Concepts of Biology-1st Canadian Edition - Molnar

Concepts of Biology-1st Canadian Edition - Molnar




About the Book

Concepts of Biology—1st Canadian Edition has been adapted by Charles Molnar and Jane Gair from the OpenStax College textbook, Concepts of Biology. For information about what was changed in this adaptation, refer to the copyright statement at the bottom of the home page. This adaptation is a part of the B.C. Open Textbook project.

The B.C. Open Textbook Project began in 2012 with the goal of making postsecondary education in British Columbia more accessible by reducing student cost through the use of openly licensed textbooks. The BC Open Textbook Project is administered by BCcampus and funded by the British Columbia Ministry of Advanced Education.

Open textbooks are open educational resources (OER); they are instructional resources created and shared in ways so that more people have access to them. This is a different model than traditionally copyrighted materials. OER are defined as teaching, learning, and research resources that reside in the public domain or have been released under an intellectual property license that permits their free use and re-purposing by others (Hewlett Foundation). Our open textbooks are openly licensed using a Creative Commons license, and are offered in various e-book formats free of charge, or as printed books that are available at cost.  For more information about this project, please contact If you are an instructor who is using this book for a course, please let us know.



Preface to the original textbook, by OpenStax College

Concepts of Biology is intended for the introductory biology course for non-science majors taught at most two- and four-year colleges. The scope, sequence, and level of the program are designed to match typical course syllabi. This text includes interesting features that make connections between scientific concepts and the everyday world of students. Concepts of Biology conveys the major themes of biology, such as a foundation in evolution, and features a rich and engaging art program.

Welcome to Concepts of Biology, an OpenStax College resource. This textbook has been created with several goals in mind: accessibility, customization, and student engagement—all while encouraging students toward high levels of academic scholarship. Instructors and students alike will find that this textbook offers a strong introduction to biology in an accessible format.

About OpenStax College

OpenStax College is a non-profit organization committed to improving student access to quality learning materials. Our free textbooks are developed and peer-reviewed by educators to ensure they are readable, accurate, and meet the scope and sequence requirements of today’s college courses. Unlike traditional textbooks, OpenStax College resources live online and are owned by the community of educators using them. Through our partnerships with companies and foundations committed to reducing costs for students, OpenStax College is working to improve access to higher education for all. OpenStax College is an initiative of Rice University and is made possible through the generous support of several philanthropic foundations.

About OpenStax College’s Resources

OpenStax College resources provide quality academic instruction. Three key features set our materials apart from others: they can be customized by instructors for each class, they are a “living” resource that grows online through contributions from science educators, and they are available free or for minimal cost.


OpenStax College learning resources are designed to be customized for each course. Our textbooks provide a solid foundation on which instructors can build, and our resources are conceived and written with flexibility in mind. Instructors can select the sections most relevant to their curricula and create a textbook that speaks directly to the needs of their classes and student body. Teachers are encouraged to expand on existing examples by adding unique context via geographically localized applications and topical connections.

Concepts of Biology can be easily customized using our online platform. Simply select the content most relevant to your syllabus and create a textbook that speaks directly to the needs of your class. Concepts of Biology is organized as a collection of sections that can be rearranged, modified, and enhanced through localized examples or to incorporate a specific theme of your course. This customization feature will help bring biology to life for your students and will ensure that your textbook truly reflects the goals of your course.


To broaden access and encourage community curation, Concepts of Biology is “open source” licensed under a Creative Commons Attribution (CC-BY) license. The scientific community is invited to submit examples, emerging research, and other feedback to enhance and strengthen the material and keep it current and relevant for today’s students. Submit your suggestions to, and check in on edition status, alternate versions, errata, and news on the StaxDash at


Our textbooks are available for free online, and in low-cost print and e-book editions.

About Concepts of Biology

Concepts of Biology is designed for the single-semester introduction to biology course for non-science majors, which for many students is their only college-level science course. As such, this course represents an important opportunity for students to develop the necessary knowledge, tools, and skills to make informed decisions as they continue with their lives. Rather than being mired down with facts and vocabulary, the typical non-science major student needs information presented in a way that is easy to read and understand. Even more importantly, the content should be meaningful. Students do much better when they understand why biology is relevant to their everyday lives. For these reasons, Concepts of Biology is grounded on an evolutionary basis and includes exciting features that highlight careers in the biological sciences and everyday applications of the concepts at hand. We also strive to show the interconnectedness of topics within this extremely broad discipline. In order to meet the needs of today’s instructors and students, we maintain the overall organization and coverage found in most syllabi for this course. A strength of Concepts of Biology is that instructors can customize the book, adapting it to the approach that works best in their classroom. Concepts of Biology also includes an innovative art program that incorporates critical thinking and clicker questions to help students understand—and apply—key concepts.

Coverage and Scope

Our Concepts of Biology textbook adheres to the scope and sequence of most one-semester non-majors courses nationwide. We also strive to make biology, as a discipline, interesting and accessible to students. In addition to a comprehensive coverage of core concepts and foundational research, we have incorporated features that draw learners into the discipline in meaningful ways. Our scope of content was developed after surveying over a hundred biology professors and listening to their coverage needs. We provide a thorough treatment of biology’s fundamental concepts with a scope that is manageable for instructors and students alike.

  • Unit 1: The Cellular Foundation of Life. Our opening unit introduces students to the sciences, including the process of science and the underlying concepts from the physical sciences that provide a framework within which learners comprehend biological processes. Additionally, students will gain solid understanding of the structures, functions, and processes of the most basic unit of life: the cell.
  • Unit 2: Cell Division and Genetics. Our genetics unit takes learners from the foundations of cellular reproduction to the experiments that revealed the basis of genetics and laws of inheritance.
  • Unit 3: Molecular Biology and Biotechnology. Students will learn the intricacies of DNA, protein synthesis, and gene regulation and current applications of biotechnology and genomics.
  • Unit 4: Evolution and the Diversity of Life. The core concepts of evolution are discussed in this unit with examples illustrating evolutionary processes. Additionally, the evolutionary basis of biology reappears throughout the textbook in general discussion and is reinforced through special call-out features highlighting specific evolution-based topics. The diversity of life is explored with detailed study of various organisms and discussion of emerging phylogenetic relationships between and among bacteria, protist kingdoms, fungi, plants, and animals.
  • Unit 5: Animal Structure and Function. An introduction to the form and function of the animal body is followed by chapters on the immune system and animal development. This unit touches on the biology of all organisms while maintaining an engaging focus on human anatomy and physiology that helps students connect to the topics.
  • Unit 6: Ecology. Ecological concepts are broadly covered in this unit, with features highlighting localized, real-world issues of conservation and biodiversity.

Pedagogical Foundation and Features

Because of the impact science has on students and society, an important goal of science education is to achieve a scientifically literate population that consistently makes informed decisions. Scientific literacy transcends a basic understanding of scientific principles and processes to include the ability to make sense of the myriad instances where people encounter science in day-to-day life. Thus, a scientifically literate person is one who uses science content knowledge to make informed decisions, either personally or socially, about topics or issues that have a connection with science. Concepts of Biology is grounded on a solid scientific base and designed to promote scientific literacy. Throughout the text, you will find features that engage the students in scientific inquiry by taking selected topics a step further.

  • Evolution in Action features uphold the importance of evolution to all biological study through discussions like “Global Decline of Coral Reefs” and “The Red Queen Hypothesis.”
  • Career in Action features present information on a variety of careers in the biological sciences, introducing students to the educational requirements and day-to-day work life of a variety of professions, such as forensic scientists, registered dietitians, and biogeographers.
  • Biology in Action features tie biological concepts to emerging issues and discuss science in terms of everyday life. Topics include “Invasive Species” and “Photosynthesis at the Grocery Store.”

Art and Animations that Engage

Our art program takes a straightforward approach designed to help students learn the concepts of biology through simple, effective illustrations, photos, and micrographs. Concepts of Biology also incorporates links to relevant animations and interactive exercises that help bring biology to life for students.

  • Concepts in Action features direct students to online interactive exercises and animations to add a fuller context and examples to core content.

About Our Team

Concepts of Biology would not be possible if not for the tremendous contributions of the authors and community reviewing team

Senior Contributors

Samantha Fowler Clayton State University
Rebecca Roush Sandhills Community College
James Wise Hampton University

Faculty Contributors and Reviewers

Mark Belk Brigham Young University
Lisa Boggs Southwestern Oklahoma State University
Sherryl Broverman Duke University
David Byres Florida State College at Jacksonville
Aaron Cassill The University of Texas at San Antonio
Karen Champ College of Central Florida
Sue Chaplin University of St. Thomas
Diane Day Clayton State University
Jean DeSaix University of North Carolina at Chapel Hill
David Hunnicutt St. Norbert College
Barbara Kuehner Hawaii Community College
Brenda Leady University of Toledo
Bernie Marcus Genesee Community College
Flora Mhlanga Lipscomb University
Madeline Mignone Dominican College
Elizabeth Nash Long Beach City College
Mark Newton San Jose City College
Diana Oliveras University of Colorado Boulder
Ann Paterson Williams Baptist College
Joel Piperberg Millersville University
Nick Reeves Mt. San Jacinto College
Ann Reisenauer San Jose State University
Lynn Rumfelt Gordon College
Michael Rutledge Middle Tennessee State University
Edward Saiff Ramapo College of New Jersey
Brian Shmaefsky Kingwood College
Gary Shultz Marshall University
Donald Slish SUNY Plattsburgh
Anh-Hue Tu Georgia Southwestern State University
Elena Zoubina Bridgewater State University


Preface to the 1st Canadian Edition

Preface to the 1st Canadian Edition, by Charles Molnar and Jane Gair, adapters of Concepts of Biology

In this survey text, directed at those not majoring in biology, we dispel the assumption that a little learning is a dangerous thing. We hope that by skimming the surface of a very deep subject, biology, we may inspire you to drink more deeply and make more informed choices relating to your health, the environment, politics, and the greatest subject that all of us are entwined in, life itself.

In the adapted textbook, Concepts of Biology — 1st Canadian Edition, you will find the following units:

Adaptations to the original textbook Concepts of Biology by OpenStax College include:

Thanks to BCcampus and Camosun College for funding and support. We are most grateful to the Let’s Talk Science organization from their trove of science links.


Unit 1. The Cellular Foundation of Life


Chapter 1: Introduction to Biology


Figure 1.1 This NASA image is a composite of several satellite-based views of Earth. To make the whole-Earth image, NASA scientists combine observations of different parts of the planet. (credit: modification of work by NASA)

Viewed from space, Earth  offers few clues about the diversity of life forms that reside there. The first forms of life on Earth are thought to have been microorganisms that existed for billions of years before plants and animals appeared. The mammals, birds, and flowers so familiar to us are all relatively recent, originating 130 to 200 million years ago. Humans have inhabited this planet for only the last 2.5 million years, and only in the last 200,000 years have humans started looking like we do today.


1.1 Themes and Concepts of Biology

Learning Objectives

By the end of this section, you will be able to:

  • Identify and describe the properties of life
  • Describe the levels of organization among living things
  • List examples of different sub disciplines in biology

Biology is the science that studies life. What exactly is life? This may sound like a silly question with an obvious answer, but it is not easy to define life. For example, a branch of biology called virology studies viruses, which exhibit some of the characteristics of living entities but lack others. It turns out that although viruses can attack living organisms, cause diseases, and even reproduce, they do not meet the criteria that biologists use to define life.

From its earliest beginnings, biology has wrestled with four questions: What are the shared properties that make something “alive”? How do those various living things function? When faced with the remarkable diversity of life, how do we organize the different kinds of organisms so that we can better understand them? And, finally—what biologists ultimately seek to understand—how did this diversity arise and how is it continuing? As new organisms are discovered every day, biologists continue to seek answers to these and other questions.

Properties of Life

All groups of living organisms share several key characteristics or functions: order, sensitivity or response to stimuli, reproduction, adaptation, growth and development, regulation, homeostasis, and energy processing. When viewed together, these eight characteristics serve to define life.


Organisms are highly organized structures that consist of one or more cells. Even very simple, single-celled organisms are remarkably complex. Inside each cell, atoms make up molecules. These in turn make up cell components or organelles. Multicellular organisms, which may consist of millions of individual cells, have an advantage over single-celled organisms in that their cells can be specialized to perform specific functions, and even sacrificed in certain situations for the good of the organism as a whole. How these specialized cells come together to form organs such as the heart, lung, or skin in organisms like the toad shown in Figure 1. 2 will be discussed later.

A photo shows a light-colored toad covered in bright green spots.

Figure 1.2 A toad represents a highly organized structure consisting of cells, tissues, organs, and organ systems. (credit: “Ivengo(RUS)”/Wikimedia Commons)

Sensitivity or Response to Stimuli

Organisms respond to diverse stimuli. For example, plants can bend toward a source of light or respond to touch. Even tiny bacteria can move toward or away from chemicals (a process called chemotaxis) or light (phototaxis). Movement toward a stimulus is considered a positive response, while movement away from a stimulus is considered a negative response.

A photograph of the Mimosa pudica shows a plant with many tiny leaves.

Figure 1.3 The leaves of this sensitive plant (Mimosa pudica) will instantly droop and fold when touched. After a few minutes, the plant returns to its normal state. (credit: Alex Lomas)

Concept in Action

QR Code representing a URL

Watch this video to see how the sensitive plant responds to a touch stimulus.


Single-celled organisms reproduce by first duplicating their DNA, which is the genetic material, and then dividing it equally as the cell prepares to divide to form two new cells. Many multicellular organisms (those made up of more than one cell) produce specialized reproductive cells that will form new individuals. When reproduction occurs, DNA containing genes is passed along to an organism’s offspring. These genes are the reason that the offspring will belong to the same species and will have characteristics similar to the parent, such as fur color and blood type.


All living organisms exhibit a “fit” to their environment. Biologists refer to this fit as adaptation and it is a consequence of evolution by natural selection, which operates in every lineage of reproducing organisms. Examples of adaptations are diverse and unique, from heat-resistant Archaea that live in boiling hot springs to the tongue length of a nectar-feeding moth that matches the size of the flower from which it feeds. All adaptations enhance the reproductive potential of the individual exhibiting them, including their ability to survive to reproduce. Adaptations are not constant. As an environment changes, natural selection causes the characteristics of the individuals in a population to track those changes.

Growth and Development

Organisms grow and develop according to specific instructions coded for by their genes. These genes provide instructions that will direct cellular growth and development, ensuring that a species’ young will grow up to exhibit many of the same characteristics as its parents.

A photograph depicts four kittens: one has an orange and white tabby coat, another is entirely black, the third and fourth have a black, white and orange tabby coat but with different patterning.

Figure 1.4 Although no two look alike, these kittens have inherited genes from both parents and share many of the same characteristics. (credit: Pieter & Renée Lanser)


Even the smallest organisms are complex and require multiple regulatory mechanisms to coordinate internal functions, such as the transport of nutrients, response to stimuli, and coping with environmental stresses. For example, organ systems such as the digestive or circulatory systems perform specific functions like carrying oxygen throughout the body, removing wastes, delivering nutrients to every cell, and cooling the body.


To function properly, cells require appropriate conditions such as proper temperature, pH, and concentrations of diverse chemicals. These conditions may, however, change from one moment to the next. Organisms are able to maintain internal conditions within a narrow range almost constantly, despite environmental changes, through a process called homeostasis or “steady state”—the ability of an organism to maintain constant internal conditions. For example, many organisms regulate their body temperature in a process known as thermoregulation. Organisms that live in cold climates, such as the polar bear, have body structures that help them withstand low temperatures and conserve body heat. In hot climates, organisms have methods (such as perspiration in humans or panting in dogs) that help them to shed excess body heat.

This photo shows a white, furry polar bear.

Figure 1.5 Polar bears and other mammals living in ice-covered regions maintain their body temperature by generating heat and reducing heat loss through thick fur and a dense layer of fat under their skin. (credit: “longhorndave”/Flickr)

Energy Processing

All organisms (such as the California condor shown in Figure 1.6) use a source of energy for their metabolic activities. Some organisms capture energy from the sun and convert it into chemical energy in food; others use chemical energy from molecules they take in.

This photo shows a California condor in flight with a tag on its wing.

Figure 1.6 A lot of energy is required for a California condor to fly. Chemical energy derived from food is used to power flight. California condors are an endangered species; scientists have strived to place a wing tag on each bird to help them identify and locate each individual bird. (credit: Pacific Southwest Region U.S. Fish and Wildlife)

Levels of Organization of Living Things

Living things are highly organized and structured, following a hierarchy on a scale from small to large. The atom is the smallest and most fundamental unit of matter. It consists of a nucleus surrounded by electrons. Atoms form molecules. A molecule is a chemical structure consisting of at least two atoms held together by a chemical bond. Many molecules that are biologically important are macromolecules, large molecules that are typically formed by combining smaller units called monomers. An example of a macromolecule is deoxyribonucleic acid (DNA), which contains the instructions for the functioning of the organism that contains it.

Molecular model depicts a DNA molecule, showing its double helix structure.

Figure 1.7 A molecule, like this large DNA molecule, is composed of atoms. (credit: “Brian0918″/Wikimedia Commons)

Concept in Action

QR Code representing a URL

To see an animation of this DNA molecule, click here.

Some cells contain aggregates of macromolecules surrounded by membranes; these are called organelles. Organelles are small structures that exist within cells and perform specialized functions. All living things are made of cells; the cell itself is the smallest fundamental unit of structure and function in living organisms. (This requirement is why viruses are not considered living: they are not made of cells. To make new viruses, they have to invade and hijack a living cell; only then can they obtain the materials they need to reproduce.) Some organisms consist of a single cell and others are multicellular. Cells are classified as prokaryotic or eukaryotic. Prokaryotes are single-celled organisms that lack organelles surrounded by a membrane and do not have nuclei surrounded by nuclear membranes; in contrast, the cells of eukaryotes do have membrane-bound organelles and nuclei.

In most multicellular organisms, cells combine to make tissues, which are groups of similar cells carrying out the same function. Organs are collections of tissues grouped together based on a common function. Organs are present not only in animals but also in plants. An organ system is a higher level of organization that consists of functionally related organs. For example vertebrate animals have many organ systems, such as the circulatory system that transports blood throughout the body and to and from the lungs; it includes organs such as the heart and blood vessels. Organisms are individual living entities. For example, each tree in a forest is an organism. Single-celled prokaryotes and single-celled eukaryotes are also considered organisms and are typically referred to as microorganisms.

A flow chart shows the hierarchy of living organisms. From smallest to largest, this hierarchy includes: 1 An atom, with protons, neutrons and electrons. 2 Molecules such as the phospholipid shown, made up of atoms. 3 Organelles, such as Golgi apparatus and nuclei, that exist inside cells. 4 Cells, such as a red blood cell. 5 Tissues, such as human skin tissue. 6 Organs such as the stomach and intestine make up the human digestive system, an example of an organ system. 7 Organisms, populations and communities. In a park, each person is an organism. Together, all the people make up a population. All the plant and animal species in the park comprise a community. 8 Ecosystems: The ecosystem of Central Park in New York includes living organisms and the environment in which they live. 9 The biosphere: encompasses all the ecosystems on Earth.

Figure 1.8 From an atom to the entire Earth, biology examines all aspects of life. (credit “molecule”: modification of work by Jane Whitney; credit “organelles”: modification of work by Louisa Howard; credit “cells”: modification of work by Bruce Wetzel, Harry Schaefer, National Cancer Institute; credit “tissue”: modification of work by “Kilbad”/Wikimedia Commons; credit “organs”: modification of work by Mariana Ruiz Villareal, Joaquim Alves Gaspar; credit “organisms”: modification of work by Peter Dutton; credit “ecosystem”: modification of work by “gigi4791″/Flickr; credit “biosphere”: modification of work by NASA)

Which of the following statements is false?

  1. Tissues exist within organs which exist within organ systems.
  2. Communities exist within populations which exist within ecosystems.
  3. Organelles exist within cells which exist within tissues.
  4. Communities exist within ecosystems which exist in the biosphere.

All the individuals of a species living within a specific area are collectively called a population. For example, a forest may include many white pine trees. All of these pine trees represent the population of white pine trees in this forest. Different populations may live in the same specific area. For example, the forest with the pine trees includes populations of flowering plants and also insects and microbial populations. A community is the set of populations inhabiting a particular area. For instance, all of the trees, flowers, insects, and other populations in a forest form the forest’s community. The forest itself is an ecosystem. An ecosystem consists of all the living things in a particular area together with the abiotic, or non-living, parts of that environment such as nitrogen in the soil or rainwater. At the highest level of organization, the biosphere is the collection of all ecosystems, and it represents the zones of life on Earth. It includes land, water, and portions of the atmosphere.

The Diversity of Life

The science of biology is very broad in scope because there is a tremendous diversity of life on Earth. The source of this diversity is evolution, the process of gradual change during which new species arise from older species. Evolutionary biologists study the evolution of living things in everything from the microscopic world to ecosystems.

In the 18th century, a scientist named Carl Linnaeus first proposed organizing the known species of organisms into a hierarchical taxonomy. In this system, species that are most similar to each other are put together within a grouping known as a genus. Furthermore, similar genera (the plural of genus) are put together within a family. This grouping continues until all organisms are collected together into groups at the highest level. The current taxonomic system now has eight levels in its hierarchy, from lowest to highest, they are: species, genus, family, order, class, phylum, kingdom, and domain. Thus species are grouped within genera, genera are grouped within families, families are grouped within orders, and so on.

A chart shows the eight levels of taxonomic hierarchy for the dog, Canis lupus.

Figure 1.9 This diagram shows the levels of taxonomic hierarchy for a dog, from the broadest category—domain—to the most specific—species.

The highest level, domain, is a relatively new addition to the system since the 1990s. Scientists now recognize three domains of life, the Eukarya, the Archaea, and the Bacteria. The domain Eukarya contains organisms that have cells with nuclei. It includes the kingdoms of fungi, plants, animals, and several kingdoms of protists. The Archaea, are single-celled organisms without nuclei and include many extremophiles that live in harsh environments like hot springs. The Bacteria are another quite different group of single-celled organisms without nuclei. Both the Archaea and the Bacteria are prokaryotes, an informal name for cells without nuclei. The recognition in the 1990s that certain “bacteria,” now known as the Archaea, were as different genetically and biochemically from other bacterial cells as they were from eukaryotes, motivated the recommendation to divide life into three domains. This dramatic change in our knowledge of the tree of life demonstrates that classifications are not permanent and will change when new information becomes available.

In addition to the hierarchical taxonomic system, Linnaeus was the first to name organisms using two unique names, now called the binomial naming system. Before Linnaeus, the use of common names to refer to organisms caused confusion because there were regional differences in these common names. Binomial names consist of the genus name (which is capitalized) and the species name (all lower-case). Both names are set in italics when they are printed. Every species is given a unique binomial which is recognized the world over, so that a scientist in any location can know which organism is being referred to. For example, the North American blue jay is known uniquely as Cyanocitta cristata. Our own species is Homo sapiens.

Photos depict: A: bacterial cells. B: a natural hot vent. C: a sunflower. D: a lion.

Figure 1.10 These images represent different domains. The scanning electron micrograph shows (a) bacterial cells belong to the domain Bacteria, while the (b) extremophiles, seen all together as colored mats in this hot spring, belong to domain Archaea. Both the (c) sunflower and (d) lion are part of domain Eukarya. (credit a: modification of work by Rocky Mountain Laboratories, NIAID, NIH; credit b: modification of work by Steve Jurvetson; credit c: modification of work by Michael Arrighi; credit d: modification of work by Frank Vassen)

Evolution in Action

Carl Woese and the Phylogenetic Tree

The evolutionary relationships of various life forms on Earth can be summarized in a phylogenetic tree. A phylogenetic tree is a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both. A phylogenetic tree is composed of branch points, or nodes, and branches. The internal nodes represent ancestors and are points in evolution when, based on scientific evidence, an ancestor is thought to have diverged to form two new species. The length of each branch can be considered as estimates of relative time.

In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. The pioneering work of American microbiologist Carl Woese in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains—Bacteria, Archaea, and Eukarya. Woese proposed the domain as a new taxonomic level and Archaea as a new domain, to reflect the new phylogenetic tree. Many organisms belonging to the Archaea domain live under extreme conditions and are called extremophiles. To construct his tree, Woese used genetic relationships rather than similarities based on morphology (shape). Various genes were used in phylogenetic studies. Woese’s tree was constructed from comparative sequencing of the genes that are universally distributed, found in some slightly altered form in every organism, conserved (meaning that these genes have remained only slightly changed throughout evolution), and of an appropriate length.

This phylogenetic tree shows that the three domains of life, bacteria, archaea and eukarya, all arose from a common ancestor.

Figure 1.11 This phylogenetic tree was constructed by microbiologist Carl Woese using genetic relationships. The tree shows the separation of living organisms into three domains: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are organisms without a nucleus or other organelles surrounded by a membrane and, therefore, are prokaryotes. (credit: modification of work by Eric Gaba)

Branches of Biological Study

The scope of biology is broad and therefore contains many branches and sub disciplines. Biologists may pursue one of those sub disciplines and work in a more focused field. For instance, molecular biology studies biological processes at the molecular level, including interactions among molecules such as DNA, RNA, and proteins, as well as the way they are regulated. Microbiology is the study of the structure and function of microorganisms. It is quite a broad branch itself, and depending on the subject of study, there are also microbial physiologists, ecologists, and geneticists, among others.

Another field of biological study, neurobiology, studies the biology of the nervous system, and although it is considered a branch of biology, it is also recognized as an interdisciplinary field of study known as neuroscience. Because of its interdisciplinary nature, this sub discipline studies different functions of the nervous system using molecular, cellular, developmental, medical, and computational approaches.

Photo depicts scientists digging fossils out of the dirt.

Figure 1.12 Researchers work on excavating dinosaur fossils at a site in Castellón, Spain. (credit: Mario Modesto)

Paleontology, another branch of biology, uses fossils to study life’s history. Zoology and botany are the study of animals and plants, respectively. Biologists can also specialize as biotechnologists, ecologists, or physiologists, to name just a few areas. Biotechnologists apply the knowledge of biology to create useful products. Ecologists study the interactions of organisms in their environments. Physiologists study the workings of cells, tissues and organs. This is just a small sample of the many fields that biologists can pursue. From our own bodies to the world we live in, discoveries in biology can affect us in very direct and important ways. We depend on these discoveries for our health, our food sources, and the benefits provided by our ecosystem. Because of this, knowledge of biology can benefit us in making decisions in our day-to-day lives.

The development of technology in the twentieth century that continues today, particularly the technology to describe and manipulate the genetic material, DNA, has transformed biology. This transformation will allow biologists to continue to understand the history of life in greater detail, how the human body works, our human origins, and how humans can survive as a species on this planet despite the stresses caused by our increasing numbers. Biologists continue to decipher huge mysteries about life suggesting that we have only begun to understand life on the planet, its history, and our relationship to it. For this and other reasons, the knowledge of biology gained through this textbook and other printed and electronic media should be a benefit in whichever field you enter.

Forensic Scientist

Forensic science is the application of science to answer questions related to the law. Biologists as well as chemists and biochemists can be forensic scientists. Forensic scientists provide scientific evidence for use in courts, and their job involves examining trace material associated with crimes. Interest in forensic science has increased in the last few years, possibly because of popular television shows that feature forensic scientists on the job. Also, the development of molecular techniques and the establishment of DNA databases have updated the types of work that forensic scientists can do. Their job activities are primarily related to crimes against people such as murder, rape, and assault. Their work involves analyzing samples such as hair, blood, and other body fluids and also processing DNA found in many different environments and materials. Forensic scientists also analyze other biological evidence left at crime scenes, such as insect parts or pollen grains. Students who want to pursue careers in forensic science will most likely be required to take chemistry and biology courses as well as some intensive math courses.

Photo depicts a scientist working in a lab.

Figure 1.13 This forensic scientist works in a DNA extraction room at the U.S. Army Criminal Investigation Laboratory. (credit: U.S. Army CID Command Public Affairs)

Section Summary

Biology is the science of life. All living organisms share several key properties such as order, sensitivity or response to stimuli, reproduction, adaptation, growth and development, regulation, homeostasis, and energy processing. Living things are highly organized following a hierarchy that includes atoms, molecules, organelles, cells, tissues, organs, and organ systems. Organisms, in turn, are grouped as populations, communities, ecosystems, and the biosphere. Evolution is the source of the tremendous biological diversity on Earth today. A diagram called a phylogenetic tree can be used to show evolutionary relationships among organisms. Biology is very broad and includes many branches and sub disciplines. Examples include molecular biology, microbiology, neurobiology, zoology, and botany, among others.


Which of the following statements is false?

A) Tissues exist within organs which exist within organ systems.

B) Communities exist within populations which exist within ecosystems.

C) Organelles exist within cells which exist within tissues.

D) Communities exist within ecosystems which exist in the biosphere.


Multiple Choice

The smallest unit of biological structure that meets the functional requirements of “living” is the ________.

A) organ

B) organelle

C) cell

D) macromolecule


Which of the following sequences represents the hierarchy of biological organization from the most complex to the least complex level?

A ) organelle, tissue, biosphere, ecosystem, population

B) organ, organism, tissue, organelle, molecule

C) organism, community, biosphere, molecule, tissue, organ

D) biosphere, ecosystem, community, population, organism


Free Response

Using examples, explain how biology can be studied from a microscopic approach to a global approach.

Researchers can approach biology from the smallest to the largest, and everything in between. For instance, an ecologist may study a population of individuals, the population’s community, the community’s ecosystem, and the ecosystem’s part in the biosphere. When studying an individual organism, a biologist could examine the cell and its organelles, the tissues that the cells make up, the organs and their respective organ systems, and the sum total—the organism itself.



atom: a basic unit of matter that cannot be broken down by normal chemical reactions

biology: the study of living organisms and their interactions with one another and their environments

biosphere: a collection of all ecosystems on Earth

cell: the smallest fundamental unit of structure and function in living things

community: a set of populations inhabiting a particular area

ecosystem: all living things in a particular area together with the abiotic, nonliving parts of that environment

eukaryote: an organism with cells that have nuclei and membrane-bound organelles

evolution: the process of gradual change in a population that can also lead to new species arising from older species

homeostasis: the ability of an organism to maintain constant internal conditions

macromolecule: a large molecule typically formed by the joining of smaller molecules

molecule: a chemical structure consisting of at least two atoms held together by a chemical bond

organ: a structure formed of tissues operating together to perform a common function

organ system: the higher level of organization that consists of functionally related organs

organelle: a membrane-bound compartment or sac within a cell

organism: an individual living entity

phylogenetic tree: a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both

population: all individuals within a species living within a specific area

prokaryote: a unicellular organism that lacks a nucleus or any other membrane-bound organelle

tissue: a group of similar cells carrying out the same function


1.2 The Process of Science

Learning Objectives

By the end of this section, you will be able to:

  • Identify the shared characteristics of the natural sciences
  • Understand the process of scientific inquiry
  • Compare inductive reasoning with deductive reasoning
  • Describe the goals of basic science and applied science
Photo A depicts round colonies of blue-green algae. Photo B depicts round fossil structures called stromatalites along a watery shoreline.

Figure 1.14 Formerly called blue-green algae, the (a) cyanobacteria seen through a light microscope are some of Earth’s oldest life forms. These (b) stromatolites along the shores of Lake Thetis in Western Australia are ancient structures formed by the layering of cyanobacteria in shallow waters. (credit a: modification of work by NASA; scale-bar data from Matt Russell; credit b: modification of work by Ruth Ellison)

Like geology, physics, and chemistry, biology is a science that gathers knowledge about the natural world. Specifically, biology is the study of life. The discoveries of biology are made by a community of researchers who work individually and together using agreed-on methods. In this sense, biology, like all sciences is a social enterprise like politics or the arts. The methods of science include careful observation, record keeping, logical and mathematical reasoning, experimentation, and submitting conclusions to the scrutiny of others. Science also requires considerable imagination and creativity; a well-designed experiment is commonly described as elegant, or beautiful. Like politics, science has considerable practical implications and some science is dedicated to practical applications, such as the prevention of disease. Other science proceeds largely motivated by curiosity. Whatever its goal, there is no doubt that science, including biology, has transformed human existence and will continue to do so.

Scanning electronic micrograph depicts E. coli bacteria aggregated together.

Figure 1.15 Biologists may choose to study Escherichia coli (E. coli), a bacterium that is a normal resident of our digestive tracts but which is also sometimes responsible for disease outbreaks. In this micrograph, the bacterium is visualized using a scanning electron microscope and digital colorization. (credit: Eric Erbe; digital colorization by Christopher Pooley, USDA-ARS)

The Nature of Science

Biology is a science, but what exactly is science? What does the study of biology share with other scientific disciplines? Science (from the Latin scientia, meaning “knowledge”) can be defined as knowledge about the natural world.

Science is a very specific way of learning, or knowing, about the world. The history of the past 500 years demonstrates that science is a very powerful way of knowing about the world; it is largely responsible for the technological revolutions that have taken place during this time. There are however, areas of knowledge and human experience that the methods of science cannot be applied to. These include such things as answering purely moral questions, aesthetic questions, or what can be generally categorized as spiritual questions. Science has cannot investigate these areas because they are outside the realm of material phenomena, the phenomena of matter and energy, and cannot be observed and measured.

The scientific method is a method of research with defined steps that include experiments and careful observation. The steps of the scientific method will be examined in detail later, but one of the most important aspects of this method is the testing of hypotheses. A hypothesis is a suggested explanation for an event, which can be tested. Hypotheses, or tentative explanations, are generally produced within the context of a scientific theory. A scientific theory is a generally accepted, thoroughly tested and confirmed explanation for a set of observations or phenomena. Scientific theory is the foundation of scientific knowledge. In addition, in many scientific disciplines (less so in biology) there are scientific laws, often expressed in mathematical formulas, which describe how elements of nature will behave under certain specific conditions. There is not an evolution of hypotheses through theories to laws as if they represented some increase in certainty about the world. Hypotheses are the day-to-day material that scientists work with and they are developed within the context of theories. Laws are concise descriptions of parts of the world that are amenable to formulaic or mathematical description.

Natural Sciences

What would you expect to see in a museum of natural sciences? Frogs? Plants? Dinosaur skeletons? Exhibits about how the brain functions? A planetarium? Gems and minerals? Or maybe all of the above? Science includes such diverse fields as astronomy, biology, computer sciences, geology, logic, physics, chemistry, and mathematics. However, those fields of science related to the physical world and its phenomena and processes are considered natural sciences. Thus, a museum of natural sciences might contain any of the items listed above.

Some fields of science include astronomy, biology, computer science, geology, logic, physics, chemistry, and mathematics. (credit: "Image Editor/Flickr)"

Figure 1.16 Some fields of science include astronomy, biology, computer science, geology, logic, physics, chemistry, and mathematics. (credit: “Image Editor”/Flickr)

There is no complete agreement when it comes to defining what the natural sciences include. For some experts, the natural sciences are astronomy, biology, chemistry, earth science, and physics. Other scholars choose to divide natural sciences into life sciences, which study living things and include biology, and physical sciences, which study nonliving matter and include astronomy, physics, and chemistry. Some disciplines such as biophysics and biochemistry build on two sciences and are interdisciplinary.

Scientific Inquiry

One thing is common to all forms of science: an ultimate goal “to know.” Curiosity and inquiry are the driving forces for the development of science. Scientists seek to understand the world and the way it operates. Two methods of logical thinking are used: inductive reasoning and deductive reasoning.

Inductive reasoning is a form of logical thinking that uses related observations to arrive at a general conclusion. This type of reasoning is common in descriptive science. A life scientist such as a biologist makes observations and records them. These data can be qualitative (descriptive) or quantitative (consisting of numbers), and the raw data can be supplemented with drawings, pictures, photos, or videos. From many observations, the scientist can infer conclusions (inductions) based on evidence. Inductive reasoning involves formulating generalizations inferred from careful observation and the analysis of a large amount of data. Brain studies often work this way. Many brains are observed while people are doing a task. The part of the brain that lights up, indicating activity, is then demonstrated to be the part controlling the response to that task.

Deductive reasoning or deduction is the type of logic used in hypothesis-based science. In deductive reasoning, the pattern of thinking moves in the opposite direction as compared to inductive reasoning. Deductive reasoning is a form of logical thinking that uses a general principle or law to forecast specific results. From those general principles, a scientist can extrapolate and predict the specific results that would be valid as long as the general principles are valid. For example, a prediction would be that if the climate is becoming warmer in a region, the distribution of plants and animals should change. Comparisons have been made between distributions in the past and the present, and the many changes that have been found are consistent with a warming climate. Finding the change in distribution is evidence that the climate change conclusion is a valid one.

Both types of logical thinking are related to the two main pathways of scientific study: descriptive science and hypothesis-based science. Descriptive (or discovery) science aims to observe, explore, and discover, while hypothesis-based science begins with a specific question or problem and a potential answer or solution that can be tested. The boundary between these two forms of study is often blurred, because most scientific endeavors combine both approaches. Observations lead to questions, questions lead to forming a hypothesis as a possible answer to those questions, and then the hypothesis is tested. Thus, descriptive science and hypothesis-based science are in continuous dialogue.

Hypothesis Testing

Biologists study the living world by posing questions about it and seeking science-based responses. This approach is common to other sciences as well and is often referred to as the scientific method. The scientific method was used even in ancient times, but it was first documented by England’s Sir Francis Bacon (1561–1626), who set up inductive methods for scientific inquiry. The scientific method is not exclusively used by biologists but can be applied to almost anything as a logical problem-solving method.

Painting depicts Sir Francis Bacon in a long cloak.

Figure1.17 Sir Francis Bacon is credited with being the first to document the scientific method.

The scientific process typically starts with an observation (often a problem to be solved) that leads to a question. Let’s think about a simple problem that starts with an observation and apply the scientific method to solve the problem. One Monday morning, a student arrives at class and quickly discovers that the classroom is too warm. That is an observation that also describes a problem: the classroom is too warm. The student then asks a question: “Why is the classroom so warm?”

Recall that a hypothesis is a suggested explanation that can be tested. To solve a problem, several hypotheses may be proposed. For example, one hypothesis might be, “The classroom is warm because no one turned on the air conditioning.” But there could be other responses to the question, and therefore other hypotheses may be proposed. A second hypothesis might be, “The classroom is warm because there is a power failure, and so the air conditioning doesn’t work.”

Once a hypothesis has been selected, a prediction may be made. A prediction is similar to a hypothesis but it typically has the format “If . . . then . . . .” For example, the prediction for the first hypothesis might be, “If the student turns on the air conditioning, then the classroom will no longer be too warm.”

A hypothesis must be testable to ensure that it is valid. For example, a hypothesis that depends on what a bear thinks is not testable, because it can never be known what a bear thinks. It should also be falsifiable, meaning that it can be disproven by experimental results. An example of an unfalsifiable hypothesis is “Botticelli’s Birth of Venus is beautiful.” There is no experiment that might show this statement to be false. To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate one or more of the hypotheses. This is important. A hypothesis can be disproven, or eliminated, but it can never be proven. Science does not deal in proofs like mathematics. If an experiment fails to disprove a hypothesis, then we find support for that explanation, but this is not to say that down the road a better explanation will not be found, or a more carefully designed experiment will be found to falsify the hypothesis.

Each experiment will have one or more variables and one or more controls. A variable is any part of the experiment that can vary or change during the experiment. A control is a part of the experiment that does not change. Look for the variables and controls in the example that follows. As a simple example, an experiment might be conducted to test the hypothesis that phosphate limits the growth of algae in freshwater ponds. A series of artificial ponds are filled with water and half of them are treated by adding phosphate each week, while the other half are treated by adding a salt that is known not to be used by algae. The variable here is the phosphate (or lack of phosphate), the experimental or treatment cases are the ponds with added phosphate and the control ponds are those with something inert added, such as the salt. Just adding something is also a control against the possibility that adding extra matter to the pond has an effect. If the treated ponds show lesser growth of algae, then we have found support for our hypothesis. If they do not, then we reject our hypothesis. Be aware that rejecting one hypothesis does not determine whether or not the other hypotheses can be accepted; it simply eliminates one hypothesis that is not valid . Using the scientific method, the hypotheses that are inconsistent with experimental data are rejected.

A flow chart shows the steps in the scientific method. In step 1, an observation is made. In step 2, a question is asked about the observation. In step 3, an answer to the question, called a hypothesis, is proposed. In step 4, a prediction is made based on the hypothesis. In step 5, an experiment is done to test the prediction. In step 6, the results are analyzed to determine whether or not the hypothesis is supported. If the hypothesis is not supported, another hypothesis is made. In either case, the results are reported.

Figure 1.18 The scientific method is a series of defined steps that include experiments and careful observation. If a hypothesis is not supported by data, a new hypothesis can be proposed.

In the example below, the scientific method is used to solve an everyday problem. Which part in the example below is the hypothesis? Which is the prediction? Based on the results of the experiment, is the hypothesis supported? If it is not supported, propose some alternative hypotheses.

  1. My toaster doesn’t toast my bread.
  2. Why doesn’t my toaster work?
  3. There is something wrong with the electrical outlet.
  4. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.
  5. I plug my coffeemaker into the outlet.
  6. My coffeemaker works.

In practice, the scientific method is not as rigid and structured as it might at first appear. Sometimes an experiment leads to conclusions that favor a change in approach; often, an experiment brings entirely new scientific questions to the puzzle. Many times, science does not operate in a linear fashion; instead, scientists continually draw inferences and make generalizations, finding patterns as their research proceeds. Scientific reasoning is more complex than the scientific method alone suggests.

Basic and Applied Science

The scientific community has been debating for the last few decades about the value of different types of science. Is it valuable to pursue science for the sake of simply gaining knowledge, or does scientific knowledge only have worth if we can apply it to solving a specific problem or bettering our lives? This question focuses on the differences between two types of science: basic science and applied science.

Basic science or “pure” science seeks to expand knowledge regardless of the short-term application of that knowledge. It is not focused on developing a product or a service of immediate public or commercial value. The immediate goal of basic science is knowledge for knowledge’s sake, though this does not mean that in the end it may not result in an application.

In contrast, applied science or “technology,” aims to use science to solve real-world problems, making it possible, for example, to improve a crop yield, find a cure for a particular disease, or save animals threatened by a natural disaster. In applied science, the problem is usually defined for the researcher.

Some individuals may perceive applied science as “useful” and basic science as “useless.” A question these people might pose to a scientist advocating knowledge acquisition would be, “What for?” A careful look at the history of science, however, reveals that basic knowledge has resulted in many remarkable applications of great value. Many scientists think that a basic understanding of science is necessary before an application is developed; therefore, applied science relies on the results generated through basic science. Other scientists think that it is time to move on from basic science and instead to find solutions to actual problems. Both approaches are valid. It is true that there are problems that demand immediate attention; however, few solutions would be found without the help of the knowledge generated through basic science.

One example of how basic and applied science can work together to solve practical problems occurred after the discovery of DNA structure led to an understanding of the molecular mechanisms governing DNA replication. Strands of DNA, unique in every human, are found in our cells, where they provide the instructions necessary for life. During DNA replication, new copies of DNA are made, shortly before a cell divides to form new cells. Understanding the mechanisms of DNA replication enabled scientists to develop laboratory techniques that are now used to identify genetic diseases, pinpoint individuals who were at a crime scene, and determine paternity. Without basic science, it is unlikely that applied science would exist.

Another example of the link between basic and applied research is the Human Genome Project, a study in which each human chromosome was analyzed and mapped to determine the precise sequence of DNA subunits and the exact location of each gene. (The gene is the basic unit of heredity; an individual’s complete collection of genes is his or her genome.) Other organisms have also been studied as part of this project to gain a better understanding of human chromosomes. The Human Genome Project  relied on basic research carried out with non-human organisms and, later, with the human genome. An important end goal eventually became using the data for applied research seeking cures for genetically related diseases.

The human genome project’s logo is shown, depicting a human being inside a DNA double helix. The words chemistry, biology, physics, ethics, informatics and engineering surround the circular image.

Figure 1.19 The Human Genome Project was a 13-year collaborative effort among researchers working in several different fields of science. The project was completed in 2003. (credit: the U.S. Department of Energy Genome Programs)

While research efforts in both basic science and applied science are usually carefully planned, it is important to note that some discoveries are made by serendipity, that is, by means of a fortunate accident or a lucky surprise. Penicillin was discovered when biologist Alexander Fleming accidentally left a petri dish of Staphylococcus bacteria open. An unwanted mold grew, killing the bacteria. The mold turned out to be Penicillium, and a new antibiotic was discovered. Even in the highly organized world of science, luck—when combined with an observant, curious mind—can lead to unexpected breakthroughs.

Reporting Scientific Work

Whether scientific research is basic science or applied science, scientists must share their findings for other researchers to expand and build upon their discoveries. Communication and collaboration within and between sub disciplines of science are key to the advancement of knowledge in science. For this reason, an important aspect of a scientist’s work is disseminating results and communicating with peers. Scientists can share results by presenting them at a scientific meeting or conference, but this approach can reach only the limited few who are present. Instead, most scientists present their results in peer-reviewed articles that are published in scientific journals. Peer-reviewed articles are scientific papers that are reviewed, usually anonymously by a scientist’s colleagues, or peers. These colleagues are qualified individuals, often experts in the same research area, who judge whether or not the scientist’s work is suitable for publication. The process of peer review helps to ensure that the research described in a scientific paper or grant proposal is original, significant, logical, and thorough. Grant proposals, which are requests for research funding, are also subject to peer review. Scientists publish their work so other scientists can reproduce their experiments under similar or different conditions to expand on the findings. The experimental results must be consistent with the findings of other scientists.

There are many journals and the popular press that do not use a peer-review system. A large number of online open-access journals, journals with articles available without cost, are now available many of which use rigorous peer-review systems, but some of which do not. Results of any studies published in these forums without peer review are not reliable and should not form the basis for other scientific work. In one exception, journals may allow a researcher to cite a personal communication from another researcher about unpublished results with the cited author’s permission.

Section Summary

Biology is the science that studies living organisms and their interactions with one another and their environments. Science attempts to describe and understand the nature of the universe in whole or in part. Science has many fields; those fields related to the physical world and its phenomena are considered natural sciences.

A hypothesis is a tentative explanation for an observation. A scientific theory is a well-tested and consistently verified explanation for a set of observations or phenomena. A scientific law is a description, often in the form of a mathematical formula, of the behavior of an aspect of nature under certain circumstances. Two types of logical reasoning are used in science. Inductive reasoning uses results to produce general scientific principles. Deductive reasoning is a form of logical thinking that predicts results by applying general principles. The common thread throughout scientific research is the use of the scientific method. Scientists present their results in peer-reviewed scientific papers published in scientific journals.

Science can be basic or applied. The main goal of basic science is to expand knowledge without any expectation of short-term practical application of that knowledge. The primary goal of applied research, however, is to solve practical problems.


In the example below, the scientific method is used to solve an everyday problem. Which part in the example below is the hypothesis? Which is the prediction? Based on the results of the experiment, is the hypothesis supported? If it is not supported, propose some alternative hypotheses.

  1. My toaster doesn’t toast my bread.
  2. Why doesn’t my toaster work?
  3. There is something wrong with the electrical outlet.
  4. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.
  5. I plug my coffeemaker into the outlet.
  6. My coffeemaker works.

The hypothesis is #3 (there is something wrong with the electrical outlet), and the prediction is #4 (if something is wrong with the outlet, then the coffeemaker also won’t work when plugged into the outlet). The original hypothesis is not supported, as the coffee maker works when plugged into the outlet. Alternative hypotheses may include (1) the toaster might be broken or (2) the toaster wasn’t turned on.

Multiple Choice

A suggested and testable explanation for an event is called a ________.

A) hypothesis

B) variable

C) theory

D) control


The type of logical thinking that uses related observations to arrive at a general conclusion is called ________.

A) deductive reasoning

B) the scientific method

C) hypothesis-based science

D) inductive reasoning


Free Response

Give an example of how applied science has had a direct effect on your daily life.

Answers will vary. One example of how applied science has had a direct effect on daily life is the presence of vaccines. Vaccines to prevent diseases such polio, measles, tetanus, and even the influenza affect daily life by contributing to individual and societal health.



applied science: a form of science that solves real-world problems

basic science: science that seeks to expand knowledge regardless of the short-term application of that knowledge

control: a part of an experiment that does not change during the experiment

deductive reasoning: a form of logical thinking that uses a general statement to forecast specific results

descriptive science: a form of science that aims to observe, explore, and find things out

falsifiable: able to be disproven by experimental results

hypothesis: a suggested explanation for an event, which can be tested

hypothesis-based science: a form of science that begins with a specific explanation that is then tested

inductive reasoning: a form of logical thinking that uses related observations to arrive at a general conclusion

life science: a field of science, such as biology, that studies living things

natural science: a field of science that studies the physical world, its phenomena, and processes

peer-reviewed article: a scientific report that is reviewed by a scientist’s colleagues before publication

physical science: a field of science, such as astronomy, physics, and chemistry, that studies nonliving matter

science: knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method

scientific law: a description, often in the form of a mathematical formula, for the behavior of some aspect of nature under certain specific conditions

scientific method: a method of research with defined steps that include experiments and careful observation

scientific theory: a thoroughly tested and confirmed explanation for observations or phenomena

variable: a part of an experiment that can vary or change


Chapter 1 PowerPoint

Chapter 1 PowerPoint


Chapter 2: Introduction to the Chemistry of Life

Photo shows a variety of cheeses, fruits, and breads served on a tray.

Figure 2.1 Foods such as bread, fruit, and cheese are rich sources of biological macromolecules. (credit: modification of work by Bengt Nyman)

The elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus are the key building blocks of the chemicals found in living things. They form the carbohydrates, nucleic acids, proteins, and lipids (all of which will be defined later in this chapter) that are the fundamental molecular components of all organisms. In this chapter, we will discuss these important building blocks and learn how the unique properties of the atoms of different elements affect their interactions with other atoms to form the molecules of life.  These interactions determine what atoms combine and the ultimate shape of the molecules and macromolecules, that shape will determine their function.

Food provides an organism with nutrients—the matter it needs to survive. Many of these critical nutrients come in the form of biological macromolecules, or large molecules necessary for life. These macromolecules are built from different combinations of smaller organic molecules. What specific types of biological macromolecules do living things require? How are these molecules formed? What functions do they serve? In this chapter, we will explore these questions.


2.1 The Building Blocks of Molecules

Learning Objectives

By the end of this section, you will be able to:

  • Describe matter and elements
  • Describe the interrelationship between protons, neutrons, and electrons, and the ways in which electrons can be donated or shared between atoms

At its most fundamental level, life is made up of matter. Matter occupies space and has mass. All matter is composed of elements, substances that cannot be broken down or transformed chemically into other substances. Each element is made of atoms, each with a constant number of protons and unique properties. A total of 118 elements have been defined; however, only 92 occur naturally, and fewer than 30 are found in living cells. The remaining 26 elements are unstable and, therefore, do not exist for very long or are theoretical and have yet to be detected.

Each element is designated by its chemical symbol (such as H, N, O, C, and Na), and possesses unique properties. These unique properties allow elements to combine and to bond with each other in specific ways.


An atom is the smallest component of an element that retains all of the chemical properties of that element. For example, one hydrogen atom has all of the properties of the element hydrogen, such as it exists as a gas at room temperature, and it bonds with oxygen to create a water molecule. Hydrogen atoms cannot be broken down into anything smaller while still retaining the properties of hydrogen. If a hydrogen atom were broken down into subatomic particles, it would no longer have the properties of hydrogen.

At the most basic level, all organisms are made of a combination of elements. They contain atoms that combine together to form molecules. In multicellular organisms, such as animals, molecules can interact to form cells that combine to form tissues, which make up organs. These combinations continue until entire multicellular organisms are formed.

All atoms contain protons, electrons, and neutrons. The only exception is hydrogen (H), which is made of one proton and one electron. A proton is a positively charged particle that resides in the nucleus (the core of the atom) of an atom and has a mass of 1 and a charge of +1. An electron is a negatively charged particle that travels in the space around the nucleus. In other words, it resides outside of the nucleus. It has a negligible mass and has a charge of –1.

Atoms are made up of protons and neutrons located within the nucleus, and electrons surrounding the nucleus.

Figure 2.2 Atoms are made up of protons and neutrons located within the nucleus, and electrons surrounding the nucleus.


Neutrons, like protons, reside in the nucleus of an atom. They have a mass of 1 and no charge. The positive (protons) and negative (electrons) charges balance each other in a neutral atom, which has a net zero charge.

Because protons and neutrons each have a mass of 1, the mass of an atom is equal to the number of protons and neutrons of that atom. The number of electrons does not factor into the overall mass, because their mass is so small.

As stated earlier, each element has its own unique properties. Each contains a different number of protons and neutrons, giving it its own atomic number and mass number. The atomic number of an element is equal to the number of protons that element contains. The mass number, or atomic mass, is the number of protons plus the number of neutrons of that element. Therefore, it is possible to determine the number of neutrons by subtracting the atomic number from the mass number.

These numbers provide information about the elements and how they will react when combined. Different elements have different melting and boiling points, and are in different states (liquid, solid, or gas) at room temperature. They also combine in different ways. Some form specific types of bonds, whereas others do not. How they combine is based on the number of electrons present. Because of these characteristics, the elements are arranged into the periodic table of elements, a chart of the elements that includes the atomic number and relative atomic mass of each element. The periodic table also provides key information about the properties of elements —often indicated by color-coding. The arrangement of the table also shows how the electrons in each element are organized and provides important details about how atoms will react with each other to form molecules.

Isotopes are different forms of the same element that have the same number of protons, but a different number of neutrons. Some elements, such as carbon, potassium, and uranium, have naturally occurring isotopes. Carbon-12, the most common isotope of carbon, contains six protons and six neutrons. Therefore, it has a mass number of 12 (six protons and six neutrons) and an atomic number of 6 (which makes it carbon). Carbon-14 contains six protons and eight neutrons. Therefore, it has a mass number of 14 (six protons and eight neutrons) and an atomic number of 6, meaning it is still the element carbon. These two alternate forms of carbon are isotopes. Some isotopes are unstable and will lose protons, other subatomic particles, or energy to form more stable elements. These are called radioactive isotopes or radioisotopes.

Periodic table of elements.

Figure 2.3 Arranged in columns and rows based on the characteristics of the elements, the periodic table provides key information about the elements and how they might interact with each other to form molecules. Most periodic tables provide a key or legend to the information they contain.

How many neutrons do (K) potassium-39 and potassium-40 have, respectively?

Evolution in Action

Carbon Dating 

Carbon-14 (14C) is a naturally occurring radioisotope that is created in the atmosphere by cosmic rays. This is a continuous process, so more 14C is always being created. As a living organism develops, the relative level of 14C in its body is equal to the concentration of 14C in the atmosphere. When an organism dies, it is no longer ingesting 14C, so the ratio will decline. 14C decays to 14N by a process called beta decay; it gives off energy in this slow process.

After approximately 5,730 years, only one-half of the starting concentration of 14C will have been converted to 14N. The time it takes for half of the original concentration of an isotope to decay to its more stable form is called its half-life. Because the half-life of 14C is long, it is used to age formerly living objects, such as fossils. Using the ratio of the 14C concentration found in an object to the amount of 14C detected in the atmosphere, the amount of the isotope that has not yet decayed can be determined. Based on this amount, the age of the fossil can be calculated to about 50,000 years. Isotopes with longer half-lives, such as potassium-40, are used to calculate the ages of older fossils. Through the use of carbon dating, scientists can reconstruct the ecology and biogeography of organisms living within the past 50,000 years.

Photograph shows scientists digging pygmy mammoth skeleton fossils from the ground.

Figure 2.4 The age of remains that contain carbon and are less than about 50,000 years old, such as this pygmy mammoth, can be determined using carbon dating. (credit: Bill Faulkner/NPS)

Concept in Action

QR Code representing a URL

To learn more about atoms and isotopes, and how you can tell one isotope from another, visit this site and run the simulation.

Chemical Bonds

How elements interact with one another depends on how their electrons are arranged and how many openings for electrons exist at the outermost region where electrons are present in an atom. Electrons exist at energy levels that form shells around the nucleus. The closest shell can hold up to two electrons. The closest shell to the nucleus is always filled first, before any other shell can be filled. Hydrogen has one electron; therefore, it has only one spot occupied within the lowest shell. Helium has two electrons; therefore, it can completely fill the lowest shell with its two electrons. If you look at the periodic table, you will see that hydrogen and helium are the only two elements in the first row. This is because they only have electrons in their first shell. Hydrogen and helium are the only two elements that have the lowest shell and no other shells.

The second and third energy levels can hold up to eight electrons. The eight electrons are arranged in four pairs and one position in each pair is filled with an electron before any pairs are completed.

Looking at the periodic table again, you will notice that there are seven rows. These rows correspond to the number of shells that the elements within that row have. The elements within a particular row have increasing numbers of electrons as the columns proceed from left to right. Although each element has the same number of shells, not all of the shells are completely filled with electrons. If you look at the second row of the periodic table, you will find lithium (Li), beryllium (Be), boron (B), carbon (C), nitrogen (N), oxygen (O), fluorine (F), and neon (Ne). These all have electrons that occupy only the first and second shells. Lithium has only one electron in its outermost shell, beryllium has two electrons, boron has three, and so on, until the entire shell is filled with eight electrons, as is the case with neon.

Not all elements have enough electrons to fill their outermost shells, but an atom is at its most stable when all of the electron positions in the outermost shell are filled. Because of these vacancies in the outermost shells, we see the formation of chemical bonds, or interactions between two or more of the same or different elements that result in the formation of molecules. To achieve greater stability, atoms will tend to completely fill their outer shells and will bond with other elements to accomplish this goal by sharing electrons, accepting electrons from another atom, or donating electrons to another atom. Because the outermost shells of the elements with low atomic numbers (up to calcium, with atomic number 20) can hold eight electrons, this is referred to as the octet rule. An element can donate, accept, or share electrons with other elements to fill its outer shell and satisfy the octet rule.

When an atom does not contain equal numbers of protons and electrons, it is called an ion. Because the number of electrons does not equal the number of protons, each ion has a net charge. Positive ions are formed by losing electrons and are called cations. Negative ions are formed by gaining electrons and are called anions.

For example, sodium only has one electron in its outermost shell. It takes less energy for sodium to donate that one electron than it does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons and only 10 electrons, leaving it with an overall charge of +1. It is now called a sodium ion.

The chlorine atom has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one electron than to lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons and 18 electrons, giving it a net negative (–1) charge. It is now called a chloride ion. This movement of electrons from one element to another is referred to as electron transfer. As illustrates, a sodium atom (Na) only has one electron in its outermost shell, whereas a chlorine atom (Cl) has seven electrons in its outermost shell. A sodium atom will donate its one electron to empty its shell, and a chlorine atom will accept that electron to fill its shell, becoming chloride. Both ions now satisfy the octet rule and have complete outermost shells. Because the number of electrons is no longer equal to the number of protons, each is now an ion and has a +1 (sodium) or –1 (chloride) charge.

Diagram shows electron transfer between elements.

Figure 2.5 Elements tend to fill their outermost shells with electrons. To do this, they can either donate or accept electrons from other elements.

Ionic Bonds

There are four types of bonds or interactions: ionic, covalent, hydrogen bonds, and van der Waals interactions. Ionic and covalent bonds are strong interactions that require a larger energy input to break apart. When an element donates an electron from its outer shell, as in the sodium atom example above, a positive ion is formed. The element accepting the electron is now negatively charged. Because positive and negative charges attract, these ions stay together and form an ionic bond, or a bond between ions. The elements bond together with the electron from one element staying predominantly with the other element. When Na+ and Cl ions combine to produce NaCl, an electron from a sodium atom stays with the other seven from the chlorine atom, and the sodium and chloride ions attract each other in a lattice of ions with a net zero charge.

Covalent Bonds

Another type of strong chemical bond between two or more atoms is a covalent bond. These bonds form when a pair of  electrons is shared between two elements and are the strongest and most common form of chemical bond in living organisms. Covalent bonds form between the elements that make up the biological molecules in our cells. Unlike ionic bonds, covalent bonds do not dissociate in water.

The hydrogen and oxygen atoms that combine to form water molecules are bound together by covalent bonds. The electron from the hydrogen atom divides its time between the outer shell of the hydrogen atom and the incomplete outer shell of the oxygen atom. To completely fill the outer shell of an oxygen atom, two electrons from two hydrogen atoms are needed, hence the subscript “2” in H2O. The electrons are shared between the atoms, dividing their time between them to “fill” the outer shell of each. This sharing is a lower energy state for all of the atoms involved than if they existed without their outer shells filled.

There are two types of covalent bonds: polar and nonpolar. Nonpolar covalent bonds form between two atoms of the same element or between different elements that share the electrons equally. For example, an oxygen atom can bond with another oxygen atom to fill their outer shells. This association is nonpolar because the electrons will be equally distributed between each oxygen atom. Two covalent bonds form between the two oxygen atoms because oxygen requires two shared electrons to fill its outermost shell. Nitrogen atoms will form three covalent bonds (also called triple covalent) between two atoms of nitrogen because each nitrogen atom needs three electrons to fill its outermost shell. Another example of a nonpolar covalent bond is found in the methane (CH4) molecule. The carbon atom has four electrons in its outermost shell and needs four more to fill it. It gets these four from four hydrogen atoms, each atom providing one. These elements all share the electrons equally, creating four nonpolar covalent bonds.

In a polar covalent bond, the electrons shared by the atoms spend more time closer to one nucleus than to the other nucleus. Because of the unequal distribution of electrons between the different nuclei, a slightly positive (δ+) or slightly negative (δ–) charge develops. The covalent bonds between hydrogen and oxygen atoms in water are polar covalent bonds. The shared electrons spend more time near the oxygen nucleus, giving it a small negative charge, than they spend near the hydrogen nuclei, giving these molecules a small positive charge.

Hydrogen Bonds

Ionic and covalent bonds are strong bonds that require considerable energy to break. However, not all bonds between elements are ionic or covalent bonds. Weaker bonds can also form. These are attractions that occur between positive and negative charges that do not require much energy to break. Two weak bonds that occur frequently are hydrogen bonds and van der Waals interactions. These bonds give rise to the unique properties of water and the unique structures of DNA and proteins.

When polar covalent bonds containing a hydrogen atom form, the hydrogen atom in that bond has a slightly positive charge. This is because the shared electron is pulled more strongly toward the other element and away from the hydrogen nucleus. Because the hydrogen atom is slightly positive (δ+), it will be attracted to neighboring negative partial charges (δ–). When this happens, a weak interaction occurs between the δ+ charge of the hydrogen atom of one molecule and the δ– charge of the other molecule. This interaction is called a hydrogen bond. This type of bond is common; for example, the liquid nature of water is caused by the hydrogen bonds between water molecules. Hydrogen bonds give water the unique properties that sustain life. If it were not for hydrogen bonding, water would be a gas rather than a liquid at room temperature.


Diagram showing hydrogen bonds formed between adjacent water molecules.

Figure 2.6 Hydrogen bonds form between slightly positive (δ+) and slightly negative (δ–) charges of polar covalent molecules, such as water.


Hydrogen bonds can form between different molecules and they do not always have to include a water molecule. Hydrogen atoms in polar bonds within any molecule can form bonds with other adjacent molecules. For example, hydrogen bonds hold together two long strands of DNA to give the DNA molecule its characteristic double-stranded structure. Hydrogen bonds are also responsible for some of the three-dimensional structure of proteins.

van der Waals Interactions

Like hydrogen bonds, van der Waals interactions are weak attractions or interactions between molecules. They occur between polar, covalently bound, atoms in different molecules. Some of these weak attractions are caused by temporary partial charges formed when electrons move around a nucleus. These weak interactions between molecules are important in biological systems.

Radiography Technicians

Have you or anyone you know ever had a magnetic resonance imaging (MRI) scan, a mammogram, or an X-ray? These tests produce images of your soft tissues and organs (as with an MRI or mammogram) or your bones (as happens in an X-ray) by using either radio waves or special isotopes (radiolabeled or fluorescently labeled) that are ingested or injected into the body. These tests provide data for disease diagnoses by creating images of your organs or skeletal system.

MRI imaging works by subjecting hydrogen nuclei, which are abundant in the water in soft tissues, to fluctuating magnetic fields, which cause them to emit their own magnetic field. This signal is then read by sensors in the machine and interpreted by a computer to form a detailed image.

Some radiography technologists and technicians specialize in computed tomography, MRI, and mammography. They produce films or images of the body that help medical professionals examine and diagnose. Radiologists work directly with patients, explaining machinery, preparing them for exams, and ensuring that their body or body parts are positioned correctly to produce the needed images. Physicians or radiologists then analyze the test results.

Radiography technicians can work in hospitals, doctors’ offices, or specialized imaging centers. Training to become a radiography technician happens at hospitals, colleges, and universities that offer certificates, associate’s degrees, or bachelor’s degrees in radiography.

Section Summary

Matter is anything that occupies space and has mass. It is made up of atoms of different elements. All of the 92 elements that occur naturally have unique qualities that allow them to combine in various ways to create compounds or molecules. Atoms, which consist of protons, neutrons, and electrons, are the smallest units of an element that retain all of the properties of that element. Electrons can be donated or shared between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions.


How many neutrons do (K) potassium-39 and potassium-40 have, respectively?

Potassium-39 has twenty neutrons. Potassium-40 has twenty-one neutrons.

Multiple Choice

Magnesium has an atomic number of 12. Which of the following statements is true of a neutral magnesium atom?

A) It has 12 protons, 12 electrons, and 12 neutrons.

B) It has 12 protons, 12 electrons, and six neutrons.

C) It has six protons, six electrons, and no neutrons.

D) It has six protons, six electrons, and six neutrons.


Which type of bond represents a weak chemical bond?

A) hydrogen bond

B) ionic bond

C) covalent bond

D) polar covalent bond


An isotope of sodium (Na) has a mass number of 22. How many neutrons does it have?

A) 11

B) 12

C) 22

D) 44


Free Response

Why are hydrogen bonds and van der Waals interactions necessary for cells?

Hydrogen bonds and van der Waals interactions form weak associations between different molecules. They provide the structure and shape necessary for proteins and DNA within cells so that they function properly. Hydrogen bonds also give water its unique properties, which are necessary for life.



anion: a negative ion formed by gaining electrons

atomic number: the number of protons in an atom

cation: a positive ion formed by losing electrons

chemical bond: an interaction between two or more of the same or different elements that results in the formation of molecules

covalent bond: a type of strong bond between two or more of the same or different elements; forms when electrons are shared between elements

electron: a negatively charged particle that resides outside of the nucleus in the electron orbital; lacks functional mass and has a charge of –1

electron transfer: the movement of electrons from one element to another

element: one of 118 unique substances that cannot be broken down into smaller substances and retain the characteristic of that substance; each element has a specified number of protons and unique properties

hydrogen bond: a weak bond between partially positively charged hydrogen atoms and partially negatively charged elements or molecules

ion: an atom or compound that does not contain equal numbers of protons and electrons, and therefore has a net charge

ionic bond: a chemical bond that forms between ions of opposite charges

isotope: one or more forms of an element that have different numbers of neutrons

mass number: the number of protons plus neutrons in an atom

matter: anything that has mass and occupies space

neutron: a particle with no charge that resides in the nucleus of an atom; has a mass of 1

nonpolar covalent bond: a type of covalent bond that forms between atoms when electrons are shared equally between atoms, resulting in no regions with partial charges as in polar covalent bonds

nucleus: (chemistry) the dense center of an atom made up of protons and (except in the case of a hydrogen atom) neutrons

octet rule: states that the outermost shell of an element with a low atomic number can hold eight electrons

periodic table of elements: an organizational chart of elements, indicating the atomic number and mass number of each element; also provides key information about the properties of elements

polar covalent bond:a type of covalent bond in which electrons are pulled toward one atom and away from another, resulting in slightly positive and slightly negative charged regions of the molecule

proton: a positively charged particle that resides in the nucleus of an atom; has a mass of 1 and a charge of +1

radioactive isotope: an isotope that spontaneously emits particles or energy to form a more stable element

van der Waals interaction: a weak attraction or interaction between molecules caused by slightly positively charged or slightly negatively charged atoms


2.2 Water

Learning Objectives

By the end of this section, you will be able to:

  • Describe the properties of water that are critical to maintaining life

Do you ever wonder why scientists spend time looking for water on other planets? It is because water is essential to life; even minute traces of it on another planet can indicate that life could or did exist on that planet. Water is one of the more abundant molecules in living cells and the one most critical to life as we know it. Approximately 60–70 percent of your body is made up of water. Without it, life simply would not exist.

Water Is Polar

The hydrogen and oxygen atoms within water molecules form polar covalent bonds. The shared electrons spend more time associated with the oxygen atom than they do with hydrogen atoms. There is no overall charge to a water molecule, but there is a slight positive charge on each hydrogen atom and a slight negative charge on the oxygen atom. Because of these charges, the slightly positive hydrogen atoms repel each other and form the unique shape. Each water molecule attracts other water molecules because of the positive and negative charges in the different parts of the molecule. Water also attracts other polar molecules (such as sugars), forming hydrogen bonds. When a substance readily forms hydrogen bonds with water, it can dissolve in water and is referred to as hydrophilic (“water-loving”). Hydrogen bonds are not readily formed with nonpolar substances like oils and fats . These nonpolar compounds are hydrophobic (“water-fearing”) and will not dissolve in water.

Picture of oil in water.

Figure 2.7 As this macroscopic image of oil and water shows, oil is a nonpolar compound and, hence, will not dissolve in water. Oil and water do not mix. (credit: Gautam Dogra)

Water Stabilizes Temperature

The hydrogen bonds in water allow it to absorb and release heat energy more slowly than many other substances. Temperature is a measure of the motion (kinetic energy) of molecules. As the motion increases, energy is higher and thus temperature is higher. Water absorbs a great deal of energy before its temperature rises. Increased energy disrupts the hydrogen bonds between water molecules. Because these bonds can be created and disrupted rapidly, water absorbs an increase in energy and temperature changes only minimally. This means that water moderates temperature changes within organisms and in their environments. As energy input continues, the balance between hydrogen-bond formation and destruction swings toward the destruction side. More bonds are broken than are formed. This process results in the release of individual water molecules at the surface of the liquid (such as a body of water, the leaves of a plant, or the skin of an organism) in a process called evaporation. Evaporation of sweat, which is 90 percent water, allows for cooling of an organism, because breaking hydrogen bonds requires an input of energy and takes heat away from the body.

Conversely, as molecular motion decreases and temperatures drop, less energy is present to break the hydrogen bonds between water molecules. These bonds remain intact and begin to form a rigid, lattice-like structure (e.g., ice) (Figure 2.8 a). When frozen, ice is less dense than liquid water (the molecules are farther apart). This means that ice floats on the surface of a body of water (Figure 2.8 b). In lakes, ponds, and oceans, ice will form on the surface of the water, creating an insulating barrier to protect the animal and plant life beneath from freezing in the water. If this did not happen, plants and animals living in water would freeze in a block of ice and could not move freely, making life in cold temperatures difficult or impossible.

Part A shows the lattice-like molecular structure of ice. Part B is a photo of ice on water.

Figure 2.8 (a) The lattice structure of ice makes it less dense than the freely flowing molecules of liquid water. Ice’s lower density enables it to (b) float on water. (credit a: modification of work by Jane Whitney; credit b: modification of work by Carlos Ponte)

Concepts in Action

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Click here to see a 3-D animation of the structure of an ice lattice. (credit: image created by Jane Whitney using Visual Molecular Dynamics (VMD) software1)

Water Is an Excellent Solvent

Because water is polar, with slight positive and negative charges, ionic compounds and polar molecules can readily dissolve in it. Water is, therefore, what is referred to as a solvent—a substance capable of dissolving another substance. The charged particles will form hydrogen bonds with a surrounding layer of water molecules. This is referred to as a sphere of hydration and serves to keep the particles separated or dispersed in the water. In the case of table salt (NaCl) mixed in water, the sodium and chloride ions separate, or dissociate, in the water, and spheres of hydration are formed around the ions. A positively charged sodium ion is surrounded by the partially negative charges of oxygen atoms in water molecules. A negatively charged chloride ion is surrounded by the partially positive charges of hydrogen atoms in water molecules. These spheres of hydration are also referred to as hydration shells. The polarity of the water molecule makes it an effective solvent and is important in its many roles in living systems.

