Molecular Biology of the Cell, 5th Edition

Molecular Biology ofTHE CELL Fifth Edition Molecular Biology of THE CELL Fifth Edition Bruce Alberts Alexander Johnson Julian Lewis Martin Raff Keith Roberts Peter Walter With problems by John Wilson Tim Hunt Garland Science Vice President: Denise Schanck Assistant Editor: Sigrid Masson Production Editor and Layout: Emma Jeffcock Senior Publisher: Jackie Harbor Illustrator: Nigel Orme Designer: Matthew McClements, Blink Studio, Ltd. Editors: Marjorie Anderson and Sherry Granum Copy Editor: Bruce Goatly Indexer: Merrall-Ross International, Ltd. Permissions Coordinator: Mary Dispenza Cell Biology Interactive Artistic and Scientific Direction: Peter Walter Narrated by: Julie Theriot Production Design and Development: Michael Morales © 2008, 2002 by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter. © 1983, 1989, 1994 by Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts, and James D. Watson. Bruce Alberts received his Ph.D. from Harvard University and is Professor of Biochemistry and Biophysics at the University of California, San Francisco. For 12 years, he served as President of the U.S. National Academy of Sciences (1993–2005). 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. 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 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. 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 book covered by the copyright heron may be reproduced or used in any format in any form or by any means—graphic, electronic, or mechanical, including photocopying, recording, taping, or information storage and retrieval systems—without permission of the publisher. Library of Congress Cataloging-in-Publication Data Molecular biology of the cell / Bruce Alberts … [et al.].-- 5th ed. p. cm ISBN 978-0-8153-4105-5 (hardcover)---ISBN 978-0-8153-4106-2 (paperback) 1. Cytology. 2. Molecular biology. I. Alberts, Bruce. QH581.2 .M64 2008 571.6--dc22 2007005475 CIP 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. Printed in the United States of America 15 14 13 12 11 10 9 8 7 6 5 4 3 2 The goal is to learn how to put the facts to use—to reason. To help readers on the way to an active understanding. With each edition of this book. A companion volume. and to control the behavior of living systems.v Preface In many respects. we hailed the identification of a single protein—a signal receptor. This provides hundreds of movies and animations. we have included new material on many topics. We know the complete genome sequences of these and many other species. Fifth Edition: The Problems Book (ISBN 978-0-8153-4110-9). cell biologists face even greater challenges for the future. we have for the first time incorporated end-of-chapter problems. working together as a system. and recording the results of their experiments in the genetic instructions they pass on to their progeny. Stars may be 1043 times bigger. gives complete answers to these problems and also contains more than 1700 additional problems and solutions. although there are great achievements to report. the more we realize how much remains to be understood. cell-cycle control. with all their interlocking control loops. but we still cannot predict how a cell will behave if we mutate a previously unstudied gene. written by John Wilson and Tim Hunt. for about 20% of the age of the universe—living cells have been progressively refining and extending their molecular machinery. As in previous editions. cytoskeletal dynamics. In the days of our innocence. This means going beyond the recitation of facts. the disc also now includes all the figures and tables from the main . by the same authors. apoptosis. ranging from epigenetics. histone modifications. Molecular Biology of the Cell. including many that are new in this edition. showing cells and cellular processes in action and bringing the text to life. and held in specific positions by binding to scaffold proteins that give the chemical factory a definite spatial structure. we marvel at the new information that cell biologists have gathered in just a few years. and more astonishing products of the laws of physics and chemistry. Scientists can calculate the age of the Sun and predict when it will cease to shine. we have tried above all to give readers a conceptual framework for the mass of information that we now have about cells. Through heredity and natural selection. stem cells. operating from the beginnings of life on Earth to the present day—that is. Genome sequencing has given us virtually complete molecular parts-lists for many different organisms. but cells are more complex. we understand the structure of the universe better than the workings of living cells. to predict. and novel cancer therapies. but we have only the most primitive grasp of the dynamics of these biochemical systems. But we are even more amazed and daunted at the sophistication of the mechanisms that we encounter. small RNAs. say—as a great step forward. In this edition. more intricately structured. These emphasize a quantitative approach and the art of reasoning from experiments. but we cannot explain how it is that a human being may live for eighty years but a mouse for only two. and comparative genomics. working on the first edition. A further major adjunct to the main book is the attached Media DVD-ROM disc. The deeper we probe into the cell. Now we appreciate that each protein is generally part of a complex with many others. regulating one another’s activities in subtle ways. Therefore. genetics and biochemistry have told us a great deal about what those parts are capable of individually and which ones interact with which others. to genetic noise. Jackie Harbor and Sigrid Masson kept us organized. In an effort to make the standard Student Edition somewhat more portable. . Adam Sendroff kept us aware of our readers and their needs and reactions. we could not have produced any of the editions of this book. available to qualified instructors. covering multicellular systems. Other ancillaries available for the book include a bank of test questions and lecture outlines. containing the full set of chapters as printed pages. and with no less gratitude. We also owe a huge debt to the staff of Garland Science and others who helped convert writers’ efforts into a polished final product. and other materials into a user-friendly DVD-ROM. we thank our spouses. friends and colleagues. As always. including the back cover. and Nicholas Harberd for the plant section of Chapter 15. Eleanor Lawrence and Sherry Granum updated and enlarged the glossary. is also available for those who prefer it. as did Maynard Olson for the genomics section of Chapter 4. skill. and Sherry Granum combed the text for obscurities. Wallace Marshall and Laura Attardi provided substantial help with Chapters 8 and 20. Marjorie Anderson. Xiaodong Wang for Chapter 18. and David Morgan likewise for Chapter 17 (Cell Cycle). while retaining in the printed volume Chapters 1–20. and errors. and a set of 200 full-color overhead transparencies. But we should emphasize that the final chapters have been revised and updated as thoroughly as the rest of the book and we sincerely hope that they will be read! A Reference Edition (ISBN 978-0-8153-4111-6). Full details of the conventions adopted in the book are given in the Note to the Reader that follows this Preface. not only for their professional skill and dedication and for efficiency far surpassing our own. pre-loaded into PowerPoint® presentations.vi Preface book. we use the same style. Without their patient. and Innate Immunity). As explained there. Emma Jeffcock laid out its pages with extraordinary speed and unflappable efficiency. Perhaps the biggest change is in the physical structure of the book. respectively. Matthew McClements designed the book and its front cover. we are indebted to many people. and often in defiance of the usual species-specific conventions. We thank them all. dealing impeccably with innumerable corrections. Michael Morales managed the transformation of a mass of animations. covering the core of the usual cell biology curriculum. in electronic (PDF) form on the accompanying disc. Nigel Orme put the artwork into its final form and supervised the visual aspects of the book. infelicities. video clips. but we must here single out some exceptionally important contributions: Julie Theriot is almost entirely responsible for Chapters 16 (Cytoskeleton) and 24 (Pathogens. but also for their unfailing helpfulness and friendship: they have made it a pleasure to work on the book. families. Bruce Goatly. Full acknowledgments for scientific help are given separately. Denise Schanck directed the whole enterprise and shepherded the wayward authors along the road with wisdom. with his usual flair. regardless of species. we have taken a drastic approach in confronting the different rules for the writing of gene names in different species: throughout this book. Lastly. enduring support. we are providing Chapters 21–25. and kindness. Infection. and Fertilization Development of Multicellular Organisms Specialized Tissues. and RNA Visualizing Cells PART IV 10. Infection. 16. 22. Glossary Index Tables CELLS IN THEIR SOCIAL CONTEXT Cell Junctions. 11. 25. Repair. 9. BASIC GENETIC MECHANISMS DNA. and Recombination How Cells Read the Genome: From DNA to Protein Control of Gene Expression PART III 8. 13. and the Extracellular Matrix Cancer Chapters 21–25 available on Media DVD-ROM Sexual Reproduction: Meiosis. Amino Acids . 17. 24. 18. 15. 2. 14. 5. 7. Cell Adhesion. 6. and Innate Immunity The Adaptive Immune System The Genetic Code. and Genomes DNA Replication. INTERNAL ORGANIZATION OF THE CELL Membrane Structure Membrane Transport of Small Molecules and the Electrical Properties of Membranes Intracellular Compartments and Protein Sorting Intracellular Vesicular Traffic Energy Conversion: Mitochondria and Chloroplasts Mechanisms of Cell Communication The Cytoskeleton The Cell Cycle Apoptosis PART V 19. Chromosomes.vii Contents Special Features Detailed Contents Acknowledgments A Note to the Reader viii ix xxvi xxxi PART I 1. 23. DNA. and Tissue Renewal Pathogens. 21. 20. 3. Germ Cells. Stem Cells. METHODS Manipulating Proteins. 12. INTRODUCTION TO THE CELL Cells and Genomes Cell Chemistry and Biosynthesis Proteins 1 45 125 195 263 329 411 501 579 617 651 695 749 813 879 965 1053 1115 1131 1205 1269 1305 1417 1485 1539 G–1 I–1 T–1 PART II 4. viii Special Features Table 1–1 Table 1–2 Table 2–1 Table 2–2 Table 2–3 Table 2–4 Panel 2–1 Panel 2–2 Panel 2–3 Panel 2–4 Panel 2–5 Panel 2–6 Panel 2–7 Panel 2–8 Panel 2–9 Panel 3–1 Panel 3–2 Table 3–1 Panel 3–3 Table 4–1 Table 5–3 Table 6–1 Panel 8–1 Table 10–1 Table 11–1 Panel 11–2 Panel 11–3 Table 12–1 Table 12–2 Table 14–1 Panel 14–1 Table 15–5 Panel 16–2 Panel 16–3 Table 17–2 Panel 17–1 Some Genomes That Have Been Completely Sequenced p. 18 The Numbers of Gene Families, Classified by Function, That Are Common to All Three Domains of the Living World p. 24 Covalent and Noncovalent Chemical Bonds p. 53 The Types of Molecules That Form a Bacterial Cell p. 55 Approximate Chemical Compositions of a Typical Bacterium and a Typical Mammalian Cell p. 63 Relationship Between the Standard Free-Energy Change, DG°, and the Equilibrium Constant p. 77 Chemical Bonds and Groups Commonly Encountered in Biological Molecules pp. 106–107 Water and Its Influence on the Behavior of Biological Molecules pp. 108–109 The Principal Types of Weak Noncovalent Bonds that Hold Macromolecules Together pp. 110–111 An Outline of Some of the Types of Sugars Commonly Found in Cells pp. 112–113 Fatty Acids and Other Lipids pp. 114–115 A Survey of the Nucleotides pp. 116–117 Free Energy and Biological Reactions pp. 118–119 Details of the 10 Steps of Glycolysis pp. 120–121 The Complete Citric Acid Cycle pp. 122–123 The 20 Amino Acids Found in Proteins pp. 128–129 Four Different Ways of Depicting a Small Protein, the SH2 Domain pp. 132–133 Some Common Types of Enzymes p. 159 Some of the Methods Used to Study Enzymes pp. 162–163 Some Vital Statistics for the Human Genome p. 206 Three Major Classes of Transposable Elements p. 318 Principal Types of RNAs Produced in Cells p. 336 Review of Classical Genetics pp. 554–555 Approximate Lipid Compositions of Different Cell Membranes p. 624 A Comparison of Ion Concentrations Inside and Outside a Typical Mammalian Cell p. 652 The Derivation of the Nernst Equation p. 670 Some Classical Experiments on the Squid Giant Axon p. 679 Relative Volumes Occupied by the Major Intracellular Compartments in a Liver Cell (Hepatocyte) p. 697 Relative Amounts of Membrane Types in Two Kinds of Eucaryotic Cells p. 697 Product Yields from the Oxidation of Sugars and Fats p. 824 Redox Potentials p. 830 The Ras Superfamily of Monomeric GTPases p. 926 The Polymerization of Actin and Tubulin pp. 978–979 Accessory Proteins that Control the Assembly and Position of Cytoskeletal Filaments pp. 994–995 Summary of the Major Cell-Cycle Regulatory Proteins p. 1066 The Principle Stages of M Phase (Mitosis and Cytokinesis) in an Animal Cell pp. 1072–1073 ix Detailed Contents Chapter 1 Cells and Genomes THE UNIVERSAL FEATURES OF CELLS ON EARTH All Cells Store Their Hereditary Information in the Same Linear Chemical Code (DNA) All Cells Replicate Their Hereditary Information by Templated Polymerization All Cells Transcribe Portions of Their Hereditary Information into the Same Intermediary Form (RNA) All Cells Use Proteins as Catalysts All Cells Translate RNA into Protein in the Same Way The Fragment of Genetic Information Corresponding to One Protein Is One Gene Life Requires Free Energy All Cells Function as Biochemical Factories Dealing with the Same Basic Molecular Building Blocks All Cells Are Enclosed in a Plasma Membrane Across Which Nutrients and Waste Materials Must Pass A Living Cell Can Exist with Fewer Than 500 Genes Summary 1 1 2 3 4 5 6 7 8 8 9 10 11 The World of Animal Cells Is Represented By a Worm, a Fly, a Mouse, and a Human Studies in Drosophila Provide a Key to Vertebrate Development The Vertebrate Genome Is a Product of Repeated Duplication Genetic Redundancy Is a Problem for Geneticists, But It Creates Opportunities for Evolving Organisms The Mouse Serves as a Model for Mammals Humans Report on Their Own Peculiarities We Are All Different in Detail Summary Problems References 36 37 38 39 39 40 41 42 42 44 Chapter 2 Cell Chemistry and Biosynthesis THE CHEMICAL COMPONENTS OF A CELL Cells Are Made From a Few Types of Atoms The Outermost Electrons Determine How Atoms Interact Covalent Bonds Form by the Sharing of Electrons There Are Different Types of Covalent Bonds An Atom Often Behaves as if It Has a Fixed Radius Water Is the Most Abundant Substance in Cells Some Polar Molecules Are Acids and Bases Four Types of Noncovalent Attractions Help Bring Molecules Together in Cells A Cell Is Formed from Carbon Compounds Cells Contain Four Major Families of Small Organic Molecules Sugars Provide an Energy Source for Cells and Are the Subunits of Polysaccharides Fatty Acids Are Components of Cell Membranes, as Well as a Source of Energy Amino Acids Are the Subunits of Proteins Nucleotides Are the Subunits of DNA and RNA The Chemistry of Cells Is Dominated by Macromolecules with Remarkable Properties Noncovalent Bonds Specify Both the Precise Shape of a Macromolecule and its Binding to Other Molecules Summary 45 45 45 46 48 50 51 51 52 53 54 55 55 58 59 61 62 63 65 THE DIVERSITY OF GENOMES AND THE TREE OF LIFE Cells Can Be Powered by a Variety of Free Energy Sources Some Cells Fix Nitrogen and Carbon Dioxide for Others The Greatest Biochemical Diversity Exists Among Procaryotic Cells The Tree of Life Has Three Primary Branches: Bacteria, Archaea, and Eucaryotes Some Genes Evolve Rapidly; Others Are Highly Conserved Most Bacteria and Archaea Have 1000–6000 Genes New Genes Are Generated from Preexisting Genes Gene Duplications Give Rise to Families of Related Genes Within a Single Cell Genes Can Be Transferred Between Organisms, Both in the Laboratory and in Nature Sex Results in Horizontal Exchanges of Genetic Information Within a Species The Function of a Gene Can Often Be Deduced from Its Sequence More Than 200 Gene Families Are Common to All Three Primary Branches of the Tree of Life Mutations Reveal the Functions of Genes Molecular Biologists Have Focused a Spotlight on E. coli Summary 11 12 13 14 15 16 17 18 19 21 22 22 23 23 24 26 CATALYSIS AND THE USE OF ENERGY BY CELLS Cell Metabolism Is Organized by Enzymes 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 Enzymes Lower the Barriers That Block Chemical Reactions How Enzymes Find Their Substrates: The Enormous Rapidity of Molecular Motions The Free-Energy Change for a Reaction Determines Whether It Can Occur The Concentration of Reactants Influences the Free-Energy Change and a Reaction’s Direction For Sequential Reactions, DG° Values Are Additive Activated Carrier Molecules Are Essential for Biosynthesis The Formation of an Activated Carrier Is Coupled to an Energetically Favorable Reaction 65 66 66 68 70 71 72 74 75 76 77 78 79 GENETIC INFORMATION IN EUCARYOTES Eucaryotic Cells May Have Originated as Predators Modern Eucaryotic Cells Evolved from a Symbiosis Eucaryotes Have Hybrid Genomes Eucaryotic Genomes Are Big Eucaryotic Genomes Are Rich in Regulatory DNA The Genome Defines the Program of Multicellular Development Many Eucaryotes Live as Solitary Cells: the Protists A Yeast Serves as a Minimal Model Eucaryote The Expression Levels of All The Genes of An Organism Can Be Monitored Simultaneously To Make Sense of Cells, We Need Mathematics, Computers, and Quantitative Information Arabidopsis Has Been Chosen Out of 300,000 Species As a Model Plant 26 26 27 30 30 31 31 32 33 34 35 36 x Detailed Contents 80 81 82 83 84 87 Molecular Tunnels Channel Substrates in Enzymes with Multiple Catalytic Sites Multienzyme Complexes Help to Increase the Rate of Cell Metabolism The Cell Regulates the Catalytic Activities of its Enzymes Allosteric Enzymes Have Two or More Binding Sites That Interact Two Ligands Whose Binding Sites Are Coupled Must Reciprocally Affect Each Other’s Binding Symmetric Protein Assemblies Produce Cooperative Allosteric Transitions The Allosteric Transition in Aspartate Transcarbamoylase Is Understood in Atomic Detail Many Changes in Proteins Are Driven by Protein Phosphorylation A Eucaryotic Cell Contains a Large Collection of Protein Kinases and Protein Phosphatases The Regulation of Cdk and Src Protein Kinases Shows How a Protein Can Function as a Microchip Proteins That Bind and Hydrolyze GTP Are Ubiquitous Cellular Regulators Regulatory Proteins Control the Activity of GTP-Binding Proteins by Determining Whether GTP or GDP Is Bound Large Protein Movements Can Be Generated From Small Ones Motor Proteins Produce Large Movements in Cells Membrane-Bound Transporters Harness Energy to Pump Molecules Through Membranes Proteins Often Form Large Complexes That Function as Protein Machines Protein Machines with Interchangeable Parts Make Efficient Use of Genetic Information The Activation of Protein Machines Often Involves Positioning Them at Specific Sites Many Proteins Are Controlled by Multisite Covalent Modification A Complex Network of Protein Interactions Underlies Cell Function Summary Problems References ATP Is the Most Widely Used Activated Carrier Molecule Energy Stored in ATP Is Often Harnessed to Join Two Molecules Together NADH and NADPH Are Important Electron Carriers There Are Many Other Activated Carrier Molecules in Cells The Synthesis of Biological Polymers Is Driven by ATP Hydrolysis Summary 167 168 169 171 171 172 173 175 176 177 178 179 179 181 182 184 184 185 186 187 190 191 193 HOW CELLS OBTAIN ENERGY FROM FOOD Glycolysis Is a Central ATP-Producing Pathway Fermentations Produce ATP in the Absence of Oxygen Glycolysis Illustrates How Enzymes Couple Oxidation to Energy Storage Organisms Store Food Molecules in Special Reservoirs Most Animal Cells Derive Their Energy from Fatty Acids Between Meals Sugars and Fats Are Both Degraded to Acetyl CoA in Mitochondria The Citric Acid Cycle Generates NADH by Oxidizing Acetyl Groups to CO2 Electron Transport Drives the Synthesis of the Majority of the ATP in Most Cells Amino Acids and Nucleotides Are Part of the Nitrogen Cycle Metabolism Is Organized and Regulated Summary Problems References 88 88 89 91 91 95 96 97 100 100 101 103 103 124 Chapter 3 Proteins 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 The a Helix and the b Sheet Are Common Folding Patterns Protein Domains Are Modular Units from which Larger Proteins Are Built Few of the Many Possible Polypeptide Chains Will Be Useful to Cells Proteins Can Be Classified into Many Families Sequence Searches Can Identify Close Relatives Some Protein Domains Form Parts of Many Different Proteins Certain Pairs of Domains Are Found Together in Many Proteins The Human Genome Encodes a Complex Set of Proteins, Revealing Much That Remains Unknown Larger Protein Molecules Often Contain More Than One Polypeptide Chain Some Proteins Form Long Helical Filaments Many Protein Molecules Have Elongated, Fibrous Shapes Many Proteins Contain a Surprisingly Large Amount of Unstructured Polypeptide Chain Covalent Cross-Linkages Often Stabilize Extracellular Proteins Protein Molecules Often Serve as Subunits for the Assembly of Large Structures Many Structures in Cells Are Capable of Self-Assembly Assembly Factors Often Aid the Formation of Complex Biological Structures Summary 125 125 125 130 131 135 136 137 139 140 141 142 142 143 145 146 147 148 149 151 152 Chapter 4 DNA, Chromosomes, and Genomes THE STRUCTURE AND FUNCTION OF DNA A DNA Molecule Consists of Two Complementary Chains of Nucleotides The Structure of DNA Provides a Mechanism for Heredity In Eucaryotes, DNA Is Enclosed in a Cell Nucleus Summary 195 197 197 199 200 201 CHROMOSOMAL DNA AND ITS PACKAGING IN THE CHROMATIN FIBER Eucaryotic DNA Is Packaged into a Set of Chromosomes Chromosomes Contain Long Strings of Genes The Nucleotide Sequence of the Human Genome Shows How Our Genes Are Arranged Genome Comparisons Reveal Evolutionarily Conserved DNA Sequences Chromosomes Exist in Different States Throughout the Life of a Cell Each DNA Molecule That Forms a Linear Chromosome Must Contain a Centromere, Two Telomeres, and Replication Origins DNA Molecules Are Highly Condensed in Chromosomes Nucleosomes Are a Basic Unit of Eucaryotic Chromosome Structure The Structure of the Nucleosome Core Particle Reveals How DNA Is Packaged Nucleosomes Have a Dynamic Structure, and Are Frequently Subjected to Changes Catalyzed by ATP-Dependent ChromatinRemodeling Complexes Nucleosomes Are Usually Packed Together into a Compact Chromatin Fiber Summary 202 202 204 205 207 208 209 210 211 212 PROTEIN FUNCTION All Proteins Bind to Other Molecules The Surface Conformation of a Protein Determines Its Chemistry Sequence Comparisons Between Protein Family Members Highlight Crucial Ligand-Binding Sites Proteins Bind to Other Proteins Through Several Types of Interfaces Antibody Binding Sites Are Especially Versatile The Equilibrium Constant Measures Binding Strength Enzymes Are Powerful and Highly Specific Catalysts Substrate Binding Is the First Step in Enzyme Catalysis Enzymes Speed Reactions by Selectively Stabilizing Transition States Enzymes Can Use Simultaneous Acid and Base Catalysis Lysozyme Illustrates How an Enzyme Works Tightly Bound Small Molecules Add Extra Functions to Proteins 152 153 154 155 156 156 157 158 159 160 160 161 166 215 216 218 THE REGULATION OF CHROMATIN STRUCTURE Some Early Mysteries Concerning Chromatin Structure 219 220 Detailed Contents Heterochromatin Is Highly Organized and Unusually Resistant to Gene Expression 220 The Core Histones Are Covalently Modified at Many Different Sites 222 Chromatin Acquires Additional Variety through the Site-Specific Insertion of a Small Set of Histone Variants 224 The Covalent Modifications and the Histone Variants Act in Concert to Produce a “Histone Code” That Helps to Determine Biological Function 224 A Complex of Code-Reader and Code-Writer Proteins Can Spread Specific Chromatin Modifications for Long Distances Along a Chromosome 226 Barrier DNA Sequences Block the Spread of Reader–Writer Complexes and Thereby Separate Neighboring Chromatin Domains 227 The Chromatin in Centromeres Reveals How Histone Variants Can Create Special Structures 228 Chromatin Structures Can Be Directly Inherited 230 Chromatin Structures Add Unique Features to Eucaryotic Chromosome Function 231 Summary 233 xi DNA REPLICATION MECHANISMS Base-Pairing Underlies DNA Replication and DNA Repair The DNA Replication Fork Is Asymmetrical The High Fidelity of DNA Replication Requires Several Proofreading Mechanisms Only DNA Replication in the 5’-to-3’ Direction Allows Efficient Error Correction A Special Nucleotide-Polymerizing Enzyme Synthesizes Short RNA Primer Molecules on the Lagging Strand Special Proteins Help to Open Up the DNA Double Helix in Front of the Replication Fork A Sliding Ring Holds a Moving DNA Polymerase onto the DNA The Proteins at a Replication Fork Cooperate to Form a Replication Machine A Strand-Directed Mismatch Repair System Removes Replication Errors That Escape from the Replication Machine DNA Topoisomerases Prevent DNA Tangling During Replication DNA Replication Is Fundamentally Similar in Eucaryotes and Bacteria Summary 266 266 266 268 271 272 273 273 275 276 278 280 281 THE GLOBAL STRUCTURE OF CHROMOSOMES Chromosomes Are Folded into Large Loops of Chromatin Polytene Chromosomes Are Uniquely Useful for Visualizing Chromatin Structures There Are Multiple Forms of Heterochromatin Chromatin Loops Decondense When the Genes Within Them Are Expressed Chromatin Can Move to Specific Sites Within the Nucleus to Alter Their Gene Expression Networks of Macromolecules Form a Set of Distinct Biochemical Environments inside the Nucleus Mitotic Chromosomes Are Formed from Chromatin in Its Most Condensed State Summary 233 234 236 238 239 239 241 243 245 THE INITIATION AND COMPLETION OF DNA REPLICATION IN CHROMOSOMES DNA Synthesis Begins at Replication Origins Bacterial Chromosomes Typically Have a Single Origin of DNA Replication Eucaryotic Chromosomes Contain Multiple Origins of Replication In Eucaryotes DNA Replication Takes Place During Only One Part of the Cell Cycle Different Regions on the Same Chromosome Replicate at Distinct Times in S Phase Highly Condensed Chromatin Replicates Late, While Genes in Less Condensed Chromatin Tend to Replicate Early Well-Defined DNA Sequences Serve as Replication Origins in a Simple Eucaryote, the Budding Yeast A Large Multisubunit Complex Binds to Eucaryotic Origins of Replication The Mammalian DNA Sequences That Specify the Initiation of Replication Have Been Difficult to Identify New Nucleosomes Are Assembled Behind the Replication Fork The Mechanisms of Eucaryotic Chromosome Duplication Ensure That Patterns of Histone Modification Can Be Inherited Telomerase Replicates the Ends of Chromosomes Telomere Length Is Regulated by Cells and Organisms Summary 281 281 282 282 284 285 285 286 287 288 289 290 292 293 294 HOW GENOMES EVOLVE Genome Alterations Are Caused by Failures of the Normal Mechanisms for Copying and Maintaining DNA The Genome Sequences of Two Species Differ in Proportion to the Length of Time That They Have Separately Evolved Phylogenetic Trees Constructed from a Comparison of DNA Sequences Trace the Relationships of All Organisms A Comparison of Human and Mouse Chromosomes Shows How the Structures of Genomes Diverge The Size of a Vertebrate Genome Reflects the Relative Rates of DNA Addition and DNA Loss in a Lineage We Can Reconstruct the Sequence of Some Ancient Genomes Multispecies Sequence Comparisons Identify Important DNA Sequences of Unknown Function Accelerated Changes in Previously Conserved Sequences Can Help Decipher Critical Steps in Human Evolution Gene Duplication Provides an Important Source of Genetic Novelty During Evolution Duplicated Genes Diverge The Evolution of the Globin Gene Family Shows How DNA Duplications Contribute to the Evolution of Organisms Genes Encoding New Proteins Can Be Created by the Recombination of Exons Neutral Mutations Often Spread to Become Fixed in a Population, with a Probability that Depends on Population Size A Great Deal Can Be Learned from Analyses of the Variation Among Humans Summary Problems References 245 246 247 248 249 251 251 252 253 253 254 256 257 257 258 260 260 262 DNA REPAIR Without DNA Repair, Spontaneous DNA Damage Would Rapidly Change DNA Sequences The DNA Double Helix Is Readily Repaired DNA Damage Can Be Removed by More Than One Pathway Coupling DNA Repair to Transcription Ensures That the Cell’s Most Important DNA Is Efficiently Repaired The Chemistry of the DNA Bases Facilitates Damage Detection Special DNA Polymerases Are Used in Emergencies to Repair DNA Double-Strand Breaks Are Efficiently Repaired DNA Damage Delays Progression of the Cell Cycle Summary 295 296 296 297 299 300 302 302 303 304 HOMOLOGOUS RECOMBINATION Homologous Recombination Has Many Uses in the Cell Homologous Recombination Has Common Features in All Cells DNA Base-Pairing Guides Homologous Recombination The RecA Protein and its Homologs Enable a DNA Single Strand to Pair with a Homologous Region of DNA Double Helix Branch Migration Can Either Enlarge Hetroduplex Regions or Release Newly Synthesized DNA as a Single Strand Homologous Recombination Can Flawlessly Repair DoubleStranded Breaks in DNA Cells Carefully Regulate the Use of Homologous Recombination in DNA Repair Holliday Junctions Are Often Formed During Homologous Recombination Events 304 304 305 305 307 308 308 310 311 Chapter 5 DNA Replication, Repair, and Recombination THE MAINTENANCE OF DNA SEQUENCES Mutation Rates Are Extremely Low Low Mutation Rates Are Necessary for Life as We Know It Summary 263 263 263 265 265 but Lack a Protein Coat 320 A Large Fraction of the Human Genome Is Composed of Nonretroviral Retrotransposons 321 Different Transposable Elements Predominate in Different Organisms 322 Genome Sequences Reveal the Approximate Times that Transposable Elements Have Moved 323 Conservative Site-Specific Recombination Can Reversibly Rearrange DNA 323 Conservative Site-Specific Recombination Was Discovered in Bacteriophage l 324 Conservative Site-Specific Recombination Can Be Used to Turn Genes On or Off 324 Summary 326 Problems 327 References 328 Chapter 6 How Cells Read the Genome: From DNA to Protein FROM DNA TO RNA 329 331 332 333 335 336 338 339 340 342 343 345 346 347 349 349 351 352 353 355 355 357 358 360 362 363 366 Portions of DNA Sequence Are Transcribed into RNA Transcription Produces RNA Complementary to One Strand of DNA Cells Produce Several Types of RNA Signals Encoded in DNA Tell RNA Polymerase Where to Start and Stop Transcription Start and Stop Signals Are Heterogeneous in Nucleotide Sequence Transcription Initiation in Eucaryotes Requires Many Proteins RNA Polymerase II Requires General Transcription Factors Polymerase II Also Requires Activator. Mediator. Mobile Genetic Elements Can Insert Into Any DNA Sequence 317 DNA-Only Transposons Move by Both Cut-and-Paste and Replicative Mechanisms 317 Some Viruses Use a Transposition Mechanism to Move Themselves into Host Cell Chromosomes 319 Retroviral-like Retrotransposons Resemble Retroviruses.xii Detailed Contents FROM RNA TO PROTEIN 312 314 315 316 An mRNA Sequence Is Decoded in Sets of Three Nucleotide tRNA Molecules Match Amino Acids to Codons in mRNA tRNAs Are Covalently Modified Before They Exit from the Nucleus Specific Enzymes Couple Each Amino Acid to Its Appropriate tRNA Molecule Editing by RNA Synthetases Ensures Accuracy Amino Acids Are Added to the C-terminal End of a Growing Polypeptide Chain The RNA Message Is Decoded in Ribosomes Elongation Factors Drive Translation Forward and Improve Its Accuracy The Ribosome Is a Ribozyme Nucleotide Sequences in mRNA Signal Where to Start Protein Synthesis Stop Codons Mark the End of Translation Proteins Are Made on Polyribosomes There Are Minor Variations in the Standard Genetic Code Inhibitors of Procaryotic Protein Synthesis Are Useful as Antibiotics Accuracy in Translation Requires the Expenditure of Free Energy Quality Control Mechanisms Act to Prevent Translation of Damaged mRNAs Some Proteins Begin to Fold While Still Being Synthesized Molecular Chaperones Help Guide the Folding of Most Proteins Exposed Hydrophobic Regions Provide Critical Signals for Protein Quality Control The Proteasome Is a Compartmentalized Protease with Sequestered Active Sites An Elaborate Ubiquitin-Conjugating System Marks Proteins for Destruction Many Proteins Are Controlled by Regulated Destruction Abnormally Folded Proteins Can Aggregate to Cause Destructive Human Diseases There Are Many Steps From DNA to Protein Summary Meiotic Recombination Begins with a Programmed DoubleStrand Break Homologous Recombination Often Results in Gene Conversion Mismatch Proofreading Prevents Promiscuous Recombination Between Two Poorly Matched DNA Sequences Summary 366 367 368 369 370 371 373 373 377 378 379 381 381 382 383 385 385 387 388 390 391 393 395 396 399 399 TRANSPOSITION AND CONSERVATIVE SITE-SPECIFIC RECOMBINATION 316 Through Transposition. and ChromatinModifying Proteins Transcription Elongation Produces Superhelical Tension in DNA Transcription Elongation in Eucaryotes Is Tightly Coupled to RNA Processing RNA Capping Is the First Modification of Eucaryotic Pre-mRNAs RNA Splicing Removes Intron Sequences from Newly Transcribed Pre-mRNAs Nucleotide Sequences Signal Where Splicing Occurs RNA Splicing Is Performed by the Spliceosome The Spliceosome Uses ATP Hydrolysis to Produce a Complex Series of RNA–RNA Rearrangements Other Properties of Pre-mRNA and Its Synthesis Help to Explain the Choice of Proper Splice Sites A Second Set of snRNPs Splice a Small Fraction of Intron Sequences in Animals and Plants RNA Splicing Shows Remarkable Plasticity Spliceosome-Catalyzed RNA Splicing Probably Evolved from Self-Splicing Mechanisms RNA-Processing Enzymes Generate the 3¢ End of Eucaryotic mRNAs Mature Eucaryotic mRNAs Are Selectively Exported from the Nucleus Many Noncoding RNAs Are Also Synthesized and Processed in the Nucleus The Nucleolus Is a Ribosome-Producing Factory The Nucleus Contains a Variety of Subnuclear Structures Summary THE RNA WORLD AND THE ORIGINS OF LIFE Life Requires Stored Information Polynucleotides Can Both Store Information and Catalyze Chemical Reactions A Pre-RNA World May Predate the RNA World Single-Stranded RNA Molecules Can Fold into Highly Elaborate Structures Self-Replicating Molecules Undergo Natural Selection How Did Protein Synthesis Evolve? All Present-Day Cells Use DNA as Their Hereditary Material Summary Problems References 400 401 401 402 403 404 407 408 408 409 410 Chapter 7 Control of Gene Expression AN OVERVIEW OF GENE CONTROL The Different Cell Types of a Multicellular Organism Contain the Same DNA Different Cell Types Synthesize Different Sets of Proteins External Signals Can Cause a Cell to Change the Expression of Its Genes Gene Expression Can Be Regulated at Many of the Steps in the Pathway from DNA to RNA to Protein Summary 411 411 411 412 413 415 415 DNA-BINDING MOTIFS IN GENE REGULATORY PROTEINS Gene Regulatory Proteins Were Discovered Using Bacterial Genetics The Outside of the DNA Helix Can Be Read by Proteins Short DNA Sequences Are Fundamental Components of Genetic Switches Gene Regulatory Proteins Contain Structural Motifs That Can Read DNA Sequences The Helix–Turn–Helix Motif Is One of the Simplest and Most Common DNA-Binding Motifs 416 416 416 418 418 419 . and RNA 501 ISOLATING CELLS AND GROWING THEM IN CULTURE Cells Can Be Isolated from Intact Tissues Cells Can Be Grown in Culture Eucaryotic Cell Lines Are a Widely Used Source of Homogeneous Cells Embryonic Stem Cells Could Revolutionize Medicine Somatic Cell Nuclear Transplantation May Provide a Way to Generate Personalized Stem Cells Hybridoma Cell Lines Are Factories That Produce Monoclonal Antibodies Summary 501 502 502 505 505 507 508 510 THE MOLECULAR GENETIC MECHANISMS THAT CREATE SPECIALIZED CELL TYPES DNA Rearrangements Mediate Phase Variation in Bacteria A Set of Gene Regulatory Proteins Determines Cell Type in a Budding Yeast Two Proteins That Repress Each Other’s Synthesis Determine the Heritable State of Bacteriophage Lambda Simple Gene Regulatory Circuits Can Be Used to Make Memory Devices Transcriptional Circuits Allow the Cell to Carry Out Logic Operations Synthetic Biology Creates New Devices from Existing Biological Parts Circadian Clocks Are Based on Feedback Loops in Gene Regulation A Single Gene Regulatory Protein Can Coordinate the Expression of a Set of Genes 454 454 455 457 458 459 460 460 462 PURIFYING PROTEINS Cells Can Be Separated into Their Component Fractions Cell Extracts Provide Accessible Systems to Study Cell Functions Proteins Can Be Separated by Chromatography Affinity Chromatography Exploits Specific Binding Sites on Proteins Genetically-Engineered Tags Provide an Easy Way to Purify Proteins 510 510 511 512 513 514 .Detailed Contents Homeodomain Proteins Constitute a Special Class of Helix–Turn– Helix Proteins There Are Several Types of DNA-Binding Zinc Finger Motifs b sheets Can Also Recognize DNA Some Proteins Use Loops That Enter the Major and Minor Groove to Recognize DNA The Leucine Zipper Motif Mediates Both DNA Binding and Protein Dimerization Heterodimerization Expands the Repertoire of DNA Sequences That Gene Regulatory Proteins Can Recognize The Helix–Loop–Helix Motif Also Mediates Dimerization and DNA Binding It Is Not Yet Possible to Predict the DNA Sequences Recognized by All Gene Regulatory Proteins A Gel-Mobility Shift Assay Readily Detects Sequence-Specific DNA-Binding Proteins DNA Affinity Chromatography Facilitates the Purification of Sequence-Specific DNA-Binding Proteins The DNA Sequence Recognized by a Gene Regulatory Protein Can Be Determined Experimentally Phylogenetic Footprinting Identifies DNA Regulatory Sequences Through Comparative Genomics Chromatin Immunoprecipitation Identifies Many of the Sites That Gene Regulatory Proteins Occupy in Living Cells Summary Expression of a Critical Gene Regulatory Protein Can Trigger the Expression of a Whole Battery of Downstream Genes Combinatorial Gene Control Creates Many Different Cell Types in Eucaryotes A Single Gene Regulatory Protein Can Trigger the Formation of an Entire Organ The Pattern of DNA Methylation Can Be Inherited When Vertebrate Cells Divide Genomic Imprinting Is Based on DNA Methylation CG-Rich Islands Are Associated with Many Genes in Mammals Epigenetic Mechanisms Ensure That Stable Patterns of Gene Expression Can Be Transmitted to Daughter Cells Chromosome-Wide Alterations in Chromatin Structure Can Be Inherited The Control of Gene Expression is Intrinsically Noisy Summary xiii 420 421 422 423 423 424 425 426 427 428 429 431 431 432 463 464 465 467 468 470 471 473 476 477 POST-TRANSCRIPTIONAL CONTROLS Transcription Attenuation Causes the Premature Termination of Some RNA Molecules Riboswitches Might Represent Ancient Forms of Gene Control Alternative RNA Splicing Can Produce Different Forms of a Protein from the Same Gene The Definition of a Gene Has Had to Be Modified Since the Discovery of Alternative RNA Splicing Sex Determination in Drosophila Depends on a Regulated Series of RNA Splicing Events A Change in the Site of RNA Transcript Cleavage and Poly-A Addition Can Change the C-terminus of a Protein RNA Editing Can Change the Meaning of the RNA Message RNA Transport from the Nucleus Can Be Regulated Some mRNAs Are Localized to Specific Regions of the Cytoplasm The 5’ and 3’ Untranslated Regions of mRNAs Control Their Translation The Phosphorylation of an Initiation Factor Regulates Protein Synthesis Globally Initiation at AUG Codons Upstream of the Translation Start Can Regulate Eucaryotic Translation Initiation Internal Ribosome Entry Sites Provide Opportunities for Translation Control Changes in mRNA Stability Can Regulate Gene Expression Cytoplasmic Poly-A Addition Can Regulate Translation Small Noncoding RNA Transcripts Regulate Many Animal and Plant Genes RNA Interference Is a Cell Defense Mechanism RNA Interference Can Direct Heterochromatin Formation RNA Interference Has Become a Powerful Experimental Tool Summary Problems References 477 477 478 479 480 481 482 483 485 486 488 488 489 491 492 493 493 495 496 497 497 497 499 HOW GENETIC SWITCHES WORK The Tryptophan Repressor Is a Simple Switch That Turns Genes On and Off in Bacteria Transcriptional Activators Turn Genes On A Transcriptional Activator and a Transcriptional Repressor Control the Lac Operon DNA Looping Occurs During Bacterial Gene Regulation Bacteria Use Interchangeable RNA Polymerase Subunits to Help Regulate Gene Transcription Complex Switches Have Evolved to Control Gene Transcription in Eucaryotes A Eucaryotic Gene Control Region Consists of a Promoter Plus Regulatory DNA Sequences Eucaryotic Gene Activator Proteins Promote the Assembly of RNA Polymerase and the General Transcription Factors at the Startpoint of Transcription Eucaryotic Gene Activator Proteins Also Modify Local Chromatin Structure Gene Activator Proteins Work Synergistically Eucaryotic Gene Repressor Proteins Can Inhibit Transcription in Various Ways Eucaryotic Gene Regulatory Proteins Often Bind DNA Cooperatively Complex Genetic Switches That Regulate Drosophila Development Are Built Up from Smaller Modules The Drosophila Eve Gene Is Regulated by Combinatorial Controls Complex Mammalian Gene Control Regions Are Also Constructed from Simple Regulatory Modules Insulators Are DNA Sequences That Prevent Eucaryotic Gene Regulatory Proteins from Influencing Distant Genes Gene Switches Rapidly Evolve Summary 432 433 435 435 437 438 439 440 441 442 444 445 445 447 448 450 452 453 453 Chapter 8 Manipulating Proteins. DNA. 2 mm Apart Living Cells Are Seen Clearly in a Phase-Contrast or a DifferentialInterference-Contrast Microscope Images Can Be Enhanced and Analyzed by Digital Techniques Intact Tissues Are Usually Fixed and Sectioned before Microscopy Specific Molecules Can Be Located in Cells by Fluorescence Microscopy Antibodies Can Be Used to Detect Specific Molecules Imaging of Complex Three-Dimensional Objects Is Possible with the Optical Microscope The Confocal Microscope Produces Optical Sections by Excluding Out-of-Focus Light Fluorescent Proteins Can Be Used to Tag Individual Proteins in Living Cells and Organisms Protein Dynamics Can Be Followed in Living Cells Light-Emitting Indicators Can Measure Rapidly Changing Intracellular Ion Concentrations Several Strategies Are Available by Which Membrane-Impermeant Substances Can Be Introduced into Cells Light Can Be Used to Manipulate Microscopic Objects As Well As to Image Them Single Molecules Can Be Visualized by Using Total Internal Reflection Fluorescence Microscopy Individual Molecules Can Be Touched and Moved Using Atomic Force Microscopy Molecules Can Be Labeled with Radioisotopes Radioisotopes Are Used to Trace Molecules in Cells and Organisms Summary 579 579 580 583 583 585 586 588 589 590 592 593 596 597 598 599 600 600 602 603 ANALYZING AND MANIPULATING DNA Restriction Nucleases Cut Large DNA Molecules into Fragments Gel Electrophoresis Separates DNA Molecules of Different Sizes Purified DNA Molecules Can Be Specifically Labeled with Radioisotopes or Chemical Markers in vitro Nucleic Acid Hybridization Reactions Provide a Sensitive Way of Detecting Specific Nucleotide Sequences Northern and Southern Blotting Facilitate Hybridization with Electrophoretically Separated Nucleic Acid Molecules Genes Can Be Cloned Using DNA Libraries Two Types of DNA Libraries Serve Different Purposes cDNA Clones Contain Uninterrupted Coding Sequences Genes Can Be Selectively Amplified by PCR Cells Can Be Used As Factories to Produce Specific Proteins Proteins and Nucleic Acids Can Be Synthesized Directly by Chemical Reactions DNA Can Be Rapidly Sequenced Nucleotide Sequences Are Used to Predict the Amino Acid Sequences of Proteins The Genomes of Many Organisms Have Been Fully Sequenced Summary 532 532 534 535 535 538 540 541 544 544 546 548 548 550 551 552 LOOKING AT CELLS AND MOLECULES IN THE ELECTRON MICROSCOPE The Electron Microscope Resolves the Fine Structure of the Cell Biological Specimens Require Special Preparation for the Electron Microscope Specific Macromolecules Can Be Localized by Immunogold Electron Microscopy Images of Surfaces Can Be Obtained by Scanning Electron Microscopy Metal Shadowing Allows Surface Features to Be Examined at High Resolution by Transmission Electron Microscopy Negative Staining and Cryoelectron Microscopy Both Allow Macromolecules to Be Viewed at High Resolution Multiple Images Can Be Combined to Increase Resolution Different Views of a Single Object Can Be Combined to Give a Three-Dimensional Reconstruction Summary Problems References 604 604 605 606 607 608 610 610 612 612 614 615 STUDYING GENE EXPRESSION AND FUNCTION Classical Genetics Begins by Disrupting a Cell Process by Random Mutagenesis Genetic Screens Identify Mutants with Specific Abnormalities Mutations Can Cause Loss or Gain of Protein Function Complementation Tests Reveal Whether Two Mutations Are in the Same Gene or Different Genes Genes Can Be Ordered in Pathways by Epistasis Analysis Genes Identified by Mutations Can Be Cloned Human Genetics Presents Special Problems and Special Opportunities Human Genes Are Inherited in Haplotype Blocks.xiv Detailed Contents Large Collections of Tagged Knockouts Provide a Tool for Examining the Function of Every Gene in an Organism RNA Interference Is a Simple and Rapid Way to Test Gene Function Reporter Genes and In Situ Hybridization Reveal When and Where a Gene Is Expressed Expression of Individual Genes Can Be Measured Using Quantitative RT-PCR Microarrays Monitor the Expression of Thousands of Genes at Once Single-Cell Gene Expression Analysis Reveals Biological “Noise” Summary Problems References Purified Cell-Free Systems Are Required for the Precise Dissection of Molecular Functions 516 Summary 516 569 571 572 573 574 575 576 576 578 ANALYZING PROTEINS Proteins Can Be Separated by SDS Polyacrylamide-Gel Electrophoresis Specific Proteins Can Be Detected by Blotting with Antibodies Mass Spectrometry Provides a Highly Sensitive Method for Identifying Unknown Proteins Two-Dimensional Separation Methods are Especially Powerful Hydrodynamic Measurements Reveal the Size and Shape of a Protein Complex Sets of Interacting Proteins Can Be Identified by Biochemical Methods Protein–Protein Interactions Can Also Be Identified by a Two-Hybrid Technique in Yeast Combining Data Derived from Different Techniques Produces Reliable Protein-Interaction Maps Optical Methods Can Monitor Protein Interactions in Real Time Some Techniques Can Monitor Single Molecules Protein Function Can Be Selectively Disrupted with Small Molecules Protein Structure Can Be Determined Using X-Ray Diffraction NMR Can Be Used to Determine Protein Structure in Solution Protein Sequence and Structure Provide Clues About Protein Function Summary 517 517 518 519 521 522 523 523 524 524 526 527 527 529 530 531 Chapter 9 Visualizing Cells LOOKING AT CELLS IN THE LIGHT MICROSCOPE The Light Microscope Can Resolve Details 0. Which Can Aid in the Search for Mutations That Cause Disease Complex Traits Are Influenced by Multiple Genes Reverse Genetics Begins with a Known Gene and Determines Which Cell Processes Require Its Function Genes Can Be Re-Engineered in Several Ways Engineered Genes Can Be Inserted into the Germ Line of Many Organisms Animals Can Be Genetically Altered Transgenic Plants Are Important for Both Cell Biology and Agriculture 553 553 556 557 558 558 559 560 561 563 563 564 565 566 568 Chapter 10 Membrane Structure THE LIPID BILAYER Phosphoglycerides. and Sterols Are the Major Lipids in Cell Membranes Phospholipids Spontaneously Form Bilayers 617 617 618 620 . Sphingolipids. Detailed Contents The Lipid Bilayer Is a Two-Dimensional Fluid The Fluidity of a Lipid Bilayer Depends on Its Composition Despite Their Fluidity. Lipid Bilayers Can Form Domains of Different Compositions Lipid Droplets Are Surrounded by a Phospholipid Monolayer The Asymmetry of the Lipid Bilayer Is Functionally Important Glycolipids Are Found on the Surface of All Plasma Membranes Summary 621 622 624 625 626 628 629 Patch-Clamp Recording Indicates That Individual Gated Channels Open in an All-or-Nothing Fashion Voltage-Gated Cation Channels Are Evolutionarily and Structurally Related Transmitter-Gated Ion Channels Convert Chemical Signals into Electrical Ones at Chemical Synapses Chemical Synapses Can Be Excitatory or Inhibitory The Acetylcholine Receptors at the Neuromuscular Junction Are Transmitter-Gated Cation Channels Transmitter-Gated Ion Channels Are Major Targets for Psychoactive Drugs Neuromuscular Transmission Involves the Sequential Activation of Five Different Sets of Ion Channels Single Neurons Are Complex Computation Devices Neuronal Computation Requires a Combination of at Least Three Kinds of K+ Channels Long-Term Potentiation (LTP) in the Mammalian Hippocampus Depends on Ca2+ Entry Through NMDA-Receptor Channels Summary Problems References xv 680 682 682 684 684 686 687 688 689 691 692 693 694 MEMBRANE PROTEINS Membrane Proteins Can Be Associated with the Lipid Bilayer in Various Ways Lipid Anchors Control the Membrane Localization of Some Signaling Proteins In Most Transmembrane Proteins the Polypeptide Chain Crosses the Lipid Bilayer in an a-Helical Conformation Transmembrane a Helices Often Interact with One Another Some b Barrels Form Large Transmembrane Channels Many Membrane Proteins Are Glycosylated Membrane Proteins Can Be Solubilized and Purified in Detergents Bacteriorhodopsin Is a Light-Driven Proton Pump That Traverses the Lipid Bilayer as Seven a Helices Membrane Proteins Often Function as Large Complexes Many Membrane Proteins Diffuse in the Plane of the Membrane Cells Can Confine Proteins and Lipids to Specific Domains Within a Membrane The Cortical Cytoskeleton Gives Membranes Mechanical Strength and Restrict Membrane Protein Diffusion Summary Problems References 629 629 630 631 632 634 635 636 640 642 642 645 646 648 648 650 Chapter 12 Intracellular Compartments and Protein Sorting THE COMPARTMENTALIZATION OF CELLS All Eucaryotic Cells Have the Same Basic Set of MembraneEnclosed Organelles Evolutionary Origins Explain the Topological Relationships of Organelles Proteins Can Move Between Compartments in Different Ways Signal Sequences Direct Proteins to the Correct Cell Address Most Organelles Cannot Be Constructed De Novo: They Require Information in the Organelle Itself Summary 695 695 695 697 699 701 702 704 Chapter 11 Membrane Transport of Small Molecules and the Electrical Properties of Membranes 651 PRINCIPLES OF MEMBRANE TRANSPORT Protein-Free Lipid Bilayers Are Highly Impermeable to Ions There Are Two Main Classes of Membrane Transport Proteins: Transporters and Channels Active Transport Is Mediated by Transporters Coupled to an Energy Source Summary 651 652 652 653 654 THE TRANSPORT OF MOLECULES BETWEEN THE NUCLEUS AND THE CYTOSOL Nuclear Pore Complexes Perforate the Nuclear Envelope Nuclear Localization Signals Direct Nuclear Proteins to the Nucleus Nuclear Import Receptors Bind to Both Nuclear Localization Signals and NPC proteins Nuclear Export Works Like Nuclear Import. But in Reverse The Ran GTPase Imposes Directionality on Transport Through NPCs Transport Through NPCs Can Be Regulated by Controlling Access to the Transport Machinery During Mitosis the Nuclear Envelope Disassembles Summary 704 705 705 707 708 708 709 710 712 TRANSPORTERS AND ACTIVE MEMBRANE TRANSPORT Active Transport Can Be Driven by Ion Gradients Transporters in the Plasma Membrane Regulate Cytosolic pH An Asymmetric Distribution of Transporters in Epithelial Cells Underlies the Transcellular Transport of Solutes There Are Three Classes of ATP-Driven Pumps The Ca2+ Pump Is the Best-Understood P-type ATPase The Plasma Membrane P-type Na+-K+ Pump Establishes the Na+ Gradient Across the Plasma Membrane ABC Transporters Constitute the Largest Family of Membrane Transport Proteins Summary 654 656 657 658 659 660 661 663 667 THE TRANSPORT OF PROTEINS INTO MITOCHONDRIA AND CHLOROPLASTS Translocation into Mitochondria Depends on Signal Sequences and Protein Translocators Mitochondrial Precursor Proteins Are Imported as Unfolded Polypeptide Chains ATP Hydrolysis and a Membrane Potential Drive Protein Import Into the Matrix Space Bacteria and Mitochondria Use Similar Mechanisms to Insert Porins into their Outer Membrane Transport Into the Inner Mitochondrial Membrane and Intermembrane Space Occurs Via Several Routes Two Signal Sequences Direct Proteins to the Thylakoid Membrane in Chloroplasts Summary 713 713 715 716 717 717 719 720 ION CHANNELS AND THE ELECTRICAL PROPERTIES OF MEMBRANES 667 Ion Channels Are Ion-Selective and Fluctuate Between Open and Closed States 667 The Membrane Potential in Animal Cells Depends Mainly on K+ Leak Channels and the K+ Gradient Across the Plasma Membrane 669 The Resting Potential Decays Only Slowly When the Na+-K+ Pump Is Stopped 669 The Three-Dimensional Structure of a Bacterial K+ Channel Shows How an Ion Channel Can Work 671 Aquaporins Are Permeable to Water But Impermeable to Ions 673 The Function of a Neuron Depends on Its Elongated Structure 675 Voltage-Gated Cation Channels Generate Action Potentials in Electrically Excitable Cells 676 Myelination Increases the Speed and Efficiency of Action Potential Propagation in Nerve Cells 678 PEROXISOMES Peroxisomes Use Molecular Oxygen and Hydrogen Peroxide to Perform Oxidative Reactions A Short Signal Sequence Directs the Import of Proteins into Peroxisomes Summary 721 721 722 723 . a Single Internal ER Signal Sequence Remains in the Lipid Bilayer as a Membrane-Spanning a Helix Combinations of Start-Transfer and Stop-Transfer Signals Determine the Topology of Multipass Transmembrane Proteins Translocated Polypeptide Chains Fold and Assemble in the Lumen of the Rough ER Most Proteins Synthesized in the Rough ER Are Glycosylated by the Addition of a Common N-Linked Oligosaccharide Oligosaccharides Are Used as Tags to Mark the State of Protein Folding Improperly Folded Proteins Are Exported from the ER and Degraded in the Cytosol Misfolded Proteins in the ER Activate an Unfolded Protein Response Some Membrane Proteins Acquire a Covalently Attached Glycosylphosphatidylinositol (GPI) Anchor The ER Assembles Most Lipid Bilayers Summary Problems References TRANSPORT FROM THE TRANS GOLGI NETWORK TO LYSOSOMES Lysosomes Are the Principal Sites of Intracellular Digestion Lysosomes Are Heterogeneous Plant and Fungal Vacuoles Are Remarkably Versatile Lysosomes Multiple Pathways Deliver Materials to Lysosomes A Mannose 6-Phosphate Receptor Recognizes Lysosomal Proteins in the Trans Golgi Network The M6P Receptor Shuttles Between Specific Membranes A Signal Patch in the Hydrolase Polypeptide Chain Provides the Cue for M6P Addition Defects in the GlcNAc Phosphotransferase Cause a Lysosomal Storage Disease in Humans Some Lysosomes Undergo Exocytosis Summary 779 779 780 781 782 783 784 785 785 786 786 732 734 736 736 738 739 740 742 743 745 746 748 TRANSPORT INTO THE CELL FROM THE PLASMA MEMBRANE: ENDOCYTOSIS Specialized Phagocytic Cells Can Ingest Large Particles Pinocytic Vesicles Form from Coated Pits in the Plasma Membrane Not All Pinocytic Vesicles Are Clathrin-Coated Cells Use Receptor-Mediated Endocytosis to Import Selected Extracellular Macromolecules Endocytosed Materials That Are Not Retrieved from Endosomes End Up in Lysosomes Specific Proteins Are Retrieved from Early Endosomes and Returned to the Plasma Membrane Multivesicular Bodies Form on the Pathway to Late Endosomes Transcytosis Transfers Macromolecules Across Epithelial Cell Sheets Epithelial Cells Have Two Distinct Early Endosomal Compartments but a Common Late Endosomal Compartment Summary 787 787 789 790 791 792 793 795 797 798 799 Chapter 13 Intracellular Vesicular Traffic THE MOLECULAR MECHANISMS OF MEMBRANE TRANSPORT AND THE MAINTENANCE OF COMPARTMENTAL DIVERSITY There Are Various Types of Coated Vesicles The Assembly of a Clathrin Coat Drives Vesicle Formation Not All Coats Form Basket-like Structures Phosphoinositides Mark Organelles and Membrane Domains Cytoplasmic Proteins Regulate the Pinching-Off and Uncoating of Coated Vesicles Monomeric GTPases Control Coat Assembly Not All Transport Vesicles Are Spherical Rab Proteins Guide Vesicle Targeting SNAREs Mediate Membrane Fusion Interacting SNAREs Need to Be Pried Apart Before They Can Function Again Viral Fusion Proteins and SNAREs May Use Similar Fusion Mechanisms Summary 749 TRANSPORT FROM THE TRANS GOLGI NETWORK TO THE CELL EXTERIOR: EXOCYTOSIS 750 751 754 755 757 757 758 760 760 762 764 764 766 799 TRANSPORT FROM THE ER THROUGH THE GOLGI APPARATUS Proteins Leave the ER in COPII-Coated Transport Vesicles Only Proteins That Are Properly Folded and Assembled Can Leave the ER Vesicular Tubular Clusters Mediate Transport from the ER to the Golgi Apparatus The Retrieval Pathway to the ER Uses Sorting Signals Many Proteins Are Selectively Retained in the Compartments in Which They Function The Golgi Apparatus Consists of an Ordered Series of Compartments Oligosaccharide Chains Are Processed in the Golgi Apparatus Proteoglycans Are Assembled in the Golgi Apparatus What Is the Purpose of Glycosylation? Transport Through the Golgi Apparatus May Occur by Vesicular Transport or Cisternal Maturation Golgi Matrix Proteins Help Organize the Stack Summary 766 767 767 768 769 771 771 773 775 776 777 778 779 Many Proteins and Lipids Seem to Be Carried Automatically from the Golgi Apparatus to the Cell Surface 800 Secretory Vesicles Bud from the Trans Golgi Network 801 Proteins Are Often Proteolytically Processed During the Formation of Secretory Vesicles 803 Secretory Vesicles Wait Near the Plasma Membrane Until Signaled to Release Their Contents 803 Regulated Exocytosis Can Be a Localized Response of the Plasma Membrane and Its Underlying Cytoplasm 804 Secretory Vesicle Membrane Components Are Quickly Removed from the Plasma Membrane 805 Some Regulated Exocytosis Events Serve to Enlarge the Plasma Membrane 805 Polarized Cells Direct Proteins from the Trans Golgi Network to the Appropriate Domain of the Plasma Membrane 805 Different Strategies Guide Membrane Proteins and Lipids Selectively to the Correct Plasma Membrane Domains 806 Synaptic Vesicles Can Form Directly from Endocytic Vesicles 807 Summary 809 Problems 810 References 812 Chapter 14 Energy Conversion: Mitochondria and Chloroplasts THE MITOCHONDRION The Mitochondrion Contains an Outer Membrane. and Two Internal Compartments The Citric Acid Cycle Generates High-Energy Electrons A Chemiosmotic Process Converts Oxidation Energy into ATP NADH Transfers its Electrons to Oxygen Through Three Large Respiratory Enzyme Complexes As Electrons Move Along the Respiratory Chain.xvi Detailed Contents 723 724 726 727 730 731 THE ENDOPLASMIC RETICULUM The ER Is Structurally and Functionally Diverse Signal Sequences Were First Discovered in Proteins Imported into the Rough ER A Signal-Recognition Particle (SRP) Directs ER Signal Sequences to a Specific Receptor in the Rough ER Membrane The Polypeptide Chain Passes Through an Aqueous Pore in the Translocator Translocation Across the ER Membrane Does Not Always Require Ongoing Polypeptide Chain Elongation In Single-Pass Transmembrane Proteins. an Inner Membrane. Energy Is Stored as an Electrochemical Proton Gradient Across the Inner Membrane The Proton Gradient Drives ATP Synthesis 813 815 816 817 817 819 820 821 . Light Energy Captured by Chlorophyll Creates a Strong Electron Donor from a Weak One Noncyclic Photophosphorylation Produces Both NADPH and ATP Chloroplasts Can Make ATP by Cyclic Photophosphorylation Without Making NADPH Photosystems I and II Have Related Structures. Chloroplasts Make Most of Theirs Mitochondria May Contribute to the Aging of Cells and Organisms Why Do Mitochondria and Chloroplasts Have Their Own Genetic Systems? Summary xvii 859 859 861 862 863 863 864 866 866 867 867 868 868 870 822 822 823 824 826 827 ELECTRON-TRANSPORT CHAINS AND THEIR PROTON PUMPS 827 Protons Are Unusually Easy to Move 827 The Redox Potential Is a Measure of Electron Affinities 828 Electron Transfers Release Large Amounts of Energy 829 Spectroscopic Methods Identified Many Electron Carriers in the Respiratory Chain 829 The Respiratory Chain Includes Three Large Enzyme Complexes Embedded in the Inner Membrane 831 An Iron–Copper Center in Cytochrome Oxidase Catalyzes Efficient O2 Reduction 832 Electron Transfers in the Inner Mitochondrial Membrane Are Mediated by Electron Tunneling during Random Collisions 834 A Large Drop in Redox Potential Across Each of the Three Respiratory Enzyme Complexes Provides the Energy for H+ Pumping 835 The H+ Pumping Occurs by Distinct Mechanisms in the Three Major Enzyme Complexes 835 H+ Ionophores Uncouple Electron Transport from ATP Synthesis 836 Respiratory Control Normally Restrains Electron Flow Through the Chain 837 Natural Uncouplers Convert the Mitochondria in Brown Fat into Heat-Generating Machines 838 The Mitochondrion Plays Many Critical Roles in Cell Metabolism 838 Bacteria Also Exploit Chemiosmotic Mechanisms to Harness Energy 839 Summary 840 THE EVOLUTION OF ELECTRON-TRANSPORT CHAINS The Earliest Cells Probably Used Fermentation to Produce ATP Electron-Transport Chains Enabled Anaerobic Bacteria to Use Nonfermentable Molecules as Their Major Source of Energy By Providing an Inexhaustible Source of Reducing Power. and Specificity of the Response 897 Modular Interaction Domains Mediate Interactions Between Intracellular Signaling Proteins 897 Cells Can Use Multiple Mechanisms to Respond Abruptly to a Gradually Increasing Concentration of an Extracellular Signal 899 Intracellular Signaling Networks Usually Make Use of Feedback Loops 901 Cells Can Adjust Their Sensitivity to a Signal 902 Summary 903 THE GENETIC SYSTEMS OF MITOCHONDRIA AND PLASTIDS 855 Mitochondria and Chloroplasts Contain Complete Genetic Systems 856 Organelle Growth and Division Determine the Number of Mitochondria and Plastids in a Cell 857 . G-Protein-Coupled. and Enzyme-Coupled Receptors 891 Most Activated Cell-Surface Receptors Relay Signals Via Small Molecules and a Network of Intracellular Signaling Proteins 893 Many Intracellular Signaling Proteins Function as Molecular Switches That Are Activated by Phosphorylation or GTP Binding 895 Intracellular Signaling Complexes Enhance the Speed.Detailed Contents The Proton Gradient Drives Coupled Transport Across the Inner Membrane Proton Gradients Produce Most of the Cell’s ATP Mitochondria Maintain a High ATP:ADP Ratio in Cells A Large Negative Value of DG for ATP Hydrolysis Makes ATP Useful to the Cell ATP Synthase Can Function in Reverse to Hydrolyze ATP and Pump H+ Summary Mitochondria and Chloroplasts Have Diverse Genomes Mitochondria and Chloroplasts Probably Both Evolved from Endosymbiotic Bacteria Mitochondria Have a Relaxed Codon Usage and Can Have a Variant Genetic Code Animal Mitochondria Contain the Simplest Genetic Systems Known Some Organelle Genes Contain Introns The Chloroplast Genome of Higher Plants Contains About 120 Genes Mitochondrial Genes Are Inherited by a Non-Mendelian Mechanism Organelle Genes Are Maternally Inherited in Many Organisms Petite Mutants in Yeasts Demonstrate the Overwhelming Importance of the Cell Nucleus for Mitochondrial Biogenesis Mitochondria and Plastids Contain Tissue-Specific Proteins that Are Encoded in the Cell Nucleus Mitochondria Import Most of Their Lipids. and Also Resemble Bacterial Photosystems The Proton-Motive Force Is the Same in Mitochondria and Chloroplasts Carrier Proteins in the Chloroplast Inner Membrane Control Metabolite Exchange with the Cytosol Chloroplasts Also Perform Other Crucial Biosyntheses Summary 840 841 842 843 844 845 846 847 848 849 850 853 853 853 854 855 855 Chapter 15 Mechanisms of Cell Communication 879 GENERAL PRINCIPLES OF CELL COMMUNICATION 879 Extracellular Signal Molecules Bind to Specific Receptors 880 Extracellular Signal Molecules Can Act Over Either Short or Long Distances 881 Gap Junctions Allow Neighboring Cells to Share Signaling Information 884 Each Cell Is Programmed to Respond to Specific Combinations of Extracellular Signal Molecules 884 Different Types of Cells Usually Respond Differently to the Same Extracellular Signal Molecule 885 The Fate of Some Developing Cells Depends on Their Position in Morphogen Gradients 886 A Cell Can Alter the Concentration of an Intracellular Molecule Quickly Only If the Lifetime of the Molecule Is Short 886 Nitric Oxide Gas Signals by Directly Regulating the Activity of Specific Proteins Inside the Target Cell 887 Nuclear Receptors Are Ligand-Modulated Gene Regulatory Proteins 889 The Three Largest Classes of Cell-Surface Receptor Proteins Are IonChannel-Coupled. Efficiency. Photosynthetic Bacteria Overcame a Major Evolutionary Obstacle The Photosynthetic Electron-Transport Chains of Cyanobacteria Produced Atmospheric Oxygen and Permitted New Life-Forms Summary Problems References 870 870 871 872 873 875 877 878 CHLOROPLASTS AND PHOTOSYNTHESIS The Chloroplast Is One Member of the Plastid Family of Organelles Chloroplasts Resemble Mitochondria But Have an Extra Compartment Chloroplasts Capture Energy from Sunlight and Use It to Fix Carbon Carbon Fixation Is Catalyzed by Ribulose Bisphosphate Carboxylase Each CO2 Molecule That Is Fixed Consumes Three Molecules of ATP and Two Molecules of NADPH Carbon Fixation in Some Plants Is Compartmentalized to Facilitate Growth at Low CO2 Concentrations Photosynthesis Depends on the Photochemistry of Chlorophyll Molecules A Photochemical Reaction Center Plus an Antenna Complex Form a Photosystem In a Reaction Center. Providing a Fast Track to the Nucleus Protein Tyrosine Phosphatases Reverse Tyrosine Phosphorylations Signal Proteins of the TGFb Superfamily Act Through Receptor Serine/Threonine Kinases and Smads Serine/Threonine and Tyrosine Protein Kinases Are Structurally Related Bacterial Chemotaxis Depends on a Two-Component Signaling Pathway Activated by Histidine-Kinase-Associated Receptors Receptor Methylation Is Responsible for Adaptation in Bacterial Chemotaxis Summary 921 922 923 924 926 927 928 930 931 932 934 935 935 937 938 939 941 941 943 944 HOW CELLS REGULATE THEIR CYTOSKELETAL FILAMENTS 992 SIGNALING