The world of the cell / 4th ed.

About the Authors p. v
Preface p. vii
Acknowledgments p. xi
Guide to Techniques and Methods p. xiii
The World of the Cell: An Overview of Structure and Function p. 1
A Preview of the Cell p. 2
The Cell Theory: A Brief History p. 2
The Emergence of Modern Cell Biology p. 4
Units of Measurement in Cell Biology p. 3
Further Insights: Biology, "Facts," and the Scientific Method p. 12
The Chemistry of the Cell p. 17
The Importance of Carbon p. 17
The Importance of Water p. 21
The Importance of Selectively Permeable Membranes p. 24
The Importance of Synthesis by Polymerization p. 26
The Importance of Self-Assembly p. 31
Further Insights: Tempus Fugit and the Fine Art of Watchmaking p. 38
The Macromolecules of the Cell p. 43
Proteins p. 43
Nucleic Acids p. 55
Polysaccharides p. 63
Lipids p. 65
Historical Perspectives: On the Trail of the Double Helix p. 60
Cells and Organelles p. 78
Properties and Strategies of Cells p. 78
The Eukaryotic Cell in Overview: Pictures at an Exhibition p. 86
Viruses, Viroids, and Prions: Agents That Invade Cells p. 102
Historical Perspectives: Discovering Organelles: The Importance of Centrifuges and Chance Observations p. 95
Bioenergetics: The Flow of Energy in the Cell p. 110
The Importance of Energy p. 110
Bioenergetics p. 116
Understanding [Delta]G p. 125
Life and the Steady State: Reactions That Move Toward Equilibrium Without Ever Getting There p. 129
Further Insights: Jumping Beans and Free Energy p. 121
Historical Perspectives: Energy and Entropy: The Greek Connection p. 123
Enzymes: The Catalysts of Life p. 134
Activation Energy and the Metastable State p. 134
Enzymes as Biological Catalysts p. 136
Enzyme Kinetics p. 144
Enzyme Regulation p. 151
RNA Molecules as Enzymes: Ribozymes p. 157
Further Insights: Monkeys and Peanuts p. 145
Historical Perspective: ATCase: Experimental Support for Allosteric Regulation p. 155
Membranes and Cell Signaling p. 163
Membranes: Their Structure, Function, and Chemistry p. 164
The Functions of Membranes p. 164
Models of Membrane Structure: An Experimental Perspective p. 166
Membrane Lipids: The "Fluid" Part of the Model p. 172
Membrane Proteins: The "Mosaic" Part of the Model p. 181
Contemporary Techniques: Revolutionizing the Study of Membrane Proteins: The Impact of Molecular Biology p. 188
Transport Across Membranes: Overcoming the Permeability Barrier p. 201
Cells and Transport Processes p. 201
Simple Diffusion: Unassisted Movement Down the Gradient p. 203
Facilitated Diffusion: Protein-Mediated Movement Down the Gradient p. 209
Active Transport: Protein-Mediated Movement Up the Gradient p. 213
Examples of Active Transport p. 217
The Energetics of Transport p. 222
On to Nerve Cells p. 226
Further Insights: Osmosis: The Special Case of Water Transport p. 206
Clinical Applications: Membrane Transport, Cystic Fibrosis, and the Prospects For Gene Therapy p. 218
Signal Transduction Mechanisms: I. Electrical Signals in Nerve Cells p. 232
The Nervous System p. 232
Understanding Membrane Potential p. 234
Electrical Excitability p. 240
The Action Potential p. 243
Synaptic Transmission p. 251
Integration and Processing of Nerve Signals p. 260
Clinical Applications: Poisoned Arrows, Snakebites and Nerve Gases p. 259
Signal Transduction Mechanisms: II. Messengers and Receptors p. 266
Chemical Signals and Cellular Receptors p. 266
G Protein-Linked Receptors p. 269
Protein Kinase-Associated Receptors p. 280
Growth Factors as Messengers p. 284
The Endocrine and Paracrine Hormone Systems p. 288
Further Insights: G Proteins and Vision p. 270
Further Insights: Cell Signals and Programmed Cell Death p. 287
Beyond the Cell: Extracellular Structures, Cell Adhesion, and Cell Junctions p. 299
The Extracellular Matrix of Animal Cells p. 299
Fibronectins Bind Cells to the Matrix and Guide Cellular Movement p. 305
Cell-Cell Recognition and Adhesion p. 309
Cell Junctions p. 311
The Plant Cell Surface p. 320
Clinical Applications: Understanding Blood Type: A Matter of Molecular Recognition p. 313
Intracellular Compartments: The Endoplasmic Reticulum, Golgi Complex, Endosomes, Lysosomes, and Peroxisomes p. 329