Illustration of spheres of hydration around sodium and chlorine ions.

Figure 2.9 When table salt (NaCl) is mixed in water, spheres of hydration form around the ions.

Water Is Cohesive

Have you ever filled up a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water actually forms a dome-like shape above the rim of the glass. This water can stay above the glass because of the property of cohesion. In cohesion, water molecules are attracted to each other (because of hydrogen bonding), keeping the molecules together at the liquid-air (gas) interface, although there is no more room in the glass. Cohesion gives rise to surface tension, the capacity of a substance to withstand rupture when placed under tension or stress. When you drop a small scrap of paper onto a droplet of water, the paper floats on top of the water droplet, although the object is denser (heavier) than the water. This occurs because of the surface tension that is created by the water molecules. Cohesion and surface tension keep the water molecules intact and the item floating on the top. It is even possible to “float” a steel needle on top of a glass of water if you place it gently, without breaking the surface tension.

Picture of a needle floating on top of water because of cohesion and surface tension.

Figure 2.10 The weight of a needle on top of water pulls the surface tension downward; at the same time, the surface tension of the water is pulling it up, suspending the needle on the surface of the water and keeping it from sinking. Notice the indentation in the water around the needle. (credit: Cory Zanker)

These cohesive forces are also related to the water’s property of adhesion, or the attraction between water molecules and other molecules. This is observed when water “climbs” up a straw placed in a glass of water. You will notice that the water appears to be higher on the sides of the straw than in the middle. This is because the water molecules are attracted to the straw and therefore adhere to it.

Cohesive and adhesive forces are important for sustaining life. For example, because of these forces, water can flow up from the roots to the tops of plants to feed the plant.

Concept in Action

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To learn more about water, visit the U.S. Geological Survey Water Science for Schools: All About Water! website.

Buffers, pH, Acids, and Bases

The pH of a solution is a measure of its acidity or alkalinity. You have probably used litmus paper, paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator, to test how much acid or base (alkalinity) exists in a solution. You might have even used some to make sure the water in an outdoor swimming pool is properly treated. In both cases, this pH test measures the amount of hydrogen ions that exists in a given solution. High concentrations of hydrogen ions yield a low pH, whereas low levels of hydrogen ions result in a high pH. The overall concentration of hydrogen ions is inversely related to its pH and can be measured on the pH scale (Figure 2.11). Therefore, the more hydrogen ions present, the lower the pH; conversely, the fewer hydrogen ions, the higher the pH.

The pH scale ranges from 0 to 14. A change of one unit on the pH scale represents a change in the concentration of hydrogen ions by a factor of 10, a change in two units represents a change in the concentration of hydrogen ions by a factor of 100. Thus, small changes in pH represent large changes in the concentrations of hydrogen ions. Pure water is neutral. It is neither acidic nor basic, and has a pH of 7.0. Anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is alkaline. The blood in your veins is slightly alkaline (pH = 7.4). The environment in your stomach is highly acidic (pH = 1 to 2). Orange juice is mildly acidic (pH = approximately 3.5), whereas baking soda is basic (pH = 9.0).

The pH scale with representative substances and their pHs.

Figure 2.11 The pH scale measures the amount of hydrogen ions (H+) in a substance. (credit: modification of work by Edward Stevens)

Acids are substances that provide hydrogen ions (H+) and lower pH, whereas bases provide hydroxide ions (OH) and raise pH. The stronger the acid, the more readily it donates H+. For example, hydrochloric acid and lemon juice are very acidic and readily give up H+ when added to water. Conversely, bases are those substances that readily donate OH. The OH ions combine with H+ to produce water, which raises a substance’s pH. Sodium hydroxide and many household cleaners are very alkaline and give up OH rapidly when placed in water, thereby raising the pH.

Most cells in our bodies operate within a very narrow window of the pH scale, typically ranging only from 7.2 to 7.6. If the pH of the body is outside of this range, the respiratory system malfunctions, as do other organs in the body. Cells no longer function properly, and proteins will break down. Deviation outside of the pH range can induce coma or even cause death.

So how is it that we can ingest or inhale acidic or basic substances and not die? Buffers are the key. Buffers readily absorb excess H+ or OH, keeping the pH of the body carefully maintained in the aforementioned narrow range. Carbon dioxide is part of a prominent buffer system in the human body; it keeps the pH within the proper range. This buffer system involves carbonic acid (H2CO3) and bicarbonate (HCO3) anion. If too much H+ enters the body, bicarbonate will combine with the H+ to create carbonic acid and limit the decrease in pH. Likewise, if too much OH is introduced into the system, carbonic acid will rapidly dissociate into bicarbonate and H+ ions. The H+ ions can combine with the OH ions, limiting the increase in pH. While carbonic acid is an important product in this reaction, its presence is fleeting because the carbonic acid is released from the body as carbon dioxide gas each time we breathe. Without this buffer system, the pH in our bodies would fluctuate too much and we would fail to survive.

Section Summary

Water has many properties that are critical to maintaining life. It is polar, allowing for the formation of hydrogen bonds, which allow ions and other polar molecules to dissolve in water. Therefore, water is an excellent solvent. The hydrogen bonds between water molecules give water the ability to hold heat better than many other substances. As the temperature rises, the hydrogen bonds between water continually break and reform, allowing for the overall temperature to remain stable, although increased energy is added to the system. Water’s cohesive forces allow for the property of surface tension. All of these unique properties of water are important in the chemistry of living organisms.

The pH of a solution is a measure of the concentration of hydrogen ions in the solution. A solution with a high number of hydrogen ions is acidic and has a low pH value. A solution with a high number of hydroxide ions is basic and has a high pH value. The pH scale ranges from 0 to 14, with a pH of 7 being neutral. Buffers are solutions that moderate pH changes when an acid or base is added to the buffer system. Buffers are important in biological systems because of their ability to maintain constant pH conditions.


Multiple Choice

Which of the following statements is not true?

A) Water is polar.

B) Water stabilizes temperature.

C) Water is essential for life.

D) Water is the most abundant atom in Earth’s atmosphere.


Using a pH meter, you find the pH of an unknown solution to be 8.0. How would you describe this solution?

A) weakly acidic

B) strongly acidic

C) weakly basic

D) strongly basic


The pH of lemon juice is about 2.0, whereas tomato juice’s pH is about 4.0. Approximately how much of an increase in hydrogen ion concentration is there between tomato juice and lemon juice?

A) 2 times

B) 10 times

C) 100 times

D) 1000 times


Free Response

Why can some insects walk on water?

Some insects can walk on water, although they are heavier (denser) than water, because of the surface tension of water. Surface tension results from cohesion, or the attraction between water molecules at the surface of the body of water [the liquid-air (gas) interface].

Explain why water is an excellent solvent.

Water molecules are polar, meaning they have separated partial positive and negative charges. Because of these charges, water molecules are able to surround charged particles created when a substance dissociates. The surrounding layer of water molecules stabilizes the ion and keeps differently charged ions from reassociating, so the substance stays dissolved.



acid: a substance that donates hydrogen ions and therefore lowers pH

adhesion: the attraction between water molecules and molecules of a different substance

base: a substance that absorbs hydrogen ions and therefore raises pH

buffer: a solution that resists a change in pH by absorbing or releasing hydrogen or hydroxide ions

cohesion: the intermolecular forces between water molecules caused by the polar nature of water; creates surface tension

evaporation: the release of water molecules from liquid water to form water vapor

hydrophilic: describes a substance that dissolves in water; water-loving

hydrophobic: describes a substance that does not dissolve in water; water-fearing

litmus paper: filter paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator

pH scale: a scale ranging from 0 to 14 that measures the approximate concentration of hydrogen ions of a substance

solvent: a substance capable of dissolving another substance

surface tension: the cohesive force at the surface of a body of liquid that prevents the molecules from separating

temperature: a measure of molecular motion



1 Humphrey, W., Dalke, A. and Schulten, K., “VMD—Visual Molecular Dynamics”, J. Molec. Graphics, 1996, vol. 14, pp. 33-38.


2.3 Biological Molecules

Learning Objectives

By the end of this section, you will be able to:

  • Describe the ways in which carbon is critical to life
  • Explain the impact of slight changes in amino acids on organisms
  • Describe the four major types of biological molecules
  • Understand the functions of the four major types of molecules

The large molecules necessary for life that are built from smaller organic molecules are called biological macromolecules. There are four major classes of biological macromolecules (carbohydrates, lipids, proteins, and nucleic acids), and each is an important component of the cell and performs a wide array of functions. Combined, these molecules make up the majority of a cell’s mass. Biological macromolecules are organic, meaning that they contain carbon. In addition, they may contain hydrogen, oxygen, nitrogen, phosphorus, sulfur, and additional minor elements.


It is often said that life is “carbon-based.” This means that carbon atoms, bonded to other carbon atoms or other elements, form the fundamental components of many, if not most, of the molecules found uniquely in living things. Other elements play important roles in biological molecules, but carbon certainly qualifies as the “foundation” element for molecules in living things. It is the bonding properties of carbon atoms that are responsible for its important role.

Carbon Bonding

Carbon contains four electrons in its outer shell. Therefore, it can form four covalent bonds with other atoms or molecules. The simplest organic carbon molecule is methane (CH4), in which four hydrogen atoms bind to a carbon atom.

Diagram of a methane molecule.

Figure 2.12 Carbon can form four covalent bonds to create an organic molecule. The simplest carbon molecule is methane (CH4), depicted here.

However, structures that are more complex are made using carbon. Any of the hydrogen atoms can be replaced with another carbon atom covalently bonded to the first carbon atom. In this way, long and branching chains of carbon compounds can be made (Figure 2.13 a). The carbon atoms may bond with atoms of other elements, such as nitrogen, oxygen, and phosphorus (Figure 2.13 b). The molecules may also form rings, which themselves can link with other rings (Figure 2.13 c). This diversity of molecular forms accounts for the diversity of functions of the biological macromolecules and is based to a large degree on the ability of carbon to form multiple bonds with itself and other atoms.

Examples of three different carbon-containing molecules.

Figure 2.13 These examples show three molecules (found in living organisms) that contain carbon atoms bonded in various ways to other carbon atoms and the atoms of other elements. (a) This molecule of stearic acid has a long chain of carbon atoms. (b) Glycine, a component of proteins, contains carbon, nitrogen, oxygen, and hydrogen atoms. (c) Glucose, a sugar, has a ring of carbon atoms and one oxygen atom.


Carbohydrates are macromolecules with which most consumers are somewhat familiar. To lose weight, some individuals adhere to “low-carb” diets. Athletes, in contrast, often “carb-load” before important competitions to ensure that they have sufficient energy to compete at a high level. Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and vegetables are all natural sources of carbohydrates. Carbohydrates provide energy to the body, particularly through glucose, a simple sugar. Carbohydrates also have other important functions in humans, animals, and plants.

Carbohydrates can be represented by the formula (CH2O)n, where n is the number of carbon atoms in the molecule. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides.

Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars, the most common of which is glucose. In monosaccharides, the number of carbon atoms usually ranges from three to six. Most monosaccharide names end with the suffix -ose. Depending on the number of carbon atoms in the sugar, they may be known as trioses (three carbon atoms), pentoses (five carbon atoms), and hexoses (six carbon atoms).

Monosaccharides may exist as a linear chain or as ring-shaped molecules; in aqueous solutions, they are usually found in the ring form.

The chemical formula for glucose is C6H12O6. In most living species, glucose is an important source of energy. During cellular respiration, energy is released from glucose, and that energy is used to help make adenosine triphosphate (ATP). Plants synthesize glucose using carbon dioxide and water by the process of photosynthesis, and the glucose, in turn, is used for the energy requirements of the plant. The excess synthesized glucose is often stored as starch that is broken down by other organisms that feed on plants.

Galactose (part of lactose, or milk sugar) and fructose (found in fruit) are other common monosaccharides. Although glucose, galactose, and fructose all have the same chemical formula (C6H12O6), they differ structurally and chemically (and are known as isomers) because of differing arrangements of atoms in the carbon chain.

Chemical structures of glucose, galactose, and fructose.

Figure 2.14 Glucose, galactose, and fructose are isomeric monosaccharides, meaning that they have the same chemical formula but slightly different structures.

Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction (a reaction in which the removal of a water molecule occurs). During this process, the hydroxyl group (–OH) of one monosaccharide combines with a hydrogen atom of another monosaccharide, releasing a molecule of water (H2O) and forming a covalent bond between atoms in the two sugar molecules.

Common disaccharides include lactose, maltose, and sucrose. Lactose is a disaccharide consisting of the monomers glucose and galactose. It is found naturally in milk. Maltose, or malt sugar, is a disaccharide formed from a dehydration reaction between two glucose molecules. The most common disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and fructose.

A long chain of monosaccharides linked by covalent bonds is known as a polysaccharide (poly- = “many”). The chain may be branched or unbranched, and it may contain different types of monosaccharides. Polysaccharides may be very large molecules. Starch, glycogen, cellulose, and chitin are examples of polysaccharides.

Starch is the stored form of sugars in plants and is made up of amylose and amylopectin (both polymers of glucose). Plants are able to synthesize glucose, and the excess glucose is stored as starch in different plant parts, including roots and seeds. The starch that is consumed by animals is broken down into smaller molecules, such as glucose. The cells can then absorb the glucose.

Glycogen is the storage form of glucose in humans and other vertebrates, and is made up of monomers of glucose. Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever glucose levels decrease, glycogen is broken down to release glucose.

Cellulose is one of the most abundant natural biopolymers. The cell walls of plants are mostly made of cellulose, which provides structural support to the cell. Wood and paper are mostly cellulosic in nature. Cellulose is made up of glucose monomers that are linked by bonds between particular carbon atoms in the glucose molecule.

Every other glucose monomer in cellulose is flipped over and packed tightly as extended long chains. This gives cellulose its rigidity and high tensile strength—which is so important to plant cells. Cellulose passing through our digestive system is called dietary fiber. While the glucose-glucose bonds in cellulose cannot be broken down by human digestive enzymes, herbivores such as cows, buffalos, and horses are able to digest grass that is rich in cellulose and use it as a food source. In these animals, certain species of bacteria reside in the rumen (part of the digestive system of herbivores) and secrete the enzyme cellulase. The appendix also contains bacteria that break down cellulose, giving it an important role in the digestive systems of ruminants. Cellulases can break down cellulose into glucose monomers that can be used as an energy source by the animal.

Carbohydrates serve other functions in different animals. Arthropods, such as insects, spiders, and crabs, have an outer skeleton, called the exoskeleton, which protects their internal body parts. This exoskeleton is made of the biological macromolecule chitin, which is a nitrogenous carbohydrate. It is made of repeating units of a modified sugar containing nitrogen.

Thus, through differences in molecular structure, carbohydrates are able to serve the very different functions of energy storage (starch and glycogen) and structural support and protection (cellulose and chitin).

Chemical structures of starch, glycogen, cellulose, and chitin.

Figure 2.15 Although their structures and functions differ, all polysaccharide carbohydrates are made up of monosaccharides and have the chemical formula (CH2O)n.

Registered Dietitian: Obesity is a worldwide health concern, and many diseases, such as diabetes and heart disease, are becoming more prevalent because of obesity. This is one of the reasons why registered dietitians are increasingly sought after for advice. Registered dietitians help plan food and nutrition programs for individuals in various settings. They often work with patients in health-care facilities, designing nutrition plans to prevent and treat diseases. For example, dietitians may teach a patient with diabetes how to manage blood-sugar levels by eating the correct types and amounts of carbohydrates. Dietitians may also work in nursing homes, schools, and private practices.

To become a registered dietitian, one needs to earn at least a bachelor’s degree in dietetics, nutrition, food technology, or a related field. In addition, registered dietitians must complete a supervised internship program and pass a national exam. Those who pursue careers in dietetics take courses in nutrition, chemistry, biochemistry, biology, microbiology, and human physiology. Dietitians must become experts in the chemistry and functions of food (proteins, carbohydrates, and fats).


Lipids include a diverse group of compounds that are united by a common feature. Lipids are hydrophobic (“water-fearing”), or insoluble in water, because they are nonpolar molecules. This is because they are hydrocarbons that include only nonpolar carbon-carbon or carbon-hydrogen bonds. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of lipids called fats. Lipids also provide insulation from the environment for plants and animals. For example, they help keep aquatic birds and mammals dry because of their water-repelling nature. Lipids are also the building blocks of many hormones and are an important constituent of the plasma membrane. Lipids include fats, oils, waxes, phospholipids, and steroids.

A photo of a river otter in the water

Figure 2.16 Hydrophobic lipids in the fur of aquatic mammals, such as this river otter, protect them from the elements. (credit: Ken Bosma)

A fat molecule, such as a triglyceride, consists of two main components—glycerol and fatty acids. Glycerol is an organic compound with three carbon atoms, five hydrogen atoms, and three hydroxyl (–OH) groups. Fatty acids have a long chain of hydrocarbons to which an acidic carboxyl group is attached, hence the name “fatty acid.” The number of carbons in the fatty acid may range from 4 to 36; most common are those containing 12–18 carbons. In a fat molecule, a fatty acid is attached to each of the three oxygen atoms in the –OH groups of the glycerol molecule with a covalent bond.

Chemical structures of starch, glycogen, cellulose, and chitin.

Figure 2.17 Lipids include fats, such as triglycerides, which are made up of fatty acids and glycerol, phospholipids, and steroids.

During this covalent bond formation, three water molecules are released. The three fatty acids in the fat may be similar or dissimilar. These fats are also called triglycerides because they have three fatty acids. Some fatty acids have common names that specify their origin. For example, palmitic acid, a saturated fatty acid, is derived from the palm tree. Arachidic acid is derived from Arachis hypogaea, the scientific name for peanuts.

Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there are only single bonds between neighboring carbons in the hydrocarbon chain, the fatty acid is saturated. Saturated fatty acids are saturated with hydrogen; in other words, the number of hydrogen atoms attached to the carbon skeleton is maximized.

When the hydrocarbon chain contains a double bond, the fatty acid is an unsaturated fatty acid.

Most unsaturated fats are liquid at room temperature and are called oils. If there is one double bond in the molecule, then it is known as a monounsaturated fat (e.g., olive oil), and if there is more than one double bond, then it is known as a polyunsaturated fat (e.g., canola oil).

Saturated fats tend to get packed tightly and are solid at room temperature. Animal fats with stearic acid and palmitic acid contained in meat, and the fat with butyric acid contained in butter, are examples of saturated fats. Mammals store fats in specialized cells called adipocytes, where globules of fat occupy most of the cell. In plants, fat or oil is stored in seeds and is used as a source of energy during embryonic development.

Unsaturated fats or oils are usually of plant origin and contain unsaturated fatty acids. The double bond causes a bend or a “kink” that prevents the fatty acids from packing tightly, keeping them liquid at room temperature. Olive oil, corn oil, canola oil, and cod liver oil are examples of unsaturated fats. Unsaturated fats help to improve blood cholesterol levels, whereas saturated fats contribute to plaque formation in the arteries, which increases the risk of a heart attack.

In the food industry, oils are artificially hydrogenated to make them semi-solid, leading to less spoilage and increased shelf life. Simply speaking, hydrogen gas is bubbled through oils to solidify them. During this hydrogenation process, double bonds of the cis-conformation in the hydrocarbon chain may be converted to double bonds in the trans-conformation. This forms a trans-fat from a cis-fat. The orientation of the double bonds affects the chemical properties of the fat.

Two images show the molecular structure of a fat in the cis-conformation and the trans-conformation.

Figure 2.18 During the hydrogenation process, the orientation around the double bonds is changed, making a trans-fat from a cis-fat. This changes the chemical properties of the molecule.

Margarine, some types of peanut butter, and shortening are examples of artificially hydrogenated trans-fats. Recent studies have shown that an increase in trans-fats in the human diet may lead to an increase in levels of low-density lipoprotein (LDL), or “bad” cholesterol, which, in turn, may lead to plaque deposition in the arteries, resulting in heart disease. Many fast food restaurants have recently eliminated the use of trans-fats, and U.S. food labels are now required to list their trans-fat content.

Essential fatty acids are fatty acids that are required but not synthesized by the human body. Consequently, they must be supplemented through the diet. Omega-3 fatty acids fall into this category and are one of only two known essential fatty acids for humans (the other being omega-6 fatty acids). They are a type of polyunsaturated fat and are called omega-3 fatty acids because the third carbon from the end of the fatty acid participates in a double bond.

Salmon, trout, and tuna are good sources of omega-3 fatty acids. Omega-3 fatty acids are important in brain function and normal growth and development. They may also prevent heart disease and reduce the risk of cancer.

Like carbohydrates, fats have received a lot of bad publicity. It is true that eating an excess of fried foods and other “fatty” foods leads to weight gain. However, fats do have important functions. Fats serve as long-term energy storage. They also provide insulation for the body. Therefore, “healthy” unsaturated fats in moderate amounts should be consumed on a regular basis.

Phospholipids are the major constituent of the plasma membrane. Like fats, they are composed of fatty acid chains attached to a glycerol or similar backbone. Instead of three fatty acids attached, however, there are two fatty acids and the third carbon of the glycerol backbone is bound to a phosphate group. The phosphate group is modified by the addition of an alcohol.

A phospholipid has both hydrophobic and hydrophilic regions. The fatty acid chains are hydrophobic and exclude themselves from water, whereas the phosphate is hydrophilic and interacts with water.

Cells are surrounded by a membrane, which has a bilayer of phospholipids. The fatty acids of phospholipids face inside, away from water, whereas the phosphate group can face either the outside environment or the inside of the cell, which are both aqueous.

Steroids and Waxes

Unlike the phospholipids and fats discussed earlier, steroids have a ring structure. Although they do not resemble other lipids, they are grouped with them because they are also hydrophobic. All steroids have four, linked carbon rings and several of them, like cholesterol, have a short tail.

Cholesterol is a steroid. Cholesterol is mainly synthesized in the liver and is the precursor of many steroid hormones, such as testosterone and estradiol. It is also the precursor of vitamins E and K. Cholesterol is the precursor of bile salts, which help in the breakdown of fats and their subsequent absorption by cells. Although cholesterol is often spoken of in negative terms, it is necessary for the proper functioning of the body. It is a key component of the plasma membranes of animal cells.

Waxes are made up of a hydrocarbon chain with an alcohol (–OH) group and a fatty acid. Examples of animal waxes include beeswax and lanolin. Plants also have waxes, such as the coating on their leaves, that helps prevent them from drying out.

Concept in Action

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For an additional perspective on lipids, explore “Biomolecules: The Lipids” through this interactive animation.


Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of different proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a linear sequence.

The functions of proteins are very diverse because there are 20 different chemically distinct amino acids that form long chains, and the amino acids can be in any order. For example, proteins can function as enzymes or hormones. Enzymes, which are produced by living cells, are catalysts in biochemical reactions (like digestion) and are usually proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) upon which it acts. Enzymes can function to break molecular bonds, to rearrange bonds, or to form new bonds. An example of an enzyme is salivary amylase, which breaks down amylose, a component of starch.

Hormones are chemical signaling molecules, usually proteins or steroids, secreted by an endocrine gland or group of endocrine cells that act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that maintains blood glucose levels.

Proteins have different shapes and molecular weights; some proteins are globular in shape whereas others are fibrous in nature. For example, hemoglobin is a globular protein, but collagen, found in our skin, is a fibrous protein. Protein shape is critical to its function. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape of the protein, leading to a loss of function or denaturation (to be discussed in more detail later). All proteins are made up of different arrangements of the same 20 kinds of amino acids.

Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. Every amino acid also has another variable atom or group of atoms bonded to the central carbon atom known as the R group. The R group is the only difference in structure between the 20 amino acids; otherwise, the amino acids are identical.

The fundamental molecular structure of an amino acid is shown. Also shown are the molecular structures of alanine, valine, lysine, and aspartic acid, which vary only in the structure of the R group

Figure 2.19 Amino acids are made up of a central carbon bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. The central carbon’s fourth bond varies among the different amino acids, as seen in these examples of alanine, valine, lysine, and aspartic acid.

The chemical nature of the R group determines the chemical nature of the amino acid within its protein (that is, whether it is acidic, basic, polar, or nonpolar).

The sequence and number of amino acids ultimately determine a protein’s shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration reaction. The carboxyl group of one amino acid and the amino group of a second amino acid combine, releasing a water molecule. The resulting bond is the peptide bond.

The products formed by such a linkage are called polypeptides. While the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have combined together, have a distinct shape, and have a unique function.

Evolution in Action

The Evolutionary Significance of Cytochrome cCytochrome c is an important component of the molecular machinery that harvests energy from glucose. Because this protein’s role in producing cellular energy is crucial, it has changed very little over millions of years. Protein sequencing has shown that there is a considerable amount of sequence similarity among cytochrome c molecules of different species; evolutionary relationships can be assessed by measuring the similarities or differences among various species’ protein sequences.

For example, scientists have determined that human cytochrome c contains 104 amino acids. For each cytochrome c molecule that has been sequenced to date from different organisms, 37 of these amino acids appear in the same position in each cytochrome c. This indicates that all of these organisms are descended from a common ancestor. On comparing the human and chimpanzee protein sequences, no sequence difference was found. When human and rhesus monkey sequences were compared, a single difference was found in one amino acid. In contrast, human-to-yeast comparisons show a difference in 44 amino acids, suggesting that humans and chimpanzees have a more recent common ancestor than humans and the rhesus monkey, or humans and yeast.

Protein Structure

As discussed earlier, the shape of a protein is critical to its function. To understand how the protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary.

The unique sequence and number of amino acids in a polypeptide chain is its primary structure. The unique sequence for every protein is ultimately determined by the gene that encodes the protein. Any change in the gene sequence may lead to a different amino acid being added to the polypeptide chain, causing a change in protein structure and function. In sickle cell anemia, the hemoglobin β chain has a single amino acid substitution, causing a change in both the structure and function of the protein. What is most remarkable to consider is that a hemoglobin molecule is made up of two alpha chains and two beta chains that each consist of about 150 amino acids. The molecule, therefore, has about 600 amino acids. The structural difference between a normal hemoglobin molecule and a sickle cell molecule—that dramatically decreases life expectancy in the affected individuals—is a single amino acid of the 600.

Because of this change of one amino acid in the chain, the normally biconcave, or disc-shaped, red blood cells assume a crescent or “sickle” shape, which clogs arteries. This can lead to a myriad of serious health problems, such as breathlessness, dizziness, headaches, and abdominal pain for those who have this disease.

Folding patterns resulting from interactions between the non-R group portions of amino acids give rise to the secondary structure of the protein. The most common are the alpha (α)-helix and beta (β)-pleated sheet structures. Both structures are held in shape by hydrogen bonds. In the alpha helix, the bonds form between every fourth amino acid and cause a twist in the amino acid chain.

In the β-pleated sheet, the “pleats” are formed by hydrogen bonding between atoms on the backbone of the polypeptide chain. The R groups are attached to the carbons, and extend above and below the folds of the pleat. The pleated segments align parallel to each other, and hydrogen bonds form between the same pairs of atoms on each of the aligned amino acids. The α-helix and β-pleated sheet structures are found in many globular and fibrous proteins.

The unique three-dimensional structure of a polypeptide is known as its tertiary structure. This structure is caused by chemical interactions between various amino acids and regions of the polypeptide. Primarily, the interactions among R groups create the complex three-dimensional tertiary structure of a protein. There may be ionic bonds formed between R groups on different amino acids, or hydrogen bonding beyond that involved in the secondary structure. When protein folding takes place, the hydrophobic R groups of nonpolar amino acids lay in the interior of the protein, whereas the hydrophilic R groups lay on the outside. The former types of interactions are also known as hydrophobic interactions.

In nature, some proteins are formed from several polypeptides, also known as subunits, and the interaction of these subunits forms the quaternary structure. Weak interactions between the subunits help to stabilize the overall structure. For example, hemoglobin is a combination of four polypeptide subunits.


Figure 2.20 The four levels of protein structure can be observed in these illustrations. (credit: modification of work by National Human Genome Research Institute)

Each protein has its own unique sequence and shape held together by chemical interactions. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape in what is known as denaturation as discussed earlier. Denaturation is often reversible because the primary structure is preserved if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to a loss of function. One example of protein denaturation can be seen when an egg is fried or boiled. The albumin protein in the liquid egg white is denatured when placed in a hot pan, changing from a clear substance to an opaque white substance. Not all proteins are denatured at high temperatures; for instance, bacteria that survive in hot springs have proteins that are adapted to function at those temperatures.

Concept in Action

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For an additional perspective on proteins, explore “Biomolecules: The Proteins” through this interactive animation.

Nucleic Acids

Nucleic acids are key macromolecules in the continuity of life. They carry the genetic blueprint of a cell and carry instructions for the functioning of the cell.

The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals.

The other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules never leave the nucleus, but instead use an RNA intermediary to communicate with the rest of the cell. Other types of RNA are also involved in protein synthesis and its regulation.

DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide, DNA or RNA. Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group . Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to a phosphate group.

Structure of a nucleotide.

Figure 2.21 A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and a phosphate group.

DNA Double-Helical Structure

DNA has a double-helical structure. It is composed of two strands, or polymers, of nucleotides. The strands are formed with bonds between phosphate and sugar groups of adjacent nucleotides. The strands are bonded to each other at their bases with hydrogen bonds, and the strands coil about each other along their length, hence the “double helix” description, which means a double spiral.

Figure 2.22 Chemical structure of DNA, with colored label identifying the four bases as well as the phosphate and deoxyribose components of the backbone.

Figure 2.22 Chemical structure of DNA, with colored label identifying the four bases as well as the phosphate and deoxyribose components of the backbone. (Chemical Structure of DNA by Madeleine Price Ball is CC0).

The alternating sugar and phosphate groups lie on the outside of each strand, forming the backbone of the DNA. The nitrogenous bases are stacked in the interior, like the steps of a staircase, and these bases pair; the pairs are bound to each other by hydrogen bonds. The bases pair in such a way that the distance between the backbones of the two strands is the same all along the molecule.  The rule is that nucleotide A pairs with nucleotide T, and G with C, see section 9.1 for more details.

Section Summary

Living things are carbon-based because carbon plays such a prominent role in the chemistry of living things. The four covalent bonding positions of the carbon atom can give rise to a wide diversity of compounds with many functions, accounting for the importance of carbon in living things. Carbohydrates are a group of macromolecules that are a vital energy source for the cell, provide structural support to many organisms, and can be found on the surface of the cell as receptors or for cell recognition. Carbohydrates are classified as monosaccharides, disaccharides, and polysaccharides, depending on the number of monomers in the molecule.

Lipids are a class of macromolecules that are nonpolar and hydrophobic in nature. Major types include fats and oils, waxes, phospholipids, and steroids. Fats and oils are a stored form of energy and can include triglycerides. Fats and oils are usually made up of fatty acids and glycerol.

Proteins are a class of macromolecules that can perform a diverse range of functions for the cell. They help in metabolism by providing structural support and by acting as enzymes, carriers or as hormones. The building blocks of proteins are amino acids. Proteins are organized at four levels: primary, secondary, tertiary, and quaternary. Protein shape and function are intricately linked; any change in shape caused by changes in temperature, pH, or chemical exposure may lead to protein denaturation and a loss of function.

Nucleic acids are molecules made up of repeating units of nucleotides that direct cellular activities such as cell division and protein synthesis. Each nucleotide is made up of a pentose sugar, a nitrogenous base, and a phosphate group. There are two types of nucleic acids: DNA and RNA.


Multiple Choice

An example of a monosaccharide is ________.

A) fructose

B) glucose

C) galactose

all of the above


Cellulose and starch are examples of ________.

A) monosaccharides

B) disaccharides

C) lipids

D) polysaccharides


Phospholipids are important components of __________.

A) the plasma membrane of cells

B) the ring structure of steroids

C) the waxy covering on leaves

D) the double bond in hydrocarbon chains


The monomers that make up proteins are called _________.

A) nucleotides

B) disaccharides

C) amino acids

D) chaperones


Free Response

Explain at least three functions that lipids serve in plants and/or animals.

Fat serves as a valuable way for animals to store energy. It can also provide insulation. Phospholipids and steroids are important components of cell membranes.

Explain what happens if even one amino acid is substituted for another in a polypeptide chain. Provide a specific example.

A change in gene sequence can lead to a different amino acid being added to a polypeptide chain instead of the normal one. This causes a change in protein structure and function. For example, in sickle cell anemia, the hemoglobin β chain has a single amino acid substitution. Because of this change, the disc-shaped red blood cells assume a crescent shape, which can result in serious health problems.



amino acid: a monomer of a protein

carbohydrate: a biological macromolecule in which the ratio of carbon to hydrogen to oxygen is 1:2:1; carbohydrates serve as energy sources and structural support in cells

cellulose: a polysaccharide that makes up the cell walls of plants and provides structural support to the cell

chitin: a type of carbohydrate that forms the outer skeleton of arthropods, such as insects and crustaceans, and the cell walls of fungi

denaturation: the loss of shape in a protein as a result of changes in temperature, pH, or exposure to chemicals

deoxyribonucleic acid (DNA): a double-stranded polymer of nucleotides that carries the hereditary information of the cell

disaccharide: two sugar monomers that are linked together by a peptide bond

enzyme: a catalyst in a biochemical reaction that is usually a complex or conjugated protein

fat: a lipid molecule composed of three fatty acids and a glycerol (triglyceride) that typically exists in a solid form at room temperature

glycogen: a storage carbohydrate in animals

hormone: a chemical signaling molecule, usually a protein or steroid, secreted by an endocrine gland or group of endocrine cells; acts to control or regulate specific physiological processes

lipids: a class of macromolecules that are nonpolar and insoluble in water

macromolecule: a large molecule, often formed by polymerization of smaller monomers

monosaccharide: a single unit or monomer of carbohydrates

nucleic acid: a biological macromolecule that carries the genetic information of a cell and carries instructions for the functioning of the cell

nucleotide: a monomer of nucleic acids; contains a pentose sugar, a phosphate group, and a nitrogenous base

oil: an unsaturated fat that is a liquid at room temperature

phospholipid: a major constituent of the membranes of cells; composed of two fatty acids and a phosphate group attached to the glycerol backbone

polypeptide: a long chain of amino acids linked by peptide bonds

polysaccharide: a long chain of monosaccharides; may be branched or unbranched

protein: a biological macromolecule composed of one or more chains of amino acids

ribonucleic acid (RNA): a single-stranded polymer of nucleotides that is involved in protein synthesis

saturated fatty acid: a long-chain hydrocarbon with single covalent bonds in the carbon chain; the number of hydrogen atoms attached to the carbon skeleton is maximized

starch: a storage carbohydrate in plants

steroid: a type of lipid composed of four fused hydrocarbon rings

trans-fat: a form of unsaturated fat with the hydrogen atoms neighboring the double bond across from each other rather than on the same side of the double bond

triglyceride: a fat molecule; consists of three fatty acids linked to a glycerol molecule

unsaturated fatty acid: a long-chain hydrocarbon that has one or more than one double bonds in the hydrocarbon chain


Chapter 2 PowerPoint

Chapter 2 Powerpoint


Chapter 3: Introduction to Cell Structure and Function

Left: Human nasal sinus cells as viewed by light microscopy have an irregular round shape and a well-defined nucleus that takes up about one-half of the cell. Middle: Onion skin cells, also viewed by light microscopy, are long and thin with a rectangular shape defined by a cell wall. They are about as wide as a nasal sinus cell, but at least five times as long. The cell wall and nucleus are well defined in the micrograph. The onion skin nucleus is about the same size as the nasal sinus cell nucleus. Right: In this scanning electron micrograph of bacterial cells, the cell surface has a three-dimensional shape. Three of the bacteria are oval in shape. The fourth is round and has protrusions called pili. One pilus connects this bacterium to another.

Figure 3.1 (a) Nasal sinus cells (viewed with a light microscope), (b) onion cells (viewed with a light microscope), and (c) Vibrio tasmaniensis bacterial cells (viewed using a scanning electron microscope) are from very different organisms, yet all share certain characteristics of basic cell structure. (credit a: modification of work by Ed Uthman, MD; credit b: modification of work by Umberto Salvagnin; credit c: modification of work by Anthony D’Onofrio; scale-bar data from Matt Russell)

Close your eyes and picture a brick wall. What is the basic building block of that wall? It is a single brick, of course. Like a brick wall, your body is composed of basic building blocks, and the building blocks of your body are cells.  An average human is thought to have 37.2 trillion cells.

Your body has many kinds of cells, each specialized for a specific purpose. Just as a home is made from a variety of building materials, the human body is constructed from many cell types. For example, epithelial cells protect the surface of the body and cover the organs and body cavities within. Bone cells help to support and protect the body. Cells of the immune system fight invading bacteria. Additionally, red blood cells carry oxygen throughout the body. Each of these cell types plays a vital role during the growth, development, and day-to-day maintenance of the body. In spite of their enormous variety, however, all cells share certain fundamental characteristics.


3.1 How Cells Are Studied

Learning Objectives

By the end of this section, you will be able to:

  • Describe the roles of cells in organisms
  • Compare and contrast light microscopy and electron microscopy
  • Summarize the cell theory

A cell is the smallest unit of a living thing. A living thing, like you, is called an organism. Thus, cells are the basic building blocks of all organisms.

In multicellular organisms, several cells of one particular kind interconnect with each other and perform shared functions to form tissues (for example, muscle tissue, connective tissue, and nervous tissue), several tissues combine to form an organ (for example, stomach, heart, or brain), and several organs make up an organ system (such as the digestive system, circulatory system, or nervous system). Several systems functioning together form an organism (such as an elephant, for example).

There are many types of cells, and all are grouped into one of two broad categories: prokaryotic and eukaryotic. Animal cells, plant cells, fungal cells, and protist cells are classified as eukaryotic, whereas bacteria and archaea cells are classified as prokaryotic. Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, let us first examine how biologists study cells.


Cells vary in size. With few exceptions, individual cells are too small to be seen with the naked eye, so scientists use microscopes to study them. A microscope is an instrument that magnifies an object. Most images of cells are taken with a microscope and are called micrographs.

Light Microscopes

To give you a sense of the size of a cell, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as µm) in diameter; the head of a pin is about two thousandths of a meter (millimeters, or mm) in diameter. That means that approximately 250 red blood cells could fit on the head of a pin.

The optics of the lenses of a light microscope changes the orientation of the image. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when viewed through a microscope, and vice versa. Similarly, if the slide is moved left while looking through the microscope, it will appear to move right, and if moved down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image. Due to the manner in which light travels through the lenses, this system of lenses produces an inverted image (binoculars and a dissecting microscope work in a similar manner, but include an additional magnification system that makes the final image appear to be upright).

Most student microscopes are classified as light microscopes (Figure 3.2 a). Visible light both passes through and is bent by the lens system to enable the user to see the specimen. Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells.

Light microscopes commonly used in the undergraduate college laboratory magnify up to approximately 400 times. Two parameters that are important in microscopy are magnification and resolving power. Magnification is the degree of enlargement of an object. Resolving power is the ability of a microscope to allow the eye to distinguish two adjacent structures as separate; the higher the resolution, the closer those two objects can be, and the better the clarity and detail of the image. When oil immersion lenses are used, magnification is usually increased to 1,000 times for the study of smaller cells, like most prokaryotic cells. Because light entering a specimen from below is focused onto the eye of an observer, the specimen can be viewed using light microscopy. For this reason, for light to pass through a specimen, the sample must be thin or translucent.

Concept in Action

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For another perspective on cell size, try the HowBig interactive.

A second type of microscope used in laboratories is the dissecting microscope (Figure 3.2 b). These microscopes have a lower magnification (20 to 80 times the object size) than light microscopes and can provide a three-dimensional view of the specimen. Thick objects can be examined with many components in focus at the same time. These microscopes are designed to give a magnified and clear view of tissue structure as well as the anatomy of the whole organism. Like light microscopes, most modern dissecting microscopes are also binocular, meaning that they have two separate lens systems, one for each eye. The lens systems are separated by a certain distance, and therefore provide a sense of depth in the view of their subject to make manipulations by hand easier. Dissecting microscopes also have optics that correct the image so that it appears as if being seen by the naked eye and not as an inverted image. The light illuminating a sample under a dissecting microscope typically comes from above the sample, but may also be directed from below.

Part a: This light microscope has binocular lenses and three objective lenses. The sample stage is directly beneath the objective lens. The light microscope sits on a tabletop. Part b: The dissecting microscope has binocular eyepieces, one objective lens, and light sources from both above and below the sample stage. There is room on the stage for a three-dimensional specimen.

Figure 3.2 (a) Most light microscopes used in a college biology lab can magnify cells up to approximately 400 times. (b) Dissecting microscopes have a lower magnification than light microscopes and are used to examine larger objects, such as tissues.

Electron Microscopes

In contrast to light microscopes, electron microscopes use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure 3.4), it also provides higher resolving power. Preparation of a specimen for viewing under an electron microscope will kill it; therefore, live cells cannot be viewed using this type of microscopy. In addition, the electron beam moves best in a vacuum, making it impossible to view living materials.

In a scanning electron microscope, a beam of electrons moves back and forth across a cell’s surface, rendering the details of cell surface characteristics by reflection. Cells and other structures are usually coated with a metal like gold. In a transmission electron microscope, the electron beam is transmitted through the cell and provides details of a cell’s internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than are light microscopes.

Part a: Salmonella viewed through a light microscope appear as tiny purple dots.

Figure 3.3 Salmonella bacteria are viewed with a light microscope. (modification of work by CDC, Armed Forces Institute of Pathology, Charles N. Farmer)

Part b: In this scanning electron micrograph, the bacteria appear as three-dimensional red ovals. The human cells are much larger with a complex, folded appearance. Some of the bacteria lie on the surfaces of the human cells, and some are squeezed between them.

Figure 3.4 This scanning electron micrograph shows Salmonella bacteria (in red) invading human cells. (modification of work by Rocky Mountain Laboratories, NIAID, NIH; scale-bar data from Matt Russell)

Cytotechnologist: Have you ever heard of a medical test called a Pap smear? In this test, a doctor takes a small sample of cells from the uterine cervix of a patient and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection.

Cytotechnologists (cyto– = cell) are professionals who study cells through microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits or are abnormal. Their focus is not limited to cervical cells; they study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, who is a medical doctor who can make a clinical diagnosis.

Cytotechnologists play vital roles in saving people’s lives. When abnormalities are discovered early, a patient’s treatment can begin sooner, which usually increases the chances of successful treatment.

Both normal cells and cells infected with HPV have an irregular, round shape and a well-defined nucleus. The infected cells, however, are two to three times as large as uninfected cells, and some have two nuclei.

Figure 3.5 These uterine cervix cells, viewed through a light microscope, were obtained from a Pap smear. Normal cells are on the left. The cells on the right are infected with human papillomavirus. (credit: modification of work by Ed Uthman; scale-bar data from Matt Russell)

Cell Theory

The microscopes we use today are far more complex than those used in the 1600s by Antony van Leeuwenhoek, a Dutch shopkeeper who had great skill in crafting lenses. Despite the limitations of his now-ancient lenses, van Leeuwenhoek observed the movements of protists (a type of single-celled organism) and sperm, which he collectively termed “animalcules.”

In a 1665 publication called Micrographia, experimental scientist Robert Hooke coined the term “cell” (from the Latin cella, meaning “small room”) for the box-like structures he observed when viewing cork tissue through a lens. In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses and microscope construction enabled other scientists to see different components inside cells.

By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that all living things are composed of one or more cells, that the cell is the basic unit of life, and that all new cells arise from existing cells. These principles still stand today.

Section Summary

A cell is the smallest unit of life. Most cells are so small that they cannot be viewed with the naked eye. Therefore, scientists must use microscopes to study cells. Electron microscopes provide higher magnification, higher resolution, and more detail than light microscopes. The unified cell theory states that all organisms are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells.


Multiple Choice

When viewing a specimen through a light microscope, scientists use _________ to distinguish the individual components of cells.

A) a beam of electrons

B) radioactive isotopes

C) special stains

D) high temperatures


The ___________ is the basic unit of life.

A) organism

B) cell

C) tissue

D) organ


Free Response

What are the advantages and disadvantages of light, transmission, and scanning electron microscopes?

The advantages of light microscopes are that they are easily obtained, and the light beam does not kill the cells. However, typical light microscopes are somewhat limited in the amount of detail that they can reveal. Electron microscopes are ideal because you can view intricate details, but they are bulky and costly, and preparation for the microscopic examination kills the specimen. Transmission electron microscopes are designed to examine the internal structures of a cell, whereas a scanning electron microscope only allows visualization of the surface of a structure.



microscope: the instrument that magnifies an object

unified cell theory: the biological concept that states that all organisms are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells


3.2 Comparing Prokaryotic and Eukaryotic Cells

Learning Objectives

By the end of this section, you will be able to:

  • Name examples of prokaryotic and eukaryotic organisms
  • Compare and contrast prokaryotic cells and eukaryotic cells
  • Describe the relative sizes of different kinds of cells


Cells fall into one of two broad categories: prokaryotic and eukaryotic. The predominantly single-celled organisms of the domains Bacteria and Archaea are classified as prokaryotes (pro– = before; –karyon– = nucleus). Animal cells, plant cells, fungi, and protists are eukaryotes (eu– = true).

Components of Prokaryotic Cells

All cells share four common components: 1) a plasma membrane, an outer covering that separates the cell’s interior from its surrounding environment; 2) cytoplasm, consisting of a jelly-like region within the cell in which other cellular components are found; 3) DNA, the genetic material of the cell; and 4) ribosomes, particles that synthesize proteins. However, prokaryotes differ from eukaryotic cells in several ways.

A prokaryotic cell is a simple, single-celled (unicellular) organism that lacks a nucleus, or any other membrane-bound organelle. We will shortly come to see that this is significantly different in eukaryotes. Prokaryotic DNA is found in the central part of the cell: a darkened region called the nucleoid.

In this illustration, the prokaryotic cell has an oval shape. The circular chromosome is concentrated in a region called the nucleoid. The fluid inside the cell is called the cytoplasm. Ribosomes, depicted as small circles, float in the cytoplasm. The cytoplasm is encased in a plasma membrane, which in turn is encased by a cell wall. A capsule surrounds the cell wall. The bacterium depicted has a flagellum protruding from one narrow end. Pili are small protrusions that extend from the capsule in all directions.

Figure 3.6 This figure shows the generalized structure of a prokaryotic cell.

Unlike Archaea and eukaryotes, bacteria have a cell wall made of peptidoglycan, comprised of sugars and amino acids, and many have a polysaccharide capsule (Figure 3.6). The cell wall acts as an extra layer of protection, helps the cell maintain its shape, and prevents dehydration. The capsule enables the cell to attach to surfaces in its environment. Some prokaryotes have flagella, pili, or fimbriae. Flagella are used for locomotion, while most pili are used to exchange genetic material during a type of reproduction called conjugation.

Eukaryotic Cells

In nature, the relationship between form and function is apparent at all levels, including the level of the cell, and this will become clear as we explore eukaryotic cells. The principle “form follows function” is found in many contexts. For example, birds and fish have streamlined bodies that allow them to move quickly through the medium in which they live, be it air or water. It means that, in general, one can deduce the function of a structure by looking at its form, because the two are matched.

A eukaryotic cell is a cell that has a membrane-bound nucleus and other membrane-bound compartments or sacs, called organelles, which have specialized functions. The word eukaryotic means “true kernel” or “true nucleus,” alluding to the presence of the membrane-bound nucleus in these cells. The word “organelle” means “little organ,” and, as already mentioned, organelles have specialized cellular functions, just as the organs of your body have specialized functions.

Cell Size

At 0.1–5.0 µm in diameter, prokaryotic cells are significantly smaller than eukaryotic cells, which have diameters ranging from 10–100 µm (Figure 3.7). The small size of prokaryotes allows ions and organic molecules that enter them to quickly spread to other parts of the cell. Similarly, any wastes produced within a prokaryotic cell can quickly move out. However, larger eukaryotic cells have evolved different structural adaptations to enhance cellular transport. Indeed, the large size of these cells would not be possible without these adaptations. In general, cell size is limited because volume increases much more quickly than does cell surface area. As a cell becomes larger, it becomes more and more difficult for the cell to acquire sufficient materials to support the processes inside the cell, because the relative size of the surface area across which materials must be transported declines.

Relative sizes on a logarithmic scale, from 0.1 nm to 1 m, are shown. Objects are shown from smallest to largest. The smallest object shown, an atom, is about 1 nm in size. The next largest objects shown are lipids and proteins; these molecules are between 1 and 10 nm. Bacteria are about 100 nm, and mitochondria are about 1 µm. Plant and animal cells are both between 10 and 100 µm. A human egg is between 100 µm and 1 mm. A frog egg is about 1 mm, a chicken egg and an ostrich egg are both between 10 and 100 mm, but a chicken egg is larger. For comparison, a human is approximately 1 m tall.

Figure 3.7 This figure shows the relative sizes of different kinds of cells and cellular components. An adult human is shown for comparison.

Section Summary

Prokaryotes are predominantly single-celled organisms of the domains Bacteria and Archaea. All prokaryotes have plasma membranes, cytoplasm, ribosomes, a cell wall, DNA, and lack membrane-bound organelles. Many also have polysaccharide capsules. Prokaryotic cells range in diameter from 0.1–5.0 µm.

Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes, but a eukaryotic cell is typically larger than a prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a membrane), and has other membrane-bound organelles that allow for compartmentalization of functions. Eukaryotic cells tend to be 10 to 100 times the size of prokaryotic cells.


Multiple Choice

Which of these do all prokaryotes and eukaryotes share?

A) nuclear envelope

B) cell walls

C) organelles

D) plasma membrane


A typical prokaryotic cell __________________ compared to a eukaryotic cell.

A) is smaller in size by a factor of 100

B) is similar in size

C) is smaller in size by a factor of one million

D) is larger in size by a factor of 10


Free Response

Describe the structures that are characteristic of a prokaryote cell.

Prokaryotic cells are surrounded by a plasma membrane and have DNA, cytoplasm, and ribosomes, like eukaryotic cells. They also have cell walls and may have a cell capsule. Prokaryotes have a single large chromosome that is not surrounded by a nuclear membrane. Prokaryotes may have flagella or motility, pili for conjugation, and fimbriae for adhesion to surfaces.



eukaryotic cell: a cell that has a membrane-bound nucleus and several other membrane-bound compartments or sacs

organelle: a membrane-bound compartment or sac within a cell

prokaryotic cell: a unicellular organism that lacks a nucleus or any other membrane-bound organelle



3.3 Eukaryotic Cells

Learning Objectives

By the end of this section, you will be able to:

  • Describe the structure of eukaryotic plant and animal cells
  • State the role of the plasma membrane
  • Summarize the functions of the major cell organelles
  • Describe the cytoskeleton and extracellular matrix


At this point, it should be clear that eukaryotic cells have a more complex structure than do prokaryotic cells. Organelles allow for various functions to occur in the cell at the same time. Before discussing the functions of organelles within a eukaryotic cell, let us first examine two important components of the cell: the plasma membrane and the cytoplasm.

Part a: This illustration shows a typical eukaryotic cell, which is egg shaped. The fluid inside the cell is called the cytoplasm, and the cell is surrounded by a cell membrane. The nucleus takes up about one-half of the width of the cell. Inside the nucleus is the chromatin, which is comprised of DNA and associated proteins. A region of the chromatin is condensed into the nucleolus, a structure in which ribosomes are synthesized. The nucleus is encased in a nuclear envelope, which is perforated by protein-lined pores that allow entry of material into the nucleus. The nucleus is surrounded by the rough and smooth endoplasmic reticulum, or ER. The smooth ER is the site of lipid synthesis. The rough ER has embedded ribosomes that give it a bumpy appearance. It synthesizes membrane and secretory proteins. Besides the ER, many other organelles float inside the cytoplasm. These include the Golgi apparatus, which modifies proteins and lipids synthesized in the ER. The Golgi apparatus is made of layers of flat membranes. Mitochondria, which produce energy for the cell, have an outer membrane and a highly folded inner membrane. Other, smaller organelles include peroxisomes that metabolize waste, lysosomes that digest food, and vacuoles. Ribosomes, responsible for protein synthesis, also float freely in the cytoplasm and are depicted as small dots. The last cellular component shown is the cytoskeleton, which has four different types of components: microfilaments, intermediate filaments, microtubules, and centrosomes. Microfilaments are fibrous proteins that line the cell membrane and make up the cellular cortex. Intermediate filaments are fibrous proteins that hold organelles in place. Microtubules form the mitotic spindle and maintain cell shape. Centrosomes are made of two tubular structures at right angles to one another. They form the microtubule-organizing center.Figure_03_03_01a_new

Figure 3.8 (a) This figure shows a typical animal cell

Part b: This illustration depicts a typical eukaryotic plant cell. The nucleus of a plant cell contains chromatin and a nucleolus, the same as in an animal cell. Other structures that a plant cell has in common with an animal cell include rough and smooth ER, the Golgi apparatus, mitochondria, peroxisomes, and ribosomes. The fluid inside the plant cell is called the cytoplasm, just as in an animal cell. The plant cell has three of the four cytoskeletal components found in animal cells: microtubules, intermediate filaments, and microfilaments. Plant cells do not have centrosomes. Plants have five structures not found in animals cells: plasmodesmata, chloroplasts, plastids, a central vacuole, and a cell wall. Plasmodesmata form channels between adjacent plant cells. Chloroplasts are responsible for photosynthesis; they have an outer membrane, an inner membrane, and stack of membranes inside the inner membrane. The central vacuole is a very large, fluid-filled structure that maintains pressure against the cell wall. Plastids store pigments. The cell wall is localized outside the cell membrane.

Figure 3.8 (b) This figures shows a typical plant cell.

What structures does a plant cell have that an animal cell does not have? What structures does an animal cell have that a plant cell does not have? Plant cells have plasmodesmata, a cell wall, a large central vacuole, chloroplasts, and plastids. Animal cells have lysosomes and centrosomes.

The Plasma Membrane

Like prokaryotes, eukaryotic cells have a plasma membrane (Figure 3.9) made up of a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment. A phospholipid is a lipid molecule composed of two fatty acid chains, a glycerol backbone, and a phosphate group. The plasma membrane regulates the passage of some substances, such as organic molecules, ions, and water, preventing the passage of some to maintain internal conditions, while actively bringing in or removing others. Other compounds move passively across the membrane.

the plasma membrane is composed of a phospholipid bilayer. in the bilayer, the two long hydrophobic tails of phospholipids face toward the center, and the hydrophilic head group faces the exterior. Integral membrane proteins and protein channels span the entire bilayer. Protein channels have a pore in the middle. Peripheral membrane proteins sit on the surface of the phospholipids and are associated with the head groups. On the exterior side of the membrane, carbohydrates are attached to certain proteins and lipids. Filaments of the cytoskeleton line the interior of the membrane.

Figure 3.9 The plasma membrane is a phospholipid bilayer with embedded proteins. There are other components, such as cholesterol and carbohydrates, which can be found in the membrane in addition to phospholipids and protein.

The plasma membranes of cells that specialize in absorption are folded into fingerlike projections called microvilli (singular = microvillus). This folding increases the surface area of the plasma membrane. Such cells are typically found lining the small intestine, the organ that absorbs nutrients from digested food. This is an excellent example of form matching the function of a structure.

People with celiac disease have an immune response to gluten, which is a protein found in wheat, barley, and rye. The immune response damages microvilli, and thus, afflicted individuals cannot absorb nutrients. This leads to malnutrition, cramping, and diarrhea. Patients suffering from celiac disease must follow a gluten-free diet.

The Cytoplasm

The cytoplasm comprises the contents of a cell between the plasma membrane and the nuclear envelope (a structure to be discussed shortly). It is made up of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals. Even though the cytoplasm consists of 70 to 80 percent water, it has a semi-solid consistency, which comes from the proteins within it. However, proteins are not the only organic molecules found in the cytoplasm. Glucose and other simple sugars, polysaccharides, amino acids, nucleic acids, fatty acids, and derivatives of glycerol are found there too. Ions of sodium, potassium, calcium, and many other elements are also dissolved in the cytoplasm. Many metabolic reactions, including protein synthesis, take place in the cytoplasm.

The Cytoskeleton

If you were to remove all the organelles from a cell, would the plasma membrane and the cytoplasm be the only components left? No. Within the cytoplasm, there would still be ions and organic molecules, plus a network of protein fibers that helps to maintain the shape of the cell, secures certain organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move independently. Collectively, this network of protein fibers is known as the cytoskeleton. There are three types of fibers within the cytoskeleton: microfilaments, also known as actin filaments, intermediate filaments, and microtubules (Figure 3.10).

Microfilaments line the inside of the plasma membrane, whereas microfilaments radiate out from the center of the cell. Intermediate filaments form a network throughout the cell that holds organelles in place.

Figure 3.10 Microfilaments, intermediate filaments, and microtubules compose a cell’s cytoskeleton.

Microfilaments are the thinnest of the cytoskeletal fibers and function in moving cellular components, for example, during cell division. They also maintain the structure of microvilli, the extensive folding of the plasma membrane found in cells dedicated to absorption. These components are also common in muscle cells and are responsible for muscle cell contraction. Intermediate filaments are of intermediate diameter and have structural functions, such as maintaining the shape of the cell and anchoring organelles. Keratin, the compound that strengthens hair and nails, forms one type of intermediate filament. Microtubules are the thickest of the cytoskeletal fibers. These are hollow tubes that can dissolve and reform quickly. Microtubules guide organelle movement and are the structures that pull chromosomes to their poles during cell division. They are also the structural components of flagella and cilia. In cilia and flagella, the microtubules are organized as a circle of nine double microtubules on the outside and two microtubules in the center.

The centrosome is a region near the nucleus of animal cells that functions as a microtubule-organizing center. It contains a pair of centrioles, two structures that lie perpendicular to each other. Each centriole is a cylinder of nine triplets of microtubules.

The centrosome replicates itself before a cell divides, and the centrioles play a role in pulling the duplicated chromosomes to opposite ends of the dividing cell. However, the exact function of the centrioles in cell division is not clear, since cells that have the centrioles removed can still divide, and plant cells, which lack centrioles, are capable of cell division.

Flagella and Cilia

Flagella (singular = flagellum) are long, hair-like structures that extend from the plasma membrane and are used to move an entire cell, (for example, sperm, Euglena). When present, the cell has just one flagellum or a few flagella. When cilia (singular = cilium) are present, however, they are many in number and extend along the entire surface of the plasma membrane. They are short, hair-like structures that are used to move entire cells (such as paramecium) or move substances along the outer surface of the cell (for example, the cilia of cells lining the fallopian tubes that move the ovum toward the uterus, or cilia lining the cells of the respiratory tract that move particulate matter toward the throat that mucus has trapped).

The Endomembrane System

The endomembrane system (endo = within) is a group of membranes and organelles in eukaryotic cells that work together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, vesicles, endoplasmic reticulum and the Golgi apparatus, which we will cover shortly. Although not technically within the cell, the plasma membrane is included in the endomembrane system because, as you will see, it interacts with the other endomembranous organelles.

The Nucleus

Typically, the nucleus is the most prominent organelle in a cell. The nucleus (plural = nuclei) houses the cell’s DNA in the form of chromatin and directs the synthesis of ribosomes and proteins. Let us look at it in more detail (Figure 3.11).

In this illustration, chromatin floats in the nucleoplasm. The nucleoid is depicted as a dense, circular region inside the nucleus. The double nuclear membrane is perforated with protein-lined pores

Figure 3.11 The outermost boundary of the nucleus is the nuclear envelope. Notice that the nuclear envelope consists of two phospholipid bilayers (membranes)—an outer membrane and an inner membrane—in contrast to the plasma membrane ([link]), which consists of only one phospholipid bilayer. (credit: modification of work by NIGMS, NIH)

The nuclear envelope is a double-membrane structure that constitutes the outermost portion of the nucleus (Figure 3.11). Both the inner and outer membranes of the nuclear envelope are phospholipid bilayers.

The nuclear envelope is punctuated with pores that control the passage of ions, molecules, and RNA between the nucleoplasm and the cytoplasm.

To understand chromatin, it is helpful to first consider chromosomes. Chromosomes are structures within the nucleus that are made up of DNA, the hereditary material, and proteins. This combination of DNA and proteins is called chromatin. In eukaryotes, chromosomes are linear structures. Every species has a specific number of chromosomes in the nucleus of its body cells. For example, in humans, the chromosome number is 46, whereas in fruit flies, the chromosome number is eight.

Chromosomes are only visible and distinguishable from one another when the cell is getting ready to divide. When the cell is in the growth and maintenance phases of its life cycle, the chromosomes resemble an unwound, jumbled bunch of threads.

This image shows various levels of the organization of chromatin (DNA and protein).

Figure 3.12 This image shows various levels of the organization of chromatin (DNA and protein).


This image shows paired chromosomes

Figure 3.13 This image shows paired chromosomes. (credit: modification of work by NIH; scale-bar data from Matt Russell)

We already know that the nucleus directs the synthesis of ribosomes, but how does it do this? Some chromosomes have sections of DNA that encode ribosomal RNA. A darkly stained area within the nucleus, called the nucleolus (plural = nucleoli), aggregates the ribosomal RNA with associated proteins to assemble the ribosomal subunits that are then transported through the nuclear pores into the cytoplasm.

The Endoplasmic Reticulum

The endoplasmic reticulum (ER) is a series of interconnected membranous tubules that collectively modify proteins and synthesize lipids. However, these two functions are performed in separate areas of the endoplasmic reticulum: the rough endoplasmic reticulum and the smooth endoplasmic reticulum, respectively.

The hollow portion of the ER tubules is called the lumen or cisternal space. The membrane of the ER, which is a phospholipid bilayer embedded with proteins, is continuous with the nuclear envelope.

The rough endoplasmic reticulum (RER) is so named because the ribosomes attached to its cytoplasmic surface give it a studded appearance when viewed through an electron microscope.

The ribosomes synthesize proteins while attached to the ER, resulting in the transfer of their newly synthesized proteins into the lumen of the RER where they undergo modifications such as folding or addition of sugars. The RER also makes phospholipids for cell membranes.

If the phospholipids or modified proteins are not destined to stay in the RER, they will be packaged within vesicles and transported from the RER by budding from the membrane. Since the RER is engaged in modifying proteins that will be secreted from the cell, it is abundant in cells that secrete proteins, such as the liver.

The smooth endoplasmic reticulum (SER) is continuous with the RER but has few or no ribosomes on its cytoplasmic surface. The SER’s functions include synthesis of carbohydrates, lipids (including phospholipids), and steroid hormones; detoxification of medications and poisons; alcohol metabolism; and storage of calcium ions.

The Golgi Apparatus

We have already mentioned that vesicles can bud from the ER, but where do the vesicles go? Before reaching their final destination, the lipids or proteins within the transport vesicles need to be sorted, packaged, and tagged so that they wind up in the right place. The sorting, tagging, packaging, and distribution of lipids and proteins take place in the Golgi apparatus (also called the Golgi body), a series of flattened membranous sacs.

In this transmission electron micrograph, the Golgi apparatus appears as a stack of membranes surrounded by unnamed organelles.

Figure 3.14 The Golgi apparatus in this transmission electron micrograph of a white blood cell is visible as a stack of semicircular flattened rings in the lower portion of this image. Several vesicles can be seen near the Golgi apparatus. (credit: modification of work by Louisa Howard; scale-bar data from Matt Russell)

The Golgi apparatus has a receiving face near the endoplasmic reticulum and a releasing face on the side away from the ER, toward the cell membrane. The transport vesicles that form from the ER travel to the receiving face, fuse with it, and empty their contents into the lumen of the Golgi apparatus. As the proteins and lipids travel through the Golgi, they undergo further modifications. The most frequent modification is the addition of short chains of sugar molecules. The newly modified proteins and lipids are then tagged with small molecular groups to enable them to be routed to their proper destinations.

Finally, the modified and tagged proteins are packaged into vesicles that bud from the opposite face of the Golgi. While some of these vesicles, transport vesicles, deposit their contents into other parts of the cell where they will be used, others, secretory vesicles, fuse with the plasma membrane and release their contents outside the cell.

The amount of Golgi in different cell types again illustrates that form follows function within cells. Cells that engage in a great deal of secretory activity (such as cells of the salivary glands that secrete digestive enzymes or cells of the immune system that secrete antibodies) have an abundant number of Golgi.

In plant cells, the Golgi has an additional role of synthesizing polysaccharides, some of which are incorporated into the cell wall and some of which are used in other parts of the cell.


In animal cells, the lysosomes are the cell’s “garbage disposal.” Digestive enzymes within the lysosomes aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles. In single-celled eukaryotes, lysosomes are important for digestion of the food they ingest and the recycling of organelles. These enzymes are active at a much lower pH (more acidic) than those located in the cytoplasm. Many reactions that take place in the cytoplasm could not occur at a low pH, thus the advantage of compartmentalizing the eukaryotic cell into organelles is apparent.

Lysosomes also use their hydrolytic enzymes to destroy disease-causing organisms that might enter the cell. A good example of this occurs in a group of white blood cells called macrophages, which are part of your body’s immune system. In a process known as phagocytosis, a section of the plasma membrane of the macrophage invaginates (folds in) and engulfs a pathogen. The invaginated section, with the pathogen inside, then pinches itself off from the plasma membrane and becomes a vesicle. The vesicle fuses with a lysosome. The lysosome’s hydrolytic enzymes then destroy the pathogen (Figure 3.15).

In this illustration, a eukaryotic cell is shown consuming a bacterium. As the bacterium is consumed, it is encapsulated into a vesicle. The vesicle fuses with a lysosome, and proteins inside the lysosome digest the bacterium.

Figure 3.15 A macrophage has phagocytized a potentially pathogenic bacterium into a vesicle, which then fuses with a lysosome within the cell so that the pathogen can be destroyed. Other organelles are present in the cell, but for simplicity, are not shown.

Vesicles and Vacuoles

Vesicles and vacuoles are membrane-bound sacs that function in storage and transport. Vacuoles are somewhat larger than vesicles, and the membrane of a vacuole does not fuse with the membranes of other cellular components. Vesicles can fuse with other membranes within the cell system. Additionally, enzymes within plant vacuoles can break down macromolecules.

This figure shows the nucleus, rough ER, Golgi apparatus, vesicles, and plasma membrane. The right side of the rough ER is shown with an integral membrane protein embedded in it. The part of the protein facing the inside of the ER has a carbohydrate attached to it. The protein is shown leaving the ER in a vesicle that fuses with the cis face of the Golgi apparatus. The Golgi apparatus consists of several layers of membranes, called cisternae. As the protein passes through the cisternae, it is further modified by the addition of more carbohydrates. Eventually, it leaves the trans face of the Golgi in a vesicle. The vesicle fuses with the cell membrane so that the carbohydrate that was on the inside of the vesicle faces the outside of the membrane. At the same time, the contents of the vesicle are released from the cell.

Figure 3.16 The endomembrane system works to modify, package, and transport lipids and proteins. (credit: modification of work by Magnus Manske)

Why does the cis face of the Golgi not face the plasma membrane?

<!– Because that face receives chemicals from the ER, which is toward the center of the cell. –>


Ribosomes are the cellular structures responsible for protein synthesis. When viewed through an electron microscope, free ribosomes appear as either clusters or single tiny dots floating freely in the cytoplasm. Ribosomes may be attached to either the cytoplasmic side of the plasma membrane or the cytoplasmic side of the endoplasmic reticulum. Electron microscopy has shown that ribosomes consist of large and small subunits. Ribosomes are enzyme complexes that are responsible for protein synthesis.

Because protein synthesis is essential for all cells, ribosomes are found in practically every cell, although they are smaller in prokaryotic cells. They are particularly abundant in immature red blood cells for the synthesis of hemoglobin, which functions in the transport of oxygen throughout the body.


Mitochondria (singular = mitochondrion) are often called the “powerhouses” or “energy factories” of a cell because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. The formation of ATP from the breakdown of glucose is known as cellular respiration. Mitochondria are oval-shaped, double-membrane organelles (Figure 3.17) that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner layer has folds called cristae, which increase the surface area of the inner membrane. The area surrounded by the folds is called the mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration.

In keeping with our theme of form following function, it is important to point out that muscle cells have a very high concentration of mitochondria because muscle cells need a lot of energy to contract.

This transmission electron micrograph of a mitochondrion shows an oval, outer membrane and an inner membrane with many folds called cristae. Inside of the inner membrane is a space called the mitochondrial matrix.

Figure 3.17 This transmission electron micrograph shows a mitochondrion as viewed with an electron microscope. Notice the inner and outer membranes, the cristae, and the mitochondrial matrix. (credit: modification of work by Matthew Britton; scale-bar data from Matt Russell)


Peroxisomes are small, round organelles enclosed by single membranes. They carry out oxidation reactions that break down fatty acids and amino acids. They also detoxify many poisons that may enter the body. Alcohol is detoxified by peroxisomes in liver cells. A byproduct of these oxidation reactions is hydrogen peroxide, H2O2, which is contained within the peroxisomes to prevent the chemical from causing damage to cellular components outside of the organelle. Hydrogen peroxide is safely broken down by peroxisomal enzymes into water and oxygen.

Animal Cells versus Plant Cells

Despite their fundamental similarities, there are some striking differences between animal and plant cells (see Table 3.1). Animal cells have centrioles, centrosomes (discussed under the cytoskeleton), and lysosomes, whereas plant cells do not. Plant cells have a cell wall, chloroplasts, plasmodesmata, and plastids used for storage, and a large central vacuole, whereas animal cells do not.

The Cell Wall

In Figure 3.8 b, the diagram of a plant cell, you see a structure external to the plasma membrane called the cell wall. The cell wall is a rigid covering that protects the cell, provides structural support, and gives shape to the cell. Fungal and protist cells also have cell walls.

While the chief component of prokaryotic cell walls is peptidoglycan, the major organic molecule in the plant cell wall is cellulose, a polysaccharide made up of long, straight chains of glucose units. When nutritional information refers to dietary fiber, it is referring to the cellulose content of food.


Like mitochondria, chloroplasts also have their own DNA and ribosomes. Chloroplasts function in photosynthesis and can be found in eukaryotic cells such as plants and algae. In photosynthesis, carbon dioxide, water, and light energy are used to make glucose and oxygen. This is the major difference between plants and animals: Plants (autotrophs) are able to make their own food, like glucose, whereas animals (heterotrophs) must rely on other organisms for their organic compounds or food source.

Like mitochondria, chloroplasts have outer and inner membranes, but within the space enclosed by a chloroplast’s inner membrane is a set of interconnected and stacked, fluid-filled membrane sacs called thylakoids (Figure 3.18). Each stack of thylakoids is called a granum (plural = grana). The fluid enclosed by the inner membrane and surrounding the grana is called the stroma.

This illustration shows a chloroplast, which has an outer membrane and an inner membrane. The space between the outer and inner membranes is called the intermembrane space. Inside the inner membrane are flat, pancake-like structures called thylakoids. The thylakoids form stacks called grana. The liquid inside the inner membrane is called the stroma, and the space inside the thylakoid is called the thylakoid space.

Figure 3.18 This simplified diagram of a chloroplast shows the outer membrane, inner membrane, thylakoids, grana, and stroma.

The chloroplasts contain a green pigment called chlorophyll, which captures the energy of sunlight for photosynthesis. Like plant cells, photosynthetic protists also have chloroplasts. Some bacteria also perform photosynthesis, but they do not have chloroplasts. Their photosynthetic pigments are located in the thylakoid membrane within the cell itself.

Evolution in Action

Endosymbiosis: We have mentioned that both mitochondria and chloroplasts contain DNA and ribosomes. Have you wondered why? Strong evidence points to endosymbiosis as the explanation.

Symbiosis is a relationship in which organisms from two separate species live in close association and typically exhibit specific adaptations to each other. Endosymbiosis (endo-= within) is a relationship in which one organism lives inside the other. Endosymbiotic relationships abound in nature. Microbes that produce vitamin K live inside the human gut. This relationship is beneficial for us because we are unable to synthesize vitamin K. It is also beneficial for the microbes because they are protected from other organisms and are provided a stable habitat and abundant food by living within the large intestine.

