Biology 2e

Biology 2e

Mary Ann Clark, Jung Choi, and Matthew Douglas

OpenStax Biology 2nd Edition

Houston, TX

Contents

1

Preface

Learning Objectives

Biology is designed for multi-semester biology courses for science majors. It 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. To meet the needs of today’s instructors and students, some content has been strategically condensed while maintaining the overall scope and coverage of traditional texts for this course. Instructors can customize the book, adapting it to the approach that works best in their classroom. Biology also includes an innovative art program that incorporates critical thinking and clicker questions to help students understand—and apply—key concepts.

Welcome to Biology 2e (2nd edition), an OpenStax resource. This textbook was written to increase student access to high-quality learning materials, maintaining highest standards of academic rigor at little to no cost.

About OpenStax

OpenStax is a nonprofit based at Rice University, and it’s our mission to improve student access to education. Our first openly licensed college textbook was published in 2012, and our library has since scaled to over 25 books for college and AP® courses used by hundreds of thousands of students. OpenStax Tutor, our low-cost personalized learning tool, is being used in college courses throughout the country. Through our partnerships with philanthropic foundations and our alliance with other educational resource organizations, OpenStax is breaking down the most common barriers to learning and empowering students and instructors to succeed.

About OpenStax resources

Customization

Biology 2e is licensed under a Creative Commons Attribution 4.0 International (CC BY) license, which means that you can distribute, remix, and build upon the content, as long as you provide attribution to OpenStax and its content contributors.

Because our books are openly licensed, you are free to use the entire book or pick and choose the sections that are most relevant to the needs of your course. Feel free to remix the content by assigning your students certain chapters and sections in your syllabus, in the order that you prefer. You can even provide a direct link in your syllabus to the sections in the web view of your book.

Instructors also have the option of creating a customized version of their OpenStax book. The custom version can be made available to students in low-cost print or digital form through their campus bookstore. Visit the Instructor Resources section of your book page on OpenStax.org for more information.

Errata

All OpenStax textbooks undergo a rigorous review process. However, like any professional-grade textbook, errors sometimes occur. Since our books are web based, we can make updates periodically when deemed pedagogically necessary. If you have a correction to suggest, submit it through the link on your book page on OpenStax.org. Subject matter experts review all errata suggestions. OpenStax is committed to remaining transparent about all updates, so you will also find a list of past errata changes on your book page on OpenStax.org.

Format

You can access this textbook for free in web view or PDF through OpenStax.org, and for a low cost in print.

About Biology 2e

Biology 2e (2nd edition) is designed to cover the scope and sequence requirements of a typical two-semester biology course for science majors. The text provides comprehensive coverage of foundational research and core biology concepts through an evolutionary lens. Biology includes rich features that engage students in scientific inquiry, highlight careers in the biological sciences, and offer everyday applications. The book also includes various types of practice and homework questions that help students understand — and apply — key concepts.

The 2nd edition has been revised to incorporate clearer, more current, and more dynamic explanations, while maintaining the same organization as the first edition. Art and illustrations have been substantially improved, and the textbook features additional assessments and related resources.

Coverage and scope

Biology was one of the first textbooks published by OpenStax and has been used by hundreds of faculty and thousands of students since 2012. We mined our adopters’ extensive and helpful feedback to identify the most significant revision needs while maintaining the organization that many instructors had incorporated into their courses. Specific surveys, focus groups, and pre-revision reviews, as well as data from our OpenStax Tutor users, all aided in planning the revision.

The result is a book that thoroughly treats biology’s foundational concepts while adding current and meaningful coverage in specific areas. Biology 2e retains its manageable scope and contains ample features to draw learners into the discipline.

Structurally, the textbook remains similar to the first edition, with no chapter reorganization and very targeted changes at the section level (mostly in biodiversity).

  • Unit 1: The Chemistry of Life. Our opening unit introduces students to the sciences, including the scientific method and the fundamental concepts of chemistry and physics that provide a framework within which learners comprehend biological processes.
  • Unit 2: The Cell. Students will gain solid understanding of the structures, functions, and processes of the most basic unit of life: the cell.
  • Unit 3: Genetics. Our comprehensive genetics unit takes learners from the earliest experiments that revealed the basis of genetics through the intricacies of DNA to current applications in the emerging studies of biotechnology and genomics.
  • Unit 4: Evolutionary Processes. 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.
  • Unit 5: Biological Diversity. The diversity of life is explored with detailed study of various organisms and discussion of emerging phylogenetic relationships. This unit moves from viruses to living organisms like bacteria, discusses the organisms formerly grouped as protists, and devotes multiple chapters to plant and animal life.
  • Unit 6: Plant Structure and Function. Our plant unit thoroughly covers the fundamental knowledge of plant life essential to an introductory biology course.
  • Unit 7: Animal Structure and Function. An introduction to the form and function of the animal body is followed by chapters on specific body systems and processes. 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 8: Ecology. Ecological concepts are broadly covered in this unit, with features highlighting localized, real-world issues of conservation and biodiversity.

Changes to the Second Edition

OpenStax only undertakes second editions when significant modifications to the text are necessary. In the case of Biology 2e, user feedback indicated that we needed to focus on a few key areas, which we have done in the following ways:

  • Content revisions for clarity, accuracy, and currency. The revision plan varied by chapter based on need. About twenty chapters were wholly revised with significant updates to conceptual coverage, research-informed data, and clearer language. In about fifteen other chapters, the revisions focused mostly on readability and clearer language with fewer conceptual and factual changes.
  • Additional end-of-chapter questions. The authors added new assessments to nearly every chapter, including both review and critical thinking questions. The additions total over 350 new items.
  • Art and illustrations. Under the guidance of the authors and expert scientific illustrators, especially those well versed in creating accessible art, the OpenStax team made changes to most of the art in Biology. You will find examples in the section below. The revisions fall into the following categories:
    • Revisions for accuracy
    • Redesigns for greater understanding and impact
    • Recoloring art for overall consistency
  • Accessibility improvements. As with all OpenStax books, the first edition of Biology was created with a focus on accessibility. We have emphasized and improved that approach in the second edition.
    • To accommodate users of specific assistive technologies, all alternative text was reviewed and revised for comprehensiveness and clarity.
    • Many illustrations were revised to improve the color contrast, which is important for some visually impaired students.
    • Overall, the OpenStax platform has been continually upgraded to improve accessibility.

A transition guide will be available on OpenStax.org to highlight the specific chapter-level changes to the second edition.

Pedagogical foundation

The pedagogical choices, chapter arrangements, and learning objective fulfillment were developed and vetted with the feedback of another one hundred reviewers, who thoroughly read the material and offered detailed critical commentary.

  • Evolution Connection features uphold the importance of evolution to all biological study through discussions like “The Evolution of Metabolic Pathways” and “Algae and Evolutionary Paths to Photosynthesis.”
  • Scientific Method Connection call-outs walk students through actual or thought experiments that elucidate the steps of the scientific process as applied to the topic. Features include “Determining the Time Spent in Cell Cycle Stages” and “Testing the Hypothesis of Independent Assortment.”
  • Career Connection 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 microbiologist, ecologist, neurologist, and forensic scientist.
  • Everyday Connection features tie biological concepts to emerging issues and discuss science in terms of everyday life. Topics include “Chesapeake Bay” and “Can Snail Venom Be Used as a Pharmacological Pain Killer?”

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. Biology 2e also incorporates links to relevant animations and interactive exercises that help bring biology to life for students.

  • Visual Connection features call out core figures in each chapter for student study. Questions about key figures, including clicker questions that can be used in the classroom, engage students’ critical thinking and analytical abilities to ensure their genuine understanding.
  • Link to Learning features direct students to online interactive exercises and animations to add a fuller context and examples to core content.

Below are a few examples of the revised art for Biology 2e:


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Additional resources

Student and instructor resources

We’ve compiled additional resources for both students and instructors, including Getting Started Guides, an instructor solution guide, and PowerPoint lecture slides. Instructor resources require a verified instructor account, which you can apply for when you log in or create your account on OpenStax.org. Take advantage of these resources to supplement your OpenStax book.

Community Hubs

OpenStax partners with the Institute for the Study of Knowledge Management in Education (ISKME) to offer Community Hubs on OER Commons – a platform for instructors to share community-created resources that support OpenStax books, free of charge. Through our Community Hubs, instructors can upload their own materials or download resources to use in their own courses, including additional ancillaries, teaching material, multimedia, and relevant course content. We encourage instructors to join the hubs for the subjects most relevant to your teaching and research as an opportunity both to enrich your courses and to engage with other faculty.

To reach the Community Hubs, visit www.oercommons.org/hubs/OpenStax.

Technology partners

As allies in making high-quality learning materials accessible, our technology partners offer optional low-cost tools that are integrated with OpenStax books. To access the technology options for your text, visit your book page on OpenStax.org.

About the authors

Second edition authors and reviewers

Senior Contributing Authors

Mary Ann Clark, Texas Wesleyan University

Jung Choi, Georgia Institute of Technology

Matthew Douglas, Grand Rapids Community College

Reviewers

Kathleen Berlyn, Baltimore City Community College

Bridgett Brinton, Armstrong State University

Jennifer Chase, Northwest Nazarene University

Amy Hoffman, Grayson County College

Olga Kopp, Utah Valley University

Jennifer Larson, Capital University

Jason Locklin, Austin Community College

Hongmei Ma, American University

Melissa Masse, Tulsa Community College

Shannon McDermott, Central Virginia Community College

Bryan Monesson-Olson, University of Massachusetts Amherst

Amber Reece, California State University Fresno

Monique Reed, Texas A&M University

Jeffrey Roberts, American River College

Matthew Smith, North Dakota State University

Dawn Wankowski, Cardinal Stritch University

First edition authors and reviewers

Senior Contributing Authors

Yael Avissar (Cell Biology), Rhode Island College

Jung Choi (Genetics), Georgia Institute of Technology

Jean DeSaix (Evolution), University of North Carolina at Chapel Hill

Vladimir Jurukovski (Animal Physiology), Suffolk County Community College

Robert Wise (Plant Biology), University of Wisconsin, Oshkosh

Connie Rye (General Content Lead), East Mississippi Community College

Contributing Authors and Reviewers

Julie Adams, Aurora University

Summer Allen, Brown University

James Bader, Case Western Reserve University

David Bailey, St. Norbert College

Mark Belk, Brigham Young University

Nancy Boury, Iowa State University

Lisa Bonneau, Metropolitan Community College – Blue River

Graciela Brelles-Marino, California State University Pomona

Mark Browning, Purdue University

Sue Chaplin, University of St. Thomas

George Cline, Jacksonville State University

Deb Cook, Georgia Gwinnett College

Diane Day, Clayton State University

Frank Dirrigl, The University of Texas Pan American

Waneene Dorsey, Grambling State University

Nick Downey, University of Wisconsin La Crosse

Rick Duhrkopf, Baylor University

Kristy Duran, Adams State University

Stan Eisen, Christian Brothers University

Brent Ewers, University of Wyoming

Myriam Feldman, Lake Washington Institute of Technology

Michael Fine, Virginia Commonwealth University

Linda Flora, Delaware County Community College

Thomas Freeland, Walsh University

David Grisé, Texas A & M University – Corpus Christi

Andrea Hazard, SUNY Cortland

Michael Hedrick, University of North Texas

Linda Hensel, Mercer University

Mark Kopeny, University of Virginia

Norman Johnson, University of Massachusetts Amherst

Grace Lasker, Lake Washington Institute of Technology; Walden University

Sandy Latourelle, SUNY Plattsburgh

Theo Light, Shippensburg University

Clark Lindgren, Grinnell College

James Malcolm, University of Redlands

Mark Meade, Jacksonville State University

Richard Merritt, Houston Community College

James Mickle, North Carolina State University

Jasleen Mishra, Houston Community College

Dudley Moon, Albany College of Pharmacy and Health Sciences

Shobhana Natarajan, Brookhaven College

Jonas Okeagu, Fayetteville State University

Diana Oliveras, University of Colorado Boulder

John Peters, College of Charleston

Joel Piperberg, Millersville University

Johanna Porter-Kelley, Winston-Salem State University

Robyn Puffenbarger, Bridgewater College

Dennis Revie, California Lutheran University

Ann Rushing, Baylor University

Sangha Saha, City College of Chicago

Edward Saiff, Ramapo College of New Jersey

Brian Shmaefsky, Lone Star College System

Robert Sizemore, Alcorn State University

Marc Smith, Sinclair Community College

Frederick Spiegel, University of Arkansas

Frederick Sproull, La Roche College

Bob Sullivan, Marist College

Mark Sutherland, Hendrix College

Toure Thompson, Alabama A&M University

Scott Thomson, University of Wisconsin – Parkside

Allison van de Meene, University of Melbourne

Mary White, Southeastern Louisiana University

Steven Wilt, Bellarmine University

James Wise, Hampton University

Renna Wolfe

Virginia Young, Mercer University

Leslie Zeman, University of Washington

Daniel Zurek, Pittsburg State University

Shobhana Natarajan, Alcon Laboratories, Inc.

I

The Study of Life

1

Introduction

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: NASA/GSFC/NOAA/USGS)


Photo depicts Earth from space.

Viewed from space, Earth offers no clues about the diversity of life forms that reside there. Scientists believe that the first forms of life on Earth were microorganisms that existed for billions of years in the ocean before plants and animals appeared. The mammals, birds, and flowers so familiar to us are all relatively recent, originating 130 to 250 million years ago. The earliest representatives of the genus Homo, to which we belong, have inhabited this planet for only the last 2.5 million years, and only in the last 300,000 years have humans started looking like we do today.

2

The Science of Biology

Learning Objectives

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

  • Identify the shared characteristics of the natural sciences
  • Summarize the steps of the scientific method
  • Compare inductive reasoning with deductive reasoning
  • Describe the goals of basic science and applied science
Formerly called blue-green algae, these (a) cyanobacteria, magnified 300x under 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 layering cyanobacteria in shallow waters. (credit a: modification of work by NASA; credit b: modification of work by Ruth Ellison; scale-bar data from Matt Russell)


Photo A depicts round colonies of blue-green algae. Each algae cell is about 5 microns across. Photo B depicts round fossil structures called stromatalites along a watery shoreline.

What is biology? In simple terms, biology is the study of living organisms and their interactions with one another and their environments. This is a very broad definition because the scope of biology is vast. Biologists may study anything from the microscopic or submicroscopic view of a cell to ecosystems and the whole living planet ((Figure)). Listening to the daily news, you will quickly realize how many aspects of biology we discuss every day. For example, recent news topics include Escherichia coli ((Figure)) outbreaks in spinach and Salmonella contamination in peanut butter. Other subjects include efforts toward finding a cure for AIDS, Alzheimer’s disease, and cancer. On a global scale, many researchers are committed to finding ways to protect the planet, solve environmental issues, and reduce the effects of climate change. All of these diverse endeavors are related to different facets of the discipline of biology.

Escherichia coli (E. coli) bacteria, in this scanning electron micrograph, are normal residents of our digestive tracts that aid in absorbing vitamin K and other nutrients. However, virulent strains are sometimes responsible for disease outbreaks. (credit: Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU)


Photo depicts E. coli bacteria aggregated together.

The Process of Science

Biology is a science, but what exactly is science? What does the study of biology share with other scientific disciplines? We can define science (from the Latin scientia, meaning “knowledge”) as knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method. It becomes clear from this definition that applying scientific method plays a major role in science. The scientific method is a method of research with defined steps that include experiments and careful observation.

We will examine scientific method steps in detail later, but one of the most important aspects of this method is the testing of hypotheses by means of repeatable experiments. A hypothesis is a suggested explanation for an event, which one can test. Although using the scientific method is inherent to science, it is inadequate in determining what science is. This is because it is relatively easy to apply the scientific method to disciplines such as physics and chemistry, but when it comes to disciplines like archaeology, psychology, and geology, the scientific method becomes less applicable as repeating experiments becomes more difficult.

These areas of study are still sciences, however. Consider archaeology—even though one cannot perform repeatable experiments, hypotheses may still be supported. For instance, an archaeologist can hypothesize that an ancient culture existed based on finding a piece of pottery. He or she could make further hypotheses about various characteristics of this culture, which could be correct or false through continued support or contradictions from other findings. A hypothesis may become a verified theory. A theory is a tested and confirmed explanation for observations or phenomena. Therefore, we may be better off to define science as fields of study that attempt to comprehend the nature of the universe.

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? Maybe all of the above? Science includes such diverse fields as astronomy, biology, computer sciences, geology, logic, physics, chemistry, and mathematics ((Figure)). However, scientists consider those fields of science related to the physical world and its phenomena and processes natural sciences. Thus, a museum of natural sciences might contain any of the items listed above.

The diversity of scientific fields includes astronomy, biology, computer science, geology, logic, physics, chemistry, mathematics, and many other fields. (credit: “Image Editor”/Flickr)


A collage includes a photo of planets in our solar system, a DNA molecule, scientific equipment, a cross-section of the ocean floor, scientific symbols, a magnetic field, beakers of fluid, and a geometry problem.

There is no complete agreement when it comes to defining what the natural sciences include, however. 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, geology, physics, and chemistry. Some disciplines such as biophysics and biochemistry build on both life and physical sciences and are interdisciplinary. Some refer to natural sciences as “hard science” because they rely on the use of quantitative data. Social sciences that study society and human behavior are more likely to use qualitative assessments to drive investigations and findings.

Not surprisingly, the natural science of biology has many branches or subdisciplines. Cell biologists study cell structure and function, while biologists who study anatomy investigate the structure of an entire organism. Those biologists studying physiology, however, focus on the internal functioning of an organism. Some areas of biology focus on only particular types of living things. For example, botanists explore plants, while zoologists specialize in animals.

Scientific Reasoning

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. To do this, they use two methods of logical thinking: 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 or quantitative, and one can supplement the raw data 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 analyzing a large amount of data. Brain studies provide an example. In this type of research, scientists observe many live brains while people are engaged in a specific activity, such as viewing images of food. The scientist then predicts the part of the brain that “lights up” during this activity to be the part controlling the response to the selected stimulus, in this case, images of food. Excess absorption of radioactive sugar derivatives by active areas of the brain causes the various areas to “light up”. Scientists use a scanner to observe the resultant increase in radioactivity. Then, researchers can stimulate that part of the brain to see if similar responses result.

Deductive reasoning or deduction is the type of logic used in hypothesis-based science. In deductive reason, 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. Studies in climate change can illustrate this type of reasoning. For example, scientists may predict that if the climate becomes warmer in a particular region, then the distribution of plants and animals should change.

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, which is usually inductive, aims to observe, explore, and discover, while hypothesis-based science, which is usually deductive, begins with a specific question or problem and a potential answer or solution that one can test. The boundary between these two forms of study is often blurred, and most scientific endeavors combine both approaches. The fuzzy boundary becomes apparent when thinking about how easily observation can lead to specific questions. For example, a gentleman in the 1940s observed that the burr seeds that stuck to his clothes and his dog’s fur had a tiny hook structure. On closer inspection, he discovered that the burrs’ gripping device was more reliable than a zipper. He eventually experimented to find the best material that acted similar, and produced the hook-and-loop fastener popularly known today as Velcro. Descriptive science and hypothesis-based science are in continuous dialogue.

The Scientific Method

Biologists study the living world by posing questions about it and seeking science-based responses. Known as scientific method, this approach is common to other sciences as well. The scientific method was used even in ancient times, but England’s Sir Francis Bacon (1561–1626) first documented it ((Figure)). He set up inductive methods for scientific inquiry. The scientific method is not used only by biologists; researchers from almost all fields of study can apply it as a logical, rational problem-solving method.

Historians credit Sir Francis Bacon (1561–1626) as the first to define the scientific method. (credit: Paul van Somer)


Painting depicts Sir Francis Bacon in a long robe.

The scientific process typically starts with an observation (often a problem to solve) 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?”

Proposing a Hypothesis

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

Once one has selected a hypothesis, the student can make a prediction. 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.”

Testing a Hypothesis

A valid hypothesis must be testable. It should also be falsifiable, meaning that experimental results can disprove it. Importantly, science does not claim to “prove” anything because scientific understandings are always subject to modification with further information. This step—openness to disproving ideas—is what distinguishes sciences from non-sciences. The presence of the supernatural, for instance, is neither testable nor falsifiable. To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate one or more of the hypotheses. 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. The control group contains every feature of the experimental group except it is not given the manipulation that the researcher hypothesizes. Therefore, if the experimental group’s results differ from the control group, the difference must be due to the hypothesized manipulation, rather than some outside factor. Look for the variables and controls in the examples that follow. To test the first hypothesis, the student would find out if the air conditioning is on. If the air conditioning is turned on but does not work, there should be another reason, and the student should reject this hypothesis. To test the second hypothesis, the student could check if the lights in the classroom are functional. If so, there is no power failure and the student should reject this hypothesis. The students should test each hypothesis by carrying out appropriate experiments. Be aware that rejecting one hypothesis does not determine whether or not one can accept the other hypotheses. It simply eliminates one hypothesis that is not valid ((Figure)). Using the scientific method, the student rejects the hypotheses that are inconsistent with experimental data.

While this “warm classroom” example is based on observational results, other hypotheses and experiments might have clearer controls. For instance, a student might attend class on Monday and realize she had difficulty concentrating on the lecture. One observation to explain this occurrence might be, “When I eat breakfast before class, I am better able to pay attention.” The student could then design an experiment with a control to test this hypothesis.

In hypothesis-based science, researchers predict specific results from a general premise. We call this type of reasoning deductive reasoning: deduction proceeds from the general to the particular. However, the reverse of the process is also possible: sometimes, scientists reach a general conclusion from a number of specific observations. We call this type of reasoning inductive reasoning, and it proceeds from the particular to the general. Researchers often use inductive and deductive reasoning in tandem to advance scientific knowledge ((Figure)).

Visual Connection
The scientific method consists of a series of well-defined steps. If a hypothesis is not supported by experimental data, one can propose a new hypothesis.


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 correct. If the hypothesis is incorrect, another hypothesis is made. In either case, the results are reported.

In the example below, the scientific method is used to solve an everyday problem. Order the scientific method steps (numbered items) with the process of solving the everyday problem (lettered items). Based on the results of the experiment, is the hypothesis correct? If it is incorrect, propose some alternative hypotheses.

  1. Observation
  2. Question
  3. Hypothesis (answer)
  4. Prediction
  5. Experiment
  6. Result
  1. There is something wrong with the electrical outlet.
  2. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.
  3. My toaster doesn’t toast my bread.
  4. I plug my coffee maker into the outlet.
  5. My coffeemaker works.
  6. Why doesn’t my toaster work?
Visual Connection
Scientists use two types of reasoning, inductive and deductive reasoning, to advance scientific knowledge. As is the case in this example, the conclusion from inductive reasoning can often become the premise for deductive reasoning.


Diagram defines two types of reasoning. In inductive reasoning, a general conclusion is drawn from a number of observations. In deductive reasoning, specific results are predicted from a general premise. An example of inductive reasoning is given. In this example, three observations are made: (1) Members of a species are not all the same. (2) Individuals compete for resources. (3) Species are generally adapted to their environment. From these observations, the following conclusion is drawn: Individuals most adapted to their environment are more likely to survive and pass their traits on to the next generation. An example of deductive reasoning is also given. In this example, the general premise is that individuals most adapted to their environment are more likely to survive and pass their traits on to the next generation. From this premise, it is predicted that, if global climate change causes the temperature in an ecosystem to increase, those individuals better adapted to a warmer climate will outcompete those that are not.

Decide if each of the following is an example of inductive or deductive reasoning.

  1. All flying birds and insects have wings. Birds and insects flap their wings as they move through the air. Therefore, wings enable flight.
  2. Insects generally survive mild winters better than harsh ones. Therefore, insect pests will become more problematic if global temperatures increase.
  3. Chromosomes, the carriers of DNA, are distributed evenly between the daughter cells during cell division. Therefore, each daughter cell will have the same chromosome set as the mother cell.
  4. Animals as diverse as humans, insects, and wolves all exhibit social behavior. Therefore, social behavior must have an evolutionary advantage.

The scientific method may seem too rigid and structured. It is important to keep in mind that, although scientists often follow this sequence, there is flexibility. 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. Notice, too, that we can apply the scientific method to solving problems that aren’t necessarily scientific in nature.

Two Types of Science: Basic Science 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 to 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, although this does not mean that, in the end, it may not result in a practical 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 ((Figure)). In applied science, the problem is usually defined for the researcher.

After Hurricane Irma struck the Caribbean and Florida in 2017, thousands of baby squirrels like this one were thrown from their nests. Thanks to applied science, scientists knew how to rehabilitate the squirrel. (credit: audreyjm529, Flickr)


Image shows a squirrel being held by a person.

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?” However, a careful look at the history of science 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 researchers develop an application therefore, applied science relies on the results that researchers generate through basic science. Other scientists think that it is time to move on from basic science in order to find solutions to actual problems. Both approaches are valid. It is true that there are problems that demand immediate attention; however, scientists would find few solutions without the help of the wide knowledge foundation that basic science generates.

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. DNA strands, unique in every human, are in our cells, where they provide the instructions necessary for life. When DNA replicates, it produces new copies of itself, shortly before a cell divides. Understanding DNA replication mechanisms enabled scientists to develop laboratory techniques that researchers now use 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 researchers analyzed and mapped each human chromosome to determine the precise sequence of DNA subunits and each gene’s exact location. (The gene is the basic unit of heredity. An individual’s complete collection of genes is his or her genome.) Researchers have studied other less complex organisms as part of this project in order to gain a better understanding of human chromosomes. The Human Genome Project ((Figure)) relied on basic research with simple organisms and, later, with the human genome. An important end goal eventually became using the data for applied research, seeking cures and early diagnoses for genetically related diseases.

The Human Genome Project was a 13-year collaborative effort among researchers working in several different science fields. Researchers completed the project, which sequenced the entire human genome, in 2003. (credit: the U.S. Department of Energy Genome Programs (http://genomics.energy.gov)


The human genome projects logo is shown, depicting a human being inside a D N A double helix. The words chemistry, biology, physics, ethics, informatics, and engineering surround the circular image.

While scientists usually carefully plan research efforts in both basic science and applied science, note that some discoveries are made by serendipity, that is, by means of a fortunate accident or a lucky surprise. Scottish biologist Alexander Fleming discovered penicillin when he accidentally left a petri dish of Staphylococcus bacteria open. An unwanted mold grew on the dish, killing the bacteria. Fleming’s curiosity to investigate the reason behind the bacterial death, followed by his experiments, led to the discovery of the antibiotic penicillin, which is produced by the fungus Penicillium. 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 in order for other researchers to expand and build upon their discoveries. Collaboration with other scientists—when planning, conducting, and analyzing results—are all important for scientific research. For this reason, important aspects of a scientist’s work are communicating with peers and disseminating results to peers. Scientists can share results by presenting them at a scientific meeting or conference, but this approach can reach only the select few who are present. Instead, most scientists present their results in peer-reviewed manuscripts that are published in scientific journals. Peer-reviewed manuscripts are scientific papers that a scientist’s colleagues or peers review. 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 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.

A scientific paper is very different from creative writing. Although creativity is required to design experiments, there are fixed guidelines when it comes to presenting scientific results. First, scientific writing must be brief, concise, and accurate. A scientific paper needs to be succinct but detailed enough to allow peers to reproduce the experiments.

The scientific paper consists of several specific sections—introduction, materials and methods, results, and discussion. This structure is sometimes called the “IMRaD” format. There are usually acknowledgment and reference sections as well as an abstract (a concise summary) at the beginning of the paper. There might be additional sections depending on the type of paper and the journal where it will be published. For example, some review papers require an outline.

The introduction starts with brief, but broad, background information about what is known in the field. A good introduction also gives the rationale of the work. It justifies the work carried out and also briefly mentions the end of the paper, where the researcher will present the hypothesis or research question driving the research. The introduction refers to the published scientific work of others and therefore requires citations following the style of the journal. Using the work or ideas of others without proper citation is plagiarism.

The materials and methods section includes a complete and accurate description of the substances the researchers use, and the method and techniques they use to gather data. The description should be thorough enough to allow another researcher to repeat the experiment and obtain similar results, but it does not have to be verbose. This section will also include information on how the researchers made measurements and the types of calculations and statistical analyses they used to examine raw data. Although the materials and methods section gives an accurate description of the experiments, it does not discuss them.

Some journals require a results section followed by a discussion section, but it is more common to combine both. If the journal does not allow combining both sections, the results section simply narrates the findings without any further interpretation. The researchers present results with tables or graphs, but they do not present duplicate information. In the discussion section, the researchers will interpret the results, describe how variables may be related, and attempt to explain the observations. It is indispensable to conduct an extensive literature search to put the results in the context of previously published scientific research. Therefore, researchers include proper citations in this section as well.

Finally, the conclusion section summarizes the importance of the experimental findings. While the scientific paper almost certainly answers one or more scientific questions that the researchers stated, any good research should lead to more questions. Therefore, a well-done scientific paper allows the researchers and others to continue and expand on the findings.

Review articles do not follow the IMRAD format because they do not present original scientific findings, or primary literature. Instead, they summarize and comment on findings that were published as primary literature and typically include extensive reference sections.

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 by rational means. Science has many fields. Those fields related to the physical world and its phenomena are natural sciences.

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.

Science uses two types of logical reasoning. Inductive reasoning uses particular 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 using the scientific method, a step-based process that consists of making observations, defining a problem, posing hypotheses, testing these hypotheses, and drawing one or more conclusions. The testing uses proper controls. Scientists present their results in peer-reviewed scientific papers published in scientific journals. A scientific research paper consists of several well-defined sections: introduction, materials and methods, results, and, finally, a concluding discussion. Review papers summarize the conducted research in a particular field over a period of time.

Visual Connection Questions

(Figure) In the example below, the scientific method is used to solve an everyday problem. Order the scientific method steps (numbered items) with the process of solving the everyday problem (lettered items). Based on the results of the experiment, is the hypothesis correct? If it is incorrect, propose some alternative hypotheses.

  1. Observation
  2. Question
  3. Hypothesis (answer)
  4. Prediction
  5. Experiment
  6. Result
  1. There is something wrong with the electrical outlet.
  2. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.
  3. My toaster doesn’t toast my bread.
  4. I plug my coffee maker into the outlet.
  5. My coffeemaker works.
  6. Why doesn’t my toaster work?

(Figure) 1: C; 2: F; 3: A; 4: B; 5: D; 6: E. The original hypothesis is incorrect, as the coffeemaker works when plugged into the outlet. Alternative hypotheses include that the toaster might be broken or that the toaster wasn’t turned on.

(Figure) Decide if each of the following is an example of inductive or deductive reasoning.

  1. All flying birds and insects have wings. Birds and insects flap their
    wings as they move through the air. Therefore, wings enable
    flight.
  2. Insects generally survive mild winters better than harsh ones. Therefore, insect pests will become more problematic if global temperatures increase.
  3. Chromosomes, the carriers of DNA, separate into daughter cells during cell division. Therefore, each daughter cell will have the same chromosome set as the mother cell.
  4. Animals as diverse as humans, insects, and wolves all exhibit social behavior. Therefore, social behavior must have an evolutionary advantage.

(Figure) 1: inductive; 2: deductive; 3: deductive; 4: inductive.

Review Questions

The first forms of life on Earth were ________.

  1. plants
  2. microorganisms
  3. birds
  4. dinosaurs

B

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

  1. hypothesis
  2. variable
  3. theory
  4. control

A

Which of the following sciences is not considered a natural science?

  1. biology
  2. astronomy
  3. physics
  4. computer science

D

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

  1. deductive reasoning
  2. the scientific method
  3. hypothesis-based science
  4. inductive reasoning

D

The process of ________ helps to ensure that a scientist’s research is original, significant, logical, and thorough.

  1. publication
  2. public speaking
  3. peer review
  4. the scientific method

C

A person notices that her houseplants that are regularly exposed to music seem to grow more quickly than those in rooms with no music. As a result, she determines that plants grow better when exposed to music. This example most closely resembles which type of reasoning?

  1. inductive reasoning
  2. deductive reasoning
  3. neither, because no hypothesis was made
  4. both inductive and deductive reasoning

A

Critical Thinking Questions

Although the scientific method is used by most of the sciences, it can also be applied to everyday situations. Think about a problem that you may have at home, at school, or with your car, and apply the scientific method to solve it.

Answers will vary, but should apply the steps of the scientific method. One possibility could be a car which doesn’t start. The hypothesis could be that the car doesn’t start because the battery is dead. The experiment would be to change the battery or to charge the battery and then check whether the car starts or not. If it starts, the problem was due to the battery, and the hypothesis is accepted.

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 influenza affect daily life by contributing to individual and societal health.

Name two topics that are likely to be studied by biologists, and two areas of scientific study that would fall outside the realm of biology.

Answers will vary. Topics that fall inside the area of biological study include how diseases affect human bodies, how pollution impacts a species’ habitat, and how plants respond to their environments. Topics that fall outside of biology (the “study of life”) include how metamorphic rock is formed and how planetary orbits function.

Thinking about the topic of cancer, write a basic science question and an applied science question that a researcher interested in this topic might ask.

Answers will vary. Basic science: What evolutionary purpose might cancer serve? Applied science: What strategies might be found to prevent cancer from reproducing at the cellular level?

Glossary

abstract
opening section of a scientific paper that summarizes the research and conclusions
applied science
form of science that aims to solve real-world problems
basic science
science that seeks to expand knowledge and understanding regardless of the short-term application of that knowledge
biology
the study of living organisms and their interactions with one another and their environments
conclusion
section of a scientific paper that summarizes the importance of the experimental findings
control
part of an experiment that does not change during the experiment
deductive reasoning
form of logical thinking that uses a general inclusive statement to forecast specific results
descriptive science
(also, discovery science) form of science that aims to observe, explore, and investigate
discussion
section of a scientific paper in which the author interprets experimental results, describes how variables may be related, and attempts to explain the phenomenon in question
falsifiable
able to be disproven by experimental results
hypothesis
suggested explanation for an observation, which one can test
hypothesis-based science
form of science that begins with a specific question and potential testable answers
inductive reasoning
form of logical thinking that uses related observations to arrive at a general conclusion
introduction
opening section of a scientific paper, which provides background information about what was known in the field prior to the research reported in the paper
life science
field of science, such as biology, that studies living things
materials and methods
section of a scientific paper that includes a complete description of the substances, methods, and techniques that the researchers used to gather data
natural science
field of science that is related to the physical world and its phenomena and processes
peer-reviewed manuscript
scientific paper that a scientist’s colleagues review who are experts in the field of study
physical science
field of science, such as geology, astronomy, physics, and chemistry, that studies nonliving matter
plagiarism
using other people’s work or ideas without proper citation, creating the false impression that those are the author’s original ideas
results
section of a scientific paper in which the author narrates the experimental findings and presents relevant figures, pictures, diagrams, graphs, and tables, without any further interpretation
review article
paper that summarizes and comments on findings that were published as primary literature
science
knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method
scientific method
method of research with defined steps that include observation, formulation of a hypothesis, testing, and confirming or falsifying the hypothesis
serendipity
fortunate accident or a lucky surprise
theory
tested and confirmed explanation for observations or
phenomena
variable
part of an experiment that the experimenter can vary or
change

3

Themes and Concepts of Biology

Learning Objectives

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

  • Identify and describe the properties of life
  • Describe the levels of organization among living things
  • Recognize and interpret a phylogenetic tree
  • List examples of different subdisciplines in biology

Biology is the science that studies life, but what exactly is life? This may sound like a silly question with an obvious response, but it is not always 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. Although viruses can attack living organisms, cause diseases, and even reproduce, they do not meet the criteria that biologists use to define life. Consequently, virologists are not biologists, strictly speaking. Similarly, some biologists study the early molecular evolution that gave rise to life. Since the events that preceded life are not biological events, these scientists are also excluded from biology in the strict sense of the term.

From its earliest beginnings, biology has wrestled with three questions: What are the shared properties that make something “alive”? Once we know something is alive, how do we find meaningful levels of organization in its structure? Finally, when faced with the remarkable diversity of life, how do we organize the different kinds of organisms so that we can better understand them? As scientists discover new organisms every day, biologists continue to seek answers to these and other questions.

Properties of Life

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

Order

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


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

Organisms are highly organized, coordinated structures that consist of one or more cells. Even very simple, single-celled organisms are remarkably complex: inside each cell, atoms comprise molecules. These in turn comprise cell organelles and other cellular inclusions. In multicellular organisms ((Figure)), similar cells form tissues. Tissues, in turn, collaborate to create organs (body structures with a distinct function). Organs work together to form organ systems.

Sensitivity or Response to Stimuli

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


A photograph of the Mimosa pudica shows a plant with many tiny leaves connected to a central stem. Four of these stems connect together.

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

Link to Learning

Watch this video to see how plants respond to a stimulus—from opening to light, to wrapping a tendril around a branch, to capturing prey.

Reproduction

Single-celled organisms reproduce by first duplicating their DNA, and then dividing it equally as the cell prepares to divide to form two new cells. Multicellular organisms often produce specialized reproductive germline, gamete, oocyte, and sperm cells. After fertilization (the fusion of an oocyte and a sperm cell), a new individual develops. When reproduction occurs, DNA containing genes are passed along to an organism’s offspring. These genes ensure that the offspring will belong to the same species and will have similar characteristics, such as size and shape.

Growth and Development

Organisms grow and develop as a result of genes providing specific instructions that will direct cellular growth and development. This ensures that a species’ young ((Figure)) will grow up to exhibit many of the same characteristics as its parents.

Although no two look alike, these kittens have inherited genes from both parents and share many of the same characteristics. (credit: Rocky Mountain Feline Rescue)


A photograph depicts a mother cat nursing three kittens: one has an orange and white tabby coat, another is black with a white foot, while the third has a black and white tabby coat.

Regulation

Even the smallest organisms are complex and require multiple regulatory mechanisms to coordinate internal functions, respond to stimuli, and cope with environmental stresses. Two examples of internal functions regulated in an organism are nutrient transport and blood flow. Organs (groups of tissues working together) perform specific functions, such as carrying oxygen throughout the body, removing wastes, delivering nutrients to every cell, and cooling the body.

Homeostasis

Polar bears (Ursus maritimus) 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)


A photos shows a white, furry polar bear.

In order to function properly, cells require appropriate conditions such as proper temperature, pH, and appropriate concentration 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 homeostasis (literally, “steady state”). For example, an organism needs to regulate body temperature through the thermoregulation process. Organisms that live in cold climates, such as the polar bear ((Figure)), have body structures that help them withstand low temperatures and conserve body heat. Structures that aid in this type of insulation include fur, feathers, blubber, and fat. In hot climates, organisms have methods (such as perspiration in humans or panting in dogs) that help them to shed excess body heat.

Energy Processing

The California condor (Gymnogyps californianus) uses chemical energy derived from food to power flight. California condors are an endangered species. This bird has a wing tag that helps biologists identify the individual. (credit: Pacific Southwest Region U.S. Fish and Wildlife Service)


Photo shows a large bird with an extremely wide wingspan in flight. It is a California condor, and it has a tag on its wing.

All organisms 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 in molecules they take in as food ((Figure)).

Levels of Organization of Living Things

Living things are highly organized and structured, following a hierarchy that we can examine 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 one or more chemical bonds. Many molecules that are biologically important are macromolecules, large molecules that are typically formed by polymerization (a polymer is a large molecule that is made by combining smaller units called monomers, which are simpler than macromolecules). An example of a macromolecule is deoxyribonucleic acid (DNA) ((Figure)), which contains the instructions for the structure and functioning of all living organisms.

All molecules, including this DNA molecule, are comprised of atoms. (credit: “brian0918”/Wikimedia Commons)


Molecular model depicts a D N A molecule, showing its double helix structure. The double helix is made up of two separate vertical strands of small particles, or atoms. These strands are connected by horizontal bands of particles. The vertical strands are twisted, and the structure has the shape of a spiral staircase.

Link to Learning

Watch this video that animates the three-dimensional structure of the DNA molecule in (Figure).

Some cells contain aggregates of macromolecules surrounded by membranes. We call these organelles. Organelles are small structures that exist within cells. Examples of organelles include mitochondria and chloroplasts, which carry out indispensable functions: mitochondria produce energy to power the cell, while chloroplasts enable green plants to utilize the energy in sunlight to make sugars. 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 scientists do not consider viruses living: they are not made of cells. To make new viruses, they have to invade and hijack the reproductive mechanism of 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. Scientists classify cells as prokaryotic or eukaryotic. Prokaryotes are single-celled or colonial organisms that do not have membrane-bound nuclei. In contrast, the cells of eukaryotes do have membrane-bound organelles and a membrane-bound nucleus.

In larger organisms, cells combine to make tissues, which are groups of similar cells carrying out similar or related functions. Organs are collections of tissues grouped together performing 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. Mammals have many organ systems. For instance, the circulatory system transports blood through 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 organisms, which biologists typically call microorganisms.

Biologists collectively call all the individuals of a species living within a specific area a population. For example, a forest may include many pine trees, which represent the population of 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, insects, and microbial populations. A community is the sum 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, nonliving parts of that environment such as nitrogen in the soil or rain water. At the highest level of organization ((Figure)), the biosphere is the collection of all ecosystems, and it represents the zones of life on Earth. It includes land, water, and even the atmosphere to a certain extent.

Visual Connection
shows the biological levels of organization of living things. From a single organelle to the entire biosphere, living organisms are parts of a highly structured hierarchy. (credit “organelles”: modification of work by Umberto Salvagnin; credit “cells”: modification of work by Bruce Wetzel, Harry Schaefer/ National Cancer Institute; credit “tissues”: modification of work by Kilbad; Fama Clamosa; Mikael Häggström; credit “organs”: modification of work by Mariana Ruiz Villareal; credit “organisms”: modification of work by “Crystal”/Flickr; credit “ecosystems”: modification of work by US Fish and Wildlife Service Headquarters; credit “biosphere”: modification of work by NASA)


A flow chart shows the hierarchy of living organisms. From smallest to largest, this hierarchy includes: (1) Organelles, such as nuclei, that exist inside cells. (2) Cells, such as a red blood cell. (3) Tissues, such as human skin tissue. (4) Organs such as the stomach make up the human digestive system, an example of an organ system. (5) Organisms, populations, and communities. In a forest, each pine tree is an organism. Together, all the pine trees make up a population. All the plant and animal species in the forest comprise a community. (6) Ecosystems: the coastal ecosystem in the Southeastern United States includes living organisms and the environment in which they live. (7) The biosphere: encompasses all the ecosystems on Earth.

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.

The Diversity of Life

The fact that biology, as a science, has such a broad scope has to do with the 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.

A phylogenetic tree ((Figure)) can summarize the evolution of various life forms on Earth. It is a diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or physical traits or both. Nodes and branches comprise a phylogenetic tree. The internal nodes represent ancestors and are points in evolution when, based on scientific evidence, researchers believe an ancestor has diverged to form two new species. The length of each branch is proportional to the time elapsed since the split.

Microbiologist Carl Woese constructed this phylogenetic tree using data that he obtained from sequencing ribosomal RNA genes. The tree shows the separation of living organisms into three domains: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are prokaryotes, single-celled organisms lacking intracellular organelles. (credit: Eric Gaba; NASA Astrobiology Institute)


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

Evolution Connection

Carl Woese and the Phylogenetic TreeIn the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. They based the organizational scheme mainly on physical features, as opposed to physiology, biochemistry, or molecular biology, all of which modern systematics use. American microbiologist Carl Woese’s pioneering work in the early 1970s has shown, however, that life on Earth has evolved along three lineages, now called domains—Bacteria, Archaea, and Eukarya. The first two are prokaryotic cells with microbes that lack membrane-enclosed nuclei and organelles. The third domain contains the eukaryotes and includes unicellular microorganisms (protists), together with the three remaining kingdoms (fungi, plants, and animals). Woese defined Archaea as a new domain, and this resulted in a new taxonomic tree ((Figure)). 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).

Woese constructed his tree from universally distributed comparative gene sequencing that are present in every organism, and conserved (meaning that these genes have remained essentially unchanged throughout evolution). Woese’s approach was revolutionary because comparing physical features are insufficient to differentiate between the prokaryotes that appear fairly similar in spite of their tremendous biochemical diversity and genetic variability ((Figure)). Comparing homologous DNA and RNA sequences provided Woese with a sensitive device that revealed the extensive variability of prokaryotes, and which justified separating the prokaryotes into two domains: bacteria and archaea.

These images represent different domains. The (a) bacteria in this micrograph belong to Domain Bacteria, while the (b) extremophiles (not visible) living in this hot vent belong to Domain Archaea. Both the (c) sunflower and (d) lion are part of Domain Eukarya. (credit a: modification of work by Drew March; credit b: modification of work by Steve Jurvetson; credit c: modification of work by Michael Arrighi; credit d: modification of work by Leszek Leszcynski)


There are four photos shown. The first photo is a micrograph, showing tubelike bacterial. The second photo shows a steaming body of water, refered to as a hot vent. Some of the water is a typical blue, while the outer edges are rust colored. The third picture shows a tall sunflower, with a thick stem and bright yellow petals. The fourth photo shows a muscular lion that has a thick mane of hair around its neck and head.

Branches of Biological Study

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

Career Connection

Forensic ScientistForensic 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 materials 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, developing molecular techniques and establishing DNA databases have expanded 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 ((Figure)) found in many different environments and materials. Forensic scientists also analyze other biological evidence left at crime scenes, such as insect larvae or pollen grains. Students who want to pursue careers in forensic science will most likely have to take chemistry and biology courses as well as some intensive math courses.

This forensic scientist works in a DNA extraction room at the U.S. Army Criminal Investigation Laboratory at Fort Gillem, GA. (credit: United States Army CID Command Public Affairs)


Photo depicts a scientist working in the lab.

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

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


Photo depicts scientist digging fossils out of the dirt.

Paleontology, another branch of biology, uses fossils to study life’s history ((Figure)). 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. This is just a small sample of the many fields that biologists can pursue.

Biology is the culmination of the achievements of the natural sciences from their inception to today. Excitingly, it is the cradle of emerging sciences, such as the biology of brain activity, genetic engineering of custom organisms, and the biology of evolution that uses the laboratory tools of molecular biology to retrace the earliest stages of life on Earth. A scan of news headlines—whether reporting on immunizations, a newly discovered species, sports doping, or a genetically-modified food—demonstrates the way biology is active in and important to our everyday world.

Section Summary

Biology is the science of life. All living organisms share several key properties such as order, sensitivity or response to stimuli, reproduction, growth and development, regulation, homeostasis, and energy processing. Living things are highly organized parts of a hierarchy that includes atoms, molecules, organelles, cells, tissues, organs, and organ systems. In turn, biologists group organisms as populations, communities, ecosystems, and the biosphere. The great diversity of life today evolved from less-diverse ancestral organisms over billions of years. We can use a phylogenetic tree to show evolutionary relationships among organisms.

Biology is very broad and includes many branches and subdisciplines. Examples include molecular biology, microbiology, neurobiology, zoology, and botany, among others.

Visual Connection Questions

(Figure) 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.

(Figure) Communities exist within populations which exist within ecosystems.

Review Questions

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

  1. organ
  2. organelle
  3. cell
  4. macromolecule

C

Viruses are not considered living because they ________.

  1. are not made of cells
  2. lack cell nuclei
  3. do not contain DNA or RNA
  4. cannot reproduce

A

The presence of a membrane-enclosed nucleus is a characteristic of ________.

  1. prokaryotic cells
  2. eukaryotic cells
  3. living organisms
  4. bacteria

B

A group of individuals of the same species living in the same area is called a(n) ________.

  1. family
  2. community
  3. population
  4. ecosystem

C

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

  1. organelle, tissue, biosphere, ecosystem, population
  2. organ, organism, tissue, organelle, molecule
  3. organism, community, biosphere, molecule, tissue, organ
  4. biosphere, ecosystem, community, population, organism

D

Where in a phylogenetic tree would you expect to find the organism that had evolved most recently?

  1. at the base
  2. within the branches
  3. at the nodes
  4. at the branch tips

D

Critical Thinking Questions

Select two items that biologists agree are necessary in order to consider an organism “alive.” For each, give an example of a nonliving object that otherwise fits the definition of “alive.”

Answers will vary. Layers of sedimentary rock have order but are not alive. Technology is capable of regulation but is not, of itself, alive.

Consider the levels of organization of the biological world, and place each of these items in order from smallest level of organization to most encompassing: skin cell, elephant, water molecule, planet Earth, tropical rainforest, hydrogen atom, wolf pack, liver.

Smallest level of organization to largest: hydrogen atom, water molecule, skin cell, liver, elephant, wolf pack, tropical rainforest, planet Earth

You go for a long walk on a hot day. Give an example of a way in which homeostasis keeps your body healthy.

During your walk, you may begin to perspire, which cools your body and helps your body to maintain a constant internal temperature. You might also become thirsty and pause long enough for a cool drink, which will help to restore the water lost during perspiration.

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.

Glossary

atom
smallest and most fundamental unit of matter
biochemistry
study of the chemistry of biological organisms
biosphere
collection of all the ecosystems on Earth
botany
study of plants
cell
smallest fundamental unit of structure and function in living things
community
set of populations inhabiting a particular area
ecosystem
all the living things in a particular area together with the abiotic, nonliving parts of that environment
eukaryote
organism with cells that have nuclei and membrane-bound organelles
evolution
process of gradual change during which new species arise from older species and some species become extinct
homeostasis
ability of an organism to maintain constant internal conditions
macromolecule
large molecule, typically formed by the joining of smaller molecules
microbiology
study of the structure and function of microorganisms
molecule
chemical structure consisting of at least two atoms held together by one or more chemical bonds
molecular biology
study of biological processes and their regulation at the molecular level, including interactions among molecules such as DNA, RNA, and proteins
neurobiology
study of the biology of the nervous system
organ
collection of related tissues grouped together performing a common function
organ system
level of organization that consists of functionally related interacting organs
organelle
small structures that exist within cells and carry out cellular functions
organism
individual living entity
paleontology
study of life’s history by means of fossils
phylogenetic tree
diagram showing the evolutionary relationships among various biological species based on similarities and differences in genetic or physical traits or both; in essence, a hypothesis concerning evolutionary connections
population
all of the individuals of a species living within a specific area
prokaryote
single-celled organism that lacks organelles and does not have nuclei surrounded by a nuclear membrane
tissue
group of similar cells carrying out related functions
zoology
study of animals

II

The Chemical Foundation of Life

4

Introduction

Atoms are the building blocks of molecules in the universe—air, soil, water, rocks . . . and also the cells of all living organisms. In this model of an organic molecule, the atoms of carbon (black), hydrogen (white), nitrogen (blue), oxygen (red), and sulfur (yellow) are in proportional atomic size. The silver rods indicate chemical bonds. (credit: modification of work by Christian Guthier)


A molecular model shows hundreds of atoms, represented by yellow, red, black, blue and white balls, connected together by rods to form a molecule. The molecule has a complex but very specific three-dimensional structure with rings and branches.

Elements in various combinations comprise all matter, including living things. Some of the most abundant elements in living organisms include carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. These form the nucleic acids, proteins, carbohydrates, and lipids that are the fundamental components of living matter. Biologists must understand these important building blocks and the unique structures of the atoms that comprise molecules, allowing for cells, tissues, organ systems, and entire organisms to form.

All biological processes follow the laws of physics and chemistry, so in order to understand how biological systems work, it is important to understand the underlying physics and chemistry. For example, the flow of blood within the circulatory system follows the laws of physics that regulate the modes of fluid flow. The breakdown of the large, complex molecules of food into smaller molecules—and the conversion of these to release energy to be stored in adenosine triphosphate (ATP)—is a series of chemical reactions that follow chemical laws. The properties of water and the formation of hydrogen bonds are key to understanding living processes. Recognizing the properties of acids and bases is important, for example, to our understanding of the digestive process. Therefore, the fundamentals of physics and chemistry are important for gaining insight into biological processes.

5

Atoms, Isotopes, Ions, and Molecules: The Building Blocks

Learning Objectives

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

  • Define matter and elements
  • Describe the interrelationship between protons, neutrons, and electrons
  • Compare the ways in which electrons can be donated or shared between atoms
  • Explain the ways in which naturally occurring elements combine to create molecules, cells, tissues, organ systems, and organisms

At its most fundamental level, life is made up of matter. Matter is any substance that occupies space and has mass. Elements are unique forms of matter with specific chemical and physical properties that cannot break down into smaller substances by ordinary chemical reactions. There are 118 elements, but only 98 occur naturally. The remaining elements are unstable and require scientists to synthesize them in laboratories.

Each element is designated by its chemical symbol, which is a single capital letter or, when the first letter is already “taken” by another element, a combination of two letters. Some elements follow the English term for the element, such as C for carbon and Ca for calcium. Other elements’ chemical symbols derive from their Latin names. For example, the symbol for sodium is Na, referring to natrium, the Latin word for sodium.

The four elements common to all living organisms are oxygen (O), carbon (C), hydrogen (H), and nitrogen (N). In the nonliving world, elements are found in different proportions, and some elements common to living organisms are relatively rare on the earth as a whole, as (Figure) shows. For example, the atmosphere is rich in nitrogen and oxygen but contains little carbon and hydrogen, while the earth’s crust, although it contains oxygen and a small amount of hydrogen, has little nitrogen and carbon. In spite of their differences in abundance, all elements and the chemical reactions between them obey the same chemical and physical laws regardless of whether they are a part of the living or nonliving world.

Approximate Percentage of Elements in Living Organisms (Humans) Compared to the Nonliving World
Element Life (Humans) Atmosphere Earth’s Crust
Oxygen (O) 65% 21% 46%
Carbon (C) 18% trace trace
Hydrogen (H) 10% trace 0.1%
Nitrogen (N) 3% 78% trace

The Structure of the Atom

To understand how elements come together, we must first discuss the element’s smallest component or building block, the atom. An atom is the smallest unit of matter that retains all of the element’s chemical properties. For example, one gold atom has all of the properties of gold in that it is a solid metal at room temperature. A gold coin is simply a very large number of gold atoms molded into the shape of a coin and contains small amounts of other elements known as impurities. We cannot break down gold atoms into anything smaller while still retaining the properties of gold.

An atom is composed of two regions: the nucleus, which is in the atom’s center and contains protons and neutrons. The atom’s outermost region holds its electrons in orbit around the nucleus, as (Figure) illustrates. Atoms contain protons, electrons, and neutrons, among other subatomic particles. The only exception is hydrogen (H), which is made of one proton and one electron with no neutrons.

Elements, such as helium, depicted here, are made up of atoms. Atoms are made up of protons and neutrons located within the nucleus, with electrons in orbitals surrounding the nucleus.

This illustration shows that, like planets orbiting the sun, electrons orbit the nucleus of an atom. The nucleus contains two neutrally charged neutrons, and two positively charged protons represented by spheres. A single, circular orbital surrounding the nucleus contains two negatively charged electrons on opposite sides.

Protons and neutrons have approximately the same mass, about 1.67 × 10-24 grams. Scientists arbitrarily define this amount of mass as one atomic mass unit (amu) or one Dalton, as (Figure) shows. Although similar in mass, protons and neutrons differ in their electric charge. A proton is positively charged; whereas, a neutron is uncharged. Therefore, the number of neutrons in an atom contributes significantly to its mass, but not to its charge. Electrons are much smaller in mass than protons, weighing only 9.11 × 10-28 grams, or about 1/1800 of an atomic mass unit. Hence, they do not contribute much to an element’s overall atomic mass. Therefore, when considering atomic mass, it is customary to ignore the mass of any electrons and calculate the atom’s mass based on the number of protons and neutrons alone. Although not significant contributors to mass, electrons do contribute greatly to the atom’s charge, as each electron has a negative charge equal to the proton’s positive charge. In uncharged, neutral atoms, the number of electrons orbiting the nucleus is equal to the number of protons inside the nucleus. In these atoms, the positive and negative charges cancel each other out, leading to an atom with no net charge.

Accounting for the sizes of protons, neutrons, and electrons, most of the atom’s volume—greater than 99 percent—is empty space. With all this empty space, one might ask why so-called solid objects do not just pass through one another. The reason they do not is that the electrons that surround all atoms are negatively charged and negative charges repel each other.

Protons, Neutrons, and Electrons
Charge Mass (amu) Location
Proton +1 1 nucleus
Neutron 0 1 nucleus
Electron –1 0 orbitals

Atomic Number and Mass

Atoms of each element contain a characteristic number of protons and electrons. The number of protons determines an element’s atomic number, which scientists use to distinguish one element from another. The number of neutrons is variable, resulting in isotopes, which are different forms of the same atom that vary only in the number of neutrons they possess. Together, the number of protons and neutrons determine an element’s mass number, as (Figure) illustrates. Note that we disregard the small contribution of mass from electrons in calculating the mass number. We can use this approximation of mass to easily calculate how many neutrons an element has by simply subtracting the number of protons from the mass number. Since an element’s isotopes will have slightly different mass numbers, scientists also determine the atomic mass, which is the calculated mean of the mass number for its naturally occurring isotopes. Often, the resulting number contains a fraction. For example, the atomic mass of chlorine (Cl) is 35.45 because chlorine is composed of several isotopes, some (the majority) with atomic mass 35 (17 protons and 18 neutrons) and some with atomic mass 37 (17 protons and 20 neutrons).

Visual Connection
Carbon has an atomic number of six, and two stable isotopes with mass numbers of twelve and thirteen, respectively. Its relative atomic mass is 12.011

Carbon is indicated by its atomic symbol, a capital C. Carbon has the atomic number six and two stable isotopes, carbon-12 and carbon-13.

How many neutrons do carbon-12 and carbon-13 have, respectively?

<!–<para> Carbon-12 has six neutrons. Carbon-13 has seven neutrons.–>

Isotopes

Isotopes are different forms of an 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 contains six protons, six neutrons, and six electrons; therefore, it has a mass number of 12 (six protons and six neutrons). Carbon-14 contains six protons, eight neutrons, and six electrons; its atomic mass is 14 (six protons and eight neutrons). These two alternate forms of carbon are isotopes. Some isotopes may emit neutrons, protons, and electrons, and attain a more stable atomic configuration (lower level of potential energy); these are radioactive isotopes, or radioisotopes. Radioactive decay (carbon-14 decaying to eventually become nitrogen-14) describes the energy loss that occurs when an unstable atom’s nucleus releases radiation.

Evolution Connection

Carbon Dating
Carbon is normally present in the atmosphere in the form of gaseous compounds like carbon dioxide and methane. Carbon-14 (14C) is a naturally occurring radioisotope that is created in the atmosphere from atmospheric 14N (nitrogen) by the addition of a neutron and the loss of a proton because of cosmic rays. This is a continuous process, so more 14C is always being created. As a living organism incorporates 14C initially as carbon dioxide fixed in the process of photosynthesis, the relative amount 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 between 14C and 12C will decline as 14C decays gradually to 14N by a process called beta decay—electrons or positrons emission. This decay emits energy in a slow process.

