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Cell and Molecular Biology: Concepts and Experiments, 5th Edition
by
Karp, Gerald, Formerly of the Univ. of Florida, Gainesville
Publisher: John Wiley & Sons
Publishing Date: 2007/02/26
eText ISBN-10
0-470-37270-2
eText ISBN-13
978-0-470-37270-8
Print ISBN-10
0-470-04217-6
Print ISBN-13
978-0-470-04217-5
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Cell and Molecular Biology: Concepts and Experiments, 5th Edition
by
Karp, Gerald, Formerly of the Univ. of Florida, Gainesville
eTextbook $77.50
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About the Authors, iv
Copyright, vi
Preface to the Fifth Edit...
1. Introduction to the St...
2. The Chemical Basis of ...
3. Bioenergetics, Enzymes...
4. The Structure of Funct...
5. Aerobic Respiration an...
6. Photosynthesis and the...
7. Interactions Between C...
8. Cytoplasmic Membrane S...
9. The Cytoskeleton and C...
10. The Nature of the Gen...
11. Gene Expression: From...
12. The Cell Nucleus and ...
13. DNA Replication and R...
14. Cellular Reproduction...
15. Cell Signaling and Si...
16. Cancer, 662
17. The Immune Response, ...
18. Techniques in Cell an...
Glossary, G-1
Index, I-1
Table of Contents
About the Authors, iv
Copyright, vi
Preface to the Fifth Edition, vii
1. Introduction to the Study of Cell and Molecular Biology, 1
1.1. The Discovery of Cells, 2
1.2. Basic Properties of Cells, 3
Cells are Highly Complex and Organized, 3
Cells Possess a Genetic Program and the Means to Use It, 5
Cells Are Capable of Producing More of Themselves, 5
Cells Acquire and Utilize Energy, 5
Cells Carry Out a Variety of Chemical Reactions, 6
Cells Engage in Mechanical Activities, 6
Cells Are Able to Respond to Stimuli, 6
Cells Are Capable of Self-Regulation, 6
Cells Evolve, 7
1.3. Two Fundamentally Different Classes of Cells, 7
Characteristics That Distinguish Prokaryotic and Eukaryotic Cells, 9
Types of Prokaryotic Cells, 13
Types of Eukaryotic Cells: Cell Specialization, 15
THE HUMAN PERSPECTIVE: The Prospect of Cell Replacement Therapy, 18
The Sizes of Cells and Their Components, 20
1.4. Viruses, 21
Viroids, 24
EXPERIMENTAL PATHWAYS: The Origin of Eukaryotic Cells, 25
2. The Chemical Basis of Life, 31
2.1. Covalent Bonds, 32
Polar and Nonpolar Molecules, 33
Ionization, 33
2.2. Noncovalent Bonds, 33
THE HUMAN PERSPECTIVE: Free Radicals as a Cause of Aging, 34
Ionic Bonds: Attractions Between Charged Atoms, 35
Hydrogen Bonds, 35
Hydrophobic Interactions and van der Waals Forces, 35
The Life-Supporting Properties of Water, 37
2.3. Acids, Bases, and Buffers, 38
2.4. The Nature of Biological Molecules, 40
Functional Groups, 40
A Classification of Biological Molecules by Function, 41
2.5. Four Types of Biological Molecules, 42
Carbohydrates, 42
Lipids, 47
Proteins, 49
THE HUMAN PERSPECTIVE: Protein Folding Can Have Deadly Consequences, 65
Nucleic Acids, 75
2.6. The Formation of Complex Macromolecular Structures, 77
The Assembly of Tobacco Mosaic Virus Particles and Ribosomal Subunits, 77
EXPERIMENTAL PATHWAYS: Chaperones: Helping Proteins Reach Their Proper Folded State, 78
3. Bioenergetics, Enzymes, and Metabolism, 85
3.1. Bioenergetics, 86
The Laws of Thermodynamics and the Concept of Entropy, 86
