Karp's Cell and Molecular Biology Concepts and Experiments 8th Edition PDF

An easy way to help students learn, collaborate, and grow. Designed to engage today’s student, WileyPLUS Learning Space will transform any course into a vibrant, collaborative learning community. Identify which students Facilitate student Measure outcomes are str...

An easy way to help students learn, collaborate, and grow. Designed to engage today’s student, WileyPLUS Learning Space will transform any course into a vibrant, collaborative learning community. Identify which students Facilitate student Measure outcomes are struggling early in the engagement both in and to promote continuous semester. outside of class. improvement. Educators assess the real-time Educators can quickly organize With visual reports, it’s easy for engagement and performance of learning activities, manage student both students and educators to each student to inform teaching collaboration, and customize gauge problem areas and act on decisions. Students always know their course. what’s most important. what they need to work on. www.wileypluslearningspace.com KARP’S CELL AND MOLECULAR BIOLOGY CONCEPTS AND EXPERIMENTS EIGHTH EDITION JANET IWASA WALLACE MARSHALL University of Utah University of California, San Francisco Vice President & Director Petra Recter Director Kevin Witt Senior Acquisitions Editor Bonnie Roth Executive Marketing Manager Clay Stone Product Designer Melissa Edwards Program Assistant Carrie Thompson Content Manager Kevin Holm Senior Production Editor Sandra Dumas Design Director Harry Nolan Senior Designer Maureen Eide Photo Editor Billy Ray Production Management Services SPi Global Cover Photo Credit Janet Iwasa This book was set in 10/12 Minion Pro by SPi Global and printed and bound by Quad Graphics Versailles. 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Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030‐5774, (201) 748‐6011, fax (201) 748‐6008. Evaluation copies are provided to qualified academics and professionals for review purposes only, for use in their courses during the next academic year. These copies are licensed and may not be sold or transferred to a third party. Upon completion of the review period, please return the evaluation copy to Wiley. Return instructions and a free of charge return shipping label are available at www.wiley.com/go/returnlabel. Outside of the United States, please contact your local representative. ISBN: 978‐1‐118‐88614‐4 BRV ISBN: 978‐1‐118‐30179‐1 Printed in the United States of America 10 9 8 7 6 5 4 3 2 1  About the Authors JANET IWASA is a faculty member in the Biochemistry Department at the University of Utah. She received her bachelor’s degree from Williams College and a Ph.D. in Cell Biology from the University of California, San Francisco, where she first became interested in the visualiza- tion of biological processes. As a postdoctoral fellow, she was awarded a fellowship from the National Science Foundation to create a multimedia exhibit with Nobel Laureate Jack Szostak (Harvard University) and the Museum of Science, Boston. She later joined Harvard Medical School as a faculty member in the Department of Cell Biology, where she utilized visualization tools to aid in scientific communication, exploration and outreach. Janet’s award‐winning illustrations and animations have appeared in scientific journals including Nature, Science and Cell, as well as in the New York Times. WALLACE MARSHALL is Professor of Biochemistry and Biophysics at the University of California San Francisco. A native Long‐Islander, he received his bachelor’s degrees in Electrical Engineering and Biochemistry from the State University of New York at Stony Brook, and his Ph.D. in Biochemistry from UC San Francisco, where he studied organization of chromosomes within the nucleus with John Sedat. He then moved to Yale University for postdoctoral studies with Joel Rosenbaum, where he became interested in questions of organelle size control and cell organization, using cilia, flagella, and centrioles as model systems. In 2003, he joined the faculty at UCSF where he continues to study questions of cellular organization in a variety of model organisms including green algae, yeast, ciliates, and mammalian cells. In addition to his cell biology research, Dr. Marshall teaches Human Metabolism for the UCSF School of Pharmacy, Cell Biology for the UCSF Graduate Division, and runs a two week lab course on cell behavior. In 2014, he served as Program Committee Chair organizing the annual meeting of the American Society for Cell Biology. He is currently co‐director of the Physiology summer course at the Marine Biological Laboratory in Woods Hole, Massachusetts. ABOUT THE COVER The cover image shows an illustration, created by Janet Iwasa, of an idealized mammalian cell with different subcel- lular compartments highlighted and digitally rendered to appear as a paper cut-out. An interactive version of this illustration can be viewed at the website of the Cell Image Library (http://cellimagelibrary.org), where the selection of any compartment will allow the user to view microscopic images of that compartment taken from real cells. Preface to the Eighth Edition For the past two decades, Dr. Gerald Karp has written Cell and Working on the 8th edition side by side with Dr. Karp has given Molecular Biology: Concepts and Experiments. During this time, us renewed admiration for his writing and his ability to keep track he has maintained a consistent focus on combining rigor with of the cutting edge in the full range of topics that comprise cell and accessibility, so that even students without prior training in cell molecular biology. In this and future editions of Karp’s Cell and biology, molecular biology, or biochemistry have been able to Molecular Biology: Concepts and Experiments, we are dedicated to learn cell biology not just as a collection of facts but as a process carrying out Dr. Karp’s original mission of providing an interesting, of discovery. The value of this approach is that the lessons modern and readable text that is grounded in the experimental learned extend far beyond the field of cell biology, and provide a approach. We welcome your ideas and feedback as we continue our way for students to learn how science works, how new experi- work on this text, so please feel free to get in touch. ments can overturn previous dogmas, and how new techniques can lead to groundbreaking discovery. This approach makes cell Janet Iwasa ([email protected]) biology come alive. Wallace Marshall ([email protected]) After seven editions, Dr. Karp is ready to move on to other adventures. We are excited to take on the challenge of continuing Dr. Karp’s unique approach to teaching cell biology, while continu- ing to put students first. Our goal for this revision was to build WileyPLUS Learning Space connects the text to carefully-selected upon Karp’s hallmark experimental approach by bringing in our media examples such as video, animations, and diagrams, and own unique perspectives and harnessing today’s technology. With provides students a multitude of tools and content for self-study our new Experimental Walkthrough feature, available in and