PATHWAYS DEPENDENT ON REGULATED PROTEOLYSIS OF LATENT GENE REGULATORY PROTEINS The Receptor Protein Notch Is a Latent Gene Regulatory Protein Wnt Proteins Bind to Frizzled Receptors and Inhibit the Degradation of b-Catenin Hedgehog Proteins Bind to Patched Relieving Its Inhibition of Smoothened Many Stressful and Inflammatory Stimuli Act Through an NFkB-Dependent Signaling Pathway Summary 946 946 948 950 A Protein Complex Containing g-Tubulin Nucleates Microtubules 992 Microtubules Emanate from the Centrosome in Animal Cells 992 Actin Filaments Are Often Nucleated at the Plasma Membrane 996 The Mechanism of Nucleation Influences Large-Scale Filament Organization 998 Proteins That Bind to the Free Subunits Modify Filament Elongation 999 Severing Proteins Regulate the Length and Kinetic Behavior of Actin Filaments and Microtubules 1000 Proteins That Bind Along the Sides of Filaments Can Either Stabilize or Destabilize Them 1001 Proteins That Interact with Filament Ends Can Dramatically Change Filament Dynamics 1002 Different Kinds of Proteins Alter the Properties of Rapidly Growing Microtubule Ends 1003 Filaments Are Organized into Higher-Order Structures in Cells 1005 Intermediate Filaments Are Cross-Linked and Bundled Into Strong Arrays 1005 Cross-Linking Proteins with Distinct Properties Organize Different Assemblies of Actin Filaments 1006 Filamin and Spectrin Form Actin Filament Webs 1008 Cytoskeletal Elements Make Many Attachments to Membrane 1009 Summary 1010 MOLECULAR MOTORS 952 954 Actin-Based Motor Proteins Are Members of the Myosin Superfamily There Are Two Types of Microtubule Motor Proteins: Kinesins and Dyneins The Structural Similarity of Myosin and Kinesin Indicates a Common Evolutionary Origin Motor Proteins Generate Force by Coupling ATP Hydrolysis to Conformational Changes 1010 1011 1014 1015 1016 SIGNALING IN PLANTS Multicellularity and Cell Communication Evolved Independently in Plants and Animals Receptor Serine/Threonine Kinases Are the Largest Class of Cell-Surface Receptors in Plants 955 955 956 .xviii Detailed Contents Ethylene Blocks the Degradation of Specific Gene Regulatory Proteins in the Nucleus Regulated Positioning of Auxin Transporters Patterns Plant Growth Phytochromes Detect Red Light. and Cryptochromes Detect Blue Light Summary Problems References SIGNALING THROUGH G-PROTEIN-COUPLED CELLSURFACE RECEPTORS (GPCRS) AND SMALL INTRACELLULAR MEDIATORS Trimeric G Proteins Relay Signals from GPCRs Some G Proteins Regulate the Production of Cyclic AMP Cyclic-AMP-Dependent Protein Kinase (PKA) Mediates Most of the Effects of Cyclic AMP Some G Proteins Activate An Inositol Phospholipid Signaling Pathway by Activating Phospholipase C-b Ca2+ Functions as a Ubiquitous Intracellular Mediator The Frequency of Ca2+ Oscillations Influences a Cell’s Response Ca2+/Calmodulin-Dependent Protein Kinases (CaM-Kinases) Mediate Many of the Responses to Ca2+ Signals in Animal Cells Some G Proteins Directly Regulate Ion Channels Smell and Vision Depend on GPCRs That Regulate CyclicNucleotide-Gated Ion Channels Intracellular Mediators and Enzymatic Cascades Amplify Extracellular Signals GPCR Desensitization Depends on Receptor Phosphorylation Summary 904 905 905 908 909 912 912 914 916 917 919 920 921 957 959 960 961 962 964 Chapter 16 The Cytoskeleton THE SELF-ASSEMBLY AND DYNAMIC STRUCTURE OF CYTOSKELETAL FILAMENTS Cytoskeletal Filaments Are Dynamic and Adaptable The Cytoskeleton Can Also Form Stable Structures Each Type of Cytoskeletal Filament Is Constructed from Smaller Protein Subunits Filaments Formed from Multiple Protofilaments Have Advantageous Properties Nucleation Is the Rate-Limiting Step in the Formation of a Cytoskeletal Polymer The Tubulin and Actin Subunits Assemble Head-to-Tail to Create Polar Filaments Microtubules and Actin Filaments Have Two Distinct Ends That Grow at Different Rates Filament Treadmilling and Dynamic Instability Are Consequences of Nucleotide Hydrolysis by Tubulin and Actin Treadmilling and Dynamic Instability Aid Rapid Cytoskeletal Rearrangement Tubulin and Actin Have Been Highly Conserved During Eucaryotic Evolution Intermediate Filament Structure Depends on The Lateral Bundling and Twisting of Coiled Coils Intermediate Filaments Impart Mechanical Stability to Animal Cells Drugs Can Alter Filament Polymerization Bacterial Cell Organization and Cell Division Depend on Homologs of the Eucaryotic Cytoskeleton Summary 965 965 966 969 970 971 973 973 975 976 980 982 983 985 987 989 991 SIGNALING THROUGH ENZYME-COUPLED CELL-SURFACE RECEPTORS Activated Receptor Tyrosine Kinases (RTKs) Phosphorylate Themselves Phosphorylated Tyrosines on RTKs Serve as Docking Sites for Intracellular Signaling Proteins Proteins with SH2 Domains Bind to Phosphorylated Tyrosines Ras Belongs to a Large Superfamily of Monomeric GTPases RTKs Activate Ras Via Adaptors and GEFs: Evidence from the Developing Drosophila Eye Ras Activates a MAP Kinase Signaling Module Scaffold Proteins Help Prevent Cross-Talk Between Parallel MAP Kinase Modules Rho Family GTPases Functionally Couple Cell-Surface Receptors to the Cytoskeleton PI 3-Kinase Produces Lipid Docking Sites in the Plasma Membrane The PI-3-Kinase–Akt Signaling Pathway Stimulates Animal Cells to Survive and Grow The Downstream Signaling Pathways Activated By RTKs and GPCRs Overlap Tyrosine-Kinase-Associated Receptors Depend on Cytoplasmic Tyrosine Kinases Cytokine Receptors Activate the JAK–STAT Signaling Pathway. Except in Cancer Cells Organism and Organ Growth Depend on Cell Growth Proliferating Cells Usually Coordinate Their Growth and Division Neighboring Cells Compete for Extracellular Signal Proteins Animals Control Total Cell Mass by Unknown Mechanisms Summary Problems References 1101 1102 1103 1103 1105 1007 1107 1108 1108 1110 1111 1112 1112 1113 THE CELL-CYCLE CONTROL SYSTEM The Cell-Cycle Control System Triggers the Major Events of the Cell Cycle The Cell-Cycle Control System Depends on Cyclically Activated Cyclin-Dependent Protein Kinases (Cdks) Inhibitory Phosphorylation and Cdk Inhibitory Proteins (CKIs) Can Suppress Cdk Activity The Cell-Cycle Control System Depends on Cyclical Proteolysis Cell-Cycle Control Also Depends on Transcriptional Regulation The Cell-Cycle Control System Functions as a Network of Biochemical Switches Summary 1060 1060 1062 1063 1064 1065 1065 1067 Chapter 18 Apoptosis 1115 1115 1117 1118 1120 1121 1121 1124 1126 1127 1128 1128 1129 S PHASE S-Cdk Initiates DNA Replication Once Per Cycle Chromosome Duplication Requires Duplication of Chromatin Structure Cohesins Help Hold Sister Chromatids Together Summary 1067 1067 1069 1070 1071 MITOSIS M-Cdk Drives Entry Into Mitosis Dephosphorylation Activates M-Cdk at the Onset of Mitosis Condensin Helps Configure Duplicated Chromosomes for Separation The Mitotic Spindle Is a Microtubule-Based Machine 1071 1071 1074 1075 1075 Programmed Cell Death Eliminates Unwanted Cells Apoptotic Cells Are Biochemically Recognizable Apoptosis Depends on an Intracellular Proteolytic Cascade That Is Mediated by Caspases Cell-Surface Death Receptors Activate the Extrinsic Pathway of Apoptosis The Intrinsic Pathway of Apoptosis Depends on Mitochondria Bcl2 Proteins Regulate the Intrinsic Pathway of Apoptosis IAPs Inhibit Caspases Extracellular Survival Factors Inhibit Apoptosis in Various Ways Either Excessive or Insufficient Apoptosis Can Contribute to Disease Summary Problems References .Detailed Contents Motor Protein Kinetics Are Adapted to Cell Functions Motor Proteins Mediate the Intracellular Transport of MembraneEnclosed Organelles The Cytoskeleton Localizes Specific RNA Molecules Cells Regulate Motor Protein Function Summary 1020 1021 1022 1023 1025 Microtubule-Dependent Motor Proteins Govern Spindle Assembly and Function Two Mechanisms Collaborate in the Assembly of a Bipolar Mitotic Spindle Centrosome Duplication Occurs Early in the Cell Cycle M-Cdk Initiates Spindle Assembly in Prophase The Completion of Spindle Assembly in Animal Cells Requires Nuclear Envelope Breakdown Microtubule Instability Increases Greatly in Mitosis Mitotic Chromosomes Promote Bipolar Spindle Assembly Kinetochores Attach Sister Chromatids to the Spindle Bi-Orientation Is Achieved by Trial and Error Multiple Forces Move Chromosomes on the Spindle The APC/C Triggers Sister-Chromatid Separation and the Completion of Mitosis Unattached Chromosomes Block Sister-Chromatid Separation: The Spindle Assembly Checkpoint Chromosomes Segregate in Anaphase A and B Segregated Chromosomes Are Packaged in Daughter Nuclei at Telophase Meiosis Is a Special Form of Nuclear Division Involved in Sexual Reproduction Summary xix 1077 1077 1078 1078 1079 1080 1081 1082 1083 1085 1087 1088 1089 1090 1090 1092 THE CYTOSKELETON AND CELL BEHAVIOR 1025 Sliding of Myosin II and Actin Filaments Causes Muscles to Contract 1026 A Sudden Rise in Cytosolic Ca2+ Concentration Initiates Muscle Contraction 1028 Heart Muscle Is a Precisely Engineered Machine 1031 Cilia and Flagella Are Motile Structures Built from Microtubules and Dyneins 1031 Construction of the Mitotic Spindle Requires Microtubule Dynamics and the Interactions of Many Motor Proteins 1034 Many Cells Can Crawl Across A Solid Substratum 1036 Actin Polymerization Drives Plasma Membrane Protrusion 1037 Cell Adhesion and Traction Allow Cells to Pull Themselves Forward 1040 Members of the Rho Protein Family Cause Major Rearrangements of the Actin Cytoskeleton 1041 Extracellular Signals Can Activate the Three Rho Protein Family Members 1043 External Signals Can Dictate the Direction of Cell Migration 1045 Communication Between the Microtubule and Actin Cytoskeletons Coordinates Whole-Cell Polarization and Locomotion 1046 The Complex Morphological Specialization of Neurons Depends on the Cytoskeleton 1047 Summary 1050 Problems 1050 References 1052 CYTOKINESIS Actin and Myosin II in the Contractile Ring Generate the Force for Cytokinesis Local Activation of RhoA Triggers Assembly and Contraction of the Contractile Ring The Microtubules of the Mitotic Spindle Determine the Plane of Animal Cell Division The Phragmoplast Guides Cytokinesis in Higher Plants Membrane-Enclosed Organelles Must Be Distributed to Daughter Cells During Cytokinesis Some Cells Reposition Their Spindle to Divide Asymmetrically Mitosis Can Occur Without Cytokinesis The G1 Phase Is a Stable State of Cdk Inactivity Summary 1092 1093 1094 1095 1097 1098 1099 1099 1100 1101 Chapter 17 The Cell Cycle OVERVIEW OF THE CELL CYCLE The Eucaryotic Cell Cycle Is Divided into Four Phases Cell-Cycle Control Is Similar in All Eucaryotes Cell-Cycle Control Can Be Dissected Genetically by Analysis of Yeast Mutants Cell-Cycle Control Can Be Analyzed Biochemically in Animal Embryos Cell-Cycle Control Can Be Studied in Cultured Mammalian Cells Cell-Cycle Progression Can Be Studied in Various Ways Summary 1053 1054 1054 1056 1056 1057 1059 1059 1060 CONTROL OF CELL DIVISION AND CELL GROWTH Mitogens Stimulate Cell Division Cells Can Delay Division by Entering a Specialized Nondividing State Mitogens Stimulate G1-Cdk and G1/S-Cdk Activities DNA Damage Blocks Cell Division: The DNA Damage Response Many Human Cells Have a Built-In Limitation on the Number of Times They Can Divide Abnormal Proliferation Signals Cause Cell-Cycle Arrest or Apoptosis. and the Extracellular Matrix CADHERINS AND CELL–CELL ADHESION Cadherins Mediate Ca2+-Dependent Cell–Cell Adhesion in All Animals The Cadherin Superfamily in Vertebrates Includes Hundreds of Different Proteins. Plasmodesmata Perform Many of the Same Functions as Gap Junctions Summary 1158 1158 Chapter 20 Cancer 1159 1161 1161 1162 1163 1205 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1217 1218 1220 1220 1222 1223 1223 CANCER AS A MICROEVOLUTIONARY PROCESS Cancer Cells Reproduce Without Restraint and Colonize Other Tissues Most Cancers Derive from a Single Abnormal Cell Cancer Cells Contain Somatic Mutations A Single Mutation Is Not Enough to Cause Cancer Cancers Develop Gradually from Increasingly Aberrant Cells Cervical Cancers Are Prevented by Early Detection Tumor Progression Involves Successive Rounds of Random Inherited Change Followed by Natural Selection The Epigenetic Changes That Accumulate in Cancer Cells Involve Inherited Chromatin Structures and DNA Methylation Human Cancer Cells Are Genetically Unstable Cancerous Growth Often Depends on Defective Control of Cell Death. Including Many with Signaling Functions Cadherins Mediate Homophilic Adhesion Selective Cell–Cell Adhesion Enables Dissociated Vertebrate Cells to Reassemble into Organized Tissues Cadherins Control the Selective Assortment of Cells Twist Regulates Epithelial-Mesenchymal Transitions Catenins Link Classical Cadherins to the Actin Cytoskeleton Adherens Junctions Coordinate the Actin-Based Motility of Adjacent Cells Desmosome Junctions Give Epithelia Mechanical Strength Cell–Cell Junctions Send Signals into the Cell Interior Selectins Mediate Transient Cell–Cell Adhesions in the Bloodstream Members of the Immunoglobulin Superfamily of Proteins Mediate Ca2+-Independent Cell–Cell Adhesion Many Types of Cell Adhesion Molecules Act in Parallel to Create a Synapse Scaffold Proteins Organize Junctional Complexes Summary 1131 1133 1135 1178 1179 1179 1180 1181 1182 1183 1184 1186 1187 1187 1189 1189 1191 1191 1193 1193 1194 1195 1136 1137 1139 1140 1141 1142 1142 1143 1145 1145 1146 1147 1148 1149 TIGHT JUNCTIONS AND THE ORGANIZATION OF EPITHELIA Tight Junctions Form a Seal Between Cells and a Fence Between Membrane Domains Scaffold Proteins in Junctional Complexes Play a Key Part in the Control of Cell Proliferation Cell-Cell Junctions and the Basal Lamina Govern Apico-Basal Polarity in Epithelia A Separate Signaling System Controls Planar Cell Polarity Summary 1150 1150 1153 1155 1157 1158 THE PLANT CELL WALL The Composition of the Cell Wall Depends on the Cell Type The Tensile Strength of the Cell Wall Allows Plant Cells to Develop Turgor Pressure The Primary Cell Wall Is Built from Cellulose Microfibrils Interwoven with a Network of Pectic Polysaccharides Oriented Cell-Wall Deposition Controls Plant Cell Growth Microtubules Orient Cell-Wall Deposition Summary Problems References 1195 1195 1197 1197 1199 1200 1202 1202 1204 PASSAGEWAYS FROM CELL TO CELL: GAP JUNCTIONS AND PLASMODESMATA Gap Junctions Couple Cells Both Electrically and Metabolically A Gap-Junction Connexon Is Made Up of Six Transmembrane Connexin Subunits Gap Junctions Have Diverse Functions Cells Can Regulate the Permeability of Their Gap Junctions In Plants. Malignant Cancer Cells Must Survive and Proliferate in a Foreign Environment Tumors Induce Angiogenesis The Tumor Microenvironment Influences Cancer Development Many Properties Typically Contribute to Cancerous Growth Summary THE BASAL LAMINA Basal Laminae Underlie All Epithelia and Surround Some Nonepithelial Cell Types Laminin Is a Primary Component of the Basal Lamina Type IV Collagen Gives the Basal Lamina Tensile Strength Basal Laminae Have Diverse Functions Summary 1164 1164 1165 1166 1167 1169 INTEGRINS AND CELL-MATRIX ADHESION Integrins Are Transmembrane Heterodimers That Link to the Cytoskeleton Integrins Can Switch Between an Active and an Inactive Conformation Integrin Defects Are Responsible for Many Different Genetic Diseases Integrins Cluster to Form Strong Adhesions Extracellular Matrix Attachments Act Through Integrins to Control Cell Proliferation and Survival Integrins Recruit Intracellular Signaling Proteins at Sites of CellSubstratum Adhesion Integrins Can Produce Localized Intracellular Effects Summary 1169 1170 1170 1172 1174 1175 1176 1177 1178 . as Well as Make it Matrix Degradation Is Localized to the Vicinity of Cells Summary Chapter 19 Cell Junctions. or Both Cancer Cells Are Usually Altered in Their Responses to DNA Damage and Other Forms of Stress Human Cancer Cells Escape a Built-In Limit to Cell Proliferation A Small Population of Cancer Stem Cells Maintains Many Tumors How Do Cancer Stem Cells Arise? To Metastasize. Cell Adhesion. Cell Differentiation.xx Detailed Contents THE EXTRACELLULAR MATRIX OF ANIMAL CONNECTIVE TISSUES The Extracellular Matrix Is Made and Oriented by the Cells Within It Glycosaminoglycan (GAG) Chains Occupy Large Amounts of Space and Form Hydrated Gels Hyaluronan Acts as a Space Filler and a Facilitator of Cell Migration During Tissue Morphogenesis and Repair Proteoglycans Are Composed of GAG Chains Covalently Linked to a Core Protein Proteoglycans Can Regulate the Activities of Secreted Proteins Cell-Surface Proteoglycans Act as Co-Receptors Collagens Are the Major Proteins of the Extracellular Matrix Collagen Chains Undergo a Series of Post-Translational Modifications Propeptides Are Clipped Off Procollagen After Its Secretion to Allow Assembly of Fibrils Secreted Fibril-Associated Collagens Help Organize the Fibrils Cells Help Organize the Collagen Fibrils They Secrete by Exerting Tension on the Matrix Elastin Gives Tissues Their Elasticity Fibronectin Is an Extracellular Protein That Helps Cells Attach to the Matrix Tension Exerted by Cells Regulates Assembly of Fibronectin Fibrils Fibronectin Binds to Integrins Through an RGD Motif Cells Have to Be Able to Degrade Matrix. Detailed Contents THE PREVENTABLE CAUSES OF CANCER Many. But Not All. Tumor Promoters Do Not Viruses and Other Infections Contribute to a Significant Proportion of Human Cancers Identification of Carcinogens Reveals Ways to Avoid Cancer Summary xxi 1224 1225 1226 1227 1229 1230 There Is Still Much More to Do Summary Problems References 1264 1265 1265 1267 Chapters 21–25 available on Media DVD-ROM Chapter 21 Sexual Reproduction: Meiosis. Cancer-Causing Agents Damage DNA Tumor Initiators Damage DNA. Germ Cells. KinetochoreAssociated Proteins Meiosis Frequently Goes Wrong Crossing-Over Enhances Genetic Reassortment Crossing-Over Is Highly Regulated Meiosis Is Regulated Differently in Male and Female Mammals Summary 1272 1272 1274 1275 1276 1278 1279 1280 1280 1281 THE MOLECULAR BASIS OF CANCER-CELL BEHAVIOR Studies of Both Developing Embryos and Genetically Engineered Mice Have Helped to Uncover the Function of Cancer-Critical Genes Many Cancer-Critical Genes Regulate Cell Proliferation Distinct Pathways May Mediate the Disregulation of Cell-Cycle Progression and the Disregulation of Cell Growth in Cancer Cells Mutations in Genes That Regulate Apoptosis Allow Cancer Cells to Survive When They Should Not Mutations in the p53 Gene Allow Many Cancer Cells to Survive and Proliferate Despite DNA Damage DNA Tumor Viruses Block the Action of Key Tumor Suppressor Proteins The Changes in Tumor Cells That Lead to Metastasis Are Still Largely a Mystery Colorectal Cancers Evolve Slowly Via a Succession of Visible Changes A Few Key Genetic Lesions Are Common to a Large Fraction of Colorectal Cancers Some Colorectal Cancers Have Defects in DNA Mismatch Repair The Steps of Tumor Progression Can Often Be Correlated with Specific Mutations Each Case of Cancer Is Characterized by Its Own Array of Genetic Lesions Summary 1240 1241 1242 PRIMORDIAL GERM CELLS AND SEX DETERMINATION IN MAMMALS Signals from Neighbors Specify PGCs in Mammalian Embryos PGCs Migrate into the Developing Gonads The Sry Gene Directs the Developing Mammalian Gonad to Become a Testis Many Aspects of Sexual Reproduction Vary Greatly between Animal Species Summary 1282 1282 1283 1283 1285 1286 1244 1245 1246 1247 1249 1250 1251 1254 1254 1256 1256 EGGS An Egg Is Highly Specialized for Independent Development Eggs Develop in Stages Oocytes Use Special Mechanisms to Grow to Their Large Size Most Human Oocytes Die Without Maturing Summary 1287 1287 1288 1290 1291 1292 SPERM Sperm Are Highly Adapted for Delivering Their DNA to an Egg Sperm Are Produced Continuously in the Mammalian Testis Sperm Develop as a Syncytium Summary 1292 1292 1293 1294 1296 CANCER TREATMENT: PRESENT AND FUTURE The Search for Cancer Cures Is Difficult but Not Hopeless Traditional Therapies Exploit the Genetic Instability and Loss of Cell-Cycle Checkpoint Responses in Cancer Cells New Drugs Can Exploit the Specific Cause of a Tumor’s Genetic Instability Genetic Instability Helps Cancers Become Progressively More Resistant to Therapies New Therapies Are Emerging from Our Knowledge of Cancer Biology Small Molecules Can Be Designed to Inhibit Specific Oncogenic Proteins Tumor Blood Vessels Are Logical Targets for Cancer Therapy Many Cancers May Be Treatable by Enhancing the Immune Response Against a Specific Tumor Treating Patients with Several Drugs Simultaneously Has Potential Advantages for Cancer Therapy Gene Expression Profiling Can Help Classify Cancers into Clinically Meaningful Subgroups 1256 1257 1257 1257 1259 1260 1260 1262 1262 1263 FERTILIZATION 1297 Ejaculated Sperm Become Capacitated in the Female Genital Tract 1297 Capacitated Sperm Bind to the Zona Pellucida and Undergo an Acrosome Reaction 1298 The Mechanism of Sperm–Egg Fusion Is Still Unknown 1298 Sperm Fusion Activates the Egg by Increasing Ca2+ in the Cytosol 1299 The Cortical Reaction Helps Ensure That Only One Sperm Fertilizes the Egg 1300 The Sperm Provides Centrioles as Well as Its Genome to the Zygote 1301 IVF and ICSI Have Revolutionized the Treatment of Human Infertility 1301 Summary 1303 References 1304 Chapter 22 Development of Multicellular Organisms UNIVERSAL MECHANISMS OF ANIMAL DEVELOPMENT Animals Share Some Basic Anatomical Features 1305 1305 1307 1264 . and Fertilization OVERVIEW OF SEXUAL REPRODUCTION The Haploid Phase in Higher Eucaryotes Is Brief Meiosis Creates Genetic Diversity Sexual Reproduction Gives Organisms a Competitive Advantage Summary FINDING THE CANCER-CRITICAL GENES The Identification of Gain-of-Function and Loss-of-Function Mutations Requires Different Methods Retroviruses Can Act as Vectors for Oncogenes That Alter Cell Behavior Different Searches for Oncogenes Have Converged on the Same Gene—Ras Studies of Rare Hereditary Cancer Syndromes First Identified Tumor Suppressor Genes Tumor Suppressor Genes Can Also Be Identified from Studies of Tumors Both Genetic and Epigenetic Mechanisms Can Inactivate Tumor Suppressor Genes Genes Mutated in Cancer Can Be Made Overactive in Many Ways The Hunt for Cancer-Critical Genes Continues Summary 1230 1231 1232 1233 1234 1235 1235 1237 1239 1240 1269 1269 1269 1271 1271 1272 MEIOSIS Gametes Are Produced by Two Meiotic Cell Divisions Duplicated Homologs (and Sex Chromosomes) Pair During Early Prophase I Homolog Pairing Culminates in the Formation of a Synaptonemal Complex Homolog Segregation Depends on Meiosis-Specific. Gap. While the Neural Plate Rolls Up to Form the Neural Tube A Gene-Expression Oscillator Controls Segmentation of the Mesoderm Into Somites Delayed Negative Feedback May Generate the Oscillations of the Segmentation Clock Embryonic Tissues Are Invaded in a Strictly Controlled Fashion by Migratory Cells The Distribution of Migrant Cells Depends on Survival Factors as Well as Guidance Cues 1363 1364 1365 1365 1366 1367 1368 1369 1370 1371 1373 1373 1375 DROSOPHILA AND THE MOLECULAR GENETICS OF PATTERN FORMATION: GENESIS OF THE BODY PLAN 1328 The Insect Body Is Constructed as a Series of Segmental Units 1329 Drosophila Begins Its Development as a Syncytium 1330 Genetic Screens Define Groups of Genes Required for Specific Aspects of Early Patterning 1332 Interactions of the Oocyte With Its Surroundings Define the Axes of the Embryo: the Role of the Egg-Polarity Genes 1333 The Dorsoventral Signaling Genes Create a Gradient of a Nuclear Gene Regulatory Protein 1334 Dpp and Sog Set Up a Secondary Morphogen Gradient to Refine the Pattern of the Dorsal Part of the Embryo 1336 The Insect Dorsoventral Axis Corresponds to the Vertebrate Ventrodorsal Axis 1336 Three Classes of Segmentation Genes Refine the Anterior–Posterior Maternal Pattern and Subdivide the Embryo 1336 The Localized Expression of Segmentation Genes Is Regulated by a Hierarchy of Positional Signals 1337 The Modular Nature of Regulatory DNA Allows Genes to Have Multiple Independently Controlled Functions 1339 . Hedgehog. Controls Developmental Patterning Morphogens Are Long-Range Inducers That Exert Graded Effects Extracellular Inhibitors of Signal Molecules Shape the Response to the Inducer Developmental Signals Can Spread Through Tissue in Several Different Ways Programs That Are Intrinsic to a Cell Often Define the Time-Course of its Development Initial Patterns Are Established in Small Fields of Cells and Refined by Sequential Induction as the Embryo Grows Summary 1308 1309 1310 1311 1311 1312 1313 1313 1314 1315 1316 1316 1317 1318 1319 1319 1320 1340 1341 HOMEOTIC SELECTOR GENES AND THE PATTERNING OF THE ANTEROPOSTERIOR AXIS The Hox Code Specifies Anterior-Posterior Differences Homeotic Selector Genes Code for DNA-Binding Proteins That Interact with Other Gene Regulatory Proteins The Homeotic Selector Genes Are Expressed Sequentially According to Their Order in the Hox Complex The Hox Complex Carries a Permanent Record of Positional Information The Anteroposterior Axis Is Controlled by Hox Selector Genes in Vertebrates Also Summary 1341 1342 1342 1343 1344 1344 1347 ORGANOGENESIS AND THE PATTERNING OF APPENDAGES Conditional and Induced Somatic Mutations Make it Possible to Analyze Gene Functions Late in Development Body Parts of the Adult Fly Develop From Imaginal Discs Homeotic Selector Genes Are Essential for the Memory of Positional Information in Imaginal Disc Cells Specific Regulatory Genes Define the Cells That Will Form an Appendage The Insect Wing Disc Is Divided into Compartments Four Familiar Signaling Pathways Combine to Pattern the Wing Disc: Wingless. Gene Cloning and Sequencing Reveal Its Molecular Mechanisms Cells Change Over Time in Their Responsiveness to Developmental Signals Heterochronic Genes Control the Timing of Development Cells Do Not Count Cell Divisions in Timing Their Internal Programs Selected Cells Die by Apoptosis as Part of the Program of Development Summary 1321 1321 1322 1323 1324 1325 1325 1326 1327 1327 1328 CELL MOVEMENTS AND THE SHAPING OF THE VERTEBRATE BODY The Polarity of the Amphibian Embryo Depends on the Polarity of the Egg Cleavage Produces Many Cells from One Gastrulation Transforms a Hollow Ball of Cells into a Three-Layered Structure with a Primitive Gut The Movements of Gastrulation Are Precisely Predictable Chemical Signals Trigger the Mechanical Processes Active Changes of Cell Packing Provide a Driving Force for Gastrulation Changing Patterns of Cell Adhesion Molecules Force Cells Into New Arrangements The Notochord Elongates. Others Can Activate the Program for Creation of an Entire Organ Summary 1347 1348 1349 1351 1351 1352 1353 1353 1355 1356 1357 1357 1358 1359 1361 1362 1362 1363 CAENORHABDITIS ELEGANS: DEVELOPMENT FROM THE PERSPECTIVE OF THE INDIVIDUAL CELL Caenorhabditis elegans Is Anatomically Simple Cell Fates in the Developing Nematode Are Almost Perfectly Predictable Products of Maternal-Effect Genes Organize the Asymmetric Division of the Egg Progressively More Complex Patterns Are Created by Cell–Cell Interactions Microsurgery and Genetics Reveal the Logic of Developmental Control. and Pair-Rule Genes Create a Transient Pattern That Is Remembered by Other Genes Summary Multicellular Animals Are Enriched in Proteins Mediating Cell Interactions and Gene Regulation Regulatory DNA Defines the Program of Development Manipulation of the Embryo Reveals the Interactions Between Its Cells Studies of Mutant Animals Identify the Genes That Control Developmental Processes A Cell Makes Developmental Decisions Long Before It Shows a Visible Change Cells Have Remembered Positional Values That Reflect Their Location in the Body Inductive Signals Can Create Orderly Differences Between Initially Identical Cells Sister Cells Can Be Born Different by an Asymmetric Cell Division Positive Feedback Can Create Asymmetry Where There Was None Before Positive Feedback Generates Patterns. and Notch The Size of Each Compartment Is Regulated by Interactions Among Its Cells Similar Mechanisms Pattern the Limbs of Vertebrates Localized Expression of Specific Classes of Gene Regulatory Proteins Foreshadows Cell Differentiation Lateral Inhibition Singles Out Sensory Mother Cells Within Proneural Clusters Lateral Inhibition Drives the Progeny of the Sensory Mother Cell Toward Different Final Fates Planar Polarity of Asymmetric Divisions is Controlled by Signaling via the Receptor Frizzled Asymmetric Stem-Cell Divisions Generate Additional Neurons in the Central Nervous System Asymmetric Neuroblast Divisions Segregate an Inhibitor of Cell Division into Just One of the Daughter Cells Notch Signaling Regulates the Fine-Grained Pattern of Differentiated Cell Types in Many Different Tissues Some Key Regulatory Genes Define a Cell Type. and Provides Memory A Small Set of Signaling Pathways. Dpp.xxii Detailed Contents Egg-Polarity. Creates All-or-None Outcomes. Used Repeatedly. AND REGENERATION OF SKELETAL MUSCLE Myoblasts Fuse to Form New Skeletal Muscle Fibers 1463 1464 . Notch Signaling Between Endothelial Cells Regulates the Response Signals from Endothelial Cells Control Recruitment of Pericytes and Smooth Muscle Cells to Form the Vessel Wall Summary 1445 1445 1446 1447 1448 1450 1450 RENEWAL BY MULTIPOTENT STEM CELLS: BLOOD CELL FORMATION The Three Main Categories of White Blood Cells Are Granulocytes. and Macrophages Collaborate to Keep the Airways Clean The Lining of the Small Intestine Renews Itself Faster Than Any Other Tissue Wnt Signaling Maintains the Gut Stem-Cell Compartment Notch Signaling Controls Gut Cell Diversification Ephrin–Eph Signaling Controls the Migrations of Gut Epithelial Cells Wnt. Stem Cells. MODULATION. AND ENDOTHELIAL CELLS Endothelial Cells Line All Blood Vessels and Lymphatics Endothelial Tip Cells Pioneer Angiogenesis Different Types of Endothelial Cells Form Different Types of Vessel Tissues Requiring a Blood Supply Release VEGF. and BMP Signaling Pathways Combine to Delimit the Stem-Cell Niche The Liver Functions as an Interface Between the Digestive Tract and the Blood Liver Cell Loss Stimulates Liver Cell Proliferation Tissue Renewal Does Not Have to Depend on Stem Cells: InsulinSecreting Cells in the Pancreas Summary 1434 1434 1434 1436 1438 1439 1440 1441 1442 1443 1444 1445 PLANT DEVELOPMENT Arabidopsis Serves as a Model Organism for Plant Molecular Genetics The Arabidopsis Genome Is Rich in Developmental Control Genes Embryonic Development Starts by Establishing a Root–Shoot Axis and Then Halts Inside the Seed The Parts of a Plant Are Generated Sequentially by Meristems Development of the Seedling Depends on Environmental Signals Long-Range Hormonal Signals Coordinate Developmental Events in Separate Parts of the Plant The Shaping of Each New Structure Depends on Oriented Cell Division and Expansion Each Plant Module Grows From a Microscopic Set of Primordia in a Meristem Polarized Auxin Transport Controls the Pattern of Primordia in the Meristem Cell Signaling Maintains the Meristem Regulatory Mutations Can Transform Plant Topology by Altering Cell Behavior in the Meristem The Switch to Flowering Depends on Past and Present Environmental Cues Homeotic Selector Genes Specify the Parts of a Flower Summary References 1398 1398 1399 1400 1403 1403 1403 1406 1407 1408 1409 1410 1412 1413 1415 1415 BLOOD VESSELS. Hedgehog. and Lymphocytes The Production of Each Type of Blood Cell in the Bone Marrow Is Individually Controlled Bone Marrow Contains Hemopoietic Stem Cells A Multipotent Stem Cell Gives Rise to All Classes of Blood Cells Commitment Is a Stepwise Process Divisions of Committed Progenitor Cells Amplify the Number of Specialized Blood Cells Stem Cells Depend on Contact Signals From Stromal Cells Factors That Regulate Hemopoiesis Can Be Analyzed in Culture Erythropoiesis Depends on the Hormone Erythropoietin Multiple CSFs Influence Neutrophil and Macrophage Production The Behavior of a Hemopoietic Cell Depends Partly on Chance Regulation of Cell Survival Is as Important as Regulation of Cell Proliferation Summary 1450 1451 1453 1454 1456 1456 1457 1458 1459 1459 1460 1461 1462 1462 Chapter 23 Specialized Tissues. LYMPHATICS. PDGF. Monocytes. and Tissue Renewal EPIDERMIS AND ITS RENEWAL BY STEM CELLS 1417 1417 1419 1420 1420 1421 Epidermal Cells Form a Multilayered Waterproof Barrier Differentiating Epidermal Cells Express a Sequence of Different Genes as They Mature Stem Cells in the Basal Layer Provide for Renewal of the Epidermis The Two Daughters of a Stem Cell Do Not Always Have to Become Different GENESIS.Detailed Contents Left–Right Asymmetry of the Vertebrate Body Derives From Molecular Asymmetry in the Early Embryo Summary The Basal Layer Contains Both Stem Cells and Transit Amplifying Cells Transit amplifying Divisions Are Part of the Strategy of Growth Control Stem Cells of Some Tissues Selectively Retain Original DNA Strands The Rate of Stem-Cell Division Can Increase Dramatically When New Cells Are Needed Urgently Many Interacting Signals Govern Epidermal Renewal The Mammary Gland Undergoes Cycles of Development and Regression Summary xxiii 1376 1377 1422 1423 1424 1425 1426 1426 1428 THE MOUSE Mammalian Development Begins With a Specialized Preamble The Early Mammalian Embryo Is Highly Regulative Totipotent Embryonic Stem Cells Can Be Obtained From a Mammalian Embryo Interactions Between Epithelium and Mesenchyme Generate Branching Tubular Structures Summary 1378 1378 1380 1380 1381 1382 NEURAL DEVELOPMENT Neurons Are Assigned Different Characters According to the Time and Place Where They Are Born The Character Assigned to a Neuron at Its Birth Governs the Connections It Will Form Each Axon or Dendrite Extends by Means of a Growth Cone at Its Tip The Growth Cone Pilots the Developing Neurite Along a Precisely Defined Path In Vivo Growth Cones Can Change Their Sensibilities as They Travel Target Tissues Release Neurotrophic Factors That Control Nerve Cell Growth and Survival Neuronal Specificity Guides the Formation of Orderly Neural Maps Axons From Different Regions of the Retina Respond Differently to a Gradient of Repulsive Molecules in the Tectum Diffuse Patterns of Synaptic Connections Are Sharpened by Activity-Dependent Remodeling Experience Molds the Pattern of Synaptic Connections in the Brain Adult Memory and Developmental Synapse Remodeling May Depend on Similar Mechanisms Summary 1383 1383 1385 1386 1387 1389 1389 1391 1392 1393 1395 1396 1397 SENSORY EPITHELIA Olfactory Sensory Neurons Are Continually Replaced Auditory Hair Cells Have to Last a Lifetime Most Permanent Cells Renew Their Parts: the Photoreceptor Cells of the Retina Summary 1429 1429 1430 1432 1433 THE AIRWAYS AND THE GUT Adjacent Cell Types Collaborate in the Alveoli of the Lungs Goblet Cells. Ciliated Cells. T Lymphocytes Develop in the Thymus The Adaptive Immune System Works by Clonal Selection Most Antigens Activate Many Different Lymphocyte Clones Immunological Memory Involves Both Clonal Expansion and Lymphocyte Differentiation Immunological Tolerance Ensures That Self Antigens Are Not Normally Attacked Lymphocytes Continuously Circulate Through Peripheral Lymphoid Organs Summary 1539 1540 1540 1541 1543 1544 1545 1545 1547 1549 1551 Chapter 24 Pathogens. Pore Formation. Each with Different Biological Properties The Strength of an Antibody–Antigen Interaction Depends on Both the Number and the Affinity of the Antigen-Binding Sites Antibody Light and Heavy Chains Consist of Constant and Variable Regions The Light and Heavy Chains Are Composed of Repeating Ig Domains An Antigen-Binding Site Is Constructed from Hypervariable Loops Summary 1551 1552 1552 1552 1553 CELL BIOLOGY OF INFECTION 1501 1557 1558 1559 1560 1561 Pathogens Cross Protective Barriers to Colonize the Host 1501 Pathogens That Colonize Epithelia Must Avoid Clearance by the Host 1502 Intracellular Pathogens Have Mechanisms for Both Entering and Leaving Host Cells 1504 Virus Particles Bind to Molecules Displayed on the Host Cell Surface 1505 Virions Enter Host Cells by Membrane Fusion. or Membrane Disruption 1506 Bacteria Enter Host Cells by Phagocytosis 1507 Intracellular Eucaryotic Parasites Actively Invade Host Cells 1508 Many Pathogens Alter Membrane Traffic in the Host Cell 1511 Viruses and Bacteria Use the Host Cell Cytoskeleton for Intracellular Movement 1514 Viral Infections Take Over the Metabolism of the Host Cell 1517 Pathogens Can Alter the Behavior of the Host Organism to Facilitate the Spread of the Pathogen 1518 THE GENERATION OF ANTIBODY DIVERSITY Antibody Genes Are Assembled From Separate Gene Segments During B Cell Development Imprecise Joining of Gene Segments Greatly Increases the Diversity of V Regions The Control of V(D)J Recombination Ensures That B Cells Are Monospecific Antigen-Driven Somatic Hypermutation Fine-Tunes Antibody Responses B Cells Can Switch the Class of Antibody They Make Summary 1562 1562 1564 1565 1566 1567 1568 . Infection. Heart Disease. and Other Chronic Illnesses Summary 1485 1486 1486 1487 1488 1489 1494 1496 1498 1499 1501 B CELLS AND ANTIBODIES B Cells Make Antibodies as Both Cell-Surface Antigen Receptors and Secreted Proteins A Typical Antibody Has Two Identical Antigen-Binding Sites An Antibody Molecule Is Composed of Heavy and Light Chains There Are Five Classes of Antibody Heavy Chains. and Innate Immunity INTRODUCTION TO PATHOGENS Pathogens Have Evolved Specific Mechanisms for Interacting with Their Hosts The Signs and Symptoms of Infection May Be Caused by the Pathogen or by the Host’s Responses Pathogens Are Phylogenetically Diverse Bacterial Pathogens Carry Specialized Virulence Genes Fungal and Protozoan Parasites Have Complex Life Cycles with Multiple Forms All Aspects of Viral Propagation Depend on Host Cell Machinery Prions Are Infectious Proteins Infectious Disease Agents Are Linked To Cancer. Engulf.xxiv Detailed Contents Pathogens Evolve Rapidly Antigenic Variation in Pathogens Occurs by Multiple Mechanisms Error-Prone Replication Dominates Viral Evolution Drug-Resistant Pathogens Are a Growing Problem Summary 1518 1519 1520 1521 1524 Muscle Cells Can Vary Their Properties by Changing the Protein Isoforms They Contain Skeletal Muscle Fibers Secrete Myostatin to Limit Their Own Growth Some Myoblasts Persist as Quiescent Stem Cells in the Adult Summary 1465 1465 1466 1467 FIBROBLASTS AND THEIR TRANSFORMATIONS: THE CONNECTIVE-TISSUE CELL FAMILY Fibroblasts Change Their Character in Response to Chemical Signals The Extracellular Matrix May Influence Connective-Tissue Cell Differentiation by Affecting Cell Shape and Attachment Osteoblasts Make Bone Matrix Most Bones Are Built Around Cartilage Models Bone Is Continually Remodeled by the Cells Within It Osteoclasts Are Controlled by Signals From Osteoblasts Fat Cells Can Develop From Fibroblasts Leptin Secreted by Fat Cells Provides Feedback to Regulate Eating Summary 1467 1467 1468 1469 1470 1472 1473 1474 1475 1476 BARRIERS TO INFECTION AND THE INNATE IMMUNE SYSTEM Epithelial Surfaces and Defensins Help Prevent Infection Human Cells Recognize Conserved Features of Pathogens Complement Activation Targets Pathogens for Phagocytosis or Lysis Toll-like Proteins and NOD Proteins Are an Ancient Family of Pattern Recognition Receptors Phagocytic Cells Seek. and Destroy Pathogens Activated Macrophages Contribute to the Inflammatory Response at Sites of Infection Virus-Infected Cells Take Drastic Measures to Prevent Viral Replication Natural Killer Cells Induce Virus-Infected Cells to Kill Themselves Dendritic Cells Provide the Link Between the Innate and Adaptive Immune Systems Summary References 1524 1525 1526 1528 1530 1531 1533 1534 1535 1536 1537 1537 STEM-CELL ENGINEERING Hemopoietic Stem Cells Can Be Used to Replace Diseased Blood Cells with Healthy Ones Epidermal Stem Cell Populations Can Be Expanded in Culture for Tissue Repair Neural Stem Cells Can Be Manipulated in Culture Neural Stem Cells Can Repopulate the Central Nervous System Stem Cells in the Adult Body Are Tissue-Specific ES Cells Can Make Any Part of the Body Patient-Specific ES Cells Could Solve the Problem of Immune Rejection ES Cells Are Useful for Drug Discovery and Analysis of Disease Summary References 1476 1477 1477 1478 1478 1479 1480 1481 1482 1482 1483 Chapter 25 The Adaptive Immune System LYMPHOCYTES AND THE CELLULAR BASIS OF ADAPTIVE IMMUNITY Lymphocytes Are Required for Adaptive Immunity The Innate and Adaptive Immune Systems Work Together B Lymphocytes Develop in the Bone Marrow. Detailed Contents T CELLS AND MHC PROTEINS T Cell Receptors (TCRs) Are Antibodylike Heterodimers Antigen Presentation by Dendritic Cells Can Either Activate or Tolerize T Cells Effector Cytotoxic T Cells Induce Infected Target Cells to Kill Themselves Effector Helper T Cells Help Activate Other Cells of the Innate and Adaptive Immune Systems Regulatory T Cells Suppress the Activity of Other T Cells T Cells Recognize Foreign Peptides Bound to MHC Proteins MHC Proteins Were Identified in Transplantation Reactions Before Their Functions Were Known Class I and Class II MHC Proteins Are Structurally Similar Heterodimers An MHC Protein Binds a Peptide and Interacts with a T Cell Receptor MHC Proteins Help Direct T Cells to Their Appropriate Targets CD4 and CD8 Co-Receptors Bind to Invariant Parts of MHC Proteins Cytotoxic T Cells Recognize Fragments of Foreign Cytosolic Proteins in Association with Class I MHC Proteins Helper T Cells Respond to Fragments of Endocytosed Foreign Protein Associated with Class II MHC Proteins Potentially Useful T Cells Are Positively Selected in the Thymus xxv 1569 1570 1571 1572 1573 1574 1575 1575 1576 1577 1579 1580 1581 1583 1585 Most Developing Cytotoxic and Helper T Cells That Could Be Activated by Self-Peptide–MHC Complexes Are Eliminated in the Thymus Some Organ-Specific Proteins Are Ectopically Expressed in the Thymus Medulla The Function of MHC Proteins Helps Explain Their Polymorphism Summary 1586 1587 1588 1588 HELPER T CELLS AND LYMPHOCYTE ACTIVATION Activated Dendritic Cells Use Multiple Mechanisms to Activate T Cells The Activation of T Cells Is Controlled by Negative Feedback The Subclass of Effector Helper T Cell Determines the Nature of the Adaptive Immune Response TH1 Cells Activate Infected Macrophages and Stimulate An Inflammatory Response Antigen Binding to B Cell Receptors (BCRs) Is Only One Step in B Cell Activation Antigen-Specific Helper T Cells Are Essential for Activating Most B Cells A Special Class of B Cells Recognize T-Cell-Independent Antigens Immune Recognition Molecules Belong to the Ancient Ig Superfamily Summary References 1589 1590 1591 1592 1594 1595 1597 1598 1599 1600 1600 . Hiten Madhani (University of California. San Francisco).) Chapter 1: W. Peter Shaw (John Innes Centre. San Francisco). San Francisco). San Francisco). Douglas Kellogg (University of California. San Francisco). Bertil Hille (University of Washington). Ulrich Laemmli (University of Geneva. Rick Wood (University of Pittsburgh) Chapter 6: Raul Andino (University of California. David Bartel (Massachusetts Institute of Technology). second. Canada). Germany). Robert Stroud (University of California. Santa Cruz). Thomas Lindahl (Cancer Research. Martinsried). San Francisco). Martinsried). Alexander Varshavsky (California Institute of Technology). San Francisco). Janet Thornton (European Bioinformatics Institute. Roger Kornberg (Stanford University). Eugene Koonin (National Institutes of Health). San Francisco). Roy Parker (University of Arizona). Mitchell Sogin (Woods Hole Institute) Chapter 2: Michael Cox (University of Wisconsin. Ken Sawin (The Wellcome Trust Centre for Cell Biology. Louise Johnson (University of Oxford). Jonathan Weissman (University of California. David Tollervey (University of Edinburgh. San Francisco). Maynard Olson (University of Washington) Chapter 5: Elizabeth Blackburn (University of California. San Francisco). Steven West (Cancer Research. Robert Sauer (Massachusetts Institute of Technology). San Francisco). Lily Jan (University of California. Switzerland). Mark Ptashne (Memorial Sloan-Kettering Center). Douglas Koshland (Carnegie Institution of Washington. Ronald Vale (University of California. Berkeley). Joachim Li (University of California. UK). Christine Guthrie (University of California. (Those who helped on this edition are listed first. Robert Edwards (University of California. Frankfurt am Main). UK). Reinhard Lührman (Max Planck Institute of Biophysical Chemistry. Adrian Bird (Wellcome Trust Centre. UK). Elliott Margulies (National Institutes of Health). Madison). San Francisco). Jennifer Frazier (Exploratorium®. Nikolaus Pfanner (University of Freiburg. Christopher Mathews (Oregon State University). Richard Ebright (Rutgers University). Frank Holstege (University Medical Center. Jennifer Lippincott-Schwartz (National Institutes of Health) Chapter 10: Ari Helenius (Swiss Federal Institute of Technology Zürich. Steve Harrison (Harvard University). as well as those who helped in preparing the first. those who helped with the first. Daniel Finley (Harvard University). San Francisco) Chapter 7: Raul Andino (University of California. Roger Nicoll (University of California. Geeta Narlikar (University of California. second. Aziz Sancar (University of North Carolina. Donald Voet (University of Pennsylvania). Jack Szostak (Harvard Medical School. Ueli Schibler (University of Geneva. Greg Petsko (Brandeis University). Karsten Weis (University of California. San Francisco). Frankfurt am Main). San Francisco). James Haber (Brandeis University). Robert Stroud (University of California. Quinn Mitrovich (University of California. Joseph Gall (Carnegie Institution of Washington). Daniel Schnell (University of Massachusetts. Susan Wente (Vanderbilt University . Carol Gross (University of California. Ramanujan Hegde (National Institutes of Health). (Harry Noller (University of California. third and fourth editions follow. Hiten Madhani (University of California. Howard Hughes Medical Institute). Werner Kühlbrandt (Max Planck Institute of Biophysics. Los Angeles). Switzerland). Susan Gasser (University of Geneva. Roger Kornberg (Stanford University). Michael Green (University of Massachusetts Medical School). Santa Cruz). Ford Doolittle (Dalhousie University. Gary Felsenfeld (National Institutes of Health). San Francisco). Baltimore). Rodney Rothstein (Columbia University). Michael Bulger (University of Rochester Medical Center). Carol Gross (University of California. Dieter Osterhelt (Max Planck Institute of Biochemistry. Michael Green (University of Massachusetts Medical School). UK). Michael Lynch (Indiana University). Bruce Stillman (Cold Spring Harbor Laboratory). Switzerland). We would like to thank the following for their suggestions in preparing this edition. Amherst). Nancy Kleckner (Harvard University). David Bartel (Massachusetts Institute of Technology). The Netherlands). San Francisco). Barbara Panning (University of California. Art Horwich (Yale University School of Medicine). Dresden) Chapter 11: Wolfhard Almers (Oregon Health and Science University). third and fourth editions. Amherst) Chapter 12: Larry Gerace (The Scripps Research Institute). San Francisco). San Francisco) Chapter 9: Wolfgang Baumeister (Max Planck Institute of Biochemistry. Kai Simons (Max Planck Institute of Molecular Cell Biology and Genetics. Joan Steitz (Yale University). San Francisco). Patrick Williamson (University of Massachusetts. San Francisco). Azim Surani (University of Cambridge) Chapter 8: Wallace Marshall [major contribution] (University of California. John Wilson (Baylor College of Medicine) Chapter 3: David Eisenberg (University of California. Eric Green (National Institutes of Health). UK). Chapel Hill). Göttingen). UK). Switzerland). UK) Chapter 4: David Allis (The Rockefeller University). Werner Kühlbrandt (Max Planck Institute of Biophysics.xxvi Acknowledgments In writing this book we have benefited greatly from the advice of many biologists and biochemists. Chapel Hill). San Francisco) Chapter 17: David Morgan [major contribution] (University of California. Joseph Lipsick (Stanford University School of Medicine). San Francisco). Berkeley). UK). St. Morgan Sheng (Massachusetts Institute of Technology). Berkeley). Dennis Bray (University of Cambridge). Ben Glick (University of Chicago). John Couchman (Imperial College. Johann De-Bono (The Institute of Cancer Research. Ralph Steinman (The Rockefeller University). Douglas Hanahan (University of California. Douglas Fearon (University of Cambridge). Ira Mellman (Yale University). Alfred Gilman (The University of Texas Southwestern Medical Center). Craig Thompson (Abramson Family Cancer Research Institute. Nicolas Tapon (London Research Institute) Chapter 23: Ralf Adams (London Research Institute). Cambridge). Kenneth Yamada (National Institutes of Health) Chapter 20: Laura Attardi [substantial contribution] (Stanford University). Jude Children’s Hospital) Chapter 18: Xiaodong Wang [substantial contribution] (The University of Texas Southwestern Medical School). Philippa Marrack (National Jewish Medical and Research Center. Diana Myles (University of California. UK). Francois Schweisguth (French National Centre for Scientific Research. UK). Arshad Desai (University of California. Frankfurt am Main). Michael Nussenzweig (Rockefeller University). Anton Berns (Netherlands Cancer Institute. Berkeley). Anne McLaren (Wellcome/ Cancer Research Campaign Institute. Caetano Reis e Sousa (Cancer Research. UK). Len Stephens (The Babraham Institute. Japan) Chapter 19: Jeffrey Axelrod (Stanford University Medical Center). Dresden). Larry Goldstein (University of California. Eric Karsenti (European Molecular Biology Laboratory. Johnson (The Gurdon Institute. Renee Reijo (University of California. Seattle). Denver). Richard Harland (University of California. Lewis Lanier (University of California. Scott Lowe (Cold Spring Harbor Laboratory). Azim Surani (The Gurdon Institute. Daniel St. Julie Pitcher (University College London). Charles Sherr (St. Terry Orr-Weaver (Massachusetts Institute of Technology). Graham Warren (Yale University). University of Pennsylvania). San Francisco). San Diego) Chapter 15: Nicholas Harberd [substantial contribution] (John Innes Centre. Ronald Vale (University of California. UK). Stuart Orkin (Harvard Medical School). UK) Chapter 24: Julie Theriot [major contribution] (Stanford University). Matthew Freeman (Laboratory of Molecular Biology. Charles Streuli (The University of Manchester. Brigid Hogan (Duke University). Alan Hall (MRC Laboratory for Molecular Biology and Cell Biology. San Francisco). Jude Children’s Hospital). San Diego). San Francisco). San Francisco). Robin Irvine (University of Cambridge). Douglas Green (St. Seattle). Roel Nusse (Stanford University). Daniel Goodenough (Harvard Medical School). Simon Hughes (Kings College. Lynn Enquist (Princeton University). San Diego). UK). Joe Howard (Max Planck Institute of Molecular Cell Biology and Genetics. Richard Hynes (Massachusetts Institute of Technology). Henry Bourne (University of California. Nancy Kleckner (Harvard University). Germany). Fred Bunz (Johns Hopkins). Stan Falkow (Stanford University). Michael Bishop (University of California. UK). Ari Helenius (Swiss Federal Institute of Technology Zürich. Fiona Watt (Cancer Research Institute. France). Bruce Edgar (Fred Hutchinson Cancer Research Center. Thomas Reh (University of Washington. Davis). San Diego). John Carroll (University College London). Matthias Falk (Lehigh University). Toronto). Daniel Portnoy (University of California. Alan Hall (Memorial Sloan-Kettering Cancer Center). Sankar Ghosh (Yale University School of Medicine). UK) Chapter 16: Julie Theriot [major contribution] (Stanford University). Germany). Michael Neuberger (University of Cambridge). Berkeley). Scott Hawley (Stowers Institute for Medical Research. Australia). San Diego). San Francisco). Elliott Meyerowitz (California Institute of Technology). Jerry Adams (The Walter and Eliza Hall Institute of Medical Research. Frankfurt am Main) Chapter 14: Michael Gray (Dalhousie University). Marino Zerial (Max Planck Institute of Molecular Cell Biology and Genetics. Caroline Damsky (University of California. Andrew Halestrap (University of Bristol. San Francisco). Walter Birchmeier (Max-Delbrück Center for Molecular Medicine. Abby Dernburg (University of Califonia. Japan). Switzerland). Michael Bishop (University of California. France). Neil Hunter (University of California. Cambridge). Kenneth Irvine (Rutgers University). Craig Thompson (University of Pennsylvania). Jonathan Pines (Gurdon Institute. Louis). Kansas City). Paul Edwards (University of Cambridge). San Francisco). Konrad Basler (University of Zürich. San Francisco). UK). Jeffrey Gordon (Washington University. UK). Sweden). Harald von Boehmer (Harvard Medical School). Pat Williamson (University of Massachusetts. Jim Smith (The Gurdon Institute. Daniel Louvard (Institut Curie. Carl-Henrik Heldin (Ludwig Institute for Cancer Research. Michael Karin (University of California. Michael Yaffe (University of California. Michael Glotzer (University of Chicago). UK). Hans Clevers (Hubrecht Institute. James Briscoe (National Institute for Medical Research. The Netherlands). Ian Tomlinson (Cancer Research. Davis). Douglas Fearon (University of Cambridge). UK). Shigekazu Nagata (Kyoto University. Martin Humphries (University of Manchester. Ken Keegstra (Michigan State University). San Diego). UK). Henry Bourne (University of California. Bjorn Olsen (Harvard Medical School). William McGinnis (University of California. San Francisco). UK). Kim Nasmyth (University of Oxford).Acknowledgments Medical Center). Hugh Pelham (The Medical Research Council. William Paul (National Institutes of . Austin Smith (University of Edinburgh. UK). Giampietro Schiavo (London Research Institute). UK). Amherst) Chapter 13: Scott Emr (University of California. San Francisco). Timothy Mitchison (Harvard Medical School). Charles Streuli (University of Manchester. Paul Wassarman (Mount Sinai School of Medicine) Chapter 22: Julie Ahringer (The Gurdon Institute. The Netherlands). Canada). Robert Weinberg (Massachusetts Institute of Technology) Chapter 21: Patricia Calarco (University of California. San Francisco). Richard Locksley (University of California. James Ferrell (Stanford University). Tony Pawson (Mount Sinai Hospital. Gerald Schatten (Pittsburgh Development Center). UK). Elliott Meyerowitz (California Institute of Technology). Masatoshi Takeichi (RIKEN xxvii Kobe Institute. Rebecca Heald (University of California. Switzerland). UK). Cambridge). UK). David Garrod (University of Manchester. UK). Keith Burridge (University of North Carolina. Bruce Ponder (University of Cambridge). Lewis Lanier (University of California. Gary Ward (University of Vermont) Chapter 25: Harald von Boehmer (Harvard Medical School). Laura Machesky (The University of Birmingham. Elizabeth Robertson (The Wellcome Trust Centre for Human Genetics. John Dick (University of Toronto. UK). UK). Holger Gerhardt (London Research Institute). Werner Kühlbrandt (Max Planck Institute of Biophysics. Henry Bourne (University of California. Michael Bennett (Albert Einstein College of Medicine). Michael Akam (University of Cambridge). San Francisco). John Hopfield (Princeton University). Nancy Hollingsworth (State University of New York. Nick Rudzik (University of Toronto. Ernst Hafen (Universitat Zurich). Ira Herskowitz (deceased). Daniel Goodenough (Harvard Medical School). Michael Dexter (The Wellcome Trust. Adelaide Carpenter (University of California. Stony Brook). Mark Bretscher (MRC Laboratory of Molecular Biology. Robert Cohen (University of California. Glossary Eleanor Lawrence. Michael Carey (University of California. Joseph Gall (Yale University). Sherry Granum Readers David Kashatus (Duke University). San Francisco). San Francisco). Andre Brandli (Swiss Federal Institute of Technology. UK). Los Angeles). Madison). Michael Glotzer (University of Vienna. UK). Boston). Christopher Dobson (University of Cambridge). Germany). Robert Brooks (King’s College London). Ray Evert (University of Wisconsin. Mario Capecchi (University of Utah). Canada). and fourth editions David Agard (University of California. Seattle). Boulder). Fred Alt (CBR Institute for Biomedical Research. Larry Gerace (The Scripps Research Institute). Caetano Reis e Sousa (Cancer Research. Klaus Rajewsky (Harvard Medical School). Gary Felsenfeld (National Institutes of Health). Adrian Harwood (MRC Laboratory for Molecular Cell Biology and Cell Biology Unit. Marianne BronnerFraser (California Institute of Technology). John Hall (University of Southampton. Pierre Chambon (University of Strasbourg). Alan Hinnebusch (National Institutes of Health. Los Angeles). Zacheus Cande (University of California. Rehovot. London). Steve Burden (New York University of Medicine). Martinsried). San Francisco). Russell Doolittle (University of California. Jonathan Howard (University of Washington. Stanley Falkow (Stanford University). Graham Hardie (University of Dundee. Peter Gould (Middlesex Hospital Medical School. David Eisenberg (University of California. Chapel Hill). David Bartel (Massachusetts Institute of Technology). Daniel Friend (University of California. Carol Gross (University of California. John Heath (University of Birmingham. Ruth Ellman (Institute of Cancer Research. Graham Dunn (MRC Cell Biophysics Unit. David Birk (UMNDJ—Robert Wood Johnson Medical School). Richard Henderson (MRC Laboratory of Molecular Biology. Nicholas Harberd (John Innes Centre. Tim Bliss (National Institute for Medical Research. Jonathan Ashmore (University College London). London). Seattle). Berkeley). Anthony DeFranco (University of California. Linda Amos (MRC Laboratory of Molecular Biology. London). Leroy Hood (Institute for Systems Biology. Michael Brown (University of Oxford). Norwich. Robert Edwards (University of California. Tim Hunt Health). St. Richard Harland (University of California. Tom Cavalier-Smith (King’s College London). Charles Gilvarg (Princeton University). Seattle). Walter Gratzer (King’s College London). Bastien Gomperts (University College Hospital Medical School. Lewis Cantley (Harvard Medical School). Philip Cohen (University of Dundee. Christine Field (Harvard Medical School). San Francisco). Michael Ashburner (University of Cambridge). The Netherlands). Simon Hughes (King’s College London). Zach Hall (University of California. Austria). John Harris (University of Otago. Berkeley). Michael Bishop (University of California. San Francisco). Alan Grafen (University of Oxford). London). UK). Irvine). Ben Barres (Stanford University). Cambridge). The Netherlands). San Francisco). UK). Leslie Grivell (University of Amsterdam. Israel). Keith Dudley (King’s College London). Robert Fletterick (University of California. Oxford). Roger Cooke (University of California. San Francisco). Peter Baker (deceased). Cambridge). Elaine Fuchs (University of Chicago). David Epel (Stanford University). Charles Emerson (University of Virginia). San Diego). Hans Bode (University of California. Emmanuel Kreidl (University of Vienna. Merton Bernfield (Harvard Medical School). Brian Gunning (Australian National University. Bethesda). Stuart Cull-Candy (University College London). Comprehensive Cancer Center). Canada). Alan Hall (MRC Laboratory for Molecular Biology and Cell Biology. San Francisco). New Zealand). David Baldwin (Stanford University). Stephen Cohen (EMBL Heidelberg. Amherst). David Housman (Massachusetts Institute of Technology). London). Anthony Gardner-Medwin (University College London). James Crow (University of Wisconsin. San Francisco). Martha Arnaud (University of California.xxviii Acknowledgments Sarah Elgin (Washington University. Stuart Ferguson (University of Oxford). Jim Goodrich (University of Colorado. second. Jim Dunwell (John Innes Institute. Louis). Ralph Steinman (The Rockefeller University). San Francisco). Judah Folkman (Harvard Medical School). Christine Guthrie (University of California. Barry Brown (King’s College London). San Diego). Dea Shahinas (University of Toronto. University of Basel). Michael Banda (University of California. Roderick Capaldi (University of Oregon). London). Darwin Berg (University of California. UK). Julian Downward (Cancer Research. UK). James Hudspeth (The Rockefeller University). San Diego). Max Burger (University of Basel). Piet Borst (Jan Swammerdam Institute. Cambridge). third. Los Angeles). University of Amsterdam). Bernie Gilula (deceased). Louis). Stephen Burley (SGX Pharmaceuticals). London). Nancy Craig (Johns Hopkins University). UK). Austria). Canada) First. San Francisco). UK). San Francisco). Frank Grosveld (Erasmus Universiteit. Alan Boyde (University College London). Paul Edwards (University of Cambridge). UK). Charles Cantor (Columbia University). Scott Emr (University of California. Raul Andino (University of California. Sankar Ghosh (Yale University School of Medicine). Norwich. Zurich). Leslie Dale (University College London). Amherst). Richard Gardner (University of Oxford). Beverly Emerson (The Salk Institute). Sutton. Benny Geiger (Weizmann Institute of Science. Carl Branden (deceased). . Spyros ArtavanisTsakonas (Harvard Medical School). London). David Hanke (University of Cambridge). Frank Gertler (Massachusetts Institute of Technology). San Francisco). Norwich. Scotland). San Diego). Leland Hartwell (University of Washington. UK). Clay Armstrong (University of Pennsylvania). Berkeley). Berkeley). Ari Helenius (Yale University). Seattle). Larry Goldstein (University of California. Michael Berridge (The Babraham Institute. Keith Burridge (University of North Carolina. Canberra). Barry Gumbiner (Memorial Sloan-Kettering Cancer Center). Bertil Hille (University of Washington. Günther Gerisch (Max Planck Institute of Biochemistry. Tayna Awabdy (University of California. David Haig (Harvard University). San Diego). Madison). Peter Garland (Institute of Cancer Research. Walter Gehring (Biozentrum. Sharyn Endow (Duke University). Harvey Florman (Tufts University). Michael Grunstein (University of California. John Cairns (Radcliffe Infirmary. San Francisco). Howard Green (Harvard University). Jeffrey Hall (Brandeis University). Michael Green (University of Massachusetts. Gerard Evan (University of California. Stephen Harrison (Harvard University). Scotland). Gary Firestone (University of California. Glenn Herrick (University of Utah). Gerald Fischbach (Columbia University). John Gerhart (University of California. Larry Fowke (University of Saskatchewan. UK). Martin Humphries (University of Manchester. St. Cambridge). Martin Brand (University of Cambridge). San Francisco). Cornelia Bargmann (University of California. Enrico Coen (John Innes Institute. Tariq Enver (Institute of Cancer Research. Adrian Harris (Cancer Research. Reid Gilmore (University of Massachusetts. Robert Horvitz (Massachusetts Institute of Technology). John Cooper (Washington University School of Medicine. San Francisco). Jesse Roth (National Institutes of Health). Gordon Peters (Cancer Research. Gary Ruvkun (Massachusetts General Hospital). Richard Klausner (National Institutes of Health). Mark Mooseker (Yale University). Seattle). Harry Noller (University of California. Jeremy Hyams (University College London). Gail Martin (University of California. San Francisco). San Francisco). Peter Sarnow (Stanford University). Joseph Schlessinger (New York University Medical Center). Berkeley). Robin Lovell-Badge (National Institute for Medical Research. London). Richard Losick (Harvard University). Robert Kypta (MRC Laboratory for Molecular Cell Biology. Patrick O’Farrell (University of California. Tim Mitchison (Harvard Medical School). Berkeley). Eugene Koonin (National Institutes of Health). UK). Louis Reichardt (University of California. Philadelphia). Ron Kaback (University of California. San Diego). Chapel Hill). University of Basel). Howard Schachman (University of California. Berkeley). Paul Nurse (Cancer Research. Murdoch Mitchison (Harvard University). Dan Portnoy (University of California. J. Judith Kimble (University of Wisconsin. Terence Partridge (MRC Clinical Sciences Centre. James Priess (University of Washington. Tomas Lindahl (Cancer Research. Parson (University of Washington. Philip Ingham (University of Sheffield. Jane Langdale (University of Oxford). Montrose Moses (Duke University). Julie Pitcher (University College London). Cynthia Kenyon (University of California. Toronto). Maynard Olson (University of Washington. Joshua Sanes (Harvard University). Peter Lawrence (MRC Laboratory of Molecular Biology. UK). Chris Miller (Brandeis University). Barbara Panning (University of California. Nancy Kleckner (Harvard University). Ray Keller (University of California. Richard Hynes (Massachusetts Institute of Technology). Israel). Dan Littman (New York University School of Medicine). Boston). Michael Schramm (Hebrew University). Bethesda). Berkeley). Lefkowitz (Duke University). UK). Martin Rechsteiner (University of Utah. Andrew Murray (Harvard University). UK). Robert Mishell (University of Birmingham. Philippa Marrack (National Jewish Medical and Research Center. San Francisco). Trevor Lamb (University of Cambridge). Nelson (University of Illinois. Mark Marsh (Institute of Cancer Research. Tom Pollard (Yale University). San Francisco). Jordan Raff (Wellcome/CRC Institute. John Owen (University of Birmingham. Louis). UK). Hartmut Land (Cancer Research. Jim Rothman (Memorial Sloan-Kettering Cancer Center). San Francisco). Diana Myles (University of California. Cambridge). Charles Janeway (deceased). Jeffrey Pollard (Albert Einstein College of Medicine). Richard Myers (Stanford University). Barbara Meyer (University of California. Lisa Satterwhite (Duke University Medical School). Tom Jessell (Columbia University). David Phillips (The Rockefeller University). San Francisco). Laurence Hurst (University of Bath. Berkeley). Berkeley). David Nicholls (University of Dundee. Michael Levine (University of California. UK). George Palade (deceased). Frank McNally (University of California. Robert J. Tony Hyman (Max Planck Institute of Molecular Cell Biology & Genetics. Seattle). Avrion Mitchison (University College London). Anne McLaren (Wellcome/Cancer Research Campaign Institute. xxix N. UK). Switzerland). Hugh Pelham (MRC Laboratory of Molecular Biology. Robert Kingston (Massachusetts General Hospital). Arthur Johnson (Texas A & M University). Salt Lake City). Klaus Rajewsky (University of Cologne. Urbana-Champaign).Acknowledgments (Cancer Research. Jeremy