The cell book index
Transcript of 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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