ESSENTIAL
`CELL BIOLOGY
`
`third edition
`
`Alberts Bray Hopkin Johnson Lewis Raff Roberts Walter
`Mylan v. Genentech
`IPR2016-00710
`Genentech Exhibit 2081
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`ESSENTIAL third edition
`CELL BIOLOGY
`
`

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`

`
`ESSENTIAL third edition
`CELL BIOLOGY
`
`Alberts Bray Hopkin Johnson Lewis Raff Roberts Walter
`
`

`
`Essential Cell Biology Interactive
`Artistic and Scientifi c Direction: Peter Walter
`Narrated by: Julie Theriot
`Producer: Michael Morales
`Interface Design: Matthew McClements, Blink Studio
`Programming: Tom McElderry
`
`Julian Lewis received his D.Phil. from the University of
`Oxford and is a Principal Scientist at the London Research
`Institute of Cancer Research UK.
`Martin Raff received his M.D. from McGill University and is
`at the Medical Research Council Laboratory for Molecular
`Cell Biology and Cell Biology Unit and in the Biology
`Department at University College London.
`Keith Roberts received his Ph.D. from the University of
`Cambridge and is Emeritus Fellow at the John Innes Centre,
`Norwich.
`Peter Walter received his Ph.D. from The Rockefeller
`University in New York and is Professor and Chairman
`of the Department of Biochemistry and Biophysics at the
`University of California, San Francisco, and an Investigator
`of the Howard Hughes Medical Institute.
`
`Garland Science
`Vice President: Denise Schanck
`Senior Editor: Michael Morales
`Production Editor and Layout: Emma Jeffcock
`Project Editor: Sigrid Masson
`Assistant Editor: Katherine Ghezzi
`Editorial Assistant: Monica Toledo
`Text Editors: Eleanor Lawrence, Sherry Granum, Elizabeth Zayatz
`Copyeditor: Bruce Goatly
`Book and Cover Design: Matthew McClements, Blink Studio
`Illustrator: Nigel Orme
`Cover Illustration: Jose Ortega
`Indexer: Liza Furnival
`Permission Coordinator: Mary Dispenza
`
`Bruce Alberts received his Ph.D. from Harvard University and
`is Professor of Biochemistry and Biophysics at the University
`of California, San Francisco. He is the editor-in-chief of Science
`magazine. For 12 years he served as President of the
`U.S. National Academy of Sciences (1993-2005).
`Dennis Bray received his Ph.D. from Massachusetts Institute
`of Technology and is currently an active emeritus professor at
`University of Cambridge. In 2006 he was awarded the Microsoft
`European Science Award.
`Karen Hopkin received her Ph.D. in biochemistry from the
`Albert Einstein College of Medicine and is a science writer in
`Somerville, Massachusetts.
`Alexander Johnson received his Ph.D. from Harvard University
`and is Professor of Microbiology and Immunology and Director
`of the Biochemistry, Cell Biology, Genetics, and Developmental
`Biology Graduate Program at the University of California,
`San Francisco.
`
`© 2010 by Bruce Alberts, Dennis Bray, Karen Hopkin,
`Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts,
`and Peter Walter
`© 2004 by Bruce Alberts, Dennis Bray, Karen Hopkin,
`Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts,
`and Peter Walter
`© 1998 by Bruce Alberts, Dennis Bray, Alexander Johnson,
`Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter
`
`This book contains information obtained from authentic and
`highly regarded sources. Reprinted material is quoted with
`permission, and sources are indicated. A wide variety of
`references are listed. Reasonable efforts have been made to
`publish reliable data and information, but the author and the
`publisher cannot assume responsibility for the validity of all
`materials or for the consequences of their use.
`
`All rights reserved. No part of this publication may be
`reproduced, stored in a retrieval system or transmitted in any
`form or by any means—electronic, mechanical, photocopying,
`recording, or otherwise—without the prior written permission of
`the copyright holder.
`
`Published by Garland Science, Taylor & Francis Group,
`LLC, an informa business, 270 Madison Avenue,
`New York, NY 10016, USA, and 2 Park Square, Milton Park,
`Abingdon, OX14 4RN, UK.