PickettHeaps (The University of Melbourne. Vishu Lingappa (University of California. San Francisco). San Francisco). Terri Orr-Weaver (Massachusetts Institute of Technology). Los Angeles). Berkeley). Michelle Moritz (University of California. Roger Keynes (University of Cambridge). Walter Neupert (University of Munich. David Sabatini (New York University). San Francisco). Giampietro Schiavo (Cancer Research. Peter Mombaerts (The Rockefeller University). Albany). Scotland). Erin O’Shea (Harvard University). Irvine). San Francisco). San Francisco). Mike Klymkowsky (University of Colorado. Stuart Orkin (Children’s Hospital. Gottfried Schatz (Biozentrum. E. UK). UK). Paul Martin (University College London). Dale Purves (Duke University). San Francisco). Suzanne Noble (University of California. William E. Madison). Davis). Joan Massagué (Memorial Sloan-Kettering Cancer Center). Richard McCarty (Cornell University). Warren Levinson (University of California. Scotland). Brian McCarthy (University of California. Cambridge). Janet Rossant (Mount Sinai Hospital. Jennifer Lippincott-Schwartz (National Institutes of Health. Berkeley). Duncan O’Dell (deceased). Jay Lash (University of Pennsylvania). Douglas Kellogg (University of California. Elaine Robson (University of Reading. Seattle). Greg Petsko (Brandeis University). UK). Werner Kühlbrandt (Max Planck Institute for Biophysics. Andy Johnston (John Innes Institute. London). London). San Francisco). Mark Krasnow (Stanford University). Alex Levitzki (Hebrew University. Santa Cruz). San Francisco). Kelly Komachi (University of California. Basel). Alan Munro (University of Cambridge). Fred Richards (Yale University). London). Marilyn Kozak (University of Pittsburgh). Randy Schekman (University of California. UK). Australia). UK). Ulrich Laemmli (University of Geneva. Jordan (Queen Elizabeth College. Ira Mellman (Yale University). Mark E. Peter Lachmann (MRC Center. Robert Schreiber (Scripps Clinic and Research Institute). Norman Iscove (Ontario Cancer Institute. Joel Rosenbaum (Yale University). Erkki Ruoslahti (La Jolla Cancer Research Foundation). James Schwartz (Columbia . UK). UK). Elliot Meyerowitz (California Institute of Technology). Cambridge). Alan Sachs (University of California. Cambridge). Davis). Davis). San Francisco). Michael Neuberger (MRC Laboratory of Molecular Biology. UK). John Kuriyan (University of California. Stuart Kornfeld (Washington University.A. Regis Kelly (University of California. Daniel Koshland (University of California. Toronto). Marc Kirschner (Harvard University). Elio Raviola (Harvard Medical School). Boulder). Bruce Ponder (University of Cambridge). William Otto (Cancer Research.G. Tom Maniatis (Harvard University). St. Tony Pawson (Mount Sinai Hospital. Berkeley). Juan Korenbrot (University of California. Germany). Paul (National Institutes of Health). San Francisco). Dresden). Santa Cruz). Conly Rieder (Wadsworth Center. Laura Machesky (University of Birmingham. David Ish-Horowicz (Cancer Research. Dale Oxender (University of Michigan). William W. Denver). Joachim Li (University of California. Berkeley). Richard Scheller (Stanford University). Keith Mostov (University of California. San Francisco). Cambridge). Lily Jan (University of California. Jodi Nunnari (University of California. San Francisco). Ottoline Leyser (University of York. Cambridge). George Ratcliffe (University of Oxford). Davis). Efraim Racker (Cornell University). Shirley Lowe (University of California. Paul Lazarow (Mount Sinai School of Medicine). Tucson). Darwin Prockop (Tulane University). Hans Müller-Eberhard (Scripps Clinic and Research Institute). James Maller (University of Colorado Medical School). Robert Perry (Institute of Cancer Research. John Kendrick-Jones (MRC Laboratory of Molecular Biology. Freiderick Meins (Freiderich Miescher Institut. Phillips Robbins (Massachusetts Institute of Technology). London). Norwich. Alan Sachs (University of California. UK). Mitchison (University College London). UK). David Rees (National Institute for Medical Research. Clive Lloyd (John Innes Institute. Anne Mudge (University College London). Roy Parker (University of Arizona. Stephanie Mel (University of California. Colin Manoil (Harvard Medical School). Robert Roeder (The Rockefeller University). Cambridge). Edward Salmon (University of North Carolina. Toronto). Germany). Frankfurt am Main). Tom Kornberg (University of California. David Morgan (University of California. William McGinnis (University of California. Norwich. London). David Lane (University of Dundee. Graham Warren (Yale University School of Medicine). Sandra Wolin (Yale University School of Medicine). UK). Abraham Worcel (University of Rochester). UK). Lewis Tilney (University of Pennsylvania). Philippe Sengel (University of Grenoble. Wilfred Stein (Hebrew University. Peter Shaw (John Innes Institute.Victor Vacquier (University of California. Gregg Semenza (Johns Hopkins University). Keith Willison (Chester Beatty Laboratories. Lewis T. Masatoshi Takeichi (Kyoto University). Tom Vanaman (University of Kentucky). Jack Szostak (Massachusetts General Hospital). UK). UK). Charles Yocum (University of Michigan. Scotland). Robert Trelstad (UMDNJ. Germany). Robert Stroud (University of California. Philadelphia). Paul Travers (Anthony Nolan Research Institute. Malcolm Steinberg (Princeton University). Irving Weissman (Stanford University). France). Norman Wessells (Stanford University). Michael Wilcox (deceased). Harold Weintraub (deceased). France). Rosalind Zalin (University College London). Paul Sternberg (California Institute of Technology). Glasgow). San Francisco). Yu-Lie Wang (Worcester Foundation for Biomedical Research). John Scott (University of Manchester. Samuel Silverstein (Columbia University). Paul Wassarman (Mount Sinai School of Medicine). Ronald Schwartz (National Institutes of Health). San Diego). The Netherlands). San Francisco). Jonathan Weissman (University of California. University). Fiona Watt (Cancer Research. John Sedat (University of California. Lewis Wolpert (University College London). Göttingen). Melvin I. St. Norfolk. Israel). Chuck Stevens (The Salk Institute). Robert Wood Johnson Medical School). Kai Simons (Max Planck Institute of Molecular Cell Biology and Genetics. Anne Warner (University College London). Cambridge).xxx Acknowledgments Medicine. Louis). Michael Stryker (University of California. London). Nick Tonks (Cold Spring Harbor Laboratory). Trevor Wang (John Innes Institute. John Maynard Smith (University of Sussex. Roger Thomas (University of Bristol. Germany). Oxford). Berkeley). William Wickner (Dartmouth College). Keith Yamamoto (University of California. Scott Stachel (University of California. Boulder). Mathias Sprinzl (University of Bayreuth. UK). Alison Smith (John Innes Institute. Berkeley). Nigel Unwin (MRC Laboratory of Molecular Biology. Simon (California Institute of Technology). Paris). Alexander Varshavsky (California Institute of Technology). Murray Stewart (MRC Laboratory of Molecular Biology. Andrew Staehelin (University of Colorado. UK). UK). San Francisco). UK). Karsten Weis (University of California. Nick Wright (Cancer Research. Judy White (University of Virginia). Margaret Stanley (University of Cambridge). Martha Stark (University of California. Julie Theriot (Stanford University). Michael Sheetz (Columbia University). Ann Arbor). Vernon Thornton (King’s College London). Cheryll Tickle (University of Dundee. UK). Scotland). San Francisco). Daniel Szollosi (Institut National de la Recherche Agronomique. Norwich. Virginia Walbot (Stanford University). Clifford Tabin (Harvard Medical School). David Shima (Cancer Research. François Schweisguth (ENS. Monroe Strickberger (University of Missouri. Martin Weigert (Institute of Cancer Research. Williams (Chiron Corporation). Jonathan Slack (Cancer Research. Frank Solomon (Massachusetts Institute of Technology). Robert Wood Johnson Medical School). UK). Peter Yurchenco (UMDNJ. San Francisco). Steven West (Cancer Research. UK). Berkeley). Klaus Weber (Max Planck Institute for Biophysical Chemistry. Santa Cruz). Chapel Hill). Dresden). John Wilson (Baylor University). Peter Selby (Cancer Research. London). John Radcliffe Hospital. Zvi Sellinger (Hebrew University. San Francisco). Norwich. Rick Wood (Cancer Research. Timothy Springer (Harvard Medical School). UK). UK). John Wyke (Beatson Institute for Cancer Research. Anthony Trewavas (Edinburgh University. William Sullivan (University of California. Cambridge). Frank Walsh (Glaxo-Smithkline-Beecham. Harry van der Westen (Wageningen. Fiona Watt (Cancer Research. John Watts (John Innes Institute. Diethard Tautz (University of Cologne. Alan Wolffe (deceased). Bruce Spiegelman (Harvard Medical School). Clare Waterman-Storer (The Scripps Research Institute). David Standring (University of California. Jim Till (Ontario Cancer Institute. Michael Solursh (University of Iowa). Israel). UK). Norwich. Patricia Zambryski (University of California. Madhu Wahi (University of California. San Francisco). Richard Wolfenden (University of North Carolina. Alain Townsend (Institute of Molecular . UK). San Francisco). Harold Varmus (Sloan-Kettering Institute). UK). Toronto). like this <ATCG>. They can serve either as an introduction for those who have not studied biochemistry or as a refresher course for those who have. These references frequently include the original papers in which important discoveries were first reported. providing increased portability for students. boldface type has been used to highlight key terms at the point in a chapter where the main discussion of them occurs. Chapters 21–25 can be found on the Media DVD-ROM which is packaged with each book. Italic is used to set off important terms with a lesser degree of emphasis. covering technical terms that are part of the common currency of cell biology. At the end of the book is the expanded glossary. Part IV discusses the internal organization of the cell. When the code is typed into the interface. expression and transmission of genetic information. all in lower case. the only common feature is that they are always set in italics. The first three chapters of Part I cover elementary principles and basic biochemistry. it is intended as a first resort for a reader who encounters an unfamiliar term used without explanation.xxxi A Note to the Reader Structure of the Book Although the chapters of this book can be read independently of one another. Part III deals with the principles of the main experimental methods for investigating cells. gene names are spelled out all in capital letters. The four-letter codes are enclosed in brackets and highlighted in color. These are arranged in alphabetical order under the main chapter section headings. Chapter 8 includes several tables giving the dates of crucial developments along with the names of the scientists involved. It is not necessary to read these two chapters in order to understand the later chapters. the corresponding media item will load into the media player. End-of-Chapter Problems A selection of problems. In some species (such as humans). Part II deals with the storage. in yet others (most mouse genes). Media Codes Media codes are integrated throughout the text to indicate when relevant videos and animations are available on the DVD-ROM. Nomenclature for Genes and Proteins Each species has its own conventions for naming genes. References A concise list of selected references is included at the end of each chapter. they are arranged in a logical sequence of five parts. Glossary Terms Throughout the book. now appears in the text at the end of each chapter. Elsewhere in the book the policy has been to avoid naming individual scientists. but a reader will find it a useful reference. Fifth Edition: The Problems Book. The interface for the Cell Biology Interactive media player on the DVD-ROM contains a window where you enter the 4-letter code. with the first letter in upper . in other species (such as zebrafish). written by John Wilson and Tim Hunt. Part V follows the behavior of cells in multicellular systems. The complete solutions to these problems can be found in Molecular Biology of the Cell. starting with cell–cell junctions and extracellular matrix and concluding with two chapters on the immune system. or (as in Drosophila) with different combinations of upper and lower case. or BMP4. but all in italics. Itga1 HOXA4 cyclops. We cannot independently define a fresh convention for each of the next few million species whose genes we may wish to study. RecA. catalase). unless they are acronyms (such as GFP . Bmp4. GFP . Cdc28p Cdc2. Gfp. Sev Human Zebrafish Caenorhabditis Drosophila Deformed. Cyc UNC-6 Sevenless. Dfd (named after dominant mutant phenotype) CDC28 Cdc2 GAI uvrA PROTEIN Hoxa4 BMP4 integrin a1 HOXA4 Cyclops. Cdc2. according to whether the first mutant allele to be discovered gave a dominant or recessive phenotype. but in roman rather than italic letters: Apc. Cyc Unc6 Sevenless. Many of them have names in their own right. SPECIES-SPECIFIC CONVENTION ORGANISM Mouse GENE Hoxa4 Bmp4 integrin a-1. etc. For completeness. the Table below shows some of the official conventions for individual species—conventions that we shall mostly violate in this book. nylon). Catalase. for Green Fluorescent Protein. and we shall simply write them in the traditional way (actin. Egl1. Cdc2p GAI UvrA Cdc28 Cdc2 Gai UvrA Cdc28 Cdc2 GAI UvrA . Dishevelled. coli Cdc28. in the manner shown. or the hippopotamus version.). for those genes we put that letter in upper case if it is usual to do so (LacZ. the intention will generally be clear from the context. Egl1. Such protein names take many forms. HoxA4). with the first letter in upper case and the rest in lower case. assigned to them before the gene was named. Dfd Deformed. Cdc2.xxxii A Note to the Reader case and rest in lower case. SEV UNIFIED CONVENTION USED IN THIS BOOK GENE PROTEIN HoxA4 Bmp4 Integrin a1. there are many occasions. we list a few further details of naming rules that we shall follow. For the corresponding gene names in all these cases. What convention then should we use? We have decided in this book to cast aside the conventions for individual species and follow a uniform rule: we write all gene names. We use no hyphen to separate added letters or numbers from the rest of the name. Sev HoxA4 BMP4 integrin a1 HoxA4 Cyclops. Itga1 HoxA4 Cyclops. In some instances an added letter in the gene name is traditionally used to distinguish between genes that are related by function or evolution. Hemoglobin. where we need to refer to a gene generically. because they are all equivalent for the purposes of the discussion. To force all such protein names into a uniform style would do too much violence to established usages. Occasionally in our book we need to highlight a protein name by setting it in italics for emphasis. especially in a book such as this. thus: Apc. Proteins are more of a problem. we shall nevertheless follow our standard rule: Actin. Moreover. Dfd Yeast Saccharomyces cerevisiae (budding yeast) Schizosaccharomyces pombe (fission yeast) Arabidopsis E. sev (named after recessive mutant phenotype) Deformed. Cyc Unc6 Sevenless. it is also unsustainable. cyc unc-6 sevenless. without specifying the mouse version. the chick version. like the names of people and places. For those who wish to know them. will be written in the same way. Dishevelled. Bazooka. the human version. Bazooka. like the names of ordinary substances (cheese. The corresponding protein. When it is necessary to specify the organism. DFD Deformed. This typographical chaos drives everyone crazy. although most of them traditionally begin with a lower-case letter (actin. this can be done with a prefix to the gene name. hemoglobin. where it is named after the gene. It is not just tiresome and absurd. for Bone Morphogenetic Protein #4). Conventions for naming protein products are equally varied. ) Adobe and Acrobat are either registered trademarks or trademarks of Adobe Systems Incorporated in the United States and/or other countries PowerPoint is either a registered trademark or trademark of Microsoft Corporation in the United States and/or other countries . Garland Science Classwire™ All of the teaching supplements on the DVD-ROM (these include figures in PowerPoint and JPEG format.com. Garland Science Classwire™ offers access to other instructional resources from all of the Garland Science textbooks. It provides problems to accompany Chapters 1–20 of Molecular Biology of the Cell. Each chapter of problems is divided into sections that correspond to those of the main textbook and review key terms. teaching supplements for Molecular Biology of the Cell are available to qualified instructors. The chapters are in PDF format and can be easily printed or searched using Adobe® Acrobat® Reader or other PDF software. a PDF file located on the root level of the DVD-ROM and in the Appendix of the media player. MBoC5 Lecture Outlines Lecture outlines created from the concept heads for the text are provided. California) and Linda Huang (University of Massachusetts. The DVD-ROM also contains Chapters 21–25 which cover multicellular systems. It could even provide ideas for exam questions. tables. Teaching Supplements Upon request. For additional information. and movies) and the test questions and lecture outlines are available to qualified instructors online at the Garland Science Classwire™ Web site. The multimedia can be accessed either as individual files or through the Cell Biology Interactive media player. animations. and high-resolution micrographs on the DVD. and micrograph in JPEG format. There are also over 125 videos. table. one for each chapter. test for understanding basic concepts.com/garlandscience or e-mail science@garland. MBoC5 Media DVD-ROM The DVD included with every copy of the book contains the figures. MBoC5 Transparency Set Provides 200 full-color overhead acetate transparencies of the most important figures from the book. (Classwire is a trademark of Chalkfree. A complete table of contents and overview of all electronic resources is contained in the MBoC5 Media Viewing Guide. Solutions for the end-of-chapter problems in the main textbook are also found in The Problems Book. Fifth Edition: The Problems Book should be useful for homework assignments and as a basis for class discussion. Molecular Biology of the Cell. A separate folder contains individual versions of each figure. pre-loaded into PowerPoint® presentations. The panels are available in PDF format. Written by Kirsten Benjamin (Amyris Biotechnologies. and micrographs from the book.A Note to the Reader xxxiii Ancillaries Molecular Biology of the Cell. As discussed above. please visit http://www. molecular structure tutorials. Solutions for all of the problems are provided on the CD-ROM which accompanies the book. The authors have chosen to include material that not only reinforces basic concepts but also expands the content and scope of the book. and provides free online course management tools. MBoC5 Test Questions A selection of test questions will be available. Boston). these thought questions will test students’ understanding of the chapter material. the media player has been programmed to work with the Media Codes integrated throughout the book. 125 videos. Chapters 21–25 in PDF format. animations. and pose research-based problems. Inc.classwire. Fifth Edition: The Problems Book by John Wilson and Tim Hunt (ISBN: 978-0-8153-4110-9) The Problems Book is designed to help students appreciate the ways in which experiments and simple calculations can lead to an understanding of how cells work. Emeryville. 1001 cofilin see Cofilin (actin depolymerizing factor) D-form (ADP-bound). clathrin-coated vesicles. 656. 903. 979F yeast actin patches. 1002F filament elongation and. 994F. 988T dynamic behavior. 84T formation. 885F neurotransmitter function. 882 different effects on different cells. pathogen-induced. 1036F. 982–983 minus end. 166 see also Enzyme catalysis serine proteases. 996 pathogen-induced mechanism. 690 photoreceptors. 1000F severing proteins. 969. 1013 polymerization see Actin polymerization properties. 903F. 1009F filament dynamics and. 72. 1042–1043. 966. 1515F. 660F multidrug resistance protein. 996–998 nucleotide hydrolysis. 996–998 protrusion model of cell movement. 689F propagation. 665–666 Abl gene. 976 plasma membrane protrusion. 654F. 1437. 1567F. 803F. 301F RNA structure. page numbers with an F refer to a figure. 968F. 1394 conformational changes. 663–667 antigen presentation. 685 structural model. 997. vs means compare/comparison. 1582 ATP binding. 919 Adaptin. 1437F. 1568 Active site. 1293 Acrosome reaction. 1170F via catenins. 979. 974. 1297. 1206 Adenomatous polyposis coli see APC (adenomatous polyposis coli) gene/protein Adenosine deaminase(s) (ADARs). 1206 Adenoma. 1007. 122F Acquired immunodeficiency syndrome (AIDS). 1516F at plasma membrane. 1009 evolutionary conservation. page numbers with a T refer to a table. 1039F pushing force. 96 fatty acid oxidation. 1581 see also HIV Acquired immunological tolerance. 96–97 energy storage. 1135T Actinomycin. 899. 1006–1007. 73F. 92F see also Glycolysis reaction coupling. 1037 elongation. 197. 1142. 1002–1003. pages 1269–1601 are found in the Chapters 21–25 folder on the DVD that accompanies this book. 97F. 1299F ACTH (adrenocorticotrophic hormone). 1516F see also Actin polymerization isoforms. 927 ADARs see Adenosine deaminase(s) (ADARs) Adenine. 666F bacterial vs. 679FF definition. 165–166 Activation-induced deaminase (AID). 684–686 Acetyl CoA (Acetyl Coenzyme A). Page numbers in boldface refer to a major text discussion of the entry. 1436 in water. with an FF to figures that follow consecutively. 1508. 684. 164F. 1261. 977F. 973F subunits. 1095F depolymerization. 484F reaction rates. 656. 1095. 109F measurement see pH secretion. 808 receptors see Acetylcholine receptors (AChRs) structure. 903F. 1142F arrays. 74F lysozyme. 1006–1007. tropomodulin. 1387F nucleation see Actin polymerization nucleotide-binding site. 977FF. 684–686. 665 auxiliary transport. 916 resting potential. 678. 160. 1039 rate. 1507 microtubule-based movement in axons. 166 role in catalysis. 965 Saccharomyces cerevisiae. 1506F. 917–918 receptor down-regulation. 685 selectivity. 1135T adhesion belt (zona adherens). 975 subunits. 1134. 822. 679. adaptive Adaptor proteins. 774F. 980 drugs affecting. 824–825 see also specific carriers Activation energy. secondary. myosin. 73F lowering by enzymes. 337F Absorptive (brush-border) cells. 679F Activated carriers in metabolism. 969–970. 154. 920 visual transduction. 971 T-form (ATP-bound). 677. 1026–1028 neuronal growth cones. 1003. 1003 myosin movement. 53F Acid anhydrides. 685F history. 756F Adaptive immune response see Immune response/system. histones. 656 symporters. 52–53. 684 mode of action. 1168 sequential activation. lysosomes. 161F Adenosine diphosphate see ADP Adenosine triphosphate see ATP Adenovirus(es). 160F lysozyme. 1142. 944 calcium ion activated potassium ion channel. 966. 1011–1014 see also Myosin Actin-binding protein(s). 1394 Adaptation bacterial chemotaxis. 1006 assembly see Actin polymerization axon structure. 1037–1038. 660. 823F antibiotic resistance and. 976–980. 1135T adherens junctions and cell motility. 974F organization. 290 Acetylcholine (ACh) blood vessels nitric oxide. 969–970 structure. 677F saltatory conduction. in yeast. 994F. 665F molecular design. 628F. 1006–1008 cross-linking. 970F Actin depolymerization factor see Cofilin (actin depolymerizing factor) a-Actinin. 885. 775F Achaete gene. 676 initiation. definition. 656F. 685 as transmitter-gated channels. stomach. 1516. 885F Acetylcholine receptors (AChRs). 982–983 growth rate of plus/minus ends. 978F Actin-related protein (ARP). 916 neuromuscular junction. 687F basal lamina and. 1006. 1170. 318T Acetylation. 1007F web/gel-forming. Rho and Cdc42 effects. 1261F Abortive transcription initiation. 79–8082–83. 1037–1038. 83F N-Acetylneuraminic acid. 165F. 1515F nucleation mechanism. 1547 see also Immunological tolerance Acrosomal vesicle. 755 Acid hydrolases. modification by proteins. 679F schematic. 107F Acid hydrolase receptors. 145F. 976 induction/assembly. 999–1000 ERM protein regulation. 685 muscarinic. 968. 223F. T cells. 1022 Actin-rich cortex. 1517 Adherens junction(s). 817 see also Citric acid cycle structure. retromers. 888 concentration in synaptic cleft. 1133T. 974. 1143F cadherins see Cadherin(s) . 656F see also Carrier protein(s) Activity-dependent synapse elimination. definition. 301F base-pairing. 1516F bacterial invasion process. 1007F bundling. 1043F plant cell wall deposition. 332 Adenocarcinoma. 84T. 980 treadmilling. 997F lamellipodia. 990F capping. 676F squid giant axon experiments. 1093–1094 RhoA and. 999F. 1356 Acid(s). 680 recording. 659 uniporters. 1037 contractile ring (cytokinesis). 1142 integrin attachment. 1202 plus end capping protein.Index If you are using ISBN: 0-8153-4105-5 or ISBN: 0-8153-4106-2 (located on the bar code on the back cover). 686F structure. 971 time course. 1000 Actin cables. 20F. 656–657 primary vs. 920 receptor sequestration. 907T Actin/actin filaments. 155F spliceosomes. 352 Active transport. 970F Actin-based motor proteins. 97F mitochondrial production. in chronic myelogenous leukemia. 1042F. 1515–1516. 1003F cell cortex. 1003 muscle contraction. 1013 Accessory receptor. 1523F antiporters see Antiporters ion gradient driven. 78–79 glycolysis. eucaryotic. 687–688 nicotinic. 611F. 1509F nucleation. 385T Actin polymerization bacterial intracellular movement. 973F ARP complex role. actin filament packing. 72–73. 999–1000. 679. 1298. 990. signaling pathways. 965F accessory proteins see Actin-binding protein(s) anchoring junction attachment. 1133T. 484. 653–667. 1438F Acanthamoeba castellanii. 1048 bacterial homolog. A ABC transporter(s). 1496F entry and uncoating. 779–780 Aconitase. 1522. 689 postsynaptic potential. 1039F regulation. 1008–1009. 116F. 1580 Ac-Ds elements. 994F. 903F receptor inactivation. 1515–1516. 987. 679F voltage clamping. 1007F Actin-linked cell–matrix adhesion. 1134. 198F deamination. 1036F. 79–86. 983F. 1037 Action potential(s). 96. Rac. 973. 803F. 90F Aldehydes. 384F. 404–406 phospholipids. 1142 occurrence. 12. 157F. 384. 1142 see also Cell adhesion Adhesins bacterial adhesion to epithelium. definition. 646 Aneuploidy meiotic nondisjunction. 112F Alexa dyes. 1087. 1519–1520. 479F gene definition modification. 1262 process. 171. neurofilament assembly. 980 production from ATP. 1332F. 92F Aldolase. 369. 1552F. 1590 catenin interactions. 1142 columnar epithelium. 27. 839 see also Glycolysis pathogenic. 839. 1434 Alveoli lung. 1089–1090 anaphase B. 429F. 1566. 128F. 368F. 172F see also Feedback regulation Alport syndrome. 129F Albinism (hypopigmentation). 1435F mammary gland. 128. 12. 369F Antigen(s). 80. 172F phosphorylation-mediated. cytoskeletal. 1413. Integrin(s). 1064 Ancestor tracing. 1036 osmosis regulation. 837F ribozymes. 1524 resistance. hippocampus. 1089–1090 spindle assembly checkpoint and. 58–59 Amphiphilic molecules. 1175–1176. 129F polar (uncharged). 1030 Adrenocorticotrophic hormone (ACTH). 428–429. 1100–1101 targets/mechanism of action. 480 Alu elements. 107F Amino acid(s). 22 mobile genetic elements. 1448–1449 capillary sprouting. 99. 562F Allelic exclusion. 369F. 1493F Antibiotics. 515F Affinity constant (Ka). 370. 349F. 59–60. 396–397 Amyloplasts. 1558F Antigenic variation. 1182F. types I/II. 385T Ames test. 428–429 protein–protein interactions. 372F structure. 1413F Agamous gene. 513–514. oxidation in glycolysis. 1559F. 1494F. 1068 geminin destruction. 161F Amine groups. 128. 235F see also Xenopus. 597F Aerobic metabolism. 1447F inhibitors. 870–872 formic acid oxidation. 479–480. 97–98 bacterial. 152 side-chain effects. 1427F Alzheimer’s disease. 1066T chromatid separation and completion of mitosis. 1448 Anion. 125–127 see also Protein(s). mobile genetic elements. 1434. 508–509 Antigen–antibody binding. 618 Ampicillin resistance. 1519F Antigen presentation. 1064 S-cyclins. 175F . 1100F regulated proteolysis. lymphocyte recirculation. 1558 Affinity maturation. 479–480. hydrolysis. 385T Antibodies see Immunoglobulin(s) Anticodon(s). 1553F. 156. 318F Amyloid protein. 871F glycolysis. 663 spread of Legionnaire’s disease. 587. NMJ. 835–836. 1434–1436 Akt (protein kinase B). 1347F Anthrax. 397. 907T Aequoria victoria. 1087. 479F post-transcriptional gene regulation. 370. 534 Age/aging premature. 1341–1347. 1134F coordination of cell motility. 371F proofreading. 558 frequency. 101 see also Citric acid cycle essential. genome size. 199–200. individual species Amphipathic molecules evolutionary significance. 1501 Anaphase meiosis anaphase I. 1300 Angiogenesis. 1449F response to wounding and damage. 348. 1184T Agrin. 1552. 1133T. 1132. 1225. 479F optional intron. 479F patterns. 1523 transfer. 1331–1334. 1064. 1414F Agarose gel electrophoresis. 1554F. specific types Anchor proteins. 293–294 see also Cancer Aggrecan. 377 wobble. 1566 Aflatoxin B1. 1142. 1576 natural selection effects. DNA repair defects. 128F side chains. 1581 see also HIV AIDS virus see HIV Airways. 80F Adrenaline (epinephrine). 1331F. 587F Algae. 1508 AMP (adenosine monophosphate) cyclic see Cyclic AMP production from ATP. 1522. histology. 370–371 accuracy. 875F Allele(s). 1522. 129F nitrogen cycle. 172–173 Allosteric regulation. 480 mutually exclusive exons. 86F AMPA receptor(s). 429F matrices. 100–101 optical isomers. 1064 securin destruction. 1088F G1 phase and. 1557 monoclonal specificity. 1087F. 314. 1364–1369 polarity. 1366 role of homeotic selector genes. 370. 1539 ADP (adenosine diphosphate) ATP:ADP ratio. 1146–1147 optional exon. 171–172. 144F Alcohol. 322. 1278–1279 polyspermy. 1088 Anaphase promoting complex (APC/C). 1065F. 561–562. 1167 Alternative splicing. 125 aminoacylation. in cancer therapy. 175 proton pumps. 1089F anaphase A. 1100 DNA replication initiation and. 479F regulation. 1509F Adhesion belt (zona adherens). 30–31 lampbrush chromosomes. 200F see also Genetic code energy sources. 1225. 1168 AIDS (acquired immunodeficiency syndrome). intracellular ion concentration. 848F Anteroposterior axis development Drosophila. 234F. 554F. mutation rate data. 539–540 Alcohol dehydrogenase. 373F synthetic ribozymes. 515F see also Protein tags protein tagging. 1523F environmental reservoirs. 407 see also Transfer RNA Amniotic sac. 1132F. structure. 32 evolution. 371–372. 1134. 247. 101. 375F Aminoacyl-tRNA synthetases. 18T Affinity. 1502 phagocytosis induction by bacteria. 871. 1575 All-or-none response. 479 Dscam gene. 1225F Amide bond. 248F Anchorage dependence. 130. 1560–1561 Antigenic determinants (epitopes). 1427–1428. 1557. 841F Amyotrophic lateral sclerosis (ALS). 154F protein structure role. 59. 1477. 904 smooth muscle control. 1334F role of homeotic selector genes. 1343F vertebrates amphibian embryo. 562F of MHC proteins. 1557F Allograft(s). 5. 404 cooperative transitions. 514F DNA-binding proteins. 59F. 15F Anabolism see Biosynthesis Anaerobic organisms. 1578–1579. 295T relation to telomere shortening. peptide binding to MHC protein. 1493. 158F antigen–antibody binding. 173F. 1135T see also Cadherin(s). 428–429. 101F families. 839F evolution. 130F protein functional role. 839. 691 Amphibians embryos gastrulation. 125–137 protein subunits. 371F see also Transfer RNA analysis. 1054. haplotype blocks. 1143F Adhesion receptors. 1558F affinity constant (Ka). production by fermentation. 1171 linkage. 1558 Affinity chromatography. 1508. 1364 see also Xenopus laevis development genome size. aggregation. 126F structure. 1521–1522 misuse. 874. 1522–1523 targets/mechanisms of action. 354 Agamous Arabidopsis mutant. 1523F horizontal gene transfer. 1071. 1342F. 156. 371–372. 127F. 512. 534F principles. 349. 1553F Antigen-binding site. 60F coding for. 1073F. 900 G-protein-linked receptors. 156–157. 1590–1591 B7 proteins. 1379 Amoebae. 1344–1347. 349F a-tropomyosin gene. 1142 Anemia. 1091. 171–176 conformational changes. 1133–1150. 987 Anabaena. 848. 1447F endothelial cells role. 173–174. 372. 318F R-gene product. 368–369. 479F neural cell adhesion molecule (NCAM). 1521–1524 active pumping. 900 Allosteric cooperative transitions see Allosteric regulation Allosteric proteins. individual amino acids Aminoacyl-tRNA–ribosome binding. 1561F structure. 1091F mitosis. 1001. 1523–1524 enzyme alteration. 1562. 873–874 Aeropyrum pernix. antibody for antigenic determinant. 479F intron sequence ambiguity. 128F nonpolar. 1558 determinant number. 59–60. 1539. 452. 1068–1069 M-cyclins. 154–155. 1565 Allergy/allergic reactions. 1100–1101. 348 advantages. 6. 480F splicing signals. 823–824 D-form Actin. 1091F anaphase II. 264 charge (pK values). 1522. 1522F protein synthesis inhibitors. 934 in cancer. 523 protein separation/purification. 786 Albumin. 7F. 120F Aldoses. gene characterization. 377–378 catalytic reaction. protein aggregates. 1229 African sleeping sickness. antibody production. 1448F tumor growth and. 1446. structure. 907T glycogen breakdown. 371. 1021 a-Amanitin. 1447. 1244 Alanine. 385T Antenna complex. 839F evolutionary significance. 323F Alveolar cells. 90. 174F. 1545. 596–597. 841. 1556. 1446–1447. 1066.I:2 INDEX see also Cooperativity (protein interactions) integrins. 395. 480. 171. 86. 1175F Anchor amino acid. 1550–1551 Adipocytes see Fat cells Adjuvant(s). 33F cell crawling. 127F. 1523F selective pressure. 1226F. 1579F Anchoring junction(s). 129F basic. 128F protein folding role. 60F. 128 acidic. 47 Anisomycin. 1448. 375. 480–481 internal splice site. 396F regulation. 1446. 1181. 592 Aequorin. 1064. 1346F. 1066T. 1220–1221. 1182. 657 see also specific types Antirrhinum (snapdragon). 158F. 1399F. 1099F oocytes. 81F. 47 ATP (adenosine triphosphate). 1573F. 243 coupled to DNA replication. 1116. 100F. 526 Associative learning. 1076F Astral relaxation model. 16F. 1327 mouse paws. 61F. 1215–1216. 81F mitochondrial protein import. 1122–1123 Bcl2 proteins. 1163. 881 Autoimmune disease. 1117F DNA damage. 1399–1400 size. . 823–824 ATPases (ion transport). 791. 1413. 1289. 1252 colorectal cancer. 1389–1390 phagocytosis. 168 ATP:ADP ratio. 541. 1362 insects. 351–352 ATP-mediated phosphorylation. 447F see also DNA bending ARF protein(s). 822–823 mitochondrial localization. 915F. 16F Arabidopsis thaliana (wall cress). 836 see also Electrochemical proton gradients. 18T bacteriorhodopsin. 920–921. 633F. 1105 Attenuation. 295T. 884. dominant negative mutations. 117F energy carrier. 1542. 1445F Arthritis. 1489F Ascaris lumbricoides. 1106 Atherosclerosis. 51 Atomic weight. 1120F. 144F. 1038F pathogen movement. 1106 Fas ligand/Fas receptor. 1117. 737F. 997. 550. 18T Architectural protein(s). 1571. 1588 Autocatalysis. 81. 603F synthesis see ATP synthesis transport. 48F atomic interactions. 1432 Atomic force microscopy (AFM). 1023F A-site (ribosome binding). 1108F Apaf-1. 128F Argonaute protein. page numbers with an F refer to a figure. epithelial apicobasal polarity. 78. 1347–1363 fine-grained patterning. 47F. 86. 1594 procaspases. 299F Apyrimidinic sites. 813. 86. 1121 associated diseases. 1408F. 87F energetics. protein glycosylation. 1023. apoptosis. 494. 871–872 cyanobacteria. 1124–1125 pro-apoptotic proteins. 821–822. 1289F stem cells. 174F catalytic mechanism. 7F. 826–827 sodium-driven. 1410F root. 81 biosynthetic role. 1118. 660. 1120–1121 hemopoiesis. definition. 354F Ataxia telangiectasia (AT). 1431FF Aurora B kinase. 1410F maintenance by Wuschel and Clavata signaling. 824–825 nucleic acids. 855F mechanism of action. 46–48 atomic radius. 93F. 656F sodium-calcium exchanger. 1353 Apurinic sites. chronic infections. 1355–1356 see also specific appendages Apterous gene. 675 structure. bacterial gene regulation. 1403. 129F Aspartate transcarbamoylase allosteric cooperative transitions. 32 Antisense RNA. 1127 cancer and. 247F. 1500 Arthropods ECM polysaccharides. 821F uncoupling. 1414F Apical meristem. structure. 1400. 1125F IRES-mediated production of cell-death proteins. elegans. 737. 657–658 sodium–potassium pump (ATPase). 8–9 abundance. 550F Autonomously replicating sequence (ARS). 601F Atomic modeling. 17. 915. 1409–1410. 1122F APC/C see Anaphase promoting complex (APC/C) APC (adenomatous polyposis coli) gene/protein. 80 evolution. 1402 genome. 304 mutation. 885F cellular changes. 273. 821–823. 665 see also specific pumps/proteins ATP caps. 791. 1489 Asexual reproduction. 826F bacteria. 1096–1097. biochemical. 1402F transgenic. 673F mode of action. 1409–1410. 759. 1116F activation/induction abnormal mitogenic stimulation. 568–569. 37–39.INDEX CD28. 825F glutamine synthase. 674. 1542F. 872–875 fermentation. 1289F Asymmetric cell division. 1126 C. 1421. 287F Artery. 45 I:3 Atoms. 173–174. 129F Aspartate (aspartic acid). 1252T. 496 ARP (actin-related protein). 45–48. 371 ATP synthase. 1540. 90 hydrolysis see ATP hydrolysis radiolabeling. 51 atomic structure. 295T. 1127. resistance see Antibiotics. 600. 1122–1123 Appendages. 1516 Arrestin. 659–660. 850–853. 1121. 494F. with an FF to figures that follow consecutively. 1584–1585 Antigen-presenting cells. 286. 299F Apetala2 Arabidopsis mutant. 215–216 sperm motility. 564F Antiserum. 175F structure. 129F Association constant (Ka). 850–853 cyclic photophosphorylation. 627 proteolytic cascade. 1269F Ash1 gene regulatory protein. 1216F. 298. 824–825. 1413. 1428 membrane potential. 845F chromosome condensation. 1411F Aplysia. 674. 822F see also ATP hydrolysis. 1413F Apetala3 gene. 1180 infections transmitted by. 1076. 784F Autophagy. 286. structure. 1118F extrinsic pathway. 1117 development. 1429. 95F. 1040 APOBEC. 1084 Aurora kinases. 1115–1117 cell recognition. 589 Antral follicles. 819F proton gradients. 994F. mutation transforming flower to leafy shoot. 852FF see also ATP synthase. 656 mechanism. DNA damage and. 353–354. 1398FF embryogenesis. 845. 1462 intrinsic pathway. 1099. 1126 Autophosphorylation. 1534F Astral microtubules. 674F Aquifex genome size. 376 Asparagine-linked oligosaccharide(s). 1408FF. 1035F. 401 Autocrine signaling. 491 macrophage scavenging. 1115 phosphatidylserine. 174F Aspartic acid. 1414F model plant. 661–663. 1245–1246 cell elimination. 18T homeotic selector gene expression in flower. 1096. evolutionary relationships. 84F ATP synthase. immunological tolerance. 173. resistance Anti-Müllerian hormone. Glycolysis ATR protein kinase. 1409–1410. 81. 1289–1290. 640–642 membrane composition. structure. 80–81 historical aspects. cell movement. 1549 Automated DNA sequencing. 997. 1413F Apetala2/ethylene-responsive-element binding protein. 1105 mutation. 657–658 sodium independent chloride–hydrogen carbonate exchanger. 46F electrons see Electron(s) space-filling models. 1500. 1535 Apoptosis (programmed cell death). 782–783. 1356–1362 vertebrates. 304. 660 sodium-driven chloride–hydrogen carbonate exchanger. 1156 Auditory hair cells. 295T. structure. 92F. 920F ARS (autonomously replicating sequence). 1253 Ape(s). development. 477–478 Atypical protein kinase C (aPKC). 1163. 1074 Autimmune regulator (AIRE) protein. 950. 919. 247. 839–840 structure. proteins. 1400T Apaf1. 922 Page numbers in boldface refer to a major text discussion of the entry. ATP synthesis ATP synthesis. 1400T Apetala2 gene. 817–819. 81. 248F AP endonuclease. 1412F homeotic mutations. 86F aminoacyl-tRNA synthetases. 673–675. 45–46. 1285. 1107–1108. 147. 784F apoptosis. 1500 ATM protein kinase defects. 782–783. 787. 1347–1355. NMR. vs means compare/comparison. 839 energetics. 839 chloroplast localization. 1407F shoot. 1116F tadpole metamorphosis. 91. 1487. 62F. 826. 979F ATP hydrolysis. 1402. 1117–1118 cell signaling. 158F Association rate. 529 Atomic radius. 1121. 1292 AP2/EREBP gene regulatory proteins. 287F Autophagosome(s). 716–717 nucleosome sliding. genome size. 173–174. 1539. 1401F. 997F in lamellipodia. 299F Aquaporin channel(s). 121F see also Glycolysis mitochondrial see Oxidative phosphorylation photosynthetic. 949. 1122F DNA damage. 80F alternative route. 81F chemical structure. 855F oxidative phosphorylation. page numbers with a T refer to a table. 51 valences. helper T-cells. Electron transport chain(s) energetics. 18T in tree of life. 1269. 783F. base excision repair (BER). 273F coupling to biosynthetic reactions. 826F carbon fixation. 1431F. 822 utilization measurement. 1022 ARP complex (ARP 2/3 complex). 821F reversibility. 1121. 1106 Atoh1 gene. 564. 1096F Astral stimulation model. 1096F Asymmetrical division. 1396–1397 Asthma. 1118 mitochondrial proteins. 1115 plasma membrane. 1590 cross presentation. 1038. 1107 Arginine. 1124F. 1286F Antiporters. 36. 1121–1124 IAP proteins. DNA cloning vectors. 542F Ascaris. 1293 spliceosomes. 856 neurons. 821. 1119F. 814F bacterial. 1414F Apetala3 Arabidopsis mutant. 1400T genetic screen. 624 Archaeoglobus fulgidus. 1116. 1356–1358. 1572F see also Macrophage(s) Antimicrobial drugs. 1413F gene regulatory proteins in. 61. 870–876 anaerobes. 1571F costimulatory molecules. 1398–1399 mutant seedlings. 1571–1572. 142. 80 electron transport-driven. 1352. 826–827. 445–446. 1120. 304 DNA damage and. 39F. 979. actin filaments. 747F Asparagine. 787 in mammary gland. 36f. 870–871 glycolytic pathway. 1421F AT–AC spliceosome. oocytes. 1584 cytotoxic vs. 1115–1129. 1500 Atherosclerotic plaques. 16. 86F. 569. 1402F flowers. 839–840 sodium–proton exchanger. 1430–1432. caspases see Caspase(s) regulation anti-apoptotic proteins. origin of life. 46. 527–531 Atomic nuclei. 569 Archaea (archaebacteria). 1501–1502 see also individual species Artificial chromosomes. 853 noncyclic photophosphorylation. 375F. 94–95. 458. 1488 Gram-negative. 556. 202.I:4 INDEX opportunistic pathogens. 458F see also Cro repressor. 1491–1492 see also individual viruses Bacteriophage lambda bacterial adhesion. 1271 Auxin. cytochrome oxidase binding. 457–458. 416 see also Genetic switches. 211. 1490F ribosomes. 552 Bacterial gene expression regulation. 1131. 1599 B2 cells. 1015. 1047 myelin sheath. 541. 1127. 839–840. DNA rearrangement. Photosynthesis. 1166–1167 synthesis.. Lambda repressor life cycle. 1568F. 1165–1166 type IV collagen. 1505 chemical composition. 1165 Base(s) (chemical). 1527 Gram-positive. 1426 functional roles. 14F. 401 RNA and. 24–25. 1033. 18T Bacillus anthracis. 1493. 1492F obligate pathogens.. 640F. 336–338. 1596F T-cell receptor vs. 959. 1490 phase variation. 1261 Gleevec and. 1261F “Beads on a string” chromatin. 20F BACs (bacterial artificial chromosomes). 269. 1540 activation. 1552. 478–479 structure(s). 197–199. coli as model. 325F gene regulation. 1543–1544. 1167–1169 kidney glomerulus. 612F see also Protein synthesis. 211F. 55T. 1262F Bcr gene. 142F sequence recognition. 1362. 612F shapes. 282. 1416F. 418T repressors. 294. 282–283. 16. 1553–1554. 1493 mechanism of action. membrane integrity. 1494F archaea and eucaryotes vs. 453F Beggiatoa. 1419. 1565–1566 recirculation. 323F B7 proteins. 1047–1050 see also Axonal transport development. lymph node lymphoid follicles. 1387–1389. 1490–1491 . 18T. 1047 action potential propagation. 1597F antibody synthesis. 1391–1393 microtubule orientation. 473 Basal cell carcinoma. 270F unnatural. 457. 689 Azide. 324. 1505 genome integration. 14F. 1490F sizes. 197–199. 324. 457–458. 1501 pathogenic. 1490F pili (fimbriae). 640–642. 325F excision. 282. 45–46 Axil. apoptosis. role in cancer. 457. 1147. 1121–1124. 324 heritable state. DNA cloning vectors. 1552 post-transcriptional control. 603 Autosome(s). 1507–1508. 603F electron microscopy. ion channels. 1501 BAD protein. 284F 2D-PAGE. 472 gene expression. 1596 resting. 21. 384. 333F. 1565–1566. 1164F epidermal stem-cell maintenance. 473. 268–269.. 1165. 1356. 1491F origin of replication. Fc receptor signaling. 1048 herpes viruses. 380 inhibitors. 1164F. 1596F class switching. 1386–1387. 421F lambda repressor. 1386 guidance mechanisms. 1165F. 1554F antibody gene-pool selection. 298. 1410. 1164 barrier functions. 1516F Axonemal dyneins. 951 Basal cells epidermis. 1452F. 1568. 1509F lithotrophic. 454–455 photosynthetic. 522F 3H-thymidine. 116F RNA. 1574–1575. 508–509. 1503 type III secretion system for. 839–840. 1416F. 1408–1409 indole-3-acetic acid. 1543F. 1493–1494 cAMP overproduction due to. 284F 3H-uridine. 541. 1566F class switching. 296. 296F natural. 380. 839F chromosomes. 458F dimerization. 601. 1491 viruses of see Bacteriophage(s) see also specific organisms Bacterial artificial chromosomes (BACs). 1164–1165. 25F electron transport. 1490F. 1566F B-cell receptor. at hydrothermal vents. 477–478 see also Transcription Bacterial toxins. 351 see also Ribosomal RNA. 301F nucleotide structure. 268–269 see also DNA replication. 1490F cell wall. 266F. 116F pairing see Base-pairing purine see Purine base(s) pyrimidine. 1504–1505 diarrhea due to. 457. 12 mRNA. 1488. 16F. 1490 genome organization. 387F virulence genes and factors. 198F. 871–872 see also Electron transport chain(s) energy sources. 61. chronic myelogenous leukemia. 306. 198FF see also DNA structure DNA synthesis and. 1123F in cancer. 1492 Bacillus anthracis. 332. 345F. 1592T. 482–483 B1 cells. mRNA export. 458F corepression. 416. 325F excisionase. 22F Bacteriorhodopsin. 17. 1516–1517. 280. 61. 1596F Bcl2 proteins. 1489–1494 facultative pathogens. 458. 359F Ball-and-chain model. 1122–1123 Bcr–Abl protein. 459 Bacteriophage T4. 1493 Bacillus subtilis. 1406F transport in plants. 1550 regulation. 1493 lethal toxin (anthrax). 834 B B1 elements. sperm. 1590 CTLA4 binding. 1168F mammary gland. 15 DNA replication. 283F see also DNA replication DNA sequences as immunostimulants. 1293. 198F. 266. 1177. 1167F laminins. 1591F Bacilli. 1403–1404. Repressor protein(s) operons. 359. 306F Basement membrane see Basal lamina Base-pairing (nucleotides) DNA structure and. 16. 53. 416 DNA sequence recognition. 1421. 1411F Axin. 1166F. 1490F capsules. 1400T Basophils. 458F Cro repressor. 557F Benzopyrene. 15F Behavioral mutants. 1410 Axillary bud. 1419F olfactory epithelia. voltage-gated potassium ion channels inactivation. 1494F. 872–875 see also Cyanobacteria. 1492F invasion. 675 see also Dendrite(s) Axonal transport anterograde vs. 109F measurement see PH Base(s) (nucleic acid) DNA. 1428 structure/composition. 1546 monospecificity. 680F neurosignaling. 1261. 387. 324. 1507–1511 nonpathogens vs. 1167 mechanical. 863. 333F wobble base-pairing. 1486. 324. 1557F Bax. 1490F. 246 Basic helix-loop-helix (bHLH) proteins. 17 toxins see Bacterial toxins transcription see under Transcription translation quality control. 1596F antibody gene-pool selection. 840. 1527 flagella see Flagella outer membrane. 1552. 949 Axon(s). 1591–1592 T-cell activation. 385T see also Antibiotics ribosomes. 1492F bacterial adhesion. 325F lytic state. 1493–1494 Bacteriophage(s). 1543–1544. 18T size. 1492. 1429F. Translation riboswitches. 1419F distribution/occurrence. 63T chemiosmotic coupling. 1490F Bacillus. 1164–1169. retrograde. 325F see also Transposition virulence gene transfer. 1599 B-cell receptor. 1595–1596 co-receptors. 300 Base excision repair (BER). 1596F development. 1543F. 1491 edema toxin (anthrax). 346F. 1597T memory. 1514–1517 invasion of host cells. 552 Bacteria. 18T. 1387F differentiation from dendrites. 1532 cell-surface projections. 418T. 680F. 1245 Bcl-XL protein. 458F integration. 1597–1598. 1140. 458F transcription circuits. 345F gene regulatory proteins. 17F bacteriophage adhesion. 339F. 1527 E. PI 3-kinase signaling. 14. 421F. 677F see also Action potential(s) cytoskeleton. 509F immunological synapse. 142. 1490F. 458F prophage. 381F normal flora. 1489–1490 antibiotic action and targets. 554F. 282–283. 1554F. 1565–1566. 1168 diversity. 1507–1508 epigenetics. 198FF damage. 678F Barr body. 1568F see also Immunoglobulin(s) hybridoma production. 959–961 Avogadro’s number. 1594–1595. 1595–1596. 334F splicing mechanism. 1504 type IV secretion system for. 1165. apoptosis. 16F. 212F BEAF insulator-binding protein. 1132F. 1595F antigen presentation. 345F see also Transcription gene regulation see Bacterial gene expression regulation genomes sequenced. 1492. 1033F Axoneme. 717. 641F Bacteroides. 482–483. 482–483 helper T-cells (TH). 1122 B cell(s). Purple bacteria porin insertion. 300F. 873F evolution. 1168–1169. 602–603. 1595. 332 RNA folding. 301F tautomers. 326 integrase. 1388F retinotectal projection. 1164–1165. 1490F plasma membrane. X-inactivation. 1556. 959F. 1122 Balbiani rings. 1527 intracellular movement. 1493 cholera. 369F Base substitution mutation(s). 297–298. 1594. 603F eucaryotic replication forks. 1293F Axon hillock(s). 299F Base-flipping. 1165 regeneration and. DNA synthesis origin of life. 717F protein synthesis. 1505 conservative site-specific recombination. 1430 Basal lamina. 839 entry into host cells by phagocytosis. 934. 1544F signaling events. 934F Bak. RNA structure unusual. 678. 462–463 see also Lac operon (Escherichia coli) transcription attenuation. 1225 Autoradiography. 433F. 22F. 283F diversity. protein analysis. 1330–1331. 596–597 Biosynthesis. 1330F Blastomere. 552 hermaphrodites. 1336. sensory maps. 1503F Blastocyst. DNA repair disorders. 1136–1137. 1454 Blood vessels. 1469–1470 development. 1324F. 1365F. 1184T Beta-sheet motif. 538–539. endochondral. 1276F Black membranes. 846–847. 1470 joints. role. 1453T formation see Hemopoiesis functions. 838 Brown. 39F. 1301 46BR patient. 1452F. 1323F cell death. apoptosis. 34 as model eucaryote. 1138T. 1193 stress response. 1229 infections. 1059. 1472–1473. 1459 see also Hemopoiesis blood sinuses. 1324 cell patterning. 539–540. 1388 selective adhesion. 1321 microtubules. 1321 apoptosis. 1385–1386. 1208F Breathless gene. 1322F. 64F. 846 a-Bungarotoxin. neuronal. 1470F remodeling. 1382 Branch migration. 67F see also Thermodynamics Bioluminescence. 1210F. 457F see also Mating-type switching E. 476F for multicellular development. 318T Budding yeast(s). 188 RNA interference (RNAi). 1137. 1135. 1140–1141. 1386F 1. 1388 homophilic adhesion. 847F C4 plants. 1321. 1438F Bs1 transposon. 1324FF ABp cell. uropathogenic E. development. 571F sex determination. Drosophila. disintegrins. 1138T signaling functions. 39 molt cycle. 1145 structure. 504F BZIP gene regulatory proteins. apoptosis. 1136. vs means compare/comparison. 1229F typical growth. 1124 Bidirectional signaling. 531F Blastula. 1321 development see Caenorhabditis elegans development gene regulatory proteins. 1137 catenin link to actin cytoskeleton. 1425 Breast cancer Brca1/Brac2 proteins. 1451–1453. 1452–1453. 1122. 1141. 1456. 1249–1250 N-cadherin. 1138T. 1446 endothelial cells see Endothelial cells formation and sprouting see Angiogenesis see also specific types Bloom syndrome. 448–449. 1395–1396 Biological order. 1456F X-ray effect on. . diploid state. 475. 1324FF asymmetric cell division. 1388 P-cadherin. 685 Burkitt’s lymphoma translocation activating Myc gene. 1138T Fat proteins. 1455F stromal cells. in visual cortex. origin. in neuronal guidance. 1136. 1334. 1136. 922 Binocularly driven cells. 1138F binding affinity. 310 chromosome abnormalities. 1453–1456. 1139F VE-cadherin. 1333F. 20T.. 1541F control. 1379F Blastopore. 1140–1141 “Velcro principle. 66 activated carriers. 1142F distribution. 455–457. 1336. 1345 Branching morphogenesis. 1445F. 1141F. 1388 nonclassical cadherins. 1381–1382. 65F thermodynamics. 1138T. 1469–1474 canaliculi. 1136F diversity. 1367–1368. 1381F Blastoderm. 531. 1322. 1400T C3 plants. 1445–1450. 1136F. 1366. 1441 Bone(s). 1145 developmental expression embryo compaction. 34F alternative splicing. 1137. 1342F Bivalent formation. 34 haploid vs. 1136. 957 Bride-of-sevenless mutant. 1471 secretion by osteoblasts. 1138 tissue segregation and. Louise. 1193 ECM degradation. 456F. 1138T signaling. 135F DNA-binding. 982F as model organism. 1379–1380. 308. 1138T Flamingo protein. 1504 Borrelia burgdorferi. 131. 564F protein interaction maps. Protein transport Biotin. 1136. 1139–1140. 1137 desmocollins. 1138T family members. 1139F cadherin domain motif. 1142F E-cadherin. 121F Bithorax complex. 67F cholesterol. 1136–1137. 847F C6 (Zn finger) gene regulatory proteins. 1422 muscle cell division. 1500 Boundary elements see Insulator elements Bovine spongiform encephalopathy (BSE). 310 BrdU (bromodeoxyuridine) cell cycle analysis. 1140F. 1470–1471. 295T Brush-border. 1138T genes. 1286 sexual reproduction. 1137–1138 classical cadherins. 1177T cadherin 23. 571. 1470F cartilage replacement by. 1508 b-catenin and. 1361 Brca1/Brac2 proteins. 1471F matrix erosion by osteoclasts. 1324. ICE. 1363F. 1365 Blie. 479–480 cell type specification. 1474 repair. 1370 Brain. 1323 see also under Caenorhabditis elegans development genome.INDEX Beta-barrel proteins. 1470 long. 1473F ECM degradation. 1137F. 1138T.. 583 Bromodeoxyuridine see BrdU (bromodeoxyuridine) Bronchiole. 539F Southern blotting. 1239 viral causation. 1145 protocadherins. 1323–1324. 18T. 1324F. 1059F epidermal cell division. 1437F. 1489 Caenorhabditis elegans development. 1138T. 84–87 see also specific pathways Biosynthetic–secretory pathway(s). page numbers with a T refer to a table. coli. 1324. 1148 see also specific types Caenorhabditis elegans. 1142 Ca2+-mediated cell–cell adhesion. 1469–1470. 413F see also Saccharomyces cerevisiae Bundle-sheath cells. 1403 Brat protein. Eph receptors and ephrins. 1367F BLAST sequence alignment. 770F see also Exocytosis. coli vs. 1321–1328. 736. 1139F nervous tissue. 1453–1462. 1321 size. 1228. 557F. 1470–1471. 307F. 1456. 295T incidence dependent on reproductive history. 295T Blotting membranes. 1435F Brown fat. 1470–1471. 1400T C2H2 (Zn finger) gene regulatory proteins. 170F macromolecules. 1503. 1456F Bone morphogenetic proteins (BMPs). 1136–1137. 36–37. 1274F. 1137F. 622. 519F see also DNA hybridization B lymphocyte leukemia. 1136. 37f. 1137–1139. 1471F ECM production. 1453F. 84F. 1145 T-cadherin. 1138T. 736. 1444F Betaglycan. 286. 1123–1124 BH123 proteins. 3-Bisphosphoglycerate. 135. 18T. 1321–1328 ABa cell. 134F. 1502. 1229. 1145 structure. 1382F Branchless gene. in bone marrow. 806. 1365. 622F Bladder cancer. 1022–1023 Bid. 1136. 1324FF Page numbers in boldface refer to a major text discussion of the entry. 81F see also specific carriers biological order. 1470F Bone marrow apoptosis. 65–87 catabolism vs. 1400T I:5 C C2C2 (Zn finger)/GATA gene regulatory proteins. 1467. as transmembrane proteins. 1468. 350F Brassinosteroids. 397–398. 1400T Ca2+ ATPase see Calcium pump (Ca2+-ATPase) Ca2+/calmodulin see under Calmodulin Ca2+ pump see Calcium pump (Ca2+-ATPase) Cadherin(s). 1138T cadherin domain repeats. DNA repair disorders. 1453T see also individual types Blood coagulation anti-clotting agents. 79F. 1444. 770. 1324. effect on acetylcholine receptors. 1184. 1471 uncalcified (osteoid). 1334F Drosophila development. 170. 423F see also Protein structure BH3-only proteins. 1443 Blood cells. 1324 E cell. 1140F selective assortment. 1498 see also Prion proteins (PrP) Brachyury (“short tail”) protein. Osteoclast(s) composition. 287F reproductive cycles.” 1138–1139. 1342. 767 Birthdays. 1400T genes dosage compensation. 1471F cells. 1474 structure. family members in different eucaryotes. 1138 intracellular domains. 1327–1328. 1392FF Branchial arches. 33–34 replication origins. 1138T desmogelins. 83F feedback inhibition. 1179 fibroblasts transformation to. 1133–1150 bacterial invasion and. 927 Brightfield microscopy. 422. 1469–1471 formation. 749–787. 1136–1137. 1327F cell fate. 1177T cadherin domain repeats. 1117 blood cell production. cell culture micrograph. 1469–1470 as source of signal proteins. 1333. 1142 synapse formation and. 1499 BY2 immortal cell lines. 1138T signaling. 750F. 67. 957. chronic illness. 1441 Bordetella pertussis. 81. 949. 1136F neural development. 1135–1136. 1274. 1219 B lymphocytes see B cell(s) BMP (bone morphogenetic protein) family. 66–68 entropy. 1470–1472 cartilage model. 1451F. 1118 cell numbers. 1322 cell lineage. 800 pH control. 1322 mutants. 1382 BRI1 receptor kinase. 1136. 1215F DNA repair defects. 1137 conformational changes. 1282F. 308F. 449F mRNA localization. 846–847. 1470F see also Osteoblast(s). 167T BiP. 1456F transplantation. 65–87 structural. 1141F. 312F Branch point-binding protein (BBP). 1194 Blood sinuses. 1123F Bicoid protein. 538 Northern blotting. 1022–1023 eve gene activator. 1136–1137. 1136. 539F western blotting. 1379FF. 1322F adult anatomy. 285F. 1140. 1454 histology. 1455–1456. 285. 63 energy requirements. 1391–1395. 1139F. apoptosis. 635F see also specific proteins Beta-cells (insulin-secreting). 1471–1472 lacunae. 34 genome. 1228T. with an FF to figures that follow consecutively. 1446F branching mechanism. page numbers with an F refer to a figure. 486–487. 632. 167. 1470. 1458–1459 transfusion. 1136. 1448 development. 1142. 148F. 816F mutational effects. 344. weighing risks. 913 calmodulin and. 1210 cell proliferation. 1324. 71F. 915. 346–347 guanyl transferase reaction. 363–364. 1286 Vasa protein. 1206. 840. zinc ion dependence. 1209. 1212–1213 oxygen as limiting factor. carbon fixation. 767 Calreticulin. 241F. 804. 597F as intracellular messenger. 845F ribulose bisphosphate carboxylase. dependence. 1322 sex determination. 265. 1026 Cardiolipin. 1226. 659–660. 295T. 658–659 ATP-driven pumps. 845F reactions. 1008 cell division rate. 1224–1230 somatic mutations. 912 Calcium pump (Ca2+-ATPase). 1207F causes/pathogenesis. 1218–1219 properties. 1205–1267 angiogenesis in cornea. 167 Carcinogenesis. 1135–1136 cytosolic concentrations. 1206–1207 stem cells. 1324 Wnt signaling pathway. 1489F. 912–913 signaling see Calcium signaling storage. 1232–1233 chromosome abnormalities. 1161–1162 intracellular measurement. 914F. 595F. 1208 cancer after exposure. 1255F genetic instability effect. 1229–1230 epigenetic vs. 1217–1218 origin. 912F. 1223 defective cell death. 98–99 see also Citric acid cycle Carbon dioxide (CO2) pump. 912–916 Ca2+-induced Ca2+ release. 867–867. 844 see also Carbon fixation see also Polysaccharides. 277–278. fertilization. 1322F inductive cell–cell interactions. 912F Calcium signaling. of actin filaments see Actin/actin filaments 5¢ Capping of eucaryotic mRNA. 1003 Capsid(s) (viral). 346–347 decapping. 725–726 transmitter release at synapses. 738–739 Calvin cycle see Carbon-fixation cycle CaM-kinase (Ca2+/calmodulin-dependent protein kinase). 1260 evolution of resistance to therapy. DNA microarrays. 1142 cells. 1299 calcium release. as intercellular signal. 1324. 846–847 Carbon fixation. 1234–1235. 660–661 autophosphorylation. 1325 Caged molecules. 365F. genetic change. 1209 cell lines. 661F muscle contraction. 1257 see also Mutation(s). 1193 invasiveness. 844–847. 1234–1235 loss of heterozygosity. 54–55 double bonds between. 910. protein chaperone function. 1207 progression. molecular tunneling. 1227 origin from single mutant cell. 1448F see also Angiogenesis Capping. 1229–1230 industrial. 845. 161F Carbon monoxide. 1324F. 889 Carboxylated biotin. hereditary. 1104–1105. 913 IP3-gated Ca2+-release channels. phagocytosis resistance mechanisms. 346–347. 1217 Cancer-critical genes. 1323 heterochronic genes and timing. 915–916. 492 functions. 1234–1236 see also Mutation(s). microtubule-based movement in axons. 1326F maternal effect. 1214F epithelial–mesenchymal transitions. 915F. 346 pre-mRNA ordering. 1031 adherens junctions. 1325 precision. 913F Ca2+ spikes. 912–914. 1207–1208. 1141 growth/progression. 1212F. 844–845 CO2 pump. 1225 USA. 1497. 1324FF P granules. 1463–1464. specific cancers Cancer cells. 596F Cajal bodies. 1323F polarizing signal. 846–847 cyanobacteria. 660F egg cell. 1215–1216 defective cell differentiation. 347F Capping protein. 1218F heritable properties. 414F reproduction without restraint. 1532 CapZ protein. 1207F. 1234–1235. 988 traditional therapies. 1233–1234 Rb gene. 914 Ca2+ oscillations. 916F CAMP see Cyclic AMP Canaliculi. 346F cap-binding complex. 1262 cell crawling. 1127 benign vs. 1224F epigenetic change. 1448 apoptosis. 915F Bordetella adenylyl cyclase binding. 914–916. 913F Ca2+ wave. 1209 see also Oncogene(s). 913. DNA methylation. 912 ubiquitous intracellular messenger. 1324. 843–848 CO2 (carbon dioxide). 167–168. 844. 506T colonization without restraint. 1219 stem cells. 1233 p53 gene/protein and. 106F skeletons. 149F. 1208 Carcinogens.I:6 INDEX 1216–1217 see also DNA repair environmental factors. 1107–1108 contributing properties. 106F Carbon dioxide (CO2) fixation see Carbon fixation metabolic production. fatty acids. 1208. 912F oscillation frequency. 1229F variation between countries. 1224. 845F chloroplasts. 352 reaction. 1212–1213. 1225 identification for cancer avoidance. 1442 Cancer. 1030 entry into cytosol. 1513 Cap snatching. 1222F natural selection. egg cells. 1213 genes see Cancer-critical genes preventable. 912 Calcium wave. 1326–1327. malignant. 1106 Rb gene/protein. 1463F mitochondria. 1231–1232 dominant vs recessive (oncogene vs tumor suppressor gene). 914–916 action on CaM-kinase II. 1031F sarcomeres. 1225. 1236 Ras gene. 750F. 1322–1323. 656F. 1220 see also Metastases metastasis see Metastases natural selection. 1205–1224 mortality. 911 at synapses. 912. 1446F response to wounding. 660 mechanism. 1212–1213 propagation. 912–913 Calcium channel(s). 844–847. 844F Carbon-fixation cycle. 1500 Cargo. 144F Calnexin. 1256–1265 antibodies targeting oncogenic proteins. 1030 Ca2+/calmodulin. 873–875 evolution. 1225–1229 Carcinoma. 1299 gap junction permeability. 1257–1360 sensitivity. 1222. 660 egg activation. 1208. 911 ryanodine receptors. 652–667 active transport. 910. 1322 gene regulatory proteins. 1250–1255. 1324FF epithelial apico-basal polarity mechanisms. 1297 Cap-binding complex (CBC). 1323 gut. 168F Carbohydrates. 1209F see also Cancer cells ECM degradation. 912–916 regulation of concentration in cytosol. 1241–1242 cell proliferation regulation. 754 Carrier protein(s). 912F. 1448. 912–913 regulation of cytosol concentration. 1003 Carbamoyl phosphate synthase. 1232F hereditary cancer syndromes. 912. 1259 new therapies. 1218. 1215–1216 ECM degradation. Sugars Carbon atomic structure. 1212 incidence environmental factors. 1294. 912. 910. sarcoplasmic reticulum. 808. 654–667 asymmetric cellular distribution. 1227 as a microevolutionary process. 1224. 412. 1228T initiation. 71F. 346–347 Capillaries. 1208 carcinogens see Carcinogens DNA repair defects. 1155–1156 founder cells. 1336F retroviruses. 1323–1324. 1206 prevention. 1299 Callus formation. 690 Calcium/calcium ion (Ca2+) cadherin-mediated cell–cell adhesion. 1503 Ca2+ binding. 1225F types. stem cell role. Tumor suppressor genes (TSGs) cells see Cancer cells clonality clonal evolution. 912–914 PKC and. 1400T genes. 1214–1215 microenvironment. Oncogene(s). 1224–1230 primary. 1229F nomenclature. 912. 346 methyl transferase reaction. 346. . 661F Calcium-sensitive fluorescent indicators. USA. 1225. 1218 recurrence. 1325 pop (plenty of pharynx). 69. 265. 915F. reaction rates. 868F Cardiovascular disease. 1209F Mormons. 1194F epidemiology. 1323–1324 mom (more mesoderm). 84F Carboxyl groups. 13. 1324F. 845. 106F Carbon–carbon double bonds. actin filament. 660 structure. 46F cell components. 504–505. 1206. 1241–1242 analysis in transgenic mice. 1219 taxol. 1323 EMS cell. 1213 fluorescence-activated cell sorter. 1517 Capsules. 346 phosphatase reaction. 1344F varied types of mutation. 660–661. 69 ATP hydrolysis. 845F Carbonic anhydrase. 1446–1447. 148. 1210 colorectal cancer. 150F. 1194. 1324. 1217–1219 telomerase activity. 1233F molecular characterization. 594F Calcium-activated potassium channel(s). 910F see also Inositol phospholipid(s) mechanisms keeping cytosolic Ca2+ levels low. 910–912 see also Calcium channel(s) IP3-mediated. 241. 738–739. 914 structure. 1220 growth rate. 1230 metabolic activation. 1206 loss of contact inhibition. 1517 Capacitation. 1323 pop-1. 1234 Cardiac muscle. 13. 594–595. 1241–1255 blood supply. 1324FF P2 cell. 1210. 55 biosynthesis. 1219 treatment. as chaperone protein. 767F Cargo receptor(s). 1224F as function of age. 1210F. 1324FF MS cells. 295–296. 872–875 NADPH. Tumor suppressor genes (TSGs). 596–597. 1206–1207 epigenetic changes. 749. 912. 114F Carboxypeptidase. individual genes Cancer syndromes. 1225F mutagenicity. 1230–1241 analysis in developing embryos. 1242–1244 identification. 1324. 1234–1235 Canine parvovirus. 1230–1241 cell transformation assay. 568 Calmodulin. 1325 see also individual genes germ cells. plant cells. 1282F. 401 catalysts. Cell–matrix adhesions. 1063. specific types Cell adhesion. 1573F caspase recruitment domain. 1145 synapse formation and. 1327F Ced4 gene. 1071. 1505F role in viral entry into cells. 1592T. 1597. Cell–cell adhesion cell–matrix adhesion. 288. 13FF light sources (phototrophic cells). 8 inorganic chemical sources (lithotrophic cells). 1458 capillary sprouting. 887–889. page numbers with a T refer to a table. 1599F negative selection. Cell junction(s) Cell coat (glycocalyx). 1592T. 402. 285F. 12 genome see Genome(s) isolation. 1469F defective in achondroplasia. 1472–1473 growth. 1592T CD40 ligand. 67F definition. 1327. 1590. 1040F see also Cell motility/movement Cell culture. 568 primary cultures. 1142F see also Cell lines. 1057F Cdh1. 407F ribosomes. 1053–1113. homophilic binding. 502–504 historical aspects. 100F citric acid cycle see Citric acid cycle glycolysis see Glycolysis oxidative phosphorylation see Oxidative phosphorylation sugars. 1146–1147 integrins. 402F self-replication. 1471F replacement by bone. 1119 Catabolism. 1145. 1146. 1133–1150 dendritic cells. 1470–1471. 1127 interleukin-1-converting enzyme. 653F. Signal transduction. 1471 ‘models’ in bone development. Cell I:7 junction(s). 1145 classical cadherin link to actin filaments. 12. 1064. 1025–1050 see also Cell motility/movement chemical components. 1142F signaling. 24T plasma membrane. 1505F CD3 complex. 1505. 1064. 404. 1592T Cdc6. 543. 554F. 656F coupling to proton gradients. ORC binding. 1068 Ced3 gene. specific proteins Cartilage. 790. 574 Cdt1. 883 plants. 1470. 1177T cadherins see Cadherin(s) cell–cell adhesion. 1151 mechanism. 1597 CD40 receptor protein. 1598T on macrophage. 1059. 1118. 1066T. 1059–1060. 45–65 carbon compounds. 885F endocrine. 1592T immunoglobulin superfamily. 543F. 1471F Casein kinase 1. cadherin binding. Neurotransmitter(s). 1594 CD80. 1131–1204. T cells. 1118 signaling pathways. in dynamic instability. 1036. 3F gene families in common. 55 free energy information transmission. Ribozymes Catalytic antibodies. Tissue culture Cell cycle. page numbers with an F refer to a figure. cytoskeleton shape. . Extracellular matrix (ECM) Cell adhesion molecules (CAMs). 