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Cell Biology E-Book

Cell Biology E-Book

Thomas D. Pollard | William C. Earnshaw | Jennifer Lippincott-Schwartz

(2007)

Additional Information

Book Details

Abstract

A masterful introduction to the cell biology that you need to know! This critically acclaimed textbook offers you a modern and unique approach to the study of cell biology. It emphasizes that cellular structure, function, and dysfunction ultimately result from specific macromolecular interactions. You'll progress from an explanation of the "hardware" of molecules and cells to an understanding of how these structures function in the organism in both healthy and diseased states. The exquisite art program helps you to better visualize molecular structures.

  • Covers essential concepts in a more efficient, reader-friendly manner than most other texts on this subject.
  • Makes cell biology easier to understand by demonstrating how cellular structure, function, and dysfunction result from specific macromole¬cular interactions.
  • Progresses logically from an explanation of the "hardware" of molecules and cells to an understanding of how these structures function in the organism in both healthy and diseased states.
  • Helps you to visualize molecular structures and functions with over 1500 remarkable full-color illustrations that present physical structures to scale.
  • Explains how molecular and cellular structures evolved in different organisms.
  • Shows how molecular changes lead to the development of diseases through numerous Clinical Examples throughout.
  • Includes STUDENT CONSULT access at no additional charge, enabling you to consult the textbook online, anywhere you go · perform quick searches · add your own notes and bookmarks · follow Integration Links to related bonus content from other STUDENT CONSULT titles—to help you see the connections between diverse disciplines · test your knowledge with multiple-choice review questions · and more!
  • New keystone chapter on the origin and evolution of life on earth probably the best explanation of evolution for cell biologists available!
  • Spectacular new artwork by gifted artist Graham Johnson of the Scripps Research Institute in San Diego. 200 new and 500 revised figures bring his keen insight to Cell Biology illustration and further aid the reader’s understanding.
  • New chapters and sections on the most dynamic areas of cell biology - Organelles and membrane traffic by Jennifer Lippincott-Schwartz; RNA processing (including RNAi) by David Tollervey., updates on stem cells and DNA Repair.
  • ,More readable than ever. Improved organization and an accessible new design increase the focus on understanding concepts and mechanisms.
  • New guide to figures featuring specific organisms and specialized cells paired with a list of all of the figures showing these organisms. Permits easy review of cellular and molecular mechanisms.
  • New glossary with one-stop definitions of over 1000 of the most important terms in cell biology.

