TheCell6

THE CELL A Molecular Approach Sixth Edition

Geoffrey M. Cooper • Robert E. Hausman Boston University

Sinauer Associates, Inc. • Publishers Sunderland, Massachusetts U.S.A. ©2013 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured or disseminated in any form without express written permission from the publisher.

Brief Contents

PART I

PART III

Introduction

1

Chapter 1 An Overview of Cells and Cell Research 3 Chapter 2 The Composition of Cells 43 Chapter 3 Cell Metabolism 73 Chapter 4 Fundamentals of Molecular Biology 103

PART II

Cell Structure and Function

343

Chapter 9 The Nucleus 345 Chapter 10 Protein Sorting and Transport 373 Chapter 11 Bioenergetics and Metabolism 421 Chapter 12 The Cytoskeleton and Cell Movement 459 Chapter 13 The Plasma Membrane 515

The Flow of Genetic Information 151 Chapter 5 The Organization and Sequences of Cellular Genomes 153 Chapter 6 Replication, Maintenance, and Rearrangements of Genomic DNA 191

Chapter 14 Cell Walls, the Extracellular Matrix, and Cell Interactions 557

PART IV

Cell Regulation

587

Chapter 15 Cell Signaling 589

Chapter 7 RNA Synthesis and Processing 239

Chapter 16 The Cell Cycle 641

Chapter 8 Protein Synthesis, Processing, and Regulation 297

Chapter 17 Cell Death and Cell Renewal 681 Chapter 18 Cancer 713

©2013 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured or disseminated in any form without express written permission from the publisher.

Contents Preface xix Organization and Features of The Cell xxi Media and Supplements to Accompany The Cell xxiii

Part I

Introduction

1

CHAPTER 1

An Overview of Cells and Cell Research 3 The Origin and Evolution of Cells 4 The first cell 4 The evolution of metabolism 6 Present-day prokaryotes 8 Eukaryotic cells 9 The origin of eukaryotes 10 The development of multicellular organisms 13

Cells as Experimental Models E. coli 17 Yeasts 18 Caenorhabditis elegans 18 Drosophila melanogaster 19 Arabidopsis thaliana 19 Vertebrates 20

Tools of Cell Biology 22 Light microscopy 22 Electron microscopy 28 Subcellular fractionation 31 Growth of animal cells in culture 32 Culture of plant cells 36 Viruses 36 KEY EXPERIMENT

Animal Cell Culture 34 MOLECULAR MEDICINE

Viruses and Cancer 37

17

Summary and Key Terms 39 Questions 40 References and Further Reading 41

CHAPTER 2

The Composition of Cells 43 The Molecules of Cells 43 Carbohydrates 44 Lipids 46 Nucleic acids 49 Proteins 52

Cell Membranes 58 Membrane lipids 58 Membrane proteins 59 Transport across cell membranes 62

Proteomics: Large-Scale Analysis of Cell Proteins 65 Identification of cell proteins 65 Global analysis of protein localization 67 Protein interactions 68

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Contents

KEY EXPERIMENT

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CHAPTER 4

The Folding of Polypeptide Chains 54 KEY EXPERIMENT

The Structure of Cell Membranes 62

Summary and Key Terms 70 Questions 71 References and Further Reading 71

CHAPTER 3

Cell Metabolism

73

The Central Role of Enzymes as Biological Catalysts 73 The catalytic activity of enzymes 73 Mechanisms of enzymatic catalysis 74 Coenzymes 76 Regulation of enzyme activity 79

Metabolic Energy 81 Free energy and ATP 81 The generation of ATP from glucose 84 The derivation of energy from other organic molecules 89 Photosynthesis 90

The Biosynthesis of Cell Constituents 91 Carbohydrates 92 Lipids 93 Proteins 94 Nucleic acids 98 KEY EXPERIMENT