Scientists have long noticed that bacteria, mitochondria, and chloroplasts are similar in size. We also know that mitochondria and chloroplasts have DNA and ribosomes, just as bacteria do and they resemble the types found in bacteria. Scientists believe that host cells and bacteria formed a mutually beneficial endosymbiotic relationship when the host cells ingested aerobic bacteria and cyanobacteria but did not destroy them. Through evolution, these ingested bacteria became more specialized in their functions, with the aerobic bacteria becoming mitochondria and the photosynthetic bacteria becoming chloroplasts.

The Central Vacuole

Previously, we mentioned vacuoles as essential components of plant cells. If you look at Figure 3.8 b, you will see that plant cells each have a large, central vacuole that occupies most of the cell. The central vacuole plays a key role in regulating the cell’s concentration of water in changing environmental conditions. In plant cells, the liquid inside the central vacuole provides turgor pressure, which is the outward pressure caused by the fluid inside the cell. Have you ever noticed that if you forget to water a plant for a few days, it wilts? That is because as the water concentration in the soil becomes lower than the water concentration in the plant, water moves out of the central vacuoles and cytoplasm and into the soil. As the central vacuole shrinks, it leaves the cell wall unsupported. This loss of support to the cell walls of a plant results in the wilted appearance. Additionally, this fluid has a very bitter taste, which discourages consumption by insects and animals. The central vacuole also functions to store proteins in developing seed cells.

Extracellular Matrix of Animal Cells

Most animal cells release materials into the extracellular space. The primary components of these materials are glycoproteins and the protein collagen. Collectively, these materials are called the extracellular matrix (Figure 3.19). Not only does the extracellular matrix hold the cells together to form a tissue, but it also allows the cells within the tissue to communicate with each other.

This illustration shows the plasma membrane. Embedded in the plasma membrane are integral membrane proteins called integrins. On the exterior of the cell is a vast network of collagen fibers, which are attached to the integrins via a protein called fibronectin. Proteoglycan complexes also extend from the plasma membrane into the extracellular matrix. A magnified view shows that each proteoglycan complex is composed of a polysaccharide core. Proteins branch from this core, and carbohydrates branch from the proteins. The inside of the cytoplasmic membrane is lined with microfilaments of the cytoskeleton.

Figure 3.19 The extracellular matrix consists of a network of substances secreted by cells.

Blood clotting provides an example of the role of the extracellular matrix in cell communication. When the cells lining a blood vessel are damaged, they display a protein receptor called tissue factor. When tissue factor binds with another factor in the extracellular matrix, it causes platelets to adhere to the wall of the damaged blood vessel, stimulates adjacent smooth muscle cells in the blood vessel to contract (thus constricting the blood vessel), and initiates a series of steps that stimulate the platelets to produce clotting factors.

Intercellular Junctions

Cells can also communicate with each other by direct contact, referred to as intercellular junctions. There are some differences in the ways that plant and animal cells do this. Plasmodesmata (singular = plasmodesma) are junctions between plant cells, whereas animal cell contacts include tight and gap junctions, and desmosomes.

In general, long stretches of the plasma membranes of neighboring plant cells cannot touch one another because they are separated by the cell walls surrounding each cell. Plasmodesmata are numerous channels that pass between the cell walls of adjacent plant cells, connecting their cytoplasm and enabling signal molecules and nutrients to be transported from cell to cell (Figure 3.20 a).

Part a shows two plant cells side-by-side. A channel, or plasmodesma, in the cell wall allows fluid and small molecules to pass from the cytoplasm of one cell to the cytoplasm of another. Part b shows two cell membranes joined together by a matrix of tight junctions. Part c shows two cells fused together by a desmosome. Cadherins extend out from each cell and join the two cells together. Intermediate filaments connect to cadherins on the inside of the cell. Part d shows two cells joined together with protein pores called gap junctions that allow water and small molecules to pass through.

Figure 3.20 There are four kinds of connections between cells. (a) A plasmodesma is a channel between the cell walls of two adjacent plant cells. (b) Tight junctions join adjacent animal cells. (c) Desmosomes join two animal cells together. (d) Gap junctions act as channels between animal cells. (credit b, c, d: modification of work by Mariana Ruiz Villareal)

A tight junction is a watertight seal between two adjacent animal cells (Figure 3.20 b). Proteins hold the cells tightly against each other. This tight adhesion prevents materials from leaking between the cells. Tight junctions are typically found in the epithelial tissue that lines internal organs and cavities, and composes most of the skin. For example, the tight junctions of the epithelial cells lining the urinary bladder prevent urine from leaking into the extracellular space.

Also found only in animal cells are desmosomes, which act like spot welds between adjacent epithelial cells (Figure 3.20 c). They keep cells together in a sheet-like formation in organs and tissues that stretch, like the skin, heart, and muscles.

Gap junctions in animal cells are like plasmodesmata in plant cells in that they are channels between adjacent cells that allow for the transport of ions, nutrients, and other substances that enable cells to communicate (Figure 3.20 d). Structurally, however, gap junctions and plasmodesmata differ.

Table 3.1 This table provides the components of prokaryotic and eukaryotic cells and their respective functions.

Components of Prokaryotic and Eukaryotic Cells and Their Functions

Cell Component


Present in Prokaryotes?

Present in Animal Cells?

Present in Plant Cells?

Plasma membrane Separates cell from external environment; controls passage of organic molecules, ions, water, oxygen, and wastes into and out of the cell Yes Yes Yes
Cytoplasm Provides structure to cell; site of many metabolic reactions; medium in which organelles are found Yes Yes Yes
Nucleoid Location of DNA Yes No No
Nucleus Cell organelle that houses DNA and directs synthesis of ribosomes and proteins No Yes Yes
Ribosomes Protein synthesis Yes Yes Yes
Mitochondria ATP production/cellular respiration No Yes Yes
Peroxisomes Oxidizes and breaks down fatty acids and amino acids, and detoxifies poisons No Yes Yes
Vesicles and vacuoles Storage and transport; digestive function in plant cells No Yes Yes
Centrosome Unspecified role in cell division in animal cells; organizing center of microtubules in animal cells No Yes No
Lysosomes Digestion of macromolecules; recycling of worn-out organelles No Yes No
Cell wall Protection, structural support and maintenance of cell shape Yes, primarily peptidoglycan in bacteria but not Archaea No Yes, primarily cellulose
Chloroplasts Photosynthesis No No Yes
Endoplasmic reticulum Modifies proteins and synthesizes lipids No Yes Yes
Golgi apparatus Modifies, sorts, tags, packages, and distributes lipids and proteins No Yes Yes
Cytoskeleton Maintains cell’s shape, secures organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move independently Yes Yes Yes
Flagella Cellular locomotion Some Some No, except for some plant sperm.
Cilia Cellular locomotion, movement of particles along extracellular surface of plasma membrane, and filtration No Some No

Section Summary

Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes, but a eukaryotic cell is typically larger than a prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a membrane), and has other membrane-bound organelles that allow for compartmentalization of functions. The plasma membrane is a phospholipid bilayer embedded with proteins. The nucleolus within the nucleus is the site for ribosome assembly. Ribosomes are found in the cytoplasm or are attached to the cytoplasmic side of the plasma membrane or endoplasmic reticulum. They perform protein synthesis. Mitochondria perform cellular respiration and produce ATP. Peroxisomes break down fatty acids, amino acids, and some toxins. Vesicles and vacuoles are storage and transport compartments. In plant cells, vacuoles also help break down macromolecules.

Animal cells also have a centrosome and lysosomes. The centrosome has two bodies, the centrioles, with an unknown role in cell division. Lysosomes are the digestive organelles of animal cells.

Plant cells have a cell wall, chloroplasts, and a central vacuole. The plant cell wall, whose primary component is cellulose, protects the cell, provides structural support, and gives shape to the cell. Photosynthesis takes place in chloroplasts. The central vacuole expands, enlarging the cell without the need to produce more cytoplasm.

The endomembrane system includes the nuclear envelope, the endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, as well as the plasma membrane. These cellular components work together to modify, package, tag, and transport membrane lipids and proteins.

The cytoskeleton has three different types of protein elements. Microfilaments provide rigidity and shape to the cell, and facilitate cellular movements. Intermediate filaments bear tension and anchor the nucleus and other organelles in place. Microtubules help the cell resist compression, serve as tracks for motor proteins that move vesicles through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. They are also the structural elements of centrioles, flagella, and cilia.

Animal cells communicate through their extracellular matrices and are connected to each other by tight junctions, desmosomes, and gap junctions. Plant cells are connected and communicate with each other by plasmodesmata.


What structures does a plant cell have that an animal cell does not have? What structures does an animal cell have that a plant cell does not have?

Plant cells have plasmodesmata, a cell wall, a large central vacuole, chloroplasts, and plastids. Animal cells have lysosomes and centrosomes.

Why does the cis face of the Golgi not face the plasma membrane?

Because that face receives chemicals from the ER, which is toward the center of the cell.

Multiple Choice

Which of the following is found both in eukaryotic and prokaryotic cells?

A) nucleus

B) mitochondrion

C) vacuole

D) ribosome


Which of the following is not a component of the endomembrane system?

A) mitochondrion

B) Golgi apparatus

C) endoplasmic reticulum

D) lysosome


Free Response

In the context of cell biology, what do we mean by form follows function? What are at least two examples of this concept?

“Form follows function” refers to the idea that the function of a body part dictates the form of that body part. As an example, organisms like birds or fish that fly or swim quickly through the air or water have streamlined bodies that reduce drag. At the level of the cell, in tissues involved in secretory functions, such as the salivary glands, the cells have abundant Golgi.



cell wall: a rigid cell covering made of cellulose in plants, peptidoglycan in bacteria, non-peptidoglycan compounds in Archaea, and chitin in fungi that protects the cell, provides structural support, and gives shape to the cell

central vacuole: a large plant cell organelle that acts as a storage compartment, water reservoir, and site of macromolecule degradation

chloroplast: a plant cell organelle that carries out photosynthesis

cilium: (plural: cilia) a short, hair-like structure that extends from the plasma membrane in large numbers and is used to move an entire cell or move substances along the outer surface of the cell

cytoplasm: the entire region between the plasma membrane and the nuclear envelope, consisting of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals

cytoskeleton: the network of protein fibers that collectively maintains the shape of the cell, secures some organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move

cytosol: the gel-like material of the cytoplasm in which cell structures are suspended

desmosome: a linkage between adjacent epithelial cells that forms when cadherins in the plasma membrane attach to intermediate filaments

endomembrane system: the group of organelles and membranes in eukaryotic cells that work together to modify, package, and transport lipids and proteins

endoplasmic reticulum (ER): a series of interconnected membranous structures within eukaryotic cells that collectively modify proteins and synthesize lipids

extracellular matrix: the material, primarily collagen, glycoproteins, and proteoglycans, secreted from animal cells that holds cells together as a tissue, allows cells to communicate with each other, and provides mechanical protection and anchoring for cells in the tissue

flagellum: (plural: flagella) the long, hair-like structure that extends from the plasma membrane and is used to move the cell

gap junction: a channel between two adjacent animal cells that allows ions, nutrients, and other low-molecular weight substances to pass between the cells, enabling the cells to communicate

Golgi apparatus: a eukaryotic organelle made up of a series of stacked membranes that sorts, tags, and packages lipids and proteins for distribution

lysosome: an organelle in an animal cell that functions as the cell’s digestive component; it breaks down proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles

mitochondria: (singular: mitochondrion) the cellular organelles responsible for carrying out cellular respiration, resulting in the production of ATP, the cell’s main energy-carrying molecule

nuclear envelope: the double-membrane structure that constitutes the outermost portion of the nucleus

nucleolus: the darkly staining body within the nucleus that is responsible for assembling ribosomal subunits

nucleus: the cell organelle that houses the cell’s DNA and directs the synthesis of ribosomes and proteins

peroxisome: a small, round organelle that contains hydrogen peroxide, oxidizes fatty acids and amino acids, and detoxifies many poisons

plasma membrane: a phospholipid bilayer with embedded (integral) or attached (peripheral) proteins that separates the internal contents of the cell from its surrounding environment

plasmodesma:(plural: plasmodesmata) a channel that passes between the cell walls of adjacent plant cells, connects their cytoplasm, and allows materials to be transported from cell to cell

ribosome: a cellular structure that carries out protein synthesis

rough endoplasmic reticulum (RER): the region of the endoplasmic reticulum that is studded with ribosomes and engages in protein modification

smooth endoplasmic reticulum (SER): the region of the endoplasmic reticulum that has few or no ribosomes on its cytoplasmic surface and synthesizes carbohydrates, lipids, and steroid hormones; detoxifies chemicals like pesticides, preservatives, medications, and environmental pollutants, and stores calcium ions

tight junction: a firm seal between two adjacent animal cells created by protein adherence

vacuole: a membrane-bound sac, somewhat larger than a vesicle, that functions in cellular storage and transport

vesicle: a small, membrane-bound sac that functions in cellular storage and transport; its membrane is capable of fusing with the plasma membrane and the membranes of the endoplasmic reticulum and Golgi apparatus


3.4 The Cell Membrane

Learning Objectives

By the end of this section, you will be able to:

  • Understand the fluid mosaic model of membranes
  • Describe the functions of phospholipids, proteins, and carbohydrates in membranes

A cell’s plasma membrane defines the boundary of the cell and determines the nature of its contact with the environment. Cells exclude some substances, take in others, and excrete still others, all in controlled quantities. Plasma membranes enclose the borders of cells, but rather than being a static bag, they are dynamic and constantly in flux. The plasma membrane must be sufficiently flexible to allow certain cells, such as red blood cells and white blood cells, to change shape as they pass through narrow capillaries. These are the more obvious functions of a plasma membrane. In addition, the surface of the plasma membrane carries markers that allow cells to recognize one another, which is vital as tissues and organs form during early development, and which later plays a role in the “self” versus “non-self” distinction of the immune response.

The plasma membrane also carries receptors, which are attachment sites for specific substances that interact with the cell. Each receptor is structured to bind with a specific substance. For example, surface receptors of the membrane create changes in the interior, such as changes in enzymes of metabolic pathways. These metabolic pathways might be vital for providing the cell with energy, making specific substances for the cell, or breaking down cellular waste or toxins for disposal. Receptors on the plasma membrane’s exterior surface interact with hormones or neurotransmitters, and allow their messages to be transmitted into the cell. Some recognition sites are used by viruses as attachment points. Although they are highly specific, pathogens like viruses may evolve to exploit receptors to gain entry to a cell by mimicking the specific substance that the receptor is meant to bind. This specificity helps to explain why human immunodeficiency virus (HIV) or any of the five types of hepatitis viruses invade only specific cells.

Fluid Mosaic Model

In 1972, S. J. Singer and Garth L. Nicolson proposed a new model of the plasma membrane that, compared to earlier understanding, better explained both microscopic observations and the function of the plasma membrane. This was called the fluid mosaic model. The model has evolved somewhat over time, but still best accounts for the structure and functions of the plasma membrane as we now understand them. The fluid mosaic model describes the structure of the plasma membrane as a mosaic of components—including phospholipids, cholesterol, proteins, and carbohydrates—in which the components are able to flow and change position, while maintaining the basic integrity of the membrane. Both phospholipid molecules and embedded proteins are able to diffuse rapidly and laterally in the membrane. The fluidity of the plasma membrane is necessary for the activities of certain enzymes and transport molecules within the membrane. Plasma membranes range from 5–10 nm thick. As a comparison, human red blood cells, visible via light microscopy, are approximately 8 µm thick, or approximately 1,000 times thicker than a plasma membrane.

the plasma membrane is composed of a phospholipid bilayer. in the bilayer, the two long hydrophobic tails of phospholipids face toward the center, and the hydrophilic head group faces the exterior. Integral membrane proteins and protein channels span the entire bilayer. Protein channels have a pore in the middle. Peripheral membrane proteins sit on the surface of the phospholipids and are associated with the head groups. On the exterior side of the membrane, carbohydrates are attached to certain proteins and lipids. Filaments of the cytoskeleton line the interior of the membrane.

Figure 3.21 The fluid mosaic model of the plasma membrane structure describes the plasma membrane as a fluid combination of phospholipids, cholesterol, proteins, and carbohydrates.

The plasma membrane is made up primarily of a bilayer of phospholipids with embedded proteins, carbohydrates, glycolipids, and glycoproteins, and, in animal cells, cholesterol. The amount of cholesterol in animal plasma membranes regulates the fluidity of the membrane and changes based on the temperature of the cell’s environment. In other words, cholesterol acts as antifreeze in the cell membrane and is more abundant in animals that live in cold climates.

The main fabric of the membrane is composed of two layers of phospholipid molecules, and the polar ends of these molecules (which look like a collection of balls in an artist’s rendition of the model) (Figure 3.22) are in contact with aqueous fluid both inside and outside the cell. Thus, both surfaces of the plasma membrane are hydrophilic. In contrast, the interior of the membrane, between its two surfaces, is a hydrophobic or nonpolar region because of the fatty acid tails. This region has no attraction for water or other polar molecules.

This phospholipid molecule is composed of a hydrophilic head and two hydrophobic tails. The hydrophilic head group consists of a phosphate-containing group attached to a glycerol molecule. The hydrophobic tails, each containing either a saturated or an unsaturated fatty acid, are long hydrocarbon chains.

Figure 3.22 This phospholipid molecule is composed of a hydrophilic head and two hydrophobic tails. The hydrophilic head group consists of a phosphate-containing group attached to a glycerol molecule. The hydrophobic tails, each containing either a saturated or an unsaturated fatty acid, are long hydrocarbon chains.


Proteins make up the second major chemical component of plasma membranes. Integral proteins are embedded in the plasma membrane and may span all or part of the membrane. Integral proteins may serve as channels or pumps to move materials into or out of the cell. Peripheral proteins are found on the exterior or interior surfaces of membranes, attached either to integral proteins or to phospholipid molecules. Both integral and peripheral proteins may serve as enzymes, as structural attachments for the fibers of the cytoskeleton, or as part of the cell’s recognition sites.

Carbohydrates are the third major component of plasma membranes. They are always found on the exterior surface of cells and are bound either to proteins (forming glycoproteins) or to lipids (forming glycolipids). These carbohydrate chains may consist of 2–60 monosaccharide units and may be either straight or branched. Along with peripheral proteins, carbohydrates form specialized sites on the cell surface that allow cells to recognize each other.

Evolution in Action

How Viruses Infect Specific OrgansSpecific glycoprotein molecules exposed on the surface of the cell membranes of host cells are exploited by many viruses to infect specific organs. For example, HIV is able to penetrate the plasma membranes of specific kinds of white blood cells called T-helper cells and monocytes, as well as some cells of the central nervous system. The hepatitis virus attacks only liver cells.

These viruses are able to invade these cells, because the cells have binding sites on their surfaces that the viruses have exploited with equally specific glycoproteins in their coats. (Figure 3.23). The cell is tricked by the mimicry of the virus coat molecules, and the virus is able to enter the cell. Other recognition sites on the virus’s surface interact with the human immune system, prompting the body to produce antibodies. Antibodies are made in response to the antigens (or proteins associated with invasive pathogens). These same sites serve as places for antibodies to attach, and either destroy or inhibit the activity of the virus. Unfortunately, these sites on HIV are encoded by genes that change quickly, making the production of an effective vaccine against the virus very difficult. The virus population within an infected individual quickly evolves through mutation into different populations, or variants, distinguished by differences in these recognition sites. This rapid change of viral surface markers decreases the effectiveness of the person’s immune system in attacking the virus, because the antibodies will not recognize the new variations of the surface patterns.

This illustration shows the plasma membrane of a T cell. CD4 receptors extend from the membrane into the extracellular space. The HIV virus recognizes part of the CD4 receptor and attaches to it.

Figure 3.23 HIV docks at and binds to the CD4 receptor, a glycoprotein on the surface of T cells, before entering, or infecting, the cell. (credit: modification of work by US National Institutes of Health/National Institute of Allergy and Infectious Diseases)

Section Summary

The modern understanding of the plasma membrane is referred to as the fluid mosaic model. The plasma membrane is composed of a bilayer of phospholipids, with their hydrophobic, fatty acid tails in contact with each other. The landscape of the membrane is studded with proteins, some of which span the membrane. Some of these proteins serve to transport materials into or out of the cell. Carbohydrates are attached to some of the proteins and lipids on the outward-facing surface of the membrane. These form complexes that function to identify the cell to other cells. The fluid nature of the membrane owes itself to the configuration of the fatty acid tails, the presence of cholesterol embedded in the membrane (in animal cells), and the mosaic nature of the proteins and protein-carbohydrate complexes, which are not firmly fixed in place. Plasma membranes enclose the borders of cells, but rather than being a static bag, they are dynamic and constantly in flux.


Multiple Choice

Which plasma membrane component can be either found on its surface or embedded in the membrane structure?

A) protein

B) cholesterol

C) carbohydrate

D) phospholipid


The tails of the phospholipids of the plasma membrane are composed of _____ and are _______?

A) phosphate groups; hydrophobic

B) fatty acid groups; hydrophilic

C) phosphate groups; hydrophilic

D) fatty acid groups; hydrophobic


Free Response

Why is it advantageous for the cell membrane to be fluid in nature?

The fluidity of the cell membrane is necessary for the operation of some enzymes and transport mechanisms within the membrane.



fluid mosaic model: a model of the structure of the plasma membrane as a mosaic of components, including phospholipids, cholesterol, proteins, and glycolipids, resulting in a fluid rather than static character


3.5 Passive Transport

Learning Objectives

By the end of this section, you will be able to:

  • Explain why and how passive transport occurs
  • Understand the processes of osmosis and diffusion
  • Define tonicity and describe its relevance to passive transport

Plasma membranes must allow certain substances to enter and leave a cell, while preventing harmful material from entering and essential material from leaving. In other words, plasma membranes are selectively permeable—they allow some substances through but not others. If they were to lose this selectivity, the cell would no longer be able to sustain itself, and it would be destroyed. Some cells require larger amounts of specific substances than do other cells; they must have a way of obtaining these materials from the extracellular fluids. This may happen passively, as certain materials move back and forth, or the cell may have special mechanisms that ensure transport. Most cells expend most of their energy, in the form of adenosine triphosphate (ATP), to create and maintain an uneven distribution of ions on the opposite sides of their membranes. The structure of the plasma membrane contributes to these functions, but it also presents some problems.

The most direct forms of membrane transport are passive. Passive transport is a naturally occurring phenomenon and does not require the cell to expend energy to accomplish the movement. In passive transport, substances move from an area of higher concentration to an area of lower concentration in a process called diffusion. A physical space in which there is a different concentration of a single substance is said to have a concentration gradient.

Selective Permeability

Plasma membranes are asymmetric, meaning that despite the mirror image formed by the phospholipids, the interior of the membrane is not identical to the exterior of the membrane. Integral proteins that act as channels or pumps work in one direction. Carbohydrates, attached to lipids or proteins, are also found on the exterior surface of the plasma membrane. These carbohydrate complexes help the cell bind substances that the cell needs in the extracellular fluid. This adds considerably to the selective nature of plasma membranes.

Recall that plasma membranes have hydrophilic and hydrophobic regions. This characteristic helps the movement of certain materials through the membrane and hinders the movement of others. Lipid-soluble material can easily slip through the hydrophobic lipid core of the membrane. Substances such as the fat-soluble vitamins A, D, E, and K readily pass through the plasma membranes in the digestive tract and other tissues. Fat-soluble drugs also gain easy entry into cells and are readily transported into the body’s tissues and organs. Molecules of oxygen and carbon dioxide have no charge and pass through by simple diffusion.

Polar substances, with the exception of water, present problems for the membrane. While some polar molecules connect easily with the outside of a cell, they cannot readily pass through the lipid core of the plasma membrane. Additionally, whereas small ions could easily slip through the spaces in the mosaic of the membrane, their charge prevents them from doing so. Ions such as sodium, potassium, calcium, and chloride must have a special means of penetrating plasma membranes. Simple sugars and amino acids also need help with transport across plasma membranes.


Diffusion is a passive process of transport. A single substance tends to move from an area of high concentration to an area of low concentration until the concentration is equal across the space. You are familiar with diffusion of substances through the air. For example, think about someone opening a bottle of perfume in a room filled with people. The perfume is at its highest concentration in the bottle and is at its lowest at the edges of the room. The perfume vapor will diffuse, or spread away, from the bottle, and gradually, more and more people will smell the perfume as it spreads. Materials move within the cell’s cytosol by diffusion, and certain materials move through the plasma membrane by diffusion (Figure 3.24). Diffusion expends no energy. Rather the different concentrations of materials in different areas are a form of potential energy, and diffusion is the dissipation of that potential energy as materials move down their concentration gradients, from high to low.

The left part of this illustration shows a substance on one side of a membrane only. The middle part shows that, after some time, some of the substance has diffused across the plasma membrane. The right part shows that, after more time, an equal amount of the substance is on each side of the membrane.

Figure 3.24 Diffusion through a permeable membrane follows the concentration gradient of a substance, moving the substance from an area of high concentration to one of low concentration. (credit: modification of work by Mariana Ruiz Villarreal)

Each separate substance in a medium, such as the extracellular fluid, has its own concentration gradient, independent of the concentration gradients of other materials. Additionally, each substance will diffuse according to that gradient.

Several factors affect the rate of diffusion.

  • Extent of the concentration gradient: The greater the difference in concentration, the more rapid the diffusion. The closer the distribution of the material gets to equilibrium, the slower the rate of diffusion becomes.
  • Mass of the molecules diffusing: More massive molecules move more slowly, because it is more difficult for them to move between the molecules of the substance they are moving through; therefore, they diffuse more slowly.
  • Temperature: Higher temperatures increase the energy and therefore the movement of the molecules, increasing the rate of diffusion.
  • Solvent density: As the density of the solvent increases, the rate of diffusion decreases. The molecules slow down because they have a more difficult time getting through the denser medium.

Concept in Action

For an animation of the diffusion process in action, view this short video on cell membrane transport.

Facilitated transport

In facilitated transport, also called facilitated diffusion, material moves across the plasma membrane with the assistance of transmembrane proteins down a concentration gradient (from high to low concentration) without the expenditure of cellular energy. However, the substances that undergo facilitated transport would otherwise not diffuse easily or quickly across the plasma membrane. The solution to moving polar substances and other substances across the plasma membrane rests in the proteins that span its surface. The material being transported is first attached to protein or glycoprotein receptors on the exterior surface of the plasma membrane. This allows the material that is needed by the cell to be removed from the extracellular fluid. The substances are then passed to specific integral proteins that facilitate their passage, because they form channels or pores that allow certain substances to pass through the membrane. The integral proteins involved in facilitated transport are collectively referred to as transport proteins, and they function as either channels for the material or carriers.


Osmosis is the diffusion of water through a semipermeable membrane according to the concentration gradient of water across the membrane. Whereas diffusion transports material across membranes and within cells, osmosis transports only water across a membrane and the membrane limits the diffusion of solutes in the water. Osmosis is a special case of diffusion. Water, like other substances, moves from an area of higher concentration to one of lower concentration. Imagine a beaker with a semipermeable membrane, separating the two sides or halves (Figure 3.25). On both sides of the membrane, the water level is the same, but there are different concentrations on each side of a dissolved substance, or solute, that cannot cross the membrane. If the volume of the water is the same, but the concentrations of solute are different, then there are also different concentrations of water, the solvent, on either side of the membrane.

Two beakers are shown, each divided into left and right halves by a semipermeable membrane. The first beaker has the same amount of water on both sides, but more solute in the water on the right side of the membrane and less solute in the water on the left side. In the second beaker, the water has moved from the left side of the membrane to the right side, making the solute concentration the same on both sides, but the water level much lower on the left side.

Figure 3.25 In osmosis, water always moves from an area of higher concentration (of water) to one of lower concentration (of water). In this system, the solute cannot pass through the selectively permeable membrane.

A principle of diffusion is that the molecules move around and will spread evenly throughout the medium if they can. However, only the material capable of getting through the membrane will diffuse through it. In this example, the solute cannot diffuse through the membrane, but the water can. Water has a concentration gradient in this system. Therefore, water will diffuse down its concentration gradient, crossing the membrane to the side where it is less concentrated. This diffusion of water through the membrane—osmosis—will continue until the concentration gradient of water goes to zero. Osmosis proceeds constantly in living systems.


Tonicity describes the amount of solute in a solution. The measure of the tonicity of a solution, or the total amount of solutes dissolved in a specific amount of solution, is called its osmolarity. Three terms—hypotonic, isotonic, and hypertonic—are used to relate the osmolarity of a cell to the osmolarity of the extracellular fluid that contains the cells. In a hypotonic solution, such as tap water, the extracellular fluid has a lower concentration of solutes than the fluid inside the cell, and water enters the cell. (In living systems, the point of reference is always the cytoplasm, so the prefix hypo– means that the extracellular fluid has a lower concentration of solutes, or a lower osmolarity, than the cell cytoplasm.) It also means that the extracellular fluid has a higher concentration of water than does the cell. In this situation, water will follow its concentration gradient and enter the cell. This may cause an animal cell to burst, or lyse.

In a hypertonic solution (the prefix hyper– refers to the extracellular fluid having a higher concentration of solutes than the cell’s cytoplasm), the fluid contains less water than the cell does, such as seawater. Because the cell has a lower concentration of solutes, the water will leave the cell. In effect, the solute is drawing the water out of the cell. This may cause an animal cell to shrivel, or crenate.

In an isotonic solution, the extracellular fluid has the same osmolarity as the cell. If the concentration of solutes of the cell matches that of the extracellular fluid, there will be no net movement of water into or out of the cell. Blood cells in hypertonic, isotonic, and hypotonic solutions take on characteristic appearances (Figure 3.26).

Illustration of red blood cells in hypotonic, isotonic, and hypertonic solutions. In the hypertonic solution, the cells shrivel and take on a spiky appearance. In the isotonic solution, the cells are normal in appearance. In the hypotonic solution, the cells swell and one has ruptured.

Figure 3.26 Osmotic pressure changes the shape of red blood cells in hypertonic, isotonic, and hypotonic solutions. (credit: modification of work by Mariana Ruiz Villarreal)

A doctor injects a patient with what the doctor thinks is isotonic saline solution. The patient dies, and autopsy reveals that many red blood cells have been destroyed. Do you think the solution the doctor injected was really isotonic?

<!– No, it must have been hypotonic, as a hypotonic solution would cause water to enter the cells, thereby making them burst. –>

Some organisms, such as plants, fungi, bacteria, and some protists, have cell walls that surround the plasma membrane and prevent cell lysis. The plasma membrane can only expand to the limit of the cell wall, so the cell will not lyse. In fact, the cytoplasm in plants is always slightly hypertonic compared to the cellular environment, and water will always enter a cell if water is available. This influx of water produces turgor pressure, which stiffens the cell walls of the plant (Figure 3.27). In nonwoody plants, turgor pressure supports the plant. If the plant cells become hypertonic, as occurs in drought or if a plant is not watered adequately, water will leave the cell. Plants lose turgor pressure in this condition and wilt.

The left part of this image shows a plant cell bathed in a hypertonic solution so that the plasma membrane has pulled away completely from the cell wall, and the central vacuole has shrunk. The middle part shows a plant cell bathed in an isotonic solution; the plasma membrane has pulled away from the cell wall a bit, and the central vacuole has shrunk. The right part shows a plant cell in a hypotonic solution. The central vacuole is large, and the plasma membrane is pressed against the cell wall.

Figure 3.27 The turgor pressure within a plant cell depends on the tonicity of the solution that it is bathed in. (credit: modification of work by Mariana Ruiz Villarreal)

Section Summary

The passive forms of transport, diffusion and osmosis, move material of small molecular weight. Substances diffuse from areas of high concentration to areas of low concentration, and this process continues until the substance is evenly distributed in a system. In solutions of more than one substance, each type of molecule diffuses according to its own concentration gradient. Many factors can affect the rate of diffusion, including concentration gradient, the sizes of the particles that are diffusing, and the temperature of the system.

In living systems, diffusion of substances into and out of cells is mediated by the plasma membrane. Some materials diffuse readily through the membrane, but others are hindered, and their passage is only made possible by protein channels and carriers. The chemistry of living things occurs in aqueous solutions, and balancing the concentrations of those solutions is an ongoing problem. In living systems, diffusion of some substances would be slow or difficult without membrane proteins.


A doctor injects a patient with what he thinks is isotonic saline solution. The patient dies, and autopsy reveals that many red blood cells have been destroyed. Do you think the solution the doctor injected was really isotonic?

No, it must have been hypotonic, as a hypotonic solution would cause water to enter the cells, thereby making them burst.

Multiple Choice

Water moves via osmosis _________.

A) throughout the cytoplasm

B) from an area with a high concentration of other solutes to a lower one

C) from an area with a low concentration of solutes to an area with a higher one

D) from an area with a low concentration of water to one of higher concentration


The principal force driving movement in diffusion is __________.

A) temperature

B) particle size

C) concentration gradient

D) membrane surface area

Free Response

Why does osmosis occur?

Water moves through a semipermeable membrane in osmosis because there is a concentration gradient across the membrane of solute and solvent. The solute cannot effectively move to balance the concentration on both sides of the membrane, so water moves to achieve this balance.



concentration gradient: an area of high concentration across from an area of low concentration

diffusion: a passive process of transport of low-molecular weight material down its concentration gradient

facilitated transport: a process by which material moves down a concentration gradient (from high to low concentration) using integral membrane proteins

hypertonic: describes a solution in which extracellular fluid has higher osmolarity than the fluid inside the cell

hypotonic: describes a solution in which extracellular fluid has lower osmolarity than the fluid inside the cell

isotonic: describes a solution in which the extracellular fluid has the same osmolarity as the fluid inside the cell

osmolarity: the total amount of substances dissolved in a specific amount of solution

osmosis: the transport of water through a semipermeable membrane from an area of high water concentration to an area of low water concentration across a membrane

passive transport: a method of transporting material that does not require energy

selectively permeable: the characteristic of a membrane that allows some substances through but not others

solute: a substance dissolved in another to form a solution

tonicity: the amount of solute in a solution.


3.6 Active Transport

Learning Objectives

By the end of this section, you will be able to:

  • Understand how electrochemical gradients affect ions
  • Describe endocytosis, including phagocytosis, pinocytosis, and receptor-mediated endocytosis
  • Understand the process of exocytosis

 Active transport mechanisms require the use of the cell’s energy, usually in the form of adenosine triphosphate (ATP). If a substance must move into the cell against its concentration gradient, that is, if the concentration of the substance inside the cell must be greater than its concentration in the extracellular fluid, the cell must use energy to move the substance. Some active transport mechanisms move small-molecular weight material, such as ions, through the membrane.

In addition to moving small ions and molecules through the membrane, cells also need to remove and take in larger molecules and particles. Some cells are even capable of engulfing entire unicellular microorganisms. You might have correctly hypothesized that the uptake and release of large particles by the cell requires energy. A large particle, however, cannot pass through the membrane, even with energy supplied by the cell.

Electrochemical Gradient

We have discussed simple concentration gradients—differential concentrations of a substance across a space or a membrane—but in living systems, gradients are more complex. Because cells contain proteins, most of which are negatively charged, and because ions move into and out of cells, there is an electrical gradient, a difference of charge, across the plasma membrane. The interior of living cells is electrically negative with respect to the extracellular fluid in which they are bathed; at the same time, cells have higher concentrations of potassium (K+) and lower concentrations of sodium (Na+) than does the extracellular fluid. Thus, in a living cell, the concentration gradient and electrical gradient of Na+ promotes diffusion of the ion into the cell, and the electrical gradient of Na+ (a positive ion) tends to drive it inward to the negatively charged interior. The situation is more complex, however, for other elements such as potassium. The electrical gradient of K+ promotes diffusion of the ion into the cell, but the concentration gradient of K+ promotes diffusion out of the cell (Figure 3.28). The combined gradient that affects an ion is called its electrochemical gradient, and it is especially important to muscle and nerve cells.

A cell membrane is shown with a protein channel that allows passage of ions into and out of the cell. The cytoplasm has a higher concentration of potassium, and the extracellular fluid has a higher concentration of sodium. An arrow shows movement of a potassium ion out of the cell through the protein channel.

Figure 3.28 Electrochemical gradients arise from the combined effects of concentration gradients and electrical gradients. (credit: modification of work by “Synaptitude”/Wikimedia Commons)

Moving Against a Gradient

To move substances against a concentration or an electrochemical gradient, the cell must use energy. This energy is harvested from ATP that is generated through cellular metabolism. Active transport mechanisms, collectively called pumps or carrier proteins, work against electrochemical gradients. With the exception of ions, small substances constantly pass through plasma membranes. Active transport maintains concentrations of ions and other substances needed by living cells in the face of these passive changes. Much of a cell’s supply of metabolic energy may be spent maintaining these processes. Because active transport mechanisms depend on cellular metabolism for energy, they are sensitive to many metabolic poisons that interfere with the supply of ATP.

Two mechanisms exist for the transport of small-molecular weight material and macromolecules. Primary active transport moves ions across a membrane and creates a difference in charge across that membrane. The primary active transport system uses ATP to move a substance, such as an ion, into the cell, and often at the same time, a second substance is moved out of the cell. The sodium-potassium pump, an important pump in animal cells, expends energy to move potassium ions into the cell and a different number of sodium ions out of the cell (Figure 3.29). The action of this pump results in a concentration and charge difference across the membrane.

This illustration shows the sodium-potassium pump. Initially, the pump’s opening faces the cytoplasm, where three sodium ions bind to it. The pump hydrolyzes ATP to ADP and, as a result, undergoes a conformational change. The sodium ions are released into the extracellular space. Two potassium ions from the extracellular space now bind the pump, which changes conformation again, releasing the potassium ions into the cytoplasm.

Figure 3.29 The sodium-potassium pump move potassium and sodium ions across the plasma membrane. (credit: modification of work by Mariana Ruiz Villarreal)

Secondary active transport describes the movement of material using the energy of the electrochemical gradient established by primary active transport. Using the energy of the electrochemical gradient created by the primary active transport system, other substances such as amino acids and glucose can be brought into the cell through membrane channels. ATP itself is formed through secondary active transport using a hydrogen ion gradient in the mitochondrion.


Endocytosis is a type of active transport that moves particles, such as large molecules, parts of cells, and even whole cells, into a cell. There are different variations of endocytosis, but all share a common characteristic: The plasma membrane of the cell invaginates, forming a pocket around the target particle. The pocket pinches off, resulting in the particle being contained in a newly created vacuole that is formed from the plasma membrane.

Three types of endocytosis are shown: (a) phagocytosis, (b) pinocytosis, and (c) receptor-mediated endocytosis. Part a shows the plasma membrane forming a pocket around a particle in the extracellular fluid. The membrane subsequently engulfs the particle, which becomes trapped in a vacuole. Part b shows a plasma membrane forming a pocket around fluid in the extracellular fluid. The membrane subsequently engulfs the fluid, which becomes trapped in a vacuole. Part c shows a part of the plasma membrane that is clathrin-coated on the cytoplasmic side and has receptors on the extracellular side. The receptors bind a substance, then pinch off to form a coated vesicle.

Figure 3.30 Three variations of endocytosis are shown. (a) In one form of endocytosis, phagocytosis, the cell membrane surrounds the particle and pinches off to form an intracellular vacuole. (b) In another type of endocytosis, pinocytosis, the cell membrane surrounds a small volume of fluid and pinches off, forming a vesicle. (c) In receptor-mediated endocytosis, uptake of substances by the cell is targeted to a single type of substance that binds at the receptor on the external cell membrane. (credit: modification of work by Mariana Ruiz Villarreal)

Phagocytosis is the process by which large particles, such as cells, are taken in by a cell. For example, when microorganisms invade the human body, a type of white blood cell called a neutrophil removes the invader through this process, surrounding and engulfing the microorganism, which is then destroyed by the neutrophil (Figure 3.30).

A variation of endocytosis is called pinocytosis. This literally means “cell drinking” and was named at a time when the assumption was that the cell was purposefully taking in extracellular fluid. In reality, this process takes in solutes that the cell needs from the extracellular fluid (Figure 3.30).

A targeted variation of endocytosis employs binding proteins in the plasma membrane that are specific for certain substances (Figure 3.30). The particles bind to the proteins and the plasma membrane invaginates, bringing the substance and the proteins into the cell. If passage across the membrane of the target of receptor-mediated endocytosis is ineffective, it will not be removed from the tissue fluids or blood. Instead, it will stay in those fluids and increase in concentration. Some human diseases are caused by a failure of receptor-mediated endocytosis. For example, the form of cholesterol termed low-density lipoprotein or LDL (also referred to as “bad” cholesterol) is removed from the blood by receptor-mediated endocytosis. In the human genetic disease familial hypercholesterolemia, the LDL receptors are defective or missing entirely. People with this condition have life-threatening levels of cholesterol in their blood, because their cells cannot clear the chemical from their blood.

Concept in Action

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See receptor-mediated endocytosis in action and click on different parts for a focused animation to learn more.


In contrast to these methods of moving material into a cell is the process of exocytosis. Exocytosis is the opposite of the processes discussed above in that its purpose is to expel material from the cell into the extracellular fluid. A particle enveloped in membrane fuses with the interior of the plasma membrane. This fusion opens the membranous envelope to the exterior of the cell, and the particle is expelled into the extracellular space (Figure 3.31).

A vesicle containing waste products is shown in the cytoplasm. The vesicle migrates to the cell membrane. The membrane of the vesicle fuses with the cell membrane, and the contents of the vesicle are released to the extracellular fluid.

Figure 3.31 In exocytosis, a vesicle migrates to the plasma membrane, binds, and releases its contents to the outside of the cell. (credit: modification of work by Mariana Ruiz Villarreal)


Section Summary

The combined gradient that affects an ion includes its concentration gradient and its electrical gradient. Living cells need certain substances in concentrations greater than they exist in the extracellular space. Moving substances up their electrochemical gradients requires energy from the cell. Active transport uses energy stored in ATP to fuel the transport. Active transport of small molecular-size material uses integral proteins in the cell membrane to move the material—these proteins are analogous to pumps. Some pumps, which carry out primary active transport, couple directly with ATP to drive their action. In secondary transport, energy from primary transport can be used to move another substance into the cell and up its concentration gradient.

Endocytosis methods require the direct use of ATP to fuel the transport of large particles such as macromolecules; parts of cells or whole cells can be engulfed by other cells in a process called phagocytosis. In phagocytosis, a portion of the membrane invaginates and flows around the particle, eventually pinching off and leaving the particle wholly enclosed by an envelope of plasma membrane. Vacuoles are broken down by the cell, with the particles used as food or dispatched in some other way. Pinocytosis is a similar process on a smaller scale. The cell expels waste and other particles through the reverse process, exocytosis. Wastes are moved outside the cell, pushing a membranous vesicle to the plasma membrane, allowing the vesicle to fuse with the membrane and incorporating itself into the membrane structure, releasing its contents to the exterior of the cell.


Multiple Choice

Active transport must function continuously because __________.

  1. plasma membranes wear out
  2. cells must be in constant motion
  3. facilitated transport opposes active transport
  4. diffusion is constantly moving the solutes in the other direction


Free Response

Where does the cell get energy for active transport processes?

The cell harvests energy from ATP produced by its own metabolism to power active transport processes, such as pumps.



active transport: the method of transporting material that requires energy

electrochemical gradient: a gradient produced by the combined forces of the electrical gradient and the chemical gradient

endocytosis: a type of active transport that moves substances, including fluids and particles, into a cell

exocytosis: a process of passing material out of a cell

phagocytosis: a process that takes macromolecules that the cell needs from the extracellular fluid; a variation of endocytosis

pinocytosis: a process that takes solutes that the cell needs from the extracellular fluid; a variation of endocytosis

receptor-mediated endocytosis: a variant of endocytosis that involves the use of specific binding proteins in the plasma membrane for specific molecules or particles


Chapter 3 PowerPoint

Chapter 3 PowerPoint


Chapter 4: Introduction to How Cells Obtain Energy

In this photo, a hummingbird drinks from a feeder.

Figure 4.1 A hummingbird needs energy to maintain prolonged flight. The bird obtains its energy from taking in food and transforming the energy contained in food molecules into forms of energy to power its flight through a series of biochemical reactions. (credit: modification of work by Cory Zanker)


Virtually every task performed by living organisms requires energy. Energy is needed to perform heavy labor and exercise, but humans also use energy while thinking, and even during sleep. In fact, the living cells of every organism constantly use energy. Nutrients and other molecules are imported into the cell, metabolized (broken down) and possibly synthesized into new molecules, modified if needed, transported around the cell, and possibly distributed to the entire organism. For example, the large proteins that make up muscles are built from smaller molecules imported from dietary amino acids. Complex carbohydrates are broken down into simple sugars that the cell uses for energy. Just as energy is required to both build and demolish a building, energy is required for the synthesis and breakdown of molecules as well as the transport of molecules into and out of cells. In addition, processes such as ingesting and breaking down pathogenic bacteria and viruses, exporting wastes and toxins, and movement of the cell require energy. From where, and in what form, does this energy come? How do living cells obtain energy, and how do they use it? This chapter will discuss different forms of energy and the physical laws that govern energy transfer. This chapter will also describe how cells use energy and replenish it, and how chemical reactions in the cell are performed with great efficiency.


4.1 Energy and Metabolism

Learning Objectives

By the end of this section, you will be able to:

  • Explain what metabolic pathways are
  • State the first and second laws of thermodynamics
  • Explain the difference between kinetic and potential energy
  • Describe endergonic and exergonic reactions
  • Discuss how enzymes function as molecular catalysts

Scientists use the term bioenergetics to describe the concept of energy flow (Figure 4.2) through living systems, such as cells. Cellular processes such as the building and breaking down of complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Just as living things must continually consume food to replenish their energy supplies, cells must continually produce more energy to replenish that used by the many energy-requiring chemical reactions that constantly take place. Together, all of the chemical reactions that take place inside cells, including those that consume or generate energy, are referred to as the cell’s metabolism.

This diagram shows energy from the sun being transferred to producers, such as plants. The producers in turn transfer energy to consumers and decomposers. Animals also transfer energy to decomposers.

Figure 4.2 Ultimately, most life forms get their energy from the sun. Plants use photosynthesis to capture sunlight, and herbivores eat the plants to obtain energy. Carnivores eat the herbivores, and eventual decomposition of plant and animal material contributes to the nutrient pool.

Metabolic Pathways

Consider the metabolism of sugar. This is a classic example of one of the many cellular processes that use and produce energy. Living things consume sugars as a major energy source, because sugar molecules have a great deal of energy stored within their bonds. For the most part, photosynthesizing organisms like plants produce these sugars. During photosynthesis, plants use energy (originally from sunlight) to convert carbon dioxide gas (CO2) into sugar molecules (like glucose: C6H12O6). They consume carbon dioxide and produce oxygen as a waste product. This reaction is summarized as:

6CO2 + 6H2O + energy ——-> C6H12O6+ 6O2

Because this process involves synthesizing an energy-storing molecule, it requires energy input to proceed. During the light reactions of photosynthesis, energy is provided by a molecule called adenosine triphosphate (ATP), which is the primary energy currency of all cells. Just as the dollar is used as currency to buy goods, cells use molecules of ATP as energy currency to perform immediate work. In contrast, energy-storage molecules such as glucose are consumed only to be broken down to use their energy. The reaction that harvests the energy of a sugar molecule in cells requiring oxygen to survive can be summarized by the reverse reaction to photosynthesis. In this reaction, oxygen is consumed and carbon dioxide is released as a waste product. The reaction is summarized as:

C6H12O6 + 6O2 ——> 6CO2 + 6H2O + energy

Both of these reactions involve many steps.

The processes of making and breaking down sugar molecules illustrate two examples of metabolic pathways. A metabolic pathway is a series of chemical reactions that takes a starting molecule and modifies it, step-by-step, through a series of metabolic intermediates, eventually yielding a final product. In the example of sugar metabolism, the first metabolic pathway synthesized sugar from smaller molecules, and the other pathway broke sugar down into smaller molecules. These two opposite processes—the first requiring energy and the second producing energy—are referred to as anabolic pathways (building polymers) and catabolic pathways (breaking down polymers into their monomers), respectively. Consequently, metabolism is composed of synthesis (anabolism) and degradation (catabolism) (Figure 4.3).

It is important to know that the chemical reactions of metabolic pathways do not take place on their own. Each reaction step is facilitated, or catalyzed, by a protein called an enzyme. Enzymes are important for catalyzing all types of biological reactions—those that require energy as well as those that release energy.

Anabolic and metabolic pathways are shown. In the anabolic pathway, four small molecules have energy added to them to make one large molecule. In the catabolic pathway, one large molecule is broken down into two components: four small molecules plus energy.

Figure 4.3 Catabolic pathways are those that generate energy by breaking down larger molecules. Anabolic pathways are those that require energy to synthesize larger molecules. Both types of pathways are required for maintaining the cell’s energy balance.


Thermodynamics refers to the study of energy and energy transfer involving physical matter. The matter relevant to a particular case of energy transfer is called a system, and everything outside of that matter is called the surroundings. For instance, when heating a pot of water on the stove, the system includes the stove, the pot, and the water. Energy is transferred within the system (between the stove, pot, and water). There are two types of systems: open and closed. In an open system, energy can be exchanged with its surroundings. The stovetop system is open because heat can be lost to the air. A closed system cannot exchange energy with its surroundings.

Biological organisms are open systems. Energy is exchanged between them and their surroundings as they use energy from the sun to perform photosynthesis or consume energy-storing molecules and release energy to the environment by doing work and releasing heat. Like all things in the physical world, energy is subject to physical laws. The laws of thermodynamics govern the transfer of energy in and among all systems in the universe.

In general, energy is defined as the ability to do work, or to create some kind of change. Energy exists in different forms. For example, electrical energy, light energy, and heat energy are all different types of energy. To appreciate the way energy flows into and out of biological systems, it is important to understand two of the physical laws that govern energy.


The first law of thermodynamics states that the total amount of energy in the universe is constant and conserved. In other words, there has always been, and always will be, exactly the same amount of energy in the universe. Energy exists in many different forms. According to the first law of thermodynamics, energy may be transferred from place to place or transformed into different forms, but it cannot be created or destroyed. The transfers and transformations of energy take place around us all the time. Light bulbs transform electrical energy into light and heat energy. Gas stoves transform chemical energy from natural gas into heat energy. Plants perform one of the most biologically useful energy transformations on earth: that of converting the energy of sunlight to chemical energy stored within organic molecules (Figure 4.2). Some examples of energy transformations are shown in Figure 4.4.

The challenge for all living organisms is to obtain energy from their surroundings in forms that they can transfer or transform into usable energy to do work. Living cells have evolved to meet this challenge. Chemical energy stored within organic molecules such as sugars and fats is transferred and transformed through a series of cellular chemical reactions into energy within molecules of ATP. Energy in ATP molecules is easily accessible to do work. Examples of the types of work that cells need to do include building complex molecules, transporting materials, powering the motion of cilia or flagella, and contracting muscle fibers to create movement.

The left side of this diagram depicts energy being transferred from an ice cream cone to two boys riding bikes. The right side depicts a plant converting light energy into chemical energy: Light energy is represented by the sun, and the chemical energy is represented by a green leaf on a branch.

Figure 4.4 Shown are some examples of energy transferred and transformed from one system to another and from one form to another. The food we consume provides our cells with the energy required to carry out bodily functions, just as light energy provides plants with the means to create the chemical energy they need. (credit “ice cream”: modification of work by D. Sharon Pruitt; credit “kids”: modification of work by Max from Providence; credit “leaf”: modification of work by Cory Zanker)

A living cell’s primary tasks of obtaining, transforming, and using energy to do work may seem simple. However, the second law of thermodynamics explains why these tasks are harder than they appear. All energy transfers and transformations are never completely efficient. In every energy transfer, some amount of energy is lost in a form that is unusable. In most cases, this form is heat energy. Thermodynamically, heat energy is defined as the energy transferred from one system to another that is not work. For example, when a light bulb is turned on, some of the energy being converted from electrical energy into light energy is lost as heat energy. Likewise, some energy is lost as heat energy during cellular metabolic reactions.

An important concept in physical systems is that of order and disorder. The more energy that is lost by a system to its surroundings, the less ordered and more random the system is. Scientists refer to the measure of randomness or disorder within a system as entropy. High entropy means high disorder and low energy. Molecules and chemical reactions have varying entropy as well. For example, entropy increases as molecules at a high concentration in one place diffuse and spread out. The second law of thermodynamics says that energy will always be lost as heat in energy transfers or transformations.

Living things are highly ordered, requiring constant energy input to be maintained in a state of low entropy.

Potential and Kinetic Energy

When an object is in motion, there is energy associated with that object. Think of a wrecking ball. Even a slow-moving wrecking ball can do a great deal of damage to other objects. Energy associated with objects in motion is called kinetic energy (Figure 4.5). A speeding bullet, a walking person, and the rapid movement of molecules in the air (which produces heat) all have kinetic energy.

Now what if that same motionless wrecking ball is lifted two stories above ground with a crane? If the suspended wrecking ball is unmoving, is there energy associated with it? The answer is yes. The energy that was required to lift the wrecking ball did not disappear, but is now stored in the wrecking ball by virtue of its position and the force of gravity acting on it. This type of energy is called potential energy (Figure 4.5). If the ball were to fall, the potential energy would be transformed into kinetic energy until all of the potential energy was exhausted when the ball rested on the ground. Wrecking balls also swing like a pendulum; through the swing, there is a constant change of potential energy (highest at the top of the swing) to kinetic energy (highest at the bottom of the swing). Other examples of potential energy include the energy of water held behind a dam or a person about to skydive out of an airplane.

The photo on the left shows water behind a dam as potential energy. The photo on the right shows a waterfall as kinetic energy.

Figure 4.5 Still water has potential energy; moving water, such as in a waterfall or a rapidly flowing river, has kinetic energy. (credit “dam”: modification of work by “Pascal”/Flickr; credit “waterfall”: modification of work by Frank Gualtieri)

Potential energy is not only associated with the location of matter, but also with the structure of matter. Even a spring on the ground has potential energy if it is compressed; so does a rubber band that is pulled taut. On a molecular level, the bonds that hold the atoms of molecules together exist in a particular structure that has potential energy. Remember that anabolic cellular pathways require energy to synthesize complex molecules from simpler ones and catabolic pathways release energy when complex molecules are broken down. The fact that energy can be released by the breakdown of certain chemical bonds implies that those bonds have potential energy. In fact, there is potential energy stored within the bonds of all the food molecules we eat, which is eventually harnessed for use. This is because these bonds can release energy when broken. The type of potential energy that exists within chemical bonds, and is released when those bonds are broken, is called chemical energy. Chemical energy is responsible for providing living cells with energy from food. The release of energy occurs when the molecular bonds within food molecules are broken.

Concept in Action

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Visit the site and select “Pendulum” from the “Work and Energy” menu to see the shifting kinetic and potential energy of a pendulum in motion.

Free and Activation Energy

After learning that chemical reactions release energy when energy-storing bonds are broken, an important next question is the following: How is the energy associated with these chemical reactions quantified and expressed? How can the energy released from one reaction be compared to that of another reaction? A measurement of free energy is used to quantify these energy transfers. Recall that according to the second law of thermodynamics, all energy transfers involve the loss of some amount of energy in an unusable form such as heat. Free energy specifically refers to the energy associated with a chemical reaction that is available after the losses are accounted for. In other words, free energy is usable energy, or energy that is available to do work.

If energy is released during a chemical reaction, then the change in free energy, signified as ∆G (delta G) will be a negative number. A negative change in free energy also means that the products of the reaction have less free energy than the reactants, because they release some free energy during the reaction. Reactions that have a negative change in free energy and consequently release free energy are called exergonic reactions. Think: exergonic means energy is exiting the system. These reactions are also referred to as spontaneous reactions, and their products have less stored energy than the reactants. An important distinction must be drawn between the term spontaneous and the idea of a chemical reaction occurring immediately. Contrary to the everyday use of the term, a spontaneous reaction is not one that suddenly or quickly occurs. The rusting of iron is an example of a spontaneous reaction that occurs slowly, little by little, over time.

If a chemical reaction absorbs energy rather than releases energy on balance, then the ∆G for that reaction will be a positive value. In this case, the products have more free energy than the reactants. Thus, the products of these reactions can be thought of as energy-storing molecules. These chemical reactions are called endergonic reactions and they are non-spontaneous. An endergonic reaction will not take place on its own without the addition of free energy.

Four photos, from left to right, show a compost pile, a baby chick emerging from a fertilized egg, a teabag’s dark-colored contents diffusing into a clear mug of water, and a ball rolling downhill.

Figure 4.6 Shown are some examples of endergonic processes (ones that require energy) and exergonic processes (ones that release energy). (credit a: modification of work by Natalie Maynor; credit b: modification of work by USDA; credit c: modification of work by Cory Zanker; credit d: modification of work by Harry Malsch)

Look at each of the processes shown and decide if it is endergonic or exergonic.

There is another important concept that must be considered regarding endergonic and exergonic reactions. Exergonic reactions require a small amount of energy input to get going, before they can proceed with their energy-releasing steps. These reactions have a net release of energy, but still require some energy input in the beginning. This small amount of energy input necessary for all chemical reactions to occur is called the activation energy.

Concept in Action

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Watch an animation of the move from free energy to transition state of the reaction.


A substance that helps a chemical reaction to occur is called a catalyst, and the molecules that catalyze biochemical reactions are called enzymes. Most enzymes are proteins and perform the critical task of lowering the activation energies of chemical reactions inside the cell. Most of the reactions critical to a living cell happen too slowly at normal temperatures to be of any use to the cell. Without enzymes to speed up these reactions, life could not persist. Enzymes do this by binding to the reactant molecules and holding them in such a way as to make the chemical bond-breaking and -forming processes take place more easily. It is important to remember that enzymes do not change whether a reaction is exergonic (spontaneous) or endergonic. This is because they do not change the free energy of the reactants or products. They only reduce the activation energy required for the reaction to go forward (Figure 4.7). In addition, an enzyme itself is unchanged by the reaction it catalyzes. Once one reaction has been catalyzed, the enzyme is able to participate in other reactions.

This plot shows that a catalyst decreases the activation energy for a reaction but does not change the Gibbs free energy.

Figure 4.7 Enzymes lower the activation energy of the reaction but do not change the free energy of the reaction.

The chemical reactants to which an enzyme binds are called the enzyme’s substrates. There may be one or more substrates, depending on the particular chemical reaction. In some reactions, a single reactant substrate is broken down into multiple products. In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction and both become modified, but they leave the reaction as two products. The location within the enzyme where the substrate binds is called the enzyme’s active site. The active site is where the “action” happens. Since enzymes are proteins, there is a unique combination of amino acid side chains within the active site. Each side chain is characterized by different properties. They can be large or small, weakly acidic or basic, hydrophilic or hydrophobic, positively or negatively charged, or neutral. The unique combination of side chains creates a very specific chemical environment within the active site. This specific environment is suited to bind to one specific chemical substrate (or substrates).

Active sites are subject to influences of the local environment. Increasing the environmental temperature generally increases reaction rates, enzyme-catalyzed or otherwise. However, temperatures outside of an optimal range reduce the rate at which an enzyme catalyzes a reaction. Hot temperatures will eventually cause enzymes to denature, an irreversible change in the three-dimensional shape and therefore the function of the enzyme. Enzymes are also suited to function best within a certain pH and salt concentration range, and, as with temperature, extreme pH, and salt concentrations can cause enzymes to denature.

For many years, scientists thought that enzyme-substrate binding took place in a simple “lock and key” fashion. This model asserted that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a model called induced fit (Figure 4.8). The induced-fit model expands on the lock-and-key model by describing a more dynamic binding between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild shift in the enzyme’s structure that forms an ideal binding arrangement between enzyme and substrate.

Concept in Action

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View an animation of induced fit.

When an enzyme binds its substrate, an enzyme-substrate complex is formed. This complex lowers the activation energy of the reaction and promotes its rapid progression in one of multiple possible ways. On a basic level, enzymes promote chemical reactions that involve more than one substrate by bringing the substrates together in an optimal orientation for reaction. Another way in which enzymes promote the reaction of their substrates is by creating an optimal environment within the active site for the reaction to occur. The chemical properties that emerge from the particular arrangement of amino acid R groups within an active site create the perfect environment for an enzyme’s specific substrates to react.

The enzyme-substrate complex can also lower activation energy by compromising the bond structure so that it is easier to break. Finally, enzymes can also lower activation energies by taking part in the chemical reaction itself. In these cases, it is important to remember that the enzyme will always return to its original state by the completion of the reaction. One of the hallmark properties of enzymes is that they remain ultimately unchanged by the reactions they catalyze. After an enzyme has catalyzed a reaction, it releases its product(s) and can catalyze a new reaction.

In this diagram, a substrate binds the active site of an enzyme and, in the process, both the shape of the enzyme and the shape of the substrate change. The substrate is converted to product, which leaves the active site.

Figure 4.8 The induced-fit model is an adjustment to the lock-and-key model and explains how enzymes and substrates undergo dynamic modifications during the transition state to increase the affinity of the substrate for the active site.

It would seem ideal to have a scenario in which all of an organism’s enzymes existed in abundant supply and functioned optimally under all cellular conditions, in all cells, at all times. However, a variety of mechanisms ensures that this does not happen. Cellular needs and conditions constantly vary from cell to cell, and change within individual cells over time. The required enzymes of stomach cells differ from those of fat storage cells, skin cells, blood cells, and nerve cells. Furthermore, a digestive organ cell works much harder to process and break down nutrients during the time that closely follows a meal compared with many hours after a meal. As these cellular demands and conditions vary, so must the amounts and functionality of different enzymes.

Since the rates of biochemical reactions are controlled by activation energy, and enzymes lower and determine activation energies for chemical reactions, the relative amounts and functioning of the variety of enzymes within a cell ultimately determine which reactions will proceed and at what rates. This determination is tightly controlled in cells. In certain cellular environments, enzyme activity is partly controlled by environmental factors like pH, temperature, salt concentration, and, in some cases, cofactors or coenzymes.

Enzymes can also be regulated in ways that either promote or reduce enzyme activity. There are many kinds of molecules that inhibit or promote enzyme function, and various mechanisms by which they do so. In some cases of enzyme inhibition, an inhibitor molecule is similar enough to a substrate that it can bind to the active site and simply block the substrate from binding. When this happens, the enzyme is inhibited through competitive inhibition, because an inhibitor molecule competes with the substrate for binding to the active site.

On the other hand, in noncompetitive inhibition, an inhibitor molecule binds to the enzyme in a location other than the active site, called an allosteric site, but still manages to block substrate binding to the active site. Some inhibitor molecules bind to enzymes in a location where their binding induces a conformational change that reduces the affinity of the enzyme for its substrate. This type of inhibition is called allosteric inhibition (Figure 4.9). Most allosterically regulated enzymes are made up of more than one polypeptide, meaning that they have more than one protein subunit. When an allosteric inhibitor binds to a region on an enzyme, all active sites on the protein subunits are changed slightly such that they bind their substrates with less efficiency. There are allosteric activators as well as inhibitors. Allosteric activators bind to locations on an enzyme away from the active site, inducing a conformational change that increases the affinity of the enzyme’s active site(s) for its substrate(s) (Figure 4.9).

The left part of this diagram shows allosteric inhibition. The allosteric inhibitor binds to the enzyme at a site other than the active site. The shape of the active site is altered so that the enzyme can no longer bind to the substrate. The right part of this diagram shows allosteric activation. The allosteric activator binds to the enzyme at a site other than the active site. The shape of the active site is changed, allowing substrate to bind.

Figure 4.9 Allosteric inhibition works by indirectly inducing a conformational change to the active site such that the substrate no longer fits. In contrast, in allosteric activation, the activator molecule modifies the shape of the active site to allow a better fit of the substrate.

Pharmaceutical Drug Developer

This photo shows several red capsule pills.

Figure 4.10 Have you ever wondered how pharmaceutical drugs are developed? (credit: Deborah Austin)

Enzymes are key components of metabolic pathways. Understanding how enzymes work and how they can be regulated are key principles behind the development of many of the pharmaceutical drugs on the market today. Biologists working in this field collaborate with other scientists to design drugs (Figure 4.10).

Consider statins for example—statins is the name given to one class of drugs that can reduce cholesterol levels. These compounds are inhibitors of the enzyme HMG-CoA reductase, which is the enzyme that synthesizes cholesterol from lipids in the body. By inhibiting this enzyme, the level of cholesterol synthesized in the body can be reduced. Similarly, acetaminophen, popularly marketed under the brand name Tylenol, is an inhibitor of the enzyme cyclooxygenase. While it is used to provide relief from fever and inflammation (pain), its mechanism of action is still not completely understood.

How are drugs discovered? One of the biggest challenges in drug discovery is identifying a drug target. A drug target is a molecule that is literally the target of the drug. In the case of statins, HMG-CoA reductase is the drug target. Drug targets are identified through painstaking research in the laboratory. Identifying the target alone is not enough; scientists also need to know how the target acts inside the cell and which reactions go awry in the case of disease. Once the target and the pathway are identified, then the actual process of drug design begins. In this stage, chemists and biologists work together to design and synthesize molecules that can block or activate a particular reaction. However, this is only the beginning: If and when a drug prototype is successful in performing its function, then it is subjected to many tests from in vitro experiments to clinical trials before it can get approval from the U.S. Food and Drug Administration to be on the market.

Many enzymes do not work optimally, or even at all, unless bound to other specific non-protein helper molecules. They may bond either temporarily through ionic or hydrogen bonds, or permanently through stronger covalent bonds. Binding to these molecules promotes optimal shape and function of their respective enzymes. Two examples of these types of helper molecules are cofactors and coenzymes. Cofactors are inorganic ions such as ions of iron and magnesium. Coenzymes are organic helper molecules, those with a basic atomic structure made up of carbon and hydrogen. Like enzymes, these molecules participate in reactions without being changed themselves and are ultimately recycled and reused. Vitamins are the source of coenzymes. Some vitamins are the precursors of coenzymes and others act directly as coenzymes. Vitamin C is a direct coenzyme for multiple enzymes that take part in building the important connective tissue, collagen. Therefore, enzyme function is, in part, regulated by the abundance of various cofactors and coenzymes, which may be supplied by an organism’s diet or, in some cases, produced by the organism.

Shown are the molecular structures for Vitamin A, folic acid, Vitamin B1, Vitamin C, Vitamin B2, Vitamin D2, Vitamin B6, and Vitamin E.

Figure 4.11 Vitamins are important coenzymes or precursors of coenzymes, and are required for enzymes to function properly. Multivitamin capsules usually contain mixtures of all the vitamins at different percentages.


Feedback Inhibition in Metabolic Pathways

Molecules can regulate enzyme function in many ways. The major question remains, however: What are these molecules and where do they come from? Some are cofactors and coenzymes, as you have learned. What other molecules in the cell provide enzymatic regulation such as allosteric modulation, and competitive and non-competitive inhibition? Perhaps the most relevant sources of regulatory molecules, with respect to enzymatic cellular metabolism, are the products of the cellular metabolic reactions themselves. In a most efficient and elegant way, cells have evolved to use the products of their own reactions for feedback inhibition of enzyme activity. Feedback inhibition involves the use of a reaction product to regulate its own further production (Figure 4.12). The cell responds to an abundance of the products by slowing down production during anabolic or catabolic reactions. Such reaction products may inhibit the enzymes that catalyzed their production through the mechanisms described above.

This diagram shows a metabolic pathway in which three enzymes convert a substrate, in three steps, into a final product. The final product inhibits the first enzyme in the pathway by feedback inhibition.

Figure 4.12 Metabolic pathways are a series of reactions catalyzed by multiple enzymes. Feedback inhibition, where the end product of the pathway inhibits an upstream process, is an important regulatory mechanism in cells.


The production of both amino acids and nucleotides is controlled through feedback inhibition. Additionally, ATP is an allosteric regulator of some of the enzymes involved in the catabolic breakdown of sugar, the process that creates ATP. In this way, when ATP is in abundant supply, the cell can prevent the production of ATP. On the other hand, ADP serves as a positive allosteric regulator (an allosteric activator) for some of the same enzymes that are inhibited by ATP. Thus, when relative levels of ADP are high compared to ATP, the cell is triggered to produce more ATP through sugar catabolism.

Section Summary

Cells perform the functions of life through various chemical reactions. A cell’s metabolism refers to the combination of chemical reactions that take place within it. Catabolic reactions break down complex chemicals into simpler ones and are associated with energy release. Anabolic processes build complex molecules out of simpler ones and require energy.

In studying energy, the term system refers to the matter and environment involved in energy transfers. Entropy is a measure of the disorder of a system. The physical laws that describe the transfer of energy are the laws of thermodynamics. The first law states that the total amount of energy in the universe is constant. The second law of thermodynamics states that every energy transfer involves some loss of energy in an unusable form, such as heat energy. Energy comes in different forms: kinetic, potential, and free. The change in free energy of a reaction can be negative (releases energy, exergonic) or positive (consumes energy, endergonic). All reactions require an initial input of energy to proceed, called the activation energy.

Enzymes are chemical catalysts that speed up chemical reactions by lowering their activation energy. Enzymes have an active site with a unique chemical environment that fits particular chemical reactants for that enzyme, called substrates. Enzymes and substrates are thought to bind according to an induced-fit model. Enzyme action is regulated to conserve resources and respond optimally to the environment.


Look at each of the processes shown and decide if it is endergonic or exergonic.

A compost pile decomposing is an exergonic process. A baby developing from a fertilized egg is an endergonic process. Tea dissolving into water is an exergonic process. A ball rolling downhill is an exergonic process.

Review Questions

Which of the following is not an example of an energy transformation?

A) Heating up dinner in a microwave

B) Solar panels at work

C) Formation of static electricity

D) None of the above


Which of the following is not true about enzymes?

A) They are consumed by the reactions they catalyze.

B) They are usually made of amino acids.

C) They lower the activation energy of chemical reactions.

D) Each one is specific to the particular substrate(s) to which it binds.


Free Response

Does physical exercise to increase muscle mass involve anabolic and/or catabolic processes? Give evidence for your answer.

Physical exercise involves both anabolic and catabolic processes. Body cells break down sugars to provide ATP to do the work necessary for exercise, such as muscle contractions. This is catabolism. Muscle cells also must repair muscle tissue damaged by exercise by building new muscle. This is anabolism.

Explain in your own terms the difference between a spontaneous reaction and one that occurs instantaneously, and what causes this difference.

A spontaneous reaction is one that has a negative ∆G and thus releases energy. However, a spontaneous reaction need not occur quickly or suddenly like an instantaneous reaction. It may occur over long periods of time due to a large energy of activation, which prevents the reaction from occurring quickly.

With regard to enzymes, why are vitamins and minerals necessary for good health? Give examples.

Most vitamins and minerals act as cofactors and coenzymes for enzyme action. Many enzymes require the binding of certain cofactors or coenzymes to be able to catalyze their reactions. Since enzymes catalyze many important reactions, it is critical to obtain sufficient vitamins and minerals from diet and supplements. Vitamin C (ascorbic acid) is a coenzyme necessary for the action of enzymes that build collagen.



activation energy: the amount of initial energy necessary for reactions to occur

active site: a specific region on the enzyme where the substrate binds

allosteric inhibition: the mechanism for inhibiting enzyme action in which a regulatory molecule binds to a second site (not the active site) and initiates a conformation change in the active site, preventing binding with the substrate

anabolic: describes the pathway that requires a net energy input to synthesize complex molecules from simpler ones

bioenergetics: the concept of energy flow through living systems

catabolic: describes the pathway in which complex molecules are broken down into simpler ones, yielding energy as an additional product of the reaction

competitive inhibition: a general mechanism of enzyme activity regulation in which a molecule other than the enzyme’s substrate is able to bind the active site and prevent the substrate itself from binding, thus inhibiting the overall rate of reaction for the enzyme

endergonic: describes a chemical reaction that results in products that store more chemical potential energy than the reactants

enzyme: a molecule that catalyzes a biochemical reaction

exergonic: describes a chemical reaction that results in products with less chemical potential energy than the reactants, plus the release of free energy

feedback inhibition: a mechanism of enzyme activity regulation in which the product of a reaction or the final product of a series of sequential reactions inhibits an enzyme for an earlier step in the reaction series

heat energy: the energy transferred from one system to another that is not work

kinetic energy: the type of energy associated with objects in motion

metabolism: all the chemical reactions that take place inside cells, including those that use energy and those that release energy

noncompetitive inhibition: a general mechanism of enzyme activity regulation in which a regulatory molecule binds to a site other than the active site and prevents the active site from binding the substrate; thus, the inhibitor molecule does not compete with the substrate for the active site; allosteric inhibition is a form of noncompetitive inhibition

potential energy: the type of energy that refers to the potential to do work

substrate: a molecule on which the enzyme acts

thermodynamics: the science of the relationships between heat, energy, and work



4.2 Glycolysis

Learning Objectives

By the end of this section, you will be able to:

  • Explain how ATP is used by the cell as an energy source
  • Describe the overall result in terms of molecules produced of the breakdown of glucose by glycolysis

Energy production within a cell involves many coordinated chemical pathways. Most of these pathways are combinations of oxidation and reduction reactions. Oxidation and reduction occur in tandem. An oxidation reaction strips an electron from an atom in a compound, and the addition of this electron to another compound is a reduction reaction. Because oxidation and reduction usually occur together, these pairs of reactions are called oxidation-reduction reactions, or redox reactions.