After approximately 5,730 years, half of the starting concentration of 14C will convert back to 14N. We call the time it takes for half of the original concentration of an isotope to decay back to its more stable form its half-life. Because the half-life of 14C is long, scientists use it to date formerly living objects such as old bones or wood. Comparing the ratio of the 14C concentration in an object to the amount of 14C in the atmosphere, scientists can determine the amount of the isotope that has not yet decayed. On the basis of this amount, (Figure) shows that we can calculate the age of the material, such as the pygmy mammoth, with accuracy if it is not much older than about 50,000 years. Other elements have isotopes with different half lives. For example, 40K (potassium-40) has a half-life of 1.25 billion years, and 235U (Uranium 235) has a half-life of about 700 million years. Through the use of radiometric dating, scientists can study the age of fossils or other remains of extinct organisms to understand how organisms have evolved from earlier species.

Scientists can determine the age of carbon-containing remains less than about 50,000 years old, such as this pygmy mammoth, using carbon dating. (credit: Bill Faulkner, NPS)

Photo shows scientists unearthing a mammoth skeleton.

Link to Learning

To learn more about atoms, isotopes, and how to tell one isotope from another, run the simulation.

The Periodic Table

The periodic table organizes and displays different elements. Devised by Russian chemist Dmitri Mendeleev (1834–1907) in 1869, the table groups elements that, although unique, share certain chemical properties with other elements. The properties of elements are responsible for their physical state at room temperature: they may be gases, solids, or liquids. Elements also have specific chemical reactivity, the ability to combine and to chemically bond with each other.

In the periodic table in (Figure), the elements are organized and displayed according to their atomic number and are arranged in a series of rows and columns based on shared chemical and physical properties. In addition to providing the atomic number for each element, the periodic table also displays the element’s atomic mass. Looking at carbon, for example, its symbol (C) and name appear, as well as its atomic number of six (in the upper left-hand corner) and its atomic mass of 12.11.

The periodic table shows each element’s atomic mass and atomic number. The atomic number appears above the symbol for the element and the approximate atomic mass appears below it.

The periodic table consists of eighteen groups and seven periods. Each element has its own square. Within each square is the following information; the atomic number, the symbol, the relative atomic mass, and the name. For example, hydrogen's atomic number is 1, symbol is the letter H; relative atomic mass is 1.01, and name is hydrogen. Two additional rows of elements, known as the lanthanides and actinides, are placed beneath the main table. The lanthanides include elements 57 through 71 and belong in period seven between groups three and four. The actinides include elements 89 through 98 and belong in period eight between the same groups. These elements are placed separately to make the table more compact. For each element, the name, atomic symbol, atomic number, and atomic mass are provided. The atomic number is a whole number that represents the number of protons. The atomic mass, which is the average mass of different isotopes, is estimated to two decimal places. The elements are divided into three categories: metals, nonmetals and metalloids. These form a diagonal line from period two, group thirteen to period seven, group sixteen. All elements to the left of the metalloids are metals, and all elements to the right are nonmetals.

The periodic table groups elements according to chemical properties. Scientists base the differences in chemical reactivity between the elements on the number and spatial distribution of an atom’s electrons. Atoms that chemically react and bond to each other form molecules. Molecules are simply two or more atoms chemically bonded together. Logically, when two atoms chemically bond to form a molecule, their electrons, which form the outermost region of each atom, come together first as the atoms form a chemical bond.

Electron Shells and the Bohr Model

Note that there is a connection between the number of protons in an element, the atomic number that distinguishes one element from another, and the number of electrons it has. In all electrically neutral atoms, the number of electrons is the same as the number of protons. Thus, each element, at least when electrically neutral, has a characteristic number of electrons equal to its atomic number.

In 1913, Danish scientist Niels Bohr (1885–1962) developed an early model of the atom. The Bohr model shows the atom as a central nucleus containing protons and neutrons, with the electrons in circular orbitals at specific distances from the nucleus, as (Figure) illustrates. These orbits form electron shells or energy levels, which are a way of visualizing the number of electrons in the outermost shells. These energy levels are designated by a number and the symbol “n.” For example, 1n represents the first energy level located closest to the nucleus.

In 1913, Niels Bohrs developed the Bohr model in which electrons exist within principal shells. An electron normally exists in the lowest energy shell available, which is the one closest to the nucleus. Energy from a photon of light can bump it up to a higher energy shell, but this situation is unstable, and the electron quickly decays back to the ground state. In the process, it releases a photon of light.

Three concentric circles around the nucleus of a hydrogen atom represent principal shells. These are named 1 n, 2 n, and 3 n in order of increasing distance from the nucleus. An electron orbits in the shell closest to the nucleus, 1 n.

Electrons fill orbitals in a consistent order: they first fill the orbitals closest to the nucleus, then they continue to fill orbitals of increasing energy further from the nucleus. If there are multiple orbitals of equal energy, they fill with one electron in each energy level before adding a second electron. The electrons of the outermost energy level determine the atom’s energetic stability and its tendency to form chemical bonds with other atoms to form molecules.

Under standard conditions, atoms fill the inner shells first, often resulting in a variable number of electrons in the outermost shell. The innermost shell has a maximum of two electrons but the next two electron shells can each have a maximum of eight electrons. This is known as the octet rule, which states, with the exception of the innermost shell, that atoms are more stable energetically when they have eight electrons in their valence shell, the outermost electron shell. (Figure) shows examples of some neutral atoms and their electron configurations. Notice that in (Figure), helium has a complete outer electron shell, with two electrons filling its first and only shell. Similarly, neon has a complete outer 2n shell containing eight electrons. In contrast, chlorine and sodium have seven and one in their outer shells, respectively, but theoretically they would be more energetically stable if they followed the octet rule and had eight.

Visual Connection
Bohr diagrams indicate how many electrons fill each principal shell. Group 18 elements (helium, neon, and argon) have a full outer, or valence, shell. A full valence shell is the most stable electron configuration. Elements in other groups have partially filled valence shells and gain or lose electrons to achieve a stable electron configuration.

Bohr diagrams of elements from groups 1, 14, 17 and 18, and periods 1, 2 and 3 are shown. Period 1, in which the 1n shell is filling, contains hydrogen and helium. Hydrogen, in group 1, has one valence electron. Helium, in group 18, has two valence electrons. The 1n shell holds a maximum of two electrons, so the shell is full and the electron configuration is stable. Period 2, in which the 2n shell is filling, contains lithium, carbon, fluorine, and neon. Lithium, in group 1, has 1 valence electron. Carbon, in group 14, has 4 valence electrons. Fluorine, in group 17, has 7 valence electrons. Neon, in group 18, has 8 valence electrons, a full octet. Period 3, in which the 3n shell is filling, contains sodium, silicon, chlorine, and argon. Sodium, in group 1, has 1 valence electron. Silicon, in group 14, has 4 valence electrons. Chlorine, in group 17, has 7 valence electrons. Argon, in group 18, has 8 valence electrons, a full octet.

An atom may give, take, or share electrons with another atom to achieve a full valence shell, the most stable electron configuration. Looking at this figure, how many electrons do elements in group 1 need to lose in order to achieve a stable electron configuration? How many electrons do elements in groups 14 and 17 need to gain to achieve a stable configuration?

<!–<para>Elements in group 1 need to lose one electron to achieve a stable electron configuration. Elements in groups 14 and 17 need to gain four and one electrons, respectively, to achieve a stable configuration.–>

Understanding that the periodic table’s organization is based on the total number of protons (and electrons) helps us know how electrons distribute themselves among the shells. The periodic table is arranged in columns and rows based on the number of electrons and their location. Examine more closely some of the elements in the table’s far right column in (Figure). The group 18 atoms helium (He), neon (Ne), and argon (Ar) all have filled outer electron shells, making it unnecessary for them to share electrons with other atoms to attain stability. They are highly stable as single atoms. Because they are non reactive, scientists coin them inert (or noble gases). Compare this to the group 1 elements in the left-hand column. These elements, including hydrogen (H), lithium (Li), and sodium (Na), all have one electron in their outermost shells. That means that they can achieve a stable configuration and a filled outer shell by donating or sharing one electron with another atom or a molecule such as water. Hydrogen will donate or share its electron to achieve this configuration, while lithium and sodium will donate their electron to become stable. As a result of losing a negatively charged electron, they become positively charged ions. Group 17 elements, including fluorine and chlorine, have seven electrons in their outmost shells, so they tend to fill this shell with an electron from other atoms or molecules, making them negatively charged ions. Group 14 elements, of which carbon is the most important to living systems, have four electrons in their outer shell allowing them to make several covalent bonds (discussed below) with other atoms. Thus, the periodic table’s columns represent the potential shared state of these elements’ outer electron shells that is responsible for their similar chemical characteristics.

Electron Orbitals

Although useful to explain the reactivity and chemical bonding of certain elements, the Bohr model does not accurately reflect how electrons spatially distribute themselves around the nucleus. They do not circle the nucleus like the earth orbits the sun, but we find them in electron orbitals. These relatively complex shapes result from the fact that electrons behave not just like particles, but also like waves. Mathematical equations from quantum mechanics, which scientists call wave functions, can predict within a certain level of probability where an electron might be at any given time. Scientists call the area where an electron is most likely to be found its orbital.

Recall that the Bohr model depicts an atom’s electron shell configuration. Within each electron shell are subshells, and each subshell has a specified number of orbitals containing electrons. While it is impossible to calculate exactly an electron’s location, scientists know that it is most probably located within its orbital path. The letter s, p, d, and f designate the subshells. The s subshell is spherical in shape and has one orbital. Principal shell 1n has only a single s orbital, which can hold two electrons. Principal shell 2n has one s and one p subshell, and can hold a total of eight electrons. The p subshell has three dumbbell-shaped orbitals, as (Figure) illustrates. Subshells d and f have more complex shapes and contain five and seven orbitals, respectively. We do not show these in the illustration. Principal shell 3n has s, p, and d subshells and can hold 18 electrons. Principal shell 4n has s, p, d and f orbitals and can hold 32 electrons. Moving away from the nucleus, the number of electrons and orbitals in the energy levels increases. Progressing from one atom to the next in the periodic table, we can determine the electron structure by fitting an extra electron into the next available orbital.

The s subshells are shaped like spheres. Both the 1n and 2n principal shells have an s orbital, but the size of the sphere is larger in the 2n orbital. Each sphere is a single orbital. Three dumbbell-shaped orbitals comprise p subshells. Principal shell 2n has a p subshell, but shell 1 does not.

Illustration shows 1 n s, 2 n s and 2 n p subshells. The 1 n s subshell and 2 n s subshells are both spheres, but the 2 n s sphere is larger than the 1 n s sphere. The 2 n p subshell is made up of three dumbbells that radiate out from the center of the atom.

The closest orbital to the nucleus, the 1s orbital, can hold up to two electrons. This orbital is equivalent to the Bohr model’s innermost electron shell. Scientists call it the 1s orbital because it is spherical around the nucleus. The 1s orbital is the closest orbital to the nucleus, and it is always filled first, before any other orbital fills. Hydrogen has one electron; therefore, it occupies only one spot within the 1s orbital. We designate this as 1s1, where the superscripted 1 refers to the one electron within the 1s orbital. Helium has two electrons; therefore, it can completely fill the 1s orbital with its two electrons. We designate this as 1s2, referring to the two electrons of helium in the 1s orbital. On the periodic table (Figure), hydrogen and helium are the only two elements in the first row (period). This is because they only have electrons in their first shell, the 1s orbital. Hydrogen and helium are the only two elements that have the 1s and no other electron orbitals in the electrically neutral state.

The second electron shell may contain eight electrons. This shell contains another spherical s orbital and three “dumbbell” shaped p orbitals, each of which can hold two electrons, as (Figure) shows. After the 1s orbital fills, the second electron shell fills, first filling its 2s orbital and then its three p orbitals. When filling the p orbitals, each takes a single electron. Once each p orbital has an electron, it may add a second. Lithium (Li) contains three electrons that occupy the first and second shells. Two electrons fill the 1s orbital, and the third electron then fills the 2s orbital. Its electron configuration is 1s22s1. Neon (Ne), alternatively, has a total of ten electrons: two are in its innermost 1s orbital and eight fill its second shell (two each in the 2s and three p orbitals). Thus it is an inert gas and energetically stable as a single atom that will rarely form a chemical bond with other atoms. Larger elements have additional orbitals, comprising the third electron shell. While the concepts of electron shells and orbitals are closely related, orbitals provide a more accurate depiction of an atom’s electron configuration because the orbital model specifies the different shapes and special orientations of all the places that electrons may occupy.

Link to Learning

Watch this visual animation to see the spatial arrangement of the p and s orbitals.

Chemical Reactions and Molecules

All elements are most stable when their outermost shell is filled with electrons according to the octet rule. This is because it is energetically favorable for atoms to be in that configuration and it makes them stable. However, since not all elements have enough electrons to fill their outermost shells, atoms form chemical bonds with other atoms thereby obtaining the electrons they need to attain a stable electron configuration. When two or more atoms chemically bond with each other, the resultant chemical structure is a molecule. The familiar water molecule, H2O, consists of two hydrogen atoms and one oxygen atom. These bond together to form water, as (Figure) illustrates. Atoms can form molecules by donating, accepting, or sharing electrons to fill their outer shells.

Two or more atoms may bond with each other to form a molecule. When two hydrogens and an oxygen share electrons via covalent bonds it forms a water molecule.

In the first image, an oxygen atom is shown with six valence electrons. Four of these valence electrons form pairs at the top and right sides of the valence shell. The other two electrons are alone on the bottom and left sides. A hydrogen atom sits next to each the lone electron of the oxygen. Each hydrogen has only one valence electron. An arrow indicates that a reaction takes place. After the reaction, in the second image, each unpaired electron in the oxygen joins an electron from one of the hydrogen atoms so that the valence rings are now connected together. The bond that forms between oxygen and hydrogen can also be represented by a dash.

Chemical reactions occur when two or more atoms bond together to form molecules or when bonded atoms break apart. Scientists call the substances used in the beginning of a chemical reaction reactants (usually on the left side of a chemical equation), and we call the substances at the end of the reaction products (usually on the right side of a chemical equation). We typically draw an arrow between the reactants and products to indicate the chemical reaction’s direction. This direction is not always a “one-way street.” To create the water molecule above, the chemical equation would be:

An example of a simple chemical reaction is breaking down hydrogen peroxide molecules, each of which consists of two hydrogen atoms bonded to two oxygen atoms (H2O2). The reactant hydrogen peroxide breaks down into water, containing one oxygen atom bound to two hydrogen atoms (H2O), and oxygen, which consists of two bonded oxygen atoms (O2). In the equation below, the reaction includes two hydrogen peroxide molecules and two water molecules. This is an example of a balanced chemical equation, wherein each element’s number of atoms is the same on each side of the equation. According to the law of conservation of matter, the number of atoms before and after a chemical reaction should be equal, such that no atoms are, under normal circumstances, created or destroyed.

Even though all of the reactants and products of this reaction are molecules (each atom remains bonded to at least one other atom), in this reaction only hydrogen peroxide and water are representatives of compounds: they contain atoms of more than one type of element. Molecular oxygen, alternatively, as (Figure) shows, consists of two doubly bonded oxygen atoms and is not classified as a compound but as a hononuclear molecule.

A double bond joins the oxygen atoms in an O2 molecule.

Two oxygen atoms are shown side-by-side. Each has six valence electrons, two that are paired and two that are unpaired. An arrow indicates that a reaction takes place. After the reaction, the four unpaired electrons join to form a double bond. This double bond can also be depicted by an equal sign between two Os.

Some chemical reactions, such as the one above, can proceed in one direction until they expend all the reactants. The equations that describe these reactions contain a unidirectional arrow and are irreversible. Reversible reactions are those that can go in either direction. In reversible reactions, reactants turn into products, but when the product’s concentration goes beyond a certain threshold (characteristic of the particular reaction), some of these products convert back into reactants. At this point, product and reactant designations reverse. This back and forth continues until a certain relative balance between reactants and products occurs—a state called equilibrium. A chemical equation with a double headed arrow pointing towards both the reactants and products often denote these reversible reaction situations.

For example, in human blood, excess hydrogen ions (H+) bind to bicarbonate ions (HCO3) forming an equilibrium state with carbonic acid (H2CO3). If we added carbonic acid to this system, some of it would convert to bicarbonate and hydrogen ions.

{{\text{HCO}}_{3}}^{-}{\text{+ H}}^{+}\text{}↔{\text{H}}_{2}{\text{CO}}_{3}

However, biological reactions rarely obtain equilibrium because the concentrations of the reactants or products or both are constantly changing, often with one reaction’s product a reactant for another. To return to the example of excess hydrogen ions in the blood, forming carbonic acid will be the reaction’s major direction. However, the carbonic acid can also leave the body as carbon dioxide gas (via exhalation) instead of converting back to bicarbonate ion, thus driving the reaction to the right by the law of mass action. These reactions are important for maintaining homeostasis in our blood.

Ions and Ionic Bonds

Some atoms are more stable when they gain or lose an electron (or possibly two) and form ions. This fills their outermost electron shell and makes them energetically more stable. Because the number of electrons does not equal the number of protons, each ion has a net charge. Cations are positive ions that form by losing electrons. Negative ions form by gaining electrons, which we call anions. We designate anions by their elemental name and change the ending to “-ide”, thus the anion of chlorine is chloride, and the anion of sulfur is sulfide.

Scientists refer to this movement of electrons from one element to another as electron transfer. As (Figure) illustrates, sodium (Na) only has one electron in its outer electron 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, 11 neutrons, and only 10 electrons, leaving it with an overall charge of +1. We now refer to it as a sodium ion. Chlorine (Cl) in its lowest energy state (called the ground state) 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, 17 neutrons, and 18 electrons, giving it a net negative (–1) charge. We now refer to it as a chloride ion. In this example, sodium will donate its one electron to empty its shell, and chlorine will accept that electron to fill its shell. 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 cation) or –1 (chloride anion) charge. Note that these transactions can normally only take place simultaneously: in order for a sodium atom to lose an electron, it must be in the presence of a suitable recipient like a chlorine atom.

In the formation of an ionic compound, metals lose electrons and nonmetals gain electrons to achieve an octet.

A sodium and a chlorine atom sit side by side. The sodium atom has one valence electron, and the chlorine atom has seven. Six of chlorines electrons form pairs at the top, bottom and right sides of the valence shell. The seventh electron sits alone on the left side. The sodium atom transfers its valence electron to chlorines valence shell, where it pairs with the unpaired left electron. An arrow indicates a reaction takes place. After the reaction takes place, the sodium becomes a cation with a charge of plus one and an empty valence shell, while the chlorine becomes an anion with a charge of minus one and a full valence shell containing eight electrons.

Ionic bonds form between ions with opposite charges. For instance, positively charged sodium ions and negatively charged chloride ions bond together to make crystals of sodium chloride, or table salt, creating a crystalline molecule with zero net charge.

Physiologists refer to certain salts as electrolytes (including sodium, potassium, and calcium), ions necessary for nerve impulse conduction, muscle contractions, and water balance. Many sports drinks and dietary supplements provide these ions to replace those lost from the body via sweating during exercise.

Covalent Bonds and Other Bonds and Interactions

Another way to satisfy the octet rule by sharing electrons between atoms to form covalent bonds. These bonds are stronger and much more common than ionic bonds in the molecules of living organisms. We commonly find covalent bonds in carbon-based organic molecules, such as our DNA and proteins. We also find covalent bonds in inorganic molecules like H2O, CO2, and O2. The bonds may share one, two, or three pairs of electrons, making single, double, and triple bonds, respectively. The more covalent bonds between two atoms, the stronger their connection. Thus, triple bonds are the strongest.

The strength of different levels of covalent bonding is one of the main reasons living organisms have a difficult time in acquiring nitrogen for use in constructing their molecules, even though molecular nitrogen, N2, is the most abundant gas in the atmosphere. Molecular nitrogen consists of two nitrogen atoms triple bonded to each other and, as with all molecules, sharing these three pairs of electrons between the two nitrogen atoms allows for filling their outer electron shells, making the molecule more stable than the individual nitrogen atoms. This strong triple bond makes it difficult for living systems to break apart this nitrogen in order to use it as constituents of proteins and DNA.

Forming water molecules provides an example of covalent bonding. Covalent bonds bind the hydrogen and oxygen atoms that combine to form water molecules as (Figure) shows. The electron from the hydrogen splits its time between the hydrogen atoms’ incomplete outer shell and the oxygen atoms’ incomplete outer shell. To completely fill the oxygen’s outer shell, which has six electrons but which would be more stable with eight, two electrons (one from each hydrogen atom) are needed: hence, the well-known formula H2O. The two elements share the electrons to fill the outer shell of each, making both elements more stable.

Link to Learning

View this short video to see an animation of ionic and covalent bonding.

Polar Covalent Bonds

There are two types of covalent bonds: polar and nonpolar. In a polar covalent bond, (Figure) shows atoms unequally share the electrons and are attracted more to one nucleus than the other. Because of the unequal electron distribution between the atoms of different elements, a slightly positive (δ+) or slightly negative (δ–) charge develops. This partial charge is an important property of water and accounts for many of its characteristics.

Water is a polar molecule, with the hydrogen atoms acquiring a partial positive charge and the oxygen a partial negative charge. This occurs because the oxygen atom’s nucleus is more attractive to the hydrogen atoms’ electrons than the hydrogen nucleus is to the oxygen’s electrons. Thus, oxygen has a higher electronegativity than hydrogen and the shared electrons spend more time near the oxygen nucleus than the hydrogen atoms’ nucleus, giving the oxygen and hydrogen atoms slightly negative and positive charges, respectively. Another way of stating this is that the probability of finding a shared electron near an oxygen nucleus is more likely than finding it near a hydrogen nucleus. Either way, the atom’s relative electronegativity contributes to developing partial charges whenever one element is significantly more electronegative than the other, and the charges that these polar bonds generate may then be used to form hydrogen bonds based on the attraction of opposite partial charges. (Hydrogen bonds, which we discuss in detail below, are weak bonds between slightly positively charged hydrogen atoms to slightly negatively charged atoms in other molecules.) Since macromolecules often have atoms within them that differ in electronegativity, polar bonds are often present in organic molecules.

Nonpolar Covalent Bonds

Nonpolar covalent bonds form between two atoms of the same element or between different elements that share electrons equally. For example, molecular oxygen (O2) is nonpolar because the electrons distribute equally between the two oxygen atoms.

(Figure) also shows another example of a nonpolar covalent bond—methane (CH4). Carbon has four electrons in its outermost shell and needs four more to fill it. It obtains these four from four hydrogen atoms, each atom providing one, making a stable outer shell of eight electrons. Carbon and hydrogen do not have the same electronegativity but are similar; thus, nonpolar bonds form. The hydrogen atoms each need one electron for their outermost shell, which is filled when it contains two electrons. These elements share the electrons equally among the carbons and the hydrogen atoms, creating a nonpolar covalent molecule.

Whether a molecule is polar or nonpolar depends both on bond type and molecular shape. Both water and carbon dioxide have polar covalent bonds, but carbon dioxide is linear, so the partial charges on the molecule cancel each other out.

Table compares water, methane and carbon dioxide molecules. In water, oxygen has a stronger pull on electrons than hydrogen resulting in a polar covalent O-H bond. Likewise in carbon dioxide the oxygen has a stronger pull on electrons than carbon and the bond is polar covalent. However, water has a bent shape because two lone pairs of electrons push the hydrogen atoms together so the molecule is polar. By contrast carbon dioxide has two double bonds that repel each other, resulting in a linear shape. The polar bonds in carbon dioxide cancel each other out, resulting in a nonpolar molecule. In methane, the bond between carbon and hydrogen is nonpolar and the molecule is a symmetrical tetrahedron with hydrogens spaced as far apart as possible on the three-dimensional sphere. Since methane is symmetrical with nonpolar bonds, it is a nonpolar molecule.

Hydrogen Bonds and Van Der Waals Interactions

Ionic and covalent bonds between elements require energy to break. Ionic bonds are not as strong as covalent, which determines their behavior in biological systems. However, not all bonds are ionic or covalent bonds. Weaker bonds can also form between molecules. Two weak bonds that occur frequently are hydrogen bonds and van der Waals interactions. Without these two types of bonds, life as we know it would not exist. Hydrogen bonds provide many of the critical, life-sustaining properties of water and also stabilize the structures of proteins and DNA, the building block of cells.

When polar covalent bonds containing hydrogen form, the hydrogen in that bond has a slightly positive charge because hydrogen’s electron is pulled more strongly toward the other element and away from the hydrogen. Because the hydrogen is slightly positive, it will be attracted to neighboring negative charges. When this happens, a weak interaction occurs between the hydrogen’s δ+ from one molecule and another molecule’s δ– charge on the more electronegative atoms, usually oxygen or nitrogen, or within the same molecule. Scientists call this interaction a hydrogen bond. This type of bond is common and occurs regularly between water molecules. Individual hydrogen bonds are weak and easily broken; however, they occur in very large numbers in water and in organic polymers, creating a major force in combination. Hydrogen bonds are also responsible for zipping together the DNA double helix.

Like hydrogen bonds, van der Waals interactions are weak attractions or interactions between molecules. Van der Waals attractions can occur between any two or more molecules and are dependent on slight fluctuations of the electron densities, which are not always symmetrical around an atom. For these attractions to happen, the molecules need to be very close to one another. These bonds—along with ionic, covalent, and hydrogen bonds—contribute to the proteins’ three-dimensional structure in our cells that is necessary for their proper function.

Career Connection

Pharmaceutical Chemist
Pharmaceutical chemists are responsible for developing new drugs and trying to determine the mode of action of both old and new drugs. They are involved in every step of the drug development process. We can find drugs in the natural environment or we can synthesize them in the laboratory. In many cases, chemists chemically change potential drugs from nature chemically in the laboratory to make them safer and more effective, and sometimes synthetic versions of drugs substitute for the version we find in nature.

After a drug’s initial discovery or synthesis, the chemist then develops the drug, perhaps chemically altering it, testing it to see if it is toxic, and then designing methods for efficient large-scale production. Then, the process of approving the drug for human use begins. In the United States, the Food and Drug Administration (FDA) handles drug approval. This involves a series of large-scale experiments using human subjects to ensure the drug is not harmful and effectively treats the condition for which it is intended. This process often takes several years and requires the participation of physicians and scientists, in addition to chemists, to complete testing and gain approval.

An example of a drug that was originally discovered in a living organism is Paclitaxel (Taxol), an anti-cancer drug used to treat breast cancer. This drug was discovered in the bark of the pacific yew tree. Another example is aspirin, originally isolated from willow tree bark. Finding drugs often means testing hundreds of samples of plants, fungi, and other forms of life to see if they contain any biologically active compounds. Sometimes, traditional medicine can give modern medicine clues as to where to find an active compound. For example, mankind has used willow bark to make medicine for thousands of years, dating back to ancient Egypt. However, it was not until the late 1800s that scientists and pharmaceutical companies purified and marketed the aspirin molecule, acetylsalicylic acid, for human use.

Occasionally, drugs developed for one use have unforeseen effects that allow usage in other, unrelated ways. For example, scientists originally developed the drug minoxidil (Rogaine) to treat high blood pressure. When tested on humans, researchers noticed that individuals taking the drug would grow new hair. Eventually the pharmaceutical company marketed the drug to men and women with baldness to restore lost hair.

A pharmaceutical chemist’s career may involve detective work, experimentation, and drug development, all with the goal of making human beings healthier.

Section Summary

Matter is anything that occupies space and has mass. It is comprised of elements. All of the 98 elements that occur naturally have unique qualities that allow them to combine in various ways to create molecules, which in turn combine to form cells, tissues, organ systems, and organisms. 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 transfer, share, or cause charge disparities between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van der Waals interactions.

Visual Connection Questions

(Figure) How many neutrons do carbon-12 and carbon-13 have, respectively?

(Figure) Carbon-12 has six neutrons. Carbon-13 has seven neutrons.

(Figure) An atom may give, take, or share electrons with another atom to achieve a full valence shell, the most stable electron configuration. Looking at this figure, how many electrons do elements in group 1 need to lose in order to achieve a stable electron configuration? How many electrons do elements in groups 14 and 17 need to gain to achieve a stable configuration?

(Figure) Elements in group 1 need to lose one electron to achieve a stable electron configuration. Elements in groups 14 and 17 need to gain four and one electrons, respectively, to achieve a stable configuration.

Review Questions

If xenon has an atomic number of 54 and a mass number of 108, how many neutrons does it have?

  1. 54
  2. 27
  3. 100
  4. 108

A

Atoms that vary in the number of neutrons found in their nuclei are called ________.

  1. ions
  2. neutrons
  3. neutral atoms
  4. isotopes

D

Potassium has an atomic number of 19. What is its electron configuration?

  1. shells 1 and 2 are full, and shell 3 has nine electrons
  2. shells 1, 2 and 3 are full and shell 4 has three electrons
  3. shells 1, 2 and 3 are full and shell 4 has one electron
  4. shells 1, 2 and 3 are full and no other electrons are present

C

Which type of bond represents a weak chemical bond?

  1. hydrogen bond
  2. atomic bond
  3. covalent bond
  4. nonpolar covalent bond

A

Critical Thinking Questions

What makes ionic bonds different from covalent bonds?

Ionic bonds are created between ions. The electrons are not shared between the atoms, but rather are associated more with one ion than the other. Ionic bonds are strong bonds, but are weaker than covalent bonds, meaning it takes less energy to break an ionic bond compared with a covalent one.

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 or within different regions of the same molecule. They provide the structure and shape necessary for proteins and DNA within cells so that they function properly.

Glossary

anion
negative ion that is formed by an atom gaining one or more electrons
atom
the smallest unit of matter that retains all of the chemical properties of an element
atomic mass
calculated mean of the mass number for an element’s isotopes
atomic number
total number of protons in an atom
balanced chemical equation
statement of a chemical reaction with the number of each type of atom equalized for both the products and reactants
cation
positive ion that is formed by an atom losing one or more electrons
chemical bond
interaction between two or more of the same or different atoms that results in forming molecules
chemical reaction
process leading to rearranging atoms in molecules
chemical reactivity
the ability to combine and to chemically bond with each other
compound
substance composed of molecules consisting of atoms of at least two different elements
covalent bond
type of strong bond formed between two atoms of the same or different elements; forms when electrons are shared between atoms
electrolyte
ion necessary for nerve impulse conduction, muscle contractions, and water balance
electron
negatively charged subatomic particle that resides outside of the nucleus in the electron orbital; lacks functional mass and has a negative charge of –1 unit
electron configuration
arrangement of electrons in an atom’s electron shell (for example, 1s22s22p6)
electron orbital
how electrons are spatially distributed surrounding the nucleus; the area where we are most likely to find an electron
electron transfer
movement of electrons from one element to another; important in creating ionic bonds
electronegativity
ability of some elements to attract electrons (often of hydrogen atoms), acquiring partial negative charges in molecules and creating partial positive charges on the hydrogen atoms
element
one of 118 unique substances that cannot break down into smaller substances; each element has unique properties and a specified number of protons
equilibrium
steady state of relative reactant and product concentration in reversible chemical reactions in a closed system
hydrogen bond
weak bond between slightly positively charged hydrogen atoms and slightly negatively charged atoms in other molecules
inert gas
(also, noble gas) element with filled outer electron shell that is unreactive with other atoms
ion
atom or chemical group that does not contain equal numbers of protons and electrons
ionic bond
chemical bond that forms between ions with opposite charges (cations and anions)
irreversible chemical reaction
chemical reaction where reactants proceed unidirectionally to form products
isotope
one or more forms of an element that have different numbers of neutrons
law of mass action
chemical law stating that the rate of a reaction is proportional to the concentration of the reacting substances
mass number
total number of protons and neutrons in an atom
matter
anything that has mass and occupies space
molecule
two or more atoms chemically bonded together
neutron
uncharged particle that resides in an atom’s nucleus; has a mass of one amu
noble gas
see inert gas
nonpolar covalent bond
type of covalent bond that forms between atoms when electrons are shared equally between them
nucleus
core of an atom; contains protons and neutrons
octet rule
rule that atoms are most stable when they hold eight electrons in their outermost shells
orbital
region surrounding the nucleus; contains electrons
periodic table
organizational chart of elements indicating each element’s atomic number and atomic mass; provides key information about the elements’ properties
polar covalent bond
type of covalent bond that forms as a result of unequal electron sharing, resulting in creating slightly positive and negative charged molecule regions
product
molecule that is result of chemical reaction
proton
positively charged particle that resides in the atom’s nucleus; has a mass of one amu and a charge of +1
radioisotope
isotope that emits radiation comprised of subatomic particles to form more stable elements
reactant
molecule that takes part in a chemical reaction
reversible chemical reaction
chemical reaction that functions bidirectionally, where products may turn into reactants if their concentration is great enough
valence shell
outermost shell of an atom
van der Waals interaction
very weak interaction between molecules due to temporary charges attracting atoms that are very close together

6

Water

Learning Objectives

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

  • Describe the properties of water that are critical to maintaining life
  • Explain why water is an excellent solvent
  • Provide examples of water’s cohesive and adhesive properties
  • Discuss the role of acids, bases, and buffers in homeostasis

Why do scientists spend time looking for water on other planets? Why is water so important? It is because water is essential to life as we know it. Water is one of the more abundant molecules and the one most critical to life on Earth. Water comprises approximately 60–70 percent of the human body. Without it, life as we know it simply would not exist.

The polarity of the water molecule and its resulting hydrogen bonding make water a unique substance with special properties that are intimately tied to the processes of life. Life originally evolved in a watery environment, and most of an organism’s cellular chemistry and metabolism occur inside the watery contents of the cell’s cytoplasm. Special properties of water are its high heat capacity and heat of vaporization, its ability to dissolve polar molecules, its cohesive and adhesive properties, and its dissociation into ions that leads to generating pH. Understanding these characteristics of water helps to elucidate its importance in maintaining life.

Water’s Polarity

One of water’s important properties is that it is composed of polar molecules: the hydrogen and oxygen within water molecules (H2O) form polar covalent bonds. While there is no net charge to a water molecule, water’s polarity creates a slightly positive charge on hydrogen and a slightly negative charge on oxygen, contributing to water’s properties of attraction. Water generates charges because oxygen is more electronegative than hydrogen, making it more likely that a shared electron would be near the oxygen nucleus than the hydrogen nucleus, thus generating the partial negative charge near the oxygen.

As a result of water’s polarity, each water molecule attracts other water molecules because of the opposite charges between water molecules, forming hydrogen bonds. Water also attracts or is attracted to other polar molecules and ions. We call a polar substance that interacts readily with or dissolves in water hydrophilic (hydro- = “water”; -philic = “loving”). In contrast, nonpolar molecules such as oils and fats do not interact well with water, as (Figure) shows. A good example of this is vinegar and oil salad dressing (an acidic water solution). We call such nonpolar compounds hydrophobic (hydro- = “water”; -phobic = “fearing”).

Oil and water do not mix. As this macro image of oil and water shows, oil does not dissolve in water but forms droplets instead. This is because it is a nonpolar compound. (credit: Gautam Dogra).

Image shows oil droplets floating in water. The oil droplets act like prisms that bend the light into all the colors of the rainbow.

Water’s States: Gas, Liquid, and Solid

The formation of hydrogen bonds is an important quality of the liquid water that is crucial to life as we know it. As water molecules make hydrogen bonds with each other, water takes on some unique chemical characteristics compared to other liquids and, since living things have a high water content, understanding these chemical features is key to understanding life. In liquid water, hydrogen bonds constantly form and break as the water molecules slide past each other. The water molecules’ motion (kinetic energy) causes the bonds to break due to the heat contained in the system. When the heat rises as water boils, the water molecules’ higher kinetic energy causes the hydrogen bonds to break completely and allows water molecules to escape into the air as gas (steam or water vapor). Alternatively, when water temperature reduces and water freezes, the water molecules form a crystalline structure maintained by hydrogen bonding (there is not enough energy to break the hydrogen bonds) that makes ice less dense than liquid water, a phenomenon that we do not see when other liquids solidify.

Water’s lower density in its solid form is due to the way hydrogen bonds orient as they freeze: the water molecules push farther apart compared to liquid water. With most other liquids, solidification when the temperature drops includes lowering kinetic energy between molecules, allowing them to pack even more tightly than in liquid form and giving the solid a greater density than the liquid.

The lower density of ice, as (Figure) depicts, an anomaly causes it to float at the surface of liquid water, such as in an iceberg or ice cubes in a glass of water. In lakes and ponds, ice will form on the water’s surface creating an insulating barrier that protects the animals and plant life in the pond from freezing. Without this insulating ice layer, plants and animals living in the pond would freeze in the solid block of ice and could not survive. The expansion of ice relative to liquid water causes the detrimental effect of freezing on living organisms. The ice crystals that form upon freezing rupture the delicate membranes essential for living cells to function, irreversibly damaging them. Cells can only survive freezing if another liquid like glycerol temporarily replaces the water in them.

Hydrogen bonding makes ice less dense than liquid water. The (a) lattice structure of ice makes it less dense than the liquid water’s freely flowing molecules, enabling it to (b) float on water. (credit a: modification of work by Jane Whitney, image created using Visual Molecular Dynamics (VMD) software1; credit b: modification of work by Carlos Ponte)

Ice floes float on ocean water near a mountain range that rises out of the water. The molecular structure shows the molecules are arranged in a hexagon, and are bonded to other hexagonal arrangements with a good deal of space between them.

Link to Learning

Click here to see a 3-D animation of an ice lattice structure. (Image credit: Jane Whitney. Image created using Visual Molecular Dynamics VMD software.2)

Water’s High Heat Capacity

Water’s high heat capacity is a property that hydrogen bonding among water molecules causes. Water has the highest specific heat capacity of any liquids. We define specific heat as the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius. For water, this amount is one calorie. It therefore takes water a long time to heat and a long time to cool. In fact, water’s specific heat capacity is about five times more than that of sand. This explains why the land cools faster than the sea. Due to its high heat capacity, warm blooded animals use water to more evenly disperse heat in their bodies: it acts in a similar manner to a car’s cooling system, transporting heat from warm places to cool places, causing the body to maintain a more even temperature.

Water’s Heat of Vaporization

Water also has a high heat of vaporization, the amount of energy required to change one gram of a liquid substance to a gas. A considerable amount of heat energy (586 cal) is required to accomplish this change in water. This process occurs on the water’s surface. As liquid water heats up, hydrogen bonding makes it difficult to separate the liquid water molecules from each other, which is required for it to enter its gaseous phase (steam). As a result, water acts as a heat sink or heat reservoir and requires much more heat to boil than does a liquid such as ethanol (grain alcohol), whose hydrogen bonding with other ethanol molecules is weaker than water’s hydrogen bonding. Eventually, as water reaches its boiling point of 100° Celsius (212° Fahrenheit), the heat is able to break the hydrogen bonds between the water molecules, and the kinetic energy (motion) between the water molecules allows them to escape from the liquid as a gas. Even when below its boiling point, water’s individual molecules acquire enough energy from other water molecules such that some surface water molecules can escape and vaporize: we call this process evaporation.

The fact that hydrogen bonds need to be broken for water to evaporate means that bonds use a substantial amount of energy in the process. As the water evaporates, energy is taken up by the process, cooling the environment where the evaporation is taking place. In many living organisms, including in humans, the evaporation of sweat, which is 90 percent water, allows the organism to cool so that it can maintain homeostasis of body temperature.

Water’s Solvent Properties

Since water is a polar molecule with slightly positive and slightly negative charges, ions and polar molecules can readily dissolve in it. Therefore, we refer to water as a solvent, a substance capable of dissolving other polar molecules and ionic compounds. The charges associated with these molecules will form hydrogen bonds with water, surrounding the particle with water molecules. We refer to this as a sphere of hydration, or a hydration shell, as (Figure) illustrates and serves to keep the particles separated or dispersed in the water.

When we add ionic compounds to water, the individual ions react with the water molecules’ polar regions and their ionic bonds are disrupted in the process of dissociation. Dissociation occurs when atoms or groups of atoms break off from molecules and form ions. Consider table salt (NaCl, or sodium chloride): when we add NaCl crystals to water, the NaCl molecules dissociate into Na+ and Cl ions, and spheres of hydration form around the ions, as (Figure) illustrates. The partially negative charge of the water molecule’s oxygen surrounds the positively charged sodium ion. The hydrogen’s partially positive charge on the water molecule surrounds the negatively charged chloride ion.

When we mix table salt (NaCl) in water, it forms spheres of hydration around the ions.

When sodium chloride dissolves in water, the positively charged sodium ions interact with the oxygen of water, and the negatively charged chlorine ions interact with the hydrogen of water.

Water’s Cohesive and Adhesive Properties

Have you ever filled a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water 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-gas (water-air) interface, although there is no more room in the glass.

Cohesion allows for surface tension, the capacity of a substance to withstand rupturing when placed under tension or stress. This is also why water forms droplets when on a dry surface rather than flattening by gravity. When we place a small scrap of paper onto a water droplet, the paper floats on top even though paper is denser (heavier) than the water. Cohesion and surface tension keep the water molecules’ hydrogen bonds intact and support the item floating on the top. It’s even possible to “float” a needle on top of a glass of water if you place it gently without breaking the surface tension, as (Figure) shows.

A needle’s weight pulls the surface downward. At the same time, the surface tension pulls it up, suspending it on the water’s surface preventing it from sinking. Notice the indentation in the water around the needle. (credit: Cory Zanker)

A photograph shows a needle floating at the surface of a glass of water. Though the needle floats, it appears to be slightly sinking below the surface.

These cohesive forces are related to water’s property of adhesion, or the attraction between water molecules and other molecules. This attraction is sometimes stronger than water’s cohesive forces, especially when the water is exposed to charged surfaces such as those on the inside of thin glass tubes known as capillary tubes. We observe adhesion when water “climbs” up the tube placed in a glass of water: notice that the water appears to be higher on the tube’s sides than in the middle. This is because the water molecules are attracted to the capillary’s charged glass walls more than they are to each other and therefore adhere to it. We call this type of adhesion capillary action, as (Figure) illustrates.

The adhesive forces exerted by the glass’ internal surface exceeding the cohesive forces between the water molecules themselves causes capillary action in a glass tube. (credit: modification of work by Pearson-Scott Foresman, donated to the Wikimedia Foundation)

A thin hollow tube sits in a beaker of water. The water level inside the tube is higher than the water level in the beaker due to capillary action.

Why are cohesive and adhesive forces important for life? Cohesive and adhesive forces are important for transporting water from the roots to the leaves in plants. These forces create a “pull” on the water column. This pull results from the tendency of water molecules evaporating on the plant’s surface to stay connected to water molecules below them, and so they are pulled along. Plants use this natural phenomenon to help transport water from their roots to their leaves. Without these properties of water, plants would be unable to receive the water and the dissolved minerals they require. In another example, insects such as the water strider, as (Figure) shows, use the water’s surface tension to stay afloat on the water’s surface layer and even mate there.

Water’s cohesive and adhesive properties allow this water strider (Gerris sp.) to stay afloat. (credit: Tim Vickers)

Photo shows an insect with long, thin legs standing on the surface of water.

pH, Buffers, Acids, and Bases

The pH of a solution indicates its acidity or alkalinity.

{\text{H}}_{2}\text{O}\left(\text{I}\right)↔{\text{H}}^{+}\left(\text{aq}\right)+\text{O}{\text{H}}^{-}\left(\text{aq}\right)

You may have used litmus or pH paper, filter paper treated with a natural water-soluble dye for use as a pH indicator, tests how much acid (acidity) or base (alkalinity) exists in a solution. You might have even used some to test whether the water in a swimming pool is properly treated. In both cases, the pH test measures hydrogen ions’ concentration in a given solution.

Hydrogen ions spontaneously generate in pure water by the dissociation (ionization) of a small percentage of water molecules into equal numbers of hydrogen (H+) ions and hydroxide (OH) ions. While the hydroxide ions are kept in solution by their hydrogen bonding with other water molecules, the hydrogen ions, consisting of naked protons, immediately attract to un-ionized water molecules, forming hydronium ions (H3O+). Still, by convention, scientists refer to hydrogen ions and their concentration as if they were free in this state in liquid water.

The concentration of hydrogen ions dissociating from pure water is 1 × 10-7 moles H+ ions per liter of water. Moles (mol) are a way to express the amount of a substance (which can be atoms, molecules, ions, etc.). One mole represents the atomic weight of a substance, expressed in grams, which equals the amount of the substance containing as many units as there are atoms in 12 grams of 12C. Mathematically, one mole is equal to 6.02 × 1023 particles of the substance. Therefore, 1 mole of water is equal to 6.02 × 1023 water molecules. We calculate the pH as the negative of the base 10 logarithm of this concentration. The log10 of 1 × 10-7 is -7.0, and the negative of this number (indicated by the “p” of “pH”) yields a pH of 7.0, which is also a neutral pH. The pH inside of human cells and blood are examples of two body areas where near-neutral pH is maintained.

Non-neutral pH readings result from dissolving acids or bases in water. Using the negative logarithm to generate positive integers, high concentrations of hydrogen ions yield a low pH number; whereas, low levels of hydrogen ions result in a high pH. An acid is a substance that increases hydrogen ions’ (H+) concentration in a solution, usually by having one of its hydrogen atoms dissociate. A base provides either hydroxide ions (OH) or other negatively charged ions that combine with hydrogen ions, reducing their concentration in the solution and thereby raising the pH. In cases where the base releases hydroxide ions, these ions bind to free hydrogen ions, generating new water molecules.

The stronger the acid, the more readily it donates H+. For example, hydrochloric acid (HCl) completely dissociates into hydrogen and chloride ions and is highly acidic; whereas the acids in tomato juice or vinegar do not completely dissociate and are weak acids. Conversely, strong bases are those substances that readily donate OHor take up hydrogen ions. Sodium hydroxide (NaOH) and many household cleaners are highly alkaline and give up OH rapidly when we place them in water, thereby raising the pH. An example of a weak basic solution is seawater, which has a pH near 8.0 This is close enough to a neutral pH that marine organisms have adapted in order to live and thrive in a saline environment.

The pH scale is, as we previously mentioned, an inverse logarithm and ranges from 0 to 14 ((Figure)). 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. Extremes in pH in either direction from 7.0 are usually inhospitable to life. The pH inside cells (6.8) and the pH in the blood (7.4) are both very close to neutral. However, the environment in the stomach is highly acidic, with a pH of 1 to 2. As a result, how do stomach cells survive in such an acidic environment? How do they homeostatically maintain the near neutral pH inside them? The answer is that they cannot do it and are constantly dying. The stomach constantly produces new cells to replace dead ones, which stomach acids digest. Scientists estimate that the human body completely replaces the stomach lining every seven to ten days.

The pH scale measures hydrogen ions’ (H+) concentration in a solution. (credit: modification of work by Edward Stevens)

The lower case p upper case H scale, which ranges from zero to 14, sits next to a bar with the colors of the rainbow. The p H of common substances are given. These include gastric acid with a p H around one, lemon juice with a p H around two, orange juice with a p H around three, tomato juice with a p H around four, black coffee with a p H around five, urine with a p H around six, distilled water with a p H around seven, sea water with a p H around eight, baking soda with a p H around nine, milk of magnesia with a p H around ten, ammonia solution with a p H around 11, soapy water with a p H around 12, and bleach with a p H around 13.

Link to Learning

Watch this video for a straightforward explanation of pH and its logarithmic scale.

How can organisms whose bodies require a near-neutral pH ingest acidic and basic substances (a human drinking orange juice, for example) and survive? Buffers are the key. Buffers readily absorb excess H+ or OH, keeping the body’s pH carefully maintained in the narrow range required for survival. Maintaining a constant blood pH is critical to a person’s well-being. The buffer maintaining the pH of human blood involves carbonic acid (H2CO3), bicarbonate ion (HCO3), and carbon dioxide (CO2). When bicarbonate ions combine with free hydrogen ions and become carbonic acid, it removes hydrogen ions and moderates pH changes. Similarly, as (Figure) shows, excess carbonic acid can convert to carbon dioxide gas which we exhale through the lungs. This prevents too many free hydrogen ions from building up in the blood and dangerously reducing the blood’s pH. Likewise, if too much OH enters into the system, carbonic acid will combine with it to create bicarbonate, lowering the pH. Without this buffer system, the body’s pH would fluctuate enough to put survival in jeopardy.

This diagram shows the body’s buffering of blood pH levels. The blue arrows show the process of raising pH as more CO2 is made. The purple arrows indicate the reverse process: the lowering of pH as more bicarbonate is created.

An upper case H subscript 2 baseline upper case O molecule can combine with an upper case C upper case O subscript 2 baseline molecule to form H subscript 2 baseline C O subscript 3 baseline, or carbonic acid. A proton may dissociate from H subscript 2 baseline C O subscript 3 baseline, forming bicarbonate, or H C O subscript 3 baseline superscript negative, in the process. The reaction is reversible so that if acid is added protons combined with bicarbonate to form carbonic acid.

Other examples of buffers are antacids that some people use to combat excess stomach acid. Many of these over-the-counter medications work in the same way as blood buffers, usually with at least one ion capable of absorbing hydrogen and moderating pH, bringing relief to those who suffer “heartburn” after eating. Water’s unique properties that contribute to this capacity to balance pH—as well as water’s other characteristics—are essential to sustaining life on Earth.

Link to Learning

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

Section Summary

Water has many properties that are critical to maintaining life. It is a polar molecule, allowing for forming hydrogen bonds. Hydrogen bonds allow ions and other polar molecules to dissolve in water. Therefore, water is an excellent solvent. The hydrogen bonds between water molecules cause the water to have a high heat capacity, meaning it takes considerable added heat to raise its temperature. As the temperature rises, the hydrogen bonds between water continually break and form anew. This allows for the overall temperature to remain stable, although energy is added to the system. Water also exhibits a high heat of vaporization, which is key to how organisms cool themselves by evaporating sweat. Water’s cohesive forces allow for the property of surface tension; whereas, we see its adhesive properties as water rises inside capillary tubes. The pH value is a measure of hydrogen ion concentration in a solution and is one of many chemical characteristics that is highly regulated in living organisms through homeostasis. Acids and bases can change pH values, but buffers tend to moderate the changes they cause. These properties of water are intimately connected to the biochemical and physical processes performed by living organisms, and life would be very different if these properties were altered, if it could exist at all.

Review Questions

Which of the following statements is not true?

  1. Water is polar.
  2. Water stabilizes temperature.
  3. Water is essential for life.
  4. Water is the most abundant molecule in the Earth’s atmosphere.

D

When acids are added to a solution, the pH should ________.

  1. decrease
  2. increase
  3. stay the same
  4. cannot tell without testing

A

We call a molecule that binds up excess hydrogen ions in a solution a(n) ________.

  1. acid
  2. isotope
  3. base
  4. donator

C

Which of the following statements is true?

  1. Acids and bases cannot mix together.
  2. Acids and bases will neutralize each other.
  3. Acids, but not bases, can change the pH of a solution.
  4. Acids donate hydroxide ions (OH); bases donate hydrogen ions (H+).

B

Critical Thinking Questions

Discuss how buffers help prevent drastic swings in pH.

Buffers absorb the free hydrogen ions and hydroxide ions that result from chemical reactions. Because they can bond these ions, they prevent increases or decreases in pH. An example of a buffer system is the bicarbonate system in the human body. This system is able to absorb hydrogen and hydroxide ions to prevent changes in pH and keep cells functioning properly.

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).

Footnotes

  • 1W. Humphrey W., A. Dalke, and K. Schulten, “VMD—Visual Molecular Dynamics,” Journal of Molecular Graphics 14 (1996): 33-38.
  • 2W. Humphrey W., A. Dalke, and K. Schulten, “VMD—Visual Molecular Dynamics,” Journal of Molecular Graphics 14 (1996): 33-38.

Glossary

acid
molecule that donates hydrogen ions and increases the concentration of hydrogen ions in a solution
adhesion
attraction between water molecules and other molecules
base
molecule that donates hydroxide ions or otherwise binds excess hydrogen ions and decreases the hydrogen ions’ concentration in a solution
buffer
substance that prevents a change in pH by absorbing or releasing hydrogen or hydroxide ions
calorie
amount of heat required to change the temperature of one gram of water by one degree Celsius
capillary action
occurs because water molecules are attracted to charges on the inner surfaces of narrow tubular structures such as glass tubes, drawing the water molecules to the tubes’ sides
cohesion
intermolecular forces between water molecules caused by the polar nature of water; responsible for surface tension
dissociation
release of an ion from a molecule such that the original molecule now consists of an ion and the charged remains of the original, such as when water dissociates into H+ and OH
evaporation
change from liquid to gaseous state at a body of water’s surface, plant leaves, or an organism’s skin
heat of vaporization of water
high amount of energy required for liquid water to turn into water vapor
hydrophilic
describes ions or polar molecules that interact well with other polar molecules such as water
hydrophobic
describes uncharged nonpolar molecules that do not interact well with polar molecules such as water
litmus paper
(also, pH paper) filter paper treated with a natural water-soluble dye that changes its color as the pH of the environment changes in order to use it as a pH indicator
pH paper
see litmus paper
pH scale
scale ranging from zero to 14 that is inversely proportional to the hydrogen ions’ concentration in a solution
solvent
substance capable of dissolving another substance
specific heat capacity
the amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius
sphere of hydration
when a polar water molecule surrounds charged or polar molecules thus keeping them dissolved and in solution
surface tension
tension at the surface of a body of liquid that prevents the molecules from separating; created by the attractive cohesive forces between the liquid’s molecules

7

Carbon

Learning Objectives

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

  • Explain why carbon is important for life
  • Describe the role of functional groups in biological molecules

Many complex molecules called macromolecules, such as proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids comprise cells. The macromolecules are a subset of organic molecules (any carbon-containing liquid, solid, or gas) that are especially important for life. The fundamental component for all of these macromolecules is carbon. The carbon atom has unique properties that allow it to form covalent bonds to as many as four different atoms, making this versatile element ideal to serve as the basic structural component, or “backbone,” of the macromolecules.

Individual carbon atoms have an incomplete outermost electron shell. With an atomic number of 6 (six electrons and six protons), the first two electrons fill the inner shell, leaving four in the second shell. Therefore, carbon atoms can form up to four covalent bonds with other atoms to satisfy the octet rule. The methane molecule provides an example: it has the chemical formula CH4. Each of its four hydrogen atoms forms a single covalent bond with the carbon atom by sharing a pair of electrons. This results in a filled outermost shell.

Hydrocarbons

Hydrocarbons are organic molecules consisting entirely of carbon and hydrogen, such as methane (CH4) described above. We often use hydrocarbons in our daily lives as fuels—like the propane in a gas grill or the butane in a lighter. The many covalent bonds between the atoms in hydrocarbons store a great amount of energy, which releases when these molecules burn (oxidize). Methane, an excellent fuel, is the simplest hydrocarbon molecule, with a central carbon atom bonded to four different hydrogen atoms, as (Figure) illustrates. The shape of its electron orbitals determines the shape of the methane molecule’s geometry, where the atoms reside in three dimensions. The carbons and the four hydrogen atoms form a tetrahedron, with four triangular faces. For this reason, we describe methane as having tetrahedral geometry.

Methane has a tetrahedral geometry, with each of the four hydrogen atoms spaced 109.5° apart.


Methane, the simplest hydrocarbon, is composed of four hydrogen atoms surrounding a central carbon. The bond between the four hydrogen atoms and the central carbon spaced as far apart as possible. The resulting in a tetrahedral shape with hydrogen atoms projecting upward and off to three sides around the central carbon.

As the backbone of the large molecules of living things, hydrocarbons may exist as linear carbon chains, carbon rings, or combinations of both. Furthermore, individual carbon-to-carbon bonds may be single, double, or triple covalent bonds, and each type of bond affects the molecule’s geometry in a specific way. This three-dimensional shape or conformation of the large molecules of life (macromolecules) is critical to how they function.

Hydrocarbon Chains

Successive bonds between carbon atoms form hydrocarbon chains. These may be branched or unbranched. Furthermore, a molecule’s different geometries of single, double, and triple covalent bonds alter the overall molecule’s geometry as (Figure) illustrates. The hydrocarbons ethane, ethene, and ethyne serve as examples of how different carbon-to-carbon bonds affect the molecule’s geometry. The names of all three molecules start with the prefix “eth-,” which is the prefix for two carbon hydrocarbons. The suffixes “-ane,” “-ene,” and “-yne” refer to the presence of single, double, or triple carbon-carbon bonds, respectively. Thus, propane, propene, and propyne follow the same pattern with three carbon molecules, butane, butene, and butyne for four carbon molecules, and so on. Double and triple bonds change the molecule’s geometry: single bonds allow rotation along the bond’s axis; whereas, double bonds lead to a planar configuration and triple bonds to a linear one. These geometries have a significant impact on the shape a particular molecule can assume.

When carbon forms single bonds with other atoms, the shape is tetrahedral. When two carbon atoms form a double bond, the shape is planar, or flat. Single bonds, like those in ethane, are able to rotate. Double bonds, like those in ethene cannot rotate, so the atoms on either side are locked in place.


Methane, the simplest hydrocarbon, is composed of four hydrogen atoms surrounding a central carbon. The bond between the four hydrogen atoms and the central carbon spaced as far apart as possible. This results in a tetrahedral shape with hydrogen atoms projecting upward and off to three sides around the central carbon. Ethane is composed of two carbons connected by a single bond. Each carbon also has three hydrogen atoms connected to it. The hydrogens are spaced as far apart from each other and from the other carbon so again the shape is tetrahedral. Ethene, like ethane, is composed of two carbon atoms, but in this case the carbons are connected by a double bond. Each carbon also has two hydrogen atoms connected to it, for a total of three bonds. The three bonds are spaced as far apart as possible around carbon, which means they are all on the same plane and pointing off in three directions. As a result, the molecule is planar, or flat.

Hydrocarbon Rings

So far, the hydrocarbons we have discussed have been aliphatic hydrocarbons, which consist of linear chains of carbon atoms. Another type of hydrocarbon, aromatic hydrocarbons, consists of closed rings of carbon atoms. We find ring structures in hydrocarbons, sometimes with the presence of double bonds, which we can see by comparing cyclohexane’s structure to benzene in (Figure). Examples of biological molecules that incorporate the benzene ring include some amino acids and cholesterol and its derivatives, including the hormones estrogen and testosterone. We also find the benzene ring in the herbicide 2,4-D. Benzene is a natural component of crude oil and has been classified as a carcinogen. Some hydrocarbons have both aliphatic and aromatic portions. Beta-carotene is an example of such a hydrocarbon.