Antimetabolites and Chemotherapy 97 MOLECULAR MEDICINE

Phenylketonuria 98

Summary and Key Terms 99 Questions 100 References and Further Reading 101

Fundamentals of Molecular Biology

103

Heredity, Genes, and DNA 103 Genes and chromosomes 103 Genes and enzymes 105 Identification of DNA as the genetic material 107 The structure of DNA 108 Replication of DNA 109

Expression of Genetic Information 110 Colinearity of genes and proteins 111 The role of messenger RNA 112 The genetic code 113 RNA viruses and reverse transcription 115

Recombinant DNA 118 Restriction endonucleases 118 Generation of recombinant DNA molecules 120 Vectors for recombinant DNA 122 DNA sequencing 124 Expression of cloned genes 126

Detection of Nucleic Acids and Proteins 127 Amplification of DNA by the polymerase chain reaction 127 Nucleic acid hybridization 129 Antibodies as probes for proteins 132

Gene Function in Eukaryotes 135 Genetic analysis in yeasts 135 Gene transfer in plants and animals 136 Mutagenesis of cloned DNAs 139 Introducing mutations into cellular genes 140 Interfering with cellular gene expression 142 KEY EXPERIMENT

The DNA Provirus Hypothesis 117 KEY EXPERIMENT

RNA Interference 144

Summary and Key Terms 146 Questions 148 References and Further Reading 148

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Contents

Part II The Flow of Genetic Information

151

CHAPTER 5

The Organization and Sequences of Cellular Genomes 153

CHAPTER 6

The Complexity of Eukaryotic Genomes 153 Introns and exons 155 Repetitive DNA sequences 159 Gene duplication and pseudogenes 161

The Sequences of Complete Genomes 162 The genomes of bacteria and yeast 163 The genomes of Caenorhabditis elegans, Drosophila melanogaster, and other invertebrates 165 Plant genomes 166 The human genome 166 The genomes of other vertebrates 169

Chromosomes and Chromatin 171 Chromatin 172 Centromeres 176 Telomeres 180

Replication, Maintenance, and Rearrangements of Genomic DNA 191 DNA Replication 191 DNA polymerases 192 The replication fork 193 The fidelity of replication 200 Origins and the initiation of replication 201 Telomeres and telomerase: maintaining the ends of chromosomes 205

DNA Repair 207

Bioinformatics and Systems Biology 181 Systematic screens of gene function 181 Regulation of gene expression 182 Variation among individuals and genomic medicine 184 KEY EXPERIMENT

The Discovery of Introns 156 KEY EXPERIMENT

The Human Genome 167

Summary and Key Terms 186 Questions 187 References and Further Reading 188

Direct reversal of DNA damage 208 Excision repair 210 Base-excision repair 210 Nucleotide-excision repair 210 Transcription-coupled repair 213 Mismatch repair 213 Translesion DNA synthesis 216 Repair of double-strand breaks 216

DNA Rearrangements

219

Site-specific recombination 219 Transposition via DNA intermediates 227 Transposition via RNA intermediates 228 Gene amplification 232 MOLECULAR MEDICINE

Colon Cancer and DNA Repair 215 KEY EXPERIMENT

Rearrangement of Immunoglobulin Genes 220

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Contents

Summary and Key Terms 233 Questions 235 References and Further Reading 236

KEY EXPERIMENT

CHAPTER 7

Summary and Key Terms 291 Questions 293 References and Further Reading 294

RNA Synthesis and Processing 239 Transcription in Prokaryotes 239 RNA polymerase and transcription 240 Repressors and negative control of transcription 243 Positive control of transcription 245

Eukaryotic RNA Polymerases and General Transcription Factors 245 Eukaryotic RNA polymerases 246 General transcription factors and initiation of transcription by RNA polymerase II 246 Transcription by RNA polymerases I and III 250

Regulation of Transcription in Eukaryotes 251 cis-acting regulatory sequences: promoters and enhancers 251 Transcription factor binding sites 255 Transcriptional regulatory proteins 258 Structure and function of transcriptional activators 260 Eukaryotic repressors 263 Regulation of elongation 264 Relationship of chromatin structure to transcription 266 Regulation of transcription by noncoding RNAs 271 DNA methylation 273