`
`Library of Congress Cataloguing-in-Publication Data
`
`Essential cell biology / Bruce Alberts ... [et al.]. -- 3rd ed.
` p. cm.
`ISBN 978-0-8153-4129-1 (hardcover) -- ISBN 978-0-8153-
`4130-7 (pbk.)
`1. Cytology. 2. Molecular biology. 3. Biochemistry. I.
`Alberts, Bruce.
`QH581.2.E78 2009
`571.6--dc22
`
`2009001400
`
`Printed in the United States of America
`15 14 13 12 11 10 9 8 7 6 5 4 3 2
`
`Visit our website at http://www.garlandscience.com
`
`

`
`Preface
`
`v
`
`In our world there is no form of matter more astonishing than the living
`cell: tiny, fragile, marvelously intricate, continually made afresh, yet pre-
`serving in its DNA a record of information dating back more than three
`billion years, to a time when our planet had barely cooled from the hot
`materials of the nascent solar system. Ceaselessly re-engineered and
`diversified by evolution, extraordinarily versatile and adaptable, the cell
`still retains a core of complex self-replicating chemical machinery that is
`shared and endlessly repeated by every living organism on the face of the
`Earth, in every animal, every leaf, every bacterium in a piece of cheese,
`every yeast in a vat of wine.
`
`Curiosity, if nothing else, should drive us to study cell biology; but there
`are practical reasons, too, why cell biology should be a part of everyone’s
`education. We are made of cells, we feed on cells, and our world is made
`habitable by cells. We need to understand cell biology to understand our-
`selves; to look after our health; to take care of our food supplies; and
`to protect our endangered ecosystems. The challenge for scientists is to
`deepen knowledge and find new ways to apply it. But all of us, as citizens,
`need to know something of the subject to grapple with the modern world,
`from our own health affairs to the great public issues of environmental
`change, biomedical technologies, agriculture, and epidemic disease.
`
`Cell biology is a big subject, and it has links with almost every other branch
`of science. The study of cell biology therefore provides a great scientific
`education. However, it is easy to become lost in the detail and distracted
`by an overload of information and technical terminology. In this book we
`therefore focus on providing a digestible, straightforward, and engaging
`account of only the essential principles. We seek to explain, in a way that
`can be understood even by a reader approaching modern biology for the
`first time, how the living cell works: to show how the molecules of the
`cell—especially the protein, DNA, and RNA molecules—cooperate to cre-
`ate this remarkable system that feeds, responds to stimuli, moves, grows,
`divides, and duplicates itself.
`
`The need for a clear account of the essentials of cell biology became
`apparent to us while we were writing Molecular Biology of the Cell (MBoC),
`now in its fifth edition. MBoC is a large book aimed at advanced under-
`graduates and graduate students specializing in the life sciences or
`medicine. Many students and educated lay people who require an intro-
`ductory account of cell biology would find MBoC too detailed for their
`needs. Essential Cell Biology (ECB), in contrast, is designed to provide the
`fundamentals of cell biology that are required by anyone to understand
`both the biomedical and the broader biological issues that affect our
`lives.
`
`In this third edition, we have brought every part of the book up to date,
`with new material on chromosome structure and epigenetics, microRNAs
`
`

`
`vi
`
`Preface
`
`and RNAi, protein quality control, cell-cell recognition, genetic varia-
`tion, stem cells and their medical potential, rational cancer treatments,
`genome evolution, and many other topics. We have improved our discus-
`sion of energetics and thermodynamics, integrated the cell cycle and cell
`division into a single chapter, and updated the “How We Know” sections,
`describing experiments that illustrate how biologists tackle important
`questions and how their experimental results shape future ideas.
`
`As before, the diagrams in ECB emphasize central concepts and are
`stripped of unnecessary details. The key terms introduced in each chap-
`ter are highlighted when they first appear and are collected together at
`the end of the book in a large, illustrated glossary. We have not listed
`references for further reading: those wishing to explore a subject in
`greater depth are encouraged to consult the reading lists in MBoC5 or
`look for recent reviews in the current literature through one of the pow-
`erful search engines, such as Pubmed (http://www.ncbi.nlm.nih.gov) or
`Google Scholar (http://scholar.google.com).