Electrons and Energy

The removal of an electron from a molecule, oxidizing it, results in a decrease in potential energy in the oxidized compound. The electron (sometimes as part of a hydrogen atom) does not remain unbonded, however, in the cytoplasm of a cell. Rather, the electron is shifted to a second compound, reducing the second compound. The shift of an electron from one compound to another removes some potential energy from the first compound (the oxidized compound) and increases the potential energy of the second compound (the reduced compound). The transfer of electrons between molecules is important because most of the energy stored in atoms and used to fuel cell functions is in the form of high-energy electrons. The transfer of energy in the form of electrons allows the cell to transfer and use energy in an incremental fashion—in small packages rather than in a single, destructive burst. This chapter focuses on the extraction of energy from food. You will see that as you track the path of the transfers, you are tracking the path of electrons moving through metabolic pathways.

Electron Carriers

In living systems, a small class of compounds functions as electron shuttles: they bind and carry high-energy electrons between compounds in pathways. The principal electron carriers we will consider are derived from the B vitamin group and are derivatives of nucleotides. These compounds can be easily reduced (that is, they accept electrons) or oxidized (they lose electrons). Nicotinamide adenine dinucleotide (NAD) (Figure 4.13) is derived from vitamin B3, niacin. NAD+ is the oxidized form of the molecule; NADH is the reduced form of the molecule after it has accepted two electrons and a proton (which together are the equivalent of a hydrogen atom with an extra electron).

NAD+ can accept electrons from an organic molecule according to the general equation:

RH (Reducing Agent) + NAD + (Oxidizing Agent) —-> NADH (Reduced) + R (Oxidized)

When electrons are added to a compound, they are reduced. A compound that reduces another is called a reducing agent. In the above equation, RH is a reducing agent, and NAD+ is reduced to NADH. When electrons are removed from compound, it is oxidized. A compound that oxidizes another is called an oxidizing agent. In the above equation, NAD+ is an oxidizing agent, and RH is oxidized to R.

Similarly, flavin adenine dinucleotide (FAD+) is derived from vitamin B2, also called riboflavin. Its reduced form is FADH2. A second variation of NAD, NADP, contains an extra phosphate group. Both NAD+ and FAD+ are extensively used in energy extraction from sugars, and NADP plays an important role in anabolic reactions and photosynthesis.

This illustration shows the molecular structure of NAD^{+} and NADH. Both compounds are composed of an adenine nucleotide and a nicotinamide nucleotide, which bond together to form a dinucleotide. The nicotinamide nucleotide is at the 5' end, and the adenine nucleotide is at the 3’ end. Nicotinamide is a nitrogenous base, meaning it has nitrogen in a six-membered carbon ring. In NADH, one extra hydrogen is associated with this ring, which is not found in NAD^{+}.

Figure 4.13 The oxidized form of the electron carrier (NAD+) is shown on the left and the reduced form (NADH) is shown on the right. The nitrogenous base in NADH has one more hydrogen ion and two more electrons than in NAD+.

ATP in Living Systems

A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell, which would result in excessive thermal motion that could damage and then destroy the cell. Rather, a cell must be able to handle that energy in a way that enables the cell to store the energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. How? It functions similarly to a rechargeable battery.

When ATP is broken down, usually by the removal of its terminal phosphate group, energy is released. The cell uses the energy to do work, usually by the released phosphate binding to another molecule, activating it. For example, in the mechanical work of muscle contraction, ATP supplies the energy to move the contractile muscle proteins. Recall the active transport work of the sodium-potassium pump in cell membranes. ATP alters the structure of the integral protein that functions as the pump, changing its affinity for sodium and potassium. In this way, the cell performs work, pumping ions against their electrochemical gradients.

ATP Structure and Function

At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to a ribose molecule and a single phosphate group (Figure 4.14). Ribose is a five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in the formation of adenosine diphosphate (ADP); the addition of a third phosphate group forms adenosine triphosphate (ATP).

This illustration shows the molecular structure of ATP. This molecule is an adenine nucleotide with a string of three phosphate groups attached to it. The phosphate groups are named alpha, beta, and gamma in order of increasing distance from the ribose sugar to which they are attached.

Figure 4.14 ATP (adenosine triphosphate) has three phosphate groups that can be removed by hydrolysis to form ADP (adenosine diphosphate) or AMP (adenosine monophosphate).The negative charges on the phosphate group naturally repel each other, requiring energy to bond them together and releasing energy when these bonds are broken.

The addition of a phosphate group to a molecule requires energy. Phosphate groups are negatively charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. This repulsion makes the ADP and ATP molecules inherently unstable. The release of one or two phosphate groups from ATP, a process called dephosphorylation, releases energy.

Even exergonic, energy-releasing reactions require a small amount of activation energy to proceed. However, consider endergonic reactions, which require much more energy input because their products have more free energy than their reactants. Within the cell, where does energy to power such reactions come from? The answer lies with an energy-supplying molecule called adenosine triphosphate, or ATP. ATP is a small, relatively simple molecule, but within its bonds contains the potential for a quick burst of energy that can be harnessed to perform cellular work. This molecule can be thought of as the primary energy currency of cells in the same way that money is the currency that people exchange for things they need. ATP is used to power the majority of energy-requiring cellular reactions.

ATP in Living Systems

A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell, which would denature enzymes and other proteins, and thus destroy the cell. Rather, a cell must be able to store energy safely and release it for use only as needed. Living cells accomplish this using ATP, which can be used to fill any energy need of the cell. How? It functions as a rechargeable battery.

When ATP is broken down, usually by the removal of its terminal phosphate group, energy is released. This energy is used to do work by the cell, usually by the binding of the released phosphate to another molecule, thus activating it. For example, in the mechanical work of muscle contraction, ATP supplies energy to move the contractile muscle proteins.

ATP Structure and Function

At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to both a ribose molecule and a single phosphate group (Figure 4.15). Ribose is a five-carbon sugar found in RNA and AMP is one of the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in adenosine diphosphate (ADP); the addition of a third phosphate group forms adenosine triphosphate (ATP).

This illustration shows the molecular structure of ATP. This molecule is an adenine nucleotide with ribose and a string of three phosphate groups attached to it. The phosphate groups are named alpha, beta, and gamma in order of increasing distance from the ribose sugar to which they are attached.

Figure 4.15 The structure of ATP shows the basic components of a two-ring adenine, five-carbon ribose, and three phosphate groups.

The addition of a phosphate group to a molecule requires a high amount of energy and results in a high-energy bond. Phosphate groups are negatively charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. This repulsion makes the ADP and ATP molecules inherently unstable. The release of one or two phosphate groups from ATP, a process called hydrolysis, releases energy.


You have read that nearly all of the energy used by living things comes to them in the bonds of the sugar, glucose. Glycolysis is the first step in the breakdown of glucose to extract energy for cell metabolism. Many living organisms carry out glycolysis as part of their metabolism. Glycolysis takes place in the cytoplasm of most prokaryotic and all eukaryotic cells.

Glycolysis begins with the six-carbon, ring-shaped structure of a single glucose molecule and ends with two molecules of a three-carbon sugar called pyruvate. Glycolysis consists of two distinct phases. In the first part of the glycolysis pathway, energy is used to make adjustments so that the six-carbon sugar molecule can be split evenly into two three-carbon pyruvate molecules. In the second part of glycolysis, ATP and nicotinamide-adenine dinucleotide (NADH) are produced (Figure 4.16).

If the cell cannot catabolize the pyruvate molecules further, it will harvest only two ATP molecules from one molecule of glucose. For example, mature mammalian red blood cells are only capable of glycolysis, which is their sole source of ATP. If glycolysis is interrupted, these cells would eventually die.

A graphic shows glucose at the top with an arrow pointing down to fructose diphosphate, which then splits into two glyceraldehyde 3-phosphate molecules. Each of these forms one NADH and two ATP molecules in the process of each becoming a pyruvate molecule.

Figure 4.16 In glycolysis, a glucose molecule is converted into two pyruvate molecules.


Section Summary

ATP functions as the energy currency for cells. It allows cells to store energy briefly and transport it within itself to support endergonic chemical reactions. The structure of ATP is that of an RNA nucleotide with three phosphate groups attached. As ATP is used for energy, a phosphate group is detached, and ADP is produced. Energy derived from glucose catabolism is used to recharge ADP into ATP.

Glycolysis is the first pathway used in the breakdown of glucose to extract energy. Because it is used by nearly all organisms on earth, it must have evolved early in the history of life. Glycolysis consists of two parts: The first part prepares the six-carbon ring of glucose for separation into two three-carbon sugars. Energy from ATP is invested into the molecule during this step to energize the separation. The second half of glycolysis extracts ATP and high-energy electrons from hydrogen atoms and attaches them to NAD+. Two ATP molecules are invested in the first half and four ATP molecules are formed during the second half. This produces a net gain of two ATP molecules per molecule of glucose for the cell.


Multiple Choice

Energy is stored long-term in the bonds of _____ and used short-term to perform work from a(n) _____ molecule.

A) ATP : glucose

B) an anabolic molecule : catabolic molecule

C) glucose : ATP

D) a catabolic molecule : anabolic molecule


The energy currency used by cells is _____.




D) adenosine


The glucose that enters the glycolysis pathway is split into two molecules of _________.


B) phosphate


D) pyruvate


Free Response

Both prokaryotic and eukaryotic organisms carry out some form of glycolysis. How does that fact support or not support the assertion that glycolysis is one of the oldest metabolic pathways?

If glycolysis evolved relatively late, it likely would not be as universal in organisms as it is. It probably evolved in very primitive organisms and persisted, with the addition of other pathways of carbohydrate metabolism that evolved later.



ATP: (also, adenosine triphosphate) the cell’s energy currency

glycolysis: the process of breaking glucose into two three-carbon molecules with the production of ATP and NADH


4.3 Citric Acid Cycle and Oxidative Phosphorylation

Learning Objectives

By the end of this section, you will be able to:

  • Describe the location of the citric acid cycle and oxidative phosphorylation in the cell
  • Describe the overall outcome of the citric acid cycle and oxidative phosphorylation in terms of the products of each
  • Describe the relationships of glycolysis, the citric acid cycle, and oxidative phosphorylation in terms of their inputs and outputs.

The Citric Acid Cycle

In eukaryotic cells, the pyruvate molecules produced at the end of glycolysis are transported into mitochondria, which are sites of cellular respiration. If oxygen is available, aerobic respiration will go forward. In mitochondria, pyruvate will be transformed into a two-carbon acetyl group (by removing a molecule of carbon dioxide) that will be picked up by a carrier compound called coenzyme A (CoA), which is made from vitamin B5. The resulting compound is called acetyl CoA. (Figure 4.17). Acetyl CoA can be used in a variety of ways by the cell, but its major function is to deliver the acetyl group derived from pyruvate to the next pathway in glucose catabolism.

A graphic shows pyruvate becoming a two-carbon acetyl group by removing one molecule of carbon dioxide. The two-carbon acetyl group is picked up by coenzyme A to become acetyl CoA. The acetyl CoA then enters the citric acid cycle. Three NADH, one FADH2, one ATP, and two carbon dioxide molecules are produced during this cycle.

Figure 4.17 Pyruvate is converted into acetyl-CoA before entering the citric acid cycle.

Like the conversion of pyruvate to acetyl CoA, the citric acid cycle in eukaryotic cells takes place in the matrix of the mitochondria. Unlike glycolysis, the citric acid cycle is a closed loop: The last part of the pathway regenerates the compound used in the first step. The eight steps of the cycle are a series of chemical reactions that produces two carbon dioxide molecules, one ATP molecule (or an equivalent), and reduced forms (NADH and FADH2) of NAD+ and FAD+, important coenzymes in the cell. Part of this is considered an aerobic pathway (oxygen-requiring) because the NADH and FADH2 produced must transfer their electrons to the next pathway in the system, which will use oxygen. If oxygen is not present, this transfer does not occur.

Two carbon atoms come into the citric acid cycle from each acetyl group. Two carbon dioxide molecules are released on each turn of the cycle; however, these do not contain the same carbon atoms contributed by the acetyl group on that turn of the pathway. The two acetyl-carbon atoms will eventually be released on later turns of the cycle; in this way, all six carbon atoms from the original glucose molecule will be eventually released as carbon dioxide. It takes two turns of the cycle to process the equivalent of one glucose molecule. Each turn of the cycle forms three high-energy NADH molecules and one high-energy FADH2 molecule. These high-energy carriers will connect with the last portion of aerobic respiration to produce ATP molecules. One ATP (or an equivalent) is also made in each cycle. Several of the intermediate compounds in the citric acid cycle can be used in synthesizing non-essential amino acids; therefore, the cycle is both anabolic and catabolic.

This illustration shows the structure of a mitochondrion, which has an outer membrane and an inner membrane. The inner membrane has many folds, called cristae. The space between the outer membrane and the inner membrane is called the intermembrane space, and the central space of the mitochondrion is called the matrix. ATP synthase enzymes and the electron transport chain are located in the inner membrane

Figure 4.18 In eukaryotes, oxidative phosphorylation takes place in mitochondria. In prokaryotes, this process takes place in the plasma membrane. (Credit: modification of work by Mariana Ruiz Villareal)

Oxidative Phosphorylation

You have just read about two pathways in glucose catabolism—glycolysis and the citric acid cycle—that generate ATP. Most of the ATP generated during the aerobic catabolism of glucose, however, is not generated directly from these pathways. Rather, it derives from a process that begins with passing electrons through a series of chemical reactions to a final electron acceptor, oxygen. These reactions take place in specialized protein complexes located in the inner membrane of the mitochondria of eukaryotic organisms and on the inner part of the cell membrane of prokaryotic organisms. The energy of the electrons is harvested and used to generate a electrochemical gradient across the inner mitochondrial membrane. The potential energy of this gradient is used to generate ATP. The entirety of this process is called oxidative phosphorylation.

The electron transport chain (Figure 4.19 a) is the last component of aerobic respiration and is the only part of metabolism that uses atmospheric oxygen. Oxygen continuously diffuses into plants for this purpose. In animals, oxygen enters the body through the respiratory system. Electron transport is a series of chemical reactions that resembles a bucket brigade in that electrons are passed rapidly from one component to the next, to the endpoint of the chain where oxygen is the final electron acceptor and water is produced. There are four complexes composed of proteins, labeled I through IV in Figure 4.19 c, and the aggregation of these four complexes, together with associated mobile, accessory electron carriers, is called the electron transport chain. The electron transport chain is present in multiple copies in the inner mitochondrial membrane of eukaryotes and in the plasma membrane of prokaryotes. In each transfer of an electron through the electron transport chain, the electron loses energy, but with some transfers, the energy is stored as potential energy by using it to pump hydrogen ions across the inner mitochondrial membrane into the intermembrane space, creating an electrochemical gradient.

Part a: This illustration shows the electron transport chain embedded in the inner mitochondrial membrane. The electron transport chain consists of four electron complexes. Complex I oxidizes NADH to NAD+ and simultaneously pumps a proton across the membrane into the intermembrane space. The two electrons released from NADH are shuttled to coenzyme Q, then to complex III, to cytochrome c, to complex IV, then to molecular oxygen. In the process, two more protons are pumped across the membrane into the intermembrane space, and molecular oxygen is reduced to form water. Complex II removes two electrons from FADH2, thereby forming FAD. The electrons are shuttled to coenzyme Q, then to complex III, cytochrome c, complex I, and molecular oxygen as in the case of NADH oxidation. Part b: This illustration shows an ATP synthase enzyme embedded in the inner mitochondrial membrane. ATP synthase allows protons to move from an area of high concentration in the intermembrane space to an area of low concentration in the mitochondrial matrix. The energy derived from this exergonic process is used to synthesize ATP from ADP and inorganic phosphate. Part c: This illustration shows the electron transport chain and ATP synthase enzyme embedded in the inner mitochondrial membrane, and the citric acid cycle in the mitochondrial matrix. The citric acid cycle feeds NADH and FADH2 into the electron transport chain. The electron transport chain oxidizes these substrates and, in the process, pumps protons into the intermembrane space. ATP synthase allows protons to leak back into the matrix and synthesizes ATP.

Figure 4.19 (a) The electron transport chain is a set of molecules that supports a series of oxidation-reduction reactions. (b) ATP synthase is a complex, molecular machine that uses an H+ gradient to regenerate ATP from ADP. (c) Chemiosmosis relies on the potential energy provided by the H+ gradient across the membrane.

Cyanide inhibits cytochrome c oxidase, a component of the electron transport chain. If cyanide poisoning occurs, would you expect the pH of the intermembrane space to increase or decrease? What affect would cyanide have on ATP synthesis?

Electrons from NADH and FADH2 are passed to protein complexes in the electron transport chain. As they are passed from one complex to another (there are a total of four), the electrons lose energy, and some of that energy is used to pump hydrogen ions from the mitochondrial matrix into the intermembrane space. In the fourth protein complex, the electrons are accepted by oxygen, the terminal acceptor. The oxygen with its extra electrons then combines with two hydrogen ions, further enhancing the electrochemical gradient, to form water. If there were no oxygen present in the mitochondrion, the electrons could not be removed from the system, and the entire electron transport chain would back up and stop. The mitochondria would be unable to generate new ATP in this way, and the cell would ultimately die from lack of energy. This is the reason we must breathe to draw in new oxygen.

In the electron transport chain, the free energy from the series of reactions just described is used to pump hydrogen ions across the membrane. The uneven distribution of H+ ions across the membrane establishes an electrochemical gradient, owing to the H+ ions’ positive charge and their higher concentration on one side of the membrane.

Hydrogen ions diffuse through the inner membrane through an integral membrane protein called ATP synthase (Figure 4.19 b). This complex protein acts as a tiny generator, turned by the force of the hydrogen ions diffusing through it, down their electrochemical gradient from the intermembrane space, where there are many mutually repelling hydrogen ions to the matrix, where there are few. The turning of the parts of this molecular machine regenerate ATP from ADP. This flow of hydrogen ions across the membrane through ATP synthase is called chemiosmosis.

Chemiosmosis (Figure 4.19 c) is used to generate 90 percent of the ATP made during aerobic glucose catabolism. The result of the reactions is the production of ATP from the energy of the electrons removed from hydrogen atoms. These atoms were originally part of a glucose molecule. At the end of the electron transport system, the electrons are used to reduce an oxygen molecule to oxygen ions. The extra electrons on the oxygen ions attract hydrogen ions (protons) from the surrounding medium, and water is formed. The electron transport chain and the production of ATP through chemiosmosis are collectively called oxidative phosphorylation.

ATP Yield

The number of ATP molecules generated from the catabolism of glucose varies. For example, the number of hydrogen ions that the electron transport chain complexes can pump through the membrane varies between species. Another source of variance stems from the shuttle of electrons across the mitochondrial membrane. The NADH generated from glycolysis cannot easily enter mitochondria. Thus, electrons are picked up on the inside of the mitochondria by either NAD+ or FAD+. Fewer ATP molecules are generated when FAD+ acts as a carrier. NAD+ is used as the electron transporter in the liver and FAD+ in the brain, so ATP yield depends on the tissue being considered.

Another factor that affects the yield of ATP molecules generated from glucose is that intermediate compounds in these pathways are used for other purposes. Glucose catabolism connects with the pathways that build or break down all other biochemical compounds in cells, and the result is somewhat messier than the ideal situations described thus far. For example, sugars other than glucose are fed into the glycolytic pathway for energy extraction. Other molecules that would otherwise be used to harvest energy in glycolysis or the citric acid cycle may be removed to form nucleic acids, amino acids, lipids, or other compounds. Overall, in living systems, these pathways of glucose catabolism extract about 34 percent of the energy contained in glucose.

Mitochondrial Disease Physician

What happens when the critical reactions of cellular respiration do not proceed correctly? Mitochondrial diseases are genetic disorders of metabolism. Mitochondrial disorders can arise from mutations in nuclear or mitochondrial DNA, and they result in the production of less energy than is normal in body cells. Symptoms of mitochondrial diseases can include muscle weakness, lack of coordination, stroke-like episodes, and loss of vision and hearing. Most affected people are diagnosed in childhood, although there are some adult-onset diseases. Identifying and treating mitochondrial disorders is a specialized medical field. The educational preparation for this profession requires a college education, followed by medical school with a specialization in medical genetics. Medical geneticists can be board certified by the American Board of Medical Genetics and go on to become associated with professional organizations devoted to the study of mitochondrial disease, such as the Mitochondrial Medicine Society and the Society for Inherited Metabolic Disease.

Section Summary

The citric acid cycle is a series of chemical reactions that removes high-energy electrons and uses them in the electron transport chain to generate ATP. One molecule of ATP (or an equivalent) is produced per each turn of the cycle.

The electron transport chain is the portion of aerobic respiration that uses free oxygen as the final electron acceptor for electrons removed from the intermediate compounds in glucose catabolism. The electrons are passed through a series of chemical reactions, with a small amount of free energy used at three points to transport hydrogen ions across the membrane. This contributes to the gradient used in chemiosmosis. As the electrons are passed from NADH or FADH2 down the electron transport chain, they lose energy. The products of the electron transport chain are water and ATP. A number of intermediate compounds can be diverted into the anabolism of other biochemical molecules, such as nucleic acids, non-essential amino acids, sugars, and lipids. These same molecules, except nucleic acids, can serve as energy sources for the glucose pathway.


Cyanide inhibits cytochrome c oxidase, a component of the electron transport chain. If cyanide poisoning occurs, would you expect the pH of the intermembrane space to increase or decrease? What affect would cyanide have on ATP synthesis?

After cyanide poisoning, the electron transport chain can no longer pump electrons into the intermembrane space. The pH of the intermembrane space would increase, and ATP synthesis would stop.

Multiple Choice

What do the electrons added to NAD+ do?

A) They become part of a fermentation pathway.

B) They go to another pathway for ATP production.

C) They energize the entry of the acetyl group into the citric acid cycle.

D) They are converted into NADP.


Chemiosmosis involves

A) the movement of electrons across the cell membrane

B) the movement of hydrogen atoms across a mitochondrial membrane

C) the movement of hydrogen ions across a mitochondrial membrane

D) the movement of glucose through the cell membrane


Free Response

We inhale oxygen when we breathe and exhale carbon dioxide. What is the oxygen used for and where does the carbon dioxide come from?

The oxygen we inhale is the final electron acceptor in the electron transport chain and allows aerobic respiration to proceed, which is the most efficient pathway for harvesting energy in the form of ATP from food molecules. The carbon dioxide we breathe out is formed during the citric acid cycle when the bonds in carbon compounds are broken.


acetyl CoA: the combination of an acetyl group derived from pyruvic acid and coenzyme A which is made from pantothenic acid (a B-group vitamin)

ATP synthase: a membrane-embedded protein complex that regenerates ATP from ADP with energy from protons diffusing through it

chemiosmosis: the movement of hydrogen ions down their electrochemical gradient across a membrane through ATP synthase to generate ATP

citric acid cycle: a series of enzyme-catalyzed chemical reactions of central importance in all living cells that harvests the energy in carbon-carbon bonds of sugar molecules to generate ATP; the citric acid cycle is an aerobic metabolic pathway because it requires oxygen in later reactions to proceed

electron transport chain: a series of four large, multi-protein complexes embedded in the inner mitochondrial membrane that accepts electrons from donor compounds and harvests energy from a series of chemical reactions to generate a hydrogen ion gradient across the membrane

oxidative phosphorylation: the production of ATP by the transfer of electrons down the electron transport chain to create a proton gradient that is used by ATP synthase to add phosphate groups to ADP molecules


4.4 Fermentation

Learning Objectives

By the end of this section, you will be able to:

  • Discuss the fundamental difference between anaerobic cellular respiration and fermentation
  • Describe the type of fermentation that readily occurs in animal cells and the conditions that initiate that fermentation

In aerobic respiration, the final electron acceptor is an oxygen molecule, O2. If aerobic respiration occurs, then ATP will be produced using the energy of the high-energy electrons carried by NADH or FADH2 to the electron transport chain. If aerobic respiration does not occur, NADH must be reoxidized to NAD+ for reuse as an electron carrier for glycolysis to continue. How is this done? Some living systems use an organic molecule as the final electron acceptor. Processes that use an organic molecule to regenerate NAD+ from NADH are collectively referred to as fermentation. In contrast, some living systems use an inorganic molecule as a final electron acceptor; both methods are a type of anaerobic cellular respiration. Anaerobic respiration enables organisms to convert energy for their use in the absence of oxygen.

Lactic Acid Fermentation

The fermentation method used by animals and some bacteria like those in yogurt is lactic acid fermentation (Figure 4.20). This occurs routinely in mammalian red blood cells and in skeletal muscle that has insufficient oxygen supply to allow aerobic respiration to continue (that is, in muscles used to the point of fatigue). In muscles, lactic acid produced by fermentation must be removed by the blood circulation and brought to the liver for further metabolism. The chemical reaction of lactic acid fermentation is the following:

Pyruvic acid +NADH↔lactic acid+NAD+Pyruvic acid +NADH↔lactic acid+NAD+

The enzyme that catalyzes this reaction is lactate dehydrogenase. The reaction can proceed in either direction, but the left-to-right reaction is inhibited by acidic conditions. This lactic acid build-up causes muscle stiffness and fatigue. Once the lactic acid has been removed from the muscle and is circulated to the liver, it can be converted back to pyruvic acid and further catabolized for energy.

Lactic acid fermentation is common in muscles that have become exhausted by use.

Figure 4.20


Tremetol, a metabolic poison found in white snake root plant, prevents the metabolism of lactate. When cows eat this plant, Tremetol is concentrated in the milk. Humans who consume the milk become ill. Symptoms of this disease, which include vomiting, abdominal pain, and tremors, become worse after exercise. Why do you think this is the case?

<!– The illness is caused by lactic acid build-up. Lactic acid levels rise after exercise, making the symptoms worse. Milk sickness is rare today, but was common in the Midwestern United States in the early 1800s. –>

Alcohol Fermentation

Another familiar fermentation process is alcohol fermentation (Figure 4.21), which produces ethanol, an alcohol. The alcohol fermentation reaction is the following:

Graphic showing the alcohol fermentation reaction in an equation.

Figure 4.21 The reaction resulting in alcohol fermentation is shown.

In the first reaction, a carboxyl group is removed from pyruvic acid, releasing carbon dioxide as a gas. The loss of carbon dioxide reduces the molecule by one carbon atom, making acetaldehyde. The second reaction removes an electron from NADH, forming NAD+ and producing ethanol from the acetaldehyde, which accepts the electron. The fermentation of pyruvic acid by yeast produces the ethanol found in alcoholic beverages (Figure 4.22). If the carbon dioxide produced by the reaction is not vented from the fermentation chamber, for example in beer and sparkling wines, it remains dissolved in the medium until the pressure is released. Ethanol above 12 percent is toxic to yeast, so natural levels of alcohol in wine occur at a maximum of 12 percent.

This photo shows large, silver-colored, cylindrical fermentation tanks.

Figure 4.22 Fermentation of grape juice to make wine produces CO2 as a byproduct. Fermentation tanks have valves so that pressure inside the tanks can be released.

Anaerobic Cellular Respiration

Certain prokaryotes, including some species of bacteria and Archaea, use anaerobic respiration. For example, the group of Archaea called methanogens reduces carbon dioxide to methane to oxidize NADH. These microorganisms are found in soil and in the digestive tracts of ruminants, such as cows and sheep. Similarly, sulfate-reducing bacteria and Archaea, most of which are anaerobic (Figure 4.23), reduce sulfate to hydrogen sulfide to regenerate NAD+ from NADH.

This photo shows a bloom of green bacteria in water.

Figure 4.23 The green color seen in these coastal waters is from an eruption of hydrogen sulfide. Anaerobic, sulfate-reducing bacteria release hydrogen sulfide gas as they decompose algae in the water. (credit: NASA image courtesy Jeff Schmaltz, MODIS Land Rapid Response Team at NASA GSFC)

Concept in Action

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Visit this site to see anaerobic cellular respiration in action.

Other fermentation methods occur in bacteria. Many prokaryotes are facultatively anaerobic. This means that they can switch between aerobic respiration and fermentation, depending on the availability of oxygen. Certain prokaryotes, like Clostridia bacteria, are obligate anaerobes. Obligate anaerobes live and grow in the absence of molecular oxygen. Oxygen is a poison to these microorganisms and kills them upon exposure. It should be noted that all forms of fermentation, except lactic acid fermentation, produce gas. The production of particular types of gas is used as an indicator of the fermentation of specific carbohydrates, which plays a role in the laboratory identification of the bacteria. The various methods of fermentation are used by different organisms to ensure an adequate supply of NAD+ for the sixth step in glycolysis. Without these pathways, that step would not occur, and no ATP would be harvested from the breakdown of glucose.

Section Summary

If NADH cannot be metabolized through aerobic respiration, another electron acceptor is used. Most organisms will use some form of fermentation to accomplish the regeneration of NAD+, ensuring the continuation of glycolysis. The regeneration of NAD+ in fermentation is not accompanied by ATP production; therefore, the potential for NADH to produce ATP using an electron transport chain is not utilized.


Tremetol, a metabolic poison found in white snake root plant, prevents the metabolism of lactate. When cows eat this plant, Tremetol is concentrated in the milk. Humans who consume the milk become ill. Symptoms of this disease, which include vomiting, abdominal pain, and tremors, become worse after exercise. Why do you think this is the case?

The illness is caused by lactic acid build-up. Lactic acid levels rise after exercise, making the symptoms worse. Milk sickness is rare today, but was common in the Midwestern United States in the early 1800s.

Review Questions

Which of the following fermentation methods can occur in animal skeletal muscles?

A) lactic acid fermentation

B) alcohol fermentation

C) mixed acid fermentation

D) propionic fermentation


Free Response

When muscle cells run out of oxygen, what happens to the potential for energy extraction from sugars and what pathways do the cell use?

Without oxygen, oxidative phosphorylation and the citric acid cycle stop, so ATP is no longer generated through this mechanism, which extracts the greatest amount of energy from a sugar molecule. In addition, NADH accumulates, preventing glycolysis from going forward because of an absence of NAD+. Lactic acid fermentation uses the electrons in NADH to generate lactic acid from pyruvate, which allows glycolysis to continue and thus a smaller amount of ATP can be generated by the cell.



anaerobic cellular respiration: the use of an electron acceptor other than oxygen to complete metabolism using electron transport-based chemiosmosis

fermentation: the steps that follow the partial oxidation of glucose via glycolysis to regenerate NAD+; occurs in the absence of oxygen and uses an organic compound as the final electron acceptor


4.5 Connections to Other Metabolic Pathways

Learning Objectives

By the end of this section, you will be able to:

  • Discuss the way in which carbohydrate metabolic pathways, glycolysis, and the citric acid cycle interrelate with protein and lipid metabolic pathways
  • Explain why metabolic pathways are not considered closed systems

You have learned about the catabolism of glucose, which provides energy to living cells. But living things consume more than just glucose for food. How does a turkey sandwich, which contains protein, provide energy to your cells? This happens because all of the catabolic pathways for carbohydrates, proteins, and lipids eventually connect into glycolysis and the citric acid cycle pathways (Figure 4.24 ). Metabolic pathways should be thought of as porous—that is, substances enter from other pathways, and other substances leave for other pathways. These pathways are not closed systems. Many of the products in a particular pathway are reactants in other pathways.

Connections of Other Sugars to Glucose Metabolism

Glycogen, a polymer of glucose, is a short-term energy storage molecule in animals. When there is adequate ATP present, excess glucose is converted into glycogen for storage. Glycogen is made and stored in the liver and muscle. Glycogen will be taken out of storage if blood sugar levels drop. The presence of glycogen in muscle cells as a source of glucose allows ATP to be produced for a longer time during exercise.

Sucrose is a disaccharide made from glucose and fructose bonded together. Sucrose is broken down in the small intestine, and the glucose and fructose are absorbed separately. Fructose is one of the three dietary monosaccharides, along with glucose and galactose (which is part of milk sugar, the disaccharide lactose), that are absorbed directly into the bloodstream during digestion. The catabolism of both fructose and galactose produces the same number of ATP molecules as glucose.

Connections of Proteins to Glucose Metabolism

Proteins are broken down by a variety of enzymes in cells. Most of the time, amino acids are recycled into new proteins. If there are excess amino acids, however, or if the body is in a state of famine, some amino acids will be shunted into pathways of glucose catabolism. Each amino acid must have its amino group removed prior to entry into these pathways. The amino group is converted into ammonia. In mammals, the liver synthesizes urea from two ammonia molecules and a carbon dioxide molecule. Thus, urea is the principal waste product in mammals from the nitrogen originating in amino acids, and it leaves the body in urine.

Connections of Lipids to Glucose Metabolism

The lipids that are connected to the glucose pathways are cholesterol and triglycerides. Cholesterol is a lipid that contributes to cell membrane flexibility and is a precursor of steroid hormones. The synthesis of cholesterol starts with acetyl CoA and proceeds in only one direction. The process cannot be reversed, and ATP is not produced.

Triglycerides are a form of long-term energy storage in animals. Triglycerides store about twice as much energy as carbohydrates. Triglycerides are made of glycerol and three fatty acids. Animals can make most of the fatty acids they need. Triglycerides can be both made and broken down through parts of the glucose catabolism pathways. Glycerol can be phosphorylated and proceeds through glycolysis. Fatty acids are broken into two-carbon units that enter the citric acid cycle.

This illustration shows that glycogen, fats, and proteins can be catabolized via aerobic respiration. Glycogen is broken down into glucose, which feeds into glycolysis. Fats are broken down into glycerol, which is processed by glycolysis, and fatty acids, which are converted into acetyl CoA. Proteins are broken down into amino acids, which are processed at various stages of aerobic respiration, including glycolysis, acetyl CoA formation, and the citric acid cycle.

Figure 4.24 Glycogen from the liver and muscles, together with fats, can feed into the catabolic pathways for carbohydrates.

Evolution in Action

Pathways of Photosynthesis and Cellular Metabolism Photosynthesis and cellular metabolism consist of several very complex pathways. It is generally thought that the first cells arose in an aqueous environment—a “soup” of nutrients. If these cells reproduced successfully and their numbers climbed steadily, it follows that the cells would begin to deplete the nutrients from the medium in which they lived, as they shifted the nutrients into their own cells. This hypothetical situation would have resulted in natural selection favoring those organisms that could exist by using the nutrients that remained in their environment and by manipulating these nutrients into materials that they could use to survive. Additionally, selection would favor those organisms that could extract maximal value from the available nutrients.

An early form of photosynthesis developed that harnessed the sun’s energy using compounds other than water as a source of hydrogen atoms, but this pathway did not produce free oxygen. It is thought that glycolysis developed prior to this time and could take advantage of simple sugars being produced, but these reactions were not able to fully extract the energy stored in the carbohydrates. A later form of photosynthesis used water as a source of hydrogen ions and generated free oxygen. Over time, the atmosphere became oxygenated. Living things adapted to exploit this new atmosphere and allowed respiration as we know it to evolve. When the full process of photosynthesis as we know it developed and the atmosphere became oxygenated, cells were finally able to use the oxygen expelled by photosynthesis to extract more energy from the sugar molecules using the citric acid cycle.

Section Summary

The breakdown and synthesis of carbohydrates, proteins, and lipids connect with the pathways of glucose catabolism. The carbohydrates that can also feed into glucose catabolism include galactose, fructose, and glycogen. These connect with glycolysis. The amino acids from proteins connect with glucose catabolism through pyruvate, acetyl CoA, and components of the citric acid cycle. Cholesterol synthesis starts with acetyl CoA, and the components of triglycerides are picked up by acetyl CoA and enter the citric acid cycle.


Multiple Choice

The cholesterol synthesized by cells uses which component of the glycolytic pathway as a starting point?

A) glucose

B) acetyl CoA

C) pyruvate

D) carbon dioxide


Beta oxidation is ________.

A) the breakdown of sugars

B) the assembly of sugars

C) the breakdown of fatty acids

D) the removal of amino groups from amino acids


Free Response

Would you describe metabolic pathways as inherently wasteful or inherently economical, and why?

They are very economical. The substrates, intermediates, and products move between pathways and do so in response to finely tuned feedback inhibition loops that keep metabolism overall on an even keel. Intermediates in one pathway may occur in another, and they can move from one pathway to another fluidly in response to the needs of the cell.




Chapter 4 PowerPoint

Chapter 4 PowerPoint


Chapter 5: Introduction to Photosynthesis

This photo shows a sage thrasher eating a berry.

Figure 5.1 This sage thrasher’s diet, like that of almost all organisms, depends on photosynthesis. (credit: modification of work by Dave Menke, U.S. Fish and Wildlife Service)

No matter how complex or advanced a machine, such as the latest cellular phone, the device cannot function without energy. Living things, similar to machines, have many complex components; they too cannot do anything without energy, which is why humans and all other organisms must “eat” in some form or another. That may be common knowledge, but how many people realize that every bite of every meal ingested depends on the process of photosynthesis?


5.1: Overview of Photosynthesis

Learning Objectives

By the end of this section, you will be able to:

  • Summarize the process of photosynthesis
  • Explain the relevance of photosynthesis to other living things
  • Identify the reactants and products of photosynthesis
  • Describe the main structures involved in photosynthesis
All living organisms on earth consist of one or more cells. Each cell runs on the chemical energy found mainly in carbohydrate molecules (food), and the majority of these molecules are produced by one process: photosynthesis. Through photosynthesis, certain organisms convert solar energy (sunlight) into chemical energy, which is then used to build carbohydrate molecules. The energy used to hold these molecules together is released when an organism breaks down food. Cells then use this energy to perform work, such as cellular respiration.

The energy that is harnessed from photosynthesis enters the ecosystems of our planet continuously and is transferred from one organism to another. Therefore, directly or indirectly, the process of photosynthesis provides most of the energy required by living things on earth.

Photosynthesis also results in the release of oxygen into the atmosphere. In short, to eat and breathe, humans depend almost entirely on the organisms that carry out photosynthesis.

Concept in Action

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Click the following link to learn more about photosynthesis.

Solar Dependence and Food Production

Some organisms can carry out photosynthesis, whereas others cannot. An autotroph is an organism that can produce its own food. The Greek roots of the word autotroph mean “self” (auto) “feeder” (troph). Plants are the best-known autotrophs, but others exist, including certain types of bacteria and algae (Figure 5.2). Oceanic algae contribute enormous quantities of food and oxygen to global food chains. Plants are also photoautotrophs, a type of autotroph that uses sunlight and carbon from carbon dioxide to synthesize chemical energy in the form of carbohydrates. All organisms carrying out photosynthesis require sunlight.

Photo a shows a green fern leaf. Photo b shows a pier protruding into a large body of still water; the water near the pier is colored green with visible algae. Photo c is a micrograph of cyanobacteria.

Figure 5.2 (a) Plants, (b) algae, and (c) certain bacteria, called cyanobacteria, are photoautotrophs that can carry out photosynthesis. Algae can grow over enormous areas in water, at times completely covering the surface. (credit a: Steve Hillebrand, U.S. Fish and Wildlife Service; credit b: “eutrophication&hypoxia”/Flickr; credit c: NASA; scale-bar data from Matt Russell)

Heterotrophs are organisms incapable of photosynthesis that must therefore obtain energy and carbon from food by consuming other organisms. The Greek roots of the word heterotroph mean “other” (hetero) “feeder” (troph), meaning that their food comes from other organisms. Even if the food organism is another animal, this food traces its origins back to autotrophs and the process of photosynthesis. Humans are heterotrophs, as are all animals. Heterotrophs depend on autotrophs, either directly or indirectly. Deer and wolves are heterotrophs. A deer obtains energy by eating plants. A wolf eating a deer obtains energy that originally came from the plants eaten by that deer. The energy in the plant came from photosynthesis, and therefore it is the only autotroph in this example (Figure 5.3). Using this reasoning, all food eaten by humans also links back to autotrophs that carry out photosynthesis.

This photo shows deer running through tall grass at the edge of a forest.

Figure 5.3 The energy stored in carbohydrate molecules from photosynthesis passes through the food chain. The predator that eats these deer is getting energy that originated in the photosynthetic vegetation that the deer consumed. (credit: Steve VanRiper, U.S. Fish and Wildlife Service)

Biology in Action

Photosynthesis at the Grocery Store

This photo shows people shopping in a grocery store

Figure 5.4 Photosynthesis is the origin of the products that comprise the main elements of the human diet. (credit: Associação Brasileira de Supermercados)

Major grocery stores in the United States are organized into departments, such as dairy, meats, produce, bread, cereals, and so forth. Each aisle contains hundreds, if not thousands, of different products for customers to buy and consume (Figure 5.4).

Although there is a large variety, each item links back to photosynthesis. Meats and dairy products link to photosynthesis because the animals were fed plant-based foods. The breads, cereals, and pastas come largely from grains, which are the seeds of photosynthetic plants. What about desserts and drinks? All of these products contain sugar—the basic carbohydrate molecule produced directly from photosynthesis. The photosynthesis connection applies to every meal and every food a person consumes.

Main Structures and Summary of Photosynthesis

Photosynthesis requires sunlight, carbon dioxide, and water as starting reactants (Figure 5.5). After the process is complete, photosynthesis releases oxygen and produces carbohydrate molecules, most commonly glucose. These sugar molecules contain the energy that living things need to survive.

Photosynthesis is the origin of the products that comprise the main elements of the human diet. (credit: Associação Brasileira de Supermercados)

Figure 5.5 Photosynthesis uses solar energy, carbon dioxide, and water to release oxygen to produce energy-storing sugar molecules. Photosynthesis is the origin of the products that comprise the main elements of the human diet. (credit: Associação Brasileira de Supermercados)

The complex reactions of photosynthesis can be summarized by the chemical equation shown in Figure 5.6.

The photosynthesis equation is shown. According to this equation, six carbon dioxide molecules and six water molecules produce one sugar molecule and one oxygen molecule. The sugar molecule is made of 6 carbons, 12 hydrogens, and 6 oxygens. Sunlight is used as an energy source.

Figure 5.6 The process of photosynthesis can be represented by an equation, wherein carbon dioxide and water produce sugar and oxygen using energy from sunlight.

Although the equation looks simple, the many steps that take place during photosynthesis are actually quite complex, as in the way that the reaction summarizing cellular respiration represented many individual reactions. Before learning the details of how photoautotrophs turn sunlight into food, it is important to become familiar with the physical structures involved.

In plants, photosynthesis takes place primarily in leaves, which consist of many layers of cells and have differentiated top and bottom sides. The process of photosynthesis occurs not on the surface layers of the leaf, but rather in a middle layer called the mesophyll (Figure 5.7). The gas exchange of carbon dioxide and oxygen occurs through small, regulated openings called stomata.

In all autotrophic eukaryotes, photosynthesis takes place inside an organelle called a chloroplast. In plants, chloroplast-containing cells exist in the mesophyll. Chloroplasts have a double (inner and outer) membrane. Within the chloroplast is a third membrane that forms stacked, disc-shaped structures called thylakoids. Embedded in the thylakoid membrane are molecules of chlorophyll, a pigment (a molecule that absorbs light) through which the entire process of photosynthesis begins. Chlorophyll is responsible for the green color of plants. The thylakoid membrane encloses an internal space called the thylakoid space. Other types of pigments are also involved in photosynthesis, but chlorophyll is by far the most important. As shown in Figure 5.7, a stack of thylakoids is called a granum, and the space surrounding the granum is called stroma (not to be confused with stomata, the openings on the leaves).

The upper part of this illustration shows a leaf cross-section. In the cross-section, the mesophyll is sandwiched between an upper epidermis and a lower epidermis. The mesophyll has an upper part with rectangular cells aligned in a row, and a lower part with oval-shaped cells. An opening called a stomata exists in the lower epidermis. The middle part of this illustration shows a plant cell with a prominent central vacuole, a nucleus, ribosomes, mitochondria, and chloroplasts. The lower part of this illustration shows the chloroplast, which has pancake-like stacks of membranes inside.

Figure 5.7 Not all cells of a leaf carry out photosynthesis. Cells within the middle layer of a leaf have chloroplasts, which contain the photosynthetic apparatus. (credit “leaf”: modification of work by Cory Zanker)

On a hot, dry day, plants close their stomata to conserve water. What impact will this have on photosynthesis?

The Two Parts of Photosynthesis

Photosynthesis takes place in two stages: the light-dependent reactions and the Calvin cycle. In the light-dependent reactions, which take place at the thylakoid membrane, chlorophyll absorbs energy from sunlight and then converts it into chemical energy with the use of water. The light-dependent reactions release oxygen from the hydrolysis of water as a byproduct. In the Calvin cycle, which takes place in the stroma, the chemical energy derived from the light-dependent reactions drives both the capture of carbon in carbon dioxide molecules and the subsequent assembly of sugar molecules. The two reactions use carrier molecules to transport the energy from one to the other. The carriers that move energy from the light-dependent reactions to the Calvin cycle reactions can be thought of as “full” because they bring energy. After the energy is released, the “empty” energy carriers return to the light-dependent reactions to obtain more energy.

Section Summary

The process of photosynthesis transformed life on earth. By harnessing energy from the sun, photosynthesis allowed living things to access enormous amounts of energy. Because of photosynthesis, living things gained access to sufficient energy, allowing them to evolve new structures and achieve the biodiversity that is evident today.

Only certain organisms, called autotrophs, can perform photosynthesis; they require the presence of chlorophyll, a specialized pigment that can absorb light and convert light energy into chemical energy. Photosynthesis uses carbon dioxide and water to assemble carbohydrate molecules (usually glucose) and releases oxygen into the air. Eukaryotic autotrophs, such as plants and algae, have organelles called chloroplasts in which photosynthesis takes place.


On a hot, dry day, plants close their stomata to conserve water. What impact will this have on photosynthesis?

Levels of carbon dioxide (a reactant) will fall, and levels of oxygen (a product) will rise. As a result, the rate of photosynthesis will slow down.

Multiple Choice

What two products result from photosynthesis?

A) water and carbon dioxide

B) water and oxygen

C) glucose and oxygen

D) glucose and carbon dioxide


Which statement about thylakoids in eukaryotes is not correct?

A) Thylakoids are assembled into stacks.

B) Thylakoids exist as a maze of folded membranes.

C) The space surrounding thylakoids is called stroma.

D) Thylakoids contain chlorophyll.


From where does a heterotroph directly obtain its energy?

A) the sun

B) the sun and eating other organisms

C) eating other organisms

D) simple chemicals in the environment


Free Response

What is the overall purpose of the light reactions in photosynthesis?

To convert solar energy into chemical energy that cells can use to do work.

Why are carnivores, such as lions, dependent on photosynthesis to survive?

Because lions eat animals that eat plants.



autotroph: an organism capable of producing its own food

chlorophyll: the green pigment that captures the light energy that drives the reactions of photosynthesis

chloroplast: the organelle where photosynthesis takes place

granum: a stack of thylakoids located inside a chloroplast

heterotroph: an organism that consumes other organisms for food

light-dependent reaction:the first stage of photosynthesis where visible light is absorbed to form two energy-carrying molecules (ATP and NADPH)

mesophyll: the middle layer of cells in a leaf

photoautotroph: an organism capable of synthesizing its own food molecules (storing energy), using the energy of light

pigment: a molecule that is capable of absorbing light energy

stoma: the opening that regulates gas exchange and water regulation between leaves and the environment; plural: stomata

stroma: the fluid-filled space surrounding the grana inside a chloroplast where the Calvin cycle reactions of photosynthesis take place

thylakoid: a disc-shaped membranous structure inside a chloroplast where the light-dependent reactions of photosynthesis take place using chlorophyll embedded in the membranes


5.2: The Light-Dependent Reactions of Photosynthesis

Learning Objectives

By the end of this section, you will be able to:

  • Explain how plants absorb energy from sunlight
  • Describe how the wavelength of light affects its energy and color
  • Describe how and where photosynthesis takes place within a plant

How can light be used to make food? It is easy to think of light as something that exists and allows living organisms, such as humans, to see, but light is a form of energy. Like all energy, light can travel, change form, and be harnessed to do work. In the case of photosynthesis, light energy is transformed into chemical energy, which autotrophs use to build carbohydrate molecules. However, autotrophs only use a specific component of sunlight (Figure 5.8).

A photo shows the silhouette of a grassy plant against the sun at sunset.

Figure 5.8 Autotrophs can capture light energy from the sun, converting it into chemical energy used to build food molecules. (credit: modification of work by Gerry Atwell, U.S. Fish and Wildlife Service)

Concept in Action

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Visit this site and click through the animation to view the process of photosynthesis within a leaf.

What Is Light Energy?

The sun emits an enormous amount of electromagnetic radiation (solar energy). Humans can see only a fraction of this energy, which is referred to as “visible light.” The manner in which solar energy travels can be described and measured as waves. Scientists can determine the amount of energy of a wave by measuring its wavelength, the distance between two consecutive, similar points in a series of waves, such as from crest to crest or trough to trough (Figure 5.9).

This illustration shows two waves. The distance between the crests (shown as the uppermost part, in contrast to the trough at the bottom) is the wavelength.

Figure 5.9 The wavelength of a single wave is the distance between two consecutive points along the wave.

Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun. The electromagnetic spectrum is the range of all possible wavelengths of radiation (Figure 5.10). Each wavelength corresponds to a different amount of energy carried.

This illustration lists the types of electromagnetic radiation in order of decreasing wavelength. These are gamma rays, X-rays, ultraviolet, visible, infrared, and radio

Figure 5.10 The sun emits energy in the form of electromagnetic radiation. This radiation exists in different wavelengths, each of which has its own characteristic energy. Visible light is one type of energy emitted from the sun.

Each type of electromagnetic radiation has a characteristic range of wavelengths. The longer the wavelength (or the more stretched out it appears), the less energy is carried. Short, tight waves carry the most energy. This may seem illogical, but think of it in terms of a piece of moving rope. It takes little effort by a person to move a rope in long, wide waves. To make a rope move in short, tight waves, a person would need to apply significantly more energy.

The sun emits (Figure 5.10) a broad range of electromagnetic radiation, including X-rays and ultraviolet (UV) rays. The higher-energy waves are dangerous to living things; for example, X-rays and UV rays can be harmful to humans.

Absorption of Light

Light energy enters the process of photosynthesis when pigments absorb the light. In plants, pigment molecules absorb only visible light for photosynthesis. The visible light seen by humans as white light actually exists in a rainbow of colors. Certain objects, such as a prism or a drop of water, disperse white light to reveal these colors to the human eye. The visible light portion of the electromagnetic spectrum is perceived by the human eye as a rainbow of colors, with violet and blue having shorter wavelengths and, therefore, higher energy. At the other end of the spectrum toward red, the wavelengths are longer and have lower energy.

Understanding Pigments

Different kinds of pigments exist, and each absorbs only certain wavelengths (colors) of visible light. Pigments reflect the color of the wavelengths that they cannot absorb.

All photosynthetic organisms contain a pigment called chlorophyll a, which humans see as the common green color associated with plants. Chlorophyll a absorbs wavelengths from either end of the visible spectrum (blue and red), but not from green. Because green is reflected, chlorophyll appears green.

Other pigment types include chlorophyll b (which absorbs blue and red-orange light) and the carotenoids. Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light, which is its absorption spectrum.

Many photosynthetic organisms have a mixture of pigments; between them, the organism can absorb energy from a wider range of visible-light wavelengths. Not all photosynthetic organisms have full access to sunlight. Some organisms grow underwater where light intensity decreases with depth, and certain wavelengths are absorbed by the water. Other organisms grow in competition for light. Plants on the rainforest floor must be able to absorb any bit of light that comes through, because the taller trees block most of the sunlight (Figure 5.11).

This photo shows undergrowth in a forest.

Figure 5.11 Plants that commonly grow in the shade benefit from having a variety of light-absorbing pigments. Each pigment can absorb different wavelengths of light, which allows the plant to absorb any light that passes through the taller trees. (credit: Jason Hollinger)

How Light-Dependent Reactions Work

The overall purpose of the light-dependent reactions is to convert light energy into chemical energy. This chemical energy will be used by the Calvin cycle to fuel the assembly of sugar molecules.

The light-dependent reactions begin in a grouping of pigment molecules and proteins called a photosystem. Photosystems exist in the membranes of thylakoids. A pigment molecule in the photosystem absorbs one photon, a quantity or “packet” of light energy, at a time.

A photon of light energy travels until it reaches a molecule of chlorophyll. The photon causes an electron in the chlorophyll to become “excited.” The energy given to the electron allows it to break free from an atom of the chlorophyll molecule. Chlorophyll is therefore said to “donate” an electron (Figure 5.12).

To replace the electron in the chlorophyll, a molecule of water is split. This splitting releases an electron and results in the formation of oxygen (O2) and hydrogen ions (H+) in the thylakoid space. Technically, each breaking of a water molecule releases a pair of electrons, and therefore can replace two donated electrons.

This illustration shows photosystem II, which has a light-harvesting complex surrounding the reaction center. Chlorophyll molecules are found in the light-harvesting complex. In the reaction center, an excited electron is passed to the primary electron acceptor. A molecule of water is split, releasing one oxygen, two protons, and an electron. The electron replaces the one donated to the primary electron acceptor.

Figure 5.12 Light energy is absorbed by a chlorophyll molecule and is passed along a pathway to other chlorophyll molecules. The energy culminates in a molecule of chlorophyll found in the reaction center. The energy “excites” one of its electrons enough to leave the molecule and be transferred to a nearby primary electron acceptor. A molecule of water splits to release an electron, which is needed to replace the one donated. Oxygen and hydrogen ions are also formed from the splitting of water.

The replacing of the electron enables chlorophyll to respond to another photon. The oxygen molecules produced as byproducts find their way to the surrounding environment. The hydrogen ions play critical roles in the remainder of the light-dependent reactions.

Keep in mind that the purpose of the light-dependent reactions is to convert solar energy into chemical carriers that will be used in the Calvin cycle. In eukaryotes and some prokaryotes, two photosystems exist. The first is called photosystem II, which was named for the order of its discovery rather than for the order of the function.

After the photon hits, photosystem II transfers the free electron to the first in a series of proteins inside the thylakoid membrane called the electron transport chain. As the electron passes along these proteins, energy from the electron fuels membrane pumps that actively move hydrogen ions against their concentration gradient from the stroma into the thylakoid space. This is quite analogous to the process that occurs in the mitochondrion in which an electron transport chain pumps hydrogen ions from the mitochondrial stroma across the inner membrane and into the intermembrane space, creating an electrochemical gradient. After the energy is used, the electron is accepted by a pigment molecule in the next photosystem, which is called photosystem I (Figure 5.13).

This illustration shows the components involved in the light reactions. Photosystem II uses light to excite an electron, which is passed on to the chloroplast electron transport chain. The electron is then passed on to photosystem I and to NADP+ reductase, which makes NADPH. This process forms an electrochemical gradient that is used by ATP synthase enzyme to make ATP.

Figure 5.13 From photosystem II, the electron travels along a series of proteins. This electron transport system uses the energy from the electron to pump hydrogen ions into the interior of the thylakoid. A pigment molecule in photosystem I accepts the electron.

Generating an Energy Carrier: ATP

In the light-dependent reactions, energy absorbed by sunlight is stored by two types of energy-carrier molecules: ATP and NADPH. The energy that these molecules carry is stored in a bond that holds a single atom to the molecule. For ATP, it is a phosphate atom, and for NADPH, it is a hydrogen atom. Recall that NADH was a similar molecule that carried energy in the mitochondrion from the citric acid cycle to the electron transport chain. When these molecules release energy into the Calvin cycle, they each lose atoms to become the lower-energy molecules ADP and NADP+.

The buildup of hydrogen ions in the thylakoid space forms an electrochemical gradient because of the difference in the concentration of protons (H+) and the difference in the charge across the membrane that they create. This potential energy is harvested and stored as chemical energy in ATP through chemiosmosis, the movement of hydrogen ions down their electrochemical gradient through the transmembrane enzyme ATP synthase, just as in the mitochondrion.

The hydrogen ions are allowed to pass through the thylakoid membrane through an embedded protein complex called ATP synthase. This same protein generated ATP from ADP in the mitochondrion. The energy generated by the hydrogen ion stream allows ATP synthase to attach a third phosphate to ADP, which forms a molecule of ATP in a process called photophosphorylation. The flow of hydrogen ions through ATP synthase is called chemiosmosis, because the ions move from an area of high to low concentration through a semi-permeable structure.

Generating Another Energy Carrier: NADPH

The remaining function of the light-dependent reaction is to generate the other energy-carrier molecule, NADPH. As the electron from the electron transport chain arrives at photosystem I, it is re-energized with another photon captured by chlorophyll. The energy from this electron drives the formation of NADPH from NADP+ and a hydrogen ion (H+). Now that the solar energy is stored in energy carriers, it can be used to make a sugar molecule.

Section Summary

In the first part of photosynthesis, the light-dependent reaction, pigment molecules absorb energy from sunlight. The most common and abundant pigment is chlorophyll a. A photon strikes photosystem II to initiate photosynthesis. Energy travels through the electron transport chain, which pumps hydrogen ions into the thylakoid space. This forms an electrochemical gradient. The ions flow through ATP synthase from the thylakoid space into the stroma in a process called chemiosmosis to form molecules of ATP, which are used for the formation of sugar molecules in the second stage of photosynthesis. Photosystem I absorbs a second photon, which results in the formation of an NADPH molecule, another energy carrier for the Calvin cycle reactions.


Multiple Choice

What is the energy of a photon first used to do in photosynthesis?

A) split a water molecule

B) energize an electron

C) produce ATP

D) synthesize glucose


Which molecule absorbs the energy of a photon in photosynthesis?


B) glucose

C) chlorophyll

D) water


Plants produce oxygen when they photosynthesize. Where does the oxygen come from?

A) splitting water molecules

B) ATP synthesis

C) the electron transport chain

D) chlorophyll


Which color(s) of light does chlorophyll a reflect?

A) red and blue

B) green

C) red

D) blue


Free Response

Describe the pathway of energy in light-dependent reactions.

The energy is present initially as light. A photon of light hits chlorophyll, causing an electron to be energized. The free electron travels through the electron transport chain, and the energy of the electron is used to pump hydrogen ions into the thylakoid space, transferring the energy into the electrochemical gradient. The energy of the electrochemical gradient is used to power ATP synthase, and the energy is transferred into a bond in the ATP molecule. In addition, energy from another photon can be used to create a high-energy bond in the molecule NADPH.



absorption spectrum: the specific pattern of absorption for a substance that absorbs electromagnetic radiation

chlorophyll a: the form of chlorophyll that absorbs violet-blue and red light

chlorophyll b: the form of chlorophyll that absorbs blue and red-orange light

electromagnetic spectrum: the range of all possible frequencies of radiation

photon: a distinct quantity or “packet” of light energy

photosystem: a group of proteins, chlorophyll, and other pigments that are used in the light-dependent reactions of photosynthesis to absorb light energy and convert it into chemical energy

wavelength: the distance between consecutive points of a wave


5.3: The Calvin Cycle

Learning Objectives

By the end of this section, you will be able to:

  • Describe the Calvin cycle
  • Define carbon fixation
  • Explain how photosynthesis works in the energy cycle of all living organisms

After the energy from the sun is converted and packaged into ATP and NADPH, the cell has the fuel needed to build food in the form of carbohydrate molecules. The carbohydrate molecules made will have a backbone of carbon atoms. Where does the carbon come from? The carbon atoms used to build carbohydrate molecules comes from carbon dioxide, the gas that animals exhale with each breath. The Calvin cycle is the term used for the reactions of photosynthesis that use the energy stored by the light-dependent reactions to form glucose and other carbohydrate molecules.

The Interworkings of the Calvin Cycle

In plants, carbon dioxide (CO2) enters the chloroplast through the stomata and diffuses into the stroma of the chloroplast—the site of the Calvin cycle reactions where sugar is synthesized. The reactions are named after the scientist who discovered them, and reference the fact that the reactions function as a cycle. Others call it the Calvin-Benson cycle to include the name of another scientist involved in its discovery (Figure 5.14).

This illustration shows that ATP and NADPH produced in the light reactions are used in the Calvin cycle to make sugar.

Figure 5.14 Light-dependent reactions harness energy from the sun to produce ATP and NADPH. These energy-carrying molecules travel into the stroma where the Calvin cycle reactions take place.

The Calvin cycle reactions (Figure 5.15) can be organized into three basic stages: fixation, reduction, and regeneration. In the stroma, in addition to CO2, two other chemicals are present to initiate the Calvin cycle: an enzyme abbreviated RuBisCO, and the molecule ribulose bisphosphate (RuBP). RuBP has five atoms of carbon and a phosphate group on each end.

RuBisCO catalyzes a reaction between CO2 and RuBP, which forms a six-carbon compound that is immediately converted into two three-carbon compounds. This process is called carbon fixation, because CO2 is “fixed” from its inorganic form into organic molecules.

ATP and NADPH use their stored energy to convert the three-carbon compound, 3-PGA, into another three-carbon compound called G3P. This type of reaction is called a reduction reaction, because it involves the gain of electrons. A reduction is the gain of an electron by an atom or molecule. The molecules of ADP and NAD+, resulting from the reduction reaction, return to the light-dependent reactions to be re-energized.

One of the G3P molecules leaves the Calvin cycle to contribute to the formation of the carbohydrate molecule, which is commonly glucose (C6H12O6). Because the carbohydrate molecule has six carbon atoms, it takes six turns of the Calvin cycle to make one carbohydrate molecule (one for each carbon dioxide molecule fixed). The remaining G3P molecules regenerate RuBP, which enables the system to prepare for the carbon-fixation step. ATP is also used in the regeneration of RuBP.

This illustration shows a circular cycle with three stages. Three molecules of carbon dioxide enter the cycle. In the first stage, the enzyme RuBisCO incorporates the carbon dioxide into an organic molecule. Six ATP molecules are converted into six ADP molecules. In the second stage, the organic molecule is reduced. Six NADPH molecules are converted into six NADP+ ions and one hydrogen ion. Sugar is produced. In stage three, RuBP is regenerated, and three ATP molecules are converted into three ADP molecules. RuBP then starts the cycle again.

Figure 5.15 The Calvin cycle has three stages. In stage 1, the enzyme RuBisCO incorporates carbon dioxide into an organic molecule. In stage 2, the organic molecule is reduced. In stage 3, RuBP, the molecule that starts the cycle, is regenerated so that the cycle can continue.

In summary, it takes six turns of the Calvin cycle to fix six carbon atoms from CO2. These six turns require energy input from 12 ATP molecules and 12 NADPH molecules in the reduction step and 6 ATP molecules in the regeneration step.

Concept in Action

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The following is a link to an animation of the Calvin cycle. Click Stage 1, Stage 2, and then Stage 3 to see G3P and ATP regenerate to form RuBP.


The shared evolutionary history of all photosynthetic organisms is conspicuous, as the basic process has changed little over eras of time. Even between the giant tropical leaves in the rainforest and tiny cyanobacteria, the process and components of photosynthesis that use water as an electron donor remain largely the same. Photosystems function to absorb light and use electron transport chains to convert energy. The Calvin cycle reactions assemble carbohydrate molecules with this energy.

However, as with all biochemical pathways, a variety of conditions leads to varied adaptations that affect the basic pattern. Photosynthesis in dry-climate plants (Figure 5.16) has evolved with adaptations that conserve water. In the harsh dry heat, every drop of water and precious energy must be used to survive. Two adaptations have evolved in such plants. In one form, a more efficient use of CO2 allows plants to photosynthesize even when CO2 is in short supply, as when the stomata are closed on hot days. The other adaptation performs preliminary reactions of the Calvin cycle at night, because opening the stomata at this time conserves water due to cooler temperatures. In addition, this adaptation has allowed plants to carry out low levels of photosynthesis without opening stomata at all, an extreme mechanism to face extremely dry periods.

This photo shows a cactus.

Figure 5.16 Living in the harsh conditions of the desert has led plants like this cactus to evolve variations in reactions outside the Calvin cycle. These variations increase efficiency and help conserve water and energy. (credit: Piotr Wojtkowski)

Photosynthesis in Prokaryotes

The two parts of photosynthesis—the light-dependent reactions and the Calvin cycle—have been described, as they take place in chloroplasts. However, prokaryotes, such as cyanobacteria, lack membrane-bound organelles. Prokaryotic photosynthetic autotrophic organisms have infoldings of the plasma membrane for chlorophyll attachment and photosynthesis (Figure 5.17). It is here that organisms like cyanobacteria can carry out photosynthesis.

This illustration shows a green ribbon, representing a folded membrane, with many folds stacked on top of another like a rope or hose. The photo shows an electron micrograph of a cleaved thylakoid membrane with similar folds from a unicellular organism

Figure 5.17 A photosynthetic prokaryote has infolded regions of the plasma membrane that function like thylakoids. Although these are not contained in an organelle, such as a chloroplast, all of the necessary components are present to carry out photosynthesis. (credit: scale-bar data from Matt Russell)

The Energy Cycle

Living things access energy by breaking down carbohydrate molecules. However, if plants make carbohydrate molecules, why would they need to break them down? Carbohydrates are storage molecules for energy in all living things. Although energy can be stored in molecules like ATP, carbohydrates are much more stable and efficient reservoirs for chemical energy. Photosynthetic organisms also carry out the reactions of respiration to harvest the energy that they have stored in carbohydrates, for example, plants have mitochondria in addition to chloroplasts.

You may have noticed that the overall reaction for photosynthesis:


is the reverse of the overall reaction for cellular respiration:


Photosynthesis produces oxygen as a byproduct, and respiration produces carbon dioxide as a byproduct.

In nature, there is no such thing as waste. Every single atom of matter is conserved, recycling indefinitely. Substances change form or move from one type of molecule to another, but never disappear (Figure 5.18).

CO2 is no more a form of waste produced by respiration than oxygen is a waste product of photosynthesis. Both are byproducts of reactions that move on to other reactions. Photosynthesis absorbs energy to build carbohydrates in chloroplasts, and aerobic cellular respiration releases energy by using oxygen to break down carbohydrates. Both organelles use electron transport chains to generate the energy necessary to drive other reactions. Photosynthesis and cellular respiration function in a biological cycle, allowing organisms to access life-sustaining energy that originates millions of miles away in a star.

This photograph shows a giraffe eating leaves from a tree. Labels indicate that the giraffe consumes oxygen and releases carbon dioxide, whereas the tree consumes carbon dioxide and releases oxygen.

Figure 5.18 In the carbon cycle, the reactions of photosynthesis and cellular respiration share reciprocal reactants and products. (credit: modification of work by Stuart Bassil)

Section Summary

Using the energy carriers formed in the first stage of photosynthesis, the Calvin cycle reactions fix CO2 from the environment to build carbohydrate molecules. An enzyme, RuBisCO, catalyzes the fixation reaction, by combining CO2 with RuBP. The resulting six-carbon compound is broken down into two three-carbon compounds, and the energy in ATP and NADPH is used to convert these molecules into G3P. One of the three-carbon molecules of G3P leaves the cycle to become a part of a carbohydrate molecule. The remaining G3P molecules stay in the cycle to be formed back into RuBP, which is ready to react with more CO2. Photosynthesis forms a balanced energy cycle with the process of cellular respiration. Plants are capable of both photosynthesis and cellular respiration, since they contain both chloroplasts and mitochondria.


Multiple Choice

Where in plant cells does the Calvin cycle take place?

A) thylakoid membrane

B) thylakoid space

C) stroma

D) granum


Which statement correctly describes carbon fixation?

A) the conversion of CO2 to an organic compound

B) the use of RUBISCO to form 3-PGA

C) the production of carbohydrate molecules from G3P

D) the formation of RuBP from G3P molecules

E) the use of ATP and NADPH to reduce CO2


What is the molecule that leaves the Calvin cycle to be converted into glucose?


B) G3P


D) 3-PGA


Free Response

Which part of the Calvin cycle would be affected if a cell could not produce the enzyme RuBisCO?

None of the cycle could take place, because RuBisCO is essential in fixing carbon dioxide. Specifically, RuBisCO catalyzes the reaction between carbon dioxide and RuBP at the start of the cycle.

Explain the reciprocal nature of the net chemical reactions for photosynthesis and respiration.

Photosynthesis takes the energy of sunlight and combines water and carbon dioxide to produce sugar and oxygen as a waste product. The reactions of respiration take sugar and consume oxygen to break it down into carbon dioxide and water, releasing energy. Thus, the reactants of photosynthesis are the products of respiration, and vice versa.


Calvin cycle: the reactions of photosynthesis that use the energy stored by the light-dependent reactions to form glucose and other carbohydrate molecules

carbon fixation: the process of converting inorganic CO2 gas into organic compounds


Chapter 5 PowerPoint

Chapter 5 PowerPoint


Unit 2: Cell Division and Genetics


Chapter 6: Introduction to Reproduction at the Cellular Level

Image A shows two conjoined cells forming a dumbbell shape; the fertilization envelope has been removed so that the mesh-like outer layer can be seen. Image B shows the sea urchin embryo when it has divided into 16 conjoined cells; the overall shape is rounder than in image A. Image C shows a “water melon” sea urchin which appears as a peach-colored ball covered in white protruding spines.

Figure 6.1 A sea urchin begins life as a single cell that (a) divides to form two cells, visible by scanning electron microscopy. After four rounds of cell division, (b) there are 16 cells, as seen in this SEM image. After many rounds of cell division, the individual develops into a complex, multicellular organism, as seen in this (c) mature sea urchin. (credit a: modification of work by Evelyn Spiegel, Louisa Howard; credit b: modification of work by Evelyn Spiegel, Louisa Howard; credit c: modification of work by Marco Busdraghi; scale-bar data from Matt Russell)

The individual sexually reproducing organism—including humans—begins life as a fertilized egg, or zygote. Trillions of cell divisions subsequently occur in a controlled manner to produce a complex, multicellular human. In other words, that original single cell was the ancestor of every other cell in the body. Once a human individual is fully grown, cell reproduction is still necessary to repair or regenerate tissues. For example, new blood and skin cells are constantly being produced. All multicellular organisms use cell division for growth, and in most cases, the maintenance and repair of cells and tissues. Single-celled organisms use cell division as their method of reproduction.


6.1 The Genome

Learning Objectives

By the end of this section, you will be able to:

  • Describe the prokaryotic and eukaryotic genome
  • Distinguish between chromosomes, genes, and traits

The continuity of life from one cell to another has its foundation in the reproduction of cells by way of the cell cycle. The cell cycle is an orderly sequence of events in the life of a cell from the division of a single parent cell to produce two new daughter cells, to the subsequent division of those daughter cells. The mechanisms involved in the cell cycle are highly conserved across eukaryotes. Organisms as diverse as protists, plants, and animals employ similar steps.

Genomic DNA

Before discussing the steps a cell undertakes to replicate, a deeper understanding of the structure and function of a cell’s genetic information is necessary. A cell’s complete complement of DNA is called its genome. In prokaryotes, the genome is composed of a single, double-stranded DNA molecule in the form of a loop or circle. The region in the cell containing this genetic material is called a nucleoid. Some prokaryotes also have smaller loops of DNA called plasmids that are not essential for normal growth.

