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

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

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

ix

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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or disseminated in any form without express written permission from the publisher.

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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or disseminated in any form without express written permission from the publisher.

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

xi

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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xii

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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or disseminated in any form without express written permission from the publisher.

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:
Lebers Hereditary Optic Neuropathy 426
KEY EXPERIMENT

The Chemiosmotic Theory 434

Summary and Key Terms 455

xiii

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

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or disseminated in any form without express written permission from the publisher.

Part IV Cell Regulation

587
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

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 Cdks 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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xvi

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

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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.

xvii