Table of Contents
1 Introduction to Cell Biology 1
1.1 The Discovery of Cells 2
Microscopy 2
Cell Theory 3
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 8
1.4 Types of Prokaryotic Cells 14
Domain Archaea and Domain Bacteria 14
Prokaryotic Diversity 14
1.5 Types of Eukaryotic Cells 15
Cell Differentiation 16
Model Organisms 16
1.6 The Sizes of Cells and Their Components 18
1.7 Viruses 19
Viroids 22
THE HUMAN PERSPECTIVE 23
The Prospect of Cell Replacement Therapy 23
EXPERIMENTAL PATHWAYS 27
The Origin of Eukaryotic Cells 27
2 The Structure and Functions of Biological Molecules 33
2.1 Covalent Bonds 34
Polar and Nonpolar Molecules 35
Ionization 36
2.2 Noncovalent Bonds 36
Ionic Bonds: Attractions between Charged Atoms 36
Hydrogen Bonds 36
Hydrophobic Interactions and van der Waals Forces 37
The Life-Supporting Properties of Water 38
2.3 Acids, Bases, and Buffers 39
2.4 The Nature of Biological Molecules 40
Functional Groups 41
A Classification of Biological Molecules by Function 41
2.5 Carbohydrates 42
The Structure of Simple Sugars 43
Stereoisomerism 43
Linking Sugars Together 44
Polysaccharides 45
2.6 Lipids 47
Fats 47
Steroids 48
Phospholipids 48
2.7 Building Blocks of Proteins 49
The Structures of Amino Acids 50
The Properties of the Side Chains 51
2.8 Primary and Secondary Structures of Proteins 54
Primary Structure 54
Secondary Structure 55
2.9 Tertiary Structure of Proteins 56
Myoglobin: The First Globular Protein Whose Tertiary Structure Was Determined 57
Tertiary Structure May Reveal Unexpected Similarities between Proteins 58
Protein Domains 58
Dynamic Changes within Proteins 59
2.10 Quaternary Structure of Proteins 60
The Structure of Hemoglobin 60
Protein–Protein Interactions 61
2.11 Protein Folding 61
Dynamics of Protein Folding 62
The Role of Molecular Chaperones 63
2.12 Proteomics and Interactomics 64
Proteomics 64
Interactomics 66
2.13 Protein Engineering 67
Production of Novel Proteins 67
Structure-Based Drug Design 68
2.14 Protein Adaptation and Evolution 69
2.15 Nucleic Acids 71
2.16 The Formation of Complex Macromolecular Structures 72
The Assembly of Tobacco Mosaic Virus Particles 73
The Assembly of Ribosomal Subunits 73
THE HUMAN PERSPECTIVE 73
I. Do Free Radicals Cause Aging? 73
II. Protein Misfolding Can Have Deadly Consequences 74
EXPERIMENTAL PATHWAYS 79
Chaperones - Helping Proteins Reach Their Proper Folded State 79
3 Bioenergetics, Enzymes, and Metabolism 87
3.1 Bioenergetics 88
The First Law of Thermodynamics 88
The Second Law of Thermodynamics 89
3.2 Free Energy 90
Free‐Energy Changes in Chemical Reactions 91
Free‐Energy Changes in Metabolic Reactions 92
3.3 Coupling Endergonic and Exergonic Reactions 94
3.4 Equilibrium versus Steady‐State Metabolism 94
3.5 Enzymes as Biological Catalysts 95
The Properties of Enzymes 96
Overcoming the Activation Energy Barrier 96
The Active Site 98
3.6 Mechanisms of Enzyme Catalysis 99
Substrate Orientation 100
Changing Substrate Reactivity 100
Inducing Strain in the Substrate 100
3.7 Enzyme Kinetics 103
The Michaelis‐Menten Model of Enzyme Kinetics 103
Enzyme Inhibitors 105
3.8 Metabolism 106
Oxidation and Reduction: A Matter of Electrons 107
The Capture and Utilization of Energy 108
3.9 Glycolysis and ATP Production 108
ATP Production in Glycolysis 109
Anaerobic Oxidation of Pyruvate: The Process of Fermentation 111
3.10 Reducing Power 112
3.11 Metabolic Regulation 113
Altering Enzyme Activity by Covalent Modification 113
Altering Enzyme Activity by Allosteric Modulation 113
3.12 Separating Catabolic and Anabolic Pathways 114
THE HUMAN PERSPECTIVE 115
I. The Growing Problem of Antibiotic Resistance 115
II. Caloric Restriction and Longevity 118
4 Genes, Chromosomes, and Genomes 123
4.1 The Concept of a Gene as a Unit of Inheritance 124
4.2 The Discovery of Chromosomes 125
4.3 Chromosomes: The Physical Carriers of the Genes 126