Free Energy, 88
3.2. Enzymes as Biological Catalysts, 94
The Properties of Enzymes, 94
Overcoming the Activation Energy Barrier, 95
The Active Site, 96
Mechanisms of Enzyme Catalysis, 99
Enzyme Kinetics, 101
THE HUMAN PERSPECTIVE: The Growing Problem of Antibiotic Resistance, 105
3.3. Metabolism, 107
An Overview of Metabolism, 107
Oxidation and Reduction: A Matter of Electrons, 108
The Capture and Utilization of Energy, 108
Metabolic Regulation, 114
4. The Structure of Function of the Plasma Membrane, 120
4.1. An Overview of Membrane Functions, 121
4.2. A Brief History of Studies on Plasma Membrane Structure, 123
4.3. The Chemical Composition of Membranes, 125
Membrane Lipids, 125
Membrane Carbohydrates, 129
4.4. The Structure and Functions of Membrane Proteins, 130
Integral Membrane Proteins, 130
Studying the Structure and Properties of Integral Membrane Proteins, 132
Peripheral Membrane Proteins, 136
Lipid-Anchored Membrane Proteins, 136
4.5. Membrane Lipids and Membrane Fluidity, 136
The Importance of Membrane Fluidity, 137
Maintaining Membrane Fluidity, 138
The Asymmetry of Membrane Lipids, 138
Lipid Rafts, 138
4.6. The Dynamic Nature of the Plasma Membrane, 139
The Diffusion of Membrane Proteins after Cell Fusion, 140
Restrictions on Protein and Lipid Mobility, 141
The Red Blood Cell: An Example of Plasma Membrane Structure, 144
4.7. The Movement of Substances Across Cell Membranes, 147
The Energetics of Solute Movement, 147
Diffusion of Substances through Membranes, 148
Facilitated Diffusion, 156
Active Transport, 157
THE HUMAN PERSPECTIVE: Defects in Ion Channels as a Cause of Inherited Disease, 160
4.8. Membrane Potentials and Nerve Impulses, 163
The Resting Potential, 164
The Action Potential, 165
Propagation of Action Potentials as an Impulse, 166
Neurotransmission: Jumping the Synaptic Cleft, 168
EXPERIMENTAL PATHWAYS: The Acetylcholine Receptor, 171
5. Aerobic Respiration and the Mitochondrion, 179
5.1. Mitochondrial Structure and Function, 180
Mitochondrial Membranes, 182
The Mitochondrial Matrix, 182
5.2. Oxidative Metabolism in the Mitochondrion, 183
The Tricarboxylic Acid (TCA) Cycle, 185
The Importance of Reduced Coenzymes in the Formation of ATP, 187
THE HUMAN PERSPECTIVE: The Role of Anaerobic and Aerobic Metabolism in Exercise, 188
5.3. The Role of Mitochondria in the Formation of ATP, 188
Oxidation–Reduction Potentials, 189
Electron Transport, 191
Types of Electron Carriers, 191
5.4. Translocation of Protons and the Establishment of a Proton-motive Force, 198
5.5. The Machinery for ATP Formation, 199
The Structure of ATP Synthase, 200
The Basis of ATP Formation According to the Binding Change Mechanism, 202
Other Roles for the Proton-motive Force in Addition to ATP Synthesis, 206
5.6. Peroxisomes, 207
THE HUMAN PERSPECTIVE: Diseases that Result from Abnormal Mitochrondrial or Peroxisomal Function, 208
6. Photosynthesis and the Chloroplast, 214
6.1. Chloroplast Structure and Function, 216
6.2. An Overview of Photosynthetic Metabolism, 217
6.3. The Absorption of Light, 219
Photosynthetic Pigments, 219
6.4. Photosynthetic Units and Reaction Centers, 221
Oxygen Formation: Coordinating the Action of Two Different Photosynthetic Systems, 222