practice. Instructors can customize their course content for WileyPLUS Learning Space, students can see first-hand how key students, create online homework and quizzes, and have insight experimental techniques are performed in the lab. These offer a into student activity through data analytics and reporting features. mix of video, which show how researchers carry out experiments, To try it, visit http://www.wileypluslearningspace.com. Here are and 3D animations that show a molecular-level view of how the some of the resources available in WileyPLUS Learning Space: experiments work. These Walkthroughs provide context and a vis- ual explanation that helps make these important experimental Experimental Walkthrough Videos techniques more concrete. Quantitative Tutorial Videos A solid understanding of quantitative concepts is becoming Cell View Animations increasingly important within cell biology, but is an area that Video Library many students struggle with. To address this issue, we have also added another new video feature, called Quantitative Tutorials, Biology Basics Animations to visually illustrate how to solve specific analytical questions at Instructor’s Manual by Joel Piperberg, Millersville University the end of each chapter. The Quantitative Tutorial provides an Clicker Questions by Leocadia Paliulis, Bucknell University accessible, student‐friendly review of basic mathematical concepts and Omar Quintero, University of Richmond used within the context of a biological problem, and will expand Lecture PowerPoint Presentations by Edmund B. Rucker, the available resources for quantitative and physical concepts University of Kentucky within this 8th edition. One key feature of the past editions was to highlight how cell Testbank and Answer Key by Robert Seiser, Roosevelt University biology impacts our daily lives, in terms of medicine and other areas of society. The Human Perspectives sections highlight ACKNOWLEDGEMENTS human interest stories to reinforce and review basic cell biology, and also provide examples of how fundamental discoveries have Gerald Karp, who dedicated many years to carefully and thought- progressed into clinical practice. We have expanded this feature fully writing and editing this text, has left a remarkable legacy that so that now every chapter has at least one Human Perspectives we are grateful to inherit. In putting together this edition, we are section. As part of this feature we report on the latest clinical tri- thankful for his insight, wisdom and advice that was always cheer- als for various cell biology‐based therapies and drugs, a feature fully and generously provided to us. that we hope will inspire students who are pursuing careers in We are grateful to many individuals at John Wiley & Sons health sciences fields. In addition to the full Human Perspectives who made this edition possible. Kevin Witt brought us on board at sections, each chapter is now introduced with a short “chapter the beginning stages and infused us with his enthusiasm for the opener” designed to generate enthusiasm about the science in project. Bonnie Roth provided superb leadership, guidance and each chapter through provocative issues or questions. We hope support throughout the writing and editing process. Carrie that this will give our readers the opportunity to think more Thompson, Melissa Edwards, Beth Pearson, and Liz Baird helped about the links between science, society, and our place in the to keep us on organized and on track with the text and the various universe. media elements. Patty Donovan of SPI Global played a central role in coordinating the production of the text, incorporating changes to Adam, Aki and Kenzo, and the lifelong encouragement of her vii the text and numerous illustrations and images. Billy Ray led the parents, Kuni and Mieko. team in obtaining new images used in this edition. Maureen Eide Wallace Marshall thanks his scientific mentors, Rolf Sternglanz, skillfully designed the interior and front cover. John Sedat, and Joel Rosenbaum, for launching him in the direction PREFACE Janet Iwasa thanks Rob Savage, Dyche Mullins and Jack Szostak, that he went. He thanks his parents, Clifford and Adele Marshall for for inspiring and guiding her along the path towards becoming a making him who he is. And he thanks his family, Jennifer and Wyeth, biologist. Janet is particularly grateful for the support of her family, for continued inspiration and support. viii We also wish to thank all reviewers of this and previous editions: PREFACE STEVE ALAS DENNIS O. CLEGG REBECCA HEALD California State Polytechnic University, University of California—Santa Barbara University of California, Berkeley Pomona KATE COOPER ROBERT HELLING RAVI ALLADA Loras College University of Michigan Northwestern University RONALD H. COOPER MARK HENS DEREK APPLEWHITE University of California—Los Angeles University of North Carolina, Greensboro Reed College PHILIPPA D. DARBRE ARTHUR HORWICH LINDA AMOS University of Reading Yale University School of Medicine MRC Laboratory of Molecular Biology ROGER W. DAVENPORT JEN‐CHIH HSIEH KARL J. AUFDERHEIDE University of Maryland State University of New York at Stony Brook Texas A&M University SUSAN DESIMONE JOEL A. HUBERMAN GERALD T. BABCOCK Middlebury College Roswell Park Cancer Institute Michigan State University LINDA DEVEAUX GREGORY D. D. HURST WILLIAM E. BALCH Idaho State University University College London The Scripps Research Institute RICHARD E. DEARBORN KEN JACOBSON KENNETH J. BALAZOVICH Albany College of Pharmacy University of North Carolina University of Michigan BARRY J. DICKSON MARIE JANICKE JAMES BARBER Research Institute of Molecular Pathology University at Buffalo—SUNY Imperial College of Science— DAVID DOE MICHAEL JONZ Wolfson Laboratories Westfield State College University of Ottawa JOHN D. BELL ROBERT S. DOTSON ROLAND KAUNAS Brigham Young University Tulane University Texas A&M University WENDY A. BICKMORE JENNIFER A. DOUDNA HAIG H. KAZAZIAN, JR. Medical Research Council, Yale University University of Pennsylvania United Kingdom MICHAEL EDIDIN LAURA R. KELLER ASHOK BIDWAI Johns Hopkins University Florida State University West Virginia University EVAN E. EICHLER TOM KELLER ALLAN BLAKE University of Washington Florida State University Seton Hall University ARRI EISEN REBECCA KELLUM MARTIN BOOTMAN Emory University University of Kentucky Babraham Institute ROBERT FILLINGAME GREG M. KELLY DAVID BOURGAIZE University of Wisconsin Medical School University of Western Ontario Whittier College ORNA COHEN-FIX NEMAT O. KEYHANI DANIEL BRANTON National Institute of Health, Laboratory University of Florida Harvard University of Molecular and Cellular Biology KIM KIRBY THOMAS R. BREEN JACEK GAERTIG University of Guelph Southern Illinois University University of Georgia NANCY KLECKNER SHARON K. BULLOCK BENJAMIN GLICK Harvard University Virginia Commonwealth University The University of Chicago WERNER KÜHLBRANDT RODERICK A. CAPALDI REGINALD HALABY Max‐Planck‐Institut fÜr Biophysik University of Oregon Montclair State University JAMES LAKE GORDON G. CARMICHAEL MICHAEL HAMPSEY University of California—Los Angeles University of Connecticut Health Center University of Medicine and Dentistry