`
`A central feature of the book is the many questions that are presented in
`the text margins and at the end of each chapter. These are designed to
`provoke students to think about what they have read and to encourage
`them to pause and test their understanding. Many questions challenge
`the student to place the newly acquired information in a broader biologi-
`cal context, and some have more than one valid answer. Others invite
`speculation. Answers to all the questions are given at the end of the book;
`in many cases these provide a commentary or an alternative perspective
`on material presented in the main text.
`
`For those who want to develop their active grasp of cell biology further
`and to get a deeper understanding of how cell biologists extract con-
`clusions from experiments, we recommend Molecular Biology of the Cell,
`Fifth Edition: A Problems Approach, by John Wilson and Tim Hunt. Though
`written as a companion to MBoC, this contains questions at all levels of
`difficulty and is a goldmine of thought-provoking problems for teachers
`and students. We have drawn upon it for some of the questions in ECB,
`and we are very grateful to its authors.
`
`The explosion of new imaging and computer technologies continues to
`give fresh and spectacular views of the inner workings of living cells.
`We have tried to capture some of the excitement of these advances in a
`revised and enlarged version of the Essential Cell Biology Interactive media
`player on the DVD-ROM included with each copy of the book. It contains
`over 130 video clips, animations, molecular structures, and high-resolu-
`tion micrographs—all designed to complement the material in individual
`book chapters. One cannot watch cells crawling, dividing, segregating
`their chromosomes, or rearranging their surface without a sense of won-
`der at the molecular mechanisms that underlie these processes. For a
`vivid sense of the marvel that science reveals beneath the surface of eve-
`ryday things, it is hard to match the movie of DNA replication included
`on the DVD. We hope that ECB Interactive will motivate and intrigue stu-
`dents while reinforcing basic concepts covered in the text, and thereby
`will make the learning of cell biology both easier and more rewarding.
`
`As with MBoC, each chapter of ECB is the product of communal effort, with
`individual drafts circulating from one author to another. In addition, many
`people have helped us, and these are credited in the Acknowledgments
`that follow. Despite our best efforts, it is inevitable that there will be
`errors in the book. We encourage readers who find them to let us know
`at science@garland.com, so that we can correct these errors in the next
`printing.
`
`

`
`Acknowledgments
`
`vii
`
`The authors acknowledge the many contributions of
`professors and students from around the world in the
`creation of this Third Edition. In particular, we are
`grateful to the students who participated in the focus
`groups; they provided invaluable feedback about their
`experiences using the book and multimedia, and many
`of their suggestions were implemented in this edition.
`
`We would also like to thank the professors who helped
`organize the focus groups at their schools: Chris
`Brandl at University of Western Ontario, David L. Gard
`at University of Utah, Juliet Spencer at University of
`San Francisco, and Keren Witkin and Linda Huang
`at University of Massachusetts, Boston. We greatly
`appreciate their hospitality.
`
`We also received detailed reviews from instructors
`using the second edition, and we would like to thank
`them for their work: Margarida D. Amaral, University
`of Lisbon; Lynne Arneson, American University; Karl
`Aufderheide, Texas A&M University; David K. Banfield,
`The Hong Kong University of Science and Technology;
`Stephen F. Baron, Bridgewater College; Deborah
`Bielser, University of Illinois at Urbana-Champaign;
`Barbara D. Boyan, Georgia Institute of Technology;
`Chris Brandl, University of Western Ontario; Keith
`Brown, University of Bristol; Jane Bruner, California
`State University Stanislaus; Patrick Bryan, Middlesex
`Community College; Sharon K. Bullock, Virginia
`Commonwealth University; Mike Clemens, St. George’s
`Hospital Medical School, University of London; Anne
`Cordon, University of Toronto at Mississauga; Andrew
`Dalby, University of Exeter; Dan Eshel, Brooklyn
`College; Nicolas Forraz, Kingston University; David
`L. Gard, University of Utah; Mark Grimes, University
`of Montana; Hollie Hale-Donze, Louisiana State
`University; Lynn Hannum, Colby College; Na’il M.