RNA Processing and Turnover 275 Processing of ribosomal and transfer RNAs 275 Processing of mRNA in eukaryotes 277 Splicing mechanisms 279 Alternative splicing 286 RNA editing 288 RNA degradation 289

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Isolation of a Eukaryotic Transcription Factor 259 KEY EXPERIMENT

The Discovery of snRNPs 284

CHAPTER 8

Protein Synthesis, Processing, and Regulation 297 Translation of mRNA 297 Transfer RNAs 298 The ribosome 299 The organization of mRNAs and the initiation of translation 305 The process of translation 307 Regulation of translation 313

Protein Folding and Processing 319 Chaperones and protein folding 319 Enzymes that catalyze protein folding 322 Protein cleavage 323 Glycosylation 325 Attachment of lipids 327

Regulation of Protein Function 329 Regulation by small molecules 329 Protein phosphorylation and other modifications 330 Protein-protein interactions 335

Protein Degradation 335 The ubiquitin-proteasome pathway 335 Lysosomal proteolysis 338 KEY EXPERIMENT

Catalytic Role of Ribosomal RNA 304 KEY EXPERIMENT

The Discovery of Protein-Tyrosine Kinases 333

Summary and Key Terms 339 Questions 340 References and Further Reading 341

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Contents

Part III Cell Structure and Function 343 CHAPTER 9

The Nucleus

345

The Nuclear Envelope and Traffic between the Nucleus and the Cytoplasm 345 Structure of the nuclear envelope 346 The nuclear pore complex 350 Selective transport of proteins to and from the nucleus 353 Regulation of nuclear protein import 356 Transport of RNAs 357

Internal Organization of the Nucleus 359 Chromosome organization and gene expression 359 Sub-compartments within the nucleus 362

The Nucleolus and rRNA Processing 365 Ribosomal RNA genes and the organization of the nucleolus 365 Transcription and processing of rRNA 367 Ribosome assembly 368 Additional functions of the nucleolus 369 MOLECULAR MEDICINE

Nuclear Lamina Diseases 348 KEY EXPERIMENT

Identification of Nuclear Localization Signals 352

Summary and Key Terms 370 Questions 371 References and Further Reading 372

CHAPTER 10

Protein Sorting and Transport 373 The Endoplasmic Reticulum 373 The endoplasmic reticulum and protein secretion 374 Targeting proteins to the endoplasmic reticulum 376 Insertion of proteins into the ER membrane 381 Protein folding and processing in the ER 386 Quality control in the ER 389 The smooth ER and lipid synthesis 392 Export of proteins and lipids from the ER 395

The Golgi Apparatus 398 Organization of the Golgi 398 Protein glycosylation within the Golgi 400 Lipid and polysaccharide metabolism in the Golgi 402 Protein sorting and export from the Golgi apparatus 403

The Mechanism of Vesicular Transport 406 Experimental approaches to understanding vesicular transport 406 Cargo selection, coat proteins, and vesicle budding 407 Vesicle fusion 410

Lysosomes 412 Lysosomal acid hydrolases 412 Endocytosis and lysosome formation 414 Phagocytosis and autophagy 416

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Contents

KEY EXPERIMENT

The Signal Hypothesis 378 MOLECULAR MEDICINE

Gaucher Disease 413

Questions 457 References and Further Reading 458

CHAPTER 12

Summary and Key Terms 417 Questions 419 References and Further Reading 419

The Cytoskeleton and Cell Movement 459

CHAPTER 11

Structure and Organization of Actin Filaments 459

Bioenergetics and Metabolism 421 Mitochondria 421 Organization and function of mitochondria 422 The genetic system of mitochondria 424 Protein import and mitochondrial assembly 425

The Mechanism of Oxidative Phosphorylation 431 The electron transport chain 431 Chemiosmotic coupling 432 Transport of metabolites across the inner membrane 436

Chloroplasts and Other Plastids 438 The structure and function of chloroplasts 438 The chloroplast genome 440 Import and sorting of chloroplast proteins 441 Other plastids 444