The Endoplasmic Reticulum p. 329
The Golgi Complex p. 339
Roles of the ER and Golgi Complex in Protein Glycosylation p. 342
Roles of the ER and Golgi Complex in Protein Sorting p. 344
Exocytosis and Endocytosis: Transporting Material Across the Plasma Membrane p. 348
Coated Vesicles in Cellular Transport Processes p. 355
Lysosomes and Cellular Digestion p. 359
The Plant Vacuole: A Multifunctional Organelle p. 363
Peroxisomes p. 364
Contemporary Techniques: Centrifugation: An Indispensable Technique of Cell Biology p. 332
Clinical Applications: Cholesterol, the LDL Receptor, and Receptor-Mediated Endocytosis p. 352
Energy Flow in Cells p. 375
Chemotrophic Energy Metabolism: Glycolysis and Fermentation p. 376
Metabolic Pathways p. 376
ATP: The Universal Energy Coupler p. 377
Chemotrophic Energy Metabolism p. 380
Glycolysis and Fermentation: ATP Generation Without the Involvement of Oxygen p. 386
Alternative Substrates for Glycolysis p. 393
Gluconeogenesis p. 395
The Regulation of Glycolysis and Gluconeogenesis p. 397
Further Insights: "What Happens to the Sugar?" p. 384
Chemotrophic Energy Metabolism: Aerobic Respiration p. 405
Cellular Respiration: Maximizing ATP Yields p. 405
The Mitochondrion: Where the Action Takes Place p. 407
The Tricarboxylic Acid Cycle: Oxidation in the Round p. 412
Electron Transport: Electron Flow from Coenzymes to Oxygen p. 423
The Electrochemical Proton Gradient: Key to Energy Coupling p. 433
ATP Synthesis: Putting It All Together p. 437
Aerobic Respiration: Summing It All Up p. 440
Further Insights: The Glyoxylate Cycle, Glyoxysomes, and Seed Germination p. 424
Phototrophic Energy Metabolism: Photosynthesis p. 451
An Overview of Photosynthesis p. 451
The Chloroplast: A Photosynthetic Organelle p. 453
Photosynthetic Energy Transduction p. 455
Photoreduction (NADPH Synthesis) in Oxygenic Phototrophs p. 462
Photophosphorylation (ATP Synthesis) in Oxygenic Phototrophs p. 465
A Photosynthetic Reaction Center from a Purple Bacterium p. 468
Photosynthetic Carbon Assimilation: The Calvin Cycle p. 469
Photosynthetic Energy Transduction and the Calvin Cycle p. 473
Carbohydrate Synthesis p. 473
Other Photosynthetic Assimilation Pathways p. 475
Rubisco's Oxygenase Activity Decreases Photosynthetic Efficiency p. 475
Further Insights: The Endosymbiont Theory and the Evolution of Mitochondria and Chloroplasts from Ancient Bacteria p. 456
Information Flow in Cells p. 487
The Structural Basis of Cellular Information: DNA, Chromosomes, and the Nucleus p. 488
The Chemical Nature of the Genetic Material p. 488
DNA Structure p. 496
The Organization of DNA in Genomes p. 501
DNA Packaging p. 514
The Nucleus p. 521
Further Insights: Phages: Model Systems for Studying Genes p. 492
Further Insights: A Closer Look at Restriction Enzymes p. 504
Contemporary Techniques: DNA Fingerprinting p. 512
The Cell Cycle: DNA Replication, Mitosis, and Cancer p. 533
An Overview of the Cell Cycle p. 533
DNA Replication p. 535
DNA Damage and Repair p. 550
Nuclear and Cell Division p. 554
Regulation of the Cell Cycle p. 564
Growth Control and Cancer p. 573
Contemporary Techniques: The PCR Revolution p. 544
Clinical Applications: Attacking a Tumor's Blood Supply p. 581
Sexual Reproduction, Meiosis, and Genetic Recombination p. 589
Sexual Reproduction p. 589
Meiosis p. 591
Genetic Variability: Segregation and Assortment of Alleles p. 602
Genetic Variability: Recombination and Crossing Over p. 606
Genetic Recombination in Bacteria and Viruses p. 610
Molecular Mechanism of Homologous Recombination p. 613
Recombinant DNA Technology and Gene Cloning p. 618
Genetic Engineering p. 626
Historical Perspectives: Supermouse, an Early Transgenic Triumph p. 628
Gene Expression: I. The Genetic Code and Transcription p. 634
The Directional Flow of Genetic Information p. 634
The Genetic Code p. 635
Transcription in Prokaryotic Cells p. 646
Transcription in Eukaryotic Cells p. 651
RNA Processing p. 655
Key Aspects of mRNA Metabolism p. 665
Further Insights: Reverse Transcription, Retroviruses, and Retrotransposons p. 636