1006. 1253 p120-Catenin. 880. 1590 CD8 T-cell(s). Active transport. 1145. 655F coupled carriers. 7F terminal differentiation. 14–15. 66. 418T. Receptor(s). 955 extracellular signals. 1580–1581. 378–379 spliceosome active site. 885.. 1571 see also specific types Cell–cell adhesion assays. 822–823. 1058F BrdU labeling. 1592T. 1054F analysis animal embryos. 504 mammalian cell cycle analysis. 1119 Caspase recruitment domain (CARD). 1580. 1059. 6F ribosomal machinery for protein synthesis. 1587F see also Cytotoxic T-cells (TC) CD9. 1118–1120 activation. 656F localization. combinatorial actions. 1592T. 1146 selectins. 1586. 1177T see also Cadherin(s). 1139–1140. 1147–1148 T-cell function. 73. 8–9 DNA as hereditary information store. Ribozymes in controlled energy use by cells. 1141F. 1060F Page numbers in boldface refer to a major text discussion of the entry. HIV receptor. 1467. Notch receptor protein different responses in target cell types. 1594. 1327. 1177T cadherins. caspases. 285. 25. 1138F scaffold proteins. 881. definition. 886–887. 8–9. 47 Cation-transporting ATPases see Calcium pump (Ca2+-ATPase) Caulobacter cresentus. 1057–1058. 88 oxidation of organic molecules. 1059F DNA microarrays. 1071F Cdc42. 790F Caveolin. 504F definitions. 1586. 1587F positive selection. 15F self-reproduction by autocatalysis. 1156. 949. 920F autocrine. 1580T. 1153–1155 heterophilic vs. 1087. 1471–1472. 16 bacterial cells. 8F RNA as intermediary in information transfer. specific components. 1057. 1119T inhibition. 1468–1469. 920. 1147–1149. 72–73 by RNA see Catalytic RNA. 541F cells in culture. 1140F. 14F. Integrin(s) ICAMs. 826F specificity. 1036 leading edge. 55–58. diversity. 1068 Cdc20. 2. 2 see also entries beginning cell/cellular. 881F see also Ephrin(s). sperm–egg binding. 45–123 vehicle for hereditary information. 501–517 mixed suspensions. 1468–1469 bone repair. 1580T. 4. 885F gap junctions. 401. 655 kinetics. Signaling molecule(s)/pathway(s). 352 see also Ribozymes. 542 clones. 1107 plant. 1140–1141. 7F. 420F. 14F. 1469F see also Chondrocytes erosion by osteoclasts. 1581F. 1140F selective assortment. 1508 cell–cell see Cell–cell adhesion cell–matrix see Cell–matrix adhesions traction for cell movement. 1043. 23. 161F Catalytic RNA origin of life. 1080 Catenin(s) b-Catenin cadherin binding. 884. 1145–1146 synapse formation and. 70. 1244F cDNA. 826–827. 1008. 1142 cell–cell adhesion and intracellular signaling. 25F eucaryotic cells. 1145. vs means compare/comparison. 880F carbon monoxide. 1599F negative selection. 1135 Ca2+ role. 1587F positive selection. 88–103 activated carriers. 1059. 1590 HIV receptor. 289F. 1327F C. 1057F. mating. 1066T. 1599F antigen presentation. 1040–1041 see also Cell adhesion molecules (CAMs). 1580–1581. 765F CD4 T-cell(s). 1468–1469. 1 universal properties ATP as energy currency. 502. 879–903 adaptation.’ 1059 replicative senescence. 637F Cell communication. 1142. 1066.INDEX conformational changes. 1103 tree of life archaean cells. 790 CBC (cap-binding complex). 79F anabolism vs. 1056–1057 temperature-sensitive mutants. 158–159 see also Enzyme(s). 1142 g-Catenin (plakoglobin). 1593F. 1047 bone marrow. 503F. with an FF to figures that follow consecutively. 883F see also Hormones evolution. cloning vector production. 1140–1141. 1101 Cdk (cyclin-dependent kinase) see Cyclindependent kinases (Cdks) Cdk4. 823F evolution. 546F libraries. 1177T bacterial invasion of host cells. 1595F. 1175F bacterial. 1146–1147 integrin superfamily see Integrin(s) selectins. 1119F. 652 see also ABC transporter(s). 15–16. 655F light-driven pumps. 1148–1149 selective adhesion. 949. 502 separation techniques. 543F. 5–6. 721 Catalysis autocatalysis and origin of life. 5F small molecules and fundamental chemistry. elegans see Caenorhabditis elegans Cell(s) behavior cytoskeleton involvement. 1592T CD86. 503FF origins of life. 144F. 9–10. 14. 902. 1080 Catastrophe. in cancer. 636. 411. 1590F. 6–7. 54–55 small molecules. 1471 cells. 12 from living organisms (organotrophic cells). 881 budding yeast. 1119 human. 1100 Cdc25 phosphatase. Extracellular matrix (ECM) Cell–cell contact actin polymerization via Rac. 347 C-Cbl protein. 1135–1136 cell adhesion molecules. 1177T see also Cell–matrix adhesions. 1134. 926 CCR5. 881. 1505–1506. 542. 1587. 10F proteins as catalysts and executive molecules. 1599F antigen presentation. 1003. 991 Caveolae. 1036F activities involved. 1448 see also Cell–cell adhesion. 882–883. 1120F see also Procaspase(s) caspase-3. 1119 caspase-8. 65–87 energy barriers. 1591F. 882F. 436 Catalase. 1590. 542. 1139F. 655F membrane transport. 1580. 26–32 unit of living matter. 955–962 speed of response. 540. 1298–1299 CD28. 1587F see also Helper T-cell(s) (TH) CD8 protein. 1581F. 400–408 polarization see Polarity/polarization procaryotes. 544 synthesis. 543F. 1059F ‘immortalized. 1142 colorectal cancer. 1592T. 88 Catabolite activator protein (CAP). 887F see also Cell junction(s). 1142F Cation. 1587. 504 tissue segregation in. 1472F mineralization. APC/C regulation. 1592T. 15F. 501–517 anchorage dependence. 888F paracrine. 884. 504–505. 1592T on B cell. 1516 Cdc genes. 889 cell-surface receptors see Cell-surface receptor(s) contact dependent. 1145–1146 cell proliferation and. 655. 160. 1590. 1145. 1065 flow cytometry. 544 PCR cloning. 1327F Ced9 gene. APC/C regulation. 1571 immunoglobulin superfamily. 1175–1176. 882F. 1042F. 884F nitric oxide. 1149F see also Cell junction(s). individual signaling molecules and pathways Cell crawling. 652–643 reversibility. 504 secondary cultures. Self-splicing RNA Catastrophe factors. 1327. 1142. 1124–1125. 1243. 655. 949 Caspase(s). 1599F CD4 protein. 285 see also DNA replication universal characteristics. 411–412. 1133–1135 see also Epithelia functional classification. 1135T cell–cell. 1289F plant development. 1133T. 284. 454–477 cancer and. 1385F see also Cell motility/movement Cell motility/movement in animal development. 1233–1234 see also Replicative cell senescence plane of. 1100F mitogen actions. 464–465. 1169–1178 actin-linked. 1158–1164 gap junction see Gap junction(s) plasmodesmata. 1215–1216 common processes. 1109F organ growth. 1110F DNA damage response. 1362 Cell division. 1135T. T cell receptor(s) Cell memory. 1132. telomere length. 1059F meiotic. 817F ultracentrifugation. 1039F traction. 583 protrusion. 1137. 1135T adherens junction see Adherens junction(s) desmosome see Desmosome(s) immunoglobulin superfamily. 1061. 1061. 1175–1176 limitation. 1132. 1216–1217 DNA damage. 1066. 285F. 293 mammalian cell culture. 506T. 1145–1146 selective adhesion. 1102 cell number and. 510–511. 1132F. 413F patterns of gene expression. 1145 see also Cadherin(s) cell–matrix. 1135T focal adhesions. 1110. 1132. 1060–1067. 1133T chemical synapse see Chemical synapse(s) immunological synapse. 1244F checkpoints. 1041F via actin polymerization. 1056 functions. 1105 Rb proteins. 1069 as timer/clock. 465–466 Cell differentiation. 1389–1390 . 1132. 1060. Development contribution of myosin II. 1170 hemidesmosomes see Hemidesmosome(s) see also Integrin(s) intermediate filament attachment. 1071 spindle assembly checkpoint. 1056–1057. 1138F occluding junctions. 511F mitochondria. 1053 anchorage dependence. 1057–1058. 510. 1311–1312. 1103–1105 inhibitory phosphorylation. 303. 1061. 1133T. 1140. 1056F. 1088. 1037–1038. 1058F importance. 1062. 505. 454. 1066. 1099. 1070–1071 timing. 1108–1110. 1110. 1233–1234 limits. 1363–1378 see also Cell migration. 1132 transmembrane signaling. 1069–1070 DNA replication. 1068F molecular/biochemical switches. 516 vesicular transport study. 1053. 1248. 1139–1140. Gene expression regulation Cell diversification. 1057F. 1163F epithelial. DNA replication. 1061 defects making cancer cells vulnerable. 1057F cancer and. secondary. 1103 density-dependent inhibition (contact inhibition). 1100–1101. 363. 1061F transcriptional regulation. 208–209. 1170–1171 neuronal. 1054–1060 phases. 1103 G2 phase. 1132. 1175–1176. 1133T transmembrane adhesion proteins. 1140–1141. 1133T. 1146–1147 selectins. 1131–1204 anchoring junctions. 1400 cell death balance. 1103 male gametes. 285F. 1132. specific types see also Cell adhesion. 1272 sister chromatid cohesion. 1193. 1095–1097 plant cell(s). 1281 cancer cells. 1140F. 488–489. 1108 see also Cell cycle. 1194F external signals/guidance molecules. 1145–1146 see also Cell adhesion molecules (CAMs). 1055F G0 (G zero). 512 Cell fate determinants. 506T hybrid cells. 1063–1064 p53 and. 1158. 208F. 1109F cytoskeletal role. 177–178. 1140F selective assortment. 1145. 1575 see also MHC (major histocompatibility complex). 1195 stem cells. 1065–1066. 412 terminal. 1105 meiotic. 1059. 1323F oocytes. 1175–1176. 1102 Cell plate. 1067. 1054–1055. 752F Cell growth. 1134F. 1099F C. Cytokinesis. 1135T CAMs. 1177T fibronectin and. 1105–1107 G2/M checkpoint. 1133T. 1037–1039 Cell number. 1133T. 1540. 1105 cyclical proteolysis. 464F. 1104F ubiquitin ligases see Ubiquitin ligase(s) see also specific proteins resetting. 1104–1105. 1105 timing. 1055 M phase. 1101–1112 density-dependent (contact inhibition). 1053 abnormal signals. 1111–1112 see also Cell cycle. 1133T homophilic vs. 455f genome constancy. 1175F control. 1102 defective in cancer. 511–512. 1175F cancer cells. 412 differing response to extracellular signals. 1139F. 454–455. 512F see also Protein analysis Cell-free systems biological process reconstruction. 1055 interphase. 1108F DNA damage and. 521–522 macromolecule/organelle separation. 1133–1150. 285F. 1108 organism growth. heterophilic. 504F. 1107–1108. 967F delay. 1103 eIF-2 regulation. 1194. 209. 208F. 285F. 458F. 1071 cytokinesis see Cytokinesis mitosis see Mitosis see also Meiosis S phase (DNA synthesis). 1281 metaphase-to-anaphase transition. 1065. 208F. 1169–1178 actin-linked. 1059F yeast mutants. 1105–1106. 209–210. 752. 1146. 1056 see also Cell division. 1145. Cell proliferation. 1110. 1140 gut epithelial cells. 1440F integrins and. 1133T see also Cell–cell adhesion. 510F. 1540–1551. 1132F. Cell division. 289–290 labelled cells. 1312F combinatorial control. 1217 DNA tumor virus proteins. 1045. 1061 abnormal proliferation signals and. 1134–1135. from crypts to villi. 1132. 1102 control. 512 Cell junction(s). 1133–1150 immunoglobulin superfamily. 1053 mammalian cell culture. 1059. 1101–1112 coordinated growth and division. 1068F. 1146–1147 integrin superfamily. 1104. 1099 Cell fractionation. 510. 1134F. 509F see also Hybridomas immortal. 1067–1069 histone synthesis. 966–967. 1060–1061 intracellular triggering of cell-cycle events. 464 DNA rearrangement. 1066T Cdks see Cyclin-dependent kinases (CDKs) cyclins see Cyclin(s) E2F proteins. 411. 1169–1178 selectins. 1133T. 1142F signaling. specific types Cell lines eucaryotic. 1373–1375 ECM degradation. 1104F Cell death apoptotic see Apoptosis (programmed cell death) cell number and. 1059. 1066F analysis animal embryos. 1107–1108 checkpoints see Cell cycle control chromosome changes. 1215–1216 neurons. 1249F see also Cancer coordinated growth and division. 1039F crawling see Cell crawling microscopy. 488–489 G1 phase. 516 cell cycle analysis. 512–514 electrophoresis. 1132F. 1141F. 505. 489. 1107 density-dependent. 1323–1324. 1108–1110 density-dependent inhibition. 1572 transplantation reactions. T cell(s). 1097 Cell proliferation. 1090. 506T see also Cell culture Cell–matrix adhesions. 579 Cell extracts (homogenates ). 1154–1155. Cell proliferation Cell homogenate(s). 1058. 1140F. 1059 primary vs. 285F. 1134. elegans embryo. 1133T. 1065F. Extracellular matrix (ECM). 1064. 415. 1055. 1057F arrest. 303–304. 1243. 1216–1217. 1061. Cell proliferation Cell cycle control. 1110. 1191 hemidesmosomes see Hemidesmosome(s) see also Cell–cell adhesion. bacterial phase variation. 1110F integrins and. 1425 total cell mass control. 1065F eucaryotic similarities. 1058F cell fractionation. 1061. 1106F G0 phase. 1103 see also Developmental genetics. 510 chromatography. 363F overview. 504 transformed. 1075 regulatory proteins. cell cycle arrest. 1154F tight junction see Tight junction(s) signal-relaying junctions. 1056F. 465F see also Combinatorial control protein differences. 1055. Mitosis Cell doctrine. 1133T. asymmetric cell division. 1105–1107 mitogens see Mitogen(s) see also specific factors coordinated growth and division. 1134. 1135T. 1064. 1145.I:8 INDEX see also specific types Cell determination. 466 see also Cell differentiation Cell migration developmental. 1067–1071 chromatin protein production. 209F control systems see Cell cycle control nucleolar changes. 1054. Extracellular matrix (ECM). 510–511. 1056–1057. 1053 start (restriction) point. 1055. 1133–1150. 1135T cadherin superfamily. 1134. 285. 1055F asymmetric. Cell junction(s). 1150–1158 septate. 1054F. Cell growth. 1088F start (restriction point). 510–512 cell-free systems see Cell-free systems cell lysis. 1054. 1040–1041. 1107–1108. Integrin(s) Cell-mediated immune responses. 1067–1069. 1066. 1162–1163. 1108–1110. 1059F progression analysis. 1066. Meiosis. role of Notch. 517. 511F. 412 specialization. 208F. 1059 yeast mutants. Cell–matrix adhesions channel-forming junctions. 1540F. 284. Cell growth. 505. 505. 1132F. 412. 518F. 1066T APC/C see Anaphase promoting complex (APC/C) SCF enzyme complex. 458. 1107–1108 anchorage dependence. 1289–1290. 1569–1589 intracellular pathogens. 1134. 1074 chromosome duplication. 684 acetylcholine receptors. 867 photosynthesis see Photosynthesis protein import. 230F structure. 1105. 1196. 869F genome. 1079 microtubules emanating from. 527 Chemical bonds. 996F composition. 1381F Chimeric proteins. 511. 1370 Chordin. 1527 DNA damage. 1512F. 1391 neuronal migration. 945F growth cone guidance. 1543F Central nervous system (CNS) apoptosis. 286. 244F remodeling see Chromatin remodeling structure see Chromatin structure see also Chromosome structure. 956. 35F Cellularization. 442F Chimpanzee(s). 682. 843F transport. 48F. 522 Centriole(s). 216. 874. 239–240. 1201 Cell wall(s) plant see Plant cell wall procaryotes. 220 heterochromatin see Heterochromatin immunoprecipitation. 1199T microtubules and deposition. 1111–1112 see also Cell cycle. 1392F Cervical cancer. control. 813–814. 891–895. 1386F protein aggregation vulnerability. 1096F. 864F maternal inheritance. 1313F. 875F endosymbiont hypothesis. Replicative cell senescence Cell renewal and turnover epidermis. 397 repair. 1336 Chromatids see Sister chromatid(s) Chromatin. 819F see also ATP synthesis bacterial. 859–860. 229F Centrosome. 1098 electron transport see Photosynthetic electron transport chain(s) energy interconversions. 666 Cholecystokinin. 956–960 see also individual types Cell survival integrins and. 216F. 83F. 1468–1469. 35–36. 1530 CGN see Cis Golgi network (CGN) Ch4 elements. 859–860. 470 role in innate immunity. biosynthesis. 1076. 1550F in inflammatory response. 958F G-protein linked see G protein-coupled receptors (GPCRs) intracellular receptors vs. 248F Chk1 protein kinase. 866F mutants. 1385F somatosensory region. 1513 Chlamydomonas. 684 inhibitory. 241F packing. 290 condensation. 210F. 1140 bacterial. mouse. 1206 Chordates.. in cell locomotion. 620. 243. 716F. 673. 1158–1164 see also specific types Channel protein(s). 1492. 300–301. 1079 maturation. 215F. 232F Central dogma. 231. 941–945. 1076. 839F see also Electron transport chain(s) Chemokine(s). page numbers with a T refer to a table. 1530 plants. 390F eucaryotic. 1380. 866F see also Non-Mendelian inheritance glycolysis. 232F histones. 231–233. 1048 CheA. 365F chromatin assembly factors (CAFs). 859 evolution. 1132. Heterochromatin euchromatin. 30F. 1070 see also Chromosome condensation. 1099 Cellulase. 864 higher plants. 1078. 849–850. 683F see also Neuromuscular junction (NMJ). 881. 684 cell signaling. 857T. 716–717. 1199–1200 Cesium chloride gradients. 1301. 229–230. 857. 992–996. Plasmodium falciparum resistance. 993F. 1179. 717 mitochondrial protein import. transmission. 1105. 855 cell-free systems. 1504 Cholera. 1200F. flagella. H3 CENP-A variant. 331 Central lymphoid organ. 1490F. 715.. 1078. 512F molecular weight determination. 344 histones.” 226–227. 1436F. 1196. 944F Checkpoints in cell-cycle see under Cell cycle control Chemical biology. 46–50. 431–432. in enteroendocrine cells. 1543. 470 evolution. 1082. 1084F Ceramide. 522–523 sedimentation coefficient. 744–745. 652–653 conformational changes. evolutionary relationships. 1355 see also Limb buds (vertebrate) neural development. 1437 Cholera toxin. specific types Chaperones bacterial. 114F Chondroblasts. 842F. definition. 1133T. 231F heterochromatin. Cell division. 620. 215–216. 841. 432F nuclear sites. 867 replication. 1388F neutrophils. 1211F Cesa (cellulose synthase) genes. 1500. 1367F progenitor cells. 1198F. 1076F center-seeking behavior. 432. 1388. 240F. 940. 1045F Chiasma formation. 343. 107F Chemical reactions. 629. 229–230 plasticity. 863–864 maintenance. 666. 840–841. 1276F Chick embryo limb development. 653. 1199F structure. 1406 microfibrils. 1245F scaffold proteins and junctional complexes. mathematical modelling. for oncogenes. 1180. ECM production. . 434. 839–840. 210. 1493. protein structure. 1198F cross-linking glycans. 843F nuclear-encoded tissue-specific proteins. 698. DNA sequencing. 243. 1200–1202. 864F gene transfer. Nucleosome(s) Chromatin assembly factors (CAFs). 75F Chemical synapse(s). 901 general principles. 14. 868–870. 993F reorientation. 1426–1428 small intestine. 856F. 29. 1045. 842–843. 1211–1212. 1232 Cellular interactions. 1274. 384. Stem cell(s) Cell senescence macrophage scavenging. 867 biosynthetic reactions. 1106F Chlamydia pneumoniae. 1045. 1443 mammary gland. 1175–1176 regulation of hemopoiesis. 46–47 energy carriers. 858 diversity. 635 biogenesis. 893F. 233F see also Chromatin chromosome replication. vs means compare/comparison. 230–231. 854–855 see also Chlorophyll(s) Chloroquine. 1511F. 879–903 see also Cell communication. Signaling molecule(s)/pathway(s). 1436–1438. 290 Chromatin remodeling. 859–860. 856–857. 1197–1198. 906. 226–227 Page numbers in boldface refer to a major text discussion of the entry. 620FF transport see Low-density lipoproteins (LDLs) Choline. HIV binding. 1372F Chickenpox virus. 432. 229–230. 247. 470–471. 239F. 868–870 genes. 69F see also ATP (adenosine triphosphate) Chemical groups. 228F complexes. 720F protein synthesis. 388–390 see also specific molecules Charcot–Marie–Tooth disease. 1500F Chlamydia trachomatis. 388–390. 1183 receptor. 1199–1200. 857–858 lipid synthesis. 1439 see also Regeneration. 864F introns. 1509 Chain-terminating nucleotides. 1153–1155 total cell mass control. 228–230 chromatin structure. 1198F. 1276. 443F “barrier sequences. 31F. 293 Cell signaling. 1199T direction of growth and. 529F Cellulose control of oriented plant cell expansion. 863–864.” 227–228 “code-writer enzyme. 993. 850F see also Photosynthesis. 879–974 all-or-none response. 227F. 863 b barrel proteins. 684 mechanism of action. 882 excitatory. 1301F Centromere(s). 787 replicative see Replicative cell senescence telomere shortening. 1106F Chk2 protein kinase. 1076F DNA sequence. 856. mixed. 106F electron interactions. 1076. 1197F plant cell wall. 848F I:9 photochemistry. 1197. 866. 1033 Chloramphenicol. 847–848. 1516–1517 Chimeras. 894F. 510F. 1386F homunculus. 1274F. 859–860 function. 868–870 organelle–nuclear gene transfer. 1388 Chondroma. 866. 510–511. 881F ion-channel-linked see Ion channel(s) in NFkB pathway (Toll family).INDEX requirements. transcription activator proteins. 620F. 699F distribution during cytokinesis. 848F. 1140 Chemotaxis. 1115–1116 early embryonic origins. 719–720. 1187 Chondroitin sulfate. 1197–1198. 1078F zygote. page numbers with an F refer to a figure. 230–231. 442–443. 434. 943F. 869F starch granules. 318T Chagas’ disease. 653F passive transport. 1479 see also Nervous system Central spindle stimulation model. 502 Cell transformation assay. 94F. 743. 1533–1534. 288. 1078F. 863 liverwort. 842F structure. 1550–1551. 854–855 growth and division. 858 variegation and. 856–870 copy number. 1199–1200. 95. 1527 CENP-A. 511 development. definition. 944. GroEL. 1206 Chondrosarcoma. 654F see also Ion channel(s). 1453–1454 proteoglycans and. 674F Chlorophyll(s). 385T Chloride channels. with an FF to figures that follow consecutively. 765F Chemorepulsion. 1469F Chondrodysplasias. 842–843. Cell growth. 791 membranes. 867 mitochondria vs. 511 CG (CpG) islands. 943. 61. 1032. 1244. 550 Channel-forming junctions. 744–745 Cerebral cortex. 247F. 1312–1313. 840–855 bacterial resemblance. 623 structure. 849F. 202. 433F position effect variegation. Genome(s). 216. Neurotransmitter(s) Chemiosmotic coupling. 209–210. 1132F. 1417–1428 in liver. Signal transduction Cell size. 1541F. 713F. 817–819. 1046 ‘search and capture’ of chromosomes. 1097F Centrifugation techniques. 715. 1491 Cholesterol biosynthesis. 1201F Cellulose synthase. free energy. 228–229. 856F. 842 evolutionary origin. 696 genetic system. 215. 1462 see also Cell death Cell suspension(s). 433F nucleosomes. 210. Photosystem(s) see also Chloroplast(s) Chloroplast(s). 1198. 936F enzyme-linked. 511F. 1380F. 716F protein folding role. 390F. 1384F somites. 863. 1109–1110 Cell-surface receptor(s). 814F ATP production. 130–131. 1076F replication. 232F memory circuits. 1179 Chondrocytes. 992 duplication and spindle assembly. 208F chromosome 12 translocation. 98. 1236F genome evolution. 84T. 243. 209F. 474F see also X-inactivation Coated vesicle(s). 1067 see also Chromosome replication. 1288 mitotic see Mitotic chromosome(s) packaging. 535F. Replication origin(s) telomere see Telomere(s) X-inactivation see X-inactivation Chromosome translocation. polyadenylation. 98F. 791F. homologous recombination. 246–247 stop codons. 282. 225–226. 380. 957F Coactivator(s). 1208. 534. 755F. 245 regulation. 1376F. 208F. 247 wobble. 243F see also Cell cycle. 1054 chromatin duplication. 234. 755F vesicular traffic. 754F Clathrin. 205F. 1548. 771F. 285–286 see also Chromosome condensation control see Cell cycle control duplication during S phase of cell cycle. 167. 1208. 806 flagella comparison. 994F. 216–218. 276F Classical genetics see Genetics. 122F Citric acid. 1153 CLAVATA 1. 482–483 Clonal anergy. Mitosis. 212F centromeric see Centromere(s) direct inheritance. 575. 1546 Clonal inactivation. 135F. 458. 1033F hereditary defects. 239F see also Polytene chromosome(s) Chromosome replication. 956. 208F. 208–209. 208–209. 1208F. 122F Citric acid cycle. 751. 1435F primary. 211F. individual chromosomes Chromosome abnormalities analysis see Cytogenetics. DNA synthesis. 357F. 209. shoot meristem. 1031–1032. 246–247 Chromosome duplication centrosome duplication vs. 403F Cocci. 508 vectors (DNA) see under DNA cloning Cloverleaf structure. 482–483 V(D)J recombination vs. 123F Clamp loader. 207. 144F Cilia. 754. 357–358. 367F. 203FF. 462F Cis Golgi network (CGN) (intermediate compartment). 83F. 196 homologous see Homologous chromosomes (homologs) human. 957F CLV3 (CLAVATA 3). 1069–1070 regulation of. 575F CLV1 (CLAVATA 1). 756F cargo receptors. 381 synonymous. Chromosome structure Chromatography. 135. 699F Chromosomal crossing-over see Homologous recombination (crossing-over) Chromosomal instability. 367F. 202–203. 1131. 122F. RNA structure. 210F replication and. 249F replication origins. 831. 210 see also Cell cycle. 759–760 Sar1 protein. Drosophila polytene chromosomes. 211F. 218F. 754F see also specific types Coat-recruitment GTPase(s). 1087. 369F see also Anticodon(s) Coenzyme A (CoA). 283F. 1002 Cohesin(s). 590F see also specific techniques autosomes. 1545F Cloning. 210. 1033F of epithelial cell apical domain.I:10 INDEX X-chromosome inactivation see X-inactivation see also Mitotic chromosome(s) Chromosome deletion cancer role. adaptive immunity. 122–123FF. 1071 . 243 cell cycle variation. 202. 367. specific rearrangements replication see Chromosome replication sex chromosomes see Sex chromosome(s) species differences. 1070–1071. 1254F meiotic errors. 196F. 772. 758F regulation. 309 genome evolution. 203F. 443 RNA polymerase(s). 349F Coilin. 97–99. 1093F Cleavage stimulation factor F (CstF). 28F Circadian clocks. 145. 1070 chromatin packing. 865. 507–508 DNA cloning see DNA cloning reproductive see Reproductive cloning therapeutic. 1467 in bone.. 239F see also Polytene chromosome(s) rearrangements. 754 formation ARF-proteins. 755F. 209 chromatin condensation. 244F condensins see Condensin(s) M-Cdk role. 1261. 1261F. 138F. 1410. 209. 832F. 1090 see also Chromatin. 1410F CLAVATA 3. 758F adaptin. 1032F motility. 1054 replication origin. 235F Chromoplast(s). 1077 Chromomeres. 1078 S phase of cell cycle. 817 electron generation. 202–218. 754. 790F LDL endocytosis. 1032F. 988T. 235F mitotic chromosomes. 861–862 redundancy. 1276–1278 failure (nondisjunction). 751. 6. 817 pathway. 368F Candida CUG codon. 795 structure. 204F DNA repair. 759 vesicular transport. 756F see also Clathrin-coated pit(s). of beating in respiratory tract. 1271. 195F. 754. 357F Cleavage furrow. 167T see also specific types Cofilin (actin depolymerizing factor). 461F. 211–219 30nm fiber. 1031 in left-right asymmetry. 300 Code reader complex. 489–491 mitochondrial genome. 1002F lamellipodia. 534F see also Protein purification. 1469 degradation. 210F centromere. 211. Chromosome condensation. Karyotype cancer. 217F. 117F see also Acetyl CoA Coenzyme Q. 102F. 743F. 445. 98F. 1068F Chromosome puffs. 207.” 367 Codons. 209F. 243. 237F Chromokinesins. 220 inheritance. 243. 204F chromosome 22. 210F see also Telomere(s) yeast. 751. 204F see also Genome(s) historical research. 1033 Ciliated cells. 1278–1279 mitotic. 1262F translocation activating Myc gene. 239. 1069 DNA. 249–250. 234. 237FF Chromosome condensation. structure. 754F. 1021 Collagen(s). 445. 202–205. of Golgi transport. 1033. 287–288 replication rate. 1067. Nucleosome(s) “beads on a string. 957F Clavata3 protein. repressor protein-mediated. 1093. 208–209. 233–245 chromatin see Chromatin condensation see Chromosome condensation loops. 1490F Cockayne’s syndrome. 1231 see also Chromosome abnormalities. 205F mouse vs. 237FF. 789F Clathrin-coated vesicle(s). 1034 Ciliary (axonemal) dynein. 754–755 formation. 202–219 global (higher order). 365F Co-immunoprecipitation. 1548F see also Immunological tolerance Clonal expansion. 474. development. 235F polyteny see Polytene chromosome(s) linear. 1038F nucleotide hydrolysis. 234–236. 220–222. 208F gene content. 446F Chromatin structure. 219–233 see also Chromatin remodeling. 243F. 209–210. 1278–1279 see also specific types Chromosome bands. 1031. Interphase chromosome(s). 1186T. 1208F. 210F segregation during see Chromosome segregation sister chromatids see Sister chromatid(s) structural changes needed. 512–514. 523 Colchicine (colcemid). 1544. 1272 N-terminal degradation. 754–755. 202–218. 513F. 1568 Clathrin coat(s). 395 structure. Mitosis Chromosome segregation meiotic (homologous chromosomes). 1075F ATP hydrolysis. nuclear localization. 756F pinching-off.classical Class switching. Mitotic chromosome(s) centromere see Centromere(s) chromatin see Chromatin DNA packaging. 230–234. 285–286 epigenetics. 367F. 791–792. 1567–1568 B cell activation. 383 initiation codon. 865F. 220–222. 202. 1031F polarity. 793F pinocytosis. 1218. 778 Citrate synthase. 957F Clavata1 protein. 232F duplication during S phase. 1491F biological functions. Clathrin-coated vesicle(s) Clathrin-coated pit(s). 755–757. 473–476 see also Heterochromatin interphase. Karyotype. 246–247 Chronic myelogenous leukemia (CML). 209–210. 1089–1090. Sister chromatid(s) Chromosome structure. 1069–1070 effect on replication timing. 1262F Chymotrypsin. 204 evolution. 205F structure see Chromosome structure see also Cytogenetics. 1261 Philadelphia chromosome in CML. 275F. 244F. 758–760 see also GTP-binding proteins (GTPases) Coaxial stack. 1231. 234–236. loops. 1215F. 368F Cluster analysis of gene expression.. 274. 1239 chromosome 12 and. 987. 212F. 507F. tRNAs. 211–218. 1070F Coiled-coil motif. 283 see also Human genome lampbrush chromosomes. 1434–1436 Ciliates. 1234–1236. 759 coat-recruitment GTPases. 835 Coenzymes. 209–210. 203FF. 209. 234F.. 234F. 196. 1548. 554F cell cycle changes. 1194 RNA interference (RNAi). 203F. 754–755. 756F. 202–219 post-mitotic chromosomes. 528F cancer role. 83–84. 1067 telomere. 357–358. 1210. 1217 see also Genetic instability Chromosome(s). 368. 789–790. 1410F Cleavage and polyadenylation specificity factor (CPSF). 1377 microtubule arrangement. 1284F bacterial. 202–203. 206T evolution. 208F gene organization. 1031–1034 basal bodies. respiratory tract. 1548F Clonal selection theory. 203FF chromosome 3 evolution. 433 transcriptional. 778F Cisternal maturation model. 222 see also Histone(s). 1548F see also Immunological tolerance Clonal deletion. 210. 210F chromatin condensation and timing. 554F aberrant see Chromosome abnormalities analysis. 235F. Chromosome structure polytene chromosomes see Polytene chromosome(s) puffs. specific types Chromocenter. 1410. DNA replication. 225F “Coding problem. 285F. 239. 204–205. 472 historical aspects. 460–462. 1001. 1089F see also Meiosis. 956. 755F Claudins. 1236F. 1184–1186. 204–205. 1261F. 447F Coat coloration. 1261. 751. maternal effects. 195–196. 210F. 369.” 211. 1548. 195–196. 357F Cranial sensory ganglia. 106F bond length. 905–906 regulation of PKA. 1186 tensile strength. 146 post-translational modification. 1551–1552. 1271–1272. 50F ionic bonds vs. 1352F detection and screening. 93F see also individual types Covalent modification of proteins. 1188–1189 genes. 917–918. 1396 Cro repressor. 1300. 1394F sexual reproduction and. 425 cell determination. 357. 1131. 1161 Connexins. 22. 1187 type IV. 1388. 1016–1019 negative feedback (feedback inhibition). 908. 1384F CRE (Cyclic AMP response element). 1290 Connexons. 1239. 961 Crypts of Langerhans. 1563FF Cre/Lox system. 450F Combinatorial diversification. 318T Copy number variation. 611–612 X-ray see X-ray crystallography CstF (cleavage stimulation factor F). 1580–1581. cytochrome oxidase binding. 1348. 397F. 421F. 1571. 324F. 1186T. 801F see also Exocytosis Contact-dependent signaling. 1189. 1571 lymphocyte activation. 463. 1189F fibrillar vs. 1528F early components. 1557T late components. 352. 470F C-terminal domain (CTD). 357F promoter elements. 1187. role. 1448. 464–465. 173–174. 1150–1151 Combinatorial control. 889. T-cell regulation. 906F. 908. 1185. 171. 1518 Common evolutionary ancestor. 1503 cyclic-AMP-gated cation channels. 610 Cryptdins. 1239F Comparative genomics. 377 integrins. 173F. 431F phylogenetic tree creation. 587. 181F.. 1187. 873–875 photosynthesis. prevention between MAP kinases. 355. 247F Compartment(s). 1496F Corral(s). 53T bond strength. 84–87. 357–358. evolutionary see Evolutionary conservation Conservative site-specific recombination. 449–450. 907T bacterial toxin action. 908F synthesis and degradation. 1194 Colloidal gold. 1528–1529. 1188F pro-a chains. 1559F.. 1233. 349. 397–398 Crick. 117F. 917F response to NO. 1596. 1156. 1352. 1432F Confocal microscope. 1387–1388 Contact inhibition. cells see Cell culture Cut-and-paste transposition. 448–450. 447F. 325F transgenic applications. 1467F differentiation. angiogenesis. 175F see also Allosteric regulation DNA replication fork. 1256 mismatch repair defects. 1165. 528F Complementation tests. 1187 structure. 1432. 1110. 1352F Columnar epithelia. 256F COPI-coated vesicle(s). 1255F steps in progression. 1184–1189. 1388F Commissureless protein. 1187–1189. 918 Page numbers in boldface refer to a major text discussion of the entry. 1505–1506. tumour cell identification. 1184–1185 evolution. 1157F Cryoelectron microscopy. 1234F Contractile bundles. vs means compare/comparison. 1185. 1166–1167. 767. 1185F fibrils. 908F C region exons. 352F. 277. 1178–1195 cell differentiation influence.. 606 Colon cancer see Colorectal cancer Colorectal cancer. 1186T. 773–775. 1006–1007. 1467. 1469 type III. 1563 Combinatorial regulation. 930 Crumbs complex. 751. 1187. CD40 ligand dendritic cells. 1254 sequence of mutations. 245–260 human vs chimpanzee. 48–50. 881F see also Ephrin(s). 295T. permanent. 1189 type XVII. 1185. Francis H. 1379F Compaction ratio. 908F CREB-binding protein (CBP). 245F. 1251–1252 genetic abnormalities. 767F Copia element. 952F Culture. 61. microRNA (miRNA). proteins. 494–495 Combustion. 1467–1474. 142. 464 CREB (CRE-binding protein). 888F Cyclic-GMP phosphodiesterase. 1528–1529 cascade. 1186T type IX. 1584 Cross-strand exchange see Holliday junctions Cross-talk. 273. 517. 424–425. 341–342 CTLA4. 1057F Cones (cone photoreceptors). 50 geometry. 1075 Conditional mutation. 445. 951 Costimulatory signals I:11 antigen-presenting cells. 567–568. 1526F Crypts. 1542 activation. 324 gene control mechanism. 1165. 295T Connective tissue. 325–326 reversible DNA rearrangement. 1178F basal lamina and see Basal lamina cells. 1369F Coomassie blue. 1560F Constitutive secretory pathway. 57F Condensin(s). 908 Cyclic GMP (cGMP) cyclic-GMP-gated Na+ channel. T cell. 1529F phagocytosis. 647. 1187F. 48F phosphate bond energies. epithelial apico-basal polarity. 1138 EF-Tu elongation factor. 1252T. 1185. 827F. 1185F. 458F see also Lambda repressor Cross-beta filaments. 1393–1394. 1187 type II. 759F. specific types CpG motifs see CG (CpG) islands CPI. 56. 1300F Corticotropin (ACTH). 1528F adaptive immunity. 1186T type VII. 951. 324. 61–62. 338–339. 1441F Crystallization. 834 Cyanobacteria evolutionary significance. 1007F see also Actin/actin filaments Contractile ring see Cytokinesis Convergent extension. 1470F Compaction. 881. 1528 Ig activation. 518F Cooperativity (protein interactions) allosteric transitions. 1375. 1189. of small intestine. 1529F membrane attack complex. 1436. 1186. 653 Condensation. 557F. 1528–1529. 587. 85F sugars. 905–909. 316. 751. 1250–1255. 53T dipoles. 1592T CTXf bacteriophage. 258 genome evolution. page numbers with an F refer to a figure. 142F. 1186 collagen fibrils. 1255. 1448F Coronaviruses. 1299. 210–211 Comparative genomic hybridization (CGH). 248F human vs mouse. 1352–1355. 1596F C3 activation. 457–458. 1353–1354 intracellular see Intracellular compartments Competition between axons for synaptic territory. 431. 1467F see also individual cell types collagen see Collagen(s) extracellular matrix. 800. 907F Cyclic-AMP response element (CRE). 1159–1161. 1189 type I. 1186T type XII. 357F. 909F regulation. 1186T type V. 48. 319F. 1188–1189 fibrillar. 1133. 326F Conserved synteny. 342F splicing signals. 648F Cortical reaction. 1468–1470 see also Extracellular matrix (ECM) see also Epithelia Connexin-26. 668F motor protein(s). 1492F Cubitus interruptus (Ci) protein. 862 Compact bone. 917 photoreceptors. 887. 51F. 1389 Common cold. 1159–1161. 774F Complex traits. 558 Complement-binding co-receptor complex. B7 binding. 338F RNA polymerase start sites. with an FF to figures that follow consecutively. 244F. 465–466 cell differentiation. 1172F ion channel(s). b-Globin gene expression. 357–358. 1185. 1185. 1254–1256. 591F Confocal microscopy. 1368. 259–260. 93F phosphoanhydride bonds. 274F. 196 Critical period. 1468–1470 types. 1528 C3b and C3a. 186–187. 1132F. 1160F. 1186 procollagen. 349F Conservation. 247. 398 ribozymes. 590–592. G protein. 406F tryptophan repressor. 433–434 Congenital abnormality. 1186T. 355F Cryptochrome. 1529. 1562. 1160F Consensus sequences polyadenylation signals. Ig heavy chain. 1548 Coupled reactions see Reaction coupling Covalent bonds. 482–483 CTCF protein. antigen presentation. 1580T. 1542F. antibody chains. 1110F. 557. 1444 Creutzfeldt–Jacob disease (CJD). 1352F compartmentalization of cell. 247. 256. 243. 425F. protein staining. chromosomes see Chromosome condensation Condensation reactions (macromolecule polymerization). 186T see also Posttranslational modification. 465F complex formation. 695–704 of imaginal discs. page numbers with a T refer to a table. 754FF COPII-coated vesicle(s). 587F Cy5 fluorescence. 93F phosphodiester. 754. 458F see also Cooperativity (protein interactions) Corn see Maize Corneal tumor. 1185. 397F Crossing-over see Homologous recombination (crossing-over) Cross presentation. 528F temperature-sensitive. 276 hemoglobin. 788 Complex oligosaccharide(s). 592F Conformational changes allosteric regulation see Allosteric regulation cadherins. 1572F. 1168. 404. . 1581F Corepressor(s). 1187 propeptides. 906. 144F. 207. 449F heterodimerization.. 1438 heterogeneity. Notch receptor protein Contact guidance. 174F. 917 gene activation by. 587F Cyanide. 208F Constant domain. 50F. 1251–1253. DNA packaging. 907F. 180–181. 1185. 891F Costal2 protein. 907F Cyclic-AMP phosphodiesterases. 1436F. 1271F Complementary DNA see cDNA Complementation. 528 Crystallography electron. 49. 1593F see also B7 proteins. 1185. 447. 1170–1172. 458–459. 1185–1186 mutations. 207. RNA polymerase II. 1189F type XI. electron microscopy. 172F prion protein (PrP). 1596 Complement system. 259F Co-receptor. 1505F Cy3 fluorescence.C. 528F. 908. 908 Creatine phosphokinase. 146F. 1167F. 1140. 905–906. 820F Commissural axon(s). 754F. 1250–1252. 447FF Drosophila Eve gene. DNA repair defects. 1189F fibrous protein. 1186T fibril-associated vs. 397. 591F.INDEX fibril-associated. 1379. 48–49. 47. 451F CPSF (cleavage and polyadenylation specificity factor). 563 Concentration gradient. 1186T type XVIII. 325–326. myoblast specialization. 1057. 463 receptor. 1187F synthesis. 1529F lesions in red blood cells. 889F gene expression regulation. 16F Cyclic AMP (cAMP). antibody genes. 1184. 1437 Cryptic splicing signals. 425FF promoter integration. 457–458. 249F phylogenetic footprinting. 1591–1592 CTLA-4 protein. 803F Cortisol. 1187–1188. 1186T Collagenases. membrane partitioning. 1186. 840 in tree of life. 320F see also DNA-only transposons CXCR4. 177–178. photosystem II. 395. 1581–1582 activation. 1067–1069. 203FF. 988T Cytochrome(s). 1571F activation. 1066T. 1087. 1068 see also Cyclin(s). 1534 dendritic cells. 296. 1062. 1093F dynamic behavior. 1571. 116F. 1583F helper T-cells vs. protein. 145 influencing cell behavior. 1591 Toll-like receptors (TLR). 484. 1064. 1062–1063 activation by dephosphorylation. 1184T Default pathway. 1074. 484 deamination. 1063. 1580–1581. 1097 midbody. 1063. 1097–1098. 1533–1534 T cells. 1063F Cyclin–Cdk complexes. 1290F. 1418F. 522 Deoxyribonucleic acid see DNA Deoxyribonucleoside triphosphates (dNTPs). 1022–1023 spectrin (membrane cytoskeleton). 1099. 466F Dachsous. 834. 369F. 652 Cytochalasin. 1047. 177F vertebrates. 1062. 1581F virus-infected cells. 1073F. 1062–1063. 1387F microtubule orientation. 697T Cytotoxic T-cells (TC). 965 Rho proteins. 973. 26. 1064F. 833F poisoning. 950 . 1093F actin and myosin II as force generators. 1025–1050 integrin attachment. 265 structure. 1514–1517 properties. 973 nucleation. 992 rate of subunit addition. 1005–1008 dynamic behavior. 965–1053. 1170F intracellular anchor proteins. 1099F D Dac (dachsund) gene. 1062. 831. 832–833. 992–1010 organization. spermatogenesis regulation. 782F see also Cytosol. 75F. T-cell receptor. 1063F yeast. elegans early embryo. 1055. 1063F yeast. Intermediate filament(s). 1296F Cytoplasmic dyneins. 987–989. 1418. 833F essential nature. 203F. 177–178. 1054. 1050F. 834 oxygen reduction. Cytoskeletal filaments. 1592 selection in thymus. 1080 mechanism of action. protein(s). 1590–1591 cell–cell adhesion molecules. 1014 Cytoplasmic inheritance see Non-Mendelian inheritance Cytoplasmic tyrosine kinases. 1452 self-reactive T-cell elimination. 1120. carcinogen activation. 1094. 1594 maturation. 492. 1571 MHC expression. 143. 666 Cystinuria. electron microscopy. 1063–1064 G1-Cdk. planar cell polarity. 1121F. Notch signaling pathway Denaturation. 1536 nonactivated. apoptosis. 1098 phragmoplast role in higher plants. 1062 gene expression. 492 Decorin. 301F inosine production. structure. 965–991. 74–75. 301F DNA methylation role. 144F Cytochrome oxidase complex. 1161 Deamination. 969. 1571. 1066. 1142 motor proteins see Motor protein(s) pathogen utilization. 1324 Drosophila sensory bristle development. 1063F see also Serine/threonine kinases. 834 mammalian. 1095–1097 astral relaxation model. 1103–1105 G1/S-Cdk. 988T kinetics.. 1096. 1536 Cytoplasm. 560. 1100–1101 phosphorylation. 1093–1094. 422F Cysteine. 1063F. DNA methylation. 1572–1573. 833F. 204F Cytokine(s) antagonists. 832–834. 1096F astral stimulation model. 268F Deoxyribose. 787. 1122F mutation rate. 1388F Deadenylation-independent mRNA decay. 947F. 1062 APC/C and. 1078–1079. 1049 neuronal computation. 970–971 see also Actin polymerization behavior. 661–662 volume. 1074F cyclical changes in activity. 1359 lateral inhibition.I:12 INDEX cleavage furrow. 492. 965–991 subunits. 977 self-assembly. 332F Dephosphorylation. 298F. 1074F entry into mitosis. 1062F S-Cdk. Microtubule(s). 530–531 Daz gene/protein. 1080 spindle assembly role. 1097F organelle distribution. 511. specific components Cytosol. 492F Deafness. 1477 Desensitization see Adaptation Desert Hedgehog protein. 976 nucleation regulation. 137F Cytochrome b-c1 complex. 1062F. 835 Q-cycle. 1170. 1590 NOD proteins. definition. 1062. 1063 G1-cyclins. 1571 functions. 385T Cyclostome see Anaphase promoting complex (APC/C) Cys–Cys–His–His zinc finger proteins. 266. 1531. 583 Databases. 666. 657–658. Myosin assembly. 296. 1074 microtubule dynamics and. 1103–1105 M-Cdk. 1062. 1182F. 1158 Dally/Dally-like genes. 116F. 1064F. 1092–1101. 296. 384. 689 Deletion cassettes. 1536. 570 Deletions. 1542. 300–301. 1079F. 297F. 972F. 1593F. 1071. 1584 CD8 co-receptor role. 1055F. Microtubule(s) Cytoskeleton. 470 mutagenesis mechanism. 75F. 675 Dendritic cells. 1353. 1533 Degradation signals. specific molecules Cytokinesis. 1063–1064. 130 Dendrite(s). 1062. 197. 1582 see also Interleukin(s). 1542F. Intermediate filament(s). 1062 G1/S-cyclins. 587F Darkfield microscopy. 1062. 768 Cystic fibrosis transmembrane conductance regulator protein (CFTR). 1386–1387. 1066. 833F apoptosis. 332 Cytoskeletal filaments. 492F DAPI fluorescence. 1093F contractile ring. specific components Cytoplasmic bridges. 45 DAN enzyme. 1002–1003 see also Actin/actin filaments. viral-encoded. 177F vertebrates. 300. 833F proton pumping. 297F. 101. 1571 pattern recognition receptors. 1422F Dermatan sulfate. helper T-cells (TH). 1571 phagocytosis. 177–178. 833F. 1095F site of assembly. 301F RNA structure. 1066. 1063F CKI binding. 978F. 1184T Dalton. 1096. 177. 1097F. 1179 Dermis. 969 see also Actin/actin filaments. 1571 distribution. yeast mutagenesis. 1574–1575 antigen presentation. 832. 71F. 301F base-pairing. 1525–1526. 1101 M-cyclins. 177F G2/M checkpoint. 1142F cellular polarity. 1093. 1536 De novo DNA methyltransferases. apoptosis. 1388. 1335 Decapentaplegic protein (Dpp). 1118. 1560–1561. 836F Cytochrome c. specific kinases Cycloheximide. 1353F Decapping. 1096F. 829. 297–298. 1181–1182. 1098F plasma membrane enlargement. 1001–1002 subunit stoichiometries. 1094F mitotic spindle and plane of division in animal cells. 1586 cell killing mechanism. 1225 Cytogenetics. Cyclin-dependent kinases (Cdks) Cyclin-dependent kinase-activating kinase (CAK). 301F hypoxanthine production. 805 timing. 1063–1064. 834F Cytochrome P-450 oxidase. 1063F. 935 Cytosine. 484F 5-methylcytosine. 198F C-to-U editing. 1062. 608 Depurination. 1001. 1003F cross-linking. 1535. 1533. 696 pH regulation. 834 structure. 834 iron–copper center. 512F. 1413F. 467 Dense-core vesicles see Secretory vesicle(s) Density gradient centrifugation. 1096–1097. 1101 S-cyclins. 800. 1581–1582. 1066T regulation. of viruses. 1093F asymmetric. 853 Cyclin(s). 1121. 1066 activation by dephosphorylation. 1592–1593 inflammatory response. 300–301 Death (of cells) see Cell death Death inducing signaling complex (DISC). chromosomal see Chromosome deletion d chain. 832. 1064. 1062. 1572–1573. 1358FF see also Notch receptor protein. 1002–1003 elongated. 1581F. 298F. 1066T. 966–969 capping. 1585–1586. 1571 co-stimulatory proteins. 647F stability. 492F Deadenylation-mediated mRNA decay. 299F Dermal papillae. 1131. 965–1053 assembly/formation drug-induced changes. 647. 1087 signal integrating device. 1335F. 177F. 1142. 946–947. 1290. 1044 function. 835–836 structure. 1095 see also Mitosis Cytolytic effects. 1005–1008 stabilization. 1101 Cyclin-dependent kinases (Cdks). 1120F Decapentaplegic (Dpp) gene. 965 helical filaments. 1335. 176F see also Protein phosphatase(s) Depth of field. 1587F transfer experiments. 1581F see also CD8 T-cell(s) Cyclic-nucleotide-gated ion channels. 1094–1095. 648F. 1062 inactivation/inhibition G1 phase. 966 RhoA role. 297F. 1120F Death receptor(s). 1287 strands in plant cells. 1542. 1496 Cytomegalovirus (CMV). 1093–1094 see also Actin/actin filaments. 696 division of see Cytokinesis egg (ovum). 852F see also individual cytochromes Cytochrome b6-f complex. 1295–1296 DCC receptor protein. MHC class I protein translocation inhibition. 1062. 1003. connexin-26 mutations. 916. 646. 1062 cyclin complexes see Cyclin–Cdk complexes evolution. 298F. 1571–1572. 1573F interferon-g effects. 1096F central spindle stimulation model. 688F neurosignaling. 1087 Cdk complexes see Cyclin–Cdk complexes cyclical changes. 396F Dehydrogenation reactions. 369. 1066T Cyclin-dependent kinase inhibitory proteins (CKIs). 1120–1121. 129F Cystic fibrosis. 606. 1294. 1571 Delta G (DG) see Free energy change Delta G (DG) Delta–Notch signaling see Notch signaling pathway Delta protein C. 917 Cyclic photophosphorylation. 965F cell junction attachment. 801F see also Exocytosis Defensins. 851. 72 Delayed K+ channel(s). 852F Cytochrome b562. 202–203. 1074–1075. 1184. 176. 1041–1043 RNA localization. 1074–1075. 199F as universal information store. 1269. 422F. 1318F mouse see Mouse development nervous system. 1307. 1238 DNA (deoxyribonucleic acid). 424. Genome(s) labeling. 417F. vs means compare/comparison. 1276 Diapedesis see Lymphocyte(s). 424F minor groove-binding. 464 see also Cell differentiation. 197. with an FF to figures that follow consecutively. 466F regulatory DNA defines program. 1310–1311. 1310. 1314. 211 location. 447F see also DNA-binding proteins DNA-binding dyes. 74. page numbers with an F refer to a figure.development plants see Plant development and growth positional controls. 273F transcription. 910 Diakinesis. 423F see also DNA replication. random nature. 1135T. 408 see also DNA sequence. 422. proteins see Retrotranslocation. 430F gel-mobility shift assay. 451F. 526 Distal-less gene. 1307 experimental embryology. 1307F inductive interactions and signals. 416–454 b sheet motif. 1041. DNA libraries DnaC protein. 1270F see also Meiosis yeast life cycle. 1289F. 425F DNA-binding motifs see DNA-binding motifs DNA structure relationship. 540–541. 142F functional role. 1312F. 243. 1212 see also Cancer. 198F Streptococcus pneumoniae experiments. 196F. 450–451. 368F. Genetic code. 1111 positional values. 1309–1310. 296. 195–197. 987 Desmocollins. tRNA modification. 418–419 base-pair recognition. 1306F gap junctions. 333 see also entries beginning DNA DNA array(s) see DNA microarray(s) DNA bending nucleosome–DNA interactions. 1289–1290. 112F Dihydroxyacetone phosphate. 1148–1149. 197. 1045 myosin I and II localization in crawling amoeba. Anton van. 50 Disaccharides. 201F see also Nucleus maintenance. 202–218. 1140. 461F see also Circadian clocks Divergence (evolutionary) mutation rate analysis. individual organisms and processes Developmental genetics and gene regulation. 297F DNA damage. Chromosome structure polarity. 1111 vertebrates see Vertebrate development Xenopus laevis see Xenopus laevis development see also Embryo(s)/embryogenesis. page numbers with a T refer to a table. 416–417. 56. 296F. 423. 1148F. Nucleosome(s) compaction. 129F. RNA interference (RNAi). 1136. 16F chemotaxis. 419 see also DNA structure helix-turn-helix proteins. 298F proteins. 419. 428–429. 554F sexual reproduction. 3–4. 1226. 501F Divisional asymmetry. 264 phylogenetics. 1545F Diploid cells classical genetics. 1421F DMBA (dimethylbenz[a]anthracene). 101 Differential-interference microscopy. 263. 296. 420–421. 1238 2. 1308 genetic screens. DNA damage. 1383–1397 see also Neuron(s). 1308. 432. 198F structure elucidation. 147–148. 424F protein–DNA interaction. 428–429. 3. 636–640 see also specific detergents Determination see Cell determination Detoxification reaction(s). 1143F epithelial–mesenchymal transitions. 1161 genetics see Developmental genetics and gene regulation germ layers and gastrulation. 528. 1545. 541F restriction fragments. 163. . 427–428. 329. 1311 morphogens and gradients. paired domains. 1319–1320. 419. 62F chemical synthesis. 142. 1491 enteropathogenic E. 836 Dinitrophenyl. 147F Diurnal rhythms. 329 hybridization see DNA hybridization information coding. 421–422. 986 Desmotubule. 423F see also Protein–DNA interactions DNA-binding proteins. 88. 540 reverse genetics. 1436 see also Lysosome(s) Dihydrofolate reductase. 2. 465F Drosophila see under Drosophila development genes specially required. 1193 Dislocation. 1351. 1311F cell memory. 428F zinc finger interactions. 1071 cell macromolecule. 1138T Desmogelins. 273. 446. 417. 1154 Dishevelled gene/protein. Mutation(s) genome evolution. 1309. 1312. cell cycle analysis. 639F ionic vs. 426 dimerization. 540–541 cloning vectors. 1288 Dipoles. 120F Dimer formation DNA damage. 420F homeodomain proteins see Homeodomain proteins histones see Histone(s) leucine zipper proteins. 1138T Desmosome(s). Signaling molecule(s)/pathway(s). as mutagenic chemical carcinogen. 1320F timekeeping. 1351F. 546. 200–201. 518F protein stability. 429F cloning see DNA cloning compaction. 419–420 homeodomain. nitrogen. 1309. 432F DNA sequence determination. 429–431. 423 heterodimerization. 423. 425–426. 1306F. 195–196. 549–550 Didinium. 1226. 1504 Salmonella enterica spread. 1134. 1319. 425FF homodimerization. 34. 1143–1144. 75F Digestion. 169 Diffusion.recirculation Diarrhea bloody. 199–200. 246–247 I:13 see also DNA repair manipulation see Recombinant DNA technology noncoding see Noncoding DNA packaging. 210–211 see also Chromosome(s). 427F SSBs see Single-strand DNA-binding proteins (SSBs) zinc finger proteins. 420F leucine zipper motif. 1280. planar cell polarity. 1315F mitosis in absence of cytokinesis. 1309–1310. 540–541. 583 see also Phase-contrast microscopy Differentiation of cells see Cell differentiation Diffraction patterns. 113F Discs large (Dlg) protein. 423F DNA-binding homeodomains. 1260 Dihydrouridine. 1177T keratin filaments. covalent bonds. 424F. 1275. 1162 Detergent(s). 1355 Disulfide bonds amino acids. 57F. 430F affinity chromatography. 420. 417F see also DNA structure zinc finger motifs. 464–4695. 460–462. 532–553 bending see DNA bending catenation. misfolded proteins Dissociation constant (Kd). 542F ligation reaction. 1275–1276. 141 gene regulatory proteins. in dysentery. 296 unwinding replication. 1487–1488 Dicer protein. 1041F Dideoxy DNA sequencing. 421F see also Homeodomain proteins recognition helix. 1314F C. 158F Dissociation rate. 422F. 532. 283F DNA crosslinks. 1099. 331. 34F Diplotene. 418T helix-loop-helix motif. Protein–DNA interactions DnaB protein.” Leeuwenhoek. 283F DNA catenation. 985T. 1136. 1142. 725 Development. 1310 Drosophila melanogaster see Drosophila development epithelial folding.INDEX Desmin. 244F see also Chromatin. 517F. 142F see also DNA-binding proteins Dimethylbenz[a]anthracene (DMBA). 3F thermal stability. 1309F sequential induction. 534 linker. 331 DNA makes RNA makes protein. 1311–1312 cell lineage tracing. 1359 Disintegrins. enhancesome formation. 575 see also cDNA. 1311–1312. 1305–1320 asymmetric cell division. 1305. 331F relation to proteins. 281F historical research. 1071 DNA cloning. 297. 195–196. 1518 spread of infection. 329 identification as genetic material. 265. 1313. 540. Gene regulatory protein(s). 420–421. 421–422. 297F Page numbers in boldface refer to a major text discussion of the entry. 1421. 427F binding site prediction. 541FF. 147–148 electrophoresis. 496 Dickkopf protein. 196F. 517. 195–196. 199–200. 248F see also Gene duplication(s) “Diverse animalcules. 163T. 247. 1307 descriptive embryology. 1312F cell fate. 4-Dinitrophenol. 1310. 547F helix-passing reaction. 426F helix-turn-helix motif. 422 Cro repressor. 1309F transcriptional synergy. 214F proteins. 1316T lateral inhibition. 247F. 1320F total cell mass. 330F. 1140F cleavage of egg. 1310F four essential processes. 465–466. 1313–1315. 1313F regulatory DNA defines program. 417. 636 membrane protein solubility. 369F Dihydroxyacetone. 1315 cell migration. DNA topoisomerase II. nonionic. 429F chromatin immunoprecipitation. 1305. 1308 organ formation. 28F Dietary requirements. 423. 465F combinatorial gene control. 1144F. 423. 1549 Diacylglycerol. 638F. cancer treatment. 1312–1313. 1059 DNA-binding motifs (proteins). 210–211 complementary see cDNA damage see DNA damage fingerprinting. 196. 1313F. smooth endoplasmic reticulum. 420F structure. specific genes Diabetes mellitus type 1. coli. 3F protein interactions see Protein–DNA interactions recombination see Recombination regulatory see Regulatory DNA repair see DNA repair repeats see Repetitive DNA replication see DNA replication structure see DNA structure synthesis see DNA synthesis telomeric. 202–219 chromatin packing. 418–419. in stem cell production. 528F Diffusion-limited enzyme catalysis. 548 chromatography. 424–425. 542F genomic library production. 1134F. 1309 cell differentiation. 1158. elegans see Caenorhabditis elegans development cell determination. 295T. 425F major groove-binding. 1099–1100 model organisms. 464–465. 1316–1317. 1316T Dictyostelium. 424F sequence-specific. 1141 evolutionary conservation among animals. 158F. 263–265 failure. DNA-binding proteins. 420F. 296. 210 see also Telomere(s) templated polymerization. 3F amplification via PCR see Polymerase chain reaction (PCR) analysis. 574 DNA mismatch repair see Mismatch repair DNA-only transposons. 1067 prereplication complex. 551 open reading frame prediction. 539F see also DNA probe(s) DNA labels. 283F mechanism of action. 199F. 268F eucaryotic. 536–537. 416–417 DNA sequencing. 295T. 575. 272F. 246–247 whole genome. 303. 319F. 1213 CG (CpG) islands. 1264 cluster analysis. 543F. 298 cancer and. 295T DnaB protein. 1246 see also Carcinogens. 273–274 proofreading. 300F DnaG protein. DNA topoisomerase II. 536F nucleic acid detection. specific rearrangements DNA recombination see Recombination DNA renaturation see DNA hybridization DNA repair. individual components DNA replication initiation. 544 in yeast two-hybrid system. 295T. 270F see also Mismatch repair RNA polymerases vs. 271–272. 281F. 62F. 323. 1067 regulation. 1105–1107. 438F. 437F. individual repair pathways DNA repair disorders. 303–304 cross-link repair. 19. 283F DNA probe(s). 299–300 translesion synthesis. 298F see also Mutation(s) spontaneous alterations. 480–481 DNA melting. 268F strand recognition. 248F intron–exon recognition. Mutation(s) eucaryotic. 295–304 base excision repair (BER). 272 reaction mechanism. 284F restriction–modification systems. 537. 19F DNA sequence. 472F cancer cells. 272. 298. 266F. 285F bacterial. 1527 evolutionary conservation. 282. 323 cut-and-paste transposition. 284F eucaryotic. Mutation(s) repair see DNA repair replication. as immunostimulant. 200F recognition. 304. 267 role in repair. 276F cooperativity. 297–298 mechanism. 294F. 199F. 275F mitochondrial. 283F TFIIH transcription factors. 1067. 412 metastases. 418T see also DNA-binding motifs structural effects. 274F DNA ligase. coupled to packaging. 467–468. 197–199. 297F failure to repair. 266F antiparallel nature. 38–39. 266–267 incorrect model of DNA replication. DNA repair defects. 273F DNA looping. 280 mechanism of action. 467 eucaryotes. 283F eucaryotic. 201F. 269F initiation see DNA replication initiation machinery. 544 genomic. 269–270. 535F genomic see Genome sequencing historical aspects. 280. 534. 283F DNA helicase(s). 267. 324. 318T. 468 5-methylcytosine. 281F DNA hybridization. 302 DNA structure importance. 284F. 280 chromatin effects. 300–301 enzymes. 214F double helix. 538F see also RNA–DNA hybrids DNA segment shuffling. 255 DNA excision. 1517 see also specific enzymes DNA primases. 280 proofreading. 551 protein sequence prediction.” 278F see also Chromosome replication. 282 DNA–RNA hybridization. 574. 324F DNA fingerprinting.. 306F hybridization see DNA hybridization DNA duplication(s) chromosomes see Chromosome duplication exon recombination. 539–540. 538F Northern blotting. 324. 532 recognition functions. 282. 1068F ORC (origin recognition complex). 547F DNA footprinting. 1068F preinitiation complex. 277–278. 467. 302–303. 273F. 539F helix nucleation. 1067–1068. 1240. 318T. 534. 289–290 origins see Replication origin(s) phylogenetic conservation. 532 Southern blotting. 274–275. 539F see also DNA hybridization DNA–protein interactions see Protein–DNA interactions DNA rearrangement(s) bacterial phase variation. 549–550 human genome. 295T see also Mutagenesis DNA–DNA interactions. 295T fidelity. 284F replication forks see under Replication fork replication origins see under Replication origin(s) replication rate. 299F recognition of DNA damage. 299F error prone. 542F cDNA vs. 1249 methodology. 539–540. 532 role in mutation. 267F. 320F DNA polymerase(s). 306 chromosome paints. 295T. 277–278. 333–334 “winding problem. 295 importance. 295T see also DNA damage. 467F procaryotes. 535F DNA structure. 300–301. 532. 318F. 296F see also specific types see also DNA repair DNA-damaging agents carcinogens see Carcinogens ionizing radiation. 270FF replication fork see Replication fork replication origins see Replication origin(s) semiconservative nature. 269 thermophilic. 306F recombinant DNA technology. 273. 454–455. 338F complementary chains (strands) see DNA agents causing see DNA-damaging agents apoptosis. 268F T7 polymerase. 302 dNTP substrates. 293F. 273. 468–470 inheritance. 542. 283F end-replication. 269–270. 197–201 backbone (sugar–phosphate). 297 double-strand breaks. 280. 299F RNA polymerase coupling. 200F. 277 methylation in procaryotes see DNA methylation nicks in eucaryotes. 198F. 295T. 207. 1106 see also Cancer. 273. 201F. 296. 197–199. 246–247 analysis techniques see DNA sequencing bacterial. 273. 284F uncontrolled. 201F. 1225. 205–206 comparative. 284. 535–537. 282. 534 DNA libraries. 541–542 cDNA. 285 see also Cell cycle fidelity. 303–304 checkpoints. 283F. 535–536. 524 see also DNA cloning DNA ligase(s) DNA cloning. 142. 296F DNA methyltransferase(s). 266 deformation. 301F . 266. 856–857. 538–539. 283. 543F. 550 gel electrophoresis. 295T. 200. 299F cell-cycle delay. 257 genes see Gene duplication(s) genome evolution. 1105 bulky lesions. 1216–1217. 548–550 alignment. 295–296. 279F. 281–282 bacterial chromosomes. 857F nucleosome assembly. 296. 282. 537F model of recombinational base-pairing. 292 errors. 263. 139. 282. 335 sliding clamp. 297–298 nucleotide excision repair (NER). 274F assay. 198F. 1065 gene expression analysis. 429–431. 324F see also Recombination. site-specific recombination. 467F methylated DNA binding proteins. 276 single-strand DNA-binding proteins. 550F recombinant DNA technology. 296. 207. 283F inhibition. 285. 198F. 266–295 analysis techniques. 199. 281. 246–247. 1071 DNA synthesis see DNA synthesis DNA templating. 306F hybridization conditions. 263. 1067–1069. 430F DNA glycosylases. 438F transcription regulation. 275–276 DNA helicases. 208F. 200. 540–541. 297 role in replication.I:14 INDEX strand-directed mismatch repair. 284F.. 285. 197–199. 287 origins see Replication origin(s) origins of replication see Replication origin(s) proteins. 534. 310–311 failure see Mutagenesis homologous recombination. 277. 414F. 537F DNA methylase(s) see DNA methyltransferase(s) DNA methylation. 540–542. 277–278. 195–201. 325–326 reversible. 298 DNA polymerases. 283FF. 266 5¢-3¢ chain elongation. 275–276. 269. 266 end-replication problem. 305 identification. 467–468. 272F. 285F. 417F complementary chains (strands). 1106. DnaC protein. 1117 ATM/ATR signaling pathway. 542. 299–300 transcription coupling. 276–277 see also DNA damage. 274F. specific disorders DNA repeats see Repetitive DNA DNA replication. 275F. 295 mismatch repair see Mismatch repair multiple pathways. 199–200 alterations in genome evolution. 277F. 273F DNA polymerase see DNA polymerase(s) DNA primase.. 247F. 273. 267F. 574–575 cancer cell typing. 273. 302–303 Lagging strand DNA synthesis. 1068F timing. 278 gene expression and. 334. 200. 3. 282–283. 266–281. 198–199. 39F. 295. 1106 see also Cancer. 550F chain-terminating nucleotides. 271FT see also DNA repair historical research. 574 cell cycle analysis. 574F replication fork analysis. 550. 268F catalytic mechanism. 278F see also Single-strand DNA breaks see also Mismatch repair transcription vs. 541F DNA repair. 544 see also Polymerase chain reaction (PCR) viral. 550–551. 198F base-pairing. 273F defects. 292 DNA catenation. 250 human b-globin gene. 285–286 chromosome ends see Telomere(s) initiation see DNA replication initiation multiple replication forks. 272. 296. 530–531 automation. 340–341 DNA-helix-passing reaction. 303F enzymes. 1249. 202–203 DNA–RNA hybridization. 197. 300–301 see also Ultraviolet (UV) radiation sensitivity. 300–301. 434. 276F structure. 289F. 470–471 damage recognition. 283 S phase of cell cycle. 284F. 213. 1106F cross-linking. 266. 455F conservative site-specific recombination heritable. 268F cooperativity. 285. 297–298. 438. 546. 280F primosome. 575F human genes. 467 DNA microarray(s). 468F genomic imprinting. 295T defects in see DNA repair disorders direct chemical reversal. 275–276 DNA repair. 306F nonpairing interactions. 278. 269–270. 418–419. 276F DNA topoisomerases. 269 movement along DNA. 276F bacterial dnaG. Mutation(s) cell cycle and. 278–280. 282. 286F sizes. 247. 272. 267F. 1335. rescue. 480. 479F Dynamic instability. 1344–1347. 1355 Drk gene. 466. 1338F. 449FF. 330F gene-chromosome relationship (proof ). 1422. 466F imaginal discs. 281 mechanism. 221–222. 1334–1335. 271F deoxyribonucleoside triphosphates. 1347–1363 compartment boundaries as signaling centers. 106F Double-checking. 479 chromosome puffs. 1336–1338. 1157F Drosophila melanogaster homeotic genes. 198F see also Nucleotide(s) phosphodiester bonds. 1022. 556 sequencing. 1328F apoptosis. 1330–1331 syncytium formation. 1337–1338. 1022F axonemal. 1014 force generation. 268F 5¢-3¢ chain elongation.INDEX replication hydrogen bonds. 1354F size regulation. 442F Domains. 1099. 1339–1340. 199F. 343–345. 282–283. 1059F. page numbers with a T refer to a table. 300–301 repair. 1019. 928F Drosophila development. . 199F. 571 vertebrate homologies. of blastopore. 1332 genetic techniques. 466F homeotic genes see Drosophila melanogaster homeotic genes Ras role in eye development. 1336F genetic control/gene regulation. 1329 imaginal discs. 1353F eye development. 1333. 1019F ATP hydrolysis. 466F oocyte. 1333F gastrulation and mesoderm formation. 1342. 1014–1015. 1351 intercalary regeneration. 473. 1367–1368. 1534 Down syndrome. gap junction permeability regulation. 1334–1337. 408–409. 738F. 1466 E E2F proteins. 278–279. 927F protein interaction maps. 1342F Hox complex. 1332F follicle providing egg-polarizing signals. 1331F egg polarity genes see Egg polarity genes (Drosophila) fate map. 408 sequence effects. 528F. 1330. 429 see also Homeodomain proteins as model organism. 927. 1099. 1337F. 758F Dynein(s). 1339F. 981F Dynamin protein. 284F. 1342 Polycomb and Trithorax group genes. 1354. 1339 see also individual genes Drug-induced changes. with an FF to figures that follow consecutively. 466. 1353–1354 parasegments vs. vs means compare/comparison. 278F strand separation. 1342–1347 see also Hox complex. 1330F sex determination. 449F. 1079 power stroke. 1496F. 1019 mechanochemical cycle. 38 oogonia formation. 289–290 see also DNA replication DNA topoisomerases. 1400T position effects. 1308 wing hair mutants. 278. 737. 1335FF egg. 481–482. 197–199. 488F. cytoskeletal filaments. 305F. 1337F regulatory DNA controlling pattern (eve gene). 330F mobile genetic elements. 1080 of microtubules see Microtubule(s) nucleotide hydrolysis. 1334F dorsoventral patterning. 267F. 1003 catastrophe vs. 924 Dolichol phosphate. 1103–1105. 266–268 5¢-3¢ chain elongation (leading strand). 552 size. 416F repair. 267F. 1019F Dysentery. 308–309 defects. 1328–1341 anteroposterior patterning. 1333–1334. 1248F DNA virus(es). 1336F. 1341–1342 mutations. 1333. 278 catalytic reaction. 196. 981F. 1341–1347 bithorax and Antennapedia complexes. 1335FF. 268F see also DNA polymerase(s) relation to histone synthesis. 329. 197 protein–DNA interactions. cytoskeletal filament polymerization. 448F. 476F Double bonds. 278–280 see also DNA replication lambda integrase vs. 198–199. 16. 1344 modulated repetition strategy. epidemic. 268F see also DNA polymerase. 1356–1357 individuality specified by homeotic selector genes. 1499 Dorsal lip. 1018 linker region. 1125. 987–989. 268. 481 circadian clock. Hox genes memory mechanism. 1328–1330. 1340 morphogen gradients. 1059. 276F lagging strand see Lagging strand synthesis (DNA replication) primer strand. 1353F compartments. 271–272. 551. 87F chemistry. 38F I:15 polytene see Polytene chromosome(s) sex chromosomes. 979F rescue. 271–273. 449FF. 481F. 196 see also DNA topology DNA supercoiling see Supercoiling DNA synthesis. 1287 Domain fusion. 927F segmentation genes see Drosophila melanogaster segmentation genes see also specific genes genetic model. 278. 302–303. meiotic nondisjunction. 304–305. 188 RNA interference (RNAi). 1077. 1367F Dorsal protein. protein glycoslation. 280F Double-stranded RNA (dsRNA). 268F pyrophosphate release. 1329F vertebrate body plan vs. 967. 1338F pair-rule genes. 1290. 267F. 1290F organogenesis and patterning of appendages. 16F Dominant negative mutation(s). 278–279. 1337–1338. 1100F synopsis. 449F. 448F. 447–450. 982F catastrophe. 1306. 281F DNA topology supercoiling see Supercoiling transcription elongation. 417F see also DNA-binding motifs (proteins) RNA vs. 1077F. 1333F planar cell polarity. 197 hairpin helices. 1352–1355. 1227–1228. DNA polymerase proofreading. 447–450. Epstein–Barr virus (EBV). 1400T genome information coding. 279F DNA replication role. 988T Drug resistance. of Drosophila. 1249F Page numbers in boldface refer to a major text discussion of the entry. 296–297 see also DNA repair rotation. 1022–1023 multicellular development and. 1162F Dormancy. 312. 1344 sequential Hox gene expression. 449F. genes. 1353. 1333. Drosophila sex determination. 418T. 1022–1023 photoreceptor assembly. 1019 attachment to membrane-enclosed organelles. 1330–1331. 279F. 1341–1347 see also Drosophila melanogaster homeotic genes cell cycle analysis. 