Photosynthesis 446 Electron transport 446 ATP synthesis 449

Peroxisomes 450 Functions of peroxisomes 451 Peroxisome assembly 453 MOLECULAR MEDICINE

Diseases of Mitochondria: Leber’s Hereditary Optic Neuropathy 426 KEY EXPERIMENT

The Chemiosmotic Theory 434

Summary and Key Terms 455

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Assembly and disassembly of actin filaments 460 Organization of actin filaments 465 Association of actin filaments with the plasma membrane 467 Protrusions of the cell surface 471

Actin, Myosin, and Cell Movement

472

Muscle contraction 473 Contractile assemblies of actin and myosin in nonmuscle cells 477 Unconventional myosins 479 Formation of protrusions and cell movement 480

Microtubules 482 Structure and dynamic organization of microtubules 482 Assembly of microtubules 485 Organization of microtubules within cells 488

Microtubule Motors and Movement

490

Identification of microtubule motor proteins 490 Cargo transport and intracellular organization 493 Cilia and flagella 496 Reorganization of microtubules during mitosis 499 Chromosome movement 500

Intermediate Filaments 502 Intermediate filament proteins 502 Assembly of intermediate filaments 504 Intracellular organization of intermediate filaments 505 Functions of intermediate filaments: keratins and diseases of the skin 507 KEY EXPERIMENT

The Isolation of Kinesin 491

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xiv

Contents

KEY EXPERIMENT

CHAPTER 14

Expression of Mutant Keratin Causes Abnormal Skin Development 508

Summary and Key Terms 510 Questions 512 References and Further Reading 512

Cell Walls, the Extracellular Matrix, and Cell Interactions 557

CHAPTER 13

Cell Walls 557

The Plasma Membrane

515

Structure of the Plasma Membrane 515 The phospholipid bilayer 515 Membrane proteins 519 Mobility of membrane proteins 524 The glycocalyx 525

Transport of Small Molecules 526 Passive diffusion 526 Facilitated diffusion and carrier proteins 527 Ion channels 529 Active transport driven by ATP hydrolysis 537 Active transport driven by ion gradients 540

Endocytosis 544

Bacterial cell walls 557 Eukaryotic cell walls 557

The Extracellular Matrix and Cell-Matrix Interactions 564 Matrix structural proteins 564 Matrix polysaccharides 568 Matrix adhesion proteins 569 Cell-matrix interactions 571

Cell-Cell Interactions 574 Adhesion junctions 574 Tight junctions 577 Gap junctions 578 Plasmodesmata 581 KEY EXPERIMENT

The Characterization of Integrin 572

Phagocytosis 544 Receptor-mediated endocytosis 545 Protein trafficking in endocytosis 550 MOLECULAR MEDICINE

Cystic Fibrosis 541 KEY EXPERIMENT

MOLECULAR MEDICINE

Gap Junction Diseases 580

Summary and Key Terms 582 Questions 583 References and Further Reading 584

The LDL Receptor 548

Summary and Key Terms 553 Questions 554 References and Further Reading 555

©2013 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured or disseminated in any form without express written permission from the publisher.

Part IV Cell Regulation

587 Contents

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Part IV Cell Regulation 587 CHAPTER 15

Cell Signaling

589

Signaling Molecules and Their Receptors 589 Modes of cell-cell signaling 590 Steroid hormones and the nuclear receptor superfamily 591 Nitric oxide and carbon monoxide 593 Neurotransmitters 594 Peptide hormones and growth factors 594 Eicosanoids 596 Plant hormones 598

Functions of Cell Surface Receptors 599 G protein-coupled receptors 600 Receptor protein-tyrosine kinases 603 Cytokine receptors and nonreceptor protein-tyrosine kinases 606 Receptors linked to other enzymatic activities 607

