The cell book index

8/19/2019 The cell book index

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T H E C E L L

Fifth Edition

GEOFFREY M . COOPER • ROBERT E. HAUSM AN

Boston University

ASM PRESS

Washington, D.C.

1

SINAUER ASSOCIATES, INC.

Sunderland, Massachusetts


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r i e f C o n t e n t s

PARTI

Introduction 1

C h a p t e r

1

A n O v e r v i e w o f C e l ls a n d C e l l R e s e a rc h 3

C h a p te r 2 T h e C o m p o s i t i o n o f C e l ls 43

C h a p te r 3 C e l l M e t a b o l i s m 73

C h a p te r 4 F u n d a m e n t a l s o f M o l e c u l a r B io l o g y 1 0 3

P R T I I The Flow of Genetic Inform ation 153

C h a p te r 5 T h e O r g a n i z a t i o n a n d S e q u e n c e s o f C e l lu l a r G e n o m e s 1 5 5

C h a p te r 6 R e p l ic a t io n M a i n t e n a n c e a n d R e a r r a n g e m e n t s o f G e n o m i c D N A 2 0 1

C h a p te r 7 R N A S y n t h e s i s a n d P r o c e s s in g 251

C h a p te r 8 P r o t e i n S y n t h e s i s P r o c e s s i n g a n d R e g u l a t io n 309

P R T I I I Cell Structure and Function 353

C h a p te r 9 T h e N u c le u s 3 5 5

C h a p te r 1 0 P r o t e in S o r t in g a n d T r a n s p o r t :

T h e E n d o p l a s m ic R e t i c u l u m G o l g i A p p a r a t u s a n d L y s o s o m e s 3 8 3

C h a p t e r

1 1

B i o e n e r g e t ic s a n d M e t a b o l i s m :

M i t o c h o n d r i a C h l o r o p la s t s a n d P e r o x is o m e s 4 3 3

C h a p te r 1 2 T h e C y t o s k e l e to n a n d C e l l M o v e m e n t 4 7 3

C h a p te r 1 3 T h e P la s m a M e m b r a n e 5 2 9

C h a p te r 1 4 C e l l W a l ls t h e E x t ra c e l lu l a r M a t r i x a n d C e l l I n t e r a c t i o n s 5 7 1