Killing Weeds by Inhibiting Electron Transport, 228
6.5. Photophosphorylation, 228
Noncyclic Versus Cyclic Photophosphorylation, 229
6.6. Carbon Dioxide Fixation and the Synthesis of Carbohydrate, 229
Carbohydrate Synthesis in C
3
Plants, 230
Carbohydrate Synthesis in C
4
Plants, 234
Carbohydrate Synthesis in CAM Plants, 236
7. Interactions Between Cells and Their Environment, 239
7.1. The Extracellular Space, 240
The Extracellular Matrix, 240
7.2. Interactions of Cells with Extracellular Materials, 248
Integrins, 248
Focal Adhesions and Hemidesmosomes: Anchoring Cells to Their Substratum, 252
7.3. Interactions of Cells with Other Cells, 254
Selectins, 255
Immunoglobulins, 256
Cadherins, 257
THE HUMAN PERSPECTIVE: The Role of Cell Adhesion in Inflammation and Metastasis, 259
Adherens Junctions and Desmosomes: Anchoring Cells to Other Cells, 260
The Role of Cell-Adhesion Receptors in Transmembrane Signaling, 262
7.4. Tight Junctions: Sealing the Extracellular Space, 264
7.5. Gap Junctions and Plasmodesmata: Mediating Intercellular Communication, 266
Plasmodesmata, 268
7.6. Cell Walls, 268
8. Cytoplasmic Membrane Systems: Structure, Function, and Membrane Trafficking, 274
8.1. An Overview of the Endomembrane System, 275
8.2. A Few Approaches to the Study of Endomembranes, 277
Insights Gained from Autoradiography, 277
Insights Gained from the Use of the Green Fluorescent Protein, 277
Insights Gained from the Biochemical Analysis of Subcellular Fractions, 279
Insights Gained from the Use of Cell-Free Systems, 280
Insights Gained from the Study of Mutants, 281
8.3. The Endoplasmic Reticulum, 282
The Smooth Endoplasmic Reticulum, 284
Functions of the Rough Endoplasmic Reticulum, 284
From the ER to the Golgi Complex: The First Step in Vesicular Transport, 293
8.4. The Golgi Complex, 293
Glycosylation in the Golgi Complex, 296
The Movement of Materials through the Golgi Complex, 296
8.5. Types of Vesicle Transport and Their Functions, 298
COPII-Coated Vesicles: Transporting Cargo from the ER to the Golgi Complex, 299
COPI-Coated Vesicles: Transporting Escaped Proteins Back to the ER, 300
Beyond the Golgi Complex: Sorting Proteins at the TGN, 302
Targeting Vesicles to a Particular Compartment, 304
8.6. Lysosomes, 307
THE HUMAN PERSPECTIVE: Disorders Resulting from Defects in Lysosomal Function, 309
8.7. Plant Cell Vacuoles, 310
8.8. The Endocytic Pathway: Moving Membrane and Materials into the Cell Interior, 311
Endocytosis, 311
Phagocytosis, 317
8.9. Posttranslational Uptake of Proteins by Peroxisomes, Mitochondria, and Chloroplasts, 318
Uptake of Proteins into Peroxisomes, 318
Uptake of Proteins into Mitochondria, 318
Uptake of Proteins into Chloroplasts, 320
EXPERIMENTAL PATHWAYS: Receptor-Mediated Endocytosis, 321
9. The Cytoskeleton and Cell Motility, 328
9.1. Overview of the Major Functions of the Cytoskeleton, 329
9.2. The Study of the Cytoskeleton, 330
The Use of Live-Cell Fluorescence Imaging, 330
The Use of In Vitro Single Molecule Motility Assays, 332
The Use of Cells with Altered Gene Expression, 332
9.3. Microtubules, 333
Structure and Composition, 333
Microtubule-Associated Proteins, 334
Microtubules as Structural Supports and Organizers, 335
Microtubules as Agents of Intracellular Motility, 336