`Hasan, Birzeit University; Jeannette M. Loutsch,
`Arkansas State University; Charles Mallery, University
`of Miami; Kathy Martin-Troy, Central Connecticut State
`University; Gordon T.A. McEwan, Institute of Medical
`Sciences, University of Aberdeen; Colin McGuckin,
`Kingston University; Gerard McNeil, York College,
`The City University of New York; Roger W. Melvold,
`University of North Dakota, School of Medicine
`& Health Sciences; Cristina Murga, Universidad
`Autónoma de Madrid; T. Page Owen, Jr., Connecticut
`College; Martin Rumsby, University of York; Esther
`
`Siegfried, University of Pittsburgh at Johnstown; Roger
`D. Sloboda, Dartmouth College; Julio Soto, San Jose
`State University; Juliet Spencer, University of San
`Francisco; Paul H. Tomasek, California State University
`Northridge; Gary Wessel, Brown University; Esther
`F. Wheeler, Texas Tech University; Keren Witkin,
`University of Massachusetts, Boston.
`
`Special thanks go to David Morgan for his help in
`formulating and reviewing the reorganized chapter on
`cell division.
`
`We are very grateful, too, to the readers who alerted us
`to errors they had found in the previous edition.
`
`Many Garland staff contributed to the creation of this
`book and made our work on it a pleasure. First of all,
`we owe a special debt to Michael Morales, our editor,
`who coordinated the whole enterprise. He organized
`the initial reviewing and the focus groups, worked
`closely with the authors on their chapters, urged us
`on when we fell behind, and played a major part in
`the design, assembly, and production of Essential Cell
`Biology Interactive. Sigrid Masson managed the flow
`of chapters through the production process, proof-
`read the entire book, and oversaw the writing of the
`accompanying question bank. Kate Ghezzi and
`Monica Toledo gave editorial assistance. Nigel Orme
`took original drawings created by author Keith Roberts
`and redrew them on a computer, or occasionally by
`hand, with skill and flair. To Matt McClements goes
`the credit for the graphic design of the book and of
`the DVD. Emma Jeffcock did a brilliant job in laying
`out the whole book and meticulously incorporating
`our endless corrections. Eleanor Lawrence and
`Sherry Granum did the developmental editing of
`individual chapters, repairing many rough edges, and
`Eleanor not only read the book from beginning to
`end for clarity and consistency, but also revised and
`extended the Glossary. Adam Sendroff and Lucy Brodie
`gathered user feedback and launched the book into
`the wide world. Denise Schanck, the Vice President
`of Garland Science, orchestrated all of this with great
`taste and diplomacy. We give our thanks to everyone
`in this long list.
`
`Last but not least, we are grateful, yet again, to our
`families, our colleagues, and our childminders for their
`support and tolerance.
`
`

`
`viii
`
`Instructor and Student Resources
`
`Art of Essential Cell Biology, Third Edition
`The images from the book are available in two convenient
`formats: Powerpoint® and JPEG. They are located in fold-
`ers on the Media DVD-ROM that accompanies the book
`or can be downloaded on the Web from Classwire™. On
`Classwire the individual JPEGs are searchable by figure
`number, figure name, or by keywords used in the figure
`legend from the book.
`
`Media DVD-ROM
`Every copy of the book includes a DVD-ROM with the
`following student and instructor resources:
`Essential Cell Biology Interactive
`This multimedia player contains over 130 movies (anima-
`tions, videos, and molecular tutorials), a self-test quiz for
`every chapter, and a cell explorer program that facilitates
`investigation of high-resolution micrographs. The mov-
`ies are referenced directly in the textbook through movie
`“call outs” highlighted in red, for example (Movie 1.1). If
`you enter the movie number from the book into the movie-
`locator window in the media player, the relevant movie will
`automatically appear. This feature, which was requested
`by students, should make it easier to integrate movies into
`an active learning process.
`
`Student Self-Quizzes
`The quizzing feature, which is new to this edition, allows
`students to test themselves in basic reading comprehen-
`sion of each chapter. It is accessed through the Essential
`Cell Biology Interactive media player.
`
`The Art of Essential Cell Biology, Third Edition
`This folder archive contains the figures from the book in
`JPEG and PowerPoint format as described above.
`
`Movie Vault
`This archive contains all of the movies from the Essential
`Cell Biology Interactive media player in three handy formats:
`WMV, QuickTime®, and iPod®. The WMV versions are suit-
`able for importing movies into PowerPoint for Windows®.