In eukaryotes, the genome comprises several double-stranded, linear DNA molecules (Figure 6.2) bound with proteins to form complexes called chromosomes. Each species of eukaryote has a characteristic number of chromosomes in the nuclei of its cells. Human body cells (somatic cells) have 46 chromosomes. A somatic cell contains two matched sets of chromosomes, a configuration known as diploid. The letter n is used to represent a single set of chromosomes; therefore a diploid organism is designated 2n. Human cells that contain one set of 23 chromosomes are called gametes, or sex cells; these eggs and sperm are designated n, or haploid.

Chromosomes from a human female are shown in a nucleus, scattered outside the nucleus, and arranged in numerical order, from 1–22 followed by X. Each chromosome is stained a different color.

Figure 6.2 There are 23 pairs of homologous chromosomes in a female human somatic cell. These chromosomes are viewed within the nucleus (top), removed from a cell in mitosis (right), and arranged according to length (left) in an arrangement called a karyotype. In this image, the chromosomes were exposed to fluorescent stains to distinguish them. (credit: “718 Bot”/Wikimedia Commons, National Human Genome Research)

The matched pairs of chromosomes in a diploid organism are called homologous chromosomes. Homologous chromosomes are the same length and have specific nucleotide segments called genes in exactly the same location, or locus. Genes, the functional units of chromosomes, determine specific characteristics by coding for specific proteins. Traits are the different forms of a characteristic. For example, the shape of earlobes is a characteristic with traits of free or attached.

Each copy of the homologous pair of chromosomes originates from a different parent; therefore, the copies of each of the genes themselves may not be identical. The variation of individuals within a species is caused by the specific combination of the genes inherited from both parents. For example, there are three possible gene sequences on the human chromosome that codes for blood type: sequence A, sequence B, and sequence O. Because all diploid human cells have two copies of the chromosome that determines blood type, the blood type (the trait) is determined by which two versions of the marker gene are inherited. It is possible to have two copies of the same gene sequence, one on each homologous chromosome (for example, AA, BB, or OO), or two different sequences, such as AB.

Minor variations in traits such as those for blood type, eye color, and height contribute to the natural variation found within a species. The sex chromosomes, X and Y, are the single exception to the rule of homologous chromosomes; other than a small amount of homology that is necessary to reliably produce gametes, the genes found on the X and Y chromosomes are not the same.

Section Summary

Prokaryotes have a single loop chromosome, whereas eukaryotes have multiple, linear chromosomes surrounded by a nuclear membrane. Human somatic cells have 46 chromosomes consisting of two sets of 22 homologous chromosomes and a pair of nonhomologous sex chromosomes. This is the 2n, or diploid, state. Human gametes have 23 chromosomes or one complete set of chromosomes. This is the n, or haploid, state. Genes are segments of DNA that code for a specific protein or RNA molecule. An organism’s traits are determined in large part by the genes inherited from each parent, but also by the environment that they experience. Genes are expressed as characteristics of the organism and each characteristic may have different variants called traits that are caused by differences in the DNA sequence for a gene.


Multiple Choice

A diploid cell has ________ the number of chromosomes as a haploid cell.

A) one-fourth

B) one-half

C) twice

D) four times


An organism’s traits are determined by the specific combination of inherited ________.

A) cells

B) genes

C) proteins

D) chromatids


Free Response

Compare and contrast a human somatic cell to a human gamete.

Human somatic cells have 46 chromosomes, including 22 homologous pairs and one pair of nonhomologous sex chromosomes. This is the 2n, or diploid, condition. Human gametes have 23 chromosomes, one each of 23 unique chromosomes. This is the n, or haploid, condition.


diploid: describes a cell, nucleus, or organism containing two sets of chromosomes (2n)

gamete: a haploid reproductive cell or sex cell (sperm or egg)

gene: the physical and functional unit of heredity; a sequence of DNA that codes for a specific peptide or RNA molecule

genome: the entire genetic complement (DNA) of an organism

haploid: describes a cell, nucleus, or organism containing one set of chromosomes (n)

homologous chromosomes: chromosomes of the same length with genes in the same location; diploid organisms have pairs of homologous chromosomes, and the members of each pair come from different parents

locus: the position of a gene on a chromosome



6.2 The Cell Cycle

Learning Objectives

By the end of this section, you will be able to:

  • Describe the three stages of interphase
  • Discuss the behavior of chromosomes during mitosis and how the cytoplasmic content divides during cytokinesis
  • Define the quiescent G0 phase
  • Explain how the three internal control checkpoints occur at the end of G1, at the G2–M transition, and during metaphase

The cell cycle is an ordered series of events involving cell growth and cell division that produces two new daughter cells. Cells on the path to cell division proceed through a series of precisely timed and carefully regulated stages of growth, DNA replication, and division that produce two genetically identical cells. The cell cycle has two major phases: interphase and the mitotic phase (Figure 6.3). During interphase, the cell grows and DNA is replicated. During the mitotic phase, the replicated DNA and cytoplasmic contents are separated and the cell divides.

Watch this video about the cell cycle:

This illustration shows the cell cycle, which consists of interphase and the mitotic phase. Interphase is subdivided into G1, S, and G2 phases. Cell growth occurs during G1 and G2, and DNA synthesis occurs during S. The mitotic phase consists of mitosis, in which the nuclear chromatin is divided, and cytokinesis, in which the cytoplasm is divided resulting in two daughter cells.

Figure 6.3 A cell moves through a series of phases in an orderly manner. During interphase, G1 involves cell growth and protein synthesis, the S phase involves DNA replication and the replication of the centrosome, and G2 involves further growth and protein synthesis. The mitotic phase follows interphase. Mitosis is nuclear division during which duplicated chromosomes are segregated and distributed into daughter nuclei. Usually the cell will divide after mitosis in a process called cytokinesis in which the cytoplasm is divided and two daughter cells are formed.


During interphase, the cell undergoes normal processes while also preparing for cell division. For a cell to move from interphase to the mitotic phase, many internal and external conditions must be met. The three stages of interphase are called G1, S, and G2.

G1 Phase

The first stage of interphase is called the G1 phase, or first gap, because little change is visible. However, during the G1 stage, the cell is quite active at the biochemical level. The cell is accumulating the building blocks of chromosomal DNA and the associated proteins, as well as accumulating enough energy reserves to complete the task of replicating each chromosome in the nucleus.

S Phase

Throughout interphase, nuclear DNA remains in a semi-condensed chromatin configuration. In the S phase (synthesis phase), DNA replication results in the formation of two identical copies of each chromosome—sister chromatids—that are firmly attached at the centromere region. At this stage, each chromosome is made of two sister chromatids and is a duplicated chromosome. The centrosome is duplicated during the S phase. The two centrosomes will give rise to the mitotic spindle, the apparatus that orchestrates the movement of chromosomes during mitosis. The centrosome consists of a pair of rod-like centrioles at right angles to each other. Centrioles help organize cell division. Centrioles are not present in the centrosomes of many eukaryotic species, such as plants and most fungi.

G2 Phase

In the G2 phase, or second gap, the cell replenishes its energy stores and synthesizes the proteins necessary for chromosome manipulation. Some cell organelles are duplicated, and the cytoskeleton is dismantled to provide resources for the mitotic spindle. There may be additional cell growth during G2. The final preparations for the mitotic phase must be completed before the cell is able to enter the first stage of mitosis.

The Mitotic Phase

To make two daughter cells, the contents of the nucleus and the cytoplasm must be divided. The mitotic phase is a multistep process during which the duplicated chromosomes are aligned, separated, and moved to opposite poles of the cell, and then the cell is divided into two new identical daughter cells. The first portion of the mitotic phase, mitosis, is composed of five stages, which accomplish nuclear division. The second portion of the mitotic phase, called cytokinesis, is the physical separation of the cytoplasmic components into two daughter cells.


Mitosis is divided into a series of phases—prophase, prometaphase, metaphase, anaphase, and telophase—that result in the division of the cell nucleus (Figure 6.4).

This diagram shows the five phases of mitosis, and cytokinesis. During prophase, the chromosomes condense and become visible, spindle fibers emerge from the centrosomes, the centrosomes move toward opposite poles, and the nuclear envelope breaks down. During prometaphase, the chromosomes continue to condense and kinetochores appear at the centromeres. Mitotic spindle microtubules attach to the kinetochores. During metaphase, the centrosomes are at opposite poles of the cell. Chromosomes line up at the metaphase plate and each sister chromatid is attached to spindle fibers originating from the opposite poles. During anaphase, the centromeres split in two. The sister chromatids, which are now called chromosomes, move toward opposite poles of the cell. Certain spindle fibers lengthen, elongating the cell. During telophase, the chromosomes arrive at the opposite poles and begin to decondense. The nuclear envelope re-forms. During cytokinesis in animals, a cleavage furrow separates the two daughter cells. In plants, a cell plate—the precursor to a new cell wall—separates the two daughter cells.

Figure 6.4 Animal cell mitosis is divided into five stages—prophase, prometaphase, metaphase, anaphase, and telophase—visualized here by light microscopy with fluorescence. Mitosis is usually accompanied by cytokinesis, shown here by a transmission electron microscope. (credit “diagrams”: modification of work by Mariana Ruiz Villareal; credit “mitosis micrographs”: modification of work by Roy van Heesbeen; credit “cytokinesis micrograph”: modification of work by the Wadsworth Center, NY State Department of Health; donated to the Wikimedia foundation; scale-bar data from Matt Russell)


Which of the following is the correct order of events in mitosis?

  1. Sister chromatids line up at the metaphase plate. The kinetochore becomes attached to the mitotic spindle. The nucleus re-forms and the cell divides. The sister chromatids separate.
  2. The kinetochore becomes attached to the mitotic spindle. The sister chromatids separate. Sister chromatids line up at the metaphase plate. The nucleus re-forms and the cell divides.
  3. The kinetochore becomes attached to metaphase plate. Sister chromatids line up at the metaphase plate. The kinetochore breaks down and the sister chromatids separate. The nucleus re-forms and the cell divides.
  4. The kinetochore becomes attached to the mitotic spindle. Sister chromatids line up at the metaphase plate. The kinetochore breaks apart and the sister chromatids separate. The nucleus re-forms and the cell divides.

During prophase, the “first phase,” several events must occur to provide access to the chromosomes in the nucleus. The nuclear envelope starts to break into small vesicles, and the Golgi apparatus and endoplasmic reticulum fragment and disperse to the periphery of the cell. The nucleolus disappears. The centrosomes begin to move to opposite poles of the cell. The microtubules that form the basis of the mitotic spindle extend between the centrosomes, pushing them farther apart as the microtubule fibers lengthen. The sister chromatids begin to coil more tightly and become visible under a light microscope.

During prometaphase, many processes that were begun in prophase continue to advance and culminate in the formation of a connection between the chromosomes and cytoskeleton. The remnants of the nuclear envelope disappear. The mitotic spindle continues to develop as more microtubules assemble and stretch across the length of the former nuclear area. Chromosomes become more condensed and visually discrete. Each sister chromatid attaches to spindle microtubules at the centromere via a protein complex called the kinetochore.

During metaphase, all of the chromosomes are aligned in a plane called the metaphase plate, or the equatorial plane, midway between the two poles of the cell. The sister chromatids are still tightly attached to each other. At this time, the chromosomes are maximally condensed.

During anaphase, the sister chromatids at the equatorial plane are split apart at the centromere. Each chromatid, now called a chromosome, is pulled rapidly toward the centrosome to which its microtubule was attached. The cell becomes visibly elongated as the non-kinetochore microtubules slide against each other at the metaphase plate where they overlap.

During telophase, all of the events that set up the duplicated chromosomes for mitosis during the first three phases are reversed. The chromosomes reach the opposite poles and begin to decondense (unravel). The mitotic spindles are broken down into monomers that will be used to assemble cytoskeleton components for each daughter cell. Nuclear envelopes form around chromosomes.

Concept in Action

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This page of movies illustrates different aspects of mitosis. Watch the movie entitled “DIC microscopy of cell division in a newt lung cell” and identify the phases of mitosis.


Cytokinesis is the second part of the mitotic phase during which cell division is completed by the physical separation of the cytoplasmic components into two daughter cells. Although the stages of mitosis are similar for most eukaryotes, the process of cytokinesis is quite different for eukaryotes that have cell walls, such as plant cells.

In cells such as animal cells that lack cell walls, cytokinesis begins following the onset of anaphase. A contractile ring composed of actin filaments forms just inside the plasma membrane at the former metaphase plate. The actin filaments pull the equator of the cell inward, forming a fissure. This fissure, or “crack,” is called the cleavage furrow. The furrow deepens as the actin ring contracts, and eventually the membrane and cell are cleaved in two (Figure 6.5).

In plant cells, a cleavage furrow is not possible because of the rigid cell walls surrounding the plasma membrane. A new cell wall must form between the daughter cells. During interphase, the Golgi apparatus accumulates enzymes, structural proteins, and glucose molecules prior to breaking up into vesicles and dispersing throughout the dividing cell. During telophase, these Golgi vesicles move on microtubules to collect at the metaphase plate. There, the vesicles fuse from the center toward the cell walls; this structure is called a cell plate. As more vesicles fuse, the cell plate enlarges until it merges with the cell wall at the periphery of the cell. Enzymes use the glucose that has accumulated between the membrane layers to build a new cell wall of cellulose. The Golgi membranes become the plasma membrane on either side of the new cell wall (Figure 6.5).

This illustration shows cytokinesis in a typical animal cell and a typical plant cell. In an animal cell, a contractile ring of actin filaments forms a cleavage furrow that divides the cell in two. In a plant cell, Golgi vesicles coalesce at the metaphase plate. A cell plate grows from the center outward, and the vesicles form a plasma membrane that divides the cytoplasm.

Figure 6.5 In part (a), a cleavage furrow forms at the former metaphase plate in the animal cell. The plasma membrane is drawn in by a ring of actin fibers contracting just inside the membrane. The cleavage furrow deepens until the cells are pinched in two. In part (b), Golgi vesicles coalesce at the former metaphase plate in a plant cell. The vesicles fuse and form the cell plate. The cell plate grows from the center toward the cell walls. New cell walls are made from the vesicle contents.

G0 Phase

Not all cells adhere to the classic cell-cycle pattern in which a newly formed daughter cell immediately enters interphase, closely followed by the mitotic phase. Cells in the G0 phase are not actively preparing to divide. The cell is in a quiescent (inactive) stage, having exited the cell cycle. Some cells enter G0 temporarily until an external signal triggers the onset of G1. Other cells that never or rarely divide, such as mature cardiac muscle and nerve cells, remain in G0 permanently (Figure 6.6).

In part (a), a cleavage furrow forms at the former metaphase plate in the animal cell. The plasma membrane is drawn in by a ring of actin fibers contracting just inside the membrane. The cleavage furrow deepens until the cells are pinched in two. In part (b), Golgi vesicles coalesce at the former metaphase plate in a plant cell. The vesicles fuse and form the cell plate. The cell plate grows from the center toward the cell walls. New cell walls are made from the vesicle contents.

Figure 6.6 Cells that are not actively preparing to divide enter an alternate phase called G0. In some cases, this is a temporary condition until triggered to enter G1. In other cases, the cell will remain in G0 permanently.

Control of the Cell Cycle

The length of the cell cycle is highly variable even within the cells of an individual organism. In humans, the frequency of cell turnover ranges from a few hours in early embryonic development to an average of two to five days for epithelial cells, or to an entire human lifetime spent in G0 by specialized cells such as cortical neurons or cardiac muscle cells. There is also variation in the time that a cell spends in each phase of the cell cycle. When fast-dividing mammalian cells are grown in culture (outside the body under optimal growing conditions), the length of the cycle is approximately 24 hours. In rapidly dividing human cells with a 24-hour cell cycle, the G1 phase lasts approximately 11 hours. The timing of events in the cell cycle is controlled by mechanisms that are both internal and external to the cell.

Regulation at Internal Checkpoints

It is essential that daughter cells be exact duplicates of the parent cell. Mistakes in the duplication or distribution of the chromosomes lead to mutations that may be passed forward to every new cell produced from the abnormal cell. To prevent a compromised cell from continuing to divide, there are internal control mechanisms that operate at three main cell cycle checkpoints at which the cell cycle can be stopped until conditions are favorable. These checkpoints occur near the end of G1, at the G2–M transition, and during metaphase (Figure 6.7).

This illustration shows the three major check points of the cell cycle, which occur in G1, G2, and mitosis.

Figure 6.7 The cell cycle is controlled at three checkpoints. Integrity of the DNA is assessed at the G1 checkpoint. Proper chromosome duplication is assessed at the G2 checkpoint. Attachment of each kinetochore to a spindle fiber is assessed at the M checkpoint.

The G1 Checkpoint

The G1 checkpoint determines whether all conditions are favorable for cell division to proceed. The G1 checkpoint, also called the restriction point, is the point at which the cell irreversibly commits to the cell-division process. In addition to adequate reserves and cell size, there is a check for damage to the genomic DNA at the G1 checkpoint. A cell that does not meet all the requirements will not be released into the S phase.

The G2 Checkpoint

The G2 checkpoint bars the entry to the mitotic phase if certain conditions are not met. As in the G1 checkpoint, cell size and protein reserves are assessed. However, the most important role of the G2 checkpoint is to ensure that all of the chromosomes have been replicated and that the replicated DNA is not damaged.

The M Checkpoint

The M checkpoint occurs near the end of the metaphase stage of mitosis. The M checkpoint is also known as the spindle checkpoint because it determines if all the sister chromatids are correctly attached to the spindle microtubules. Because the separation of the sister chromatids during anaphase is an irreversible step, the cycle will not proceed until the kinetochores of each pair of sister chromatids are firmly anchored to spindle fibers arising from opposite poles of the cell.

Concept in Action

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Watch what occurs at the G1, G2, and M checkpoints by visiting this animation of the cell cycle.

Section Summary

The cell cycle is an orderly sequence of events. Cells on the path to cell division proceed through a series of precisely timed and carefully regulated stages. In eukaryotes, the cell cycle consists of a long preparatory period, called interphase. Interphase is divided into G1, S, and G2 phases. Mitosis consists of five stages: prophase, prometaphase, metaphase, anaphase, and telophase. Mitosis is usually accompanied by cytokinesis, during which the cytoplasmic components of the daughter cells are separated either by an actin ring (animal cells) or by cell plate formation (plant cells).

Each step of the cell cycle is monitored by internal controls called checkpoints. There are three major checkpoints in the cell cycle: one near the end of G1, a second at the G2–M transition, and the third during metaphase.


Which of the following is the correct order of events in mitosis?

A.  Sister chromatids line up at the metaphase plate. The kinetochore becomes attached to the mitotic spindle. The nucleus re-forms and the cell divides. The sister chromatids separate.B. The kinetochore becomes attached to the mitotic spindle. The sister chromatids separate. Sister chromatids line up at the metaphase plate. The nucleus re-forms and the cell divides.

C. The kinetochore becomes attached to metaphase plate. Sister chromatids line up at the metaphase plate. The kinetochore breaks down and the sister chromatids separate. The nucleus re-forms and the cell divides.

D. The kinetochore becomes attached to the mitotic spindle. Sister chromatids line up at the metaphase plate. The kinetochore breaks apart and the sister chromatids separate. The nucleus re-forms and the cell divides.

Answer: D. The kinetochore becomes attached to the mitotic spindle. Sister chromatids line up at the metaphase plate. The kinetochore breaks apart and the sister chromatids separate. The nucleus reforms and the cell divides.

Multiple Choice

Chromosomes are duplicated during what portion of the cell cycle?

A) G1 phase

B) S phase

C) prophase

D) prometaphase


Separation of the sister chromatids is a characteristic of which stage of mitosis?

A) prometaphase

B) metaphase

C) anaphase

D) telophase


The individual chromosomes become visible with a light microscope during which stage of mitosis?

A) prophase

B) prometaphase

C) metaphase

D) anaphase


What is necessary for a cell to pass the G2 checkpoint?

A) cell has reached a sufficient size

B) an adequate stockpile of nucleotides

C) accurate and complete DNA replication

D) proper attachment of mitotic spindle fibers to kinetochores


Free Response

Describe the similarities and differences between the cytokinesis mechanisms found in animal cells versus those in plant cells.

There are very few similarities between animal cell and plant cell cytokinesis. In animal cells, a ring of actin fibers is formed around the periphery of the cell at the former metaphase plate. The actin ring contracts inward, pulling the plasma membrane toward the center of the cell until the cell is pinched in two. In plant cells, a new cell wall must be formed between the daughter cells. Because of the rigid cell walls of the parent cell, contraction of the middle of the cell is not possible. Instead, a cell plate is formed in the center of the cell at the former metaphase plate. The cell plate is formed from Golgi vesicles that contain enzymes, proteins, and glucose. The vesicles fuse and the enzymes build a new cell wall from the proteins and glucose. The cell plate grows toward, and eventually fuses with, the cell wall of the parent cell.


anaphase: the stage of mitosis during which sister chromatids are separated from each other

cell cycle: the ordered sequence of events that a cell passes through between one cell division and the next

cell cycle checkpoints: mechanisms that monitor the preparedness of a eukaryotic cell to advance through the various cell cycle stages

cell plate: a structure formed during plant-cell cytokinesis by Golgi vesicles fusing at the metaphase plate; will ultimately lead to formation of a cell wall to separate the two daughter cells

centriole: a paired rod-like structure constructed of microtubules at the center of each animal cell centrosome

cleavage furrow: a constriction formed by the actin ring during animal-cell cytokinesis that leads to cytoplasmic division

cytokinesis: the division of the cytoplasm following mitosis to form two daughter cells

G0 phase: a cell-cycle phase distinct from the G1 phase of interphase; a cell in G0 is not preparing to divide

G1 phase: (also, first gap) a cell-cycle phase; first phase of interphase centered on cell growth during mitosis

G2 phase: (also, second gap) a cell-cycle phase; third phase of interphase where the cell undergoes the final preparations for mitosis

interphase: the period of the cell cycle leading up to mitosis; includes G1, S, and G2 phases; the interim between two consecutive cell divisions

kinetochore: a protein structure in the centromere of each sister chromatid that attracts and binds spindle microtubules during prometaphase

metaphase plate: the equatorial plane midway between two poles of a cell where the chromosomes align during metaphase

metaphase: the stage of mitosis during which chromosomes are lined up at the metaphase plate

mitosis: the period of the cell cycle at which the duplicated chromosomes are separated into identical nuclei; includes prophase, prometaphase, metaphase, anaphase, and telophase

mitotic phase: the period of the cell cycle when duplicated chromosomes are distributed into two nuclei and the cytoplasmic contents are divided; includes mitosis and cytokinesis

mitotic spindle: the microtubule apparatus that orchestrates the movement of chromosomes during mitosis

prometaphase: the stage of mitosis during which mitotic spindle fibers attach to kinetochores

prophase: the stage of mitosis during which chromosomes condense and the mitotic spindle begins to form

quiescent: describes a cell that is performing normal cell functions and has not initiated preparations for cell division

S phase: the second, or synthesis phase, of interphase during which DNA replication occurs

telophase: the stage of mitosis during which chromosomes arrive at opposite poles, decondense, and are surrounded by new nuclear envelopes


6.3 Cancer and the Cell Cycle

Learning Objectives

By the end of this section, you will be able to:

  • Explain how cancer is caused by uncontrolled cell division
  • Understand how proto-oncogenes are normal cell genes that, when mutated, become oncogenes
  • Describe how tumor suppressors function to stop the cell cycle until certain events are completed
  • Explain how mutant tumor suppressors cause cancer

Cancer is a collective name for many different diseases caused by a common mechanism: uncontrolled cell division. Despite the redundancy and overlapping levels of cell-cycle control, errors occur. One of the critical processes monitored by the cell-cycle checkpoint surveillance mechanism is the proper replication of DNA during the S phase. Even when all of the cell-cycle controls are fully functional, a small percentage of replication errors (mutations) will be passed on to the daughter cells. If one of these changes to the DNA nucleotide sequence occurs within a gene, a gene mutation results. All cancers begin when a gene mutation gives rise to a faulty protein that participates in the process of cell reproduction. The change in the cell that results from the malformed protein may be minor. Even minor mistakes, however, may allow subsequent mistakes to occur more readily. Over and over, small, uncorrected errors are passed from parent cell to daughter cells and accumulate as each generation of cells produces more non-functional proteins from uncorrected DNA damage. Eventually, the pace of the cell cycle speeds up as the effectiveness of the control and repair mechanisms decreases. Uncontrolled growth of the mutated cells outpaces the growth of normal cells in the area, and a tumor can result.


The genes that code for the positive cell-cycle regulators are called proto-oncogenes. Proto-oncogenes are normal genes that, when mutated, become oncogenes—genes that cause a cell to become cancerous. Consider what might happen to the cell cycle in a cell with a recently acquired oncogene. In most instances, the alteration of the DNA sequence will result in a less functional (or non-functional) protein. The result is detrimental to the cell and will likely prevent the cell from completing the cell cycle; however, the organism is not harmed because the mutation will not be carried forward. If a cell cannot reproduce, the mutation is not propagated and the damage is minimal. Occasionally, however, a gene mutation causes a change that increases the activity of a positive regulator. For example, a mutation that allows Cdk, a protein involved in cell-cycle regulation, to be activated before it should be could push the cell cycle past a checkpoint before all of the required conditions are met. If the resulting daughter cells are too damaged to undertake further cell divisions, the mutation would not be propagated and no harm comes to the organism. However, if the atypical daughter cells are able to divide further, the subsequent generation of cells will likely accumulate even more mutations, some possibly in additional genes that regulate the cell cycle.

The Cdk example is only one of many genes that are considered proto-oncogenes. In addition to the cell-cycle regulatory proteins, any protein that influences the cycle can be altered in such a way as to override cell-cycle checkpoints. Once a proto-oncogene has been altered such that there is an increase in the rate of the cell cycle, it is then called an oncogene.

Tumor Suppressor Genes

Like proto-oncogenes, many of the negative cell-cycle regulatory proteins were discovered in cells that had become cancerous. Tumor suppressor genes are genes that code for the negative regulator proteins, the type of regulator that—when activated—can prevent the cell from undergoing uncontrolled division. The collective function of the best-understood tumor suppressor gene proteins, retinoblastoma protein (RB1), p53, and p21, is to put up a roadblock to cell-cycle progress until certain events are completed. A cell that carries a mutated form of a negative regulator might not be able to halt the cell cycle if there is a problem.

Mutated p53 genes have been identified in more than half of all human tumor cells. This discovery is not surprising in light of the multiple roles that the p53 protein plays at the G1 checkpoint. The p53 protein activates other genes whose products halt the cell cycle (allowing time for DNA repair), activates genes whose products participate in DNA repair, or activates genes that initiate cell death when DNA damage cannot be repaired. A damaged p53 gene can result in the cell behaving as if there are no mutations (Figure 6.8). This allows cells to divide, propagating the mutation in daughter cells and allowing the accumulation of new mutations. In addition, the damaged version of p53 found in cancer cells cannot trigger cell death.

This illustration shows cell cycle regulation by p53. The p53 protein normally arrests the cell cycle in response to DNA damage, cell cycle abnormalities, or hypoxia. Once the damage is repaired, the cell cycle restarts. If the damage cannot be repaired, apoptosis (programmed cell death) occurs. Mutated p53 does not arrest the cell cycle in response to cellular damage. As a result, the cell cycle continues and the cell may become cancerous.

Figure 6.8 (a) The role of p53 is to monitor DNA. If damage is detected, p53 triggers repair mechanisms. If repairs are unsuccessful, p53 signals apoptosis. (b) A cell with an abnormal p53 protein cannot repair damaged DNA and cannot signal apoptosis. Cells with abnormal p53 can become cancerous. (credit: modification of work by Thierry Soussi)

Concept in Action


Go to this website to watch an animation of how cancer results from errors in the cell cycle.

Section Summary

Cancer is the result of unchecked cell division caused by a breakdown of the mechanisms regulating the cell cycle. The loss of control begins with a change in the DNA sequence of a gene that codes for one of the regulatory molecules. Faulty instructions lead to a protein that does not function as it should. Any disruption of the monitoring system can allow other mistakes to be passed on to the daughter cells. Each successive cell division will give rise to daughter cells with even more accumulated damage. Eventually, all checkpoints become nonfunctional, and rapidly reproducing cells crowd out normal cells, resulting in tumorous growth.


Multiple Choice

________ are changes to the nucleotides in a segment of DNA that codes for a protein.

A) Proto-oncogenes

B) Tumor suppressor genes

C) Gene mutations

D) Negative regulators


A gene that codes for a positive cell cycle regulator is called a(n) ________.

A) kinase inhibitor

B) tumor suppressor gene

C) proto-oncogene

D) oncogene


Free Response

Outline the steps that lead to a cell becoming cancerous.

If one of the genes that produce regulator proteins becomes mutated, it produces a malformed, possibly non-functional, cell-cycle regulator. This increases the chance that more mutations will be left unrepaired in the cell. Each subsequent generation of cells sustains more damage. The cell cycle can speed up as a result of loss of functional checkpoint proteins. The cells can lose the ability to self-destruct.

Explain the difference between a proto-oncogene and a tumor suppressor gene.

A proto-oncogene is the segment of DNA that codes for one of the positive cell-cycle regulators. If that gene becomes mutated to a form that is overactive, it is considered an oncogene. A tumor suppressor gene is a segment of DNA that codes for one of the negative cell-cycle regulators. If that gene becomes mutated to a form that is underactive, the cell cycle will run unchecked.



oncogene: a mutated version of a proto-oncogene, which allows for uncontrolled progression of the cell cycle, or uncontrolled cell reproduction

proto-oncogene: a normal gene that controls cell division by regulating the cell cycle that becomes an oncogene if it is mutated

tumor suppressor gene: a gene that codes for regulator proteins that prevent the cell from undergoing uncontrolled division


6.4 Prokaryotic Cell Division

Learning Objectives

By the end of this section, you will be able to:

  • Describe the process of binary fission in prokaryotes
  • Explain how FtsZ and tubulin proteins are examples of homology

Prokaryotes such as bacteria propagate by binary fission. For unicellular organisms, cell division is the only method to produce new individuals. In both prokaryotic and eukaryotic cells, the outcome of cell reproduction is a pair of daughter cells that are genetically identical to the parent cell. In unicellular organisms, daughter cells are individuals.

To achieve the outcome of identical daughter cells, some steps are essential. The genomic DNA must be replicated and then allocated into the daughter cells; the cytoplasmic contents must also be divided to give both new cells the machinery to sustain life. In bacterial cells, the genome consists of a single, circular DNA chromosome; therefore, the process of cell division is simplified. Mitosis is unnecessary because there is no nucleus or multiple chromosomes. This type of cell division is called binary fission.

Binary Fission

The cell division process of prokaryotes, called binary fission, is a less complicated and much quicker process than cell division in eukaryotes. Because of the speed of bacterial cell division, populations of bacteria can grow very rapidly. The single, circular DNA chromosome of bacteria is not enclosed in a nucleus, but instead occupies a specific location, the nucleoid, within the cell. As in eukaryotes, the DNA of the nucleoid is associated with proteins that aid in packaging the molecule into a compact size. The packing proteins of bacteria are, however, related to some of the proteins involved in the chromosome compaction of eukaryotes.

The starting point of replication, the origin, is close to the binding site of the chromosome to the plasma membrane (Figure 6.9). Replication of the DNA is bidirectional—moving away from the origin on both strands of the DNA loop simultaneously. As the new double strands are formed, each origin point moves away from the cell-wall attachment toward opposite ends of the cell. As the cell elongates, the growing membrane aids in the transport of the chromosomes. After the chromosomes have cleared the midpoint of the elongated cell, cytoplasmic separation begins. A septum is formed between the nucleoids from the periphery toward the center of the cell. When the new cell walls are in place, the daughter cells separate.

This illustration shows binary fission in prokaryotes. Replication of the single, circular chromosome begins at the origin of replication and continues simultaneously in both directions. As the DNA is replicated, the cell elongates and FtsZ proteins migrate toward the center of the cell, where they form a ring. The FtsZ ring directs the formation of a septum that divides the cell in two once DNA replication is complete.

Figure 6.9 The binary fission of a bacterium is outlined in five steps. (credit: modification of work by “Mcstrother”/Wikimedia Commons)

Evolution in Action

Mitotic Spindle Apparatus

The precise timing and formation of the mitotic spindle is critical to the success of eukaryotic cell division. Prokaryotic cells, on the other hand, do not undergo mitosis and therefore have no need for a mitotic spindle. However, the FtsZ protein that plays such a vital role in prokaryotic cytokinesis is structurally and functionally very similar to tubulin, the building block of the microtubules that make up the mitotic spindle fibers that are necessary for eukaryotes. The formation of a ring composed of repeating units of a protein called FtsZ directs the partition between the nucleoids in prokaryotes. Formation of the FtsZ ring triggers the accumulation of other proteins that work together to recruit new membrane and cell-wall materials to the site. FtsZ proteins can form filaments, rings, and other three-dimensional structures resembling the way tubulin forms microtubules, centrioles, and various cytoskeleton components. In addition, both FtsZ and tubulin employ the same energy source, GTP (guanosine triphosphate), to rapidly assemble and disassemble complex structures.

FtsZ and tubulin are an example of homology, structures derived from the same evolutionary origins. In this example, FtsZ is presumed to be similar to the ancestor protein to both the modern FtsZ and tubulin. While both proteins are found in extant organisms, tubulin function has evolved and diversified tremendously since the evolution from its FtsZ-like prokaryotic origin. A survey of cell-division machinery in present-day unicellular eukaryotes reveals crucial intermediary steps to the complex mitotic machinery of multicellular eukaryotes.

The mitotic spindle fibers of eukaryotes are composed of microtubules. Microtubules are polymers of the protein tubulin. The FtsZ protein active in prokaryote cell division is very similar to tubulin in the structures it can form and its energy source. Single-celled eukaryotes (such as yeast) display possible intermediary steps between FtsZ activity during binary fission in prokaryotes and the mitotic spindle in multicellular eukaryotes, during which the nucleus breaks down and is reformed.

Mitotic Spindle Evolution
Structure of genetic material Division of nuclear material Separation of daughter cells
Prokaryotes There is no nucleus. The single, circular chromosome exists in a region of cytoplasm called the nucleoid. Occurs through binary fission. As the chromosome is replicated, the two copies move to opposite ends of the cell by an unknown mechanism. FtsZ proteins assemble into a ring that pinches the cell in two.
Some protists Linear chromosomes exist in the nucleus. Chromosomes attach to the nuclear envelope, which remains intact. The mitotic spindle passes through the envelope and elongates the cell. No centrioles exist. Microfilaments form a cleavage furrow that pinches the cell in two.
Other protists Linear chromosomes exist in the nucleus. A mitotic spindle forms from the centrioles and passes through the nuclear membrane, which remains intact. Chromosomes attach to the mitotic spindle. The mitotic spindle separates the chromosomes and elongates the cell. Microfilaments form a cleavage furrow that pinches the cell in two.
Animal cells Linear chromosomes exist in the nucleus. A mitotic spindle forms from the centrioles. The nuclear envelope dissolves.
Chromosomes attach to the mitotic spindle, which separates them and elongates the cell.
Microfilaments form a cleavage furrow that pinches the cell in two.

Section Summary

In both prokaryotic and eukaryotic cell division, the genomic DNA is replicated and each copy is allocated into a daughter cell. The cytoplasmic contents are also divided evenly to the new cells. However, there are many differences between prokaryotic and eukaryotic cell division. Bacteria have a single, circular DNA chromosome and no nucleus. Therefore, mitosis is not necessary in bacterial cell division. Bacterial cytokinesis is directed by a ring composed of a protein called FtsZ. Ingrowth of membrane and cell-wall material from the periphery of the cells results in a septum that eventually forms the separate cell walls of the daughter cells.


Multiple Choice

Which eukaryotic cell-cycle event is missing in binary fission?

A) cell growth

B) DNA duplication

C) mitosis

D) cytokinesis


FtsZ proteins direct the formation of a ________ that will eventually form the new cell walls of the daughter cells.

A) contractile ring

B) cell plate

C) cytoskeleton

D) septum


Free Response

Name the common components of eukaryotic cell division and binary fission.

The common components of eukaryotic cell division and binary fission are DNA duplication, segregation of duplicated chromosomes, and the division of the cytoplasmic contents.



binary fission: the process of prokaryotic cell division

FtsZ: a tubulin-like protein component of the prokaryotic cytoskeleton that is important in prokaryotic cytokinesis (name origin: Filamenting temperature-sensitive mutant Z)

origin: the region of the prokaryotic chromosome at which replication begins

septum: a wall formed between bacterial daughter cells as a precursor to cell separation


Chapter 6 PowerPoint

Chapter 6 PowerPoint


Chapter 7: Introduction to the Cellular Basis of Inheritance

Three images are shown. Part a shows a mother and baby hippopotamus. In part b, mature Joshua trees are pictured next to saplings. In part c, a mother and baby flamingo are shown.

Figure 7.1 Each of us, like these other large multicellular organisms, begins life as a fertilized egg. After trillions of cell divisions, each of us develops into a complex, multicellular organism. (credit a: modification of work by Frank Wouters; credit b: modification of work by Ken Cole, USGS; credit c: modification of work by Martin Pettitt)

The ability to reproduce in kind is a basic characteristic of all living things. In kind means that the offspring of any organism closely resembles its parent or parents. Hippopotamuses give birth to hippopotamus calves; Monterey pine trees produce seeds from which Monterey pine seedlings emerge; and adult flamingos lay eggs that hatch into flamingo chicks. In kind does not generally mean exactly the same. While many single-celled organisms and a few multicellular organisms can produce genetically identical clones of themselves through mitotic cell division, many single-celled organisms and most multicellular organisms reproduce regularly using another method.

Sexual reproduction is the production by parents of haploid cells and the fusion of a haploid cell from each parent to form a single, unique diploid cell. In multicellular organisms, the new diploid cell will then undergo mitotic cell divisions to develop into an adult organism. A type of cell division called meiosis leads to the haploid cells that are part of the sexual reproductive cycle. Sexual reproduction, specifically meiosis and fertilization, introduces variation into offspring that may account for the evolutionary success of sexual reproduction. The vast majority of eukaryotic organisms can or must employ some form of meiosis and fertilization to reproduce.


7.1 Sexual Reproduction

Learning Objectives

By the end of this section, you will be able to:

  • Explain that variation among offspring is a potential evolutionary advantage resulting from sexual reproduction
  • Describe the three different life-cycle strategies among sexual multicellular organisms and their commonalities
  • Understand why you could never create a gamete that would be identical to either of the gametes that made you
Sexual reproduction was an early evolutionary innovation after the appearance of eukaryotic cells. The fact that most eukaryotes reproduce sexually is evidence of its evolutionary success. In many animals, it is the only mode of reproduction. And yet, scientists recognize some real disadvantages to sexual reproduction. On the surface, offspring that are genetically identical to the parent may appear to be more advantageous. If the parent organism is successfully occupying a habitat, offspring with the same traits would be similarly successful. There is also the obvious benefit to an organism that can produce offspring by asexual budding, fragmentation, or asexual eggs. These methods of reproduction do not require another organism of the opposite sex. There is no need to expend energy finding or attracting a mate. That energy can be spent on producing more offspring. Indeed, some organisms that lead a solitary lifestyle have retained the ability to reproduce asexually. In addition, asexual populations only have female individuals, so every individual is capable of reproduction. In contrast, the males in sexual populations (half the population) are not producing offspring themselves. Because of this, an asexual population can grow twice as fast as a sexual population in theory. This means that in competition, the asexual population would have the advantage. All of these advantages to asexual reproduction, which are also disadvantages to sexual reproduction, should mean that the number of species with asexual reproduction should be more common.

However, multicellular organisms that exclusively depend on asexual reproduction are exceedingly rare. Why is sexual reproduction so common? This is one of the important questions in biology and has been the focus of much research from the latter half of the twentieth century until now. A likely explanation is that the variation that sexual reproduction creates among offspring is very important to the survival and reproduction of those offspring. The only source of variation in asexual organisms is mutation. This is the ultimate source of variation in sexual organisms. In addition, those different mutations are continually reshuffled from one generation to the next when different parents combine their unique genomes, and the genes are mixed into different combinations by the process of meiosis. Meiosis is the division of the contents of the nucleus that divides the chromosomes among gametes. Variation is introduced during meiosis, as well as when the gametes combine in fertilization.

The Red Queen Hypothesis

There is no question that sexual reproduction provides evolutionary advantages to organisms that employ this mechanism to produce offspring. The problematic question is why, even in the face of fairly stable conditions, sexual reproduction persists when it is more difficult and produces fewer offspring for individual organisms? Variation is the outcome of sexual reproduction, but why are ongoing variations necessary? Enter the Red Queen hypothesis, first proposed by Leigh Van Valen in 1973.1 The concept was named in reference to the Red Queen’s race in Lewis Carroll’s book, Through the Looking-Glass, in which the Red Queen says one must run at full speed just to stay where one is.

All species coevolve with other organisms. For example, predators coevolve with their prey, and parasites coevolve with their hosts. A remarkable example of coevolution between predators and their prey is the unique coadaptation of night flying bats and their moth prey. Bats find their prey by emitting high-pitched clicks, but moths have evolved simple ears to hear these clicks so they can avoid the bats. The moths have also adapted behaviors, such as flying away from the bat when they first hear it, or dropping suddenly to the ground when the bat is upon them. Bats have evolved “quiet” clicks in an attempt to evade the moth’s hearing. Some moths have evolved the ability to respond to the bats’ clicks with their own clicks as a strategy to confuse the bats echolocation abilities.

Each tiny advantage gained by favorable variation gives a species an edge over close competitors, predators, parasites, or even prey. The only method that will allow a coevolving species to keep its own share of the resources is also to continually improve its ability to survive and produce offspring. As one species gains an advantage, other species must also develop an advantage or they will be outcompeted. No single species progresses too far ahead because genetic variation among progeny of sexual reproduction provides all species with a mechanism to produce adapted individuals. Species whose individuals cannot keep up become extinct. The Red Queen’s catchphrase was, “It takes all the running you can do to stay in the same place.” This is an apt description of coevolution between competing species.

Life Cycles of Sexually Reproducing Organisms

Fertilization and meiosis alternate in sexual life cycles. What happens between these two events depends on the organism. The process of meiosis reduces the resulting gamete’s chromosome number by half. Fertilization, the joining of two haploid gametes, restores the diploid condition. There are three main categories of life cycles in multicellular organisms: diploid-dominant, in which the multicellular diploid stage is the most obvious life stage (and there is no multicellular haploid stage), as with most animals including humans; haploid-dominant, in which the multicellular haploid stage is the most obvious life stage (and there is no multicellular diploid stage), as with all fungi and some algae; and alternation of generations, in which the two stages, haploid and diploid, are apparent to one degree or another depending on the group, as with plants and some algae.

Nearly all animals employ a diploid-dominant life-cycle strategy in which the only haploid cells produced by the organism are the gametes. The gametes are produced from diploid germ cells, a special cell line that only produces gametes. Once the haploid gametes are formed, they lose the ability to divide again. There is no multicellular haploid life stage. Fertilization occurs with the fusion of two gametes, usually from different individuals, restoring the diploid state (Figure 7.2 a).

Part a shows the life cycle of animals. Through meiosis, adult males produce haploid (1n) sperm, and adult females produce haploid eggs. Upon fertilization, a diploid (2n) zygote forms, which grows into an adult through mitosis and cell division. Part b shows the life cycle of fungi. In fungi, the diploid (2n) zygospore undergoes meiosis to form haploid (1n) spores. Mitosis of the spores occurs to form hyphae. Hyphae can undergo asexual reproduction to form more spores, or they form plus and minus mating types that undergo nuclear fusion to form a zygospore. Part c shows the life cycle of fern plants. The diploid (2n) zygote undergoes mitosis to produce the sphorophyte, which is the familiar, leafy plant. Sporangia form on the underside of the leaves of the sphorophyte. Sporangia undergo meiosis to form haploid (1n) spores. The spores germinate and undergo mitosis to form a multicellular, leafy gametophyte. The gametophyte produces eggs and sperm. Upon fertilization, the egg and sperm form a diploid zygote.

Figure 7.2 (a) In animals, sexually reproducing adults form haploid gametes from diploid germ cells. (b) Fungi, such as black bread mold (Rhizopus nigricans), have haploid-dominant life cycles. (c) Plants have a life cycle that alternates between a multicellular haploid organism and a multicellular diploid organism. (credit c “fern”: modification of work by Cory Zanker; credit c “gametophyte”: modification of work by “Vlmastra”/Wikimedia Commons)

If a mutation occurs so that a fungus is no longer able to produce a minus mating type, will it still be able to reproduce?

Most fungi and algae employ a life-cycle strategy in which the multicellular “body” of the organism is haploid. During sexual reproduction, specialized haploid cells from two individuals join to form a diploid zygote. The zygote immediately undergoes meiosis to form four haploid cells called spores (Figure 7.2 b).

The third life-cycle type, employed by some algae and all plants, is called alternation of generations. These species have both haploid and diploid multicellular organisms as part of their life cycle. The haploid multicellular plants are called gametophytes because they produce gametes. Meiosis is not involved in the production of gametes in this case, as the organism that produces gametes is already haploid. Fertilization between the gametes forms a diploid zygote. The zygote will undergo many rounds of mitosis and give rise to a diploid multicellular plant called a sporophyte. Specialized cells of the sporophyte will undergo meiosis and produce haploid spores. The spores will develop into the gametophytes (Figure 7. 2 c).

Section Summary

Nearly all eukaryotes undergo sexual reproduction. The variation introduced into the reproductive cells by meiosis appears to be one of the advantages of sexual reproduction that has made it so successful. Meiosis and fertilization alternate in sexual life cycles. The process of meiosis produces genetically unique reproductive cells called gametes, which have half the number of chromosomes as the parent cell. Fertilization, the fusion of haploid gametes from two individuals, restores the diploid condition. Thus, sexually reproducing organisms alternate between haploid and diploid stages. However, the ways in which reproductive cells are produced and the timing between meiosis and fertilization vary greatly. There are three main categories of life cycles: diploid-dominant, demonstrated by most animals; haploid-dominant, demonstrated by all fungi and some algae; and alternation of generations, demonstrated by plants and some algae.


If a mutation occurs so that a fungus is no longer able to produce a minus mating type, will it still be able to reproduce?

Answer: Yes, it will be able to reproduce asexually.

Multiple Choice

What is a likely evolutionary advantage of sexual reproduction over asexual reproduction?

  1. sexual reproduction involves fewer steps
  2. less chance of using up the resources in a given environment
  3. sexual reproduction results in greater variation in the offspring
  4. sexual reproduction is more cost-effective


Which type of life cycle has both a haploid and diploid multicellular stage?

  1. an asexual life cycle
  2. diploid-dominant
  3. haploid-dominant
  4. alternation of generations


Which event leads to a diploid cell in a life cycle?

  1. meiosis
  2. fertilization
  3. alternation of generations
  4. mutation


Free Response

Explain the advantage that populations of sexually reproducing organisms have over asexually reproducing organisms?

The offspring of sexually reproducing organisms are all genetically unique. Because of this, sexually reproducing organisms may have more successful survival of offspring in environments that change than asexually reproducing organisms, whose offspring are all genetically identical. In addition, the rate of adaptation of sexually reproducing organisms is higher, because of their increased variation. This may allow sexually reproducing organisms to adapt more quickly to competitors and parasites, who are evolving new ways to exploit or outcompete them.

Describe the two events that are common to all sexually reproducing organisms and how they fit into the different life cycles of those organisms.

The two events common to all sexually reproducing organisms are meiosis and fertilization. Meiosis reduces a diploid cell to a haploid state. The haploid cell may divide mitotically to produce an organism, some of whose cells will combine during fertilization, or the haploid cells produced by meiosis may immediately combine in fertilization to produce a diploid cell that divides to produce an organism.



alternation of generations: a life-cycle type in which the diploid and haploid stages alternate

diploid-dominant: a life-cycle type in which the multicellular diploid stage is prevalent

haploid-dominant: a life-cycle type in which the multicellular haploid stage is prevalent

gametophyte: a multicellular haploid life-cycle stage that produces gametes

germ cell: a specialized cell that produces gametes, such as eggs or sperm

life cycle: the sequence of events in the development of an organism and the production of cells that produce offspring

meiosis: a nuclear division process that results in four haploid cells

sporophyte: a multicellular diploid life-cycle stage that produces spores


1 Leigh Van Valen, “A new evolutionary law,” Evolutionary Theory 1 (1973): 1–30.


7.2 Meiosis

Learning Objectives

By the end of this section, you will be able to:

  • Describe the behavior of chromosomes during meiosis
  • Describe cellular events during meiosis
  • Explain the differences between meiosis and mitosis
  • Explain the mechanisms within meiosis that generate genetic variation among the products of meiosis

Sexual reproduction requires fertilization, a union of two cells from two individual organisms. If those two cells each contain one set of chromosomes, then the resulting cell contains two sets of chromosomes. The number of sets of chromosomes in a cell is called its ploidy level. Haploid cells contain one set of chromosomes. Cells containing two sets of chromosomes are called diploid. If the reproductive cycle is to continue, the diploid cell must somehow reduce its number of chromosome sets before fertilization can occur again, or there will be a continual doubling in the number of chromosome sets in every generation. So, in addition to fertilization, sexual reproduction includes a nuclear division, known as meiosis, that reduces the number of chromosome sets.

Most animals and plants are diploid, containing two sets of chromosomes; in each somatic cell (the nonreproductive cells of a multicellular organism), the nucleus contains two copies of each chromosome that are referred to as homologous chromosomes. Somatic cells are sometimes referred to as “body” cells. Homologous chromosomes are matched pairs containing genes for the same traits in identical locations along their length. Diploid organisms inherit one copy of each homologous chromosome from each parent; all together, they are considered a full set of chromosomes. In animals, haploid cells containing a single copy of each homologous chromosome are found only within gametes. Gametes fuse with another haploid gamete to produce a diploid cell.

The nuclear division that forms haploid cells, which is called meiosis, is related to mitosis. As you have learned, mitosis is part of a cell reproduction cycle that results in identical daughter nuclei that are also genetically identical to the original parent nucleus. In mitosis, both the parent and the daughter nuclei contain the same number of chromosome sets—diploid for most plants and animals. Meiosis employs many of the same mechanisms as mitosis. However, the starting nucleus is always diploid and the nuclei that result at the end of a meiotic cell division are haploid. To achieve the reduction in chromosome number, meiosis consists of one round of chromosome duplication and two rounds of nuclear division. Because the events that occur during each of the division stages are analogous to the events of mitosis, the same stage names are assigned. However, because there are two rounds of division, the stages are designated with a “I” or “II.” Thus, meiosis I is the first round of meiotic division and consists of prophase I, prometaphase I, and so on. Meiosis I reduces the number of chromosome sets from two to one. The genetic information is also mixed during this division to create unique recombinant chromosomes. Meiosis II, in which the second round of meiotic division takes place in a way that is similar to mitosis, includes prophase II, prometaphase II, and so on.


Meiosis is preceded by an interphase consisting of the G1, S, and G2 phases, which are nearly identical to the phases preceding mitosis. The G1 phase is the first phase of interphase and is focused on cell growth. In the S phase, the DNA of the chromosomes is replicated. Finally, in the G2 phase, the cell undergoes the final preparations for meiosis.

During DNA duplication of the S phase, each chromosome becomes composed of two identical copies (called sister chromatids) that are held together at the centromere until they are pulled apart during meiosis II. In an animal cell, the centrosomes that organize the microtubules of the meiotic spindle also replicate. This prepares the cell for the first meiotic phase.

Meiosis I

Early in prophase I, the chromosomes can be seen clearly microscopically. As the nuclear envelope begins to break down, the proteins associated with homologous chromosomes bring the pair close to each other. The tight pairing of the homologous chromosomes is called synapsis. In synapsis, the genes on the chromatids of the homologous chromosomes are precisely aligned with each other. An exchange of chromosome segments between non-sister homologous chromatids occurs and is called crossing over. This process is revealed visually after the exchange as chiasmata (singular = chiasma) (Figure 7.3).

As prophase I progresses, the close association between homologous chromosomes begins to break down, and the chromosomes continue to condense, although the homologous chromosomes remain attached to each other at chiasmata. The number of chiasmata varies with the species and the length of the chromosome. At the end of prophase I, the pairs are held together only at chiasmata (Figure 7.3) and are called tetrads because the four sister chromatids of each pair of homologous chromosomes are now visible.

The crossover events are the first source of genetic variation produced by meiosis. A single crossover event between homologous non-sister chromatids leads to a reciprocal exchange of equivalent DNA between a maternal chromosome and a paternal chromosome. Now, when that sister chromatid is moved into a gamete, it will carry some DNA from one parent of the individual and some DNA from the other parent. The recombinant sister chromatid has a combination of maternal and paternal genes that did not exist before the crossover.

This illustration shows a pair of homologous chromosomes that are aligned. the ends of two non-sister chromatids of the homologous chromosomes cross over, and genetic material is exchanged. the non-sister chromatids between which genetic material was exchanged are called recombinant chromosomes. the other pair of non-sister chromatids that did not exchange genetic material are called non-recombinant chromosomes.

Figure 7.3 In this illustration of the effects of crossing over, the blue chromosome came from the individual’s father and the red chromosome came from the individual’s mother. Crossover occurs between non-sister chromatids of homologous chromosomes. The result is an exchange of genetic material between homologous chromosomes. The chromosomes that have a mixture of maternal and paternal sequence are called recombinant and the chromosomes that are completely paternal or maternal are called non-recombinant.

The key event in prometaphase I is the attachment of the spindle fiber microtubules to the kinetochore proteins at the centromeres. The microtubules assembled from centrosomes at opposite poles of the cell grow toward the middle of the cell. At the end of prometaphase I, each tetrad is attached to microtubules from both poles, with one homologous chromosome attached at one pole and the other homologous chromosome attached to the other pole. The homologous chromosomes are still held together at chiasmata. In addition, the nuclear membrane has broken down entirely.

During metaphase I, the homologous chromosomes are arranged in the center of the cell with the kinetochores facing opposite poles. The orientation of each pair of homologous chromosomes at the center of the cell is random.

This randomness, called independent assortment, is the physical basis for the generation of the second form of genetic variation in offspring. Consider that the homologous chromosomes of a sexually reproducing organism are originally inherited as two separate sets, one from each parent. Using humans as an example, one set of 23 chromosomes is present in the egg donated by the mother. The father provides the other set of 23 chromosomes in the sperm that fertilizes the egg. In metaphase I, these pairs line up at the midway point between the two poles of the cell. Because there is an equal chance that a microtubule fiber will encounter a maternally or paternally inherited chromosome, the arrangement of the tetrads at the metaphase plate is random. Any maternally inherited chromosome may face either pole. Any paternally inherited chromosome may also face either pole. The orientation of each tetrad is independent of the orientation of the other 22 tetrads.

In each cell that undergoes meiosis, the arrangement of the tetrads is different. The number of variations depends on the number of chromosomes making up a set. There are two possibilities for orientation (for each tetrad); thus, the possible number of alignments equals 2n where n is the number of chromosomes per set. Humans have 23 chromosome pairs, which results in over eight million (223) possibilities. This number does not include the variability previously created in the sister chromatids by crossover. Given these two mechanisms, it is highly unlikely that any two haploid cells resulting from meiosis will have the same genetic composition (Figure 7.4).

To summarize the genetic consequences of meiosis I: the maternal and paternal genes are recombined by crossover events occurring on each homologous pair during prophase I; in addition, the random assortment of tetrads at metaphase produces a unique combination of maternal and paternal chromosomes that will make their way into the gametes.

This illustration shows that, in a cell with a set of two chromosomes, four possible arrangements of chromosomes can give rise to eight different kinds of gamete. These are the eight possible arrangements of chromosomes that can occur during meiosis of two chromosomes.

Figure 7.4 To demonstrate random, independent assortment at metaphase I, consider a cell with n = 2. In this case, there are two possible arrangements at the equatorial plane in metaphase I, as shown in the upper cell of each panel. These two possible orientations lead to the production of genetically different gametes. With more chromosomes, the number of possible arrangements increases dramatically.

In anaphase I, the spindle fibers pull the linked chromosomes apart. The sister chromatids remain tightly bound together at the centromere. It is the chiasma connections that are broken in anaphase I as the fibers attached to the fused kinetochores pull the homologous chromosomes apart.

In telophase I, the separated chromosomes arrive at opposite poles. The remainder of the typical telophase events may or may not occur depending on the species. In some organisms, the chromosomes decondense and nuclear envelopes form around the chromatids in telophase I.

Cytokinesis, the physical separation of the cytoplasmic components into two daughter cells, occurs without reformation of the nuclei in other organisms. In nearly all species, cytokinesis separates the cell contents by either a cleavage furrow (in animals and some fungi), or a cell plate that will ultimately lead to formation of cell walls that separate the two daughter cells (in plants). At each pole, there is just one member of each pair of the homologous chromosomes, so only one full set of the chromosomes is present. This is why the cells are considered haploid—there is only one chromosome set, even though there are duplicate copies of the set because each homolog still consists of two sister chromatids that are still attached to each other. However, although the sister chromatids were once duplicates of the same chromosome, they are no longer identical at this stage because of crossovers.

Concept in Action

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Review the process of meiosis, observing how chromosomes align and migrate, at this site.

Meiosis II

In meiosis II, the connected sister chromatids remaining in the haploid cells from meiosis I will be split to form four haploid cells. In some species, cells enter a brief interphase, or interkinesis, that lacks an S phase, before entering meiosis II. Chromosomes are not duplicated during interkinesis. The two cells produced in meiosis I go through the events of meiosis II in synchrony. Overall, meiosis II resembles the mitotic division of a haploid cell.

In prophase II, if the chromosomes decondensed in telophase I, they condense again. If nuclear envelopes were formed, they fragment into vesicles. The centrosomes duplicated during interkinesis move away from each other toward opposite poles, and new spindles are formed. In prometaphase II, the nuclear envelopes are completely broken down, and the spindle is fully formed. Each sister chromatid forms an individual kinetochore that attaches to microtubules from opposite poles. In metaphase II, the sister chromatids are maximally condensed and aligned at the center of the cell. In anaphase II, the sister chromatids are pulled apart by the spindle fibers and move toward opposite poles.

This illustration compares chromosome alignment in meiosis I and meiosis II. In prometaphase I, homologous pairs of chromosomes are held together by chiasmata. In anaphase I, the homologous pair separates and the connections at the chiasmata are broken, but the sister chromatids remain attached at the centromere. In prometaphase II, the sister chromatids are held together at the centromere. In anaphase II, the centromere connections are broken and the sister chromatids separate.

Figure 7.5 In prometaphase I, microtubules attach to the fused kinetochores of homologous chromosomes. In anaphase I, the homologous chromosomes are separated. In prometaphase II, microtubules attach to individual kinetochores of sister chromatids. In anaphase II, the sister chromatids are separated.

In telophase II, the chromosomes arrive at opposite poles and begin to decondense. Nuclear envelopes form around the chromosomes. Cytokinesis separates the two cells into four genetically unique haploid cells. At this point, the nuclei in the newly produced cells are both haploid and have only one copy of the single set of chromosomes. The cells produced are genetically unique because of the random assortment of paternal and maternal homologs and because of the recombination of maternal and paternal segments of chromosomes—with their sets of genes—that occurs during crossover.

Comparing Meiosis and Mitosis

Mitosis and meiosis, which are both forms of division of the nucleus in eukaryotic cells, share some similarities, but also exhibit distinct differences that lead to their very different outcomes. Mitosis is a single nuclear division that results in two nuclei, usually partitioned into two new cells. The nuclei resulting from a mitotic division are genetically identical to the original. They have the same number of sets of chromosomes: one in the case of haploid cells, and two in the case of diploid cells. On the other hand, meiosis is two nuclear divisions that result in four nuclei, usually partitioned into four new cells. The nuclei resulting from meiosis are never genetically identical, and they contain one chromosome set only—this is half the number of the original cell, which was diploid.

The differences in the outcomes of meiosis and mitosis occur because of differences in the behavior of the chromosomes during each process. Most of these differences in the processes occur in meiosis I, which is a very different nuclear division than mitosis. In meiosis I, the homologous chromosome pairs become associated with each other, are bound together, experience chiasmata and crossover between sister chromatids, and line up along the metaphase plate in tetrads with spindle fibers from opposite spindle poles attached to each kinetochore of a homolog in a tetrad. All of these events occur only in meiosis I, never in mitosis.

Homologous chromosomes move to opposite poles during meiosis I so the number of sets of chromosomes in each nucleus-to-be is reduced from two to one. For this reason, meiosis I is referred to as a reduction division. There is no such reduction in ploidy level in mitosis.

Meiosis II is much more analogous to a mitotic division. In this case, duplicated chromosomes (only one set of them) line up at the center of the cell with divided kinetochores attached to spindle fibers from opposite poles. During anaphase II, as in mitotic anaphase, the kinetochores divide and one sister chromatid is pulled to one pole and the other sister chromatid is pulled to the other pole. If it were not for the fact that there had been crossovers, the two products of each meiosis II division would be identical as in mitosis; instead, they are different because there has always been at least one crossover per chromosome. Meiosis II is not a reduction division because, although there are fewer copies of the genome in the resulting cells, there is still one set of chromosomes, as there was at the end of meiosis I.

Cells produced by mitosis will function in different parts of the body as a part of growth or replacing dead or damaged cells. They may even be involved in asexual reproduction in some organisms. Cells produced by meiosis in a diploid-dominant organism such as an animal will only participate in sexual reproduction.

This illustration compares meiosis and mitosis. In meiosis, there are two rounds of cell division, whereas there is only one round of cell division in mitosis. In both mitosis and meiosis, DNA synthesis occurs during S phase. Synapsis of homologous chromosomes occurs in prophase I of meiosis, but does not occur in mitosis. Crossover of chromosomes occurs in prophase I of meiosis, but does not occur in mitosis. Homologous pairs of chromosomes line up at the metaphase plate during metaphase I of meiosis, but not during mitosis. Sister chromatids line up at the metaphase plate during metaphase II of meiosis and metaphase of mitosis. The result of meiosis is four haploid daughter cells, and the result of mitosis is two diploid daughter cells.

Figure 7.6 Meiosis and mitosis are both preceded by one round of DNA replication; however, meiosis includes two nuclear divisions. The four daughter cells resulting from meiosis are haploid and genetically distinct. The daughter cells resulting from mitosis are diploid and identical to the parent cell.

Concept in Action

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Section Summary

Sexual reproduction requires that diploid organisms produce haploid cells that can fuse during fertilization to form diploid offspring. The process that results in haploid cells is called meiosis. Meiosis is a series of events that arrange and separate chromosomes into daughter cells. During the interphase of meiosis, each chromosome is duplicated. In meiosis, there are two rounds of nuclear division resulting in four nuclei and usually four haploid daughter cells, each with half the number of chromosomes as the parent cell. During meiosis, variation in the daughter nuclei is introduced because of crossover in prophase I and random alignment at metaphase I. The cells that are produced by meiosis are genetically unique.

Meiosis and mitosis share similarities, but have distinct outcomes. Mitotic divisions are single nuclear divisions that produce daughter nuclei that are genetically identical and have the same number of chromosome sets as the original cell. Meiotic divisions are two nuclear divisions that produce four daughter nuclei that are genetically different and have one chromosome set rather than the two sets the parent cell had. The main differences between the processes occur in the first division of meiosis. The homologous chromosomes separate into different nuclei during meiosis I causing a reduction of ploidy level. The second division of meiosis is much more similar to a mitotic division.


Multiple Choice

Meiosis produces ________ daughter cells.

A) two haploid

B) two diploid

C) four haploid

D) four diploid


At which stage of meiosis are sister chromatids separated from each other?

A) prophase I

B) prophase II

C) anaphase I

D) anaphase II


The part of meiosis that is similar to mitosis is ________.

A) meiosis I

B) anaphase I

C) meiosis II

D) interkinesis


If a muscle cell of a typical organism has 32 chromosomes, how many chromosomes will be in a gamete of that same organism?

A) 8

B) 16

C) 32

D) 64


Free Response

Explain how the random alignment of homologous chromosomes during metaphase I contributes to variation in gametes produced by meiosis.

Random alignment leads to new combinations of traits. The chromosomes that were originally inherited by the gamete-producing individual came equally from the egg and the sperm. In metaphase I, the duplicated copies of these maternal and paternal homologous chromosomes line up across the center of the cell to form a tetrad. The orientation of each tetrad is random. There is an equal chance that the maternally derived chromosomes will be facing either pole. The same is true of the paternally derived chromosomes. The alignment should occur differently in almost every meiosis. As the homologous chromosomes are pulled apart in anaphase I, any combination of maternal and paternal chromosomes will move toward each pole. The gametes formed from these two groups of chromosomes will have a mixture of traits from the individual’s parents. Each gamete is unique.

In what ways is meiosis II similar to and different from mitosis of a diploid cell?

The two divisions are similar in that the chromosomes line up along the metaphase plate individually, meaning unpaired with other chromosomes (as in meiosis I). In addition, each chromosome consists of two sister chromatids that will be pulled apart. The two divisions are different because in meiosis II there are half the number of chromosomes that are present in a diploid cell of the same species undergoing mitosis. This is because meiosis I reduced the number of chromosomes to a haploid state.



chiasmata: (singular = chiasma) the structure that forms at the crossover points after genetic material is exchanged

crossing over: (also, recombination) the exchange of genetic material between homologous chromosomes resulting in chromosomes that incorporate genes from both parents of the organism forming reproductive cells

fertilization: the union of two haploid cells typically from two individual organisms

interkinesis: a period of rest that may occur between meiosis I and meiosis II; there is no replication of DNA during interkinesis

meiosis I: the first round of meiotic cell division; referred to as reduction division because the resulting cells are haploid

meiosis II: the second round of meiotic cell division following meiosis I; sister chromatids are separated from each other, and the result is four unique haploid cells

recombinant: describing something composed of genetic material from two sources, such as a chromosome with both maternal and paternal segments of DNA

reduction division: a nuclear division that produces daughter nuclei each having one-half as many chromosome sets as the parental nucleus; meiosis I is a reduction division

somatic cell: all the cells of a multicellular organism except the gamete-forming cells

synapsis: the formation of a close association between homologous chromosomes during prophase I

tetrad: two duplicated homologous chromosomes (four chromatids) bound together by chiasmata during prophase I


7.3 Errors in Meiosis

Learning Objectives

By the end of this section, you will be able to:

  • Explain how nondisjunction leads to disorders in chromosome number
  • Describe how errors in chromosome structure occur through inversions and translocations

Inherited disorders can arise when chromosomes behave abnormally during meiosis. Chromosome disorders can be divided into two categories: abnormalities in chromosome number and chromosome structural rearrangements. Because even small segments of chromosomes can span many genes, chromosomal disorders are characteristically dramatic and often fatal.

Disorders in Chromosome Number

The isolation and microscopic observation of chromosomes forms the basis of cytogenetics and is the primary method by which clinicians detect chromosomal abnormalities in humans. A karyotype is the number and appearance of chromosomes, including their length, banding pattern, and centromere position. To obtain a view of an individual’s karyotype, cytologists photograph the chromosomes and then cut and paste each chromosome into a chart, or karyogram (Figure 7.7).

This is a karyotype of a human female. There are 22 homologous pairs of chromosomes and a pair of X chromosomes.

Figure 7.7 This karyogram shows the chromosomes of a female human immune cell during mitosis. (credit: Andreas Bolzer, et al)

Geneticists Use Karyograms to Identify Chromosomal Aberrations

The karyotype is a method by which traits characterized by chromosomal abnormalities can be identified from a single cell. To observe an individual’s karyotype, a person’s cells (like white blood cells) are first collected from a blood sample or other tissue. In the laboratory, the isolated cells are stimulated to begin actively dividing. A chemical is then applied to the cells to arrest mitosis during metaphase. The cells are then fixed to a slide.

The geneticist then stains chromosomes with one of several dyes to better visualize the distinct and reproducible banding patterns of each chromosome pair. Following staining, chromosomes are viewed using bright-field microscopy. An experienced cytogeneticist can identify each band. In addition to the banding patterns, chromosomes are further identified on the basis of size and centromere location. To obtain the classic depiction of the karyotype in which homologous pairs of chromosomes are aligned in numerical order from longest to shortest, the geneticist obtains a digital image, identifies each chromosome, and manually arranges the chromosomes into this pattern.

At its most basic, the karyogram may reveal genetic abnormalities in which an individual has too many or too few chromosomes per cell. Examples of this are Down syndrome, which is identified by a third copy of chromosome 21, and Turner syndrome, which is characterized by the presence of only one X chromosome in women instead of two. Geneticists can also identify large deletions or insertions of DNA. For instance, Jacobsen syndrome, which involves distinctive facial features as well as heart and bleeding defects, is identified by a deletion on chromosome 11. Finally, the karyotype can pinpoint translocations, which occur when a segment of genetic material breaks from one chromosome and reattaches to another chromosome or to a different part of the same chromosome. Translocations are implicated in certain cancers, including chronic myelogenous leukemia.

By observing a karyogram, geneticists can actually visualize the chromosomal composition of an individual to confirm or predict genetic abnormalities in offspring even before birth.

Nondisjunctions, Duplications, and Deletions

Of all the chromosomal disorders, abnormalities in chromosome number are the most easily identifiable from a karyogram. Disorders of chromosome number include the duplication or loss of entire chromosomes, as well as changes in the number of complete sets of chromosomes. They are caused by nondisjunction, which occurs when pairs of homologous chromosomes or sister chromatids fail to separate during meiosis. The risk of nondisjunction increases with the age of the parents.

Nondisjunction can occur during either meiosis I or II, with different results (Figure 7.8). If homologous chromosomes fail to separate during meiosis I, the result is two gametes that lack that chromosome and two gametes with two copies of the chromosome. If sister chromatids fail to separate during meiosis II, the result is one gamete that lacks that chromosome, two normal gametes with one copy of the chromosome, and one gamete with two copies of the chromosome.

This illustration shows nondisjunction during meiosis I and meiosis II. Nondisjunction during meiosis I occurs when a homologous pair fails to separate, and results in two gametes with n + 1 chromosomes, and two gametes with n – 1 chromosomes. Nondisjunction during meiosis II occurs when sister chromatids fail to separate, and results in one gamete with n + 1 chromosomes, one gamete with n – 1 chromosomes, and two normal gametes.

Figure 7.8 Following meiosis, each gamete has one copy of each chromosome. Nondisjunction occurs when homologous chromosomes (meiosis I) or sister chromatids (meiosis II) fail to separate during meiosis.

An individual with the appropriate number of chromosomes for their species is called euploid; in humans, euploidy corresponds to 22 pairs of autosomes and one pair of sex chromosomes. An individual with an error in chromosome number is described as aneuploid, a term that includes monosomy (loss of one chromosome) or trisomy (gain of an extraneous chromosome). Monosomic human zygotes missing any one copy of an autosome invariably fail to develop to birth because they have only one copy of essential genes. Most autosomal trisomies also fail to develop to birth; however, duplications of some of the smaller chromosomes (13, 15, 18, 21, or 22) can result in offspring that survive for several weeks to many years. Trisomic individuals suffer from a different type of genetic imbalance: an excess in gene dose. Cell functions are calibrated to the amount of gene product produced by two copies (doses) of each gene; adding a third copy (dose) disrupts this balance. The most common trisomy is that of chromosome 21, which leads to Down syndrome. Individuals with this inherited disorder have characteristic physical features and developmental delays in growth and cognition. The incidence of Down syndrome is correlated with maternal age, such that older women are more likely to give birth to children with Down syndrome (Figure 7.9).

This graph shows the risk of Down’s syndrome in the fetus by maternal age. Risk dramatically increases past a maternal age of 35.

Figure 7.9 The incidence of having a fetus with trisomy 21 increases dramatically with maternal age.

Concept in Action

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Visualize the addition of a chromosome that leads to Down syndrome in this video simulation.