Pathways of Intracellular Signal Transduction 608 The cAMP pathway: second messengers and protein phosphorylation 608 Cyclic GMP 611 Phospholipids and Ca2+ 612 The PI 3-kinase/Akt and mTOR pathways 615 MAP kinase pathways 617 The JAK/STAT and TGF-b/Smad pathways 623 NF-kB signaling 625 The Hedgehog, Wnt, and Notch pathways 625

Signal Transduction and the Cytoskeleton 628 Integrins and signal transduction 628 Signaling from cell adhesion molecules 630 Regulation of the actin cytoskeleton 630

Signaling Networks 632 Feedback and crosstalk 632

Networks of cellular signal transduction 634 KEY EXPERIMENT

G Protein-Coupled Receptors and Odor Detection 601 MOLECULAR MEDICINE

Cancer: Signal Transduction and the ras Oncogenes 620

Summary and Key Terms 635 Questions 637 References and Further Reading 638

CHAPTER 16

The Cell Cycle

641

The Eukaryotic Cell Cycle 641 Phases of the cell cycle 642 Regulation of the cell cycle by cell growth and extracellular signals 644 Cell cycle checkpoints 646 Restricting DNA replication to once per cell cycle 647

Regulators of Cell Cycle Progression 647 Protein kinases and cell cycle regulation 647 Families of cyclins and cyclin-dependent kinases 653 Growth factors and the regulation of G1 Cdk’s 655 DNA damage checkpoints 658

The Events of M Phase 659 Stages of mitosis 659 Entry into mitosis 662 The spindle assembly checkpoint and progression to anaphase 666

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Contents

Cytokinesis 667

KEY EXPERIMENT

Meiosis and Fertilization 668

Culture of Embryonic Stem Cells 702

The process of meiosis 668 Regulation of oocyte meiosis 671 Fertilization 673

Summary and Key Terms 708 Questions 710 References and Further Reading 710

KEY EXPERIMENT

The Discovery of MPF 649 KEY EXPERIMENT

The Identification of Cyclin 652

Summary and Key Terms 675 Questions 677 References and Further Reading 677

CHAPTER 17

Cell Death and Cell Renewal 681 Programmed Cell Death 681 The events of apoptosis 682 Caspases: the executioners of apoptosis 685 Central regulators of apoptosis: the Bcl-2 family 686 Signaling pathways that regulate apoptosis 689 Alternative pathways of programmed cell death 692

Stem Cells and the Maintenance of Adult Tissues 692 Proliferation of differentiated cells 693 Stem cells 695 Medical applications of adult stem cells 701

Pluripotent Stem Cells, Cellular Reprogramming, and Regenerative Medicine 703 Embryonic stem cells 704 Somatic cell nuclear transfer 705 Induced pluripotent stem cells 707 Transdifferentiation of somatic cells 708

CHAPTER 18

Cancer

713

The Development and Causes of Cancer 713 Types of cancer 713 The development of cancer 715 Causes of cancer 717 Properties of cancer cells 718 Transformation of cells in culture 722

Tumor Viruses 723 Hepatitis B and C viruses 723 Small DNA tumor viruses 724 Herpesviruses 726 Retroviruses 726

Oncogenes 727 Retroviral oncogenes 727 Proto-oncogenes 728 Oncogenes in human cancer 731 Functions of oncogene products 735

Tumor Suppressor Genes 741 Identification of tumor suppressor genes 741 Functions of tumor suppressor gene products 745 Roles of oncogenes and tumor suppressor genes in tumor development 748

Molecular Approaches to Cancer Treatment 749 Prevention and early detection 749 Treatment 750 KEY EXPERIMENT

The Discovery of Proto-Oncogenes 730

KEY EXPERIMENT

Identification of Genes Required for Programmed Cell Death 684

MOLECULAR MEDICINE

Imatinib: Cancer Treatment Targeted against the bcr/abl Oncogene 752

©2013 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured or disseminated in any form without express written permission from the publisher.

Contents

Summary and Key Terms 755 Questions 757 References and Further Reading 757

Answers to Questions 761

Glossary 773 Illustration Credits 797 Index 799

©2013 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured or disseminated in any form without express written permission from the publisher.

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