CLAIRE M. LEONARD RATNA CHAKRABARTI of New Jersey William Paterson University University of Central Florida MICHAEL HARRINGTON ROBERT C. LIDDINGTON KENT D. CHAPMAN University of Alberta Burnham Institute University of North Texas MARCIA HARRISON FAITH LIEBL K. H. ANDY CHOO Marshall University Southern Illinois University, Edwardsville Royal Children’s Hospitals— R. SCOTT HAWLEY VISHWANATH R. LINGAPPA The Murdoch Institute American Cancer Society Research Professor University of California—San Francisco JEANNETTE M. LOUTSCH CHARLES PUTNAM ADRIANA STOICA ix Arkansas State University University of Arizona Georgetown University JON LOWRANCE DAVID REISMAN ANN STURTEVANT Lipscomb University University of South Carolina University of Michigan‐Flint PREFACE MARGARET LYNCH DONNA RITCH COLLEEN TALBOT Tufts University University of Wisconsin— California State Univerity, CHARLES MALLERY Green Bay San Bernardino University of Miami JOEL L. ROSENBAUM WILLIAM TERZAGHI MICHAEL A. MCALEAR Yale University Wilkes University Wesleyan University WOLFRAM SAENGER GISELLE THIBAUDEAU ARDYTHE A. MCCRACKEN Freie Universitat Berlin Mississippi State University University of Nevada—Reno SHIVENDRA V. SAHI JEFFREY L. TRAVIS THOMAS MCKNIGHT Western Kentucky University University at Albany—SUNY Texas A&M University JAMIE SANFORD PAUL TWIGG JOANN MEERSCHAERT Ohio Northern University University of Nebraska‐Kearney St. Cloud State University JOSHUA SANDQUIST NIGEL UNWIN JOHN MENNINGER Grinnell College MRC Laboratory of Molecular Biology University of Iowa PRASANNA SATPUTE‐KRISHNAN AJIT VARKI KIRSTEN MONSEN National Institute of Health University of California—San Diego Montclair State University INDER M. SAXENA JOSE VAZQUEZ ANDREW NEWMAN University of Texas, Austin New York University Cambridge University RANDY SCHEKMAN CLAIRE E. WALCZAK MICHELLE MORITZ University of California—Berkeley Indiana University University of California—San Francisco SANDRA SCHMID PAUL E. WANDA ROBERT MORRIS The Scripps Research Institute Southern Illinois University, Wheaton College TRINA SCHROER Edwardsville ALAN NIGHORN Johns Hopkins University JENNIFER WATERS University of Arizona TIM SCHUH Harvard University ROBERT M. NISSEN St. Cloud State University CHRIS WATTERS California State University, Los Angeles DAVID SCHULTZ Middlebury College JONATHAN NUGENT University of Louisville ANDREW WEBBER University of London ROD SCOTT Arizona State University VERONICA C. NWOSU Wheaton College BEVERLY WENDLAND North Carolina Central University KATIE SHANNON Johns Hopkins University MIKE O’DONNELL University of North Carolina— GARY M. WESSEL Rockefeller University Chapel Hill Brown University GREG ODORIZZI JOEL B. SHEFFIELD ERIC V. WONG University of Colorado, Boulder Temple University University of Louisville LEOCADIA PALIULIS ERIC SHELDEN ANDREW WOOD Bucknell University Washington State University Southern Illinois University JAMES G. PATTON DENNIS SHEVLIN GARY YELLEN Vanderbilt University College of New Jersey Harvard Medical School HUGH R. B. PELHAM JEFF SINGER MASASUKE YOSHIDA MRC Laboratory of Molecular Biology Portland State University Tokyo Institute of Technology JONATHAN PINES ROGER D. SLOBODA DANIELA ZARNESCU Wellcome/CRC Institute Dartmouth College University of Arizona DEBRA PIRES HARRIETT E. SMITH‐SOMERVILLE JIANZHI ZHANG University of California—Los Angeles University of Alabama University of Michigan MITCH PRICE BRUCE STILLMAN ROBERT A. ZIMMERMAN Pennsylvania State University Cold Spring Harbor Laboratory University of Massachusetts  Contents Hydrophobic Interactions and van der Waals Forces 36 1 Introduction to the Study of Cell and The Life-Supporting Properties of Water 37 Molecular Biology 1 2.4 Acids, Bases, and Buffers 38 1.1 The Discovery of Cells 2 2.5 The Nature of Biological Molecules 39 Microscopy 2 Functional Groups 40 Cell Theory 2 A Classification of Biological Molecules by Function 40 1.2 Basic Properties of Cells 3 2.6 Carbohydrates 42 Cells Are Highly Complex and Organized 3 The Structure of Simple Sugars 42 Cells Possess a Genetic Program and the Means Stereoisomerism 42 to Use It 5 Linking Sugars Together 43 Cells Are Capable of Producing More of Themselves 5 Polysaccharides 44 Cells Acquire and Utilize Energy 5 Cells Carry Out a Variety of Chemical Reactions 6 2.7 Lipids 46 Cells Engage in Mechanical Activities 6 Fats 46 Cells Are Able to Respond to Stimuli 6 Steroids 47 Cells Are Capable of Self-Regulation 6 Phospholipids 47 Cells Evolve 7 2.8 Building Blocks of Proteins 48 1.3 Characteristics That Distinguish Prokaryotic The Structures of Amino Acids 49 and Eukaryotic Cells 8 The Properties of the Side Chains 50 1.4 Types of Prokaryotic Cells 13 2.9 Primary and Secondary Structures of Proteins 53 Domain Archaea and Domain Bacteria 13 Primary Structure 53 Prokaryotic Diversity 14 Secondary Structure 53 1.5 Types of Eukaryotic Cells 15 2.10 Tertiary Structure of Proteins 55 Cell Differentiation 15 Myoglobin: The First Globular Protein Whose Tertiary Model Organisms 16 Structure Was Determined 56 1.6 T HE HUM AN P E R S P E CTIVE: Tertiary Structure May Reveal Unexpected Similarities The Prospect of Cell Replacement Therapy 17 between Proteins 56 Protein Domains 57 1.7 The Sizes of Cells and Their Components 21 Dynamic Changes within Proteins 58 1.8 Viruses and Viroids 23 2.11 Quaternary Structure of Proteins 58 1.9 E X P E R IM E N TAL PAT HWAY S: The Structure of Hemoglobin 59 The Origin of Eukaryotic Cells 26 Protein–Protein Interactions 59 2.12 Protein Folding 60 Dynamics of Protein Folding 60 2 The Chemical Basis of Life 31 The Role of Molecular Chaperones 62 2.1 Covalent Bonds 32 2.13 TH E H UMAN P ERSPECTI V E: Polar and Nonpolar Molecules 33 Protein Misfolding Can Have Deadly Consequences 62 Ionization 33 2.14 EX P ERIMEN TAL PATHWAYS: 2.2 T HE HUM AN P E R S P E CTIVE: Chaperones—Helping Proteins Reach Their Proper Folded Do Free Radicals Cause Aging? 34 State 67 2.3 Noncovalent Bonds 35 2.15 Proteomics and Interactomics 71 Ionic Bonds: Attractions between Charged Atoms 35 Proteomics 71 Hydrogen Bonds 35 Interactomics 72 xii 2.16 Protein Engineering 73 3.13 Separating Catabolic and Anabolic Production of Novel Proteins 74 Pathways 110 Structure-Based Drug Design 75 3.14 TH E H UMAN P ERSPECTI V E: CONTENTS Caloric Restriction and Longevity 111 2.17 Protein Adaptation and Evolution 76 2.18 Nucleic Acids 77 2.19 The Formation of Complex Macromolecular 4 The Structure and Function of the Structures 79 Plasma Membrane 114 The Assembly of Tobacco Mosaic Virus Particles 79 The Assembly of Ribosomal Subunits 79 4.1 Introduction to the Plasma Membrane 115 An Overview of Membrane Functions 115 A Brief History of Studies on Plasma Membrane 3 Bioenergetics, Enzymes, Structure 116 and Metabolism 81 4.2 The Lipid Composition of Membranes 118 Membrane Lipids 119 3.1 The Laws of Thermodynamics 82 The Nature and Importance of the Lipid Bilayer 120 The First Law of Thermodynamics 82 The Asymmetry of Membrane Lipids 121 The Second Law of Thermodynamics 83 4.3 Membrane Carbohydrates 122 3.2 Free Energy 85 4.4 Membrane Proteins 123 Free-Energy Changes in Chemical Reactions 85 Integral Membrane Proteins 124 Free-Energy Changes in Metabolic Reactions 86 Peripheral Membrane Proteins 125 3.3 Coupling Endergonic and Exergonic Reactions 88 Lipid-Anchored Membrane Proteins 125 3.4 Equilibrium versus Steady-State 4.5 Studying the Structure and Properties of Integral Metabolism 88 Membrane Proteins 126 3.5 Enzymes as Biological Catalysts 89 Identifying Transmembrane Domains 127 The Properties of Enzymes 90 Experimental Approaches to Identifying Conformational Changes within an Integral Membrane Protein 128 Overcoming the Activation Energy Barrier 90 The Active Site 92 4.6 Membrane Lipids and Membrane Fluidity 130 3.6 Mechanisms of Enzyme Catalysis 93 The Importance of Membrane Fluidity 131 Maintaining Membrane Fluidity 131 Substrate Orientation 94 Lipid Rafts 131 Changing Substrate Reactivity 94 Inducing Strain in the Substrate 94 4.7 The Dynamic Nature of the Plasma 3.7 Enzyme Kinetics 97 Membrane 132 The Diffusion of Membrane Proteins after Cell Fusion 133 The Michaelis-Menten Model of Enzyme Kinetics 97 Restrictions on Protein and Lipid Mobility 133 Enzyme Inhibitors 98 3. 