The Chromosome as a Linkage Group 127
4.4 Genetic Analysis in Drosophila 127
Crossing Over and Recombination 128
Mutagenesis and Giant Chromosomes 129
4.5 The Structure of DNA 129
The Watson‐Crick Proposal 132
The Importance of the Watson‐Crick Proposal 132
4.6 DNA Supercoiling 134
4.7 The Structure of the Genome 136
DNA Denaturation 137
DNA Renaturation 137
4.8 The Stability of the Genome 141
Whole‐Genome Duplication (Polyploidization) 141
Duplication and Modification of DNA Sequences 141
Evolution of Globin Genes 142
4.9 “Jumping Genes” and the Dynamic Nature of the Genome 143
Transposons 144
The Role of Mobile Genetic Elements in Genome Evolution 144
4.10 Sequencing Genomes: The Footprints of Biological Evolution 146
4.11 Comparative Genomics: “If It’s Conserved, It Must Be Important” 148
4.12 The Genetic Basis of “Being Human” 148
4.13 Genetic Variation within the Human Species Population 150
DNA Sequence Variation 150
Structural Variation 151
Copy Number Variation 152
THE HUMAN PERSPECTIVE 152
I. Diseases That Result from Expansion of Trinucleotide Repeats 152
II. Application of Genomic Analyses to Medicine 154
EXPERIMENTAL PATHWAYS 157
The Chemical Nature of the Gene 157
5 The Path to Gene Expression 165
5.1 The Relationship between Genes, Proteins, and RNAs 166
Evidence That DNA Is the Genetic Material 166
An Overview of the Flow of Information through the Cell 167
5.2 The Role of RNA Polymerases in Transcription 169
5.3 An Overview of Transcription in Both Prokaryotic and Eukaryotic Cells 171
Transcription in Bacteria 171
Transcription and RNA Processing in Eukaryotic Cells 172
5.4 Synthesis and Processing of Eukaryotic Ribosomal and Transfer RNAs 174
Synthesis and Processing of the rRNA Precursor 174
The Role of snoRNAs in the Processing of Pre‐rRNA 176
Synthesis and Processing of the 5S rRNA 176
Transfer RNAs 177
5.5 Synthesis and Structure of Eukaryotic Messenger RNAs 178
The Formation of Heterogeneous Nuclear RNA (hnRNA) 178
The Machinery for mRNA Transcription 178
The Structure of mRNAs 181
5.6 Split Genes: An Unexpected Finding 181
5.7 The Processing of Eukaryotic Messenger RNAs 184
5′ Caps and 3′ Poly(A) Tails 185
RNA Splicing: Removal of Introns from a Pre‐RNA 186
5.8 Evolutionary Implications of Split Genes and RNA Splicing 189
5.9 Creating New Ribozymes in the Laboratory 191
5.10 Small Regulatory RNAs and RNA Silencing Pathway 191
5.11 Small RNAs: miRNAs and piRNAs 193
miRNAs: A Class of Small RNAs that Regulate Gene Expression 193
piRNAs: A Class of Small RNAs that Function in Germ Cells 194
5.12 CRISPR and other Noncoding RNAs 195
CRISPR: Noncoding RNA in Bacteria 195
Other Noncoding RNAs 195
5.13 Encoding Genetic Information 196
The Properties of the Genetic Code 196
Identifying the Codons 197
5.14 Decoding the Codons: The Role of Transfer RNAs 198
The Structure of tRNAs 198
tRNA Charging 200
5.15 Translating Genetic Information: Initiation 201
Initiation of Translation in Prokaryotes 202
Initiation of Translation in Eukaryotes 203
The Role of the Ribosome 203
5.16 Translating Genetic Information: Elongation and Termination 205
Elongation Step 1: Aminoacyl‐tRNA Selection 205
Elongation Step 2: Peptide Bond Formation 205
Elongation Step 3: Translocation 205
Elongation Step 4: Releasing the Deacylated tRNA 206
Termination 207
5.17 mRNA Surveillance and Quality Control 208
5.18 Polyribosomes 209
THE HUMAN PERSPECTIVE 210
Clinical Applications of RNA Interference 210
EXPERIMENTAL PATHWAYS 212
The Role of RNA as a Catalyst 212
6 Controlling Gene Expression 220
6.1 Control of Gene Expression in Bacteria 221
Organization of Bacterial Genomes 221
The Bacterial Operon 221
Riboswitches 224
6.2 Control of Gene Expression in Eukaryotes: Structure and Function of the Cell Nucleus 225
The Nuclear Pore Complex and Its Role in Nucleocytoplasmic Trafficking 227
RNA Transport 230