Contemporary Techniques: The Footprinting Method for Identifying Protein-Binding Sites on DNA p. 649
Gene Expression: II. Protein Synthesis and Sorting p. 670
Translation: The Cost of Characters p. 670
The Mechanism of Translation p. 676
Nonsense Mutations and Suppressor tRNA p. 682
Posttranslational Processing p. 684
Protein Targeting and Sorting p. 686
Clinical Applications: Protein-Folding Diseases p. 683
A Mutation Primer p. 685
The Regulation of Gene Expression p. 701
Gene Regulation in Prokaryotes p. 701
Comparison of Gene Regulation in Prokaryotes and Eukaryotes p. 711
Eukaryotic Gene Regulation: Genomic Control p. 715
Eukaryotic Gene Regulation: Transcriptional Control p. 724
Eukaryotic Gene Regulation: Posttranscriptional Control p. 737
Further Insights: Dolly: A Lamb with No Father p. 717
Contemporary Techniques: Discriminating Among Multiple Levels of Control p. 743
The Cytoskeleton and Cell Motility p. 751
Cytoskeletal Systems p. 752
The Major Structural Elements of the Cytoskeleton p. 752
Techniques for Studying the Cytoskeleton p. 754
Microtubules p. 754
Microfilaments p. 766
Intermediate Filaments p. 771
The Cytoskeleton and the Tensegrity Architecture of Cells p. 775
Clinical Applications: Intermediate Filaments and the Diagnosis of Tumors p. 774
Cellular Movement: Motility and Contractility p. 781
Motile Systems p. 781
Intracellular Microtubule-Based Movement: Kinesin and Dynein p. 782
Microtubule-Based Motility p. 785
Actin-Based Cell Movement: The Myosins p. 789
Filament-Based Movement in Muscle p. 791
Actin-Based Motility in Nonmuscle Cells p. 803
Clinical Applications: Cytoskeletal Motor Proteins and Human Disease p. 790
Principles and Techniques of Microscopy p. 817
Optical Principles of Microscopy p. 817
The Illuminating Wavelength Sets a Limit on How Small an Object Can Be Seen p. 817
Resolution Refers to the Ability to Distinguish Adjacent Objects as Separate from One Another p. 819
The Practical Limit of Resolution Is Roughly 200 nm for Light Microscopy and 2 nm for Electron Microscopy p. 820
The Light Microscope p. 821
Compound Microscopes Use Several Lenses in Combination p. 821
Phase-Contrast Microscopy Detects Differences in Refractive Index and Thickness p. 822
Differential Interference Contrast (DIC) Microscopy Utilizes a Split Light Beam to Detect Phase Differences p. 823
Fluorescence Microscopy Can Detect the Presence of Specific Molecules or Ions Within Cells p. 824
Confocal Microscopy Minimizes Blurring by Focusing the Illuminating Beam on a Single Plane p. 827
Digital Video Microscopy Can Record Enhanced Time-Lapse Images p. 829
Sample Preparation Techniques for Light Microscopy p. 830
Specimen Preparation Often Involves Fixation, Sectioning, and Staining p. 830
Microscopic Autoradiography Locates Radioactive Molecules Inside Cells p. 831
The Electron Microscope p. 831
Transmission Electron Microscopy Forms an Image from Electrons That Pass Through the Specimen p. 833
Scanning Electron Microscopy Reveals the Surface Architecture of Cells and Organelles p. 835
Sample Preparation Techniques for Electron Microscopy p. 835
Ultrathin Sectioning and Staining Are Common Preparation Techniques for Transmission Electron Microscopy p. 835
Radioisotopes and Antibodies Can Localize Molecules in Electron Micrographs p. 837
Negative Staining Can Highlight Small Objects in Relief Against a Stained Background p. 837
Shadowing Techniques Use Metal Vapor Sprayed Across a Specimen's Surface p. 838
Freeze Fracturing and Freeze Etching Are Useful for Examining the Interior of Membranes p. 838
Stereo Electron Microscopy Allows Specimens to Be Viewed in Three Dimensions p. 841
Specimen Preparation for Scanning Electron Microscopy Involves Fixation but Not Sectioning p. 841
Other Imaging Methods p. 842
Scanning Probe Microscopy Reveals the Surface Features of Individual Molecules p. 842
X-Ray Diffraction Allows the Three-Dimensional Structure of Macromolecules to Be Determined p. 843
Key Terms for Self-Testing p. 844
Suggested Reading p. 845
Photo, Illustration, and Text Credits p. 847
Index p. 851