8 THE HUM AN P E R S P E CT IV E : 4.8 The Red Blood Cell: An Example of Plasma The Growing Problem of Antibiotic Resistance 100 Membrane Structure 137 3.9 An Overview of Metabolism 103 Integral Proteins of the Erythrocyte Membrane 137 The Erythrocyte Membrane Skeleton 137 Oxidation and Reduction: A Matter of Electrons 103 The Capture and Utilization of Energy 103 4.9 Solute Movement across Cell Membranes 139 3.10 Glycolysis and Fermentation 105 The Energetics of Solute Movement 139 Formation of an Electrochemical Gradient 140 ATP Production in Glycolysis 105 Anaerobic Oxidation of Pyruvate: The Process of 4.10 Diffusion through the Lipid Bilayer 140 Fermentation 108 Diffusion of Substances through Membranes 140 3.11 Reducing Power 109 The Diffusion of Water through Membranes 141 3.12 Metabolic Regulation 109 4.11 The Diffusion of Ions through Membranes 143 Altering Enzyme Activity by Covalent Modification 109 4.12 EX P ERIMEN TAL PATHWAYS: Altering Enzyme Activity by Allosteric Modulation 110 The Acetylcholine Receptor 147 4.13 Facilitated Diffusion 151 5.9 Using the Proton Gradient 192 xiii 4.14 Active Transport 152 The Role of the Fo Portion of ATP Synthase in ATP Synthesis 192 Primary Active Transport: Coupling Transport to ATP CONTENTS Other Roles for the Proton-Motive Force in Addition to ATP Hydrolysis 152 Synthesis 193 Other Primary Ion Transport Systems 154 Using Light Energy to Actively Transport Ions 155 5.10 Peroxisomes 193 Secondary Active Transport (or Cotransport): Coupling 5.11 TH E H UMAN P ERSPECTI V E: Transport to Existing Ion Gradients 155 Diseases that Result from Abnormal Mitochondrial or 4.1 5 T HE HUM AN P E R S P E CTIVE: Peroxisomal Function 195 Defects in Ion Channels and Transporters as a Cause of Inherited Disease 157 4.16 Membrane Potentials 159 6 Photosynthesis and the The Resting Potential 159 Chloroplast 199 The Action Potential 160 6.1 The Origin of Photosynthesis 200 4.17 Propagation of Action Potentials as an 6.2 Chloroplast Structure 201 Impulse 161 6.3 An Overview of Photosynthetic Metabolism 202 4.18 Neurotransmission: Jumping the Synaptic Cleft 162 6.4 The Absorption of Light 203 Actions of Drugs on Synapses 165 6.5 Coordinating the Action of Two Different Synaptic Plasticity 165 Photosynthetic Systems 205 6.6 The Operations of Photosystem II and Photosystem I 207 5 Aerobic Respiration PSII Operations: Obtaining Electrons by and the Mitochondrion 168 Splitting Water 207 PSI Operations: The Production of NADPH 210 5.1 Mitochondrial Structure and Function 169 Mitochondrial Membranes 170 6.7 An Overview of Photosynthetic Electron The Mitochondrial Matrix 172 Transport 211 5.2 Aerobic Metabolism in the Mitochondrion 172 6.8 Photophosphorylation 212 The Tricarboxylic Acid (TCA) Cycle 173 6.9 Carbohydrate Synthesis in C3 Plants 213 The Importance of Reduced Coenzymes in the Redox Control 215 Formation of ATP 175 Photorespiration 216 5.3 T HE HUM AN P E R S P E CTIVE: Peroxisomes and Photorespiration 217 The Role of Anaerobic and Aerobic Metabolism in Exercise 177 6.10 Carbohydrate Synthesis in C4 and CAM 5.4 Oxidative Phosphorylation in the Formation of Plants 218 ATP 178 6.11 TH E H UMAN P ERSPECTI V E: Oxidation–Reduction Potentials 179 Global Warming and Carbon Sequestration 219 Electron Transport 180 Types of Electron Carriers 180 5.5 Electron-Transport Complexes 182 7 Interactions between Cells and their Complex I (NADH Dehydrogenase) 184 Environment 222 Complex II (succinate dehydrogenase) 185 Complex III (cytochrome bc1) 185 7.1 Overview of Extracellular Interactions 223 Complex IV (cytochrome c oxidase) 185 7.2 The Extracellular Matrix 224 5.6 Establishment of a Proton-Motive Force 186 7.3 Components of the Extracellular Matrix 226 5.7 The Structure of ATP Synthase 187 Collagen 226 Proteoglycans 228 5.8 The Binding Change Mechanism of ATP Fibronectin 229 Formation 189 Laminin 229 Components of the Binding Change Hypothesis 189 Evidence to Support the Binding Change Mechanism and 7.4 Dynamic Properties of the Extracellular Rotary Catalysis 190 Matrix 231 xiv 7.5 Integrins 231 8.5 Membrane Biosynthesis in the Endoplasmic 7.6 Anchoring Cells to Their Substratum 234 Reticulum 271 Focal Adhesions 234 8.6 Glycosylation in the Rough Endoplasmic CONTENTS Hemidesmosomes 236 Reticulum 273 7.7 Interactions of Cells with Other Cells 237 8.7 Mechanisms That Ensure the Destruction of Selectins 238 Misfolded Proteins 275 The Immunoglobulin Superfamily 239 8.8 ER to Golgi Vesicular Transport 276 Cadherins 239 8.9 The Golgi Complex 276 7. 8 T HE HUM AN P E R S P E CT IV E : Glycosylation in the Golgi Complex 278 The Role of Cell Adhesion in Inflammation and Metastasis 241 The Movement of Materials through the Golgi 7.9 Adherens Junctions and Desmosomes 244 Complex 278 7.10 The Role of Cell-Adhesion Receptors in 8.10 Types of Vesicle Transport 280 Transmembrane Signaling 245 COPII-Coated Vesicles: Transporting Cargo from the ER to the Golgi Complex 281 7.11 Tight Junctions: Sealing the Extracellular COPI-Coated Vesicles: Transporting Escaped Proteins Back Space 245 to the ER 284 7.12 Gap Junctions and Plasmodesmata: Mediating 8.11 Beyond the Golgi Complex: Sorting Proteins at Intercellular Communication 247 the TGN 285 Gap Junctions 248 Sorting and Transport of Lysosomal Enzymes 285 Plasmodesmata 250 Sorting and Transport of Nonlysosomal Proteins 286 7. 