6.3 Chromosomes and Chromatin 230
Nucleosomes: The Lowest Level of Chromosome Organization 230
Higher Levels of Chromatin Structure 232
6.4 Heterochromatin and Euchromatin 234
X Chromosome Inactivation 234
The Histone Code and Formation of Heterochromatin 235
6.5 The Structure of a Mitotic Chromosome 238
Telomeres 240
Centromeres 243
6.6 Epigenetics: There’s More to Inheritance than DNA 243
6.7 The Nucleus as an Organized Organelle 244
6.8 An Overview of Gene Regulation in Eukaryotes 247
6.9 Transcriptional Control 248
DNA Microarrays 249
RNA Sequencing 251
6.10 The Role of Transcription Factors in Regulating Gene Expression 252
The Role of Transcription Factors in Determining a Cell’s Phenotype 252
6.11 The Structure of Transcription Factors 253
Transcription Factor Motifs 253
6.12 DNA Sites Involved in Regulating Transcription 256
6.13 The Glucocorticoid Receptor: An Example of Transcriptional Activation 258
6.14 Transcriptional Activation: The Role of Enhancers, Promoters, and Coactivators 259
Coactivators That Interact with the Basal Transcription Machinery 260
Coactivators That Alter Chromatin Structure 260
6.15 Transcriptional Activation from Paused Polymerases 263
6.16 Transcriptional Repression 264
DNA Methylation 264
Genomic Imprinting 265
Long Noncoding RNAs (lncRNAs) as Transcriptional Repressors 266
6.17 RNA Processing Control 267
6.18 Translational Control 269
Initiation of Translation 269
Cytoplasmic Localization of mRNAs 270
The Control of mRNA Stability 271
6.19 The Role of MicroRNAs in Translational Control 273
6.20 Posttranslational Control: Determining Protein Stability 274
THE HUMAN PERSPECTIVE 275
Chromosomal Aberrations and Human Disorders 275
7 DNA Replication and Repair 282
7.1 DNA Replication 283
7.2 DNA Replication in Bacterial Cells 286
Replication Forks and Bidirectional Replication 287
Unwinding the Duplex and Separating the Strands 287
The Properties of DNA Polymerases 288
Semidiscontinuous Replication 289
7.3 The Machinery Operating at the Replication Fork 291
7.4 The Structure and Functions of DNA Polymerases 293
Exonuclease Activities of DNA Polymerases 293
Ensuring High Fidelity during DNA Replication 294
7.5 Replication in Viruses 296
7.6 DNA Replication in Eukaryotic Cells 296
Initiation of Replication in Eukaryotic Cells 297
Restricting Replication to Once Per Cell Cycle 297
The Eukaryotic Replication Fork 298
Replication and Nuclear Structure 300
7.7 Chromatin Structure and Replication 300
7.8 DNA Repair 302
Nucleotide Excision Repair 302
Base Excision Repair 303
Mismatch Repair 304
Double‐Strand Breakage Repair 304
7.9 Between Replication and Repair 305
THE HUMAN PERSPECTIVE 306
Consequences of DNA Repair Deficiencies 306
8 Cellular Membrane 311
8.1 Introduction to the Plasma Membrane 312
An Overview of Membrane Functions 312
A Brief History of Studies on Plasma Membrane Structure 313
8.2 The Chemical Composition of Membranes 315
Membrane Lipids 316
The Nature and Importance of the Lipid Bilayer 317
The Asymmetry of Membrane Lipids 319
8.3 Membrane Carbohydrates 319
8.4 The Structure and Functions of Membrane Proteins 320
Integral Membrane Proteins 321
Peripheral Membrane Proteins 322
Lipid‐Anchored Membrane Proteins 322
8.5 Studying the Structure and Properties of Integral Membrane Proteins 323
Identifying Transmembrane Domains 324
Experimental Approaches to Identifying Conformational Changes within an Integral Membrane Protein 325
8.6 Membrane Lipids and Membrane Fluidity 327
The Importance of Membrane Fluidity 328
Maintaining Membrane Fluidity 328
Lipid Rafts 329
8.7 The Dynamic Nature of the Plasma Membrane 329
The Diffusion of Membrane Proteins after Cell Fusion 330
Restrictions on Protein and Lipid Mobility 331
8.8 The Red Blood Cell: An Example of Plasma Membrane Structure 334
Integral Proteins of the Erythrocyte Membrane 334