Carbon can form five- and six-membered rings. Single or double bonds may connect the carbons in the ring, and nitrogen may be substituted for carbon.


Four molecular structures are shown. Cyclopentane is a ring consisting of five carbons, each with two hydrogens attached. Cyclohexane is a ring of six carbons, each with two hydrogens attached. Benzene is a six-carbon ring with alternating double bonds. Each carbon has one hydrogen attached. Pyridine is the same as benzene, but a nitrogen is substituted for one of the carbons. No hydrogens are attached to the nitrogen.

Isomers

The three-dimensional placement of atoms and chemical bonds within organic molecules is central to understanding their chemistry. We call molecules that share the same chemical formula but differ in the placement (structure) of their atoms and/or chemical bonds isomers. Structural isomers (like butane and isobutene in (Figure)a) differ in the placement of their covalent bonds: both molecules have four carbons and ten hydrogens (C4H10), but the different atom arrangement within the molecules leads to differences in their chemical properties. For example, butane is suited for use as a fuel for cigarette lighters and torches; whereas, isobutene is suited for use as a refrigerant and a propellant in spray cans.

Geometric isomers, alternatively have similar placements of their covalent bonds but differ in how these bonds are made to the surrounding atoms, especially in carbon-to-carbon double bonds. In the simple molecule butene (C4H8), the two methyl groups (CH3) can be on either side of the double covalent bond central to the molecule, as (Figure)b illustrates. When the carbons are bound on the same side of the double bond, this is the cis configuration. If they are on opposite sides of the double bond, it is a trans configuration. In the trans configuration, the carbons form a more or less linear structure; whereas, the carbons in the cis configuration make a bend (change in direction) of the carbon backbone.

Visual Connection
We call molecules that have the same number and type of atoms arranged differently isomers. (a) Structural isomers have a different covalent arrangement of atoms. (b) Geometric isomers have a different arrangement of atoms around a double bond. (c) Enantiomers are mirror images of each other.


Part A shows butane and isobutene are structural isomers. Both molecules have four carbons and ten hydrogens, but in butane the carbons form a single chain, while in isobutene the carbons form a branched chain. Part B shows cis dash 2 butene and trans dash 2 butene each consist of a four-carbon chain. The two central carbons are connected by a double bond resulting in a planar, or flat shape. In the cis isomer, both terminal upper case C upper case H subscript 3 baseline groups are on the same side of the plane, and two hydrogen atoms are on the opposite side. Imagine a person with arms stretched out and upwards and legs spread apart, with a glove on the left hand and a sock on the left foot: this represents a cis configuration. In cis-butene the terminal upper C upper H subscript 3 baseline groups are on opposite sides of the plane. Now, imagine a person with outstretched arms and legs, but this time with a glove on the left hand and a sock on the right foot: this is what a trans configuration looks like. Part C shows two enantiomers, each with different arrangement of hydrogen, bromine, chlorine and fluorine around a central carbon. The molecules are mirror images of one another.

Which of the following statements is false?

  1. Molecules with the formulas CH3CH2COOH and C3H6O2 could be structural isomers.
  2. Molecules must have a double bond to be cistrans isomers.
  3. To be enantiomers, a molecule must have at least three different atoms or groups connected to a central carbon.
  4. To be enantiomers, a molecule must have at least four different atoms or groups connected to a central carbon.

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In triglycerides (fats and oils), long carbon chains known as fatty acids may contain double bonds, which can be in either the cis or trans configuration, as (Figure) illustrates. Fats with at least one double bond between carbon atoms are unsaturated fats. When some of these bonds are in the cis configuration, the resulting bend in the chain’s carbon backbone means that triglyceride molecules cannot pack tightly, so they remain liquid (oil) at room temperature. Alternatively, triglycerides with trans double bonds (popularly called trans fats), have relatively linear fatty acids that are able to pack tightly together at room temperature and form solid fats. In the human diet, trans fats are linked to an increased risk of cardiovascular disease, so many food manufacturers have reduced or eliminated their use in recent years. In contrast to unsaturated fats, we call triglycerides without double bonds between carbon atoms saturated fats, meaning that they contain all the hydrogen atoms available. Saturated fats are a solid at room temperature and usually of animal origin.

These space-filling models show a cis (oleic acid) and a trans (eliadic acid) fatty acid. Notice the bend in the molecule caused by the cis configuration.


Oleic acid and eliadic acid both consist of a long carbon chain. In oleic acid the chain is kinked due to the presence of a double bond about half way down, while in eliadic acid the chain is straight.

Enantiomers

Enantiomers are molecules that share the same chemical structure and chemical bonds but differ in the three-dimensional placement of atoms so that they are non-superimposable mirror images. (Figure) shows an amino acid alanine example, where the two structures are nonsuperimposable. In nature, only the L-forms of amino acids make proteins. Some D forms of amino acids are seen in the cell walls of bacteria, but never in their proteins. Similarly, the D-form of glucose is the main product of photosynthesis and we rarely see the molecule’s L-form in nature.

D-alanine and L-alanine are examples of enantiomers or mirror images. Only the L-forms of amino acids are used to make proteins.


Molecular models of D-and L-alanine are shown. The two molecules, which contain the same number of carbon, hydrogen, nitrogen atoms, are mirror images of one another.

Functional Groups

Functional groups are groups of atoms that occur within molecules and confer specific chemical properties to those molecules. We find them along the “carbon backbone” of macromolecules. Chains and/or rings of carbon atoms with the occasional substitution of an element such as nitrogen or oxygen form this carbon backbone. Molecules with other elements in their carbon backbone are substituted hydrocarbons.

The functional groups in a macromolecule are usually attached to the carbon backbone at one or several different places along its chain and/or ring structure. Each of the four types of macromolecules—proteins, lipids, carbohydrates, and nucleic acids—has its own characteristic set of functional groups that contributes greatly to its differing chemical properties and its function in living organisms.

A functional group can participate in specific chemical reactions. (Figure) shows some of the important functional groups in biological molecules. They include: hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl. These groups play an important role in forming molecules like DNA, proteins, carbohydrates, and lipids. We usually classify functional groups as hydrophobic or hydrophilic depending on their charge or polarity characteristics. An example of a hydrophobic group is the nonpolar methyl molecule. Among the hydrophilic functional groups is the carboxyl group in amino acids, some amino acid side chains, and the fatty acids that form triglycerides and phospholipids. This carboxyl group ionizes to release hydrogen ions (H+) from the COOH group resulting in the negatively charged COO group. This contributes to the hydrophilic nature of whatever molecule on which it is found. Other functional groups, such as the carbonyl group, have a partially negatively charged oxygen atom that may form hydrogen bonds with water molecules, again making the molecule more hydrophilic.

These functional groups are in many different biological molecules. R, also known as R-group, is an abbreviation for any group in which a carbon or hydrogen atom is attached to the rest of the molecule.


Table shows the structure and properties of different functional groups. Hydroxyl groups, which consist of upper case O upper case H attached to a carbon chain, are polar. Methyl groups, which consist of three hydrogens attached to a carbon chain, are nonpolar. Carbonyl groups, which consist of an oxygen double bonded to a carbon in the middle of a hydrocarbon chain, are polar. Carboxyl groups, which consist of a carbon with a double bonded oxygen and an upper O upper H group attached to a carbon chain, are able to ionize, releasing H positive ions into solution. Carboxyl groups are considered acidic. Amino groups, which consist of two hydrogens attached to a nitrogen, are able to accept H positive ions from solution, forming H subscript 3 baseline positive. Amino groups are considered basic. Phosphate groups consist of a phosphorous with one double bonded oxygen and two upper O upper H groups. Another oxygen forms a link from the phosphorous to a carbon chain. Both upper O upper H groups in phosphorous can lose an H positive ion, and phosphate groups are considered acidic.

Hydrogen bonds between functional groups (within the same molecule or between different molecules) are important to the function of many macromolecules and help them to fold properly into and maintain the appropriate shape for functioning. Hydrogen bonds are also involved in various recognition processes, such as DNA complementary base pairing and the binding of an enzyme to its substrate, as (Figure) illustrates.

Hydrogen bonds connect two strands of DNA together to create the double-helix structure.


Molecular models show hydrogen bonding between thymine and adenine, and between cytosine and guanine. These four DNA bases are organic molecules containing carbon, nitrogen, oxygen, and hydrogen in complex ring structures. Hydrogen bonds between the bases hold them together.

Section Summary

The unique properties of carbon make it a central part of biological molecules. Carbon binds to oxygen, hydrogen, and nitrogen covalently to form the many molecules important for cellular function. Carbon has four electrons in its outermost shell and can form four bonds. Carbon and hydrogen can form hydrocarbon chains or rings. Functional groups are groups of atoms that confer specific properties to hydrocarbon (or substituted hydrocarbon) chains or rings that define their overall chemical characteristics and function.

Visual Connection Questions

(Figure) Which of the following statements is false?

  1. Molecules with the formulas CH3CH2COOH and C3H6O2 could be structural isomers.
  2. Molecules must have a double bond to be cistrans isomers.
  3. To be enantiomers, a molecule must have at least three different atoms or groups connected to a central carbon.
  4. To be enantiomers, a molecule must have at least four different atoms or groups connected to a central carbon.

Review Questions

Each carbon molecule can bond with as many as________ other atom(s) or molecule(s).

  1. one
  2. two
  3. six
  4. four

D

Which of the following is not a functional group that can bond with carbon?

  1. sodium
  2. hydroxyl
  3. phosphate
  4. carbonyl

A

Critical Thinking Questions

What property of carbon makes it essential for organic life?

Carbon is unique and found in all living things because it can form up to four covalent bonds between atoms or molecules. These can be nonpolar or polar covalent bonds, and they allow for the formation of long chains of carbon molecules that combine to form proteins and DNA.

Compare and contrast saturated and unsaturated triglycerides.

Saturated triglycerides contain no double bonds between carbon atoms; they are usually solid at room temperature. Unsaturated triglycerides contain at least one double bond between carbon atoms and are usually liquid at room temperature.

Glossary

aliphatic hydrocarbon
hydrocarbon consisting of a linear chain of carbon atoms
aromatic hydrocarbon
hydrocarbon consisting of closed rings of carbon atoms
enantiomers
molecules that share overall structure and bonding patterns, but differ in how the atoms are three dimensionally placed such that they are mirror images of each other
functional group
group of atoms that provides or imparts a specific function to a carbon skeleton
geometric isomer
isomer with similar bonding patterns differing in the placement of atoms alongside a double covalent bond
hydrocarbon
molecule that consists only of carbon and hydrogen
isomers
molecules that differ from one another even though they share the same chemical formula
organic molecule
any molecule containing carbon (except carbon dioxide)
structural isomers
molecules that share a chemical formula but differ in the placement of their chemical bonds
substituted hydrocarbon
hydrocarbon chain or ring containing an atom of another element in place of one of the backbone carbons

III

Biological Macromolecules

8

Introduction

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


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

Food provides the body with the nutrients it needs to survive. Many of these critical nutrients are biological macromolecules, or large molecules, necessary for life. Different smaller organic molecule (monomer) combinations build these macromolecules (polymers). What specific biological macromolecules do living things require? How do these molecules form? What functions do they serve? We explore these questions in this chapter.

9

Synthesis of Biological Macromolecules

Learning Objectives

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

  • Understand macromolecule synthesis
  • Explain dehydration (or condensation) and hydrolysis reactions

As you’ve learned, biological macromolecules are large molecules, necessary for life, that are built from smaller organic molecules. There are four major biological macromolecule classes (carbohydrates, lipids, proteins, and nucleic acids). Each is an important cell component and performs a wide array of functions. Combined, these molecules make up the majority of a cell’s dry mass (recall that water makes up the majority of its complete mass). Biological macromolecules are organic, meaning they contain carbon. In addition, they may contain hydrogen, oxygen, nitrogen, and additional minor elements.

Dehydration Synthesis

Most macromolecules are made from single subunits, or building blocks, called monomers. The monomers combine with each other using covalent bonds to form larger molecules known as polymers. In doing so, monomers release water molecules as byproducts. This type of reaction is dehydration synthesis, which means “to put together while losing water.”

In the dehydration synthesis reaction above, two glucose molecules link to form the disaccharide maltose. In the process, it forms a water molecule.


Shown is the reaction of two glucose monomers to form maltose. When maltose is formed, a water molecules is released. The components of the linkage are upper case O upper case H from one glucose molecule combining with one upper case H from the second glucose molecule.

In a dehydration synthesis reaction ((Figure)), the hydrogen of one monomer combines with the hydroxyl group of another monomer, releasing a water molecule. At the same time, the monomers share electrons and form covalent bonds. As additional monomers join, this chain of repeating monomers forms a polymer. Different monomer types can combine in many configurations, giving rise to a diverse group of macromolecules. Even one kind of monomer can combine in a variety of ways to form several different polymers. For example, glucose monomers are the constituents of starch, glycogen, and cellulose.

Hydrolysis

Polymers break down into monomers during hydrolysis. A chemical reaction occurs when inserting a water molecule across the bond. Breaking a covalent bond with this water molecule in the compound achieves this ((Figure)). During these reactions, the polymer breaks into two components: one part gains a hydrogen atom (H+) and the other gains a hydroxyl molecule (OH–) from a split water molecule.

In the hydrolysis reaction here, the disaccharide maltose breaks down to form two glucose monomers by adding a water molecule. Note that this reaction is the reverse of the synthesis reaction in (Figure).


Shown is the breakdown of maltose to form two glucose monomers. Water is a reactant. The water molecule, upper case H subscript 2 baseline upper case O, breaks apart, with upper O upper H obtained by one of the glucose molecules, and upper H obtained by the second glucose molecule.

Dehydration and hydrolysis reactions are catalyzed, or “sped up,” by specific enzymes; dehydration reactions involve the formation of new bonds, requiring energy, while hydrolysis reactions break bonds and release energy. These reactions are similar for most macromolecules, but each monomer and polymer reaction is specific for its class. For example, catalytic enzymes in the digestive system hydrolyze or break down the food we ingest into smaller molecules. This allows cells in our body to easily absorb nutrients in the intestine. A specific enzyme breaks down each macromolecule. For instance, amylase, sucrase, lactase, or maltase break down carbohydrates. Enzymes called proteases, such as pepsin and peptidase, and hydrochloric acid break down proteins. Lipases break down lipids. These broken down macromolecules provide energy for cellular activities.

Link to Learning

Visit this site to see visual representations of dehydration synthesis and hydrolysis.

Section Summary

Proteins, carbohydrates, nucleic acids, and lipids are the four major classes of biological macromolecules—large molecules necessary for life that are built from smaller organic molecules. Macromolecules are comprised of single units scientists call monomers that are joined by covalent bonds to form larger polymers. The polymer is more than the sum of its parts: it acquires new characteristics, and leads to an osmotic pressure that is much lower than that formed by its ingredients. This is an important advantage in maintaining cellular osmotic conditions. A monomer joins with another monomer with water molecule release, leading to a covalent bond forming. Scientists call these dehydration or condensation reactions. When polymers break down into smaller units (monomers), they use a water molecule for each bond broken by these reactions. Such reactions are hydrolysis reactions. Dehydration and hydrolysis reactions are similar for all macromolecules, but each monomer and polymer reaction is specific to its class. Dehydration reactions typically require an investment of energy for new bond formation, while hydrolysis reactions typically release energy by breaking bonds.

Review Questions

Dehydration synthesis leads to formation of

  1. monomers
  2. polymers
  3. water and polymers
  4. none of the above

C

During the breakdown of polymers, which of the following reactions takes place?

  1. hydrolysis
  2. dehydration
  3. condensation
  4. covalent bond

A

The following chemical reactants produce the ester ethyl ethanoate (C4H8O2):

C2H6O + CH3COOH

What type of reaction occurs to make ethyl ethanoate?

  1. condensation
  2. hydrolysis
  3. combustion
  4. acid-base reaction

A

Critical Thinking Questions

Why are biological macromolecules considered organic?

Biological macromolecules are organic because they contain carbon.

What role do electrons play in dehydration synthesis and hydrolysis?

In a dehydration synthesis reaction, the hydrogen of one monomer combines with the hydroxyl group of another monomer, releasing a molecule of water. This creates an opening in the outer shells of atoms in the monomers, which can share electrons and form covalent bonds.

Amino acids have the generic structure seen below, where R represents different carbon-based side chains.

Describe how the structure of amino acids allows them to be linked into long peptide chains to form proteins.

Amino acids can be linked into long chains through condensation reactions. One of the hydrogen atoms bonded to the nitrogen atom of an amino acid reacts with the –OH group attached to the terminal carbon on another amino acid. Since both ends of the molecule can participate in condensation reactions, peptide bonds can be made in both directions to create a long amino acid chain.

Glossary

biological macromolecule
large molecule necessary for life that is built from smaller organic molecules
dehydration synthesis
(also, condensation) reaction that links monomer molecules, releasing a water molecule for each bond formed
hydrolysis
reaction that causes breakdown of larger molecules into smaller molecules by utilizing water
monomer
smallest unit of larger molecules that are polymers
polymer
chain of monomer residues that covalent bonds link; polymerization is the process of polymer formation from monomers by condensation

10

Carbohydrates

Learning Objectives

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

  • Discuss the role of carbohydrates in cells and in the extracellular materials of animals and plants
  • Explain carbohydrate classifications
  • List common monosaccharides, disaccharides, and polysaccharides

Most people are familiar with carbohydrates, one type of macromolecule, especially when it comes to what we eat. To lose weight, some individuals adhere to “low-carb” diets. Athletes, in contrast, often “carb-load” before important competitions to ensure that they have enough energy to compete at a high level. Carbohydrates are, in fact, an essential part of our diet. Grains, fruits, and vegetables are all natural carbohydrate sources that provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. Carbohydrates also have other important functions in humans, animals, and plants.

Molecular Structures

The stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule represents carbohydrates. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This formula also explains the origin of the term “carbohydrate”: the components are carbon (“carbo”) and the components of water (hence, “hydrate”). Scientists classify carbohydrates into three subtypes: monosaccharides, disaccharides, and polysaccharides.

Monosaccharides

Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars, the most common of which is glucose. In monosaccharides, the number of carbons usually ranges from three to seven. Most monosaccharide names end with the suffix -ose. If the sugar has an aldehyde group (the functional group with the structure R-CHO), it is an aldose, and if it has a ketone group (the functional group with the structure RC(=O)R’), it is a ketose. Depending on the number of carbons in the sugar, they can be trioses (three carbons), pentoses (five carbons), and/or hexoses (six carbons). (Figure) illustrates monosaccharides.

Scientists classify monosaccharides based on the position of their carbonyl group and the number of carbons in the backbone. Aldoses have a carbonyl group (indicated in green) at the end of the carbon chain, and ketoses have a carbonyl group in the middle of the carbon chain. Trioses, pentoses, and hexoses have three-, five-, and six- carbon backbones, respectively.


The molecular structures of glyceraldehyde, an aldose, and dihydroxyacetone, a ketose, are shown. Both sugars have a three-carbon backbone. Glyceraldehyde has a carbonyl group (c double bonded to O) at one end of the carbon chain with hydroxyl (OH) groups attached to the other carbons. Dihydroxyacetone has a carbonyl group in the middle of the chain and alcohol groups at each end. The molecular structures of linear forms of ribose, a pentose, and glucose, a hexose, are also shown. Both ribose and glucose are aldoses with a carbonyl group at the end of chain,and hydroxyl groups attached to the other carbons.

The chemical formula for glucose is C6H12O6. In humans, glucose is an important source of energy. During cellular respiration, energy releases from glucose, and that energy helps make adenosine triphosphate (ATP). Plants synthesize glucose using carbon dioxide and water, and glucose in turn provides energy requirements for the plant. Humans and other animals that feed on plants often store excess glucose as catabolized (cell breakdown of larger molecules) starch.

Galactose (part of lactose, or milk sugar) and fructose (found in sucrose, 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 isomers) because of the different arrangement of functional groups around the asymmetric carbon. All these monosaccharides have more than one asymmetric carbon ((Figure)).

Visual Connection
Glucose, galactose, and fructose are all hexoses. They are structural isomers, meaning they have the same chemical formula (C6H12O6) but a different atom arrangement.


The molecular structures of the linear forms of glucose, galactose, and fructose are shown. Glucose and galactose are both aldoses with a carbonyl group (carbon double-bonded to oxygen) at one end of the molecule. A hydroxyl (OH) group is attached to each of the other residues. In glucose, the hydroxyl group attached to the second carbon is on the left side of the molecular structure and all other hydroxyl groups are on the right. In galactose, the hydroxyl groups attached to the third and fourth carbons are on the left, and the hydroxyl groups attached to the second, fifth and sixth carbon are on the right. Frucose is a ketose with C doubled bonded to O at the second carbon. All other carbons have hydroxyl groups associated with them. The hydroxyl group associated with the third carbon is on the left, and all the other hydroxyl groups are on the right.

What kind of sugars are these, aldose or ketose?

Glucose, galactose, and fructose are isomeric monosaccharides (hexoses), meaning they have the same chemical formula but have slightly different structures. Glucose and galactose are aldoses, and fructose is a ketose.

Monosaccharides can exist as a linear chain or as ring-shaped molecules. In aqueous solutions they are usually in ring forms ((Figure)). Glucose in a ring form can have two different hydroxyl group arrangements (OH) around the anomeric carbon (carbon 1 that becomes asymmetric in the ring formation process). If the hydroxyl group is below carbon number 1 in the sugar, it is in the alpha (α) position, and if it is above the plane, it is in the beta (β) position.

Five and six carbon monosaccharides exist in equilibrium between linear and ring forms. When the ring forms, the side chain it closes on locks into an α or β position. Fructose and ribose also form rings, although they form five-membered rings as opposed to the six-membered ring of glucose.


The conversion of glucose between linear and ring forms is shown. The glucose ring has five carbons and an oxygen. In alpha glucose, the first hydroxyl group is locked in a down position, and in beta glucose, the ring is locked in an up position. Structures for ring forms of ribose and fructose are also shown. Both sugars have a ring with four carbons and an oxygen.

Disaccharides

Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction (or a condensation reaction or dehydration synthesis). During this process, one monosaccharide’s hydroxyl group combines with another monosaccharide’s hydrogen, releasing a water molecule and forming a covalent bond. A covalent bond forms between a carbohydrate molecule and another molecule (in this case, between two monosaccharides). Scientists call this a glycosidic bond ((Figure)). Glycosidic bonds (or glycosidic linkages) can be an alpha or beta type. An alpha bond is formed when the OH group on the carbon-1 of the first glucose is below the ring plane, and a beta bond is formed when the OH group on the carbon-1 is above the ring plane.

Sucrose forms when a glucose monomer and a fructose monomer join in a dehydration reaction to form a glycosidic bond. In the process, a water molecule is lost. By convention, the carbon atoms in a monosaccharide are numbered from the terminal carbon closest to the carbonyl group. In sucrose, a glycosidic linkage forms between carbon 1 in glucose and carbon 2 in fructose.


The formation of sucrose from glucose and fructose is shown. In sucrose, the number one carbon of the glucose ring is connected to the number two carbon of fructose via an oxygen.

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

Common disaccharides include maltose (grain sugar), lactose (milk sugar), and sucrose (table sugar).


The chemical structures of maltose, lactose, and sucrose are shown. Both maltose and lactose are made from two glucose monomers joined together in ring form. In maltose, the oxygen in the glycosidic bond points downward. In lactose, the oxygen in the glycosidic bond points upward. Sucrose is made from glucose and fructose monomers. The oxygen in the glycosidic bond points downward.

Polysaccharides

A long chain of monosaccharides linked by glycosidic bonds is a polysaccharide (poly- = “many”). The chain may be branched or unbranched, and it may contain different types of monosaccharides. The molecular weight may be 100,000 daltons or more depending on the number of joined monomers. Starch, glycogen, cellulose, and chitin are primary examples of polysaccharides.

Plants store starch in the form of sugars. In plants, an amylose and amylopectic mixture (both glucose polymers) comprise these sugars. Plants are able to synthesize glucose, and they store the excess glucose, beyond the their immediate energy needs, as starch in different plant parts, including roots and seeds. The starch in the seeds provides food for the embryo as it germinates and can also act as a food source for humans and animals. Enzymes break down the starch that humans consume. For example, an amylase present in saliva catalyzes, or breaks down this starch into smaller molecules, such as maltose and glucose. The cells can then absorb the glucose.

Glucose starch comprises monomers that are joined by α 1-4 or α 1-6 glycosidic bonds. The numbers 1-4 and 1-6 refer to the carbon number of the two residues that have joined to form the bond. As (Figure) illustrates, unbranched glucose monomer chains (only α 1-4 linkages) form the starch; whereas, amylopectin is a branched polysaccharide (α 1-6 linkages at the branch points).

Amylose and amylopectin are two different starch forms. Unbranched glucose monomer chains comprise amylose by α 1-4 glycosidic linkages. Unbranched glucose monomer chains comprise amylopectin by α 1-4 and α 1-6 glycosidic linkages. Because of the way the subunits are joined, the glucose chains have a helical structure. Glycogen (not shown) is similar in structure to amylopectin but more highly branched.


The chemical structures of amylose and amylopectin are shown. Amylose consists of unbranched chains of glucose subunits, and amylopectin consists of branched chains of glucose subunits.

Glycogen is the storage form of glucose in humans and other vertebrates and is comprised 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 blood glucose levels decrease, glycogen breaks down to release glucose in a process scientists call glycogenolysis.

Cellulose is the most abundant natural biopolymer. Cellulose mostly comprises a plant’s cell wall. This provides the cell structural support. Wood and paper are mostly cellulosic in nature. Glucose monomers comprise cellulose that β 1-4 glycosidic bonds link ((Figure)).

In cellulose, glucose monomers are linked in unbranched chains by β 1-4 glycosidic linkages. Because of the way the glucose subunits are joined, every glucose monomer is flipped relative to the next one resulting in a linear, fibrous structure.


The chemical structure of cellulose is shown. Cellulose consists of unbranched chains of glucose subunits. The cellulose fibers are long, tubular, and have a slight wave shape.

As (Figure) shows, every other glucose monomer in cellulose is flipped over, and the monomers are packed tightly as extended long chains. This gives cellulose its rigidity and high tensile strength—which is so important to plant cells. While human digestive enzymes cannot break down the β 1-4 linkage, herbivores such as cows, koalas, and buffalos are able, with the help of the specialized flora in their stomach, to digest plant material that is rich in cellulose and use it as a food source. In some of these animals, certain species of bacteria and protists reside in the rumen (part of the herbivore’s digestive system) and secrete the enzyme cellulase. The appendix of grazing animals also contains bacteria that digest cellulose, giving it an important role in ruminants’ digestive systems. Cellulases can break down cellulose into glucose monomers that animals use as an energy source. Termites are also able to break down cellulose because of the presence of other organisms in their bodies that secrete cellulases.

Carbohydrates serve various functions in different animals. Arthropods (insects, crustaceans, and others) have an outer skeleton, the exoskeleton, which protects their internal body parts (as we see in the bee in (Figure)). This exoskeleton is made of the biological macromolecule chitin, which is a polysaccharide-containing nitrogen. It is made of repeating N-acetyl-β-d-glucosamine units, which are a modified sugar. Chitin is also a major component of fungal cell walls. Fungi are neither animals nor plants and form a kingdom of their own in the domain Eukarya.

Insects have a hard outer exoskeleton made of chitin, a type of polysaccharide. (credit: Louise Docker)


A photograph shows a bee in flight, getting nectar from a flower.

Career Connections

Registered DietitianObesity 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 people increasingly seek out registered dietitians for advice. Registered dietitians help plan nutrition programs for individuals in various settings. They often work with patients in health care facilities, designing nutrition plans to treat and prevent 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 physiology (biological functions) of food (proteins, carbohydrates, and fats).

Benefits of Carbohydrates

Are carbohydrates good for you? Some often tell people who wish to lose weight that carbohydrates are bad and they should avoid them. Some diets completely forbid carbohydrate consumption, claiming that a low-carbohydrate diet helps people to lose weight faster. However, carbohydrates have been an important part of the human diet for thousands of years. Artifacts from ancient civilizations show the presence of wheat, rice, and corn in our ancestors’ storage areas.

As part of a well balanced diet, we should supplement carbohydrates with proteins, vitamins, and fats. Calorie-wise, a gram of carbohydrate provides 4.3 Kcal. For comparison, fats provide 9 Kcal/g, a less desirable ratio. Carbohydrates contain soluble and insoluble elements. The insoluble part, fiber, is mostly cellulose. Fiber has many uses. It promotes regular bowel movement by adding bulk, and it regulates the blood glucose consumption rate. Fiber also helps to remove excess cholesterol from the body. Fiber binds to the cholesterol in the small intestine, then attaches to the cholesterol and prevents the cholesterol particles from entering the bloodstream. Cholesterol then exits the body via the feces. Fiber-rich diets also have a protective role in reducing the occurrence of colon cancer. In addition, a meal containing whole grains and vegetables gives a feeling of fullness. As an immediate source of energy, glucose breaks down during the cellular respiration process, which produces ATP, the cell’s energy currency. Without consuming carbohydrates, we reduce the availability of “instant energy”. Eliminating carbohydrates from the diet is not the best way to lose weight. A low-calorie diet that is rich in whole grains, fruits, vegetables, and lean meat, together with plenty of exercise and plenty of water, is the more sensible way to lose weight.

Link to Learning

For an additional perspective on carbohydrates, explore “Biomolecules: the Carbohydrates” through this interactive animation.

Section Summary

Carbohydrates are a group of macromolecules that are a vital energy source for the cell and provide structural support to plant cells, fungi, and all of the arthropods that include lobsters, crabs, shrimp, insects, and spiders. Scientists classify carbohydrates as monosaccharides, disaccharides, and polysaccharides depending on the number of monomers in the molecule. Monosaccharides are linked by glycosidic bonds that form as a result of dehydration reactions, forming disaccharides and polysaccharides with eliminating a water molecule for each bond formed. Glucose, galactose, and fructose are common monosaccharides; whereas, common disaccharides include lactose, maltose, and sucrose. Starch and glycogen, examples of polysaccharides, are the storage forms of glucose in plants and animals, respectively. The long polysaccharide chains may be branched or unbranched. Cellulose is an example of an unbranched polysaccharide; whereas, amylopectin, a constituent of starch, is a highly branched molecule. Glucose storage, in the form of polymers like starch of glycogen, makes it slightly less accessible for metabolism; however, this prevents it from leaking out of the cell or creating a high osmotic pressure that could cause the cell to uptake excessive water.

Visual Connection Questions

(Figure) What kind of sugars are these, aldose or ketose?

(Figure) Glucose and galactose are aldoses. Fructose is a ketose.

Review Questions

An example of a monosaccharide is ________.

  1. fructose
  2. glucose
  3. galactose
  4. all of the above

D

Cellulose and starch are examples of:

  1. monosaccharides
  2. disaccharides
  3. lipids
  4. polysaccharides

D

Plant cell walls contain which of the following in abundance?

  1. starch
  2. cellulose
  3. glycogen
  4. lactose

B

Lactose is a disaccharide formed by the formation of a ________ bond between glucose and ________.

  1. glycosidic; lactose
  2. glycosidic; galactose
  3. hydrogen; sucrose
  4. hydrogen; fructose

B

Which of the following is not an extracellular matrix role of carbohydrates?

  1. protect an insect’s internal organs from external trauma
  2. prevent plant cells from lysing after the plant is watered
  3. maintain the shape of a fungal spore
  4. provide energy for muscle movement

D

Critical Thinking Questions

Describe the similarities and differences between glycogen and starch.

Glycogen and starch are polysaccharides. They are the storage form of glucose. Glycogen is stored in animals in the liver and in muscle cells, whereas starch is stored in the roots, seeds, and leaves of plants. Starch has two different forms, one unbranched (amylose) and one branched (amylopectin), whereas glycogen is a single type of a highly branched molecule.

Why is it impossible for humans to digest food that contains cellulose?

The β 1-4 glycosidic linkage in cellulose cannot be broken down by human digestive enzymes. Herbivores such as cows, koalas, and buffalos are able to digest grass that is rich in cellulose and use it as a food source because bacteria and protists in their digestive systems, especially in the rumen, secrete the enzyme cellulase. Cellulases can break down cellulose into glucose monomers that can be used as an energy source by the animal.

Draw the ketose and aldose forms of a monosaccharide with the chemical formula C3H6O3. How is the structure of the monosaccharide changed from one form to the other in the human body?

The human body switches carbohydrates between their aldose and ketose forms using a family of enzymes called isomerases. The ketose triose is called dihydroxyacetone, and has the oxygen double-bonded to the center carbon:

The aldose is called glyceraldehyde, and can have the oxygen double-bonded to the first or third carbon of the molecule:

Glossary

carbohydrate
biological macromolecule in which the ratio of carbon to hydrogen and to oxygen is 1:2:1; carbohydrates serve as energy sources and structural support in cells and form arthropods’ cellular exoskeleton
cellulose
polysaccharide that comprises the plants’ cell wall; provides structural support to the cell
chitin
type of carbohydrate that forms the outer skeleton of all arthropods that include crustaceans and insects; it also forms fungi cell walls
disaccharide
two sugar monomers that a glycosidic bond links
glycogen
storage carbohydrate in animals
glycosidic bond
bond formed by a dehydration reaction between two monosaccharides with eliminating a water molecule
monosaccharide
single unit or monomer of carbohydrates
polysaccharide
long chain of monosaccharides; may be branched or unbranched
starch
storage carbohydrate in plants

11

Lipids

Learning Objectives

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

  • Describe the four major types of lipids
  • Explain the role of fats in storing energy
  • Differentiate between saturated and unsaturated fatty acids
  • Describe phospholipids and their role in cells
  • Define the basic structure of a steroid and some steroid functions
  • Explain how cholesterol helps maintain the plasma membrane’s fluid nature

Lipids include a diverse group of compounds that are largely nonpolar in nature. This is because they are hydrocarbons that include mostly nonpolar carbon–carbon or carbon–hydrogen bonds. Non-polar molecules are hydrophobic (“water fearing”), or insoluble in water. Lipids perform many different functions in a cell. Cells store energy for long-term use in the form of fats. Lipids also provide insulation from the environment for plants and animals ((Figure)). For example, they help keep aquatic birds and mammals dry when forming a protective layer over fur or feathers because of their water-repellant hydrophobic nature. Lipids are also the building blocks of many hormones and are an important constituent of all cellular membranes. Lipids include fats, oils, waxes, phospholipids, and steroids.

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


Photo shows a river otter swimming. The river otter has thick fur that is smooth and wet.

Fats and Oils

A fat molecule consists of two main components—glycerol and fatty acids. Glycerol is an organic compound (alcohol) with three carbons, five hydrogens, and three hydroxyl (OH) groups. Fatty acids have a long chain of hydrocarbons to which a carboxyl group is attached, hence the name “fatty acid.” The number of carbons in the fatty acid may range from 4 to 36. The most common are those containing 12–18 carbons. In a fat molecule, the fatty acids attach to each of the glycerol molecule’s three carbons with an ester bond through an oxygen atom ((Figure)).

Joining three fatty acids to a glycerol backbone in a dehydration reaction forms triacylglycerol. Three water molecules release in the process.


The structures of glycerol, a fatty acid, and a triacylglycerol are shown. Glycerol is a chain of three carbons, with a hydroxyl (upper O upper H) group attached to each carbon. A fatty acid has an acetyl (upper C upper O upper O upper H) group attached to a long carbon chain. In triacylglycerol, a fatty acid is attached to each of glycerols three hydroxyl groups via the carboxyl group. A water molecule is lost in the reaction so the structure of the linkage is C dash O dash C, with an oxygen double bonded to the second carbon.

During this ester bond formation, three water molecules are released. The three fatty acids in the triacylglycerol may be similar or dissimilar. We also call fats triacylglycerols or triglycerides because of their chemical structure. 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 hypogea, the scientific name for groundnuts or 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. Stearic acid is an example of a saturated fatty acid ((Figure)).

Stearic acid is a common saturated fatty acid.


The structure of stearic acid is shown. This fatty acid has a hydrocarbon chain seventeen residues long attached to an acetyl group. All bonds between the carbons are single bonds.

When the hydrocarbon chain contains a double bond, the fatty acid is unsaturated. Oleic acid is an example of an unsaturated fatty acid ((Figure)).

Oleic acid is a common unsaturated fatty acid.


The structure of oleic acid is shown. This fatty acid has a hydrocarbon chain seventeen residues long attached to an acetyl group. The bond between carbon eight and carbon nine is a double bond.

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

When a fatty acid has no double bonds, it is a saturated fatty acid because it is not possible to add more hydrogen to the chain’s carbon atoms. A fat may contain similar or different fatty acids attached to glycerol. Long straight fatty acids with single bonds generally pack tightly and are solid at room temperature. Animal fats with stearic acid and palmitic acid (common in meat) and the fat with butyric acid (common in butter) are examples of saturated fats. Mammals store fats in specialized cells, or adipocytes, where fat globules occupy most of the cell’s volume. Plants store fat or oil in many seeds and use them as a source of energy during seedling development. Unsaturated fats or oils are usually of plant origin and contain cis unsaturated fatty acids. Cis and trans indicate the configuration of the molecule around the double bond. If hydrogens are present in the same plane, it is a cis fat. If the hydrogen atoms are on two different planes, it is a trans fat. The cis double bond causes a bend or a “kink” that prevents the fatty acids from packing tightly, keeping them liquid at room temperature ((Figure)). Olive oil, corn oil, canola oil, and cod liver oil are examples of unsaturated fats. Unsaturated fats help to lower blood cholesterol levels; whereas, saturated fats contribute to plaque formation in the arteries.

Saturated fatty acids have hydrocarbon chains connected by single bonds only. Unsaturated fatty acids have one or more double bonds. Each double bond may be in a cis or trans configuration. In the cis configuration, both hydrogens are on the same side of the hydrocarbon chain. In the trans configuration, the hydrogens are on opposite sides. A cis double bond causes a kink in the chain.


A comparison of saturated and unsaturated fatty acids is shown. Stearic acid, a saturated fatty acid, has a hydrocarbon chain seventeen residues long attached to an acetyl group. Oleic acid also has a seventeen-residue hydrocarbon chain, but a double bond exists between the eighth and ninth carbon in the chain. In cis oleic acid, the hydrogens are on the same side of the double bond. In the cis oleic acid, the 2 hydrogens on the same side cuase the chain to bend. In trans oleic acid, they are on opposite sides.

Trans Fats

The food industry artificially hydrogenates oils to make them semi-solid and of a consistency desirable for many processed food products. 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 convert to double bonds in the trans– conformation.

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 higher levels of low-density lipoproteins (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 banned using trans fats, and food labels are required to display the trans fat content.

Omega Fatty Acids

Essential fatty acids are those that the human body requires but does not synthesize. Consequently, they have to be supplemented through ingestion via the diet. Omega-3 fatty acids (like those in (Figure)) fall into this category and are one of only two known for humans (the other is omega-6 fatty acid). These are polyunsaturated fatty acids and are omega-3 because a double bond connects the third carbon from the hydrocarbon chain’s end to its neighboring carbon.

Alpha-linolenic acid is an example of an omega-3 fatty acid. It has three cis double bonds and, as a result, a curved shape. For clarity, the diagram does not show the carbons. Each singly bonded carbon has two hydrogens associated with it, which the diagram also does not show.


The molecular structures of alpha-linolenic acid, an omega-3 fatty acid is shown. Alpha-linolenic acid has three double bonds located eight, eleven, and fourteen residues from the acetyl group. It has a hooked shape.

The farthest carbon away from the carboxyl group is numbered as the omega (ω) carbon, and if the double bond is between the third and fourth carbon from that end, it is an omega-3 fatty acid. Nutritionally important because the body does not make them, omega-3 fatty acids include alpha-linoleic acid (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), all of which are polyunsaturated. Salmon, trout, and tuna are good sources of omega-3 fatty acids. Research indicates that omega-3 fatty acids reduce the risk of sudden death from heart attacks, lower triglycerides in the blood, decrease blood pressure, and prevent thrombosis by inhibiting blood clotting. They also reduce inflammation, and may help lower the risk of some cancers in animals.

Like carbohydrates, fats have received considerable 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. Many vitamins are fat soluble, and fats serve as a long-term storage form of fatty acids: a source of energy. They also provide insulation for the body. Therefore, we should consume “healthy” fats in moderate amounts on a regular basis.

Waxes

Wax covers some aquatic birds’ feathers and some plants’ leaf surfaces. Because of waxes’ hydrophobic nature, they prevent water from sticking on the surface ((Figure)). Long fatty acid chains esterified to long-chain alcohols comprise waxes.

Lipids comprise waxy coverings on some leaves. (credit: Roger Griffith)


The photo shows leaves on a plant; the leaves appear thick, shiny, and waxy.

Phospholipids

Phospholipids are major plasma membrane constituents that comprise cells’ outermost layer. Like fats, they are comprised of fatty acid chains attached to a glycerol or sphingosine backbone. However, instead of three fatty acids attached as in triglycerides, there are two fatty acids forming diacylglycerol, and a modified phosphate group occupies the glycerol backbone’s third carbon ((Figure)). A phosphate group alone attached to a diaglycerol does not qualify as a phospholipid. It is phosphatidate (diacylglycerol 3-phosphate), the precursor of phospholipids. An alcohol modifies the phosphate group. Phosphatidylcholine and phosphatidylserine are two important phospholipids that are in plasma membranes.

A phospholipid is a molecule with two fatty acids and a modified phosphate group attached to a glycerol backbone. Adding a charged or polar chemical group may modify the phosphate.


The molecular structure of a phospholipid is shown. It consists of two fatty acids attached to the first and second carbons in glycerol, and a phosphate group attached to the third position. The phosphate group may be further modified by addition of another molecule to one of its oxygens. Two molecules that may modify the phosphate group, choline and serine, are shown. Choline consists of a two-carbon chain with a hydroxy group attached to one end and a nitrogen attached to the other. The nitrogen, in turn, has three methyl groups attached to it and has a charge of plus one. Serine consists of a two-carbon chain with a hydroxyl group attached to one end. An amino group and a carboxyl group are attached to the other end.

A phospholipid is an amphipathic molecule, meaning it has a hydrophobic and a hydrophilic part. The fatty acid chains are hydrophobic and cannot interact with water; whereas, the phosphate-containing group is hydrophilic and interacts with water ((Figure)).

The phospholipid bilayer is the major component of all cellular membranes. The hydrophilic head groups of the phospholipids face the aqueous solution. The hydrophobic tails are sequestered in the middle of the bilayer.


An illustration of a phospholipids bilayer is shown. The phospholipids bilayer consists of two layers of phospholipids. The hydrophobic tails of the phospholipids face one another while the hydrophilic head groups face outward.

The head is the hydrophilic part, and the tail contains the hydrophobic fatty acids. In a membrane, a bilayer of phospholipids forms the structure’s matrix, phospholipids’ fatty acid tails face inside, away from water; whereas, the phosphate group faces the outside, aqueous side ((Figure)).

Phospholipids are responsible for the plasma membrane’s dynamic nature. If a drop of phospholipids is placed in water, it spontaneously forms a structure that scientists call a micelle, where the hydrophilic phosphate heads face the outside and the fatty acids face the structure’s interior.

Steroids

Unlike the phospholipids and fats that we discussed earlier, steroids have a fused ring structure. Although they do not resemble the other lipids, scientists group them with them because they are also hydrophobic and insoluble in water. All steroids have four linked carbon rings and several of them, like cholesterol, have a short tail ((Figure)). Many steroids also have the –OH functional group, which puts them in the alcohol classification (sterols).

Four fused hydrocarbon rings comprise steroids such as cholesterol and cortisol.


The structures of cholesterol and cortisol are shown. Each of these molecules is composed of three six-carbon rings fused to a five-carbon ring. Cholesterol has a branched hydrocarbon attached to the five-carbon ring, and a hydroxyl group attached to the terminal six-carbon ring. Cortisol has a two-carbon chain modified with a double-bonded oxygen, a hydroxyl group attached to the five-carbon ring, and an oxygen double-bonded to the terminal six-carbon ring.

Cholesterol is the most common steroid. The liver synthesizes cholesterol and is the precursor to many steroid hormones such as testosterone and estradiol, which gonads and endocrine glands secrete. It is also the precursor to Vitamin D. Cholesterol is also the precursor of bile salts, which help emulsifying fats and their subsequent absorption by cells. Although lay people often speak negatively about cholesterol, it is necessary for the body’s proper functioning. Sterols (cholesterol in animal cells, phytosterol in plants) are components of the plasma membrane of cells and are found within the phospholipid bilayer.

Link to Learning

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

Section Summary

Lipids are a class of macromolecules that are nonpolar and hydrophobic in nature. Major types include fats and oils, waxes, phospholipids, and steroids. Fats are a stored form of energy and are also known as triacylglycerols or triglycerides. Fats are comprised of fatty acids and either glycerol or sphingosine. Fatty acids may be unsaturated or saturated, depending on the presence or absence of double bonds in the hydrocarbon chain. If only single bonds are present, they are saturated fatty acids. Unsaturated fatty acids may have one or more double bonds in the hydrocarbon chain. Phospholipids comprise the membrane’s matrix. They have a glycerol or sphingosine backbone to which two fatty acid chains and a phosphate-containing group are attached. Steroids are another class of lipids. Their basic structure has four fused carbon rings. Cholesterol is a type of steroid and is an important constituent of the plasma membrane, where it helps to maintain the membrane’s fluid nature. It is also the precursor of steroid hormones such as testosterone.

Review Questions

Saturated fats have all of the following characteristics except:

  1. they are solid at room temperature
  2. they have single bonds within the carbon chain
  3. they are usually obtained from animal sources
  4. they tend to dissolve in water easily

D

Phospholipids are important components of ________.

  1. the plasma membrane of cells
  2. the ring structure of steroids
  3. the waxy covering on leaves
  4. the double bond in hydrocarbon chains

A

Cholesterol is an integral part of plasma membranes. Based on its structure, where is it found in the membrane?

  1. on the extracellular surface
  2. embedded with the phospholipid heads
  3. within the tail bilayer
  4. attached to the intracellular surface

C

Critical Thinking Questions

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. Waxes can protect plant leaves and mammalian fur from getting wet. Phospholipids and steroids are important components of animal cell membranes, as well as plant, fungal, and bacterial membranes.

Why have trans fats been banned from some restaurants? How are they created?

Trans fats are created artificially when hydrogen gas is bubbled through oils to solidify them. The double bonds of the cis conformation in the hydrocarbon chain may be converted to double bonds in the trans configuration. Some restaurants are banning trans fats because they cause higher levels of LDL, or “bad”cholesterol.

Why are fatty acids better than glycogen for storing large amounts of chemical energy?

Fats have a higher energy density than carbohydrates (averaging 9kcal/gram versus 4.3kcal/gram respectively). Thus, on a per gram basis, more energy can be stored in fats than can be stored in carbohydrates. Additionally, fats are packaged into spherical globules to minimize interactions with the water-based plasma membrane, while glycogen is a large branched carbohydrate that cannot be compacted for storage.

Part of cortisol’s role in the body involves passing through the plasma membrane to initiate signaling inside a cell. Describe how the structures of cortisol and the plasma membrane allow this to occur.

Cortisol is a small, generally hydrophobic molecule, while the phospholipids that create plasma membranes have a hydrophilic head and hydrophobic tails. Since cortisol is hydrophobic, it can interact with the sequestered tails of the phospholipids in the center of the plasma membrane. This, along with its small size, allows cortisol to move through the plasma membrane to the inside of the cell.

Glossary

lipid
macromolecule that is nonpolar and insoluble in water
omega fat
type of polyunsaturated fat that the body requires; numbering the carbon omega starts from the methyl end or the end that is farthest from the carboxylic end
phospholipid
membranes’ major constituent; comprised of two fatty acids and a phosphate-containing group attached to a glycerol backbone
saturated fatty acid
long-chain hydrocarbon with single covalent bonds in the carbon chain; the number of hydrogen atoms attached to the carbon skeleton is maximized
steroid
type of lipid comprised of four fused hydrocarbon rings forming a planar structure
trans fat
fat formed artificially by hydrogenating oils, leading to a different arrangement of double bond(s) than those in naturally occurring lipids
triacylglycerol (also, triglyceride)
fat molecule; consists of three fatty acids linked to a glycerol molecule
unsaturated fatty acid
long-chain hydrocarbon that has one or more double bonds in the hydrocarbon chain
wax
lipid comprised of a long-chain fatty acid that is esterified to a long-chain alcohol; serves as a protective coating on some feathers, aquatic mammal fur, and leaves

12

Proteins

Learning Objectives

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

  • Describe the functions proteins perform in the cell and in tissues
  • Discuss the relationship between amino acids and proteins
  • Explain the four levels of protein organization
  • Describe the ways in which protein shape and function are linked

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 proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.

Types and Functions of Proteins

Enzymes, which living cells produce, are catalysts in biochemical reactions (like digestion) and are usually complex or conjugated proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) upon which it acts. The enzyme may help in breakdown, rearrangement, or synthesis reactions. We call enzymes that break down their substrates catabolic enzymes. Those that build more complex molecules from their substrates are anabolic enzymes, and enzymes that affect the rate of reaction are catalytic enzymes. Note that all enzymes increase the reaction rate and, therefore, are organic catalysts. An example of an enzyme is salivary amylase, which hydrolyzes its substrate amylose, a component of starch.

Hormones are chemical-signaling molecules, usually small proteins or steroids, secreted by 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 helps regulate the blood glucose level. (Figure) lists the primary types and functions of proteins.

Protein Types and Functions
Type Examples Functions
Digestive Enzymes Amylase, lipase, pepsin, trypsin Help in food by catabolizing nutrients into monomeric units
Transport Hemoglobin, albumin Carry substances in the blood or lymph throughout the body
Structural Actin, tubulin, keratin Construct different structures, like the cytoskeleton
Hormones Insulin, thyroxine Coordinate different body systems’ activity
Defense Immunoglobulins Protect the body from foreign pathogens
Contractile Actin, myosin Effect muscle contraction
Storage Legume storage proteins, egg white (albumin) Provide nourishment in early embryo development and the seedling

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, located in our skin, is a fibrous protein. Protein shape is critical to its function, and many different types of chemical bonds maintain this shape. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the protein’s shape, leading to loss of function, or denaturation. Different arrangements of the same 20 types of amino acids comprise all proteins. Two rare new amino acids were discovered recently (selenocystein and pirrolysine), and additional new discoveries may be added to the list.

Amino Acids

Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group ((Figure)).

Amino acids have a central asymmetric carbon to which an amino group, a carboxyl group, a hydrogen atom, and a side chain (R group) are attached.


The molecular structure of an amino acid is given. An amino acid has an alpha carbon to which an amino group, a carboxyl group, a hydrogen, and a side chain are attached. The side chain varies for different amino acids, and is designated as the R - group.

Scientists use the name “amino acid” because these acids contain both amino group and carboxyl-acid-group in their basic structure. As we mentioned, there are 20 common amino acids present in proteins. Nine of these are essential amino acids in humans because the human body cannot produce them and we obtain them from our diet. For each amino acid, the R group (or side chain) is different ((Figure)).

Visual Connection
There are 20 common amino acids commonly found in proteins, each with a different R group (variant group) that determines its chemical nature.


The molecular structures of the twenty amino acids commonly found in proteins are given. These are divided into five categories: nonpolar aliphatic, polar uncharged, positively charged, negatively charged, and aromatic. Nonpolar aliphatic amino acids include glycine, alanine, valine, leucine, methionine, and isoleucine. Polar uncharged amino acids include serine, threonine, cysteine, proline, asparagine, and glutamine. Positively charged amino acids include lysine, arginine, and histidine. Negatively charged amino acids include aspartate and glutamate. Aromatic amino acids include phenylalanine, tyrosine, and tryptophan. For example, in the amino acid glycine, the R group is a single hydrogen; but in alanine the R group is upper C upper H subscript 3 baseline.

Which categories of amino acid would you expect to find on a soluble protein’s surface and which would you expect to find in the interior? What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer?

The chemical nature of the side chain determines the amino acid’s nature (that is, whether it is acidic, basic, polar, or nonpolar). For example, the amino acid glycine has a hydrogen atom as the R group. Amino acids such as valine, methionine, and alanine are nonpolar or hydrophobic in nature, while amino acids such as serine, threonine, and cysteine are polar and have hydrophilic side chains. The side chains of lysine and arginine are positively charged, and therefore these amino acids are also basic amino acids. Proline has an R group that is linked to the amino group, forming a ring-like structure. Proline is an exception to the amino acid’s standard structure since its amino group is not separate from the side chain ((Figure)).

A single upper case letter or a three-letter abbreviation represents amino acids. For example, the letter V or the three-letter symbol val represent valine. Just as some fatty acids are essential to a diet, some amino acids also are necessary. These essential amino acids in humans include isoleucine, leucine, and cysteine. Essential amino acids refer to those necessary to build proteins in the body, but not those that the body produces. Which amino acids are essential varies from organism to organism.

The sequence and the number of amino acids ultimately determine the protein’s shape, size, and function. A covalent bond, or peptide bond, attaches to each amino acid, which a dehydration reaction forms. One amino acid’s carboxyl group and the incoming amino acid’s amino group combine, releasing a water molecule. The resulting bond is the peptide bond ((Figure)).

Peptide bond formation is a dehydration synthesis reaction. The carboxyl group of one amino acid is linked to the incoming amino acid’s amino group. In the process, it releases a water molecule.


The formation of a peptide bond between two amino acids is shown. When the peptide bond forms, the carbon from the carbonyl group becomes attached to the nitrogen from the amino group. The upper O upper H from the carboxyl group and an upper H from the amino group form a molecule of water.

The products that such linkages form are peptides. As more amino acids join to this growing chain, the resulting chain is a polypeptide. Each polypeptide has a free amino group at one end. This end the N terminal, or the amino terminal, and the other end has a free carboxyl group, also the C or carboxyl terminal. 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, often have bound non-peptide prosthetic groups, have a distinct shape, and have a unique function. After protein synthesis (translation), most proteins are modified. These are known as post-translational modifications. They may undergo cleavage, phosphorylation, or may require adding other chemical groups. Only after these modifications is the protein completely functional.

Link to Learning

Click through the steps of protein synthesis in this interactive tutorial.

Evolution Connection

The Evolutionary Significance of Cytochrome cCytochrome c is an important component of the electron transport chain, a part of cellular respiration, and it is normally located in the cellular organelle, the mitochondrion. This protein has a heme prosthetic group, and the heme’s central ion alternately reduces and oxidizes during electron transfer. Because this essential 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 cytochrome c amino acid sequence homology among different species. In other words, we can assess evolutionary kinship by measuring the similarities or differences among various species’ DNA or protein sequences.

Scientists have determined that human cytochrome c contains 104 amino acids. For each cytochrome c molecule from different organisms that scientists have sequenced to date, 37 of these amino acids appear in the same position in all cytochrome c samples. This indicates that there may have been a common ancestor. On comparing the human and chimpanzee protein sequences, scientists did not find a sequence difference. When researchers compared human and rhesus monkey sequences, the single difference was in one amino acid. In another comparison, human to yeast sequencing shows a difference in the 44th position.

Protein Structure

As we discussed earlier, a protein’s shape is critical to its function. For example, an enzyme can bind to a specific substrate at an active site. If this active site is altered because of local changes or changes in overall protein structure, the enzyme may be unable to bind to the substrate. 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.

Primary Structure

Amino acids’ unique sequence in a polypeptide chain is its primary structure. For example, the pancreatic hormone insulin has two polypeptide chains, A and B, and they are linked together by disulfide bonds. The N terminal amino acid of the A chain is glycine; whereas, the C terminal amino acid is asparagine ((Figure)). The amino acid sequences in the A and B chains are unique to insulin.

Bovine serum insulin is a protein hormone comprised of two peptide chains, A (21 amino acids long) and B (30 amino acids long). In each chain, three-letter abbreviations that represent the amino acids’ names in the order they are present indicate primary structure. The amino acid cysteine (cys) has a sulfhydryl (SH) group as a side chain. Two sulfhydryl groups can react in the presence of oxygen to form a disulfide (S-S) bond. Two disulfide bonds connect the A and B chains together, and a third helps the A chain fold into the correct shape. Note that all disulfide bonds are the same length, but we have drawn them different sizes for clarity.


The amino acid sequences for the A chain and B chain of bovine insulin are shown. The A chain is 21 amino acids in length, and the B chain is 30 amino acids in length. One disulfide, or S S bond, connects two cysteine residues in the A chain. Two other disulfide linkages connect the A chain to the B chain.

The gene encoding the protein ultimately determines the unique sequence for every protein. A change in nucleotide sequence of the gene’s coding region may lead to adding a different amino acid to the growing polypeptide chain, causing a change in protein structure and function. In sickle cell anemia, the hemoglobin β chain (a small portion of which we show in (Figure)) has a single amino acid substitution, causing a change in protein structure and function. Specifically, valine in the β chain substitutes the amino acid glutamic. What is most remarkable to consider is that a hemoglobin molecule is comprised of two alpha 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—which dramatically decreases life expectancy—is a single amino acid of the 600. What is even more remarkable is that three nucleotides each encode those 600 amino acids, and a single base change (point mutation), 1 in 1800 bases causes the mutation.

The beta chain of hemoglobin is 147 residues in length, yet a single amino acid substitution leads to sickle cell anemia. In normal hemoglobin, the amino acid at position seven is glutamate. In sickle cell hemoglobin, a valine replaces glutamate.


A portion of the hemoglobin amino acid sequence is shown. The normal hemoglobin beta chain has a glutamate at position six. The sickle cell beta chain has a valine at this position.

Because of this change of one amino acid in the chain, hemoglobin molecules form long fibers that distort the biconcave, or disc-shaped, red blood cells and causes them to assume a crescent or “sickle” shape, which clogs blood vessels ((Figure)). This can lead to myriad serious health problems such as breathlessness, dizziness, headaches, and abdominal pain for those affected by this disease.

In this blood smear, visualized at 535x magnification using bright field microscopy, sickle cells are crescent shaped, while normal cells are disc-shaped. (credit: modification of work by Ed Uthman; scale-bar data from Matt Russell)


This electron micrograph shows red blood cells from a patient with sickle cell anemia. Most of the cells have a normal, disk shape, but about one in five has a sickle shape. A normal blood cell is eight microns across.

Secondary Structure

The local folding of the polypeptide in some regions gives rise to the secondary structure of the protein. The most common are the α-helix and β-pleated sheet structures ((Figure)). Both structures are held in shape by hydrogen bonds. The hydrogen bonds form between the oxygen atom in the carbonyl group in one amino acid and another amino acid that is four amino acids farther along the chain.