Table of Contents

Section Title Page Action Price
Front cover Cover
Title page iii
Copyright page iv
To Patty and Margarete and our families v
Contributors vii
Preface to the Second Edition ix
Organization of the Book ix
Preface to the First Edition xi
Acknowledgments xv
Contents xvii
Guide to Figures Featuring Specific Organisms and Specialized Cells xix
SECTION I: Introduction to Cell Biology 1
CHAPTER 1: Introduction to Cells 3
Features That Distinguish Eukaryotic and Prokaryotic Cells 4
Some Universal Principles of Living Cells 6
Overview of Eukaryotic Cellular Organization and Functions 11
CHAPTER 2: Evolution of Life on Earth 17
Prebiotic Chemistry Leading to an RNA World 18
Divergent Evolution from the Last Universal Common Ancestor of Life 19
Evolution of Prokaryotes 20
Origin of Eukaryotes 21
Origin and Evolution of Mitochondria 23
The First Billion Years of Eukaryotic Evolution 23
Origins and Evolution of Chloroplasts 25
Evolution of Multicellular Eukaryotes 26
Looking Back in Time 28
SECTION II: Chemical and Physical Background 29
CHAPTER 3: Molecules: Structures and Dynamics 33
Water 33
Proteins 34
Nucleic Acids 46
Carbohydrates 52
The Aqueous Phase of Cytoplasm 55
CHAPTER 4: Biophysical Principles 57
First-Order Reactions 57
Second-Order Reactions 58
Reversible Reactions 60
Thermodynamic Considerations 61
Linked Reactions 62
Chemical Bonds 63
A Strategy for Understanding Cellular Functions 64
Analysis of an Enzyme Mechanism: The Ras GTPase 64
CHAPTER 5: Macromolecular Assembly 69
Assembly of Macromolecular Structures from Subunits 70
Specifi city by Multiple Weak Bonds on Complementary Surfaces 71
Symmetrical Structures Constructed from Identical Subunits with Equivalent (or Quasi-equivalent) Bonds 72
New Properties from Sequential Assembly Pathways 73
Regulation at Multiple Steps on Sequential Assembly Pathways 74
CHAPTER 6: Research Strategies 85
Imaging 86
Choice of Organisms for Biological Research 92
Inventory: Gene and Protein Discovery 94
Molecular Structure 102
Partners and Pathways 102
Rates and Affinities 105
Tests of Physiological Function 105
Mathematical Models of Systems 107
SECTION III: Membrane Structure and Function 109
CHAPTER 7: Membrane Structure and Dynamics 113
Development of Ideas about Membrane Structure 113
Lipids 114
Physical Structure of the Fluid Membrane Bilayer 117
Membrane Proteins 120
CHAPTER 8: Membrane Pumps 127
Membrane Permeability: An Introduction 127
Membrane Pumps 128
Diversity of Membrane Pumps 128
Light-Driven Proton Pumping by Bacteriorhodopsin 129
ATP-Driven Pumps 130
CHAPTER 9: Membrane Carriers 139
Diversity of Carrier Proteins 139
Structure of MFS Carrier Proteins 140
Carrier Physiology and Mechanisms 142
CHAPTER 10: Membrane Channels 147
Channel Diversity and Evolution 149
Channel Structure 149
Channel Activity 151
Channels with One Transmembrane Segment 153
Channels with Two Transmembrane Segments 153
Voltage-Gated Cation Channels 155
TRP Channels 158
Channels Gated by Intracellular Ligands 159
Ion Channels Gated by Extracellular Ligands 160
ClC Chloride Channels 162
Ammonia Channels 163
Water Channels 164
Porins 165
APPENDIX 10-1: Electrical Recordings in Biology 166
Single-Channel Recordings with Patch Electrodes 166
Measurement of Membrane Potentials with Intracellular Microelectrodes and Fluorescent Dyes 167
Extracellular Electrical Measurements 167
APPENDIX 10-2: The Biophysical Basis of Membrane Potentials 167
Diffusion Potentials 167
Quantitative Relationships 168
Nernst Potential for Various Ions 169
APPENDIX 10-3: Charging and Discharging the Membrane 169
Membrane Capacitance 169
Charge Movement for a Small Cell 170
Rate of Charge Movement through Channels 170
Net Current through Ion-Selective Channels 170
Consequence of Multiple Channel Types Opening Simultaneously 171
Charge Redistribution by Electrical Conduction 172
CHAPTER 11: Membrane Physiology 173
Chemiosmotic Cycles 173
Epithelial Transport 174
Cellular Volume Regulation 176
Excitable Membranes 177
Synaptic Transmission 179
Cardiac Membrane Physiology 185
SECTION IV: Chromatin, Chromosomes, and the Cell Nucleus 189