`The QuickTime versions are suitable for importing the
`movies into PowerPoint for the Macintosh®. And the iPod
`versions have been formatted specifically for iPod and
`iTunes® use.
`Media Guide
`This PDF overviews the contents of the DVD and contains
`the text of the voice-over narration for all of the movies.
`
`Figure-Integrated Lecture Outlines
`The section headings, concept headings, and figures from
`the text have been integrated into PowerPoint presenta-
`tions. These will be useful for instructors who would like
`a head start creating lectures for their course. Like all of
`our PowerPoint presentations, the lecture outlines can be
`customized. For example, the content of these presenta-
`tions can be combined with videos from the DVD-ROM and
`questions from the book or “Question Bank,” in order to
`create unique lectures that facilitate interactive learning in
`the classroom. This resource is available on Classwire.
`Question Bank
`Written by Linda Huang, University of Massachusetts,
`Boston, and Cheryl D. Vaughan, Harvard University Division
`of Continuing Education, the revised and expanded question
`bank includes a variety of question formats: multiple-
`choice, fill-in-the-blank, true-false, matching, essay, and
`challenging “thought” questions. There are approximately
`50-60 questions per chapter, and a large number of the
`multiple-choice questions will be suitable for use with per-
`sonal response systems (i.e., clickers). The Question Bank
`was created with the philosophy that a good exam should
`do much more than simply test students’ ability to memo-
`rize information; it should require them to reflect upon and
`integrate information as a part of a sound understanding. It
`provides a comprehensive sampling of questions that can
`be used either directly or as inspiration for instructors to
`write their own test questions. Instructors can obtain the
`Question Bank by emailing: science@garland.com.
`Exploring the Living Cell DVD-Video
`Created by Christian Sardet, Centre National de la Recherche
`Scientifique (CNRS), and directed by Véronique Kleiner, this
`unique DVD takes us on a journey through the basic unit
`of life: the cell. Using the earliest drawings and exciting
`imagery taken with today’s microscopes, renowned biolo-
`gists and young scientists explain their research and share
`their discoveries. Learn how cells were discovered, how
`they function, how they relate to health and disease, and
`what the future holds.
`Classwire™
`The Classwire course management system, available at
`www.classwire.com/garlandscience, allows instructors to
`build Websites for their courses easily. It also serves as an
`online archive for instructor’s resources. After registering for
`Classwire, you will be able to download all the figures from
`the book, as well as the movies from the DVD. Additional
`instructor’s resources for Garland Science textbooks are
`also available on Classwire. Please contact science@
`garland.com for information on accessing the Classwire
`system. (Classwire™ is a trademark of Chalkfree, Inc.)
`
`

`
`Contents and Special Features
`
`ix
`
`Introduction to Cells
`Chapter 1
`Panel 1–1 Microscopy
`Panel 1–2
`Cell architecture
`How We Know: Life’s common mechanisms
`
`Chapter 2 Chemical Components of Cells
`How We Know: What are macromolecules?