The α-helix and β-pleated sheet are secondary structures of proteins that form because of hydrogen bonding between carbonyl and amino groups in the peptide backbone. Certain amino acids have a propensity to form an α-helix, while others have a propensity to form a β-pleated sheet.


The illustration shows an alpha helix protein structure, which coils like a spring, and a beta-pleated sheet structure, which forms flat sheets stacked together. In an alpha-helix, hydrogen bonding occurs between the carbonyl group of one amino acid and the amino group of the amino acid that occurs four residues later. In a beta-pleated sheet, hydrogen bonding occurs between two different lengths of peptide that are antiparallel to one another.

Every helical turn in an alpha helix has 3.6 amino acid residues. The polypeptide’s R groups (the variant groups) protrude out from the α-helix chain. In the β-pleated sheet, hydrogen bonding between atoms on the polypeptide chain’s backbone form the “pleats”. The R groups are attached to the carbons and extend above and below the pleat’s folds. The pleated segments align parallel or antiparallel to each other, and hydrogen bonds form between the partially positive nitrogen atom in the amino group and the partially negative oxygen atom in the peptide backbone’s carbonyl group. The α-helix and β-pleated sheet structures are in most globular and fibrous proteins and they play an important structural role.

Tertiary Structure

The polypeptide’s unique three-dimensional structure is its tertiary structure ((Figure)). This structure is in part due to chemical interactions at work on the polypeptide chain. Primarily, the interactions among R groups create the protein’s complex three-dimensional tertiary structure. The nature of the R groups in the amino acids involved can counteract forming the hydrogen bonds we described for standard secondary structures. For example, R groups with like charges repel each other and those with unlike charges are attracted to each other (ionic bonds). When protein folding takes place, the nonpolar amino acids’ hydrophobic R groups lie in the protein’s interior; whereas, the hydrophilic R groups lie on the outside. Scientists also call the former interaction types hydrophobic interactions. Interaction between cysteine side chains forms disulfide linkages in the presence of oxygen, the only covalent bond that forms during protein folding.

A variety of chemical interactions determine the proteins’ tertiary structure. These include hydrophobic interactions, ionic bonding, hydrogen bonding, and disulfide linkages.


This illustration shows a polypeptide backbone folded into a three-dimensional structure. Chemical interactions between amino acid side chains maintain its shape. These include an ionic bond between an amino group and a carboxyl group, hydrophobic interactions between two hydrophobic side chains, a hydrogen bond between a hydroxyl group and a carbonyl group, and a disulfide linkage.

All of these interactions, weak and strong, determine the protein’s final three-dimensional shape. When a protein loses its three-dimensional shape, it may no longer be functional.

Quaternary Structure

In nature, some proteins form from several polypeptides, or subunits, and the interaction of these subunits forms the quaternary structure. Weak interactions between the subunits help to stabilize the overall structure. For example, insulin (a globular protein) has a combination of hydrogen and disulfide bonds that cause it to mostly clump into a ball shape. Insulin starts out as a single polypeptide and loses some internal sequences in the presence of post-translational modification after forming the disulfide linkages that hold the remaining chains together. Silk (a fibrous protein), however, has a β-pleated sheet structure that is the result of hydrogen bonding between different chains.

(Figure) illustrates the four levels of protein structure (primary, secondary, tertiary, and quaternary).

Observe the four levels of protein structure in these illustrations. (credit: modification of work by National Human Genome Research Institute)


Shown are the four levels of protein structure. The primary structure is the amino acid sequence. Secondary structure is a regular folding pattern due to hydrogen bonding. Two types of secondary structure are shown: a beta pleated sheet, which is flat with regular ripples, and an alpha helix, which coils like a spring. Tertiary structure is the three-dimensional folding pattern of the protein due to interactions between amino acid side chains. Quaternary structure is the interaction of two or more polypeptide chains.

Denaturation and Protein Folding

Each protein has its own unique sequence and shape that chemical interactions hold together. If the protein is subject to changes in temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape without losing its primary sequence in what scientists call denaturation. Denaturation is often reversible because the polypeptide’s primary structure is conserved in the process if the denaturing agent is removed, allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to loss of function. One example of irreversible protein denaturation is frying an egg. The albumin protein in the liquid egg white denatures when placed in a hot pan. Not all proteins denature at high temperatures. For instance, bacteria that survive in hot springs have proteins that function at temperatures close to boiling. The stomach is also very acidic, has a low pH, and denatures proteins as part of the digestion process; however, the stomach’s digestive enzymes retain their activity under these conditions.

Protein folding is critical to its function. Scientists originally thought that the proteins themselves were responsible for the folding process. Only recently researchers discovered that often they receive assistance in the folding process from protein helpers, or chaperones (or chaperonins) that associate with the target protein during the folding process. They act by preventing polypeptide aggregation that comprise the complete protein structure, and they disassociate from the protein once the target protein is folded.

Link to Learning

For an additional perspective on proteins, view this animation called “Biomolecules: The Proteins.”

Section Summary

Proteins are a class of macromolecules that perform a diverse range of functions for the cell. They help in metabolism by acting as enzymes, carriers, or hormones, and provide structural support. The building blocks of proteins (monomers) are amino acids. Each amino acid has a central carbon that bonds to an amino group, a carboxyl group, a hydrogen atom, and an R group or side chain. There are 20 commonly occurring amino acids, each of which differs in the R group. A peptide bond links each amino acid to its neighbors. A long amino acid chain is a polypeptide.

Proteins are organized at four levels: primary, secondary, tertiary, and (optional) quaternary. The primary structure is the amino acids’ unique sequence. The polypeptide’s local folding to form structures such as the α-helix and β-pleated sheet constitutes the secondary structure. The overall three-dimensional structure is the tertiary structure. When two or more polypeptides combine to form the complete protein structure, the configuration is the protein’s quaternary structure. Protein shape and function are intricately linked. Any change in shape caused by changes in temperature or pH may lead to protein denaturation and a loss in function.

Visual Connection Questions

(Figure) Which categories of amino acid would you expect to find on the surface of a soluble protein, and which would you expect to find in the interior? What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer?

(Figure) Polar and charged amino acid residues (the remainder after peptide bond formation) are more likely to be found on the surface of soluble proteins where they can interact with water, and nonpolar (e.g., amino acid side chains) are more likely to be found in the interior where they are sequestered from water. In membrane proteins, nonpolar and hydrophobic amino acid side chains associate with the hydrophobic tails of phospholipids, while polar and charged amino acid side chains interact with the polar head groups or with the aqueous solution. However, there are exceptions. Sometimes, positively and negatively charged amino acid side chains interact with one another in the interior of a protein, and polar or charged amino acid side chains that interact with a ligand can be found in the ligand binding pocket.

Review Questions

The monomers that make up proteins are called ________.

  1. nucleotides
  2. disaccharides
  3. amino acids
  4. chaperones

C

The α-helix and the β-pleated sheet are part of which protein structure?

  1. primary
  2. secondary
  3. tertiary
  4. quaternary

B

Mad cow disease is an infectious disease where one misfolded protein causes all other copies of the protein to begin misfolding. This is an example of a disease impacting ____ structure.

  1. primary
  2. secondary
  3. tertiary
  4. quaternary

C

Critical Thinking Questions

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—the amino acid glutamic acid in position six is substituted by valine. Because of this change, hemoglobin molecules form aggregates, and the disc-shaped red blood cells assume a crescent shape, which results in serious health problems.

Describe the differences in the four protein structures.

The sequence and number of amino acids in a polypeptide chain is its primary structure. The local folding of the polypeptide in some regions is the secondary structure of the protein. The three-dimensional structure of a polypeptide is known as its tertiary structure, created in part by chemical interactions such as hydrogen bonds between polar side chains, van der Waals interactions, disulfide linkages, and hydrophobic interactions. Some proteins are formed from multiple polypeptides, also known as subunits, and the interaction of these subunits forms the quaternary structure.

Aquaporins are proteins embedded in the plasma membrane that allow water molecules to move between the extracellular matrix and the intracellular space. Based on its function and location, describe the key features of the protein’s shape and the chemical characteristics of its amino acids.

The protein must form a channel in the plasma membrane that allows water into the cell since water cannot cross the plasma membrane by itself. Since aquaporins are embedded in the plasma membrane and connect with both the intracellular and extracellular spaces, it must be amphipathic like the plasma membrane. The top and bottom of the protein must contain charged or polar amino acids (hydrophilic) to interact with the aqueous environments. The exterior transmembrane region must contain non-polar amino acids (hydrophobic) that can interact with the phospholipid tails. However, the inside of this channel must contain hydrophilic amino acids since they will interact with the traveling water molecules.

Glossary

alpha-helix structure (α-helix)
type of secondary protein structure formed by folding the polypeptide into a helix shape with hydrogen bonds stabilizing the structure
amino acid
a protein’s monomer; has a central carbon or alpha carbon to which an amino group, a carboxyl group, a hydrogen, and an R group or side chain is attached; the R group is different for all 20 common amino acids
beta-pleated sheet (β-pleated)
secondary structure in proteins in which hydrogen bonding forms “pleats” between atoms on the polypeptide chain’s backbone
chaperone
(also, chaperonin) protein that helps nascent protein in the folding process
denaturation
loss of shape in a protein as a result of changes in temperature, pH, or chemical exposure
enzyme
catalyst in a biochemical reaction that is usually a complex or conjugated protein
hormone
chemical signaling molecule, usually protein or steroid, secreted by endocrine cells that act to control or regulate specific physiological processes
peptide bond
bond formed between two amino acids by a dehydration reaction
polypeptide
long chain of amino acids that peptide bonds link
primary structure
linear sequence of amino acids in a protein
protein
biological macromolecule comprised of one or more amino acid chains
quaternary structure
association of discrete polypeptide subunits in a protein
secondary structure
regular structure that proteins form by intramolecular hydrogen bonding between the oxygen atom of one amino acid residue and the hydrogen attached to the nitrogen atom of another amino acid residue
tertiary structure
a protein’s three-dimensional conformation, including interactions between secondary structural elements; formed from interactions between amino acid side chains

13

Nucleic Acids

Learning Objectives

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

  • Describe nucleic acids’ structure and define the two types of nucleic acids
  • Explain DNA’s structure and role
  • Explain RNA’s structure and roles

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell’s genetic blueprint and carry instructions for its functioning.

DNA and RNA

The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope.

The cell’s entire genetic content is its genome, and the study of genomes is genomics. In eukaryotic cells but not in prokaryotes, DNA forms a complex with histone proteins to form chromatin, the substance of eukaryotic chromosomes. A chromosome may contain tens of thousands of genes. Many genes contain the information to make protein products. Other genes code for RNA products. DNA controls all of the cellular activities by turning the genes “on” or “off.”

The other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules never leave the nucleus but instead use an intermediary to communicate with the rest of the cell. This intermediary is the messenger RNA (mRNA). Other types of RNA—like rRNA, tRNA, and microRNA—are involved in protein synthesis and its regulation.

DNA and RNA are comprised of monomers that scientists call nucleotides. The nucleotides combine with each other to form a polynucleotide, DNA or RNA. Three components comprise each nucleotide: a nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group ((Figure)). Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.

Three components comprise a nucleotide: a nitrogenous base, a pentose sugar, and one or more phosphate groups. Carbon residues in the pentose are numbered 1′ through 5′ (the prime distinguishes these residues from those in the base, which are numbered without using a prime notation). The base is attached to the ribose’s 1′ position, and the phosphate is attached to the 5′ position. When a polynucleotide forms, the incoming nucleotide’s 5′ phosphate attaches to the 3′ hydroxyl group at the end of the growing chain. Two types of pentose are in nucleotides, deoxyribose (found in DNA) and ribose (found in RNA). Deoxyribose is similar in structure to ribose, but it has an H instead of an OH at the 2′ position. We can divide bases into two categories: purines and pyrimidines. Purines have a double ring structure, and pyrimidines have a single ring.


The molecular structure of a nucleotide is shown. The core of the nucleotide is a pentose whose carbon residues are numbered one prime through five prime. The base is attached to the one prime carbon, and the phosphate is attached to the five prime carbon. Two kinds of pentose are found in nucleotides: ribose and deoxyribose. Deoxyribose has an H instead of O H at the two prime position. Five kinds of base are found in nucleotides. Two of these, adenine and guanine, are purine bases with two rings fused together. The other three, cytosine, thymine and uracil, have one six-membered ring.

The nitrogenous bases, important components of nucleotides, are organic molecules and are so named because they contain carbon and nitrogen. They are bases because they contain an amino group that has the potential of binding an extra hydrogen, and thus decreasing the hydrogen ion concentration in its environment, making it more basic. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T).

Scientists classify adenine and guanine as purines. The purine’s primary structure is two carbon-nitrogen rings. Scientists classify cytosine, thymine, and uracil as pyrimidines which have a single carbon-nitrogen ring as their primary structure ((Figure)). Each of these basic carbon-nitrogen rings has different functional groups attached to it. In molecular biology shorthand, we know the nitrogenous bases by their symbols A, T, G, C, and U. DNA contains A, T, G, and C; whereas, RNA contains A, U, G, and C.

The pentose sugar in DNA is deoxyribose, and in RNA, the sugar is ribose ((Figure)). The difference between the sugars is the presence of the hydroxyl group on the ribose’s second carbon and hydrogen on the deoxyribose’s second carbon. The carbon atoms of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”). The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′–3′ phosphodiester linkage. A simple dehydration reaction like the other linkages connecting monomers in macromolecules does not form the phosphodiester linkage. Its formation involves removing two phosphate groups. A polynucleotide may have thousands of such phosphodiester linkages.

DNA Double-Helix Structure

DNA has a double-helix structure ((Figure)). The sugar and phosphate lie on the outside of the helix, forming the DNA’s backbone. The nitrogenous bases are stacked in the interior, like a pair of staircase steps. Hydrogen bonds bind the pairs to each other. Every base pair in the double helix is separated from the next base pair by 0.34 nm. The helix’s two strands run in opposite directions, meaning that the 5′ carbon end of one strand will face the 3′ carbon end of its matching strand. (Scientists call this an antiparallel orientation and is important to DNA replication and in many nucleic acid interactions.)

Native DNA is an antiparallel double helix. The phosphate backbone (indicated by the curvy lines) is on the outside, and the bases are on the inside. Each base from one strand interacts via hydrogen bonding with a base from the opposing strand. (credit: Jerome Walker/Dennis Myts)


The molecular structure of D N A is shown. D N A consists of two antiparallel strands twisted in a double helix. The phosphate backbone is on the outside, and the nitrogenous bases face one another on the inside. The bases appear as strands between the phosphate backbone of the double helix.

Only certain types of base pairing are allowed. For example, a certain purine can only pair with a certain pyrimidine. This means A can pair with T, and G can pair with C, as (Figure) shows. This is the base complementary rule. In other words, the DNA strands are complementary to each other. If the sequence of one strand is AATTGGCC, the complementary strand would have the sequence TTAACCGG. During DNA replication, each strand copies itself, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand.

Visual Connection
In a double stranded DNA molecule, the two strands run antiparallel to one another so that one strand runs 5′ to 3′ and the other 3′ to 5′. The phosphate backbone is located on the outside, and the bases are in the middle. Adenine forms hydrogen bonds (or base pairs) with thymine, and guanine base pairs with cytosine.


Hydrogen bonding between thymine and adenine and between guanine and cytosine is shown. Thymine forms two hydrogen bonds with adenine, and guanine forms three hydrogen bonds with cytosine. The phosphate backbones of each strand are on the outside and run in opposite directions.

A mutation occurs, and adenine replaces cytosine. What impact do you think this will have on the DNA structure?

RNA

Ribonucleic acid, or RNA, is mainly involved in the process of protein synthesis under the direction of DNA. RNA is usually single-stranded and is comprised of ribonucleotides that are linked by phosphodiester bonds. A ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of the four nitrogenous bases (A, U, G, and C), and the phosphate group.

There are four major types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and microRNA (miRNA). The first, mRNA, carries the message from DNA, which controls all of the cellular activities in a cell. If a cell requires synthesizing a certain protein, the gene for this product turns “on” and the messenger RNA synthesizes in the nucleus. The RNA base sequence is complementary to the DNA’s coding sequence from which it has been copied. However, in RNA, the base T is absent and U is present instead. If the DNA strand has a sequence AATTGCGC, the sequence of the complementary RNA is UUAACGCG. In the cytoplasm, the mRNA interacts with ribosomes and other cellular machinery ((Figure)).

A ribosome has two parts: a large subunit and a small subunit. The mRNA sits in between the two subunits. A tRNA molecule recognizes a codon on the mRNA, binds to it by complementary base pairing, and adds the correct amino acid to the growing peptide chain.


An illustration of a ribosome is shown. m R N A sits between the large and small subunits. t R N A molecules bind the ribosome and add amino acids to the growing peptide chain.

The mRNA is read in sets of three bases known as codons. Each codon codes for a single amino acid. In this way, the mRNA is read and the protein product is made. Ribosomal RNA (rRNA) is a major constituent of ribosomes on which the mRNA binds. The rRNA ensures the proper alignment of the mRNA and the Ribosomes. The ribosome’s rRNA also has an enzymatic activity (peptidyl transferase) and catalyzes peptide bond formation between two aligned amino acids. Transfer RNA (tRNA) is one of the smallest of the four types of RNA, usually 70–90 nucleotides long. It carries the correct amino acid to the protein synthesis site. It is the base pairing between the tRNA and mRNA that allows for the correct amino acid to insert itself in the polypeptide chain. MicroRNAs are the smallest RNA molecules and their role involves regulating gene expression by interfering with the expression of certain mRNA messages. (Figure) summarizes DNA and RNA features.

DNA and RNA Features
DNA RNA
Function Carries genetic information Involved in protein synthesis
Location Remains in the nucleus Leaves the nucleus
Structure Double helix Usually single-stranded
Sugar Deoxyribose Ribose
Pyrimidines Cytosine, thymine Cytosine, uracil
Purines Adenine, guanine Adenine, guanine

Even though the RNA is single stranded, most RNA types show extensive intramolecular base pairing between complementary sequences, creating a predictable three-dimensional structure essential for their function.

As you have learned, information flow in an organism takes place from DNA to RNA to protein. DNA dictates the structure of mRNA in a process scientists call transcription, and RNA dictates the protein’s structure in a process scientists call translation. This is the Central Dogma of Life, which holds true for all organisms; however, exceptions to the rule occur in connection with viral infections.

Link to Learning

To learn more about DNA, explore the Howard Hughes Medical Institute BioInteractive animations on the topic of DNA.

Section Summary

Nucleic acids are molecules comprised of nucleotides that direct cellular activities such as cell division and protein synthesis. Pentose sugar, a nitrogenous base, and a phosphate group comprise each nucleotide. There are two types of nucleic acids: DNA and RNA. DNA carries the cell’s genetic blueprint and passes it on from parents to offspring (in the form of chromosomes). It has a double-helical structure with the two strands running in opposite directions, connected by hydrogen bonds, and complementary to each other. RNA is a single-stranded polymer composed of linked nucleotides made up of a pentose sugar (ribose), a nitrogenous base, and a phosphate group. RNA is involved in protein synthesis and its regulation. Messenger RNA (mRNA) copies from the DNA, exports itself from the nucleus to the cytoplasm, and contains information for constructing proteins. Ribosomal RNA (rRNA) is a part of the ribosomes at the site of protein synthesis; whereas, transfer RNA (tRNA) carries the amino acid to the site of protein synthesis. The microRNA regulates using mRNA for protein synthesis.

Visual Connection Questions

(Figure) A mutation occurs, and cytosine is replaced with adenine. What impact do you think this will have on the DNA structure?

(Figure) Adenine is larger than cytosine and will not be able to base pair properly with the guanine on the opposing strand. This will cause the DNA to bulge. DNA repair enzymes may recognize the bulge and replace the incorrect nucleotide.

Review Questions

A nucleotide of DNA may contain ________.

  1. ribose, uracil, and a phosphate group
  2. deoxyribose, uracil, and a phosphate group
  3. deoxyribose, thymine, and a phosphate group
  4. ribose, thymine, and a phosphate group

C

The building blocks of nucleic acids are ________.

  1. sugars
  2. nitrogenous bases
  3. peptides
  4. nucleotides

D

How does the double helix structure of DNA support its role in encoding the genome?

  1. The sugar-phosphate backbone provides a template for DNA replication.
  2. tRNA pairing with the template strand creates proteins encoded by the genome.
  3. Complementary base pairing creates a very stable structure.
  4. Complementary base pairing allows for easy editing of both strands of DNA.

C

Critical Thinking Questions

What are the structural differences between RNA and DNA?

DNA has a double-helix structure. The sugar and the phosphate are on the outside of the helix and the nitrogenous bases are in the interior. The monomers of DNA are nucleotides containing deoxyribose, one of the four nitrogenous bases (A, T, G and C), and a phosphate group. RNA is usually single-stranded and is made of ribonucleotides that are linked by phosphodiester linkages. A ribonucleotide contains ribose (the pentose sugar), one of the four nitrogenous bases (A,U, G, and C), and the phosphate group.

What are the four types of RNA and how do they function?

The four types of RNA are messenger RNA, ribosomal RNA, transfer RNA, and microRNA. Messenger RNA carries the information from the DNA that controls all cellular activities. The mRNA binds to the ribosomes that are constructed of proteins and rRNA, and tRNA transfers the correct amino acid to the site of protein synthesis. microRNA regulates the availability of mRNA for translation.

Glossary

deoxyribonucleic acid (DNA)
double-helical molecule that carries the cell’s hereditary information
messenger RNA (mRNA)
RNA that carries information from DNA to ribosomes during protein synthesis
nucleic acid
biological macromolecule that carries the cell’s genetic blueprint and carries instructions for the cell’s functioning
nucleotide
monomer of nucleic acids; contains a pentose sugar, one or more phosphate groups, and a nitrogenous base
phosphodiester
linkage covalent chemical bond that holds together the polynucleotide chains with a phosphate group linking neighboring nucleotides’ two pentose sugars
polynucleotide
long chain of nucleotides
purine
type of nitrogenous base in DNA and RNA; adenine and guanine are purines
pyrimidine
type of nitrogenous base in DNA and RNA; cytosine, thymine, and uracil are pyrimidines
ribonucleic acid (RNA)
single-stranded, often internally base paired, molecule that is involved in protein synthesis
ribosomal RNA (rRNA)
RNA that ensures the proper alignment of the mRNA and the ribosomes during protein synthesis and catalyzes forming the peptide linkage
transcription
process through which messenger RNA forms on a template of DNA
transfer RNA (tRNA)
RNA that carries activated amino acids to the site of protein synthesis on the ribosome
translation
process through which RNA directs the protein’s formation

IV

Cell Structure

14

Introduction

(a) Nasal sinus cells (viewed with a light microscope), (b) onion cells (viewed with a light microscope), and (c) Vibrio tasmaniensis bacterial cells (seen through a scanning electron microscope) are from very different organisms, yet all share certain basic cell structure characteristics. (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, William H. Fowle, Eric J. Stewart, and Kim Lewis of the Lewis Lab at Northeastern University; scale-bar data from Matt Russell)


Part a: Human cheek 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. Part b: 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 cheek cell, but at least five times as long. The cell wall and nucleus are well defined in the micrograph. The onion cell nucleus is about the same size as the cheek cell nucleus. Part c: 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.

Close your eyes and picture a brick wall. What is the wall’s basic building block? It is a single brick. Like a brick wall, cells are the building blocks that make up your body.

Your body has many kinds of cells, each specialized for a specific purpose. Just as we use a variety of materials to build a home, the human body is constructed from many cell types. For example, epithelial cells protect the body’s surface and cover the organs and body cavities within. Bone cells help to support and protect the body. Immune system cells fight invading bacteria. Additionally, blood and blood cells carry nutrients and oxygen throughout the body while removing carbon dioxide. Each of these cell types plays a vital role during the body’s growth, development, and day-to-day maintenance. In spite of their enormous variety, however, cells from all organisms—even ones as diverse as bacteria, onion, and human—share certain fundamental characteristics.

15

Studying Cells

Learning Objectives

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

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

A cell is the smallest unit of a living thing. Whether comprised of one cell (like bacteria) or many cells (like a human), we call it an organism. Thus, cells are the basic building blocks of all organisms.

Several cells of one kind that interconnect with each other and perform a shared function form tissues. These tissues combine to form an organ (your stomach, heart, or brain), and several organs comprise an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being). Here, we will examine the structure and function of cells.

There are many types of cells, which scientists group into one of two broad categories: prokaryotic and eukaryotic. For example, we classify both animal and plant cells as eukaryotic cells; whereas, we classify bacterial cells as prokaryotic. Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, we will first examine how biologists study cells.

Microscopy

Cells vary in size. With few exceptions, we cannot see individual cells with the naked eye, so scientists use microscopes (micro- = “small”; -scope = “to look at”) to study them. A microscope is an instrument that magnifies an object. We photograph most cells with a microscope, so we can call these images micrographs.

The optics of a microscope’s lenses change the image orientation that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when one views through a microscope, and vice versa. Similarly, if one moves the slide left while looking through the microscope, it will appear to move right, and if one moves it down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image. Because of the manner by which light travels through the lenses, this two lens system produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright).

Light Microscopes

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

Most student microscopes are light microscopes ((Figure)a). Visible light passes and bends through 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 that undergraduates commonly use in the laboratory magnify up to approximately 400 times. Two parameters that are important in microscopy are magnification and resolving power. Magnification is the process of enlarging an object in appearance. Resolving power is the microscope’s ability to distinguish two adjacent structures as separate: the higher the resolution, the better the image’s clarity and detail. When one uses oil immersion lenses to study small objects, magnification usually increases to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes.

(a) Most light microscopes in a college biology lab can magnify cells up to approximately 400 times and have a resolution of about 200 nanometers. (b) Electron microscopes provide a much higher magnification, 100,000x, and a have a resolution of 50 picometers. (credit a: modification of work by “GcG”/Wikimedia Commons; credit b: modification of work by Evan Bench)


Part a: This light microscope has binocular lenses and four objective lenses. The sample stage is directly beneath the objective lens. The light microscope sits on a tabletop and can be easily carried. Part b: The electron microscope shown here sits in a museum. It is about the size of a desk, and a person can sit in front of it to operate it. A column taller than a person rises from the center of the scope.

Electron Microscopes

In contrast to light microscopes, electron microscopes ((Figure)b) use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail ((Figure)), it also provides higher resolving power. The method to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so we cannot view living cells with an electron microscope.

In a scanning electron microscope, a beam of electrons moves back and forth across a cell’s surface, creating details of cell surface characteristics. In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell’s internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes.

(a) These Salmonella bacteria appear as tiny purple dots when viewed with a light microscope. (b) This scanning electron microscope micrograph shows Salmonella bacteria (in red) invading human cells (yellow). Even though subfigure (b) shows a different Salmonella specimen than subfigure (a), you can still observe the comparative increase in magnification and detail. (credit a: modification of work by CDC/Armed Forces Institute of Pathology, Charles N. Farmer, Rocky Mountain Laboratories; credit b: modification of work by NIAID, NIH; scale-bar data from Matt Russell)


Part a: Salmonella through a light microscope appear as tiny purple dots. Part b: In this scanning electron micrograph, bacteria appear as three-dimensional ovals. The human cells are much larger with a complex, folded appearance. Some of the bacteria lie on the surface of the human cells, and some are squeezed between them.

Link to Learning

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

Cell Theory

The microscopes we use today are far more complex than those that Dutch shopkeeper Antony van Leeuwenhoek, used in the 1600s. Skilled in crafting lenses, van Leeuwenhoek observed the movements of single-celled organisms, which he collectively termed “animalcules.”

In the 1665 publication Micrographia, experimental scientist Robert Hooke coined the term “cell” 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, microscope construction, and staining techniques enabled other scientists to see some 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 one or more cells comprise all living things, the cell is the basic unit of life, and new cells arise from existing cells. Rudolf Virchow later made important contributions to this theory.

Career Connection

CytotechnologistHave you ever heard of a medical test called a Pap smear ((Figure))? In this test, a doctor takes a small sample of cells from the patient’s uterine cervix 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 via microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits and which 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, a medical doctor who interprets and diagnoses changes that disease in body tissue and fluids cause.

Cytotechnologists play a vital role in saving people’s lives. When doctors discover abnormalities early, a patient’s treatment can begin sooner, which usually increases the chances of a successful outcome.

These uterine cervix cells, viewed through a light microscope, are from a Pap smear. Normal cells are on the left. The cells on the right are infected with human papillomavirus (HPV). Notice that the infected cells are larger. Also, two of these cells each have two nuclei instead of one, the normal number. (credit: modification of work by Ed Uthman, MD; scale-bar data from Matt Russell)


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

Section Summary

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

Review Questions

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

  1. a beam of electrons
  2. radioactive isotopes
  3. special stains
  4. high temperatures

C

The ________ is the basic unit of life.

  1. organism
  2. cell
  3. tissue
  4. organ

B

Critical Thinking Questions

In your everyday life, you have probably noticed that certain instruments are ideal for certain situations. For example, you would use a spoon rather than a fork to eat soup because a spoon is shaped for scooping, while soup would slip between the tines of a fork. The use of ideal instruments also applies in science. In what situation(s) would the use of a light microscope be ideal, and why?

A light microscope would be ideal when viewing a small living organism, especially when the cell has been stained to reveal details.

In what situation(s) would the use of a scanning electron microscope be ideal, and why?

A scanning electron microscope would be ideal when you want to view the minute details of a cell’s surface, because its beam of electrons moves back and forth over the surface to convey the image.

In what situation(s) would a transmission electron microscope be ideal, and why?

A transmission electron microscope would be ideal for viewing the cell’s internal structures, because many of the internal structures have membranes that are not visible by the light microscope.

What are the advantages and disadvantages of each of these types of 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 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.

Explain how the formation of an adult human follows the cell theory.

The cell theory states:

  1. All living things are made of cells.;
  2. Cells are the most basic unit of life.;
  3. New cells arise from existing cells.

All humans are multicellular organisms whose smallest building blocks are cells. Adult humans begin with the fusion of a male gamete cell with a female gamete cell to form a fertilized egg (single cell). That cell then divides into two cells, which each divides into two more cells, and so forth until all the cells of a human embryo are made. As the embryo passes through all the developmental stages to make an adult human, the cells that are added arise from division of existing cells.

Glossary

cell theory
see unified cell theory
electron microscope
an instrument that magnifies an object using an electron beam that passes and bends through a lens system to visualize a specimen
light microscope
an instrument that magnifies an object using a beam of visible light that passes and bends through a lens system to visualize a specimen
microscope
an instrument that magnifies an object
unified cell theory
a biological concept that states that one or more cells comprise all organisms; the cell is the basic unit of life; and new cells arise from existing cells

16

Prokaryotic Cells

Learning Objectives

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

  • Name examples of prokaryotic and eukaryotic organisms
  • Compare and contrast prokaryotic and eukaryotic cells
  • Describe the relative sizes of different cells
  • Explain why cells must be small

Cells fall into one of two broad categories: prokaryotic and eukaryotic. We classify only the predominantly single-celled organisms Bacteria and Archaea as prokaryotes (pro- = “before”; -kary- = “nucleus”). Animal cells, plants, fungi, and protists are all 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 cytosol within the cell in which there are other cellular components; 3) DNA, the cell’s genetic material; and 4) ribosomes, which synthesize proteins. However, prokaryotes differ from eukaryotic cells in several ways.

A prokaryote is a simple, mostly 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 in the cell’s central part: the nucleoid ((Figure)).

This figure shows the generalized structure of a prokaryotic cell. All prokaryotes have chromosomal DNA localized in a nucleoid, ribosomes, a cell membrane, and a cell wall. The other structures shown are present in some, but not all, bacteria.


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 by 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 project from the capsule in all directions.

Most prokaryotes have a peptidoglycan cell wall and many have a polysaccharide capsule ((Figure)). 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. Pili exchange genetic material during conjugation, the process by which one bacterium transfers genetic material to another through direct contact. Bacteria use fimbriae to attach to a host cell.

Career Connection

MicrobiologistThe most effective action anyone can take to prevent the spread of contagious illnesses is to wash his or her hands. Why? Because microbes (organisms so tiny that they can only be seen with microscopes) are ubiquitous. They live on doorknobs, money, your hands, and many other surfaces. If someone sneezes into his hand and touches a doorknob, and afterwards you touch that same doorknob, the microbes from the sneezer’s mucus are now on your hands. If you touch your hands to your mouth, nose, or eyes, those microbes can enter your body and could make you sick.

However, not all microbes (also called microorganisms) cause disease; most are actually beneficial. You have microbes in your gut that make vitamin K. Other microorganisms are used to ferment beer and wine.

Microbiologists are scientists who study microbes. Microbiologists can pursue a number of careers. Not only do they work in the food industry, they are also employed in the veterinary and medical fields. They can work in the pharmaceutical sector, serving key roles in research and development by identifying new antibiotic sources that can treat bacterial infections.

Environmental microbiologists may look for new ways to use specially selected or genetically engineered microbes to remove pollutants from soil or groundwater, as well as hazardous elements from contaminated sites. We call using these microbes bioremediation technologies. Microbiologists can also work in the bioinformatics field, providing specialized knowledge and insight for designing, developing, and specificity of computer models of, for example, bacterial epidemics.

Cell Size

At 0.1 to 5.0 μm in diameter, prokaryotic cells are significantly smaller than eukaryotic cells, which have diameters ranging from 10 to 100 μm ((Figure)). The prokaryotes’ small size allows ions and organic molecules that enter them to quickly diffuse to other parts of the cell. Similarly, any wastes produced within a prokaryotic cell can quickly diffuse. This is not the case in eukaryotic cells, which have developed different structural adaptations to enhance intracellular transport.

This figure shows relative sizes of microbes on a logarithmic scale (recall that each unit of increase in a logarithmic scale represents a 10-fold increase in the quantity measured).


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

Small size, in general, is necessary for all cells, whether prokaryotic or eukaryotic. Let’s examine why that is so. First, we’ll consider the area and volume of a typical cell. Not all cells are spherical in shape, but most tend to approximate a sphere. You may remember from your high school geometry course that the formula for the surface area of a sphere is 4πr2, while the formula for its volume is 4πr3/3. Thus, as the radius of a cell increases, its surface area increases as the square of its radius, but its volume increases as the cube of its radius (much more rapidly). Therefore, as a cell increases in size, its surface area-to-volume ratio decreases. This same principle would apply if the cell had a cube shape ((Figure)). If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume. In other words, as a cell grows, it becomes less efficient. One way to become more efficient is to divide. Another way is to develop organelles that perform specific tasks. These adaptations lead to developing more sophisticated cells, which we call eukaryotic cells.

Visual Connection
Notice that as a cell increases in size, its surface area-to-volume ratio decreases. When there is insufficient surface area to support a cell’s increasing volume, a cell will either divide or die. The cell on the left has a volume of 1 mm3 and a surface area of 6 mm2, with a surface area-to-volume ratio of 6 to 1; whereas, the cell on the right has a volume of 8 mm3 and a surface area of 24 mm2, with a surface area-to-volume ratio of 3 to 1.


On the left, a sphere 1 mm in diameter is encased in a box of the same width. On the right, the same sphere is encased in a box 2 mm in diameter.

Prokaryotic cells are much smaller than eukaryotic cells. What advantages might small cell size confer on a cell? What advantages might large cell size have?

Section Summary

Prokaryotes are single-celled organisms of the domains Bacteria and Archaea. All prokaryotes have plasma membranes, cytoplasm, ribosomes, and DNA that is not membrane-bound. Most have peptidoglycan cell walls and many have polysaccharide capsules. Prokaryotic cells range in diameter from 0.1 to 5.0 μm.

As a cell increases in size, its surface area-to-volume ratio decreases. If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume.

Visual Connection Questions

(Figure) Prokaryotic cells are much smaller than eukaryotic cells. What advantages might small cell size confer on a cell? What advantages might large cell size have?

(Figure) Substances can diffuse more quickly through small cells. Small cells have no need for organelles and therefore do not need to expend energy getting substances across organelle membranes. Large cells have organelles that can separate cellular processes, enabling them to build molecules that are more complex.

Review Questions

Prokaryotes depend on ________ to obtain some materials and to get rid of wastes.

  1. ribosomes
  2. flagella
  3. cell division
  4. diffusion

D

Bacteria that lack fimbriae are less likely to ________.

  1. adhere to cell surfaces
  2. swim through bodily fluids
  3. synthesize proteins
  4. retain the ability to divide

A

Which of the following organisms is a prokaryote?

  1. amoeba
  2. influenza A virus
  3. charophyte algae
  4. E. coli

D

Critical Thinking Questions

Antibiotics are medicines that are used to fight bacterial infections. These medicines kill prokaryotic cells without harming human cells. What part or parts of the bacterial cell do you think antibiotics target? Why?

The cell wall would be targeted by antibiotics as well as the bacteria’s ability to replicate. This would inhibit the bacteria’s ability to reproduce, and it would compromise its defense mechanisms.

Explain why not all microbes are harmful.

Some microbes are beneficial. For instance, E. coli bacteria populate the human gut and help break down fiber in the diet. Some foods such as yogurt are formed by bacteria.

Glossary

nucleoid
central part of a prokaryotic cell’s central part where the chromosome is located
prokaryote
unicellular organism that lacks a nucleus or any other membrane-bound organelle

17

Eukaryotic Cells

Learning Objectives

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

  • Describe the structure of eukaryotic cells
  • Compare animal cells with plant cells
  • State the role of the plasma membrane
  • Summarize the functions of the major cell organelles

Have you ever heard the phrase “form follows function?” It’s a philosophy that many industries follow. In architecture, this means that buildings should be constructed to support the activities that will be carried out inside them. For example, a skyscraper should include several elevator banks. A hospital should have its emergency room easily accessible.

Our natural world also utilizes the principle of form following function, especially in cell biology, and this will become clear as we explore eukaryotic cells ((Figure)). Unlike prokaryotic cells, eukaryotic cells have: 1) a membrane-bound nucleus; 2) numerous membrane-bound organelles such as the endoplasmic reticulum, Golgi apparatus, chloroplasts, mitochondria, and others; and 3) several, rod-shaped chromosomes. Because a membrane surrounds eukaryotic cell’s nucleus, it has a “true nucleus.” The word “organelle” means “little organ,” and, as we already mentioned, organelles have specialized cellular functions, just as your body’s organs have specialized functions.

At this point, it should be clear to you that eukaryotic cells have a more complex structure than prokaryotic cells. Organelles allow different functions to be compartmentalized in different areas of the cell. Before turning to organelles, let’s first examine two important components of the cell: the plasma membrane and the cytoplasm.

Visual Connection
These figures show the major organelles and other cell components of (a) a typical animal cell and (b) a typical eukaryotic plant cell. The plant cell has a cell wall, chloroplasts, plastids, and a central vacuole—structures not in animal cells. Most cells do not have lysosomes or centrosomes.

Part a: This illustration shows a typical eukaryotic animal 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 the width of the cell. Inside the nucleus is the chromatin, which is composed of DNA and associated proteins. A region of the chromatin is condensed into the nucleolus, a structure where 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. In addition to 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 food 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.

Part b: This illustration depicts a typical eukaryotic plant cell. The nucleus of a plant cell contains chromatin and a nucleolus, the same as an animal cell. Other structures that the plant cell has in common with the animal cell include rough and smooth endoplasmic reticulum, the Golgi apparatus, mitochondria, peroxisomes, and ribosomes. The fluid inside the plant cell is called the cytoplasm, just as it is 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. Plant cells have four structures not found in animals cells: chloroplasts, plastids, a central vacuole, and a cell wall. 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 outside the cell membrane.

If the nucleolus were not able to carry out its function, what other cellular organelles would be affected?

The Plasma Membrane

Like prokaryotes, eukaryotic cells have a plasma membrane ((Figure)), a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment. A phospholipid is a lipid molecule with two fatty acid chains and a phosphate-containing group. The plasma membrane controls the passage of organic molecules, ions, water, and oxygen into and out of the cell. Wastes (such as carbon dioxide and ammonia) also leave the cell by passing through the plasma membrane.

The eukaryotic plasma membrane is a phospholipid bilayer with proteins and cholesterol embedded in it.


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 phospholipid 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.

The plasma membranes of cells that specialize in absorption fold into fingerlike projections that we call microvilli (singular = microvillus); ((Figure)). Such cells typically line the small intestine, the organ that absorbs nutrients from digested food. This is an excellent example of form following function.
People with celiac disease have an immune response to gluten, which is a protein 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.

Microvilli, as they appear on cells lining the small intestine, increase the surface area available for absorption. These microvilli are only on the area of the plasma membrane that faces the cavity from which substances will be absorbed. (credit “micrograph”: modification of work by Louisa Howard)


The left part of this figure is a transmission electron micrograph of microvilli, which appear as long, slender stalks extending from the plasma membrane. The right side illustrates cells containing microvilli. The microvilli cover the surface of the cell facing the interior of the small intestine.

The Cytoplasm

The cytoplasm is the cell’s entire region between the plasma membrane and the nuclear envelope (a structure we will discuss shortly). It is comprised of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals ((Figure)). 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 in the cytoplasm. Glucose and other simple sugars, polysaccharides, amino acids, nucleic acids, fatty acids, and derivatives of glycerol are also there. Ions of sodium, potassium, calcium, and many other elements also dissolve in the cytoplasm. Many metabolic reactions, including protein synthesis, take place in the cytoplasm.

The Nucleus

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

The nucleus stores chromatin (DNA plus proteins) in a gel-like substance called the nucleoplasm. The nucleolus is a condensed chromatin region where ribosome synthesis occurs. We call the nucleus’ boundary the nuclear envelope. It consists of two phospholipid bilayers: an outer and an inner membrane. The nuclear membrane is continuous with the endoplasmic reticulum. Nuclear pores allow substances to enter and exit the nucleus.


The two-dimensional image depicts the nucleus of a cell as a circular object with two membranes; several gaps appear in the circle, representing nuclear pores. Surrounding the nucleus are membranous sacks representing the endoplasmic reticulum. Inside the nucleus is another circle, approximately ten percent of the total size of the nucleus, representing the nucleolus.

The Nuclear Envelope

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

The nuclear envelope is punctuated with pores that control the passage of ions, molecules, and RNA between the nucleoplasm and cytoplasm. The nucleoplasm is the semi-solid fluid inside the nucleus, where we find the chromatin and the nucleolus.

Chromatin and Chromosomes

To understand chromatin, it is helpful to first explore chromosomes, structures within the nucleus that are made up of DNA, the hereditary material. You may remember that in prokaryotes, DNA is organized into a single circular chromosome. In eukaryotes, chromosomes are linear structures. Every eukaryotic species has a specific number of chromosomes in the nucleus of each cell. For example, in humans, the chromosome number is 46, while in fruit flies, it 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, proteins attach to chromosomes, and they resemble an unwound, jumbled bunch of threads. We call these unwound protein-chromosome complexes chromatin ((Figure)). Chromatin describes the material that makes up the chromosomes both when condensed and decondensed.

(a) This image shows various levels of chromatin’s organization (DNA and protein). (b) This image shows paired chromosomes. (credit b: modification of work by NIH; scale-bar data from Matt Russell)


Part a: In this illustration, DNA tightly coiled into two thick cylinders is shown in the upper right. A close-up shows how the DNA is coiled around proteins called histones. Part b: This image shows paired chromosomes. The chromosomes are shown as a collection of slender tubes.

The Nucleolus

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 staining 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 out through the pores in the nuclear envelope to the cytoplasm.

Ribosomes

Ribosomes are the cellular structures responsible for protein synthesis. When we view them through an electron microscope, ribosomes appear either as clusters (polyribosomes) or single, tiny dots that float freely in the cytoplasm. They may be attached to the plasma membrane’s cytoplasmic side or the endoplasmic reticulum’s cytoplasmic side and the nuclear envelope’s outer membrane ((Figure)). Electron microscopy shows us that ribosomes, which are large protein and RNA complexes, consist of two subunits, large and small ((Figure)). Ribosomes receive their “orders” for protein synthesis from the nucleus where the DNA transcribes into messenger RNA (mRNA). The mRNA travels to the ribosomes, which translate the code provided by the sequence of the nitrogenous bases in the mRNA into a specific order of amino acids in a protein. Amino acids are the building blocks of proteins.

A large subunit (top) and a small subunit (bottom) comprise ribosomes. During protein synthesis, ribosomes assemble amino acids into proteins.


The ribosome consists of a small subunit and a large subunit, which is about three times as big as the small one. The large subunit sits on top of the small one. A chain of m R N A threads between the large and small subunits. A protein chain extends from the top of the large subunit.

Because protein synthesis is an essential function of all cells (including enzymes, hormones, antibodies, pigments, structural components, and surface receptors), there are ribosomes in practically every cell. Ribosomes are particularly abundant in cells that synthesize large amounts of protein. For example, the pancreas is responsible for creating several digestive enzymes and the cells that produce these enzymes contain many ribosomes. Thus, we see another example of form following function.

Mitochondria

Scientists often call mitochondria (singular = mitochondrion) the cell’s “powerhouses” or “energy factories” because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. ATP represents the cell’s short-term stored energy. Cellular respiration is the process of making ATP using the chemical energy in glucose and other nutrients. In mitochondria, this process uses oxygen and produces carbon dioxide as a waste product. In fact, the carbon dioxide that you exhale with every breath comes from the cellular reactions that produce carbon dioxide as a byproduct.

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 that produce ATP. Your muscle cells need considerable energy to keep your body moving. When your cells don’t get enough oxygen, they do not make much ATP. Instead, producing lactic acid accompanies the small amount of ATP they make in the absence of oxygen.

Mitochondria are oval-shaped, double membrane organelles ((Figure)) that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner layer has folds called cristae. We call the area surrounded by the folds the mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration.

This electron micrograph shows a mitochondrion through an electron microscope. This organelle has an outer membrane and an inner membrane. The inner membrane contains folds, called cristae, which increase its surface area. We call the space between the two membranes the intermembrane space, and the space inside the inner membrane the mitochondrial matrix. ATP synthesis takes place on the inner membrane. (credit: modification of work by Matthew Britton; scale-bar data from Matt Russell)


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

Peroxisomes

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. (Many of these oxidation reactions release hydrogen peroxide, H2O2, which would be damaging to cells; however, when these reactions are confined to peroxisomes, enzymes safely break down the H2O2 into oxygen and water.) For example, peroxisomes in liver cells detoxify alcohol. Glyoxysomes, which are specialized peroxisomes in plants, are responsible for converting stored fats into sugars. Plant cells contain many different types of peroxisomes that play a role in metabolism, pathogene defense, and stress response, to mention a few.

Vesicles and Vacuoles

Vesicles and vacuoles are membrane-bound sacs that function in storage and transport. Other than the fact that vacuoles are somewhat larger than vesicles, there is a very subtle distinction between them. Vesicle membranes can fuse with either the plasma membrane or other membrane systems within the cell. Additionally, some agents such as enzymes within plant vacuoles break down macromolecules. The vacuole’s membrane does not fuse with the membranes of other cellular components.

Animal Cells versus Plant Cells

At this point, you know that each eukaryotic cell has a plasma membrane, cytoplasm, a nucleus, ribosomes, mitochondria, peroxisomes, and in some, vacuoles, but there are some striking differences between animal and plant cells. While both animal and plant cells have microtubule organizing centers (MTOCs), animal cells also have centrioles associated with the MTOC: a complex we call the centrosome. Animal cells each have a centrosome and lysosomes; whereas, most plant cells do not. Plant cells have a cell wall, chloroplasts and other specialized plastids, and a large central vacuole; whereas, animal cells do not.

The Centrosome

The centrosome is a microtubule-organizing center found near the nuclei of animal cells. It contains a pair of centrioles, two structures that lie perpendicular to each other ((Figure)). Each centriole is a cylinder of nine triplets of microtubules.

The centrosome consists of two centrioles that lie at right angles to each other. Each centriole is a cylinder comprised of nine triplets of microtubules. Nontubulin proteins (indicated by the green lines) hold the microtubule triplets together.


The image depicts two tube-like structures, one on top of the other, at right angles. Each of the tubes is labeled as the centriole. Each tube is composed of smaller tubes grouped in threes; these are labeled 'microtubule triplet.' Each centriole tube is composed of nine triplets arranged to form the wall of the tube.

The centrosome (the organelle where all microtubules originate) replicates itself before a cell divides, and the centrioles appear to have some role in pulling the duplicated chromosomes to opposite ends of the dividing cell. However, the centriole’s exact function in cell division isn’t clear, because cells that have had the centrosome removed can still divide, and plant cells, which lack centrosomes, are capable of cell division.

Lysosomes

Animal cells have another set of organelles that most plant cells do not: lysosomes. The lysosomes are the cell’s “garbage disposal.” In plant cells, the digestive processes take place in vacuoles. Enzymes within the lysosomes aid in breaking down proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles. These enzymes are active at a much lower pH than the cytoplasm’s. Therefore, the pH within lysosomes is more acidic than the cytoplasm’s pH. Many reactions that take place in the cytoplasm could not occur at a low pH, so again, the advantage of compartmentalizing the eukaryotic cell into organelles is apparent.

The Cell Wall

If you examine (Figure), the plant cell diagram, you will see a structure external to the plasma membrane. This is the cell wall, a rigid covering that protects the cell, provides structural support, and gives shape to the cell. Fungal and some protistan cells also have cell walls. While the prokaryotic cell walls’ chief component is peptidoglycan, the major organic molecule in the plant (and some protists’) cell wall is cellulose ((Figure)), a polysaccharide comprised of glucose units. Have you ever noticed that when you bite into a raw vegetable, like celery, it crunches? That’s because you are tearing the celery cells’ rigid cell walls with your teeth.

Cellulose is a long chain of β-glucose molecules connected by a 1-4 linkage. The dashed lines at each end of the figure indicate a series of many more glucose units. The size of the page makes it impossible to portray an entire cellulose molecule.


This illustration shows three glucose subunits that are attached together. Dashed lines at each end indicate that many more subunits make up an entire cellulose fiber. Each glucose subunit is a closed ring composed of carbon, hydrogen, and oxygen atoms.

Chloroplasts

Like the mitochondria, chloroplasts have their own DNA and ribosomes, but chloroplasts have an entirely different function. Chloroplasts are plant cell organelles that carry out photosynthesis. Photosynthesis is the series of reactions that use carbon dioxide, water, and light energy to make glucose and oxygen. This is a major difference between plants and animals. Plants (autotrophs) are able to make their own food, like sugars, while animals (heterotrophs) must ingest their food.

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 we call thylakoids ((Figure)). Each thylakoid stack is a granum (plural = grana). We call the fluid enclosed by the inner membrane that surrounds the grana the stroma.

The chloroplast has an outer membrane, an inner membrane, and membrane structures – thylakoids that are stacked into grana. We call the space inside the thylakoid membranes the thylakoid space. The light harvesting reactions take place in the thylakoid membranes, and sugar synthesis takes place in the fluid inside the inner membrane, which we call the stroma. Chloroplasts also have their own genome, which is contained on a single circular chromosome.


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 thylakoids is called the thylakoid space.

The chloroplasts contain a green pigment, chlorophyll, which captures the light energy that drives the reactions of photosynthesis. Like plant cells, photosynthetic protists also have chloroplasts. Some bacteria perform photosynthesis, but their chlorophyll is not relegated to an organelle.

Evolution Connection

EndosymbiosisWe 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 depend on each other for their survival. Endosymbiosis (endo- = “within”) is a mutually beneficial relationship in which one organism lives inside the other. Endosymbiotic relationships abound in nature. We have already mentioned that 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 from drying out, and they receive abundant food from the environment of the large intestine.

Scientists have long noticed that bacteria, mitochondria, and chloroplasts are similar in size. We also know that bacteria have DNA and ribosomes, just like mitochondria and chloroplasts. Scientists believe that host cells and bacteria formed an endosymbiotic relationship when the host cells ingested both aerobic and autotrophic bacteria (cyanobacteria) but did not destroy them. Through many millions of years of evolution, these ingested bacteria became more specialized in their functions, with the aerobic bacteria becoming mitochondria and the autotrophic bacteria becoming chloroplasts.

The Central Vacuole

Previously, we mentioned vacuoles as essential components of plant cells. If you look at (Figure)b, you will see that plant cells each have a large central vacuole that occupies most of the cell’s area. The central vacuole plays a key role in regulating the cell’s concentration of water in changing environmental conditions. Have you ever noticed that if you forget to water a plant for a few days, it wilts? That’s 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. As the central vacuole shrinks, it leaves the cell wall unsupported. This loss of support to the plant’s cell walls results in the wilted appearance.

The central vacuole also supports the cell’s expansion. When the central vacuole holds more water, the cell becomes larger without having to invest considerable energy in synthesizing new cytoplasm.

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 a membrane surrounds its DNA), and has other membrane-bound organelles that allow for compartmentalizing functions. The plasma membrane is a phospholipid bilayer embedded with proteins. The nucleus’s nucleolus is the site of ribosome assembly. We find ribosomes either in the cytoplasm or attached to the cytoplasmic side of the plasma membrane or endoplasmic reticulum. They perform protein synthesis. Mitochondria participate in cellular respiration. They are responsible for the majority of ATP produced in the cell. Peroxisomes hydrolyze 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 perpendicular to each other, the centrioles, and has an unknown purpose in cell division. Lysosomes are the digestive organelles of animal cells.

Plant cells and plant-like cells each 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 the cell shape. Photosynthesis takes place in chloroplasts. The central vacuole can expand without having to produce more cytoplasm.

Visual Connection Questions

(Figure) If the nucleolus were not able to carry out its function, what other cellular organelles would be affected?

(Figure) Free ribosomes and rough endoplasmic reticulum (which contains ribosomes) would not be able to form.

Review Questions

Which of the following is surrounded by two phospholipid bilayers?

  1. the ribosomes
  2. the vesicles
  3. the cytoplasm
  4. the nucleoplasm

D

Peroxisomes got their name because hydrogen peroxide is:

  1. used in their detoxification reactions
  2. produced during their oxidation reactions
  3. incorporated into their membranes
  4. a cofactor for the organelles’ enzymes

B

In plant cells, the function of the lysosomes is carried out by __________.

  1. vacuoles
  2. peroxisomes
  3. ribosomes
  4. nuclei

A

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

  1. nucleus
  2. mitochondrion
  3. vacuole
  4. ribosomes

D

Tay-Sachs disease is a genetic disorder that results in the destruction of neurons due to a buildup of sphingolipids in the cells. Which organelle is malfunctioning in Tay-Sachs?

  1. lysosome
  2. endoplasmic reticulum
  3. peroxisome
  4. mitochondria

A

Critical Thinking Questions

You already know that ribosomes are abundant in red blood cells. In what other cells of the body would you find them in great abundance? Why?

Ribosomes are abundant in muscle cells as well because muscle cells are constructed of the proteins made by the ribosomes.

What are the structural and functional similarities and differences between mitochondria and chloroplasts?

Both are similar in that they are enveloped in a double membrane, both have an intermembrane space, and both make ATP. Both mitochondria and chloroplasts have DNA, and mitochondria have inner folds called cristae and a matrix, while chloroplasts have chlorophyll and accessory pigments in the thylakoids that form stacks (grana) and a stroma.

Why are plasma membranes arranged as a bilayer rather than a monolayer?

The plasma membrane is a bilayer because the phospholipids that create it are amphiphilic (hydrophilic head, hydrophobic tail). If the plasma membrane was a monolayer, the hydrophobic tails of the phospholipids would be in direct contact with the inside of the cell. Since the cytoplasm is largely made of water, this interaction would not be stable, and would disrupt the plasma membrane of the cell as the tails were repulsed by the cytoplasm (in water, phospholipids spontaneously form spherical droplets with the hydrophilic heads facing outward to isolate the hydrophobic tails from the water). By having a bilayer, the hydrophilic heads are exposed to the aqueous cytoplasm and extracellular space, while the hydrophobic tails interact with each other in the middle of the membrane.

Glossary

cell wall
rigid cell covering comprised of various molecules that protects the cell, provides structural support, and gives shape to the cell
central vacuole
large plant cell organelle that regulates the cell’s storage compartment, holds water, and plays a significant role in cell growth as the site of macromolecule degradation
centrosome
region in animal cells made of two centrioles that serves as an organizing center for microtubules
chlorophyll
green pigment that captures the light energy that drives the light reactions of photosynthesis
chloroplast
plant cell organelle that carries out photosynthesis
chromatin
protein-DNA complex that serves as the chromosomes’ building material
chromosome
structure within the nucleus that comprises chromatin that contains DNA, the hereditary material
cytoplasm
entire region between the plasma membrane and the nuclear envelope, consisting of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals
cytosol
the cytoplasm’s gel-like material in which cell structures are suspended
eukaryotic cell
cell that has a membrane-bound nucleus and several other membrane-bound compartments or sacs
lysosome
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) cellular organelles responsible for carrying out cellular respiration, resulting in producing ATP, the cell’s main energy-carrying molecule
nuclear envelope
double-membrane structure that constitutes the nucleus’ outermost portion
nucleolus
darkly staining body within the nucleus that is responsible for assembling ribosome subunits
nucleoplasm
semi-solid fluid inside the nucleus that contains the chromatin and nucleolus
nucleus
cell organelle that houses the cell’s DNA and directs ribosome and protein synthesis
organelle
compartment or sac within a cell
peroxisome
small, round organelle that contains hydrogen peroxide, oxidizes fatty acids and amino acids, and detoxifies many poisons
plasma membrane
phospholipid bilayer with embedded (integral) or attached (peripheral) proteins, and separates the cell’s internal content from its surrounding environment
ribosome
cellular structure that carries out protein synthesis
vacuole
membrane-bound sac, somewhat larger than a vesicle, which functions in cellular storage and transport
vesicle
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

18

The Endomembrane System and Proteins

Learning Objectives

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

  • List the components of the endomembrane system
  • Recognize the relationship between the endomembrane system and its functions

The endomembrane system (endo = “within”) is a group of membranes and organelles ((Figure)) in eukaryotic cells that works together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, and vesicles, which we have already mentioned, and the endoplasmic reticulum and 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 endomembrane system does not include either mitochondria or chloroplast membranes.