1019 mitotic spindles. 294 Dystrophin. 37–38 mRNA localization. 1244F E6 viral oncogene/protein. 220–222 dosage compensation. 1347–1362. 1335F Dosage compensation. 237F chromosome 2. 268F. 1425 ATP requirement. 1248. 266. 1344. 267F. 1162. 1346F. 475–476. 1349–1351. 1286 syncytial to cellular transition. 269 Doublesex (Dsx) gene. 448F. 1497F in cancer. 1228T see also DNA tumor virus(es) dNTPs see Deoxyribonucleoside triphosphates (dNTPs) Docking proteins. 1100F early embryo and genesis of body plan. 1353F. 1015F. 448F. 1015 ciliary beating and left-right asymmetry. 221F gene regulatory proteins. 1330FF body axis specification. 303F. 416–417. 1329 genetic screening for early patterning. 482F Drosophila melanogaster adult anatomy. 1306F. 447–450. 273 mechanism for heredity. 447.. 1353–1355. 747F Dolly the sheep. 115F Dolichol. 197–198. 416–417 see also DNA bending X-ray diffraction analysis. 1346FF see also specific genes Drosophila melanogaster segmentation genes. carbon–carbon. 1157F regulatory hierarchy. 1338F segmentation genes see Drosophila melanogaster segmentation genes sex determination. 1350F. 482F Double-strand breaks (DSBs) homologous pairing/meiotic recombination. segments. 198F 3¢ to 5¢ polarity.. 1335F. viruses. 756F. 1333–1334. 1334FF. 266–268 analysis autoradiography. 279F topoisomerase II. 1157–1158. 1328–1341 blastoderm. 1275. 1352FF. 1338F gap genes. 285F. alternative splicing. 980. living world. 602–603 BrdU staining. 324 mechanisms of action. page numbers with an F refer to a figure. 1126 chromosomes. 1336 mRNA localization. 1280 production. 195–196. 980. 1334F oocyte. 1345F positional values. 198F. 266–267. 1335F. 1340F segment polarity genes. 295T see also Homologous recombination (crossing-over) topoisomerase II production. 564 RNA interference. 344F see also Nucleosome(s) DNA transfer see Horizontal gene transfer DNA tumor virus(es). 1331F. 1330. 1018. 1332F. 1335. 461–462. 967F. activator proteins. 268F template strand. 267. 199F polarity. 86. 195–196. 462F cytoskeleton. 271F. 1058 cellularization. 1331 see also under Imaginal discs key to developmental mechanisms in other animals.. 62. 18T see also chromosomes (above) homeodomain proteins. 1337F. insulin receptor substrate (IRS-1). 273 turns. 199 elucidation. 280F. 757–758. 268F. 465–466. 280F topoisomerase I. 1157. 449FF Even-skipped see Eve (Even-skipped) gene Ey gene. 1491 Dyskeratosis congenita. 267F. 564F Dopamine. 980. 318T. 1278–1279 Dpp (decapentaplegic) gene/protein. 1343F vertebrate homologies. 285. 564F genetic engineering. 268F DNA replication. 1247–1249. 1521–1524 Dscam gene. 481F. 417 major groove. 564F antisense RNA. 1377 cytoplasmic. 1343–1344. 487. 1333–1334. 199–200 see also Gene(s) nucleotides. DNA synthesis initiation. 416F minor groove. 199F. 37–38. 475 gene regulatory proteins. 983 development see Drosophila development gene expression alternative splicing. 820–821. 612F autoradiography. 853–854 across bacterial membranes. 819F. 1283 Embryonic stem (ES) cells. 1480 “personalized. 702. 743. 831. 413F parthenogenesis. 697T membrane proteins. 181F. 612F. 635 microsomes. 744–745 cholesterol synthesis. 1481–1482 “therapeutic cloning. 604–613 3-D reconstruction. 1437F in respiratory epithelium. 1298 Ca2+ increases. 1514F protein degradation see Proteasome(s) protein folding. 288F. 181F. 751F. 534. 1036 cell cycle analysis. 1189–1191. 835F. 1552F Efflux transporter proteins. 820–821 evolution. 138F Elastic fibers. 511. 830F see also ATP (adenosine triphosphate) mitochondria vs. 744F lipid metabolism. 882–883. 1139F. 827–828. 823F chemiosmosis. 605 freeze-etch. 1402. 181. 1288 cortical reaction. 1543. 739–742. 662. X-ray diffraction analysis. 609F tomography. 850F. 518F. 653. 1435 Endocrine signaling. 870–876 anaerobic bacteria. 1400. 744–745 COPII-coated vesicle formation. 1098 evolution. 1583F calcium store. chloroplasts. electron microscopy. 1481–1482 Encephalitis. Electron transfer Electrophoresis. 1303F. 604–605. 606. 793F receptor-mediated see Receptor-mediated endocytosis signal. 789 Endocytic pathway. 49 orbitals. 1191F structure. 46. 704 distribution during cytokinesis. 100F. 793 see also Endocytic pathway Endoderm. 827–840. 828. 522FF pulsed-field. amounts. 611. 605F history. 534. 741F unfolded protein response. 180–181. 604 electron scattering. 1364–1369 plant. 814. 848. 1282 Egg polarity genes (Drosophila). 598. 815F Electron scattering. 814F coupling to active transport. 604T imaging. 1283 control of differentiation by different factors. 1493 Edema toxin. 822–824 see also ATP synthase bacterial flagellum. embryonic origin. 1535 eIF4E. 1552F Effector T cells. in synapse maintenance and elimination. cell entry. 716F noncyclic photophosphorylation. 607F. 1287–1288. Proton pumps bacterial. 534 blotting see Blotting DNA sequencing. 839F. 608F. 1136. 534 cell fractionation. 836 see also ATP synthase. 795F Endocytosis. 411. 517. 821F mitochondrial protein import. 181F conformational change. 612F. gap junctions. 535F polyacrylamide gel see Polyacrylamide gel electrophoresis (PAGE) protein analysis. 100. 775F Endoplasmic reticulum (ER). 821F. 1334F Ehlers–Danlos syndrome. 828F redox potentials. 1365 Edema. 1299 cortical granules. 1481 drug discovery. 1470 Endocrine cells. 819F proton gradients. 1332–1335. 871–872 chloroplasts see Photosynthetic electron transport chain(s) cyanobacteria. 791–792. 1057–1058. 100F. 608 electron lens. 821F proton movement. 1493 Edge effects. 700F glycolipid synthesis. 1402F polarity. 100. 610F negative staining. 517 protein purification. 534 recombinant DNA technology. 1300. 611F cryoelectron microscopy. 835. 821–823. 813. 873–875 energetics. 818–819. 1241–1242 cell crawling. 46. 871–872 cyanobacteria. 377F EGF see Epidermal growth factor (EGF) Egg (ovum). 839F ATP production. 607F heavy metal stains. 377F EF-2 elongation factor. viral. 606. 839F Electrogenic pumps. 814F energetics. 608–609. 607F Electron transfer. 518F. 817–819. 959 EF-G elongation factor. 517. 521–522 gel staining. 1300F see also Fertilization C. 8734F evolutionary implications. 743. 883F Endocytic–exocytic cycle. 486. 819. coli see Escherichia coli Ectoderm. 100. 521F. 518FF. 852F. 626 membrane. 506F differentiated cell production in vitro. 782. 1323–1324 development stages. 725–726 ceramide synthesis. 750F. 180–181. 610. 1384F. 517 agarose gel. 609F SEM see Scanning electron microscopy (SEM) single-particle reconstruction. 146F. 610 colloidal gold. 744–745 lipid bilayer assembly. 1365 Endoglycosidase H (Endo H). 850–851. 820–821. 749. 488–489. 828F. 792 fluid-phase. 1290–1291. 380F eIF-2. 490F. 82F. 608 sample preparation. 737F. 377F Embryo(s)/embryogenesis anteroposterior axis see Anteroposterior axis development cadherins. 1290F specialized cell structure. 48F Elongation factor(s). 611F. 377. 882 gut (enteroendocrine cells). 815F NADH/NADPH carriers. 775F Endo H-resistant oligosaccharides. 488–489. 1140F experimental embryology. 829. 611–612 Electron density maps. 821. 598F Electrostatic interactions. 767F development. 604F. 239 contrast generation. 101 mitochondria see Mitochondrial electron transport chain(s)(s) photosynthesis see Photosynthetic electron transport chain(s) see also ATP (adenosine triphosphate). 1136F cancer-critical gene function analysis. 377–378. 491 eIF4G. 818F see also Activated carriers in metabolism oxidative phosphorylation. 505–507. 1299. 768F antigen processing/presentation. 604 molecular localization. 852F pH gradient. 820–821. 610–612 immunogold. 522FF protein denaturation. specific stages Embryonic germ cells. 1191F synthesis. 654F Electrochemical proton gradients. 1310. 605–606. chromatin condensation effect. membrane organization. 1310F G1 phase of cell cycle. individual species. 1481F derivation. 1136. 745 position in cell. 1482 immune rejection problem. 1287 size. elegans. 813. 376F. 613F surface analysis. 1291F oocytes see Oocytes PGCs see Primordial germ cells (PGCs) timing. 819F photochemical reaction centers. 606. 603F chromosome puffs. 1100 gastrulation. 521–522. 747F glycosphingolipid synthesis. 745 phospholipid synthesis. 611–612 EM-tomography. 742–743. 873–875 fermentation. 1190 Electrical activity.” 1303. 736–738. 567F. 775F phospholipid exchange proteins. 1546F. 1481–1482 mouse. 605. 747F E7 viral oncogene/protein. 1546F. Electrochemical proton gradients. 853 see also Electron transport chain(s). 791F. 380. 697 protein assembly. cell separation techniques. 610F grids. 1502 Endochondral bone formation. 882F. 872. 822. 742F virus assembly and. 377F EF-Tu elongation factor. 671 Electron(s) atomic interactions. 1310 dissociation experiments. 551 pulsed-field gels. 1287F. 607–608. 1249F Ear. 736 GPI anchor attachment. 827–840 ATP synthesis. 817–819. 737F. 377 protein synthesis. 640. neuron(s). 723–745 antibody synthesis. 1187 eIFs (eucaryotic initiation factors). 1291F. 749. 821F proton-motive force. 743–745. 146–147. 565–566. 726 microtubule motors. 1364 stem cells see Embryonic stem (ES) cells see also Development. 47F. 829F uncoupling. 535F Electroporation. 1249–1250 epithelial–mesenchymal transitions. 146F. 1058F descriptive embryology. 610 depth of field. 1546. 820–821. 1298F totipotency. 736 misfolded protein fate. 54 Elements (chemical). 179–180 EF-G see EF-G elongation factor EF-Tu see EF-Tu elongation factor transcriptional. 872. 343–345 translational. oligosaccharide processing. multivesicular bodies. 1287. Oxidative phosphorylation Electron transport chain(s). 1288 enucleation.” 507 in tissue repair. 1287. 608F. 1179. 1098 Early genes. 1544F. 1298F. 1332F. 829. 605F scanning electron microscopy (SEM). 377–378. 1496F Ebola virus. 518. 45. 490F see also Cap-binding complex (CBC) Elastase. 377 GTP-binding protein. 377F Effector B cells. 46 Electron crystallography. 535F. 740–742 see also Protein folding protein glycosylation. 675 Electrical synapses. 743F phospholipid transport. 1289F. 528 . 612. 534. 1189–1191. 1057F. 1393–1397 Electrical potential. 789 late endosomes. 606. 100F. 767. 1307. 612. 870–871 photosynthetic bacteria. 1190–1191. 505–507. 1021 oligosaccharide processing. 71–72. 180. 872 iron–sulfur centers. 1546. 606 metal shadowing. 46–48 see also Chemical bonds electron shell. 716–717. 1298–1299. 521–522. 1437. 1513. 852F protons. 490–491. 82–83. 285–286 Eastern equine encephalitis virus. 606. 606–607 resolution. 1139–1140. 655. 1543. 532. 814. 605 Electron stains. 1307. 662–663. 736–738. 1141 E. 1300F sperm binding to. 1248. 502 EF-1 elongation factor. 582F EDTA. 813–814. 630. 607F microscope. 821F see also Proton pumps membranes and. 1161 Electrochemical gradients.I:16 INDEX Electron microscopy. 1270F. 1138T in cancer invasiveness. 823F generation. 517. 380 regulation by phosphorylation. 607–609. 1287–1292 activation. 839. 1190F Elastin. 48F. 744–745 glycoprotein synthesis. 613F transmission see Transmission electron microscopy (TEM) Electron-motive force. 1288–1290. 797 E-cadherin. 1401F. 606–607. 611F. 782 LDLs. 839–840. 821–822. 1429 Early cell plate. auxin transport. 787–799 early endosomes. 170F cooperativity. 585F Eph B. 159–160. 1426 stem cell distribution. 1419. 1447F embryonic origin. 160. 922. 1429–1433 structure. 645 microvilli formation. 74. 472F bacteria. 1157–1158. 1156F occluding junctions. 784F. 803 Enolase. 1236F twin studies. 1150 see also Connective tissue Epithelial cell(s) apical domain. 160F Enzyme-linked immunosorbent assay (ELISA). 697T Endoplasmic reticulum (ER). 166F enzyme–substrate interaction see Enzyme–substrate interactions equilibrium points. 167 energetics. 1228T. 61. 472F mono-allelic expression. 794F. 1418. 696. 169–171. gut epithelial cell migration. 391. 166. 921–945 classes of. 731F signal recognition particle (SRP). 1143F host defenses. 732 stop-transfer signal. 447. 160. 158F. 473F see also Genomic imprinting Epigenome. 76. 163. 1521 Environmental reservoirs. 70 see also Chloroplast(s). 798. protein transport. 161F diffusion-limited. 729F mechanism of action. 62–63. 892. 69F forms. 1437F Entropy (S). 725F. 1352F protein structure vs. 168F Enzyme-coupled receptor(s). 77T. 163 Km. 735F post-translational translocation.INDEX quality control. Cell junction(s). 732F. 74F kinetics see Enzyme kinetics lysozyme catalysis. 1556 lineage and formation. 121F Enteroendocrine cells. 49F. 162F. 1404F renewal by stem cells. 1236. 1238 Epidermal growth factor receptor (EGFR). 794F. 803F Endosome(s) antigen processing/presentation. proteolytic processing. 74F multienzyme complexes. 471–473. 472 in cancer. 164–165. 1523F catalysis see Enzyme catalysis classification. 782. 162F see also Enzyme kinetics lysozyme. 159. 159–169 catalytic antibodies. 797–798. 769–770. 931 receptors see Eph receptors signaling. 806. 1142. 160F. 1417–1428. 1532F cytokinesis. 160. 1155–1157. specific uses chemical bonds. 75F. 1306F. 1514F volume. 733. 1583F early. 472F silencing of tumor suppressor genes. 794F apical and basolateral. 1525 as permeability barriers. 1417–1428 associated signaling pathways. 726. 88–103 catalysis. Cadherin(s). 160 transition state. 1392–1393 Ephrin(s). 1402. 72–75. yeast alpha2 protein. 813–815 oxidation reactions. 1499 Epulopiscium fishelsoni. 160F. 161F inhibitory ligands. 163 fit. 767–768 resident proteins. 1150 sensory. 164F Eosinophils attack on schistosomes. 163T. HIV (human immunodeficiency virus). 65–87 energy conversion. 747F. 447F Enkephalins. page numbers with a T refer to a table. 219F histone modification see Histone modification imprinting see Genomic imprinting inheritance see Inheritance mechanisms. 74 enzyme–product complex. 798. 162F Vmax. 697T protein sorting. 1525–1526. 558–559 Epithelia. 806. 78F floating ball analogies. 1340F. 1452F upregulation in parasitic infection. 1340–1341. 732F. 1487 I:17 Epidermal cells. 1007 tight junctions. 164F. 724F T-cell receptor assembly. 164F diffusion. 892. 696 late. voltage-gated cation channels. 736 retrieval pathway. 799F epithelial cells. 799F. 160 see also Metabolic pathway(s). 138F Enhancers. 511. 737F. 158–159 antibiotic resistance and. 799F membrane amounts. 893F. 159–160. 1419–1420 Epidermal growth factor (EGF). 512F ERGIC53 protein. 740F Sec61 protein translocator complex. 1010F Page numbers in boldface refer to a major text discussion of the entry. 69F electrical energy. inhibition by viruses. 1532. 69F. 1534 structure. 770F selective retention. 69F Engrailed gene/protein. 1392–1393 Ephrin B2. 472 DNA methylation see DNA methylation eucaryotes. 1505 see also specific viruses Env gene. 173F multienzyme complexes. 72–73 mechanism of action. gut epithelium. 770–771. 516F see also Protein tags Epstein-Barr virus (EBV). 794. 1513. 726F smooth ER. 1503 cell–cell adhesion and cell junctions. 73F. 1502. ER to Golgi apparatus transport. 1558F Epitope tagging. 48–49. 159F Equilibrium sedimentation. 157–159 relation to free energy changes. 162F. 798. 1155F. 798. 173. 62F see also Activated carriers in metabolism. 1445 Endothelin-3. 766–787. 727–730. 725F. 163 Kcat. 782. 588–589 Enzyme–substrate interactions. 1446 inflammatory response. 1441F Ephexin. gut epithelial cell migration. 1141 folding. 1420 signaling. 170 tetrahedral intermediate. 1418–1419 plants.. 219. page numbers with an F refer to a figure. 157. 730–731. 162F–163F turnover number. with an FF to figures that follow consecutively. 923T. 169 steady-state. Cell adhesion. staining. 813 kinetic energy. 1440–1441. 160F free energy. 723. 76–77. 1451 Eosin. 1422F waterproof barrier. 1441F see also specific types Ephrin A2. 741F multipass transmembrane protein integration. 724–725. 767. 72. 67F. 806F surface area. 1134F. 72 active site see Active site regulatory sites. 1141 Epitopes (antigenic determinants). 175–176 see also Allosteric regulation. 74. 159. 733F b-Endorphin. 740–742 virus assembly and. 798. 1133–1150 apico-basal polarity mechanisms. 164F. uptake by endocytosis. 806F endocytosis. 768 unfolded protein response. 733F SRP receptor. 173F phosphorylation. 1208 chromatin structure. 728. 1157F see also Adherens junction(s). radixin. 1133–1135. 628 IgA transport. 473 Epilepsy. 929F ERM (ezrin. 1426 rate. 172–173. ATP (adenosine triphosphate) cell use catabolism. 798F transport to lysosomes. 697T see also Endocytosis Endosymbiont hypothesis. 162F. 69F see also Photosynthesis potential energy. 723–745 co-translational translocation. 1536 misfolded protein fate. 1437. 739–740. 1393 Ephrin A5. production. organelle evolutionary origin. 799F glycolipids. 791–792 volume. 169F receptor coupling see Enzyme-coupled receptor(s) regulation. 739–741. 770F rough ER. 1419–1420 granular layer. 167–168. vs means compare/comparison. 473 positive feedback loop. 793F. 792–794 function. 164F substrate binding. 76. 1007 polarity. 1523–1524 Enzyme(s). 767–768 retrotranslocation. 67–68. 859–860 Endothelial cells. 986. 1545. 1445–1450. 163 Michaelis–Menten kinetics. antibiotic resistance. 799F. 744–745 structure. 730 signal sequences. 931 Eph receptors. 1375 End-replication problem. 166F molecular tunneling. mechanism. 1005 Epididymis. 168–169. 921 see also individual receptors Enzyme kinetics. mesin) family of proteins. 799F material retrieval. 159–160. 76. 1132F bacterial adhesion. 1440–1441 Epidemics. 1133 epithelial–mesenchymal transitions. 1447–1448 Ephrin B family. 1131. 77F free energy changes. 1418F associated structures/appendages. retinotectal axon guidance. 1522. 471. 69F see also Thermodynamics interconversions. 767 Erk (MAP-kinase). 515F. 169 energetics. 438F. 163–165 mechanisms. 1556F membrane protein distribution. capillary sprouting. 1134F anchoring junctions. 77F Equilibrium constant (K). 1392 Ephrin A proteins. 473. 770–771. 160 kinetics effects. 6. 797F. 736 quality control. 794 Epidermis. 472–473. 74F. 736. 728 start-transfer signal. 70. 66–67. 292 Energy ATP as carrier. 1009. Mitochondria. 1419F interfollicular. 1103. 923T. 771 retention signal. 163 reaction rates. 768–769 MHC class I proteins. 806 Epithelial–mesenchymal transitions. 1440–1441. retinotectal axon guidance. 164–165. 922. 724–725. 72 heat energy. 1352. 1418 cells. 726F see also Sarcoplasmic reticulum sphingomyelin synthesis. 784F. 807F recycling. Desmosome(s) columnar. 1420–1421 Epidermolysis bullosa simplex. 159–160. 162–163FF double reciprocal plot. 732F to Golgi apparatus. 1526F microbial evasion of. 72–73 activation energy. 119F Enveloped viruses. 159T coenzymes/cofactors. 1497. 472 genetic inheritance vs. 69F light energy. 14F Equilibrium chemical. Feedback regulation structure. . 726–727. 1150–1158 planar cell polarity mechanisms. 1294 Epigenetic phenomena. 1309 Enhancesome. 1502–1504 mucus and. 734–736. 160. 472F protein aggregation state. 1452F structure. 733–734 single pass transmembrane protein integration. 514. 69F free energy see Free energy heat energy. individual enzymes Enzyme catalysis. 682 Epinephrine see Adrenaline (epinephrine) Epistasis analysis. 730F. 159–160. 159–160. 791. 295T FAP (familial adenomatous polyposis coli). 31F non-coding DNA. 412 coordination. 439T lactose (Lac) operon see Lac operon (Escherichia coli) genome. 292 histones. 1387 Fasciclin3. 1031 Fanconi anaemia groups A-G. 97F see also Lipid(s). 18T as model organism. 872–875 cancer as a microevolutionary process. 1185–1186 duplication/divergence see Gene duplication(s) see also Genome evolution genomes see Genome evolution Hemoglobin (Hb). 1529F cytoskeleton. nonsensemediated mRNA decay. 94. 506T cell types. 1180. 269–270. 1253. 485. 30–31.” 352. Cell junction(s) Extracellular signal molecule(s)/pathway(s). 270F Exosome. 1166F see also Glycoprotein(s). 485 Experimental embryology. 1339F Evolution Algae. 1459 synthesis. 1474–1476. 873–874 carbon fixation. 1192F plant(s). 246. 1459. 889 combinatorial action. 1307 Evolutionary time. 1573F. genetic control. 1524 major events. 145–146. 97F structure. units. 1271F tree of life. 1253F Fascicles (fiber tracts). Transcription gene structure see Gene structure.eucaryotic transcription see Transcription Euchromatin. glucocorticoids. 358–359. 1337. 1176–1177. 1178–1195 basal lamina see Basal lamina cell adhesion/interaction see Cell–matrix adhesions cell secreting/synthesis. 800. 840–841 proteins see Protein evolution sexual reproduction and. 801F default pathway. 1179F components. 1008–1009 development. 1475FF gene expression regulation. as polygenic trait. 58–59 see also Fatty acids digestion. 1306F. 646 phospholipids. 284F strand-directed mismatch repair. 1190F fibronectin fibril assembly and. 697–699. 359F Expressed (DNA) sequences see Exon(s) Extracellular matrix (ECM). 1459F Erythrocyte(s). protein folding. 353F recombination in evolution. 14F double membrane. 942. 1475F. 1503F E-selectin. 63T compartmentalization. 1169 see also Integrin(s) mechanical interactions. 220. 1292–1293 colony-stimulating factors role. 449F. 1205–1224 carrier protein(s). 347 gene structure (eucaryotic). 1042F. 176–177 protein synthesis see Translation RNA polymerase(s) see RNA polymerase(s) rRNAs see Ribosomal RNA. 25F. gonad specification. 1310F. 30 Regulatory DNA. 327. 420–421 meiosis. DNA polymerase. 278 hybrid. 803 regulated see Regulated secretory pathway secretory proteins. 283F. 1189. 448–449. 663. 625. 1490 FAD/FADH2 citric acid cycle. 1110. 688 Exocytosis. 305 innate immune system. 25F mutations. 502 Ethylene receptor. 346. 1015–1016 organelle(s). 955 ATP synthesis. receptor. 283F clamp loader structure. 16F P pili. 817 electron carrier. 200–201 see also Nucleus intracellular membranes. 466FF. 1571. 99F FAK (focal adhesion kinase). 169 see also Organelle(s). 1180–1181 degradation. 1460T target cells and receptors. 1520–1521 plant(s). 36. 466F see also specific genes Ey (Eyeless) gene/protein. 982–983 genome sequence. 841 Eubacteria see Bacteria Eucaryote(s). 1502. 1594 FASTA sequence alignment. 345F. 1462 erythropoietin role. 943F gene expression regulation. 16F cells see Eucaryotic cell(s) epigenetics. 958 Etioplasts. 433F. 655 conservation in see Evolutionary conservation electron transport chain(s). 169 mRNA see Messenger RNA. 1103. 505. 1178 exocytosis. 91. 449F modular control of expression pattern. 800 secretory vesicles see Secretory vesicle(s) Exon(s). 1179. 872–875 molecular see Molecular evolution multicellularity and cell communication. synapse formation. 874. 91. 767 Facultative pathogens. 96. 155F Excisionase. 385T Erythropoiesis. 94 structure. 255 skipping. 1459–1460 cells responsive to. 448–450. 1187–1189 tissue morphogenesis and repair. mammalian. 17. 747F Error correction. 1460T ES cells see Embryonic stem (ES) cells Escherichia coli. 1103. 875F animal–plant divergence. 277 transposons. 26–32. Chromosome(s) DNA replication see DNA replication gene expression. 870–872 aerobic metabolism. 282. 1453T. 1102. 268F refractory period. 24–25.eucaryotic protein phosphorylation. 1474 Fat proteins (cadherin superfamily). 1146 Estradiol. 26–27 transmembrane proteins. 1459–1460 Erythropoietin. protein analysis. phage lambda. 18T. 889 inhibitory. 1454. 276–277 phylogenetics. 800 matrix receptors. 96 energy source. 1302–1303 Ethylene. 207. 1137. 889F Estrogen. 1111F mitogens see Mitogen(s) NO. 1286 multicellular development. 1310–1311. 256–257. 1191–1193. 386 Exonucleolytic proofreading. Cell adhesion. 1459. 700F see also specific organelles pathogens. specific compartments division see Cell division DNA packaging. 348F. 264 see also Mutation rates myosin and kinesins. 800. 1280. 1189F. 462. 870–876 gene(s). 269–270. 937. 737F. 357. 887–889. 282. 326 Excitatory postsynaptic potential (EPSP). 1459F see also Erythropoiesis lifespan and turnover. 14. protein family binding-sites. tree of life. 552 size. 958F Ethylenediaminetetraacetic acid (EDTA). 27F genomes DNA methylation. 411 see also Cell differentiation chemical composition. 1352 Ezrin. 824T storage. 531 Fat(s) composition. specific types Fat cells. 1120. 1571. 957–959. 870–876. 1459.eucaryotic metabolic rate. 250. 284F sequencing. HIV mRNA transport. 1165 fibrous proteins. 338F RecA protein see RecA protein replication. 282. neuronal. 23 see also Origin of life Evolutionary conservation. tumbling. 880–881. 1193 localisation. 1147 Fas ligand. 270FF Erythroblasts. 169 DNA localization. 1194 diversity. 353F Exon–junction complexes (EJC). 155–156. reproductive cloning. 818–819. 626 osmolarity regulation. 15–17. 1110 development. 1194 matrix metalloproteinases. 31–32 size. 318T uropathogenic. secretion from ER. 1502 promoter sequences. 213 homeodomain proteins. 1271–1272. 8F. 355F “Exon definition hypothesis. 663F Erythromycin. 1070 see also Heterochromatin Euglena. 750F. 466. specific macromolecules compressive forces and. 799–809 constitutive. 885 cell size/number regulation. 358. 888F survival factors see Survival factor(s) see also specific types/pathways Extracellular space. 1009 ERp57. 275F DNA polymerase structure. 1283 growth factors see Growth factors hydrophobic. 204 see also Noncoding DNA predators. 208F. 955 mutation rate analysis. 265 Evolutionary tracing. 206 length variation. 871–872. 646. 282 chromosome. 1253. 1459 membrane. 1194 serine proteinases. 17F cytoskeletal elements. 1504. 819F fatty acid oxidation. 416. 618F. 1180–1181 see also Bone. 466F Eye color. 352. 26–27 general features. 884 competition for. 1459–1460. 1306F. 653 FACS see Fluorescence-activated cell sorter Factor V. 256F homologous recombination and. DNA repair disorders. 16F Eve (Even-skipped) gene combinatorial control. 98. 486F Export-ready mRNA. 1103. 39–40. 1311F Exportin(s). 352.I:18 INDEX see also Gene expression. 27. 16–17 collagen genes. 1339. 415 Fat droplets. 1457F. 1179 see also specific proteins shapes/sizes. 147F. 12. 138F. 1253F Familial hypertrophic cardiomyopathy. 635 Eucaryotic cell(s) cell cycle see Cell cycle cell lines. 874F metabolic pathway(s). 1176F Familial adenomatous polyposis coli (FAP). 466. 1164 Eya (Eyes absent) gene. 472 evolutionary origin. 880–886 cell response. 202–203 see also Chromatin. 31. tree of life. 1504F flagella. 665F enteropathogenic. 1459 complement lesion. 264. 881–883 CO. 891F Ethical issues. 563 Eye development. 1594 Fas receptor protein. 767 Factor VIII. 801F extracellular matrix. 439. 16F. 1138T . 355. 1195 see also Plant cell wall tensile forces and. 463F regulatory proteins see under Gene regulatory protein(s) transcriptional regulation see Transcriptional control of gene expression F F0F1 ATPase see ATP synthase Facilitated diffusion. 448F. 1491F replication. 800 neurotransmitters see Synaptic vesicle(s) proteolytic processing of cargo. 1102 classified by range of action. 459. 1290–1291. 1555F. Cytoskeletal filaments Filamin actin filament packing. Page numbers in boldface refer to a major text discussion of the entry. 72. 590–592. 1033. 1187–1189. 547F Formaldehyde. 588F. 170–171. 1033 gene rearrangements. 1467–1468 ECM organization. 1401F development. 994F actin filament web formation. 1388. 123F Fumarate. 1449 FGF8 protein. 1574 Fractionation see Cell fractionation Frameshifting. membrane fusion. 1387 Fibril-associated collagen(s). 643. 1218F Fluorescence in situ hybridization (FISH). with an FF to figures that follow consecutively. page numbers with an F refer to a figure. 76. 1062 G1 phase of cell cycle see Cell cycle. 912F. 1559 Feedback regulation. 943F. 1325 planar cell polarity. 599. 1301. 1359 Frog(s). of spinal cord. 592F fluorescent dyes. 1297–1303 capacitation and. 14F. 942. 586–587 Fluorescence. 1413–1414 specification by homeotic selector genes. 764–765 see also Protein tags. 1176–1177. 1179F functions. 593–594. 585. 587. 248 Founder cell. 6-bisphosphate. 75–78. 264 Fibroblast(s) cell crawling. 1324. 100 Flagella. 293 transformation to cartilage and bone. psychoactive drug effects. 825F sequential reactions. 1103–1105 G1/S-cyclins. 1165 collagen see Collagen(s) ECM see Extracellular matrix (ECM) see also specific proteins Field emission guns. 587F Foam cells. 1062 G2/M checkpoint. 605F nitrogen. 75F. 119F calculation. 1048F replicative senescence. activation. 821–822. 684. 1298–1299 marine invertebrates. 871F Formin. 643. 1292 Follistatin. 1191–1193. 569–571 Fungi antibiotic production. 1501 Flow cytometry. 1337 Fusion proteins virus. 605. 1031 motility. 88–103. redox potentials. 1293. 1468–1469 differentiation and changes. 1387–1389 Fimbriae. 1005 Filaments. 1105 G2 phase of cell cycle see Cell cycle GABA (g-aminobutyric acid) neurotransmitter role. 1145. 1186T fibril-associated vs. 587F. 1062. 753F Fluorescence resonance energy transfer (FRET). 585 Formic acid oxidation. 1414F Flowering plants see Plant(s) FLP recombinase. 872 obtaining energy. 1191 structure. 455F Flamingo protein. 1298F acrosome reaction. 1057 zygote formation. 989FF F-type pumps (ATPases). 1449 steering neuronal growth cone. elegans. 1299. 464. 635 Fermentation(s). 587F immunofluorescence. 1488. 1094 Formylmethionine. 1500. 1299 cortical reaction. 1302F Xenopus embryo. 1103–1105 G1-cyclins. 586. 940 Food molecules nonfermentable. transcription circuits. 1554F. 1066. 375F. 365F Fibrillin. 1297. 825. 1388F Flora. 1270F. 1176F I:19 Follicle cells. 77T reaction concentration effects. 411. 947 Frizzled gene/protein. 1031–1034 bacterial. 459F F elements. 1599F phagocytosis role. antibody molecule. tagged knockouts. 1494 evolutionary origin. 1183 Fibronectin. 874. 1322–1323 Foxp3. 457. 1193F gene. . 586–587. 1297 egg activation and sperm binding. 1064 Fc receptor(s). 912. 413F see also Xenopus laevis Frozen sections. of human body. 1555. 576 total internal. 1271. 1191. 1176F Focal adhesions. 1298. fibrinopeptides. 609 Filaggrin protein. 1467–1468 mature and immature. 830 electron transfer. 141F soluble form. 595F Fluorescent analog cytochemistry. 1301 Fertilization. normal microbial. 1193 Fibrous proteins basal lamina. 1475F in wound repair. reduced. 1301F. 78F. 824–825. regulatory T cell(s). 90 pathways. 120F Fructose 6-phosphate. structure. 1059–1060. 1138T. 120F Fructose. translational see Translational frameshifting FRAP see Fluorescence recovery after photobleaching (FRAP) Free energy. 1531 Fossil record. 318T FepA protein. 95. 1552F. 75F. 586 Fluorescence-activated cell sorter (FACS). 600F Fluorescence recovery after photobleaching (FRAP). Negative feedback (feedback inhibition). 77–78 Free radicals. 797F Fc region. 586–589 applications. 1297 pronuclei fusion. 1036 cell culture. 1395 Fission yeast cell cycle. 998. 58F. 1498F. 1170.. sexual reproduction and. 1192 tension effects. 1316T C. 823F. 1301F in vitro (IVF) and related procedures. 597 Fluorescent dyes. 94–95 Forensic genetics. 839 earliest cells. 1500F Focal adhesion kinase (FAK). in lung development. abnormal cell motility. 1066. 13. 1467 Fibroblast growth factor (FGF) in angiogenesis. 576. 1190–1191 Fibrin. 591F nanoparticles. individual fusions G Delta G (DG) see Free energy change Delta G (DG) G0 phase of cell cycle see Cell cycle G1-Cdk. vs means compare/comparison. page numbers with a T refer to a table. 1301. 1486. 1300F sperm–egg fusion mechanism. 588F single-cell expression analysis. 1596. 1381–1382. 585 Fructose 1. 937. 1006. 989–991. 586–587. 1031F sperm. 91. 686 Gag (viral capsid) proteins. Drosophila. 112F Fruit fly see Drosophila melanogaster F-site (ribosome binding). for synapse modification. 789 Fluorescein. 591F. 503F. cytoskeletal see Actin/actin filaments. 59F see also Membrane(s). 114–115FF cell membrane components. 1371 FGF10. 586F. 644F. 1297 pronuclei fusion. 100F see also Catabolism storage. 1191. 398 Fushi tarazu mutant. 1008–1009 loss. 1502F FLIP. 96–97. 994F. 458F. 1413. 1218. 644F. 29–30 pathogenic. phylogenetic tree comparisons. 852. 75–78. 1061. 788 transcytosis. 1000F. 588–589. 1348 Fluid-phase endocytosis. 1468–1471 to fat cells. 587 confocal. 825F importance for life. 1348. 1287. 839–840. 660F Fugu rubripes see Puffer fish (Fugu rubripes) Fumarase. in C. 383. 1176–1177. 1158 polarity-signaling pathway. 1192F. 1294. plague transmission. 1062. 1502. nuclear localization. in growth cone guidance. 239 Fluorescence loss in photobleaching (FLIP). 1290F Follicle stimulating hormone (FSH). 1158 Fleas. 1382F heparan sulfate binding. 1302F sperm-donated centrioles. chromosome puffs. 1179. 1299F Ca2+ increases and egg activation. evolution of ability to use. 996 angiogenesis. 1298. 96F oxidation. 1188–1189 see also Collagen(s) Fibrillarin. 1301–1303 capacitation. 852F Fertility. 380. 58–59. tissue fixation. 1009F Filopodia. Regulatory cascades Feed-forward loops. 1191 integrin binding via RGD motif. 97F synthesis. 1056–1057. elegans development. 1300. 1494 prion proteins. 1490F proton gradients. 15F. 1293F Flagellin. 170–171 metabolic pathways. structure. 58–59. 595. 659–660. 852F Ferridoxin. 12 translation accuracy. 504F chondrocyte transformation into. 587. 1555. 839F cilia comparison. 1060F Flower(s).INDEX Fatty acids. 999F. 485F. 385 Free energy change Delta G (DG). 1066. 1007F actin filament packing. 610F FRET see Fluorescence resonance energy transfer (FRET) Fringe family of glycosyltransferases. 13. 989F. 526. 383–384 dimorphism. 96 F-box proteins. Cell cycle control G1/S-Cdk. 1062. 1007. 1188 fibril assembly integrins and. 90F see also Glycolysis Ferredoxin-NADPH reductase. 1191 basal lamina. 604. fluorescence loss in photobleaching (FLIP) Flip-flop switch. 123F Functional genomics. 90. 1165 connective tissue. 164 see also Enzyme catalysis changes in see Free energy change Delta G (DG) favorable vs. 384F. 832–833. phase-contrast microscopy. 1037 actin filament nucleation. 1. 588F quantum dots. 1049. translational frameshifting. 1596F. 1371 Fiber tracts (fascicles). formation. 1184–1189. 1271F Fixation carbon dioxide see Carbon fixation microscopy sample preparation. 753F Fluorescence microscopy. 1137. 1192F type III fibronectin repeat. 1534 FGF see Fibroblast growth factor (FGF) FGF8 protein. telomeric repeats. 122F. 1387. 1185. 994F Firing rule. SCF regulation. 526F. 24F see also Schizosaccharomyces pombe Fitness (evolutionary). 1532 Freeze-etch electron microscopy. 466 Floor plate. for organotrophs vs phototrophs vs lithotrophs. 596F. 829 equilibrium constants. 76 reaction coupling. 1189 ECM synthesis. 808 receptors. 855 see also specific types Fatty acyl CoA. 454–455. 1490F Fimbrin actin cross-linking. 264 Fibrinopeptides. neuronal. 1269 see also Zygote Fever. Phospholipid(s) mobilization. 1193 protein modules. 1056F shape mutants. 871. 1008. 8 sources. 118–119FF catalysis. 870–871 lactic acid production. 376 FtsZ protein. 1526. 1349F FLP recombinase target (FRT). 589F microscopes. 1189F Fibrillar collagen(s). 502. unfavorable reactions. 1555F. mutation rate. 837–838 positive see Positive feedback see also Allosteric regulation. 264 Fibrinogen. 1468 organization of microtubules. 448F. 560F see also specific methods imprinted see Genomic imprinting localization see Genetic mapping . 19–21 duplication and divergence. 463f heritability. 449F in mammals. 20–21. 427–428. 364. 412 see also Transcription. 464F DNA structure role. 1400T Gastric acid secretion. 345F. 444–445. 202 see also DNA structure. 465F controllable steps. 441F enhancers. 574–575. Drosophila development Gene families common to archaea. 20F. 334F. 466 see also DNA methylation. 601 Gel(s) GAGs and. 446F modular nature. 7–8. 557–558. 570 functional genomics. 1160–1161. 463. 1307F Xenopus see Xenopus laevis development GATA-1. bacteria. 429–430. 1159F. 1236F Gene duplication(s). 438F. Translation Gene expression regulation. and eucaryotes. 414FF. 199F. 200F analysis. 553 see also Genetics DNA microarrays. 462–463. 465. 884F channel proteins. 412 transcription units. 1350F DNA sequence recognition. between nucleus and cytoplasm. 442F. 447FF. 412. 255 globin genes. 35F Gene regulatory protein(s). 38–39. 23. 336 see also entries beginning gene/genetic Gene activator proteins see Transcriptional activator(s) Gene batteries. 451F promoters see Promoter elements regulatory modules in Drosophila (eve gene). 204. 176 in protein module shuffling. destruction by APC/C. 1159–1160 GARP gene regulatory proteins. 1232 see also Cancer-critical genes manipulation see Recombinant DNA technology. 430F gel mobility shift assay. 255 see also Gene families. 1159. 447–448. 628F Galactose. 40F. 465F see also Drosophila development regulation. 628 GAP see GTPase-activating proteins (GAPs) Gap genes. 461F General recombination see Homologous recombination Gene regulatory circuits. 24T evolution. 462–463. Genetic code evolutionary innovation. 246. 20–21. 285–286 heterochromatin role.general (TFII) transcription regulation see Transcriptional control of gene expression see also specific proteins Gene replacement. Helicobacter pylori association. Transgenic organism(s) numbers. 318F biochemical analysis. coordinated by critical regulatory protein. 438F. 34–35. 336–340 see also Gene control region(s) efficiency. 1159. 432F DNA sequence determination. 428F Gelsolin. 463–464 Gene clock. 415 coordinated control. 445F. 773F Gamete(s). 468F DNA signals for transcription. Gene silencing. 343F. 1000 Gel transfer see Blotting Geminin. 463F manipulation site-specific recombination. 419F see also DNA-binding motifs (proteins). Chromosome condensation. 438F insulators. 464–465 see also Combinatorial control coordinated gene control. 629 membranes. 20F. 464. 700. 412 position effects. 512. 448. 450–453. 439–440 gene control regions see Gene control region(s) genetic switches see Genetic switches hormonal. ion channels see Ion channel(s) Gcn4 protein. mathematical modeling. 412. 427–428. 1162F plasmodesmata vs. 701F Gating. 195. 440. 429. 528F. 429F chromatin immunoprecipitation. 314–315 Holliday junctions. 141F rates. 329. 425. 570 targeted mutations. 454. 23–24. 311. 480–481 DNA structure and. 1237–1239 chromatin condensation. 365F Gene(s) amplification in cancer. 1185–1186 fate of duplicates. 1160F see also Connexins structure–function relationship. 442F. 255 vertebrate evolution. 416. 449FF multicellular development and. 1307. 336 variation between cell types. 345F proportion of genome expressed. 884. 434. 332F eucaryotic. 445–447. 567F. 6. 418T prediction. 418–419. 418T. 566F 1521F GAGs see Glycosaminoglycans (GAGs) Gain-of-function mutation(s). 1161–1162. 442. 418T analysis techniques affinity chromatography. 1281 production by cell division see Meiosis see also Egg (ovum). 424F. 416 DNA sequence recognition. 480–481 modification. 221F procaryotic. 451F combinatorial control. 379F. 564F Gal4 gene/protein.general (TFII) heterodimerization. 566–568. 1009F Gel-filtration chromatography. 445. 575F cluster analysis. 256–257. 417F. 416–417. glucocorticoid regulation. 379–471. 204. 1436 Gastric cancer. 21F pseudogenes see Pseudogenes sequencing see DNA sequencing structure see Gene structure transcription units. 38–39 Xenopus genome. 412. 553–576 2D-PAGE. 1068–1069 GEMS (gemini of coiled bodies). 1338F Gap junction(s). 255 functional divergence. 1159F structure. 1158–1159 oocyte–follicle cell. 572–573. 40F. 461F Gene cloning. Pseudogenes Gene expression. 140–141. 1179–1180 gel-forming proteins. 315F in tumor suppressor gene loss. family members in different eucaryotes. Epigenetic phenomena. 199–200. 458F. 418–419. 424–425. 1337F. 545F “shotgun” approach. 451F. 452F. 1237–1239 PCR see Polymerase chain reaction (PCR) cancer-critical see Cancer-critical genes chromosomal location. 574F. 21F. 221F position effect variegation (PEV). 434. 414F approaches. 19 expression see Gene expression function(s) antibiotic resistance. 628F. 569–571 mouse. 542 PCR cloning. 425F see also Combinatorial control latent see Latent gene regulatory proteins negative control. 343. 444F. 1400T mechanisms. 462F. 554F history of concept. 465. 1269 haploid state. 470 prediction from sequence homology. 567F Gene oscillation. 207. 204–205. 1333. 415. 18–19 homologs. 463–464 enhancesome. in N-linked oligosaccharides. 464. 461F post-transcriptional see Post-transcriptional regulation protein activity control. 1163 size determination. 1456 Gated transport. 204F. 331. 1134F dynamics/turnover. 428. 447. 554F see also Genetic mapping definition. 440–441 activators see Transcriptional activator(s) complex assembly. 418T GAL4/UAS technique. cancer cells. 220. 325–326 memory devices. 431–432. Spermatozoa Gamma aminobutyric acid (GABA) see GABA (g-aminobutyric acid) Ganglioside(s) GM1. 22 generation from pre-existing genes. 461. 994F. Gene silencing human. Heterochromatin control/regulation see Gene expression regulation DNA methylation and. 667 columnar epithelium. 453 LCRs. 220 see also Chromatin. 1350F Galactocerebroside. 572F cancer and. 451F repressors see Repressor protein(s) transcriptional synergy. 449FF diversity. 448. 1307F sea urchin. 1158–1159 functions. 221. 463F. 253–254 protein kinase evolution. 20–21. 450F. 458F mRNA degradation control.. Protein–DNA interactions protein–protein interactions see Combinatorial control recognition sites see Genetic switches transcription factors see Transcription factors. 23–24 deduction from mutant phenotype. 425F. 450–452. 452F see also Gene regulatory protein(s) Gene conversion. 1503 Gastrula. 534F protein purification. 417F evolution. 1337–1338. 379F. 1363F Gastrulation. 434. 424–425. 21F paralogs. 414F. 314–315 mismatch conversion. 430F see also DNA-binding motifs eucaryotic. 458. 451F. 39F zebrafish genomes. 1160F electrical coupling. 428F discovery. 256F see also Globin genes see also Protein families Gene knockouts deletion cassettes. 568F production. 18. 575F reporter gene assay. 514F matrices. 467–468.I:20 INDEX loss. 436F see also Transcriptional activator(s) protein–DNA interactions. 254–255 see also Gene families genome evolution. 542 see also DNA cloning Gene control region(s). oncogenes. 434. 19F. 411–499. 463. Genetic redundancy. 1272. 462.” 476–477 oscillatory devices. 1158–1164 cell communication. 1290 permeability regulation. 458. 463F major families. 426 sequence determination. 446–447. 222. synthetic biology. 415. 204F orthologs. 1159–1161. 464–465 see also Transcription factors. 464F developmental expression. 418T. 1161 metabolic coupling. 575. 35. 1307 gut origin by. 575 housekeeping. 1006. 436F see also Repressor protein(s) positive control. 490–491 GEF see Guanine nucleotide exchange factor Geiger counter. 1269. 428–429. 1134. 415 regulatory proteins see Gene regulatory protein(s) transcriptional see Transcriptional control of gene expression see also Chromosome puffs. 399–409. 492–493 “noise. 246 identification. 31 downstream gene batteries. 363–364. 412. 544–546. 440. 246 collagen genes. 429–430. 537. 379F. genetic engineering. 553 tagged knockouts. 20F. 450–451. 447F glucocorticoid receptor protein. 535F Gel-mobility shift assay. 247F see also Comparative genomics size changes. 1491F operons. 1283 Genome(s). 251 synteny blocks. 564FF gene replacement. chronic myelogenous leukemia therapy. 1566 Germination. 556. 1254. 450–452. 1174 GlcNAc phosphotransferase. 468–470. antibody affinity maturation. 565F techniques. 546F Genomic DNA libraries. 21F. 329 conserved synteny. 195–197 homozygote. 433F. 348F exons see Exon(s) gene control region see Gene control region(s) human. 18T. Translation potential. 553. 1348 Genetic recombination see Recombination Genetic redundancy. Repetitive DNA. page numbers with an F refer to a figure. 300. 543F. Genetic engineering Genetic screens. 553. 680F. 1217 prevention. 553 haploid–diploid cycle. 470 chromosome(s). 199 evolution. 207. 1282. 1499 Glanzmann’s disease. 436F operators. fueling life. 250F. 205–207. 863–864. 256 fetal. 38–39 evolution see Genome evolution HIV. 248–249 phylogenetic trees. 247F. 207. 330F. 551–552 comparative see Comparative genomics conserved vs. 18T. 558 genes see Gene(s) genotype. 434. 1279–1280. 1238 Gli protein. vs means compare/comparison. 565F RNA interference (RNAi). 249F human vs puffer fish. 462–463 Genetic code. 140–141. 142. 295T prevention. 786F Gleevec (STI-751). 220. 288 gene expression regulation. I:21 252F conserved synteny. 206T. 564. 331. 251F intron–exon gene structure. 249F molecular clock hypothesis. 554–527 chromosomes see Chromosome(s) complementation tests. 348 see also Genome evolution see also DNA (deoxyribonucleic acid). 354. 451F. 256 abnormal pre-mRNA processing. 265F gene replacement see Transgenic organism(s) mutations. 565–566 inducible promoters. 256F genes see Globin genes homologies and evolutionary tree. 434F repressors see Repressor protein(s) transcriptional activators see Transcriptional activator(s) Genital ridge. 448F see also Eve (even-skipped) gene DNA sequences. 142. 860F. 207. 347 see also Splicing procaryotic bacterial chromosomes. 265. 246 human variation. 1282F gene insertion. 1322–1323 determinants. 564 protein sequence alteration. Spermatozoa Germinal centers. 252–253. 367 variations. 246 exon shuffling. 16F Gibberellic acid (GA3). 1287 as epigenetic phenomena. 264. 208F. DNA damage. 1172–1174 somatic nuclear transplantation. 253–254 gene number vs complexity. 472–473 insulin-like growth factor-2. 1323–1324 Vasa protein in determination of. 554F linkage analysis. 485F human see Human genome. 451F human DNA sequence. X-inactivation Genomic plasticity. 8. 245–260 accelerated change. 254F additions. 39–40 single nucleotide polymorphisms (SNPs). 559–560. 30–31. 565F sequence tags. with an FF to figures that follow consecutively. 348F Globin genes expression regulation. 570–571 see also Genome evolution transposon movements. specific techniques Genetic exchange. 555 mutant identification. DNA libraries completely sequenced organisms. 249–250. Gene expression. 785. 207 homology searches. 250 mammals. 528F see also Complementation tests reverse. 352. 383. 258 mechanisms. 1365F Germ-line DNA. X-inactivation Gene structure eucaryotic. 563–564. 39–40. 862. 433F. Genetic code mitochondrial see Mitochondrial genome mouse see Mouse multicellular development control. 451F. 199F. 556–557 behavioral. 323F mutations. 256. 554F historical aspects. 246 conserved sequence identification. 528F. 353F composition. 382–383 Candida CUG codon. 542 PCR cloning. energy reserves. 563. 18T complexity. 469–470 see also Gene silencing. 38–39. epidermal growth factor (EGF). antibody genes. 383. 367. . 247. 859–860. 1563F functions. 864F noncoding regions see Noncoding DNA variation in intron/exon length. 557F Genetic switches complex developmental. 452F Page numbers in boldface refer to a major text discussion of the entry. 250F. 32F organelles chloroplast see Chloroplast(s). 253. 208F. 199–200 codons see Codons DNA structure and heredity. Transgenic organism(s) germ-line mutations. 565–566 see also Egg (ovum). meiosis role. 251 minimal for life. 288. 347. 10. 545F. 470–471 gene numbers in different organisms. 450–451. 560F see also Genome evolution Genomic DNA clone. 248F human vs mouse. 447–448. 564–568 dominant negative mutant generation. b-globin abnormalities structure. nonconserved regions. 221F mating-type switching in yeast. Epstein–Barr virus (EBV). genome mitochondrial see Mitochondrial genome replication. 258 CG (CpG) islands. 566F germ cell gene insertion. 456. 957. 678 radial. Xenopus. 570 transgenic organisms see Transgenic organism(s) see also Genetics. Gamete(s). 564FF gain-of-function mutant generation. 12 Germ cell(s). 544–546. 248F human–mouse. 323F zebrafish. 407–408 reading frames. 1236F see also DNA methylation. cDNA. 247. page numbers with a T refer to a table.INDEX Gene repressor proteins see Repressor protein(s) Gene silencing CG (CpG) islands. 208F gene duplications. 247. 140 sequence analysis. 452 see also Thalassemia. 259F human vs chimpanzee. 542F vs. 541–542 see also DNA cloning. 246 conservation. 288F. 257 gene duplication see Gene duplication(s) genome duplication. 204–205 CG (CpG) islands. 560F mutation see Mutation(s) phenotype. Genomic imprinting. 553. 200F human vs mouse. genetic engineering. 439–440 mechanisms. 256F see also specific types b-Globin gene. Recombinant DNA technology. 31–32. 10. 250 transposons. 1254F DNA repair defects. 554F recombination see Recombination two genes or one?. 553. 368 universal. 569–571 Genotype. 542 human. 575 protein sequence alteration. Drosophila development. 532. 255 Genome instability DNA repair defects. 246. 469F. 95 Germ layers. 300–301 heterochromatin role. 554F linkage analysis. 11F minimum gene complement (Mycoplasma). Transcription. 508 Genetic diversity. 554F see also Meiosis heterozygote. 1214–1215. 355F chromatin structure. 418 see also DNA-binding motifs evolution. 247. DNA replication sequencing see Genome sequencing size variations. 39 Genetics classical. 323. 575 see also DNA cloning. 259 see also Genome sequencing sequence divergence. 432–454. 560F see also DNA sequencing Genetic mosaic. 367. 1406F Gibberellins. 951 Globin(s). 554F Geochemical energy. 348 losses. 1403 Gibbs free energy see Free energy Glandular fever. 206. 433–434. 258–260. 575 P granules role. 567F see also Recombination. 383 mitochondrial variations. in tree of life. 255 mutation see Mutation(s) see also Mutation rates neutral mutations. 384F see also Translation Genetic disease integrin mutations. 575 dominant negative mutant generation. 563–564 in vitro mutagenesis. 18T. 348 introns see Intron(s) pre-mRNA processing. 315F Genome sequencing. 11–26 duplication(s). 862T translational recoding. domain fusions. 2 not necessarily encoded in nucleic acid (prions). 368F redundancy. homologous recombination. conservation in. 1498 Genetic instability cancer. 200. 1385F Glioblastoma. 355F. 450–452. 323 see also individual species Genome evolution. 1236. 202. 553. 331F central dogma see Messenger RNA. 564–565. 249F. 1520–1521 Genomics comparative see Comparative genomics genome sequence analysis. 142 chromosomes see Chromosome(s) cloning. Human genome information coding. 452F see also Locus control region(s) gene clusters. 250. 1279F Genetic engineering. 195–196. 1271 Caenorhabditis elegans. 247 ancestor tracing. 1365–1366. 544 Genomic imprinting. 329. 315F Genetic mapping based on meiotic recombination. 250. 564F gene replacement. 257–258 organellar. 207. 1271. 295T from p53 loss after telomere shortening. 1383–1384 myelin production. retroviruses. 250 diversity. 1261 Glial cells. 1324 GFP see Green fluorescent protein (GFP) Giant chromosomes see Polytene chromosome(s) Giardia. 348F intron–exon organization. 457F tumor suppressor genes. 368. 572 site-directed mutagenesis. 575 reverse genetics. 305 Genetic information defining feature of life. 200 see also Chromosome replication. 383F. 553. 552 tagged knockouts. 861F protein module integration. 259–260. 200 Arabidopsis thaliana. 476–477 intracellular visualization see Fluorescence resonance energy transfer (FRET) structure. 771F. 888F. of epidermis. 904–921. 952F GTP (guanosine triphosphate). 635–636 cell–cell adhesion. 1490F. 1490F. 736–738. 91. 92F. 907F. 918. 775F. DNA repair defects. 1108. 773–775. 5¢ mRNA capping. Drosophila. 636 synthesis. 910T. 766–787 see also Endoplasmic reticulum (ER) transport through. 785. 92F. 1102 competition for. 905–906. 916 signal amplification. 1419. 490F functional role. endoplasmic reticulum (ER). 377F Guanine. 515F. 451. 1286F Gooseberry mutant. 747F Glycosaminoglycans (GAGs). 115F synthesis in ER. 1437. 919T Gq. 772 intestinal. 906–907 G12. 896F eIF-2 recycling. 412. 636. 949F Glycolipid(s) aggregates. 178–179. 722. 100F. 1307. 778F trans Golgi network (TGN) see Trans Golgi network (TGN) transport from ER. 824T see also Glycolysis structure. ATP hydrolysis. 1179. 452F pseudogenes. 754–758. 892. 896F GTP-binding proteins (GTPases). 178–179 structure. 197 base-pairing. importance. 91. 356. 1436–1437 development. 778F functional compartmentalization. 636 structure. 979. 121F. 760–761 Ran GTPase. 1460 Granulosa cells. specific factors Growth regulators in plants (plant hormones). 452F g-globin. phagocytic cells. 744–745 Glycolysis. 57. 1291F. 905F cyclic AMP and. 1404F Group I introns. 1440–1441. 1283–1285. 129F neurotransmitter role. 1337 Gp 120 protein. 904F. 179–180. 179. 905. 120–121FF see also specific enzymes evolution. 919T Golf. 657F. 1447F change of sensibilities. of transport through. 1110 mechanisms of action. 786F M6P addition. 920. 346. 102 Glucose disaccharide biosynthesis. 798 Glucose 6-phosphate. 798 Glucosyl transferase. 463F Glucocorticoids. 1043–1044 mitotic spindle formation. 180F microtubule association. 977. 759F trimeric (G proteins) vs. 1460T Granulocyte/macrophage CSF (GM-CSF). 896 see also specific GTPases movement generators. 594F gene expression regulation. 1165 compressive forces. 854 carbon-fixation cycle. G protein(s) (trimeric GTP-binding proteins/ATPases) GTP caps. 593F vesicular and intracellular transport studies. 89F. 807 protein sorting. 488–489. membrane organization. 771–773. 605. 722F Glypican. 766 antigen processing/presentation. 301F Guanine nucleotide disocciation inhibitors (GDIs). 772 cis Golgi network (CGN) see Cis Golgi network (CGN) cisternae. 1307F. 91. 742F. 906F bg complex. 463. 1145 inositol phospholipids and. 742–743. 1049F. 904. 129F Glutamine. 772. 709F. 121F chloroplasts. 1179F. 179. 731 exit face. 1098 enzymes. 1285 Sry gene and testes development. 1419F Granules. 774F. 896. 917 photoreceptors. 737F. 1573F Grb-2 protein. 256–257. 910F. 919–921 olfactory receptors. 628–629. 1291. retardation. 92F. 1571. protein tags. 585. 957–961 Growth. 806–807 synthesis. 129F Glutamine synthase. 1081 Ras GEF. 605F GroEL chaperone. 92F enzymes. 1434–1436 Golgi apparatus. 1430 Glucagon. 823. 808 structure. Guanine nucleotide exchange factor (GEF) trimeric see G protein(s). 1180–1181 protein attachment see Proteoglycan(s) proteoglycan production. 81F Glutaraldehyde. 91. 99F GTPase see GTP-binding proteins (GTPases) GTPase-activating proteins (GAPs).. 774F Golgi apparatus (Golgi complex). 777–778 volume. gene expression regulation. 889 see also Receptor guanylyl cyclases Guide RNAs. 907T desensitization. 98 protein phosphorylation. 1460T see also Basophils. 1461F Granulocyte/macrophage (GM) progenitor cells. 932F steering developing neurite. 120F Glucose transporter. 592–593. 911FF. 919–920. 362F RNA editing. 93F. 1386–1389. 920F Graft rejection. 917. 868 Glutathione S-transferase (GST). 356F Group II introns. 198F deamination. 777–778 transport to cell surface from. self-splicing mechanism. of olfactory bulb. 919T Go. 906–907. 697 proteoglycan assembly. transcytosis. 1402. 256–257 b-globin see b-Globin gene d-globin. Eosinophils. 778F cisternal maturation model. 906F downstream effects cAMP. 180F phosphorylation vs. protein folding function. 295T GSK3b. 179F. 179F. 1021 molecular compartmentalization. 1435F structure. of transport through. 1048. 56F.I:22 INDEX mucus secretion. 845F glycolysis. 91. 775–776 selective protein retention. 917–918. 710F Ras family see Ras GTPase(s) Rho family see Rho GTPase(s) Sar1 (vesicular coat assembly). 684. 684. 1180F see also specific types Glycosphingolipid(s) lipid rafts. 911F. 88–91 anaerobic. 777 position in cell. 909–911 on ion channels. electron microscopy. 785F GlcNAc phosphotransferase. 605. 178–181 cellular regulators. 979F GTP exchange factors. neuronal. 772. 88–89. 120F. structure. 112F transport. 920. 120–121FF Glycoprotein(s). 906F activation. 778F trans face (exit face). 896. 918F see also specific receptors G protein-linked receptor kinases (GRKs). 91. 779–787. 771–772. 753F Green sulfur bacteria. 765F GPI-anchored proteins see Glycosylphosphatidylinositol (GPI) anchor G protein(s) (trimeric GTP-binding proteins/ATPases). 179–181. 697T Gonad(s). 179. 1460. 905–906 inositol-phospholipid signaling. 89. 179 RhoA activation. 920F visual transduction. 115F membranes. 949. 256–257. 1440F cell turnover. 906–907. of plants. 347F Guanylyl cyclase regulation. 356F Growth cones. 637F Glycogen. glycosylation. 1583F cellular distribution. 776 structure. 950. 783–784 vesicular transport model. 905. 88. 1532 Granulocyte(s). 1184 Goblet cells. 1437 respiratory epithelium. Neutrophil(s) Granulocyte CSF (G-CSF). microtubules. 697T membrane proteins. 1298 Granzyme B protease. 854–855 Glyceraldehyde 3-phosphate dehydrogenase. 332 structure. 463F Gluconeogenesis. 463. 415. 1575 Gram-negative bacteria. 390F Ground tissue. 906F monomeric GTPases vs G proteins. 771F. 451. 928 Green fluorescent protein (GFP). 772. 334. 1179–1180 basal lamina. 799–809 see also Exocytosis transport to lysosomes. 1183 Glyoxylate cycle. 635 microtubule motors. evolution by duplication. 1435. 892. 1527 Gram-positive bacteria. 120F total energy yield. 484F Gut cell migration. 1460T. 846 carbohydrate source. 773 oligosaccharide chain processing. 301F RNA structure. 1527 Granular layer. 180F. 931 Guanine nucleotide exchange factor (GEF). 641. 57F oxidation. 691. 102F NAD+/NADH role. 1526F . 516F Glyceraldehyde. 94. 744–745 Glycosylation. 630. 1283. 731 structure. 722 Glyoxysome(s). 257 Glomeruli. 636.. 88–89. 776–777 proteins see Protein glycosylation Glycosylphosphatidylinositol (GPI) anchor. 89 pathway. 808 Glycocalyx. 180F see also GTPase-activating proteins (GAPs). 845. 807 cell-surface proteoglycans. 907T Glucocorticoid receptor protein. 759. 906 Gi (inhibitory G protein). 356. 873F Grids. 181 regulation. 483. 917–918 regulating ion channels. 905–908. 739 Glutamate (glutamic acid) neurotransmitter role. 1322F endocrine cells (enteroendocrine cells). 1109F see also Mitogen(s). 180F. 179. 756F distribution during cytokinesis. 1283F. 91 energy storage by reaction coupling. 88 metabolic interrelationships. 121F Glycine. 758–760 Rab family (vesicle docking). 905 a subunit. 708–709. 180F monomeric. 1095 Guanosine triphosphate see GTP (guanosine triphosphate) Guanyl transferase. 919T Gt (transducin). 94F Glycogen synthase kinase 3b (GSK3b). 1387–1389 Growth factors. 785 M6P receptor. 778 clathrin-coated vesicle formation. 906F. 112F Glyceraldehyde 3-phosphate. 628F side chain diversity. 919T inactivation. 605F Glutathione dismutase. 839 see also Fermentation(s) ATP production (net gain). 920F Flamingo proteins. 361. 778F membrane amounts. 696. 903F. 256F a-globin. glyceraldehyde 3-phosphate. 514–515. 1386F. development PGC migration. 854–855 energetics. 1389 collapse. 116F. gene expression regulation. 919T Gs (stimulatory G protein). 896 receptor coupling see G protein-coupled receptors (GPCRs) G protein-coupled receptors (GPCRs). electron transport. 893F. 218F Histone H2A. 725 Hepatocyte growth factor (HGF). 446F Histone H1. 1574F. 1453–1456 cell death in. 1462 commitment. 831 iron coordination. 523 High-mannose oligosaccharide(s). 697T smooth endoplasmic reticulum. 256–257. 804F secretion. 1454–1462 cell-surface markers. antibody molecule. 221. page numbers with an F refer to a figure. 1348 proteins (HSPs). 224–226. 256F gene homologies. 211. 212 assembly. 768 Heterozygote. Listeria monocytogenes. 691–692 HIS gene. 211F. 986 Hemoglobin (Hb). 211 centromere-specific variant CENP-A. 1270F. 1454 by apoptosis. 213. 343. 1593 dendritic cell activation. 1559F. 224. 406F Head polymerization. 214F identification. 1575 see also MHC (major histocompatibility complex) Histology airways. 1436. 941–942 Histochemical staining. 1431FF Hair follicle. 1396 Hedgehog protein. 216F Histone H3. 213 fold. 1505 Hepatocyte(s). 1171F intermediate filament attachment. 256F heme groups see Heme groups see also Globin(s) subunit interactions. 213F genes. 118F brown adipose tissue. 1543 rescue of irradiated individuals. 415. 128F. 238–239. 1574–1575. 1580–1581. lymphocyte origin. 1 see also Inheritance Hermaphrodite. 1592–1593 Page numbers in boldface refer to a major text discussion of the entry. 220–222. 562F Haplotype maps (hapmaps). 1554F constant domains. 238–239. 1593F type 1 (TH1). 1269–1271. 338. 1171F keratin filaments. 86. 1514F microtubule-based movement in axons. 1583–1585 B cell activation. 420F Helix–turn–helix proteins. 1371 Half-life. viral. 159 Hexoses. 1553–1557. 547F X-inactivation. 1436–1444 liver. 1514F envelope acquisition. 774F High-performance liquid chromatography (HPLC). Hemopoietic stem cells Hemopoietic cells. 1146 homophilic vs. 1552. 1553F Hippocampus. 289 histone octamer. 474–475 Heterochromatin protein 1 (HP1). 256F evolution. 238 Heterochronic genes. 306. 256–257 globin chains. 1581F class switching. 698F glucocorticoid-mediated gene expression. 1430–1432. 143F Hemolysin. 1598T immunological synapse. 325F Heteroduplex. 1442. 1326–1327. 166F porphyrin rings. 220 I:23 see also Centromere(s) dynamics. 1516–1517. 212. 831 Hemidesmosome(s). 1593F type 2 (TH2). 643. 224F see also individual histones Histone acetyltransferases (HATs). . 1557F Histidine. 145 double (DNA) see DNA structure handedness. 221F histone modification. 290 interactions. 1326F Heteroduplex joints. 412. 1458 gene therapy potential. 366. 1456–1458 see also Transit amplifying cells control. C. 1595F dendritic cell activation. 950 Hedgehog signaling pathway. 1574F. 1592–1594. page numbers with a T refer to a table. 67–68. 1563F IgM. 324. 314. 285 see also Gene silencing. 213 protein–DNA interactions. 238F organization. 425–426. 214F modifications. 1587F TH1 vs. 1598 cytokines. RNA. 1500 colonization of stomach. 1316F Drosophila. 585F Histocompatibility molecule. 561. membrane amounts. 358 Heterophilic binding. 1436–1444. 348F Hemopoiesis. 87F. 1458–1459. 830F. 231–232. 1434–1436 blood vessels. 804F. genome sequence. 511 Hebb rule. liver cancer causation. 34 Haplotype blocks. 1281 see also Meiosis yeast. 1254 Heredity. 343F Histone chaperones see Chromatin assembly factors (CAFs) Histone code hypothesis. 1353. 20 see also Globin genes iron coordination. with an FF to figures that follow consecutively. 1400 animal development. 1505 Hepatitis B infection. 579. definition. proton) Haemophilus influenzae. 804. 554F Hexokinase. 1456 commitment. 388 see also Chaperones. 774. 1505 Herpes virus(es). 1568 cytokine production by. 1458 see also Hemopoiesis Hemopoietic tissues. 1337. 1543 Hemorrhagic fever. meiotic recombination. 426F Helix–turn–helix motif. 1456 see also Erythropoiesis. 74 Heat-shock induced somatic recombination. 643F Heterochromatin. 220–222 replication.. 420. 1593F TH1 vs. Saccharomyces cerevisiae. 601T Halobacterium salinarum. glutamate receptors. 216F variants. 69F. 314F Heterogeneous nuclear ribonucleoproteins. 804. 1436F Vibrio cholerae colonization of. 1170. 212F S phase. 425–426. 1070 inheritance following replication. 804. 1585–1586. 120F. 226F Histone deacetylases (HDACs). 218. 1135T. 1260 Hereditary nonpolyposis colorectal cancer (HNPCC). 950 absent in Arabidopsis. 881. 212. 609F. 1417–1428 gut. 1556 mast cells. 1353F in gut. 285F Histamine. 21F cooperativity. 1443 Her2 protein. 285 short tandem repeats. protein–protein interactions. 290–291. 212–213 structure. 1592–1594. 403F Hairy gene. 277. 1227T Hepatitis virus(es) chronic illness. 214F synthesis in S phase. 1557F release. 1272. 220 gene expression regulation. 1502 Heparan sulfate. 1443–1444 electron micrograph. 1456 pluripotent. 213 modification see Histone modification mutations. 1583–1585 antigen recognition. mutations. 1496F assembly. 166..INDEX 1437F histology. 232F H H+ (proton) see Hydrogen ion (H+. 1503 genome size. 561–562. 212F evolutionary conservation. 1426 Hairpin structures. radioisotopes. 419–420. 1574F. 212. in. 212. 1570. 305F. 1559 variable domains. 1134F. 1516F Hes1 gene. 1426 Helicobacter pylori chronic illness. 221F position effects and position effect variegation. 1593F TH2 vs. 463 organelles. 1321 Herpes simplex virus (HSV). 256. 1462 by colony-stimulating factors. 509F. 144F. 1574–1575. 1442–1444 sensory epithelia. 1500 liver cancer and. 1592 activation of macrophages. 1575. equilibrium sedimentation. 1511–1512 Hemophilia. 1555F repeating domains. 421F structure. 290 analysis. 166F structure. origin of lymphocytes. 211 H2A dimer. 143 properties. 1597T selection in thymus. in tree of life. 452–453 gene silencing. 1134. 838 enzyme catalysis. 830F. 1575. 1070 biological functions. 1592–1594. 291F in vitro mutagenesis. TH2 choice. 157F. 1503 activation of B cells. 922. 1558–1559. 1229 Helix common molecular structure. 1429. 214F modifications. 222. 1487–1488. 1449 Hematoxylin. 221F X-inactivation. vs means compare/comparison. 1560F gene segment pool. 1458F division rate. elegans. 353F. 513 Hinge region. 420F sequence recognition. 290 interactions. 1227–1228 receptors. 220–221 centromeric (centric). 220. 1445–1450 epidermis. 166F. 551–552 Hair cells. 1340. 1558–1559. 195 defining feature of life. 1418F. 601. T cell(s) Hemangioblastoma. 142–143. 1138F Heterotypic membrane fusion. 1371 Heterocaryon(s). 1450–1463 in bone marrow. 1594–1595. 1593F see also CD4 T-cell(s). 474–475 Histone H2B. 640–642. 1445–1450 endothelial cells. 1461F lineage diagram (scheme). 1560F Heavy isotopes. 221. 289–290 variants. 1459–1461 multiple control points. Insulator elements heritability. 1559F. 420F DNA-binding motif see Helix–turn–helix motif homeodomain proteins see Homeodomain proteins Helper T-cell(s) (TH). 213F. 238–239 multiple forms. 211–216 addition to DNA (postreplication). specific proteins see also DNA repair Heavy (H) chain (antibodies). 445. 1457F from multipotent stem cells. 211 H2B dimer. 562 HATS see Histone acetyltransferases (HATS) HDACs see Histone deacetylases (HDACs) HDV fold. 585F Heme groups. 224F. 143. 1227–1228. 1456–1458 dependence on stromal cell contact. 1441 in skin. 1429–1433 Histone(s). 18T stomach cancer causation. 212.. 1228. 554–555. 34 in sexual reproduction. 640F Haloferax.. 1144F. 426F Helix–loop–helix proteins. 1574F. 146F Helix destabilizing proteins see Single-strand DNAbinding proteins (SSBs) Helix–loop–helix motif. 373 Heart muscle see Cardiac muscle Heat energy. in cancer therapy. 166. 1535–1536 receptors. 1461–1462 Hemopoietic stem cells. 16F Haploid state diploid state vs. 112F High-density protein arrays. 1456 self-renewal. 420–421. 1496 MHC class I protein translocation inhibition. 548 Histidine-kinase-associated receptors. 256–257. 1597–1598 CD4 co-receptor role. 1574F. 1183 Hepatitis. 585. 1450–1463 bone marrow. 222. 307F base-pairing. 311. 509F Hydra. 1520–1521 Nef protein. 291F variants. 1520 evolutionary innovation. 306 meiotic recombination. 142. 306. 412. 205–207. 238F Histoplasma capsulatum. 1505F drug resistance. 388. 1274F transverse filaments. 1355 HPLC (high-performance liquid chromatography). 247. 248F. 1521F HLA (human-leucocyte-associated) antigen see MHC (major histocompatibility complex) HLA-DM protein. 1275 nondisjunction. 388. 306–307. 225F interactions. 226F transcriptional. 293F complexity. 486. 41 mitochondrial. Hox genes Homeotic mutation Arabidopsis. 716F. 1274F. 21–22 antigenic variation. 302–303. 305F. DNA double-strand break repair. 1275. 251F Huntington’s disease. 384F vaccine development. 1236F. expression in mouse. 304–316 biological functions. 556 Human genome. 1179. X-inactivation. 785 Hyaluronan (hyaluronic acid. 383. 305F common features. 1505F regulated nuclear transport. 389 Hsp60 protein. 1090. 1092F. 323F mobile elements. 