Motor Proteins That Traverse the Microtubular Cytoskeleton, 338
Microtubule-Organizing Centers (MTOCs), 342
The Dynamic Properties of Microtubules, 345
Cilia and Flagella: Structure and Function, 349
THE HUMAN PERSPECTIVE: The Role of Cilia in Development and Disease, 350
9.4. Intermediate Filaments, 357
Intermediate Filament Assembly and Disassembly, 358
Types and Functions of Intermediate Filaments, 359
9.5. Microfilaments, 360
Microfilament Assembly and Disassembly, 361
Myosin: The Molecular Motor for Actin Filaments, 363
9.6. Muscle Contractility, 368
The Sliding Filament Model of Muscle Contraction, 369
9.7. Nonmuscle Motility, 374
Actin-Binding Proteins, 374
Examples of Nonmuscle Motility and Contractility, 377
10. The Nature of the Gene and the Genome, 388
10.1. The Concept of a Gene as a Unit of Inheritance, 389
10.2. Chromosomes: The Physical Carriers of the Genes, 390
The Discovery of Chromosomes, 390
Chromosomes as the Carriers of Genetic Information, 391
Genetic Analysis in
Drosophila
, 392
Crossing Over and Recombination, 392
Mutagenesis and Giant Chromosomes, 394
10.3. The Chemical Nature of the Gene, 395
The Structure of DNA, 395
The Watson-Crick Proposal, 397
DNA Supercoiling, 400
10.4. The Structure of the Genome, 402
The Complexity of the Genome, 402
THE HUMAN PERSPECTIVE: Diseases that Result from Expansion of Trinucleotide Repeats, 405
10.5. The Stability of the Genome, 409
Whole-Genome Duplication (Polyploidization), 409
Duplication and Modification of DNA Sequences, 409
“Jumping Genes” and the Dynamic Nature of the Genome, 411
10.6. Sequencing Genomes: The Footprints of Biological Evolution, 415
Comparative Genomics: “If It's Conserved, It Must Be Important”, 416
Genetic Variation Within the Human Species Population, 418
THE HUMAN PERSPECTIVE: Application of Genomic Analyses to Medicine, 419
EXPERIMENTAL PATHWAYS: The Chemical Nature of the Gene, 421
11. Gene Expression: From Transcription to Translation, 429
11.1. The Relationship Between Genes and Proteins, 430
An Overview of the Flow of Information Through the Cell, 431
11.2. An Overview of Transcription in Both Prokaryotic and Eukaryotic Cells, 432
Transcription in Bacteria, 435
Transcription and RNA Processing in Eukaryotic Cells, 436
11.3. Synthesis and Processing of Ribosomal and Transfer RNAs, 437
Synthesizing the rRNA Precursor, 438
Processing the rRNA Precursor, 440
Synthesis and Processing of the 5S rRNA, 442
Transfer RNAs, 443
11.4. Synthesis and Processing of Messenger RNAs, 444
The Machinery for mRNA Transcription, 445
Split Genes: An Unexpected Finding, 447
The Processing of Eukaryotic Messenger RNAs, 450
Evolutionary Implications of Split Genes and RNA Splicing, 457
Creating New Ribozymes in the Laboratory, 458
11.5. Small Noncoding RNAs and RNA Interference, 459
THE HUMAN PERSPECTIVE: Clinical Applications of RNA Interference, 461
MicroRNAs: A Newly Discovered Network for Gene Regulation, 462
11.6. Encoding Genetic Information, 464
The Properties of the Genetic Code, 464
11.7. Decoding the Codons: The Role of Transfer RNAs, 467
The Structure of tRNAs, 467
11.8. Translating Genetic Information, 470
Initiation, 470
Elongation, 473
Termination, 475
mRNA Surveillance: No Nonsense Allowed, 475