Visual Connection
Membrane and secretory proteins are synthesized in the rough endoplasmic reticulum (RER). The RER also sometimes modifies proteins. In this illustration, an attachment of a (purple) carbohydrate modifies a (green) integral membrane protein in the ER. Vesicles with the integral protein bud from the ER and fuse with the Golgi apparatus’ cis face. As the protein passes along the Golgi’s cisternae, the addition of more carbohydrates further modifies it. After its synthesis is complete, it exits as an integral membrane protein of the vesicle that buds from the Golgi’s trans face. When the vesicle fuses with the cell membrane, the protein becomes an integral portion of that cell membrane. (credit: modification of work by Magnus Manske)


The left part of this figure shows the rough E R with an integral membrane protein embedded in it. The part of the protein facing the inside of the E R has a carbohydrate attached to it. The protein is shown leaving the E R in a vesicle that fuses with the cis side 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 now faces the outside of the membrane. At the same time, the contents of the vesicle are ejected from the cell.

If a peripheral membrane protein were synthesized in the lumen (inside) of the ER, would it end up on the inside or outside of the plasma membrane?

The Endoplasmic Reticulum

The endoplasmic reticulum (ER) ((Figure)) is a series of interconnected membranous sacs and tubules that collectively modifies proteins and synthesizes lipids. However, these two functions take place in separate areas of the ER: the rough ER and the smooth ER, respectively.

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

Rough ER

Scientists have named the rough endoplasmic reticulum (RER) as such because the ribosomes attached to its cytoplasmic surface give it a studded appearance when viewing it through an electron microscope ((Figure)).

This transmission electron micrograph shows the rough endoplasmic reticulum and other organelles in a pancreatic cell. (credit: modification of work by Louisa Howard)


In this transmission electron micrograph, the nucleus is the most prominent feature. The nucleolus is a circular, dark region inside the nucleus. A nuclear pore can be seen in the nuclear envelope that surrounds the nucleus. The rough endoplasmic reticulum surrounds the nucleus, appearing as many layers of membranes. A mitochondrion sits between the layers of the E R membrane.

Ribosomes transfer their newly synthesized proteins into the RER’s lumen where they undergo structural modifications, such as folding or acquiring side chains. These modified proteins incorporate into cellular membranes—the ER or the ER’s or other organelles’ membranes. The proteins can also secrete from the cell (such as protein hormones, enzymes). The RER also makes phospholipids for cellular membranes.

If the phospholipids or modified proteins are not destined to stay in the RER, they will reach their destinations via transport vesicles that bud from the RER’s membrane ((Figure)).

Since the RER is engaged in modifying proteins (such as enzymes, for example) that secrete from the cell, you would be correct in assuming that the RER is abundant in cells that secrete proteins. This is the case with liver cells, for example.

Smooth ER

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

In muscle cells, a specialized SER, the sarcoplasmic reticulum, is responsible for storing calcium ions that are needed to trigger the muscle cells’ coordinated contractions.

Link to Learning

You can watch an excellent animation of the endomembrane system here. At the end of the animation, there is a short self-assessment.

Career Connection

CardiologistHeart disease is the leading cause of death in the United States. This is primarily due to our sedentary lifestyle and our high trans-fat diets.

Heart failure is just one of many disabling heart conditions. Heart failure does not mean that the heart has stopped working. Rather, it means that the heart can’t pump with sufficient force to transport oxygenated blood to all the vital organs. Left untreated, heart failure can lead to kidney failure and other organ failure.

Cardiac muscle tissue comprises the heart’s wall. Heart failure occurs when cardiac muscle cells’ endoplasmic reticula do not function properly. As a result, an insufficient number of calcium ions are available to trigger a sufficient contractile force.

Cardiologists (cardi- = “heart”; -ologist = “one who studies”) are doctors who specialize in treating heart diseases, including heart failure. Cardiologists can diagnose heart failure via a physical examination, results from an electrocardiogram (ECG, a test that measures the heart’s electrical activity), a chest X-ray to see whether the heart is enlarged, and other tests. If the cardiologist diagnoses heart failure, he or she will typically prescribe appropriate medications and recommend a reduced table salt intake and a supervised exercise program.

The Golgi Apparatus

We have already mentioned that vesicles can bud from the ER and transport their contents elsewhere, but where do the vesicles go? Before reaching their final destination, the lipids or proteins within the transport vesicles still need sorting, packaging, and tagging so that they end up in the right place. Sorting, tagging, packaging, and distributing lipids and proteins takes place in the Golgi apparatus (also called the Golgi body), a series of flattened membranes ((Figure)).

The Golgi apparatus in this white blood cell is visible as a stack of semicircular, flattened rings in the lower portion of the image. You can see several vesicles near the Golgi apparatus. (credit: modification of work by Louisa Howard)


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

We call the Golgi apparatus’ the cis face. The opposite side is the trans face. The transport vesicles that formed from the ER travel to the cis face, fuse with it, and empty their contents into the Golgi apparatus’ lumen. As the proteins and lipids travel through the Golgi, they undergo further modifications that allow them to be sorted. The most frequent modification is adding short sugar molecule chains. These newly modified proteins and lipids then tag with phosphate groups or other small molecules in order to travel to their proper destinations.

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

In another example of form following function, cells that engage in a great deal of secretory activity (such as salivary gland cells that secrete digestive enzymes or immune system cells that secrete antibodies) have an abundance of Golgi.

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

Career Connection

GeneticistMany diseases arise from genetic mutations that prevent synthesizing critical proteins. One such disease is Lowe disease (or oculocerebrorenal syndrome, because it affects the eyes, brain, and kidneys). In Lowe disease, there is a deficiency in an enzyme localized to the Golgi apparatus. Children with Lowe disease are born with cataracts, typically develop kidney disease after the first year of life, and may have impaired mental abilities.

A mutation on the X chromosome causes Lowe disease. The X chromosome is one of the two human sex chromosomes, as these chromosomes determine a person’s sex. Females possess two X chromosomes while males possess one X and one Y chromosome. In females, the genes on only one of the two X chromosomes are expressed. Females who carry the Lowe disease gene on one of their X chromosomes are carriers and do not show symptoms of the disease. However, males only have one X chromosome and the genes on this chromosome are always expressed. Therefore, males will always have Lowe disease if their X chromosome carries the Lowe disease gene. Geneticists have identified the mutated gene’s location, as well as many other mutation locations that cause genetic diseases. Through prenatal testing, a woman can find out if the fetus she is carrying may be afflicted with one of several genetic diseases.

Geneticists analyze prenatal genetic test results and may counsel pregnant women on available options. They may also conduct genetic research that leads to new drugs or foods, or perform DNA analyses for forensic investigations.

Lysosomes

In addition to their role as the digestive component and organelle-recycling facility of animal cells, lysosomes are part of the endomembrane system. Lysosomes also use their hydrolytic enzymes to destroy pathogens (disease-causing organisms) that might enter the cell. A good example of this occurs in macrophages, a group of white blood cells which are part of your body’s immune system. In a process that scientists call phagocytosis or endocytosis, a section of the macrophage’s plasma membrane 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)).

A macrophage has engulfed (phagocytized) a potentially pathogenic bacterium and then fuses with lysosomes within the cell to destroy the pathogen. Other organelles are present in the cell but for simplicity we do not show them.


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

Section Summary

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

The RER modifies proteins and synthesizes phospholipids in cell membranes. The SER synthesizes carbohydrates, lipids, and steroid hormones; engages in the detoxification of medications and poisons; and stores calcium ions. Sorting, tagging, packaging, and distributing lipids and proteins take place in the Golgi apparatus. Budding RER and Golgi membranes create lysosomes. Lysosomes digest macromolecules, recycle worn-out organelles, and destroy pathogens.

Visual Connection Questions

(Figure) If a peripheral membrane protein were synthesized in the lumen (inside) of the ER, would it end up on the inside or outside of the plasma membrane?

(Figure) It would end up on the outside. After the vesicle passes through the Golgi apparatus and fuses with the plasma membrane, it turns inside out.

Review Questions

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

  1. mitochondrion
  2. Golgi apparatus
  3. endoplasmic reticulum
  4. lysosome

A

The process by which a cell engulfs a foreign particle is known as:

  1. endosymbiosis
  2. phagocytosis
  3. hydrolysis
  4. membrane synthesis

B

Which of the following is most likely to have the greatest concentration of smooth endoplasmic reticulum?

  1. a cell that secretes enzymes
  2. a cell that destroys pathogens
  3. a cell that makes steroid hormones
  4. a cell that engages in photosynthesis

C

Which of the following sequences correctly lists in order the steps involved in the incorporation of a proteinaceous molecule within a cell?

  1. protein synthesis of the protein on the ribosome; modification in the Golgi apparatus; packaging in the endoplasmic reticulum; tagging in the vesicle
  2. synthesis of the protein on the lysosome; tagging in the Golgi; packaging in the vesicle; distribution in the endoplasmic reticulum
  3. synthesis of the protein on the ribosome; modification in the endoplasmic reticulum; tagging in the Golgi; distribution via the vesicle
  4. synthesis of the protein on the lysosome; packaging in the vesicle; distribution via the Golgi; tagging in the endoplasmic reticulum

C

Congenital disorders of glycosylation are a growing class of rare diseases. Which organelle would be most commonly involved in the glycoprotein disorder portion of the group?

  1. RER
  2. ribosomes
  3. endosomes
  4. Golgi apparatus

D

Critical Thinking Questions

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, compare your arm to a bat’s wing. While the bones of the two correspond, the parts serve different functions in each organism and their forms have adapted to follow that function.

In your opinion, is the nuclear membrane part of the endomembrane system? Why or why not? Defend your answer.

Since the external surface of the nuclear membrane is continuous with the rough endoplasmic reticulum, which is part of the endomembrane system, then it is correct to say that it is part of the system.

Glossary

endomembrane system
group of organelles and membranes in eukaryotic cells that work together modifying, packaging, and transporting lipids and proteins
endoplasmic reticulum (ER)
series of interconnected membranous structures within eukaryotic cells that collectively modify proteins and synthesize lipids
Golgi apparatus
eukaryotic organelle comprised of a series of stacked membranes that sorts, tags, and packages lipids and proteins for distribution
rough endoplasmic reticulum (RER)
region of the endoplasmic reticulum that is studded with ribosomes and engages in protein modification and phospholipid synthesis
smooth endoplasmic reticulum (SER)
region of the endoplasmic reticulum that has few or no ribosomes on its cytoplasmic surface and synthesizes carbohydrates, lipids, and steroid hormones; detoxifies certain chemicals (like pesticides, preservatives, medications, and environmental pollutants), and stores calcium ions

19

The Cytoskeleton

Learning Objectives

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

  • Describe the cytoskeleton
  • Compare the roles of microfilaments, intermediate filaments, and microtubules
  • Compare and contrast cilia and flagella
  • Summarize the differences among the components of prokaryotic cells, animal cells, and plant cells

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 help maintain the cell’s shape, secure some organelles in specific positions, allow cytoplasm and vesicles to move within the cell, and enable cells within multicellular organisms to move. Collectively, scientists call this network of protein fibers the cytoskeleton. There are three types of fibers within the cytoskeleton: microfilaments, intermediate filaments, and microtubules ((Figure)). Here, we will examine each.

Microfilaments thicken the cortex around the cell’s inner edge. Like rubber bands, they resist tension. There are microtubules in the cell’s interior where they maintain their shape by resisting compressive forces. There are intermediate filaments throughout the cell that hold organelles in place.


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

Microfilaments

Of the three types of protein fibers in the cytoskeleton, microfilaments are the narrowest. They function in cellular movement, have a diameter of about 7 nm, and are comprised of two globular protein intertwined strands, which we call actin ((Figure)). For this reason, we also call microfilaments actin filaments.

Two intertwined actin strands comprise microfilaments.


This illustration shows two actin filaments wound together. Each actin filament is composed of many actin subunits connected together to form a chain.

ATP powers actin to assemble its filamentous form, which serves as a track for the movement of a motor protein we call myosin. This enables actin to engage in cellular events requiring motion, such as cell division in eukaryotic cells and cytoplasmic streaming, which is the cell cytoplasm’s circular movement in plant cells. Actin and myosin are plentiful in muscle cells. When your actin and myosin filaments slide past each other, your muscles contract.

Microfilaments also provide some rigidity and shape to the cell. They can depolymerize (disassemble) and reform quickly, thus enabling a cell to change its shape and move. White blood cells (your body’s infection-fighting cells) make good use of this ability. They can move to an infection site and phagocytize the pathogen.

Link to Learning

To see an example of a white blood cell in action, watch a short time-lapse video of the cell capturing two bacteria. It engulfs one and then moves on to the other.

Intermediate Filaments

Several strands of fibrous proteins that are wound together comprise intermediate filaments ((Figure)). Cytoskeleton elements get their name from the fact that their diameter, 8 to 10 nm, is between those of microfilaments and microtubules.

Intermediate filaments consist of several intertwined strands of fibrous proteins.


This illustration shows 10 intermediate filament fibers bundled together.

Intermediate filaments have no role in cell movement. Their function is purely structural. They bear tension, thus maintaining the cell’s shape, and anchor the nucleus and other organelles in place. (Figure) shows how intermediate filaments create a supportive scaffolding inside the cell.

The intermediate filaments are the most diverse group of cytoskeletal elements. Several fibrous protein types are in the intermediate filaments. You are probably most familiar with keratin, the fibrous protein that strengthens your hair, nails, and the skin’s epidermis.

Microtubules

As their name implies, microtubules are small hollow tubes. Polymerized dimers of α-tubulin and β-tubulin, two globular proteins, comprise the microtubule’s walls ((Figure)). With a diameter of about 25 nm, microtubules are cytoskeletons’ widest components. They help the cell resist compression, provide a track along which vesicles move through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. Like microfilaments, microtubules can disassemble and reform quickly.

Microtubules are hollow. Their walls consist of 13 polymerized dimers of α-tubulin and β-tubulin (right image). The left image shows the tube’s molecular structure.


The left part of this figure is a molecular model of 13 polymerized dimers of alpha- and beta-tubulin joined together to form a hollow tube. The right part of this image shows the tubulin structure as a ring of spheres connected together.

Microtubules are also the structural elements of flagella, cilia, and centrioles (the latter are the centrosome’s two perpendicular bodies). In animal cells, the centrosome is the microtubule-organizing center. In eukaryotic cells, flagella and cilia are quite different structurally from their counterparts in prokaryotes, as we discuss below.

Flagella and Cilia

The flagella (singular = flagellum) are long, hair-like structures that extend from the plasma membrane and enable an entire cell to move (for example, sperm, Euglena, and some prokaryotes). When present, the cell has just one flagellum or a few flagella. However, when cilia (singular = cilium) are present, many of them extend along the plasma membrane’s entire surface. They are short, hair-like structures that move entire cells (such as paramecia) or substances along the cell’s outer surface (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 trap particulate matter and move it toward your nostrils.)

Despite their differences in length and number, flagella and cilia share a common structural arrangement of microtubules called a “9 + 2 array.” This is an appropriate name because a single flagellum or cilium is made of a ring of nine microtubule doublets, surrounding a single microtubule doublet in the center ((Figure)).

This transmission electron micrograph of two flagella shows the microtubules’ 9 + 2 array: nine microtubule doublets surround a single microtubule doublet. (credit: modification of work by Dartmouth Electron Microscope Facility, Dartmouth College; scale-bar data from Matt Russell)


This transmission electron micrograph shows a cross section of nine microtubule doublets that form a hollow tube. Another microtubule doublet sits in the center of the tube.

You have now completed a broad survey of prokaryotic and eukaryotic cell components. For a summary of cellular components in prokaryotic and eukaryotic cells, see (Figure).

Components of Prokaryotic and Eukaryotic Cells
Cell Component Function 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 cell Yes Yes Yes
Cytoplasm Provides turgor pressure to plant cells as fluid inside the central vacuole; site of many metabolic reactions; medium in which organelles are found Yes Yes Yes
Nucleolus Darkened area within the nucleus where ribosomal subunits are synthesized. No Yes Yes
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 Oxidize and thus break down fatty acids and amino acids, and detoxify 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; microtubule source in animal cells No Yes No
Lysosomes Digestion of macromolecules; recycling of worn-out organelles No Yes Some
Cell wall Protection, structural support, and maintenance of cell shape Yes, primarily peptidoglycan 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 cell, and enables unicellular organisms to move independently Yes Yes Yes
Flagella Cellular locomotion Some Some No, except for some plant sperm cells
Cilia Cellular locomotion, movement of particles along plasma membrane’s extracellular surface, and filtration Some Some No

Section Summary

The cytoskeleton has three different protein element types. From narrowest to widest, they are the microfilaments (actin filaments), intermediate filaments, and microtubules. Biologists often associate microfilaments with myosin. They 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 element of centrioles, flagella, and cilia.

Review Questions

Which of the following have the ability to disassemble and reform quickly?

  1. microfilaments and intermediate filaments
  2. microfilaments and microtubules
  3. intermediate filaments and microtubules
  4. only intermediate filaments

B

Which of the following do not play a role in intracellular movement?

  1. microfilaments and intermediate filaments
  2. microfilaments and microtubules
  3. intermediate filaments and microtubules
  4. only intermediate filaments

D

In humans, _____ are used to move a cell within its environment while _____ are used to move the environment relative to the cell.

  1. cilia, pseudopodia
  2. flagella; cilia
  3. microtubules; flagella
  4. microfilaments; microtubules

B

Critical Thinking Questions

What are the similarities and differences between the structures of centrioles and flagella?

Centrioles and flagella are alike in that they are made up of microtubules. In centrioles, two rings of nine microtubule “triplets” are arranged at right angles to one another. This arrangement does not occur in flagella.

How do cilia and flagella differ?

Cilia and flagella are alike in that they are made up of microtubules. Cilia are short, hair-like structures that exist in large numbers and usually cover the entire surface of the plasma membrane. Flagella, in contrast, are long, hair-like structures; when flagella are present, a cell has just one or two.

Describe how microfilaments and microtubules are involved in the phagocytosis and destruction of a pathogen by a macrophage.

A macrophage engulfs a pathogen by rearranging its actin microfilaments to bend the plasma membrane around the pathogen. Once the pathogen is sealed in an endosome inside the macrophage, the vesicle is walked along microtubules until it combines with a lysosome to digest the pathogen.

Compare and contrast the boundaries that plant, animal, and bacteria cells use to separate themselves from their surrounding environment.

All three cell types have a plasma membrane that borders the cytoplasm on its interior side. In animal cells, the exterior side of the plasma membrane is in contact with the extracellular environment. However, in plant and bacteria cells, a cell wall surrounds the outside of the plasma membrane. In plants, the cell wall is made of cellulose, while in bacteria the cell wall is made of peptidoglycan. Gram-negative bacteria also have an additional capsule made of lipopolysaccharides that surrounds their cell wall.

Glossary

cilium
(plural = cilia) short, hair-like structure that extends from the plasma membrane in large numbers and functions to move an entire cell or move substances along the cell’s outer surface
cytoskeleton
protein fiber network that collectively maintains the cell’s shape, secures some organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move independently
flagellum
(plural = flagella) long, hair-like structure that extends from the plasma membrane and moves the cell
intermediate filament
cytoskeletal component, comprised of several fibrous protein intertwined strands, that bears tension, supports cell-cell junctions, and anchors cells to extracellular structures
microfilament
the cytoskeleton system’s narrowest element; it provides rigidity and shape to the cell and enables cellular movements
microtubule
the cytoskeleton system’s widest element; it helps the cell resist compression, provides a track along which vesicles move through the cell, pulls replicated chromosomes to opposite ends of a dividing cell, and is the structural element of centrioles, flagella, and cilia

20

Connections between Cells and Cellular Activities

Learning Objectives

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

  • Describe the extracellular matrix
  • List examples of the ways that plant cells and animal cells communicate with adjacent cells
  • Summarize the roles of tight junctions, desmosomes, gap junctions, and plasmodesmata

You already know that tissue is a group of similar cells working together. As you might expect, if cells are to work together, they must communicate with each other, just as you need to communicate with others if you work on a group project. Let’s take a look at how cells communicate with each other.

Extracellular Matrix of Animal Cells

While cells in most multicellular organisms release materials into the extracellular space, animal cells will be discussed as an example. The primary components of these materials are proteins, and the most abundant protein is collagen. Collagen fibers are interwoven with proteoglycans, which are carbohydrate-containing protein molecules. Collectively, we call these materials the extracellular matrix ((Figure)). 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. How can this happen?

The extracellular matrix consists of a network of proteins and carbohydrates.


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. The fibers are attached to the integrins via a protein called fibronectin. Proteoglycan complexes also extend from the plasma membrane to the extracellular matrix. A close-up 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.

Cells have protein receptors on their plasma membranes’ extracellular surfaces. When a molecule within the matrix binds to the receptor, it changes the receptor’s molecular structure. The receptor, in turn, changes the microfilaments’ conformation positioned just inside the plasma membrane. These conformational changes induce chemical signals inside the cell that reach the nucleus and turn “on” or “off” the transcription of specific DNA sections, which affects the associated protein production, thus changing the activities within the cell.

Blood clotting provides an example of the extracellular matrix’s role in cell communication. When the cells lining a blood vessel are damaged, they display a protein receptor, which we call tissue factor. When tissue factor binds with another factor in the extracellular matrix, it causes platelets to adhere to the damaged blood vessel’s wall, stimulates the 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 via direct contact, or intercellular junctions. There are differences in the ways that plant and animal and fungal cells communicate. Plasmodesmata are junctions between plant cells; whereas, animal cell contacts include tight junctions, gap junctions, and desmosomes.

Plasmodesmata

In general, long stretches of the plasma membranes of neighboring plant cells cannot touch one another because the cell wall that surrounds each cell separates them ((Figure)). How then, can a plant transfer water and other soil nutrients from its roots, through its stems, and to its leaves? Such transport uses the vascular tissues (xylem and phloem) primarily. There also exist structural modifications, which we call plasmodesmata (singular = plasmodesma). Numerous channels that pass between adjacent plant cells’ cell walls connect their cytoplasm, and enable transport of materials from cell to cell, and thus throughout the plant ((Figure)).

A plasmodesma is a channel between two adjacent plant cells’ cell walls. Plasmodesmata allow materials to pass from one plant cell’s cytoplasm to an adjacent cell’s cytoplasm.


This illustration shows two plant cells side-by-side. A gap in the cell wall, a plasmodesma, allows fluid and small molecules to pass from the cytoplasm of one cell to the cytoplasm of the other.

Tight Junctions

A tight junction is a watertight seal between two adjacent animal cells ((Figure)). Proteins (predominantly two proteins called claudins and occludins) tightly hold the cells against each other.

Tight junctions form watertight connections between adjacent animal cells. Proteins create tight junction adherence. (credit: modification of work by Mariana Ruiz Villareal)


This illustration shows two cell membranes joined together by a matrix of tight junctions.

This tight adherence prevents materials from leaking between the cells; tight junctions are typically found in epithelial tissues that line internal organs and cavities, and comprise most of the skin. For example, the tight junctions of the epithelial cells lining your urinary bladder prevent urine from leaking out into the extracellular space.

Desmosomes

Also only in animal cells are desmosomes, which act like spot welds between adjacent epithelial cells ((Figure)). Cadherins, short proteins in the plasma membrane connect to intermediate filaments to create desmosomes. The cadherins connect two adjacent cells and maintain the cells in a sheet-like formation in organs and tissues that stretch, like the skin, heart, and muscles.

A desmosome forms a very strong spot weld between cells. Linking cadherins and intermediate filaments create it. (credit: modification of work by Mariana Ruiz Villareal)


This illustration shows two cells fused together by a desmosome. Cadherins extend from each cell and join the two cells together. Intermediate filaments connect to cadherins on the inside of the cell.

Gap Junctions

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

A gap junction is a protein-lined pore that allows water and small molecules to pass between adjacent animal cells. (credit: modification of work by Mariana Ruiz Villareal)


This illustration shows two cells joined together with protein pores called gap junctions that allow water and small molecules to pass through.

Gap junctions develop when a set of six proteins (connexins) in the plasma membrane arrange themselves in an elongated donut-like configuration – a connexon. When the connexon’s pores (“doughnut holes”) in adjacent animal cells align, a channel between the two cells forms. Gap junctions are particularly important in cardiac muscle. The electrical signal for the muscle to contract passes efficiently through gap junctions, allowing the heart muscle cells to contract in tandem.

Link to Learning

To conduct a virtual microscopy lab and review the parts of a cell, work through the steps of this interactive assignment.

Section Summary

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

When protein receptors on the plasma membrane’s surface of an animal cell bind to a substance in the extracellular matrix, a chain of reactions begins that changes activities taking place within the cell. Plasmodesmata are channels between adjacent plant cells, while gap junctions are channels between adjacent animal cells. However, their structures are quite different. A tight junction is a watertight seal between two adjacent cells, while a desmosome acts like a spot weld.

Review Questions

Which of the following are only in plant cells?

  1. gap junctions
  2. desmosomes
  3. plasmodesmata
  4. tight junctions

C

The key components of desmosomes are cadherins and __________.

  1. actin
  2. microfilaments
  3. intermediate filaments
  4. microtubules

C

Diseased animal cells may produce molecules that activate death cascades to kill the cells in a controlled manner. Why would neighboring healthy cells also die?

  1. The death molecule is passed through desmosomes.
  2. The death molecule is passed through plasmodesmata.
  3. The death molecule disrupts the extracellular matrix.
  4. The death molecule passes through gap junctions.

D

Critical Thinking Questions

How does the structure of a plasmodesma differ from that of a gap junction?

They differ because plant cell walls are rigid. Plasmodesmata, which a plant cell needs for transportation and communication, are able to allow movement of really large molecules. Gap junctions are necessary in animal cells for transportation and communication.

Explain how the extracellular matrix functions.

The extracellular matrix functions in support and attachment for animal tissues. It also functions in the healing and growth of the tissue.

Pathogenic E. coli have recently been shown to degrade tight junction proteins during infection. How would this provide an advantage to the bacteria?

E. coli infections generally cause food poisoning, meaning that the invading bacteria cross from the lumen of the gut into the rest of the body. Tight junctions hold the epithelial layer that lines the digestive tract together so that the material that crosses into the body is tightly regulated. One way E. coli can avoid this regulation is to destroy the tight junctions so that it can enter the body between the epithelial cells, rather than having to go through the cells.

Glossary

desmosome
linkages between adjacent epithelial cells that form when cadherins in the plasma membrane attach to intermediate filaments
extracellular matrix
material secreted from animal or fungal cells that provides mechanical protection and anchoring for the cells in the tissue
gap junction
channel between two adjacent animal cells that allows ions, nutrients, and low molecular weight substances to pass between cells, enabling the cells to communicate
plasmodesma
(plural = plasmodesmata) channel that passes between adjacent plant cells’ cell walls, connects their cytoplasm, and allows transporting of materials from cell to cell
tight junction
protein adherence that creates a firm seal between two adjacent animal cells

V

Structure and Function of Plasma Membranes

21

Introduction

Despite its seeming hustle and bustle, Grand Central Station functions with a high level of organization: People and objects move from one location to another, they cross or are contained within certain boundaries, and they provide a constant flow as part of larger activity. Analogously, a plasma membrane’s functions involve movement within the cell and across boundaries’ activities. (credit: modification of work by Randy Le’Moine)


This photo shows the hustle and bustle of Grand Central Station.

The plasma membrane, the cell membrane, has many functions, but the most basic one is to define the cell’s borders and keep the cell functional. The plasma membrane is selectively permeable. This means that the membrane allows some materials to freely enter or leave the cell, while other materials cannot move freely, but require a specialized structure, and occasionally, even energy investment for crossing.

22

Components and Structure

Learning Objectives

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

  • Understand the cell membrane fluid mosaic model
  • Describe phospholipid, protein, and carbohydrate functions in membranes
  • Discuss membrane fluidity

A cell’s plasma membrane defines the cell, outlines its borders, and determines the nature of its interaction with its environment (see (Figure) for a summary). Cells exclude some substances, take in others, and excrete still others, all in controlled quantities. The plasma membrane must be very flexible to allow certain cells, such as red and white blood cells, to change shape as they pass through narrow capillaries. These are the more obvious plasma membrane functions. In addition, the plasma membrane’s surface carries markers that allow cells to recognize one another, which is vital for tissue and organ formation during early development, and which later plays a role in the immune response’s “self” versus “non-self” distinction.

Among the most sophisticated plasma membrane functions is the ability for complex, integral proteins, receptors to transmit signals. These proteins act both as extracellular input receivers and as intracellular processing activators. These membrane receptors provide extracellular attachment sites for effectors like hormones and growth factors, and they activate intracellular response cascades when their effectors are bound. Occasionally, viruses hijack receptors (HIV, human immunodeficiency virus, is one example) that use them to gain entry into cells, and at times, the genes encoding receptors become mutated, causing the signal transduction process to malfunction with disastrous consequences.

Fluid Mosaic Model

Scientists identified the plasma membrane in the 1890s, and its chemical components in 1915. The principal components they identified were lipids and proteins. In 1935, Hugh Davson and James Danielli proposed the plasma membrane’s structure. This was the first model that others in the scientific community widely accepted. It was based on the plasma membrane’s “railroad track” appearance in early electron micrographs. Davson and Danielli theorized that the plasma membrane’s structure resembles a sandwich. They made the analogy of proteins to bread, and lipids to the filling. In the 1950s, advances in microscopy, notably transmission electron microscopy (TEM), allowed researchers to see that the plasma membrane’s core consisted of a double, rather than a single, layer. In 1972, S.J. Singer and Garth L. Nicolson proposed a new model that provides microscopic observations and better explains plasma membrane function.

The explanation, the fluid mosaic model, has evolved somewhat over time, but it still best accounts for plasma membrane structure and function as we now understand them. The fluid mosaic model describes the plasma membrane structure as a mosaic of components—including phospholipids, cholesterol, proteins, and carbohydrates—that gives the membrane a fluid character. Plasma membranes range from 5 to 10 nm in thickness. For comparison, human red blood cells, visible via light microscopy, are approximately 8 µm wide, or approximately 1,000 times wider than a plasma membrane. The membrane does look a bit like a sandwich ((Figure)).

The plasma membrane fluid mosaic model describes the plasma membrane as a fluid combination of phospholipids, cholesterol, and proteins. Carbohydrates attached to lipids (glycolipids) and to proteins (glycoproteins) extend from the membrane’s outward-facing surface.


This illustration shows a phospholipid bilayer with proteins and cholesterol embedded in it. Integral membrane proteins span the entire membrane. Protein channels are integral membrane proteins with a central pore through which molecules can pass. Peripheral proteins are associated with the phospholipid head groups on one side of the membrane only. A glycoprotein is shown with the protein portion of the molecule embedded in the membrane and the carbohydrate portion jutting out from the membrane. A glycolipid is also shown with the lipid portion embedded in the membrane and the carbohydrate portion jutting out of the membrane.

A plasma membrane’s principal components are lipids (phospholipids and cholesterol), proteins, and carbohydrates attached to some of the lipids and proteins. A phospholipid is a molecule consisting of glycerol, two fatty acids, and a phosphate-linked head group. Cholesterol, another lipid comprised of four fused carbon rings, is situated alongside the phospholipids in the membrane’s core. The protein, lipid, and carbohydrate proportions in the plasma membrane vary with cell type, but for a typical human cell, protein accounts for about 50 percent of the composition by mass, lipids (of all types) account for about 40 percent, and carbohydrates comprise the remaining 10 percent. However, protein and lipid concentration varies with different cell membranes. For example, myelin, an outgrowth of specialized cells’ membrane that insulates the peripheral nerves’ axons, contains only 18 percent protein and 76 percent lipid. The mitochondrial inner membrane contains 76 percent protein and only 24 percent lipid. The plasma membrane of human red blood cells is 30 percent lipid. Carbohydrates are present only on the plasma membrane’s exterior surface and are attached to proteins, forming glycoproteins, or attached to lipids, forming glycolipids.

Phospholipids

The membrane’s main fabric comprises amphiphilic, phospholipid molecules. The hydrophilic or “water-loving” areas of these molecules (which look like a collection of balls in an artist’s rendition of the model) ((Figure)) are in contact with the aqueous fluid both inside and outside the cell. Hydrophobic, or water-hating molecules, tend to be non-polar. They interact with other non-polar molecules in chemical reactions, but generally do not interact with polar molecules. When placed in water, hydrophobic molecules tend to form a ball or cluster. The phospholipids’ hydrophilic regions form hydrogen bonds with water and other polar molecules on both the cell’s exterior and interior. Thus, the membrane surfaces that face the cell’s interior and exterior are hydrophilic. In contrast, the cell membrane’s interior is hydrophobic and will not interact with water. Therefore, phospholipids form an excellent two-layer cell membrane that separates fluid within the cell from the fluid outside the cell.

A phospholipid molecule ((Figure)) consists of a three-carbon glycerol backbone with two fatty acid molecules attached to carbons 1 and 2, and a phosphate-containing group attached to the third carbon. This arrangement gives the overall molecule a head area (the phosphate-containing group), which has a polar character or negative charge, and a tail area (the fatty acids), which has no charge. The head can form hydrogen bonds, but the tail cannot. Scientists call a molecule with a positively or negatively charged area and an uncharged, or non-polar, area amphiphilic or “dual-loving.”

A hydrophilic head and two hydrophobic tails comprise this phospholipid molecule. 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.


An illustration of a phospholipid shows a hydrophilic head group composed of phosphate connected to a three-carbon glycerol molecule, and two hydrophobic tails composed of long hydrocarbon chains.

This characteristic is vital to the plasma membrane’s structure because, in water, phospholipids arrange themselves with their hydrophobic tails facing each other and their hydrophilic heads facing out. In this way, they form a lipid bilayer—a double layered phospholipid barrier that separates the water and other materials on one side from the water and other materials on the other side. Phosopholipids heated in an aqueous solution usually spontaneously form small spheres or droplets (micelles or liposomes), with their hydrophilic heads forming the exterior and their hydrophobic tails on the inside ((Figure)).

In an aqueous solution, phospholipids usually arrange themselves with their polar heads facing outward and their hydrophobic tails facing inward. (credit: modification of work by Mariana Ruiz Villareal)


The image on the left shows a spherical lipid bilayer, shown as a half sphere whose surface is covered in the spherical polar heads, and thin, strandlike extend inward. In the core of the sphere is another half sphere, with the same anatomy. The image on the right shows a smaller sphere that has a single lipid layer only, made up of the spherical heads. The image at the bottom shows a lipid bilayer sheet; whose polar heads form the upper and lower surfaces, with tails extending toward each other in the middle.

Proteins

Proteins comprise the plasma membranes’ second major component. Integral proteins, or integrins, as their name suggests, integrate completely into the membrane structure, and their hydrophobic membrane-spanning regions interact with the phospholipid bilayer’s hydrophobic region ((Figure)). Single-pass integral membrane proteins usually have a hydrophobic transmembrane segment that consists of 20–25 amino acids. Some span only part of the membrane—associating with a single layer—while others stretch from one side to the other, and are exposed on either side. Up to 12 single protein segments comprise some complex proteins, which are extensively folded and embedded in the membrane ((Figure)). This protein type has a hydrophilic region or regions, and one or several mildly hydrophobic regions. This arrangement of protein regions orients the protein alongside the phospholipids, with the protein’s hydrophobic region adjacent to the phosopholipids’ tails and the protein’s hydrophilic region or regions protruding from the membrane and in contact with the cytosol or extracellular fluid.

Integral membrane proteins may have one or more alpha-helices that span the membrane (examples 1 and 2), or they may have beta-sheets that span the membrane (example 3). (credit: “Foobar”/Wikimedia Commons)


The left part of this illustration shows an integral membrane protein with a single alpha-helix that spans the membrane. The middle part shows a protein with several alpha-helices spanning the membrane. The right part shows a protein with two beta-sheets spanning the membrane.

Peripheral proteins are on the membranes’ exterior and interior surfaces, attached either to integral proteins or to phospholipids. Peripheral proteins, along with integral proteins, may serve as enzymes, as structural attachments for the cytoskeleton’s fibers, or as part of the cell’s recognition sites. Scientists sometimes refer to these as “cell-specific” proteins. The body recognizes its own proteins and attacks foreign proteins associated with invasive pathogens.

Carbohydrates

Carbohydrates are the third major plasma membrane component. They are always on the cells’ exterior surface and are bound either to proteins (forming glycoproteins) or to lipids (forming glycolipids) ((Figure)). These carbohydrate chains may consist of 2–60 monosaccharide units and can be either straight or branched. Along with peripheral proteins, carbohydrates form specialized sites on the cell surface that allow cells to recognize each other. These sites have unique patterns that allow for cell recognition, much the way that the facial features unique to each person allow individuals to recognize him or her. This recognition function is very important to cells, as it allows the immune system to differentiate between body cells (“self”) and foreign cells or tissues (“non-self”). Similar glycoprotein and glycolipid types are on the surfaces of viruses and may change frequently, preventing immune cells from recognizing and attacking them.

We collectively refer to these carbohydrates on the cell’s exterior surface—the carbohydrate components of both glycoproteins and glycolipids—as the glycocalyx (meaning “sugar coating”). The glycocalyx is highly hydrophilic and attracts large amounts of water to the cell’s surface. This aids in the cell’s interaction with its watery environment and in the cell’s ability to obtain substances dissolved in the water. As we discussed above, the glycocalyx is also important for cell identification, self/non-self determination, and embryonic development, and is used in cell to cell attachments to form tissues.

Evolution Connection

How Viruses Infect Specific OrgansGlycoprotein and glycolipid patterns on the cells’ surfaces give many viruses an opportunity for infection. HIV and hepatitis viruses infect only specific organs or cells in the human body. HIV is able to penetrate the plasma membranes of a subtype of lymphocytes called T-helper cells, as well as some monocytes and central nervous system cells. The hepatitis virus attacks liver cells.

These viruses are able to invade these cells, because the cells have binding sites on their surfaces that are specific to and compatible with certain viruses ((Figure)). 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, or in response to foreign cells, such as might occur with an organ transplant. These same sites serve as places for antibodies to attach and either destroy or inhibit the virus’ activity. Unfortunately, these recognition sites on HIV change at a rapid rate because of mutations, making an effective vaccine against the virus very difficult, as the virus evolves and adapts. A person infected with HIV will quickly develop different populations, or variants, of the virus that differences in these recognition sites distinguish. This rapid change of surface markers decreases the effectiveness of the person’s immune system in attacking the virus, because the antibodies will not recognize the surface patterns’ new variations. In the case of HIV, the problem is compounded because the virus specifically infects and destroys cells involved in the immune response, further incapacitating the host.

HIV binds to the CD4 receptor, a glycoprotein on T cell surfaces. (credit: modification of work by NIH, NIAID)


This illustration shows the plasma membrane of a T cell. C D 4 receptors extend from the membrane into the extracellular space. The H I V virus recognizes part of the C D 4 receptor and attaches to it.

Membrane Fluidity

The membrane’s mosaic characteristic helps to illustrate its nature. The integral proteins and lipids exist in the membrane as separate but loosely attached molecules. These resemble the separate, multicolored tiles of a mosaic picture, and they float, moving somewhat with respect to one another. The membrane is not like a balloon, however, that can expand and contract; rather, it is fairly rigid and can burst if penetrated or if a cell takes in too much water. However, because of its mosaic nature, a very fine needle can easily penetrate a plasma membrane without causing it to burst, and the membrane will flow and self-seal when one extracts the needle.

The membrane’s mosaic characteristics explain some but not all of its fluidity. There are two other factors that help maintain this fluid characteristic. One factor is the nature of the phospholipids themselves. In their saturated form, the fatty acids in phospholipid tails are saturated with bound hydrogen atoms. There are no double bonds between adjacent carbon atoms. This results in tails that are relatively straight. In contrast, unsaturated fatty acids do not contain a maximal number of hydrogen atoms, but they do contain some double bonds between adjacent carbon atoms. A double bond results in a bend in the carbon string of approximately 30 degrees ((Figure)).

Thus, if decreasing temperatures compress saturated fatty acids with their straight tails, they press in on each other, making a dense and fairly rigid membrane. If unsaturated fatty acids are compressed, the “kinks” in their tails elbow adjacent phospholipid molecules away, maintaining some space between the phospholipid molecules. This “elbow room” helps to maintain fluidity in the membrane at temperatures at which membranes with saturated fatty acid tails in their phospholipids would “freeze” or solidify. The membrane’s relative fluidity is particularly important in a cold environment. A cold environment usually compresses membranes comprised largely of saturated fatty acids, making them less fluid and more susceptible to rupturing. Many organisms (fish are one example) are capable of adapting to cold environments by changing the proportion of unsaturated fatty acids in their membranes in response to lower temperature.

Link to Learning

Visit this site to see animations of the membranes’ fluidity and mosaic quality.

Animals have an additional membrane constituent that assists in maintaining fluidity. Cholesterol, which lies alongside the phospholipids in the membrane, tends to dampen temperature effects on the membrane. Thus, this lipid functions as a buffer, preventing lower temperatures from inhibiting fluidity and preventing increased temperatures from increasing fluidity too much. Thus, cholesterol extends, in both directions, the temperature range in which the membrane is appropriately fluid and consequently functional. Cholesterol also serves other functions, such as organizing clusters of transmembrane proteins into lipid rafts.

Plasma Membrane Components and Functions
Component Location
Phospholipid Main membrane fabric
Cholesterol Attached between phospholipids and between the two phospholipid layers
Integral proteins (for example, integrins) Embedded within the phospholipid layer(s); may or may not penetrate through both layers
Peripheral proteins On the phospholipid bilayer’s inner or outer surface; not embedded within the phospholipids
Carbohydrates (components of glycoproteins and glycolipids) Generally attached to proteins on the outside membrane layer
Career Connection

ImmunologistThe variations in peripheral proteins and carbohydrates that affect a cell’s recognition sites are of prime interest in immunology. In developing vaccines, researchers have been able to conquer many infectious diseases, such as smallpox, polio, diphtheria, and tetanus.

Immunologists are the physicians and scientists who research and develop vaccines, as well as treat and study allergies or other immune problems. Some immunologists study and treat autoimmune problems (diseases in which a person’s immune system attacks his or her own cells or tissues, such as lupus) and immunodeficiencies, whether acquired (such as acquired immunodeficiency syndrome, or AIDS) or hereditary (such as severe combined immunodeficiency, or SCID). Immunologists also help treat organ transplantation patients, who must have their immune systems suppressed so that their bodies will not reject a transplanted organ. Some immunologists work to understand natural immunity and the effects of a person’s environment on it. Others work on questions about how the immune system affects diseases such as cancer. In the past, researchers did not understand the importance of having a healthy immune system in preventing cancer.

To work as an immunologist, one must have a PhD or MD. In addition, immunologists undertake at least two to three years of training in an accredited program and must pass the American Board of Allergy and Immunology exam. Immunologists must possess knowledge of the human body’s function as they relate to issues beyond immunization, and knowledge of pharmacology and medical technology, such as medications, therapies, test materials, and surgical procedures.

Section Summary

Modern scientists refer to the plasma membrane as the fluid mosaic model. A phospholipid bilayer comprises the plasma membrane, with hydrophobic, fatty acid tails in contact with each other. The membrane’s landscape is studded with proteins, some 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 membrane’s outward-facing surface, forming complexes that function to identify the cell to other cells. The membrane’s fluid nature is due to temperature, fatty acid tail configuration (some kinked by double bonds), cholesterol presence embedded in the membrane, and the mosaic nature of the proteins and protein-carbohydrate combinations, which are not firmly fixed in place. Plasma membranes enclose and define the cells’ borders. Not static, they are dynamic and constantly in flux.

Review Questions

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

  1. protein
  2. cholesterol
  3. carbohydrate
  4. phospholipid

A

Which characteristic of a phospholipid contributes to the fluidity of the membrane?

  1. its head
  2. cholesterol
  3. a saturated fatty acid tail
  4. double bonds in the fatty acid tail

D

What is the primary function of carbohydrates attached to the exterior of cell membranes?

  1. identification of the cell
  2. flexibility of the membrane
  3. strengthening the membrane
  4. channels through membrane

A

A scientist compares the plasma membrane composition of an animal from the Mediterranean coast with one from the Mojave Desert. Which hypothesis is most likely to be correct?

  1. The cells from the Mediterranean coast animal will have more fluid plasma membranes.
  2. The cells from the Mojave Desert animal will have a higher cholesterol concentration in the plasma membranes.
  3. The cells’ plasma membranes will be indistinguishable.
  4. The cells from the Mediterranean coast animal will have a higher glycoprotein content, while the cells from the Mojave Desert animal will have a higher lipoprotein content.

B

Critical Thinking Questions

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

The fluid characteristic of the cell membrane allows greater flexibility to the cell than it would if the membrane were rigid. It also allows the motion of membrane components, required for some types of membrane transport.

Why do phospholipids tend to spontaneously orient themselves into something resembling a membrane?

The hydrophobic, nonpolar regions must align with each other in order for the structure to have minimal potential energy and, consequently, higher stability. The fatty acid tails of the phospholipids cannot mix with water, but the phosphate “head” of the molecule can. Thus, the head orients to water, and the tail to other lipids.

How can a cell use an extracellular peripheral protein as the receptor to transmit a signal into the cell?

Peripheral proteins can bind to other molecules in the extracellular space. However, they cannot directly transmit a signal to the inside of the cell since they do not have a transmembrane domain (region that goes through the plasma membrane to the inside of the cell). They must associate with integral membrane proteins in order to pass the signal to the inside of the cell.

Glossary

amphiphilic
molecule possessing a polar or charged area and a nonpolar or uncharged area capable of interacting with both hydrophilic and hydrophobic environments
fluid mosaic model
describes the plasma membrane’s structure as a mosaic of components including phospholipids, cholesterol, proteins, glycoproteins, and glycolipids (sugar chains attached to proteins or lipids, respectively), resulting in a fluid character (fluidity)
glycolipid
combination of carbohydrates and lipids
glycoprotein
combination of carbohydrates and proteins
hydrophilic
molecule with the ability to bond with water; “water-loving”
hydrophobic
molecule that does not have the ability to bond with water; “water-hating”
integral protein
protein integrated into the membrane structure that interacts extensively with the membrane lipids’ hydrocarbon chains and often spans the membrane
peripheral protein
protein at the plasma membrane’s surface either on its exterior or interior side

23

Passive Transport

Learning Objectives

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

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

Plasma membranes must allow certain substances to enter and leave a cell, and prevent some harmful materials from entering and some essential materials from leaving. In other words, plasma membranes are selectively permeable—they allow some substances to pass 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. They must have a way of obtaining these materials from extracellular fluids. This may happen passively, as certain materials move back and forth, or the cell may have special mechanisms that facilitate transport. Some materials are so important to a cell that it spends some of its energy, hydrolyzing adenosine triphosphate (ATP), to obtain these materials. Red blood cells use some of their energy doing just that. Most cells spend the majority of their energy to maintain an imbalance of sodium and potassium ions between the cell’s interior and exterior, as well as on protein synthesis.

The most direct forms of membrane transport are passive. Passive transport is a naturally occurring phenomenon and does not require the cell to exert any of its energy to accomplish the movement. In passive transport, substances move from an area of higher concentration to an area of lower concentration. A physical space in which there is a single substance concentration range has a concentration gradient.

Selective Permeability

Plasma membranes are asymmetric: the membrane’s interior is not identical to its exterior. There is a considerable difference between the array of phospholipids and proteins between the two leaflets that form a membrane. On the membrane’s interior, some proteins serve to anchor the membrane to cytoskeleton’s fibers. There are peripheral proteins on the membrane’s exterior that bind extracellular matrix elements. Carbohydrates, attached to lipids or proteins, are also on the plasma membrane’s exterior surface. These carbohydrate complexes help the cell bind required substances in the extracellular fluid. This adds considerably to plasma membrane’s selective nature ((Figure)).

The plasma membrane’s exterior surface is not identical to its interior surface.


This illustration shows that the inside and outside of a plasma membrane are different, with the exterior covered in the spherical heads, and the interior filled with the strandlike tails.

Recall that plasma membranes are amphiphilic: They have hydrophilic and hydrophobic regions. This characteristic helps move some materials through the membrane and hinders the movement of others. Non-polar and lipid-soluble material with a low molecular weight can easily slip through the membrane’s hydrophobic lipid core. 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 and hormones also gain easy entry into cells and readily transport themselves into the body’s tissues and organs. Oxygen and carbon dioxide molecules have no charge and pass through membranes by simple diffusion.

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

Diffusion

Diffusion is a passive process of transport. A single substance moves from a high concentration to a low concentration area until the concentration is equal across a space. You are familiar with diffusion of substances through the air. For example, think about someone opening a bottle of ammonia in a room filled with people. The ammonia gas is at its highest concentration in the bottle. Its lowest concentration is at the room’s edges. The ammonia vapor will diffuse, or spread away, from the bottle, and gradually, increasingly more people will smell the ammonia as it spreads. Materials move within the cell’s cytosol by diffusion, and certain materials move through the plasma membrane by diffusion ((Figure)). Diffusion expends no energy. On the contrary, concentration gradients are a form of potential energy, which dissipates as the gradient is eliminated.

Diffusion through a permeable membrane moves a substance from a high concentration area (extracellular fluid, in this case) down its concentration gradient (into the cytoplasm). (credit: modification of work by Mariana Ruiz Villareal)


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

Each separate substance in a medium, such as the extracellular fluid, has its own concentration gradient, independent of other materials’ concentration gradients. In addition, each substance will diffuse according to that gradient. Within a system, there will be different diffusion rates of various substances in the medium.

Factors That Affect Diffusion

Molecules move constantly in a random manner, at a rate that depends on their mass, their environment, and the amount of thermal energy they possess, which in turn is a function of temperature. This movement accounts for molecule diffusion through whatever medium in which they are localized. A substance moves into any space available to it until it evenly distributes itself throughout. After a substance has diffused completely through a space, removing its concentration gradient, molecules will still move around in the space, but there will be no net movement of the number of molecules from one area to another. We call this lack of a concentration gradient in which the substance has no net movement dynamic equilibrium. While diffusion will go forward in the presence of a substance’s concentration gradient, several factors affect the diffusion rate.

  • 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 diffusion rate.
  • Mass of the molecules diffusing: Heavier molecules move more slowly; therefore, they diffuse more slowly. The reverse is true for lighter molecules.
  • Temperature: Higher temperatures increase the energy and therefore the molecules’ movement, increasing the diffusion rate. Lower temperatures decrease the molecules’ energy, thus decreasing the diffusion rate.
  • Solvent density: As the density of a solvent increases, the diffusion rate decreases. The molecules slow down because they have a more difficult time passing through the denser medium. If the medium is less dense, diffusion increases. Because cells primarily use diffusion to move materials within the cytoplasm, any increase in the cytoplasm’s density will inhibit the movement of the materials. An example of this is a person experiencing dehydration. As the body’s cells lose water, the diffusion rate decreases in the cytoplasm, and the cells’ functions deteriorate. Neurons tend to be very sensitive to this effect. Dehydration frequently leads to unconsciousness and possibly coma because of the decrease in diffusion rate within the cells.
  • Solubility: As we discussed earlier, nonpolar or lipid-soluble materials pass through plasma membranes more easily than polar materials, allowing a faster diffusion rate.
  • Surface area and plasma membrane thickness: Increased surface area increases the diffusion rate; whereas, a thicker membrane reduces it.
  • Distance travelled: The greater the distance that a substance must travel, the slower the diffusion rate. This places an upper limitation on cell size. A large, spherical cell will die because nutrients or waste cannot reach or leave the cell’s center, respectively. Therefore, cells must either be small in size, as in the case of many prokaryotes, or be flattened, as with many single-celled eukaryotes.

A variation of diffusion is the process of filtration. In filtration, material moves according to its concentration gradient through a membrane. Sometimes pressure enhances the diffusion rate, causing the substances to filter more rapidly. This occurs in the kidney, where blood pressure forces large amounts of water and accompanying dissolved substances, or solutes, out of the blood and into the renal tubules. The diffusion rate in this instance is almost totally dependent on pressure. One of the effects of high blood pressure is the appearance of protein in the urine, which abnormally high pressure “squeezes through”.

Facilitated transport

In facilitated transport, or facilitated diffusion, materials diffuse across the plasma membrane with the help of membrane proteins. A concentration gradient exists that would allow these materials to diffuse into the cell without expending cellular energy. However, these materials are polar molecule ions that the cell membrane’s hydrophobic parts repel. Facilitated transport proteins shield these materials from the membrane’s repulsive force, allowing them to diffuse into the cell.

The transported material first attaches to protein or glycoprotein receptors on the plasma membrane’s exterior surface. This allows removal of material from the extracellular fluid that the cell needs. The substances then pass to specific integral proteins that facilitate their passage. Some of these integral proteins are collections of beta-pleated sheets that form a pore or channel through the phospholipid bilayer. Others are carrier proteins which bind with the substance and aid its diffusion through the membrane.

Channels

The integral proteins involved in facilitated transport are transport proteins, and they function as either channels for the material or carriers. In both cases, they are transmembrane proteins. Channels are specific for the transported substance. Channel proteins have hydrophilic domains exposed to the intracellular and extracellular fluids. In addition, they have a hydrophilic channel through their core that provides a hydrated opening through the membrane layers ((Figure)). Passage through the channel allows polar compounds to avoid the plasma membrane’s nonpolar central layer that would otherwise slow or prevent their entry into the cell. Aquaporins are channel proteins that allow water to pass through the membrane at a very high rate.

Facilitated transport moves substances down their concentration gradients. They may cross the plasma membrane with the aid of channel proteins. (credit: modification of work by Mariana Ruiz Villareal)


This illustration shows a small substance passing through the pore of a protein channel that is embedded in the plasma membrane.

Channel proteins are either open at all times or they are “gated,” which controls the channel’s opening. When a particular ion attaches to the channel protein it may control the opening, or other mechanisms or substances may be involved. In some tissues, sodium and chloride ions pass freely through open channels; whereas, in other tissues a gate must open to allow passage. An example of this occurs in the kidney, where there are both channel forms in different parts of the renal tubules. Cells involved in transmitting electrical impulses, such as nerve and muscle cells, have gated channels for sodium, potassium, and calcium in their membranes. Opening and closing these channels changes the relative concentrations on opposing sides of the membrane of these ions, resulting in facilitating electrical transmission along membranes (in the case of nerve cells) or in muscle contraction (in the case of muscle cells).

Carrier Proteins

Another type of protein embedded in the plasma membrane is a carrier protein. This aptly named protein binds a substance and, thus triggers a change of its own shape, moving the bound molecule from the cell’s outside to its interior ((Figure)). Depending on the gradient, the material may move in the opposite direction. Carrier proteins are typically specific for a single substance. This selectivity adds to the plasma membrane’s overall selectivity. Scientists poorly understand the exact mechanism for the change of shape. Proteins can change shape when their hydrogen bonds are affected, but this may not fully explain this mechanism. Each carrier protein is specific to one substance, and there are a finite number of these proteins in any membrane. This can cause problems in transporting enough material for the cell to function properly. When all of the proteins are bound to their ligands, they are saturated and the rate of transport is at its maximum. Increasing the concentration gradient at this point will not result in an increased transport rate.

Some substances are able to move down their concentration gradient across the plasma membrane with the aid of carrier proteins. Carrier proteins change shape as they move molecules across the membrane. (credit: modification of work by Mariana Ruiz Villareal)


This illustration shows a carrier protein embedded in the membrane with an opening that initially faces the extracellular surface. After a substance binds the carrier, it changes shape so that the opening faces the cytoplasm, and the substance is released.

An example of this process occurs in the kidney. In one part, the kidney filters glucose, water, salts, ions, and amino acids that the body requires. This filtrate, which includes glucose, then reabsorbs in another part of the kidney. Because there are only a finite number of carrier proteins for glucose, if more glucose is present than the proteins can handle, the excess is not transported and the body excretes this through urine. In a diabetic individual, the term is “spilling glucose into the urine.” A different group of carrier proteins, glucose transport proteins, or GLUTs, are involved in transporting glucose and other hexose sugars through plasma membranes within the body.

Channel and carrier proteins transport material at different rates. Channel proteins transport much more quickly than carrier proteins. Channel proteins facilitate diffusion at a rate of tens of millions of molecules per second; whereas, carrier proteins work at a rate of a thousand to a million molecules per second.

Osmosis

Osmosis is the movement of water through a semipermeable membrane according to the water’s concentration gradient across the membrane, which is inversely proportional to the solutes’ concentration. While diffusion transports material across membranes and within cells, osmosis transports only water across a membrane and the membrane limits the solutes’ diffusion in the water. Not surprisingly, the aquaporins that facilitate water movement play a large role in osmosis, most prominently in red blood cells and the membranes of kidney tubules.

Mechanism

Osmosis is a special case of diffusion. Water, like other substances, moves from an area of high concentration to one of low concentration. An obvious question is what makes water move at all? Imagine a beaker with a semipermeable membrane separating the two sides or halves ((Figure)). On both sides of the membrane the water level is the same, but there are different dissolved substance concentrations, or solute, that cannot cross the membrane (otherwise the solute crossing the membrane would balance concentrations on each side). If the solution’s volume on both sides of the membrane is the same, but the solute’s concentrations are different, then there are different amounts of water, the solvent, on either side of the membrane.

In osmosis, water always moves from an area of higher water concentration to one of lower concentration. In the diagram, the solute cannot pass through the selectively permeable membrane, but the water can.


This illustration shows a container whose contents are separated by a semipermeable membrane. Initially, there is a high concentration of solute on the right side of the membrane and a low concentration of the left. Over time, water diffuses across the membrane toward the side of the container that initially had a higher concentration of solute (lower concentration of water). As a result of osmosis, the water level is higher on this side of the membrane, and the solute concentration is the same on both sides.

To illustrate this, imagine two full water glasses. One has a single teaspoon of sugar in it; whereas, the second one contains one-quarter cup of sugar. If the total volume of the solutions in both cups is the same, which cup contains more water? Because the large sugar amount in the second cup takes up much more space than the teaspoon of sugar in the first cup, the first cup has more water in it.

Returning to the beaker example, recall that it has a solute mixture on either side of the 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. Thus, 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 water’s concentration gradient goes to zero or until the water’s hydrostatic pressure balances the osmotic pressure. Osmosis proceeds constantly in living systems.

Tonicity

Tonicity describes how an extracellular solution can change a cell’s volume by affecting osmosis. A solution’s tonicity often directly correlates with the solution’s osmolarity. Osmolarity describes the solution’s total solute concentration. A solution with low osmolarity has a greater number of water molecules relative to the number of solute particles. A solution with high osmolarity has fewer water molecules with respect to solute particles. In a situation in which a membrane permeable to water, though not to the solute separates two different osmolarities, water will move from the membrane’s side with lower osmolarity (and more water) to the side with higher osmolarity (and less water). This effect makes sense if you remember that the solute cannot move across the membrane, and thus the only component in the system that can move—the water—moves along its own concentration gradient. An important distinction that concerns living systems is that osmolarity measures the number of particles (which may be molecules) in a solution. Therefore, a solution that is cloudy with cells may have a lower osmolarity than a solution that is clear, if the second solution contains more dissolved molecules than there are cells.