The Erythrocyte Membrane Skeleton 336
8.9 The Movement of Substances across Cell Membranes 336
The Energetics of Solute Movement 336
Formation of an Electrochemical Gradient 337
8.10 Diffusion through the Lipid Bilayer 338
Diffusion of Substances through Membranes 338
The Diffusion of Water through Membranes 338
8.11 The Diffusion of Ions through Membranes 340
8.12 Facilitated Diffusion 345
8.13 Active Transport 346
Primary Active Transport: Coupling Transport to ATP Hydrolysis 346
Other Primary Ion Transport Systems 347
Using Light Energy to Actively Transport Ions 348
Secondary Active Transport (or Cotransport): Coupling Transport to Existing Ion Gradients 348
8.14 Membrane Potentials 350
The Resting Potential 350
The Action Potential 352
8.15 Propagation of Action Potentials as an Impulse 353
8.16 Neurotransmission: Jumping the Synaptic Cleft 354
Actions of Drugs on Synapses 356
Synaptic Plasticity 357
THE HUMAN PERSPECTIVE 357
Defects in Ion Channels and Transporters as a Cause of Inherited Disease 357
EXPERIMENTAL PATHWAYS 359
The Acetylcholine Receptor 359
9 Mitochondrion and Aerobic Respiration 368
9.1 Mitochondrial Structure and Function 369
Mitochondrial Membranes 370
The Mitochondrial Matrix 372
9.2 Oxidative Metabolism in the Mitochondrion 372
The Tricarboxylic Acid (TCA) Cycle 373
The Importance of Reduced Coenzymes in the Formation of ATP 375
9.3 The Role of Mitochondria in the Formation of ATP 377
Oxidation–Reduction Potentials 377
Electron Transport 379
Types of Electron Carriers 379
9.4 Electron‐Transport Complexes 381
Complex I (NADH dehydrogenase) 383
Complex II (succinate dehydrogenase) 384
Complex III (cytochrome bc1) 384
Complex IV (cytochrome c oxidase) 384
9.5 Translocation of Protons and the Establishment of a Proton‐ Motive Force 385
9.6 The Machinery for ATP Formation 386
The Structure of ATP Synthase 387
9.7 The Binding Change Mechanism of ATP Formation 388
Components of the Binding Change Hypothesis 388
Evidence to Support the Binding Change Mechanism and Rotary Catalysis 389
9.8 Using the Proton Gradient 391
The Role of the Fo Portion of ATP Synthase in ATP Synthesis 391
Other Roles for the Proton‐Motive Force in Addition to ATP Synthesis 392
9.9 Peroxisomes 392
THE HUMAN PERSPECTIVE 394
I. The Role of Anaerobic and Aerobic Metabolism in Exercise 394
II. Diseases that Result from Abnormal Mitochondrial or Peroxisomal Function 395
10 Chloroplast and Photosynthesis 401
10.1 The Origin of Photosynthesis 402
10.2 Chloroplast Structure and Function 403
10.3 An Overview of Photosynthetic Metabolism 404
10.4 The Absorption of Light 405
Photosynthetic Pigments 406
10.5 Photosynthetic Units and Reaction Centers 407
Oxygen Formation: Coordinating the Action of Two Different Photosynthetic Systems 408
10.6 The Operations of Photosystem II and Photosystem I 409
PSII Operations: Obtaining Electrons by Splitting Water 409
PSI Operations: The Production of NADPH 412
10.7 An Overview of Photosynthetic Electron Transport 413
Killing Weeds by Inhibiting Electron Transport 414
10.8 Photophosphorylation 415
Noncyclic Versus Cyclic Photophosphorylation 415
10.9 Carbon Dioxide Fixation and the Carbohydrate Synthesis 415
Carbohydrate Synthesis in C3 Plants 416
Redox Control 416
Photorespiration 417
Peroxisomes and Photorespiration 418
10.10 Carbohydrate Synthesis in C4 and CAM Plants 420
THE HUMAN PERSPECTIVE 421
Global Warming and Carbon Sequestration 421
11 The Extracellular Matrix and Cell Interactions 426
11.1 Overview of Extracellular Interactions 427
11.2 The Extracellular Space 428
The Extracellular Matrix 428
11.3 Components of the Extracellular Matrix 430
Collagen 430
Proteoglycans 432
Fibronectin 433
Laminin 433
11.4 Dynamic Properties of the Extracellular Matrix 435
11.5 Interactions of Cells with Extracellular Materials 436
Integrins 436
11.6 Anchoring Cells to Their Substratum 438