Polyribosomes, 476
EXPERIMENTAL PATHWAYS: The Role of RNA as a Catalyst, 478
12. The Cell Nucleus and the Control of Gene Expression, 485
12.1. The Nucleus of a Eukaryotic Cell, 486
The Nuclear Envelope, 486
Chromosomes and Chromatin, 491
THE HUMAN PERSPECTIVE: Chromosomal Aberrations and Human Disorders, 501
Epigenetics: There's More to Inheritance than DNA, 506
The Nucleus as an Organized Organelle, 507
12.2. Control of Gene Expression in Bacteria, 509
The Bacterial Operon, 510
Riboswitches, 513
12.3. Control of Gene Expression in Eukaryotes, 513
12.4. Transcriptional-Level Control, 515
The Role of Transcription Factors in Regulating Gene Expression, 518
The Structure of Transcription Factors, 518
DNA Sites Involved in Regulating Transcription, 522
Transcriptional Activation: The Role of Enhancers, Promoters, and Coactivators, 525
Transcriptional Repression, 528
12.5. Processing-Level Control, 531
12.6. Translational-Level Control, 532
Cytoplasmic Localization of mRNAs, 532
The Control of mRNA Translation, 533
The Control of mRNA Stability, 535
12.7. Postranslational Control: Determining Protein Stability, 537
13. DNA Replication and Repair, 542
13.1. DNA Replication, 543
Semiconservative Replication, 543
Replication in Bacterial Cells, 546
The Structure and Functions of DNA Polymerases, 552
Replication in Eukaryotic Cells, 556
13.2. DNA Repair, 562
Nucleotide Excision Repair, 563
Base Excision Repair, 563
Mismatch Repair, 564
Double-Strand Breakage Repair, 565
THE HUMAN PERSPECTIVE: The Consequences of DNA Repair Deficiencies, 566
13.3. Between Replication and Repair, 567
14. Cellular Reproduction, 570
14.1. The Cell Cycle, 571
Cell Cycles in Vivo, 572
Control of the Cell Cycle, 572
14.2. M Phase: Mitosis and Cytokinesis, 579
Prophase, 581
Prometaphase, 586
Metaphase, 588
Anaphase, 590
Telophase, 594
Forces Required for Mitotic Movements, 595
Cytokinesis, 596
14.3. Meiosis, 599
The Stages of Meiosis, 602
THE HUMAN PERSPECTIVE: Meiotic Nondisjunction and Its Consequences, 606
Genetic Recombination During Meiosis, 607
EXPERIMENTAL PATHWAYS: The Discovery and Characterization of MPF, 609
15. Cell Signaling and Signal Transduction: Communication Between Cells, 616
15.1. The Basic Elements of Cell Signaling Systems, 617
15.2. A Survey of Extracellular Messengers and Their Receptors, 619
15.3. G Protein-Coupled Receptors and Their Second Messengers, 620
Signal Transduction by G Protein-Coupled Receptors, 620
THE HUMAN PERSPECTIVE: Disorders Associated with G Protein-Coupled Receptors, 623
Second Messengers, 624
The Specificity of G Protein-Coupled Responses, 628
Regulation of Blood Glucose Levels, 629
The Role of GPCRs in Sensory Perception, 632
15.4. Protein-Tyrosine Phosphorylation as a Mechanism for Signal Transduction, 634
The Ras-MAP Kinase Pathway, 638
Signaling by the Insulin Receptor, 641
Signaling Pathways in Plants, 645
15.5. The Role of Calcium as an Intracellular Messenger, 645
Regulating Calcium Concentrations in Plant Cells, 648
15.6. Convergence, Divergence, and Crosstalk Among Different Signaling Pathways, 649
Examples of Convergence, Divergence, and Crosstalk Among Signaling Pathways, 650
15.7. The Role of NO as an Intercellular Messenger, 652
15.8. Apoptosis (Programmed Cell Death), 653