13 E X P E R IM E N TAL PAT HWAY S: 8.12 TH E H UMAN P ERSPECTI V E: The Role of Gap Junctions in Intercellular Communication 251 Disorders Resulting from Defects in Lysosomal Function 286 7.14 Cell Walls 254 8.13 Targeting Vesicles to a Particular Compartment 288 8 Cytoplasmic Membrane Systems: 8.14 Exocytosis 290 Structure, Function, and Membrane 8.15 Lysosomes 291 Trafficking 257 8.16 Plant Cell Vacuoles 292 8.17 Endocytosis 293 8.1 An Overview of the Endomembrane System 258 Receptor-Mediated Endocytosis and the Role of 8.2 A Few Approaches to the Study of Coated Pits 294 Endomembranes 260 The Role of Phosphoinositides in the Regulation of Insights Gained from Autoradiography 260 Coated Vesicles 296 Insights Gained from the Use of the Green Fluorescent 8.18 EX P ERIMEN TAL PATHWAYS: Protein 260 Receptor‐Mediated Endocytosis 297 Insights Gained from the Analysis of Subcellular Fractions 262 Insights Gained from the Use 8.19 The Endocytic Pathway 300 of Cell-Free Systems 263 8.20 Phagocytosis 303 Insights Gained from the Study of Mutant Phenotypes 263 8.21 Posttranslational Uptake of Proteins by 8.3 The Endoplasmic Reticulum 265 Peroxisomes, Mitochondria, and The Smooth Endoplasmic Reticulum 266 Chloroplasts 304 The Rough Endoplasmic Reticulum 267 Uptake of Proteins into Peroxisomes 304 8.4 Functions of the Rough Endoplasmic Uptake of Proteins into Mitochondria 304 Reticulum 268 Uptake of Proteins into Chloroplasts 306 Synthesis of Proteins on Membrane-Bound versus Free Ribosomes 268 Synthesis of Secretory, Lysosomal, or Plant Vacuolar 9 The Cytoskeleton and Proteins 268 Processing of Newly Synthesized Proteins in the Endoplasmic Cell Motility 309 Reticulum 270 9.1 Overview of the Major Functions of the Synthesis of Integral Membrane Proteins on ER-Bound Ribosomes 270 Cytoskeleton 310 9.2 Structure and Function of Microtubules 311 10 The Nature of the Gene and the xv Structure and Composition of Microtubules 312 Genome 366 Microtubule-Associated Proteins 313 CONTENTS Microtubules as Structural Supports and Organizers 313 10.1 The Concept of a Gene as a Unit of Microtubules as Agents of Intracellular Motility 314 Inheritance 367 9.3 Motor Proteins: Kinesins and Dyneins 315 10.2 The Discovery of Chromosomes 368 Motor Proteins Traverse the Microtubular Cytoskeleton 315 Kinesins 316 10.3 Chromosomes as the Carriers of Genetic Cytoplasmic Dynein 317 Information 369 9.4 E X P E R IM E N TAL PAT HWAY: 10.4 Genetic Analysis in Drosophila 370 The Step Size of Kinesin 319 Crossing Over and Recombination 371 9.5 Microtubule-Organizing Centers (MTOCs) 321 Mutagenesis and Giant Chromosomes 371 Centrosomes 321 10.5 The Structure of DNA 373 Basal Bodies and Other MTOCs 322 The Watson-Crick Proposal 374 Microtubule Nucleation 322 The Importance of the 9.6 Microtubule Dynamics 323 Watson-Crick Proposal 375 The Dynamic Properties of Microtubules 323 10.6 EX P ERIMEN TAL PATHWAYS: The Underlying Basis of The Chemical Nature of the Gene 377 Microtubule Dynamics 325 10.7 DNA Supercoiling 381 9.7 Structure and Function of Cilia and Flagella 327 Structure of Cilia and Flagella 329 10.8 The Complexity of the Genome 382 Growth by Intraflagellar Transport 331 DNA Denaturation 383 The Mechanism of Ciliary DNA Renaturation 384 and Flagellar Locomotion 331 10.9 TH E H UMAN P ERSPECTI V E: 9.8 T HE HUM AN P E R S P E CTIVE: Diseases That Result from Expansion of Trinucleotide The Role of Cilia in Development and Disease 333 Repeats 387 9.9 Intermediate Filaments 335 10.10 The Stability of the Genome: Duplication 389 Intermediate Filament Assembly and Disassembly 335 Whole-Genome Duplication (Polyploidization) 389 Types and Functions of Intermediate Filaments 336 Duplication and Modification of DNA Sequences 390 9.10 Actin 338 Evolution of Globin Genes 390 Actin Structure 338 10.11 The Dynamic Nature of the Genome: “Jumping Actin Filament Assembly and Disassembly 339 Genes” 391 9.11 Myosin: The Molecular Motor of Actin 341 Transposons 392 Conventional (Type II) Myosins 341 The Role of Mobile Genetic Elements in Genome Unconventional Myosins 341 Evolution 393 9.12 Muscle Organization and Contraction 344 10.12 Sequencing Genomes: The Footprints of Organization of Sarcomeres 346 Biological Evolution 394 The Sliding Filament Model 10.13 Comparative Genomics: “If It’s Conserved, It of Muscle Contraction 346 Must Be Important” 396 9.13 Actin-Binding Proteins 351 10.14 The Genetic Basis of “Being Human” 397 9.14 Cellular Motility 353 9.1 5 E X P E R IM E N TAL PAT HWAY: 10.15 Genetic Variation within the Human Species Population 398 Studying Actin‐Based Motility without Cells 358 DNA Sequence Variation 398 9.16 Actin-dependent Processes During Structural Variation 399 Development 361 Copy Number Variation 399 Axonal Outgrowth 361 10.16 TH E H UMAN PERSPECTI V E: 9.17 The Bacterial Cytoskeleton 362 Application of Genomic Analyses to Medicine 400  The Structure of tRNAs 439 xvi 11 The Central Dogma: DNA to RNA tRNA Charging 441 to Protein 404 11.16 Translating Genetic Information: Initiation 442 CONTENTS 11.1 The Relationship between Genes, Proteins, Initiation of Translation in Prokaryotes 442 and RNAs 405 Initiation of Translation in Eukaryotes 443 Evidence That DNA Is the Genetic Material 405 The Role of the Ribosome 444 An Overview of the Flow of Information through the Cell 406 11.17 Translating Genetic Information: Elongation 11.2 The Role of RNA Polymerases in and Termination 445 Transcription 408 Elongation Step 1: Aminoacyl-tRNA Selection 445 11.3 An Overview of Transcription in Both Prokaryotic Elongation Step 2: Peptide Bond Formation 445 and Eukaryotic Cells 410 Elongation Step 3: Translocation 446 Elongation Step 4: Releasing the Deacylated tRNA 447 Transcription in Bacteria 410 Termination 448 Transcription and RNA Processing in Eukaryotic Cells 411 11.4 Synthesis and Processing of Eukaryotic 11.18 mRNA Surveillance and Quality Control 448 Ribosomal and Transfer RNAs 413 11.19 Polyribosomes 449 Synthesis and Processing of the rRNA Precursor 413 11.20 EX P ERIMEN TAL PATHWAYS : The Role of snoRNAs in the Processing of Pre-rRNA 415 The Role of RNA as a Catalyst 450 Synthesis and Processing of the 5S rRNA 415 Transfer RNAs 416 11.5 Synthesis and Structure of Eukaryotic 12 Control of Gene Expression 455 Messenger RNAs 417 The Formation of Heterogeneous Nuclear RNA 12.1 Control of Gene Expression in Bacteria 456 (hnRNA) 417 Organization of Bacterial Genomes 456 The Machinery for mRNA Transcription 417 The Bacterial Operon 456 The Structure of mRNAs 419 Riboswitches 459 11.6 Split Genes: An Unexpected Finding 420 12.2 Structure of the Nuclear Envelope 460 11.7 The Processing of Eukaryotic Messenger The Nuclear Pore Complex and Its Role in RNAs 423 Nucleocytoplasmic Trafficking 462 5′ Caps and 3′ Poly(A) Tails 423 RNA Transport 465 RNA Splicing: Removal of Introns from a Pre-RNA 425 12.3 Packaging the Eukaryotic Genome 465 11.8 Evolutionary Implications of Split Genes and Nucleosomes: The Lowest Level of Chromosome RNA Splicing 429 Organization 465 Higher Levels of Chromatin Structure 467 11.9 Creating New Ribozymes in the Laboratory 429 12.4 Heterochromatin 469 11.10 RNA Interference 430 X Chromosome Inactivation 470 11. 