Hypotonic Solutions

Scientists use three terms—hypotonic, isotonic, and hypertonic—to relate the cell’s osmolarity to the extracellular fluid’s osmolarity that contains the cells. In a hypotonic situation, the extracellular fluid has lower osmolarity 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 solute concentration, or a lower osmolarity, than the cell cytoplasm.) It also means that the extracellular fluid has a higher water concentration in the solution than does the cell. In this situation, water will follow its concentration gradient and enter the cell.

Hypertonic Solutions

As for a hypertonic solution, the prefix hyper– refers to the extracellular fluid having a higher osmolarity than the cell’s cytoplasm; therefore, the fluid contains less water than the cell does. Because the cell has a relatively higher water concentration, water will leave the cell.

Isotonic Solutions

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

Visual Connection
Osmotic pressure changes red blood cells’ shape in hypertonic, isotonic, and hypotonic solutions. (credit: Mariana Ruiz Villareal)


The left part of this illustration shows shriveled red blood cells bathed in a hypertonic solution. The middle part shows healthy red blood cells bathed in an isotonic solution, and the right part shows bloated red blood cells bathed in a hypotonic solution.

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

Link to Learning

For a video illustrating the diffusion process in solutions, visit this site.

Tonicity in Living Systems

In a hypotonic environment, water enters a cell, and the cell swells. In an isotonic condition, the relative solute and solvent concentrations are equal on both membrane sides. There is no net water movement; therefore, there is no change in the cell’s size. In a hypertonic solution, water leaves a cell and the cell shrinks. If either the hypo- or hyper- condition goes to excess, the cell’s functions become compromised, and the cell may be destroyed.

A red blood cell will burst, or lyse, when it swells beyond the plasma membrane’s capability to expand. Remember, the membrane resembles a mosaic, with discrete spaces between the molecules comprising it. If the cell swells, and the spaces between the lipids and proteins become too large, the cell will break apart.

In contrast, when excessive water amounts leave a red blood cell, the cell shrinks, or crenates. This has the effect of concentrating the solutes left in the cell, making the cytosol denser and interfering with diffusion within the cell. The cell’s ability to function will be compromised and may also result in the cell’s death.

Various living things have ways of controlling the effects of osmosis—a mechanism we call osmoregulation. Some organisms, such as plants, fungi, bacteria, and some protists, have cell walls that surround the plasma membrane and prevent cell lysis in a hypotonic solution. The plasma membrane can only expand to the cell wall’s limit, so the cell will not lyse. The cytoplasm in plants is always slightly hypertonic to the cellular environment, and water will always enter a cell if water is available. This water inflow produces turgor pressure, which stiffens the plant’s cell walls ((Figure)). In nonwoody plants, turgor pressure supports the plant. Conversly, if you do not water the plant, the extracellular fluid will become hypertonic, causing water to leave the cell. In this condition, the cell does not shrink because the cell wall is not flexible. However, the cell membrane detaches from the wall and constricts the cytoplasm. We call this plasmolysis. Plants lose turgor pressure in this condition and wilt ((Figure)).

The turgor pressure within a plant cell depends on the solution’s tonicity in which it is bathed. (credit: modification of work by Mariana Ruiz Villareal)


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.

Without adequate water, the plant on the left has lost turgor pressure, visible in its wilting. Watering the plant (right) will restore the turgor pressure. (credit: Victor M. Vicente Selvas)


The left photo shows a plant that has wilted, with dark green leaves that are shriveled, and appear dry. The photo on the right shows a healthy plant, with broad light green leaves that appear soft and pliable.

Tonicity is a concern for all living things. For example, paramecia and amoebas, which are protists that lack cell walls, have contractile vacuoles. This vesicle collects excess water from the cell and pumps it out, keeping the cell from lysing as it takes on water from its environment ((Figure)).

A paramecium’s contractile vacuole, here visualized using bright field light microscopy at 480x magnification, continuously pumps water out of the organism’s body to keep it from bursting in a hypotonic medium. (credit: modification of work by NIH; scale-bar data from Matt Russell)


A transmission electron micrograph shows an oval-shaped cell. Contractile vacuoles are prominent structures embedded in the cell membrane that pump out water.

Many marine invertebrates have internal salt levels matched to their environments, making them isotonic with the water in which they live. Fish, however, must spend approximately five percent of their metabolic energy maintaining osmotic homeostasis. Freshwater fish live in an environment that is hypotonic to their cells. These fish actively take in salt through their gills and excrete diluted urine to rid themselves of excess water. Saltwater fish live in the reverse environment, which is hypertonic to their cells, and they secrete salt through their gills and excrete highly concentrated urine.

In vertebrates, the kidneys regulate the water amount in the body. Osmoreceptors are specialized cells in the brain that monitor solute concentration in the blood. If the solute levels increase beyond a certain range, a hormone releases that slows water loss through the kidney and dilutes the blood to safer levels. Animals also have high albumin concentrations, which the liver produces, in their blood. This protein is too large to pass easily through plasma membranes and is a major factor in controlling the osmotic pressures applied to tissues.

Section Summary

The passive transport forms, diffusion and osmosis, move materials of small molecular weight across membranes. Substances diffuse from high to lower concentration areas, and this process continues until the substance evenly distributes itself in a system. In solutions containing more than one substance, each molecule type diffuses according to its own concentration gradient, independent of other substances diffusing. Many factors can affect the diffusion rate, such as concentration gradient, diffusing, particle sizes, and the system’s temperature.

In living systems, the plasma membrane mediates substances diffusing in and out of cells. Some materials diffuse readily through the membrane, but others are hindered and only can pass through due to specialized proteins such as channels and transporters. The chemistry of living things occurs in aqueous solutions, and balancing the concentrations of those solutions is an ongoing problem. In living systems, diffusing some substances would be slow or difficult without membrane proteins that facilitate transport.

Visual Connection Questions

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

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

Review Questions

Water moves via osmosis _________.

  1. throughout the cytoplasm
  2. from an area with a high concentration of other solutes to a lower one
  3. from an area with a high concentration of water to one of lower concentration
  4. from an area with a low concentration of water to higher concentration

C

The principal force driving movement in diffusion is the __________.

  1. temperature
  2. particle size
  3. concentration gradient
  4. membrane surface area

C

What problem is faced by organisms that live in fresh water?

  1. Their bodies tend to take in too much water.
  2. They have no way of controlling their tonicity.
  3. Only salt water poses problems for animals that live in it.
  4. Their bodies tend to lose too much water to their environment.

A

In which situation would passive transport not use a transport protein for entry into a cell?

  1. water flowing into a hypertonic environment
  2. glucose being absorbed from the blood
  3. an ion flowing into a nerve cell to create an electrical potential
  4. oxygen moving into a cell after oxygen deprivation

D

Critical Thinking Questions

Discuss why the following affect the rate of diffusion: molecular size, temperature, solution density, and the distance that must be traveled.

Heavy molecules move more slowly than lighter ones. It takes more energy in the medium to move them along. Increasing or decreasing temperature increases or decreases the energy in the medium, affecting molecular movement. The denser a solution is, the harder it is for molecules to move through it, causing diffusion to slow down due to friction. Living cells require a steady supply of nutrients and a steady rate of waste removal. If the distance these substances need to travel is too great, diffusion cannot move nutrients and waste materials efficiently to sustain life.

Why does water move through a membrane?

Water moves through a 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.

Both of the regular intravenous solutions administered in medicine, normal saline and lactated Ringer’s solution, are isotonic. Why is this important?

Injection of isotonic solutions ensures that there will be no perturbation of the osmotic balance, and no water taken from tissues or added to them from the blood.

Describe two ways that decreasing temperature would affect the rate of diffusion of molecules across a cell’s plasma membrane.

Decreasing temperature will decrease the kinetic energy in the system. A lower temperature means less energy in the molecules, so they will move at a slower speed. Lowering temperature also decreases the kinetic energy of the molecules in the plasma membrane, compressing them together. This increases the density of the plasma membrane, which slows diffusion into the cell.

A cell develops a mutation in its potassium channels that prevents the ions from leaving the cell. If the cell’s aquaporins are still active, what will happen to the cell? Be sure to describe the tonicity and osmolarity of the cell.

Without functional potassium channels, the potassium ions that are pumped into the cell will accumulate. This increases the osmolarity inside the cell, creating a hypotonic solution. Since the plasma membrane is still selectively permeable to water by the aquaporins, water will flow into the cell. If the potassium concentration is high enough, enough water will eventually flow into the cell to lyse it.

Glossary

aquaporin
channel protein that allows water through the membrane at a very high rate
carrier protein
membrane protein that moves a substance across the plasma membrane by changing its own shape
channel protein
membrane protein that allows a substance to pass through its hollow core across the plasma membrane
concentration gradient
area of high concentration adjacent to an area of low concentration
diffusion
passive transport process of low-molecular weight material according to its concentration gradient
facilitated transport
process by which material moves down a concentration gradient (from high to low concentration) using integral membrane proteins
hypertonic
situation in which extracellular fluid has a higher osmolarity than the fluid inside the cell, resulting in water moving out of the cell
hypotonic
situation in which extracellular fluid has a lower osmolarity than the fluid inside the cell, resulting in water moving into the cell
isotonic
situation in which the extracellular fluid has the same osmolarity as the fluid inside the cell, resulting in no net water movement into or out of the cell
osmolarity
total amount of substances dissolved in a specific amount of solution
osmosis
transport of water through a semipermeable membrane according to the water’s concentration gradient across the membrane that results from the presence of solute that cannot pass through the membrane
passive transport
method of transporting material through a membrane that does not require energy
plasmolysis
detaching the cell membrane from the cell wall and constricting the cell membrane when a plant cell is in a hypertonic solution
selectively permeable
membrane characteristic that allows some substances through
solute
substance dissolved in a liquid to form a solution
tonicity
amount of solute in a solution
transport protein
membrane protein that facilitates a substance’s passage across a membrane by binding it

24

Active Transport

Learning Objectives

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

  • Understand how electrochemical gradients affect ions
  • Distinguish between primary active transport and secondary active transport

Active transport mechanisms require 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 substance’s concentration inside the cell is greater than its concentration in the extracellular fluid (and vice versa)—the cell must use energy to move the substance. Some active transport mechanisms move small-molecular weight materials, such as ions, through the membrane. Other mechanisms transport much larger molecules.

Electrochemical Gradient

We have discussed simple concentration gradients—a substance’s differential concentrations across a space or a membrane—but in living systems, gradients are more complex. Because ions move into and out of cells and because cells contain proteins that do not move across the membrane and are mostly negatively charged, there is also 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, and at the same time, cells have higher concentrations of potassium (K+) and lower concentrations of sodium (Na+) than the extracellular fluid. Thus in a living cell, the concentration gradient of Na+ tends to drive it into the cell, and its electrical gradient (a positive ion) also drives it inward to the negatively charged interior. However, the situation is more complex for other elements such as potassium. The electrical gradient of K+, a positive ion, also drives it into the cell, but the concentration gradient of K+ drives K+out of the cell ((Figure)). We call the combined concentration gradient and electrical charge that affects an ion its electrochemical gradient.

Visual Connection
Electrochemical gradients arise from the combined effects of concentration gradients and electrical gradients. Structures labeled A represent proteins. (credit: “Synaptitude”/Wikimedia Commons)


This illustration shows a membrane bilayer with a potassium channel embedded in it. The cytoplasm has a high concentration of potassium associated with a negatively charged molecule. The extracellular fluid has a high concentration of sodium associated with chlorine ions.

Injecting a potassium solution into a person’s blood is lethal. This is how capital punishment and euthanasia subjects die. Why do you think a potassium solution injection is lethal?

Moving Against a Gradient

To move substances against a concentration or electrochemical gradient, the cell must use energy. This energy comes from ATP generated through the cell’s metabolism. Active transport mechanisms, or pumps, work against electrochemical gradients. Small substances constantly pass through plasma membranes. Active transport maintains concentrations of ions and other substances that living cells require in the face of these passive movements. A cell may spend much of its metabolic energy supply maintaining these processes. (A red blood cell uses most of its metabolic energy to maintain the imbalance between exterior and interior sodium and potassium levels that the cell requires.) Because active transport mechanisms depend on a cell’s metabolism for energy, they are sensitive to many metabolic poisons that interfere with the ATP supply.

Two mechanisms exist for transporting small-molecular weight material and small molecules. Primary active transport moves ions across a membrane and creates a difference in charge across that membrane, which is directly dependent on ATP. Secondary active transport does not directly require ATP: instead, it is the movement of material due to the electrochemical gradient established by primary active transport.

Carrier Proteins for Active Transport

An important membrane adaption for active transport is the presence of specific carrier proteins or pumps to facilitate movement: there are three protein types or transporters ((Figure)). A uniporter carries one specific ion or molecule. A symporter carries two different ions or molecules, both in the same direction. An antiporter also carries two different ions or molecules, but in different directions. All of these transporters can also transport small, uncharged organic molecules like glucose. These three types of carrier proteins are also in facilitated diffusion, but they do not require ATP to work in that process. Some examples of pumps for active transport are Na+-K+ ATPase, which carries sodium and potassium ions, and H+-K+ ATPase, which carries hydrogen and potassium ions. Both of these are antiporter carrier proteins. Two other carrier proteins are Ca2+ ATPase and H+ ATPase, which carry only calcium and only hydrogen ions, respectively. Both are pumps.

A uniporter carries one molecule or ion. A symporter carries two different molecules or ions, both in the same direction. An antiporter also carries two different molecules or ions, but in different directions. (credit: modification of work by “Lupask”/Wikimedia Commons)


This illustration shows a plasma membrane with three transport proteins embedded in it. The left image shows a uniporter that transports a substance in one direction. The middle image shows a symporter that transports two different substances in the same direction. The right image shows an antiporter that transports two different substances in opposite directions.

Primary Active Transport

The primary active transport that functions with the active transport of sodium and potassium allows secondary active transport to occur. The second transport method is still active because it depends on using energy as does primary transport ((Figure)).

Primary active transport moves ions across a membrane, creating an electrochemical gradient (electrogenic transport). (credit: modification of work by Mariana Ruiz Villareal)


This illustration shows the sodium-potassium pump. Initially, the pumps opening faces the cytoplasm, where three sodium ions bind to it. The antiporter hydrolyzes and A T P to A D P 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 antiporter, which changes conformation again, releasing the potassium ions into the cytoplasm.

One of the most important pumps in animal cells is the sodium-potassium pump (Na+-K+ ATPase), which maintains the electrochemical gradient (and the correct concentrations of Na+ and K+) in living cells. The sodium-potassium pump moves K+ into the cell while moving Na+ out at the same time, at a ratio of three Na+ for every two K+ ions moved in. The Na+-K+ ATPase exists in two forms, depending on its orientation to the cell’s interior or exterior and its affinity for either sodium or potassium ions. The process consists of the following six steps.

  1. With the enzyme oriented towards the cell’s interior, the carrier has a high affinity for sodium ions. Three ions bind to the protein.
  2. The protein carrier hydrolyzes ATP and a low-energy phosphate group attaches to it.
  3. As a result, the carrier changes shape and reorients itself towards the membrane’s exterior. The protein’s affinity for sodium decreases and the three sodium ions leave the carrier.
  4. The shape change increases the carrier’s affinity for potassium ions, and two such ions attach to the protein. Subsequently, the low-energy phosphate group detaches from the carrier.
  5. With the phosphate group removed and potassium ions attached, the carrier protein repositions itself towards the cell’s interior.
  6. The carrier protein, in its new configuration, has a decreased affinity for potassium, and the two ions moves into the cytoplasm. The protein now has a higher affinity for sodium ions, and the process starts again.

Several things have happened as a result of this process. At this point, there are more sodium ions outside the cell than inside and more potassium ions inside than out. For every three sodium ions that move out, two potassium ions move in. This results in the interior being slightly more negative relative to the exterior. This difference in charge is important in creating the conditions necessary for the secondary process. The sodium-potassium pump is, therefore, an electrogenic pump (a pump that creates a charge imbalance), creating an electrical imbalance across the membrane and contributing to the membrane potential.

Link to Learning

Watch this video to see an active transport simulation in a sodium-potassium ATPase.

Secondary Active Transport (Co-transport)

Secondary active transport brings sodium ions, and possibly other compounds, into the cell. As sodium ion concentrations build outside of the plasma membrane because of the primary active transport process, this creates an electrochemical gradient. If a channel protein exists and is open, the sodium ions will pull through the membrane. This movement transports other substances that can attach themselves to the transport protein through the membrane ((Figure)). Many amino acids, as well as glucose, enter a cell this way. This secondary process also stores high-energy hydrogen ions in the mitochondria of plant and animal cells in order to produce ATP. The potential energy that accumulates in the stored hydrogen ions translates into kinetic energy as the ions surge through the channel protein ATP synthase, and that energy then converts ADP into ATP.

Visual Connection
An electrochemical gradient, which primary active transport creates, can move other substances against their concentration gradients, a process scientists call co-transport or secondary active transport. (credit: modification of work by Mariana Ruiz Villareal)


This illustration shows a membrane bilayer with two integral membrane proteins embedded in it. The first, a sodium-potassium pump, uses energy from A T P hydrolysis to pump three sodium ions out of the cell for every two potassium ions it pumps into the cell. The result is a high concentration of sodium outside the cell and a high concentration of potassium inside the cell. There is also a high concentration of amino acids outside the cell, and a low concentration inside. A sodium-amino acid co-transporter simultaneously transports sodium and the amino acid into the cell.

If the pH outside the cell decreases, would you expect the amount of amino acids transported into the cell to increase or decrease?

Section Summary

The combined gradient that affects an ion includes its concentration gradient and its electrical gradient. A positive ion, for example, might diffuse into a new area, down its concentration gradient, but if it is diffusing into an area of net positive charge, its electrical gradient hampers its diffusion. When dealing with ions in aqueous solutions, one must consider electrochemical and concentration gradient combinations, rather than just the concentration gradient alone. Living cells need certain substances that exist inside the cell 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 this transport. Active transport of small molecular-sized materials uses integral proteins in the cell membrane to move the materials. These proteins are analogous to pumps. Some pumps, which carry out primary active transport, couple directly with ATP to drive their action. In co-transport (or secondary active transport), energy from primary transport can move another substance into the cell and up its concentration gradient.

Visual Connection Questions

(Figure) Injecting a potassium solution into a person’s blood is lethal. Capital punishment and euthanasia utilize this method in their subjects. Why do you think a potassium solution injection is lethal?

(Figure) Cells typically have a high concentration of potassium in the cytoplasm and are bathed in a high concentration of sodium. Injection of potassium dissipates this electrochemical gradient. In heart muscle, the sodium/potassium potential is responsible for transmitting the signal that causes the muscle to contract. When this potential is dissipated, the signal can’t be transmitted, and the heart stops beating. Potassium injections are also used to stop the heart from beating during surgery.

(Figure) If the pH outside the cell decreases, would you expect the amount of amino acids transported into the cell to increase or decrease?

(Figure) A decrease in pH means an increase in positively charged H+ ions, and an increase in the electrical gradient across the membrane. The transport of amino acids into the cell will increase.

Review Questions

Active transport must function continuously because __________.

  1. plasma membranes wear out
  2. not all membranes are amphiphilic
  3. facilitated transport opposes active transport
  4. diffusion is constantly moving solutes in opposite directions

D

How does the sodium-potassium pump make the interior of the cell negatively charged?

  1. by expelling anions
  2. by pulling in anions
  3. by expelling more cations than are taken in
  4. by taking in and expelling an equal number of cations

C

What is the combination of an electrical gradient and a concentration gradient called?

  1. potential gradient
  2. electrical potential
  3. concentration potential
  4. electrochemical gradient

D

Critical Thinking Questions

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 the activity of pumps.

How does the sodium-potassium pump contribute to the net negative charge of the interior of the cell?

The sodium-potassium pump forces out three (positive) Na+ ions for every two (positive) K+ ions it pumps in, thus the cell loses a positive charge at every cycle of the pump.

Glucose from digested food enters intestinal epithelial cells by active transport. Why would intestinal cells use active transport when most body cells use facilitated diffusion?

Intestinal epithelial cells use active transport to fulfill their specific role as the cells that transfer glucose from the digested food to the bloodstream. Intestinal cells are exposed to an environment with fluctuating glucose levels. Immediately after eating, glucose in the gut lumen will be high, and could accumulate in intestinal cells by diffusion. However, when the gut lumen is empty, glucose levels are higher in the intestinal cells. If glucose moved by facilitated diffusion, this would cause glucose to flow back out of the intestinal cells and into the gut. Active transport proteins ensure that glucose moves into the intestinal cells, and cannot move back into the gut. It also ensures that glucose transport continues to occur even if high levels of glucose are already present in the intestinal cells. This maximizes the amount of energy the body can harvest from food.

The sodium/calcium exchanger (NCX) transports sodium into and calcium out of cardiac muscle cells. Describe why this transporter is classified as secondary active transport.

The NCX moves sodium down its electrochemical gradient into the cell. Since sodium’s electrochemical gradient is created by the Na+/K+ pump, a transport pump that requires ATP hydrolysis to establish the gradient, the NCX is a secondary active transport process.

Glossary

active transport
method of transporting material that requires energy
antiporter
transporter that carries two ions or small molecules in different directions
electrochemical gradient
a combined electrical and chemical force that produces a gradient
electrogenic pump
pump that creates a charge imbalance
primary active transport
active transport that moves ions or small molecules across a membrane and may create a difference in charge across that membrane
pump
active transport mechanism that works against electrochemical gradients
secondary active transport
movement of material that results from primary active transport to the electrochemical gradient
symporter
transporter that carries two different ions or small molecules, both in the same direction
transporter
specific carrier proteins or pumps that facilitate movement
uniporter
transporter that carries one specific ion or molecule

25

Bulk Transport

Learning Objectives

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

  • Describe endocytosis, including phagocytosis, pinocytosis, and receptor-mediated endocytosis
  • Understand the process of exocytosis

In addition to moving small ions and molecules through the membrane, cells also need to remove and take in larger molecules and particles (see (Figure) for examples). Some cells are even capable of engulfing entire unicellular microorganisms. You might have correctly hypothesized that when a cell uptakes and releases large particles, it requires energy. A large particle, however, cannot pass through the membrane, even with energy that the cell supplies.

Endocytosis

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 endocytosis variations, but all share a common characteristic: the cell’s plasma membrane invaginates, forming a pocket around the target particle. The pocket pinches off, resulting in the particle containing itself in a newly created intracellular vesicle formed from the plasma membrane.

Phagocytosis

Phagocytosis (the condition of “cell eating”) is the process by which a cell takes in large particles, such as other cells or relatively large particles. For example, when microorganisms invade the human body, a type of white blood cell, a neutrophil, will remove the invaders through this process, surrounding and engulfing the microorganism, which the neutrophil then destroys ((Figure)).

In phagocytosis, the cell membrane surrounds the particle and engulfs it. (credit: modification of work by Mariana Ruiz Villareal)


This illustration shows a plasma membrane forming a pocket around a particle in the extracellular fluid. The membrane subsequently engulfs the particle, which becomes trapped in a vacuole.

In preparation for phagocytosis, a portion of the plasma membrane’s inward-facing surface becomes coated with the protein clathrin, which stabilizes this membrane’s section. The membrane’s coated portion then extends from the cell’s body and surrounds the particle, eventually enclosing it. Once the vesicle containing the particle is enclosed within the cell, the clathrin disengages from the membrane and the vesicle merges with a lysosome for breaking down the material in the newly formed compartment (endosome). When accessible nutrients from the vesicular contents’ degradation have been extracted, the newly formed endosome merges with the plasma membrane and releases its contents into the extracellular fluid. The endosomal membrane again becomes part of the plasma membrane.

Pinocytosis

A variation of endocytosis is pinocytosis. This literally means “cell drinking”. Discovered by Warren Lewis in 1929, this American embryologist and cell biologist described a process whereby he assumed that the cell was purposefully taking in extracellular fluid. In reality, this is a process that takes in molecules, including water, which the cell needs from the extracellular fluid. Pinocytosis results in a much smaller vesicle than does phagocytosis, and the vesicle does not need to merge with a lysosome ((Figure)).

In pinocytosis, the cell membrane invaginates, surrounds a small volume of fluid, and pinches off. (credit: modification of work by Mariana Ruiz Villareal)


This illustration 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.

A variation of pinocytosis is potocytosis. This process uses a coating protein, caveolin, on the plasma membrane’s cytoplasmic side, which performs a similar function to clathrin. The cavities in the plasma membrane that form the vacuoles have membrane receptors and lipid rafts in addition to caveolin. The vacuoles or vesicles formed in caveolae (singular caveola) are smaller than those in pinocytosis. Potocytosis brings small molecules into the cell and transports them through the cell for their release on the other side, a process we call transcytosis.

Receptor-mediated Endocytosis

A targeted variation of endocytosis employs receptor proteins in the plasma membrane that have a specific binding affinity for certain substances ((Figure)).

In receptor-mediated endocytosis, the cell’s uptake of substances targets a single type of substance that binds to the receptor on the cell membrane’s external surface. (credit: modification of work by Mariana Ruiz Villareal)


This illustration 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 vesicle.

In receptor-mediated endocytosis, as in phagocytosis, clathrin attaches to the plasma membrane’s cytoplasmic side. If a compound’s uptake is dependent on receptor-mediated endocytosis and the process is ineffective, the material will not be removed from the tissue fluids or blood. Instead, it will stay in those fluids and increase in concentration. The failure of receptor-mediated endocytosis causes some human diseases. For example, receptor mediated endocytosis removes low density lipoprotein or LDL (or “bad” cholesterol) from the blood. 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 LDL particles.

Although receptor-mediated endocytosis is designed to bring specific substances that are normally in the extracellular fluid into the cell, other substances may gain entry into the cell at the same site. Flu viruses, diphtheria, and cholera toxin all have sites that cross-react with normal receptor-binding sites and gain entry into cells.

Link to Learning

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

Exocytosis

The reverse process of moving material into a cell is the process of exocytosis. Exocytosis is the opposite of the processes we discussed above in that its purpose is to expel material from the cell into the extracellular fluid. Waste material is enveloped in a membrane and fuses with the plasma membrane’s interior. This fusion opens the membranous envelope on the cell’s exterior, and the waste material expels into the extracellular space ((Figure)). Other examples of cells releasing molecules via exocytosis include extracellular matrix protein secretion and neurotransmitter secretion into the synaptic cleft by synaptic vesicles.

In exocytosis, vesicles containing substances fuse with the plasma membrane. The contents then release to the cell’s exterior. (credit: modification of work by Mariana Ruiz Villareal)


This illustration shows vesicles fusing with the plasma membrane and releasing their contents to the extracellular fluid.

Methods of Transport, Energy Requirements, and Types of Transported Material
Transport Method Active/Passive Material Transported
Diffusion Passive Small-molecular weight material
Osmosis Passive Water
Facilitated transport/diffusion Passive Sodium, potassium, calcium, glucose
Primary active transport Active Sodium, potassium, calcium
Secondary active transport Active Amino acids, lactose
Phagocytosis Active Large macromolecules, whole cells, or cellular structures
Pinocytosis and potocytosis Active Small molecules (liquids/water)
Receptor-mediated endocytosis Active Large quantities of macromolecules

Section Summary

Active transport methods require directly using ATP to fuel the transport. In a process scientists call phagocytosis, other cells can engulf large particles, such as macromolecules, cell parts, or whole cells. In phagocytosis, a portion of the membrane invaginates and flows around the particle, eventually pinching off and leaving the particle entirely enclosed by a plasma membrane’s envelope. The cell breaks down vesicle contents, with the particles either used as food or dispatched. Pinocytosis is a similar process on a smaller scale. The plasma membrane invaginates and pinches off, producing a small envelope of fluid from outside the cell. Pinocytosis imports substances that the cell needs from the extracellular fluid. The cell expels waste in a similar but reverse manner. It pushes a membranous vacuole to the plasma membrane, allowing the vacuole to fuse with the membrane and incorporate itself into the membrane structure, releasing its contents to the exterior.

Review Questions

What happens to the membrane of a vesicle after exocytosis?

  1. It leaves the cell.
  2. It is disassembled by the cell.
  3. It fuses with and becomes part of the plasma membrane.
  4. It is used again in another exocytosis event.

C

Which transport mechanism can bring whole cells into a cell?

  1. pinocytosis
  2. phagocytosis
  3. facilitated transport
  4. primary active transport

B

In what important way does receptor-mediated endocytosis differ from phagocytosis?

  1. It transports only small amounts of fluid.
  2. It does not involve the pinching off of membrane.
  3. It brings in only a specifically targeted substance.
  4. It brings substances into the cell, while phagocytosis removes substances.

C

Many viruses enter host cells through receptor-mediated endocytosis. What is an advantage of this entry strategy?

  1. The virus directly enters the cytoplasm of the cell.
  2. The virus is protected from recognition by white blood cells.
  3. The virus only enters its target host cell type.
  4. The virus can directly inject its genome into the cell’s nucleus.

C

Which of the following organelles relies on exocytosis to complete its function?

  1. Golgi apparatus
  2. vacuole
  3. mitochondria
  4. endoplasmic reticulum

A

Imagine a cell can perform exocytosis, but only minimal endocytosis. What would happen to the cell?

  1. The cell would secrete all its intracellular proteins.
  2. The plasma membrane would increase in size over time.
  3. The cell would stop expressing integral receptor proteins in its plasma membrane.
  4. The cell would lyse.

B

Critical Thinking Questions

Why is it important that there are different types of proteins in plasma membranes for the transport of materials into and out of a cell?

The proteins allow a cell to select what compound will be transported, meeting the needs of the cell and not bringing in anything else.

Why do ions have a difficult time getting through plasma membranes despite their small size?

Ions are charged, and consequently, they are hydrophilic and cannot associate with the lipid portion of the membrane. Ions must be transported by carrier proteins or ion channels.

Glossary

caveolin
protein that coats the plasma membrane’s cytoplasmic side and participates in the liquid uptake process by potocytosis
clathrin
protein that coats the plasma membrane’s inward-facing surface and assists in forming specialized structures, like coated pits, for phagocytosis
endocytosis
type of active transport that moves substances, including fluids and particles, into a cell
exocytosis
process of passing bulk material out of a cell
pinocytosis
a variation of endocytosis that imports macromolecules that the cell needs from the extracellular fluid
potocytosis
variation of pinocytosis that uses a different coating protein (caveolin) on the plasma membrane’s cytoplasmic side
receptor-mediated endocytosis
variation of endocytosis that involves using specific binding proteins in the plasma membrane for specific molecules or particles, and clathrin-coated pits that become clathrin-coated vesicles

VI

Metabolism

26

Introduction

A hummingbird needs energy to maintain prolonged periods of flight. The bird obtains its energy from taking in food and transforming the nutrients into energy through a series of biochemical reactions. The flight muscles in birds are extremely efficient in energy production. (credit: modification of work by Cory Zanker)


In this photo, a hummingbird drinks from a feeder.

Virtually every task performed by living organisms requires energy. Organisms require energy to perform heavy labor and exercise, but humans also use considerable energy while thinking, and even during sleep. Every organism’s living cells constantly use energy. Organisms import nutrients and other molecules. They metabolize (break down) and possibly synthesize into new molecules. If necessary, molecules modify, move around the cell and may distribute themselves to the entire organism. For example, the large proteins that make up muscles are actively built from smaller molecules. Complex carbohydrates break 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 to synthesize and break down molecules. Additionally, signaling molecules such as hormones and neurotransmitters transport between cells. Cells ingest and break down bacteria and viruses. Cells must also export waste and toxins to stay healthy, and many cells must swim or move surrounding materials via the beating motion of cellular appendages like cilia and flagella.

The cellular processes that we listed above require a steady supply of 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 perform with great efficiency.

27

Energy and Metabolism

Learning Objectives

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

  • Explain metabolic pathways and describe the two major types
  • Discuss how chemical reactions play a role in energy transfer

Scientists use the term bioenergetics to discuss the concept of energy flow ((Figure)) through living systems, such as cells. Cellular processes such as building and breaking down 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 what they have used, cells must continually produce more energy to replenish that which the many energy-requiring chemical reactions that constantly take place use. All of the chemical reactions that transpire inside cells, including those that use and release energy, are the cell’s metabolism.

Most life forms on earth obtain their energy from the sun. Plants use photosynthesis to capture sunlight, and herbivores eat those plants to obtain energy. Carnivores eat the herbivores, and decomposers digest plant and animal matter.

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

Carbohydrate Metabolism

Sugar (chemical reactions) metabolism (a simple carbohydrate) is a classic example of the many cellular processes that use and produce energy. Living things consume sugar as a major energy source, because sugar molecules have considerable energy stored within their bonds. The following equation describes the breakdown of glucose, a simple sugar:

{\text{C}}_{\text{6}}{\text{H}}_{\text{12}}{\text{O}}_{\text{6}}+{\text{6O}}_{\text{2}}\to 6{\text{CO}}_{\text{2}}+{\text{6H}}_{\text{2}}\text{O}+\text{energy}

Consumed carbohydrates have their origins in photosynthesizing organisms like plants ((Figure)). During photosynthesis, plants use the energy of sunlight to convert carbon dioxide gas (CO2) into sugar molecules, like glucose (C6H12O6). Because this process involves synthesizing a larger, energy-storing molecule, it requires an energy input to proceed. The following equation (notice that it is the reverse of the previous equation) describes the synthesis of glucose:

{\text{6CO}}_{\text{2}}+{\text{6H}}_{\text{2}}\text{O}+\text{energy}\to {\text{C}}_{\text{6}}{\text{H}}_{\text{12}}{\text{O}}_{\text{6}}+{\text{6O}}_{\text{2}}

During photosynthesis chemical reactions, energy is in the form of a very high-energy molecule scientists call ATP, or adenosine triphosphate. This is the primary energy currency of all cells. Just as the dollar is the currency we use to buy goods, cells use ATP molecules as energy currency to perform immediate work. The sugar (glucose) is stored as starch or glycogen. Energy-storing polymers like these break down into glucose to supply ATP molecules.

Solar energy is required to synthesize a glucose molecule during the photosynthesis reactions. In photosynthesis, light energy from the sun initially transforms into chemical energy that temporally stores itself in the energy carrier molecules ATP and NADPH (nicotinamide adenine dinucleotide phosphate). Photosynthesis later uses the stored energy in ATP and NADPH to build one glucose molecule from six molecules of CO2. This process is analogous to eating breakfast in the morning to acquire energy for your body that you can use later in the day. Under ideal conditions, energy from 18 molecules of ATP is required to synthesize one glucose molecule during photosynthesis reactions. Glucose molecules can also combine with and convert into other sugar types. When an organism consumes sugars, glucose molecules eventually make their way into each organism’s living cell. Inside the cell, each sugar molecule breaks down through a complex series of chemical reactions. The goal of these reactions is to harvest the energy stored inside the sugar molecules. The harvested energy makes high-energy ATP molecules, which perform work, powering many chemical reactions in the cell. The amount of energy needed to make one glucose molecule from six carbon dioxide molecules is 18 ATP molecules and 12 NADPH molecules (each one of which is energetically equivalent to three ATP molecules), or a total of 54 molecule equivalents required for synthesizing one glucose molecule. This process is a fundamental and efficient way for cells to generate the molecular energy that they require.

Plants, like this oak tree and acorn, use energy from sunlight to make sugar and other organic molecules. Both plants and animals (like this squirrel) use cellular respiration to derive energy from the organic molecules that plants originally produced. (credit “acorn”: modification of work by Noel Reynolds; credit “squirrel”: modification of work by Dawn Huczek)

The photo on the left shows acorns growing on an oak tree. The photo on the right shows a squirrel eating.

Metabolic Pathways

The processes of making and breaking down sugar molecules illustrate two types of metabolic pathways. A metabolic pathway is a series of interconnected biochemical reactions that convert a substrate molecule or molecules, step-by-step, through a series of metabolic intermediates, eventually yielding a final product or products. In the case of sugar metabolism, the first metabolic pathway synthesized sugar from smaller molecules, and the other pathway broke sugar down into smaller molecules. Scientists call these two opposite processes—the first requiring energy and the second producing energy—anabolic (building) and catabolic (breaking down) pathways, respectively. Consequently, building (anabolism) and degradation (catabolism) comprise metabolism.

Evolution Connection
This tree shows the evolution of the various branches of life. The vertical dimension is time. Early life forms, in blue, used anaerobic metabolism to obtain energy from their surroundings.

At the base of the evolutionary tree is the prokaryotic ancestor. This ancestor gave rise to archaebacteria, eubacteria, and Protista, which in turn gave rise to plants, fungi, and animals.

Evolution of Metabolic PathwaysThere is more to the complexity of metabolism than understanding the metabolic pathways alone. Metabolic complexity varies from organism to organism. Photosynthesis is the primary pathway in which photosynthetic organisms like plants (planktonic algae perform the majority of global synthesis) harvest the sun’s energy and convert it into carbohydrates. The by-product of photosynthesis is oxygen, which some cells require to carry out cellular respiration. During cellular respiration, oxygen aids in the catabolic breakdown of carbon compounds, like carbohydrates. Among the products are CO2 and ATP. In addition, some eukaryotes perform catabolic processes without oxygen (fermentation); that is, they perform or use anaerobic metabolism.

Organisms probably evolved anaerobic metabolism to survive (living organisms came into existence about 3.8 billion years ago, when the atmosphere lacked oxygen). Despite the differences between organisms and the complexity of metabolism, researchers have found that all branches of life share some of the same metabolic pathways, suggesting that all organisms evolved from the same ancient common ancestor ((Figure)). Evidence indicates that over time, the pathways diverged, adding specialized enzymes to allow organisms to better adapt to their environment, thus increasing their chance to survive. However, the underlying principle remains that all organisms must harvest energy from their environment and convert it to ATP to carry out cellular functions.

Anabolic and Catabolic Pathways

Anabolic pathways require an input of energy to synthesize complex molecules from simpler ones. Synthesizing sugar from CO2 is one example. Other examples are synthesizing large proteins from amino acid building blocks, and synthesizing new DNA strands from nucleic acid building blocks. These biosynthetic processes are critical to the cell’s life, take place constantly, and demand energy that ATP and other high-energy molecules like NADH (nicotinamide adenine dinucleotide) and NADPH provide ((Figure)).

ATP is an important molecule for cells to have in sufficient supply at all times. The breakdown of sugars illustrates how a single glucose molecule can store enough energy to make a great deal of ATP, 36 to 38 molecules. This is a catabolic pathway. Catabolic pathways involve degrading (or breaking down) complex molecules into simpler ones. Molecular energy stored in complex molecule bonds release in catabolic pathways and harvest in such a way that it can produce ATP. Other energy-storing molecules, such as fats, also break down through similar catabolic reactions to release energy and make ATP ((Figure)).

It is important to know that metabolic pathway chemical reactions do not take place spontaneously. A protein called an enzyme facilitates or catalyzes each reaction step. Enzymes are important for catalyzing all types of biological reactions—those that require energy as well as those that release energy.

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

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

Section Summary

Cells perform the functions of life through various chemical reactions. A cell’s metabolism refers to the chemical reactions that take place within it. There are metabolic reactions that involve breaking down complex chemicals into simpler ones, such as breaking down large macromolecules. Scientists refer to this process as catabolism, and we associate such reactions an energy release. On the other end of the spectrum, anabolism refers to metabolic processes that build complex molecules out of simpler ones, such as macromolecule synthesis. Anabolic processes require energy. Glucose synthesis and glucose breakdown are examples of anabolic and catabolic pathways, respectively.

Multiple Choice

Energy is stored long-term in the bonds of _____ and used short-term to perform work from a(n) _____ molecule.

  1. ATP : glucose
  2. an anabolic molecule : catabolic molecule
  3. glucose : ATP
  4. a catabolic molecule : anabolic molecule

C

DNA replication involves unwinding two strands of parent DNA, copying each strand to synthesize complementary strands, and releasing the parent and daughter DNA. Which of the following accurately describes this process?

  1. This is an anabolic process.
  2. This is a catabolic process.
  3. This is both anabolic and catabolic.
  4. This is a metabolic process but is neither anabolic nor catabolic.

A

Critical Thinking Questions

Does physical exercise 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.

Name two different cellular functions that require energy that parallel human energy-requiring functions.

Energy is required for cellular motion, through beating of cilia or flagella, as well as human motion, produced by muscle contraction. Cells also need energy to perform digestion, as humans require energy to digest food.

Glossary

anabolic
(also, anabolism) pathways that require an energy input to synthesize complex molecules from simpler ones
bioenergetics
study of energy flowing through living systems
catabolic
(also, catabolism) pathways in which complex molecules break down into simpler ones
metabolism
all the chemical reactions that take place inside cells, including anabolism and catabolism

28

Potential, Kinetic, Free, and Activation Energy

Learning Objectives

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

  • Define “energy”
  • Explain the difference between kinetic and potential energy
  • Discuss the concepts of free energy and activation energy
  • Describe endergonic and exergonic reactions

We define energy as the ability to do work. As you’ve learned, energy exists in different forms. For example, electrical energy, light energy, and heat energy are all different energy types. While these are all familiar energy types that one can see or feel, there is another energy type that is much less tangible. Scientists associate this energy with something as simple as an object above the ground. In order to appreciate the way energy flows into and out of biological systems, it is important to understand more about the different energy types that exist in the physical world.

Energy Types

When an object is in motion, there is energy. For example, an airplane in flight produces considerable energy. This is because moving objects are capable of enacting a change, or doing work. Think of a wrecking ball. Even a slow-moving wrecking ball can do considerable damage to other objects. However, a wrecking ball that is not in motion is incapable of performing work. Energy with objects in motion is kinetic energy. A speeding bullet, a walking person, rapid molecule movement in the air (which produces heat), and electromagnetic radiation like light all have kinetic energy.

What if we lift that same motionless wrecking ball two stories above a car with a crane? If the suspended wrecking ball is unmoving, can we associate energy with it? The answer is yes. The suspended wrecking ball has associated energy that is fundamentally different from the kinetic energy of objects in motion. This energy form results from the potential for the wrecking ball to do work. If we release the ball it would do work. Because this energy type refers to the potential to do work, we call it potential energy. Objects transfer their energy between kinetic and potential in the following way: As the wrecking ball hangs motionless, it has 0 kinetic and 100 percent potential energy. Once it releases, its kinetic energy begins to increase because it builds speed due to gravity. Simultaneously, as it nears the ground, it loses potential energy. Somewhere mid-fall it has 50 percent kinetic and 50 percent potential energy. Just before it hits the ground, the ball has nearly lost its potential energy and has near-maximal kinetic energy. Other examples of potential energy include water’s energy held behind a dam ((Figure)), or a person about to skydive from an airplane.

Water behind a dam 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)

The photo on the left shows a river that is blocked by a giant cement wall, called a dam. The photo on the right shows a waterfall.

We associate potential energy only with the matter’s location (such as a child sitting on a tree branch), but also with the matter’s structure. A spring on the ground has potential energy if it is compressed; so does a tautly pulled rubber band. The very existence of living cells relies heavily on structural potential energy. On a chemical level, the bonds that hold the molecules’ atoms together have potential energy. Remember that anabolic cellular pathways require energy to synthesize complex molecules from simpler ones, and catabolic pathways release energy when complex molecules break down. That certain chemical bonds’ breakdown can release energy 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 we eventually harness for use. This is because these bonds can release energy when broken. Scientists call the potential energy type that exists within chemical bonds that releases when those bonds break chemical energy ((Figure)). Chemical energy is responsible for providing living cells with energy from food. Breaking the molecular bonds within fuel molecules brings about the energy’s release.

The molecules in gasoline contain chemical energy within the chemical bonds. This energy transforms into kinetic energy that allows a car to race on a racetrack. (credit “car”: modification of work by Russell Trow)

The molecular formula of octane (top), which is a chain of eight carbons and eighteen hydrogens, fuels a racecar speeding along a track (bottom).

Link to Learning

Visit this site and select “A simple pendulum” on the menu (under “Harmonic Motion”) to see the shifting kinetic (K) and potential energy (U) of a pendulum in motion.

Free Energy

After learning that chemical reactions release energy when energy-storing bonds break, an important next question is how do we quantify and express the chemical reactions with the associated energy? How can we compare the energy that releases from one reaction to that of another reaction? We use a measurement of free energy to quantitate these energy transfers. Scientists call this free energy Gibbs free energy (abbreviated with the letter G) after Josiah Willard Gibbs, the scientist who developed the measurement. Recall that according to the second law of thermodynamics, all energy transfers involve losing some energy in an unusable form such as heat, resulting in entropy. Gibbs free energy specifically refers to the energy that takes place with a chemical reaction that is available after we account for entropy. In other words, Gibbs free energy is usable energy, or energy that is available to do work.

Every chemical reaction involves a change in free energy, called delta G (∆G). We can calculate the change in free energy for any system that undergoes such a change, such as a chemical reaction. To calculate ∆G, subtract the amount of energy lost to entropy (denoted as ∆S) from the system’s total energy change. Scientists call this total energy change in the system enthalpy and we denote it as ∆H. The formula for calculating ∆G is as follows, where the symbol T refers to absolute temperature in Kelvin (degrees Celsius + 273):

\Delta \text{G}=\Delta \text{H}-\text{T}\Delta \text{S}

We express a chemical reaction’s standard free energy change as an amount of energy per mole of the reaction product (either in kilojoules or kilocalories, kJ/mol or kcal/mol; 1 kJ = 0.239 kcal) under standard pH, temperature, and pressure conditions. We generally calculate standard pH, temperature, and pressure conditions at pH 7.0 in biological systems, 25 degrees Celsius, and 100 kilopascals (1 atm pressure), respectively. Note that cellular conditions vary considerably from these standard conditions, and so standard calculated ∆G values for biological reactions will be different inside the cell.

Endergonic Reactions and Exergonic Reactions

If energy releases during a chemical reaction, then the resulting value from the above equation will be a negative number. In other words, reactions that release energy have a ∆G < 0. A negative ∆G also means that the reaction’s products have less free energy than the reactants, because they gave off some free energy during the reaction. Scientists call reactions that have a negative ∆G and consequently release free energy exergonic reactions. Think: exergonic means energy is exiting the system. We also refer to these reactions as spontaneous reactions, because they can occur without adding energy into the system. Understanding which chemical reactions are spontaneous and release free energy is extremely useful for biologists, because these reactions can be harnessed to perform work inside the cell. We must draw an important distinction between the term spontaneous and the idea of a chemical reaction that occurs immediately. Contrary to the everyday use of the term, a spontaneous reaction is not one that suddenly or quickly occurs. Rusting iron is an example of a spontaneous reaction that occurs slowly, little by little, over time.

If a chemical reaction requires an energy input rather than releasing energy, then the ∆G for that reaction will be a positive value. In this case, the products have more free energy than the reactants. Thus, we can think of the reactions’ products as energy-storing molecules. We call these chemical reactions endergonic reactions, and they are non-spontaneous. An endergonic reaction will not take place on its own without adding free energy.

Let’s revisit the example of the synthesis and breakdown of the food molecule, glucose. Remember that building complex molecules, such as sugars, from simpler ones is an anabolic process and requires energy. Therefore, the chemical reactions involved in anabolic processes are endergonic reactions. Alternatively the catabolic process of breaking sugar down into simpler molecules releases energy in a series of exergonic reactions. Like the rust example above, the sugar breakdown involves spontaneous reactions, but these reactions do not occur instantaneously. (Figure) shows some other examples of endergonic and exergonic reactions. Later sections will provide more information about what else is required to make even spontaneous reactions happen more efficiently.

Visual Connection
This figure shows some examples of endergonic processes (ones that require energy) and exergonic processes (ones that release energy). These include (a) a compost pile decomposing, (b) a chick developing from a fertilized egg, (c) sand art destruction, and (d) a ball rolling down a hill. (credit a: modification of work by Natalie Maynor; credit b: modification of work by USDA; credit c: modification of work by “Athlex”/Flickr; credit d: modification of work by Harry Malsch)

There are four photos show. The first photo shows a pile of wood chips and dirt, with small plants growing from this. The second photo shows a small baby bird breaking out of its egg as it hatches. The third photo shows a large patch of desert where someone has drawn patterns in the sand. The fourth photo shows a grassy hill outside where people climb into giant inflatable balls and roll down the hillside.

Look at each of the processes, and decide if it is endergonic or exergonic. In each case, does enthalpy increase or decrease, and does entropy increase or decrease?

An important concept in studying metabolism and energy is that of chemical equilibrium. Most chemical reactions are reversible. They can proceed in both directions, releasing energy into their environment in one direction, and absorbing it from the environment in the other direction ((Figure)). The same is true for the chemical reactions involved in cell metabolism, such as the breaking down and building up of proteins into and from individual amino acids, respectively. Reactants within a closed system will undergo chemical reactions in both directions until they reach a state of equilibrium, which is one of the lowest possible free energy and a state of maximal entropy. To push the reactants and products away from a state of equilibrium requires energy. Either reactants or products must be added, removed, or changed. If a cell were a closed system, its chemical reactions would reach equilibrium, and it would die because there would be insufficient free energy left to perform the necessary work to maintain life. In a living cell, chemical reactions are constantly moving towards equilibrium, but never reach it. This is because a living cell is an open system. Materials pass in and out, the cell recycles the products of certain chemical reactions into other reactions, and there is never chemical equilibrium. In this way, living organisms are in a constant energy-requiring, uphill battle against equilibrium and entropy. This constant energy supply ultimately comes from sunlight, which produces nutrients in the photosynthesis process.

Exergonic and endergonic reactions result in changes in Gibbs free energy. Exergonic reactions release energy. Endergonic reactions require energy to proceed.

The two plots show the change in Gibbs free energy as reactants are converted to products. Gibbs free energy decreases with time for an exergonic reaction (left), and the reaction is spontaneous. Gibbs free energy increases with time for an endergonic reaction (right), and the reaction is not spontaneous.

Activation Energy

There is another important concept that we must consider regarding endergonic and exergonic reactions. Even exergonic reactions require a small amount of energy input before they can proceed with their energy-releasing steps. These reactions have a net release of energy, but still require some initial energy. Scientists call this small amount of energy input necessary for all chemical reactions to occur the activation energy (or free energy of activation) abbreviated as EA ((Figure)).

Why would an energy-releasing, negative ∆G reaction actually require some energy to proceed? The reason lies in the steps that take place during a chemical reaction. During chemical reactions, certain chemical bonds break and new ones form. For example, when a glucose molecule breaks down, bonds between the molecule’s carbon atoms break. Since these are energy-storing bonds, they release energy when broken. However, to get them into a state that allows the bonds to break, the molecule must be somewhat contorted. A small energy input is required to achieve this contorted state. This contorted state is the transition state, and it is a high-energy, unstable state. For this reason, reactant molecules do not last long in their transition state, but very quickly proceed to the chemical reaction’s next steps. Free energy diagrams illustrate the energy profiles for a given reaction. Whether the reaction is exergonic or endergonic determines whether the products in the diagram will exist at a lower or higher energy state than both the reactants and the products. However, regardless of this measure, the transition state of the reaction exists at a higher energy state than the reactants, and thus, EA is always positive.

Link to Learning

Watch an animation of the move from free energy to transition state at this site.

From where does the activation energy that chemical reactants require come? The activation energy’s required source to push reactions forward is typically heat energy from the surroundings. Heat energy (the total bond energy of reactants or products in a chemical reaction) speeds up the molecule’s motion, increasing the frequency and force with which they collide. It also moves atoms and bonds within the molecule slightly, helping them reach their transition state. For this reason, heating a system will cause chemical reactants within that system to react more frequently. Increasing the pressure on a system has the same effect. Once reactants have absorbed enough heat energy from their surroundings to reach the transition state, the reaction will proceed.

The activation energy of a particular reaction determines the rate at which it will proceed. The higher the activation energy, the slower the chemical reaction. The example of iron rusting illustrates an inherently slow reaction. This reaction occurs slowly over time because of its high EA. Additionally, burning many fuels, which is strongly exergonic, will take place at a negligible rate unless sufficient heat from a spark overcomes their activation energy. However, once they begin to burn, the chemical reactions release enough heat to continue the burning process, supplying the activation energy for surrounding fuel molecules. Like these reactions outside of cells, the activation energy for most cellular reactions is too high for heat energy to overcome at efficient rates. In other words, in order for important cellular reactions to occur at appreciable rates (number of reactions per unit time), their activation energies must be lowered ((Figure)). Scientist refer to this as catalysis. This is a very good thing as far as living cells are concerned. Important macromolecules, such as proteins, DNA, and RNA, store considerable energy, and their breakdown is exergonic. If cellular temperatures alone provided enough heat energy for these exergonic reactions to overcome their activation barriers, the cell’s essential components would disintegrate.

Visual Connection
Activation energy is the energy required for a reaction to proceed, and it is lower if the reaction is catalyzed. This diagram’s horizontal axis describes the sequence of events in time.

This plot shows the activation energy for an exergonic reaction. As the reaction proceeds, energy initially increases to overcome the activation energy. In a catalyzed reaction, the activation energy is much lower. The energy then decreases such that the Gibbs free energy of the products is less than that of the reactants. The activation energy is the peak of the energy plot minus the energy of the reactants. The Gibbs free energy is the energy of the products minus the energy of the reactants.

If no activation energy were required to break down sucrose (table sugar), would you be able to store it in a sugar bowl?

Section Summary

Energy comes in many different forms. Objects in motion do physical work, and kinetic energy is the energy of objects in motion. Objects that are not in motion may have the potential to do work, and thus, have potential energy. Molecules also have potential energy because breaking molecular bonds has the potential to release energy. Living cells depend on harvesting potential energy from molecular bonds to perform work. Free energy is a measure of energy that is available to do work. A system’s free energy changes during energy transfers such as chemical reactions, and scientists refer to this change as ∆G.

A reaction’s ∆G can be negative or positive, meaning that the reaction releases energy or consumes energy, respectively. A reaction with a negative ∆G that gives off energy is an exergonic reaction. One with a positive ∆G that requires energy input is an endergonic reaction. Exergonic reactions are spontaneous because their products have less energy than their reactants. Endergonic reactions’ products have a higher energy state than the reactants, and so these are nonspontaneous reactions. However, all reactions (including spontaneous -∆G reactions) require an initial energy input in order to reach the transition state, at which they will proceed. This initial input of energy is the activation energy.

Visual Connection Questions

(Figure) Look at each of the processes, and decide if it is endergonic or exergonic. In each case, does enthalpy increase or decrease, and does entropy increase or decrease?

(Figure) A compost pile decomposing is an exergonic process; enthalpy increases (energy is released) and entropy increases (large molecules are broken down into smaller ones). A baby developing from a fertilized egg is an endergonic process; enthalpy decreases (energy is absorbed) and entropy decreases. Sand art being destroyed is an exergonic process; there is no change in enthalpy, but entropy increases. A ball rolling downhill is an exergonic process; enthalpy decreases (energy is released), but there is no change in entropy.

(Figure) If no activation energy were required to break down sucrose (table sugar), would you be able to store it in a sugar bowl?

(Figure) No. We can store chemical energy because of the need to overcome the barrier to its breakdown.

Review Questions

Consider a pendulum swinging. Which type(s) of energy is/are associated with the pendulum in the following instances: i. the moment at which it completes one cycle, just before it begins to fall back towards the other end, ii. the moment that it is in the middle between the two ends, and iii. just before it reaches the end of one cycle (just before instant i.).

  1. i. potential and kinetic, ii. potential and kinetic, iii. kinetic
  2. i. potential, ii. potential and kinetic, iii. potential and kinetic
  3. i. potential, ii. kinetic, iii. potential and kinetic
  4. i. potential and kinetic, ii. kinetic iii. kinetic

C

Which of the following comparisons or contrasts between endergonic and exergonic reactions is false?

  1. Endergonic reactions have a positive ∆G and exergonic reactions have a negative ∆G.
  2. Endergonic reactions consume energy and exergonic reactions release energy.
  3. Both endergonic and exergonic reactions require a small amount of energy to overcome an activation barrier.
  4. Endergonic reactions take place slowly and exergonic reactions take place quickly.

D

Which of the following is the best way to judge the relative activation energies between two given chemical reactions?

  1. Compare the ∆G values between the two reactions.
  2. Compare their reaction rates.
  3. Compare their ideal environmental conditions.
  4. Compare the spontaneity between the two reactions.

B

Critical Thinking Questions

Explain in your own words 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 due to a large energy of activation, which prevents the reaction from occurring quickly.

Describe the position of the transition state on a vertical energy scale, from low to high, relative to the position of the reactants and products, for both endergonic and exergonic reactions.

The transition state is always higher in energy than the reactants and the products of a reaction (therefore, above), regardless of whether the reaction is endergonic or exergonic.

Glossary

activation energy
energy necessary for reactions to occur
chemical energy
potential energy in chemical bonds that releases when those bonds are broken
endergonic
describes chemical reactions that require energy input
enthalpy
a system’s total energy
exergonic
describes chemical reactions that release free energy
free energy
Gibbs free energy is the usable energy, or energy that is available to do work
heat energy
total bond energy of reactants or products in a chemical reaction
kinetic energy
energy type that takes place with objects or particles in motion
potential energy
energy type that has the potential to do work; stored energy
transition state
high-energy, unstable state (an intermediate form between the substrate and the product) occurring during a chemical reaction

29

The Laws of Thermodynamics

Learning Objectives

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

  • Discuss the concept of entropy
  • Explain the first and second laws of thermodynamics

Thermodynamics refers to the study of energy and energy transfer involving physical matter. The matter and its environment relevant to a particular case of energy transfer are classified as a system, and everything outside that system is the surroundings. For instance, when heating a pot of water on the stove, the system includes the stove, the pot, and the water. Energy transfers within the system (between the stove, pot, and water). There are two types of systems: open and closed. An open system is one in which energy can transfer between the system and its surroundings. The stovetop system is open because it can lose heat into the air. A closed system is one that cannot transfer energy to its surroundings.

Biological organisms are open systems. Energy exchanges between them and their surroundings, as they consume energy-storing molecules and release energy to the environment by doing work. Like all things in the physical world, energy is subject to the laws of physics. The laws of thermodynamics govern the transfer of energy in and among all systems in the universe.

The First Law of Thermodynamics

The first law of thermodynamics deals with the total amount of energy in the universe. It states that this total amount of energy is constant. 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 transfer from place to place or transform 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 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 sunlight energy into the chemical energy stored within organic molecules ((Figure)). (Figure) examples of energy transformations.

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 very well. Chemical energy stored within organic molecules such as sugars and fats transforms through a series of cellular chemical reactions into energy within ATP molecules. 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 beating motion of cilia or flagella, contracting muscle fibers to create movement, and reproduction.