CHAPTER 12: Chromosome Organization 193
Chromosome Morphology and Nomenclature 193
One DNA Molecule per Chromosome 193
The Organization of Genes on Chromosomes 195
Transposons Make Up Much of the Human Genome 197
Pseudogenes 199
Segmental Duplications in the Human Genome 199
The Centromere: Overview 200
Variations in Centromere Organization among Species 200
Mammalian Centromere DNA 202
The Ends of the Chromosomes: Why Specialized Telomeres Are Needed 204
The Structure of Telomeric DNA 204
How Telomeres Replicate the Ends of the Chromosomal DNA 204
Structural Proteins of the Telomere 206
Telomeres, Aging, and Cancer 207
CHAPTER 13: DNA Packaging in Chromatin and Chromosomes 209
The First Level of Chromosomal DNA Packaging: The Nucleosome 209
The Second Level of Chromosomal DNA Packaging: The 30-nm Fiber 214
Higher Levels of Chromosomal DNA Packaging in Interphase Nuclei 214
Functional Compartmentation of the Nucleus: Heterochromatin and Euchromatin 214
Large-Scale Structural Compartmentation of the Nucleus 220
Higher-Order Structure of Chromosomes 221
The Nuclear Matrix 223
Specialized Chromosomal Substructures: The Kinetochore 227
Centromere Proteins of the Budding Yeast 228
Mammalian Centromere Proteins 228
Role of RNAi at Centromeres 230
Conclusions 230
CHAPTER 14: Nuclear Structure and Dynamics 231
Overall Organization of the Nucleus 232
Structure of the Nuclear Envelope 236
Traffic between Nucleus and Cytoplasm 240
Disorders Associated with Defective Nuclear Trafficking 246
Other Uses of the Importin/Ran Switch 247
SECTION V: Central Dogma: From Gene to Protein 249
CHAPTER 15: Gene Expression 253
The Transcription Cycle 254
Transcription Initiation 258
Transcription Elongation and Termination 263
Gene-Specific Transcription 265
Factor Interactions 271
Chromatin and Transcription 273
Transcription Factors and Signal Transduction 275
Transcription Factors and Human Disease 277
CHAPTER 16: Eukaryotic RNA Processing 279
Synthesis of mRNAs 279
Synthesis of Stable RNAs 288
Synthesis and Function of miRNAs 292
Conclusions 296
CHAPTER 17: Protein Synthesis and Folding 297
Protein Synthetic Machinery 297
Outline of Protein Synthesis 302
Spontaneous Protein Folding 306
Chaperone-Assisted Protein Folding 307
SECTION VI: Cellular Organelles and Membrane Trafficking 311
CHAPTER 18: Posttranslational Targeting of Proteins 315
Transport of Proteins into Mitochondria 317
Transport of Proteins into Chloroplasts 320
Transport of Proteins into Peroxisomes 321
Translocation of Eukaryotic Proteins across the Plasma Membrane by ABC Transporters 323
Targeting to the Surfaces of the Plasma Membrane 323
Bacterial Protein Export 324
APPENDIX 18-1: Peroxin Features and Known Roles 329
CHAPTER 19: Mitochondria, Chloroplasts, Peroxisomes 331
Mitochondria 331
Peroxisomes 343
CHAPTER 20: Endoplasmic Reticulum 345
Endoplasmic Reticulum Functions and Organization 346
Overview of Protein Translocation into the Endoplasmic Reticulum 347
Molecular Machinery for Protein Translocation into the Endoplasmic Reticulum 350
Protein Insertion into the Endoplasmic Reticulum Bilayer or Lumen 352
Protein Folding and Oligomerization in the Endoplasmic Reticulum 355
Protein Degradation in the Endoplasmic Reticulum and the Unfolded Protein Response 357
Lipid Biosynthesis, Metabolism, and Transport within the Endoplasmic Reticulum 360
CHAPTER 21: Secretory Membrane System and Golgi Apparatus 365
Overview of the Secretory Membrane System 365
Building and Maintaining the Secretory Membrane System 367
Secretory Transport from the Endoplasmic Reticulum to the Golgi Apparatus 377
Sorting from the Trans-Golgi Network 379
Regulated Fusion with the Plasma Membrane 383
The Golgi Apparatus: Function, Structure, and Dynamics 383
CHAPTER 22: Endocytosis and the Endosomal Membrane System 391
Phagocytosis 392
Macropinocytosis 395
Endocytosis Mediated by Caveolae 396
Clathrin-Mediated Endocytosis 397
Nonclathrin/Noncaveolar Endocytosis 401
The Endosomal Compartment and the Endocytic Pathway 401
Viruses and Protein Toxins as “Opportunistic Endocytic Ligands” 406
CHAPTER 23: Degradation of Cellular Components 409