Humans display dramatic deleterious effects with autosomal trisomies and monosomies. Therefore, it may seem counterintuitive that human females and males can function normally, despite carrying different numbers of the X chromosome. In part, this occurs because of a process called X inactivation. Early in development, when female mammalian embryos consist of just a few thousand cells, one X chromosome in each cell inactivates by condensing into a structure called a Barr body. The genes on the inactive X chromosome are not expressed. The particular X chromosome (maternally or paternally derived) that is inactivated in each cell is random, but once the inactivation occurs, all cells descended from that cell will have the same inactive X chromosome. By this process, females compensate for their double genetic dose of X chromosome.

In so-called “tortoiseshell” cats, X inactivation is observed as coat-color variegation (Figure 7.10). Females heterozygous for an X-linked coat color gene will express one of two different coat colors over different regions of their body, corresponding to whichever X chromosome is inactivated in the embryonic cell progenitor of that region. When you see a tortoiseshell cat, you will know that it has to be a female.

Photo of a tortoiseshell cat.

Figure 7.10 Embryonic inactivation of one of two different X chromosomes encoding different coat colors gives rise to the tortoiseshell phenotype in cats. (credit: Michael Bodega) Photo of a tortoiseshell cat.

In an individual carrying an abnormal number of X chromosomes, cellular mechanisms will inactivate all but one X in each of her cells. As a result, X-chromosomal abnormalities are typically associated with mild mental and physical defects, as well as sterility. If the X chromosome is absent altogether, the individual will not develop.

Several errors in sex chromosome number have been characterized. Individuals with three X chromosomes, called triplo-X, appear female but express developmental delays and reduced fertility. The XXY chromosome complement, corresponding to one type of Klinefelter syndrome, corresponds to male individuals with small testes, enlarged breasts, and reduced body hair. The extra X chromosome undergoes inactivation to compensate for the excess genetic dosage. Turner syndrome, characterized as an X0 chromosome complement (i.e., only a single sex chromosome), corresponds to a female individual with short stature, webbed skin in the neck region, hearing and cardiac impairments, and sterility.

An individual with more than the correct number of chromosome sets (two for diploid species) is called polyploid. For instance, fertilization of an abnormal diploid egg with a normal haploid sperm would yield a triploid zygote. Polyploid animals are extremely rare, with only a few examples among the flatworms, crustaceans, amphibians, fish, and lizards. Triploid animals are sterile because meiosis cannot proceed normally with an odd number of chromosome sets. In contrast, polyploidy is very common in the plant kingdom, and polyploid plants tend to be larger and more robust than euploids of their species.

Chromosome Structural Rearrangements

Cytologists have characterized numerous structural rearrangements in chromosomes, including partial duplications, deletions, inversions, and translocations. Duplications and deletions often produce offspring that survive but exhibit physical and mental abnormalities. Cri-du-chat (from the French for “cry of the cat”) is a syndrome associated with nervous system abnormalities and identifiable physical features that results from a deletion of most of the small arm of chromosome 5 (Figure 7.11). Infants with this genotype emit a characteristic high-pitched cry upon which the disorder’s name is based.

Photo shows boy with cri-du-chat syndrome at four different ages (ages two, four, nine, and twelve).

Figure 7.11 This individual with cri-du-chat syndrome is shown at various ages: (A) age two, (B) age four, (C) age nine, and (D) age 12. (credit: Paola Cerruti Mainardi)

Chromosome inversions and translocations can be identified by observing cells during meiosis because homologous chromosomes with a rearrangement in one of the pair must contort to maintain appropriate gene alignment and pair effectively during prophase I.

A chromosome inversion is the detachment, 180° rotation, and reinsertion of part of a chromosome. Unless they disrupt a gene sequence, inversions only change the orientation of genes and are likely to have more mild effects than aneuploid errors.

Evolution in Action

The Chromosome 18 InversionNot all structural rearrangements of chromosomes produce nonviable, impaired, or infertile individuals. In rare instances, such a change can result in the evolution of a new species. In fact, an inversion in chromosome 18 appears to have contributed to the evolution of humans. This inversion is not present in our closest genetic relatives, the chimpanzees.

The chromosome 18 inversion is believed to have occurred in early humans following their divergence from a common ancestor with chimpanzees approximately five million years ago. Researchers have suggested that a long stretch of DNA was duplicated on chromosome 18 of an ancestor to humans, but that during the duplication it was inverted (inserted into the chromosome in reverse orientation.

A comparison of human and chimpanzee genes in the region of this inversion indicates that two genes—ROCK1 and USP14—are farther apart on human chromosome 18 than they are on the corresponding chimpanzee chromosome. This suggests that one of the inversion breakpoints occurred between these two genes. Interestingly, humans and chimpanzees express USP14 at distinct levels in specific cell types, including cortical cells and fibroblasts. Perhaps the chromosome 18 inversion in an ancestral human repositioned specific genes and reset their expression levels in a useful way. Because both ROCK1 and USP14 code for enzymes, a change in their expression could alter cellular function. It is not known how this inversion contributed to hominid evolution, but it appears to be a significant factor in the divergence of humans from other primates.1

A translocation occurs when a segment of a chromosome dissociates and reattaches to a different, nonhomologous chromosome. Translocations can be benign or have devastating effects, depending on how the positions of genes are altered with respect to regulatory sequences. Notably, specific translocations have been associated with several cancers and with schizophrenia. Reciprocal translocations result from the exchange of chromosome segments between two nonhomologous chromosomes such that there is no gain or loss of genetic information (Figure 7.12).

Part a shows an inversion in a chromosome. Two identical chromosomes are shown, except for a small section that has been inverted in the second chromosome. Part b shows a reciprocal translocation, in which DNA is transferred from one chromosome to another. No genetic information is gained or lost in the process.

Figure 7.12 An (a) inversion occurs when a chromosome segment breaks from the chromosome, reverses its orientation, and then reattaches in the original position. A (b) reciprocal translocation occurs between two nonhomologous chromosomes and does not cause any genetic information to be lost or duplicated. (credit: modification of work by National Human Genome Research Institute (USA)

Section Summary

The number, size, shape, and banding pattern of chromosomes make them easily identifiable in a karyogram and allow for the assessment of many chromosomal abnormalities. Disorders in chromosome number, or aneuploidies, are typically lethal to the embryo, although a few trisomic genotypes are viable. Because of X inactivation, aberrations in sex chromosomes typically have milder effects on an individual. Aneuploidies also include instances in which segments of a chromosome are duplicated or deleted. Chromosome structures also may be rearranged, for example by inversion or translocation. Both of these aberrations can result in negative effects on development, or death. Because they force chromosomes to assume contorted pairings during meiosis I, inversions and translocations are often associated with reduced fertility because of the likelihood of nondisjunction.


Multiple Choice

The genotype XXY corresponds to:

A) Klinefelter syndrome

B) Turner syndrome

C) Triplo-X

D) Jacob syndrome


Abnormalities in the number of X chromosomes tend to be milder than the same abnormalities in autosomes because of ________.

A) deletions

B) nonhomologous recombination

C) synapsis

D) X inactivation


Aneuploidies are deleterious for the individual because of what phenomenon?

A) nondisjunction

B) gene dosage

C) meiotic errors

D) X inactivation


Free Response

Individuals with trisomy 21 are more likely to survive to adulthood than individuals with trisomy 18. Based on what you know about aneuploidies from this module, what can you hypothesize about chromosomes 21 and 18?

The problems caused by trisomies arise because the genes on the chromosome that is present in three copies produce more product than genes on chromosomes with only two copies. The cell does not have a way to adjust the amount of product, and the lack of balance causes problems in development and the maintenance of the individual. Each chromosome is different, and the differences in survivability could have to do with the numbers of genes on the two chromosomes. Chromosome 21 may be a smaller chromosome, so there are fewer unbalanced gene products. It is also possible that chromosome 21 carries genes whose products are less sensitive to differences in dosage than chromosome 18. The genes may be less involved in critical pathways, or the differences in dosage may make less of a difference to those pathways


aneuploid: an individual with an error in chromosome number; includes deletions and duplications of chromosome segments

autosome: any of the non-sex chromosomes

chromosome inversion: the detachment, 180° rotation, and reinsertion of a chromosome arm

euploid: an individual with the appropriate number of chromosomes for their species

karyogram: the photographic image of a karyotype

karyotype: the number and appearance of an individuals chromosomes, including the size, banding patterns, and centromere position

monosomy: an otherwise diploid genotype in which one chromosome is missing

nondisjunction: the failure of synapsed homologs to completely separate and migrate to separate poles during the first cell division of meiosis

polyploid: an individual with an incorrect number of chromosome sets

translocation: the process by which one segment of a chromosome dissociates and reattaches to a different, nonhomologous chromosome

trisomy: an otherwise diploid genotype in which one entire chromosome is duplicated

X inactivation: the condensation of X chromosomes into Barr bodies during embryonic development in females to compensate for the double genetic dose




1 V Goidts, et al., “Segmental duplication associated with the human-specific inversion of chromosome 18: a further example of the impact of segmental duplications on karyotype and genome evolution in primates,” Human Genetics, 115 (2004):116–22.


Chapter 7 PowerPoint

Chapter 7 PowerPoint


Chapter 8: Introduction to Patterns of Inheritance

A photo of light purple pea flowers.

Figure 8.1 Experimenting with thousands of garden peas, Mendel uncovered the fundamentals of genetics. (credit: modification of work by Jerry Kirkhart)

Genetics is the study of heredity. Johann Gregor Mendel set the framework for genetics long before chromosomes or genes had been identified, at a time when meiosis was not well understood. Mendel selected a simple biological system and conducted methodical, quantitative analyses using large sample sizes. Because of Mendel’s work, the fundamental principles of heredity were revealed. We now know that genes, carried on chromosomes, are the basic functional units of heredity with the ability to be replicated, expressed, or mutated. Today, the postulates put forth by Mendel form the basis of classical, or Mendelian, genetics. Not all genes are transmitted from parents to offspring according to Mendelian genetics, but Mendel’s experiments serve as an excellent starting point for thinking about inheritance.


8.1 Mendel’s Experiments

Learning Objectives

By the end of this section, you will be able to:

  • Explain the scientific reasons for the success of Mendel’s experimental work
  • Describe the expected outcomes of monohybrid crosses involving dominant and recessive alleles.
Image is a sketch of Johann Gregor Mendel.

Figure 8.2 Johann Gregor Mendel set the framework for the study of genetics.

Johann Gregor Mendel (1822–1884) was a lifelong learner, teacher, scientist, and man of faith. As a young adult, he joined the Augustinian Abbey of St. Thomas in Brno in what is now the Czech Republic. Supported by the monastery, he taught physics, botany, and natural science courses at the secondary and university levels. In 1856, he began a decade-long research pursuit involving inheritance patterns in honeybees and plants, ultimately settling on pea plants as his primary model system (a system with convenient characteristics that is used to study a specific biological phenomenon to gain understanding to be applied to other systems). In 1865, Mendel presented the results of his experiments with nearly 30,000 pea plants to the local natural history society. He demonstrated that traits are transmitted faithfully from parents to offspring in specific patterns. In 1866, he published his work, Experiments in Plant Hybridization,1 in the proceedings of the Natural History Society of Brünn.

Mendel’s work went virtually unnoticed by the scientific community, which incorrectly believed that the process of inheritance involved a blending of parental traits that produced an intermediate physical appearance in offspring. This hypothetical process appeared to be correct because of what we know now as continuous variation. Continuous variation is the range of small differences we see among individuals in a characteristic like human height. It does appear that offspring are a “blend” of their parents’ traits when we look at characteristics that exhibit continuous variation. Mendel worked instead with traits that show discontinuous variation. Discontinuous variation is the variation seen among individuals when each individual shows one of two—or a very few—easily distinguishable traits, such as violet or white flowers. Mendel’s choice of these kinds of traits allowed him to see experimentally that the traits were not blended in the offspring as would have been expected at the time, but that they were inherited as distinct traits. In 1868, Mendel became abbot of the monastery and exchanged his scientific pursuits for his pastoral duties. He was not recognized for his extraordinary scientific contributions during his lifetime; in fact, it was not until 1900 that his work was rediscovered, reproduced, and revitalized by scientists on the brink of discovering the chromosomal basis of heredity.

Mendel’s Crosses

Mendel’s seminal work was accomplished using the garden pea, Pisum sativum, to study inheritance. This species naturally self-fertilizes, meaning that pollen encounters ova within the same flower. The flower petals remain sealed tightly until pollination is completed to prevent the pollination of other plants. The result is highly inbred, or “true-breeding,” pea plants. These are plants that always produce offspring that look like the parent. By experimenting with true-breeding pea plants, Mendel avoided the appearance of unexpected traits in offspring that might occur if the plants were not true breeding. The garden pea also grows to maturity within one season, meaning that several generations could be evaluated over a relatively short time. Finally, large quantities of garden peas could be cultivated simultaneously, allowing Mendel to conclude that his results did not come about simply by chance.

Mendel performed hybridizations, which involve mating two true-breeding individuals that have different traits. In the pea, which is naturally self-pollinating, this is done by manually transferring pollen from the anther of a mature pea plant of one variety to the stigma of a separate mature pea plant of the second variety.

Plants used in first-generation crosses were called P, or parental generation, plants (Figure 8.3). Mendel collected the seeds produced by the P plants that resulted from each cross and grew them the following season. These offspring were called the F1, or the first filial (filial = daughter or son), generation. Once Mendel examined the characteristics in the F1 generation of plants, he allowed them to self-fertilize naturally. He then collected and grew the seeds from the F1 plants to produce the F2, or second filial, generation. Mendel’s experiments extended beyond the F2 generation to the F3 generation, F4 generation, and so on, but it was the ratio of characteristics in the P, F1, and F2 generations that were the most intriguing and became the basis of Mendel’s postulates.

The diagram shows a cross between pea plants that are true-breeding for purple flower color and plants that are true-breeding for white flower color. This cross-fertilization of the P generation resulted in an F_{1} generation with all violet flowers. Self-fertilization of the F_{1} generation resulted in an F_{2} generation that consisted of 705 plants with violet flowers, and 224 plants with white flowers.

Figure 8.3 Mendel’s process for performing crosses included examining flower color.

Garden Pea Characteristics Revealed the Basics of Heredity

In his 1865 publication, Mendel reported the results of his crosses involving seven different characteristics, each with two contrasting traits. A trait is defined as a variation in the physical appearance of a heritable characteristic. The characteristics included plant height, seed texture, seed color, flower color, pea-pod size, pea-pod color, and flower position. For the characteristic of flower color, for example, the two contrasting traits were white versus violet. To fully examine each characteristic, Mendel generated large numbers of F1 and F2 plants and reported results from thousands of F2 plants.

What results did Mendel find in his crosses for flower color? First, Mendel confirmed that he was using plants that bred true for white or violet flower color. Irrespective of the number of generations that Mendel examined, all self-crossed offspring of parents with white flowers had white flowers, and all self-crossed offspring of parents with violet flowers had violet flowers. In addition, Mendel confirmed that, other than flower color, the pea plants were physically identical. This was an important check to make sure that the two varieties of pea plants only differed with respect to one trait, flower color.

Once these validations were complete, Mendel applied the pollen from a plant with violet flowers to the stigma of a plant with white flowers. After gathering and sowing the seeds that resulted from this cross, Mendel found that 100 percent of the F1 hybrid generation had violet flowers. Conventional wisdom at that time would have predicted the hybrid flowers to be pale violet or for hybrid plants to have equal numbers of white and violet flowers. In other words, the contrasting parental traits were expected to blend in the offspring. Instead, Mendel’s results demonstrated that the white flower trait had completely disappeared in the F1 generation.

Importantly, Mendel did not stop his experimentation there. He allowed the F1 plants to self-fertilize and found that 705 plants in the F2 generation had violet flowers and 224 had white flowers. This was a ratio of 3.15 violet flowers to one white flower, or approximately 3:1. When Mendel transferred pollen from a plant with violet flowers to the stigma of a plant with white flowers and vice versa, he obtained approximately the same ratio irrespective of which parent—male or female—contributed which trait. This is called a reciprocal cross—a paired cross in which the respective traits of the male and female in one cross become the respective traits of the female and male in the other cross. For the other six characteristics that Mendel examined, the F1 and F2 generations behaved in the same way that they behaved for flower color. One of the two traits would disappear completely from the F1 generation, only to reappear in the F2 generation at a ratio of roughly 3:1 (Figure 8.4).

Seven characteristics of Mendel’s pea plants are illustrated. The flowers can be purple or white. The peas can be yellow or green, or smooth or wrinkled. The pea pods can be inflated or constricted, or yellow or green. The flower position can be axial or terminal. The stem length can be tall or dwarf.

Figure 8.4 Mendel identified seven pea plant characteristics.

Upon compiling his results for many thousands of plants, Mendel concluded that the characteristics could be divided into expressed and latent traits. He called these dominant and recessive traits, respectively. Dominant traits are those that are inherited unchanged in a hybridization. Recessive traits become latent, or disappear in the offspring of a hybridization. The recessive trait does, however, reappear in the progeny of the hybrid offspring. An example of a dominant trait is the violet-colored flower trait. For this same characteristic (flower color), white-colored flowers are a recessive trait. The fact that the recessive trait reappeared in the F2 generation meant that the traits remained separate (and were not blended) in the plants of the F1 generation. Mendel proposed that this was because the plants possessed two copies of the trait for the flower-color characteristic, and that each parent transmitted one of their two copies to their offspring, where they came together. Moreover, the physical observation of a dominant trait could mean that the genetic composition of the organism included two dominant versions of the characteristic, or that it included one dominant and one recessive version. Conversely, the observation of a recessive trait meant that the organism lacked any dominant versions of this characteristic.

Concept in Action

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For an excellent review of Mendel’s experiments and to perform your own crosses and identify patterns of inheritance, visit the Mendel’s Peas web lab.

Section Summary

Working with garden pea plants, Mendel found that crosses between parents that differed for one trait produced F1 offspring that all expressed one parent’s traits. The traits that were visible in the F1 generation are referred to as dominant, and traits that disappear in the F1 generation are described as recessive. When the F1 plants in Mendel’s experiment were self-crossed, the F2 offspring exhibited the dominant trait or the recessive trait in a 3:1 ratio, confirming that the recessive trait had been transmitted faithfully from the original P parent. Reciprocal crosses generated identical F1 and F2 offspring ratios. By examining sample sizes, Mendel showed that traits were inherited as independent events.


Multiple Choice

Imagine that you are performing a cross involving seed color in garden pea plants. What traits would you expect to observe in the F1 offspring if you cross true-breeding parents with green seeds and yellow seeds? Yellow seed color is dominant over green.

A) only yellow-green seeds

B) only yellow seeds

C) 1:1 yellow seeds:green seeds

D) 1:3 green seeds:yellow seeds


Imagine that you are performing a cross involving seed texture in garden pea plants. You cross true-breeding round and wrinkled parents to obtain F1 offspring. Which of the following experimental results in terms of numbers of plants are closest to what you expect in the F2 progeny?

A) 810 round seeds

B) 810 wrinkled seeds

C) 405:395 round seeds:wrinkled seeds

D) 610:190 round seeds:wrinkled seeds


Free Response

Describe one of the reasons that made the garden pea an excellent choice of model system for studying inheritance.

The garden pea has flowers that close tightly during self-pollination. This helps to prevent accidental or unintentional fertilizations that could have diminished the accuracy of Mendel’s data.


continuous variation: a variation in a characteristic in which individuals show a range of traits with small differences between them

discontinuous variation: a variation in a characteristic in which individuals show two, or a few, traits with large differences between them

dominant: describes a trait that masks the expression of another trait when both versions of the gene are present in an individual

F1: the first filial generation in a cross; the offspring of the parental generation

F2:the second filial generation produced when F1 individuals are self-crossed or fertilized with each other

hybridization: the process of mating two individuals that differ, with the goal of achieving a certain characteristic in their offspring

model system: a species or biological system used to study a specific biological phenomenon to gain understanding that will be applied to other species

P: the parental generation in a cross

recessive: describes a trait whose expression is masked by another trait when the alleles for both traits are present in an individual

reciprocal cross: a paired cross in which the respective traits of the male and female in one cross become the respective traits of the female and male in the other cross

trait: a variation in an inherited characteristic



1 Johann Gregor Mendel, “Versuche über Pflanzenhybriden.” Verhandlungen des naturforschenden Vereines in Brünn, Bd. IV für das Jahr, 1865 Abhandlungen (1866):3–47. [for English translation, see]


8.2 Laws of Inheritance

Learning Objectives

By the end of this section, you will be able to:

  • Explain the relationship between genotypes and phenotypes in dominant and recessive gene systems
  • Use a Punnett square to calculate the expected proportions of genotypes and phenotypes in a monohybrid cross
  • Explain Mendel’s law of segregation and independent assortment in terms of genetics and the events of meiosis
  • Explain the purpose and methods of a test cross

The seven characteristics that Mendel evaluated in his pea plants were each expressed as one of two versions, or traits. Mendel deduced from his results that each individual had two discrete copies of the characteristic that are passed individually to offspring. We now call those two copies genes, which are carried on chromosomes. The reason we have two copies of each gene is that we inherit one from each parent. In fact, it is the chromosomes we inherit and the two copies of each gene are located on paired chromosomes. Recall that in meiosis these chromosomes are separated out into haploid gametes. This separation, or segregation, of the homologous chromosomes means also that only one of the copies of the gene gets moved into a gamete. The offspring are formed when that gamete unites with one from another parent and the two copies of each gene (and chromosome) are restored.

For cases in which a single gene controls a single characteristic, a diploid organism has two genetic copies that may or may not encode the same version of that characteristic. For example, one individual may carry a gene that determines white flower color and a gene that determines violet flower color. Gene variants that arise by mutation and exist at the same relative locations on homologous chromosomes are called alleles. Mendel examined the inheritance of genes with just two allele forms, but it is common to encounter more than two alleles for any given gene in a natural population.

Phenotypes and Genotypes

Two alleles for a given gene in a diploid organism are expressed and interact to produce physical characteristics. The observable traits expressed by an organism are referred to as its phenotype. An organism’s underlying genetic makeup, consisting of both the physically visible and the non-expressed alleles, is called its genotype. Mendel’s hybridization experiments demonstrate the difference between phenotype and genotype. For example, the phenotypes that Mendel observed in his crosses between pea plants with differing traits are connected to the diploid genotypes of the plants in the P, F1, and F2 generations. We will use a second trait that Mendel investigated, seed color, as an example. Seed color is governed by a single gene with two alleles. The yellow-seed allele is dominant and the green-seed allele is recessive. When true-breeding plants were cross-fertilized, in which one parent had yellow seeds and one had green seeds, all of the F1 hybrid offspring had yellow seeds. That is, the hybrid offspring were phenotypically identical to the true-breeding parent with yellow seeds. However, we know that the allele donated by the parent with green seeds was not simply lost because it reappeared in some of the F2 offspring (Figure 8.5). Therefore, the F1 plants must have been genotypically different from the parent with yellow seeds.

The P plants that Mendel used in his experiments were each homozygous for the trait he was studying. Diploid organisms that are homozygous for a gene have two identical alleles, one on each of their homologous chromosomes. The genotype is often written as YY or yy, for which each letter represents one of the two alleles in the genotype. The dominant allele is capitalized and the recessive allele is lower case. The letter used for the gene (seed color in this case) is usually related to the dominant trait (yellow allele, in this case, or “Y”). Mendel’s parental pea plants always bred true because both produced gametes carried the same allele. When P plants with contrasting traits were cross-fertilized, all of the offspring were heterozygous for the contrasting trait, meaning their genotype had different alleles for the gene being examined. For example, the F1 yellow plants that received a Y allele from their yellow parent and a y allele from their green parent had the genotype Yy.

By the end of this section, you will be able to: Explain the relationship between genotypes and phenotypes in dominant and recessive gene systems Use a Punnett square to calculate the expected proportions of genotypes and phenotypes in a monohybrid cross Explain Mendel’s law of segregation and independent assortment in terms of genetics and the events of meiosis Explain the purpose and methods of a test cross

Figure 8.5 Phenotypes are physical expressions of traits that are transmitted by alleles. Capital letters represent dominant alleles and lowercase letters represent recessive alleles. The phenotypic ratios are the ratios of visible characteristics. The genotypic ratios are the ratios of gene combinations in the offspring, and these are not always distinguishable in the phenotypes.

Law of Dominance

Our discussion of homozygous and heterozygous organisms brings us to why the F1 heterozygous offspring were identical to one of the parents, rather than expressing both alleles. In all seven pea-plant characteristics, one of the two contrasting alleles was dominant, and the other was recessive. Mendel called the dominant allele the expressed unit factor; the recessive allele was referred to as the latent unit factor. We now know that these so-called unit factors are actually genes on homologous chromosomes. For a gene that is expressed in a dominant and recessive pattern, homozygous dominant and heterozygous organisms will look identical (that is, they will have different genotypes but the same phenotype), and the recessive allele will only be observed in homozygous recessive individuals.

Correspondence between Genotype and Phenotype for a Dominant-Recessive Characteristic.
Homozygous Heterozygous Homozygous
Genotype YY Yy yy
Phenotype yellow yellow green

Mendel’s law of dominance states that in a heterozygote, one trait will conceal the presence of another trait for the same characteristic. For example, when crossing true-breeding violet-flowered plants with true-breeding white-flowered plants, all of the offspring were violet-flowered, even though they all had one allele for violet and one allele for white. Rather than both alleles contributing to a phenotype, the dominant allele will be expressed exclusively. The recessive allele will remain latent, but will be transmitted to offspring in the same manner as that by which the dominant allele is transmitted. The recessive trait will only be expressed by offspring that have two copies of this allele (Figure 8.6), and these offspring will breed true when self-crossed.

Photo shows a mother with an albino child.

Figure 8.6 The allele for albinism, expressed here in humans, is recessive. Both of this child’s parents carried the recessive allele.

Monohybrid Cross and the Punnett Square

When fertilization occurs between two true-breeding parents that differ by only the characteristic being studied, the process is called a monohybrid cross, and the resulting offspring are called monohybrids. Mendel performed seven types of monohybrid crosses, each involving contrasting traits for different characteristics. Out of these crosses, all of the F1 offspring had the phenotype of one parent, and the F2 offspring had a 3:1 phenotypic ratio. On the basis of these results, Mendel postulated that each parent in the monohybrid cross contributed one of two paired unit factors to each offspring, and every possible combination of unit factors was equally likely.

The results of Mendel’s research can be explained in terms of probabilities, which are mathematical measures of likelihood. The probability of an event is calculated by the number of times the event occurs divided by the total number of opportunities for the event to occur. A probability of one (100 percent) for some event indicates that it is guaranteed to occur, whereas a probability of zero (0 percent) indicates that it is guaranteed to not occur, and a probability of 0.5 (50 percent) means it has an equal chance of occurring or not occurring.

To demonstrate this with a monohybrid cross, consider the case of true-breeding pea plants with yellow versus green seeds. The dominant seed color is yellow; therefore, the parental genotypes were YY for the plants with yellow seeds and yy for the plants with green seeds. A Punnett square, devised by the British geneticist Reginald Punnett, is useful for determining probabilities because it is drawn to predict all possible outcomes of all possible random fertilization events and their expected frequencies. Figure 8.9 shows a Punnett square for a cross between a plant with yellow peas and one with green peas. To prepare a Punnett square, all possible combinations of the parental alleles (the genotypes of the gametes) are listed along the top (for one parent) and side (for the other parent) of a grid. The combinations of egg and sperm gametes are then made in the boxes in the table on the basis of which alleles are combining. Each box then represents the diploid genotype of a zygote, or fertilized egg. Because each possibility is equally likely, genotypic ratios can be determined from a Punnett square. If the pattern of inheritance (dominant and recessive) is known, the phenotypic ratios can be inferred as well. For a monohybrid cross of two true-breeding parents, each parent contributes one type of allele. In this case, only one genotype is possible in the F1 offspring. All offspring are Yy and have yellow seeds.

When the F1 offspring are crossed with each other, each has an equal probability of contributing either a Y or a y to the F2 offspring. The result is a 1 in 4 (25 percent) probability of both parents contributing a Y, resulting in an offspring with a yellow phenotype; a 25 percent probability of parent A contributing a Y and parent B a y, resulting in offspring with a yellow phenotype; a 25 percent probability of parent A contributing a y and parent B a Y, also resulting in a yellow phenotype; and a (25 percent) probability of both parents contributing a y, resulting in a green phenotype. When counting all four possible outcomes, there is a 3 in 4 probability of offspring having the yellow phenotype and a 1 in 4 probability of offspring having the green phenotype. This explains why the results of Mendel’s F2 generation occurred in a 3:1 phenotypic ratio. Using large numbers of crosses, Mendel was able to calculate probabilities, found that they fit the model of inheritance, and use these to predict the outcomes of other crosses.

Law of Segregation

Observing that true-breeding pea plants with contrasting traits gave rise to F1 generations that all expressed the dominant trait and F2 generations that expressed the dominant and recessive traits in a 3:1 ratio, Mendel proposed the law of segregation. This law states that paired unit factors (genes) must segregate equally into gametes such that offspring have an equal likelihood of inheriting either factor. For the F2 generation of a monohybrid cross, the following three possible combinations of genotypes result: homozygous dominant, heterozygous, or homozygous recessive. Because heterozygotes could arise from two different pathways (receiving one dominant and one recessive allele from either parent), and because heterozygotes and homozygous dominant individuals are phenotypically identical, the law supports Mendel’s observed 3:1 phenotypic ratio. The equal segregation of alleles is the reason we can apply the Punnett square to accurately predict the offspring of parents with known genotypes. The physical basis of Mendel’s law of segregation is the first division of meiosis in which the homologous chromosomes with their different versions of each gene are segregated into daughter nuclei. This process was not understood by the scientific community during Mendel’s lifetime (Figure 8.7).

Homologous pairs of chromosomes line up at the metaphase plate during metaphase I of meiosis. The homologous chromosomes with their different versions of each gene are segregated into daughter nuclei.

Figure 8.7 The first division in meiosis is shown.

Test Cross

Beyond predicting the offspring of a cross between known homozygous or heterozygous parents, Mendel also developed a way to determine whether an organism that expressed a dominant trait was a heterozygote or a homozygote. Called the test cross, this technique is still used by plant and animal breeders. In a test cross, the dominant-expressing organism is crossed with an organism that is homozygous recessive for the same characteristic. If the dominant-expressing organism is a homozygote, then all F1 offspring will be heterozygotes expressing the dominant trait (Figure 8.8). Alternatively, if the dominant-expressing organism is a heterozygote, the F1 offspring will exhibit a 1:1 ratio of heterozygotes and recessive homozygotes (Figure 8.9). The test cross further validates Mendel’s postulate that pairs of unit factors segregate equally.

In a test cross, a parent with a dominant phenotype but unknown genotype is crossed with a recessive parent. If the parent with the unknown phenotype is homozygous dominant, all the resulting offspring will have at least one dominant allele. If the parent with the unknown phenotype is heterozygous, 50 percent of the offspring will inherit a recessive allele from both parents and will have the recessive phenotype.

Figure 8.8 A test cross can be performed to determine whether an organism expressing a dominant trait is a homozygote or a heterozygote.

A test cross can be performed to determine whether an organism expressing a dominant trait is a homozygote or a heterozygote.

Figure 8.9 This Punnett square shows the cross between plants with yellow seeds and green seeds. The cross between the true-breeding P plants produces F1 heterozygotes that can be self-fertilized. The self-cross of the F1 generation can be analyzed with a Punnett square to predict the genotypes of the F2 generation. Given an inheritance pattern of dominant–recessive, the genotypic and phenotypic ratios can then be determined.

In pea plants, round peas (R) are dominant to wrinkled peas (r). You do a test cross between a pea plant with wrinkled peas (genotype rr) and a plant of unknown genotype that has round peas. You end up with three plants, all which have round peas. From this data, can you tell if the parent plant is homozygous dominant or heterozygous?

You cannot be sure if the plant is homozygous or heterozygous as the data set is too small: by random chance, all three plants might have acquired only the dominant gene even if the recessive one is present.

Law of Independent Assortment

Mendel’s law of independent assortment states that genes do not influence each other with regard to the sorting of alleles into gametes, and every possible combination of alleles for every gene is equally likely to occur. Independent assortment of genes can be illustrated by the dihybrid cross, a cross between two true-breeding parents that express different traits for two characteristics. Consider the characteristics of seed color and seed texture for two pea plants, one that has wrinkled, green seeds (rryy) and another that has round, yellow seeds (RRYY). Because each parent is homozygous, the law of segregation indicates that the gametes for the wrinkled–green plant all are ry, and the gametes for the round–yellow plant are all RY. Therefore, the F1 generation of offspring all are RrYy (Figure 8.10).

This illustration shows a dihybrid cross between pea plants. In the P generation, a plant that has the homozygous dominant phenotype of yellow, round peas is crossed with a plant with the homozygous recessive phenotype of green, wrinkled peas. The resulting F_{1} offspring have a heterozygous genotype and yellow, round peas. Self-pollination of the F_{1} generation results in F_{2} offspring with a phenotypic ratio of 9:3:3:1 for round–yellow, round–green, wrinkled–yellow, and wrinkled–green peas, respectively.

Figure 8.10 A dihybrid cross in pea plants involves the genes for seed color and texture. The P cross produces F1 offspring that are all heterozygous for both characteristics. The resulting 9:3:3:1 F2 phenotypic ratio is obtained using a Punnett square.

In pea plants, purple flowers (P) are dominant to white (p), and yellow peas (Y) are dominant to green (y). What are the possible genotypes and phenotypes for a cross between PpYY and ppYy pea plants? How many squares would you need to complete a Punnett square analysis of this cross?

The possible genotypes are PpYY, PpYy, ppYY, and ppYy. The former two genotypes would result in plants with purple flowers and yellow peas, while the latter two genotypes would result in plants with white flowers with yellow peas, for a 1:1 ratio of each phenotype. You only need a 2 × 2 Punnett square (four squares total) to do this analysis because two of the alleles are homozygous.

The gametes produced by the F1 individuals must have one allele from each of the two genes. For example, a gamete could get an R allele for the seed shape gene and either a Y or a y allele for the seed color gene. It cannot get both an R and an r allele; each gamete can have only one allele per gene. The law of independent assortment states that a gamete into which an r allele is sorted would be equally likely to contain either a Y or a y allele. Thus, there are four equally likely gametes that can be formed when the RrYy heterozygote is self-crossed, as follows: RY, rY, Ry, and ry. Arranging these gametes along the top and left of a 4 × 4 Punnett square gives us 16 equally likely genotypic combinations. From these genotypes, we find a phenotypic ratio of 9 round–yellow:3 round–green:3 wrinkled–yellow:1 wrinkled–green. These are the offspring ratios we would expect, assuming we performed the crosses with a large enough sample size.

The physical basis for the law of independent assortment also lies in meiosis I, in which the different homologous pairs line up in random orientations. Each gamete can contain any combination of paternal and maternal chromosomes (and therefore the genes on them) because the orientation of tetrads on the metaphase plane is random (Figure 8.11).

Homologous pairs of chromosomes line up at the metaphase plate during metaphase I of meiosis. The homologous chromosomes, with their different versions of each gene, are randomly segregated into daughter nuclei, resulting in a variety of possible genetic arrangements.

Figure 8.11 The random segregation into daughter nuclei that happens during the first division in meiosis can lead to a variety of possible genetic arrangements.


Probability Basics

Probabilities are mathematical measures of likelihood. The empirical probability of an event is calculated by dividing the number of times the event occurs by the total number of opportunities for the event to occur. It is also possible to calculate theoretical probabilities by dividing the number of times that an event is expected to occur by the number of times that it could occur. Empirical probabilities come from observations, like those of Mendel. Theoretical probabilities come from knowing how the events are produced and assuming that the probabilities of individual outcomes are equal. A probability of one for some event indicates that it is guaranteed to occur, whereas a probability of zero indicates that it is guaranteed not to occur. An example of a genetic event is a round seed produced by a pea plant. In his experiment, Mendel demonstrated that the probability of the event “round seed” occurring was one in the F1 offspring of true-breeding parents, one of which has round seeds and one of which has wrinkled seeds. When the F1 plants were subsequently self-crossed, the probability of any given F2 offspring having round seeds was now three out of four. In other words, in a large population of F2 offspring chosen at random, 75 percent were expected to have round seeds, whereas 25 percent were expected to have wrinkled seeds. Using large numbers of crosses, Mendel was able to calculate probabilities and use these to predict the outcomes of other crosses.

The Product Rule and Sum Rule

Mendel demonstrated that the pea-plant characteristics he studied were transmitted as discrete units from parent to offspring. As will be discussed, Mendel also determined that different characteristics, like seed color and seed texture, were transmitted independently of one another and could be considered in separate probability analyses. For instance, performing a cross between a plant with green, wrinkled seeds and a plant with yellow, round seeds still produced offspring that had a 3:1 ratio of green:yellow seeds (ignoring seed texture) and a 3:1 ratio of round:wrinkled seeds (ignoring seed color). The characteristics of color and texture did not influence each other.

The product rule of probability can be applied to this phenomenon of the independent transmission of characteristics. The product rule states that the probability of two independent events occurring together can be calculated by multiplying the individual probabilities of each event occurring alone. To demonstrate the product rule, imagine that you are rolling a six-sided die (D) and flipping a penny (P) at the same time. The die may roll any number from 1–6 (D#), whereas the penny may turn up heads (PH) or tails (PT). The outcome of rolling the die has no effect on the outcome of flipping the penny and vice versa. There are 12 possible outcomes of this action, and each event is expected to occur with equal probability.

Twelve Equally Likely Outcomes of Rolling a Die and Flipping a Penny
Rolling Die Flipping Penny

Of the 12 possible outcomes, the die has a 2/12 (or 1/6) probability of rolling a two, and the penny has a 6/12 (or 1/2) probability of coming up heads. By the product rule, the probability that you will obtain the combined outcome 2 and heads is: (D2) x (PH) = (1/6) x (1/2) or 1/12. Notice the word “and” in the description of the probability. The “and” is a signal to apply the product rule. For example, consider how the product rule is applied to the dihybrid cross: the probability of having both dominant traits in the F2 progeny is the product of the probabilities of having the dominant trait for each characteristic, as shown here:


3/4 × 3/4 = 9/16

On the other hand, the sum rule of probability is applied when considering two mutually exclusive outcomes that can come about by more than one pathway. The sum rule states that the probability of the occurrence of one event or the other event, of two mutually exclusive events, is the sum of their individual probabilities. Notice the word “or” in the description of the probability. The “or” indicates that you should apply the sum rule. In this case, let’s imagine you are flipping a penny (P) and a quarter (Q). What is the probability of one coin coming up heads and one coin coming up tails? This outcome can be achieved by two cases: the penny may be heads (PH) and the quarter may be tails (QT), or the quarter may be heads (QH) and the penny may be tails (PT). Either case fulfills the outcome. By the sum rule, we calculate the probability of obtaining one head and one tail as [(PH) × (QT)] + [(QH) × (PT)] = [(1/2) × (1/2)] + [(1/2) × (1/2)] = 1/2. You should also notice that we used the product rule to calculate the probability of PH and QT, and also the probability of PT and QH, before we summed them. Again, the sum rule can be applied to show the probability of having just one dominant trait in the F2 generation of a dihybrid cross:


3/16 + 3/4 = 15/16
The Product Rule and Sum Rule
Product Rule Sum Rule
For independent events A and B, the probability (P) of them both occurring (A and B) is (PA × PB) For mutually exclusive events A and B, the probability (P) that at least one occurs (A or B) is (PA + PB)

To use probability laws in practice, it is necessary to work with large sample sizes because small sample sizes are prone to deviations caused by chance. The large quantities of pea plants that Mendel examined allowed him calculate the probabilities of the traits appearing in his F2 generation. As you will learn, this discovery meant that when parental traits were known, the offspring’s traits could be predicted accurately even before fertilization.

This is a pedigree of a family that carries the recessive disorder alkaptonuria. In the second generation, an unaffected mother and an affected father have three children. One child has the disorder, so the genotype of the mother must be Aa and the genotype of the father is aa. One unaffected child goes on to have two children, one affected and one unaffected. Because her husband was not affected, she and her husband must both be heterozygous. The genotype of their unaffected child is unknown, and is designated A?. In the third generation, the other unaffected child had no offspring, and his genotype is therefore also unknown. The affected third-generation child goes on to have one child with the disorder. Her husband is unaffected and is labeled “3.” The first generation father is affected and is labeled “1.” The first generation mother is unaffected and is labeled “2.” The Art Connection question asks the genotype of the three numbered individuals.

Figure 8.12

Alkaptonuria is a recessive genetic disorder in which two amino acids, phenylalanine and tyrosine, are not properly metabolized. Affected individuals may have darkened skin and brown urine, and may suffer joint damage and other complications. In this pedigree, individuals with the disorder are indicated in blue and have the genotype aa. Unaffected individuals are indicated in yellow and have the genotype AA or Aa. Note that it is often possible to determine a person’s genotype from the genotype of their offspring. For example, if neither parent has the disorder but their child does, they must be heterozygous. Two individuals on the pedigree have an unaffected phenotype but unknown genotype. Because they do not have the disorder, they must have at least one normal allele, so their genotype gets the “A?” designation.

What are the genotypes of the individuals labeled 1, 2 and 3?

Section Summary

When true-breeding, or homozygous, individuals that differ for a certain trait are crossed, all of the offspring will be heterozygous for that trait. If the traits are inherited as dominant and recessive, the F1 offspring will all exhibit the same phenotype as the parent homozygous for the dominant trait. If these heterozygous offspring are self-crossed, the resulting F2 offspring will be equally likely to inherit gametes carrying the dominant or recessive trait, giving rise to offspring of which one quarter are homozygous dominant, half are heterozygous, and one quarter are homozygous recessive. Because homozygous dominant and heterozygous individuals are phenotypically identical, the observed traits in the F2 offspring will exhibit a ratio of three dominant to one recessive.

Mendel postulated that genes (characteristics) are inherited as pairs of alleles (traits) that behave in a dominant and recessive pattern. Alleles segregate into gametes such that each gamete is equally likely to receive either one of the two alleles present in a diploid individual. In addition, genes are assorted into gametes independently of one another. That is, in general, alleles are not more likely to segregate into a gamete with a particular allele of another gene.


 In pea plants, round peas (R) are dominant to wrinkled peas (r). You do a test cross between a pea plant with wrinkled peas (genotype rr) and a plant of unknown genotype that has round peas. You end up with three plants, all which have round peas. From this data, can you tell if the parent plant is homozygous dominant or heterozygous?

 Answer: You cannot be sure if the plant is homozygous or heterozygous as the data set is too small: by random chance, all three plants might have acquired only the dominant gene even if the recessive one is present.

In pea plants, purple flowers (P) are dominant to white (p), and yellow peas (Y) are dominant to green (y). What are the possible genotypes and phenotypes for a cross between PpYY and ppYy pea plants? How many squares would you need to complete a Punnett square analysis of this cross?

Answer: The possible genotypes are PpYY, PpYy, ppYY, and ppYy. The former two genotypes would result in plants with purple flowers and yellow peas, while the latter two genotypes would result in plants with white flowers with yellow peas, for a 1:1 ratio of each phenotype. You only need a 2 × 2 Punnett square (four squares total) to do this analysis because two of the alleles are homozygous.

Multiple Choice

The observable traits expressed by an organism are described as its ________.

A) phenotype

B) genotype

C) alleles

D) zygote


A recessive trait will be observed in individuals that are ________ for that trait.

A) heterozygous

B) homozygous or heterozygous

C) homozygous

D) diploid


What are the types of gametes that can be produced by an individual with the genotype AaBb?

A) Aa, Bb

B) AA, aa, BB, bb

C) AB, Ab, aB, ab

D) AB, ab


What is the reason for doing a test cross?

A) to identify heterozygous individuals with the dominant phenotype

B) to determine which allele is dominant and which is recessive

C) to identify homozygous recessive individuals in the F2

D) to determine if two genes assort independently


Free Response

Use a Punnett square to predict the offspring in a cross between a dwarf pea plant (homozygous recessive) and a tall pea plant (heterozygous). What is the phenotypic ratio of the offspring?

The Punnett square would be 2 × 2 and will have T and T along the top and T and t along the left side. Clockwise from the top left, the genotypes listed within the boxes will be Tt, Tt, tt, and tt. The phenotypic ratio will be 1 tall:1 dwarf.

Use a Punnett square to predict the offspring in a cross between a tall pea plant (heterozygous) and a tall pea plant (heterozygous). What is the genotypic ratio of the offspring?

The Punnett square will be 2 × 2 and will have T and t along the top and T and t along the left side. Clockwise from the top left, the genotypes listed within the boxes will be TT, Tt, Tt, and tt. The genotypic ratio will be 1TT:2Tt:1tt.


allele: one of two or more variants of a gene that determines a particular trait for a characteristic

dihybrid: the result of a cross between two true-breeding parents that express different traits for two characteristics

genotype: the underlying genetic makeup, consisting of both physically visible and non-expressed alleles, of an organism

heterozygous: having two different alleles for a given gene on the homologous chromosomes

homozygous: having two identical alleles for a given gene on the homologous chromosomes

law of dominance: in a heterozygote, one trait will conceal the presence of another trait for the same characteristic

law of independent assortment: genes do not influence each other with regard to sorting of alleles into gametes; every possible combination of alleles is equally likely to occur

law of segregation: paired unit factors (i.e., genes) segregate equally into gametes such that offspring have an equal likelihood of inheriting any combination of factors

monohybrid: the result of a cross between two true-breeding parents that express different traits for only one characteristic

phenotype: the observable traits expressed by an organism

Punnett square: a visual representation of a cross between two individuals in which the gametes of each individual are denoted along the top and side of a grid, respectively, and the possible zygotic genotypes are recombined at each box in the grid

test cross: a cross between a dominant expressing individual with an unknown genotype and a homozygous recessive individual; the offspring phenotypes indicate whether the unknown parent is heterozygous or homozygous for the dominant trait



8.3 Extensions of the Laws of Inheritance

Learning Objectives

By the end of this section, you will be able to:

  • Identify non-Mendelian inheritance patterns such as incomplete dominance, codominance, multiple alleles, and sex linkage from the results of crosses
  • Explain the effect of linkage and recombination on gamete genotypes
  • Explain the phenotypic outcomes of epistatic effects among genes
  • Explain polygenic inheritance

Mendel studied traits with only one mode of inheritance in pea plants. The inheritance of the traits he studied all followed the relatively simple pattern of dominant and recessive alleles for a single characteristic. There are several important modes of inheritance, discovered after Mendel’s work, that do not follow the dominant and recessive, single-gene model.

Alternatives to Dominance and Recessiveness

Mendel’s experiments with pea plants suggested that: 1) two types of “units” or alleles exist for every gene; 2) alleles maintain their integrity in each generation (no blending); and 3) in the presence of the dominant allele, the recessive allele is hidden, with no contribution to the phenotype. Therefore, recessive alleles can be “carried” and not expressed by individuals. Such heterozygous individuals are sometimes referred to as “carriers.” Since then, genetic studies in other organisms have shown that much more complexity exists, but that the fundamental principles of Mendelian genetics still hold true. In the sections to follow, we consider some of the extensions of Mendelism.

Incomplete Dominance

Mendel’s results, demonstrating that traits are inherited as dominant and recessive pairs, contradicted the view at that time that offspring exhibited a blend of their parents’ traits. However, the heterozygote phenotype occasionally does appear to be intermediate between the two parents. For example, in the snapdragon, Antirrhinum majus (Figure 8.13), a cross between a homozygous parent with white flowers (CWCW) and a homozygous parent with red flowers (CRCR) will produce offspring with pink flowers (CRCW). (Note that different genotypic abbreviations are used for Mendelian extensions to distinguish these patterns from simple dominance and recessiveness.) This pattern of inheritance is described as incomplete dominance, meaning that one of the alleles appears in the phenotype in the heterozygote, but not to the exclusion of the other, which can also be seen. The allele for red flowers is incompletely dominant over the allele for white flowers. However, the results of a heterozygote self-cross can still be predicted, just as with Mendelian dominant and recessive crosses. In this case, the genotypic ratio would be 1 CRCR:2 CRCW:1 CWCW, and the phenotypic ratio would be 1:2:1 for red:pink:white. The basis for the intermediate color in the heterozygote is simply that the pigment produced by the red allele (anthocyanin) is diluted in the heterozygote and therefore appears pink because of the white background of the flower petals.

Photo is of a snapdragon with a pink flower.

Figure 8.13 These pink flowers of a heterozygote snapdragon result from incomplete dominance. (credit: “storebukkebruse”/Flickr)


A variation on incomplete dominance is codominance, in which both alleles for the same characteristic are simultaneously expressed in the heterozygote. An example of codominance occurs in the ABO blood groups of humans. The A and B alleles are expressed in the form of A or B molecules present on the surface of red blood cells. Homozygotes (IAIA and IBIB) express either the A or the B phenotype, and heterozygotes (IAIB) express both phenotypes equally. The IAIB individual has blood type AB. In a self-cross between heterozygotes expressing a codominant trait, the three possible offspring genotypes are phenotypically distinct. However, the 1:2:1 genotypic ratio characteristic of a Mendelian monohybrid cross still applies (Figure 8.14).

A Punnett square showing both parents with AB blood types. The offspring will have AA, AB, and BB blood types in a ratio of 1 to 2 to 1.

Figure 8.14 This Punnett square shows an AB/AB blood type cross

Multiple Alleles

Mendel implied that only two alleles, one dominant and one recessive, could exist for a given gene. We now know that this is an oversimplification. Although individual humans (and all diploid organisms) can only have two alleles for a given gene, multiple alleles may exist at the population level, such that many combinations of two alleles are observed. Note that when many alleles exist for the same gene, the convention is to denote the most common phenotype or genotype in the natural population as the wild type (often abbreviated “+”). All other phenotypes or genotypes are considered variants (mutants) of this typical form, meaning they deviate from the wild type. The variant may be recessive or dominant to the wild-type allele.

An example of multiple alleles is the ABO blood-type system in humans. In this case, there are three alleles circulating in the population. The IA allele codes for A molecules on the red blood cells, the IB allele codes for B molecules on the surface of red blood cells, and the i allele codes for no molecules on the red blood cells. In this case, the IA and IB alleles are codominant with each other and are both dominant over the i allele. Although there are three alleles present in a population, each individual only gets two of the alleles from their parents. This produces the genotypes and phenotypes shown in Figure 8.15. Notice that instead of three genotypes, there are six different genotypes when there are three alleles. The number of possible phenotypes depends on the dominance relationships between the three alleles.

A Punnett square showing the possible genotype and phenotypes of the ABO blood types in humans.

Figure 8.15 Inheritance of the ABO blood system in humans is shown.

Multiple Alleles Confer Drug Resistance in the Malaria Parasite

Malaria is a parasitic disease in humans that is transmitted by infected female mosquitoes, including Anopheles gambiae, and is characterized by cyclic high fevers, chills, flu-like symptoms, and severe anemia. Plasmodium falciparum and P. vivax are the most common causative agents of malaria, and P. falciparum is the most deadly. When promptly and correctly treated, P. falciparum malaria has a mortality rate of 0.1 percent. However, in some parts of the world, the parasite has evolved resistance to commonly used malaria treatments, so the most effective malarial treatments can vary by geographic region.

In Southeast Asia, Africa, and South America, P. falciparum has developed resistance to the anti-malarial drugs chloroquine, mefloquine, and sulfadoxine-pyrimethamine. P. falciparum, which is haploid during the life stage in which it is infective to humans, has evolved multiple drug-resistant mutant alleles of the dhps gene. Varying degrees of sulfadoxine resistance are associated with each of these alleles. Being haploid, P. falciparum needs only one drug-resistant allele to express this trait.

In Southeast Asia, different sulfadoxine-resistant alleles of the dhps gene are localized to different geographic regions. This is a common evolutionary phenomenon that comes about because drug-resistant mutants arise in a population and interbreed with other P. falciparum isolates in close proximity. Sulfadoxine-resistant parasites cause considerable human hardship in regions in which this drug is widely used as an over-the-counter malaria remedy. As is common with pathogens that multiply to large numbers within an infection cycle, P. falciparum evolves relatively rapidly (over a decade or so) in response to the selective pressure of commonly used anti-malarial drugs. For this reason, scientists must constantly work to develop new drugs or drug combinations to combat the worldwide malaria burden.1

Sex-Linked Traits

In humans, as well as in many other animals and some plants, the sex of the individual is determined by sex chromosomes—one pair of non-homologous chromosomes. Until now, we have only considered inheritance patterns among non-sex chromosomes, or autosomes. In addition to 22 homologous pairs of autosomes, human females have a homologous pair of X chromosomes, whereas human males have an XY chromosome pair. Although the Y chromosome contains a small region of similarity to the X chromosome so that they can pair during meiosis, the Y chromosome is much shorter and contains fewer genes. When a gene being examined is present on the X, but not the Y, chromosome, it is X-linked.

Eye color in Drosophila, the common fruit fly, was the first X-linked trait to be identified. Thomas Hunt Morgan mapped this trait to the X chromosome in 1910. Like humans, Drosophila males have an XY chromosome pair, and females are XX. In flies the wild-type eye color is red (XW) and is dominant to white eye color (Xw) (Figure 8.16). Because of the location of the eye-color gene, reciprocal crosses do not produce the same offspring ratios. Males are said to be hemizygous, in that they have only one allele for any X-linked characteristic. Hemizygosity makes descriptions of dominance and recessiveness irrelevant for XY males. Drosophila males lack the white gene on the Y chromosome; that is, their genotype can only be XWY or XwY. In contrast, females have two allele copies of this gene and can be XWXW, XWXw, or XwXw.

Photo shows two fruit flies, one with red eyes and one with white eyes.

Figure 8.16 In Drosophila, the gene for eye color is located on the X chromosome. Red eye color is wild-type and is dominant to white eye color.

In an X-linked cross, the genotypes of F1 and F2 offspring depend on whether the recessive trait was expressed by the male or the female in the P generation. With respect to Drosophila eye color, when the P male expresses the white-eye phenotype and the female is homozygously red-eyed, all members of the F1 generation exhibit red eyes (Figure 8.17). The F1 females are heterozygous (XWXw), and the males are all XWY, having received their X chromosome from the homozygous dominant P female and their Y chromosome from the P male. A subsequent cross between the XWXw female and the XWY male would produce only red-eyed females (with XWXW or XWXw genotypes) and both red- and white-eyed males (with XWY or XwY genotypes). Now, consider a cross between a homozygous white-eyed female and a male with red eyes. The F1 generation would exhibit only heterozygous red-eyed females (XWXw) and only white-eyed males (XwY). Half of the F2 females would be red-eyed (XWXw) and half would be white-eyed (XwXw). Similarly, half of the F2 males would be red-eyed (XWY) and half would be white-eyed (XwY).

This illustration shows a Punnett square analysis of fruit fly eye color, which is a sex-linked trait. A red-eyed male fruit fly with the genotype X^{w}Y is crossed with a white-eyed female fruit fly with the genotype X^{w}X^{w}. All of the female offspring acquire a dominant X^{W} allele from the father and a recessive X^{w} allele from the mother, and are therefore heterozygous dominant with red eye color. All the male offspring acquire a recessive X^{w} allele from the mother and a Y chromosome from the father and are therefore hemizygous recessive with white eye color.

Figure 8.17 Crosses involving sex-linked traits often give rise to different phenotypes for the different sexes of offspring, as is the case for this cross involving red and white eye color in Drosophila. In the diagram, w is the white-eye mutant allele and W is the wild-type, red-eye allele.

What ratio of offspring would result from a cross between a white-eyed male and a female that is heterozygous for red eye color?


Half of the female offspring would be heterozygous (XWXw) with red eyes, and half would be homozygous recessive (XwXw) with white eyes. Half of the male offspring would be hemizygous dominant (XWY) with red eyes, and half would be hemizygous recessive (XwY) with white eyes.

Discoveries in fruit fly genetics can be applied to human genetics. When a female parent is homozygous for a recessive X-linked trait, she will pass the trait on to 100 percent of her male offspring, because the males will receive the Y chromosome from the male parent. In humans, the alleles for certain conditions (some color-blindness, hemophilia, and muscular dystrophy) are X-linked. Females who are heterozygous for these diseases are said to be carriers and may not exhibit any phenotypic effects. These females will pass the disease to half of their sons and will pass carrier status to half of their daughters; therefore, X-linked traits appear more frequently in males than females.

In some groups of organisms with sex chromosomes, the sex with the non-homologous sex chromosomes is the female rather than the male. This is the case for all birds. In this case, sex-linked traits will be more likely to appear in the female, in whom they are hemizygous.

Concept in Action

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Watch this video to learn more about sex-linked traits.

Linked Genes Violate the Law of Independent Assortment

Although all of Mendel’s pea plant characteristics behaved according to the law of independent assortment, we now know that some allele combinations are not inherited independently of each other. Genes that are located on separate, non-homologous chromosomes will always sort independently. However, each chromosome contains hundreds or thousands of genes, organized linearly on chromosomes like beads on a string. The segregation of alleles into gametes can be influenced by linkage, in which genes that are located physically close to each other on the same chromosome are more likely to be inherited as a pair. However, because of the process of recombination, or “crossover,” it is possible for two genes on the same chromosome to behave independently, or as if they are not linked. To understand this, let us consider the biological basis of gene linkage and recombination.

Homologous chromosomes possess the same genes in the same order, though the specific alleles of the gene can be different on each of the two chromosomes. Recall that during interphase and prophase I of meiosis, homologous chromosomes first replicate and then synapse, with like genes on the homologs aligning with each other. At this stage, segments of homologous chromosomes exchange linear segments of genetic material (Figure 8.18). This process is called recombination, or crossover, and it is a common genetic process. Because the genes are aligned during recombination, the gene order is not altered. Instead, the result of recombination is that maternal and paternal alleles are combined onto the same chromosome. Across a given chromosome, several recombination events may occur, causing extensive shuffling of alleles.

This illustration shows a pair of homologous chromosomes. One of the pair has the alleles ABC and the other has the alleles abc. During meiosis, crossover occurs between two of the chromosomes and genetic material is exchanged, resulting in one recombinant chromosome that has the alleles ABc and another that has the alleles abC. The other two chromosomes are non-recombinant and have the same arrangement of genes as before meiosis.

Figure 8.18 The process of crossover, or recombination, occurs when two homologous chromosomes align and exchange a segment of genetic material.

When two genes are located on the same chromosome, they are considered linked, and their alleles tend to be transmitted through meiosis together. To exemplify this, imagine a dihybrid cross involving flower color and plant height in which the genes are next to each other on the chromosome. If one homologous chromosome has alleles for tall plants and red flowers, and the other chromosome has genes for short plants and yellow flowers, then when the gametes are formed, the tall and red alleles will tend to go together into a gamete and the short and yellow alleles will go into other gametes. These are called the parental genotypes because they have been inherited intact from the parents of the individual producing gametes. But unlike if the genes were on different chromosomes, there will be no gametes with tall and yellow alleles and no gametes with short and red alleles. If you create a Punnett square with these gametes, you will see that the classical Mendelian prediction of a 9:3:3:1 outcome of a dihybrid cross would not apply. As the distance between two genes increases, the probability of one or more crossovers between them increases and the genes behave more like they are on separate chromosomes. Geneticists have used the proportion of recombinant gametes (the ones not like the parents) as a measure of how far apart genes are on a chromosome. Using this information, they have constructed linkage maps of genes on chromosomes for well-studied organisms, including humans.

Mendel’s seminal publication makes no mention of linkage, and many researchers have questioned whether he encountered linkage but chose not to publish those crosses out of concern that they would invalidate his independent assortment postulate. The garden pea has seven chromosomes, and some have suggested that his choice of seven characteristics was not a coincidence. However, even if the genes he examined were not located on separate chromosomes, it is possible that he simply did not observe linkage because of the extensive shuffling effects of recombination.


Mendel’s studies in pea plants implied that the sum of an individual’s phenotype was controlled by genes (or as he called them, unit factors), such that every characteristic was distinctly and completely controlled by a single gene. In fact, single observable characteristics are almost always under the influence of multiple genes (each with two or more alleles) acting in unison. For example, at least eight genes contribute to eye color in humans.

Concept in Action

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Eye color in humans is determined by multiple alleles. Use the Eye Color Calculator to predict the eye color of children from parental eye color.

In some cases, several genes can contribute to aspects of a common phenotype without their gene products ever directly interacting. In the case of organ development, for instance, genes may be expressed sequentially, with each gene adding to the complexity and specificity of the organ. Genes may function in complementary or synergistic fashions, such that two or more genes expressed simultaneously affect a phenotype. An apparent example of this occurs with human skin color, which appears to involve the action of at least three (and probably more) genes. Cases in which inheritance for a characteristic like skin color or human height depend on the combined effects of numerous genes are called polygenic inheritance.

Genes may also oppose each other, with one gene suppressing the expression of another. In epistasis, the interaction between genes is antagonistic, such that one gene masks or interferes with the expression of another. “Epistasis” is a word composed of Greek roots meaning “standing upon.” The alleles that are being masked or silenced are said to be hypostatic to the epistatic alleles that are doing the masking. Often the biochemical basis of epistasis is a gene pathway in which expression of one gene is dependent on the function of a gene that precedes or follows it in the pathway.

An example of epistasis is pigmentation in mice. The wild-type coat color, agouti (AA) is dominant to solid-colored fur (aa). However, a separate gene C, when present as the recessive homozygote (cc), negates any expression of pigment from the A gene and results in an albino mouse (Figure 8.19). Therefore, the genotypes AAcc, Aacc, and aacc all produce the same albino phenotype. A cross between heterozygotes for both genes (AaCc x AaCc) would generate offspring with a phenotypic ratio of 9 agouti:3 black:4 albino (Figure 8.19). In this case, the C gene is epistatic to the A gene.

A cross between two agouti mice with the heterozygous genotype AaCc is shown. Each mouse produces four different kinds of gametes (AC, aC, Ac, and ac). A 4 × 4 Punnett square is used to determine the genotypic ratio of the offspring. The phenotypic ratio is 9/16 agouti, 3/16 black, and 4/16 white.

Figure 8.19 In this example of epistasis, one gene (C) masks the expression of another (A) for coat color. When the C allele is present, coat color is expressed; when it is absent (cc), no coat color is expressed. Coat color depends on the A gene, which shows dominance, with the recessive homozygote showing a different phenotype than the heterozygote or dominant homozygote.

Section Summary

Alleles do not always behave in dominant and recessive patterns. Incomplete dominance describes situations in which the heterozygote exhibits a phenotype that is intermediate between the homozygous phenotypes. Codominance describes the simultaneous expression of both of the alleles in the heterozygote. Although diploid organisms can only have two alleles for any given gene, it is common for more than two alleles for a gene to exist in a population. In humans, as in many animals and some plants, females have two X chromosomes and males have one X and one Y chromosome. Genes that are present on the X but not the Y chromosome are said to be X-linked, such that males only inherit one allele for the gene, and females inherit two.

According to Mendel’s law of independent assortment, genes sort independently of each other into gametes during meiosis. This occurs because chromosomes, on which the genes reside, assort independently during meiosis and crossovers cause most genes on the same chromosomes to also behave independently. When genes are located in close proximity on the same chromosome, their alleles tend to be inherited together. This results in offspring ratios that violate Mendel’s law of independent assortment. However, recombination serves to exchange genetic material on homologous chromosomes such that maternal and paternal alleles may be recombined on the same chromosome. This is why alleles on a given chromosome are not always inherited together. Recombination is a random event occurring anywhere on a chromosome. Therefore, genes that are far apart on the same chromosome are likely to still assort independently because of recombination events that occurred in the intervening chromosomal space.

Whether or not they are sorting independently, genes may interact at the level of gene products, such that the expression of an allele for one gene masks or modifies the expression of an allele for a different gene. This is called epistasis.


What ratio of offspring would result from a cross between a white-eyed male and a female that is heterozygous for red eye color?

Answer: Half of the female offspring would be heterozygous (XWXw) with red eyes, and half would be homozygous recessive (XwXw) with white eyes. Half of the male offspring would be hemizygous dominant (XWY) with red eyes, and half would be hemizygous recessive (XwY) with white eyes.

Multiple Choice

If black and white true-breeding mice are mated and the result is all gray offspring, what inheritance pattern would this be indicative of?

A) dominance

B) codominance

C) multiple alleles

D) incomplete dominance


The ABO blood groups in humans are expressed as the IA, IB, and i alleles. The IA allele encodes the A blood group antigen, IB encodes B, and i encodes O. Both A and B are dominant to O. If a heterozygous blood type A parent (IAi) and a heterozygous blood type B parent (IBi) mate, one quarter of their offspring are expected to have the AB blood type (IAIB) in which both antigens are expressed equally. Therefore, ABO blood groups are an example of:

A) multiple alleles and incomplete dominance

B) codominance and incomplete dominance

C) incomplete dominance only

D) multiple alleles and codominance


In a cross between a homozygous red-eyed female fruit fly and a white-eyed male fruit fly, what is the expected outcome?

A) all white-eyed male offspring

B) all white-eyed female offspring

C) all red-eyed offspring

D) half white-eyed make offspring


When a population has a gene with four alleles circulating, how many possible genotypes are there?

A) 3

B) 6

C) 10

D) 16


Free Response

Can a male be a carrier of red-green color blindness?

No, males can only express color blindness and cannot carry it because an individual needs two X chromosomes to be a carrier.

Could an individual with blood type O (genotype ii) be a legitimate child of parents in which one parent had blood type A and the other parent had blood type B?

Yes this child could have come from these parents. The child would have inherited an i allele from each parent and for this to happen the type A parent had to have genotype IAi and the type b parent had to have genotype IBi.



codominance: in a heterozygote, complete and simultaneous expression of both alleles for the same characteristic

epistasis: an interaction between genes such that one gene masks or interferes with the expression of another

hemizygous: the presence of only one allele for a characteristic, as in X-linkage; hemizygosity makes descriptions of dominance and recessiveness irrelevant

incomplete dominance: in a heterozygote, expression of two contrasting alleles such that the individual displays an intermediate phenotype

linkage: a phenomenon in which alleles that are located in close proximity to each other on the same chromosome are more likely to be inherited together

recombination: the process during meiosis in which homologous chromosomes exchange linear segments of genetic material, thereby dramatically increasing genetic variation in the offspring and separating linked genes

wild type: the most commonly occurring genotype or phenotype for a given characteristic found in a population

X-linked: a gene present on the X chromosome, but not the Y chromosome


1 Sumiti Vinayak et al., “Origin and Evolution of Sulfadoxine Resistant Plasmodium falciparum,” PLoS Pathogens 6 (2010): e1000830.


Chapter 8 PowerPoint

Chapter 8 PowerPoint


Unit 3: Molecular Biology and Biotechnology


Chapter 9: Introduction to Molecular Biology

Photo shows Dolly the sheep, which has been stuffed and placed in a glass case.

Figure 9.1 Dolly the sheep was the first cloned mammal. Photo shows Dolly the sheep, which has been stuffed and placed in a glass case.

The three letters “DNA” have now become associated with crime solving, paternity testing, human identification, and genetic testing. DNA can be retrieved from hair, blood, or saliva. With the exception of identical twins, each person’s DNA is unique and it is possible to detect differences between human beings on the basis of their unique DNA sequence.

DNA analysis has many practical applications beyond forensics and paternity testing. DNA testing is used for tracing genealogy and identifying pathogens. In the medical field, DNA is used in diagnostics, new vaccine development, and cancer therapy. It is now possible to determine predisposition to many diseases by analyzing genes.

DNA is the genetic material passed from parent to offspring for all life on Earth. The technology of molecular genetics developed in the last half century has enabled us to see deep into the history of life to deduce the relationships between living things in ways never thought possible. It also allows us to understand the workings of evolution in populations of organisms. Over a thousand species have had their entire genome sequenced, and there have been thousands of individual human genome sequences completed. These sequences will allow us to understand human disease and the relationship of humans to the rest of the tree of life. Finally, molecular genetics techniques have revolutionized plant and animal breeding for human agricultural needs. All of these advances in biotechnology depended on basic research leading to the discovery of the structure of DNA in 1953, and the research since then that has uncovered the details of DNA replication and the complex process leading to the expression of DNA in the form of proteins in the cell.


9.1 The Structure of DNA

Learning Objectives

By the end of this section, you will be able to:

  • Describe the structure of DNA
  • Describe how eukaryotic and prokaryotic DNA is arranged in the cell

In the 1950s, Francis Crick and James Watson worked together at the University of Cambridge, England, to determine the structure of DNA. Other scientists, such as Linus Pauling and Maurice Wilkins, were also actively exploring this field. Pauling had discovered the secondary structure of proteins using X-ray crystallography. X-ray crystallography is a method for investigating molecular structure by observing the patterns formed by X-rays shot through a crystal of the substance. The patterns give important information about the structure of the molecule of interest. In Wilkins’ lab, researcher Rosalind Franklin was using X-ray crystallography to understand the structure of DNA. Watson and Crick were able to piece together the puzzle of the DNA molecule using Franklin’s data (Figure 9.2). Watson and Crick also had key pieces of information available from other researchers such as Chargaff’s rules. Chargaff had shown that of the four kinds of monomers (nucleotides) present in a DNA molecule, two types were always present in equal amounts and the remaining two types were also always present in equal amounts. This meant they were always paired in some way. In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine for their work in determining the structure of DNA.

Photo in part A shows James Watson, Francis Crick, and Maclyn McCarty. The x-ray diffraction pattern in part b is symmetrical, with dots in an x-shape.

Figure 9.2 Pioneering scientists (a) James Watson and Francis Crick are pictured here with American geneticist Maclyn McCarty. Scientist Rosalind Franklin discovered (b) the X-ray diffraction pattern of DNA, which helped to elucidate its double helix structure. (credit a: modification of work by Marjorie McCarty; b: modification of work by NIH)

Now let’s consider the structure of the two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The building blocks of DNA are nucleotides, which are made up of three parts: a deoxyribose (5-carbon sugar), a phosphate group, and a nitrogenous base (Figure 9.3). There are four types of nitrogenous bases in DNA. Adenine (A) and guanine (G) are double-ringed purines, and cytosine (C) and thymine (T) are smaller, single-ringed pyrimidines. The nucleotide is named according to the nitrogenous base it contains.

(a) Each DNA nucleotide is made up of a sugar, a phosphate group, and a base.

Figure 9.3 (a) Each DNA nucleotide is made up of a sugar, a phosphate group, and a base.

(b) Cytosine and thymine are pyrimidines. Guanine and adenine are purines.

Figure 9.3 (b) Cytosine and thymine are pyrimidines. Guanine and adenine are purines.

The phosphate group of one nucleotide bonds covalently with the sugar molecule of the next nucleotide, and so on, forming a long polymer of nucleotide monomers. The sugar–phosphate groups line up in a “backbone” for each single strand of DNA, and the nucleotide bases stick out from this backbone. The carbon atoms of the five-carbon sugar are numbered clockwise from the oxygen as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”). The phosphate group is attached to the 5′ carbon of one nucleotide and the 3′ carbon of the next nucleotide. In its natural state, each DNA molecule is actually composed of two single strands held together along their length with hydrogen bonds between the bases.

Watson and Crick proposed that the DNA is made up of two strands that are twisted around each other to form a right-handed helix, called a double helix. Base-pairing takes place between a purine and pyrimidine: namely, A pairs with T, and G pairs with C. In other words, adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs. This is the basis for Chargaff’s rule; because of their complementarity, there is as much adenine as thymine in a DNA molecule and as much guanine as cytosine. Adenine and thymine are connected by two hydrogen bonds, and cytosine and guanine are connected by three hydrogen bonds. The two strands are anti-parallel in nature; that is, one strand will have the 3′ carbon of the sugar in the “upward” position, whereas the other strand will have the 5′ carbon in the upward position. The diameter of the DNA double helix is uniform throughout because a purine (two rings) always pairs with a pyrimidine (one ring) and their combined lengths are always equal. (Figure 9.4).

Part A shows an illustration of a DNA double helix, which has a sugar phosphate backbone on the outside and nitrogenous base pairs on the inside. Part B shows base-pairing between thymine and adenine, which form two hydrogen bonds, and between guanine and cytosine, which form three hydrogen bonds.