`Panel 2–1
`Chemical bonds and groups
`Panel 2–2
`The chemical properties of water
`Panel 2–3
`An outline of some of the types of sugar
`Panel 2–4
`Fatty acids and other lipids
`Panel 2–5
`The 20 amino acids found in proteins
`Panel 2–6
`A survey of the nucleotides
`Panel 2–7
`The principal types of weak noncovalent bonds
`
`Chapter 3 Energy, Catalysis, and Biosynthesis
`Panel 3–1
`Free energy and biological reactions
`How We Know: Using kinetics to model and manipulate metabolic pathways
`
`Chapter 4 Protein Structure and Function
`Panel 4–1
`A few examples of some general proteins
`Panel 4–2
`Four different ways of depicting a small protein
`Panel 4–3
`Making and using antibodies
`How We Know: Probing protein structure
`Panel 4–4
`Cell breakage and initial fractionation of cell extracts
`Panel 4–5
`Protein separation by chromatography
`Panel 4–6
`Protein separation by electrophoresis
`
`Chapter 5 DNA and Chromosomes
`How We Know: Genes are made of DNA
`
`Chapter 6 DNA Replication, Repair, and Recombination
`How We Know: The nature of replication
`
`Chapter 7 From DNA to Protein: How Cells Read the Genome
`How We Know: Cracking the genetic code
`
`Chapter 8 Control of Gene Expression
`How We Know: Gene regulation—the story of Eve
`
`1
`8–9
`25
`30–31
`
`39
`60–61
`64–65
`66–67
`68–69
`70–71
`72–73
`74–75
`76–77
`
`81
`94–95
`101–103
`
`119
`120
`128–129
`144–145
`158–160
`164–165
`166
`167
`
`171
`174–176
`
`197
`200–202
`
`231
`248–249
`
`269
`282–284
`
`

`
`x
`
`Contents and Special Features
`
`Chapter 9 How Genes and Genomes Evolve
`How We Know: Counting genes
`
`Chapter 10 Analyzing Genes and Genomes
`How We Know: Sequencing the human genome
`
`Chapter 11 Membrane Structure
`How We Know: Measuring membrane flow
`
`Chapter 12 Membrane Transport
`How We Know: Squid reveal secrets of membrane excitability
`
`Chapter 13 How Cells Obtain Energy from Food
`Panel 13–1 Details of the 10 steps of glycolysis
`How We Know: Unraveling the citric acid cycle
`Panel 13–2
`The complete citric acid cycle
`
`Chapter 14 Energy Generation in Mitochondria and Chloroplasts
`How We Know: How chemiosmotic coupling drives ATP synthesis
`Panel 14–1
`Redox potentials
`
`Chapter 15 Intracellular Compartments and Transport
`How We Know: Tracking protein and vesicle transport
`
`Chapter 16 Cell Communication
`How We Know: Untangling cell signaling pathways
`
`Chapter 17 Cytoskeleton
`Panel 17–1
`The three major types of protein filaments
`How We Know: Pursuing motor proteins
`
`Chapter 18 The Cell Division Cycle
`How We Know: Discovery of cyclins and Cdks
`Panel 18–1
`The principal stages of M phase in an animal cell
`
`Chapter 19 Sex and Genetics
`Panel 19–1
`Some essentials of classical genetics
`How We Know: Reading genetic linkage maps
`
`Chapter 20 Cellular Communities: Tissues, Stem Cells, and Cancer
`How We Know: Making sense of the genes that are critical for cancer
`
`Answers to Questions
`
`Glossary
`
`Index
`
`
`
`
`
`297
`318–319
`
`327
`348–349
`
`363
`382–383
`
`387
`412–413
`
`425
`430–431
`440–441
`442–443
`
`453
`468–469
`471
`
`495
`520–521
`
`531
`560–562
`
`571
`573
`586–588
`
`609
`615–616
`626–627
`
`651
`674
`680–681
`
`689
`725–726
`
`A:1
`
`G:1
`
`I:1
`
`

`
`Detailed Contents
`
`xi
`
`5
`
`5
`6
`
`6
`
`1
`Chapter 1 Introduction to Cells
`2
`UNITY AND DIVERSITY OF CELLS
`Cells Vary Enormously in Appearance and Function 2
`Living Cells All Have a Similar Basic Chemistry
`3
`All Present-Day Cells Have Apparently Evolved
`from the Same Ancestor
`Genes Provide the Instructions for Cellular Form,
`Function, and Complex Behavior
`CELLS UNDER THE MICROSCOPE
`The Invention of the Light Microscope Led to the
`Discovery of Cells
`Cells, Organelles, and Even Molecules Can Be
`Seen Under the Microscope
`THE PROCARYOTIC CELL
`Procaryotes Are the Most Diverse of Cells
`The World of Procaryotes Is Divided into Two
`Domains: Bacteria and Archaea
`THE EUCARYOTIC CELL
`The Nucleus Is the Information Store of the Cell
`Mitochondria Generate Usable Energy from