Here are two examples of energy transferring from one system to another and transformed from one form to another. Humans can convert the chemical energy in food, like this ice cream cone, into kinetic energy (the energy of movement to ride a bicycle). Plants can convert electromagnetic radiation (light energy) from the sun into chemical energy. (credit “ice cream”: modification of work by D. Sharon Pruitt; credit “kids on bikes”: modification of work by Michelle Riggen-Ransom; credit “leaf”: modification of work by Cory Zanker)


The left side of this diagram depicts energy being transferred from an ice cream cone to two boys riding a bike; this is described as chemical energy to kinetic energy. The right side depicts a plant converting light energy into chemical energy.

The Second Law of Thermodynamics

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. None of the energy transfers that we have discussed, along with all energy transfers and transformations in the universe, is 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, scientists define heat energy as energy that transfers from one system to another that is not doing work. For example, when an airplane flies through the air, it loses some of its energy as heat energy due to friction with the surrounding air. This friction actually heats the air by temporarily increasing air molecule speed. Likewise, some energy is lost as heat energy during cellular metabolic reactions. This is good for warm-blooded creatures like us, because heat energy helps to maintain our body temperature. Strictly speaking, no energy transfer is completely efficient, because some energy is lost in an unusable form.

An important concept in physical systems is that of order and disorder (or randomness). The more energy that a system loses to its surroundings, the less ordered and more random the system. Scientists refer to the measure of randomness or disorder within a system as entropy. High entropy means high disorder and low energy ((Figure)). To better understand entropy, think of a student’s bedroom. If no energy or work were put into it, the room would quickly become messy. It would exist in a very disordered state, one of high entropy. Energy must be put into the system, in the form of the student doing work and putting everything away, in order to bring the room back to a state of cleanliness and order. This state is one of low entropy. Similarly, a car or house must be constantly maintained with work in order to keep it in an ordered state. Left alone, a house’s or car’s entropy gradually increases through rust and degradation. Molecules and chemical reactions have varying amounts of entropy as well. For example, as chemical reactions reach a state of equilibrium, entropy increases, and as molecules at a high concentration in one place diffuse and spread out, entropy also increases.

Scientific Connection

Transfer of Energy and the Resulting EntropySet up a simple experiment to understand how energy transfers and how a change in entropy results.

  1. Take a block of ice. This is water in solid form, so it has a high structural order. This means that the molecules cannot move very much and are in a fixed position. The ice’s temperature is 0°C. As a result, the system’s entropy is low.
  2. Allow the ice to melt at room temperature. What is the state of molecules in the liquid water now? How did the energy transfer take place? Is the system’s entropy higher or lower? Why?
  3. Heat the water to its boiling point. What happens to the system’s entropy when the water is heated?

Think of all physical systems of in this way: Living things are highly ordered, requiring constant energy input to maintain themselves in a state of low entropy. As living systems take in energy-storing molecules and transform them through chemical reactions, they lose some amount of usable energy in the process, because no reaction is completely efficient. They also produce waste and by-products that are not useful energy sources. This process increases the entropy of the system’s surroundings. Since all energy transfers result in losing some usable energy, the second law of thermodynamics states that every energy transfer or transformation increases the universe’s entropy. Even though living things are highly ordered and maintain a state of low entropy, the universe’s entropy in total is constantly increasing due to losing usable energy with each energy transfer that occurs. Essentially, living things are in a continuous uphill battle against this constant increase in universal entropy.

Entropy is a measure of randomness or disorder in a system. Gases have higher entropy than liquids, and liquids have higher entropy than solids.


This diagram shows that solids have a regular packing arrangement and low entropy, whereas liquids have irregular packing and higher entropy.

Section Summary

In studying energy, scientists use the term “system” to refer to the matter and its environment involved in energy transfers. Everything outside of the system is the surroundings. Single cells are biological systems. We can think of systems as having a certain amount of order. It takes energy to make a system more ordered. The more ordered a system, the lower its entropy. Entropy is a measure of a system’s disorder. As a system becomes more disordered, the lower its energy and the higher its entropy.

The laws of thermodynamics are a series of laws that describe the properties and processes of energy transfer. The first law states that the total amount of energy in the universe is constant. This means that energy cannot be created or destroyed, only transferred or transformed. The second law of thermodynamics states that every energy transfer involves some loss of energy in an unusable form, such as heat energy, resulting in a more disordered system. In other words, no energy transfer is completely efficient, and all transfers trend toward disorder.

Review Questions

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

  1. turning on a light switch
  2. solar panels at work
  3. formation of static electricity
  4. none of the above

A

In each of the three systems, determine the state of entropy (low or high) when comparing the first and second: i. the instant that a perfume bottle is sprayed compared with 30 seconds later, ii. an old 1950s car compared with a brand new car, and iii. a living cell compared with a dead cell.

  1. i. low, ii. high, iii. low
  2. i. low, ii. high, iii. high
  3. i. high, ii. low, iii. high
  4. i. high, ii. low, iii. low

A

Critical Thinking Questions

Imagine an elaborate ant farm with tunnels and passageways through the sand where ants live in a large community. Now imagine that an earthquake shook the ground and demolished the ant farm. In which of these two scenarios, before or after the earthquake, was the ant farm system in a state of higher or lower entropy?

The ant farm had lower entropy before the earthquake because it was a highly ordered system. After the earthquake, the system became much more disordered and had higher entropy.

Energy transfers take place constantly in everyday activities. Think of two scenarios: cooking on a stove and driving. Explain how the second law of thermodynamics applies to these two scenarios.

While cooking, food is heating up on the stove, but not all of the heat goes to cooking the food, some of it is lost as heat energy to the surrounding air, increasing entropy. While driving, cars burn gasoline to run the engine and move the car. This reaction is not completely efficient, as some energy during this process is lost as heat energy, which is why the hood and the components underneath it heat up while the engine is turned on. The tires also heat up because of friction with the pavement, which is additional energy loss. This energy transfer, like all others, also increases entropy.

Glossary

entropy (S)
measure of randomness or disorder within a system
heat
energy transferred from one system to another that is not work (energy of the molecules’ motion or particles)
thermodynamics
study of energy and energy transfer involving physical matter

30

ATP: Adenosine Triphosphate

Learning Objectives

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

  • Explain ATP’s role as the cellular energy currency
  • Describe how energy releases through ATP hydrolysis

Even exergonic, energy-releasing reactions require a small amount of activation energy in order 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, from where does energy to power such reactions come? The answer lies with an energy-supplying molecule scientists call adenosine triphosphate, or ATP. This is a small, relatively simple molecule ((Figure)), but within some of its bonds, it contains the potential for a quick burst of energy that can be harnessed to perform cellular work. Think of this molecule as the cells’ primary energy currency in much the same way that money is the currency that people exchange for things they need. ATP powers the majority of energy-requiring cellular reactions.

ATP is the cell’s primary energy currency. It has an adenosine backbone with three phosphate groups attached.

The molecular structure of adenosine triphosphate is shown. Three phosphate groups, called alpha, beta, and gamma, are attached to a ribose sugar. Adenine is also attached to the ribose.

As its name suggests, adenosine triphosphate is comprised of adenosine bound to three phosphate groups ((Figure)). Adenosine is a nucleoside consisting of the nitrogenous base adenine and a five-carbon sugar, ribose. The three phosphate groups, in order of closest to furthest from the ribose sugar, are alpha, beta, and gamma. Together, these chemical groups constitute an energy powerhouse. However, not all bonds within this molecule exist in a particularly high-energy state. Both bonds that link the phosphates are equally high-energy bonds (phosphoanhydride bonds) that, when broken, release sufficient energy to power a variety of cellular reactions and processes. These high-energy bonds are the bonds between the second and third (or beta and gamma) phosphate groups and between the first and second phosphate groups. These bonds are “high-energy” because the products of such bond breaking—adenosine diphosphate (ADP) and one inorganic phosphate group (Pi)—have considerably lower free energy than the reactants: ATP and a water molecule. Because this reaction takes place using a water molecule, it is a hydrolysis reaction. In other words, ATP hydrolyzes into ADP in the following reaction:

\text{ATP}+{\text{H}}_{\text{2}}\text{O}\to \text{ADP}+{\text{P}}_{\text{i}}+\text{free energy}

Like most chemical reactions, ATP to ADP hydrolysis is reversible. The reverse reaction regenerates ATP from ADP + Pi. Cells rely on ATP regeneration just as people rely on regenerating spent money through some sort of income. Since ATP hydrolysis releases energy, ATP regeneration must require an input of free energy. This equation expresses ATP formation:

Two prominent questions remain with regard to using ATP as an energy source. Exactly how much free energy releases with ATP hydrolysis, and how does that free energy do cellular work? The calculated ∆G for the hydrolysis of one ATP mole into ADP and Pi is −7.3 kcal/mole (−30.5 kJ/mol). Since this calculation is true under standard conditions, one would expect a different value exists under cellular conditions. In fact, the ∆G for one ATP mole’s hydrolysis in a living cell is almost double the value at standard conditions: –14 kcal/mol (−57 kJ/mol).

ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP + Pi, and the free energy released during this process is lost as heat. The second question we posed above discusses how ATP hydrolysis energy release performs work inside the cell. This depends on a strategy scientists call energy coupling. Cells couple the ATP hydrolysis’ exergonic reaction allowing them to proceed. One example of energy coupling using ATP involves a transmembrane ion pump that is extremely important for cellular function. This sodium-potassium pump (Na+/K+ pump) drives sodium out of the cell and potassium into the cell ((Figure)). A large percentage of a cell’s ATP powers this pump, because cellular processes bring considerable sodium into the cell and potassium out of it. The pump works constantly to stabilize cellular concentrations of sodium and potassium. In order for the pump to turn one cycle (exporting three Na+ ions and importing two K+ ions), one ATP molecule must hydrolyze. When ATP hydrolyzes, its gamma phosphate does not simply float away, but it actually transfers onto the pump protein. Scientists call this process of a phosphate group binding to a molecule phosphorylation. As with most ATP hydrolysis cases, a phosphate from ATP transfers onto another molecule. In a phosphorylated state, the Na+/K+ pump has more free energy and is triggered to undergo a conformational change. This change allows it to release Na+ to the cell’s outside. It then binds extracellular K+, which, through another conformational change, causes the phosphate to detach from the pump. This phosphate release triggers the K+ to release to the cell’s inside. Essentially, the energy released from the ATP hydrolysis couples with the energy required to power the pump and transport Na+ and K+ ions. ATP performs cellular work using this basic form of energy coupling through phosphorylation.

Visual Connection
The sodium-potassium pump is an example of energy coupling. The energy derived from exergonic ATP hydrolysis pumps sodium and potassium ions across the cell membrane.

This illustration shows the sodium-potassium pump embedded in the cell membrane. A T P hydrolysis catalyzes a conformational change in the pump that allows sodium ions to move from the cytoplasmic side to the extracellular side of the membrane, and potassium ions to move from the extracellular side to the cytoplasmic side of the membrane as well.

One ATP molecule’s hydrolysis releases 7.3 kcal/mol of energy (∆G = −7.3 kcal/mol of energy). If it takes 2.1 kcal/mol of energy to move one Na+ across the membrane (∆G = +2.1 kcal/mol of energy), how many sodium ions could one ATP molecule’s hydrolysis move?

Often during cellular metabolic reactions, such as nutrient synthesis and breakdown, certain molecules must alter slightly in their conformation to become substrates for the next step in the reaction series. One example is during the very first steps of cellular respiration, when a sugar glucose molecule breaks down in the process of glycolysis. In the first step, ATP is required to phosphorylze glucose, creating a high-energy but unstable intermediate. This phosphorylation reaction powers a conformational change that allows the phosphorylated glucose molecule to convert to the phosphorylated sugar fructose. Fructose is a necessary intermediate for glycolysis to move forward. Here, ATP hydrolysis’ exergonic reaction couples with the endergonic reaction of converting glucose into a phosphorylated intermediate in the pathway. Once again, the energy released by breaking a phosphate bond within ATP was used for phosphorylyzing another molecule, creating an unstable intermediate and powering an important conformational change.

Link to Learning

See an interactive animation of the ATP-producing glycolysis process at this site.

Section Summary

ATP is the primary energy-supplying molecule for living cells. ATP is comprised of a nucleotide, a five-carbon sugar, and three phosphate groups. The bonds that connect the phosphates (phosphoanhydride bonds) have high-energy content. The energy released from ATP hydrolysis into ADP + Pi performs cellular work. Cells use ATP to perform work by coupling ATP hydrolysis’ exergonic reaction with endergonic reactions. ATP donates its phosphate group to another molecule via phosphorylation. The phosphorylated molecule is at a higher-energy state and is less stable than its unphosphorylated form, and this added energy from phosphate allows the molecule to undergo its endergonic reaction.

Visual Connection Questions

(Figure) One ATP molecule’s hydrolysis releases 7.3 kcal/mol of energy (∆G = −7.3 kcal/mol of energy). If it takes 2.1 kcal/mol of energy to move one Na+ across the membrane (∆G = +2.1 kcal/mol of energy), how many sodium ions could one ATP molecule’s hydrolysis move?

(Figure) Three sodium ions could be moved by the hydrolysis of one ATP molecule. The ∆G of the coupled reaction must be negative. Movement of three sodium ions across the membrane will take 6.3 kcal of energy (2.1 kcal × 3 Na+ ions = 6.3 kcal). Hydrolysis of ATP provides 7.3 kcal of energy, more than enough to power this reaction. Movement of four sodium ions across the membrane, however, would require 8.4 kcal of energy, more than one ATP molecule can provide.

Review Questions

The energy released by the hydrolysis of ATP is____

  1. primarily stored between the alpha and beta phosphates
  2. equal to −57 kcal/mol
  3. harnessed as heat energy by the cell to perform work
  4. providing energy to coupled reactions

D

Which of the following molecules is likely to have the most potential energy?

  1. sucrose
  2. ATP
  3. glucose
  4. ADP

A

Critical Thinking Questions

Do you think that the EA for ATP hydrolysis is relatively low or high? Explain your reasoning.

The activation energy for hydrolysis is very low. Not only is ATP hydrolysis an exergonic process with a large −∆G, but ATP is also a very unstable molecule that rapidly breaks down into ADP + Pi if not utilized quickly. This suggests a very low EA since it hydrolyzes so quickly.

Glossary

ATP
adenosine triphosphate, the cell’s energy currency
phosphoanhydride bond
bond that connects phosphates in an ATP molecule

31

Enzymes

Learning Objectives

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

  • Describe the role of enzymes in metabolic pathways
  • Explain how enzymes function as molecular catalysts
  • Discuss enzyme regulation by various factors

A substance that helps a chemical reaction to occur is a catalyst, and the special molecules that catalyze biochemical reactions are enzymes. Almost all enzymes are proteins, comprised of amino acid chains, and they perform the critical task of lowering the activation energies of chemical reactions inside the cell. Enzymes do this by binding to the reactant molecules, and holding them in such a way as to make the chemical bond-breaking and bond-forming processes take place more readily. It is important to remember that enzymes do not change the reaction’s ∆G. In other words, they do not change whether a reaction is exergonic (spontaneous) or endergonic. This is because they do not change the reactants’ or products’ free energy. They only reduce the activation energy required to reach the transition state ((Figure)).

Enzymes lower the reaction’s activation energy but do not change the reaction’s free energy.


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

Enzyme Active Site and Substrate Specificity

The chemical reactants to which an enzyme binds are the enzyme’s substrates. There may be one or more substrates, depending on the particular chemical reaction. In some reactions, a single-reactant substrate breaks down into multiple products. In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction, both become modified, and leave the reaction as two products. The location within the enzyme where the substrate binds is the enzyme’s active site. This is where the “action” happens. Since enzymes are proteins, there is a unique combination of amino acid residues (also side chains, or R groups) within the active site. Different properties characterize each residue. These can be large or small, weakly acidic or basic, hydrophilic or hydrophobic, positively or negatively charged, or neutral. The unique combination of amino acid residues, their positions, sequences, structures, and properties, creates a very specific chemical environment within the active site. This specific environment is suited to bind, albeit briefly, to a specific chemical substrate (or substrates). Due to this jigsaw puzzle-like match between an enzyme and its substrates (which adapts to find the best fit between the transition state and the active site), enzymes are known for their specificity. The “best fit” results from the shape and the amino acid functional group’s attraction to the substrate. There is a specifically matched enzyme for each substrate and, thus, for each chemical reaction; however, there is flexibility as well.

The fact that active sites are so perfectly suited to provide specific environmental conditions also means that they are subject to local enviromental influences. It is true that increasing the environmental temperature generally increases reaction rates, enzyme-catalyzed or otherwise. However, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site in such a way that they are less well suited to bind substrates. High temperatures will eventually cause enzymes, like other biological molecules, to denature, a process that changes the substance’s natural properties. Likewise, the local environment’s pH can also affect enzyme function. Active site amino acid residues have their own acidic or basic properties that are optimal for catalysis. These residues are sensitive to changes in pH that can impair the way substrate molecules bind. Enzymes are suited to function best within a certain pH range, and, as with temperature, extreme environmental pH values (acidic or basic) can cause enzymes to denature.

Induced Fit and Enzyme Function

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 more refined view scientists call induced fit ((Figure)). This model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild shift in the enzyme’s structure that confirms an ideal binding arrangement between the enzyme and the substrate’s transition state. This ideal binding maximizes the enzyme’s ability to catalyze its reaction.

Link to Learning

View an induced fit animation at this website.

When an enzyme binds its substrate, it forms an enzyme-substrate complex. This complex lowers the reaction’s activation energy and promotes its rapid progression in one of many ways. On a basic level, enzymes promote chemical reactions that involve more than one substrate by bringing the substrates together in an optimal orientation. The appropriate region (atoms and bonds) of one molecule is juxtaposed to the other molecule’s appropriate region with which it must react. Another way in which enzymes promote substrate reaction is by creating an optimal environment within the active site for the reaction to occur. Certain chemical reactions might proceed best in a slightly acidic or non-polar environment. The chemical properties that emerge from the particular arrangement of amino acid residues within an active site create the perfect environment for an enzyme’s specific substrates to react.

You have learned that the activation energy required for many reactions includes the energy involved in manipulating or slightly contorting chemical bonds so that they can easily break and allow others to reform. Enzymatic action can aid this process. The enzyme-substrate complex can lower the activation energy by contorting substrate molecules in such a way as to facilitate bond-breaking, helping to reach the transition state. Finally, enzymes can also lower activation energies by taking part in the chemical reaction itself. The amino acid residues can provide certain ions or chemical groups that actually form covalent bonds with substrate molecules as a necessary step of the reaction process. In these cases, it is important to remember that the enzyme will always return to its original state at the reaction’s completion. One of enzymes’ hallmark properties is that they remain ultimately unchanged by the reactions they catalyze. After an enzyme catalyzes a reaction, it releases its product(s).

According to the induced-fit model, both enzyme and substrate undergo dynamic conformational changes upon binding. The enzyme contorts the substrate into its transition state, thereby increasing the reaction’s rate.


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 products that then leave the enzymes active site.

Metabolism Control Through Enzyme Regulation

It would seem ideal to have a scenario in which all the encoded enzymes in an organism’s genome existed in abundant supply and functioned optimally under all cellular conditions, in all cells, at all times. In reality, this is far from the case. A variety of mechanisms ensure that this does not happen. Cellular needs and conditions vary from cell to cell, and change within individual cells over time. The required enzymes and energetic demands of stomach cells are different from those of fat storage cells, skin cells, blood cells, and nerve cells. Furthermore, a digestive 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 do 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 which rates. This determination is tightly controlled. In certain cellular environments, environmental factors like pH and temperature partly control enzyme activity. There are other mechanisms through which cells control enzyme activity and determine the rates at which various biochemical reactions will occur.

Molecular Regulation of Enzymes

Enzymes can be regulated in ways that either promote or reduce their activity. There are many different kinds of molecules that inhibit or promote enzyme function, and various mechanisms exist for doing so. For example, 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 active site binding ((Figure)). Alternatively, in noncompetitive inhibition, an inhibitor molecule binds to the enzyme in a location other than an allosteric site, a binding site away from the active site, and still manages to block substrate binding to the active site.

Competitive and noncompetitive inhibition affect the reaction’s rate differently. Competitive inhibitors affect the initial rate but do not affect the maximal rate; whereas, noncompetitive inhibitors affect the maximal rate.


This plot shows rate of reaction versus substrate concentration for an enzyme in the absence of inhibitor, and for enzyme in the presence of competitive and noncompetitive inhibitors. Both competitive and noncompetitive inhibitors slow the rate of reaction, but competitive inhibitors can be overcome by high concentrations of substrate, whereas noncompetitive inhibitors cannot.

Some inhibitor molecules bind to enzymes in a location where their binding induces a conformational change that reduces the enzyme’s affinity for its substrate. This type of inhibition is an allosteric inhibition ((Figure)). More than one polypeptide comprise most allosterically regulated enzymes, meaning that they have more than one protein subunit. When an allosteric inhibitor binds to an enzyme, all active sites on the protein subunits change 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).

Allosteric inhibitors modify the enzyme’s active site so that substrate binding is reduced or prevented. In contrast, allosteric activators modify the enzyme’s active site so that the affinity for the substrate increases.


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 its 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 at a higher affinity.

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


This photo shows several red capsule pills.

Drug Discovery by Looking for Inhibitors of Key Enzymes in Specific PathwaysEnzymes are key components of metabolic pathways. Understanding how enzymes work and how they can be regulated is a key principle behind developing many pharmaceutical drugs ((Figure)) on the market today. Biologists working in this field collaborate with other scientists, usually chemists, to design drugs.

Consider statins for example—which is a class of drugs that reduces cholesterol levels. These compounds are essentially inhibitors of the enzyme HMG-CoA reductase. HMG-CoA reductase is the enzyme that synthesizes cholesterol from lipids in the body. By inhibiting this enzyme, the drug reduces cholesterol levels synthesized in the body. Similarly, acetaminophen, popularly marketed under the brand name Tylenol, is an inhibitor of the enzyme cyclooxygenase. While it is effective in providing relief from fever and inflammation (pain), scientists still do not completely understand its mechanism of action.

How are drugs developed? One of the first challenges in drug development is identifying the specific molecule that the drug is intended to target. In the case of statins, HMG-CoA reductase is the drug target. Researchers identify targets through painstaking research in the laboratory. Identifying the target alone is not sufficient. Scientists also need to know how the target acts inside the cell and which reactions go awry in the case of disease. Once researchers identify the target and the pathway, then the actual drug design process begins. During this stage, chemists and biologists work together to design and synthesize molecules that can either block or activate a particular reaction. However, this is only the beginning: both if and when a drug prototype is successful in performing its function, then it must undergo many tests from in vitro experiments to clinical trials before it can obtain FDA approval to be on the market.

Many enzymes don’t work optimally, or even at all, unless bound to other specific non-protein helper molecules, either temporarily through ionic or hydrogen bonds or permanently through stronger covalent bonds. Two types of helper molecules are cofactors and coenzymes. Binding to these molecules promotes optimal conformation and function for their respective enzymes. Cofactors are inorganic ions such as iron (Fe++) and magnesium (Mg++). One example of an enzyme that requires a metal ion as a cofactor is the enzyme that builds DNA molecules, DNA polymerase, which requires a bound zinc ion (Zn++) to function. Coenzymes are organic helper molecules, with a basic atomic structure comprised of carbon and hydrogen, which are required for enzyme action. The most common sources of coenzymes are dietary vitamins ((Figure)). Some vitamins are precursors to coenzymes and others act directly as coenzymes. Vitamin C is a coenzyme for multiple enzymes that take part in building the important connective tissue component, collagen. An important step in breaking down glucose to yield energy is catalysis by a multi-enzyme complex scientists call pyruvate dehydrogenase. Pyruvate dehydrogenase is a complex of several enzymes that actually requires one cofactor (a magnesium ion) and five different organic coenzymes to catalyze its specific chemical reaction. Therefore, enzyme function is, in part, regulated by an abundance of various cofactors and coenzymes, which the diets of most organisms supply.

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.


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

Enzyme Compartmentalization

In eukaryotic cells, molecules such as enzymes are usually compartmentalized into different organelles. This allows for yet another level of regulation of enzyme activity. Enzymes required only for certain cellular processes are sometimes housed separately along with their substrates, allowing for more efficient chemical reactions. Examples of this sort of enzyme regulation based on location and proximity include the enzymes involved in the latter stages of cellular respiration, which take place exclusively in the mitochondria, and the enzymes involved in digesting cellular debris and foreign materials, located within lysosomes.

Feedback Inhibition in Metabolic Pathways

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

Metabolic pathways are a series of reactions that multiple enzymes catalyze. Feedback inhibition, where the pathway’s end product inhibits an upstream step, is an important regulatory mechanism in cells.


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.

Producing both amino acids and nucleotides is controlled through feedback inhibition. Additionally, ATP is an allosteric regulator of some of the enzymes involved in sugar’s catabolic breakdown, the process that produces ATP. In this way, when ATP is abundant, the cell can prevent its further production. Remember that ATP is an unstable molecule that can spontaneously dissociate into ADP. If too much ATP were present in a cell, much of it would go to waste. Alternatively, ADP serves as a positive allosteric regulator (an allosteric activator) for some of the same enzymes that ATP inhibits. Thus, when relative ATP levels are high compared to ATP, the cell is triggered to produce more ATP through sugar catabolism.

Section Summary

Enzymes are chemical catalysts that accelerate chemical reactions at physiological temperatures by lowering their activation energy. Enzymes are usually proteins consisting of one or more polypeptide chains. Enzymes have an active site that provides a unique chemical environment, comprised of certain amino acid R groups (residues). This unique environment is perfectly suited to convert particular chemical reactants for that enzyme, scientists call substrates, into unstable intermediates that they call transition states. Enzymes and substrates bind with an induced fit, which means that enzymes undergo slight conformational adjustments upon substrate contact, leading to full, optimal binding. Enzymes bind to substrates and catalyze reactions in four different ways: bringing substrates together in an optimal orientation, compromising the bond structures of substrates so that bonds can break down more easily, providing optimal environmental conditions for a reaction to occur, or participating directly in their chemical reaction by forming transient covalent bonds with the substrates.

Enzyme action must be regulated so that in a given cell at a given time, the desired reactions catalyze and the undesired reactions are not. Enzymes are regulated by cellular conditions, such as temperature and pH. They are also regulated through their location within a cell, sometimes compartmentalized so that they can only catalyze reactions under certain circumstances. Enzyme inhibition and activation via other molecules are other important ways that enzymes are regulated. Inhibitors can act competitively, noncompetitively, or allosterically. Noncompetitive inhibitors are usually allosteric. Activators can also enhance enzyme function allosterically. The most common method by which cells regulate the enzymes in metabolic pathways is through feedback inhibition. During feedback inhibition, metabolic pathway products serve as inhibitors (usually allosteric) of one or more of the enzymes (usually the first committed enzyme of the pathway) involved in the pathway that produces them.

Review Questions

Which of the following is not true about enzymes:

  1. They increase ∆G of reactions.
  2. They are usually made of amino acids.
  3. They lower the activation energy of chemical reactions.
  4. Each one is specific to the particular substrate(s) to which it binds.

A

An allosteric inhibitor does which of the following?

  1. Binds to an enzyme away from the active site and changes the conformation of the active site, increasing its affinity for substrate binding.
  2. Binds to the active site and blocks it from binding substrate.
  3. Binds to an enzyme away from the active site and changes the conformation of the active site, decreasing its affinity for the substrate.
  4. Binds directly to the active site and mimics the substrate.

C

Which of the following analogies best describes the induced-fit model of enzyme-substrate binding?

  1. a hug between two people
  2. a key fitting into a lock
  3. a square peg fitting through the square hole and a round peg fitting through the round hole of a children’s toy
  4. the fitting together of two jigsaw puzzle pieces

A

Critical Thinking Questions

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

Most vitamins and minerals act as coenzymes and cofactors 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 the diet and from supplements. Vitamin C (ascorbic acid) is a coenzyme necessary for the action of enzymes that build collagen, an important protein component of connective tissue throughout the body. Magnesium ion (Mg++) is an important cofactor that is necessary for the enzyme pyruvate dehydrogenase to catalyze part of the pathway that breaks down sugar to produce energy. Vitamins cannot be produced in the human body and therefore must be obtained in the diet.

Explain in your own words how enzyme feedback inhibition benefits a cell.

Feedback inhibition allows cells to control the amounts of metabolic products produced. If there is too much of a particular product relative to the cell’s needs, feedback inhibition effectively causes the cell to decrease production of that particular product. In general, this reduces the production of superfluous products and conserves energy, maximizing energy efficiency.

Glossary

active site
enzyme’s specific region to which the substrate binds
allosteric inhibition
inhibition by a binding event at a site different from the active site, which induces a conformational change and reduces the enzyme’s affinity for its substrate
coenzyme
small organic molecule, such as a vitamin or its derivative, which is required to enhance an enzyme’s activity
cofactor
inorganic ion, such as iron and magnesium ions, required for optimal enzyme activity regulation
competitive inhibition
type of inhibition in which the inhibitor competes with the substrate molecule by binding to the enzyme’s active site
denature
process that changes a subtance’s natural properties
feedback inhibition
a product’s effect of a reaction sequence to decrease its further production by inhibiting the first enzyme’s activity in the pathway that produces it
induced fit
dynamic fit between the enzyme and its substrate, in which both components modify their structures to allow for ideal binding
substrate
molecule on which the enzyme acts

VII

Cellular Respiration

32

Introduction

This geothermal energy plant transforms thermal energy from deep in the ground into electrical energy, which can be easily used. (credit: modification of work by the U.S. Department of Defense)


A photograph shows an energy plant on a hillside with clouds of white steam immediately above the plant

The electrical energy plant in (Figure) converts energy from one form to another form that can be more easily used. This type of generating plant starts with underground thermal energy (heat) and transforms it into electrical energy that will be transported to homes and factories. Like a generating plant, plants and animals also must take in energy from the environment and convert it into a form that their cells can use. Mass and its stored energy enter an organism’s body in one form and are converted into another form that can fuel the organism’s life functions. In the process of photosynthesis, plants and other photosynthetic producers take in energy in the form of light (solar energy) and convert it into chemical energy in the form of glucose, which stores this energy in its chemical bonds. Then, a series of metabolic pathways, collectively called cellular respiration, extracts the energy from the bonds in glucose and converts it into a form that all living things can use.

33

Energy in Living Systems

Learning Objectives

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

  • Discuss the importance of electrons in the transfer of energy in living systems
  • Explain how ATP is used by cells as an energy source

Energy production within a cell involves many coordinated chemical pathways. Most of these pathways are combinations of oxidation and reduction reactions, which occur at the same time. 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 high-energy 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 biochemical 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)) 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). Note that if a compound has an “H” on it, it is generally reduced (e.g., NADH is the reduced form of NAD).

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

When electrons are added to a compound, it is 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 a 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 in plants.

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+.

This illustration shows the molecular structure of N A D superscript plus sign baseline and N A D H. 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 prime end, and the adenine nucleotide is at the 3 prime end. Nicotinamide is a nitrogenous base, meaning it has nitrogen in a six-membered carbon ring. In N A D H, one extra hydrogen is associated with this ring, which is not found in N A D superscript plus sign baseline.

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 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 energy is used to do work by the cell, usually when the released phosphate binds to another molecule, thereby 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 to a single phosphate group ((Figure)). 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).

ATP (adenosine triphosphate) has three phosphate groups that can be removed by hydrolysis (addition of H2O) 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.

This illustration shows the molecular structure of A T P. 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.

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.

Energy from ATP

Hydrolysis is the process of breaking complex macromolecules apart. During hydrolysis, water is split, or lysed, and the resulting hydrogen atom (H+) and a hydroxyl group (OH), or hydroxide, are added to the larger molecule. The hydrolysis of ATP produces ADP, together with an inorganic phosphate ion (Pi), and the release of free energy. To carry out life processes, ATP is continuously broken down into ADP, and like a rechargeable battery, ADP is continuously regenerated into ATP by the reattachment of a third phosphate group. Water, which was broken down into its hydrogen atom and hydroxyl group (hydroxide) during ATP hydrolysis, is regenerated when a third phosphate is added to the ADP molecule, reforming ATP.

Obviously, energy must be infused into the system to regenerate ATP. Where does this energy come from? In nearly every living thing on Earth, the energy comes from the metabolism of glucose, fructose, or galactose, all isomers with the chemical formula C6H12O6 but different molecular configurations. In this way, ATP is a direct link between the limited set of exergonic pathways of glucose catabolism and the multitude of endergonic pathways that power living cells.

Phosphorylation

Recall that, in some chemical reactions, enzymes may bind to several substrates that react with each other on the enzyme, forming an intermediate complex. An intermediate complex is a temporary structure, and it allows one of the substrates (such as ATP) and reactants to more readily react with each other; in reactions involving ATP, ATP is one of the substrates and ADP is a product. During an endergonic chemical reaction, ATP forms an intermediate complex with the substrate and enzyme in the reaction. This intermediate complex allows the ATP to transfer its third phosphate group, with its energy, to the substrate, a process called phosphorylation. Phosphorylation refers to the addition of the phosphate (~P). This is illustrated by the following generic reaction, in which A and B represent two different substrates:

When the intermediate complex breaks apart, the energy is used to modify the substrate and convert it into a product of the reaction. The ADP molecule and a free phosphate ion are released into the medium and are available for recycling through cell metabolism.

Substrate Phosphorylation

ATP is generated through two mechanisms during the breakdown of glucose. A few ATP molecules are generated (that is, regenerated from ADP) as a direct result of the chemical reactions that occur in the catabolic pathways. A phosphate group is removed from an intermediate reactant in the pathway, and the free energy of the reaction is used to add the third phosphate to an available ADP molecule, producing ATP ((Figure)). This very direct method of phosphorylation is called substrate-level phosphorylation.

In phosphorylation reactions, the gamma (third) phosphate of ATP is attached to a protein.

This illustration shows a substrate-level phosphorylation reaction in which the gamma phosphate of A T P is attached to a protein.

Oxidative Phosphorylation

Most of the ATP generated during glucose catabolism, however, is derived from a much more complex process, chemiosmosis, which takes place in mitochondria ((Figure)) within a eukaryotic cell or the plasma membrane of a prokaryotic cell. Chemiosmosis, a process of ATP production in cellular metabolism, is used to generate 90 percent of the ATP made during glucose catabolism and is also the method used in the light reactions of photosynthesis to harness the energy of sunlight. The production of ATP using the process of chemiosmosis is called oxidative phosphorylation because of the involvement of oxygen in the process.

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)

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. A T P synthase enzymes and the electron transport chain are located in the inner membrane.

Career Connections

Mitochondrial Disease PhysicianWhat happens when the critical reactions of cellular respiration do not proceed correctly? This may happen in mitochondrial diseases, which 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. In type 2 diabetes, for instance, the oxidation efficiency of NADH is reduced, impacting oxidative phosphorylation but not the other steps of respiration. 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 diseases, such as the Mitochondrial Medicine Society and the Society for Inherited Metabolic Disorders.

Section Summary

ATP functions as the energy currency for cells. It allows the cell to store energy briefly and transport it within the cell to support endergonic chemical reactions. The structure of ATP is that of an RNA nucleotide with three phosphates attached. As ATP is used for energy, a phosphate group or two are detached, and either ADP or AMP is produced. Energy derived from glucose catabolism is used to convert ADP into ATP. When ATP is used in a reaction, the third phosphate is temporarily attached to a substrate in a process called phosphorylation. The two processes of ATP regeneration that are used in conjunction with glucose catabolism are substrate-level phosphorylation and oxidative phosphorylation through the process of chemiosmosis.

Review Questions

The energy currency used by cells is ________.

  1. ATP
  2. ADP
  3. AMP
  4. adenosine

A

A reducing chemical reaction ________.

  1. reduces the compound to a simpler form
  2. adds an electron to the substrate
  3. removes a hydrogen atom from the substrate
  4. is a catabolic reaction

B

Critical Thinking Questions

Why is it beneficial for cells to use ATP rather than energy directly from the bonds of carbohydrates? What are the greatest drawbacks to harnessing energy directly from the bonds of several different compounds?

ATP provides the cell with a way to handle energy in an efficient manner. The molecule can be charged, stored, and used as needed. Moreover, the energy from hydrolyzing ATP is delivered as a consistent amount. Harvesting energy from the bonds of several different compounds would result in energy deliveries of different quantities.

Glossary

chemiosmosis
process in which there is a production of adenosine triphosphate (ATP) in cellular metabolism by the involvement of a proton gradient across a membrane
dephosphorylation
removal of a phosphate group from a molecule
oxidative phosphorylation
production of ATP using the process of chemiosmosis in the presence of oxygen
phosphorylation
addition of a high-energy phosphate to a compound, usually a metabolic intermediate, a protein, or ADP
redox reaction
chemical reaction that consists of the coupling of an oxidation reaction and a reduction reaction
substrate-level phosphorylation
production of ATP from ADP using the excess energy from a chemical reaction and a phosphate group from a reactant

34

Glycolysis

Learning Objectives

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

  • Describe the overall result in terms of molecules produced during the chemical breakdown of glucose by glycolysis
  • Compare the output of glycolysis in terms of ATP molecules and NADH molecules produced

As you have read, nearly all of the energy used by living cells comes to them in the bonds of the sugar glucose. Glycolysis is the first step in the breakdown of glucose to extract energy for cellular metabolism. In fact, nearly all living organisms carry out glycolysis as part of their metabolism. The process does not use oxygen directly and therefore is termed anaerobic. Glycolysis takes place in the cytoplasm of both prokaryotic and eukaryotic cells. Glucose enters heterotrophic cells in two ways. One method is through secondary active transport in which the transport takes place against the glucose concentration gradient. The other mechanism uses a group of integral proteins called GLUT proteins, also known as glucose transporter proteins. These transporters assist in the facilitated diffusion of glucose.

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. The first part of the glycolysis pathway traps the glucose molecule in the cell and uses energy to modify it so that the six-carbon sugar molecule can be split evenly into the two three-carbon molecules. The second part of glycolysis extracts energy from the molecules and stores it in the form of ATP and NADH—remember: this is the reduced form of NAD.

First Half of Glycolysis (Energy-Requiring Steps)

Step 1. The first step in glycolysis ((Figure)) is catalyzed by hexokinase, an enzyme with broad specificity that catalyzes the phosphorylation of six-carbon sugars. Hexokinase phosphorylates glucose using ATP as the source of the phosphate, producing glucose-6-phosphate, a more reactive form of glucose. This reaction prevents the phosphorylated glucose molecule from continuing to interact with the GLUT proteins, and it can no longer leave the cell because the negatively charged phosphate will not allow it to cross the hydrophobic interior of the plasma membrane.

Step 2. In the second step of glycolysis, an isomerase converts glucose-6-phosphate into one of its isomers, fructose-6-phosphate (this isomer has a phosphate attached at the location of the sixth carbon of the ring). An isomerase is an enzyme that catalyzes the conversion of a molecule into one of its isomers. (This change from phosphoglucose to phosphofructose allows the eventual split of the sugar into two three-carbon molecules.)

Step 3. The third step is the phosphorylation of fructose-6-phosphate, catalyzed by the enzyme phosphofructokinase. A second ATP molecule donates a high-energy phosphate to fructose-6-phosphate, producing fructose-1,6-bisphosphate. In this pathway, phosphofructokinase is a rate-limiting enzyme. It is active when the concentration of ADP is high; it is less active when ADP levels are low and the concentration of ATP is high. Thus, if there is “sufficient” ATP in the system, the pathway slows down. This is a type of end product inhibition, since ATP is the end product of glucose catabolism.

Step 4. The newly added high-energy phosphates further destabilize fructose-1,6-bisphosphate. The fourth step in glycolysis employs an enzyme, aldolase, to cleave fructose-1,6-bisphosphate into two three-carbon isomers: dihydroxyacetone phosphate and glyceraldehyde-3-phosphate.

Step 5. In the fifth step, an isomerase transforms the dihydroxyacetone-phosphate into its isomer, glyceraldehyde-3-phosphate. Thus, the pathway will continue with two molecules of a glyceraldehyde-3-phosphate. At this point in the pathway, there is a net investment of energy from two ATP molecules in the breakdown of one glucose molecule.

The first half of glycolysis uses two ATP molecules in the phosphorylation of glucose, which is then split into two three-carbon molecules.


This illustration shows the steps in the first half of glycolysis. In step one, the enzyme hexokinase uses one A T P molecule in the phosphorylation of glucose. In step two, glucose dash 6 dash phosphate is rearranged to form fructose dash 6 dash phosphate by phosphoglucose isomerase. In step three, phosphofructokinase uses a second A T P molecule in the phosphorylation of the substrate, forming fructose dash 1, 6 dash bisphosphate. The enzyme fructose bisphosphate aldose splits the substrate into two, forming glyceraldeyde dash 3 dash phosphate and dihydroxyacetone-phosphate. In step 4, triose phosphate isomerase converts the dihydroxyacetone-phosphate into glyceraldehyde dash 3 dash phosphate.

Second Half of Glycolysis (Energy-Releasing Steps)

So far, glycolysis has cost the cell two ATP molecules and produced two small, three-carbon sugar molecules. Both of these molecules will proceed through the second half of the pathway, and sufficient energy will be extracted to pay back the two ATP molecules used as an initial investment and produce a profit for the cell of two additional ATP molecules and two even higher-energy NADH molecules.

Step 6. The sixth step in glycolysis ((Figure)) oxidizes the sugar (glyceraldehyde-3-phosphate), extracting high-energy electrons, which are picked up by the electron carrier NAD+, producing NADH. The sugar is then phosphorylated by the addition of a second phosphate group, producing 1,3-bisphosphoglycerate. Note that the second phosphate group does not require another ATP molecule.

The second half of glycolysis involves phosphorylation without ATP investment (step 6) and produces two NADH and four ATP molecules per glucose.


This illustration shows the steps in the second half of glycolysis. In step six, the enzyme glyceraldehydes dash 3 dash phosphate dehydrogenase produces one N A D H molecule and forms 1 3 dash bisphosphoglycerate. In step seven, the enzyme phosphoglycerate kinase removes a phosphate group from the substrate, forming one A T P molecule and 3 dash phosphoglycerate. In step eight, the enzyme phosphoglycerate mutase rearranges the substrate to form 2 dash phosphoglycerate. In step nine, the enzyme enolase rearranges the substrate to form phosphoenolpyruvate. In step ten, a phosphate group is removed from the substrate, forming one A T P molecule and pyruvate.

Here again is a potential limiting factor for this pathway. The continuation of the reaction depends upon the availability of the oxidized form of the electron carrier, NAD+. Thus, NADH must be continuously oxidized back into NAD+ in order to keep this step going. If NAD+ is not available, the second half of glycolysis slows down or stops. If oxygen is available in the system, the NADH will be oxidized readily, though indirectly, and the high-energy electrons from the hydrogen released in this process will be used to produce ATP. In an environment without oxygen, an alternate pathway (fermentation) can provide the oxidation of NADH to NAD+.

Step 7. In the seventh step, catalyzed by phosphoglycerate kinase (an enzyme named for the reverse reaction), 1,3-bisphosphoglycerate donates a high-energy phosphate to ADP, forming one molecule of ATP. (This is an example of substrate-level phosphorylation.) A carbonyl group on the 1,3-bisphosphoglycerate is oxidized to a carboxyl group, and 3-phosphoglycerate is formed.

Step 8. In the eighth step, the remaining phosphate group in 3-phosphoglycerate moves from the third carbon to the second carbon, producing 2-phosphoglycerate (an isomer of 3-phosphoglycerate). The enzyme catalyzing this step is a mutase (isomerase).

Step 9. Enolase catalyzes the ninth step. This enzyme causes 2-phosphoglycerate to lose water from its structure; this is a dehydration reaction, resulting in the formation of a double bond that increases the potential energy in the remaining phosphate bond and produces phosphoenolpyruvate (PEP).

Step 10. The last step in glycolysis is catalyzed by the enzyme pyruvate kinase (the enzyme in this case is named for the reverse reaction of pyruvate’s conversion into PEP) and results in the production of a second ATP molecule by substrate-level phosphorylation and the compound pyruvic acid (or its salt form, pyruvate). Many enzymes in enzymatic pathways are named for the reverse reactions, since the enzyme can catalyze both forward and reverse reactions (these may have been described initially by the reverse reaction that takes place in vitro, under nonphysiological conditions).

Link to Learning

Gain a better understanding of the breakdown of glucose by glycolysis by visiting this site to see the process in action.

Outcomes of Glycolysis

Glycolysis begins with glucose and produces two pyruvate molecules, four new ATP molecules, and two molecules of NADH. (Note: two ATP molecules are used in the first half of the pathway to prepare the six-carbon ring for cleavage, so the cell has a net gain of two ATP molecules and two NADH molecules for its use). If the cell cannot catabolize the pyruvate molecules further, it will harvest only two ATP molecules from one molecule of glucose. Mature mammalian red blood cells do not have mitochondria and thus are not capable of aerobic respiration—the process in which organisms convert energy in the presence of oxygen—and glycolysis is their sole source of ATP. If glycolysis is interrupted, these cells lose their ability to maintain their sodium-potassium pumps, and eventually, they die.

The last step in glycolysis will not occur if pyruvate kinase, the enzyme that catalyzes the formation of pyruvate, is not available in sufficient quantities. In this situation, the entire glycolysis pathway will proceed, but only two ATP molecules will be made in the second half. Thus, pyruvate kinase is a rate-limiting enzyme for glycolysis.

Section Summary

Glycolysis is the first pathway within the cytoplasm used in the breakdown of glucose to extract energy. It was probably one of the earliest metabolic pathways to evolve and is used by nearly all of the organisms on Earth. Glycolysis consists of two parts: The first part prepares the six-carbon ring of glucose for cleavage into two three-carbon sugars. ATP is invested in the process during this half 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 by substrate phosphorylation during the second half. This produces a net gain of two ATP and two NADH molecules for the cell.

Review Questions

During the second half of glycolysis, what occurs?

  1. ATP is used up.
  2. Fructose is split in two.
  3. ATP is made.
  4. Glucose becomes fructose.

C

Critical Thinking Questions

Nearly all organisms on Earth carry out some form of glycolysis. How does this 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.

Because they lose their mitochondria during development, red blood cells cannot perform aerobic respiration; however, they do perform glycolysis in the cytoplasm. Why do all cells need an energy source, and what would happen if glycolysis were blocked in a red blood cell?

All cells must consume energy to carry out basic functions, such as pumping ions across membranes. A red blood cell would lose its membrane potential if glycolysis were blocked, and it would eventually die.

Glossary

aerobic respiration
process in which organisms convert energy in the presence of oxygen
anaerobic
process that does not use oxygen
glycolysis
process of breaking glucose into two three-carbon molecules with the production of ATP and NADH
isomerase
enzyme that converts a molecule into its isomer
pyruvate
three-carbon sugar that can be decarboxylated and oxidized to make acetyl CoA, which enters the citric acid cycle under aerobic conditions; the end product of glycolysis

35

Oxidation of Pyruvate and the Citric Acid Cycle

Learning Objectives

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

  • Explain how a circular pathway, such as the citric acid cycle, fundamentally differs from a linear biochemical pathway, such as glycolysis
  • Describe how pyruvate, the product of glycolysis, is prepared for entry into the citric acid cycle

If oxygen is available, aerobic respiration will go forward. In eukaryotic cells, the pyruvate molecules produced at the end of glycolysis are transported into the mitochondria, which are the sites of cellular respiration. There, pyruvate is transformed into an acetyl group that will be picked up and activated by a carrier compound called coenzyme A (CoA). The resulting compound is called acetyl CoA. CoA is derived from vitamin B5, pantothenic acid. 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 stage of the pathway in glucose catabolism.

Breakdown of Pyruvate

In order for pyruvate, the product of glycolysis, to enter the next pathway, it must undergo several changes. The conversion is a three-step process ((Figure)).

Step 1. A carboxyl group is removed from pyruvate, releasing a molecule of carbon dioxide into the surrounding medium. This reaction creates a two-carbon hydroxyethyl group bound to the enzyme (pyruvate dehydrogenase). We should note that this is the first of the six carbons from the original glucose molecule to be removed. (This step proceeds twice because there are two pyruvate molecules produced at the end of glycolsis for every molecule of glucose metabolized anaerobically; thus, two of the six carbons will have been removed at the end of both steps.)

Step 2. The hydroxyethyl group is oxidized to an acetyl group, and the electrons are picked up by NAD+, forming NADH. The high-energy electrons from NADH will be used later to generate ATP.

Step 3. The enzyme-bound acetyl group is transferred to CoA, producing a molecule of acetyl CoA.

Upon entering the mitochondrial matrix, a multienzyme complex converts pyruvate into acetyl CoA. In the process, carbon dioxide is released, and one molecule of NADH is formed.


This illustration shows the three-step conversion of pyruvate into acetyl upper case C lower case o upper case A. In step one, a carboxyl group is removed from pyruvate, releasing carbon dioxide. In step two, a redox reaction forms acetate and N A D H. In step three, the acetate is transferred coenzyme A, forming acetyl upper C lower o upper A.

Note that during the second stage of glucose metabolism, whenever a carbon atom is removed, it is bound to two oxygen atoms, producing carbon dioxide, one of the major end products of cellular respiration.

Acetyl CoA to CO2

In the presence of oxygen, acetyl CoA delivers its acetyl (2C) group to a four-carbon molecule, oxaloacetate, to form citrate, a six-carbon molecule with three carboxyl groups; this pathway will harvest the remainder of the extractable energy from what began as a glucose molecule and release the remaining four CO2 molecules. This single pathway is called by different names: the citric acid cycle (for the first intermediate formed—citric acid, or citrate—when acetate joins to the oxaloacetate), the TCA cycle (because citric acid or citrate and isocitrate are tricarboxylic acids), and the Krebs cycle, after Hans Krebs, who first identified the steps in the pathway in the 1930s in pigeon flight muscles.

Citric Acid Cycle

Like the conversion of pyruvate to acetyl CoA, the citric acid cycle takes place in the matrix of mitochondria. Almost all of the enzymes of the citric acid cycle are soluble, with the single exception of the enzyme succinate dehydrogenase, which is embedded in the inner membrane of the mitochondrion. 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 redox, dehydration, hydration, and decarboxylation reactions that produce two carbon dioxide molecules, one GTP/ATP, and the reduced carriers NADH and FADH2 ((Figure)). This is considered an aerobic pathway because the NADH and FADH2 produced must transfer their electrons to the next pathway in the system, which will use oxygen. If this transfer does not occur, the oxidation steps of the citric acid cycle also do not occur. Note that the citric acid cycle produces very little ATP directly and does not directly consume oxygen.

In the citric acid cycle, the acetyl group from acetyl CoA is attached to a four-carbon oxaloacetate molecule to form a six-carbon citrate molecule. Through a series of steps, citrate is oxidized, releasing two carbon dioxide molecules for each acetyl group fed into the cycle. In the process, three NAD+ molecules are reduced to NADH, one FAD molecule is reduced to FADH2, and one ATP or GTP (depending on the cell type) is produced (by substrate-level phosphorylation). Because the final product of the citric acid cycle is also the first reactant, the cycle runs continuously in the presence of sufficient reactants. (credit: modification of work by “Yikrazuul”/Wikimedia Commons)


This illustration shows the eight steps of the citric acid cycle. In the first step, the acetyl group from acetyl uppercase C lower case o upper case A is transferred to a four-carbon oxaloacetate molecule to form a six-carbon citrate molecule. In the second step, citrate is rearranged to form isocitrate. In the third step, isocitrate is oxidized to alpha-ketoglutarate. In the process, one N A D H is formed from N A D superscript plus sign baseline; and one carbon dioxide is released. In the fourth step, alpha-ketoglutarate is oxidized and upper C lower o upper A is added, forming succinyl upper C lower o upper A. In the process, another N A D H is formed and another carbon dioxide is released. In the fifth step, upper C lower o upper A is released from succinyl upper C lower o upper A, forming succinate. In the process, one G T P is formed, which is later converted into A T P. In the sixth step, succinate is oxidized to fumarate, and one F A D is reduced to F A D H subscript 2 baseline. In the seventh step, fumarate is converted into malate. In the eighth step, malate is oxidized to oxaloacetate, and another N A D H is formed.

Steps in the Citric Acid Cycle

Step 1. Prior to the first step, a transitional phase occurs during which pyruvic acid is converted to acetyl CoA. Then, the first step of the cycle begins: This condensation step combines the two-carbon acetyl group with a four-carbon oxaloacetate molecule to form a six-carbon molecule of citrate. CoA is bound to a sulfhydryl group (-SH) and diffuses away to eventually combine with another acetyl group. This step is irreversible because it is highly exergonic. The rate of this reaction is controlled by negative feedback and the amount of ATP available. If ATP levels increase, the rate of this reaction decreases. If ATP is in short supply, the rate increases.

Step 2. In step two, citrate loses one water molecule and gains another as citrate is converted into its isomer, isocitrate.

Step 3. In step three, isocitrate is oxidized, producing a five-carbon molecule, α-ketoglutarate, along with a molecule of CO2 and two electrons, which reduce NAD+ to NADH. This step is also regulated by negative feedback from ATP and NADH and a positive effect of ADP.

Step 4. Steps three and four are both oxidation and decarboxylation steps, which as we have seen, release electrons that reduce NAD+ to NADH and release carboxyl groups that form CO2 molecules. Alpha-ketoglutarate is the product of step three, and a succinyl group is the product of step four. CoA binds with the succinyl group to form succinyl CoA. The enzyme that catalyzes step four is regulated by feedback inhibition of ATP, succinyl CoA, and NADH.

Step 5. In step five, a phosphate group is substituted for coenzyme A, and a high-energy bond is formed. This energy is used in substrate-level phosphorylation (during the conversion of the succinyl group to succinate) to form either guanine triphosphate (GTP) or ATP. There are two forms of the enzyme, called isoenzymes, for this step, depending upon the type of animal tissue in which they are found. One form is found in tissues that use large amounts of ATP, such as heart and skeletal muscle. This form produces ATP. The second form of the enzyme is found in tissues that have a high number of anabolic pathways, such as liver. This form produces GTP. GTP is energetically equivalent to ATP; however, its use is more restricted. In particular, protein synthesis primarily uses GTP.

Step 6. Step six is a dehydration process that converts succinate into fumarate. Two hydrogen atoms are transferred to FAD, reducing it to FADH2. (Note: the energy contained in the electrons of these hydrogens is insufficient to reduce NAD+ but adequate to reduce FAD.) Unlike NADH, this carrier remains attached to the enzyme and transfers the electrons to the electron transport chain directly. This process is made possible by the localization of the enzyme catalyzing this step inside the inner membrane of the mitochondrion.

Step 7. Water is added by hydrolysis to fumarate during step seven, and malate is produced. The last step in the citric acid cycle regenerates oxaloacetate by oxidizing malate. Another molecule of NADH is then produced in the process.

Link to Learning

Click through each step of the citric acid cycle here.

Products of the Citric Acid Cycle

Two carbon atoms come into the citric acid cycle from each acetyl group, representing four out of the six carbons of one glucose molecule. Two carbon dioxide molecules are released on each turn of the cycle; however, these do not necessarily contain the most recently added carbon atoms. The two acetyl carbon atoms will eventually be released on later turns of the cycle; thus, all six carbon atoms from the original glucose molecule are eventually incorporated into carbon dioxide. Each turn of the cycle forms three NADH molecules and one FADH2 molecule. These carriers will connect with the last portion of aerobic respiration, the electron transport chain, to produce ATP molecules. One GTP or ATP is also made in each cycle. Several of the intermediate compounds in the citric acid cycle can be used in synthesizing nonessential amino acids; therefore, the cycle is amphibolic (both catabolic and anabolic).

Section Summary

In the presence of oxygen, pyruvate is transformed into an acetyl group attached to a carrier molecule of coenzyme A. The resulting acetyl CoA can enter several pathways, but most often, the acetyl group is delivered to the citric acid cycle for further catabolism. During the conversion of pyruvate into the acetyl group, a molecule of carbon dioxide and two high-energy electrons are removed. The carbon dioxide accounts for two (conversion of two pyruvate molecules) of the six carbons of the original glucose molecule. The electrons are picked up by NAD+, and the NADH carries the electrons to a later pathway for ATP production. At this point, the glucose molecule that originally entered cellular respiration has been completely oxidized. Chemical potential energy stored within the glucose molecule has been transferred to electron carriers or has been used to synthesize a few ATPs.

The citric acid cycle is a series of redox and decarboxylation reactions that removes high-energy electrons and carbon dioxide. The electrons, temporarily stored in molecules of NADH and FADH2, are used to generate ATP in a subsequent pathway. One molecule of either GTP or ATP is produced by substrate-level phosphorylation on each turn of the cycle. There is no comparison of the cyclic pathway with a linear one.

Review Questions

What is removed from pyruvate during its conversion into an acetyl group?

  1. oxygen
  2. ATP
  3. B vitamin
  4. carbon dioxide

D

What do the electrons added to NAD+ do?

  1. They become part of a fermentation pathway.
  2. They go to another pathway for ATP production.
  3. They energize the entry of the acetyl group into the citric acid cycle.
  4. They are converted to NADP.

B

GTP or ATP is produced during the conversion of ________.

  1. isocitrate into α-ketoglutarate
  2. succinyl CoA into succinate
  3. fumarate into malate
  4. malate into oxaloacetate

B

How many NADH molecules are produced on each turn of the citric acid cycle?

  1. one
  2. two
  3. three
  4. four

C

Critical Thinking Questions

What is the primary difference between a circular pathway and a linear pathway?

In a circular pathway, the final product of the reaction is also the initial reactant. The pathway is self-perpetuating, as long as any of the intermediates of the pathway are supplied. Circular pathways are able to accommodate multiple entry and exit points, thus being particularly well suited for amphibolic pathways. In a linear pathway, one trip through the pathway completes the pathway, and a second trip would be an independent event.

Glossary

acetyl CoA
combination of an acetyl group derived from pyruvic acid and coenzyme A, which is made from pantothenic acid (a B-group vitamin)
citric acid cycle
(also Krebs cycle) series of enzyme-catalyzed chemical reactions of central importance in all living cells for extraction of energy from carbohydrates
Krebs cycle
(also citric acid cycle) alternate name for the citric acid cycle, named after Hans Krebs, who first identified the steps in the pathway in the 1930s in pigeon flight muscles; see citric acid cycle
TCA cycle
(also citric acid cycle) alternate name for the citric acid cycle, named after the group name for citric acid, tricarboxylic acid (TCA); see citric acid cycle

36

Oxidative Phosphorylation

Learning Objectives

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

  • Describe how electrons move through the electron transport chain and explain what happens to their energy levels during this process
  • Explain how a proton (H+) gradient is established and maintained by the electron transport chain

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. Instead, it is derived from a process that begins by moving electrons through a series of electron carriers that undergo redox reactions. This process causes hydrogen ions to accumulate within the matrix space. Therefore, a concentration gradient forms in which hydrogen ions diffuse out of the matrix space by passing through ATP synthase. The current of hydrogen ions powers the catalytic action of ATP synthase, which phosphorylates ADP, producing ATP.