1517 virus-induced metabolic changes. 425F homologies. 509F Hybridization. 623. 765F co-receptors. 1280F chiasma formation. 313–314 recombination complex. 1275 meiotic pairing. 390F Hsp60 protein. 304–305. 283 t-loop. 432F chromatin remodeling. 71F. 290–291 interactions. 1506F membrane traffic and pathogen strategies. 1346F sequential gene expression. 311F Homeobox genes see Homeotic (homeobox) genes Homeodomain DNA-binding motifs. 312 gene conversion. 310 regulation. 21F Homologous recombination (crossing-over). 308 Holliday junctions see Holliday junctions hybridization (synapsis). 560 Hurler’s disease. 1180–1181. 478. 315F double-strand break repair. 429 plants. 222. 205–206 comparative. 1391 Horizontal gene transfer. 426–432. 287–288 replication rate. 1271. 203FF chromosome 12 translocation. 485F. 205–206. 206T. 343F histone deactylase complexes (HDACs). 1280 non-crossovers. 213. 138F. 227–228 hsp40 proteins. 204F chromosome 22. 1507–1511. 225. 1271. 20–21. 1274. 1276F bivalent formation. 882 gene expression regulation. mitochondrial protein import. 475 Histone H4. 485F transcription attenuation. 253 Human genetics.” 310. 1276. 765F. 554F Homunculus. 308–309. 397. models. 1273–1274. 532 see also Human genome Human immunodeficiency virus see HIV Human papillomavirus. 486F microtubule-based movement in axons. 623F Hydrogenation reactions. 312F double branch migration. 1274. 1494. 323 see also Mobile genetic elements see also Noncoding DNA genes. 187F. 187. 797 chemokine receptor binding. 314 genetic diversity and. 1280 proteins. 1502–1504 antigenic variation. 214F modifications. 223F polytene chromosomes. 485F. 1521. 1276F double strand breaks. 343 histone acetyl transferases (HATs). 472F histone code hypothesis. 415. mitochondrial protein transport. 1343–1344 Drosophila see Drosophila melanogaster homeotic genes family members in different eucaryotes. 486F Rev responsive element (RRE). 211 evolutionary conservation. 1280 regulation. 205F. 1269F Hydride ions. 222F chromatin immunoprecipitation analysis. 306F strand invasion. 420–421 DNA-binding. 303 Homologous genes. 1581 cancer and. 1137–1139 heterophilic vs. 1274F. 310–311 “repair factories. 209F sequencing. 205–206 composition. 485–486. 19 Hormones. definition. 202. 305. 1519–1520 Housekeeping genes. 1274–1275. 1274F. cervical cancer. DNA see DNA hybridization Hybridomas. 1505–1506. 861–862. 311. 785 Huntingtin. 290–291. 463. 1502–1504 intracellular parasites. modification to facilitate pathogen spread. 19F. 1180F Hyaluronidase. 421 isolation. 541. 218F modifications. 1414F Hox complex see Hox complex see also Homeodomain proteins. 1505. 1342F Homing receptors. 1342. 217–218. 207. 1406 HNPCC see Hereditary nonpolyposis colorectal cancer (HNPCC) hnRNPs. 106F. 1507 multivesicular bodies. 343. 248F Human Genome Project. 20F. 205F. 1338F. 16F Humoral immune response. 305F. 432. 1525–1526 evasion by pathogens. 764–765. 1277F nondisjunction. 207F. 1521F HIV-2. 307F strand exchange see Holliday junctions strand invasion. 312. 1138F Homo sapiens see Humans (Homo sapiens) Homotypic membrane fusion. 1091–1092. 265 H3 tetramer. 314. 290–291. 1092. electron carriers. 1276. 1276F crossover control. 222. 1271. 291F variants. 1488 transcription shut-down. 314. 443FF. 1271. 207F Alu elements. 321–322 phylogeny reconstruction. 1280 genetic diversity and. 1552–1568 see also B cell(s). 1521 life cycle. 485F receptors. 485F. 768. 1277F see also Homologous recombination (crossing-over) meiotic segregation. 1228T cell entry and uncoating. 717 Hsp70 protein. 1346F HOX code. 1276–1278. 1343F insect and mammal compared. sequence comparisons. 1494F HIV (human immunodeficiency virus). 314 crossover interference. 389. 1275. 1280 double Holliday junction. 1278–1279 Homologous end-joining. 1274–1275. 486F Tat protein. 246 Homophilic adhesion. 1496F. 432. anteroposterior axis determination. 1274F. 1504–1505 bacteria.I:24 INDEX Drosophila. 308F heteroduplex joints. 205F replication origins. 205–206. 513 HS4 protein. 1508F. 142. 1274F. hyaluronate). 206T see also Gene structure genomic DNA library. 1501–1502 epithelial surfaces. 1399 Wuschel. 251F scale. 485–486. 1348 see also meiotic recombination (below) mechanism base-flipping.. 1276F synaptonemal complex. 1511–1514. 205–206. 485F. 212. 1271 axial cores. 449F Hunter’s disease. 222. 542F individual variation. 321F. 308. 421F. 72 H4 tetramer. 226. 475 Histone modification. 305 control via mismatch correction. 310F evolutionary benefit. 358 Holliday junctions. 532 size. 1279F morphological changes. 1280 Spo11. 202. 224–226. 142. 485. 1521 fusion peptide. 226F. 353F. 717 HTH motif see Helix–turn–helix motif Human accelerated regions (HARs). 206T regulatory. 206. 312F gene conversion. 312. 305 see also Linkage analysis. Immunoglobulin(s) Hunchback protein. 1550 Homologous chromosomes (homologs). 40 in tree of life. 1521 see also specific types HIV-1. 222–224. 430F evolutionary conservation. 1278–1279 pairing sites. 769F Homozygote. 223F acetylation/deacetylation. lymphocytes. 1518 Host cells invasion by pathogens. 420–421. 1345. 1342–1346 Hox complex anteroposterior axis determination. 206T gene organization. 138. 1236F. 1410F Homeotic (homeobox) genes. 1274 sex chromosomes. 1509F evasion of defenses. 508–509. 421F see also Homeodomain proteins Homeodomain proteins. 305 genetic exchange/assortment. 290 amino acid side chains. eve gene activation. 433F functional roles epigenetic. 1342–1346 expression in mouse. 472. asexual reproduction. 309F defects. 448–450. 715. 1341–1347 chromosomal ordering in Hox complexes. 20F. 1501. 463F see also individual hormones Host behavior. 305F. 420. 1498F. 312F RecA. 861F nonretroviral-like retrotransposons. 212. 222. 314–315 isomerization. 390F Hsp70 protein. 434. 1181 Hybrid cells hybridomas see Hybridomas production. 321F Rev protein. 307F. 420–421 heterodimerization. 1517–1518 Host defenses. 206T chromosomes. 1508–1511 viruses. CG (CpG) islands. 307–308. 443F. 1511F response to pathogens. 206 size. 247F. 295T heterozygosity loss. 206F. 1400T flower development. 1279F heteroduplex. 303F. 1505–1506. 486F reverse transcriptase structure. Meiosis Homology. 138F. 1274. 1279–1280. diversification and origin. 1275–1276. 1269. 1343–1344 Hox genes. 420–421. 290–291 histone code hypothesis. 1505–1506. 1413–1414. 1279–1280. 313F double-strand breaks. 206 structure. 1275F telomeres and. 82 Hydrocarbon(s). 470 HoxB complex. 318T. 1517 mutation rate. 206. 1413F . 18T Human Genome Project. 304–305. 478 translational frameshifting. 1499 Humans (Homo sapiens) genome see Human genome as model organism. 206. 314F hot spots and cold spots. 1346F expression pattern in Drosophila. 312–314. 1507 genome. 446F histone tail modification. 1275 synapsis. 1275. 224F. 1506F. 214F. 305–306 branch migration. 473–476 DNA methylation. 232F. 503F fluorescent labeling. 688 Initiation codon. 588–589 immunoprecipitation. 704 chromatin structure. 1501–1502 signs/symptoms. 596 movement. pathogen-associated. 786 Hypothalamus. 52 exchange. 1540. 398. 1487–1488 see also specific infections/organisms Infectious mononucleosis. 1059 see also Cell cycle control Immortal strand hypothesis. 127. 1573. 164–165 Hydrolytic editing.. 1557F Immunoglobulin fold. 598F monoclonal antibodies. 1571 peripheral. 1319–1320 see also specific signals Infection(s) as carcinogens. 1527. 1368F sequential. 768F in vitro via hybridomas. 953 IkB protein. 1568F evolution. 1554F. 1425F Immune complexes. 1548F self. 1559. 721 Hydrolysis. 198F. 1530 see also Phagocytosis Immunoblotting. T cell(s) innate. 509 avidity. 1559F. 1145. 157F. 1591 B cells/helper T cells. 1548F Immunoprecipitation. 835. 1552–1568. 154F protein structure. 140 structures. 1547. 1301 Inflammation/inflammatory response. 1548. 1557T allergic reactions. 1534–1536 Toll-like receptors role. 417 protein–DNA interactions. 929 Immortal cell lines/immortalization. 1547–1549 acquired. 300. 588F Induced proximityy. 1356F Imago. 1521. 140F light (L) chains see Light (L) chain (antibodies) paired domains. 1526–1527. Proton pumps pH measurement. 1524 recognition of pathogens. circadian clock. 828F Hydropathy plots. 519F Immunoglobulin a (Iga). 1555F. 606–607. 508–509. 675 ball and stick model. 1541–1542. 467F histone modifications. 372. 1554F hypervariable region. 111F. 1553 histamine secretion. 866 ‘Protein-only inheritance. 618. 1563. 1540FF adaptive vs. 1567. 1555F. 431–432. 1531 function. 1557T affinity. 502. 621F see also Water Hydrophobic chromatography. 52. 13FF Hydroxyl ion. 100F intracellular ion concentration. 1552F. 380 Innate immune response see Immune response/system. 1524. 1557T class switching. 1599F alternative splicing. 157F. 702. 1559. 1564–1565 immunoglobulin a (Iga). 341 Initiation factors (eucaryotic) see eIFs (eucaryotic initiation factors) Initiator tRNA. 1521 cell entry. 1313 gastrulation role. 1539. 130F in water. 1555. 1588 clonal deletion. 257F immunoglobulin fold. 1501–1524 chronic diseases. 1557 monoclonal see Monoclonal antibodies responses. 828. 1–5 non-Mendelian. 291F information transmission. 1563FF. 156. 108F. 1349–1351 growth control. 1560F immunoglobulin fold. 866F maternal. 1560F class switching. 1556FF. 765 entry and uncoating. 588. 1587–1588 receptor editing. 1546F see also specific types structure. 1 see also Inheritance Inheritance. 1597T signal-relaying junctions. 52. 606–607. 1560–1561 Ig domains. 1485. 154. 489–491 Initiation complex. 1507 microtubule-based movement in axons. 1546F Immunological synapse. 588 immunoelectron microscopy. 1499–1500 intracellular pathogens see Intracellular pathogens response to see Host defenses. 110F Hydrogen ion (H+. 1124–1125 Inhibitory G protein (Gi). 584F Imaginal discs. 1560. 54F bond length/strength. angiogenesis activation. 1539. 110F aquaporin(s). 587F. 57F. 1540. 1554 transmembrane. 402–403. energetics. 380. 950 IkB kinase (IKK). 1552F. page numbers with an F refer to a figure. 1557T class switching. in development. 461 Hypoxanthine. 1558 applications cell separation techniques. 370 segments. 1488 Imprinting see Genomic imprinting Inclusion-cell disease (I-cell disease). 1599F Immunoglobulin superfamily. 633F Hydrophilic molecules. 1517 pandemics.hydrolysis sugars. 372F Hydronium ion. . 401. 1559F. 1552. 1146–1147 I:25 b2 integrin ligands. 1183 Inflammatory mediators. 130F protein–ligand binding. 1159 I ICAMs see Intercellular cell adhesion molecules (ICAMs) IFNs see Interferon(s) IgA see Immunoglobulin A (IgA) IgD see Immunoglobulin D (IgD) IgE see Immunoglobulin E (IgE) IgG see Immunoglobulin G (IgG) IgM see Immunoglobulin M (IgM) IHog protein. 621F proteins. 197–198. 1553 class switching. 381 Hydrophobic molecules. exon recombination. 506T. 1562. B cell development. 1418F Hypopigmentation (albinism). 953 ILs see Interleukin(s) Image processing electron microscopy. 1553 Immunoglobulin D (IgD). 1557F class switching. 432F microinjection. 1599–1600. 290–291. 367F. 1227 cell biology. 432. 141 tail (Fc) region. 1562–1569. 1506F. 607F immunofluorescence microscopy. 1496F. 1187F Hydroxyprolines. 1533–1534 Influenza virus(es). 1540FF MHC proteins see MHC (major histocompatibility complex) Page numbers in boldface refer to a major text discussion of the entry. 195 epigenetic. 950 Indirect immunofluorescence. aminoacyl-tRNA synthetases. auxin transport. 230–234. 52. 1560F binding sites see Antigen-binding site gene-segment pool. 1526–1528 response to viruses. 1147F see also Immunoglobulin(s). 1556. 1539. 866. 620. 56. 1559F. 1221. 53. 1329 Immature naive B cell.. 1174 cell adhesion. 1558 classes. 12. 1553 Immediate early gene(s). 906–907 Inhibitory postsynaptic potential (IPSP). 620. 109F gradients to drive ATP synthesis. 1599F immunoglobulin b (Igb). innate Innexins. 1424–1426. transmembrane protein(s). 1599F Immunoglobulin b (Igb). 1557T. 1599F membrane-bound form. 959 Information transmission defining property of life. 1563F heavy (H) chain see Heavy (H) chain (antibodies) hinge region. 1557T see also specific types class switching see Class switching diversification. 301F Hypoxia. 467–468. 1567 heavy chain. 1527 Immunosuppression. 1522F Influx transporter proteins. 1547. 109F Hydroxylysines. 1553–1557. 632. 85F ATP see ATP hydrolysis macromolecules. 417. 618. 512 Hydrophobic interactions. 1567 heavy chain. Immunoglobulin(s). 1556. 1552–1561. transcriptional. 1353–1354 wing imaginal disc. 1553F.’ yeast. 1567 structure. 1146–1147. 8 molecules DNA see DNA (deoxyribonucleic acid) origin of life. 1561F Immunoglobulin-like domain. 785–786 Indian Hedgehog protein. 1553F Immune response/system adaptive. 518. 1448–1449 primary vs secondary. 109F. 1566F post-transcriptional regulation. 458 Immunostimulants. 126. 1 energetics. 583–584. 1558F. 1599 Immunoglobulin M (IgM). antibody. 1349F Inducible promoters. 597. 1554–1556. 1548. 1560F.INDEX Hydrogen. 564 Inductive signals. 1553–1554. 46F Hydrogen bonds. 1499 Infertility. 1559 synthesis in endoplasmic reticulum. atomic structure. 1526. 1553. 1560–1561 Hypodermis (subcutaneous layer). 610–612 light microscopy. specific members Immunogold electron microscopy. 835F see also Electrochemical proton gradients. 1348. collagens. 54. 1534F proteoglycans and. SMN protein mutation. 1526–1527. 1559F. 509F see also B cell(s) Immunoglobulin A (IgA). 588. 1568F complement activation. 1540F primary and secondary. 1418. 53T DNA structure. 607FF Immunological memory. 108F. 828F Hydrogen ion pump (H+ pump) see Proton pumps Hydrogen peroxide. 1546 see also B cell(s). 1599F Immunoglobulin(s). 185–186 Induced somatic recombination. 1533–1534. 257F genes gene-pool selection. 398F Inherited spinal muscular atrophy. 84–87 nucleotide see Nucleotide(s). 108F. 108F. 1548F nonactivated dendritic cells. 1187F. 390–391 see also Water Hydrothermal vents. 1524–1537. 153. 1190 5-Hydroxytryptamine (5-HT) see Serotonin (5-hydroxytryptamine. 502 FACS. 587F. 1540F complement system see Complement system innate vs. 1546. 1542F. 502. 1132 Immunological tolerance. 1186. 291. 1527 evolution. 1545 cell-mediated vs antibody. 1557T B-cell development. 417F protein folding. 364–365 Inhibitors of apoptosis (IAPs). 1553 Immunoglobulin E (IgE). 865F chloroplast(s). 1177T synapse formation and. page numbers with a T refer to a table. 402F RNA see RNA (ribonucleic acid) quantification. peroxisomes. 504F. 1546F. 1540FF elicitors. 1147–1148 evolution. tuberculosis. 1554F. 140F Immunoglobulin G (IgG). Immune response/system route. 1558–1559. 5-HT) Hypervariable region. 827–828. 199F. 1221 Hypoxia-inducible factor 1 (HIF1). 864–865. 1186. vs means compare/comparison. 1547F autimmune regulator (AIRE) protein. with an FF to figures that follow consecutively. 1. 596 water. 1567 heavy chain. proton) acids. 1540. 432F. 983 isoforms. 1511F lysosomal fusion prevention. effects on. 1118 Interleukin-2 (IL2). 573F fluorescence (FISH). 1329 Insulator-binding proteins. 1418–1419 Interleukin(s). 452–453. 47. in cancer. chromosome puffs. 1386F Internode (plant stem). 349. 1508–1511 strategies against host membrane traffic. 1584. 1406F Interfollicular epidermis. 1103 phosphorylation cf GTP-binding. 984 properties. 1591F Interleukin-2 receptor. 972F global distribution. 668 gating. 830F. 534F protein purification. 1174 bacterial invasion and. 1431. 1594. 910F phosphatidylinositol 4. 1511F. 239 Instars. 206T length variation. 1288 looping. 1431F ligand-gated see Ligand-gated ion channel(s) mutations. 668F. 1428 mutation and genetic disease. 1134. 968F. 1593. 1511–1514. 910. 965 role in cell division. 53T covalent bonds vs. 1477 Integrase. 893. 831. 1596F Invariant pocket. 597F microinjection. 1575. 1170F adhesion junctions. 177F. 1133T. 1146 inside-out activation. 353F optional. 1595F. 453. 206 group I. 1171. 1508 bi-directional signaling. 598–599 visualization electroporation. 408 In vivo. 983–985. 757. 917 Ion-exchange chromatography. 1174 b3 integrins. 667–669 transport efficiency. 26 Internal ribosome entry sites (IRESs). 1593 Interleukin-17 (IL17). 1512. 1171F Interaction domain(s). 1174–1175 counterreceptors. 596. 985–987 organization. 1171F see also Desmosome(s) assembly. 598. 966–967 structure. 217F Interference effects. 934 receptor. 598F radioisotopic tracing. 668 conformational changes. 596. 1079 Intervening (DNA) sequences see Intron(s) Intestinal defenses. 551 Invariant chain. Chromosome structure. MHC protein. 1593F. 334. 596. 1512F movement using actin polymerization. 235F. 1513–1514. 324. 318T Inosine. 933 cellular location. 651F. 680–682. 575 In vitro RNA selection experiments. 235F polyteny. 1176–1177. 217. 1177T actin linkage. 911FF egg activation role. 5-bisphosphate [PI(4. 667 voltage-gated. 1176F mitogens. 1143. 1176F in mammary gland. imprinting. 1175F clustering and strong adhesions. 1501–1502 see also Drosophila melanogaster Insertional mutagenesis. 581. 1598T receptors. 365F Interdigitated solenoid model. 352. 1512 modification by bacteria. 652T Intracellular movement. 1534–1535 interferon-b (IFNb). 880F. 596–597. 597–598. 1591F see also specific interleukins Interleukin-1-converting enzyme (ICE). 556 see also Transposon(s) In situ hybridization (ISH). 238F lampbrush chromosomes. 469–470. 1460T. 667. 897 Intercalary regeneration. 363–364. 208F.. 1514–1517 Intracellular pathogens. 598F GFP. 681FF selectivity. 484F Inositol 1. 983F subunits. 318T lambda integrase. 652T see also Electrochemical proton gradients membrane channels see Ion channel(s) see also specific ions Ion channel(s). 1461F . 1171–1172. anchorage dependence. 1093 Interphase chromosome(s). 152F receptor. 911FF see also Phospholipase C see also specific types Input–output devices (“microchips”). 668F cyclic-nucleotide-gated. 452F. 1170F. 1598T Interleukin-5 (IL5). 318T. 985 keratins see Keratin(s) lateral bundling and twisting of coiled coils. 1536 interferon-g (IFNg) cytotoxic T-cells. 1526F Intracellular compartments. 209 chromatin organization. 1021–1022 see also Cytoskeleton. 1579F Invasin. 348 fate signals. 111F bond length/strength. 627F. 538F Intron–exon recognition. 897F threshold-like response. 241F. 1174 diversity of function. 234. 1354F Intercellular cell adhesion molecules (ICAMs). 5)P2]. 1301–1303. 353F splicing signals see Splicing signals see also Splicing sequence ambiguity.intracellular Intracellular signal molecule(s)/pathway(s). protein kinases. effects on. 243 see also Heterochromatin histone modifications. 1144. 668. 830F. 910F. 909. 535F Ionic bonds. 1444F Insulin-like growth factor-1 (IGF-1). 1302F Intragenic mutation(s). 1299 membranes. 356F group II. 692T function. 319F In vitro. 1172F b1 integrins. 238. 898F signaling proteins. 1511–1512. 1244 retromers. 1354. 894F. 452–453. 910 Inositol phospholipid(s). 602–603 see also Radioisotopes see also Fluorescent dyes Intracellular receptors see Nuclear hormone receptor(s). 1512F modification by viruses. 1134. 1504–1505. 246–247 Inverted repeats. 597F. 1419 Ion(s). 984FF mechanical stability. 234F. DNA-only transposons. 1005–1006 polypeptide structure. 1192 heterophiilic binding. 1169. 900–901. 1170–1172. 491. 592–593 see also Green fluorescent protein (GFP) ion concentration. 863 protein evolution role. Receptor(s). 1080 stress fibers. 910F. 1598. 572–573. 1534–1535. 1302. definition. 236F. 48F protein folding. 325F Integrin(s). 966 elongated. 1172 intracellular signaling. 356. 1598T Interleukin-13 (IL13). 984. 1175–1176. 897. 1511F escape from phagolysosome. 1511F. 798. 356F human genes. 971 Internal membranes. invasion of host cells. 863 organellar. specific molecules signal integration. 794 Iron–sulfur center. 470F Integra (skin substitute). 257 removal by RNA splicing. 910F.5-triphosphate (IP3) IRESs see Internal ribosome entry sites (IRESs) Iron–copper center. 130F Ionizing radiation. chromatin structure. 1508 Inversion(s). 901F tyrosine phosphorylation see Tyrosine kinase(s) see also Signal transduction. 1144F. 757F. 984F cellular location. 897–899 see also Signaling molecule(s)/pathway(s). 1515–1516 parasites. 1504–1505 entry/exit from host cells. 756 signaling pathway. 1514F survival in phagolysosome. 909–911. 893 signal enhancement. DNA-damaging agents. 1172 structure. 1173T. 111F aqueous solutions. 1169 cell migration and. 1593. 1173T. 1591F. 411. 831 IS1 transposons. 480 Intron–exon mapping. 369F. 151. 1592 T-cell development. 236–238 see also Cell cycle. 47 concentration. 923T. 750–766 see also Organelle(s) Intracellular ion concentration(s). 1593F. 5-triphosphate (IP3).4. 901F second messengers. 923T. 924 secretion (b cells). 682 patch-clamp recordings. 1076F. 1594 Intermediate compartment see Cis Golgi network (CGN) Intermediate filament(s) anchoring junction attachment. 356. Motor protein(s) Intracytoplasmic sperm injection (ICSI). 695–748. 1173. 1593. 923F. 966 dynamic behavior. 1592T Intercellular gene transfer see Horizontal gene transfer Interchromatin granule clusters (speckles). 1172. Cyclic-nucleotide-gated. 1145 allosteric regulation. 404F. 1174F fibronectin binding. 1172–1174 outside-in activation. 897 signaling complexes. 1398F. 1075. 1172F tension effects. cytochrome oxidase complex. 145. 1422F b2 integrins. 1172–1174. bacteria and viruses. 924 Insulin-like growth factor-2 (IGF-2). 1146. 582F Interferon(s) interferon-a (IFNa). 345–346. 968. 1577–1578. 696F endocytic pathway. 177–178 see also Protein kinase(s) integrins. Polytene chromosome(s) Interpolar microtubules. against pathogens. 1460. cell signaling. genome evolution. 484. 512. 1407 Interphase. 144F proteolytic cleavage. 179F Insect(s) as vectors for microbial pathogens. 453F Insulin. 916 families. 1422. 180F tyrosine residues see Tyrosine kinase(s) see also Protein kinase(s) positive feedback. 352–353. 753F membrane-enclosed organelles. 234–236. 1055 chromosomes see Interphase chromosome(s) microtubule dynamics. 1170. 1176–1177. 1582 TH1 cell secretion. 1302F In vitro mutagenesis. specific molecules/pathways Intracellular transport GFP-fusion protein studies. 894F input–output devices. 910F. 1595F. 597F. 514F matrices.I:26 INDEX Interleukin-4 (IL4). 1598T viral infections. 1598T Interleukin-10 (IL10). 528F. 347–348 order. 19F Intron(s) evolution. 1513 Intracellular processes manipulation. 911F phosphoinositide 3-kinase. 1297. 206. 1172. 923F. 1591F Interleukin-3 (IL3). 832–834 Iron. 1444. 491F. endocytic uptake. 241. 1169–1178. 597F IP3 see Inositol 1. 624. 205F. 503–504 Involucrin. 358 gene structure. 1592. 667–692 abundancy. 852 Iron–sulfur proteins. 300–301 see also Ultraviolet (UV) radiation Ionotropic receptors see Ion channel(s) Ion-sensitive indicators. 1591. 758F phosphatidylinositol (PI). 743. 1517 Interneurons. definition. 453F Insulator elements. 798F. 1170–1171 cell proliferation and survival. 751F maintenance. 1598T Interleukin-12 (IL12). 893–899. 18. 4. 177–178. 503–504 In vitro fertilization (IVF) and related procedures. 676–678 see also individual types Ion channels. 924. 369. 1193 fibronectin fibril assembly. 213. basal lamina. 1552–1553. 1040 cell crawling. 1085–1087. 406F Ligation DNA cloning. 1076F meiosis I. Anton van. 1174 Leucoplasts. 1174 migration from capillaries. 1228T Kartagener’s syndrome. chromatin condensation effect. 1153. 1508 Legionnaire’s disease. 1033 Karyotype. 204. 952–954. 1556. 599. 272. 305F Junctional complexes. 1014F ATP hydrolysis. 324. 1427F Lactose permease. 1454F integrins. 1422. 1038F. 1089 Page numbers in boldface refer to a major text discussion of the entry. 276F end-replication problem. 1475 deficiency. 438 lac gene regulation. 1085F. 425F Leucocyte(s). 1451–1453 Leucocyte adhesion deficiency. 267–268. 502. 1530 Notch. 1016–1019 linker region. 1488 Lens(es) electron microscope. 1038. 986F a-keratin. 1076F. 295T Lex A protein. RNA structure. 528F Lethal toxin. 141 Krüppel mutant. 604 light microscope. 1. 1560F J Jak (Janus kinase). 1451. 1529 trans-Golgi network. 234F. 1251–1252. 950 Left-right asymmetry development. 1556F IgM. 937–939 J (joining) chain IgA. 1020–1021 Kinetochore(s). 808 Lectin complement activation pathway. 582F see also Light waves Lepromatous leprosy. 956. 1075–1076. ER retrieval pathway. 1350F Laser capture microdissection. 1329. vs means compare/comparison. 770 Knockout animals see Gene knockouts K-Ras gene. 522F Isoleucine. 1148–1149. 153 see also Substrate(s). 1555F Joint molecules (recombination) conservative site-specific recombination. 1014. development. 1288 Langerhans cell see Dendritic cells Lariat structure. 1084. 1277–1278 microtubules attachment. 325F synapsis. 418T. 448–450. 461F Lamellipodia. 140F. 280. 1014F Kinesin superfamily see Kinesin(s). 449F Kupffer cells. 1558–1559. Drosophila. 1088 structure. 436F see also Repressor protein(s) Lac repressor. 636 mannan-binding. 418T synthetic biology. 540. 1439F Latrunculin. 272 see also DNA ligase(s) Light (L) chain (antibodies). 1512F transmission. 947F Drosophila sensory bristle development. with an FF to figures that follow consecutively. 1275 Let7 gene. 423. 501F LEF1/TCF gene regulatory proteins. 269F. 203 analysis. 9F. 1164F. 1444. 1086 spindle assembly checkpoint. 56 amino acids. 599F Late genes. 403F Kit protein. 1167 Kinases see Protein kinase(s) Kinesin(s). 268. 1581. 457–458. 490 Lectin(s). 949F NFkB. 1168 structure. 420F synthetic biology. 939T Janus kinase (Jak). 949F LDLs see Low-density lipoproteins (LDLs) Leading strand synthesis (DNA replication). 123F Isocitrate dehydrogenase. 646F Lateral inhibition Delta–Notch signaling. 1016 mechanochemical cycles. 1431F neurotransmitter-gated see Transmitter-gated ion channel(s) Ligase fold.enzyme binding Ligand-gated ion channel(s) ion-channel-linked receptors. 1419 control of differentiation in culture. 418T gene regulatory protein. 264 two-signal switching. 949. 1021 central core and force generation. Motor protein(s) Kinetics enzyme catalysis see Enzyme kinetics motor proteins. 1452F types. 145 Keratin filaments. 1592T Life. 1554F. 995F. 1008 cell adhesion. wnt signaling. 281F RNA primers. 1511F. 996 actin gels. 541F lagging strand synthesis (DNA replication). 1164–1165. 347. 458F DNA sequence recognition. 281F ligation. 1376–1377 Lefty1 gene. 1000. 1298 mitotic. 985–986. 1385 Islets of Langerhans. 1076F tension. domain fusion. 9F. 248F. 1036F cofilin in. 1020 structure. 1453–1454. 268. 1219 chronic myelogenous see Chronic myelogenous leukemia (CML) DNA repair defects. 1083F Kinetochore fiber. 9F. 1001F KDEL sequence. 1529 Leeuwenhoek. 946–948 K Kaposi’s sarcoma. 1554. 770. 418T DNA looping. 1454F inflammatory response. 937–939. 210. 1508F strategy against host membrane traffic. 1419F Keratinocytes. epidermal prickle cells. 1529 glycocalyx interaction. 272F Lakritz mutant. 203FF human. 1453T adhesion to endothelial cells. 1558F constant domains. Kinesin-related proteins (KRPs). 418T. 1037F a-Ketoglutarate. 1508. 1084F forces acting on. 1165 Junk DNA. 841 Leukemia B lymphocyte leukemia. 416. 770 Keratan sulfate. 1077. 128F sugars. 1439–1440. 1590F see also Src family of protein tyrosine kinases LCRs see Locus control region(s) LDL-receptor-related protein (LRP). 1330F imaginal discs. 1082. 1357–1358 Wnt-Notch signaling. 1014. 501. 1476F gene sequence comparisons. structure. 1086F. 1037 actin filament nucleation. 123F Ketoses. 1476F function/effects. 348F. 1252T. 953F. 1082–1083 bipolarity. 1255 Krebs cycle see Citric acid cycle Kringle domain. 1040F. 416 DNA sequence recognition. 556 Lambda bacteriophage see Bacteriophage lambda Lambda repressor. 988T Lck. 424F. 1166 laminin-1 (classical laminin). 272 Okazaki fragments. 1148F. 1038F growth cones. 418T discovery. 1059 Lac operon (Escherichia coli). 436F CAP activation. 601. 1154F cell proliferation and. 1475–1476. 129F Isomers. 1016–1017. 1418F. 1564–1565 Junctional epidermolysis bullosa. 1020 processivity. 271–273. 123F a-Ketoglutarate dehydrogenase complex. 1018F microtubule-binding site. 1 autocatalytic process. 1453–1454. 946–954 Lateral diffusion (membrane proteins). 1499F I:27 proteolysis. 122F. 1037. 461F see also Repressor protein(s) Lactate production. 1327 Lethal mutation(s). 1038F Laminin(s) basal lamina. 1155F isoforms. . 442F Leydig cells. 416. 269F. 1593–1594 Leprosy. 1149F see also Scaffold protein(s) Junctional diversification. 1041 web formation by ARP complex. 1458. 1453. 1388 NMJ. 203F muntjac deer. 1557T. 1165–1166 mutations. structure. 601T radioactive see Radioisotopes Izumo protein. 1014F see also individual kinesins Kinesin-related proteins (KRPs). 90 see also Glycolysis Lactation. 1443F Kuru. 436 lac repressor see Lac repressor mutations. 285–286 Latent gene regulatory proteins b-catenin. 234. 1040F. 1508 Leishmaniasis. 1475–1476 Leptogene. 581–582. 269F. 1166F Lampbrush chromosomes. 1035F. 112F Kidney glomerulus. 272F. 271F. 892. 1228. 1167F epithelial apico-basal polarity. 1034. 249F secretion from fat cells. 267. page numbers with an F refer to a figure. 267F. 272. 205F see also Mitotic chromosome(s) Katanin. 204F. 1285 LFA1 (lymphocyte-function-associated protein 1). 276F Leaky scanning. 985T. 1083F. 658F Lagging strand synthesis (DNA replication). 350F Larva (Drosophila). origin. 1049 movement mechanism. 268F. 235F. 1512–1513. 995F mitotic spindles. 521F. 1337 Krüppel protein. 956F Leucine. 937–939 Jak-STAT signaling pathway. 420F. pre-mRNA splicing. 946–947. 1179 Keratin(s). 1076. 1079. 503F Laser tweezers. 521. 1167 neuronal guidance role. selective protein retention. 99. monosaccharides. 1008. 1039 ruffling at leading edge. 1377 Legionella pneumophilia invasion of host cells. 657. 731 Kissing hairpins. 112F Isotopes. 1015–1016 force generation. 1–11 Ligand(s) ion channel opening see Ion channel(s) protein binding sites. 527. 938F. 2D-PAGE. 1454F structure. antibody gene segment joining. 1593–1594 Leptin. 1166–1167. 123F Isoelectric focusing. mitotic spindle. 1165–1166 collagen binding. 1375. 1016 evolutionary origin. 643. 948–950. 1431. 1458F KKXX sequence. 129F Leucine zipper proteins. 1014. 1018F axonal transport. 7F universal features. 1493 Leucine-rich repeat (LRR) proteins. 1426 migratory. 416 helix-turn-helix motif. 1419. 1014F microtubule disassembly. 1037–1038 organization cf. 1444F Isocitrate. 122F. ER retrieval pathway. 860 see also Noncoding DNA L L1 elements see LINE (L1) elements Labeling index. 1349. 1427–1428. 292 see also Telomerase eucaryotic. 1082F movement speed. 987. page numbers with a T refer to a table. 893F mechanically-gated.INDEX Islet gene. 1084 Kin recognition. 1153–1155 organization. 1343F extended germ band. 1145 complement activation. 783. 1452–1453. 1453T activation. 744F see also Phospholipid(s) asymmetry. 1544 dependence on innate immune system. 1434–1436 Toll-like receptors (TLR). 888 foam cells. 787. 780F structure. 580–583. 458F Lysosomal hydrolase. 1199T Limb buds (vertebrate). 84–87 shape specification. 584F diffraction effects. 867 see also Fat(s). 1186. 791–794. 583 fluorescence see Fluorescence microscopy history. 63F. 621–624. 1543–1544 clonal selection. 306F see also DNA hybridization enzyme–substrate interactions see Enzyme–substrate interactions hydrophobic interactions. 623F origin. 1036 effect of NO. synaptic control. 1531–1532 antibody-activated. 1414 Magnesium. 1460 lineage and formation. 1511–1512 invasion of host cells. plant cell wall. 557–558 Loss of heterozygosity (LOH). 1550. 1593F. 1511F hemolysin secretion and action. 743–745. 1442–1444 cancer. 1507–1508. 781–782 see also Lysozyme Lysozyme catalysis. 94F. 1592T Lymphocytic choriomeningitis (LCM) virus. 63. 626–627. 1549F. 1541F central. 790 Lipopolysaccharide (LPS). 582F. 584F microscope. 651 black membranes. 172FF Linker DNA. 323F see also Repetitive DNA Linkage analysis. 630 Lipid bilayer(s). 617–629. 581. Lymph node(s). 1560F variable domains. 1088. 780F transport from endosomes. 164F. 165F disulfide-bonds. 624 see also Lipid bilayer. 1541F. 85F energy requirements. 1460T macrophage production role. 638 b-Lipotropin. 55F. 1595F lipopolysaccharide. 63T protein subunits. 56. 97F. 763F. 652 domain formation. 956F L-selectin. 1355F. 450–452.I:28 INDEX g-Lipotropin. 621–622. 791–792. 1575. commitment to lymphoid pathway. 583. 1549. 779–780 fusion with phagosomes. 1540. 1533 receptors. 64F subunits. 1530F recruitment of cells. 764 membrane protein association see Membrane protein(s) mobility. 148–152 see also specific types Macrophage(s) activation. 211 Linker region. 583 interference effects. 1452 HIV infection. 742–743. 1456–1457 homing receptors. 322F human genome. 1229 cells see Hepatocyte(s) structure. 1555F. phage lambda. 987 Low-density lipoprotein (LDL) receptors. 1156F Locus control region(s). 779–780 degradation pathways. 583 phase. 164–165. 1326F Lineage tracing. 1516F escape from host phagolysosome. 1560F Light energy. 848F Light microscopy. 87F cell chemistry. 1480. 791–792. 62F. 848. 697T yeast vacuoles. 1326 Lin14 gene. 1550F Luminescent molecules. 604F phase-contrast see Phase-contrast microscopy resolution. 582F. 598–599 see also Photosynthesis Light-harvesting complexes. DNA methylation. 696. 1196. 625. 956. 559–560 gene localization. 803F Liquid chromatography. 335–336 mammalian vs bacterial cells. 907T. 1120 effector cells. 1541–1542 immunological memory. 522 Listeria monocytogenes actin-based movement. peripheral. 1559. 1206F Lysine. 697T plant vacuoles. 580. 452. 652 relative permeability. effect. 1508. 783F. 1374F Limb regeneration. 795F. 164F see also Lysosome(s) generation of diversity. 295T non-Hodgkins. 1508 Mad2 protein. 792. 1480F Lim gene. 1322. 583F. 620F. 625F. 144F. 1490F immunostimulation. 1155–1156. 786 function. 1558–1559. 781F melanocytes. 581–583 3-D imaging. 84–87 orientation. protein–ligand interactions. 779–787.. 598–599 Lignin. 1500 Lymphatic vessel. 1434–1436 Luteinizing hormone (LH). 780F acid hydrolases. 626 spontaneous formation. 12. 158F protein–DNA interactions see Protein–DNA interactions protein–ligand interactions see Protein–ligand interactions see also specific methods Macromolecule(s) assembly. 1527 macrophage activation by. 1543 recirculation. 128F. 625F assembly. 1446 Lymph node(s). 452F Long interspersed nuclear element see LINE (L1) elements Long-term depression (LTD). membrane proteins. apoptosis. 1532 phagocytosis. 560F gene mapping. 1508 Lithotroph(s). 1515F. 781–782 proton pump. 626F synthesis. 782. 1443F Lkb1 gene/protein. mouse genome. 589–590 confocal microscopy. 624F diffusion. 1550. 584F darkfield. 115F. 622F. 1531 tuberculosis. . 784FF maturation. 784F distribution. 1514. 627 see also specific kinases Lipid raft(s). 1581 interleukin secretion and sensitivity. 786 Lysosomal storage diseases. 1546 T cell development. 554–555. 1551F Lymphocyte(s). 1507–1508 Salmonella enterica. 590. 780–781 exocytosis. 579 image processing. 592F image deconvolution. 581F. 583–584. 796F from Golgi apparatus. 791F. 1527F Liposome(s). 318T. 786F Lysosomal secretion. 1548 hemopoietic stem cells. 1546 origin(s). 581F. 620–621 structure. 807F assembly. 115F bilayer formation see Lipid bilayer(s) cell membrane(s). 407F permeability. 793F Lox recombination element see Cre/Lox system LPS see Lipopolysaccharide (LPS) LRR (leucin-rich repeat proteins). 786 membranes. 653F signaling. 582FF contrast generation. 548. 63–64. 15F Liver. 15. 1512F phagosomal membrane destruction. 62F composition. 1512–1513. 161. 783–784. 1227–1228. 1549F see also B cell(s). 1145. SNARE proteins. 579. 1562–1566 repeating domains. 691. 1593–1594 lifespan and turnover. 1500 function. 582F. 1551F Lymphoid organ(s). 581–582. 1292 Lyme disease. Caenorhabditis elegans. Membrane(s) droplets. 622. 559–560. 807. 1511 volume. 1434–1436 NADPH oxidase complex. 1549–1551. 115F aggregates. 310. 559–560. 1540–1551 adaptive immunity. 622. 621F fusion. 1543 peripheral. 1195. 156. 624. 62–63 abundance. 1511–1512. costimulatory signal. 791F Low-density lipoproteins (LDLs). 86. 1546 naive cells. 590F brightfield. 625F membrane protein solubility. spindle assembly checkpoint. long-term potentiation. 1534 apoptosis. 1543–1544 tolerance. 1555. 785F. newt. 1400T. 69F. 590 electron microscopy vs. 622. 609F sample preparation. 1322F LINE (L1) elements. 583 contrast generation. 510–511 interactions see Macromolecular interactions polymerisation. 780. 585F Light waves. 784F material import. 1117 cell crawling. 1531–1532 intracellular digestion. 171–172. 1385 Lin4 gene. 1434–1435. T cell(s) Lymphocyte-function-associated protein 1 (LFA1). 1016 Lipid(s). 148 functions. 148 cell fractionation. epithelial apico-basal polarity. 1594–1595 helper T-cells (TH). 1553F see also Bone marrow. 584. 163–164 structure. 1557T Mycobacterium tuberculosis. 405–406. 1540–1541 B cell development. 583F. 1546 general principles. 1543. 631. 1460–1461 Macropinosomes. 1516. 618F. 560F see also Homologous recombination (crossingover) Linkage. 691 Long-term potentiation (LTP). 1543F central vs. 617–629. 626F barrier function. 1543. 785–786 Lysosome(s). specific types Lipid anchor(s). 527 Maintenance methyltransferase. 9. 624–625 fluidity. 691 Magnetic tweezers. 1088F Mad cow disease see Bovine spongiform encephalopathy (BSE) MADS box gene regulatory proteins. 1496F Lymphoid follicles. 621–622 Lipid kinase(s). 58. 779–780. 1548 cytotoxic. 458. 207F human vs. 803F M M6P see Mannose-6-phosphate (M6P) Macromolecular interactions DNA–DNA interactions. 591. 1550 memory cells. 581F. 1593–1594 see also Antigen-presenting cells Macrophage-colony-stimulating factor (M-CSF). 582F momentum. 111F noncovalent interactions. 742F caveolae formation. 528F. 1598T leprosy. 1187F Lysis/lysogeny. 622–624. 1550. 1530F structure. 1531–1532 respiratory tract. 1457F lung. 1236 Lou Gehrig’s disease. 652F. 625–626. 148–152 biosynthesis. (kinesin). 596–597 Lung(s). 622 composition. 620–621. 1512F receptors. Thymus Lymphoma(s) Burkitt’s see Burkitt’s lymphoma DNA repair defects. 1541F. metastasis. 321–322. 788F. function. 585. 692F Loss-of-function mutation(s). 785F Trypanosoma cruzi invasion. 583 differential-interference microscopy. 779–787. 334 cap snatching. 1206 Melanosomes. synaptic plasticity. 123F Malate dehydrogenase. 866 Mathematical modelling. 1376F regulative properties of early embryo. 1107 Mechanoreceptor(s). 1273F kinetochores. 624 principles. 318T. 1286 genetic diversity and. 846 Messenger RNA (mRNA). 26. Lipid raft(s). intracellular pathogen strategies. 866. 1517 degradation. 1022F. 554F. 1271. 1074–1075. 1356F Mef2 genes/proteins. 418T genetic conservation. 1307F. 1272–1281 checkpoints. 169. 520F tandem. 671 Membrane protein(s). 990F M-Cdk. 1427–1428. 1091F. 930 NGF effects. 1023–1024 lysosomal exocytosis. 859 mRNA editing. 1546. 1273–1274. 1022. 331. 1059 Mammalian development. 645. 617–649. 1553 Mbl protein. 1297 Marker genes see Reporter gene(s) Mass spectrometry accuracy. specific types/locations Membrane attack complex. 1280. 1280–1281 timing differences. 1278–1279 evolutionary conservation. 456 Mata2 protein. 750–766 principles. 929F MAP-kinase signaling pathway. 1307. 461 Melting temperature. 485 gene expression regulation. 697T intracellular pathogen strategies. 10F see also Active transport. 1278–1279 lampbrush chromosomes. 1090–1092. 630 diffusion. 537F Membrane(s) composition fatty acids. 697T pancreatic exocrine cell. 1381–1382. 456 Maternal inheritance chloroplast genome. 1059F chemical composition. 1517 localization. 1280. 651–692 impermeant molecules. 519–521 Mast cells. 492F RNA interference. 1409–1410. Plasma membrane. 135 transmembrane see Transmembrane protein(s) see also specific types/proteins Membrane shuttle. 1391–1393. 519–520 Matrix metalloproteinases (MMPs). 763F. 1495F spread. 1105. 643F. 958 see also Ras GTPase(s) MAP-kinase-kinase (MAPKK). 866F mitochondrial genome. 821F resting. 804. individual lipids lipid to protein ratio. 617–648. Protein translocation. 1557F interleukin secretion. 1411F Major groove recognition. 653. 419F DNA-binding proteins. 1413 maintenance. 669. 455–456. 803F Melanoma. 642–645. fertilization in. 645F see also Lipid bilayer(s). 1511F liver cell (hepatocyte). 1194 Matrix receptors. individual species Mammalian genetics gene control regions. 1427F basal lamina. 346F. 630F amounts. 929FF. 784 Membrane trafficking. 1280–1281 sex differences. 783–784 lysosomal sorting. 1292 regulation. 646–648 structure. 1277–1278 prophase I stages. 455–456. 457F. 645. 742–743. 234F meiosis I. 1378–1383 branching morphogenesis (of lung). 1277F. 455–456 Mating type (yeast). 457F Mating-type switching. 1281F see also Mitosis Meiotic recombination see under Homologous recombination (crossing-over) Mek kinase. 1280 meiosis II. 425F. 1074. 1099. 742F integral. Channel protein(s) Memory B cells. 34. production. 1276–1277. 1468 Mesenchyme. 522 MALDI-TOF. 519–520 Malignancy see Cancer Mammalian cell(s) cell culture. 1103 see also specific components MAPs see Microtubule-associated proteins (MAPs) Maps (brain). 1087. 1074F entry into mitosis. 929F Erk. 517 Meristem(s). 1511–1514. 482–483 see also Polyadenylation (mRNA 3¢ end) 5¢-caps see 5¢ Capping of eucaryotic mRNA cDNA clones. 929F Melanocytes. 1169 integrins see Integrin(s) Mature naive B cell. 1278 mitosis vs. 755. Vesicular transport viscosity. 597–598 I:29 see also Membrane transport. 1403 apical see Apical meristem flower. 1106F. 544 editing. . 1410–1411. 464F Megakaryocytes. 621–622 fusion. 1418F fish. 1074 microtubule dynamics and. 520F protein analysis. 289F. 1277F oocytes. 1494–1495. 667–692 see also Membrane potential fluidity. 645F multicomponent complexes. 35F Mating factors (yeast). cells. 1078–1079. 769F intracellular. 697T strength. 1101 Mdm2 protein. 123F MALDI-TOF mass spectrometry. 936F EGF effects. 1427F myoepithelial cells. 768. 697–698. 510 electrical properties. 1269. 1092. 1273F. 1380–1381. 1468 Mesenchymal stem cells. 651–692 carrier proteins and active transport. 379F. 1455. 492–493 nonsense-mediated decay see Nonsensemediated mRNA decay pathways. 1278. 866 Mesenchymal cells (“immature” fibroblasts). 669. with an FF to figures that follow consecutively. 1290. circadian clock. 450–453 gene regulatory proteins.. Ion channel(s) vesicular traffic see Vesicular transport see also Active transport. 487F nuclear export see under Nuclear–cytoplasmic transport processing see RNA processing (eucaryotic) splicing see Splicing Page numbers in boldface refer to a major text discussion of the entry. 1068 M-cyclins. 1426–1428. 636–640 structure. 458F see also Gene conversion. 519 liquid chromatography combination. 1091F. 1001. 58–59 lipid(s). 1396 b-Mercaptoethanol. 491. 631F cell surface exposure. 1091F. 930 plants. 484 replicative senescence. 1059. 1529F Membrane potential. 423. mannose-6-phosphate (M6P) receptor(s). 956. 419. 820–821. 1428 development and regression cycles. 929F evolution. 1392–1394 Marfans syndrome. 757 proteins see Membrane protein(s) disruption. 35–36. 1501–1502 see also Plasmodium falciparum Malate. 1362 Mata1 protein. 651 intracellular. Protein transport of small molecules. 486–487. 468–470 Mammary gland alveoli. 1024F Melatonin. Channel protein(s). 519–521. adaptive immunity. 786F receptors. 929. 122F. 928–931. 1598T Master regulatory proteins. 671F. 956. 646–648 endoplasmic reticulum. 39–40 imprinting. 1529 Mannose-6-phosphate (M6P) lysosomal import. 468 glycosylation. page numbers with a T refer to a table. 1382F early stages and extraembryonic membranes. 1288. 629–630. 419. 636 lipid-linked. 63T DNA replication. 418T. 1556 histamine secretion. 929FF MAP-kinase-kinase-kinase (MAPKKK). 1280. 1451. 543F. 1379–1380. 1409–1410 MERRF. 1274. 468–487. 1453T. 487–488 3¢ end generation. 1380 see also Mouse development. 1365. 629–649. 929FF. 483–485 expression levels. 865F. 1163 regulation by CLV1. 1001F MAP-kinase(s). 1275–1276. 618F see also Lipid bilayer(s) transport across. 630 interchain disulfide bonds. 1080 Mcm proteins. 1427F Mannan-binding lectins. 764.INDEX 467 Maize. 9–10 Thermotoga maritima. 1410F plasmodesmata. 281F. Platelet(s) Meiosis. 1276F specific protein complexes. 755. 928. 1278 meiotic S phase. human cell types. 357F. 412 internal ribosome entry site (IRES). 1276–1278. 695–736 see also Endoplasmic reticulum (ER). mechanosensory bristles. 455–456 Mating-type cassette. 1272–1274. 1190–1191 Marine invertebrates. 629 association with lipid bilayer. page numbers with an F refer to a figure. 1064. 1392F retinotectal. 642–643 peripheral. 928–931. 1403 size. 1529. 644 solubility. Phospholipid(s). Carrier protein(s). 1546 Memory cells. 1141 Mesoderm. 1090–1092. 669–671. 1272. 1445 Mesophyll cells. 519–520 membrane composition. 989. 1281 errors. 995F. 1511F Membrane transport importance. 357–358. 630 single-particle tracking. 492. 420F see also DNA structure Major histocompatibility complex see MHC (major histocompatibility complex) Malaria. 283–284 mitochondrial DNA. 617–629. 1335. 1273F. 821F mitochondrial inner membrane. Protein sorting. 1080 spindle assembly role. 1279F homolog pairing see under Homologous chromosomes (homologs) homolog recombination/crossing-over see under Homologous recombination (crossing-over) homolog segregation. 1379F embryonic stem cells (ES cells). 785. 1511–1514. 635–636 glycosylphosphatidylinositol anchor. 929. 16F. 177F neuronal. vs means compare/comparison. 630 localization. 1381F left-right asymmetry. 786. Gene silencing Matrix-assisted laser desorption ionization–time-offlight (MALDI-TOF) spectrometry. 419F. 495 eucaryotic. 846 Mesophyll (parenchyma). 784F Mannose-6-phosphate (M6P) receptor(s). 1195. 456F. 629 phosphoinositides. 1454. 456F. 1062. 651–654 of proteins. 1079F. 1495. 957F sequential development. 1546F Memory. 1376–1377. 4. 644 see also Lipid bilayer(s). 786 melanosomes see Melanosomes Melanocyte stimulating hormone (MSH). 415. 804F. 1457F see also Blood cells. 491F. 1062. 424F helix-turn-helix motif. cell cycle analysis. 1090 micromanipulation experiments. 784 structure. 784 MAP2 protein. definition. 1090. 1066 activation by dephosphorylation. 929. 1071. 1391F. 315–316. 16F Methanococcus. 823–824 historical aspects. 969 configuration. 100 organization. 315F Mismatch repair. 1095–1097. 1220. 1249 monitoring. 1003 cell division and. 875F bacterial resemblance. 488 function. 1201 dynamic instability. 336. 637 Michaelis–Menten equation. 1583–1585 recognition by coreceptors. 1581–1582. 965 structure. 816F mitosis. 1581F expression on viral-infected cells. 996 bundle of actin filaments. 501. 874. 1080. 1084F spindle formation. 965F accessory proteins. 585 fixation. 1535–1536 structure. 66F. 1579F T cell interactions. 815. 579 cell cycle analysis. organization by MAPs. 815–827 apoptosis role. 1580T. 1122F. 16F. 860F. 1397F. 1190–1191. 1501 pathogenic see Pathogen(s) see also Bacteria Microdissection techniques. 1035F. 18T Methionine. 1535–1536 nonclassical. 1486. 1580T. 745 see also Mitochondrial protein import lipid import. 487. 867F cardiolipin synthesis. 1571 H-2 (histocompatibility-2) antigen. 66F regulation. 1081. 974–975. 1577–1578. 992F. communication with actin cytoskeleton. 1584–1585 specificity pocket. 1511F Microsurgery. 1510–1511. 315F Mismatch proofreading. 66. 1581. 581F sample preparation. 1250 local invasion/invasiveness. 815–827 citric acid cycle see Citric acid cycle electron transport see Mitochondrial electron transport chain(s)(s) energetics. 1220. 1121. 971 treadmilling. 1054. specific pathways Metabolic rate enhancement. 1583F recognition by coreceptors. 1581F structure. 101. 838–839. 995F. 579.nucleation. 511 cell metabolism. electron microscopy. 981F. 585F scale. 975–976. 380. 1047–1048. 699. 1250F ECM degradation. 470 DNA methylation. 1097F instability/dynamics. 1194. 277F. 992. 1206F. Translation Metabolic balance. 1014F mitochondria association. 1008F Mid-blastula transition. 1577F. 1071. 1075–1076. 1329. 1035. 726. 1516–1517 plant cells. 468 Methylation DNA see DNA methylation histone tails. 1200–1202. 243. 1048F Golgi apparatus organization. 1427. 868F cell aging. 347F Met repressor. 859 fractionation. 1575. 1577 peptide loading. 1220 barriers. 1220. 492. 1014–1015 see also Kinesin(s) Microtubule flux. 383 see also Transcription. 395 Methylated DNA binding proteins. 1001. 1577–1578. 381F. 1197–1198. 1579F. 467. 1079 see also Mitosis. 1121F. 276–278. 101–102 tissue differences. 1048F nucleation. 554–555. 585. 1325 Microtome. 1298. 583–584. 585. 362F see also Methyltransferase(s) 5-Methylcytosine. 169–171. 493–495. 1201F plus and minus ends. 1577–1579. 102 rate increases by multienzyme complexes. 491. 180–181 translation signals. 621F. 1580F see also Protein–protein interactions polymorphism. 585. 586F Microsome(s). 1580–1581. 27–28. 816F translation start sites. 1577–1578. 598F MicroRNA (miRNA). 1075–1077. 169 Metabolism. 346F. 1517 see also Protein synthesis. 696. 1250 mutations leading to. 1085F. 1588 restriction. 1066. 982F. 605 staining. 1577 subtypes. 596 Microfibrils. 102 Metabolic map(s). DNA methylation. 467F structure. 859–860. Ribosome(s) Messenger RNA–transfer RNA interactions. 277–279. 815. 1097–1098. 974. 10. 620. 1034 pathogen movement based on. 857. 1200F. 423. 102F Metabolic pathway(s) enzyme catalysis. production and secretion. 1576F. Translation Messenger RNA–ribosome interactions path through. 1365 Midbody (cytokinesis). 379–380. 168–169 regulation. 428F deamination. 976F interpolar. 969 see also mitosis (below) cell polarization. 992 see also Centrosome Microvilli actin filament nucleation. 492–493 transfer RNA interactions. 301F. 610F Metamorphosis. 1061. 424F Miranda protein. 1581F. 1083F. 380. 376 bacterial mRNA. 380 untranslated regions. gene conversion. 514 Metal-shadowing. 1087 Metastases (secondary tumors). 1206. 1352 Metaphase. 301F Methyltransferase(s) DNA see DNA methyltransferase(s) 5¢ mRNA capping. 295T see also DNA repair disorders Mitochondria. 1579F subtypes. 1578. 1250 easy and difficult steps. 423F MHC (major histocompatibility complex). 635 biogenesis. 980. 1094. 1046 endoplasmic reticulum organization. 1080 see also Mitotic chromosome(s) Metaphase plate. 858F heat production. 856. 820 see also ATP synthesis evolution. hypervariable (VNTRs). 992. 659 structure. 973. 609. 1124F. 1588 invariant pocket. 1086F. 969. 66 activated carrier molecules. 102 catabolism see Catabolism cooperation. 870–872 interrelationship. 1585–1586 transplantation reactions. 1085 Metaphase-to-anaphase transition. 162F Microbial flora normal. 867–868 localization. 1076F chromosome effects on. 976–982. 726F Microsporidia. 1085. 975 see also Microtubule(s). 379–380. 995F assembly. 1577–1578. 270F strand-directed mismatch repair. 969. 815–816 import into. 974–975. 1574F. 968. 270. 1569–1589 T cell selection. 819F oxidative phosphorylation see Oxidative phosphorylation respiratory enzyme complex. 503F Microelectrode(s). 277F dysfunction and cancer. 129F Methionine aminopeptidases. impermeant molecules. C. b sheet motif. 102FF see also Biosynthesis. 1220. 585F Microtubule(s). 223F rRNA. 67F. 1094F Migration see Cell migration Milk. 1197F Microfilaments see Actin/actin filaments b2-Microglobulin. 1576F peptide-binding. 978F properties. 605. 1406. astral. 1221F. 1569–1589. 1021. 1576F MHC class II. MHC protein/antigen interactions. Drosophila. 585. 547F Microscopy. 381F bacterial Shine–Dalgarno sequence. 1571. 1072F chromosome movement. 1579–1580 dendritic cells. 1021 growth rate of plus/minus ends. 1599F coreceptor recognition. 974F see also Tubulin subunits. 79F anabolism/biosynthetic see Biosynthesis balance. 1581–1582. 1575. 102 see also Metabolic pathway(s) Metal affinity chromatography. 1096F.I:30 INDEX class restriction. 1082. 1220. 346. 97F. 1249–1250 process (steps). 1086 chromosome structure. 1021 fibroblasts. 570–571 Minor groove-binding. 1080. 1221F Methanobacterium. 1193. elegans. 585. 361. 1361 Mismatch conversion. 501F image processing. 1085. 1081F kinetochore attachment. DNA-binding proteins. 376F ribosome binding-site. 302–303 exonucleolytic proofreading. intracellular ion measurement. 336T localization by the cytoskeleton. 1583. 243F microtubule dynamics. 511. 868 growth and division. 272 deaminated methylated cytosines. 1581F peptide loading. 272. 856F. 1080 Microtubule-dependent motor protein(s). 1046 cellular location. 1576. 101. 222. 1575 human genes. 277–278. 993 depolymerization. 1081F centrosome role. 1599F coreceptor recognition. 168–169. 29F. 1089. 1579F MHC class I. 494F Microsatellite DNA. 700F. 170F evolution. 580F in situ hybridization. 1298F membrane transport. 867–868. 1581F recognition by natural killer cells. 1581. 1121. 502. 511. 817 oxidation of food molecules. 605F sectioning. 579–591 electron microscopy see Electron microscopy historical aspects. 857–858. 1576F . 79–86. 554–555. 1577. 970F egg (ovum). 1002F capping. 295–296. 1123 b barrel proteins. 1014–1015 see also Kinesin(s) neurons. 819F high-energy electrons. 491F. 1576F. 1035. 580. 1125F membrane potential. 585F. 1580F Microinjection. 977FF Microtubule-associated proteins (MAPs). 817F see also Cell fractionation genome see Mitochondrial genome glutathione peroxidase. Mitotic spindle motor protein types. 115F. 1220. 488 internal ribosome entry site (IRES). 1022–1023 polyadenylation see Polyadenylation (mRNA 3’ end) procaryotic. 1118 protein release. Catabolism. 1089 Microtubule-organising center (MTOC). 1098 DNA see Mitochondrial genome energy conversion. 375F. 868 cell-free systems. 819. 839F distribution during cytokinesis. 866–867. 1575. generation. 1575–1576 Micelle(s). Tubulin bundles. 1082F cytokinesis and. 1059 cell structure analysis. 102F. 67F. 968F. 381F. 1194F entry into circulation. 1575. 1250F colonization of distant tissues. 1427F Minimum gene compliment. 838 high ATP:ADP ratio maintenance. 597–598. 1578F. 584F light microscopy see Light microscopy resolving power. 1035F kinesin binding site. 488 ribosome interactions see Messenger RNA–ribosome interactions splicing see Splicing stability. 29F. 180–181 see also Transfer RNA (tRNA). 1085–1087. 1054. 245–260 clock hypothesis. 75F Molecular motors see Motor protein(s) Molecular switches. 838 redox potentials. 895. 866 Mitochondrial diseases. 865F. 1103. 1075–1076. 1055F. 1077. 715. 208F. 864–865. 831–832 transport across. 1386F Motor protein(s). 819–820. 834. 717. 814. 831. 1335F Drosophila wing imaginal disc. 323FF DNA transposons. 865. definition. 508–509. 859–860. 816. 861F maintenance. 484F structure see Mitochondrial structure superoxide dismutase. 1079. 243. 1042–1043 in vesicular coat assembly. 25 Arabidopsis. 1054 assembly. 1078F. 819. 710–712. page numbers with an F refer to a figure. 861F mutations. 388F Mom (more mesoderm) mutants. Eve gene. 1074–1075. 759–760 see also individual proteins Molecular weight. 858 evolution. 856–857. Virus(es). 588F. 857 volume. 1089 unattached chromosomes and. 1065–1066. 1072FF anaphase. 1099 Cdk inactivation. 1035F instability. 1077–1082. 250F. 836 protein import see Mitochondrial protein import protein synthesis. 43F yeast. 36–37. 1099–1100 APC/C and completion. 1070 condensin role. 248F Molecular mimicry. vs means compare/comparison. 1080. 1080. 713 membrane composition. 827F. 818F. 247. 509F in cancer therapy. 1079 assembly. . 1501–1502 Motor neuron(s). specific mitogens Mitogen-activated protein kinase(s) see MAPkinase(s) Mitogen-activated protein kinase signaling see MAP-kinase signaling pathway Mitosis. 715–716. cellular) Mollusk. 1071. 713. dissociation. 867 import see Mitochondrial protein import poisons. Cytokinesis. 1084F forces acting on. 713. 820. 1082–1083. 816. 817F. 1039 length. 855F electron carriers. 716F into inner membrane/intermembrane space. coli. in yeast. 1072F prophase. 51 small cellular organic see Organic molecules (small. Transposon(s). 866 non-Mendelian inheritance. 1077F. 858F Mitochondrial structure. 862T human. 865F. 697T Mitochondrial diseases. 1026–1030 Page numbers in boldface refer to a major text discussion of the entry. 717F role in respiration. 1021. 817F. 1087. 1073F. 830F. 382F Molecular motions. 1066. 1074. 595F see also Mitotic chromosome(s) Mobile genetic elements. 713F. 697T outer membrane. 587F. 869F see also Mitochondrial genome RNA editing. 714–715 SAM complex. 318F Drosophila melanogaster. 1076F. 316 bacterial. 1084F separation. 886. 1095–1097 disassembly. 1071. 835F respiratory control. 243. 859F DNA replication. 966–967 lamellipodia vs. 713. 1352 see also specific morphogens Morula. 483. 1085F. 1090 chromosome segregation. 1452F. 1059 Mitotic spindle. 1089–1090 chromosome structure see Mitotic chromosome(s) condensin and. 37–38. 838 uncoupling. 1082–1083 meiosis vs. 861F. 243F. 715F. 1075 GTPases. 714. 821F electron tunneling. 1075 entry into Aurora kinases. 473 Monoclonal antibodies. 1077F.. 1061. 834–835 respiratory enzyme complexes. 867 variability with cell type. 836 see also Oxidative phosphorylation Mitochondrial genome. Plasmodium transmission. 1082–1083 spindle attachment. 1089F metaphase. 717 contact sites. 830F. 1075F chromatin condensation. 820–821. 1088F asymmetric cell division. 243. 1334F. 1328–1329 E. 1085F. 1034–1035. 1034–1035 muscle contraction. 718F mechanisms. 483. 717–719. 1107. 831 coenzyme Q (ubiquinone). 247F. 832F cytochromes. definition. 1494. 858 diversity. 1087. 1054. 1103–1105 G1/S-Cdk stimulation. 43F mouse.INDEX microtubule association. 816F nuclear-encoded tissue-specific proteins. 1099. 1318 Drosophila egg. 856F. 1089–1090. 867. 1083–1085. 817. 688. 244F. 1016–1019. 1272. 55. 1089–1090 sister chromatids. 859 Mitochondrial protein import. 1088. 1021–1022 axonal transport. 1088 see also Kinetochore cytokinesis plane of division. 821F electrochemical gradient. 484F. 713. 841–842. 1081 classes. 1054. 245 bipolar spindle assembly. 36F. with an FF to figures that follow consecutively. 861–862 transcription. 34F see also individual models Modular organization. 522–523 Molecule(s). 1333–1335. 857. 716FF chaperone proteins. 1076 centrosome duplication. 318T human genome. 243. 716FF OXA complex. 207F. 74–75. 815F. 718F precursor proteins. 45 Molecular weight determination. 859. 1086F. 1107–1108. 1035F bipolar array. 831–839 chloroplasts vs. 862 phylogenetics. 868 urea cycle. Pax-6. 837–838 reverse electron flow. 1010. 856–857. 208–209. 248–249. 818F matrix.. 1075–1077. 1379F Mosquitoes. 1072F prometaphase. 1074 kinetochore and. 714F. 1079 as microtubule-based machine. 1034–1035. 243F. 207F insertion mechanisms see Site-specific recombination see also Repetitive DNA. 814. 895–897. 1099F chromosome attachment. 1089 unattached chromosomes and. specific elements Model organism(s). 688F. 835. 112F Monoubiquitinylation. 48 hydrophilic. 1084F bi-orientation mechanism. 863 genetic code variation. 52 large see Macromolecule(s) representation. 815. 1078–1079 microtubule dynamics. 853–854. 823–824 energetics. 1035. 1102–1103 see also Growth factors. 858 sizes. 40. 1090 intermediate filaments. 1082–1083. 1079F. 1055. 1385. 821 see also Electron transport chain. 1081F see also Microtubule(s). 862 Molecular evolution. 712F phases. 33–34. 818F porin insertion. 24–25. 713. 818F. 1078 checkpoints. 1088 see also Cell cycle control chromosome packaging. 1260 immunofluorescence microscopy. 817F. 1110 G1-Cdk stimulation. 1091F. 1079F mitotic spindle movements. 718 TIM complex see TIM complex TOM complex see TOM complex Mitochondrial reticulum. 1071. 1081F Polo-like kinases. Microtubule(s) Mitotic chromosome(s). 594–595. 318T Alu family. 926 Morphogenic gradient(s) cell fate dependent on position. 181. 717. 248–249 mitochondria. 718F energy use. 816. 834 spectroscopy. 387–388. 25F humans. page numbers with a T refer to a table. 866 nucleoids. 1072F telophase. 1457F Monomeric GTPases see under GTP-binding proteins (GTPases) Monosaccharides. 37F. 1048F microtubule dynamics and. 815–817. 1017F see also ATP hydrolysis biological functions. 1102–1103 competition for. 243F separation/segregation. 818F chloroplasts vs. 1088 see also Kinetochore Mitotic index. 716–717. 57F. 715 signal sequences. 1081F mitotic spindle see Mitotic spindle nuclear lamina. 857T. 207F SINEs. 1100–1101 centriole function. 866 Mitochondrial DNA see Mitochondrial genome Mitochondrial electron transport chain(s)(s). 868–870. 832F see also Respiratory enzyme complexes electron tunneling. 713. 1078 condensation. release factors (translational). 1084F forces acting on. 853 matrix space. 718. 1083–1085. Meiosis. 822 intermembrane space. Motor protein(s) I:31 photoactivation visualization. 1082F. 207F LINEs. 1084F bi-orientation mechanism. 367F Drosophila melanogaster. 1090 see also specific phases see also Cell cycle. 1081–1082 centrosome duplication. 1077. 1054. 1087F. 1071–1092 in absence of cytokinesis. 1103–1105 intracellular signaling pathways. 817F inner membrane. 1306F Molten globule. 715. 1010–1025 actin-based see Myosin(s) ATP hydrolysis. 39–40. 895F cell cycle control. 862 gene expression. 1075 M-Cdk and. 829. 589 Monoclonal response (lymphocyte). 1452. 831 see also Cytochrome(s) iron–sulfur proteins. 181–182. 36. 831. 829. 831 random collisions. 367. 1453T.. 208F. 1073F. 1088 asymmetric cell division. 843F cristae. 1083–1085. 1071 metaphase. 715 protein translocators. 708–709 Rho family GTPases. 862. 1108F specificities. 1088F spindle attachment. 817. 869F copy number. 243. 381. 861F copy number. Oxidative phosphorylation see also Mitochondrial genome Mitogen(s). 714F stop-transfer sequence. 821 enzyme complexes see Respiratory enzyme complexes natural (brown fat). 209. centrifugation techniques. 1325 Mono-allelic expression. epigenetics. 179F Ran GTPase.. 1034. 179. 1080. 1379. 1339 Moesin. 46 Molecular chaperones see Chaperones Molecular clock(s). 820F energy storage. 1084 M-Cdk and. eye development. 1398–1399 Caenorhabditis elegans. 856–857. 861–862. 886F definition. 1070–1071. 1009 Molarity. 712F. 208F. 1545 Monocytes. 207F retroviral-like elements. 1085–1087. 1087F. 1276–1277. 713–719. 243FF bi-orientation mechanism. 1080 mitotic spindle assembly/function. 1061. 857F. 716F. 1273F. 52 hydrophobic. 868–870 molecular clock rate. 1087. role. 1277F microtubule instability and. 244F. 1054–1055. 1379F. 276–277 MutH protein. 169. 19F inversion. 207. 1011–1014 ATP hydrolysis. 1022 Myosin light-chain kinase (MLCK). 205F Muscarinic acetylcholine receptors (mAChRs). 11F. 1435. 833F. 1400T NADH dehydrogenase complex. 1512. 1106. 263–264 evolutionary significance. production. 570 cancer development. 265. 246 see also Genome evolution deletion. 1549 Myb gene regulatory proteins. 1109 visualizing. 1016 rigor state. 264. 1014–1015 see also Dynein(s). 303F. 1024–1025. 323F knockouts production. 1208. 1302 silent. 1169. effects. 1385 skeletal see Skeletal muscle stem cell differentiation. 1557 Multivesicular bodies. 1017F cycle of structural changes. 92F. 1013. 528F. 570 see also Mutation(s) Mutation(s). 1463–1464. 1015–1016 force generation. 296 Escherichia coli. 296. 1466 recruitment. Cancer-critical genes evolutionary innovation. 528F temperature-sensitive. 955 see also Development. 1020 regulation by phosphorylation. 263. 916 Muscle. 264 fibrinopeptides. 1103 as oncogene. 528F synonymous. 1378 chimeras. muscle fiber growth. 836 NADH/NAD+. 265 see also Cancer. 1013. 1512 transmission. 1019 structure. Extracellular matrix (ECM) cell specialization see Cell differentiation evolution. 83 generation. 1016 subtypes. 1507–1508 phagocytosis and survival inside phagocytic cells. 98. 1231 germ-line. 1026–1028. 818–819. 264 measurement. 18. 1466F mutation in mice. 18. 774F. 298F see also Mutagenesis neutral mutations. 934F mu chain. 213 identification. 1379 egg. 464F. 1503 Mucus host defense mechanism. 772. 265 gain-of-function. 1507–1508 phagosome maturation prevention. 1012. 795–797. 528F loss-of-function. 1020 muscle contraction. 252F Multiubiquitylation. 1373–1374 Myoclonic epilepsy and ragged red fiber disease (MERRF). 556 see also Mobile genetic elements random. 1029. 1238F Burkitt’s lymphoma. 1026 lever arm. 1013F Myosin II. 1015–1016 kinetics. protein kinase. 264 increases. 298f. 678 Multipotent stem cells see Stem cell(s) Multispecies conserved sequences. demyelination. 1380–1381. 1465. 364–365 Muscular dystrophy. 1089 see also Mitosis. 21F. 1017F muscle contraction. 265 underestimation. 264 mitochondrial DNA. 263–264 Caenorhabditis elegans. 1209 suppressor. 265 mammals. 263–264 Mutator gene(s). 1512F persistence. 797F Mumps virus. 1164F cardiac see Cardiac muscle cells see Muscle cell(s) classes. 1106. 1463F contraction. 1029F Muscle cell(s) cardiac. 144F Myosin(s). 246 protein. 1466 skeletal muscle fiber formation. 1464–1465. 1005. Kinesin(s) regulation. 665–666 Multienzyme complexes. 558F rate see Mutation rates recessive. Myogenic protein(s) protein isoforms. 470F see also Genomic imprinting transposons. 1465F Muscular atrophy (inherited spinal). 1064. 528F in cancer. 1231 mechanisms. effect on. 803F MTOR. 17 null. 1013. 528F lethal. 1507 Mycoplasma. 1093–1094. 557. 1110. 16–17. 1382F early stages and extraembryonic membranes. 1012–1013 power stroke. 1209. 557–558. 1380F. 1500 Mycoplasma genitalium. 1378 transgenic mouse production. 1463. mitosis without cytokinesis. 818F. 1400T Myc gene/protein. SMN protein mutation. 568F see also Gene knockouts as model organism. 1013. 1380. 1464 see also Myoblast(s). Mitotic spindle conformational changes. 464. 1463F Myofibril. 1208. 464. 566–568. 1095. 265 histones. 1026–1030 control by troponin. 1028F. 418T. 1016–1020 microtubule-based. 1261 conditional. base substitution. chromosome differences. 1039F. 1463–1467 basal lamina. 1239 mitogen activation and. 1464. 487F. 528F. 1463F syncytium. 528F point mutation. 553. 296. 1020F mechanochemical cycles. 1030 Myostatin. 464F see also MyoD gene regulatory proteins Myogenin gene regulatory protein. signals. 1464 Myoepithelial cells. 1021–1022 RNA localization. 168–169. 1023–1025 see also specific types Mouse development see Mouse development genome chromosomes. 1464. 1022–1023 spindle pole separation. 293–294 comparative genomics. 1466 Mutagenesis carcinogenesis. 1016–1019 evolutionary origins. 567F transgenic organism(s). 819–820 see also NADH/NAD+ functional roles. 565. 265. 1020. 1107. Myogenic protein(s) dilator. 464F MyoD gene regulatory proteins. 1214 dominant. 558 dominant negative see Dominant negative mutation(s) elimination by natural selection. 1012F movement speed. 43F. 564F. 819–820 glycolysis. 20. 1026. 93F production from pyruvate. 1463–1464. 682 organelle transport. 82–83. 1466F Myotendinous junctions. 469F. 528F. 204–205. 1013F see also individual types Myosin I. 1026–1028 non-muscle. 1011 cell motility. 464. 18T host cell membrane traffic and. 1496F Muntjac deer. 575 yeast. 1025F structure. 1242F Mycobacterium tuberculosis. 250 imprinting. 1020–1021 mechanisms. 19F. 679F see also Action potential(s) structure. 323. 464 MRNA see Messenger RNA MSH. IVF and. 567F Mouse development. 528F destabilizing/deleterious. 556 mechanisms. 1027F Myofibroblasts. 10. 1464F maintenance. 795 Multivalent antigen(s). Cell junction(s). 464. 1437 Multicellularity cell–cell interactions. 