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THE CELL

A Molecular Approach

Sixth Edition

Geoffrey M. Cooper • Robert E. Hausman

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PART I

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

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 7 RNA Synthesis and

Processing 239

Chapter 8 Protein Synthesis,

Processing, and Regulation 297

PART III

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

Chapter 14 Cell Walls, the Extracellular

Matrix, and Cell

Interactions 557

PART IV

Cell Regulation 587

Chapter 15 Cell

Signaling 589

Chapter 16 The Cell Cycle 641

Chapter 17 Cell Death and Cell

Renewal 681

Chapter 18 Cancer 713

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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 17

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

KEYEXPERIMENT

Animal Cell Culture 34

MOLECULARMEDICINE

Viruses and Cancer 37

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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KEYEXPERIMENT

The Folding of Polypeptide Chains 54

KEYEXPERIMENT

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

KEYEXPERIMENT

Antimetabolites and Chemotherapy 97

Phenylketonuria 98

Summary and Key Terms 99

Questions 100

References and Further Reading 101

CHAPTER 4 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

KEYEXPERIMENT

The DNA Provirus Hypothesis 117

KEYEXPERIMENT

RNA Interference 144

Summary and Key Terms 146

Questions 148

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x Contents

Part II The Flow of

Genetic Information 151

CHAPTER 5 The Organization and

Sequences of Cellular

Genomes 153

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

Bioinformatics and Systems Biology 181

Systematic screens of gene function 181 Regulation of gene expression 182 Variation among individuals and genomic

medicine 184

KEYEXPERIMENT

The Discovery of Introns 156

KEYEXPERIMENT

The Human Genome 167

Summary and Key Terms 186

Questions 187

References and Further Reading 188

CHAPTER 6 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

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

Colon Cancer and DNA Repair 215

KEYEXPERIMENT

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Summary and Key Terms 233

Questions 235

References and Further Reading 236

CHAPTER 7 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

KEYEXPERIMENT

Isolation of a Eukaryotic Transcription Factor 259

KEYEXPERIMENT

The Discovery of snRNPs 284

Summary and Key Terms 291

Questions 293

References and Further Reading 294

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

KEYEXPERIMENT

Catalytic Role of Ribosomal RNA 304

KEYEXPERIMENT

The Discovery of Protein-Tyrosine Kinases 333

Summary and Key Terms 339

Questions 340

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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

Nuclear Lamina Diseases 348

KEYEXPERIMENT

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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KEYEXPERIMENT

The Signal Hypothesis 378

Gaucher Disease 413

Summary and Key Terms 417

Questions 419

References and Further Reading 419

CHAPTER 11 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 MOLECULARMEDICINE Diseases of Mitochondria:

Leber’s Hereditary Optic Neuropathy 426

KEYEXPERIMENT

The Chemiosmotic Theory 434

Summary and Key Terms 455

Questions 457

References and Further Reading 458

CHAPTER 12 The Cytoskeleton and

Cell Movement 459

Structure and Organization of Actin

Filaments 459

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

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xiv Contents

KEYEXPERIMENT

Expression of Mutant Keratin

Causes Abnormal Skin Development 508

Summary and Key Terms 510

Questions 512

References and Further Reading 512

CHAPTER 13 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

Phagocytosis 544

Receptor-mediated endocytosis 545 Protein trafficking in endocytosis 550

Cystic Fibrosis 541

KEYEXPERIMENT

The LDL Receptor 548

Summary and Key Terms 553

Questions 554

References and Further Reading 555

CHAPTER 14 Cell Walls, the Extracellular

Matrix, and Cell

Interactions 557

Cell Walls 557

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 KEYEXPERIMENT

The Characterization of Integrin 572

Gap Junction Diseases 580

Summary and Key Terms 582

Questions 583

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Contents xv

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

KEYEXPERIMENT

G Protein-Coupled Receptors and Odor Detection 601

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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Cytokinesis 667

Meiosis and Fertilization 668

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

KEYEXPERIMENT

The Discovery of MPF 649

KEYEXPERIMENT

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

KEYEXPERIMENT

Identification of Genes Required for Programmed Cell Death 684

KEYEXPERIMENT

Culture of Embryonic Stem Cells 702

Summary and Key Terms 708

Questions 710

References and Further Reading 710

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