11 T HE HUM AN P E R S P E CT IVE: The Histone Code and Formation of Heterochromatin 470 Clinical Applications of RNA Interference 432 12.5 The Structure of a Mitotic Chromosome 473 11.12 Small RNAs: miRNAs and piRNAs 433 Telomeres 473 miRNAs: A Class of Small RNAs that Regulate Gene Centromeres 477 Expression 434 12.6 TH E H UMAN P ERSPECTI V E: piRNAs: A Class of Small RNAs that Function in Germ Cells 435 Chromosomal Aberrations and Human Disorders 478 11.13 CRISPR and other Noncoding RNAs 435 12.7 Epigenetics: There’s More to Inheritance than CRISPR: Noncoding RNA in Bacteria 435 DNA 480 Other Noncoding RNAs 436 12.8 The Nucleus as an Organized Organelle 480 11.14 Encoding Genetic Information 436 12.9 An Overview of Gene Regulation in The Properties of the Genetic Code 436 Eukaryotes 483 Identifying the Codons 437 12.10 Profiling Gene Activity 485 11.15 Decoding the Codons: The Role of Transfer DNA Microarrays 485 RNAs 439 RNA Sequencing 487 12.11 The Role of Transcription Factors in Regulating 13.6 DNA Replication in Eukaryotic Cells 526 xvii Gene Expression 488 Initiation of Replication in Eukaryotic Cells 526 12.12 The Structure of Transcription Factors 489 Restricting Replication to Once Per Cell Cycle 527 CONTENTS The Eukaryotic Replication Fork 528 The Zinc-Finger Motif 490 Replication and Nuclear Structure 530 The Helix–Loop–Helix (HLH) Motif 490 The Leucine Zipper Motif 491 13.7 Chromatin Structure and Replication 530 12.13 DNA Sites Involved in Regulating 13.8 DNA Repair 531 Transcription 492 Nucleotide Excision Repair 532 12.14 An Example of Transcriptional Activation: Base Excision Repair 532 The Glucocorticoid Receptor 494 Mismatch Repair 534 Double-Strand Breakage Repair 534 12.15 Transcriptional Activation: The Role of Enhancers, Promoters, and Coactivators 495 13.9 Between Replication and Repair 535 Coactivators That Interact with the Basal Transcription 13.10 TH E H UMAN PERSPECTI V E: Machinery 496 Consequences of DNA Repair Deficiencies 536 Coactivators That Alter Chromatin Structure 496 12.16 Transcriptional Activation from Paused Polymerases 499 14 Cell Division 539 12.17 Transcriptional Repression 499 14.1 The Cell Cycle 540 DNA Methylation 500 Phases of the Cell Cycle 540 Genomic Imprinting 501 Cell Cycles in Vivo 541 Long Noncoding RNAs (lncRNAs) as Transcriptional 14.2 Regulation of the Cell Cycle 542 Repressors 502 14.3 EX P ERIMEN TAL PATHWAYS: 12.18 RNA Processing Control 503 The Discovery and Characterization of MPF 543 12.19 Translational Control 505 14.4 Control of the Cell Cycle: The Role of Protein Initiation of Translation 505 Kinases 546 Cytoplasmic Localization of mRNAs 506 Cyclin Binding 547 The Control of mRNA Stability 506 Cdk Phosphorylation/Dephosphorylation 547 12.20 The Role of MicroRNAs in Translational Cdk Inhibitors 548 Control 508 Controlled Proteolysis 548 Subcellular Localization 548 12.21 Posttranslational Control: Determining Protein Stability 509 14.5 Control of the Cell Cycle: Checkpoints, Cdk Inhibitors, and Cellular Responses 550 14.6 Overview of M Phase: Mitosis and 13 DNA Replication and Repair 512 Cytokinesis 552 13.1 DNA Replication 513 14.7 Prophase 552 Formation of the Mitotic Chromosome 552 13.2 DNA Replication in Bacterial Cells 516 Centromeres and Kinetochores 555 Replication Forks and Bidirectional Replication 517 Formation of the Mitotic Spindle 556 Unwinding the Duplex and Separating the Strands 517 The Dissolution of the Nuclear Envelope and Partitioning The Properties of DNA Polymerases 518 of Cytoplasmic Organelles 558 Semidiscontinuous Replication 519 14.8 Prometaphase 559 13.3 The Machinery Operating at the Replication Fork 521 14.9 Metaphase 560 14.10 Anaphase 562 13.4 The Structure and Functions of DNA Polymerases 523 The Role of Proteolysis in Progression through Mitosis 562 The Events of Anaphase 564 Exonuclease Activities of DNA Polymerases 523 Forces Required for Chromosome Movements at Ensuring High Fidelity during DNA Replication 523 Anaphase 564 13.5 Replication in Viruses 526 The Spindle Assembly Checkpoint 566 xviii 14.11 Telophase and Cytokinesis 567 15.11 The Ras-MAP Kinase Pathway 607 Motor Proteins Required for Mitotic Movements 567 Accessory Proteins 608 Cytokinesis 567 Adapting the MAP Kinase to Transmit Different Types of CONTENTS Cytokinesis in Plant Cells: Formation of the Cell Plate 570 Information 610 14.12 Overview of Meiosis 571 15.12 Signaling by the Insulin Receptor 611 The Insulin Receptor Is a Protein-Tyrosine Kinase 611 14.13 The Stages of Meiosis 574 Insulin Receptor Substrates 1 and 2 611 14. 14 T HE HUM AN P E R S P E CT IVE: Glucose Transport 612 Meiotic Nondisjunction and Its Consequences 577 Diabetes Mellitus 613 14.15 Genetic Recombination during Meiosis 579 15.13 Signaling Pathways in Plants 613 15.14 The Role of Calcium as an Intracellular 15 Cell Signaling and Signal Messenger 613 IP3 and Voltage-Gated Ca2+ Channels 613 Transduction: Communication Visualizing Cytoplasmic Ca2+ Concentration in Living between Cells 582 Cells 614 Ca2+-Binding Proteins 615 15.1 The Basic Elements of Cell Signaling Regulating Calcium Concentrations in Plant Cells 617 Systems 583 15.15 Convergence, Divergence, and Cross-Talk 15.2 A Survey of Extracellular Messengers and Their among Different Signaling Pathways 617 Receptors 586 15.16 The Role of NO as an Intercellular 15.3 Signal Transduction by G Protein-Coupled Messenger 619 Receptors 587 NO as an Activator of Guanylyl Cyclase 620 Receptors 587 Inhibiting Phosphodiesterase 620 G Proteins 588 Termination of the Response 589 15.17 Apoptosis (Programmed Cell Death) 621 Bacterial Toxins 590 The Extrinsic Pathway of Apoptosis 622 The Intrinsic Pathway of Apoptosis 623 15. 4 E X P E R IM E N TAL PAT HWAY S: Necroptosis 624 The Discovery and Characterization of GTP‐Binding Signaling Cell Survival 624 Proteins 590 15. 5 T HE HUM AN P E R S P E CT IV E: Disorders Associated with G Protein‐Coupled Receptors 594 16 Cancer 627 15.6 Second Messengers 595 16.1 Basic Properties of a Cancer Cell 628 The Discovery of Cyclic AMP 595 Phosphatidylinositol-Derived Second Messengers 596 16.2 The Causes of Cancer 631 Phospholipase C 597 16.3 EX P ERIMEN TAL PATHWAYS: 15.7 The Specificity of G Protein-Coupled The Discovery of Oncogenes 632 Responses 599 16.4 Cancer: A Genetic Disorder 636 15.8 Regulation of Blood Glucose Levels 599 16.5 An Overview of Tumor-Suppressor Genes Glucose Mobilization: An Example of a Response and Oncogenes 638 Induced by cAMP 600 16.6 Tumor-Suppressor Genes: The RB Gene 640 Signal Amplification 600 Other Aspects of cAMP Signal Transduction Pathways 600 16.7 Tumor-Suppressor Genes: The TP53 Gene 642 15.9 The Role of GPCRs in Sensory Perception 603 The Role of p53: Guardian of the Genome 642 15.10 Protein-Tyrosine Phosphorylation as a The Role of p53 in Promoting Senescence 644 Mechanism for Signal Transduction 603 16.8 Other Tumor-Suppressor Genes 645 Receptor Dimerization 604 Protein Kinase Activation 604 16.9 Oncogenes 646 Phosphotyrosine-Dependent Protein–Protein Oncogenes That Encode Growth Factors or Their Interactions 604 Receptors 646 Activation of Downstream Signaling Pathways 604 Oncogenes That Encode Cytoplasmic Protein Kinases 647 Ending the Response 607 Oncogenes That Encode Transcription Factors 647  Oncogenes That Encode Proteins That Affect the Epigenetic State of Chromatin 647 18 Techniques in Cell and Molecular xix Oncogenes That Encode Metabolic Enzymes 647 Biology 692 Oncogenes That Encode Products CONTENTS That Affect Apoptosis 648 18.1 The Light Microscope 693 Resolution 694 16.10 The Mutator Phenotype: Mutant Genes Visibility 695 Involved in DNA Repair 649 18.2 Bright-Field and Phase-Contrast Microscopy 695 16.11 MicroRNAs: A New Player in the Genetics of Cancer 649 Bright-Field Light Microscopy 695 Phase-Contrast Microscopy 695 16.12 The Cancer Genome 649 18.3 Fluorescence Microscopy (and Related 16.13 Gene-Expression Analysis 651 Fluorescence-Based Techniques) 696 16.14 Strategies for Combating Cancer 654 Laser Scanning Confocal Microscopy 699 16.15 Immunotherapy 654 Super-Resolution Fluorescence Microscopy 