Electron Transport Chain

The electron transport chain ((Figure)) is the last component of aerobic respiration and is the only part of glucose metabolism that uses atmospheric oxygen. Oxygen continuously diffuses into plant tissues (typically through stomata), as well as into fungi and bacteria; however, in animals, oxygen enters the body through a variety of respiratory systems. Electron transport is a series of redox reactions that resembles a relay race or bucket brigade in that electrons are passed rapidly from one component to the next, to the endpoint of the chain where the electrons reduce molecular oxygen and, along with associated protons, produces water. There are four complexes composed of proteins, labeled I through IV in (Figure), 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 with multiple copies in the inner mitochondrial membrane of eukaryotes and within the plasma membrane of prokaryotes.

The electron transport chain is a series of electron transporters embedded in the inner mitochondrial membrane that shuttles electrons from NADH and FADH2 to molecular oxygen. In the process, protons are pumped from the mitochondrial matrix to the intermembrane space, and oxygen is reduced to form water.


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 N A D H to N A D superscript plus sign baseline; and simultaneously pumps a proton across the membrane to the inter membrane space. The two electrons released from N A D H are shuttled to coenzyme Q, then to complex I I I, to cytochrome c, to complex I V, then to molecular oxygen. In the process, two more protons are pumped across the membrane to the intermembrane space, and molecular oxygen is reduced to form water. Complex I I removes two electrons from F A D H subscript 2 baseline, thereby forming F A D. The electrons are shuttled to coenzyme Q, then to complex I I I, cytochrome c, complex I, and molecular oxygen as in the case of N A D H oxidation.

Complex I

First, two electrons are carried to the first complex via NADH. This complex, labeled I, is composed of flavin mononucleotide (FMN) and an iron-sulfur (Fe-S)-containing protein. FMN, which is derived from vitamin B2 (also called riboflavin), is one of several prosthetic groups or cofactors in the electron transport chain. A prosthetic group is a nonprotein molecule required for the activity of a protein. Prosthetic groups are organic or inorganic, nonpeptide molecules bound to a protein that facilitate its function. Prosthetic groups include coenzymes, which are the prosthetic groups of enzymes. The enzyme in complex I is NADH dehydrogenase and is a very large protein, containing 45 amino acid chains. Complex I can pump four hydrogen ions across the membrane from the matrix into the intermembrane space, and it is in this way that the hydrogen ion gradient is established and maintained between the two compartments separated by the inner mitochondrial membrane.

Q and Complex II

Complex II directly receives FADH2—which does not pass through complex I. The compound connecting the first and second complexes to the third is ubiquinone B. The Q molecule is lipid soluble and freely moves through the hydrophobic core of the membrane. Once it is reduced (QH2), ubiquinone delivers its electrons to the next complex in the electron transport chain. Q receives the electrons derived from NADH from complex I, and the electrons derived from FADH2 from complex II. This enzyme and FADH2 form a small complex that delivers electrons directly to the electron transport chain, bypassing the first complex. Since these electrons bypass and thus do not energize the proton pump in the first complex, fewer ATP molecules are made from the FADH2 electrons. The number of ATP molecules ultimately obtained is directly proportional to the number of protons pumped across the inner mitochondrial membrane.

Complex III

The third complex is composed of cytochrome b—another Fe-S protein, a Rieske center (2Fe-2S center), and cytochrome c proteins. This complex is also called cytochrome oxidoreductase. Cytochrome proteins have a prosthetic group of heme. The heme molecule is similar to the heme in hemoglobin, but it carries electrons, not oxygen. As a result, the iron ion at its core is reduced and oxidized as it passes the electrons, fluctuating between different oxidation states: Fe++ (reduced) and Fe+++ (oxidized). The heme molecules in the cytochromes have slightly different characteristics due to the effects of the different proteins binding to them, giving slightly different characteristics to each complex. Complex III pumps protons through the membrane and passes its electrons to cytochrome c for transport to the fourth complex of proteins and enzymes. (Cytochrome c receives electrons from Q; however, whereas Q carries pairs of electrons, cytochrome c can accept only one at a time.)

Complex IV

The fourth complex is composed of cytochrome proteins c, a, and a3. This complex contains two heme groups (one in each of the two cytochromes, a, and a3) and three copper ions (a pair of CuA and one CuB in cytochrome a3). The cytochromes hold an oxygen molecule very tightly between the iron and copper ions until the oxygen is completely reduced by the gain of two electrons. The reduced oxygen then picks up two hydrogen ions from the surrounding medium to make water (H2O). The removal of the hydrogen ions from the system contributes to the ion gradient that forms the foundation for the process of chemiosmosis.

Chemiosmosis

In chemiosmosis, the free energy from the series of redox reactions just described is used to pump hydrogen ions (protons) across the mitochondrial membrane. The uneven distribution of H+ ions across the membrane establishes both concentration and electrical gradients (thus, an electrochemical gradient), owing to the hydrogen ions’ positive charge and their aggregation on one side of the membrane.

If the membrane were continuously open to simple diffusion by the hydrogen ions, the ions would tend to diffuse back across into the matrix, driven by the concentrations producing their electrochemical gradient. Recall that many ions cannot diffuse through the nonpolar regions of phospholipid membranes without the aid of ion channels. Similarly, hydrogen ions in the matrix space can only pass through the inner mitochondrial membrane by an integral membrane protein called ATP synthase ((Figure)). This complex protein acts as a tiny generator, turned by the force of the hydrogen ions diffusing through it, down their electrochemical gradient. The turning of parts of this molecular machine facilitates the addition of a phosphate to ADP, forming ATP, using the potential energy of the hydrogen ion gradient.

Visual Connection
ATP synthase is a complex, molecular machine that uses a proton (H+) gradient to form ATP from ADP and inorganic phosphate (Pi). (Credit: modification of work by Klaus Hoffmeier)


This illustration shows an A T P synthase enzyme embedded in the inner mitochondrial membrane. A T P 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 A T P from A D P and inorganic phosphate.

Dinitrophenol (DNP) is an “uncoupler” that makes the inner mitochondrial membrane “leaky” to protons. It was used until 1938 as a weight-loss drug. What effect would you expect DNP to have on the change in pH across the inner mitochondrial membrane? Why do you think this might be an effective weight-loss drug?

<!– [link]Figure 07_04_02[/link]After DNP poisoning, the electron transport chain can no longer form a proton gradient, and ATP synthase can no longer make ATP. DNP is an effective diet drug because it uncouples ATP synthesis; in other words, after taking it, a person obtains less energy out of the food he or she eats. Interestingly, one of the worst side effects of this drug is hyperthermia, or overheating of the body. Since ATP cannot be formed, the energy from electron transport is lost as heat. –>

Chemiosmosis ((Figure)) is used to generate 90 percent of the ATP made during aerobic glucose catabolism; it is also the method used in the light reactions of photosynthesis to harness the energy of sunlight in the process of photophosphorylation. Recall that the production of ATP using the process of chemiosmosis in mitochondria is called oxidative phosphorylation. The overall result of these 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 pathway, the electrons are used to reduce an oxygen molecule to oxygen ions. The extra electrons on the oxygen attract hydrogen ions (protons) from the surrounding medium, and water is formed. Thus, oxygen is the final electron acceptor in the electron transport chain.

Visual Connection
In oxidative phosphorylation, the pH gradient formed by the electron transport chain is used by ATP synthase to form ATP.


This illustration shows the electron transport chain, the A T P synthase enzyme embedded in the inner mitochondrial membrane, and the citric acid cycle occurring in the mitochondrial matrix. The citric acid cycle feeds N A D H and F A D H subscript 2 baseline to the electron transport chain. The electron transport chain oxidizes these substrates and, in the process, pumps protons into the intermembrane space. A T P synthase allows protons to leak back into the matrix and synthesizes A T P.

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 effect would cyanide have on ATP synthesis?

<!– <para>After cyanide poisoning, the electron transport chain can no longer pump electrons into the intermembrane space. The pH of the intermembrane space would increase, the pH gradient would decrease, and ATP synthesis would stop. –>

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 membranes of the mitochondria. (The NADH generated from glycolysis cannot easily enter mitochondria.) Thus, electrons are picked up on the inside of mitochondria by either NAD+ or FAD+. As you have learned earlier, these FAD+ molecules can transport fewer ions; consequently, fewer ATP molecules are generated when FAD+ acts as a carrier. NAD+ is used as the electron transporter in the liver and FAD+ acts in the brain.

Another factor that affects the yield of ATP molecules generated from glucose is the fact that intermediate compounds in these pathways are also 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. In addition, the five-carbon sugars that form nucleic acids are made from intermediates in glycolysis. Certain nonessential amino acids can be made from intermediates of both glycolysis and the citric acid cycle. Lipids, such as cholesterol and triglycerides, are also made from intermediates in these pathways, and both amino acids and triglycerides are broken down for energy through these pathways. Overall, in living systems, these pathways of glucose catabolism extract about 34 percent of the energy contained in glucose, with the remainder being released as heat.

Section Summary

The electron transport chain is the portion of aerobic respiration that uses free oxygen as the final electron acceptor of the electrons removed from the intermediate compounds in glucose catabolism. The electron transport chain is composed of four large, multiprotein complexes embedded in the inner mitochondrial membrane and two small diffusible electron carriers shuttling electrons between them. The electrons are passed through a series of redox reactions, with a small amount of free energy used at three points to transport hydrogen ions across a membrane. This process contributes to the gradient used in chemiosmosis. The electrons passing through the electron transport chain gradually lose energy. High-energy electrons donated to the chain by either NADH or FADH2 complete the chain, as low-energy electrons reduce oxygen molecules and form water. The level of free energy of the electrons drops from about 60 kcal/mol in NADH or 45 kcal/mol in FADH2 to about 0 kcal/mol in water. The end products of the electron transport chain are water and ATP. A number of intermediate compounds of the citric acid cycle can be diverted into the anabolism of other biochemical molecules, such as nonessential amino acids, sugars, and lipids. These same molecules can serve as energy sources for the glucose pathways.

Visual Connection Questions

(Figure) Dinitrophenol (DNP) is an “uncoupler” that makes the inner mitochondrial membrane “leaky” to protons. It was used until 1938 as a weight-loss drug. What effect would you expect DNP to have on the change in pH across the inner mitochondrial membrane? Why do you think this might be an effective weight-loss drug?

(Figure) After DNP poisoning, the electron transport chain can no longer form a proton gradient, and ATP synthase can no longer make ATP. DNP is an effective diet drug because it uncouples ATP synthesis; in other words, after taking it, a person obtains less energy out of the food he or she eats. Interestingly, one of the worst side effects of this drug is hyperthermia, or overheating of the body. Since ATP cannot be formed, the energy from electron transport is lost as heat.

(Figure) 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 effect would cyanide have on ATP synthesis?

(Figure) After cyanide poisoning, the electron transport chain can no longer pump electrons into the intermembrane space. The pH of the intermembrane space would increase, the pH gradient would decrease, and ATP synthesis would stop.

Review Questions

What compound receives electrons from NADH?

  1. FMN
  2. ubiquinone
  3. cytochrome c1
  4. oxygen

A

Chemiosmosis involves ________.

  1. the movement of electrons across the cell membrane
  2. the movement of hydrogen atoms across a mitochondrial membrane
  3. the movement of hydrogen ions across a mitochondrial membrane
  4. the movement of glucose through the cell membrane

C

Critical Thinking Questions

How do the roles of ubiquinone and cytochrome c differ from the roles of the other components of the electron transport chain?

Q and cytochrome c are transport molecules. Their function does not result directly in ATP synthesis in that they are not pumps. Moreover, Q is the only component of the electron transport chain that is not a protein. Ubiquinone and cytochrome c are small, mobile electron carriers, whereas the other components of the electron transport chain are large complexes anchored in the inner mitochondrial membrane.

What accounts for the different number of ATP molecules that are formed through cellular respiration?

Few tissues except muscle produce the maximum possible amount of ATP from nutrients. The intermediates are used to produce needed amino acids, fatty acids, cholesterol, and sugars for nucleic acids. When NADH is transported from the cytoplasm to the mitochondria, an active transport mechanism is used, which decreases the amount of ATP that can be made. The electron transport chain differs in composition between species, so different organisms will make different amounts of ATP using their electron transport chains.

Glossary

ATP synthase
(also F1F0 ATP synthase) membrane-embedded protein complex that adds a phosphate to ADP with energy from protons diffusing through it
prosthetic group
(also prosthetic cofactor) molecule bound to a protein that facilitates the function of the protein
ubiquinone
soluble electron transporter in the electron transport chain that connects the first or second complex to the third

37

Metabolism without Oxygen

Learning Objectives

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

  • 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 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 the glycolytic pathway 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 called anaerobic cellular respiration, in which organisms convert energy for their use in the absence of oxygen.

Anaerobic Cellular Respiration

Certain prokaryotes, including some species in the domains Bacteria and Archaea, use anaerobic respiration. For example, a group of archaeans 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, most of which are anaerobic ((Figure)), reduce sulfate to hydrogen sulfide to regenerate NAD+ from NADH.

The green color seen in these coastal waters is from an eruption of hydrogen sulfide–producing bacteria. These anaerobic, sulfate-reducing bacteria release hydrogen sulfide gas as they decompose algae in the water. (credit: modification of work by NASA/Jeff Schmaltz, MODIS Land Rapid Response Team at NASA GSFC, Visible Earth Catalog of NASA images)

This photo shows a bloom of green bacteria in water.

Link to Learning

Visit this site to see anaerobic cellular respiration in action.

Lactic Acid Fermentation

The fermentation method used by animals and certain bacteria, such as those in yogurt, is lactic acid fermentation ((Figure)). This type of fermentation is used routinely in mammalian red blood cells, which do not have mitochondria, and in skeletal muscle that has an insufficient oxygen supply to allow aerobic respiration to continue (that is, in muscles used to the point of fatigue). In muscles, lactic acid accumulation must be removed by the blood circulation, and when the lactic acid loses a hydrogen, the resulting lactate is brought to the liver for further metabolism. The chemical reactions of lactic acid fermentation are the following:

\text{Pyruvic acid}+\text{NADH}↔\text{lactic acid}+{\text{NAD}}^{+}

The enzyme used in this reaction is lactate dehydrogenase (LDH). The reaction can proceed in either direction, but the reaction from left to right is inhibited by acidic conditions. Such lactic acid accumulation was once believed to cause muscle stiffness, fatigue, and soreness, although more recent research disputes this hypothesis. Once the lactic acid has been removed from the muscle and circulated to the liver, it can be reconverted into pyruvic acid and further catabolized for energy.

Visual Connection
Lactic acid fermentation is common in muscle cells that have run out of oxygen.

This illustration shows that during glycolysis, glucose is broken down into two pyruvate molecules and, in the process, two N A D H are formed from N A D superscript plus sign baseline. During lactic acid fermentation, the two pyruvate molecules are converted into lactate, and N A D H is recycled back into N A D superscript plus sign baseline.

Tremetol, a metabolic poison found in the white snakeroot plant, prevents the metabolism of lactate. When cows eat this plant, tremetol is concentrated in the milk they produce. Humans who consume the milk can become seriously ill. Symptoms of this disease, which include vomiting, abdominal pain, and tremors, become worse after exercise. Why do you think this is the case?

<!– [link]Figure 07_05_02[/link]The illness is caused by lactate accumulation. Lactate 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)), which produces ethanol. The first chemical reaction of alcohol fermentation is the following (CO2 does not participate in the second reaction):

\text{pyruvic acid}+{\text{H}}^{+}\to {\text{CO}}_{2}+\text{acetaldehyde}+\text{NADH}+{\text{H}}^{+}\to \text{ethanol}+{\text{NAD}}^{+}

The first reaction is catalyzed by pyruvate decarboxylase, a cytoplasmic enzyme, with a coenzyme of thiamine pyrophosphate (TPP, derived from vitamin B1 and also called thiamine). A carboxyl group is removed from pyruvic acid, releasing carbon dioxide as a gas. The loss of carbon dioxide reduces the size of the molecule by one carbon, producing acetaldehyde. The second reaction is catalyzed by alcohol dehydrogenase to oxidize NADH to NAD+ and reduce acetaldehyde to ethanol. The fermentation of pyruvic acid by yeast produces the ethanol found in alcoholic beverages. Ethanol tolerance of yeast is variable, ranging from about 5 percent to 21 percent, depending on the yeast strain and environmental conditions.

Fermentation of grape juice into wine produces CO2 as a byproduct. Fermentation tanks have valves so that the pressure inside the tanks created by the carbon dioxide produced can be released.

This photo shows large cylindrical fermentation tanks stacked one on top of the other.

Other Types of Fermentation

Other fermentation methods take place in bacteria. We should note that many prokaryotes are facultatively anaerobic. This means that they can switch between aerobic respiration and fermentation, depending on the availability of free oxygen. Certain prokaryotes, such as Clostridia, are obligate anaerobes. Obligate anaerobes live and grow in the absence of molecular oxygen. Oxygen is a poison to these microorganisms and kills them on exposure. We should also note 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. Various methods of fermentation are used by assorted organisms to ensure an adequate supply of NAD+ for the sixth step in glycolysis. Without these pathways, this step would not occur, and ATP could not be harvested from the breakdown of glucose.

Section Summary

If NADH cannot be oxidized 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 of NADH to produce ATP using an electron transport chain is not utilized.

Visual Connection Questions

((Figure)) Tremetol, a metabolic poison found in the white snake root plant, prevents the metabolism of lactate. When cows eat this plant, tremetol is concentrated in the milk they produce. Humans who consume the milk can become seriously ill. Symptoms of this disease, which include vomiting, abdominal pain, and tremors, become worse after exercise. Why do you think this is the case?

(Figure) The illness is caused by lactate accumulation. Lactate 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?

  1. lactic acid fermentation
  2. alcohol fermentation
  3. mixed acid fermentation
  4. propionic fermentation

A

Critical Thinking Questions

What is the primary difference between fermentation and anaerobic respiration?

Fermentation uses glycolysis only. Anaerobic respiration uses all three parts of cellular respiration, including the parts in the mitochondria like the citric acid cycle and electron transport; it also uses a different final electron acceptor instead of oxygen gas.

Glossary

anaerobic cellular respiration
process in which organisms convert energy for their use in the absence of oxygen
fermentation
process of regenerating NAD+ with either an inorganic or organic compound serving as the final electron acceptor; occurs in the absence of oxygen

38

Connections of Carbohydrate, Protein, and Lipid Metabolic Pathways

Learning Objectives

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

  • Discuss the ways 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 organic compounds other than glucose for food. How does a turkey sandwich end up as ATP in 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 (see (Figure)). Metabolic pathways should be thought of as porous and interconnecting—that is, substances enter from other pathways, and intermediates leave for other pathways. These pathways are not closed systems! Many of the substrates, intermediates, and products in a particular pathway are reactants in other pathways.

Connections of Other Sugars to Glucose Metabolism

Glycogen, a polymer of glucose, is an energy storage molecule in animals. When there is adequate ATP present, excess glucose is stored as glycogen in both liver and muscle cells. The glycogen will be hydrolyzed into glucose 1-phosphate monomers (G-1-P) if blood sugar levels drop. The presence of glycogen as a source of glucose allows ATP to be produced for a longer period of time during exercise. Glycogen is broken down into glucose-1-phosphate (G-1-P) and converted into glucose-6-phosphate (G-6-P) in both muscle and liver cells, and this product enters the glycolytic pathway.

Sucrose is a disaccharide with a molecule of glucose and a molecule of fructose bonded together with a glycosidic linkage. Fructose is one of the three “dietary” monosaccharides, along with glucose and galactose (part of the milk sugar dissacharide lactose), which 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 hydrolyzed by a variety of enzymes in cells. Most of the time, the amino acids are recycled into the synthesis of new proteins. If there are excess amino acids, however, or if the body is in a state of starvation, some amino acids will be shunted into the pathways of glucose catabolism ((Figure)). It is very important to note that 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, produced from the nitrogen originating in amino acids, and it leaves the body in urine. It should be noted that amino acids can be synthesized from the intermediates and reactants in the cellular respiration cycle.

The carbon skeletons of certain amino acids (indicated in boxes) derived from proteins can feed into the citric acid cycle. (credit: modification of work by Mikael Häggström)


This illustration shows that the amino acids alanine, glycine, threonine, cysteine, and serine can be converted into pyruvate. Leucine, lysine, phenylalanine, tyrosine, tryptophan, and isoleucine can be converted into acetyl upper case C lower case o upper case A. Arginine, proline, histidine, glutamine, and glutamate can be converted into alpha-ketoglutarate. Isoleucine, valine, methionine, and threonine can be converted into succinyl upper C lower o upper A. Tyrosine and phenylalanine can be converted into fumarate, and aspartate and asparagine can be converted into oxaloacetate.

Connections of Lipid and Glucose Metabolisms

The lipids connected to the glucose pathway include 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 groups and proceeds in only one direction. The process cannot be reversed.

Triglycerides—made from the bonding of glycerol and three fatty acids—are a form of long-term energy storage in animals. 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 to glycerol-3-phosphate, which continues through glycolysis. Fatty acids are catabolized in a process called beta-oxidation, which takes place in the matrix of the mitochondria and converts their fatty acid chains into two-carbon units of acetyl groups. The acetyl groups are picked up by CoA to form acetyl CoA that proceeds into the citric acid cycle.

Glycogen from the liver and muscles, as well as other carbohydrates, hydrolyzed into glucose-1-phosphate, together with fats and proteins, can feed into the catabolic pathways for carbohydrates.


This illustration shows that glycogen, fats, and proteins can be catabolized via aerobic respiration. Glycogen is broken down into glucose, which feeds into glycolysis at the start. Fats are broken down into glycerol, which is processed by glycolysis, and fatty acids 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.

Evolution Connection

Pathways of Photosynthesis and Cellular MetabolismThe processes of 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—possibly on the surface of some porous clays, perhaps in warm marine environments. 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 the components of their own bodies. 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 upon which they could survive. Selection would favor those organisms that could extract maximal value from the nutrients to which they had access.

An early form of photosynthesis developed that harnessed the sun’s energy using water as a source of hydrogen atoms, but this pathway did not produce free oxygen (anoxygenic photosynthesis). (Another type of anoxygenic photosynthesis did not produce free oxygen because it did not use water as the source of hydrogen ions; instead, it used materials such as hydrogen sulfide and consequently produced sulfur). It is thought that glycolysis developed at this time and could take advantage of the simple sugars being produced but that these reactions were unable to fully extract the energy stored in the carbohydrates. The development of glycolysis probably predated the evolution of photosynthesis, as it was well suited to extract energy from materials spontaneously accumulating in the “primeval soup.” A later form of photosynthesis used water as a source of electrons and hydrogen and generated free oxygen. Over time, the atmosphere became oxygenated, but not before the oxygen released oxidized metals in the ocean and created a “rust” layer in the sediment, permitting the dating of the rise of the first oxygenic photosynthesizers. Living things adapted to exploit this new atmosphere that allowed aerobic respiration as we know it to evolve. When the full process of oxygenic photosynthesis developed and the atmosphere became oxygenated, cells were finally able to use the oxygen expelled by photosynthesis to extract considerably more energy from the sugar molecules using the citric acid cycle and oxidative phosphorylation.

Section Summary

The breakdown and synthesis of carbohydrates, proteins, and lipids connect with the pathways of glucose catabolism. The simple sugars are galactose, fructose, glycogen, and pentose. These are catabolized during 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 groups, and the components of triglycerides come from glycerol-3-phosphate from glycolysis and acetyl groups produced in the mitochondria from pyruvate.

Review Questions

A major connection for sugars in glycolysis is ________.

  1. glucose-6-phosphate
  2. fructose-1,6-bisphosphate
  3. dihydroxyacetone phosphate
  4. phosphoenolpyruvate

A

Beta-oxidation is ________.

  1. the breakdown of sugars
  2. the assembly of sugars
  3. the breakdown of fatty acids
  4. the removal of amino groups from amino acids

C

Critical Thinking Questions

Would you describe metabolic pathways as inherently wasteful or inherently economical? 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 balanced overall. 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.

39

Regulation of Cellular Respiration

Learning Objectives

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

  • Describe how feedback inhibition would affect the production of an intermediate or product in a pathway
  • Identify the mechanism that controls the rate of the transport of electrons through the electron transport chain

Cellular respiration must be regulated in order to provide balanced amounts of energy in the form of ATP. The cell also must generate a number of intermediate compounds that are used in the anabolism and catabolism of macromolecules. Without controls, metabolic reactions would quickly come to a standstill as the forward and backward reactions reached a state of equilibrium. Resources would be used inappropriately. A cell does not need the maximum amount of ATP that it can make all the time: At times, the cell needs to shunt some of the intermediates to pathways for amino acid, protein, glycogen, lipid, and nucleic acid production. In short, the cell needs to control its metabolism.

Regulatory Mechanisms

A variety of mechanisms is used to control cellular respiration. Some type of control exists at each stage of glucose metabolism. Access of glucose to the cell can be regulated using the GLUT (glucose transporter) proteins that transport glucose ((Figure)). Different forms of the GLUT protein control passage of glucose into the cells of specific tissues.

GLUT4 is a glucose transporter that is stored in vesicles. A cascade of events that occurs upon insulin binding to a receptor in the plasma membrane causes GLUT4-containing vesicles to fuse with the plasma membrane so that glucose may be transported into the cell.


When insulin in the bloodstream binds the insulin receptor in the plasma membrane of a target cell, a vesicle containing the glucose transporter Glut-4 fuses with the plasma membrane. Glut-4 is a transporter that allows glucose to enter the cell.

Some reactions are controlled by having two different enzymes—one each for the two directions of a reversible reaction. Reactions that are catalyzed by only one enzyme can go to equilibrium, stalling the reaction. In contrast, if two different enzymes (each specific for a given direction) are necessary for a reversible reaction, the opportunity to control the rate of the reaction increases, and equilibrium is not reached.

A number of enzymes involved in each of the pathways—in particular, the enzyme catalyzing the first committed reaction of the pathway—are controlled by attachment of a molecule to an allosteric site on the protein. The molecules most commonly used in this capacity are the nucleotides ATP, ADP, AMP, NAD+, and NADH. These regulators—allosteric effectors—may increase or decrease enzyme activity, depending on the prevailing conditions. The allosteric effector alters the steric structure of the enzyme, usually affecting the configuration of the active site. This alteration of the protein’s (the enzyme’s) structure either increases or decreases its affinity for its substrate, with the effect of increasing or decreasing the rate of the reaction. The attachment signals to the enzyme. This binding can increase or decrease the enzyme’s activity, providing a feedback mechanism. This feedback type of control is effective as long as the chemical affecting it is attached to the enzyme. Once the overall concentration of the chemical decreases, it will diffuse away from the protein, and the control is relaxed.

Control of Catabolic Pathways

Enzymes, proteins, electron carriers, and pumps that play roles in glycolysis, the citric acid cycle, and the electron transport chain tend to catalyze nonreversible reactions. In other words, if the initial reaction takes place, the pathway is committed to proceeding with the remaining reactions. Whether a particular enzyme activity is released depends upon the energy needs of the cell (as reflected by the levels of ATP, ADP, and AMP).

Glycolysis

The control of glycolysis begins with the first enzyme in the pathway, hexokinase ((Figure)). This enzyme catalyzes the phosphorylation of glucose, which helps to prepare the compound for cleavage in a later step. The presence of the negatively charged phosphate in the molecule also prevents the sugar from leaving the cell. When hexokinase is inhibited, glucose diffuses out of the cell and does not become a substrate for the respiration pathways in that tissue. The product of the hexokinase reaction is glucose-6-phosphate, which accumulates when a later enzyme, phosphofructokinase, is inhibited.

The glycolysis pathway is primarily regulated at the three key enzymatic steps (1, 2, and 7) as indicated. Note that the first two steps that are regulated occur early in the pathway and involve hydrolysis of ATP.


This illustration shows that glycolysis is regulated via three key enzymes: hexokinase phosphofructokinase, and phosphoglycerate kinase. The first two enzymes hydrolyze an ATP and the third one produces ATP.

Phosphofructokinase is the main enzyme controlled in glycolysis. High levels of ATP or citrate or a lower, more acidic pH decreases the enzyme’s activity. An increase in citrate concentration can occur because of a blockage in the citric acid cycle. Fermentation, with its production of organic acids such as lactic acid, frequently accounts for the increased acidity in a cell; however, the products of fermentation do not typically accumulate in cells.

The last step in glycolysis is catalyzed by pyruvate kinase. The pyruvate produced can proceed to be catabolized or converted into the amino acid alanine. If no more energy is needed and alanine is in adequate supply, the enzyme is inhibited. The enzyme’s activity is increased when fructose-1,6-bisphosphate levels increase. (Recall that fructose-1,6-bisphosphate is an intermediate in the first half of glycolysis.) The regulation of pyruvate kinase involves phosphorylation by a kinase (pyruvate kinase), resulting in a less-active enzyme. Dephosphorylation by a phosphatase reactivates it. Pyruvate kinase is also regulated by ATP (a negative allosteric effect).

If more energy is needed, more pyruvate will be converted into acetyl CoA through the action of pyruvate dehydrogenase. If either acetyl groups or NADH accumulates, there is less need for the reaction, and the rate decreases. Pyruvate dehydrogenase is also regulated by phosphorylation: a kinase phosphorylates it to form an inactive enzyme, and a phosphatase reactivates it. The kinase and the phosphatase are also regulated.

Citric Acid Cycle

The citric acid cycle is controlled through the enzymes that catalyze the reactions that make the first two molecules of NADH ((Figure)). These enzymes are isocitrate dehydrogenase and α-ketoglutarate dehydrogenase. When adequate ATP and NADH levels are available, the rates of these reactions decrease. When more ATP is needed, as reflected in rising ADP levels, the rate increases. Alpha-ketoglutarate dehydrogenase will also be affected by the levels of succinyl CoA—a subsequent intermediate in the cycle—causing a decrease in activity. A decrease in the rate of operation of the pathway at this point is not necessarily negative, as the increased levels of the α-ketoglutarate not used by the citric acid cycle can be used by the cell for amino acid (glutamate) synthesis.

Electron Transport Chain

Specific enzymes of the electron transport chain are unaffected by feedback inhibition, but the rate of electron transport through the pathway is affected by the levels of ADP and ATP. Greater ATP consumption by a cell is indicated by a buildup of ADP. As ATP usage decreases, the concentration of ADP decreases, and now, ATP begins to build up in the cell. This change in the relative concentration of ADP to ATP triggers the cell to slow down the electron transport chain.

Link to Learning

Visit this site to see an animation of the electron transport chain and ATP synthesis.

For a summary of feedback controls in cellular respiration, see (Figure).

Summary of Feedback Controls in Cellular Respiration
Pathway Enzyme affected Elevated levels of effector Effect on pathway activity
glycolysis hexokinase glucose-6-phosphate decrease
phosphofructokinase low-energy charge (ATP, AMP), fructose-6-phosphate via fructose-2,6-bisphosphate increase
high-energy charge (ATP, AMP), citrate, acidic pH decrease
pyruvate kinase fructose-1,6-bisphosphate increase
high-energy charge (ATP, AMP), alanine decrease
pyruvate to acetyl CoA conversion pyruvate dehydrogenase ADP, pyruvate increase
acetyl CoA, ATP, NADH decrease
citric acid cycle isocitrate dehydrogenase ADP increase
ATP, NADH decrease
α-ketoglutarate dehydrogenase calcium ions, ADP increase
ATP, NADH, succinyl CoA decrease
electron transport chain ADP increase
ATP decrease

Section Summary

Cellular respiration is controlled by a variety of means. The entry of glucose into a cell is controlled by the transport proteins that aid glucose passage through the cell membrane. Most of the control of the respiration processes is accomplished through the control of specific enzymes in the pathways. This is a type of negative feedback mechanism, turning the enzymes off. The enzymes respond most often to the levels of the available nucleosides ATP, ADP, AMP, NAD+, and FAD. Other intermediates of the pathway also affect certain enzymes in the systems.

Review Questions

The effect of high levels of ADP is to ________ in cellular respiration.

  1. increase the activity of specific enzymes
  2. decrease the activity of specific enzymes
  3. have no effect on the activity of specific enzymes
  4. slow down the pathway

A

The control of which enzyme exerts the most control on glycolysis?

  1. hexokinase
  2. phosphofructokinase
  3. glucose-6-phosphatase
  4. aldolase

B

Critical Thinking Questions

How does citrate from the citric acid cycle affect glycolysis?

Citrate can inhibit phosphofructokinase by feedback regulation.

Why might negative feedback mechanisms be more common than positive feedback mechanisms in living cells?

Negative feedback mechanisms actually control a process; it can turn it off, whereas positive feedback accelerates the process, allowing the cell no control over it. Negative feedback naturally maintains homeostasis, whereas positive feedback drives the system away from equilibrium.

Glossary

GLUT protein
integral membrane protein that transports glucose

VIII

Photosynthesis

40

Introduction

This world map shows Earth’s distribution of photosynthetic activity determined by chlorophyll a concentrations. On land, chlorophyll is evident from terrestrial plants, and within oceanic zones, from chlorophyll from phytoplankton. (credit: modification of work by SeaWiFS Project, NASA/Goddard Space Flight Center and ORBIMAGE)


The image shows a map of the world, colored by the levels of chlorophyll a on land and in the ocean.

The metabolic processes in all organisms—from bacteria to humans—require energy. To get this energy, many organisms access stored energy by eating, that is, by ingesting other organisms. But where does the stored energy in food originate? All of this energy can be traced back to photosynthesis.

41

Overview of Photosynthesis

Learning Objectives

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

  • Explain the significance of photosynthesis to other living organisms
  • Describe the main structures involved in photosynthesis
  • Identify the substrates and products of photosynthesis

Photosynthesis is essential to all life on earth; both plants and animals depend on it. It is the only biological process that can capture energy that originates from sunlight and converts it into chemical compounds (carbohydrates) that every organism uses to power its metabolism. It is also a source of oxygen necessary for many living organisms. In brief, the energy of sunlight is “captured” to energize electrons, whose energy is then stored in the covalent bonds of sugar molecules. How long lasting and stable are those covalent bonds? The energy extracted today by the burning of coal and petroleum products represents sunlight energy captured and stored by photosynthesis 350 to 200 million years ago during the Carboniferous Period.

Plants, algae, and a group of bacteria called cyanobacteria are the only organisms capable of performing photosynthesis ((Figure)). Because they use light to manufacture their own food, they are called photoautotrophs (literally, “self-feeders using light”). Other organisms, such as animals, fungi, and most other bacteria, are termed heterotrophs (“other feeders”), because they must rely on the sugars produced by photosynthetic organisms for their energy needs. A third very interesting group of bacteria synthesize sugars, not by using sunlight’s energy, but by extracting energy from inorganic chemical compounds. For this reason, they are referred to as chemoautotrophs.

Photoautotrophs including (a) plants, (b) algae, and (c) cyanobacteria synthesize their organic compounds via photosynthesis using sunlight as an energy source. Cyanobacteria and planktonic algae can grow over enormous areas in water, at times completely covering the surface. In a (d) deep sea vent, chemoautotrophs, such as these (e) thermophilic bacteria, capture energy from inorganic compounds to produce organic compounds. The ecosystem surrounding the vents has a diverse array of animals, such as tubeworms, crustaceans, and octopuses that derive energy from the bacteria. (credit a: modification of work by Steve Hillebrand, U.S. Fish and Wildlife Service; credit b: modification of work by “eutrophication&hypoxia”/Flickr; credit c: modification of work by NASA; credit d: University of Washington, NOAA; credit e: modification of work by Mark Amend, West Coast and Polar Regions Undersea Research Center, UAF, NOAA)


Photo a shows a fern leaf. Photo b shows thick, green algae growing on water. Micrograph c shows cyanobacteria, which are green rods about 10 microns long. Photo D shows black smoke pouring out of a deep sea vent covered with red worms. Micrograph E shows rod-shaped bacteria about 1.5 microns long.

The importance of photosynthesis is not just that it can capture sunlight’s energy. After all, a lizard sunning itself on a cold day can use the sun’s energy to warm up in a process called behavioral thermoregulation. In contrast, photosynthesis is vital because it evolved as a way to store the energy from solar radiation (the “photo-” part) to energy in the carbon-carbon bonds of carbohydrate molecules (the “-synthesis” part). Those carbohydrates are the energy source that heterotrophs use to power the synthesis of ATP via respiration. Therefore, photosynthesis powers 99 percent of Earth’s ecosystems. When a top predator, such as a wolf, preys on a deer ((Figure)), the wolf is at the end of an energy path that went from nuclear reactions on the surface of the sun, to visible light, to photosynthesis, to vegetation, to deer, and finally to the wolf.

The energy stored in carbohydrate molecules from photosynthesis passes through the food chain. The predator that eats these deer receives a portion of the energy that originated in the photosynthetic vegetation that the deer consumed. (credit: modification of work by Steve VanRiper, U.S. Fish and Wildlife Service)


A photo shows deer running through tall grass beside a forest.

Main Structures and Summary of Photosynthesis

Photosynthesis is a multi-step process that requires specific wavelengths of visible sunlight, carbon dioxide (which is low in energy), and water as substrates ((Figure)). After the process is complete, it releases oxygen and produces glyceraldehyde-3-phosphate (GA3P), as well as simple carbohydrate molecules (high in energy) that can then be converted into glucose, sucrose, or any of dozens of other sugar molecules. These sugar molecules contain energy and the energized carbon that all living things need to survive.

Photosynthesis uses solar energy, carbon dioxide, and water to produce energy-storing carbohydrates. Oxygen is generated as a waste product of photosynthesis.


Photo of a tree with labels shows photosynthesis. Arrows indicate that the tree uses carbon dioxide, water, and sunlight to make sugars and oxygen. Water is absorbed through the tree's roots; sunlight is absorbed through the tree's leaves; the tree also absorbs carbon dioxide, and releases oxygen.

The following is the chemical equation for photosynthesis ((Figure)):

The basic equation for photosynthesis is deceptively simple. In reality, the process takes place in many steps involving intermediate reactants and products. Glucose, the primary energy source in cells, is made from two three-carbon GA3Ps.


The photosynthesis equation is shown. According to this equation, six carbon dioxide and six water molecules produce one sugar molecule and six oxygen molecules. The sugar molecule is made of six carbons, twelve hydrogens, and six oxygens. Sunlight is used as an energy source.

Although the equation looks simple, the many steps that take place during photosynthesis are actually quite complex. Before learning the details of how photoautotrophs turn sunlight into food, it is important to become familiar with the structures involved.

Basic Photosynthetic Structures

In plants, photosynthesis generally takes place in leaves, which consist of several layers of cells. The process of photosynthesis occurs in a middle layer called the mesophyll. The gas exchange of carbon dioxide and oxygen occurs through small, regulated openings called stomata (singular: stoma), which also play roles in the regulation of gas exchange and water balance. The stomata are typically located on the underside of the leaf, which helps to minimize water loss due to high temperatures on the upper surface of the leaf. Each stoma is flanked by guard cells that regulate the opening and closing of the stomata by swelling or shrinking in response to osmotic changes.

In all autotrophic eukaryotes, photosynthesis takes place inside an organelle called a chloroplast. For plants, chloroplast-containing cells exist mostly in the mesophyll. Chloroplasts have a double membrane envelope (composed of an outer membrane and an inner membrane), and are ancestrally derived from ancient free-living cyanobacteria. Within the chloroplast are stacked, disc-shaped structures called thylakoids. Embedded in the thylakoid membrane is chlorophyll, a pigment (molecule that absorbs light) responsible for the initial interaction between light and plant material, and numerous proteins that make up the electron transport chain. The thylakoid membrane encloses an internal space called the thylakoid lumen. As shown in (Figure), a stack of thylakoids is called a granum, and the liquid-filled space surrounding the granum is called stroma or “bed” (not to be confused with stoma or “mouth,” an opening on the leaf epidermis).

Visual Connection
Photosynthesis takes place in chloroplasts, which have an outer membrane and an inner membrane. Stacks of thylakoids called grana form a third membrane layer.


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 lumen.

On a hot, dry day, the guard cells of plants close their stomata to conserve water. What impact will this have on photosynthesis?

<!–<para> Levels of carbon dioxide (a necessary photosynthetic substrate) will fall. As a result, the rate of photosynthesis will decrease.–>

The Two Parts of Photosynthesis

Photosynthesis takes place in two sequential stages: the light-dependent reactions and the light-independent reactions. In the light-dependent reactions, energy from sunlight is absorbed by chlorophyll and that energy is converted into stored chemical energy. In the light-independent reactions, the chemical energy harvested during the light-dependent reactions drives the assembly of sugar molecules from carbon dioxide. Therefore, although the light-independent reactions do not use light as a reactant, they require the products of the light-dependent reactions to function. In addition, however, several enzymes of the light-independent reactions are activated by light. The light-dependent reactions utilize certain molecules to temporarily store the energy: These are referred to as energy carriers. The energy carriers that move energy from light-dependent reactions to light-independent reactions can be thought of as “full” because they are rich in energy. After the energy is released, the “empty” energy carriers return to the light-dependent reaction to obtain more energy. (Figure) illustrates the components inside the chloroplast where the light-dependent and light-independent reactions take place.

Photosynthesis takes place in two stages: light-dependent reactions and the Calvin cycle. Light-dependent reactions, which take place in the thylakoid membrane, use light energy to make ATP and NADPH. The Calvin cycle, which takes place in the stroma, uses energy derived from these compounds to make GA3P from CO2.


This illustration shows a chloroplast with an outer membrane, an inner membrane, and stacks of membranes inside the inner membrane called thylakoids. The entire stack is called a granum. In the light reactions, energy from sunlight is converted into chemical energy in the form of A T P and N A D P H. In the process, water is used and oxygen is produced. Energy from A T P and N A D P H are used to power the Calvin cycle, which produces G A 3 P from carbon dioxide. A T P is broken down to A D P and Pi, and N A D P H is oxidized to N A D P superscript plus sign baseline. The cycle is completed when the light reactions convert these molecules back into A T P and N A D P H.

Link to Learning

Click the link to learn more about photosynthesis.

Everyday Connection

Photosynthesis at the Grocery Store

Foods that humans consume originate from photosynthesis. (credit: Associação Brasileira de Supermercados)


A photo shows people shopping in a grocery store.

Major grocery stores in the United States are organized into departments, such as dairy, meats, produce, bread, cereals, and so forth. Each aisle ((Figure)) contains hundreds, if not thousands, of different products for customers to buy and consume.

Although there is a large variety, each item ultimately can be linked back to photosynthesis. Meats and dairy link, because the animals were fed plant-based foods. The breads, cereals, and pastas come largely from starchy grains, which are the seeds of photosynthesis-dependent plants. What about desserts and drinks? All of these products contain sugar—sucrose is a plant product, a disaccharide, a carbohydrate molecule, which is built directly from photosynthesis. Moreover, many items are less obviously derived from plants: For instance, paper goods are generally plant products, and many plastics (abundant as products and packaging) are derived from “algae” (unicellular plant-like organisms, and cyanobacteria). Virtually every spice and flavoring in the spice aisle was produced by a plant as a leaf, root, bark, flower, fruit, or stem. Ultimately, photosynthesis connects to every meal and every food a person consumes.

Section Summary

The process of photosynthesis transformed life on Earth. By harnessing energy from the sun, the evolution of photosynthesis allowed living things access to enormous amounts of energy. Because of photosynthesis, living things gained access to sufficient energy that allowed them to build new structures and achieve the biodiversity evident today.

Only certain organisms (photoautotrophs), can perform photosynthesis; they require the presence of chlorophyll, a specialized pigment that absorbs certain wavelengths of the visible spectrum and can capture energy from sunlight. Photosynthesis uses carbon dioxide and water to assemble carbohydrate molecules and release oxygen as a byproduct into the atmosphere. Eukaryotic autotrophs, such as plants and algae, have organelles called chloroplasts in which photosynthesis takes place, and starch accumulates. In prokaryotes, such as cyanobacteria, the process is less localized and occurs within folded membranes, extensions of the plasma membrane, and in the cytoplasm.

Visual Connection Questions

(Figure) On a hot, dry day, the guard cells of plants close their stomata to conserve water. What impact will this have on photosynthesis?

(Figure) Levels of carbon dioxide (a necessary photosynthetic substrate) will immediately fall. As a result, the rate of photosynthesis will be inhibited.

Review Questions

Which of the following components is not used by both plants and cyanobacteria to carry out photosynthesis?

  1. chloroplasts
  2. chlorophyll
  3. carbon dioxide
  4. water

A

What two main products result from photosynthesis?

  1. oxygen and carbon dioxide
  2. chlorophyll and oxygen
  3. sugars/carbohydrates and oxygen
  4. sugars/carbohydrates and carbon dioxide

C

In which compartment of the plant cell do the light-independent reactions of photosynthesis take place?

  1. thylakoid
  2. stroma
  3. outer membrane
  4. mesophyll

B

Which statement about thylakoids in eukaryotes is not correct?

  1. Thylakoids are assembled into stacks.
  2. Thylakoids exist as a maze of folded membranes.
  3. The space surrounding thylakoids is called stroma.
  4. Thylakoids contain chlorophyll.

B

Predict the end result if a chloroplast’s light-independent enzymes developed a mutation that prevented them from activating in response to light.

  1. GA3P accumulation
  2. ATP and NADPH accumulation
  3. Water accumulation
  4. Carbon dioxide depletion

B

How are the NADPH and GA3P molecules made during photosynthesis similar?

  1. They are both end products of photosynthesis.
  2. They are both substrates for photosynthesis.
  3. They are both produced from carbon dioxide.
  4. They both store energy in chemical bonds.

D

Critical Thinking Questions

What is the overall outcome of the light reactions in photosynthesis?

The outcome of light reactions in photosynthesis is the conversion of solar energy into chemical energy that the chloroplasts can use to do work (mostly anabolic production of carbohydrates from carbon dioxide).

Why are carnivores, such as lions, dependent on photosynthesis to survive?

Because lions eat animals that eat plants.

Why are energy carriers thought of as either “full” or “empty”?

The energy carriers that move from the light-dependent reaction to the light-independent one are “full” because they bring energy. After the energy is released, the “empty” energy carriers return to the light-dependent reaction to obtain more energy. There is not much actual movement involved. Both ATP and NADPH are produced in the stroma where they are also used and reconverted into ADP, Pi, and NADP+.

Describe how the grey wolf population would be impacted by a volcanic eruption that spewed a dense ash cloud that blocked sunlight in a section of Yellowstone National Park.

The grey wolves are apex predators in their food web, meaning they consume smaller prey animals and are not the prey of any other animal. Blocking sunlight would prevent the plants at the bottom of the food web from performing photosynthesis. This would kill many of the plants, reducing the food sources available to smaller animals in Yellowstone. A smaller prey animal population means that fewer wolves can survive in the area, and the population of grey wolves will decrease.

How does the closing of the stomata limit photosynthesis?

The stomata regulate the exchange of gases and water vapor between a leaf and its surrounding environment. When the stomata are closed, the water molecules cannot escape the leaf, but the leaf also cannot acquire new carbon dioxide molecules from the environment. This limits the light-independent reactions to only continuing until the carbon dioxide stores in the leaf are depleted.

Glossary

chemoautotroph
organism that can build organic molecules using energy derived from inorganic chemicals instead of sunlight
chloroplast
organelle in which photosynthesis takes place
granum
stack of thylakoids located inside a chloroplast
heterotroph
organism that consumes organic substances or other organisms for food
light-dependent reaction
first stage of photosynthesis where certain wavelengths of the visible light are absorbed to form two energy-carrying molecules (ATP and NADPH)
light-independent reaction
second stage of photosynthesis, through which carbon dioxide is used to build carbohydrate molecules using energy from ATP and NADPH
mesophyll
middle layer of chlorophyll-rich cells in a leaf
photoautotroph
organism capable of producing its own organic compounds from sunlight
pigment
molecule that is capable of absorbing certain wavelengths of light and reflecting others (which accounts for its color)
stoma
opening that regulates gas exchange and water evaporation between leaves and the environment, typically situated on the underside of leaves
stroma
fluid-filled space surrounding the grana inside a chloroplast where the light-independent reactions of photosynthesis take place
thylakoid
disc-shaped, membrane-bound structure inside a chloroplast where the light-dependent reactions of photosynthesis take place; stacks of thylakoids are called grana
thylakoid lumen
aqueous space bound by a thylakoid membrane where protons accumulate during light-driven electron transport

42

The Light-Dependent Reactions of Photosynthesis

Learning Objectives

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

  • Explain how plants absorb energy from sunlight
  • Describe short and long wavelengths of light
  • Describe how and where photosynthesis takes place within a plant

How can light energy be used to make food? When a person turns on a lamp, electrical energy becomes light energy. Like all other forms of kinetic energy, light can travel, change form, and be harnessed to do work. In the case of photosynthesis, light energy is converted into chemical energy, which photoautotrophs use to build basic carbohydrate molecules ((Figure)). However, autotrophs only use a few specific wavelengths of sunlight.

Photoautotrophs can capture visible light energy in specific wavelengths from the sun, converting it into the chemical energy used to build food molecules. (credit: Gerry Atwell)


A photo shows the silhouette of a grassy plant against the sun at sunset.

What Is Light Energy?

The sun emits an enormous amount of electromagnetic radiation (solar energy in a spectrum from very short gamma rays to very long radio waves). Humans can see only a tiny fraction of this energy, which we refer to as “visible light.” The manner in which solar energy travels is described as waves. Scientists can determine the amount of energy of a wave by measuring its wavelength (shorter wavelengths are more powerful than longer wavelengths)—the distance between consecutive crest points of a wave. Therefore, a single wave is measured from two consecutive points, such as from crest to crest or from trough to trough ((Figure)).

The wavelength of a single wave is the distance between two consecutive points of similar position (two crests or two troughs) along the wave.


The illustration shows two waves. The distance between the crests (or troughs) is the wavelength. The crest is the upper portion of the wave, the trough is the lower portion of the wave.

Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun and other stars. Scientists differentiate the various types of radiant energy from the sun within the electromagnetic spectrum. The electromagnetic spectrum is the range of all possible frequencies of radiation ((Figure)). The difference between wavelengths relates to the amount of energy carried by them.

The sun emits energy in the form of electromagnetic radiation. This radiation exists at different wavelengths, each of which has its own characteristic energy. All electromagnetic radiation, including visible light, is characterized by its wavelength.


The illustration lists the types of electromagnetic radiation in order of increasing wavelength. These include gamma rays, X-rays, ultraviolet, visible, infrared, and radio. Gamma rays have a very short wavelength, on the order of one thousandth of a nanometer. Radio waves have a very long wavelength, on the order of one kilometer. Visible light ranges from 380 nanometers at the violet end of the spectrum, to 750 nanometers at the red end of the spectrum.

Each type of electromagnetic radiation travels at a particular wavelength. The longer the wavelength, the less energy it carries. Short, tight waves carry the most energy. This may seem illogical, but think of it in terms of a piece of moving heavy 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 electromagnetic spectrum ((Figure)) shows several types of electromagnetic radiation originating from the sun, including X-rays and ultraviolet (UV) rays. The higher-energy waves can penetrate tissues and damage cells and DNA, which explains why both X-rays and UV rays can be harmful to living organisms.

Absorption of Light

Light energy initiates the process of photosynthesis when pigments absorb specific wavelengths of visible light. Organic pigments, whether in the human retina or the chloroplast thylakoid, have a narrow range of energy levels that they can absorb. Energy levels lower than those represented by red light are insufficient to raise an orbital electron to a excited (quantum) state. Energy levels higher than those in blue light will physically tear the molecules apart, in a process called bleaching. Our retinal pigments can only “see” (absorb) wavelengths between 700 nm and 400 nm of light, a spectrum that is therefore called visible light. For the same reasons, plants, pigment molecules absorb only light in the wavelength range of 700 nm to 400 nm; plant physiologists refer to this range for plants as photosynthetically active radiation.

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 the colors to the human eye. The visible light portion of the electromagnetic spectrum shows the 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 ((Figure)).

The colors of visible light do not carry the same amount of energy. Violet has the shortest wavelength and therefore carries the most energy, whereas red has the longest wavelength and carries the least amount of energy. (credit: modification of work by NASA)


The illustration shows the colors of visible light. In order of decreasing wavelength, these are red, orange, yellow, green, blue, indigo, and violet.

Understanding Pigments

Different kinds of pigments exist, and each absorbs only specific wavelengths (colors) of visible light. Pigments reflect or transmit the wavelengths they cannot absorb, making them appear a mixture of the reflected or transmitted light colors.

Chlorophylls and carotenoids are the two major classes of photosynthetic pigments found in plants and algae; each class has multiple types of pigment molecules. There are five major chlorophylls: a, b, c and d and a related molecule found in prokaryotes called bacteriochlorophyll. Chlorophyll a and chlorophyll b are found in higher plant chloroplasts and will be the focus of the following discussion.

With dozens of different forms, carotenoids are a much larger group of pigments. The carotenoids found in fruit—such as the red of tomato (lycopene), the yellow of corn seeds (zeaxanthin), or the orange of an orange peel (β-carotene)—are used as advertisements to attract seed dispersers. In photosynthesis, carotenoids function as photosynthetic pigments that are very efficient molecules for the disposal of excess energy. When a leaf is exposed to full sun, the light-dependent reactions are required to process an enormous amount of energy; if that energy is not handled properly, it can do significant damage. Therefore, many carotenoids reside in the thylakoid membrane, absorb excess energy, and safely dissipate that energy as heat.

Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light: This is termed the absorption spectrum. The graph in (Figure) shows the absorption spectra for chlorophyll a, chlorophyll b, and a type of carotenoid pigment called β-carotene (which absorbs blue and green light). Notice how each pigment has a distinct set of peaks and troughs, revealing a highly specific pattern of absorption. Chlorophyll a absorbs wavelengths from either end of the visible spectrum (blue and red), but not green. Because green is reflected or transmitted, chlorophyll appears green. Carotenoids absorb in the short-wavelength blue region, and reflect the longer yellow, red, and orange wavelengths.

(a) Chlorophyll a, (b) chlorophyll b, and (c) β-carotene are hydrophobic organic pigments found in the thylakoid membrane. Chlorophyll a and b, which are identical except for the part indicated in the red box, are responsible for the green color of leaves. β-carotene is responsible for the orange color in carrots. Each pigment has (d) a unique absorbance spectrum.


Chlorophyll a and chlorophyll b are made up of a long hydrocarbon chain attached to a large, complex ring made up of nitrogen and carbon. Magnesium is associated with the center of the ring. Chlorophyll b differs from chlorophyll a in that it has a C H O group instead of a C H 3 group associated with one part of the ring. Beta-carotene is a branched hydrocarbon with a six-membered carbon ring at each end. Each chart shows the absorbance spectra for chlorophyll a, chlorophyll b, and beta-carotene. The three pigments absorb blue-green and orange-red wavelengths of light but have slightly different spectra.

Many photosynthetic organisms have a mixture of pigments, and by using these pigments, the organism can absorb energy from a wider range of wavelengths. Not all photosynthetic organisms have full access to sunlight. Some organisms grow underwater where light intensity and quality decrease and change with depth. 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 absorb most of the sunlight and scatter the remaining solar radiation ((Figure)).

Plants that commonly grow in the shade have adapted to low levels of light by changing the relative concentrations of their chlorophyll pigments. (credit: Jason Hollinger)


The photo shows undergrowth in a forest.

When studying a photosynthetic organism, scientists can determine the types of pigments present by generating absorption spectra. An instrument called a spectrophotometer can differentiate which wavelengths of light a substance can absorb. Spectrophotometers measure transmitted light and compute from it the absorption. By extracting pigments from leaves and placing these samples into a spectrophotometer, scientists can identify which wavelengths of light an organism can absorb. Additional methods for the identification of plant pigments include various types of chromatography that separate the pigments by their relative affinities to solid and mobile phases.

How Light-Dependent Reactions Work

The overall function of light-dependent reactions is to convert solar energy into chemical energy in the form of NADPH and ATP. This chemical energy supports the light-independent reactions and fuels the assembly of sugar molecules. The light-dependent reactions are depicted in (Figure). Protein complexes and pigment molecules work together to produce NADPH and ATP. The numbering of the photosystems is derived from the order in which they were discovered, not in the order of the transfer of electrons.

A photosystem consists of 1) a light-harvesting complex and 2) a reaction center. Pigments in the light-harvesting complex pass light energy to two special chlorophyll a molecules in the reaction center. The light excites an electron from the chlorophyll a pair, which passes to the primary electron acceptor. The excited electron must then be replaced. In (a) photosystem II, the electron comes from the splitting of water, which releases oxygen as a waste product. In (b) photosystem I, the electron comes from the chloroplast electron transport chain discussed below.


Illustration a shows the structure of P S I I, which is embedded in the thylakoid membrane. At the core of P S I I is the reaction center. The reaction center is surrounded by the light-harvesting complex, which contains antenna pigment molecules that shunt light energy toward a pair of chlorophyll a molecules in the reaction center. As a result, an electron is excited and transferred to the primary electron acceptor. A water molecule is split, releasing two electrons which are used to replace excited electrons. Illustration b shows the structure of P S I, which is similar in structure to P S I I. However, P S I I uses an electron from the chloroplast electron transport chain also embedded in the thylakoid membrane to replace the excited electron.

The actual step that converts light energy into chemical energy takes place in a multiprotein complex called a photosystem, two types of which are found embedded in the thylakoid membrane: photosystem II (PSII) and photosystem I (PSI) ((Figure)). The two complexes differ on the basis of what they oxidize (that is, the source of the low-energy electron supply) and what they reduce (the place to which they deliver their energized electrons).

Both photosystems have the same basic structure; a number of antenna proteins to which the chlorophyll molecules are bound surround the reaction center where the photochemistry takes place. Each photosystem is serviced by the light-harvesting complex, which passes energy from sunlight to the reaction center; it consists of multiple antenna proteins that contain a mixture of 300 to 400 chlorophyll a and b molecules as well as other pigments like carotenoids. The absorption of a single photon or distinct quantity or “packet” of light by any of the chlorophylls pushes that molecule into an excited state. In short, the light energy has now been captured b