P R T I V Cell Regulation 601

C h a p te r 1 5 C e l l S ig n a l in g 6 0 3

C h a p te r 1 6 T h e C e l l C y c l e 6 5 3

C h a p te r 1 7 C e l l D e a t h a n d C e l l R e n e w a l 6 9 3

C h a p te r 1 8 C a n c e r 7 2 5


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Features of h e ell xv

lements to Accomp any The Cell xvii

PART I INTRODUCTION

An Overview of Cells

and Cell Research

3

t Cell 4

ution of Metabolism 6

ukaryotic Cells

ryotes 9

Multicellular

Organisms 12

18

18

thaliana 19

s of Cell Bio logy 21

on Microsc opy 28

owth of Anim al Cells in Culture 33

lture of Plant Cells 36

Animal Cell Culture 34

Viruses and Cancer 37

Summ ary and

K ey Terms

39

Questions

41

R efer ences a n d F ur ther R ead ing 42

2

The Composition

of Cells

43

The Molecules

of Cells 43

Carbohydrates 44

Lipids 46

Nucleic Acids 49

Proteins 52

Cell Me mbrane s 58

Membrane Lipids 58

Membrane Proteins 60

Transport across Cell Mem branes 63

Proteomics: Large-Scale

An alysis of Cell Proteins 64

Identifica tion of Cell Proteins 65

Global Analysis of Protein

Localization 67

Protein Interactions 68

KEY EXPERIMENT

The Folding of Polypeptide Chains 54

KEY EXPERIMENT

The Structure of Cell Membranes 60

Summ ary and

K ey Terms

70

Questions 71

R efer ences

a n d

F ur ther R ead ing

71

Cell Metabolism

73

The Central Role of Enzymes as

Biological Catalysts 73

The Catalytic Activ ity of Enzymes 73

Mechanisms of Enzymatic Catalysis 74

Coenzymes 76

Regulation of Enzyme Activity 79

Me tabolic Energy 81

Free Energy and ATP 81

The Generation of

ATP

from

Glucose 84

The Derivation of Energy from Other

Organic Molecules 89

Photosynthesis 89

The Biosynthesis of Cell

Consti tuents 91

Carbohydrates 92

Lipids 93

Proteins 94

Nucleic Acids 96

MOLECULAR MEDICINE

Phenylketonuria 97

KEY EXPERIMENT

Antimetabolites and Chemotherapy 98

Summ ary and

K ey

Terms 99

Questions 100

R efer ences a n d F ur ther R ead ing

1 1


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VIM CONTENTS

DNA Repair 216

Direct Reversal of DNA Damage 216

Excision Repair 219

Translesion DNA Synthesis 224

Repair of Doub le-Strand Breaks 226

Recomb ination b etween

Homologous DNA

Sequences 227

Models of Homologous

Recombination 228

Enzymes Involved in Homologous

Recombination 229

DNA Rearrangements 233

Site-Specific Recombination 234

Transposition via DNA

Intermediates 240

Transpos ition via RNA-

Intermediates 242

Gene Am plification 245

MOLECULAR MEDICINE

Colo n Cancer and DNA Repair 225

KEY EXPERIMENT

Rearrangement of Immunoglobulin

Genes 236

Summary and e y Terms 247

Que st ions 249

References

and Furthe r

Reading

24 9

7

R N A S y n t h e s is a n d

P r o c e s s i n g 251

Trans crip tion in

Prokaryotes 251

RNA Polymerase and Transcription 252

Repressors and Negative Control of

Transcription 256

Positive Co ntro l of Transcription 258

Eukaryotic RNA Polymerases

and General Transcription

Factors 258

Eukaryotic RNA Polymerases 259

General Transcription Factors and

Initiation of Transcription by RNA

Polymerase II 259

Transcription by RNA Polymerases I

and III 263

Regulation of Transcription

in Eukaryotes 265

c/5-Acting Regulatory Sequences:

Promoters and Enhancers 265

Trans cription Factor Bind ing Sites 269

Transcriptional Regulatory Proteins 270

Structure and Function of

Transcriptional Activators 273

Eukaryotic Repressors 276

Regulation of Elongation 278

Relationship of Ch rom atin Structure to

Transcription 278

Regulation of Transcription by

Noncoding RNAs 285

DNA Methylation 286

RNA Processing and

Turnover 287

Processing of Ribosomal and Transfer

RNAs 288

Processing of mRNA in Eukaryotes 290

Splicing Mechanisms 293

Alternative Splicing 298

RNA Editing 300

RNA Degrad ation 301

KEY EXPERIMENT

Isolation of a Eukaryotic Transcription

Factor 272

KEY EXPERIMENT

The Discovery of snRNPs 294

Summary and e y Terms 303

Que st ions 305

References and Further Reading 306

8

P r o t e i n S y n t h e s i s

P r o c e s s i n g a n d

R e g u l a t i o n 309

Trans lation of mRNA 309

Transfer RNAs 310

TheRibosome 311

The Organization of mRNAs and the

Initiation of Translation 317

The Process of Trans lation 318

Regulation of Translation 323

Protein Folding and

Processing 329

Chaperones and Protein Folding 330

Enzymes tha t Catalyze Protein

Folding 332

Protein Cleavage 333

Glycosylation 335

Attac hm ent of Lipids 337

Regulation of Protein

Function 340

Regulation by Small Molecules 340

Protein Phospho rylation 341

Protein-Protein Interactions 343

Protein Degradation 345

The Ubiquitin-Proteasome

Pathway 345

Lysosomal Proteolysis 348

KEY EXPERIMENT

Catalytic Role of Ribosomal RNA 316

KEY EXPERIMENT

The Discovery of Protein-Tyrosine

Kinases 344

Summ ary and e y Terms 34 9

Que st ions 351

References

and Furthe r

Reading

35 1


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CONTENTS

IX

PART

III

CELL STRUCTURE AND FUNCTION

The Nucleus

355

and

the

Nucleus

the Cytoplasm

355

of

the Nuclear Envelope

356

ear Pore Com plex

360

ective Transport

of

Proteins

to and

from

the

Nucleus

361

of Nuclear Protein

Import

367

of

RNAs

368

ernal Org anization

of

Nucleus

369

Chromatin Structure

370

the

Nucleus

372

e Nucleolus a nd rRNA

374

the

Organization

of

the Nucleolus

375

of rRNA

376

osome Assembly

378

Nuclear Lamina Diseases 358

Y EXPERIMENT

Identification

of

Nuclear Localization

Signals

362

and

K e y Terms 379

381

and Furthe r Reading 381

1

1 1 Protein Sorting

V

and

Transport:

The Endoplasmic Reticulum

Golgi Apparatus and

Lysosomes 383

The Endoplasmic

Reticulum 383

The Endoplasmic Reticulum

and

Protein

Secretion

384

Targeting Proteins

to the

Endoplasmic

Reticulum

386

Insertion

of

Proteins into

the

ER

Membrane

391

Protein Folding

and

Processing

in the

ER 396

Quality Control

in the ER 398

The Smooth

ER

and Lipid Synthesis

402

Export

of

Proteins and Lipids from

th e

ER 405

The Golgi App aratus

408

Organization

of

the Golgi

408

Protein Glycosylation w ithin

the Golgi

410

Lipid and Polysaccharide Metabolism

in

the

Golgi

412

Protein So rting and Export from

the

Golgi A pparatus

413

The Mechanism

of

Vesicular

Transport

416

Experimental Approaches

to Under-

stand ing Vesicular Transport

416

Cargo Selection, Coat Proteins,

and

Vesicle Bud ding

418

Vesicle Fusion

420

Lysosomes

423

Lysosomal Acid Hydrolases

423

Endocytosis and Lysosome Formation 426

Phagocytosis and Au tophagy

426

KEY EXPERIMENT

The Signal Hypothesis

388

MOLECULAR MEDICINE

Caucher Disease 425

Summary and

K e y

Terms 429

Questions 431

References and

Furthe r

Reading 431

1

1 Bioenergetics and

I Metabolism:

Mitochondria Chloroplasts

and Peroxisomes 433

Mitochondria 433

Organization and Function

of

Mitochondria 434

The Genetic System

of

M itochondria

435

Protein Import and Mitochondrial

Assembly 437

The Mechanism

of

O xidat ive

Phosphorylat ion

445

The Electron Transport Chain

445

Chemiosmotic Cou pling

446

Transport

of

M etabolites across

the

Inner M embrane

450

Chloroplasts and Other

Plastids

452

The Structure and F unction

of Chloroplasts

452

The Chloroplast Genome

454

Imp ort and Sorting

of

Chloroplast

Proteins

455

Othe r Plastids

457


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CONTENTS

and II 460

P Synthesis 46 4

eroxisomes 464

of Peroxisomes 465

eroxisome Assembly 467

Diseases of Mitochondria: Leber's

Hereditary Optic Neuropathy 438

EY EXPERIMENT

The Chemiosmotic Theory 448

umm ary and K ey Terms 46 9

Questions 471

References

and Further

Reading

47 1

2

The Cytoskeleton

and Cell

Movement 473

Structure and Orga nization of

Actin Filaments 473

Assembly and Disassembly of Actin

Filaments 474

Organ ization of Actin Filaments 479

Association of Actin Filaments with the

Plasma Membrane 481

Protrusions of the Ce ll Surface 485

Act in, M yosin , and Cell

Movement 487

Muscle Contraction 487

Contractile Assemblies of Actin and

Myosin in Nonm uscle Cells 492

Nonmuscle Myosins 493

Formation of Protrusions and Cell

Movement 494

Intermediate Filaments 496

Intermediate Filament Proteins 496

ssembly of Intermediate Filaments 498

Intracellular Organization of

Intermediate Filaments 499

Functions of Keratins and

Ne urofilam ents: Diseases of the Skin

and Nervous System 501

Microtubules 504

Structure and Dynamic Organization

of Microtubules 504

Assembly of Microtu bules 507

Organization of Microtubules within

Cells 509

Microtubule Motors and

Movement 511

Identification of Microtubule Motor

Proteins 511

Cargo Transport and Intracellular

Organization 515

Cilia and Flagella 516

Reorganization of Microtubules

during Mitosis 519

Chromosome Movem ent 520

KEY EXPERIMENT

Expression of Mutant Keratin Causes

Abnormal Skin Development 502

KEY EXPERIMENT

The Isolation of Kinesin 512

Summ ary and

K ey Terms

52 2

Questions 525

References and Furthe r Reading 52 5

The Plasma

Membrane

529

Structure of the Plasma

Membrane 529

The Phos pholipid Bilayer 529

Membrane Proteins 533

Mobility of Membrane Proteins 538

The Glycocalyx 540

Transport of Small

Molecules 540

Passive Diffus ion 541

Facilitated Diffusion and Carrier

Proteins 542

Ion Channels 544

Active Transport Driven by ATP

Hydrolysis 551

Active Transport Driven by Ion

Gradients 555

Endocytosis 557

Phagocytosis 557

Receptor-Mediated Endocytosis 558

Protein Trafficking in Endocytosis 563

MOLECULAR MEDICINE

Cystic Fibrosis 554

KEY EXPERIMENT

The

LDL

Receptor 560

Summ ary and

K ey Terms

56 7

Questions 568

References

and Furthe r

Reading

56 8

4

Cell Walls the

Extracellular

Matrix and Cell

Interactions

571

Cell W alls 571

Bacterial Cell Walls 571

Eukaryotic Cell Walls 572

The Extracel lular Matr ix and

Cell-Matrix Interactions 577

Matrix Structural Proteins 578

Matrix Polysaccharides 581

Ma trix Adhesion Proteins 582

Cell-Matrix Interactions 583

Cell-Cell Inte rac tions 587

Adhesion junctions 587

Tig ht Junctions 590

Gap Junctions 591

Plasmodesmata 595

KEY EXPERIMENT

The Characterization of Integrins 584

MOLECULAR MEDICINE

Gap Junction Diseases 594

Summ ary and

K ey Terms

59 6

Questions 598

References

and Further

Reading

59 8


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CONTENTS

X I

PART IV CELL REGULATION

k

ell

Signaling

603

Signaling Molecules and

Their Receptors 603

Modes of Cell-Cell Signaling 604

Steroid Hormones and the Nuclear

Receptor Superfamily 605

Nitric O xide and C arbon

Monoxide 607

Neurotransmitters 608

Peptide Hormones and Gro wth

Factors 609

Eicosanoids 610

Plant Hormones 612

Functions of Cell Surface

Receptors 613

G Protein-Coupled Receptors 613

Receptor Protein-Tyrosine Kinases 615

Cytokine Receptors and Non receptor

Protein-Tyrosine Kinases 620

Receptors Linked to Othe r Enzymatic

Activities 620

Pathways of Intracellular

Signal Transduction 621

The cAMP Pathway: Second Messengers

and Protein Phospho rylation 622

Cyclic GMP 624

Phospholipids and Ca

2+

625

The

PI

3-Kinase/Akt and mTOR

Pathways 628

MAP Kinase Pathways 630

The JAK/STAT and TGF-/3/Smad

Pathways 636

NF-JCB Signaling

637

The Hedgehog, Wnt, and No tch

Pathways 638

Signal Transduction and

the Cytoskeleton 641

Integrins and Signal Transduction 641

Regulation of the Actin

Cytoskeleton 642

Signaling Ne tworks 644

Feedback and Crosstalk 644

Networks of Cellular Signal

Transduction 646

KEY EXPERIMENT

C Protein-Coupled Receptors and Odor

Detection 616

MOLECULAR MEDICINE

Cancer: Signal Transduction and the

rasOncogenes 633

Summary and K ey Terms 64 7

Questions 650

References

and Further

Reading

65 0

16

T h e C e ll

C y c l e

653

The Eukaryotic Cell

Cycle 653

Phases of the Cell Cycle 654

Regulation of the Cell Cycle by Cell

Grow th and Extracellular Signals 655

Cell Cycle Checkpoints 657

Restricting DNA Replication to Once

per Cell Cycle 659

Regulators of Cell Cycle

Progression 659

Protein Kinases and Cell Cycle

Regulation 659

Families of Cyclins and C yclin-

Dependent Kinases 664

Gro wth Factors and the Regulation

of G, Cdk's 667

DNA Damage Checkpoints 670

The Events of M Phase 672

Stages of Mitosis 672

Cdk1

/Cyclin B and Progression to

Metaphase 675

The Spindle Assembly C heckpoint and

Progression to Anaphase 678

Cytokinesis 680

Meiosis and Fert i l izat ion 681

The Process of Meiosis 681

Regulation of Ooc yte Meiosis 684

Fertilization 687

KEY EXPERIMENT

The Discovery of MPF 660

KEY EXPERIMENT

The Identification of Cyclin 663

Summary and K ey Terms 68 8

Quest ions 690

References and Furthe r Reading 69 1

7

C e ll D e a t h

and

C e l l R e n e w a l

693

Programmed Cell Death 693

The Events of Apoptosis 694

Caspases: The Executioners

of Apoptosis 697

Central Regulators of Apoptosis:

The Bcl-2 Family 699

Signaling Pathways that Regulate

Apoptosis 701

Alternative Pathways of Programmed

Cell Death 705


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