699 Light Sheet Fluorescence Microscopy 700 16.16 Inhibiting the Activity of Cancer-Promoting Proteins 656 18.4 Transmission Electron Microscopy 701 16.17 The Concept of a Cancer Stem Cell 658 18.5 Specimen Preparation for Electron 16.18 Inhibiting the Formation of New Blood Vessels Microscopy 703 (Angiogenesis) 659 Cryofixation and the Use of Frozen Specimens 703 Negative Staining 705 Shadow Casting 705 17 The Immune Response 661 Freeze-Fracture Replication and Freeze Etching 705 17.1 An Overview of the Immune Response 662 18.6 Scanning Electron Microscopy 707 Innate Immune Responses 663 18.7 Atomic Force Microscopy 708 Adaptive Immune Responses 665 18.8 The Use of Radioisotopes 709 17.2 The Clonal Selection Theory as It Applies to B Cells 666 18.9 Cell Culture 710 1 7.3 T HE HUM AN P E R S P E CTIVE: 18.10 The Fractionation of a Cell’s Contents by Autoimmune Diseases 668 Differential Centrifugation 711 17.4 Vaccination 671 18.11 Purification and Characterization of Proteins by 1 7.5 E X P E R IM E N TAL PAT HWAY S: Liquid Column Chromatography 712 The Role of the Major Histocompatibility Complex in Antigen Ion-Exchange Chromatography 712 Presentation 672 Gel Filtration Chromatography 712 17.6 T Lymphocytes: Activation and Mechanism of Affinity Chromatography 713 Action 675 18.12 Determining Protein–Protein Interactions 714 17.7 The Modular Structure of Antibodies 678 18.13 Characterization of Proteins by Polyacrylamide 17.8 DNA Rearrangements That Produce Genes Gel Electrophoresis 715 Encoding B- and T-Cell Antigen Receptors 681 SDS–PAGE 716 17.9 Membrane-Bound Antigen Receptor Two-Dimensional Gel Electrophoresis 716 Complexes 683 18.14 Characterization of Proteins by 17.10 The Major Histocompatibility Complex 684 Spectrometry 716 17.11 Distinguishing Self from Nonself 686 18.15 Characterization of Proteins by Mass 17.12 Lymphocytes Are Activated by Cell-Surface Spectrometry 716 Signals 689 18.16 Determining the Structure of Proteins and Activation of Helper T Cells by Professional APCs 689 Multisubunit Complexes 717 Activation of B Cells by TH Cells 689 18.17 Fractionation of Nucleic Acids 719 17.13 Signal Transduction Pathways in Lymphocyte Separation of DNAs by Gel Electrophoresis 719 Activation 689 Separation of Nucleic Acids by Ultracentrifugation 719 xx 18.18 Nucleic Acid Hybridization 721 Transgenic Animals 733 Transgenic Plants 734 18.19 Chemical Synthesis of DNA 722 18.25 Gene Editing and Silencing 734 18.20 Recombinant DNA Technology 723 CONTENTS In Vitro Mutagenesis 735 Restriction Endonucleases 723 Knockout Mice 735 Formation of Recombinant DNAs 723 RNA Interference 736 DNA Cloning 724 Genome Editing Using Engineered 18.21 Enzymatic Amplification of DNA by PCR 726 Nucleases 737 Process of PCR 727 18.26 The Use of Antibodies 738 Applications of PCR 728 18.22 DNA Sequencing 728 18.23 DNA Libraries 730 Glossary G-1 Genomic Libraries 731 Additional Reading A-1 cDNA Libraries 731 18.24 DNA Transfer into Eukaryotic Cells and Index I-1 Mammalian Embryos 732  Nobel Prizes Awarded for Research in Cell and Molecular Biology Since 1958 Year Recipient* Prize Area of Research Pages in Text 2015 Tomas Lindahl Chemistry Mechanisms of DNA repair 532 Paul Modrich Aziz Sancar 2014 Eric Betzig Chemistry Development of super-resolved fluorescence microscopy 699–700 W. E. Moerner Stefan Hell 2013 James E. Rothman M&P Discoveries of machinery regulating vesicle traffic 263, 279 Randy W. Schekman Thomas C. Südhof 2012 John B. Gurdon M & P** Animal cloning, nuclear reprogramming 483 Shinya Yamanaka Cell reprogramming 20, 489 Brian K. Kobilka Chemistry G protein‐coupled receptors 588 Robert J. Lefkowitz 2011 Bruce A. Beutler M&P Innate immunity 664 Jules A. Hoffmann Ralph M. Steinman Dendritic cells and Adaptive immunity 676 2009 Venkatraman Ramakrishnan Chemistry Ribosome structure and function 453 Thomas A. Steitz Ada E. Yonath Eliazbeth H. Blackburn M&P Telomeres and telomerase 475 Carol W. Greider Jack W. Szostak 2008 Francoise Barré‐Sinoussi M&P Discovery of HIV 23 Luc Montagnier Harald zur Hausen Role of HPV in cancer 631 Martin Chalfie Chemistry Discovery and development of GFP 260, 697 Osamu Shimomura Roger Tsien 2007 Mario R. Capecchi M&P Development of techniques for knockout mice 735 Martin J. Evans Oliver Smithies 2006 Andrew Z. Fire M&P RNA Interference 430 Craig C. Mello Roger D. Kornberg Chemistry Transcription in eukaryotes 412, 465 2004 Richard Axel M&P Olfactory receptors 603 Linda B. Buck Aaron Ciechanover Chemistry Ubiquitin and proteasomes 509 Avram Hershko Irwin Rose 2003 Peter Agre Chemistry Structure of membrane channels 143, 144 Roderick MacKinnon 2002 Sydney Brenner M&P Introduction of C. elegans 16 John Sulston as a model organism H. Robert Horvitz Apoptosis in C. elegans 622 John B. Fenn Chemistry Electrospray ionization in MS 717 Koichi Tanaka MALDI in MS 717 Kurt Wüthrich NMR analysis of proteins 55 2001 Leland H. Hartwell M&P Control of the cell cycle 547, 550 Tim Hunt Paul Nurse Year Recipient* Prize Area of Research Pages in Text 2000 Arvid Carlsson M&P Synaptic transmission and signal transduction 164 Paul Greengard 614 Eric Kandel 1999 Günter Blobel M&P Protein trafficking 268 1998 Robert Furchgott M&P NO as intercellular messenger 620 Louis Ignarro Ferid Murad 1997 Jens C. Skou Chemistry Na+/K+‐ATPase 152 Paul Boyer Mechanism of ATP synthesis 189, 190 John Walker Stanley B. Prusiner M&P Protein nature of prions 63 1996 Rolf M. Zinkernagel M&P Recognition of virus‐infected cells by the immune 672 system Peter C. Doherty 1995 Edward B. Lewis M&P Genetic control of embryonic development 15 Christiane Nüsslein‐Volhard Eric Wieschaus 1994 Alfred Gilman M&P Structure and function of GTP‐binding (G) proteins 593 Martin Rodbell 1993 Kary Mullis Chemistry Polymerase chain reaction (PCR) 726 Michael Smith Site‐directed mutagenesis (SDM) 735 Richard J. Roberts M&P Intervening sequences 420 Phillip A. Sharp 1992 Edmond Fischer M&P Alteration of enzyme activity by phosphorylation/ 109, 600 dephosphorylation Edwin Krebs 1991 Erwin Neher M&P Measurement of ion flux by patch‐clamp recording 143 Bert Sakmann 1990 Joseph E. Murray M&P Organ and cell transplantation in human disease 684 E. Donnall Thomas 1989 J. Michael Bishop M&P Cellular genes capable of causing malignant 633 transformation Harold Varmus Thomas R. Cech Chemistry Ability of RNA to catalyze reactions 425, 450 Sidney Altman 1988 Johann Deisenhofer Chemistry Bacterial photosynthetic reaction center 207 Robert Huber Hartmut Michel 1987 Susumu Tonegawa M&P DNA rearrangements responsible for antibody diversity 681 1986 Rita Levi‐Montalcini M&P Factors that affect nerve outgrowth 379 Stanley Cohen 1985 Michael S. Brown M&P Regulation of cholesterol metabolism and endocytosis 319 Joseph L. Goldstein 1984 Georges Köhler M&P Monoclonal antibodies 738, 739 Cesar Milstein Niels K. Jerne Antibody formation 666 1983 Barbara McClintock M&P Mobile elements in the genome 391, 392, 394 1982 Aaron Klug Chemistry Structure of nucleic acid‐protein complexes 55 1980 Paul Berg Chemistry Recombinant DNA technology 692, 723 Walter Gilbert DNA sequencing technology 728 Frederick Sanger Baruj Bennacerraf M&P Major histocompatibility complex 684 Jean Dausset George