Characteristics of Constitutive Protein Turnover 409
Degradation in Lysosomes 410
Degradation by Proteasomes 413
Lipid Turnover and Degradation 418
APPENDIX 23-1: Lysosomal Storage Diseases 421
SECTION VII: Signaling Mechanisms 423
CHAPTER 24: Plasma Membrane Receptors 427
Seven-Helix Receptors 428
Receptor Tyrosine Kinases 431
Cytokine Receptors 433
Receptor Serine/Threonine Kinases 433
Guanylyl Cyclase Receptors 435
Tumor Necrosis Factor Receptor Family 436
Toll-Like Receptors 436
Notch Receptors 437
Hedgehog Receptors 437
APPENDIX 24-1: Receptors and Ligands 439
CHAPTER 25: Protein Hardware for Signaling 443
Protein Phosphorylation 443
Guanosine Triphosphate–Binding Proteins 451
Molecular Recognition by Adapter Domains 457
APPENDIX 25-1: Families of Protein Kinases 462
APPENDIX 25-2: Parallels among Guanosine Triphosphate-Binding Proteins 463
CHAPTER 26: Second Messengers 465
Cyclic Nucleotides 466
Lipid-Derived Second Messengers 468
Calcium 475
Nitric Oxide 482
APPENDIX 26-1: Examples of Ca2+ Regulated Proteins 485
CHAPTER 27: Integration of Signals 487
Signal Transduction by G-Protein-Coupled, Seven-Helix Transmembrane Receptors 487
Detection of Odors by the Olfactory System 488
Photon Detection by the Vertebrate Retina 491
Regulation of Metabolism through the b-Adrenergic Receptor 494
Signaling Pathways Influencing Gene Expression 497
MAP Kinase Pathways to the Nucleus 498
Growth Factor Receptor Tyrosine Kinase Pathway through Ras to Map Kinase 499
Insulin Pathways to GLUT4 and MAP Kinase 501
T-Lymphocyte Pathways through Nonreceptor Tyrosine Kinases 502
Cytokine Receptor, JAK/STAT Pathways 505
Serine/Threonine Kinase Receptor Pathways through Smads 506
Two-Component Phosphotransfer Systems 507
SECTION VIII: Cellular Adhesion and the Extracellular Matrix 513
CHAPTER 28: Cells of the Extracellular Matrix and Immune System 517
Indigenous Connective Tissue Cells 517
Origin and Development of Blood Cells 520
Cells Confined to the Blood 521
Cells Responsible for Innate and Adaptive Immunity 523
Cellular Basis of Innate Immunity 524
Cellular Basis of Adaptive Immunity 526
CHAPTER 29: Extracellular Matrix Molecules 531
Collagen 531
Elastic Fibers 536
Glycosaminoglycans and Proteoglycans 539
Adhesive Glycoproteins 541
The Basal Lamina 544
Matrix Metalloproteinases 546
APPENDIX 29-1: Collagen Families 549
APPENDIX 29-2: Proteoglycans 550
APPENDIX 29-3: Adhesive Glycoproteins 551
CHAPTER 30: Cellular Adhesion 553
General Principles of Cellular Adhesion 554
Identification and Characterization of Adhesion Receptors 555
Immunoglobulin Family of Cell Adhesion Molecules 556
Cadherin Family of Adhesion Receptors 556
Integrin Family of Adhesion Receptors 560
Selectin Family of Adhesion Receptors 565
Other Adhesion Receptors 566
Examples of Dynamic Adhesion 567
CHAPTER 31: Intercellular Junctions 571
Tight Junctions 573
Gap Junctions 575
Adherens Junctions 579
Desmosomes 579
Adhesion to the Extracellular Matrix: Hemidesmosomes and Focal Contacts 581
CHAPTER 32: Connective Tissues 583
Loose Connective Tissue 583
Dense Connective Tissue 583
Cartilage 584
Bone 586
Formation and Growth of the Skeleton 589
Repair of Wounds and Fractures 593
Plant Cell Wall 595
APPENDIX 32-1: Examples of Genetic Defects of Cartilage and Bone 598
SECTION IX: Cytoskeleton and Cellular Motility 599
CHAPTER 33: Actin and Actin-Binding Proteins 603
Actin Molecule 604
Actin-Related Proteins 606
Actin Polymerization 606
Actin-Binding Proteins 609
Actin Dynamics in Live Cells 614
Mechanical Properties of Cytoplasm 618
APPENDIX 33-1: Classification of Actin-Binding Proteins 619
CHAPTER 34: Microtubules and Centrosomes 623
Tubulin Structure 625
Tubulin Diversity 626
Structure of Microtubules 626
Microtubule Assembly from GTP Tubulin 627
Microtubule-Organizing Centers 628
Steady-State Dynamics of Microtubules in Vitro 628
Microtubule Dynamics in Cells 630
Regulation by Microtubule-Associated Proteins 631
The Centrosome 635
APPENDIX 34-1: Some Microtubule-Associated Proteins 641
APPENDIX 34-2: Some Centrosomal Proteins 643
CHAPTER 35: Intermediate Filaments 645
Structure of Intermediate Filament Subunits 646