`Food to Power the Cell
`Chloroplasts Capture Energy from Sunlight
`Internal Membranes Create Intracellular
`Compartments with Different Functions
`The Cytosol Is a Concentrated Aqueous Gel
`of Large and Small Molecules
`The Cytoskeleton Is Responsible for Directed
`Cell Movements
`The Cytoplasm Is Far from Static
`Eucaryotic Cells May Have Originated as
`Predators
`MODEL ORGANISMS
`Molecular Biologists Have Focused on E. coli
`Brewer’s Yeast Is a Simple Eucaryotic Cell
`
`7
`11
`14
`
`15
`16
`16
`
`17
`18
`
`19
`
`21
`
`22
`23
`
`23
`26
`27
`28
`
`Arabidopsis Has Been Chosen Out of 300,000
`Species as a Model Plant
`The World of Animals Is Represented by a Fly, a
`Worm, a Fish, a Mouse, and the Human Species 29
`Comparing Genome Sequences Reveals Life’s
`Common Heritage
`Essential Concepts
`End-of-Chapter Questions
`
`33
`35
`36
`
`28
`
`41
`
`Chapter 2 Chemical Components
`39
`of Cells
`40
`CHEMICAL BONDS
`Cells Are Made of Relatively Few Types of Atoms 40
`The Outermost Electrons Determine How Atoms
`Interact
`Ionic Bonds Form by the Gain and Loss of
`44
`Electrons
`Covalent Bonds Form by the Sharing of Electrons 45
`Covalent Bonds Vary in Strength
`46
`There Are Different Types of Covalent Bonds
`47
`Electrostatic Attractions Help Bring Molecules
`Together in Cells
`Water Is Held Together by Hydrogen Bonds
`Some Polar Molecules Form Acids and Bases
`in Water
`MOLECULES IN CELLS
`A Cell Is Formed from Carbon Compounds
`Cells Contain Four Major Families of Small
`Organic Molecules
`Sugars Are Energy Sources for Cells and Subunits
`52
`of Polysaccharides
`Fatty Acids Are Components of Cell Membranes 54
`Amino Acids Are the Subunits of Proteins
`55
`Nucleotides Are the Subunits of DNA and RNA
`56
`
`47
`48
`
`49
`50
`50
`
`51
`
`

`
`xii
`
`Detailed Contents
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`MACROMOLECULES IN CELLS
`Macromolecules Contain a Specific Sequence
`of Subunits
`Noncovalent Bonds Specify the Precise Shape
`of a Macromolecule
`Noncovalent Bonds Allow a Macromolecule
`to Bind Other Selected Molecules
`Essential Concepts
`End-of-Chapter Questions
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`Chapter 3 Energy, Catalysis, and
`Biosynthesis
`THE USE OF ENERGY BY CELLS
`Biological Order Is Made Possible by the Release
`of Heat Energy from Cells
`Photosynthetic Organisms Use Sunlight to
`Synthesize Organic Molecules
`Cells Obtain Energy by the Oxidation of Organic
`Molecules
`Oxidation and Reduction Involve Electron
`Transfers
`FREE ENERGY AND CATALYSIS
`Enzymes Lower the Energy Barriers That Prevent
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`Chemical Reactions from Occurring
`The Free-Energy Change for a Reaction Determines
`Whether It Can Occur
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`The Concentration of Reactants Influences the
`Free-Energy Change and a Reaction’s Direction 92
`The Standard Free-Energy Change Makes it
`Possible to Compare the Energetics of
`Different Reactions
`Cells Exist in a State of Chemical Disequilibrium
`The Equilibrium Constant is Directly Proportional
`to (cid:37)G°
`In Complex Reactions, the Equilibrium Constant
`Depends on the Concentrations of All
`Reactants and Products
`The Equilibrium Constant Indicates the Strength
`of Molecular Interactions
`For Sequential Reactions, the Changes in Free
`Energy are Additive
`Rapid Diffusion Allows Enzymes to Find Their
`Substrates
`Vmax and KM Measure Enzyme Performance
`ACTIVATED CARRIER MOLECULES AND
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`BIOSYNTHESIS
`The Formation of an Activated Carrier Is Coupled
`to an Energetically Favorable Reaction
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`ATP is the Most Widely Used Activated Carrier
`Molecule
`Energy Stored in ATP is Often Harnessed to
`Join Two Molecules Together
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`NADH and NADPH Are Important Electron
`Carriers
`Cells Make Use of Many Other Activated
`Carrier Molecules
`The Synthesis of Biological Polymers Requires