D. Snell 1978 Werner Arber M&P Restriction endonuclease technology 723 Daniel Nathans Hamilton O. Smith Peter Mitchell Chemistry Chemiosmotic mechanism of oxidative phosphorylation 176 1976 D. Carleton Gajdusek M&P Prion‐based diseases 63 1975 David Baltimore M&P Reverse transcriptase and tumor virus activity 633 Year Recipient* Prize Area of Research Pages in Text Renato Dulbecco Howasrd M. Temin 1974 Albert Claude M&P Structure and function of internal components of cells 262 Christian de Duve George E. Palade 1972 Gerald Edelman M&P Immunoglobulin structure 678 Rodney R. Porter Christian B. Anfinsen Chemistry Relationship between primary and tertiary structure of 60 proteins 1971 Earl W. Sutherland M&P Mechanism of hormone action and cyclic AMP 590, 595, 596 1970 Bernard Katz M&P Nerve impulse propagation and transmission 160 Ulf von Euler Luis F. Leloir Chemistry Role of sugar nucleotides in carbohydrate synthesis 273 1969 Max Delbrück M&P Genetic structure of viruses 23, 380 Alfred D. Hershey Salvador E. Luria 1968 H. Gobind Khorana M&P Genetic code 722‐723 Marshall W. Nirenberg Robert W. Holley Transfer RNA structure 439 1966 Peyton Rous M&P Tumor viruses 632 1965 Francois Jacob M&P Bacterial operons wand messenger RNA 406, 456 Andre M. Lwoff Jacques L. Monod 1964 Dorothy C. Hodgkin Chemistry X‐ray structure of complex biological molecules 717 1963 John C. Eccles M&P Ionic basis of nerve membrane potentials 160 Alan L. Hodgkin Andrew F. Huxley 1962 Francis H. C. Crick M&P Three‐dimensional structure of DNA 374‐377 James D. Watson Maurice H. F. Wilkins John C. Kendrew Chemistry Three‐dimensional structure of globular proteins 56 Max F. Perutz 1961 Melvin Calvin Chemistry Biochemistry of CO2 assimilation during photosynthesis 213, 214‐215 1960 F. MacFarlane Burnet M&P Clonal selection theory of antibody formation 666 Peter B. Medawar 1959 Arthur Kornberg M&P Synthesis of DNA and RNA 518, 523 Severo Ochoa 1958 George W. Beadle M&P Gene expression 405‐406 Joshua Lederberg Edward L. Tatum Frederick Sanger Chemistry Primary structure of proteins 53 *In a few cases, corecipients whose research was in an area outside of cell and molecular biology have been omitted from this list. **Medicine and Physiology  Topics of Human Interest NOTE: An f after a page denotes a figure; t denotes a table; fn denotes a footnote; HP denotes a Human Perspective; EP denotes an Experimental Pathway. Acquired immune deficiency syndrome. See Graves’ disease and thyroiditis, 669HP, Calorie-restricted diet, life span and, 632, AIDS Chapter 17 Chapter 16, 111–112HP, Chapter 3 Acute lymphoblastic leukemia (ALL), 644, 651, inflammatory bowel diseases (IBDs), 669HP, Cancer, 627–660, Chapter 16 653, Chapter 16 Chapter 17 cancer genome, 649–651, Chapter 16 Acute myeloid leukemia (AML), 647–648, 651, multiple sclerosis (MS), 669HP, Chapter 17 causes of, 631–632, Chapter 16 652f, 653f, Chapter 16 rheumatoid arthritis, 669HP, Chapter 17 cells, properties of, 628–631, 629f, Chapter 16 Adaptive (acquired) immune response, 665, systemic lupus erythematosus (SLE), 669HP, aneuploidy, 630, 630f, Chapter 16 Chapter 17 669HPf, Chapter 17 cells of origin of malignant tumors, Adenoviruses, 21HP, 23, 24f, 158HP, 420–421, treatment of, 670–671HP, Chapter 17 636–637, 637f, Chapter 16 631, 641, 643, Chapter 1, Chapter 4, type 1 diabetes (T1D), 669HP, Chapter 17 effects of serum deprivation on growth of, Chapter 11, Chapter 16 629–630, 630f, Chapter 16 Adrenoleukodystrophy (ALD), 197HP, Bacterial toxins, 590, Chapter 15 growth rate, 629, 629f, Chapter 16 Chapter 5 Bacteriophage therapy, 25, Chapter 1 metastasis, 628, 628f, Chapter 16 African populations, genomes of, 385–386, Benign tumors, 638, 644, 650, Chapter 16 combating, strategies for, 654–660, Chapter 16 Chapter 10 Biofilms, 13, 157HP, 583, Chapter 1, Chapter 4, angiogenesis, 659–660, Chapter 16 Agammaglobulinemia, 665, Chapter 17 Chapter 15 cancer stem cells, 658–659, Chapter 16 Aging Blistering diseases, 237, 245, 338, 671, chemotherapy, 628, 637, 644, 648, 653, 654, Down syndrome (trisomy 21) and, 479HP, Chapter 7, Chapter 9, Chapter 17 655, 659, Chapter 16 Chapter 14 Blood-brain barrier, 247, Chapter 7 immunotherapy, 654–656, Chapter 16 mitochondrial disorders and, 195HP, Chapter 5 Blood cell differentiation, 666f, Chapter 17 inhibiting activity of cancer-promoting premature (progeria), 461, 536HP, Chapter 12, Blood clots, 46, 49, 229, 231, 233, 233f, 281, 302, proteins, 656–658, Chapter 16 Chapter 13 392, 586, Chapter 2, Chapter 7, Chapter 8, targeted therapies, 654, Chapter 16 radicals and, 34–35HP, Chapter 2 Chapter 10, Chapter 15 diet and, 632, Chapter 16 telomeres and, 477, Chapter 12 Blood glucose, 599–602, 599f, Chapter 15 gene-expression analysis, 651–654, 652f, 653f, AIDS (acquired immune deficiency syndrome) Blood-group antigens, 122–123, 123f, 398, 684, 654f, Chapter 16 helper T cells and, 678, Chapter 17 Chapter 4, Chapter 10, Chapter 17 as genetic disorder, 636–638, Chapter 16 resistance, 595–596HP, 678, 684, 685, Bone marrow, 18HP, 197HP, 231f, 235, 242HP, microRNAs, 649, Chapter 16 Chapter 15, Chapter 17 288HP, 402HP, 475, 476, 481, 662, 662f, 665, multiple myeloma, 679, 680f, 681, 738–739, resistance to drugs, 74, 101–102HP, Chapter 2, 666f, 669HP, 686, Chapter 1, Chapter 5, 739f, Chapter 17 Chapter 3 Chapter 7, Chapter 8, Chapter 10, mutator phenotype, 649, Chapter 16 therapies for, 433HP, Chapter 11 Chapter 12, Chapter 17 new cases and deaths in US in 2015, 628, 629f, ALD (adrenoleukodystrophy), 197HP, Bone marrow transplantation, 18HP, 197HP, Chapter 16 Chapter 5 242HP, Chapter 1, Chapter 5, Chapter 7 oncogenes, 646–648, Chapter 16 ALL (Acute lymphoblastic leukemia), 644, 651, Booster shots, 671, Chapter 17 activation of proto-oncogene to, 638, 639, 653, Chapter 16 Breast cancer 639f, Chapter 16 Alzheimer’s disease (AD), 64–67HP, 66HPf, 165, BRCA1 and, 512, 645, Chapter 13, discovery of, 633–636EP, Chapter 16 Chapter 2, Chapter 4 Chapter 16 overview of, 638–639, 638f, Chapter 16 AML (Acute myeloid leukemia), 647–648, 651, cause of, 631, Chapter 16 research efforts, 628, Chapter 16 652f, 653f, Chapter 16 gene-expression analysis, 652–653, 654f, therapy, PLK1 as target for, 433HP, 433HPf, Anesthetics, 161, Chapter 4 Chapter 16 Chapter 11 Aneuploidy, 566, 577–578HP, 630, 630f, 643, genetic mutations in, 640, 642f, 644, tumor-suppressor genes, 638–646, 638f, 640t, 645, Chapter 14, Chapter 16 Chapter 16 Chapter 16 Antacid medications, 154, Chapter 4 genetics and, 636, Chapter 16 APC genes, 645, Chapter 16 Antibiotics, 100–102HP immunotherapy for, 655, Chapter 16 BRCA1/BRCA2 genes, 512, 645, Chapter 13, modes of, in clinical use, 101HPt, Chapter 3 karyotype of cell from, 630f, Chapter 16 Chapter 16 penicillin, 99, 100HP, 101HPt, 102HP, new cases and deaths in US in 2015, 629f, overview of, 638–639, Chapter 16 Chapter 3 Chapter 16 PTEN gene, 646, Chapter 16 Antidepressants, 165, Chapter 4 PI3K pathway in, 651, Chapter 16 RB gene, 640–641, 641f, Chapter 16 Anti-inflammatory drugs, and cancer, 632, Preventive mastectomy, 512, Chapter 13 TP53 gene, 642–645, 642f, Chapter 16 Chapter 16 protein-inhibiting drugs for, 657, Chapter 16 Carcinogens, 631, 632f, 643, Chapter 16 Antioxidants, 35HP, Chapter 2