Polymer Structure 647
Assembly and Dynamics of Intermediate Filaments 647
Posttranslational Modifications 649
Expression of Intermediate Filaments in Specialized Cells 649
Proteins Associated with Intermediate Filaments 650
Functions of Intermediate Filaments in Cells 650
CHAPTER 36: Motor Proteins 655
Myosins 657
Microtubule Motors 663
CHAPTER 37: Intracellular Motility 673
Strategies to Identify Tracks and Motors 674
Rapid Movements along Microtubules 674
Intracellular Movements Driven by Microtubule Polymerization 678
Bulk Movement of Cytoplasm Driven by Actin and Myosin 680
Actin-Based Movements of Organelles in Other Cells 681
Cytoplasmic Movements Driven by Actin Polymerization 681
CHAPTER 38: Cellular Motility 685
Cell Shape Changes Produced by Extension of Surface Processes 685
Cell Shape Changes Produced by Contraction 688
Locomotion by Pseudopod Extension 689
Locomotion by Cilia and Flagella 695
Bacterial Flagella 699
CHAPTER 39: Muscles 705
Skeletal Muscle 705
Cardiac Muscle 719
SECTION X: Cell Cycle 727
CHAPTER 40: Introduction to the Cell Cycle 731
Principles of Cell-Cycle Regulation 731
Phases of the Cell Cycle 733
The Biochemical Basis of Cell-Cycle Transitions 735
Role of Protein Destruction in Cell-Cycle Control 742
Changing States of the Cytoplasm during the Cell Cycle 743
APPENDIX 40-1: Inventory of the Enzymes of the Cell Cycle Engine 745
CHAPTER 41: G1 Phase and Regulation of Cell Proliferation 747
The G0 Phase and Growth Control 747
Exit from the G0 Phase 749
The Restriction Point: A Critical G1 Decision Point 750
Regulation of Cell Proliferation by the Restriction Point 751
The Restriction Point and Cancer 753
Proteolysis and G1 Cell Cycle Progression 754
Integrity of Cellular DNA Monitored by a G1 Checkpoint 755
Moving into and out of G0: Stem Cells 756
G1 Regulation: A Matter of Life and Death 760
CHAPTER 42: S Phase and DNA Replication 761
DNA Replication: A Primer 761
Origins of Replication 762
Assembly of the Prereplication Complex 765
Signals That Start Replication 767
Mechanism of DNA Synthesis 768
Higher-Order Organization of DNA Replication in the Nucleus 771
Temporal Control of Replication during the S Phase 771
The Intra-S Checkpoint 774
Synthesis of the Histone Proteins 775
Other Events of the S Phase 775
CHAPTER 43: G2 Phase and Control of Entry into Mitosis 777
Enzymology of the G2/Mitosis Transition 777
Changes in Subcellular Localization at the G2/M Transition 779
Cdk1–Cyclin A and the Initiation of Prophase 780
Summary of the Main Events of the G2/M Transition 780
The G2 Checkpoint 781
The G2 Checkpoint and Cancer 783
How the G2 Checkpoint Works 783
Transition to Mitosis 785
CHAPTER 44: Mitosis and Cytokinesis 791
Prophase 791
Prometaphase 795
Metaphase 802
Anaphase 803
Telophase 806
Cytokinesis 807
CHAPTER 45: Meiosis 815
Meiosis: An Essential Process for Sexual Reproduction 816
The Language of Meiosis 818
Recombination 818
Tracking the Homologous Chromosomes through the Stages of Meiotic Prophase I 821
Chromosomal Ikebana: The Bouquet Stage 822
Pairing and Synapsis in More Detail 823
Synaptonemal Complex Components 825
Chiasmata 826
Cohesion and Chromosomal Movements during Meiosis I 827
Behavior of the Sex Chromosomes in Meiosis 828
Cell-Cycle Regulation of Meiotic Events 829
Suppression of DNA Replication between Meiosis I and Meiosis II 829
The Metaphase II Arrest and the MAP Kinase Pathway 829
Timing of Meiosis in Humans 830
Meiotic Defects and Human Disease 831
CHAPTER 46: Programmed Cell Death 833
The Necessity for Cell Death in Multicellular Organisms 833
Programmed Cell Death versus Accidental Cell Death: Apoptosis versus Necrosis 833
Nonapoptotic Programmed Cell Death 836
Classes of Cells That Undergo Programmed Cell Death 837
Genetic Analysis of Programmed Cell Death 839
Signals and Pathways of Apoptosis 840
Protein Regulators and Effectors of Apoptosis 840
The Extrinsic Pathway of Apoptotic Death 846
Role of the Fas Death Receptor in Normal and Diseased Cells 848
Linking Apoptosis to the Cell Cycle by p53 849
Importance of Apoptosis in Human Disease 849
Glossary 851
Index 875