1209–1210. 989 Mrf4 gene regulatory protein. Genetic instability limitation on number of essential genes. 1455–1466 muscle growth control. 1379 embryo. 1427F. 92F citric acid cycle. 1027F. 1026. 1464 fusion. 1466 persistence as satellite (stem) cells. 1465–1466 somite origin. Tissue(s) Multidrug resistance. 1024. 78. 1131–1132 see also Cell adhesion. 1217 see also Cancer. 1381F genetics. 888. 1502. 277F MutS protein. 1028F development. 678–680. 557F. 246. 1026–1028 processivity. 89. 1525 secretion. 464 Myoglobin. 950 amplified in carcinoma. 1239 chromosome translocation activating. 866 MyoD gene. 1041 contractile ring (cytokinesis). 1380 embryonic stem cells (ES cells). 248–249. 1028–1030 sliding-filament model. 264. 1381–1382. 1095F filament arrangement. 1487 genome size. 1015F. 277F MutL protein. 1030F role of Ca2+. 39–40. vs. 528F. 264 DNA repair defects. IgM. 556–557. humans. 795F. 464F. 1016 motor activity of head. 862 natural selection effects. 817 electron carrier. 252–253. 1378–1383 branching morphogenesis (of lung). 464F. 1450. 1016 enzymatic digestion. 1480 see also Myoblast(s). 556 site-directed. 934. 96 . 208F. 1208 gene expression analysis. 1464 uncoordinated growth and division. 1012F Myosin V. 1111F gene mutation. 832. 1463–1464 differentiation. 1464 fibers see Muscle fiber(s) heart see Cardiac muscle insect flight muscle.I:32 INDEX structure. 1027F motor neuron innervation. 680F Myoblast(s). 1170 Myotonia. 1012. 1379. 264 germ-line. 558 screening. 1012 evolutionary origin. 1029. 1468 Myogenic protein(s). 265. 1025F. 1057F consequences. 1425 N N-acetylneuraminic acid see Sialic acid (NANA) NAC gene regulatory proteins. 1020. 1217. 570–571 Myelin sheath action potential propagation. 1261 see also specific types Mutation rates. 1238–1239. 1425 Muscle fiber(s). 249F conserved synteny. 464 cell culture micrograph. 82–83. 1057. 504F differentiation. 565F in vitro mutagenesis. 1435. 559–560 see also Genetic screens intragenic. 1173. 264 somatic. 1011F thick filament. 14F. 264. 1099 Multipass proteins see Transmembrane protein(s) Multiple sclerosis. 277F Myasthenia gravis. 1465 skeletal see Skeletal muscle smooth. voltage-gated cation channels. 247 translocations. 1553 Mucociliary escalator. 1242. 796F. vs human. 18T. 1209–1210. 1381F M phase of cell cycle see under Cell cycle MreB protein. 1026F. 264. 169F see also Protein complexes (assemblies) Multinucleated cells. 557–558. 851 NADPH synthesis. 872 noncyclic photophosphorylation. 1356–1358 Notch signaling pathway. 1384F synapse elimination and remodeling. 490F Neisseria. 777F NMDA receptors. 1395F synapse formation. 126–127. basal lamina and. 1316F Arabidopsis. 1390F neurulation. 923F. specific regions/cell types Netrin protein. 1385F specification (neurogenesis). 1386F. 110F Noncyclic photophosphorylation. 459. specific types Neuronal doctrine. C. 705–710 mechanisms. 1390F neuroblasts. 1536 Noggin protein. 1360F. 1049. 530. 1531–1532 structure. 1383. 1546F Nanos protein. 504 Neurospheres. 1360–1361. 158F van der Waals attractions see Van der Waals forces weak interactions. 670 Nerve cells see Neuron(s) Nerve growth factor (NGF). 1480. 1451 apoptosis. electron microscopy. 82–83. 1453T. 1480 Neural tube. immune response. 682. 851 Nondisjunction. 1048 organization. 1110F structure axons see Axon(s) cytoskeleton see cytoskeleton (above) dendrites see Dendrite(s) function relationship. 946. 1387F cadherins and. 1048 see also Intermediate filament(s) organization of microtubules. 538–539. absence. 1141F. 806. 396–397 see also Prion diseases see also specific diseases Neurofibromatosis. 1334. 1360–1361 Neurodegeneration. limb regeneration. 1546. 1398F. 1271 in tumor progression. 1486. 1535–1536 virus-infected cell recognition. 969F lineage and formation. 1371F. 1367F. 156. 948F. 1391–1394 neural tube. 969. 562F mutations. 360–361 see also specific RNA types Noncovalent interactions. nucleic acid hybridization. 708–709. 1383–1397 migration. 1395F. apoptosis. 1161 growth cones. 645 schematic. 1388F Neural cell adhesion molecule (NCAM). 1389–1390. 78. 1355 Notch signal protein. misfolded protein degradation. 1047 Neuroblasts. 1383 brain and spinal cord (CNS). 1278–1279 Non-Hodgkins lymphoma. 683. 303F Non-Mendelian inheritance. 1393–1395 neural migration. 866F Nonretroviral transposons. 1123 NPCs see Nuclear pore complex(es) NSF. 456 Nematodes see Caenorhabditis elegans N-end rule see N-terminal degradation Neoplasm (tumor) see Cancer Nernst equation. 987. 1383. 1536 MHC class I recognition. 1388 Nebulin. 864–865. 1429 Notch receptor protein. 1138T. 1146–1147 Neural crest cell migration. 1394F. 1358FF in skin. 1370–1371. 1126F character assignment. 331 introns see Intron(s) from mitochondria. 481 Neurotransmitter(s). 1117 cell crawling. 1148–1149. 684. 1391–1393. 1385–1386 plasma membrane. 675F size control. 1136F development see Neural development neurons see Neuron(s) see also entries beginning neuro-/neural. 1393–1394 CAMs. 16–17 alleles. 888. 946–948 angiogenesis. 1167F Nitric oxide (NO). 1136. 1334F Nasal placode. 172. 139. 1531–1532. definition. 1450 Nitric oxide synthase. 769F N-terminal degradation. 1460–1461 NADPH oxidase complex. 13. 1374F Neural development. 1532 Naîve cells. 985T. 1161 interconnections. 1384F neural crest. 1587F Negative staining. 684–686 regeneration. 1385–1386. 1046F rapid turnover by apoptosis. 1140F. 171. 709F import. 15F. 1386–1388. 710F regulation. 529–530. 902F allostery. 1392F. 1407 Nodes of Ranvier. 888F Nitrocellulose membranes. 1165. 1360F in non-neural tissue. 707–708. 1535–1536 virus-infected cell destruction. 95F. 610. 359F. 247 self-replicating molecules. 777. metastasis. 1036 cytoskeleton rearrangement. vs means compare/comparison. 1371 phases. 1370–1371. 1352F endothelial cells. 923T. 83 photosynthesis. 438F Nuclear–cytoplasmic transport directionality. basal lamina and. 709F export mechanisms. 1028F Necrosis. 1049. 1536 Natural selection. 774–775. elegans early embryo. in plants. 17 Neutrophil(s). 888F ion channel gating see Transmitter-gated ion channel(s) see also individual neurotransmitters Neutral mutations. 1049 neurofilaments. subunit association. 22. 1136. 1140. 882. 1370F. 1048F specialization dependent on cytoskeleton. 31. 137 purifying selection. 1166. 1396–1397 gap junctions. 345 Negative translational control. 1. 1384. 1478–1479. 1439F in neurogenesis. 1400 at Drosophila wing margin. 94. 1333F. 1391F Neural plate. 538–539. 172F multiple. 13. 386F Normal microbial flora. 1362 pancreas. 1426 in vertebral limb. synapse formation. 1149F. 1395–1396. 1036. 1462 receptors. 1547 see also Immunological tolerance Natural killer (NK) cell(s). 1109 Nervous system apoptosis. 1388 NCAM (neural cell adhesion molecule). 1147–1148 scaffold proteins. page numbers with an F refer to a figure. 171 transcription circuits. 888 NK cells see Natural killer (NK) cell(s) N-linked oligosaccharide(s) formation. 764F. 739F protein glycosylation. 1391FF. 1388. 82–83. 1005 see also Intermediate filament(s) Neuroligin. 53–54. 318T Nonsense-mediated mRNA decay. 264. 1316T Noise. 329F. 1161. 691–692 NMR spectroscopy. 170F. 1386–1387. 709. 985T. 1140F. 1384 see also Neural crest cell migration effects of experience. 1449 animal development. 1356F. 1367F chick embryo. 100–101 Nitrogen fixation. 1586–1587. 1393F activity-dependent remodelling. 1520 Neisseria gonorrhoeae. 459F Negative selection. 1360. 530T Nocodazole. 845F evolutionary significance. 385–387. 1047–1050 development. 204 genome rich in. 1147–1148 Neuromuscular junction (NMJ). 1388F. 1389–1390 neurotrophic factors. 865F. 1530 NGF see Nerve growth factor (NGF) N-glycanase. 1374. 143F Neurites. 953F. 887–889. embryonic origin. 1168 ion channels. 866. 173F regulation. 1453. 170F. 1236F. 583 Noncoding DNA. . 94–95. 1140. 171 rate of inhibition. 1385F neurite(s). 1391–1392. 1370. 788F. 845. 1140. 1356–1358. 519F. 1283. DNA looping. 1531 Newt. 680. 688F. 1535–1536 activation. 1383–1385 see also Neural development electrical properties. 1206F Nonhomologous end-joining. 708–709. 82F electron carriers. 529F. 1383–1385 neuron death. 1126. 764. 539F Nose. 64F. 1045F. 987F. 172F see also Allosteric regulation conformational coupling. 1386F neural crest cells see Neural crest cell migration neural map formation. 358–360. 1385F Neuraminidase. 688–690 see also Action potential(s) gap junctions. 850–853 NADPH oxidase complex. 710F receptors. 852FF ATP synthesis. 1387–1388. 1352. 1531–1532. 1393–1395. 947. 1048 protein aggregates. 1010 Neurofilaments. 302–303. 143. 1480F NFkB proteins. 669. 539F Nitrogen cycle. 1212–1213 see also Evolution N-cadherin (neural cadherin). 64. 1370–1371. 1374 peripheral nervous system (PNS). 1360. 111F ionic bonds see Ionic bonds macromolecules. 1444 in sensory bristle development. 708F. 383 Page numbers in boldface refer to a major text discussion of the entry. 916 Nidogen. 1448 gut cell differentiation. 404–406 sexual reproduction and. 1385F see also Neural crest cell migration neural plate. with an FF to figures that follow consecutively. 940. 1177 neural birthdays and diversification. 1384F Natural immunological tolerance. 888. 171. 708F. 1360F. 1393F integrins and. 561–562. 1457F. 738. 1324 Noxa. 1385–1386 cytoskeleton dynamic instability. 1141F early embryonic origins. 1360 neurogenesis. Synapse(s). 1383–1397 axon-dendrite distinction. 774F protein folding function. 94 carbon-fixation. 806F see also Neurotransmitter(s). 100 Nitroglycerine. electron microscopy. 488. 82F functional role. 1049F. 1021 Nodal protein. 1148F Neural maps. 987. 952–954. page numbers with a T refer to a table. 1376–1377 Node. 55F. interferon-b (IFNb). 1384F. 675–676. 265 see also Mutation(s) protein conformation. 740F I:33 Nicotinamide adenine dinucleotide see NADH/NAD+ Nicotinamide adenine dinucleotide phosphate see NADPH/NADP+ Nicotinic acetylcholine receptors (nAChRs). 776F three-dimensional structure. 711F mRNA export. 1168F Neuron(s) apoptosis. 1478 Neurospora.INDEX NADPH/NADP+. 1532 phagocytosis. 902. 1115 Negative feedback (feedback inhibition). 850–853. 1115–1116 cadherin expression. 344F. 1370F neural specificity. 395–396 Ntrc regulatory protein. 1005. 1109. 930. 1370. 1370F. 860 repetitive elements see Repetitive DNA Noncoding RNA. 611F Negative supercoiling. DNA double-strand break repair. 709F. 610–611 Nomanski differential-interference contrast microscopy. 1028. 680F NOD proteins. thymus. 926. 1501 Northern blotting. basal lamina. 1140–1141. 1447F guidance. 988T. 1168–1169. 1371F Neural retina see Retina Neural stem cells. gene definition. 1439–1440. 787. 1452F Toll-like receptors (TLR). 1557T polarization. 110–111FF hydrogen bonds see Hydrogen bonds hydrophobic forces. 684F acetylcholine receptors. 987F. 1049F polarized cells. 486–488. 1080. 1215.I:34 INDEX nonhistone proteins. 1287 Null mutation(s). 358. Mitochondria evolution. 707F Nuclear pores. 1241–1242 identification. 61F. 1239 overexpression. 1429–1430. 55 nucleotides see Nucleotide(s) photosynthetic synthesis. 428. 864–865 membranes. 1359F Numerical aperture. 1291F Oogonia. neural stem cells and neuronal turnover. 364–366 GEMS. 197 in tRNA. 984. 590F. 637 Ocular dominance columns. 363–364. 116–117F DNA see DNA (deoxyribonucleic acid) hybridization hybridization conditions. 490. 1281. in frog. 1400T zinc finger proteins. X-ray diffraction. 889–890. 705. 1431F Organogenesis. 421–422. 710 Nuclear lamins. 1291–1292. 537F Southern blotting. 773–775. 365F functions. 201F. 775F Golgi apparatus processing. 705–707. 551 Operator(s). 1237–1239 viral. 1288. 704. 61–62 origin of life. 1090 structure. 280. 711F shuttling proteins. 289–290 dynamic structure. 1231–1234. 1288. 269F. 710 nuclear localization signals (NLSs). specific organs Organotrophs. 1111F total cell mass control. 1497F Nucleofilaments. 214F DNA replication. 1111–1112 see also Development. 697T see also entries beginning nucleo-/nuclear Nucleus. DNA (deoxyribonucleic acid) membrane amounts. 1290–1292. 1391F Optional introns. 87F see also DNA synthesis. 1232 see also Cancer-critical genes. 200–201 see also Chromosome(s). 974. 212F see also Histone(s) DNA interactions. 62. 1107. 700F volume. 979F motor protein force generation. 434F lambda. 68–70 sugars see Sugars Organism growth cell growth and. 705–707. 307F Nucleoids. 712F structure. 1288. 113F complex. 45 Organic molecules (small. 706F structure. 977F see also ATP hydrolysis nomenclature. microscope lens. 609F see also Nuclear pore complex(es) Nuclear receptor superfamily. 254. 299F Nucleus compartments. 1291F gene expression. 747F O-linked oligosaccharide(s). 418T. 1289. Microtubule(s) Nucleic acid(s). 215–216. 362F. oogonium. 1280. 218. 1290. 871–872. 1433 Opsonization. 705F. 61. 705F. RNA polymerization. 1290–1291. 1071. 706–707. 200. 1079–1080. 86. 704. 1490–1491 Occludin. 1290F Oogenesis. 776F OMP decarboxylase. 1290F follicle/accessory cells and. . 708–709 size exclusion. 700F inheritance. 359F. 363–364. 872–875 lipid bilayers. in axon guidance. Multicellularity Organizer (Spemann’s Organizer). 200–201. 992 see also Actin polymerization. 400–408 DNA as hereditary material. 1391 Optic tectum. 891F. 707–708. 708 regulation. 709–710 Nuclear transplantation. 211–218 30-nm fiber. 1289F. 365F Cajal bodies. 486F localization mechanisms. liver. 1555. 1231 activation. 85. 332 see also DNA (deoxyribonucleic acid). protein glycosylation. 974. 859 Nucleolus. 1016–1019 treadmilling. RecA protein–DNA interactions. 1290 lampbrush chromosomes. 1290. 413F Nuclear transport receptor(s). 1430 Okazaki fragments. 114F Olfactory bulb. 1347–1363 see also Development. 425F Octylglucoside. 1391. 215–216. 296. 705 Ran GTPase. 709–710 Nuclear envelope. 1557T Optical diffraction. 1153 Occluding junction(s). 56F diffusion rate in cell. 1555F. 1520 Open reading frames (ORFs). 358–359 structure. regeneration. 704 mitotic cells. 200. 74–75 fatty acids see Fatty acids metabolism. 1107. 201F. 358. 1430 Olfactory sensory (receptor) neurons. 1110. 706F see also Nuclear lamina Nuclear export receptor(s). 1442 N-WASp. 1288–1290. 776. 359F gene expression regulation. 1102. 706–707 mRNA transport. 434. 1289F. RNA. 590–592. 1108 inhibitory factors. individual genes/proteins Oncogenesis. 1516F Nylon membranes. 212F structure determination. 344 see also Chromatin Nucleosome sliding. reaction rates. 358–359. 212F transcriptional effects. 297F energy carriers. 281F Oleic acid. 116–117FF biosynthesis. 116F. 813 see also Chloroplast(s). 1289F development (oogenesis). 211 O Obesity. 705F. 61. 1288–1289. 973. 537F Northern blotting. 527 Optic nerve. 581 Optical sectioning. 1292 primary. 705. 212–214. 255F gene regulatory proteins. 200–201. 211–213. 432. 407–408 RNA world see RNA world hypothesis self-replicating molecules autocatalysis requirement. 1430 Odorant receptor proteins. 423F Nuclear import receptor(s). 26. 636 Oligosaccharyl transferase. 429F Oligosaccharide(s). 1232 Oocytes. 211 protein binding.synthesis chemistry. 402F protein synthesis. 678 Oligonucleotides. 979. 535–536. 757 position. viral. 55 amino acids see Amino acid(s) as building blocks. 117F biosynthesis. 1290. 241F. 3F. 55–56. 532. 365F visualization. 365F transport into/out of see Nuclear–cytoplasmic transport volume. 3. 1368. membrane protein solubility. 978F.adaptive Oligodendrocyte(s). 267–268. 401 base-pairing see Base-pairing RNA see RNA (ribonucleic acid) structure. 1291F asymmetrical division. 3. 201F. 215 structural organization. 539–540. 201F. 1098 development. 215–216. 241–243. 433F. 538–539. of cytoskeletal polymer. 985T Nuclear localization signals (NLSs). 1370 Organ of Corti. 711F mitosis. 272. 1133T see also specific types Oct1 Pou domain protein. 242F DNA localization. 706F electron micrograph. 706F nuclear pore complexes see Nuclear pore complex(es) nuclear pores see Nuclear pores nucleoporins. 402–403. retroviruses. 708–709. 696. 117F nucleic acid subunits. 401–402 see also Origin of life. 405–406 pre-RNA world. 989 microtubule assembly. 1288 maturation. 212F see also Chromatin chromatin remodeling. 1358. pathogen movement. 218F historical aspects. 708F Nuclear lamina. 1002 cofilin. 12 Origin of life. 61–62. 708 Nuclear export signal(s). 296F. 1475 Obligate pathogens. 539F recombinant DNA technology. 708 Nucleation. 1102. 1290. 892F Nuclear scaffold see Nuclear matrix Nuclear shuttling protein(s). 485–486. 364. 364F ribosome synthesis see Ribosome(s) Nucleoporin(s). 329F. 706F visualization. 705 Nucleoside triphosphates. cellular). 581. 1516. 711–712. 401 export-ready mRNA. 697 topological relationships. 1238–1239. 357. 85F. egg (ovum). 504F. 1002 FtsZ protein. 737. 1288–1290. 211. Neisseria. 976. 215F Nucleotide(s). 1290F Opa membrane protein family. 220 linker DNA. 242 Nuclear membrane. 1132F. 457–458 Operons. 364. RNA (ribonucleic acid) structure. 705 mechanism of action. 708 Nuclear hormone receptor(s) gene duplication and divergence. 295T. 334 Nucleosome(s). 433F. 712F. 411. 359F. 113F ER processing. 365F nucleolus see Nucleolus speckles. 362–363. 211F. 358. 773F. 1429F Oligoclonal response. 215F histone H1 binding. 697T mitochondria see Mitochondria phosphoinositides. 697T proteins. affinity chromatography. 709F. 704 energy converting. 538–539. 582F Nurse cells. 363–364. 917. 61 see also ATP (adenosine triphosphate) hydrolysis actin filament assembly. 775F sialic acid addition. 1289F. 1290F. DNA bending. 1291F Drosophila. 408 electron transport chain evolution. 1291F. 863 ORC see Origin recognition complex (ORC) Organelle(s). 197. 1289F. 1232 new methods of identification. 298. 487F regulation. 697–699. 697T see also specific organelles Organic chemistry. 211F. 539F 738. 370F see also individual nucleotides Nucleotide excision repair (NER). 1395F Odorant receptor genes. 1292 size acquisition mechanisms. 1430. 1288. 702. 487 Ran GTPase. 462–463 see also Lac operon (Escherichia coli) Opportunistic pathogens. 161F Oncogene(s). 101 damage. 1292 secondary. 710F receptors. 709–710. 737F. 485–486 HIV. 774F side chain diversity. 1289. 528F Numb protein. 1290F Nutrient absorption. 592F Optical tweezers. 363–366. 539F see also DNA hybridization nucleotide subunits. 201F subnuclear bodies. 706F Nuclear pore complex(es). 706F Nuclear magnetic resonance (NMR) spectroscopy see NMR spectroscopy Nuclear matrix (scaffold). 1288. 433F core particle. 1291F meiosis. 117F Nucleocapsid. 1132. Northern blotting. 363F. 695–697 analysis methods. 329F. RNA world hypothesis properties. 509–512 chloroplasts see Chloroplast(s) cytokinesis and. 1490 Opsin. 1545 see also Immune response/system. 1501–1502 drug resistant. 1496F Passive transport. 21F Oscillation circadian see Circadian clocks of gene expression in somitogenesis. 1105 modes of action. eye development. 556 Pemphigus. 1472. 1291F cancer. with an FF to figures that follow consecutively. 1167F. apoptosis. 1333. peroxisome protein import. 1518 host cell membranes and. 402F Peptide transporters. 1490 host behavior modification. 1156F. 1486 Perlecan. in cancer. 547F Pathogen(s). 1444 Pancreatic exocrine cell(s). 1469–1470. 663 Ovaries accessory cells. gated channels studies. 1450 Perinuclear space. 605. 401 see also Catalytic RNA time line. 952F Patch electrodes. vs means compare/comparison. 1371–1373. 787–789. 1257 inactivation by DNA tumor virus proteins. 722 oxidative reactions. Fungi. epithelial apico-basal polarity. 1290. 1106F. 1156–1157. 1487 immune response to see Immune response/system infections see Infection(s) infectious process. 718. 418T. 721 membrane amounts. 990. 127F formation. 1470F Osteopetrosis. 820F ATP synthesis. MHC protein. 1555. 1212 Par3 gene/protein. 950. 1437–1438. 70. 1555F bacterial entry into host cells. 664. 98. 1161 Ovulation. 1249F subversion of cell-cycle control. 1464 Pax6 (and homologs). 1531–1532 phylogenetic diversity. 1437F. page numbers with an F refer to a figure. 1503 Petite mutants. 1578F. 1140. 1470. 1138T PCNA protein. influenza virus. 91. 1531F antibody-activated. 723F protein import. 1068 Orphan receptors. 1490–1491 opportunistic. 680–682. Neutrophil(s) Phagocytosis. 1280. 696. 1156 PEV (position effect variegation). 822F. 823 electron transport see Mitochondrial electron transport chain evolution. 221F P granules. 71. 1577. 1527. 1528–1529 electron micrographs. 1157F Paracellular transport. tight junction(s). bacterial. 831 see also Redox potential(s) Oxidative damage. 832–833 evolutionary significance. Drosophila. 866–867 Peutz–Jeghers syndrome. 407 Peptidyl-tRNA–ribosome binding. 88–103 see also Respiration electron transfers. 874F electron affinity. mutated in cancer. 1152 Paracortex. 664F. 1140 neuronal. 1474 Ouabain. 1489–1490 Pathogenicity islands. 72. 871F Oxygen atmospheric. 721 functions. 819. 128F. 1252T deficiency targeted in cancer therapy. 1502–1504 evolution (rapid). 1577–1579. 402. 404–406 polynucleotides. 423. 1508. 1490F. 98. 1536. 1582F Peptidoglycan(s). DNA repair defects. 1292 Ovum see Egg (ovum) OXA complex. 424F DNA damage checkpoint. 462F Pertussis. 874F free radical generation. plant cell wall. 1248 oncogenes (E6 and E7). 295T development. 275F PCR see Polymerase chain reaction (PCR) PDGF see Platelet-derived growth factor (PDGF) PDI see Protein disulfide isomerase (PDI) PDZ domains. 705F Periodic table. 721 volume. 1156–1157. 376. 1324–1325. 697T see also Glyoxysome(s) Per protein. 1470F ECM production. 1531–1534 see also Macrophage(s). 49f Peripheral lymphoid organ(s). 1579F Peptide bonds. 1372F. 889 Orthologous genes. 721–722 hydrogen peroxide. 1458. I:35 Virus(es) Pathogen-associated immunostimulants. 1511F host cytoskeleton and. 722 Oxidation–reduction (redox) reactions. 596 see also Acid(s). 1521–1524 evasion of host defenses. meiosis completion after. 1521–1522 Pentoses. cells in C. epithelial apico-basal polarity. 1526. 1373F Osmium. EM sample preparation. 1184T Permeases see Carrier protein(s) Peroxin(s). 1198. 1485–1537. 1580F see also MHC (major histocompatibility complex) Peptide nucleic acid (PNA). immune response. 1520–1521 facultative. 1361 Par4 gene/protein. process. 1490 phagocytosis. 1136. 1509F macrophages. effects on. host behavior modification. 1488–1489 primary. 832–834. 1517–1518 Pachytene. 100F. 1157F Par3/Par6/aPKC complex. 821F intracellular. 697T Pandemics. Base(s) (chemical) Phagocytic cells. 26. 1473F Osteoclast(s). 1217 DNA binding. elegans embryo. 1550. 721F. in tree of life. 52. 161 Peptide fragments. 883 Paralogous genes. 1212 Papillomas. 1243 p21 gene/protein. 1543F Peripheral tolerance. 122F. 1532 transport molecules. 1470F remodeling of bone. 407 hydrolysis. 1228T. epithelial apico-basal polarity. 1228. 1106F Mdm2 protein interactions. bacterial cell wall. 96–97. 828 peroxisomes. 1492F obligate. 1198F. 722 Peroxisome(s) electron micrograph. definition. 1446F. sodium–potassium pump effects. 906–907. 681F Patched protein. 1582. 819F. 1514–1517 host interactions. 874F see also Evolution Origin of replication see Replication origin(s) Origin recognition complex (ORC). 287. 187F mutant forms overexpressed. lymph node. 1471F Osteoblast(s). 1472F bone erosion. 1105. 1275 PAGE see Polyacrylamide gel electrophoresis (PAGE) Pair-rule genes. 833F requirement for catabolism. 296F Oxidative metabolism energetics. 1501–1502 intracellular see Intracellular pathogens nonpathogens vs. 821–822. 466F Pax7. membrane amounts. 664FF Ossification. 1496. 1330 Parasites intracellular. 1467F precursor cells. 1472F Osteogenesis imperfecta. 1541–1542 dendritic cells. 256–257 Oxytocin. 1469–1470. 1530–1531 Pax3. 1518 tissue damage. 1155–1156 Par6 gene/protein.. 721–722 phospholipid import from ER. 288. 1288 gap junctions. 1179 lineage and formation. 722 cellular energy production. 1578F. 873–875. 1573. 697T b oxidation. 1551F Paracrine signaling. 1148 Pectins. Cervical cancer. 1188F. 1290F. 1165. 20–21. 1127 colorectal cancer. 1470. 221. 16F Parasegments. 21F Paramecium. 99. 70 glycolysis. 60F bond angles. 1157F see also specific genes/proteins ParM protein. 721 production. 654F Patch-clamp recording(s). 1324FF p16 (INK4) CKI protein. 817–818 see also Aerobic metabolism toxic compounds. 1487 spread. 1543. 1488 see also Bacteria. 1489 protozoan. 1490F Peritonitis. 606 Osmium tetroxide. 788. 1539 Pathogenesis. 1471 cartilage erosion. 20–21. 1251–1252. major events. 1144 Penicillin. 1539 colonization of host. 1487–1488 human evolution. 1587–1588 Periplasmic space. 1226–1227 Papillomaviruses. 1117 P P2. 1521. 1486–1487 recognition by host cells. 1473F Osteocytes. 1248. 1246F modifications. electron microscopy stains. 1541F. 653. 28F. 318T. 1127 Page numbers in boldface refer to a major text discussion of the entry. 1526–1528 requirements to multiply in host. 1036 remodeling of bone. 828–829. 870–872. 1199T P elements. 1246 p53 gene/protein apoptosis. 466. 480. 1246. 1491. 663. 1474 Osteoporosis. 1522F Paneth cells. 1571 pathogen recognition by phagocytes. 401–402 polypeptides. 1503 Pertussis toxin. 379. 1527. 1573F Pericentriolar matrix. 1494–1495 Parathyroid hormone. 1337F Pancreas. 1470F. 784F. 527 Paternity testing. 1115. 109F gradient. 820F b oxidation. Parasites. 1123. 1464 P-cadherin. 1045. 1527 Peptidyl transferase. 1531 Toll-like proteins. 1248–1249 PAPS see 3¢-Phosphoadenosine-5¢-phosphosulfate (PAPS) Pap smear. 1581–1585 Peptide-MHC complex. 833. 1508–1511 parasitic worms. 605F Osmolarity regulation. 71F biological vs combustion. . signs/symptoms. 1579F. peroxisomes. 1511–1514. 1105. 1337–1338. 1511–1514 host response. 98F. 92F see also Glycolysis Oxidative phosphorylation. 288F. 873–874. 1491F Pathway guidance. DNA. 123F Oxidation reactions. 1166. 1440. 1246 tumor suppressor. 882F. neuroblast cell division. 379F. 1287 Parvoviruses. nuclear receptor superfamily. 788F induction by bacteria. 715. 723F enzymes.INDEX natural selection. 1106. 874 reduction by cytochrome oxidase. steric limitations. 112F Peptide-binding groove. class I MHC proteins loading. 1472–1473. 20F. 1323. 718F Oxaloacetate. 462F Perforin. 296. 881. epithelial apico-basal polarity. 256–257 Oxygen-carrying molecules. 1507–1508 complement role. 721–723 structure. 375F Per clock gene. 1428 cell-cycle arrest in response to telomere shortening. 1147. 745 plasmalogens. 1323F pH. Protozoa. 289F. page numbers with a T refer to a table. 990F Parthenogenesis. 59. 1385–1389 Pattern recognition receptors. host cell invasion. 1486–1487 host membrane traffic changes. 20F. 907T Par genes/proteins. 1228F cancer role. 1076 Pericytes. 27F. 1526F Papanicolaou technique. 820–821. 1539. 1177. 1155–1157. 1187 Osteogenic cells. 1470–1472. 1472F cell crawling. scaffold proteins. of migrating cell. 1470F Osteoid. 1290–1292. organelles. 1285. 375. 91. 853. 1097–1098. 1199–1200 primary cell walls. 121F Phosphoglycerate kinase. 9. 120F Phosphoglucose isomerase. 4)P2]. 863 evolution. 850–853. Protein kinase(s). 776. 852F. 757F Phosphoinositol kinases. 757. 1046 extracellular signaling. 1196–1197. 70. 847F. 1196. 1513. 618 aggregates. 93F phosphodiester. 789–790. 1199T proteins. 1163F transgenic. 852F. 568–569. 247F. 846 microtubules. 854F electron transfer see Photosynthetic electron transport chain(s) evolution. recent evolutionary origin. 872–875 plants see Plant(s) Photosynthetic reaction centers. 1197–1198. 863. 848. 911FF Phosphatidylinositol 4-phosphate [PI(4)P]. 846 carbon fixation see Carbon fixation. 121F 3-Phosphoglycerate. 1097–1098 Phylogenetic footprinting. 1195–1197. genome preservation. 1358. 744. 1081 culture. 1198F cross-linking glycans. as tumor promoters. 840–841. 299F Phosphodiester bonds. 1299 Phospholipid(s). 115F amphipathic molecules. 1359F. Purple bacteria carbon fixation (dark reactions) see Carbon fixation chlorophyll photochemistry. 1195–1202 composition/structure. 1158. 898. 5-bisphosphate [PI(4. ER. 852F evolution. 69. 68–70 equation. 107F bond energies. 849–850. 59F. 1162 PKC see Protein kinase C (PKC) Placenta. 1208F. 1531–1532 Phalloidin. 1226 Phosphatase(s) see Protein phosphatase(s) Phosphate bonds. 853. 1162–1163. 627 flippases. 852 see also Carbon fixation. 895 GTP-binding vs. 1261F Phorbol esters. 1097–1098. 504–505. 1117 3’-Phosphoadenosine-5’-phosphosulfate (PAPS). 744F lipid bilayer assembly. 854F photosystem II. 840–855. 222. 934 Phosphoinositide kinases. 852F Photosystem(s). 854F reaction centers see Photosynthetic reaction centers redox potentials. 850. 744F Phosphorus-32. membranes. 960–961. lipid bilayer assembly. 745 . 909. 1195 evolutionary origin. 743. 1198F. 872–875 noncyclic photophosphorylation see Noncyclic photophosphorylation photosystems see Photosystem(s) relation to respiration. 933 Phosphatidylinositol 3. 618–620 properties. effect on liver. 1195 flowering. 1010 Phosphatidylinositol 3¢-kinase (PI 3-kinase). 787–788. 1197F. 815F. 743F Phosphatidylethanolamine. 1432–1433. 627. PTB site). 619F. 61–62. 93F phosphoanhydride bonds. Cytochrome(s) Phototrophs. 854F bacterial. 1197–1198. 1043F. 58–59 bilayers. 454–455. 534 Phosphorylation ATP-mediated. 175 Phosphate transfer reactions. 848F see also Chlorophyll(s). 853 electron-transfer (light reactions) see Photosynthetic electron transport chain(s) energetics. 627F growth factor signaling. 849F. 595F. 844F. 827F. 848F photosystem I. 1196F actin filaments and. 1429. 199F Phosphoenolpyruvate. 1195. 1511–1512. 848. 872–875 mitochondrial electron transport vs. 1511F. Photosynthesis cell differentiation. Photosystem(s) chloroplast(s). 80. 848F bacterial. 569F. 909. 29 mesophyll cells. 618–620. 619F see also individual molecules Phosphoinositide-dependent protein kinase I. 176F glycolysis. 1502F Plakoglobin (g-catenin). 1195–1197 cellulose. Chloroplast(s) Photosynthetic organisms. 570F Plant cell(s). 1531–1532 resistance mechanisms. 70F stages. 1531–1532 process. 1199F cell type and. 789F Pit fields. 843–848. 1195. 16F. 851. 642. 1201F photosynthetic organelles see Chloroplast(s) plasticity. 504F. 1531–1532 respiratory burst. 743. 642 redox potentials. 1198.I:36 INDEX Phospholipid flippase(s). 630 Phosphatidylserine. 840 bacteria. 1098F development see Plant development and growth division. 853 water-splitting enzyme. 570F turgor pressure. 960–961 Photoreceptors (photoreceptor cells). 988T Phase. 407F see also Lipid bilayer(s) biosynthesis. 58. 1444 Phenol extractions. 1433F see also Cones. 61. 841–842. 121F Phosphoglyceride(s). 1198F. 853 light-harvesting complexes. 782–783. 744. 58–59. 757. 36 as model organisms see Arabidopsis thaliana (wall cress) plasmodesmata. 850F photosystem II complex. 627 see also specific phospholipases Phospholipase C (PLC). 627. 853 see also Chlorophyll(s). 93F Phosphodiesterase. 852F see also Thylakoid(s) electron carriers. circadian clock. 846–847. 619F. 223F noncyclic photophosphorylation see Noncyclic photophosphorylation oxidative see Oxidative phosphorylation protein see Protein phosphorylation Phosphotyrosine-binding domain (PTB domain. DNA rearrangement. 1200–1202. in chronic myelogenous leukemia. 121F Phosphoglycerate mutase. 618. 568 transformation. 841F totipotency. 853 electron transport see Photosynthetic electron transport chain(s) noncyclic photophosphorylation. 849 photosystem I. 1180. 744F Phospholipid transfer proteins. 1198F secondary cell walls. 848. 4-bisphosphate [PI(3. 1379 Placodes. 961F PI see Phosphatidylinositol (PI) PI 3-kinase see Phosphatidylinositol 3¢-kinase (PI 3-kinase) Pigment cells. 1109F Phosphatidylinositol 4. 538 Phenotype. 618. 1384F Plague. 560. 757. 248 Physical gene mapping. 796–797. 840–841 extracellular matrix. 744F Phospholipid scramblase. 855F reaction centers. 1197 vacuoles see Plant vacuoles Plant cell wall. 1180. 1197F pathogens. 1196. 1532 Phagolysosome. 788. 1208. Purple bacteria evolution. 1142 Planar cell polarity. structure. 431. 851F. 596F Photochemical reaction centers. 932–935 actin organization. 852F. 583 Phase transition. 642F electron transfer. 622. 852F. 431F Phylogenetic tree(s). 405–406. endoplasmic reticulum (ER). Neisseria. 850F. 872–875 see also Cyanobacteria. 846–847 see also Carbon fixation Photosynthesis. cadherin binding. 93F. 899F Photoactivation. 84F dephosphorylation. 1202 microtubules and. 618 synthesis. 554F analysis. 1198. 618. 848 antenna complex. 1490F Pilin protein. 850F. 849F. 247.. 744–745. 1200F orientation of deposition. 1502. 743–745 see also specific molecules Phospholipid exchange proteins. 176. 840. bubonic. 59F. 625–626 membrane composition. 5)P2]. 12 Phototropin. 1360F Plant(s) comparative anatomy. 850F bacterial. 853 bacterial. 1024F Pili. 129F Pheromones. 121F Phosphofructokinase. 961 Phototropism. 849–850. 93F Phosphate groups.. 627. 744–745. 1452. 743–745 scramblases. 853. 70 evolution. 1196 functional roles and specialization. 180F histone tails. 91. 626. 581. 787. 1196. 757F Phosphoinositides see Inositol phospholipid(s) Phosphoinositol (PI). 757F Phospholipase(s). 1520 Pineal gland. 743 Phosphatidylinositol (PI). 1097F. 853–854. 854F bacterial. 852F. 910F. 853–854 cyclic photophosphorylation. 107F. 1531–1532 Phagosome(s). 853 structural relationships. 620 structure. 850–853. fish. base excision repair (BER). 568 cytokinesis in. 91. 850F. 413F cel walls see Plant cell wall centrosome lack. 120F 2-Phosphoglycerate. 1157–1158. 36. Protein phosphatase(s) Phosphatidylcholine. 92F phosphorylation see Phosphorylation see also ATP (adenosine triphosphate). 84F cascades. 70F see also specific components Photosynthetic electron transport chain(s). 583 Phase-contrast microscopy. 1261. 844F. 623 Phase variation. 844F cyclic photophosphorylation. 987. 618. 909F. 1023–1024. 852FF see also Photosystem(s) Photoprotein. 560F Phytochrome. Plant development and growth evolution. 556–557 see also Genetic screens heritability see Genomic imprinting Phenylalanine. 840–841. 854F Photophosphorylation. 776F Phosphoanhydride bonds. DNA label. 594–595. 1195. cytokinesis in higher plants. 850–853. 918F. 92F. 1199T development and growth. 627. 411. nucleic acids. 114F. 909. 455F see also Site-specific recombination Phenobarbital. 848. 1199T pectins. 849–850. 873F across thylakoid membrane. 872–875 see also Cyanobacteria. 851. 961 Phragmoplast. 852FF proton-motive force. 910F. 61. 847F development see Plant development. 1199T lignin. 849–850. 461 Pinocytosis. 69–70. 917 Philadelphia chromosome. 910F Phosphatidylinositol-specific phospholipase C. 62F lipid droplets. 850F redox potentials. 867–868 cell macromolecules. 852F. 846 bundle-sheath cells. 553. 851–852. C3 vs C4 plants. 5568 plastids. 847–848. 848. 873 Z scheme. 853–854 electron transfer. 840. 619F. 1157F. 1200F. 843–844. 61–62. 1198. 1108. 745 Phospholipid translocator(s) apoptosis. Rod photoreceptors (rods) Photorespiration. 1200–1202. 86. MHC proteins. 1044 T cell(s). 933 Plectin. 386 poly-A-binding protein. 379F. 841F chloroplasts see Chloroplast(s) development. 563 Polyisoprenoid(s). 357F Polyacrylamide. 667. 1162–1163. 1194 Plasminogen activators. 492F messenger RNA 3¢ end.INDEX compression resistance. 547F Polymerases DNA see DNA polymerase(s). tight junctions. 1016 Poxviruses. 295T Pre-mRNA modifications capping see 5’ Capping of eucaryotic mRNA hnRNP packaging. 1406F meristems see Meristem(s) microtubules and. 132F Polypeptides see Protein(s) Polyprotein(s). with an FF to figures that follow consecutively. 517. 707. 405–406. 1004F PNA (peptide nucleic acid). DNA replication RNA see RNA polymerase(s) thermophilic. 717. 1289. 87F see also Macromolecule(s) Polymorphism. 39F. 1077–1078. 492. 1163F Plasmodium falciparum. 669 selectivity filter. 425F Power stroke. 144F. 1419. 699F. 617 actin filament contact. 1492F Plasmin. 1519 Point mutations. 1314–1315 cell memory. 1450 Pleckstrin homology (PH) domain. 1102. 1544F. 255. 541FF. 781–782. 722F Plasma membrane(s). 402–403 Presenilin. 717F Porphyrin rings. 637 staining. 415. 85F cell macromolecules. 408F proteoglycans. 1588 Polymorphonuclear leucocytes see Neutrophil(s) Polynucleotides DNA see DNA (deoxyribonucleic acid) origin of life. 1086F Polarity/polarization. DNA repair defects. 84–87 head polymerization. 1408F sequential. long-range. 1345F Polygenic traits. 21. 1364 see also under Drosophila development DNA strands. 1197. 172F epigenetics. 1190 function regulation. 1401. 698. 1371 Prickle cells. 485–486 translational see Translational control of gene expression Post-translational modification. 357–358. 635. 1398–1415. 1406. 925F. 1502 mitochondrial DNA. 414F. 221. 1494–1495. 957. 458F. 1406F Plant modules. 358 polyadenylation see Polyadenylation (mRNA 3’ end) splicing see Splicing Pre-pro-protein(s). 534. 288 Pre-RNA world. 546F. 221F Positive feedback control. 923T. 1035. 673F voltage-gated see Voltage-gated potassium channel(s) Potassium leak channels (K+ leak channels). 721. 1400. 1009–1010. 1513–1514. 458. 1151 enlargement. 459F Positive selection. 674F conductance. 149F entry and uncoating. 1068F Pre-replicative ORC complex. 1515F capsid. 1495F transmission and vector. 380 Polyclonal response. 1102F. 545F. 237FF deconvolution microscopy. 370–371. 407F. 1401F Arabidopsis see Arabidopsis thaliana (wall cress) cell signaling. 1392–1393 Position effects. 1557 Pop1 gene regulatory protein. 401 RNA see RNA (ribonucleic acid) see also Nucleic acid(s) Polypeptide backbone protein models. 689F Post-transcriptional regulation. 1403 sexual reproduction. 1549F. Immunoglobulin(s) Polycomb group. 1552 see also B cell(s) Plasmalogen(s). imaginal discs. 1403. 852F Plastoquinone. structure. 1575. 1047. 1102. 357–358. 699 genomes. 1496F. 901F cell asymmetry. 781F. 1545 see also Immune response/system. 402. 388F collagens. 517 Polyacrylamide gel electrophoresis (PAGE). 381–382. 379F. 1076F mitotic spindle. 357F poly-A polymerase. 9. 353F. 482–483 m RNA polyadenylation. origin of life. 1496F Pre-B cell. 535F gel-mobility shift assay. 479–480 immunoglobulin genes. 3F epithelia apico-basal polarity mechanisms. 1312–1313. 1585–1586. 1498F Poliovirus. vs means compare/comparison. 1199 plasmodesmata. 1163 Plasma cells (effector B cells). lymphocyte origin. 805. 357F CstF protein. 493 deadenylation-mediated mRNA decay. 841F etioplasts. 544–546. 737F. 996–998 domains. 806F lipids see Lipid bilayer(s) origin. 1587F Positive supercoiling. 1157F exocytosis control. 1186. asymmetric division. page numbers with a T refer to a table. eradication by vaccination. plasmodesmata and. 477F alternative splicing. 38–39. 1325 Porin(s). 544 see also DNA replication. 358 Poly-A tails see Polyadenylation (mRNA 3¢ end) Polycistronic mRNA. 357F cytoplasmic. 1489F TFIID cleavage. 38F. 672F chloride channel vs. 344F. 1413F. 115F Polymerase chain reaction (PCR). 415 RNA processing control. 477–499. 590 Polar body. 382F. in thymus. 1495F. 1400 embryogenesis. 164–165 Polyspermy. 238F insulator-binding. 1004. 795 Polyvalent antigen(s). 806F planar cell polarity mechanisms. 590F see also Chromosome structure RNA synthesis. 379F. 1111F. . 373 tail polymerization. 1549. 1081–1082 neutrophil(s). chronic illness. 831 Porphyromonas gingivalis. 859 time-dependent transcription. 88F. 357F. 1543. 1010F actin filament nucleation. 737. 1201F plant module growth from primordia. 85. 318T nonsense-mediated mRNA decay. 1491–1492. 730 see also Ribosome(s) I:37 Polysaccharides. 1046 developmental. 1158. 113F biosynthesis. 236–238. 1197. 1406. 1401F. 671–673. 357–358. 1196 tensile strength. 171. 453F microscopy. 413. 1045F Polar molecules. 1155–1157. 1414F hormonal signals. 402F Pneumocystis carinii. 1006F Ploidy variation. 1407–1408 Plant vacuoles. 1517 Pollen. 1067–1068. 466 conformational coupling. 1037–1039 universality. 841 evolution. 947 Presomitic mesoderm. 798. 1196F see under Plant cell wall egg (zygote). 841 Plastocyanin. 459. page numbers with an F refer to a figure. 9–10 see also Membrane(s) Plasmid(s). 1085. 1156F epiethial cells. 1586F. 1162–1163. 1046F Saccharomyces cerevisiae. 1199 Plant hormones (growth regulators). heme groups. 1500 Positional information. 1517 structure. 669 POU-domain. 372F Poly-A polymerase. 239F visualization. 852F Platelet(s). 1441. 592F. 901. 50. 1547. 517. 236–238 chromosome puffs. 1035F Poliomyelitis. 1507 host cell transcription shut-off. 1411FF repetitive patterning. 855–856 growth and division. 358 post-transcriptional gene regulation. 1407–1408 regulatory mutations in maize. 220–222 histone modifications. 236 see also Chromosome puffs Polyubiquitylation. 62F digestion. 728. 1409–1410 cell wall formation. 1112F Pluripotent hemopoietic stem cells. 1045F. 1399F. 388F see also specific modifications Potassium channel(s) (K+ channel) bacterial. 357F nonretroviral transposons. 1551F Postsynaptic potential (PSP). 995F. 1163F Plant development and growth. 1155F. 1200–1202. 590F gene expression. 799F. 1410–1412. 357F. 1553 Precursor oligosaccharide(s). 415. 1403 flower development. 518F. haploid cells. 1187F covalent. 517 2D-PAGE. 383. 782F Plant viruses. 56. 671 gating. 220–222 Drosophila melanogaster. 1300 Polytene chromosome(s). 86. 1074 Pol proteins. 1174 Platelet-derived growth factor (PDGF). 1344. specific enzymes Polymerization reactions actin see Actin polymerization DNA see DNA replication energetics. 472F transcription circuits. 401 see also RNA world hypothesis properties. 1157–1158. 87F. 346. 51F Polar ejection force. 857–858 leucoplasts. 477–485 see also Splicing RNA transport control. 1155 Yeast budding. 1501–1502 see also Malaria Plastid(s). 426–427. 1194 Plasminogen. 803 Polyribosome(s). 1543 Plus end tracking proteins (+TIPs). 1042 cytoskeleton and. 1005. 370. 221. 540–541. 1270 shaping and by oriented cell division. structure. 1402F environmental influences. 428F SDS-PAGE. by meristems. 1506F. 1496. 1111. 747F Preimmune antibody repertoire. 1419F Page numbers in boldface refer to a major text discussion of the entry. 345 Post-capillary venule. 841–842 amyloplasts. 707F. 221F Position effect variegation (PEV). 1413–1414. 1351 Positional value. 1044. of myosin. 1289F Polar covalent bonds. 1406 signals for seedlings. 830F.. 1519 life cycle. 246 Point spread function. microtubule formation. 1494–1495 antigenic variation. Protein phosphorylation elastin. 803 Prereplication complex (pre-RC). 471. antigenic variation. 1075–1076. 1269 Polo-like kinases. 357F CPSF protein. 672 leak channels. 357–358. 1194 Plasmodesmata. regulated secretory pathway (exocytosis). 388F see also Protein glycosylation. 1562 Preinitiation complex. 1403. 1491F. 957. 805–806 kinetochore. 974–975. 841 diversity. 1325 Pop (plenty of pharynx) mutants. 1196. 518F Polyadenylation (mRNA 3¢ end). 1403 turgor pressure and. translational frameshifting. 370–371. 52–53 Poleward flux. 186–187. 1044. 969. 1067 Premature ageing. 236–237. 521–522 DNA sequencing gels. 841. 1573 tissues. 1183–1184 protrusion driven by actin polymerization. 696. 372F RNA localization control. 880. 38. 186T noncovalent. 384F Poly-A-binding protein. 995F. 15F diversity. 513F. 140F. 392F antigen processing/presentation. 138. 270FF see also Mismatch repair Proopiomelanocortin. 139. 125–194 abundance in cells. 398 fungi. 546. 139 SDS-PAGE. 307F replication initiation. 531. eucaryotes vs. 1301. 548FF Protein families. 155 mass spectrometry. 1198F Primary cilium. 136. 515F dynamics. 267F. 1282–1286 migration into developing gonad. 398 infectivity. 1118. RNA pol II. 387 Protein function. 15 DNA methylation see DNA methylation gene expression. 397F. Bacteria Procaspase(s). 1291F Primordial germ cells (PGCs). 339 transcriptional integration. 548 classification. 154–155 Protein glycosylation. 392–393. 736–738. 449–450. 1498–1499 Procaryotes. 131F. 593. 527–529. 140–141. 145 glycosylation see Protein glycosylation identification see Protein identification as machines see Protein machines macromolecular subunits. 1072F. 345F mRNA. 307F RecA protein. 767–768 refolding. Protein–protein interactions synthesis see Protein synthesis translocation see Protein transport Protein aggregation CNS vulnerability. 269–270. 1498–1499 abnormal. 1275–1276. 172–173 see also Allosteric regulation analysis methods see Protein analysis assemblies see Protein complexes (assemblies) basic principles. 397–398. 560F domain shuffling. 391F see also Chaperones relation to synthesis. 139F Protein disulfide isomerase (PDI). 1183. 130–131 ER. 136–142 amino acid changes. 518. 1054. 381F. 1197–1198. 737F. 594F electrophoresis. 1498. 277 Translation initiation. 588 Primary antibody response. 166–167 phosphorylation see Protein phosphorylation protein interaction see Protein–protein interactions quality control. 1121. 144F binding site prediction.domains motor see Motor protein(s) movements (shape changes). 257F facilitated by introns and splicing. 143. 514F. 6F see also Enzyme(s) chemical synthesis. 142F. 1498–1499 see also Prion proteins (PrP) quality control. 391F sequencing see under Protein analysis shape/size. 739F glucosyl transferase role. 126 co-translational. 517 X-ray diffraction. 140–141. 147F structure see Protein structure subunits. 130F binding site creation. 1120F. 336–337. 1499F normal cellular PrP. 1195.. 142. 747F see also Endoplasmic reticulum (ER) Protein identification. 130. 346F. 155F sequence homology. 380. 1276F mitosis. 5–6. inducible. 282. 736 Protein–DNA interactions. 131. 504 Primary immune response. 139. 140F phosphorylation. immunofluorescence microscopy. 179–181. 521–522. 427 DNA structure effects. 153–157 see also Active site. 494. 138F. transcription. 148–152 assembly factors. 803 Prophase meiosis. 264 protein families. structural changes and. 388–390. 14 cells. 392. 447. 747F noncovalent interactions. 447FF protein-to-protein binding. 522–523 mass spectrometry. 1194. 1000F Progenitor cells. 1546 see also Immune response/system. 528F degradation see Proteolysis denaturation. 336–337. 143F.adaptive Primary cell walls. 1119F. 519–532 Primary antibodies. 398 replication. 450F Promoters. 257. 64F. 519 sequencing homology searches. 521–522. 155–156 unit evolutionary time. 152F Projection. 1546F see also Immune response/system. 517–532 NMR studies. Proteolysis amino acid side-chain role. 265 domain fusion. 276. 5 binding site(s). 1080 see also Mitotic spindle Proplastids. 397–398 misfolding/aggregation. 1282. 142–143. 380 strand-directed mismatch repair. DNA-binding proteins Protein evolution. 1291. 1288. 1573F. 139F ligand-binding site identification. 148 see also Protein complexes. 282 RNA polymerases. 397–398 neural degeneration due to. epigenetics. 142. 14F. 391F. 434–436 protein synthesis. 512–514. 37F. 257 see also Immunoglobulin superfamily mutation rates. 1583F misfolded protein degradation. 126. 736 ERp57 role. 564 Pronuclei fusion. 739–741. 149–151 viruses. 447. 1080. 739F misfolded proteins. 426 common interactions. 336. 388F monitoring. Protein identification. 1283F. 1072F. 1386F. 148F. 1289F Primary pathogens. 1582. 470–471 consensus sequences. 999–1000. 315–316 Promoter elements. 152–196 enzymes see Enzyme(s) phosphorylation effects see Protein phosphorylation protein–ligand binding see Protein–ligand interactions structure–function relationship. 519–521. 803F Pro-peptide(s). 62F aggregation see Protein aggregation allosteric. 143F see also Protein machines. 416–417 see also DNA structure enhancesome. 524F. 1183 Proteasome(s). 841 Prospero protein. 181F nonprotein components. 142–143. 137–139. 1546. 495F Procollagen. Protein purification Protein-coding RNA. 387–388. 523–524. 387–388. 141F. 397F proteolytic resistance. 1187 Profilin. 1489. 1283 specification by germ cell determinants. 126–127. 521F. 594F globular. Protein–protein interactions Protein databases. 151 dimers. 390–391. 1282–1283 Primosome. 397F Prion proteins (PrP). 520F protein–protein interactions. 392F protein quality control. 1283. 145–146 see also specific types folding see Protein folding functions see Protein function gene regulation by see Gene regulatory protein(s) GFP tagging for visualization in living cells. Protein complexes (assemblies) as catalysts. 434. 338–339 asymmetry. 426. 522F Western blotting. 416–417. 138–139. 339. 738–739 N-linked glycosylation role. 171. 145F assembly. 1187F Prometaphase. 172–173. 472F see also Prion diseases Protein analysis chromatography. 348 modules. 1361 Protease(s). 419F histones. 148 modules. 390–391. 767 . 525F proteomics. 388F energetics. 155–156. 519–521 sequence alignment. 212–213 Rad51 protein. 340T Protein complexes (assemblies). 154F calreticulin and calnexin. 397–398 positive cellular roles. 131 see also Protein structure sorting see Protein sorting stability. 1486–1487 Primer strand. 141F. 173F see also Allosteric regulation eucaryotic gene-regulatory proteins complexes. 265 Protein expression vectors. 397–398. 740F processivity of proteolysis. 14–15. 175 ribosomes. 264. 148. 548. 1527 see also Archaea (archaebacteria). 1391 Proline. 137–139 evolutionary tracing. 139. 138F see also Gene families. specific types Protein folding. 1091–1092. 149 cooperativity.I:38 INDEX structure. 1274. 283F Prion diseases. 64. 137. retinotectal. 388F prion proteins. 390F. 1078–1079. 1086 Promiscuous recombination. 187 see also Protein structure. 338–339. 1187. 345F. visualization by GFP tagging. 397–398 see also Prion proteins (PrP). 151. 517 DNA interaction see Protein–DNA interactions evolution see Protein evolution families see Protein families fibrous. 698. 418–419. 138–139 conformational changes see Conformational changes crystals. 139. 338F eucaryotic. 488 repressors see Repressor protein(s) transcription see under Transcription transcriptional control. 740F molten globule. 1282F specification by neighboring cells in mammals. 592–593. 738–739. 139. 149 self-assembly. 739. 739F. 522FF isoelectric focusing. 391–394. 391. 175. 387–390. 137. 130F pathways. 531F see also DNA sequencing structure determination. 138. 268F Primordial follicle cells. 528. 392F see also Ubiquitin pathway Protein(s). regulation. 519F hydrodynamic measurements. 1285. 338 see also DNA-binding motifs. proteolytic processing. 525–526. 339F bacterial. 1186. adaptive Primary lymphoid organ see Central lymphoid organ Primary oocytes. 738–739 chaperones. DNA synthesis. 1456–1458 see also Stem cell(s) Programmed cell death see Apoptosis (programmed cell death) Proinsulin. 155–156 see also Gene families sequence homology. 440 CG (CpG) islands. 129F. 138F. 1574 Processing bodies (P-bodies). 257. 142–143. 1194F see also Proteasome(s) Protease inhibitors. 397 state. 417F. 529–530 nuclear magnetic resonance. 1498–1499 conformational change. 139F structural resemblance vs sequence resemblance. 518FF 2D-PAGE. 447F gene regulatory proteins. 899 Primary cultures. 391–393. 130. 142F phosphorylation effects. 391. 391F. 999F. 1498 structure and aggregation. 136F. 140–141. 139. 139. 1288 pluripotency. 767 see also Chaperones constraints. 1302F Proofreading by DNA polymerase. 737F. 388F. 1301F. 397 human disease. 528F see also Microscopy. Protein phosphatase(s) functional effects. 379. 854 redox potentials. 151. 640–642 evolution. 184–185 interchangeable parts. 187F gene regulatory proteins. cell-free systems. 176–178. 517 X-ray diffraction. 660F see also Calcium pump. apoptosis. 135F. 1244 Protein kinase C (PKC). 925 PTEN phosphatase (tumor suppressor). 176.” 177–178. 136 unstructured polypeptide chains. 1183–1184 connective tissues. 248. 144F determination. 1104 Protein–protein interactions. 255. 179–180. 185–186. 1181–1182 membrane proteins. 345F. 132–133FF. 380F levels of regulation. 1165 cell surface co-receptors. 141. 938–939 Protein phosphorylation. 59–60. 126F. 1064F. 399 location see Ribosome(s) peptide bond formation. 137F evolutionary tracing.’ yeast. Protein purification Protein interaction maps. 155F antigen–antibody see Antigen–antibody binding binding sites. 827–828. 837F lysosomes. 143. 188 Protein modules. in cell movement. transfer RNA modification. 131. 396F insulin. 251F Pulse-chase experiments. 156 SH3 domain. 131. 142 interface types. 385T see also Antibiotics initiation. caspases see Caspase(s) cell cycle control. 713–718 see also Mitochondrial protein import in endoplasmic reticulum see Endoplasmic reticulum (ER) Protein translocators. 155–156. 136 coding. 373. 423F stability. Translation Protein tags affinity chromatography. 659. 139. 59. Genetic code. 938–939 Proteoglycan(s). 176. 560F large kinase domain. 1182. 597F Puromycin. 610F handedness. 1063F. 200F see also Genetic code prediction. Protein–protein interactions Protein machines. 176F. 403F Pseudomonas aeruginosa. 134F. 515F. 153F. 899F. 3446 protein tyrosine phosphatases (PTPs). 85F. page numbers with an F refer to a figure. 780. protein import signal hypothesis. 141 SH2 domain. 136F modules. 523–527 dimerization. 719–720 see also Chloroplast(s). 701F general flow. 829F allostery. 175–176 Rb protein regulation. 517–532 SDS-PAGE. 806–807 basolateral domain. 145F actin. 154F. 1293 Puffer fish (Fugu rubripes). 451F GTP-GDP exchange as alternative to phosphorylation. 807 signals. 835. 136. 526–527 subunits. 524 optical methods. 154F. 695–748 I:39 chloroplasts see Chloroplast(s). 1181F see also specific types Proteolysis. 1329 Purifying selection. 522FF Western blotting. 135F C-terminus. RNA structure. 860 Page numbers in boldface refer to a major text discussion of the entry. 177 enzymes involved. 399F evolution. 853–854 Proton pumps. 188–190. 700. 807 endosomes. 1494–1495. 1182–1183 sizes. 184–185 position in cell. 384. 33F Protocadherins. 147–148. 1181–1182. 775–776. 1136. 126F polypeptide backbone. 136F. 714–715 Protein transport across membranes. 836 atomic detail. 59. 701–702. 140F paired. 172FF noncovalent interactions. 380. 139. 153. 1181F basal lamina. 602F Pulsed-field gel electrophoresis. 381. 972F Proton see Hydrogen ion (H+. 524–526 quaternary structure. 155F regulation. 636 as molecular sieves. 699–701 peroxisomes see Peroxisome(s). 368. 176F tyrosine kinases see Tyrosine kinase(s) see also individual enzymes Protein kinase B (Akt.INDEX mass spectrometry. 1184T aggregates. 1064 degradation signals. 376F ER and see under Endoplasmic reticulum (ER) eucaryotic. 535F electrophoresis. 375–376. 1123 Pumps see Carrier protein(s) Pupa. 518F Protein structure. 373F. 184 see also Protein complexes (assemblies) Protein microarrays. Transmembrane protein(s). 728F studies. 821. 176. 60F. 154 see also Protein–DNA interactions. 131. 1231. 156F map construction. 397 regulated destruction. 380F. 512–514. 173F see also Allosteric regulation enzyme–substrate see Enzyme–substrate interactions linkage. 199–200. 30. 971–972. 125 primary structure. 178–179 GTP-mediated see GTP-binding proteins (GTPases) phosphorylation cycles. 141F. 154–155. 727F. 517. 380 reading frames. 189F. 186F scaffold proteins. 176F see also Protein kinase(s). 395–396. 145F see also Actin/actin filaments assembly. DNA-binding motifs see DNAbinding motifs (proteins) ‘Protein-only inheritance. PKB). 702T. 177F regulation. 512 inhibitors. 135F b sheets. 32–34. 177F. 142–143. 199F. 154. 125. 699. 153 amino acid side-chains. 145F electron microscopy. 780F photosynthesis. 155. 154–155. 188 Protists. 125–152 amino acid sequence. 1182–1183 protein regulation by. 144F. 348 3-D models. 515 GST. 154F. 422. 176–177. 175–176 Protein motifs. 148F Protein purification chromatography. 143 limited fold numbers. 482–483 depicting. 142–143. 375F. 147F structure–function relationship. 851. . 136 SH2 domains see SH2 domain (Src homology 2 domain) single molecules. 157–158 see also Equilibrium constant (K) cooperativity. 933 P-type pumps (ATPases). Ubiquitin pathway Proteomics. 835F see also Respiratory enzyme complexes Proto-oncogenes. 934. 398F Protein phosphatase(s). 534 Puma. 126F computational analysis. 185–186 gene minimization. 31F. role. 297F see also Adenine. 146–147 see also Peptide bonds. 184–185. 1145–1146 Pseudogenes. “microchips. 136 a helix. 61. 186–187. 131. 548 see also Affinity chromatography. 385T Purple bacteria mitochondrial evolution. 701F. 136F helical filaments. 135. 1074–1075 5’ mRNA capping. 1508–1511 Protrusion. 381F see also Protein folding. 296. 871 general mechanism. 247 Purine base(s). 177F structure. Guanine Purkinje cell. 32–33 as parasites. 125–137 see also Amino acid(s) analysis. 821F. 686. 137. 184–186 activation. 145. 1037 Pseudouridine. 701F mitochondria see Mitochondrial protein import nucleus see Nuclear–cytoplasmic transport between organelles. 807 lipid rafts. 175–176. 85. 141F. 59. 527–529. 155F binding strength. Vesicular transport Protein tyrosine kinases see Tyrosine kinase(s) Protein tyrosine phosphatases (PTPs). 155F. 519F see also Protein analysis. 450. 140–141. 135. 135 noncovalent forces. 807F glycosphingolipids. 368F relation to DNA see Gene expression. Epitope tagging Protein translocation. 1066T. 395–396 see also Proteasome(s). 140F. 602. 132–133FF. 376. 690 PTB domain (phosphotyrosine-binding domain). Drosophila. 519–521 see also Protein analysis. 177 phosphorylation site as recognition signal for protein binding. 187–190 analysis methods. 1448 P-selectin. 1181. 139. 1182F. 1183F assembly/synthesis. 155F see also Allosteric regulation. proton) Proton gradients see Electrochemical proton gradients Proton-motive force. 136–137 membrane spanning regions. 139 components. 84F energetics. 703F through secretory pathway. 898. vs means compare/comparison. Sodium–potassium pump (ATPase) Puberty. 153F. 391 apoptosis (programmed cell death). 1292. 171–172. 154–155 Protein synthesis. 376 Psychoactive drugs. 257F fusion. 379F steps.protein import across mitochondrial membranes. 185. 1063–1064. 703F trans Golgi network. 1288–1289. 514–515. 407–408 experimental analysis. 130–131. 377F peptidyl transferase. 749–787 see also Protein sorting. 528F domains. 143F tertiary structure. 626. 185–186 structure. 116F depurination. 377F elongation factors. 345F. 152F protein aggregate resistance. 153 water exclusion. 190F Protein kinase(s). 140F. 516F histidine tag. page numbers with a T refer to a table. Coomassie blue. 154–155 subunits. protein import endoplasmic reticulum see Endoplasmic reticulum (ER). 140–141. 179F sequence homology. 135. 518FF. 515F cleavable. Conformational changes core structure. 807F Protein stains. 1179. 398. 396F regulatory function. 169–170 allostery see Allosteric regulation specificity. 134F. of actin meshwork at leading edge. protein transport gated. 172–173. 1066T evolution. 132–133FF. 1039F Prox1 protein. 373F post-translational alterations see Posttranslational modification procaryotic. 895 Cdk activation. 521–522. 376F. 1063. 257 Pseudoknot. 384. 139F conformation. Messenger RNA termination. intracellular calcium. 835 bacteriorhodopsin. 153. 368F P-site (ribosome binding). 517. 131. 131. 895 Cdk inactivation. with an FF to figures that follow consecutively. 703F across chloroplast membranes. 136 secondary structure. 550–551 quaternary structure. 911 Protein–ligand interactions. 156. 154F. 188–190. 379–380. 1491 Pseudopodia. Recombinant proteins Protein sorting apical domain. 175–178 ATP as phosphate donor. 126–127 N-terminus. 1237. Protein folding Protein structure–function relationship. 726–727. 347F. 1237F Protozoa. 377–378. 366–400 elongation cycle. 1138T Protofilament. 28F. 1387 Rad51 protein. 84F Pyruvate decarboxylase. 1233–1234. 210F DNA sequences. 200. 1463–1467 Regulated secretory pathway (exocytosis). 828 Redox potential(s). 934 active and inactive forms. 269. 881. 1340F patterning of Drosophila embryo. 791–792. 116F see also Cytosine. 266F see also DNA replication Replication origin(s). 922 see also Protein tyrosine phosphatases (PTPs) Receptor-mediated endocytosis. 268 bacterial. DNA effects. hypervariable microsatellites. 1564. 1535 “Repair factories. 315–316 site-specific see Site-specific recombination Recombination complex. 78F. 281–282 eucaryotic. 307F Receptor(s) cell-surface see Cell-surface receptor(s) down-regulation. DNA topoisomerases structure. 532 DNA cloning see DNA cloning DNA labeling. 1239 RAG protein. 1234. 708 Ran-guanine exchange factor (Ran-GEF). 308. 603F see also Autoradiography measurement. 200F. 1241 normal Ras proteins. 91 mechanical model. 922 Receptor-like tyrosine phosphatase. 482–483. 1234 as oncogene. 543F DNA microarrays. 307F synapsis. 187F Regulatory cascades. Thymine. 601T applications. 532–533. 709F. 828–829. 96. 1316F docking with SH2-domain proteins. 831. 1107. 180F. 794F receptor recycling. in frog. 284F histone association. 602–603. specific types Replication errors. 1242F Ras GTPase(s). 89F. 186–187. 210. 1242. 307F homologs. 929. 601 Radiolabeling. 323F repeat-induced recombination. Meiosis promiscuous. 925F animal development. 1081 nuclear transport. 835.” homologous recombination. 538F. 71F. 761. 850. 922–924. 79–80 ATP role. biotin use. 556 Ran-GAP. 708–709. 1563. 602. 1564F Red blood cell(s) see Erythrocyte(s) Redox pairs. 96F transport. 1518 receptor. 792–794. 266. 1574–1575 Release factors (translational). 929F activation of PI 3-kinase. 286F eucaryotic. 290 mammalian. 929FF Recessive mutation(s). 90F citric acid cycle. 325–326 transgenic organisms see Transgenic organism(s) see also Genetic engineering. 267–268. 402F Pyrimidine base(s). 852F. 1548. 209. 827F. 310 protein–DNA interactions. 1564F. 179. 532. 1046–1047 epithelial apico-basal polarity. 180F Ras guanine nucleotide exchange factor (Ras GEF). 381F. 266. 315F RNA pol II CTD. 269F template strand. 276–277 see also Mismatch repair Replication fork. 1067 chromatin assembly factors (CAFs). 1280 Recombination signal sequences. 537F. 828–829. 828 Redundancy. 1156 growth cone steering. 181F mitogen activation. 532 PCR. 282 cooperativity. GEFs. 711 Ran GTPase(s) compartmentalization. 7–8. 829. 534F RNA production. 602–603. 928–930. 1543–1544. gene expression analysis. 96. 1103. 573F Quantum dots. 793F. 1168–1169. 121F Q Q-cycle. 308F Brca1/Brac2 proteins. 283. 1354. 276F. 862 Recombinant DNA technology. 300–301 see also Ultraviolet (UV) radiation Radiofrequency. 269F. 927. 924F. 534. 927. 1565. 794 extracellular macromolecule import. 830 electron transfer. 761T Rabies virus. 1242 regulation by phosphorylation. genetic. 835F. 540–542. 514–516. 532. 288 see also Human genome nucleic acid hybridization. 553. 545F. 558 Reclinomonas. 881F see also Nuclear hormone receptor(s) ligand-gated ion channels see Ligand-gated ion channel(s) see also Receptor-mediated endocytosis. 127F Random mutagenesis. 832F. 573–574. 61. 269F. 541–542. 924FF. 824–825 activated carrier formation. 804 localization. 1103–1105. 710F Ran-GTPase-activating protein (Ran-GAP). 546 site-specific recombination applications. 272. 791–799 EGF uptake. 929F. homologous end-joining (DSB repair). 925F Ras pathway activation. 533T human replication origin identification. 1236F . 708 Ran-GEF. 307F. 1233–1234. 286. 308F Radiation. 793F membrane protein sorting. 285. 1104F. evolution. 708 Ras gene. 266. 923T. 31–32 Regulatory myosin light chain (RMLC). 1104 ways of losing. 795 editing. 1332 programming of development and. 928F Ras–MAP-kinase signaling pathway. 170. 1067 bacterial. 282. 537 DNA sequencing see DNA sequencing electrophoresis see Electrophoresis historical aspects. 1095 Regulatory T cell(s). 925. 210–211 genetic markers. 281F. 1107 regulation. 928F structure. 89–90. 708 Ran-GTP. 1505 Rac GTPase(s). 269F arrangement. 835–836 Quantitative reverse transcriptase polymerase chain reaction (RT-PCR). 305F. 806F see also Exocytosis Regulation by multisite modifications. 830. 266. 924–925. 835. microtubules role. 284F chromosomal. 71–72. coli replication. 281F strand separation. 306–307. 761F Rab GTPase(s). 804F plasma membrane enlargement. 1176 Rb (retinoblastoma) gene/protein cancer. 1393 Reoviruses. 1496F. E. 1104–1105. 854F Pus. 75F. 39 Refractory period. 548 expression vectors. 931 activation. 760–761. 805. 534. 268. specific techniques Recombinant proteins applications. 709F mitotic spindle formation. 310. VNTRs. 800. 762. 121F oxidation to acetyl CoA. 289–290 nucleosome interaction. 276F. 287F. 1564–1565 DNA repair role. 307–308. 381. 1391 skeletal muscle. 122F glycolysis. 546. 81 glycolysis. 936F activation of MAP-kinase pathway. 1309. 830F concentration changes. 307–308. 762F Rab effector(s). 600–601. 1517. 547F telomeric sequences. host defences. 368F RecA protein homologous recombination. 1107. 923F. 288 DNA synthesis. 928F. 276–277. 201F. 542F. 1354F optic nerve. 280 initiation. 323F multiplication in genome. 96F Pyruvate dehydrogenase complex. 382F Remodeling. 801F. 482F Regulatory DNA. 210. 926–930. 851. 587. 1569–1570. 547F human genome. 830T Reduction–oxidation (redox) reactions. 529 Radioisotopes. 177F Receptor tyrosine kinases (RTK). 282F. Recombinant proteins. 284F Regeneration basal lamina and. 284 nucleosome assembly. 554F antibody chains. 830 DG calculation. 275–276 DNA microarray analysis. specific types Receptor guanylyl cyclases. 1105 experimental analysis. 784. 797–798. 1565 see also Immunological tolerance intracellular. 271–272. 1155F. 831 Reduction reactions. 1309F as speciality of eucaryotes. 929F. 263. 1043 effect on actin organization. 290 DNA damage response. 794 material degradation. 793F iron uptake. 926–927. 276F asymmetry. 761. 603F Radixin. 532. 282. 546. 272F. 852F R Rab5. 1009 Raf kinase (MAP-kinase-kinase-kinase). Rhomediated phosphorylation. DNA synthesis. 1244F knock-out in mice. 546F protein production see Recombinant proteins reporter genes see Reporter gene(s) restriction enzymes. NMR. 1241. 310F Repeat-induced recombination. peptide bond angles. 281F leading strand synthesis. 853 measurement. 850F. 1548F. 280. 346 short tandem repeats. Uracil Pyrophosphate release.I:40 INDEX Reaction coupling. 206 eve gene modular organization. 368. 804. 1531 Pyranosyl-RNA (p-RNA). 539F in situ hybridization. 288 photosynthetic reaction centers. 292 see also Transposon(s). 602F. 283–284 movement rate. 792 transcytosis. 1600 Ramachandran plot. 1168F intercalary. 532–553 basic principles. 548 see also Protein purification Recombination. 1042F. 267–268. 303 general (homologous) see Homologous recombination (crossing-over) genetic engineering see Recombinant DNA technology meiotic see Homologous recombination (crossing-over). 793F signal peptides. 80F see also Free energy Reading frames open see Open reading frames (ORFs) protein synthesis. 1103 mutated in cancers. 282F see also Replication origin(s) lagging strand synthesis. 283FF hemimethylation. 282. 268F Pyruvate anaerobic breakdown. 285F human. 534. 830F standard. 281. 282. 96F Pyruvate kinase. prevention. 315F Repetitive DNA centromeric sequences. 822 Pyruvate carboxylase. 544–546. 797F Receptor proteins see Receptor(s) Receptor serine kinase family. 548F protein tags. 88. 136 Quinone(s). 207F. 268. 1235 cell cycle control. 273 see also DNA helicase(s). 588F Quaternary structure. of synaptic connections. 307F see also RecA protein Rad52 protein. 536F see also DNA probe(s) DNA libraries. V(D)J joining. 488 bacterial. 374F. 4–8. 362F see also specific types composition. 362F see also SnoRNAs synthesis. 612F eucaryotic. 378. 488. 735F retinal binding. 