Figure 9.4 DNA (a) forms a double stranded helix, and (b) adenine pairs with thymine and cytosine pairs with guanine. (credit a: modification of work by Jerome Walker, Dennis Myts)

The Structure of RNA

There is a second nucleic acid in all cells called ribonucleic acid, or RNA. Like DNA, RNA is a polymer of nucleotides. Each of the nucleotides in RNA is made up of a nitrogenous base, a five-carbon sugar, and a phosphate group. In the case of RNA, the five-carbon sugar is ribose, not deoxyribose. Ribose has a hydroxyl group at the 2′ carbon, unlike deoxyribose, which has only a hydrogen atom (Figure 9.5).

A figure showing the structure of ribose and deoxyribose sugars. In ribose, the OH at the 2' position is highlighted in red. In deoxyribose, the H at the 2' position is highlighted in red.

Figure 9.5 The difference between the ribose found in RNA and the deoxyribose found in DNA is that ribose has a hydroxyl group at the 2′ carbon.

RNA nucleotides contain the nitrogenous bases adenine, cytosine, and guanine. However, they do not contain thymine, which is instead replaced by uracil, symbolized by a “U.” RNA exists as a single-stranded molecule rather than a double-stranded helix. Molecular biologists have named several kinds of RNA on the basis of their function. These include messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)—molecules that are involved in the production of proteins from the DNA code.

How DNA Is Arranged in the Cell

DNA is a working molecule; it must be replicated when a cell is ready to divide, and it must be “read” to produce the molecules, such as proteins, to carry out the functions of the cell. For this reason, the DNA is protected and packaged in very specific ways. In addition, DNA molecules can be very long. Stretched end-to-end, the DNA molecules in a single human cell would come to a length of about 2 meters. Thus, the DNA for a cell must be packaged in a very ordered way to fit and function within a structure (the cell) that is not visible to the naked eye. The chromosomes of prokaryotes are much simpler than those of eukaryotes in many of their features (Figure 9.6). Most prokaryotes contain a single, circular chromosome that is found in an area in the cytoplasm called the nucleoid.

Illustration shows a eukaryotic cell, which has a membrane-bound nucleus containing chromatin and a nucleolus, and a prokaryotic cell, which has DNA contained in an area of the cytoplasm called the nucleoid. The prokaryotic cell is much smaller than the eukaryotic cell.

Figure 9.6 A eukaryote contains a well-defined nucleus, whereas in prokaryotes, the chromosome lies in the cytoplasm in an area called the nucleoid.

The size of the genome in one of the most well-studied prokaryotes, Escherichia coli, is 4.6 million base pairs, which would extend a distance of about 1.6 mm if stretched out. So how does this fit inside a small bacterial cell? The DNA is twisted beyond the double helix in what is known as supercoiling. Some proteins are known to be involved in the supercoiling; other proteins and enzymes help in maintaining the supercoiled structure.

Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus. At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The DNA is wrapped tightly around the histone core. This nucleosome is linked to the next one by a short strand of DNA that is free of histones. This is also known as the “beads on a string” structure; the nucleosomes are the “beads” and the short lengths of DNA between them are the “string.” The nucleosomes, with their DNA coiled around them, stack compactly onto each other to form a 30-nm–wide fiber. This fiber is further coiled into a thicker and more compact structure. At the metaphase stage of mitosis, when the chromosomes are lined up in the center of the cell, the chromosomes are at their most compacted. They are approximately 700 nm in width, and are found in association with scaffold proteins.

In interphase, the phase of the cell cycle between mitoses at which the chromosomes are decondensed, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. There is a tightly packaged region that stains darkly, and a less dense region. The darkly staining regions usually contain genes that are not active, and are found in the regions of the centromere and telomeres. The lightly staining regions usually contain genes that are active, with DNA packaged around nucleosomes but not further compacted.

Illustration shows levels of organization of eukaryotic chromosomes, starting with the DNA double helix, which wraps around histone proteins. The entire DNA molecule wraps around many clusters of histone proteins, forming a structure that looks like beads on a string. The chromatin is further condensed by wrapping around a protein core. The result is a compact chromosome, shown in duplicated form.

Figure 9.7 These figures illustrate the compaction of the eukaryotic chromosome.

Concept in Action

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Watch this animation of DNA packaging.

Section Summary

The model of the double-helix structure of DNA was proposed by Watson and Crick. The DNA molecule is a polymer of nucleotides. Each nucleotide is composed of a nitrogenous base, a five-carbon sugar (deoxyribose), and a phosphate group. There are four nitrogenous bases in DNA, two purines (adenine and guanine) and two pyrimidines (cytosine and thymine). A DNA molecule is composed of two strands. Each strand is composed of nucleotides bonded together covalently between the phosphate group of one and the deoxyribose sugar of the next. From this backbone extend the bases. The bases of one strand bond to the bases of the second strand with hydrogen bonds. Adenine always bonds with thymine, and cytosine always bonds with guanine. The bonding causes the two strands to spiral around each other in a shape called a double helix. Ribonucleic acid (RNA) is a second nucleic acid found in cells. RNA is a single-stranded polymer of nucleotides. It also differs from DNA in that it contains the sugar ribose, rather than deoxyribose, and the nucleotide uracil rather than thymine. Various RNA molecules function in the process of forming proteins from the genetic code in DNA.

Prokaryotes contain a single, double-stranded circular chromosome. Eukaryotes contain double-stranded linear DNA molecules packaged into chromosomes. The DNA helix is wrapped around proteins to form nucleosomes. The protein coils are further coiled, and during mitosis and meiosis, the chromosomes become even more greatly coiled to facilitate their movement. Chromosomes have two distinct regions which can be distinguished by staining, reflecting different degrees of packaging and determined by whether the DNA in a region is being expressed (euchromatin) or not (heterochromatin).


Multiple Choice

Which of the following does cytosine pair with?

A) guanine

B) thymine

C) adenine

D) a pyrimidine


Prokaryotes contain a ________chromosome, and eukaryotes contain ________ chromosomes.

A) single-stranded circular; single-stranded linear

B) single-stranded linear; single-stranded circular

C) double-stranded circular; double-stranded linear

D) double-stranded linear; double-stranded circular


Free Response

Describe the organization of the eukaryotic chromosome.

The DNA is wound around proteins called histones. The histones then stack together in a compact form that creates a fiber that is 30-nm thick. The fiber is further coiled for greater compactness. During metaphase of mitosis, the chromosome is at its most compact to facilitate chromosome movement. During interphase, there are denser areas of chromatin, called heterochromatin, that contain DNA that is not expressed, and less dense euchromatin that contains DNA that is expressed.

Describe the structure and complementary base pairing of DNA.

A single strand of DNA is a polymer of nucleic acids joined covalently between the phosphate group of one and the deoxyribose sugar of the next to for a “backbone” from which the nitrogenous bases stick out. In its natural state, DNA has two strands wound around each other in a double helix. The bases on each strand are bonded to each other with hydrogen bonds. Only specific bases bond with each other; adenine bonds with thymine, and cytosine bonds with guanine.


deoxyribose: a five-carbon sugar molecule with a hydrogen atom rather than a hydroxyl group in the 2′ position; the sugar component of DNA nucleotides

double helix: the molecular shape of DNA in which two strands of nucleotides wind around each other in a spiral shape

nitrogenous base: a nitrogen-containing molecule that acts as a base; often referring to one of the purine or pyrimidine components of nucleic acids

phosphate group: a molecular group consisting of a central phosphorus atom bound to four oxygen atoms


9.2 DNA Replication

Learning Objectives

By the end of this section, you will be able to:

  • Explain the process of DNA replication
  • Explain the importance of telomerase to DNA replication
  • Describe mechanisms of DNA repair

When a cell divides, it is important that each daughter cell receives an identical copy of the DNA. This is accomplished by the process of DNA replication. The replication of DNA occurs during the synthesis phase, or S phase, of the cell cycle, before the cell enters mitosis or meiosis.

The elucidation of the structure of the double helix provided a hint as to how DNA is copied. Recall that adenine nucleotides pair with thymine nucleotides, and cytosine with guanine. This means that the two strands are complementary to each other. For example, a strand of DNA with a nucleotide sequence of AGTCATGA will have a complementary strand with the sequence TCAGTACT (Figure 9.8).

Figure shows the ladder-like structure of DNA, with complementary bases making up the rungs of the ladder.

Figure 9.8 The two strands of DNA are complementary, meaning the sequence of bases in one strand can be used to create the correct sequence of bases in the other strand.

Because of the complementarity of the two strands, having one strand means that it is possible to recreate the other strand. This model for replication suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied (Figure 9.9).

Illustration shows the semiconservative model of DNA synthesis. In the semi-conservative model, each newly synthesized strand pairs with a parent strand.

Figure 9.9 The semiconservative model of DNA replication is shown. Gray indicates the original DNA strands, and blue indicates newly synthesized DNA.

During DNA replication, each of the two strands that make up the double helix serves as a template from which new strands are copied. The new strand will be complementary to the parental or “old” strand. Each new double strand consists of one parental strand and one new daughter strand. This is known as semiconservative replication. When two DNA copies are formed, they have an identical sequence of nucleotide bases and are divided equally into two daughter cells.

DNA Replication in Eukaryotes

Because eukaryotic genomes are very complex, DNA replication is a very complicated process that involves several enzymes and other proteins. It occurs in three main stages: initiation, elongation, and termination.

Recall that eukaryotic DNA is bound to proteins known as histones to form structures called nucleosomes. During initiation, the DNA is made accessible to the proteins and enzymes involved in the replication process. How does the replication machinery know where on the DNA double helix to begin? It turns out that there are specific nucleotide sequences called origins of replication at which replication begins. Certain proteins bind to the origin of replication while an enzyme called helicase unwinds and opens up the DNA helix. As the DNA opens up, Y-shaped structures called replication forks are formed (Figure 9.10). Two replication forks are formed at the origin of replication, and these get extended in both directions as replication proceeds. There are multiple origins of replication on the eukaryotic chromosome, such that replication can occur simultaneously from several places in the genome.

During elongation, an enzyme called DNA polymerase adds DNA nucleotides to the 3′ end of the template. Because DNA polymerase can only add new nucleotides at the end of a backbone, a primer sequence, which provides this starting point, is added with complementary RNA nucleotides. This primer is removed later, and the nucleotides are replaced with DNA nucleotides. One strand, which is complementary to the parental DNA strand, is synthesized continuously toward the replication fork so the polymerase can add nucleotides in this direction. This continuously synthesized strand is known as the leading strand. Because DNA polymerase can only synthesize DNA in a 5′ to 3′ direction, the other new strand is put together in short pieces called Okazaki fragments. The Okazaki fragments each require a primer made of RNA to start the synthesis. The strand with the Okazaki fragments is known as the lagging strand. As synthesis proceeds, an enzyme removes the RNA primer, which is then replaced with DNA nucleotides, and the gaps between fragments are sealed by an enzyme called DNA ligase.

The process of DNA replication can be summarized as follows:

  1. DNA unwinds at the origin of replication.
  2. New bases are added to the complementary parental strands. One new strand is made continuously, while the other strand is made in pieces.
  3. Primers are removed, new DNA nucleotides are put in place of the primers and the backbone is sealed by DNA ligase.
Illustration shows a replication bubble. Helicase unwinds the helix. An RNA primer starts the synthesis, and DNA polymerase extends the DNA strand from the RNA primer. DNA synthesis occurs only in the 5' to 3' direction. On the leading strand, DNA synthesis occurs continuously. On the lagging strand, DNA synthesis restarts many times as the helix unwinds, resulting in many short fragments called Okazaki fragments.

Figure 9.10 A replication fork is formed by the opening of the origin of replication, and helicase separates the DNA strands. An RNA primer is synthesized, and is elongated by the DNA polymerase. On the leading strand, DNA is synthesized continuously, whereas on the lagging strand, DNA is synthesized in short stretches. The DNA fragments are joined by DNA ligase (not shown).

You isolate a cell strain in which the joining together of Okazaki fragments is impaired and suspect that a mutation has occurred in an enzyme found at the replication fork. Which enzyme is most likely to be mutated?

Telomere Replication

Because eukaryotic chromosomes are linear, DNA replication comes to the end of a line in eukaryotic chromosomes. As you have learned, the DNA polymerase enzyme can add nucleotides in only one direction. In the leading strand, synthesis continues until the end of the chromosome is reached; however, on the lagging strand there is no place for a primer to be made for the DNA fragment to be copied at the end of the chromosome. This presents a problem for the cell because the ends remain unpaired, and over time these ends get progressively shorter as cells continue to divide. The ends of the linear chromosomes are known as telomeres, which have repetitive sequences that do not code for a particular gene. As a consequence, it is telomeres that are shortened with each round of DNA replication instead of genes. For example, in humans, a six base-pair sequence, TTAGGG, is repeated 100 to 1000 times. The discovery of the enzyme telomerase (Figure 9.11) helped in the understanding of how chromosome ends are maintained. The telomerase attaches to the end of the chromosome, and complementary bases to the RNA template are added on the end of the DNA strand. Once the lagging strand template is sufficiently elongated, DNA polymerase can now add nucleotides that are complementary to the ends of the chromosomes. Thus, the ends of the chromosomes are replicated.

Telomerase has an associated RNA that complements the 5' overhang at the end of the chromosome. The RNA template is used to synthesize the complementary strand. Telomerase then shifts, and the process is repeated. Next, primase and DNA polymerase synthesize the rest of the complementary strand.

Figure 9.11 The ends of linear chromosomes are maintained by the action of the telomerase enzyme.

Telomerase is typically found to be active in germ cells, adult stem cells, and some cancer cells. For her discovery of telomerase and its action, Elizabeth Blackburn (Figure 9.12) received the Nobel Prize for Medicine and Physiology in 2009.

Photo shows Elizabeth Blackburn.

Figure 9.12 Elizabeth Blackburn, 2009 Nobel Laureate, was the scientist who discovered how telomerase works. (credit: U.S. Embassy, Stockholm, Sweden)

Telomerase is not active in adult somatic cells. Adult somatic cells that undergo cell division continue to have their telomeres shortened. This essentially means that telomere shortening is associated with aging. In 2010, scientists found that telomerase can reverse some age-related conditions in mice, and this may have potential in regenerative medicine.1 Telomerase-deficient mice were used in these studies; these mice have tissue atrophy, stem-cell depletion, organ system failure, and impaired tissue injury responses. Telomerase reactivation in these mice caused extension of telomeres, reduced DNA damage, reversed neurodegeneration, and improved functioning of the testes, spleen, and intestines. Thus, telomere reactivation may have potential for treating age-related diseases in humans.

DNA Replication in Prokaryotes

Recall that the prokaryotic chromosome is a circular molecule with a less extensive coiling structure than eukaryotic chromosomes. The eukaryotic chromosome is linear and highly coiled around proteins. While there are many similarities in the DNA replication process, these structural differences necessitate some differences in the DNA replication process in these two life forms.

DNA replication has been extremely well-studied in prokaryotes, primarily because of the small size of the genome and large number of variants available. Escherichia coli has 4.6 million base pairs in a single circular chromosome, and all of it gets replicated in approximately 42 minutes, starting from a single origin of replication and proceeding around the chromosome in both directions. This means that approximately 1000 nucleotides are added per second. The process is much more rapid than in eukaryotes. The table below summarizes the differences between prokaryotic and eukaryotic replications.

Differences between Prokaryotic and Eukaryotic Replications
Property Prokaryotes Eukaryotes
Origin of replication Single Multiple
Rate of replication 1000 nucleotides/s 50 to 100 nucleotides/s
Chromosome structure circular linear
Telomerase Not present Present

Concept in Action

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Click through a tutorial on DNA replication.

DNA Repair

DNA polymerase can make mistakes while adding nucleotides. It edits the DNA by proofreading every newly added base. Incorrect bases are removed and replaced by the correct base, and then polymerization continues (Figure 9.13 a). Most mistakes are corrected during replication, although when this does not happen, the mismatch repair mechanism is employed. Mismatch repair enzymes recognize the wrongly incorporated base and excise it from the DNA, replacing it with the correct base (Figure 9.13 b). In yet another type of repair, nucleotide excision repair, the DNA double strand is unwound and separated, the incorrect bases are removed along with a few bases on the 5′ and 3′ end, and these are replaced by copying the template with the help of DNA polymerase (Figure 9.13 c). Nucleotide excision repair is particularly important in correcting thymine dimers, which are primarily caused by ultraviolet light. In a thymine dimer, two thymine nucleotides adjacent to each other on one strand are covalently bonded to each other rather than their complementary bases. If the dimer is not removed and repaired it will lead to a mutation. Individuals with flaws in their nucleotide excision repair genes show extreme sensitivity to sunlight and develop skin cancers early in life.

Part a shows DNA polymerase replicating a strand of DNA. The enzyme has accidentally inserted G opposite A, resulting in a bulge. The enzyme backs up to fix the error. In part b, the top illustration shows a replicated DNA strand with a G–T base mismatch. The bottom illustration shows the repaired DNA, which has the correct G–C base pairing. Part c shows a DNA strand in which a thymine dimer has formed. An excision repair enzyme cuts out the section of DNA that contains the dimer so that it can be replaced with a normal base pair.

Figure 9.13 Proofreading by DNA polymerase (a) corrects errors during replication. In mismatch repair (b), the incorrectly added base is detected after replication. The mismatch repair proteins detect this base and remove it from the newly synthesized strand by nuclease action. The gap is now filled with the correctly paired base. Nucleotide excision (c) repairs thymine dimers. When exposed to UV, thymines lying adjacent to each other can form thymine dimers. In normal cells, they are excised and replaced.

Most mistakes are corrected; if they are not, they may result in a mutation—defined as a permanent change in the DNA sequence. Mutations in repair genes may lead to serious consequences like cancer.

Section Summary

DNA replicates by a semi-conservative method in which each of the two parental DNA strands act as a template for new DNA to be synthesized. After replication, each DNA has one parental or “old” strand, and one daughter or “new” strand.

Replication in eukaryotes starts at multiple origins of replication, while replication in prokaryotes starts from a single origin of replication. The DNA is opened with enzymes, resulting in the formation of the replication fork. Primase synthesizes an RNA primer to initiate synthesis by DNA polymerase, which can add nucleotides in only one direction. One strand is synthesized continuously in the direction of the replication fork; this is called the leading strand. The other strand is synthesized in a direction away from the replication fork, in short stretches of DNA known as Okazaki fragments. This strand is known as the lagging strand. Once replication is completed, the RNA primers are replaced by DNA nucleotides and the DNA is sealed with DNA ligase.

The ends of eukaryotic chromosomes pose a problem, as polymerase is unable to extend them without a primer. Telomerase, an enzyme with an inbuilt RNA template, extends the ends by copying the RNA template and extending one end of the chromosome. DNA polymerase can then extend the DNA using the primer. In this way, the ends of the chromosomes are protected. Cells have mechanisms for repairing DNA when it becomes damaged or errors are made in replication. These mechanisms include mismatch repair to replace nucleotides that are paired with a non-complementary base and nucleotide excision repair, which removes bases that are damaged such as thymine dimers.


You isolate a cell strain in which the joining together of Okazaki fragments is impaired and suspect that a mutation has occurred in an enzyme found at the replication fork. Which enzyme is most likely to be mutated?

Answer: Ligase, as this enzyme joins together Okazaki fragments.

Multiple Choice

DNA replicates by which of the following models?

A) conservative

B) semiconservative

C) dispersive

D) none of the above


The initial mechanism for repairing nucleotide errors in DNA is ________.

A) mismatch repair

B) DNA polymerase proofreading

C) nucleotide excision repair

D) thymine dimers


Free Response

How do the linear chromosomes in eukaryotes ensure that its ends are replicated completely?

Telomerase has an inbuilt RNA template that extends the 3′ end, so a primer is synthesized and extended. Thus, the ends are protected.


DNA ligase: the enzyme that catalyzes the joining of DNA fragments together

DNA polymerase: an enzyme that synthesizes a new strand of DNA complementary to a template strand

helicase: an enzyme that helps to open up the DNA helix during DNA replication by breaking the hydrogen bonds

lagging strand: during replication of the 3′ to 5′ strand, the strand that is replicated in short fragments and away from the replication fork

leading strand: the strand that is synthesized continuously in the 5′ to 3′ direction that is synthesized in the direction of the replication fork

mismatch repair: a form of DNA repair in which non-complementary nucleotides are recognized, excised, and replaced with correct nucleotides

mutation: a permanent variation in the nucleotide sequence of a genome

nucleotide excision repair: a form of DNA repair in which the DNA molecule is unwound and separated in the region of the nucleotide damage, the damaged nucleotides are removed and replaced with new nucleotides using the complementary strand, and the DNA strand is resealed and allowed to rejoin its complement

Okazaki fragments: the DNA fragments that are synthesized in short stretches on the lagging strand
primer: a short stretch of RNA nucleotides that is required to initiate replication and allow DNA polymerase to bind and begin replication

replication fork: the Y-shaped structure formed during the initiation of replication

semiconservative replication: the method used to replicate DNA in which the double-stranded molecule is separated and each strand acts as a template for a new strand to be synthesized, so the resulting DNA molecules are composed of one new strand of nucleotides and one old strand of nucleotides

telomerase: an enzyme that contains a catalytic part and an inbuilt RNA template; it functions to maintain telomeres at chromosome ends

telomere: the DNA at the end of linear chromosomes



1 Mariella Jaskelioff, et al., “Telomerase reactivation reverses tissue degeneration in aged telomerase-deficient mice,” Nature, 469 (2011):102–7.


9.3 Transcription

Learning Objectives

By the end of this section, you will be able to:

  • Explain the central dogma
  • Explain the main steps of transcription
  • Describe how eukaryotic mRNA is processed

In both prokaryotes and eukaryotes, the second function of DNA (the first was replication) is to provide the information needed to construct the proteins necessary so that the cell can perform all of its functions. To do this, the DNA is “read” or transcribed into an mRNA molecule. The mRNA then provides the code to form a protein by a process called translation. Through the processes of transcription and translation, a protein is built with a specific sequence of amino acids that was originally encoded in the DNA. This module discusses the details of transcription.

The Central Dogma: DNA Encodes RNA; RNA Encodes Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma (Figure 9.14), which states that genes specify the sequences of mRNAs, which in turn specify the sequences of proteins.

A flow chart shows DNA, with an arrow to RNA, which has an arrow to protein.

Figure 9.14 The central dogma states that DNA encodes RNA, which in turn encodes protein.

The copying of DNA to mRNA is relatively straightforward, with one nucleotide being added to the mRNA strand for every complementary nucleotide read in the DNA strand. The translation to protein is more complex because groups of three mRNA nucleotides correspond to one amino acid of the protein sequence. However, as we shall see in the next module, the translation to protein is still systematic, such that nucleotides 1 to 3 correspond to amino acid 1, nucleotides 4 to 6 correspond to amino acid 2, and so on.

Transcription: from DNA to mRNA

Both prokaryotes and eukaryotes perform fundamentally the same process of transcription, with the important difference of the membrane-bound nucleus in eukaryotes. With the genes bound in the nucleus, transcription occurs in the nucleus of the cell and the mRNA transcript must be transported to the cytoplasm. The prokaryotes, which include bacteria and archaea, lack membrane-bound nuclei and other organelles, and transcription occurs in the cytoplasm of the cell. In both prokaryotes and eukaryotes, transcription occurs in three main stages: initiation, elongation, and termination.


Transcription requires the DNA double helix to partially unwind in the region of mRNA synthesis. The region of unwinding is called a transcription bubble. The DNA sequence onto which the proteins and enzymes involved in transcription bind to initiate the process is called a promoter. In most cases, promoters exist upstream of the genes they regulate. The specific sequence of a promoter is very important because it determines whether the corresponding gene is transcribed all of the time, some of the time, or hardly at all (Figure 9.15).

Illustration shows a template strand and nontemplate strand of DNA, with a promoter section in red on the template strand. Downstream of the promoter is an RNA polymerase where RNA is being synthesized.

Figure 9.15 The initiation of transcription begins when DNA is unwound, forming a transcription bubble. Enzymes and other proteins involved in transcription bind at the promoter.


Transcription always proceeds from one of the two DNA strands, which is called the template strand. The mRNA product is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate strand, with the exception that RNA contains a uracil (U) in place of the thymine (T) found in DNA. During elongation, an enzyme called RNA polymerase proceeds along the DNA template adding nucleotides by base pairing with the DNA template in a manner similar to DNA replication, with the difference that an RNA strand is being synthesized that does not remain bound to the DNA template. As elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and rewound behind it (Figure 9.16).

Illustration shows RNA synthesis by RNA polymerase. The RNA strand is synthesized in the 5' to 3' direction.

Figure 9.16 During elongation, RNA polymerase tracks along the DNA template, synthesizes mRNA in the 5′ to 3′ direction, and unwinds then rewinds the DNA as it is read.


Once a gene is transcribed, the prokaryotic polymerase needs to be instructed to dissociate from the DNA template and liberate the newly made mRNA. Depending on the gene being transcribed, there are two kinds of termination signals, but both involve repeated nucleotide sequences in the DNA template that result in RNA polymerase stalling, leaving the DNA template, and freeing the mRNA transcript.

On termination, the process of transcription is complete. In a prokaryotic cell, by the time termination occurs, the transcript would already have been used to partially synthesize numerous copies of the encoded protein because these processes can occur concurrently using multiple ribosomes (polyribosomes) (Figure 9.17). In contrast, the presence of a nucleus in eukaryotic cells precludes simultaneous transcription and translation.

Illustration shows multiple mRNAs being transcribed off one gene. Ribosomes attach to the mRNA before transcription is done and begin making protein.

Figure 9.17 Multiple polymerases can transcribe a single bacterial gene while numerous ribosomes concurrently translate the mRNA transcripts into polypeptides. In this way, a specific protein can rapidly reach a high concentration in the bacterial cell.

Eukaryotic RNA Processing

The newly transcribed eukaryotic mRNAs must undergo several processing steps before they can be transferred from the nucleus to the cytoplasm and translated into a protein. The additional steps involved in eukaryotic mRNA maturation create a molecule that is much more stable than a prokaryotic mRNA. For example, eukaryotic mRNAs last for several hours, whereas the typical prokaryotic mRNA lasts no more than five seconds.

The mRNA transcript is first coated in RNA-stabilizing proteins to prevent it from degrading while it is processed and exported out of the nucleus. This occurs while the pre-mRNA still is being synthesized by adding a special nucleotide “cap” to the 5′ end of the growing transcript. In addition to preventing degradation, factors involved in protein synthesis recognize the cap to help initiate translation by ribosomes.

Once elongation is complete, an enzyme then adds a string of approximately 200 adenine residues to the 3′ end, called the poly-A tail. This modification further protects the pre-mRNA from degradation and signals to cellular factors that the transcript needs to be exported to the cytoplasm.

Eukaryotic genes are composed of protein-coding sequences called exons (ex-on signifies that they are expressed) and intervening sequences called introns (int-ron denotes their intervening role). Introns are removed from the pre-mRNA during processing. Intron sequences in mRNA do not encode functional proteins. It is essential that all of a pre-mRNA’s introns be completely and precisely removed before protein synthesis so that the exons join together to code for the correct amino acids. If the process errs by even a single nucleotide, the sequence of the rejoined exons would be shifted, and the resulting protein would be nonfunctional. The process of removing introns and reconnecting exons is called splicing (Figure 9.18). Introns are removed and degraded while the pre-mRNA is still in the nucleus.

Illustration shows a primary RNA transcript with three exons and two introns. In the spliced transcript, the introns are removed and the exons are fused together. A 5' cap and poly-A tail have also been added.

Figure 9.18 Eukaryotic mRNA contains introns that must be spliced out. A 5′ cap and 3′ tail are also added.

Section Summary

In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template. Elongation synthesizes new mRNA. Termination liberates the mRNA and occurs by mechanisms that stall the RNA polymerase and cause it to fall off the DNA template. Newly transcribed eukaryotic mRNAs are modified with a cap and a poly-A tail. These structures protect the mature mRNA from degradation and help export it from the nucleus. Eukaryotic mRNAs also undergo splicing, in which introns are removed and exons are reconnected with single-nucleotide accuracy. Only finished mRNAs are exported from the nucleus to the cytoplasm.


Multiple Choice

A promoter is ________.

A) a specific sequence of DNA nucleotides

B) a specific sequence of RNA nucleotides

C) a protein that binds to DNA

D) an enzyme that synthesizes RNA


Portions of eukaryotic mRNA sequence that are removed during RNA processing are ________.

A) exons

B) caps

C) poly-A tails

D) introns



exon: a sequence present in protein-coding mRNA after completion of pre-mRNA splicing

intron: non–protein-coding intervening sequences that are spliced from mRNA during processing

mRNA: messenger RNA; a form of RNA that carries the nucleotide sequence code for a protein sequence that is translated into a polypeptide sequence

nontemplate strand: the strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that T nucleotides in the DNA are replaced by U nucleotides in the mRNA

promoter: a sequence on DNA to which RNA polymerase and associated factors bind and initiate transcription

RNA polymerase: an enzyme that synthesizes an RNA strand from a DNA template strand

splicing: the process of removing introns and reconnecting exons in a pre-mRNA

template strand: the strand of DNA that specifies the complementary mRNA molecule

transcription bubble: the region of locally unwound DNA that allows for transcription of mRNA




9.4 Translation

Learning Objectives

By the end of this section, you will be able to:

  • Describe the different steps in protein synthesis
  • Discuss the role of ribosomes in protein synthesis
  • Describe the genetic code and how the nucleotide sequence determines the amino acid and the protein sequence

The synthesis of proteins is one of a cell’s most energy-consuming metabolic processes. In turn, proteins account for more mass than any other component of living organisms (with the exception of water), and proteins perform a wide variety of the functions of a cell. The process of translation, or protein synthesis, involves decoding an mRNA message into a polypeptide product. Amino acids are covalently strung together in lengths ranging from approximately 50 amino acids to more than 1,000.

The Protein Synthesis Machinery

In addition to the mRNA template, many other molecules contribute to the process of translation. The composition of each component may vary across species; for instance, ribosomes may consist of different numbers of ribosomal RNAs (rRNA) and polypeptides depending on the organism. However, the general structures and functions of the protein synthesis machinery are comparable from bacteria to human cells. Translation requires the input of an mRNA template, ribosomes, tRNAs, and various enzymatic factors (Figure 9.19).

Illustration of the molecules involved in protein translation. A ribosome is shown with mRNA and tRNA. Amino acids are emerging to form a protein chain.

Figure 9.19 The protein synthesis machinery includes the large and small subunits of the ribosome, mRNA, and tRNA. (credit: modification of work by NIGMS, NIH)

In E. coli, there are 200,000 ribosomes present in every cell at any given time. A ribosome is a complex macromolecule composed of structural and catalytic rRNAs, and many distinct polypeptides. In eukaryotes, the nucleolus is completely specialized for the synthesis and assembly of rRNAs.

Ribosomes are located in the cytoplasm in prokaryotes and in the cytoplasm and endoplasmic reticulum of eukaryotes. Ribosomes are made up of a large and a small subunit that come together for translation. The small subunit is responsible for binding the mRNA template, whereas the large subunit sequentially binds tRNAs, a type of RNA molecule that brings amino acids to the growing chain of the polypeptide. Each mRNA molecule is simultaneously translated by many ribosomes, all synthesizing protein in the same direction.

Depending on the species, 40 to 60 types of tRNA exist in the cytoplasm. Serving as adaptors, specific tRNAs bind to sequences on the mRNA template and add the corresponding amino acid to the polypeptide chain. Therefore, tRNAs are the molecules that actually “translate” the language of RNA into the language of proteins. For each tRNA to function, it must have its specific amino acid bonded to it. In the process of tRNA “charging,” each tRNA molecule is bonded to its correct amino acid.

The Genetic Code

To summarize what we know to this point, the cellular process of transcription generates messenger RNA (mRNA), a mobile molecular copy of one or more genes with an alphabet of A, C, G, and uracil (U). Translation of the mRNA template converts nucleotide-based genetic information into a protein product. Protein sequences consist of 20 commonly occurring amino acids; therefore, it can be said that the protein alphabet consists of 20 letters. Each amino acid is defined by a three-nucleotide sequence called the triplet codon. The relationship between a nucleotide codon and its corresponding amino acid is called the genetic code.

Given the different numbers of “letters” in the mRNA and protein “alphabets,” combinations of nucleotides corresponded to single amino acids. Using a three-nucleotide code means that there are a total of 64 (4 × 4 × 4) possible combinations; therefore, a given amino acid is encoded by more than one nucleotide triplet (Figure 9.20).

Figure shows all 64 codons. Sixty-two of these code for amino acids, and three are stop codons shown in red. The start codon, AUG, is colored green.

Figure 9.20 This figure shows the genetic code for translating each nucleotide triplet, or codon, in mRNA into an amino acid or a termination signal in a nascent protein. (credit: modification of work by NIH)

Three of the 64 codons terminate protein synthesis and release the polypeptide from the translation machinery. These triplets are called stop codons. Another codon, AUG, also has a special function. In addition to specifying the amino acid methionine, it also serves as the start codon to initiate translation. The reading frame for translation is set by the AUG start codon near the 5′ end of the mRNA. The genetic code is universal. With a few exceptions, virtually all species use the same genetic code for protein synthesis, which is powerful evidence that all life on Earth shares a common origin.

The Mechanism of Protein Synthesis

Just as with mRNA synthesis, protein synthesis can be divided into three phases: initiation, elongation, and termination. The process of translation is similar in prokaryotes and eukaryotes. Here we will explore how translation occurs in E. coli, a representative prokaryote, and specify any differences between prokaryotic and eukaryotic translation.

Protein synthesis begins with the formation of an initiation complex. In E. coli, this complex involves the small ribosome subunit, the mRNA template, three initiation factors, and a special initiator tRNA. The initiator tRNA interacts with the AUG start codon, and links to a special form of the amino acid methionine that is typically removed from the polypeptide after translation is complete.

In prokaryotes and eukaryotes, the basics of polypeptide elongation are the same, so we will review elongation from the perspective of E. coli. The large ribosomal subunit of E. coli consists of three compartments: the A site binds incoming charged tRNAs (tRNAs with their attached specific amino acids). The P site binds charged tRNAs carrying amino acids that have formed bonds with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA. The E site releases dissociated tRNAs so they can be recharged with free amino acids. The ribosome shifts one codon at a time, catalyzing each process that occurs in the three sites. With each step, a charged tRNA enters the complex, the polypeptide becomes one amino acid longer, and an uncharged tRNA departs. The energy for each bond between amino acids is derived from GTP, a molecule similar to ATP (Figure 9.21). Amazingly, the E. coli translation apparatus takes only 0.05 seconds to add each amino acid, meaning that a 200-amino acid polypeptide could be translated in just 10 seconds.

Illustration shows the steps of protein synthesis. First, an initiator tRNA recognizes the sequence AUG on the mRNA that is associated with the small ribosomal subunit. The large subunit joins the complex. Next, a second tRNA is recruited at the A site. A peptide bond is formed between the first amino acid, which is at the P site, and the second amino acid, which is at the A site. The mRNA then shifts and the first tRNA is moved to the E site, where it dissociates from the ribosome. Another tRNA binds the A site, and the process is repeated.

Figure 9.21 Translation begins when a tRNA anticodon recognizes a codon on the mRNA. The large ribosomal subunit joins the small subunit, and a second tRNA is recruited. As the mRNA moves relative to the ribosome, the polypeptide chain is formed. Entry of a release factor into the A site terminates translation and the components dissociate.

Termination of translation occurs when a stop codon (UAA, UAG, or UGA) is encountered. When the ribosome encounters the stop codon, the growing polypeptide is released and the ribosome subunits dissociate and leave the mRNA. After many ribosomes have completed translation, the mRNA is degraded so the nucleotides can be reused in another transcription reaction.

Concept in Action

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Transcribe a gene and translate it to protein using complementary pairing and the genetic code at this site.

Section Summary

The central dogma describes the flow of genetic information in the cell from genes to mRNA to proteins. Genes are used to make mRNA by the process of transcription; mRNA is used to synthesize proteins by the process of translation. The genetic code is the correspondence between the three-nucleotide mRNA codon and an amino acid. The genetic code is “translated” by the tRNA molecules, which associate a specific codon with a specific amino acid. The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three stop codons. This means that more than one codon corresponds to an amino acid. Almost every species on the planet uses the same genetic code.

The players in translation include the mRNA template, ribosomes, tRNAs, and various enzymatic factors. The small ribosomal subunit binds to the mRNA template. Translation begins at the initiating AUG on the mRNA. The formation of bonds occurs between sequential amino acids specified by the mRNA template according to the genetic code. The ribosome accepts charged tRNAs, and as it steps along the mRNA, it catalyzes bonding between the new amino acid and the end of the growing polypeptide. The entire mRNA is translated in three-nucleotide “steps” of the ribosome. When a stop codon is encountered, a release factor binds and dissociates the components and frees the new protein.


Multiple Choice

The RNA components of ribosomes are synthesized in the ________.

A) cytoplasm

B) nucleus

C) nucleolus

D) endoplasmic reticulum


How long would the peptide be that is translated from this MRNA sequence: 5′-AUGGGCUACCGA-3′?

A) 0

B) 2

C) 3

D) 4


Free Response

Transcribe and translate the following DNA sequence (nontemplate strand): 5′-ATGGCCGGTTATTAAGCA-3′

The mRNA would be: 5′-AUGGCCGGUUAUUAAGCA-3′. The protein would be: MAGY. Even though there are six codons, the fifth codon corresponds to a stop, so the sixth codon would not be translated.


codon: three consecutive nucleotides in mRNA that specify the addition of a specific amino acid or the release of a polypeptide chain during translation

genetic code: the amino acids that correspond to three-nucleotide codons of mRNA

rRNA: ribosomal RNA; molecules of RNA that combine to form part of the ribosome

stop codon: one of the three mRNA codons that specifies termination of translation

start codon: the AUG (or, rarely GUG) on an mRNA from which translation begins; always specifies methionine

tRNA: transfer RNA; an RNA molecule that contains a specific three-nucleotide anticodon sequence to pair with the mRNA codon and also binds to a specific amino acid


9.5 How Genes Are Regulated

Learning Objectives

By the end of this section, you will be able to:

  • Discuss why every cell does not express all of its genes
  • Describe how prokaryotic gene expression occurs at the transcriptional level
  • Understand that eukaryotic gene expression occurs at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels

For a cell to function properly, necessary proteins must be synthesized at the proper time. All organisms and cells control or regulate the transcription and translation of their DNA into protein. The process of turning on a gene to produce RNA and protein is called gene expression. Whether in a simple unicellular organism or in a complex multicellular organism, each cell controls when and how its genes are expressed. For this to occur, there must be a mechanism to control when a gene is expressed to make RNA and protein, how much of the protein is made, and when it is time to stop making that protein because it is no longer needed.

Cells in multicellular organisms are specialized; cells in different tissues look very different and perform different functions. For example, a muscle cell is very different from a liver cell, which is very different from a skin cell. These differences are a consequence of the expression of different sets of genes in each of these cells. All cells have certain basic functions they must perform for themselves, such as converting the energy in sugar molecules into energy in ATP. Each cell also has many genes that are not expressed, and expresses many that are not expressed by other cells, such that it can carry out its specialized functions. In addition, cells will turn on or off certain genes at different times in response to changes in the environment or at different times during the development of the organism. Unicellular organisms, both eukaryotic and prokaryotic, also turn on and off genes in response to the demands of their environment so that they can respond to special conditions.

The control of gene expression is extremely complex. Malfunctions in this process are detrimental to the cell and can lead to the development of many diseases, including cancer.

Prokaryotic versus Eukaryotic Gene Expression

To understand how gene expression is regulated, we must first understand how a gene becomes a functional protein in a cell. The process occurs in both prokaryotic and eukaryotic cells, just in slightly different fashions.

Because prokaryotic organisms lack a cell nucleus, the processes of transcription and translation occur almost simultaneously. When the protein is no longer needed, transcription stops. As a result, the primary method to control what type and how much protein is expressed in a prokaryotic cell is through the regulation of DNA transcription into RNA. All the subsequent steps happen automatically. When more protein is required, more transcription occurs. Therefore, in prokaryotic cells, the control of gene expression is almost entirely at the transcriptional level.

The first example of such control was discovered using E. coli in the 1950s and 1960s by French researchers and is called the lac operon. The lac operon is a stretch of DNA with three adjacent genes that code for proteins that participate in the absorption and metabolism of lactose, a food source for E. coli. When lactose is not present in the bacterium’s environment, the lac genes are transcribed in small amounts. When lactose is present, the genes are transcribed and the bacterium is able to use the lactose as a food source. The operon also contains a promoter sequence to which the RNA polymerase binds to begin transcription; between the promoter and the three genes is a region called the operator. When there is no lactose present, a protein known as a repressor binds to the operator and prevents RNA polymerase from binding to the promoter, except in rare cases. Thus very little of the protein products of the three genes is made. When lactose is present, an end product of lactose metabolism binds to the repressor protein and prevents it from binding to the operator. This allows RNA polymerase to bind to the promoter and freely transcribe the three genes, allowing the organism to metabolize the lactose.

Eukaryotic cells, in contrast, have intracellular organelles and are much more complex. Recall that in eukaryotic cells, the DNA is contained inside the cell’s nucleus and it is transcribed into mRNA there. The newly synthesized mRNA is then transported out of the nucleus into the cytoplasm, where ribosomes translate the mRNA into protein. The processes of transcription and translation are physically separated by the nuclear membrane; transcription occurs only within the nucleus, and translation only occurs outside the nucleus in the cytoplasm. The regulation of gene expression can occur at all stages of the process (Figure 9.22). Regulation may occur when the DNA is uncoiled and loosened from nucleosomes to bind transcription factors (epigenetic level), when the RNA is transcribed (transcriptional level), when RNA is processed and exported to the cytoplasm after it is transcribed (post-transcriptional level), when the RNA is translated into protein (translational level), or after the protein has been made (post-translational level).

Illustration shows the steps of protein synthesis in three steps: transcription, RNA processing, and translation. In transcription, the RNA strand is synthesized by RNA polymerase in the 5' to 3' direction. In RNA processing, a primary RNA transcript with three exons and two introns is shown. In the spliced transcript, the introns are removed and the exons are fused together. A 5' cap and poly-A tail have also been added. In translation, an initiator tRNA recognizes the sequence AUG on the mRNA that is associated with the small ribosomal subunit. The large subunit joins the complex. Next, a second tRNA is recruited at the A site. A peptide bond is formed between the first amino acid, which is at the P site, and the second amino acid, which is at the A site. The mRNA then shifts and the first tRNA is moved to the E site, where it dissociates from the ribosome. Another tRNA binds the A site, and the process is repeated.

Figure 9.22 Eukaryotic gene expression is regulated during transcription and RNA processing, which take place in the nucleus, as well as during protein translation, which takes place in the cytoplasm. Further regulation may occur through post-translational modifications of proteins.

The differences in the regulation of gene expression between prokaryotes and eukaryotes are summarized in the table below.

Differences in the Regulation of Gene Expression of Prokaryotic and Eukaryotic Organisms
Prokaryotic organisms Eukaryotic organisms
Lack nucleus Contain nucleus
RNA transcription and protein translation occur almost simultaneously
  • RNA transcription occurs prior to protein translation, and it takes place in the nucleus. RNA translation to protein occurs in the cytoplasm.
  • RNA post-processing includes addition of a 5′ cap, poly-A tail, and excision of introns and splicing of exons.
Gene expression is regulated primarily at the transcriptional level Gene expression is regulated at many levels (epigenetic, transcriptional, post-transcriptional, translational, and post-translational)

Alternative RNA Splicing

In the 1970s, genes were first observed that exhibited alternative RNA splicing. Alternative RNA splicing is a mechanism that allows different protein products to be produced from one gene when different combinations of introns (and sometimes exons) are removed from the transcript (Figure 9.23). This alternative splicing can be haphazard, but more often it is controlled and acts as a mechanism of gene regulation, with the frequency of different splicing alternatives controlled by the cell as a way to control the production of different protein products in different cells, or at different stages of development. Alternative splicing is now understood to be a common mechanism of gene regulation in eukaryotes; according to one estimate, 70% of genes in humans are expressed as multiple proteins through alternative splicing.

Illustration of segments of pre-mRNA with exons shown in blue, red, orange, and pink. Five basic modes of alternative splicing are generally recognized. Each segment of pre-mRNA can be spliced to produce a variety of new mature mRNA segments; two are shown for each here. In the case of exon skipping, an exon may be spliced out or retained. In the case of mutually exclusive exons, one of two exons is retained in mRNAs after splicing, but not both. In the case of an alternative donor site, an alternative 5' splice junction (donor site) is used, changing the 3' boundary of the upstream exon. In the case of an alternative acceptor site, an alternative 3' splice junction (acceptor site) is used, changing the 5' boundary of the downstream exon. In the case of intron retention, a sequence may be spliced out as an intron or simply retained. This is distinguished from exon skipping because the retained sequence is not flanked by introns. The pink portion is considered an intron when skipped (top) and an exon when included (bottom).

Figure 9.23 There are five basic modes of alternative splicing. Segments of pre-mRNA with exons shown in blue, red, orange, and pink can be spliced to produce a variety of new mature mRNA segments.

How could alternative splicing evolve? Introns have a beginning and ending recognition sequence, and it is easy to imagine the failure of the splicing mechanism to identify the end of an intron and find the end of the next intron, thus removing two introns and the intervening exon. In fact, there are mechanisms in place to prevent such exon skipping, but mutations are likely to lead to their failure. Such “mistakes” would more than likely produce a nonfunctional protein. Indeed, the cause of many genetic diseases is alternative splicing rather than mutations in a sequence. However, alternative splicing would create a protein variant without the loss of the original protein, opening up possibilities for adaptation of the new variant to new functions. Gene duplication has played an important role in the evolution of new functions in a similar way—by providing genes that may evolve without eliminating the original functional protein.

Section Summary

While all somatic cells within an organism contain the same DNA, not all cells within that organism express the same proteins. Prokaryotic organisms express the entire DNA they encode in every cell, but not necessarily all at the same time. Proteins are expressed only when they are needed. Eukaryotic organisms express a subset of the DNA that is encoded in any given cell. In each cell type, the type and amount of protein is regulated by controlling gene expression. To express a protein, the DNA is first transcribed into RNA, which is then translated into proteins. In prokaryotic cells, these processes occur almost simultaneously. In eukaryotic cells, transcription occurs in the nucleus and is separate from the translation that occurs in the cytoplasm. Gene expression in prokaryotes is regulated only at the transcriptional level, whereas in eukaryotic cells, gene expression is regulated at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels.


Multiple Choice

Control of gene expression in eukaryotic cells occurs at which level(s)?

A) only the transcriptional level

B) epigenetic and transcriptional levels

C) epigenetic, transcriptional, and translational levels

D) epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels


Post-translational control refers to:

A) regulation of gene expression after transcription

B) regulation of gene expression after translation

C) control of epigenetic activation

D) period between transcription and translation


Free Response

Describe how controlling gene expression will alter the overall protein levels in the cell.

The cell controls which protein is expressed, and to what level that protein is expressed, in the cell. Prokaryotic cells alter the transcription rate to turn genes on or off. This method will increase or decrease protein levels in response to what is needed by the cell. Eukaryotic cells change the accessibility (epigenetic), transcription, or translation of a gene. This will alter the amount of RNA, and the lifespan of the RNA, to alter the amount of protein that exists. Eukaryotic cells also change the protein’s translation to increase or decrease its overall levels. Eukaryotic organisms are much more complex and can manipulate protein levels by changing many stages in the process.



alternative RNA splicing: a post-transcriptional gene regulation mechanism in eukaryotes in which multiple protein products are produced by a single gene through alternative splicing combinations of the RNA transcript

epigenetic: describing non-genetic regulatory factors, such as changes in modifications to histone proteins and DNA that control accessibility to genes in chromosomes

gene expression: processes that control whether a gene is expressed

post-transcriptional: control of gene expression after the RNA molecule has been created but before it is translated into protein

post-translational: control of gene expression after a protein has been created


Chapter 9 PowerPoint

Chapter 9 PowerPoint


Chapter 10: Introduction to Biotechnology

In part A, a PCR machine sits on a desk. It has a digital screen on the front and buttons, and “caution, hot base” is written on the front. Part B shows a hot spring in Yellowstone.

Figure 10.1 (a) A thermal cycler, such as the one shown here, is a basic tool used to study DNA in a process called the polymerase chain reaction (PCR). The polymerase enzyme most often used with PCR comes from a strain of bacteria that lives in (b) the hot springs of Yellowstone National Park. (credit a: modification of work by Magnus Manske; credit b: modification of work by Jon Sullivan)


The latter half of the twentieth century began with the discovery of the structure of DNA, then progressed to the development of the basic tools used to study and manipulate DNA. These advances, as well as advances in our understanding of and ability to manipulate cells, have led some to refer to the twenty-first century as the biotechnology century. The rate of discovery and of the development of new applications in medicine, agriculture, and energy is expected to accelerate, bringing huge benefits to humankind and perhaps also significant risks. Many of these developments are expected to raise significant ethical and social questions that human societies have not yet had to consider.


10.1 Cloning and Genetic Engineering

Learning Objectives

By the end of this section, you will be able to:

  • Explain the basic techniques used to manipulate genetic material
  • Explain molecular and reproductive cloning

Biotechnology is the use of artificial methods to modify the genetic material of living organisms or cells to produce novel compounds or to perform new functions. Biotechnology has been used for improving livestock and crops since the beginning of agriculture through selective breeding. Since the discovery of the structure of DNA in 1953, and particularly since the development of tools and methods to manipulate DNA in the 1970s, biotechnology has become synonymous with the manipulation of organisms’ DNA at the molecular level. The primary applications of this technology are in medicine (for the production of vaccines and antibiotics) and in agriculture (for the genetic modification of crops). Biotechnology also has many industrial applications, such as fermentation, the treatment of oil spills, and the production of biofuels, as well as many household applications such as the use of enzymes in laundry detergent.

Manipulating Genetic Material

To accomplish the applications described above, biotechnologists must be able to extract, manipulate, and analyze nucleic acids.

Review of Nucleic Acid Structure

To understand the basic techniques used to work with nucleic acids, remember that nucleic acids are macromolecules made of nucleotides (a sugar, a phosphate, and a nitrogenous base). The phosphate groups on these molecules each have a net negative charge. An entire set of DNA molecules in the nucleus of eukaryotic organisms is called the genome. DNA has two complementary strands linked by hydrogen bonds between the paired bases.

Unlike DNA in eukaryotic cells, RNA molecules leave the nucleus. Messenger RNA (mRNA) is analyzed most frequently because it represents the protein-coding genes that are being expressed in the cell.

Isolation of Nucleic Acids

To study or manipulate nucleic acids, the DNA must first be extracted from cells. Various techniques are used to extract different types of DNA (Figure 10.2). Most nucleic acid extraction techniques involve steps to break open the cell, and then the use of enzymatic reactions to destroy all undesired macromolecules. Cells are broken open using a detergent solution containing buffering compounds. To prevent degradation and contamination, macromolecules such as proteins and RNA are inactivated using enzymes. The DNA is then brought out of solution using alcohol. The resulting DNA, because it is made up of long polymers, forms a gelatinous mass.

Four test tubes are illustrated, showing four steps in extracting DNA. In the first, cells are lysed using a detergent that disrupts the plasma membrane. In the second, cell contents are treated with protease to destroy protein, and RNase to destroy RNA. In the third, cell debris is pelleted in a centrifuge. The supernatant (liquid) containing the DNA is transferred to a clean tube. In the fourth test tube, the DNA is precipitated with ethanol. It forms viscous strands that can be spooled on a glass rod.

Figure 10.2 This diagram shows the basic method used for the extraction of DNA.

RNA is studied to understand gene expression patterns in cells. RNA is naturally very unstable because enzymes that break down RNA are commonly present in nature. Some are even secreted by our own skin and are very difficult to inactivate. Similar to DNA extraction, RNA extraction involves the use of various buffers and enzymes to inactivate other macromolecules and preserve only the RNA.

Gel Electrophoresis

Because nucleic acids are negatively charged ions at neutral or alkaline pH in an aqueous environment, they can be moved by an electric field. Gel electrophoresis is a technique used to separate charged molecules on the basis of size and charge. The nucleic acids can be separated as whole chromosomes or as fragments. The nucleic acids are loaded into a slot at one end of a gel matrix, an electric current is applied, and negatively charged molecules are pulled toward the opposite end of the gel (the end with the positive electrode). Smaller molecules move through the pores in the gel faster than larger molecules; this difference in the rate of migration separates the fragments on the basis of size. The nucleic acids in a gel matrix are invisible until they are stained with a compound that allows them to be seen, such as a dye. Distinct fragments of nucleic acids appear as bands at specific distances from the top of the gel (the negative electrode end) that are based on their size (Figure 10.3). A mixture of many fragments of varying sizes appear as a long smear, whereas uncut genomic DNA is usually too large to run through the gel and forms a single large band at the top of the gel.

Photo shows a black background with 9 faint gray vertical bands (lanes). In those bands are horizontal white slightly blurry bands of varying thicknesses and brightness. The faint gray lanes on the left and right edges have a lot of horizontal bands, and the 7 in the middle have only a few each, in different positions.

Figure 10.3 Shown are DNA fragments from six samples run on a gel, stained with a fluorescent dye and viewed under UV light. (credit: modification of work by James Jacob, Tompkins Cortland Community College)

Polymerase Chain Reaction

DNA analysis often requires focusing on one or more specific regions of the genome. It also frequently involves situations in which only one or a few copies of a DNA molecule are available for further analysis. These amounts are insufficient for most procedures, such as gel electrophoresis. Polymerase chain reaction (PCR) is a technique used to rapidly increase the number of copies of specific regions of DNA for further analyses (Figure 10.4). PCR uses a special form of DNA polymerase, the enzyme that replicates DNA, and other short nucleotide sequences called primers that base pair to a specific portion of the DNA being replicated. PCR is used for many purposes in laboratories. These include: 1) the identification of the owner of a DNA sample left at a crime scene; 2) paternity analysis; 3) the comparison of small amounts of ancient DNA with modern organisms; and 4) determining the sequence of nucleotides in a specific region.

Figure showing PCR in 4 steps. First, the double strand of DNA is denatured at 95 degrees Celsius to separate the strands. The 2 strands are then annealed at approximately 50 degrees Celsius using primers. DNA polymerase then extends the new strands at 72 degrees Celsius. The fourth step shows that this procedure takes place many times, resulting in an increase in copies of the original DNA.

Figure 10.4 Polymerase chain reaction, or PCR, is used to produce many copies of a specific sequence of DNA using a special form of DNA polymerase. Figure showing PCR in 4 steps. First, the double strand of DNA is denatured at 95 degrees Celsius to separate the strands. The 2 strands are then annealed at approximately 50 degrees Celsius using primers. DNA polymerase then extends the new strands at 72 degrees Celsius. The fourth step shows that this procedure takes place many times, resulting in an increase in copies of the original DNA.


In general, cloning means the creation of a perfect replica. Typically, the word is used to describe the creation of a genetically identical copy. In biology, the re-creation of a whole organism is referred to as “reproductive cloning.” Long before attempts were made to clone an entire organism, researchers learned how to copy short stretches of DNA—a process that is referred to as molecular cloning.

Molecular Cloning

Cloning allows for the creation of multiple copies of genes, expression of genes, and study of specific genes. To get the DNA fragment into a bacterial cell in a form that will be copied or expressed, the fragment is first inserted into a plasmid. A plasmid (also called a vector in this context) is a small circular DNA molecule that replicates independently of the chromosomal DNA in bacteria. In cloning, the plasmid molecules can be used to provide a “vehicle” in which to insert a desired DNA fragment. Modified plasmids are usually reintroduced into a bacterial host for replication. As the bacteria divide, they copy their own DNA (including the plasmids). The inserted DNA fragment is copied along with the rest of the bacterial DNA. In a bacterial cell, the fragment of DNA from the human genome (or another organism that is being studied) is referred to as foreign DNA to differentiate it from the DNA of the bacterium (the host DNA).

Plasmids occur naturally in bacterial populations (such as Escherichia coli) and have genes that can contribute favorable traits to the organism, such as antibiotic resistance (the ability to be unaffected by antibiotics). Plasmids have been highly engineered as vectors for molecular cloning and for the subsequent large-scale production of important molecules, such as insulin. A valuable characteristic of plasmid vectors is the ease with which a foreign DNA fragment can be introduced. These plasmid vectors contain many short DNA sequences that can be cut with different commonly available restriction enzymes. Restriction enzymes (also called restriction endonucleases) recognize specific DNA sequences and cut them in a predictable manner; they are naturally produced by bacteria as a defense mechanism against foreign DNA. Many restriction enzymes make staggered cuts in the two strands of DNA, such that the cut ends have a 2- to 4-nucleotide single-stranded overhang. The sequence that is recognized by the restriction enzyme is a four- to eight-nucleotide sequence that is a palindrome. Like with a word palindrome, this means the sequence reads the same forward and backward. In most cases, the sequence reads the same forward on one strand and backward on the complementary strand. When a staggered cut is made in a sequence like this, the overhangs are complementary (Figure 10.5).

In part A, the figure shows a strand of ladder-like DNA. In part B, the DNA is cut on both strands between the two guanines. In part C, the 2 strands have separated, leaving complementary sticky ends on each with unattached 5' to 3' G, A, T, and C nucleotides.

Figure 10.5 In this (a) six-nucleotide restriction enzyme recognition site, notice that the sequence of six nucleotides reads the same in the 5′ to 3′ direction on one strand as it does in the 5′ to 3′ direction on the complementary strand. This is known as a palindrome. (b) The restriction enzyme makes breaks in the DNA strands, and (c) the cut in the DNA results in “sticky ends”. Another piece of DNA cut on either end by the same restriction enzyme could attach to these sticky ends and be inserted into the gap made by this cut.

Because these overhangs are capable of coming back together by hydrogen bonding with complementary overhangs on a piece of DNA cut with the same restriction enzyme, these are called “sticky ends.” The process of forming hydrogen bonds between complementary sequences on single strands to form double-stranded DNA is called annealing. Addition of an enzyme called DNA ligase, which takes part in DNA replication in cells, permanently joins the DNA fragments when the sticky ends come together. In this way, any DNA fragment can be spliced between the two ends of a plasmid DNA that has been cut with the same restriction enzyme (Figure 10.6).

An illustration showing the steps in creating recombinant DNA plasmids, inserting them into bacteria, and then selecting only the bacteria that have successfully taken up the recombinant plasmid. The steps are as follows: both foreign DNA and a plasmid are cut with the same restriction enzyme. The restriction site occurs only once in the plasmid in the middle of a gene for an enzyme (lacZ). The restriction enzyme leaves complementary sticky ends on the foreign DNA fragment and the plasmid. This allows the foreign DNA to be inserted into the plasmid when the sticky ends anneal. Adding DNA ligase reattaches the DNA backbones. These are recombinant plasmids. The plasmids are combined with a culture of living bacteria. Many of the bacteria do not take any plasmids into their cells, many take plasmids that do not have the foreign DNA in them, and a few take up the recombinant plasmid. The bacteria that take up the recombinant plasmid cannot make the enzyme from the gene that the fragment was inserted into (lacZ). They also carry a gene for resistance to the antibiotic ampicillin, which was on the original plasmid. To find the bacteria with the recombinant plasmid, the bacteria are grown on a plate with the antibiotic ampicillin and a substance that changes color when exposed to the enzyme produced by the lacZ gene. The ampicillin will kill any bacteria that did not take up a plasmid. The color of the substance will not change when the gene for lacZ contains the foreign DNA insert. These are the bacteria with the recombinant plasmid that we want to grow.

Figure 10.6 This diagram shows the steps involved in molecular cloning.

Plasmids with foreign DNA inserted into them are called recombinant DNA molecules because they contain new combinations of genetic material. Proteins that are produced from recombinant DNA molecules are called recombinant proteins. Not all recombinant plasmids are capable of expressing genes. Plasmids may also be engineered to express proteins only when stimulated by certain environmental factors, so that scientists can control the expression of the recombinant proteins.

Reproductive Cloning

Reproductive cloning is a method used to make a clone or an identical copy of an entire multicellular organism. Most multicellular organisms undergo reproduction by sexual means, which involves the contribution of DNA from two individuals (parents), making it impossible to generate an identical copy or a clone of either parent. Recent advances in biotechnology have made it possible to reproductively clone mammals in the laboratory.

Natural sexual reproduction involves the union, during fertilization, of a sperm and an egg. Each of these gametes is haploid, meaning they contain one set of chromosomes in their nuclei. The resulting cell, or zygote, is then diploid and contains two sets of chromosomes. This cell divides mitotically to produce a multicellular organism. However, the union of just any two cells cannot produce a viable zygote; there are components in the cytoplasm of the egg cell that are essential for the early development of the embryo during its first few cell divisions. Without these provisions, there would be no subsequent development. Therefore, to produce a new individual, both a diploid genetic complement and an egg cytoplasm are required. The approach to producing an artificially cloned individual is to take the egg cell of one individual and to remove the haploid nucleus. Then a diploid nucleus from a body cell of a second individual, the donor, is put into the egg cell. The egg is then stimulated to divide so that development proceeds. This sounds simple, but in fact it takes many attempts before each of the steps is completed successfully.

The first cloned agricultural animal was Dolly, a sheep who was born in 1996. The success rate of reproductive cloning at the time was very low. Dolly lived for six years and died of a lung tumor (Figure 10.7). There was speculation that because the cell DNA that gave rise to Dolly came from an older individual, the age of the DNA may have affected her life expectancy. Since Dolly, several species of animals (such as horses, bulls, and goats) have been successfully cloned.

There have been attempts at producing cloned human embryos as sources of embryonic stem cells. In the procedure, the DNA from an adult human is introduced into a human egg cell, which is then stimulated to divide. The technology is similar to the technology that was used to produce Dolly, but the embryo is never implanted into a surrogate mother. The cells produced are called embryonic stem cells because they have the capacity to develop into many different kinds of cells, such as muscle or nerve cells. The stem cells could be used to research and ultimately provide therapeutic applications, such as replacing damaged tissues. The benefit of cloning in this instance is that the cells used to regenerate new tissues would be a perfect match to the donor of the original DNA. For example, a leukemia patient would not require a sibling with a tissue match for a bone-marrow transplant.

The illustration shows the steps in cloning the sheep named Dolly. An enucleated egg cell from one sheep is fused with a mammary cell from another sheep. This fused cell then divides to the blastocyst stage and is placed in the uterus of the surrogate ewe, where it develops into the lamb, Dolly. Dolly is the genetic clone of the mammary cell donor.

Figure 10.7 Dolly the sheep was the first agricultural animal to be cloned. To create Dolly, the nucleus was removed from a donor egg cell. The enucleated egg was placed next to the other cell, then they were shocked to fuse. They were shocked again to start division. The cells were allowed to divide for several days until an early embryonic stage was reached, before being implanted in a surrogate mother.

Why was Dolly a Finn-Dorset and not a Scottish Blackface sheep?

Because even though the original cell came from a Scottish Blackface sheep and the surrogate mother was a Scottish Blackface, the DNA came from a Finn-Dorset.

Genetic Engineering

Using recombinant DNA technology to modify an organism’s DNA to achieve desirable traits is called genetic engineering. Addition of foreign DNA in the form of recombinant DNA vectors that are generated by molecular cloning is the most common method of genetic engineering. An organism that receives the recombinant DNA is called a genetically modified organism (GMO). If the foreign DNA that is introduced comes from a different species, the host organism is called transgenic. Bacteria, plants, and animals have been genetically modified since the early 1970s for academic, medical, agricultural, and industrial purposes. These applications will be examined in more detail in the next module.

Concept in Action

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Watch this short video explaining how scientists create a transgenic animal.

Although the classic methods of studying the function of genes began with a given phenotype and determined the genetic basis of that phenotype, modern techniques allow researchers to start at the DNA sequence level and ask: “What does this gene or DNA element do?” This technique, called reverse genetics, has resulted in reversing the classical genetic methodology. One example of this method is analogous to damaging a body part to determine its function. An insect that loses a wing cannot fly, which means that the wing’s function is flight. The classic genetic method compares insects that cannot fly with insects that can fly, and observes that the non-flying insects have lost wings. Similarly in a reverse genetics approach, mutating or deleting genes provides researchers with clues about gene function. Alternately, reverse genetics can be used to cause a gene to overexpress itself to determine what phenotypic effects may occur.

Section Summary

Nucleic acids can be isolated from cells for the purposes of further analysis by breaking open the cells and enzymatically destroying all other major macromolecules. Fragmented or whole chromosomes can be separated on the basis of size by gel electrophoresis. Short stretches of DNA can be amplified by PCR. DNA can be cut (and subsequently re-spliced together) using restriction enzymes. The molecular and cellular techniques of biotechnology allow researchers to genetically engineer organisms, modifying them to achieve desirable traits.

Cloning may involve cloning small DNA fragments (molecular cloning), or cloning entire organisms (reproductive cloning). In molecular cloning with bacteria, a desired DNA fragment is inserted into a bacterial plasmid using restriction enzymes and the plasmid is taken up by a bacterium, which will then express the foreign DNA. Using other techniques, foreign genes can be inserted into eukaryotic organisms. In each case, the organisms are called transgenic organisms. In reproductive cloning, a donor nucleus is put into an enucleated egg cell, which is then stimulated to divide and develop into an organism.

In reverse genetics methods, a gene is mutated or removed in some way to identify its effect on the phenotype of the whole organism as a way to determine its function.


Why was Dolly a Finn-Dorset and not a Scottish Blackface sheep?

Answer: Because even though the original cell came from a Scottish Blackface sheep and the surrogate mother was a Scottish Blackface, the DNA came from a Finn-Dorset.

Multiple Choice

In gel electrophoresis of DNA, the different bands in the final gel form because the DNA molecules ________.

A) are from different organisms

B) have different lengths

C) have different nucleotide compositions

D) have different genes


In the reproductive cloning of an animal, the genome of the cloned individual comes from ________.

A) a sperm cell

B) an egg cell

C) any gamete cell

D) a body cell


What carries a gene from one organism into a bacteria cell?

A) a plasmid

B) an electrophoresis gel

C) a restriction enzyme

D) polymerase chain reaction


Free Response

What is the purpose and benefit of the polymerase chain reaction?

The polymerase chain reaction is used to quickly produce many copies of a specific segment of DNA when only one or a very few copies are originally present. The benefit of PCR is that there are many instances in which we would like to know something about a sample of DNA when only very small amounts are available. PCR allows us to increase the number of DNA molecules so that other tests, such as sequencing, can be performed with it.


anneal: in molecular biology, the process by which two single strands of DNA hydrogen bond at complementary nucleotides to form a double-stranded molecule

biotechnology: the use of artificial methods to modify the genetic material of living organisms or cells to produce novel compounds or to perform new functions

cloning: the production of an exact copy—specifically, an exact genetic copy—of a gene, cell, or organism

gel electrophoresis: a technique used to separate molecules on the basis of their ability to migrate through a semisolid gel in response to an electric current

genetic engineering: alteration of the genetic makeup of an organism using the molecular methods of biotechnology
genetically modified organism (GMO): an organism whose genome has been artificially changed

plasmid: a small circular molecule of DNA found in bacteria that replicates independently of the main bacterial chromosome; plasmids code for some important traits for bacteria and can be used as vectors to transport DNA into bacteria in genetic engineering applications

polymerase chain reaction (PCR): a technique used to make multiple copies of DNA

recombinant DNA: a combination of DNA fragments generated by molecular cloning that does not exist in nature
strong>recombinant protein: a protein that is expressed from recombinant DNA molecules

restriction enzyme: an enzyme that recognizes a specific nucleotide sequence in DNA and cuts the DNA double strand at that recognition site, often with a staggered cut leaving short single strands or “sticky” ends

reverse genetics: a form of genetic analysis that manipulates DNA to disrupt or affect the product of a gene to analyze the gene’s function

reproductive cloning: cloning of entire organisms
transgenic: describing an organism that receives DNA from a different species


10.2 Biotechnology in Medicine and Agriculture

Learning Objectives

By the end of this section, you will be able to:

  • Describe uses of biotechnology in medicine
  • Describe uses of biotechnology in agriculture

It is easy to see how biotechnology can be used for medicinal purposes. Knowledge of the genetic makeup of our species, the genetic basis of heritable diseases, and the invention of technology to manipulate and fix mutant genes provides methods to treat diseases. Biotechnology in agriculture can enhance resistance to disease, pests, and environmental stress to improve both crop yield and quality.

Genetic Diagnosis and Gene Therapy

The process of testing for suspected genetic defects before administering treatment is called genetic diagnosis by genetic testing. In some cases in which a genetic disease is present in an individual’s family, family members may be advised to undergo genetic testing. For example, mutations in the BRCA genes may increase the likelihood of developing breast and ovarian cancers in women and some other cancers in women and men. A woman with breast cancer can be screened for these mutations. If one of the high-risk mutations is found, her female relatives may also wish to be screened for that particular mutation, or simply be more vigilant for the occurrence of cancers. Genetic testing is also offered for fetuses (or embryos with in vitro fertilization) to determine the presence or absence of disease-causing genes in families with specific debilitating diseases.

Concept in Action

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See how human DNA is extracted for uses such as genetic testing.

Gene therapy is a genetic engineering technique that may one day be used to cure certain genetic diseases. In its simplest form, it involves the introduction of a non-mutated gene at a random location in the genome to cure a disease by replacing a protein that may be absent in these individuals because of a genetic mutation. The non-mutated gene is usually introduced into diseased cells as part of a vector transmitted by a virus, such as an adenovirus, that can infect the host cell and deliver the foreign DNA into the genome of the targeted cell (Figure 10.8). To date, gene therapies have been primarily experimental procedures in humans. A few of these experimental treatments have been successful, but the methods may be important in the future as the factors limiting its success are resolved.

An illustration showing a virus containing viral DNA combined with a healthy non-mutated gene. The virus enters the targeted call and injects the non-mutated gene into the target cell nucleus.

Figure 10.8 This diagram shows the steps involved in curing disease with gene therapy using an adenovirus vector. (credit: modification of work by NIH)

Production of Vaccines, Antibiotics, and Hormones

Traditional vaccination strategies use weakened or inactive forms of microorganisms or viruses to stimulate the immune system. Modern techniques use specific genes of microorganisms cloned into vectors and mass-produced in bacteria to make large quantities of specific substances to stimulate the immune system. The substance is then used as a vaccine. In some cases, such as the H1N1 flu vaccine, genes cloned from the virus have been used to combat the constantly changing strains of this virus.

Antibiotics kill bacteria and are naturally produced by microorganisms such as fungi; penicillin is perhaps the most well-known example. Antibiotics are produced on a large scale by cultivating and manipulating fungal cells. The fungal cells have typically been genetically modified to improve the yields of the antibiotic compound.

Recombinant DNA technology was used to produce large-scale quantities of the human hormone insulin in E. coli as early as 1978. Previously, it was only possible to treat diabetes with pig insulin, which caused allergic reactions in many humans because of differences in the insulin molecule. In addition, human growth hormone (HGH) is used to treat growth disorders in children. The HGH gene was cloned from a cDNA (complementary DNA) library and inserted into E. coli cells by cloning it into a bacterial vector.

Transgenic Animals

Although several recombinant proteins used in medicine are successfully produced in bacteria, some proteins need a eukaryotic animal host for proper processing. For this reason, genes have been cloned and expressed in animals such as sheep, goats, chickens, and mice. Animals that have been modified to express recombinant DNA are called transgenic animals (Figure 10.9).

A photo shows 3 mice under ultraviolet light. All three have white fur that looks purple in the UV light. The middle mouse is non-transgenic and is non-fluorescing. The mice on the left and right are transgenic, and their eyes, ears, nose, and tail fluoresce green under the UV light.

Figure 10.9 It can be seen that two of these mice are transgenic because they have a gene that causes them to fluoresce under a UV light. The non-transgenic mouse does not have the gene that causes fluorescence. (credit: Ingrid Moen et al.)

Several human proteins are expressed in the milk of transgenic sheep and goats. In one commercial example, the FDA has approved a blood anticoagulant protein that is produced in the milk of transgenic goats for use in humans. Mice have been used extensively for expressing and studying the effects of recombinant genes and mutations.