`an Energy Input
`Essential Concepts
`End-of-Chapter Questions
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`Chapter 4 Protein Structure and
`Function
`THE SHAPE AND STRUCTURE OF PROTEINS
`The Shape of a Protein Is Specified by Its
`Amino Acid Sequence
`Proteins Fold into a Conformation of Lowest
`Energy
`Proteins Come in a Wide Variety of Complicated
`Shapes
`The (cid:66)(cid:1)Helix and the (cid:67) Sheet Are Common
`Folding Patterns
`Helices Form Readily in Biological Structures
`(cid:67) Sheets Form Rigid Structures at the Core
`of Many Proteins
`Proteins Have Several Levels of Organization
`Few of the Many Possible Polypeptide Chains
`Will Be Useful
`Proteins Can Be Classified into Families
`Large Protein Molecules Often Contain More
`Than One Polypeptide Chain
`Proteins Can Assemble into Filaments, Sheets,
`or Spheres
`Some Types of Proteins Have Elongated Fibrous
`Shapes
`Extracellular Proteins Are Often Stabilized by
`Covalent Cross-Linkages
`HOW PROTEINS WORK
`All Proteins Bind to Other Molecules
`The Binding Sites of Antibodies Are Especially
`Versatile
`Enzymes Are Powerful and Highly Specific
`Catalysts
`Lysozyme Illustrates How an Enzyme Works
`Most Drugs Inhibit Enzymes
`Tightly Bound Small Molecules Add Extra
`Functions to Proteins
`HOW PROTEINS ARE CONTROLLED
`The Catalytic Activities of Enzymes Are Often
`Regulated by Other Molecules
`Allosteric Enzymes Have Binding Sites That
`Influence One Another
`Phosphorylation Can Control Protein Activity by
`Triggering a Conformational Change
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`GTP-Binding Proteins Are Also Regulated
`by the Cyclic Gain and Loss of a Phosphate
`Group
`Nucleotide Hydrolysis Allows Motor Proteins
`to Produce Large Movements in Cells
`Proteins Often Form Large Complexes That
`Function as Protein Machines
`Covalent Modification Controls the Location and
`Assembly of Protein Machines
`HOW PROTEINS ARE STUDIED
`Cells Can Be Grown in a Culture Dish
`Purification Techniques Allow Homogeneous
`Protein Preparations to Be Obtained from
`Cell Homogenates
`Large Amounts of Almost Any Protein Can be
`Produced by Genetic Engineering Techniques 163
`Automated Studies of Protein Structure and
`Function Are Increasing the Pace of Discovery 163
`Essential Concepts
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`End-of-Chapter Questions
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`Chapter 5 DNA and Chromosomes
`172
`THE STRUCTURE AND FUNCTION OF DNA
`A DNA Molecule Consists of Two Complementary
`Chains of Nucleotides
`173
`The Structure of DNA Provides a Mechanism for
`Heredity
`THE STRUCTURE OF EUCARYOTIC
`CHROMOSOMES
`Eucaryotic DNA Is Packaged into Multiple
`Chromosomes
`Chromosomes Contain Long Strings of Genes
`Chromosomes Exist in Different States
`Throughout the Life of a Cell
`Interphase Chromosomes Are Organized Within
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`the Nucleus
`The DNA in Chromosomes Is Highly Condensed 184
`Nucleosomes Are the Basic Units of Eucaryotic
`185
`Chromosome Structure
`Chromosome Packing Occurs on Multiple Levels 187
`THE REGULATION OF CHROMOSOME
`STRUCTURE
`Changes in Nucleosome Structure Allow Access
`to DNA
`Interphase Chromosomes Contain Both
`Condensed and More Extended Forms
`of Chromatin
`Changes in Chromatin Structure Can Be
`Inherited
`Essential Concepts
`End-of-Chapter Questions
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`Chapter 6 DNA Replication, Repair,
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`and Recombination
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`DNA REPLICATION
`198
`Base-Pairing Enables DNA Replication
`199
`DNA Synthesis Begins at Replication Origins
`New DNA Synthesis Occurs at Replication Forks 203
`The Replication Fork Is Asymmetrical
`204
`DNA Polymerase Is Self-correcting
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`Short Lengths of RNA Act as Primers for DNA
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`Synthesis
`Proteins at a Rep