The Extensive Pathway of Apoptosis, 654
The Intrinsic Pathway of Apoptosis, 655
16. Cancer, 662
16.1. Basic Properties of a Cancer Cell, 663
16.2. The Causes of Cancer, 665
16.3. The Genetics of Cancer, 666
Tumor-Suppressor Genes and Oncogenes: Brakes and Accelerators, 670
16.4. New Strategies for Combating Cancer, 682
Immunotherapy, 683
Inhibiting the Activity of Cancer-Promoting Proteins, 684
Inhibiting the Formation of New Blood Vessels (Angiogenesis), 685
EXPERIMENTAL PATHWAYS: The Discovery of Oncogenes, 686
17. The Immune Response, 693
17.1. An Overview of the Immune Response, 694
Innate Immune Responses, 694
Adaptive Immune Responses, 696
17.2. The Clonal Selection Theory as It Applies to B Cells, 697
Vaccination, 700
17.3. T Lymphocytes: Activation and Mechanism of Action, 701
17.4. Selected Topics on the Cellular and Molecular Basis of Immunity, 703
The Molecular Structure of Antibodies, 703
DNA Rearrangement of Genes Encoding B- and T-Cell Antigen Receptors, 706
Membrane-Bound Antigen Receptor Complexes, 709
The Major Histocompatibility Complex, 709
Distinguishing Self from Nonself, 715
Lymphocytes Are Activated by Cell-Surface Signals, 716
Signal Transduction Pathways Used in Lymphocyte Activation, 717
THE HUMAN PERSPECTIVE: Autoimmune Diseases, 718
EXPERIMENTAL PATHWAYS: The Role of the Major Histocompatibility Complex in Antigen Presentation, 720
18. Techniques in Cell and Molecular Biology, 727
18.1. The Light Microscope, 728
Resolution, 728
Visibility, 729
Preparation of Specimens for Bright-Field Light Microscopy, 730
Phase-Contrast Microscopy, 730
Fluorescence Microscopy (and Related Fluorescence-Based Techniques), 731
Video Microscopy and Image Processing, 733
Laser Scanning Confocal Microscopy, 733
18.2. Transmission Electron Microscopy, 734
Specimen Preparation for Electron Microscopy, 736
18.3. Scanning Electron and Atomic Force Microscopy, 740
Atomic Force Microscopy, 741
18.4. The Use of Radioisotopes, 742
18.5. Cell Culture, 743
18.6. The Fractionation of a Cell's Contents by Differential Centrifugation, 744
18.7. Isolation, Purification, and Fractionation of Proteins, 746
Selective Precipitation, 746
Liquid Column Chromatography, 746
Polyacrylamide Gel Electrophoresis, 749
Measurement of Protein Concentration, 751
18.8. Determining the Structure of Proteins and Multisubunit Complexes, 752
18.9. Purification of Nucleic Acids, 753
18.10. Fractionation of Nucleic Acids, 754
Separation of DNAs by Gel Electrophoresis, 754
Separation of Nucleic Acids by Ultracentrifugation, 754
18.11. Nucleic Acid Hybridization, 756
18.12. Chemical Synthesis of DNA, 758
18.13. Recombinant DNA Technology, 758
Restriction Endonucleases, 758
Formation of Recombinant DNAs, 760
DNA Cloning, 760
18.14. Enzymatic Amplification of DNA by PCR, 763
Applications of PCR, 765
18.15. DNA Sequencing, 765
18.16. DNA Libraries, 767
Genomic Libraries, 767
cDNA Libraries, 768
18.17. DNA Transfer into Eukaryotic Cells and Mammalian Embryos, 769
18.18. Determining Eukaryotic Gene Function by Gene Elimination, 769
In Vitro Mutagenesis, 772
Knockout Mice, 772
RNA Interference, 774
18.19. The Use of Antibodies, 774
Glossary, G-1
Index, I-1
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