Transgenic Plants

Manipulating the DNA of plants (creating genetically modified organisms, or GMOs) has helped to create desirable traits such as disease resistance, herbicide, and pest resistance, better nutritional value, and better shelf life (Figure 10.10). Plants are the most important source of food for the human population. Farmers developed ways to select for plant varieties with desirable traits long before modern-day biotechnology practices were established.

A photo of cobs of corn with kernels of varying shape and color.

Figure 10.10 Corn, a major agricultural crop used to create products for a variety of industries, is often modified through plant biotechnology. (credit: Keith Weller, USDA)

Transgenic plants have received DNA from other species. Because they contain unique combinations of genes and are not restricted to the laboratory, transgenic plants and other GMOs are closely monitored by government agencies to ensure that they are fit for human consumption and do not endanger other plant and animal life. Because foreign genes can spread to other species in the environment, particularly in the pollen and seeds of plants, extensive testing is required to ensure ecological stability. Staples like corn, potatoes, and tomatoes were the first crop plants to be genetically engineered.

Transformation of Plants Using Agrobacterium tumefaciens

In plants, tumors caused by the bacterium Agrobacterium tumefaciens occur by transfer of DNA from the bacterium to the plant. The artificial introduction of DNA into plant cells is more challenging than in animal cells because of the thick plant cell wall. Researchers used the natural transfer of DNA from Agrobacterium to a plant host to introduce DNA fragments of their choice into plant hosts. In nature, the disease-causing A. tumefaciens have a set of plasmids that contain genes that integrate into the infected plant cell’s genome. Researchers manipulate the plasmids to carry the desired DNA fragment and insert it into the plant genome.

The Organic Insecticide Bacillus thuringiensis

Bacillus thuringiensis (Bt) is a bacterium that produces protein crystals that are toxic to many insect species that feed on plants. Insects that have eaten Bt toxin stop feeding on the plants within a few hours. After the toxin is activated in the intestines of the insects, death occurs within a couple of days. The crystal toxin genes have been cloned from the bacterium and introduced into plants, therefore allowing plants to produce their own crystal Bt toxin that acts against insects. Bt toxin is safe for the environment and non-toxic to mammals (including humans). As a result, it has been approved for use by organic farmers as a natural insecticide. There is some concern, however, that insects may evolve resistance to the Bt toxin in the same way that bacteria evolve resistance to antibiotics.

FlavrSavr Tomato

The first GM crop to be introduced into the market was the FlavrSavr Tomato produced in 1994. Molecular genetic technology was used to slow down the process of softening and rotting caused by fungal infections, which led to increased shelf life of the GM tomatoes. Additional genetic modification improved the flavor of this tomato. The FlavrSavr tomato did not successfully stay in the market because of problems maintaining and shipping the crop.

Section Summary

Genetic testing is performed to identify disease-causing genes, and can be used to benefit affected individuals and their relatives who have not developed disease symptoms yet. Gene therapy—by which functioning genes are incorporated into the genomes of individuals with a non-functioning mutant gene—has the potential to cure heritable diseases. Transgenic organisms possess DNA from a different species, usually generated by molecular cloning techniques. Vaccines, antibiotics, and hormones are examples of products obtained by recombinant DNA technology. Transgenic animals have been created for experimental purposes and some are used to produce some human proteins.

Genes are inserted into plants, using plasmids in the bacterium Agrobacterium tumefaciens, which infects plants. Transgenic plants have been created to improve the characteristics of crop plants—for example, by giving them insect resistance by inserting a gene for a bacterial toxin.


Multiple Choice

What is a genetically modified organism (GMO)?

A) a plant with certain genes removed

B) an organism with an artificially altered genome

C) a hybrid organism

D) any agricultural organism produced by breeding or biotechnology


What is the role of Agrobacterium tumefaciens in the production of transgenic plants?

A) Genes from A. tumefaciens are inserted into plant DNA to give the plant different traits.

B) Transgenic plants have been given resistance to the pest A. tumefaciens.

C) A. tumefaciens is used as a vector to move genes into plant cells.

D) Plant genes are incorporated into the genome of Agrobacterium tumefaciens.


Free Response

Today, it is possible for a diabetic patient to purchase human insulin from a pharmacist. What technology makes this possible and why is it a benefit over how things used to be?

The human insulin comes from the gene that produces insulin in humans, which has been spliced into a bacterial genome using recombinant DNA technology. The bacterium produces the insulin, which is then purified for human use. Before there was genetically engineered human insulin, diabetics were given insulin extracted from pig pancreases, which was similar to, but not exactly like, human insulin. Because it was not exactly like human insulin, the pig insulin caused complications in some diabetic patients.


gene therapy: the technique used to cure heritable diseases by replacing mutant genes with good genes

genetic testing: identifying gene variants in an individual that may lead to a genetic disease in that individual


10.3 Genomics and Proteomics

Learning Objectives

By the end of this section, you will be able to:

  • Define genomics and proteomics
  • Define whole genome sequencing
  • Explain different applications of genomics and proteomics

The study of nucleic acids began with the discovery of DNA, progressed to the study of genes and small fragments, and has now exploded to the field of genomics. Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. The advances in genomics have been made possible by DNA sequencing technology. Just as information technology has led to Google Maps that enable us to get detailed information about locations around the globe, genomic information is used to create similar maps of the DNA of different organisms.

Mapping Genomes

Genome mapping is the process of finding the location of genes on each chromosome. The maps that are created are comparable to the maps that we use to navigate streets. A genetic map is an illustration that lists genes and their location on a chromosome. Genetic maps provide the big picture (similar to a map of interstate highways) and use genetic markers (similar to landmarks). A genetic marker is a gene or sequence on a chromosome that shows genetic linkage with a trait of interest. The genetic marker tends to be inherited with the gene of interest, and one measure of distance between them is the recombination frequency during meiosis. Early geneticists called this linkage analysis.

Physical maps get into the intimate details of smaller regions of the chromosomes (similar to a detailed road map) (Figure 10.11). A physical map is a representation of the physical distance, in nucleotides, between genes or genetic markers. Both genetic linkage maps and physical maps are required to build a complete picture of the genome. Having a complete map of the genome makes it easier for researchers to study individual genes. Human genome maps help researchers in their efforts to identify human disease-causing genes related to illnesses such as cancer, heart disease, and cystic fibrosis, to name a few. In addition, genome mapping can be used to help identify organisms with beneficial traits, such as microbes with the ability to clean up pollutants or even prevent pollution. Research involving plant genome mapping may lead to methods that produce higher crop yields or to the development of plants that adapt better to climate change.

A diagram showing a human chromosome with bands revealed with a Giemsa stain. The bands are labeled with Xp and a number on the short arm and Xq and a number on the long arm. Certain genes are found within some of the bands. These genes are labeled on the right: Fanconi anemia B, Wiskott-Aldrich syndrome, Pelizaeus-Merzbacher disease, Fragile X syndrome, and G6PD deficiency[0].

Figure 10.11 This is a physical map of the human X chromosome. (credit: modification of work by NCBI, NIH)

Genetic maps provide the outline, and physical maps provide the details. It is easy to understand why both types of genome-mapping techniques are important to show the big picture. Information obtained from each technique is used in combination to study the genome. Genomic mapping is used with different model organisms that are used for research. Genome mapping is still an ongoing process, and as more advanced techniques are developed, more advances are expected. Genome mapping is similar to completing a complicated puzzle using every piece of available data. Mapping information generated in laboratories all over the world is entered into central databases, such as the National Center for Biotechnology Information (NCBI). Efforts are made to make the information more easily accessible to researchers and the general public. Just as we use global positioning systems instead of paper maps to navigate through roadways, NCBI allows us to use a genome viewer tool to simplify the data mining process.

Concept in Action

QR Code representing a URL

Online Mendelian Inheritance in Man (OMIM) is a searchable online catalog of human genes and genetic disorders. This website shows genome mapping, and also details the history and research of each trait and disorder. Click the link to search for traits (such as handedness) and genetic disorders (such as diabetes).

Whole Genome Sequencing

Although there have been significant advances in the medical sciences in recent years, doctors are still confounded by many diseases and researchers are using whole genome sequencing to get to the bottom of the problem. Whole genome sequencing is a process that determines the DNA sequence of an entire genome. Whole genome sequencing is a brute-force approach to problem solving when there is a genetic basis at the core of a disease. Several laboratories now provide services to sequence, analyze, and interpret entire genomes.

In 2010, whole genome sequencing was used to save a young boy whose intestines had multiple mysterious abscesses. The child had several colon operations with no relief. Finally, a whole genome sequence revealed a defect in a pathway that controls apoptosis (programmed cell death). A bone marrow transplant was used to overcome this genetic disorder, leading to a cure for the boy. He was the first person to be successfully diagnosed using whole genome sequencing.

The first genomes to be sequenced, such as those belonging to viruses, bacteria, and yeast, were smaller in terms of the number of nucleotides than the genomes of multicellular organisms. The genomes of other model organisms, such as the mouse (Mus musculus), the fruit fly (Drosophila melanogaster), and the nematode (Caenorhabditis elegans) are now known. A great deal of basic research is performed in model organisms because the information can be applied to other organisms. A model organism is a species that is studied as a model to understand the biological processes in other species that can be represented by the model organism. For example, fruit flies are able to metabolize alcohol like humans, so the genes affecting sensitivity to alcohol have been studied in fruit flies in an effort to understand the variation in sensitivity to alcohol in humans. Having entire genomes sequenced helps with the research efforts in these model organisms (Figure 10.12).

Five photos are of the mouse, Mus musculus; the fruit fly, Drosophila melanogaster; the nematode Caenorhabditis elegans, viewed through a scanning electron microscope; the yeast Saccharomyces cerevisiae, seen in a differential interference contrast light micrograph; and a small white flower, Arabidopsis thaliana

Figure 10.12 Much basic research is done with model organisms, such as the mouse, Mus musculus; the fruit fly, Drosophila melanogaster; the nematode Caenorhabditis elegans; the yeast Saccharomyces cerevisiae; and the common weed, Arabidopsis thaliana. (credit “mouse”: modification of work by Florean Fortescue; credit “nematodes”: modification of work by “snickclunk”/Flickr; credit “common weed”: modification of work by Peggy Greb, USDA; scale-bar data from Matt Russell)

The first human genome sequence was published in 2003. The number of whole genomes that have been sequenced steadily increases and now includes hundreds of species and thousands of individual human genomes.

Applying Genomics

The introduction of DNA sequencing and whole genome sequencing projects, particularly the Human Genome Project, has expanded the applicability of DNA sequence information. Genomics is now being used in a wide variety of fields, such as metagenomics, pharmacogenomics, and mitochondrial genomics. The most commonly known application of genomics is to understand and find cures for diseases.

Predicting Disease Risk at the Individual Level

Predicting the risk of disease involves screening and identifying currently healthy individuals by genome analysis at the individual level. Intervention with lifestyle changes and drugs can be recommended before disease onset. However, this approach is most applicable when the problem arises from a single gene mutation. Such defects only account for about 5 percent of diseases found in developed countries. Most of the common diseases, such as heart disease, are multifactorial or polygenic, which refers to a phenotypic characteristic that is determined by two or more genes, and also environmental factors such as diet. In April 2010, scientists at Stanford University published the genome analysis of a healthy individual (Stephen Quake, a scientist at Stanford University, who had his genome sequenced); the analysis predicted his propensity to acquire various diseases. A risk assessment was done to analyze Quake’s percentage of risk for 55 different medical conditions. A rare genetic mutation was found that showed him to be at risk for sudden heart attack. He was also predicted to have a 23 percent risk of developing prostate cancer and a 1.4 percent risk of developing Alzheimer’s disease. The scientists used databases and several publications to analyze the genomic data. Even though genomic sequencing is becoming more affordable and analytical tools are becoming more reliable, ethical issues surrounding genomic analysis at a population level remain to be addressed. For example, could such data be legitimately used to charge more or less for insurance or to affect credit ratings?

Genome-wide Association Studies

Since 2005, it has been possible to conduct a type of study called a genome-wide association study, or GWAS. A GWAS is a method that identifies differences between individuals in single nucleotide polymorphisms (SNPs) that may be involved in causing diseases. The method is particularly suited to diseases that may be affected by one or many genetic changes throughout the genome. It is very difficult to identify the genes involved in such a disease using family history information. The GWAS method relies on a genetic database that has been in development since 2002 called the International HapMap Project. The HapMap Project sequenced the genomes of several hundred individuals from around the world and identified groups of SNPs. The groups include SNPs that are located near to each other on chromosomes so they tend to stay together through recombination. The fact that the group stays together means that identifying one marker SNP is all that is needed to identify all the SNPs in the group. There are several million SNPs identified, but identifying them in other individuals who have not had their complete genome sequenced is much easier because only the marker SNPs need to be identified.

In a common design for a GWAS, two groups of individuals are chosen; one group has the disease, and the other group does not. The individuals in each group are matched in other characteristics to reduce the effect of confounding variables causing differences between the two groups. For example, the genotypes may differ because the two groups are mostly taken from different parts of the world. Once the individuals are chosen, and typically their numbers are a thousand or more for the study to work, samples of their DNA are obtained. The DNA is analyzed using automated systems to identify large differences in the percentage of particular SNPs between the two groups. Often the study examines a million or more SNPs in the DNA. The results of GWAS can be used in two ways: the genetic differences may be used as markers for susceptibility to the disease in undiagnosed individuals, and the particular genes identified can be targets for research into the molecular pathway of the disease and potential therapies. An offshoot of the discovery of gene associations with disease has been the formation of companies that provide so-called “personal genomics” that will identify risk levels for various diseases based on an individual’s SNP complement. The science behind these services is controversial.

Because GWAS looks for associations between genes and disease, these studies provide data for other research into causes, rather than answering specific questions themselves. An association between a gene difference and a disease does not necessarily mean there is a cause-and-effect relationship. However, some studies have provided useful information about the genetic causes of diseases. For example, three different studies in 2005 identified a gene for a protein involved in regulating inflammation in the body that is associated with a disease-causing blindness called age-related macular degeneration. This opened up new possibilities for research into the cause of this disease. A large number of genes have been identified to be associated with Crohn’s disease using GWAS, and some of these have suggested new hypothetical mechanisms for the cause of the disease.


Pharmacogenomics involves evaluating the effectiveness and safety of drugs on the basis of information from an individual’s genomic sequence. Personal genome sequence information can be used to prescribe medications that will be most effective and least toxic on the basis of the individual patient’s genotype. Studying changes in gene expression could provide information about the gene transcription profile in the presence of the drug, which can be used as an early indicator of the potential for toxic effects. For example, genes involved in cellular growth and controlled cell death, when disturbed, could lead to the growth of cancerous cells. Genome-wide studies can also help to find new genes involved in drug toxicity. The gene signatures may not be completely accurate, but can be tested further before pathologic symptoms arise.


Traditionally, microbiology has been taught with the view that microorganisms are best studied under pure culture conditions, which involves isolating a single type of cell and culturing it in the laboratory. Because microorganisms can go through several generations in a matter of hours, their gene expression profiles adapt to the new laboratory environment very quickly. On the other hand, many species resist being cultured in isolation. Most microorganisms do not live as isolated entities, but in microbial communities known as biofilms. For all of these reasons, pure culture is not always the best way to study microorganisms. Metagenomics is the study of the collective genomes of multiple species that grow and interact in an environmental niche. Metagenomics can be used to identify new species more rapidly and to analyze the effect of pollutants on the environment (Figure 10.13). Metagenomics techniques can now also be applied to communities of higher eukaryotes, such as fish.

The diagram shows 3 individual rings representing DNA, with a small portion of each in a contrasting color. The small portions represent DNA from a different species. The 3 rings have the caption “All of the genomic DNA from a particular environment is cut into fragments and ligated into a cloning vector. The fragments are sequenced, and regions of overlap are used to determine the genomic sequences.” Below the rings are many pieces of the contrasting color portions only, with an arrow pointing to solid longer lines of the 3 colors.

Figure 10.13 Metagenomics involves isolating DNA from multiple species within an environmental niche. The DNA is cut up and sequenced, allowing entire genome sequences of multiple species to be reconstructed from the sequences of overlapping pieces.

Creation of New Biofuels

Knowledge of the genomics of microorganisms is being used to find better ways to harness biofuels from algae and cyanobacteria. The primary sources of fuel today are coal, oil, wood, and other plant products such as ethanol. Although plants are renewable resources, there is still a need to find more alternative renewable sources of energy to meet our population’s energy demands. The microbial world is one of the largest resources for genes that encode new enzymes and produce new organic compounds, and it remains largely untapped. This vast genetic resource holds the potential to provide new sources of biofuels (Figure 10.14).

A photo of a large container of green fluid, with a display in the background with the heading “From Field to Fleet”.

Figure 10.14 Renewable fuels were tested in Navy ships and aircraft at the first Naval Energy Forum. (credit: modification of work by John F. Williams, US Navy)

Mitochondrial Genomics

Mitochondria are intracellular organelles that contain their own DNA. Mitochondrial DNA mutates at a rapid rate and is often used to study evolutionary relationships. Another feature that makes studying the mitochondrial genome interesting is that in most multicellular organisms, the mitochondrial DNA is passed on from the mother during the process of fertilization. For this reason, mitochondrial genomics is often used to trace genealogy.

Genomics in Forensic Analysis

Information and clues obtained from DNA samples found at crime scenes have been used as evidence in court cases, and genetic markers have been used in forensic analysis. Genomic analysis has also become useful in this field. In 2001, the first use of genomics in forensics was published. It was a collaborative effort between academic research institutions and the FBI to solve the mysterious cases of anthrax (Figure 10.15) that was transported by the US Postal Service. Anthrax bacteria were made into an infectious powder and mailed to news media and two U.S. Senators. The powder infected the administrative staff and postal workers who opened or handled the letters. Five people died, and 17 were sickened from the bacteria. Using microbial genomics, researchers determined that a specific strain of anthrax was used in all the mailings; eventually, the source was traced to a scientist at a national biodefense laboratory in Maryland.

A light microscope photo of the long rods of anthrax bacterium. Several lines of red spore dots can be seen as well.

Figure 10.15 Bacillus anthracis is the organism that causes anthrax. (credit: modification of work by CDC; scale-bar data from Matt Russell)

Genomics in Agriculture

Genomics can reduce the trials and failures involved in scientific research to a certain extent, which could improve the quality and quantity of crop yields in agriculture (Figure 10.16). Linking traits to genes or gene signatures helps to improve crop breeding to generate hybrids with the most desirable qualities. Scientists use genomic data to identify desirable traits, and then transfer those traits to a different organism to create a new genetically modified organism, as described in the previous module. Scientists are discovering how genomics can improve the quality and quantity of agricultural production. For example, scientists could use desirable traits to create a useful product or enhance an existing product, such as making a drought-sensitive crop more tolerant of the dry season.

A photo of several purple plums and the leaves of the plum tree. One plum has been cut in half to expose the yellow flesh and small brown pit.

Figure 10.16 Transgenic agricultural plants can be made to resist disease. These transgenic plums are resistant to the plum pox virus. (credit: Scott Bauer, USDA ARS)


Proteins are the final products of genes that perform the function encoded by the gene. Proteins are composed of amino acids and play important roles in the cell. All enzymes (except ribozymes) are proteins and act as catalysts that affect the rate of reactions. Proteins are also regulatory molecules, and some are hormones. Transport proteins, such as hemoglobin, help transport oxygen to various organs. Antibodies that defend against foreign particles are also proteins. In the diseased state, protein function can be impaired because of changes at the genetic level or because of direct impact on a specific protein.

A proteome is the entire set of proteins produced by a cell type. Proteomes can be studied using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. The study of the function of proteomes is called proteomics. Proteomics complements genomics and is useful when scientists want to test their hypotheses that were based on genes. Even though all cells in a multicellular organism have the same set of genes, the set of proteins produced in different tissues is different and dependent on gene expression. Thus, the genome is constant, but the proteome varies and is dynamic within an organism. In addition, RNAs can be alternatively spliced (cut and pasted to create novel combinations and novel proteins), and many proteins are modified after translation. Although the genome provides a blueprint, the final architecture depends on several factors that can change the progression of events that generate the proteome.

Genomes and proteomes of patients suffering from specific diseases are being studied to understand the genetic basis of the disease. The most prominent disease being studied with proteomic approaches is cancer (Figure 10.17). Proteomic approaches are being used to improve the screening and early detection of cancer; this is achieved by identifying proteins whose expression is affected by the disease process. An individual protein is called a biomarker, whereas a set of proteins with altered expression levels is called a protein signature. For a biomarker or protein signature to be useful as a candidate for early screening and detection of a cancer, it must be secreted in body fluids such as sweat, blood, or urine, so that large-scale screenings can be performed in a noninvasive fashion. The current problem with using biomarkers for the early detection of cancer is the high rate of false-negative results. A false-negative result is a negative test result that should have been positive. In other words, many cases of cancer go undetected, which makes biomarkers unreliable. Some examples of protein biomarkers used in cancer detection are CA-125 for ovarian cancer and PSA for prostate cancer. Protein signatures may be more reliable than biomarkers to detect cancer cells. Proteomics is also being used to develop individualized treatment plans, which involves the prediction of whether or not an individual will respond to specific drugs and the side effects that the individual may have. Proteomics is also being used to predict the possibility of disease recurrence.

Photo shows a protein pattern analyzer. It is a large piece of equipment on a desktop with pipettes at the end of long steel tubes.

Figure 10.17 This machine is preparing to do a proteomic pattern analysis to identify specific cancers so that an accurate cancer prognosis can be made. (credit: Dorie Hightower, NCI, NIH)

The National Cancer Institute has developed programs to improve the detection and treatment of cancer. The Clinical Proteomic Technologies for Cancer and the Early Detection Research Network are efforts to identify protein signatures specific to different types of cancers. The Biomedical Proteomics Program is designed to identify protein signatures and design effective therapies for cancer patients.

Section Summary

Genome mapping is similar to solving a big, complicated puzzle with pieces of information coming from laboratories all over the world. Genetic maps provide an outline for the location of genes within a genome, and they estimate the distance between genes and genetic markers on the basis of the recombination frequency during meiosis. Physical maps provide detailed information about the physical distance between the genes. The most detailed information is available through sequence mapping. Information from all mapping and sequencing sources is combined to study an entire genome.

Whole genome sequencing is the latest available resource to treat genetic diseases. Some doctors are using whole genome sequencing to save lives. Genomics has many industrial applications, including biofuel development, agriculture, pharmaceuticals, and pollution control.

Imagination is the only barrier to the applicability of genomics. Genomics is being applied to most fields of biology; it can be used for personalized medicine, prediction of disease risks at an individual level, the study of drug interactions before the conduction of clinical trials, and the study of microorganisms in the environment as opposed to the laboratory. It is also being applied to the generation of new biofuels, genealogical assessment using mitochondria, advances in forensic science, and improvements in agriculture.

Proteomics is the study of the entire set of proteins expressed by a given type of cell under certain environmental conditions. In a multicellular organism, different cell types will have different proteomes, and these will vary with changes in the environment. Unlike a genome, a proteome is dynamic and under constant flux, which makes it more complicated and more useful than the knowledge of genomes alone.


Multiple Choice

What is the most challenging issue facing genome sequencing?

A) the inability to develop fast and accurate sequencing techniques

B) the ethics of using information from genomes at the individual level

C) the availability and stability of DNA

D) all of the above


Genomics can be used in agriculture to:

A) generate new hybrid strains

B) improve disease resistance

C) improve yield

D) all of the above


What kind of diseases are studied using genome-wide association studies?

A) viral diseases

B) single-gene inherited diseases

C) diseases caused by multiple genes

D) diseases caused by environmental factors


Free Response

Describe two of the applications for genome mapping.

Genome mapping helps researchers to study disease-causing genes in humans. It also helps to identify traits of organisms that can be used in applications such as cleaning up pollution.

Identify a possible advantage and a possible disadvantage of a genetic test that would identify genes in individuals that increase their probability of having Alzheimer’s disease later in life.

The benefit of such a test is that the individual can make preparations for having the disease including taking treatments that slow the disease. The disadvantage of the test is that it might be used by insurance companies to deny coverage to the person.


biomarker: an individual protein that is uniquely produced in a diseased state

genetic map: an outline of genes and their location on a chromosome that is based on recombination frequencies between markers

genomics: the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species

metagenomics: the study of the collective genomes of multiple species that grow and interact in an environmental niche

model organism: a species that is studied and used as a model to understand the biological processes in other species represented by the model organism

pharmacogenomics: the study of drug interactions with the genome or proteome; also called toxicogenomics

physical map: a representation of the physical distance between genes or genetic markers

protein signature: a set of over- or under-expressed proteins characteristic of cells in a particular diseased tissue

proteomics: study of the function of proteomes

whole genome sequencing: a process that determines the nucleotide sequence of an entire genome


Chapter 10 PowerPoint

Chapter 10 PowerPoint


Unit 4: Animal Structure and Function

Note for Instructors, Students and other users,

This version of Concepts of Biology contain two sets of anatomy and physiology chapters and PowerPoint presentations.  Chapters 11-13 and PPTs cover materials briefly, while Chapters 14-24 and associated PPTs go into more depth.  Let your interests and course objectives guide your use of these materials.


Chapter 11: Introduction to the Body's Systems

Photo shows a white arctic fox that blends in with the snow.

Figure 11.1 An arctic fox is a complex animal, well adapted to its environment. (credit: Keith Morehouse, USFWS)

The arctic fox, a complex animal that has adapted to its environment, illustrates the relationships between an animal’s form and function. The multicellular bodies of animals consist of tissues that make up more complex organs and organ systems. The organ systems of an animal maintain homeostasis within the multicellular body. These systems are adapted to obtain the necessary nutrients and other resources needed by the cells of the body, to remove the wastes those cells produce, to coordinate the activities of the cells, tissues, and organs throughout the body, and to coordinate the many responses of the individual organism to its environment.


11.1 Homeostasis and Osmoregulation

Learning Objectives

By the end of this section, you will be able to:

  • Explain the concept of homeostasis
  • Describe thermoregulation of endothermic and ectothermic animals
  • Explain how the kidneys serve as the main osmoregulatory organs in the human body

Homeostasis refers to the relatively stable state inside the body of an animal. Animal organs and organ systems constantly adjust to internal and external changes in order to maintain this steady state. Examples of internal conditions maintained homeostatically are the level of blood glucose, body temperature, blood calcium level. These conditions remain stable because of physiologic processes that result in negative feedback relationships. If the blood glucose or calcium rises, this sends a signal to organs responsible for lowering blood glucose or calcium. The signals that restore the normal levels are examples of negative feedback. When homeostatic mechanisms fail, the results can be unfavorable for the animal. Homeostatic mechanisms keep the body in dynamic equilibrium by constantly adjusting to the changes that the body’s systems encounter. Even an animal that is apparently inactive is maintaining this homeostatic equilibrium. Two examples of factors that are regulated homeostatically are temperature and water content. The processes that maintain homeostasis of these two factors are called thermoregulation and osmoregulation.


The goal of homeostasis is the maintenance of equilibrium around a specific value of some aspect of the body or its cells called a set point. While there are normal fluctuations from the set point, the body’s systems will usually attempt to go back to this point. A change in the internal or external environment is called a stimulus and is detected by a receptor; the response of the system is to adjust the activities of the system so the value moves back toward the set point. For instance, if the body becomes too warm, adjustments are made to cool the animal. If glucose levels in the blood rise after a meal, adjustments are made to lower them and to get the nutrient into tissues that need it or to store it for later use.

When a change occurs in an animal’s environment, an adjustment must be made so that the internal environment of the body and cells remains stable. The receptor that senses the change in the environment is part of a feedback mechanism. The stimulus—temperature, glucose, or calcium levels—is detected by the receptor. The receptor sends information to a control center, often the brain, which relays appropriate signals to an effector organ that is able to cause an appropriate change, either up or down, depending on the information the sensor was sending.


Animals can be divided into two groups: those that maintain a constant body temperature in the face of differing environmental temperatures, and those that have a body temperature that is the same as their environment and thus varies with the environmental temperature. Animals that do not have internal control of their body temperature are called ectotherms. The body temperature of these organisms is generally similar to the temperature of the environment, although the individual organisms may do things that keep their bodies slightly below or above the environmental temperature. This can include burrowing underground on a hot day or resting in the sunlight on a cold day. The ectotherms have been called cold-blooded, a term that may not apply to an animal in the desert with a very warm body temperature.

An animal that maintains a constant body temperature in the face of environmental changes is called an endotherm. These animals are able to maintain a level of activity that an ectothermic animal cannot because they generate internal heat that keeps their cellular processes operating optimally even when the environment is cold.

Concept in Action

QR Code representing a URL

Watch this Discovery Channel video on thermoregulation to see illustrations of the process in a variety of animals.

Animals conserve or dissipate heat in a variety of ways. Endothermic animals have some form of insulation. They have fur, fat, or feathers. Animals with thick fur or feathers create an insulating layer of air between their skin and internal organs. Polar bears and seals live and swim in a subfreezing environment and yet maintain a constant, warm, body temperature. The arctic fox, for example, uses its fluffy tail as extra insulation when it curls up to sleep in cold weather. Mammals can increase body heat production by shivering, which is an involuntary increase in muscle activity. In addition, arrector pili muscles can contract causing individual hairs to stand up when the individual is cold. This increases the insulating effect of the hair. Humans retain this reaction, which does not have the intended effect on our relatively hairless bodies; it causes “goose bumps” instead. Mammals use layers of fat as insulation also. Loss of significant amounts of body fat will compromise an individual’s ability to conserve heat.

Ectotherms and endotherms use their circulatory systems to help maintain body temperature. Vasodilation, the opening up of arteries to the skin by relaxation of their smooth muscles, brings more blood and heat to the body surface, facilitating radiation and evaporative heat loss, cooling the body. Vasoconstriction, the narrowing of blood vessels to the skin by contraction of their smooth muscles, reduces blood flow in peripheral blood vessels, forcing blood toward the core and vital organs, conserving heat. Some animals have adaptions to their circulatory system that enable them to transfer heat from arteries to veins that are flowing next to each other, warming blood returning to the heart. This is called a countercurrent heat exchange; it prevents the cold venous blood from cooling the heart and other internal organs. The countercurrent adaptation is found in dolphins, sharks, bony fish, bees, and hummingbirds.

Some ectothermic animals use changes in their behavior to help regulate body temperature. They simply seek cooler areas during the hottest part of the day in the desert to keep from getting too warm. The same animals may climb onto rocks in the evening to capture heat on a cold desert night before entering their burrows.

Thermoregulation is coordinated by the nervous system (Figure 11.2). The processes of temperature control are centered in the hypothalamus of the advanced animal brain. The hypothalamus maintains the set point for body temperature through reflexes that cause vasodilation or vasoconstriction and shivering or sweating. The sympathetic nervous system under control of the hypothalamus directs the responses that effect the changes in temperature loss or gain that return the body to the set point. The set point may be adjusted in some instances. During an infection, compounds called pyrogens are produced and circulate to the hypothalamus resetting the thermostat to a higher value. This allows the body’s temperature to increase to a new homeostatic equilibrium point in what is commonly called a fever. The increase in body heat makes the body less optimal for bacterial growth and increases the activities of cells so they are better able to fight the infection.

Flow chart shows how normal body temperature is maintained. If the body temperature rises, blood vessels dilate, resulting in loss of heat to the environment. Sweat glands secrete fluid. As this fluid evaporates, heat is lost from the body. As a result, the body temperature falls to normal body temperature. If body temperature falls, blood vessels constrict so that heat is conserved. Sweat glands do not secrete fluid. Shivering (involuntary contraction of muscles) releases heat which warms the body. Heat is retained, and body temperature increases to normal.

Figure 11.2 The body is able to regulate temperature in response to signals from the nervous system.

When bacteria are destroyed by leukocytes, pyrogens are released into the blood. Pyrogens reset the body’s thermostat to a higher temperature, resulting in fever. How might pyrogens cause the body temperature to rise?

<!–Pyrogens increase body temperature by causing the blood vessels to constrict, inducing shivering, and stopping sweat glands from secreting fluid.–>


Osmoregulation is the process of maintaining salt and water balance (osmotic balance) across membranes within the body. The fluids inside and surrounding cells are composed of water, electrolytes, and nonelectrolytes. An electrolyte is a compound that dissociates into ions when dissolved in water. A nonelectrolyte, in contrast, does not dissociate into ions in water. The body’s fluids include blood plasma, fluid that exists within cells, and the interstitial fluid that exists in the spaces between cells and tissues of the body. The membranes of the body (both the membranes around cells and the “membranes” made of cells lining body cavities) are semipermeable membranes. Semipermeable membranes are permeable to certain types of solutes and to water, but typically cell membranes are impermeable to solutes.

The body does not exist in isolation. There is a constant input of water and electrolytes into the system. Excess water, electrolytes, and wastes are transported to the kidneys and excreted, helping to maintain osmotic balance. Insufficient fluid intake results in fluid conservation by the kidneys. Biological systems constantly interact and exchange water and nutrients with the environment by way of consumption of food and water and through excretion in the form of sweat, urine, and feces. Without a mechanism to regulate osmotic pressure, or when a disease damages this mechanism, there is a tendency to accumulate toxic waste and water, which can have dire consequences.

Mammalian systems have evolved to regulate not only the overall osmotic pressure across membranes, but also specific concentrations of important electrolytes in the three major fluid compartments: blood plasma, interstitial fluid, and intracellular fluid. Since osmotic pressure is regulated by the movement of water across membranes, the volume of the fluid compartments can also change temporarily. Since blood plasma is one of the fluid components, osmotic pressures have a direct bearing on blood pressure.

Excretory System

The human excretory system functions to remove waste from the body through the skin as sweat, the lungs in the form of exhaled carbon dioxide, and through the urinary system in the form of urine. All three of these systems participate in osmoregulation and waste removal. Here we focus on the urinary system, which is comprised of the paired kidneys, the ureter, urinary bladder and urethra (Figure 11.3). The kidneys are a pair of bean-shaped structures that are located just below the liver in the body cavity. Each of the kidneys contains more than a million tiny units called nephrons that filter blood containing the metabolic wastes from cells. All the blood in the human body is filtered about 60 times a day by the kidneys. The nephrons remove wastes, concentrate them, and form urine that is collected in the bladder.

Internally, the kidney has three regions—an outer cortex, a medulla in the middle, and the renal pelvis, which is the expanded end of the ureter. The renal cortex contains the nephrons—the functional unit of the kidney. The renal pelvis collects the urine and leads to the ureter on the outside of the kidney. The ureters are urine-bearing tubes that exit the kidney and empty into the urinary bladder.

Illustration on the left shows the placement of the kidneys and bladder in a human man. The two kidneys face one another and are located on the posterior side, about halfway up the back. A renal artery and a renal vein extend from the inside middle of each kidney, toward a major blood vessel that runs up the middle of the body. A ureter runs down from each kidney to the bladder, a sac that sits just above the pelvis. The urethra runs down from the bottom of the bladder and through the penis. The adrenal glands are lumpy masses that sit on top of the kidneys. The illustration on the right shows a kidney, shaped like a kidney bean standing on end. The inside of the kidney consists of three layers: the outer cortex, the middle medulla and the inner renal pelvis. The renal pelvis is flush with the concave side of the kidney, and empties into the ureter, a tube that runs down outside the concave side of the kidney. Several renal pyramids are embedded in the medulla, which is the thickest kidney layer. Each renal pyramid is teardrop-shaped, with the narrow end facing the renal pelvis. The renal artery and renal vein enter the concave part of the kidney, just above the ureter. The renal artery and renal vein branch into arterioles and venules, respectively, which extend into the kidney and branch into capillaries in the cortex.

Figure 11.3 The human excretory system is made up of the kidneys, ureter, urinary bladder, and urethra. The kidneys filter blood and form urine, which is stored in the bladder until it is eliminated through the urethra. On the right, the internal structure of the kidney is shown. (credit: modification of work by NCI, NIH)

Blood enters each kidney from the aorta, the main artery supplying the body below the heart, through a renal artery. It is distributed in smaller vessels until it reaches each nephron in capillaries. Within the nephron the blood comes in intimate contact with the waste-collecting tubules in a structure called the glomerulus. Water and many solutes present in the blood, including ions of sodium, calcium, magnesium, and others; as well as wastes and valuable substances such as amino acids, glucose and vitamins, leave the blood and enter the tubule system of the nephron. As materials pass through the tubule much of the water, required ions, and useful compounds are reabsorbed back into the capillaries that surround the tubules leaving the wastes behind. Some of this reabsorption requires active transport and consumes ATP. Some wastes, including ions and some drugs remaining in the blood, diffuse out of the capillaries into the interstitial fluid and are taken up by the tubule cells. These wastes are then actively secreted into the tubules. The blood then collects in larger and larger vessels and leaves the kidney in the renal vein. The renal vein joins the inferior vena cava, the main vein that returns blood to the heart from the lower body. The amounts of water and ions reabsorbed into the circulatory system are carefully regulated and this is an important way the body regulates its water content and ion levels. The waste is collected in larger tubules and then leaves the kidney in the ureter, which leads to the bladder where urine, the combination of waste materials and water, is stored.

The bladder contains sensory nerves, stretch receptors that signal when it needs to be emptied. These signals create the urge to urinate, which can be voluntarily suppressed up to a limit. The conscious decision to urinate sets in play signals that open the sphincters, rings of smooth muscle that close off the opening, to the urethra that allows urine to flow out of the bladder and the body.

Dialysis Technician

Dialysis is a medical process of removing wastes and excess water from the blood by diffusion and ultrafiltration. When kidney function fails, dialysis must be done to artificially rid the body of wastes and fluids. This is a vital process to keep patients alive. In some cases, the patients undergo artificial dialysis until they are eligible for a kidney transplant. In others who are not candidates for kidney transplants, dialysis is a lifelong necessity.

Dialysis technicians typically work in hospitals and clinics. While some roles in this field include equipment development and maintenance, most dialysis technicians work in direct patient care. Their on-the-job duties, which typically occur under the direct supervision of a registered nurse, focus on providing dialysis treatments. This can include reviewing patient history and current condition, assessing and responding to patient needs before and during treatment, and monitoring the dialysis process. Treatment may include taking and reporting a patient’s vital signs, preparing solutions and equipment to ensure accurate and sterile procedures.

Section Summary

Homeostasis is a dynamic equilibrium that is maintained in body tissues and organs. It is dynamic because it is constantly adjusting to the changes that the systems encounter. It is an equilibrium because body functions are kept within a normal range, with some fluctuations around a set point. The kidneys are the main osmoregulatory organs in mammalian systems; they function to filter blood and maintain the dissolved ion concentrations of body fluids. They are made up internally of three distinct regions—the cortex, medulla, and pelvis. The blood vessels that transport blood into and out of the kidneys arise from and merge with the aorta and inferior vena cava, respectively. The nephron is the functional unit of the kidney, which actively filters blood and generates urine. The urine leaves the kidney through the ureter and is stored in the urinary bladder. Urine is voided from the body through the urethra.


When bacteria are destroyed by leukocytes, pyrogens are released into the blood. Pyrogens reset the body’s thermostat to a higher temperature, resulting in fever. How might pyrogens cause the body temperature to rise?

Pyrogens increase body temperature by causing the blood vessels to constrict, inducing shivering, and stopping sweat glands from secreting fluid.

Review Questions

When faced with a sudden drop in environmental temperature, an endothermic animal will ________.

A) experience a drop in its body temperature

B) wait to see if it goes lower

C) increase muscle activity to generate heat

D) add fur or fat to increase insulation


How are wastes carried to the kidney for removal?

A) in cells

B) in the urine

C) in blood

D) in interstitial fluid


What is the cause of a fever of 38.3 °C (101 °F)?

A) too much heat produced by the body

B) upward adjustment of the body temperature set point

C) inadequate cooling mechanisms in the body

D) the heat caused by a viral or bacterial infection


Free Response

Describe how the body’s mechanisms maintain homeostasis?

The body has a sensor that detects a deviation of the state of the cells or the body from the set point. The information is relayed to a control center, usually the brain, where signals go to effectors. Those effectors cause a negative feedback response that moves the state of the body in a direction back toward the set point.

Why is excretion important in order to achieve osmotic balance?

Excretion allows an organism to rid itself of waste molecules that could be toxic if allowed to accumulate. It also allows the organism to keep the amount of water and dissolved solutes in balance.


ectotherm: an organism that relies primarily on environmental heat sources to maintain its body temperature
endotherm: an organism that relies primarily on internal heat sources to maintain its body temperature
interstitial fluid: the fluid found between cells in the body, similar in constitution to the fluid component of blood, but without the high concentrations of proteins
kidney: the organ that performs excretory and osmoregulatory functions
nephron: the functional unit of the kidney
osmoregulation: the mechanism by which water and solute concentrations are maintained at desired levels
osmotic balance: the appropriate values of water and solute concentrations for a healthy organism
renal artery: the artery that delivers blood to the kidney
renal vein: the vein that drains blood from the kidney
set point: the target value of a physiological state in homeostasis
ureter: the urine-bearing tubes coming out of the kidney
urethra: the tube that conducts urine from the urinary bladder to the external environment
urinary bladder: the structure that the ureters empty the urine into the appropriate values of water and solute concentrations for a healthy organism


11.2 Digestive System

Learning Objectives

By the end of this section, you will be able to:

  • Explain the processes of digestion and absorption
  • Explain the specialized functions of the organs involved in processing food in the body
  • Describe the ways in which organs work together to digest food and absorb nutrients
  • Describe the essential nutrients required for cellular function that cannot be synthesized by the animal body
  • Describe how excess carbohydrates and energy are stored in the body

All living organisms need nutrients to survive. While plants can obtain nutrients from their roots and the energy molecules required for cellular function through the process of photosynthesis, animals obtain their nutrients by the consumption of other organisms. At the cellular level, the biological molecules necessary for animal function are amino acids, lipid molecules, nucleotides, and simple sugars. However, the food consumed consists of protein, fat, and complex carbohydrates. Animals must convert these macromolecules into the simple molecules required for maintaining cellular function. The conversion of the food consumed to the nutrients required is a multistep process involving digestion and absorption. During digestion, food particles are broken down to smaller components, which are later absorbed by the body. This happens by both physical means, such as chewing, and by chemical means.

One of the challenges in human nutrition is maintaining a balance between food intake, storage, and energy expenditure. Taking in more food energy than is used in activity leads to storage of the excess in the form of fat deposits. The rise in obesity and the resulting diseases like type 2 diabetes makes understanding the role of diet and nutrition in maintaining good health all the more important.

The Human Digestive System

The process of digestion begins in the mouth with the intake of food. The teeth play an important role in masticating (chewing) or physically breaking food into smaller particles. The enzymes present in saliva also begin to chemically break down food. The food is then swallowed and enters the esophagus—a long tube that connects the mouth to the stomach. Using peristalsis, or wave-like smooth-muscle contractions, the muscles of the esophagus push the food toward the stomach. The stomach contents are extremely acidic, with a pH between 1.5 and 2.5. This acidity kills microorganisms, breaks down food tissues, and activates digestive enzymes. Further breakdown of food takes place in the small intestine where bile produced by the liver, and enzymes produced by the small intestine and the pancreas, continue the process of digestion. The smaller molecules are absorbed into the blood stream through the epithelial cells lining the walls of the small intestine. The waste material travels on to the large intestine where water is absorbed and the drier waste material is compacted into feces; it is stored until it is excreted through the anus.

The basic components of the human digestive system begins at the mouth. Food is swallowed through the esophagus and into the kidney-shaped stomach. The liver is located on top of the stomach, and the pancreas is underneath. Food passes from the stomach to the long, winding small intestine. From there it enters the wide large intestine before passing out the anus. At the junction of the small and large intestine is a pouch called the cecum.

Figure 11.4 The components of the human digestive system are shown.

Oral Cavity

Both physical and chemical digestion begin in the mouth or oral cavity, which is the point of entry of food into the digestive system. The food is broken into smaller particles by mastication, the chewing action of the teeth. All mammals have teeth and can chew their food to begin the process of physically breaking it down into smaller particles.

The chemical process of digestion begins during chewing as food mixes with saliva, produced by the salivary glands (Figure 11.5). Saliva contains mucus that moistens food and buffers the pH of the food. Saliva also contains lysozyme, which has antibacterial action. It also contains an enzyme called salivary amylase that begins the process of converting starches in the food into a disaccharide called maltose. Another enzyme called lipase is produced by cells in the tongue to break down fats. The chewing and wetting action provided by the teeth and saliva prepare the food into a mass called the bolus for swallowing. The tongue helps in swallowing—moving the bolus from the mouth into the pharynx. The pharynx opens to two passageways: the esophagus and the trachea. The esophagus leads to the stomach and the trachea leads to the lungs. The epiglottis is a flap of tissue that covers the tracheal opening during swallowing to prevent food from entering the lungs.

Illustration A shows the parts of the human oral cavity. The tongue rests in the lower part of the mouth. The flap that hangs from the back of the mouth is the uvula. The airway behind the uvula, called the pharynx, extends up to the back of the nasal cavity and down to the esophagus, which begins in the neck. Illustration B shows the two salivary glands, which are located beneath the tongue, the sublingual and the submandibular. A third salivary gland, the parotid, is located just in front of the ear.

Figure 11.5 (a) Digestion of food begins in the mouth. (b) Food is masticated by teeth and moistened by saliva secreted from the salivary glands. Enzymes in the saliva begin to digest starches and fats. With the help of the tongue, the resulting bolus is moved into the esophagus by swallowing. (credit: modification of work by Mariana Ruiz Villareal)


The esophagus is a tubular organ that connects the mouth to the stomach. The chewed and softened food passes through the esophagus after being swallowed. The smooth muscles of the esophagus undergo peristalsis that pushes the food toward the stomach. The peristaltic wave is unidirectional—it moves food from the mouth to the stomach, and reverse movement is not possible, except in the case of the vomit reflex. The peristaltic movement of the esophagus is an involuntary reflex; it takes place in response to the act of swallowing.

Ring-like muscles called sphincters form valves in the digestive system. The gastro-esophageal sphincter (or cardiac sphincter) is located at the stomach end of the esophagus. In response to swallowing and the pressure exerted by the bolus of food, this sphincter opens, and the bolus enters the stomach. When there is no swallowing action, this sphincter is shut and prevents the contents of the stomach from traveling up the esophagus. Acid reflux or “heartburn” occurs when the acidic digestive juices escape into the esophagus.


A large part of protein digestion occurs in the stomach (Figure 11.7). The stomach is a saclike organ that secretes gastric digestive juices.

Protein digestion is carried out by an enzyme called pepsin in the stomach chamber. The highly acidic environment kills many microorganisms in the food and, combined with the action of the enzyme pepsin, results in the catabolism of protein in the food. Chemical digestion is facilitated by the churning action of the stomach caused by contraction and relaxation of smooth muscles. The partially digested food and gastric juice mixture is called chyme. Gastric emptying occurs within two to six hours after a meal. Only a small amount of chyme is released into the small intestine at a time. The movement of chyme from the stomach into the small intestine is regulated by hormones, stomach distension and muscular reflexes that influence the pyloric sphincter.

The stomach lining is unaffected by pepsin and the acidity because pepsin is released in an inactive form and the stomach has a thick mucus lining that protects the underlying tissue.

Small Intestine

Chyme moves from the stomach to the small intestine. The small intestine is the organ where the digestion of protein, fats, and carbohydrates is completed. The small intestine is a long tube-like organ with a highly folded surface containing finger-like projections called the villi. The top surface of each villus has many microscopic projections called microvilli. The epithelial cells of these structures absorb nutrients from the digested food and release them to the bloodstream on the other side. The villi and microvilli, with their many folds, increase the surface area of the small intestine and increase absorption efficiency of the nutrients.

The human small intestine is over 6 m (19.6 ft) long and is divided into three parts: the duodenum, the jejunum and the ileum. The duodenum is separated from the stomach by the pyloric sphincter. The chyme is mixed with pancreatic juices, an alkaline solution rich in bicarbonate that neutralizes the acidity of chyme from the stomach. Pancreatic juices contain several digestive enzymes that break down starches, disaccharides, proteins, and fats. Bile is produced in the liver and stored and concentrated in the gallbladder; it enters the duodenum through the bile duct. Bile contains bile salts, which make lipids accessible to the water-soluble enzymes. The monosaccharides, amino acids, bile salts, vitamins, and other nutrients are absorbed by the cells of the intestinal lining.

The undigested food is sent to the colon from the ileum via peristaltic movements. The ileum ends and the large intestine begins at the ileocecal valve. The vermiform, “worm-like,” appendix is located at the ileocecal valve. The appendix of humans has a minor role in immunity.

Large Intestine

The large intestine reabsorbs the water from indigestible food material and processes the waste material (Figure 11.6). The human large intestine is much smaller in length compared to the small intestine but larger in diameter. It has three parts: the cecum, the colon, and the rectum. The cecum joins the ileum to the colon and is the receiving pouch for the waste matter. The colon is home to many bacteria or “intestinal flora” that aid in the digestive processes. The colon has four regions, the ascending colon, the transverse colon, the descending colon and the sigmoid colon. The main functions of the colon are to extract the water and mineral salts from undigested food, and to store waste material.

Illustration shows the structure of the large intestine, which begins with the ascending colon. Below the ascending colon is the cecum. The vermiform appendix is a small projection at the bottom of the cecum. The ascending colon travels up the right side of the body, then turns into the transverse colon. On the left side of the body the large intestine turns again, into the descending colon. At the bottom, the descending colon curves up; this part of the intestine is called the sigmoid colon. The sigmoid colon empties into the rectum. The rectum travels straight down, to the anus.

Figure 11.6 The large intestine reabsorbs water from undigested food and stores waste until it is eliminated. (credit: modification of work by Mariana Ruiz Villareal)

The rectum (Figure 11.6) stores feces until defecation. The feces are propelled using peristaltic movements during elimination. The anus is an opening at the far-end of the digestive tract and is the exit point for the waste material. Two sphincters regulate the exit of feces, the inner sphincter is involuntary and the outer sphincter is voluntary.

Accessory Organs

The organs discussed above are the organs of the digestive tract through which food passes. Accessory organs add secretions and enzymes that break down food into nutrients. Accessory organs include the salivary glands, the liver, the pancreas, and the gall bladder. The secretions of the liver, pancreas, and gallbladder are regulated by hormones in response to food consumption.

The liver is the largest internal organ in humans and it plays an important role in digestion of fats and detoxifying blood. The liver produces bile, a digestive juice that is required for the breakdown of fats in the duodenum. The liver also processes the absorbed vitamins and fatty acids and synthesizes many plasma proteins. The gallbladder is a small organ that aids the liver by storing bile and concentrating bile salts.

The pancreas secretes bicarbonate that neutralizes the acidic chyme and a variety of enzymes for the digestion of protein and carbohydrates.

Illustration shows the human lower digestive system, which begins with the stomach, a sac that lies above the large intestine. The stomach empties into the small intestine, which is a long, highly folded tube. The beginning of the small intestine is called the duodenum, the long middle part is called the jejunum, and the end is called the ileum. The ileum empties into the large intestine on the right side of the body. Beneath the junction of the small and large intestine is a small pouch called the cecum. The appendix is at the bottom end of the cecum. The large intestine travels up the left side of the body, across the top of the small intestine, then down the right side of the body. These parts of the large intestine are called the ascending colon, the transverse colon and the descending colon, respectively. The large intestine empties into the rectum, which is connected to the anus. The pancreas is sandwiched between the stomach and large intestine. The liver is a triangular organ that sits above and slightly to the right of the stomach. The gallbladder is a small bulb between the liver and stomach.

Figure 11.7 The stomach has an extremely acidic environment where most of the protein gets digested. (credit: modification of work by Mariana Ruiz Villareal)

Which of the following statements about the digestive system is false?

A) Chyme is a mixture of food and digestive juices that is produced in the stomach.

B) Food enters the large intestine before the small intestine.

C) In the small intestine, chyme mixes with bile, which emulsifies fats.

D) The stomach is separated from the small intestine by the pyloric sphincter.



The human diet should be well balanced to provide nutrients required for bodily function and the minerals and vitamins required for maintaining structure and regulation necessary for good health and reproductive capability (Figure 11.8).

Healthy diet logo shows a plate divided into four sections, labeled “fruits”, “vegetables” “grains,” and “protein”. The vegetables section is slightly larger than the other three. A circle to the side of the plate is labeled “dairy”. Beneath the plate is the web address “Choose My Plate dot gov”.

Figure 11.8 For humans, a balanced diet includes fruits, vegetables, grains, protein, and dairy. (credit: USDA)

Concept in Action

QR Code representing a URL

Explore this interactive United States Department of Agriculture website to learn more about each food group and the recommended daily amounts.

The organic molecules required for building cellular material and tissues must come from food. During digestion, digestible carbohydrates are ultimately broken down into glucose and used to provide energy within the cells of the body. Complex carbohydrates, including polysaccharides, can be broken down into glucose through biochemical modification; however, humans do not produce the enzyme necessary to digest cellulose (fiber). The intestinal flora in the human gut are able to extract some nutrition from these plant fibers. These plant fibers are known as dietary fiber and are an important component of the diet. The excess sugars in the body are converted into glycogen and stored for later use in the liver and muscle tissue. Glycogen stores are used to fuel prolonged exertions, such as long-distance running, and to provide energy during food shortage. Fats are stored under the skin of mammals for insulation and energy reserves.

Proteins in food are broken down during digestion and the resulting amino acids are absorbed. All of the proteins in the body must be formed from these amino-acid constituents; no proteins are obtained directly from food.

Fats add flavor to food and promote a sense of satiety or fullness. Fatty foods are also significant sources of energy, and fatty acids are required for the construction of lipid membranes. Fats are also required in the diet to aid the absorption of fat-soluble vitamins and the production of fat-soluble hormones.

While the animal body can synthesize many of the molecules required for function from precursors, there are some nutrients that must be obtained from food. These nutrients are termed essential nutrients, meaning they must be eaten, because the body cannot produce them.

The fatty acids omega-3 alpha-linolenic acid and omega-6 linoleic acid are essential fatty acids needed to make some membrane phospholipids. Vitamins are another class of essential organic molecules that are required in small quantities. Many of these assist enzymes in their function and, for this reason, are called coenzymes. Absence or low levels of vitamins can have a dramatic effect on health. Minerals are another set of inorganic essential nutrients that must be obtained from food. Minerals perform many functions, from muscle and nerve function, to acting as enzyme cofactors. Certain amino acids also must be procured from food and cannot be synthesized by the body. These amino acids are the “essential” amino acids. The human body can synthesize only 11 of the 20 required amino acids; the rest must be obtained from food.


With obesity at high rates in the United States, there is a public health focus on reducing obesity and associated health risks, which include diabetes, colon and breast cancer, and cardiovascular disease. How does the food consumed contribute to obesity?

Fatty foods are calorie-dense, meaning that they have more calories per unit mass than carbohydrates or proteins. One gram of carbohydrates has four calories, one gram of protein has four calories, and one gram of fat has nine calories. Animals tend to seek lipid-rich food for their higher energy content. Greater amounts of food energy taken in than the body’s requirements will result in storage of the excess in fat deposits.

Excess carbohydrate is used by the liver to synthesize glycogen. When glycogen stores are full, additional glucose is converted into fatty acids. These fatty acids are stored in adipose tissue cells—the fat cells in the mammalian body whose primary role is to store fat for later use.

The rate of obesity among children is rapidly rising in the United States. To combat childhood obesity and ensure that children get a healthy start in life, in 2010 First Lady Michelle Obama launched the Let’s Move! campaign. The goal of this campaign is to educate parents and caregivers on providing healthy nutrition and encouraging active lifestyles in future generations. This program aims to involve the entire community, including parents, teachers, and healthcare providers to ensure that children have access to healthy foods—more fruits, vegetables, and whole grains—and consume fewer calories from processed foods. Another goal is to ensure that children get physical activity. With the increase in television viewing and stationary pursuits such as video games, sedentary lifestyles have become the norm. Visit to learn more.

Section Summary

There are many organs that work together to digest food and absorb nutrients. The mouth is the point of ingestion and the location where both mechanical and chemical breakdown of food begins. Saliva contains an enzyme called amylase that breaks down carbohydrates. The food bolus travels through the esophagus by peristaltic movements to the stomach. The stomach has an extremely acidic environment. The enzyme pepsin digests protein in the stomach. Further digestion and absorption take place in the small intestine. The large intestine reabsorbs water from the undigested food and stores waste until elimination.

Carbohydrates, proteins, and fats are the primary components of food. Some essential nutrients are required for cellular function but cannot be produced by the animal body. These include vitamins, minerals, some fatty acids, and some amino acids. Food intake in more than necessary amounts is stored as glycogen in the liver and muscle cells, and in adipose tissue. Excess adipose storage can lead to obesity and serious health problems.


Which of the following statements about the digestive system is false?

A) Chyme is a mixture of food and digestive juices that is produced in the stomach.

B) Food enters the large intestine before the small intestine.

C) In the small intestine, chyme mixes with bile, which emulsifies fats.

D) The stomach is separated from the small intestine by the pyloric sphincter.

Answer: B

Review Questions

Where does the majority of fat digestion take place?

A) mouth

B) stomach

C) small intestine

D) large intestine


The bile from the liver is delivered to the ________.

A) stomach

B) liver

C) small intestine

D) colon


Which of the following statements is not true?

A) Essential nutrients can be synthesized by the body.

B) Vitamins are required in small quantities for bodily function.

C) Some amino acids can be synthesized by the body, while others need to be obtained from diet.

D) Vitamins come in two categories: fat-soluble and water-soluble.


Free Response

What is the role of the accessory organs in digestion?

Accessory organs play an important role in producing and delivering digestive juices to the intestine during digestion and absorption. Specifically, the salivary glands, liver, pancreas, and gallbladder play important roles. Malfunction of any of these organs can lead to disease states.

What is the role of minerals in maintaining good health?

Minerals—such as potassium, sodium, and calcium—are required for the functioning of many cellular processes. While minerals are required in trace amounts, not having minerals in the diet can be potentially harmful.

Discuss why obesity is a growing epidemic.

In the United States, obesity, particularly childhood obesity, is a growing concern. Some of the contributors to this situation include sedentary lifestyles and consuming more processed foods and less fruits and vegetables. As a result, even young children who are obese can face health concerns.


amylase: an enzyme found in saliva and secreted by the pancreas that converts carbohydrates to maltose
anus: the exit point of the digestive system for waste material
bile: a digestive juice produced by the liver; important for digestion of lipids
bolus: a mass of food resulting from chewing action and wetting by saliva
colon: the largest portion of the large intestine consisting of the ascending colon, transverse colon, and descending colon
chyme: a mixture of partially digested food and stomach juices
esophagus: a tubular organ that connects the mouth to the stomach
essential nutrient: a nutrient that cannot be synthesized by the body; it must be obtained from food
gallbladder: the organ that stores and concentrates bile
large intestine: a digestive system organ that reabsorbs water from undigested material and processes waste matter
liver: an organ that produces bile for digestion and processes vitamins and lipids
mineral: an inorganic, elemental molecule that carries out important roles in the body
oral cavity: the point of entry of food into the digestive system
pancreas: a gland that secretes digestive juices
pepsin: an enzyme found in the stomach whose main role is protein digestion
peristalsis: wave-like movements of muscle tissue
rectum: the area of the body where feces is stored until elimination
salivary gland: one of three pairs of exocrine glands in the mammalian mouth that secretes saliva, a mix of watery mucus and enzymes
small intestine: the organ where digestion of protein, fats, and carbohydrates is completed
stomach: a saclike organ containing acidic digestive juices
vitamin: an organic substance necessary in small amounts to sustain life


11.3 Circulatory and Respiratory Systems

Learning Objectives

By the end of this section, you will be able to:

  • Describe the passage of air from the outside environment to the lungs
  • Describe the function of the circulatory system
  • Describe the cardiac cycle
  • Explain how blood flows through the body

Animals are complex multicellular organisms that require a mechanism for transporting nutrients throughout their bodies and removing wastes. The human circulatory system has a complex network of blood vessels that reach all parts of the body. This extensive network supplies the cells, tissues, and organs with oxygen and nutrients, and removes carbon dioxide and waste compounds.

The medium for transport of gases and other molecules is the blood, which continually circulates through the system. Pressure differences within the system cause the movement of the blood and are created by the pumping of the heart.

Gas exchange between tissues and the blood is an essential function of the circulatory system. In humans, other mammals, and birds, blood absorbs oxygen and releases carbon dioxide in the lungs. Thus the circulatory and respiratory system, whose function is to obtain oxygen and discharge carbon dioxide, work in tandem.

The Respiratory System (Basic level)

Take a breath in and hold it. Wait several seconds and then let it out. Humans, when they are not exerting themselves, breathe approximately 15 times per minute on average. This equates to about 900 breaths an hour or 21,600 breaths per day. With every inhalation, air fills the lungs, and with every exhalation, it rushes back out. That air is doing more than just inflating and deflating the lungs in the chest cavity. The air contains oxygen that crosses the lung tissue, enters the bloodstream, and travels to organs and tissues. There, oxygen is exchanged for carbon dioxide, which is a cellular waste material. Carbon dioxide exits the cells, enters the bloodstream, travels back to the lungs, and is expired out of the body during exhalation.

Breathing is both a voluntary and an involuntary event. How often a breath is taken and how much air is inhaled or exhaled is regulated by the respiratory center in the brain in response to signals it receives about the carbon dioxide content of the blood. However, it is possible to override this automatic regulation for activities such as speaking, singing and swimming under water.

During inhalation the diaphragm descends creating a negative pressure around the lungs and they begin to inflate, drawing in air from outside the body. The air enters the body through the nasal cavity located just inside the nose (Figure 11.9). As the air passes through the nasal cavity, the air is warmed to body temperature and humidified by moisture from mucous membranes. These processes help equilibrate the air to the body conditions, reducing any damage that cold, dry air can cause. Particulate matter that is floating in the air is removed in the nasal passages by hairs, mucus, and cilia. Air is also chemically sampled by the sense of smell.

From the nasal cavity, air passes through the pharynx (throat) and the larynx (voice box) as it makes its way to the trachea (Figure 11.9). The main function of the trachea is to funnel the inhaled air to the lungs and the exhaled air back out of the body. The human trachea is a cylinder, about 25 to 30 cm (9.8–11.8 in) long, which sits in front of the esophagus and extends from the pharynx into the chest cavity to the lungs. It is made of incomplete rings of cartilage and smooth muscle. The cartilage provides strength and support to the trachea to keep the passage open. The trachea is lined with cells that have cilia and secrete mucus. The mucus catches particles that have been inhaled, and the cilia move the particles toward the pharynx.

The end of the trachea divides into two bronchi that enter the right and left lung. Air enters the lungs through the primary bronchi. The primary bronchus divides, creating smaller and smaller diameter bronchi until the passages are under 1 mm (.03 in) in diameter when they are called bronchioles as they split and spread through the lung. Like the trachea, the bronchus and bronchioles are made of cartilage and smooth muscle. Bronchi are innervated by nerves of both the parasympathetic and sympathetic nervous systems that control muscle contraction (parasympathetic) or relaxation (sympathetic) in the bronchi and bronchioles, depending on the nervous system’s cues. The final bronchioles are the respiratory bronchioles. Alveolar ducts are attached to the end of each respiratory bronchiole. At the end of each duct are alveolar sacs, each containing 20 to 30 alveoli. Gas exchange occurs only in the alveoli. The alveoli are thin-walled and look like tiny bubbles within the sacs. The alveoli are in direct contact with capillaries of the circulatory system. Such intimate contact ensures that oxygen will diffuse from the alveoli into the blood. In addition, carbon dioxide will diffuse from the blood into the alveoli to be exhaled. The anatomical arrangement of capillaries and alveoli emphasizes the structural and functional relationship of the respiratory and circulatory systems. Estimates for the surface area of alveoli in the lungs vary around 100 m2. This large area is about the area of half a tennis court. This large surface area, combined with the thin-walled nature of the alveolar cells, allows gases to easily diffuse across the cells.

The illustration shows the flow of air through the human respiratory system. The nasal cavity is a wide cavity above and behind the nostrils, and the pharynx is the passageway behind the mouth. The nasal cavity and pharynx join and enter the trachea through the larynx. The larynx is somewhat wider than the trachea and flat. The trachea has concentric, ring-like grooves, giving it a bumpy appearance. The trachea bifurcates into two primary bronchi, which are also grooved. The primary bronchi enter the lungs, and branch into secondary bronchi. The secondary bronchi in turn branch into many tertiary bronchi. The tertiary bronchi branch into bronchioles, which branch into terminal bronchioles. Each terminal bronchiole ends in an alveolar sac. Each alveolar sac contains many alveoli clustered together, like bunches of grapes. The alveolar duct is the air passage into the alveolar sac. The alveoli are hollow, and air empties into them. Pulmonary arteries bring deoxygenated blood to the alveolar sac (and thus appear blue), and pulmonary veins return oxygenated blood (and thus appear red) to the heart. Capillaries form a web around each alveolus. The diaphragm is a membrane that pushes up against the lungs.

Figure 11.9 Air enters the respiratory system through the nasal cavity, and then passes through the pharynx and the trachea into the lungs. (credit: modification of work by NCI)


 Systems of Gas Exchange

Learning Objectives

By the end of this section, you will be able to:

  • Describe the passage of air from the outside environment to the lungs
  • Explain how the lungs are protected from particulate matter

The primary function of the respiratory system is to deliver oxygen to the cells of the body’s tissues and remove carbon dioxide, a cell waste product. The main structures of the human respiratory system are the nasal cavity, the trachea, and lungs.

All aerobic organisms require oxygen to carry out their metabolic functions. Along the evolutionary tree, different organisms have devised different means of obtaining oxygen from the surrounding atmosphere. The environment in which the animal lives greatly determines how an animal respires. The complexity of the respiratory system is correlated with the size of the organism. As animal size increases, diffusion distances increase and the ratio of surface area to volume drops. In unicellular organisms, diffusion across the cell membrane is sufficient for supplying oxygen to the cell (Figure 11.10). Diffusion is a slow, passive transport process. In order for diffusion to be a feasible means of providing oxygen to the cell, the rate of oxygen uptake must match the rate of diffusion across the membrane. In other words, if the cell were very large or thick, diffusion would not be able to provide oxygen quickly enough to the inside of the cell. Therefore, dependence on diffusion as a means of obtaining oxygen and removing carbon dioxide remains feasible only for small organisms or those with highly-flattened bodies, such as many flatworms (Platyhelminthes). Larger organisms had to evolve specialized respiratory tissues, such as gills, lungs, and respiratory passages accompanied by a complex circulatory systems, to transport oxygen throughout their entire body.


Figure 11.10  The cell of the unicellular algae Ventricaria ventricosa is one of the largest known, reaching one to five centimeters in diameter. Like all single-celled organisms, V. ventricosa exchanges gases across the cell membrane.

Direct Diffusion

For small multicellular organisms, diffusion across the outer membrane is sufficient to meet their oxygen needs. Gas exchange by direct diffusion across surface membranes is efficient for organisms less than 1 mm in diameter. In simple organisms, such as cnidarians and flatworms, every cell in the body is close to the external environment. Their cells are kept moist and gases diffuse quickly via direct diffusion. Flatworms are small, literally flat worms, which ‘breathe’ through diffusion across the outer membrane (Figure 11.11). The flat shape of these organisms increases the surface area for diffusion, ensuring that each cell within the body is close to the outer membrane surface and has access to oxygen. If the flatworm had a cylindrical body, then the cells in the center would not be able to get oxygen.


Figure 11.11.  This flatworm’s process of respiration works by diffusion across the outer membrane. (credit: Stephen Childs)

Skin and Gills

Earthworms and amphibians use their skin (integument) as a respiratory organ. A dense network of capillaries lies just below the skin and facilitates gas exchange between the external environment and the circulatory system. The respiratory surface must be kept moist in order for the gases to dissolve and diffuse across cell membranes.

Organisms that live in water need to obtain oxygen from the water. Oxygen dissolves in water but at a lower concentration than in the atmosphere. The atmosphere has roughly 21 percent oxygen. In water, the oxygen concentration is much smaller than that. Fish and many other aquatic organisms have evolved gills to take up the dissolved oxygen from water (Figure 11.12). Gills are thin tissue filaments that are highly branched and folded. When water passes over the gills, the dissolved oxygen in water rapidly diffuses across the gills into the bloodstream. The circulatory system can then carry the oxygenated blood to the other parts of the body. In animals that contain coelomic fluid instead of blood, oxygen diffuses across the gill surfaces into the coelomic fluid. Gills are found in mollusks, annelids, and crustaceans.

Figure 39.4.  This common carp, like many other aquatic organisms, has gills that allow it to obtain oxygen from water. (credit: "Guitardude012"/Wikimedia Commons)

Figure 11.12. 
This common carp, like many other aquatic organisms, has gills that allow it to obtain oxygen from water. (credit: “Guitardude012″/Wikimedia Commons)

The folded surfaces of the gills provide a large surface area to ensure that the fish gets sufficient oxygen. Diffusion is a process in which material travels from regions of high concentration to low concentration until equilibrium is reached. In this case, blood with a low concentration of oxygen molecules circulates through the gills. The concentration of oxygen molecules in water is higher than the concentration of oxygen molecules in gills. As a result, oxygen molecules diffuse from water (high concentration) to blood (low concentration), as shown in Figure 11.13. Similarly, carbon dioxide molecules in the blood diffuse from the blood (high concentration) to water (low concentration).


Figure 11.13.  As water flows over the gills, oxygen is transferred to blood via the veins. (credit “fish”: modification of work by Duane Raver, NOAA)

Tracheal Systems

Insect respiration is independent of its circulatory system; therefore, the blood does not play a direct role in oxygen transport. Insects have a highly specialized type of respiratory system called the tracheal system, which consists of a network of small tubes that carries oxygen to the entire body. The tracheal system is the most direct and efficient respiratory system in active animals. The tubes in the tracheal system are made of a polymeric material called chitin.

Insect bodies have openings, called spiracles, along the thorax and abdomen. These openings connect to the tubular network, allowing oxygen to pass into the body (Figure 11.14) and regulating the diffusion of CO2 and water vapor. Air enters and leaves the tracheal system through the spiracles. Some insects can ventilate the tracheal system with body movements.


Figure 11.14.  Insects perform respiration via a tracheal system.

Mammalian Systems

In mammals, pulmonary ventilation occurs via inhalation (breathing). During inhalation, air enters the body through thenasal cavity located just inside the nose (Figure 11.15). As air passes through the nasal cavity, the air is warmed to body temperature and humidified. The respiratory tract is coated with mucus to seal the tissues from direct contact with air. Mucus is high in water. As air crosses these surfaces of the mucous membranes, it picks up water. These processes help equilibrate the air to the body conditions, reducing any damage that cold, dry air can cause. Particulate matter that is floating in the air is removed in the nasal passages via mucus and cilia. The processes of warming, humidifying, and removing particles are important protective mechanisms that prevent damage to the trachea and lungs. Thus, inhalation serves several purposes in addition to bringing oxygen into the respiratory system.


Figure 11.15.  Air enters the respiratory system through the nasal cavity and pharynx, and then passes through the trachea and into the bronchi, which bring air into the lungs. (credit: modification of work by NCI)

Which of the following statements about the mammalian respiratory system is false?

  1. When we breathe in, air travels from the pharynx to the trachea.
  2. The bronchioles branch into bronchi.
  3. Alveolar ducts connect to alveolar sacs.
  4. Gas exchange between the lung and blood takes place in the alveolus.

From the nasal cavity, air passes through the pharynx (throat) and the larynx (voice box), as it makes its way to thetrachea (Figure 11.16). The main function of the trachea is to funnel the inhaled air to the lungs and the exhaled air back out of the body. The human trachea is a cylinder about 10 to 12 cm long and 2 cm in diameter that sits in front of the esophagus and extends from the larynx into the chest cavity where it divides into the two primary bronchi at the midthorax. It is made of incomplete rings of hyaline cartilage and smooth muscle (Figure 11.17). The trachea is lined with mucus-producing goblet cells and ciliated epithelia. The cilia propel foreign particles trapped in the mucus toward the pharynx. The cartilage provides strength and support to the trachea to keep the passage open. The smooth muscle can contract, decreasing the trachea’s diameter, which causes expired air to rush upwards from the lungs at a great force. The forced exhalation helps expel mucus when we cough. Smooth muscle can contract or relax, depending on stimuli from the external environment or the body’s nervous system.