819F.reverse Reverse transcriptases. 360–361. 571 experimental applications. 378F. 571 reverse genetics. 385T Rigor state. 980. 374–375 see also Nucleolus bacterial. 360–361. 283–284 Replicative cell senescence. 832. 337F Page numbers in boldface refer to a major text discussion of the entry. 891F Retinotectal map. 335–336 degradation. 532–533 recombinant DNA technology. 391. 1193 R-gene product. 571–572 Caenorhabditis elegans. 405T RNA folding. 379F binding-sites. 415. 423F eucaryotic. 1080 Respiration evolutionary aspects. 4–5. 1095F. 490F Reproductive cloning. 483 evolutionary significance. 336. 434F. 488 Ribosomal RNA (rRNA).. 445. 1502. 404 ribosomes. 756. 543F retrotransposons. 336T. 445–447. 288F licensing. 835. 890. 505. 384F genome. 819. 292 applications. 379F. gene expression regulation. 340T Ribosome(s). 756F Retrotranslocation. 62F biosynthesis. 385T eucaryotic vs. 831–832. 838. 1067 Replication units. 495–497. 483–484 gene expression regulation. as host defense mechanism. 321F mutation rate. 1240 viral dsRNA-directed ssRNA destruction. Translation ribozyme activity. 485F. 981F. 532. 1022 ER membrane integration. 1432 binding to dynein. 264F. 485. 439–441 RNA–DNA hybrids. 87F cellular types. 334F. 485F. 586–587 Rhodopsin. 507. 1107. refinement. 540–541 sequence specificity. 1019 RISC (RNA-induced silencing complex). 507F. 1502. 548 in situ hybridization. 362–363. 368F. 361F. 404. 834F energetics. 497 mechanism of action. 381 internal ribosome entry site (IRES). 724–725 structure. 835F see also Proton pumps identification. 1042F. 378–379 rough ER. 116F. 379F translational control. 383. 334. 300 information transfer. 336T mRNA see Messenger RNA noncoding. 149–151. 832–834. 1290 modifications. 378 genes. 378F. 112F. translational frameshifting. 404F. 833F. 492. misfolded proteins. 378–379. 496 tumor cell identification. 494. 1059. 379F ribosomal location. 1503 function. 383. 434–434. 1345 Ribbon protein models. 378F. 373. 873F Reverse genetics see Genetics. 70. 335–336. 379F RNA location. 492–493. 320. 361F. 874–875 oxidation of organic molecules. 331. 1229 see also specific hormones Rescue. 132F. 360–361 see also RNA polymerase I. . 85F. 166F RhoGEF. 836 Respiratory epithelium. 360–361. 317. 492F “RNA factory” concept. 318T. page numbers with an F refer to a figure. 1061. 1217 Reporter gene(s) gene expression analysis. 378–379. 318T. 360–361. 362–363. 375 Ribosome recycling factor. 239F see also Transcription RNA cleavage regulation. 418T.. 1393–1395. 340F sigma factors. 70 relation to photosynthesis. 533 Restriction–modification systems. 1532 Respiratory chain see Electron transport chain(s) Respiratory control. 486F RGD motif. 1432–1433. 1518 RNA (ribonucleic acid). 1393F Retromers. 406F allostery. 374F composition see Ribosomal proteins. 336–337. 207F LTRs. 408 see also Catalytic RNA Ribulose. 918F. 402. 416 DNA-binding. 439. 1302–1303. 369F trypanosome mitochondrial mRNA. 485. 404F synthetic. 1432 Retinoblastoma. 1435F colonization. 572F GFP see Green fluorescent protein (GFP) LacZ. 287. of myosin. 373 bacterial. 1303F Dolly the sheep. 832. 585. 834. 835–836. 739–740. 488 see also Protein synthesis.. 335–336. size. 478–479. 415. page numbers with a T refer to a table. 406F conformational changes. 378–379. 85. 1042–1043 RhoA see RhoA GTPase(s) Rhombomeres. 1177 RhoC gene. 571. 381F Riboswitches. 438F RNA pol II vs. 7F processing see RNA processing (eucaryotic) recombinant DNA technology. 378–379 I:41 large subunit. HIV mRNA transport. 360–361. RNA polymerase III transcription. 445. with an FF to figures that follow consecutively. 300. 491 leaky scanning. 379F eucaryotic. 443 Dicer protein. 383. 483. 931. 1394F Retinotectal projection. Ribosomal RNA efficiency. 378F. 6–7. 837–838 Respiratory enzyme complexes. 378F small subunit. 166F. 408. 339–340. 495 double-stranded (dsRNA). 728. 321F see also Telomerase Reverse two-hybrid system. 420F. 586F splicing see Splicing structure see RNA structure synthesis. 361. 384F reverse transcriptase see Reverse transcriptases translational frameshifting. 494F RNA-induced transcriptional silencing complex (RITS). 833F see also Mitochondrial structure NADH dehydrogenase complex. 1432 Retinal ganglion cells. 373 bacterial. 363. 404FF. 5F. 1392–1393. 166. 1066. 918. 1095 Rho GTPase(s) actin organization. 833F. 362F transfer RNA. 18T Rickettsia rickettsia. 287F. 337F transcription cycle. cDNA cloning. 844. 538F RNA editing. vs means compare/comparison. 564F in human disease. origin of life. 112F Ribulose bisphosphate carboxylase. 1105 Retina gap junctions. 166. 318T structure. actin-based movement. 729F hydrophobic interactions. genome size. 494. 384. 408 autoradiography. 1067 prereplication complex (pre-RC) binding. 846 Rickettsia prowazekii. 338. 1515–1516 Rifamycin. 369. translational frameshifting. 374–375. 486–488 molecular conformation. 337F. 361F. 532–533. 447FF mechanisms. 70F Respiratory burst. 546. 1432–1433 neuronal specificity and retinotectal map. 863. effect on cancer incidence. 740F Retrotransposons. 1232 Pol proteins. 334F. 434F tryptophan repressor see Tryptophan repressor translational repressors. 1249 Rhodamine. 446F procaryotic Cro repressor see Cro repressor lac repressor see Lac repressor lambda repressor see Lambda repressor Met repressor. 384F see also Retroviral-like retrotransposons Reverse electron flow. RNA polymerase II. 640. 872. 408F see also RNA world hypothesis genetic material. 318T see also Retroviruses Retroviruses Gag proteins. 490 membrane-bound. in metastasis. 404. 375 electron microscopy single-particle reconstruction. 484 rRNA processing. 496 RNA interference (RNAi). 149–151 eucaryotic. 439T structure. 375 protein location. 755–756. 335F bacterial. 1387 monomeric. 361F functions. 447F. 496 Drosophila. 137F Ribonuclease. 571F chromatin remodeling.INDEX origin recognition complex (ORC). integrin–fibronectin binding. 1393F structure. 318T reverse transcriptase. 484F see also Guide RNAs RNA endonuclease. 728. 1162. in dynamic instability. 361. 332F Ribosomal proteins. HIV. 1094–1095. 361F. 478F. 536–537. 1041–1043. 1435. 1182F Ribonucleic acid see RNA (ribonucleic acid) Ribose. 421F. 532 Restriction (start) point of cell cycle. 1535 RNA-like polymers. 485–486. 486F Rev responsive element (RRE). 819–820. 379F. 270 polytene chromosome(s). 494F RITS (RNA-induced transcriptional silencing complex). 1522. 1502 mucus. 572–573. 321F see also Transposition HIV see HIV (human immunodeficiency virus) integrase see Integrase life cycle. 833F. 496 River blindness. 1234–1235. 373–376. 346. 524 Rev protein. 1432F Retinal. 378–379 ribozyme-catalysed reactions. 571–572 transposable element reduction. 445. 844F. 831–832 localization. phagocytosis. 288F replication units. 374F free. 423F operator binding. 1525 Restriction enzymes biological function. 729F polyribosomes (polysomes) see Polyribosome(s) protein synthesis. 293. 836F cytochrome oxidase complex. 1043–1045 growth cone steering. 286. 1235F Retinoblastoma gene/protein see Rb (retinoblastoma) gene/protein Retinoic acid. 378–379. 375–376. eucaryotic replication origins. 347F RNA-induced silencing complex (RISC). 831–839 cytochrome b-c1 complex. 6–7. 542. 406F protein catalysts vs. 8F. 483–485 mammalian mRNA. 322F human genome. 379F antibiotic binding. 1055. 1104. 1450 oncogenesis. 374F assembly. 889F. 331F see also Transcription localization. 323 see also Retroviral-like retrotransposons Retroviral-like retrotransposons. 1287 Reproductive hormones. 442F Repressor protein(s) discovery. 1285 Retinoic acid receptor. 384F. 436F. 1391. 283–284 S. 1162F histology and cell renewal. 497. 1523F RhoA GTPase(s). 1391. 1535 editing see RNA editing evolutionary significance. 6–7. 602 error frequency. cerevisiae. 364F. 534F. 572 technique. 332. 362F processing. 375F catalytic site. 86. 433–434. 489F Ribozymes. 321F genome integration. 402F RNA polymerase(s). 337 eucaryotic. 1356. 1064. 580. 1372–1373 Segmentation. 343 transcription termination. 983F cell cycle. 1388F. 334 orientation. 1403 Arabidopsis mutants. 1056F cell polarization. 486–488 gene expression regulation. 415. 1497F mutation rate. RNA interference (RNAi). tight junction(s). 403F Tar. 341F. 346. 379F. 1509F pathogenicity islands. 335F fidelity. skeletal muscle. 1532. 1400. 1433F response to light. 1329 Segment-polarity genes. 478 tertiary. 1546F Secondary cell walls. 1533 spread. 805 proteolytic processing of cargo. 1496F Rough endoplasmic reticulum see Endoplasmic reticulum (ER).I:42 INDEX limited genetic code?. RNAi. 1518 strategy against host membrane traffic. 715 Sar1 protein. 1067–1069. 339. 404. 9. 383F Self-assembly. destruction by APC/C. 605 Securin. 495 folding. gastrulation. 368F nucleotides. 1232.. 1044 centromere structure. 344 functions. 660. 919–920. 487–488. 1400F structure. 403–404. 339. 190F role of cytoskeleton. 408 double-stranded. 759F Sarcoma(s). 345–346 editing. 287F genome. 1087 Sedimentation coefficient. 360. 400–404. 188. 1146F Selective pressure. 338 reaction mechanism. 1228 Schistosomes. 188. 1491F phagocytosis. 1066. 517. 438–439. 1466 Satellite tobacco necrosis virus. 1511F. 343F. DNA. 340T RNA polymerase III. 340T. 338. 1163. 340T RNA polymerase I. 299–300 elongation factor association. 1546 see also Immune response/system. 334 structure. 637 see also Polyacrylamide gel electrophoresis (PAGE) Sealing strands. 803 membrane recycling. 1145–1146. cellulose synthase. 401 polypeptides. 229. 350–351. 1407F Root hairs. 1206. 440 transcriptional mediator. capsid. 340F bacterial polymerase vs. 62. 407 natural selection. 1156. 19. 184–185. 1404–1405F tip. 1195.adaptive Secondary lymphoid organ see Peripheral lymphoid organ Secondary oocytes. 1148–1149. 1289F Second messenger(s). 1177T functions. 339. 1534. bladder cancer causation. 287 protein interaction maps. 710 RNA virus(es) assembly. 404–406 self-replicating system. evolution autocatalysis requirement. Holliday junctions. 477–481 see also Alternative splicing mRNA capping. 397–398. cellular polarity. 339. 1108 Saccharomyces cerevisiae actin. 286–287. 1386F. 1429. eosinophil attack. 332. 522 Seed(s). 1433. 552 Salivary gland. 1149F tight junction(s). 339. 455F Saltatory conduction. 609F S-Cdk. 332F. 334–335 nucleoside triphosphate substrates. 379F. 340T. 236–238. 404 noncovalent interactions. 317 Self-replicating molecules. 343F. 1064. 439T. 1065F. 537 RNA processing (eucaryotic). 401 catalytic RNA. 983. 340T general transcription factors. 803. 1550F structure. 1148F PDZ domains. 336–337. 332 see also Nucleotide(s) phosphodiester backbone. 403F. 333F. membrane proteins. 64. 1390 transcription regulation. 1148 synapse formation and. DNA replication. cerevisiae see Saccharomyces cerevisiae SCF (stem-cell factor). 403–404. 864 mutants. 1512F Salmonella. 24F. 1040F RuvA. 1356FF Sensory neuron(s). 930. 487F 3¢ UTR. 364–366 polyadenylation. 1403F Segmentation genes controlling.general (TFII) evolution of. 607–608. 346 transcription initiation. 272F RNA probe(s). 1146F L-selectin. 286–287. epithelial apico-basal polarity. 1338F. 403 DNA comparison. microscopy sample preparation. 1329. 1029 Satellite cells. 286–287. 1404F Seedlings. 401 Self-splicing RNA. translational recoding. 802F formation. 1432. 351 splicing mechanism. 408F S S1 fragment. 1499 rRNA see Ribosomal RNA RTK (receptor tyrosine kinase) see Receptor tyrosine kinases (RTK) Rubisco see Ribulose bisphosphate carboxylase Ruffling. 1056–1057. 312F 1056F Schwann cell(s). 415. 339–340. 800 Secretory vesicle(s). 350F. 10F “Selfish DNA. 637 SDS-PAGE. 334–335 protein–DNA interaction. 517. 552 His gene. 237F. 1087 SDS (sodium dodecyl sulfate). 585. 402–403 see also Catalytic RNA. 1508. 1405F. 272. 518F. 1145–1146. 1356–1357. 1356F Sensory cells. 403. 800 egg (ovum). 1556F Secretory C-terminal. 363 RNA polymerase II. 266F Seminiferous tubules. 1307F Sebaceous gland. 440 chromatin remodeling. 339. 340F C-terminal domain (CTD). 383. Antibiotic resistance. 402F. 402F transition from pre-RNA world. 340T transcription regulation. 1532F Schizosaccharomyces pombe. 343–344 energetics. 1145. 335 DNA repair coupling. 342–343. 333F. 1068 S. 341–342. 1407F Rosettes. 485–486. 351F AT–AC spliceosome. 642 Rotaviruses. ion channels. coated-vesicle formation. 1145. Ribozymes Rock kinase. 334F superhelical tension generation. 1293 Semliki forest virus. 482–483 Secretory granule(s) see Secretory vesicle(s) Secretory protein(s). as transducers. 486–488 mechanisms. 488F nuclear see Nuclear–cytoplasmic transport regulation. 1407F Root cap. 1512. 486–487. 1418F Secondary antibody response. 361 RNA primers. 1028. 601 Scrapie. rough Roundabout receptor protein. 1496F RNA world hypothesis. 580F Scanning electron microscopy (SEM). 1346F. at leading edge of cells. 229F DNA replication.” 1044. 495 double-stranded RNA (dsRNA). 1232 Sarcomere. structural changes coupled to DNA-binding. 1196 Secondary cultures. 511. 433 DNA polymerases vs. 358 RNA polymerase III. 332F secondary. 894. 266. 1372F Segmentation clock. 1152F. 356–357. 477–485 3¢ changes. 1345. 401. 1201 Rotational diffusion.general (TFII) processivity. 454–455. action potential propagation. 343 transcriptional activators. 64F. 19F Selectin(s). 1507 Senescence see Cell senescence Sensory bristles. 668. 1066. myosin. 1402. 1028F Sarcoplasmic reticulum. 300. interactions with other proteins. 680 SAM complex. 1186 Scute gene. 672 Selenocysteine. 403 tRNAs. 190F Schistosoma haematobium. transcription attenuation role. 1498 Scribble complex. 339. lipid bilayers. 407F natural selection. 1330F see also Drosophila development vertebrates. 334. 1336–1338. phase variation. 1550. 1337F. 403F hairpins. 149F Scaffold protein(s). 357–358 “RNA factory” concept. 1433F renewal. 353–354 ATP hydrolysis. 346 splicing see Splicing RNA–RNA rearrangements snRNPs. 1064. 483–485 gene expression regulation. 897. 1288 exocytosis. 1157F Scurvy. 403F RNA transcripts see Messenger RNA RNA transport. 969–970 “shmoo. 1338F Drosophila see Drosophila melanogaster segmentation genes see also specific genes insect body. 1095 Rod photoreceptors (rods). 1523 Selectivity filter(s). 1062. . 1356 S-cyclins. 1375 SCF enzyme complex. 1389 Semiconservative DNA replication. 285F as model genetic organism. 185F. 1388F. sequencing. 339F promoter binding. Drosophila. 585F. 1066T protein interaction maps. 332–333. 333F base-pairing. 759. 337 proofreading. 346 nuclear subdomains. 504 Secondary immune response. 147 Scale. 440 see also Transcription factors. 270. 1145. 1339 Segment shuffling. 1044F Saccharomyces pombe. 918F Root(s) apical meristem. 1289. 1535–1536 genomes. 404–406 polynucleotides. 312F RuvB. 1491 invasion of host cells. 272. myelin production. 1333. 1429 see also specific types Sensory epithelia. 1153–1155 unstructured polypeptide chains. 340T RNA polymerase II. 1233F. 1153F Sea urchin. 339. 920F outer segment. Drosophila polyteny. 339–340. Holliday junctions. 725–726. 893 see also Cyclic AMP (cAMP) g-Secretase. 1401F in plant development. genome. 1293 synapses see Synaptic vesicle(s) Sectioning. 1389 Rous sarcoma virus. renewal. 347F structure. 351–352 RNA splicing see Splicing RNA structure. 237FF Salmonella enterica. 1429–1433 Sensory mother cell. 931F. 1152. 801F membrane fusion. 608F. 344–345. 678 Scintillation counter. 340T chromatin effects. exocytosis. 947 Secretory component. 1520–1521 structures. 1056–1057. 803F sperm. 287F. 340–342 see also Transcription factors. 343. 368. 1026. 1433F amplification of signal in visual transduction cascade. 1371–1372. 345F see also individual enzymes RNA polymerase I. 356F see also Catalytic RNA SEM see Scanning electron microscopy Semaphorin protein.” definition. 341. 482–483 splicing. 149–151 defense. 1012 S6 kinase (S6K). 801–802. 1199. 332. 517F membrane protein solubility. 343F chromatin-modifying proteins. 178. 899F. 489F “Shmoo. 177F Signal patch(es). 274F Sister chromatid(s). 562F see also Haplotype blocks physical gene mapping. 1318–1319. 1466 see also Muscle fiber(s) genesis. 1154F Septic shock. 1279–1280. 768. 937–938. 905–909 G proteins see G protein(s) (trimeric GTP-binding proteins/ATPases) NFkB. 140–141. 936 Src family. 1183 signaling proteins. 1389 SL RNP. 1271. 336 Small intestine. 1123 cancer role. page numbers with an F refer to a figure. 1029F Skin architecture. 1275 sex determination and. 1317–1318 mechanisms of signal spread. 1012F. 136F. 722 rough endoplasmic reticulum protein import. 1027F. 351 function. 1530 nuclear receptor superfamily. 1283. 527. 1524 virulence plasmid. 354F transcription. 1256 Small interfering RNA (siRNA). telomeric repeats. 276F eucaryotic. 1226 function. 1408FF. 565F mechanisms conservative. 481F. 481F. 136F. 570 Sequential induction. 1101 Sickle-cell anemia. 155. 1463–1467 modulation. 727–730. 1319–1320 see also Drosophila development Serine protease(s) active site. 762–763. 1120 extracellular see Extracellular signal molecule(s)/pathway(s) intracellular see Intracellular signal molecule(s)/pathway(s) kinases as input–output devices. 352 U4 snRNA. Drosophila. 1243F caspases. 701F M6P addition recognition. 1163. 439. 1435 neurotransmitter role. Meiosis. 275F. 243FF. 898. 455F mutations. diploid cells. “microchip” analogy. 1089F spindle attachment. 1029. 895 Signaling cell(s). 1534 Septins. 488. 273. 279F see also Strand-directed mismatch repair Single-strand DNA. 1521F Simian virus 40 (SV40). development. 349–350 assembly. 155F protein phosphorylation. page numbers with a T refer to a table. 243FF cohesion. 178F structure. 951 Smooth muscle calcium influx. 1030 cells. 1088F. 481–482. 132–133FF. 1172 developmental. 726–727. 202. 336T. 705 peroxisomes protein import. 1286F variation between species. 1269–1304 evolutionary perspective competitive advantage. Transposase Skeletal muscle. 1030 Snail gene/protein. 925. 1283F. 1436F Small-molecule inhibitors. 349. cellular) transmembrane transport. 1087. 684 Sertoli cells. 149F SINEs (short interspersed nuclear elements). 1411F “Shotgun” gene cloning. 1286F Sevenless mutant. 138–139. 1285–1286 strategy differences. 1491 actin-based movement. 1388F. 1070 SMN (survival of motor neurons) protein. 1242–1245. 1132. 274. 277F. 1132F. epithelial–mesenchymal transitions. associated mutations. 336T see also Splicing nuclear localization. 775F Sic1 protein. 719–720 mitochondrial proteins. 762–763. 1414 Separase. 354–355. 728. 1269. diversification and origin. 1286 see also Primordial germ cells (PGCs) Sex differences. 1097 Sequence tags. 902. 904 endocrine cells of respiratory epithelium. 1463–1467 structure. 154. 129F Serine/threonine kinases. 1516F antibiotic-resistant. 701F. 1089–1090. 889–891. Myosin(s) cells. 178. vs means compare/comparison. genetic engineering. 138F Serine. Arabidopsis mutant. 1054 meiotic.” of yeast. 306 DNA replication machinery. 336. 278. 960–961. 1463F blood vessels. 1409–1410. 324F. 365F transcription. 1516. structure. 1418F cancer. 701–702. 1417 Mammalian. 785 nuclear localization signals. 177 see also individual kinases Serine/threonine phosphatases. 336. 1145. 1271–1272. 482F gonad development. 364 Page numbers in boldface refer to a major text discussion of the entry. 1463–1464. 325–326 transpositional see Transposition see also Integrase. 1280–1281 Sex hormone. 177–178. 1271. 340T snRNAs. 887F see also specific pathways/components. 131. 354F Slug gene/protein.smooth Smoothened protein. 178F structure. 482F Sex-reversed mice. 763FF tetanus toxin target. 1054. 464F satellite cells. Drosophila sex determination. 701–702. 1282 SH2 domain (Src homology 2 domain) cell signaling proteins. 455. 1278 Sepsis. 961F Silent mutation(s). 1088. 1026. 273. 352 U2 snRNA. 264 Simian immunodeficiency virus (SIV). 575–576. 1133T see also specific types Signal sequence(s). 1075 separation. Y-chromosome Sex determination. 340T U1 snRNA. 178. 325–326 genome rearrangement. 473. 1418F replicative senescence. 349. 565. 277. 177F regulation. capsid. 1119 cell adhesion and. 728. 325–326 consequences gene control. 1194 protein family evolution. epithelial–mesenchymal transitions. 764F membrane fusion. 361 function. 363 see also Spliceosome snRNPs. 727F. 322 Single-cell expression analysis. 888. 324. 1141 Smad4 gene. 1284F see also X-chromosome. 1534 Septate junctions. 641. 354F recycling. 1318F see also Development. 1026F. 1325–1326 inhibitors. 1070–1071. 362F nuclear localization. 1316–1317. 243. 1273 mitotic. 365F protein complexes (snRNPs) see SnRNPs SL snRNA. 244F. 351. with an FF to figures that follow consecutively. 293 supportive functional requirements. elegans. 760 SnoRNAs. Toll-like receptors. 542. 1075. 1255 Smad-dependent signaling pathway. 1318F morphogens. 1283–1285. 1012 see also Actin/actin filaments. 651 universality. colorectal cancer. 1272–1274 see also Egg (ovum). 1463 differentiation. 705–707 Signal-recognition particle(s) (SRP) protein transport. 1141 SNARE proteins disassembly. 364–365 Smooth endoplasmic reticulum see Endoplasmic reticulum (ER). 141. 1491F Shine–Dalgarno sequence. 1417–1418 Sliding clamp. 880 Signaling molecule(s)/pathway(s) BH3-only proteins. 1147 Sigma factors. 940F Smad family. 764. 1316. 1044. 349. 927 Sev protein. 730 structure. 1084F Site-directed mutagenesis. 353–354. 702T Signal transducers. 891F photoreceptors. 22 overview. 337F. 281F Slit protein. 351. 554F meiotic pairing. 763F vesicular transport guidance. 137–138. 1090. 889F. 144F surface–string interactions. 177F proteoglycans. 140F structural homologies. 5-HT). 941 cell signaling. 349 U5 snRNA. 630–631 signal transduction see Signal transduction turnover rate of signaling molecules. 141 Shigella flexneri. 560F Single-pass proteins see Transmembrane protein(s) Single-strand DNA-binding proteins (SSBs) cooperativity.INDEX Sepallata. 565. 156F SH3 domain (Src homology 3 domain). 365F AT–AC spliceosomal. Drosophila. meiosis regulation. 891 Signal transduction adaptation (desensitization). 1279F fertilization see Fertilization gamete production. . 1401F. 713. 273. 1284–1285. 1271F genetic diversity. 1087. 178F STATs. 938 Serotonin (5-hydroxytryptamine. 1495 Sidekicks proteins. 1282–1286 Drosophila melanogaster. protein transport. 439T Signal hypothesis. 760 vesicle SNAREs. 464. 769F Rab effector interaction. 1269–1271. effect of SSBs. 1269–1272 sex determination see Sex determination species differences. 560 genome evolution. 920F cyclic AMP. 762–764. 924–926. 1317F. 940F plants. 280 structure. 295T. histology. 1278 Sialic acid (NANA). 352 U6 snRNA. 920. 1070F resolution. 763F. 243. 1136–1137. 938F evolutionary tracing. 627F. 925F. 560. 324F. 714F nuclear localization signals. 726–727 types. 156. 898. 703F chloroplast proteins. 936 regulatory role. 1463 cell size. specific types/pathways Signaling networks. 8–9 Small nuclear ribonucloproteins see SnRNPs Small nuclear RNAs see SnRNAs Small nucleolar RNAs see SnoRNAs Smallpox virus. 1083–1085. Spermatozoa germ cell development see Primordial germ cells (PGCs) haploid vs. 1270F horizontal gene transfer. 941 Small-cell lung cancer. 761 target membrane SNAREs. 576F Single-nucleotide polymorphisms (SNPs). 899F. 1154–1155. 207F. Morphogenic gradient(s) DISC. 349–350 catalytic functions. 259 inheritance tracking. 728F Signal-relaying junction(s). 175 regulatory role. 956–959 receptor-linked. 886–887. 1418. 890 Sex-lethal (Sxl) gene. 1436–1442. 527F Small molecules organic see Organic molecules (small. 1044F Shoot apical meristem. 349. 1496 SMC proteins. 155F extracellular matrix degradation. 1026. 565F Site-specific recombination I:43 applications. 364. 628F. 1463–1467 actin filaments. 939–940. 1316T C. 551 Shugoshins. 1463–1467 regeneration. 324. 939. 275F Single-strand DNA breaks (nicks). 927 Sex chromosome(s). 352. 774F. 1087F. plant photoproteins. 1450 mechanism of action. 728F Signaling cascades. synapse formation. 274F. 1284 Sexual reproduction. 274F DNA hybridization role. 380. 1003. 352 components. 1503 epithelium. 518F. 123F Succinyl-CoA synthetase. 353 SR proteins. 1270F. 609F Steroids. 353–354. 1066. 832F Sperm see Spermatozoa Spermatids. 480. 16F RNA–RNA rearrangement. 1421. membrane lipid(s). 305. 1396 Src family of protein tyrosine kinases. 843F. 539–540. 352F. 178. 720F role in tumor progression. 661–663. 1292–1293 binding to egg. 1292–1293. 1297. 354F tRNA. histochemical. 719–720. 276–278. 507F Somatosensory region. pombe. hemopoietic. 55–58. 841. 367F. 94F synthesis. 1282. 993 Spirochaetes. antibodies. 1217–1218. 70F. 136F. Drosophila. 995F. 205F sex determination. 1295–1296 spermatids. 347. tree of life. 1458F chloroplasts. 350F machinery see Spliceosome(s) release. 350F. 178F Src see Src protein structure. 1298. 647F structure. 347. 95. 504 Spinal muscular atrophy. 732 mechanism. 1385–1386. voltage-gated see Voltagegated sodium channel(s) Sodium dodecyl sulfate see SDS (sodium dodecyl sulfate) Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). infection route. 1297 mitochondria. 94F see also Starch structure. 1424F gut epithelium. 136. 354F active site. 1294–1296. 846 granules amyloplasts. 842. 418T Space-filling models. 1219 Stem cell factor (SCF). 178F Src homology 2 domain (SH2) see SH2 domain Src homology 3 domain (SH3) see SH3 domain Src-like kinase. ER protein transport. 733F Starvation. 148–152 Succinate. 1436–1437 hemopoietic see Hemopoietic stem cells immortal strand hypothesis. Splicing Sodium-calcium exchanger. 1293 meiosis in. 841. 178. 38–39 Species divergence. 353 trans-spliceosome. 55–58. 355. 352. 1335 Solvent(s). 1425 embryonic (ES) see Embryonic stem (ES) cells engineering. hemopoiesis control. 1088 Spindle pole body. 50 lysozyme. 619F. 1425F multipotent. MHC protein. water. 554–555. 355. 1285 Sp1 protein. 348F. electron carriers. 463 Stathmin. 1490F Spiroplasma. 350F. 1503 Stomata. 480F signals. 816F . 353 Sry gene/protein. 662F selectivity. cortisol release. 1285. 713F. 88F. 1294 spermatocytes see Spermatocytes spermatogonia. 906–907. 348F muscle cell isoforms. 481F. membrane lipid(s). 1293. 351F U4/5/6 triple snRNP. 352 RNA–RNA rearrangements. 1418. 744–745 Sphingosine. 919T Stomach bacterial colonization. 1293. 1105 Start-transfer signal(s). 112F. 928 SOS response. 353F trans-splicing. B-cell signaling. 1418F Substrate(s). mutation rates. 114F Steel factor (SCF. 678. 660 Sodium channel(s). 585F Staphylococcal nuclease. 55–56. 1421F division rate. 350–351. 1503 cancer.I:44 INDEX motility. 679. Helicobacter pylori association. 355–357 evolutionary advantage. 306 Stratified squamous epithelium. 1165 cells. signaling pathways. 272. 1386F tissue culture. 1283–1285. 265F heat-shock induced recombination. 354–355. 115F Sterol(s). Mutation(s) Somatic nuclear transplantation. 56 derivatives. 144F SH2 protein domain. cerebral cortex. testes development. 355F Spo11 meiosis-specific protein. 349–351. 1299F cortical reaction and. 1229. 845F see also Photosynthesis as building blocks. 1348 induced recombination. stem-cell factor). 14F. 645. 159–160 see also Ligand(s) Subunits (macromolecules). 351 lariat structure. 352. 1434 Streptococcus. 1008 Spectroscopy. 1420. 646. 355–357 fidelity mechanisms. Monosaccharides. 349F splice sites. 1293 secondary. 846 Sugars. 1375 Stem cell(s). structure. 1293 Spermatozoa. 265. 350F Splicing. 481–482. 719–720. 164F protein molecules. 347–348 mechanisms. 845–846. 123F Succinyl CoA. 351F. 1577–1578. 1299. 1596F Src protein functional role. 353–354. 354F sm proteins. 385T Stress. 1228. 277F Strand invasion. 122F. 1294 Spermatogenesis genes regulating. 1566–1567. 109F Somatic cell(s). 1421–1422. 477–481 Drosophila sex determination. 113F see also Carbohydrates. 1349F mutations. 354–355. 351–352. 351–352. 1292–1296 adaptation for DNA delivery. 1417–1484 asymmetry of daughter-cell fates. 350F RNA–RNA rearrangements. 831. 94F. 1396 Steric limitations. 637 Sodium independent chloride–hydrogen carbonate exchanger. DNA sequence recognition. 1501 Streptomycin. 1294. 161F Staphylococcus. 363 see also SnRNAs. 351–352 SL RNP. 349F. 127F Steriocillia. 619F. 679F Squint. 352 see also SnRNAs evolution. 631 regulation. 347–348. enzyme binding. 1000 Stearic acid. chronic myelogenous leukemia therapy. homologous recombination. mode of action. 1261 Stimulatory G protein (GS). 352. 1209 see also Cancer. 1428 protein transport. 1375 Stem cell niche. 352 U1snRNP. 369. 539F Sox9 gene/protein. 1424 role in cancer. 353–354. 1296F Spermatogonia. 178. 56 storage. 936 deletions leading to cancer. 1298–1299. 646F precursors see Spermatocytes production see Spermatogenesis structure. 1430. Polysaccharides. 1293 stages. 659 Sodium–potassium pump (ATPase). 669 pumping cycle. 354F Splice sites. 1298F acrosome reaction. SMN protein mutation. 1293F plasma membrane domains. cortisol release. 354F base-pairing. 369F Splicing signals. 908 Somite(s). 579. 1208. 841F chloroplasts. 1436 ulcers. 1293F Spermatozoon see Spermatozoa S phase of cell cycle see under Cell cycle Sphingolipid(s). 1209 Somatic hypermutation. 1293. 177F membranes. 1421F. 351F self-splicing see Self-splicing RNA transesterification. 1424–1426. 351. 1501 Starch biosynthesis. 178F structure. 994F actin filament web formation. 618–620 STI-751 (Gleevec). 347–348 alternative see Alternative splicing AT–AC splicing. 204–205. 1269 SPR see Surface plasmon resonance (SPR) Squames. 265. 350F. 349. 350F U5 snRNP. 179F regulation. 463 Stress fibers. reaction rates. 355. 1442F Stem-loops. 511. 1419. inherited. 1280 S. 355F evolution. 347–348. 842F structure. 348 gene expression regulation. 1371. 349–351. 351F assembly. 365F splicing mechanism. 1450–1463 production. 824T polymerization. 1286 sexual reproduction. 1372F Sonic Hedgehog protein. 366 errors. 264 Specificity pocket. 625 see also specific types Sphingomyelin. 744–745 Spinal cord development. 853 mammary gland. 1055. 350F. 113F energy source. 662F osmotic regulation. 123F Sucrose. individual sugars Sulfolobus. 1294F. 618. 346. 349. 96–97. 352–353. 1293–1294. 618–620. 352. 364–365 Spindle assembly checkpoint. 1281 primary. 310–311 see also DNA repair Southern blotting. 14F Spisula development. 350F. cell cycle analysis. 517. 1465 plasticity. 684 Subcutaneous layer (hypodermis) of skin. 1286F S–S bonds see Disulfide bonds Staining. 1058 Spliceosome(s). 350F. 1008 membrane cytoskeleton. 1061. 352F. 133F Species differences chromosomes. 1430F. 350 AT–AC spliceosome. 1441. 1458–1459. 950 Son-of-sevenless mutant. 403F Stereocilia. 351–352 catalytic RNAs. 480 regulation. classical experiments. 1093 Stroma. 1348. 381 Strand-directed mismatch repair. 350F. 1007F actin filament packing. 507–508. 1285–1286 Xenopus laevis. 1300F see also Fertilization capacitation. 95 Start (restriction) point of cell cycle. structure. 466F Sog gene. 1222 Strychnine. 354F cellular location. 1431F Stereo vision. 112–113FF biosynthesis via photosynthesis. 1208. 552 Spore(s). 846 Stop codons. 1293. 350F. 1392F Somatostatin. 671 So (sine oculis) gene. 1579F Spectrin actin cross-linking. 1295F syncytia. 1228. 1419F Squid giant axon. 350–351. 72–73. 351F U2 snRNP. 178F SRP see Signal-recognition particle(s) (SRP) SR proteins. 1417–1428 founder cell population. peptide bonds. 1271 functions. 69. 1476–1483 epidermal. 1294 Spermatocytes. RNA structure. 482F intron removal. 352 assembly. 354F ATP hydrolysis. 658 Sodium-linked symporter. 1232 evolution. 618. 351F U6 snRNP. 57F. 352 mode of action. 1567F Somatic mutation(s). 122F. 350F U4 snRNP. 628. 882F synaptic cleft. 198F dimer formation. 1569–1589 accessory receptors. 284F. 292–294 cancer. 890. 116F. 882. 868 Superoxide dismutase (SOD). capillary sprouting. 833 Supporting cells. 270 Taxol. 1170. tree of life. page numbers with an F refer to a figure. 282–283. 3–4. 1107 Telophase. 1134F. 1573 development. definition. 292 replicative loss. 139 Threonine. 528F Suprachiasmatic nucleus (SCN). 197 base-pairing. 207. DNA bases. 1393. 1142F see also Cell adhesion. 515–516 Tandem mass spectrometry. 1435F Surrogate light chains. 1401F Swinholide. 1392–1409. 342F location. 210. genome evolution. olfactory epithelium. 1395F organization/structure. 843. 698 Thylakoid space. 1396–1397 signaling. 843 membrane. 210 evolutionary conservation. 1591F antigen recognition. 1047. 988T Switch helix. aging. 1152–1153. 1429F Suppression. 714F mitochondrial protein import. 1581F see also Helper T-cell(s) (TH) CD8. 344F Superoxide. 1571 see also CD4 T-cell(s). of electrical activity in synapse modification. 1102. 1149F regeneration. 293. 1420 Terminator elements. 1138T T cell(s). 1580–1581. Extracellular matrix (ECM) cell growth and. 1283–1285. 559 Synthetic phenotype. 200F. 1152F scaffold proteins. 682 vesicles see Synaptic vesicle(s) Synapsis. 1590F. 1580F. dependence on electrical activity. 1174. 3–5. 1599F antigen presentation to. 267F. 1540 T cell receptor(s). 288F. 1572T. 907T receptor. 355F. 1579–1580 general properties. 1127F Suspensor. transcription attenuation. 250 conserved. 22F T7 polymerase. 159 Thy1 protein. 1151–1152. computational protein analysis. 1566F Survival factor(s). apoptosis. 1150–1158 epithelial cells. 1226 Tetraspanin.general TGFb superfamily see Transforming growth factor-b (TGFb) family TGN see Trans Golgi network (TGN) TH see Helper T-cell(s) (TH) TH17 cells. 1391F neuronal specificity and retinotectal map. 1595–1596 CD3 complex association. 4F. 1585F organ-specific protein expression. 1599F Thylakoid(s). 1577–1579. 200. 341F. 1126. 1391. 1591–1592. 1551F main classes. 1549. 719–720. 763F Synteny blocks. 318T Tandem affinity purification tagging (tap-tagging). 803 structure. 344F Superhelical tension. 1549–1551. 478 TATA-binding protein (TBP). 1527 Telomerase. 247 Syntaxin. 118–119FF entropy. 1599F T cell development. 1131–1132. 288. 1275. nonactivated dendritic cells. self-reactive lymphocytes. 342F Tat protein. 129F Thrombin. 293. 66–67. T T4 bacteriophage. 1390F Sympathetic neurons. 1151. 1569–1589. 559 TATA box consensus sequence. 1464 Syndecan-1. vs means compare/comparison. 293–294 senescence role. 505 cell senescence and. 1570–1571. 1118–1119 Tar RNA structure. functional genomics. 10F. 891F Thyroxine. 1598–1599 T cell-mediated immune response. 1298–1299 Tet repressor. 29 mitochondrial origins. 462F TIM complex. 294F T-loops. 293 replication. 1149F. 1586. 1599. 1540. 1148F immunological. 1099 Drosophila embryo. 842–843. 293. 1570–1571. 1170F Tam3 transposon. 1151F transmembrane adhesion proteins. 1596F Symbiosis chloroplast origins. 338. 1140F selective assortment. 87F Tail region see Fc region. 1394F formation. 682 Synaptic connections. 1590F structure. 1132F selective adhesion. 1184T Syndecans. 339 Testes development. 1153–1155. 1579F. 340–341 TFII transcription factors see Transcription factors. 713F. 1429. generation. 67–68. 1393–1395. b-globin abnormalities. 18T Synonymous mutation. 995F. 297F structure. 659 Synapse(s). 1153F transcellular transport. 507. 1174F lymph node. 1276F Synaptic cleft(s). 1103. 269 Tagged knockouts. 988. 306F. 719 Timeless protein. 1579–1580 MHC protein interaction. 66–67. 3H-thymidine autoradiography. 1543 MHC class restriction. 461F Synthetic lethality. 1152F. 1550 resting. 1136–1137. 843. circadian clock. 340. tree of life. 868 Superoxide radical. 711F. 448F. 682 chemical see Chemical synapse(s) electrical. 1168–1169. 1580T. 268F information transmission. Regulatory T cell(s).. 1139F. 1590 assembly in ER. 988T TBP see TATA-binding protein (TBP) TC see Cytotoxic T-cells (TC) TCA cycle see Citric acid cycle T-cadherin. 763F Synaptonemal complex. 843F. 3F. t-SNARE. 515–516 Target proteins. 1132 modification. 461F TFIIH transcription factors. 1393–1394 cell adhesion molecules and. 806. 1580–1581. 333. CD8 T-cell(s). 1140–1141. 340 transcription factor-binding. 86. 292F see also Reverse transcriptases Telomere(s). 569–571 Tail polymerization. 1540–1551 helper see Helper T-cell(s) (TH) integrins. 208F Synthetic biology. transcription attenuation role. 1293. 269. 1393. 3F DNA. 285 Synchrony. 201F. 210F. 1294F. 889F Tight junction(s). 557F. 718F. GTP-binding proteins. 118F see also Free energy Thermofilum. 1148–1149. 1153–1155 structure. 1150–1153 junctional complexes. 1585–1586. 1057F Templated polymerization. 656F. 508 Thermal motions. 882. 1141F. 1168F remodeling. 557. 1107 yeast. 1587–1588 T cell selection. 1549F Threading. Cell junction(s). 1580F signaling function. 529 Syncytia. mechanism. 807–808 membrane fusion. 1140–1141. 1544F selection in thymus. 1570F. 292. 1585–1586 organization. 461 Surface plasmon resonance (SPR). 1147–1148 scaffold proteins and. 1217 heterochromatin role see Heterochromatin length regulation. actin filament modification. 1274.antibody molecule Talin. transcription. 1294F Testosterone. 714–715 membrane association. 1152 as permeability barriers. 1565–1566. synthetic biology. 1581F see also Cytotoxic T-cells (TC) structure. 720F vesicles. T cell receptor(s) T cell co-receptors CD4. Transcription Teosinte. class switching. 1012F see also Myosin Thoracic duct. 250 human–mouse. 656. 1430F. 1590F g chain. 882F Synaptic vesicle(s). 1057. 1141F. 1002F Tautomeric shift. 344–345. 1154F paracellular transport. 66–67. 1585–1586 Thyroid hormone. 1055. signal-relaying junctions. 889F Tetracyclin. 342F Page numbers in boldface refer to a major text discussion of the entry. 1580–1581 activation. 118F second law. genome size. 525–526. 1183–1184 Synechocystis. 49F Thermodynamics. 525F Surfactant. 1293–1294. optic. 363 structure. NGF dependence. 1286F spermatogenesis. 519–521. 1275F Synchronized cells. 452 Therapeutic cloning. 716–717. 318F. 1575 CD4 see Helper T-cell(s) (TH) cytoskeletal polarization in. proofreading. 390F Tectorial membrane. 344–345. page numbers with a T refer to a table. 1390 Symporter(s). 1411F Teosinte branched-1 (Tb1) gene. as tumor promoter. 296. 1411 Terminal differentiation. 1543F. 1102. 1447 Tissue(s) basal lamina see Basal lamina cell–cell interactions. 1553. 1580T. 716F. 1396–1397 Synaptic signaling. 478 Tau protein. 301F. 1153 TIM23. 843F Thymidine. 719–720. colorectal cancer. 1431F Tectum. 1587F tolerance. 1274F. 332F Thymosin. 1571 TCF4 gene regulatory protein. 1090 TEM see Transmission electron microscopy Temperature-sensitive mutation(s). 1295F structure. 1594 Thalassemia. 292. . 293F see also Telomerase replicative cell senescence and. 602–603 Thymine. 1161 elimination. 1073F. 181 Switch sequences. 266F. 1434.INDEX Supercoiling. 16F Thermomicrobium. 1001. with an FF to figures that follow consecutively. 305F. 988F. 882. 1400F. 1430. 3–4. 1587F T cell-independent antigen. 718 Tim clock gene. 999 Thymus. 1548 see also Immunological tolerance Suppressor mutation(s). 1133. structure. 1571–1572. 809F see also Neurotransmitter(s) Synaptobrevin. 5F. 340–341. 1150–1151 functions. 1139–1140. 1411. 1575 recirculation. 507F. B-cell signaling. pre-B cell. 1568 Syk kinase. 27–28 Sympathetic ganglion. 462F Tip cell. 1439 TCP-I chaperone. 337. 294F meiotic homolog pairing and. 49. 334F I:45 see also DNA replication. 768 B-cell receptor vs. v-SNARE. 1108 connective see Connective tissue developmental segregation. 1587. 292–294. 1400. 1392–1393 Teichoic acids. 67F first law. 1541F. 460. 18T Thick filaments. 1330 muscle cells. 860. 1107 nucleolar assembly. 341FF. 16F Thermotoga maritima. 1543F direction to targets. 1274F repetitive DNA sequences. 522 Tap-tagging. 1574F. 1275–1276. 1585–1586. 1571 MHC protein/antigen interactions. 266. 1393–1395 Synchrotron X-ray sources. Cytotoxic T-cells (TC). 852F protein transport. 385T Tetradecanoylphorbol acetate. remodeling. 374F gene expression regulation see Translational control of gene expression historical aspects. 599. 375–376. 487–488 formylmethionine. 375F anticodons see Anticodon(s) evolutionary significance. 464–465 see also DNA-binding motifs. 716F. 368F. 343F. 503–504 spinal cord. 568 Toxin(s). 807F M6P receptor proteins. 339. 436F Transcriptional control of gene expression. 1510F Toy (twin of eyeless) gene. 159–160. 160. 343 Transcriptional repressors see Repressor protein(s) Transcriptional silencing see Gene silencing Transcriptional synergy. 438–439. 160. 1131 see also specific tissues Tissue culture. 716–717. 370F peptidyl-tRNA–ribosome binding. 801F. 442F see also DNA-binding motifs transcriptional synergy. 453 locus control regions (LCRs). 380 internal ribosome entry site (IRES). 160F analogs. 336–338. 432–477 activators see Transcriptional activator(s) eucaryotes “action at a distance. 339. 442. 782F Topoisomerases see DNA topoisomerases TOR kinase. 477–478 Transcription circuits. 339F rRNA genes. 337 elongation. 1041F Transcellular transport. 1111F loss of function mutations. 441. 1151F Transcription. 450–452. 368F see also Genetic code. 341. 778F lipid raft assembly. 1530F. enzyme catalysis. plant vacuoles. 447F complex formation. 504 see also Cell culture Tissue explants. 380. 149F TOM complex. 1104. 489–490 initiation factors (eIFs). 659F tight junction(s). 339F DNA signals. 1530–1531. 385T initiation. 1183 regulatory T cell(s). 377–378 free energy expenditure. 445. 336. 446F structure. 771F transport. 434–436 DNA looping. 4–5 Transcriptional activator(s). 1493–1494 Toxoplasma gondii conoid. 940F animal development. 477 see also Gene(s) Transcytosis. 718F Tomography. 439F.. 540–541 Transferrin receptor. 504 extracellular factors. 436. 336–340 consensus sequences. 566–568 plants. 341F. 334F. 380. 339 universal principles. 1028F Tjp protein family. 379–380. 794 Transfer RNA (tRNA). 341–342 Transcription unit(s). 798 IgA. 345–346 see also Transcription factors. 1155 renewal. as tumor promoter. 336. 481F. 333. 369F. 444–445. 1536 inflammatory response. 341F. 338F. 367. 340–341. 490 mRNA cap. 503–504 explants. 436FF. 585. 611F. 1517 1142F engineering. 337. 600F Totipotency. 1194 Titin. 1065. 436F procaryotic. 445. 1108 Torso protein. 338–339 transcriptional activators see Transcriptional activator(s) see also Promoter elements procaryotic (bacterial). 331. 807F structure. Transfer RNA eucaryotes. 1422F benefits. 1556F insulin receptor. 367F adaptor molecules. 339. 612F Tonoplast(s). 160. 4F. 340–342 activator protein interaction. 6. 1151. 447FF holoenzyme interaction. 459F. 375–376. 334F. 4F decoding. 446F TATA box-binding. 343F histone code reading. 1489F vacuole formation and replication. 444F. 384. 348F Transfection. 1479 epithelial see Epithelia explants. 270. 345F. 798F recycling endosomes. 504 requirements. 612. 440 insulators. 863 see also Genetic code ‘Transformed’ phenotype. 373F transcription. 338F RNA polymerase. 797F glucose transporters. 4F. 339. 554–555. 1400 Drosophila development.general (TFII) evolution. 444F promoters. 1530–1531 Toll-like receptors (TLRs). 340T see also RNA polymerase(s) RNA processing. 464–465 Transcription attenuation. 434–436 Lac operon see Lac operon (Escherichia coli) regulatory proteins see Gene regulatory protein(s) repressors see Repressor protein(s) see also RNA polymerase(s) Transcriptional mediator. 1533–1534 dendritic cells. 438F function. 399F ribosomes. 1103. cancer cells. 331–343. 1417–1484 variety. general (TFII) fidelity. 366–367 inhibitors. 797–798. 340 repressor protein interaction. 1154 T-loops. 570F production. 341–342. 1429 Transesterification reactions. 771F functional compartmentalization. 343F. 1040–1041. 458. 445. 7F. 161F stabilization. 1531. 434–436 promoters. 380. 337. 379F. 420F. 1334F Total cell mass. 325–326 Cre/Lox system. 482F Transforming growth factor-b (TGFb) family activation of Smad-dependent signaling pathway. 399F elongation. 339–346. 1334. 371F. electron microscope (EM). 299–300 Transcription factors. 338–339. 478 transcriptional synergy. 1333F.. 372F accuracy. 334 gene expression regulation see Transcriptional control of gene expression . 371. 371–373 origin. 334. 807. 4–8. capsid. 435–436. 1102. 490F initiator tRNA. 336T initiator tRNAs. 318T TNFa see Tumor necrosis factor-a (TNFa) Tobacco cells. 1028. 380 initiation codon. 1437 Transitional endoplasmic reticulum see Endoplasmic reticulum (ER). 477–478 eucaryotes vs. 292. 568–569. 337. 370F. 458F procaryotes (bacterial). 503F Tissue staining. 1509. 491 leaky scanning. 1316F Arabidopsis absence of. 566–568. control. 488–489. 440 see also Promoter elements regulatory elements. 570F site-specific recombination. 506T. 149 Toll-like proteins. 368–369 aminoacylation reaction. 605 specialized. 380. 337F. 343–345 initiation. 1110. 380 modification. 579. 1422–1424. 1426 Transgenic organism(s). 366–383. 784 protein sorting pathways. 341F. 164 Translation. 436F coactivators. 439–440 heritability. 1509 host cell membrane traffic. 444–445. 341–342 eucaryotic. 1111–1112 Total internal reflection fluorescence microscopy (TRIF). 1423 gut epithelium. 1470. pre-mRNA splicing. cell culture micrograph. 438F repressor interactions. 342–343. 1575 skin. 798.” 438F cell cycle control. 1542 activation. 504F Tobacco mosaic virus (TMV). 345F directionality. 343–346. Transcription factors. 341F Transcription initiation complex.. 772 electron micrograph. 418T. 336–337 abortive. microscopy sample preparation. 502. 340 nomenclature. 1104F complexity. plant cells. 337F. 338F heterogeneity. 438F. 344F eucaryotic. 336–337. 270. 438F gene regulatory proteins see under Gene regulatory protein(s) procaryotes vs. 934. 333 RNA polymerase orientation. 444–445. 1233 Transformer (Tra) gene. 368. 382 EF-Tu role. 339. 1336 inhibitor signals. 335–336 see also Messenger RNA directionality. 658–659. 569F. 504 Tissue-inhibitors of metalloproteinases (TIMPs). 1493 bacterial see Bacterial toxins cholera. 1477 sectioning. 339F promoters. 340–342. 370–371. 798 Transducers. 1140 polarity. 447. 1226 Trabecular bone. 714–715. 293F T lymphocytes (T cells) see Lymphocyte(s). 380F. 369. 567–568 see also Gene knockouts Trans Golgi network (TGN). 380. 362–363. 407–408 function. 460F Transcription-coupled repair. 339. 375F structure. 342F. 341F. 793F. 1533–1534 Tomato bushy stunt virus. 332–333. microdissection techniques. 385 basic principles. 1466 proteoglycans and. 459–460.smooth Transition state. 585F. 714F. general (TFII). 339–340. 466F TP53 see p53 gene/protein TPA (tetradecanoylphorbol acetate). 4–8. 339 transcription attenuation. 585F Tissue-type plasminogen activator (tPA). 337F terminators. 439T. T cell(s) Tn3 transposons. 339F.I:46 INDEX initiation. 347–348. 335F basic principles. 438F. 372F see also Aminoacyl-tRNA synthetases aminoacyl-tRNA–ribosome binding. 4F. 504 historical aspects. 1509. 4–5. 368. 360–361. 337. 1110 organization and maintenance. 793. 334. 1193. 477–478 rates. 1510F structure. 160 activation energy. 444F. 407 synthetase recognition. 1425–1426 growth control strategy. 1243 myostatin. 372–373. 452F TATA box see TATA box transcriptional attenuation. 361F termination. 1492 mechanism of action. 337F complex. 338–339. 380F. 435 eucaryotic. 488 eucaryotes. 376F accuracy. 444F see also RNA polymerase II mechanisms. 1194 Tissue slices. 331. 343F mitochondrial DNA. 370 replication vs. 335–336. DNA cloning vectors. 1470F Traction. 372F reading frames. 785F see also Exocytosis Transit amplifying cells. 380F bacteria. 415. 939–941. 779–787. 1512 invasion of host cells. 1102. self assembly. 368F. 1417–1484 repair. 338–339 promoters. 337F sigma factors. Drosophila sex determination. cell movement. 339. 1232. 863 RNA polymerases. 438F transcription initiation. 726 preparative ultracentrifuge. 1517–1518 see also Messenger RNA (mRNA). 524F see also Protein–protein interactions Two-hybrid system. structure. 349F. 1153 Trichomonas. 318T genes. 656F Unit evolutionary time. 1197. 1502. 1519F. 318T viral integration. 1519F. 393. 354F SL RNP. 354. 12–13. 414F isoelectric focusing step. 1135T. 607F microscope. 393–394. 1511. page numbers with an F refer to a figure. 16F. 1065F. 317. Protein synthesis. 394F. 510–511. 323 b-globin genes. 434F helix-turn-helix motif. 297F. 415 Tyrosine kinase(s). 1134F. 177F B cell receptor signaling. 361. bacterial toxins. 994F. 375F. 1227 Tumor necrosis factor-a (TNFa). splicing mechanism. splicing mechanism. 944F Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). molecular mimicry. 610F Transmitter-gated ion channel(s). 488 Upstream ORFs. 1599 bacterial genome. 354F Transverse filaments. 632 multipass. 492–493. tight junction(s). 734–735. 1388 Uncoupling agents. 1389 Unc5. mouse knockouts. 393. 1598T Tumor promoter(s). 510–511. 980 g-tubulin. growing seedling. 1232F genetic vs. 1575–1576 Transporters/transport proteins see Carrier protein(s) Transport vesicle(s). apoptotic cells. 317. 923T TrkA receptor protein (NGF receptor). 632. cell isolation techniques. 1520 Trypanosoma cruzi. confocal microscopy. 522F SDS-PAGE step. 377–378 peptidyl transferase. 524F “Two-photon” effect. 521–522 gene expression analysis. 395F ubiquitin. 1177T see also Integrin(s) domains. 992F. netrin receptor. tree of life. 1003 Tropomyosin. 953F. 354–355. 521–522 visualization. 977FF Tree of life. protein evolution. 350F U2AF spliceosomal protein. 489–491. 317. 607F immunoelectron microscopy. 992. 760 Transposable elements see Transposon(s) Transposase. 1237F hereditary cancer syndromes. 740F Ubiquitin-activating enzyme. 632. chromosomal see Chromosome translocation Transmembrane adhesion proteins. 473. 1141. 320F enzymes. 396F activation. 523–524. 502 Tryptophan. 511F microsome purification. 350F Trithorax group. 95. 473F Twist gene/protein. 350F U2 snRNP. 1169. 318T Type III secretion system. 686–687 see also specific receptors Transplantation reaction. 223F Ultracentrifugation cell fractionation. 982–983 filament assembly. 683 neuromuscular junctions. 318T DNA-only. 521F. Retroviral-like retrotransposons evolutionary movements. small molecules. 656. 295T Unc5H. 1507–1508. 350F U4 snRNP. 490 Uracil. 1234–1235 identification. 989 evolutionary conservation. 687–688 permeability changes. 636F. 608–609 metal shadowing. 1494F. 992. 488. 379F. 433–434. 317. 12–13. 318F. 922. 1509. 606–607. 632 a-helix conformation. time line see Origin of life Untranslated regions 3¢ untranslated region. 318T cut-and-paste mechanism. 632–634 hydrogen bonding. 16F Trichothiodystrophy. 1504 Tyrosine aminotransferase. 13F Tubulin(s) bacterial homolog. . 740F see also Proteasome(s) Ubiquitylation. 383. 1227 Tumor suppressor genes (TSGs). 433F Tryptophan repressor. 556 phylogenetic variation. 383F. 1064. 634 b barrel conformation. 1335 Two-component signaling pathway/system. gene expression regulation. human vs. 914F structure. 632. 1194 UTR see Untranslated regions UV light see Ultraviolet (UV) radiation Page numbers in boldface refer to a major text discussion of the entry. 1592. 653. 112F Triple response. vs means compare/comparison. 634FF. 781. 604–607. 420F T segments. 735F single-pass. 433F. 298 see also DNA damage. 492F negative. 1153 Transmembrane protein(s). 606 Urea. 373F. 521. 1350F Ubiquinone see Coenzyme Q Ubiquitin. 18T Triacylglycerols. 318T retrotransposons. 433F Tryptophan operon. autoradiography. 15–16 Treponema pallidum. 207F insertional mutagenesis. 323F transposition mechanism see Transposition see also Transposase. 992F. 1226. 387F see also Nonsense-mediated mRNA decay regulation. 382F Translocase of the inner mitochondrial membrane see TIM complex Translocase of the outer mitochondrial membrane see TOM complex Translocations. 592F Ty1 retrotransposon. 976–980. 379. 594–595. 318F Transposition. with an FF to figures that follow consecutively. 1277F Treadmilling. 1276. 1153 see also Cadherin(s) cell–matrix adhesion. 595F polymerization. 188 see also specific enzymes Ubiquitin pathway. DNA repair defects. 161F Trioses. 1388 Unc genes. 353. 604F sample preparation. 354F. 489F termination. 490F internal ribosome entry site (IRES). 393–394 protein labeling. 1593–1594 Tuberculosis. 381F viral RNA. 488. 484F Trypanosoma brucei. 395–396 proteasome targeting. 393–394. 608–609. 942. 116F. 1508 see also Mycobacterium tuberculosis Tube worms. 14F genome size. 393. 953. 522F Two-hybrid methods. 1517 peptide chain elongation. 493 initiation regulation. 1134–1135. electron microscopy stains. Ribosome(s) Translational control of gene expression. 396F cell cycle control. 523–524. 631–632. rRNA modifications. 354. 1077. 385–387. 1389 Unc6 gene. 1344 Triton. mouse. 632 hydropathy plots. 384F Translational recoding. 96F fatty acid storage. 97F. time course. membrane protein solubility. 332. 354F trypanosomes. epigenetic change. 733F transport. mitochondria. page numbers with a T refer to a table. 998 see also Microtubule(s) g-Tubulin ring complex (g-TuRC). 250F human genome. 369. 114F Tricarboxylic acid cycle see Citric acid cycle Tricellulin. specific types/locations Tumor initiators. 733–734. target membrane SNAREs Tubercle. 394F N-terminal degradation. 629–630. 58 structure. 321F Transpositional site-specific recombination see Transposition Transposon(s). 129F U U1 snRNP. 1390 tRNA see Transfer RNA tRNA-splicing endonuclease. Drosophila. 384F Translational repressors. 683 psychoactive drug effects. 1001 Trypanosoma. 684–686 localization. 1511F Trypanosome(s) antigenic variation. 394F enzymes. splicing mechanism. 383. 159–160 Twin studies. 490F see also Messenger RNA (mRNA) Translational frameshifting. 528F. 634F. netrin receptor. 483. 603 Uridine isomerization. 332F. 480. 333F Uranium. 1502 T-SNAREs see SNARE proteins. 184–185. 265 Universe. 318T see also specific enzymes mechanism see Site-specific recombination retrotransposons. 604–605. 630F assembly. 632F a-helix interactions. 935 Tyrosine. 412. 316 DNA-only transposons. 1199 Turnover number. 982 photoactivation visualization. 682–684. 379 procaryotic. 379F see also Protein synthesis quality control. 120F. 867 Urease. 350F UAS (upstream activating sequence) element. 1590F receptor-linked see Receptor tyrosine kinases (RTK) T-cell receptor signaling. 1190 Tropomodulin. 637 Trk A. 605F surface analysis. 415. 1118F Turgor pressure. splicing mechanism. 350F U6 snRNP. 734–736. 296. 382–383. 101 Urea cycle. 115F energy storage. DNA repair sensitivity. 185F. 394F Ubiquitin ligase(s). histone tails. 362F Urokinase plasminogen activator (uPA). 1234–1235 loss by mutation. 994F. 973–975 isoforms. 318T see also Retrotransposons. 490F Translation release factor (eRFI). enzyme catalysis. 604F 3-D reconstruction. meiotic homolog pairing. 568F Triglyceride(s) see Triacylglycerols Trimeric GTP-binding proteins (G proteins) see G protein(s). 651 see also Porin(s). 592. 488 cytoplasmic polyadenylation. 129F. 1066T SCF. 634–635. 1079 Tumor(s) see Cancer. 480 DNA-only transposons. 1520 tsetse flies. G protein(s) (trimeric GTP-binding proteins/ATPases) Triosephosphate isomerase. 836. individual elements Trans-splicing. 1236F see also individual genes/proteins I:47 TUNEL technique. 1493. 491 mRNA degradation.INDEX mRNA signals. 318F alternative splicing. 319F. 375–376. 1502 Trypsin. epigenetics. 393. 606. 487. 1329 Tsetse fly. 838 Uniporter(s). 381. 1231. 1488. 394F. 488. 635F cell–cell adhesion. 1235–1236 mechanisms of losing. 1527 viruses. 684–686. 370F Tropoelastin. 605–606. 510F Ultraviolet (UV) radiation DNA damage. 749. 1226. 392–393. 376F elongation factors. 1117. 957. splicing mechanism. 488F 5¢ untranslated region. specific proteins/types Transmission electron microscopy (TEM). 318F classification. 958F Triple snRNP. 892 acetylcholine receptors as. 973 T-form and D-form. 1590F see also Src family of protein tyrosine kinases Tyrosine-kinase-associated receptor. 1507 Tuberculoid leprosy. 317. 1503 3H-Uridine autoradiography. 1174 Velocity sedimentation. 1496–1497. 1253 gut stem-cell population maintenance. 1248F entry and uncoating. 1563F V(D)J recombinase. 510–511. 769F. 129F Valium. 1505–1506 replication. 43F Vertebrate development. 148. 777–778 investigations. plasmodesmata and. 1395F Visual transduction. 1516–1517 Variegation. of small intestine. 1491 anthrax. 1355F Wing imaginal disc. effects of. 828. 1395F Visual experience. 1503 CTXf bacteriophage. 1491. 1564F V-J joining process. 1505. 51–52 channel(s) see Aquaporin channel(s) chemical properties. 907T VE-cadherin. 1436F. 548FF virus transmission by. 769F. 1441 Vimentin. 1517 Valine. 1517–1518 intracellular movement. 1492F colonization of gut. 1496 Virulence factors. 541FF see also DNA cloning of pathogens. 676–677 Volvox. 1352 Wire protein models. 1496 capsids. 1356F Wingless (Wg) gene/protein. 750–766. DNA repair disorders.I:48 V INDEX formation. 1518 microtubule-based movement. 130F Van der Waals radius. 1496–1498. 1367F left-right asymmetry. 1369–1370. 1374. 1564–1566 class switching vs. definition. deficiency. 1376F mid-blastula transition. 1448F healing angiogenesis. 1497F genome integration see Mobile genetic elements. k light chain production. individual cell types Whooping cough (pertussis). 1436. 1227–1228 see also DNA tumor virus(es) cytolytic effects. 687–688 Voltage-gated ion channel(s). 611F. 108F Water-splitting enzyme. 167. 949F in bone marrow. 1363–1378 cadherins and. 1504 see also Bacterial toxins Virulence genes. 682. 1373–1375 myoblast migration. 1491 structure. 752F. 769. 1425–1426 role of TGFb. 1568 control. 772F W Wall cress see Arabidopsis thaliana Warburg effect. 1518 Worm see Caenorhabditis elegans Wound(s) angiogenesis. 1501–1502 WRKY (Zn finger) gene regulatory proteins.. 1370–1371 pigment cells. 14F bacteriophage. 1535–1536 morphology. 1489F toxin see Cholera toxin virulence genes. 873 Watson. 1502 “Velcro principle” cadherin adhesion. 1406F vaccination. 1505–1506 bacterial see Bacteriophage(s) bloodborne. family . 369F Wolbachia host behavior modification. 149F. 676–678 see also specific types Voltage-gated potassium channel(s). 763F V-type pumps (ATPases). 150F transmission by vectors. 1402. in mammalian cortex. 1426 Wobble base-pairing. 1449 role in tumour progression. 51. 1498F HIV prevention. 917–918 adaptation. influence on ocular dominance columns. 1513 icosahedral. 1502 see also specific infections/organisms Visual connections. 1496 structure. 1488 DNA tumor virus(es). 1498. 920. 1404F Vasopressin. 1502 as carcinogens. 1448. 1145 colorectal cancer. 52F. 1364F gastrulation. bacterial. mechanism of action. 1140F neural tube formation. 1492F pandemics. 918 see also Arrestin. 1374F neural crest. 687 states. actin cross-linking. 1140F. 828F solvent. 1513. 1518 infection treatment. 1043. 682 evolutionary relationship. 1521 Vaccinia virus. 762–763. 148F. 1247–1249. 1370F. 1497F. 1141F Xenopus laevis see Xenopus laevis development see also individual processes and species Vesicular transport. 891F Vitamin D3. 1365 migratory cells. 1426 infection route. 766–787 exocytosis. 1140. 799–809 see also Exocytosis to lysosomes. 1140–1141. 1497. 701. 1488. 985T Vinblastine (vincristine). 547F Varicella zoster virus. 167T see also individual vitamins Vitamin A. 1353. 770F transport from ER to Golgi apparatus. microtubule-based movement. Rhodopsin. specific infections/organisms Virion. 1369F egg asymmetries in amphibia. 753F organelle relationship. 110F bond length/strength. 1559F. 1365. 750F coated vesicles see Coated vesicle(s) docking specificity. 769. 988T Viral infection(s) interferon-g. 51–52 electron source. 108–109FF cell content. 985. 196 Wee1 kinase.and left-eye inputs. 548. 295T Western blotting. 769F retrieval pathway.” DNA replication. 1564 Voltage-gated calcium channel(s). 1496F nonenveloped. 154 proton behavior. 1523 Van der Waals forces. 1489F. 678F mutants. 512F Vertebrate(s) development see Vertebrate development times of evolutionary divergence. 1363F. 1448 control of cell turnover. 1491 chromosome. 1517–1518 evolution. 768–769 electron micrograph. 799–809 see also Exocytosis Golgi apparatus transport to cell surface. 1074. 1340 in vertebrate limb. James D. 1282 Vascular cell adhesion molecules (VCAMs). 768. 889F Vitelline layer. 1366F. 1139F integrin adhesion. 1516F. 1186 Vitamin D. 110F Variable domain genes. 676 neuromuscular junctions. 1514F enzymes encoded. 640. 150F. proteins. 1563 heavy Ig chains. 1493 type III secretion system for. 501F Von Hippel–Lindau (VHL) syndrome. 1074F Werner syndrome. 1145 Vectors DNA cloning. 1497 retroviruses see Retroviruses RNA viruses see RNA virus(es) size. 752. 1491F. 1506F enveloped. 873 functional roles. 1497. 53T protein folding. 1221 Vascular tissue blood vessels see Blood vessels of plants. ball-and-chain model. 1514–1517 life cycles. 1138–1139. 610 V(D)J joining. 769F Vibrio cholerae. 1449 V-SNAREs. 1565–1566 recombination signal sequences. 109F structure. Site-specific recombination host cell membrane traffic changes. 1183 endothelial cells. 1395. 948–950.. 1201. 1355 see also Wnt signaling pathway Wingless signaling pathway. 149 spherical. 1140. 851. 1376F somite formation. 1438–1441 planar cell polarity. 852F. 1063. 1146 Vascular endothelial growth factor (VEGF) cell–cell junctions and. 1497F self assembly. 51. 660 Vaccines/vaccination. 866F Vasa family proteins. 1400 animal development. 1158 in skin. 1501–1502 protein expression. 1365. 1448. 605. 1520–1521 genome. 1395F Visual cortex. 133F Wnt signaling pathway absent in Arabidopsis. 701F secretory vesicles see Secretory vesicle(s) SNARE proteins and see SNARE proteins Vesicular tubular clusters. 1497. 1138T. 1535–1536 receptors. 1492F Virus(es). 677 delayed. 1163 proteins. 920F amplification of signal in rod photoreceptors. 1496 diversity. 1245 WASp family. 1492F gene map. 1395–1396. 866. 1365F convergent extension. 1491 Villin. homotypic membrane fusion. resistance. 920F photoreceptor cells. 519F White blood cells see Leucocyte(s). 1517. 540–541. 678 Voltage-gated sodium channel(s) inactivating mechanism. 1365–1369. 753. 1353F in Drosophila segmentation. 678. 1505. Rod photoreceptors (rods) Vitamin(s) as coenzymes. 54. 518. 1458 cell–cell adhesion and. 612 nucleocapsid. 1007 Villi. 369. 779–787 model. ocular dominance columns. 148–149. 1353 see also Wnt signaling Wing margin. 890 Vitamin C. 760–761. 1513–1514. 1507 plant. 1516. 546. 1534–1536 adhesion to host cells. 1145 ECM binding. 1498F see also Virus(es). 1395F segregation of right. 1287 Vitreous ice. 1141F see also Cadherin(s) cell movements and shaping of body plan. 1372F see also under Xenopus laevis development mouse see Mouse development neural crest. 1373–1374. 1493. 701F. 1514F host metabolism changes. 1139–1140. 1517. 686 Vancomycin. 51F. 1496. 1497. 1496F MHC class I expression inhibition. 689 epilepsy. 682 inactivation. structure. 1559F. 1503 see also Pertussis toxin “Winding problem. 278F Wing bud. 1368–1369. 1497 protein synthesis. 1395–1396 molded by experience. 851. 1374F neurulation. 1370–1371. 1364. 1372F notochord. 1517. 890 receptor. 1496. 1366F cell adhesion and sorting-out. 1376–1377. 1560F Variable number tandem repeats (VNTRs). 1371–1372. 1498. 1517F vertical spread. development. 919–920. 1560F light Ig chains. 1363–1378 blastula. 1494F. 1375. 1516F Water. 1316F b-catenin. 1370F cleavage. 1491 Virulence plasmids. 548F. 761–762 ER to Golgi apparatus. 1514F. 474 XMAP215. 867F DNA. 1143F Zona occludens see Tight junction(s) Zona pellucida. 34F sexual reproduction. lethal toxin. 421. 1287. 1360F egg. 1300 ZO proteins. 30-nm fiber formation. 1365–1367. 1288F. 529 X-ray crystallography DNA. 1367F cell packing changes (convergent extension). haploid vs. 865F petite mutants. 427F structure. 421 Zinc protease. 1298. 295T synchrotron sources. 1004F Xpd gene/protein.. 39. 295T. 542F Yeast budding cellular polarity. 202. 475 histone H4 variants. 1298. 1298. 1044F in tree of life. 1142. 1284 Yeast(s). 781–782 Yeast artificial chromosomes (YACs). 1044 signaling pathway. 195–196. 38–39 species differences. 995F. 1400T Wuschel protein. 421–422. 1208 XIC (X-inactivation center). 703F reproductive cycles. 421. 473F mosaics. 1366F. 1298 ZP2 glycoprotein. 474–475 histone H3 variants.INDEX members in different eucaryotes. 1057–1058. 475–476 histone H2A variants. 1063F chromosome replication. 1045F Yeast genetics gene regulatory proteins. 422F. formation during cell division. 475 mechanism. 1502F. 411. 858F. 422F types. 852 Zygote. 1337 Zymogens. 1300 Z-ring. 102F mitochondria. DNA sequence recognition. 423F DNA-binding. 606F. 1271. 473. 530T IgG structure. 421–422. 1508. 1365F. 1056 vacuoles. 864–865. 1081F embryo cell cycle analysis. 1026. 1298F. 865F. 866–867 as model eucaryote. 39. 1364F cell-free systems. 1287 I:49 X X-chromosome(s). 473–474 see also Gene silencing. 880. 1410F X-ray(s). lysosomal properties. 592F. 197 electron density maps. deletion cassettes. 1056F. 857. 1027F Zebrafish. 880. 1575 Xenopus laevis. 1363 effect of blocking Notch signaling in. DNA repair defects. 139. 1045F mating types. 989F Z scheme (photosynthesis). 1057 growth. 422F Zinc finger proteins. vs means compare/comparison. 38–39 Xenopus laevis development. Genomic imprinting X-inactivation center (XIC). 1058. 473. 474 X-inactivation. 723 Zigzag model. 1410. 217F Zinc finger motifs. 1368F. 422F. 1367 Xenopus ruwenzoriensis. 210 E. 864–865. 1493 Zona adherens (adhesion belt). 34. 556. 1365–1369. 1368–1369. 1058F microtubule dynamics during mitosis. 866–867 mutagenesis. 1301F reconstruction (cloning). 16F two-hybrid methods. 523–524. 318T metabolic map. 1275 Sry gene. 473–475. 255. transplantation reactions. 1369F cell movements. microtubule formation. 1369F signals controlling. 1080. page numbers with an F refer to a figure. 1291F. 1275 Zygotic-effect genes. 528 historical aspects. 202. 1287. 1057F. 528F mitochondrial DNA. 1494 budding see Budding yeast(s) cell cycle control. protein–protein interactions. 1154 ZP1 glycoprotein. 1301. 39 Xenopus tropicalis. 473–475. 524F utility as model organisms. mouse knockouts. 793 Page numbers in boldface refer to a major text discussion of the entry. 1367F. 1284 meiotic pairing. 285. 1004. 473. 33. 1209F random chromosome choice. 527–529. 1058F gastrulation. 1269–1270. 527–528 sensitivity. diploid cells. 34 fermentations. 39F Xeroderma pigmentosum (XP). 423F zinc finger repeats. 1502. 1520 Yolk. 1290 Yolk granules. 34–35 genetics see Yeast genetics genome. 541. 413F zygotic-effect genes. 473F. 1366F. 217. 1337 see also Fertilization Zygotene. with an FF to figures that follow consecutively. . 474 XIST RNA. 1057F cleavage. 880F. 39F development see Xenopus laevis development genome duplication. 1275 Xenografts. genome preservation. 422F sequence specificity. 863 inheritance. 398F protein transport studies.” 1044. 989. 1520 Yersinia pseudotuberculosis.’ 398. 863. page numbers with a T refer to a table. 568F Z Y YACs see Yeast artificial chromosomes (YACs) Y-chromosome. 1044. 418T Zap70 tyrosine kinase. 1391F Zellweger syndrome. 1284 inactivation see X-inactivation meiotic pairing. 1590F Z disc. 1058F fertilization. coli vs. 1056–1057. 1300 ZP3 glycoprotein. 1271. 474F Barr body. 1363F cell movement during development. 1270F “shmoo. 421–422. 1561F protein structure determination. 473F. 33–34 ‘protein-only inheritance. 90 see also Glycolysis fission yeast see Schizosaccharomyces pombe gene expression analysis. 1062. 1269 centrioles. 570 Yersinia pestis. 473 dosage compensation.