Focal Adhesions 438
Hemidesmosomes 440
11.7 Interactions of Cells with Other Cells 441
Selectins 441
The Immunoglobulin Superfamily 442
Cadherins 443
11.8 Adherens Junctions and Desmosomes: Anchoring Cells to Other Cells 445
11.9 The Role of Cell‐Adhesion Receptors in Transmembrane Signaling 447
11.10 Tight Junctions: Sealing the Extracellular Space 447
11.11 Gap Junctions and Plasmodesmata: Mediating Intercellular Communication 449
Gap Junctions 449
Plasmodesmata 451
11.12 Cell Walls 453
THE HUMAN PERSPECTIVE 455
The Role of Cell Adhesion in Inflammation and Metastasis 455
EXPERIMENTAL PATHWAYS 457
The Role of Gap Junctions in Intercellular Communication 457
12 Cellular Organelles and Membrane Trafficking 463
12.1 An Overview of the Endomembrane System 464
12.2 A Few Approaches to the Study of Endomembranes 466
Insights Gained from Autoradiography 466
Insights Gained from the Use of the Green Fluorescent Protein 467
Insights Gained from the Analysis of Subcellular Fractions 468
Insights Gained from the Use of Cell‐Free Systems 469
Insights Gained from the Study of Mutant Phenotypes 470
12.3 The Endoplasmic Reticulum 472
The Smooth Endoplasmic Reticulum 473
The Rough Endoplasmic Reticulum 473
12.4 Functions of the Rough Endoplasmic Reticulum 473
Synthesis of Proteins on Membrane‐Bound versus Free Ribosomes 473
Synthesis of Secretory, Lysosomal, or Plant Vacuolar Proteins 475
Processing of Newly Synthesized Proteins in the Endoplasmic Reticulum 476
Synthesis of Integral Membrane Proteins on ER‐Bound Ribosomes 476
12.5 Membrane Biosynthesis in the Endoplasmic Reticulum 477
12.6 Glycosylation in the Rough Endoplasmic Reticulum 479
12.7 Mechanisms That Ensure the Destruction of Misfolded Proteins 481
12.8 ER to Golgi Vesicular Transport 482
12.9 The Golgi Complex 482
Glycosylation in the Golgi Complex 484
The Movement of Materials through the Golgi Complex 485
12.10 Types of Vesicle Transport and Their Functions 487
COPII‐Coated Vesicles: Transporting Cargo from the ER to the Golgi Complex 488
COPI‐Coated Vesicles: Transporting Escaped Proteins Back to the ER 489
12.11 Beyond the Golgi Complex: Sorting Proteins at the TGN 491
Sorting and Transport of Lysosomal Enzymes 491
Sorting and Transport of Nonlysosomal Proteins 493
12.12 Targeting Vesicles to a Particular Compartment 493
12.13 Exocytosis 496
12.14 Lysosomes 496
12.15 Plant Cell Vacuoles 498
12.16 Endocytosis 498
Receptor‐Mediated Endocytosis and the Role of Coated Pits 499
The Role of Phosphoinositides in the Regulation of Coated Vesicles 501
12.17 The Endocytic Pathway 502
12.18 Phagocytosis 505
12.19 Posttranslational Uptake of Proteins by Peroxisomes, Mitochondria, and Chloroplasts 505
Uptake of Proteins into Peroxisomes 506
Uptake of Proteins into Mitochondria 506
Uptake of Proteins into Chloroplasts 507
THE HUMAN PERSPECTIVE 508
Disorders Resulting from Defects in Lysosomal Function 508
EXPERIMENTAL PATHWAYS 510
Receptor‐Mediated Endocytosis 510
13 The Cytoskeleton 517
13.1 Overview of the Major Functions of the Cytoskeleton 518
13.2 Microtubules: Structure and Function 520
Structure and Composition of Microtubules 520
Microtubule‐Associated Proteins 521
Microtubules as Structural Supports and Organizers 521
Microtubules as Agents of Intracellular Motility 522
13.3 Motor Proteins: Kinesins and Dyneins 524
Motor Proteins Traverse the Microtubular Cytoskeleton 524
Kinesins 524
Cytoplasmic Dynein 526
13.4 Microtubule‐Organizing Centers (MTOCs) 527
Centrosomes 528
Basal Bodies and Other MTOCs 530
Microtubule Nucleation 530
13.5 Microtubule Dynamics 530
The Dynamic Properties of Microtubules 530
The Underlying Basis of Microtubule Dynamics 532
13.6 Cilia and Flagella: Structure and Function 534
Structure of Cilia and Flagella 535
Growth by Intraflagellar Transport 537
The Mechanism of Ciliary and Flagellar Locomotion 539
13.7 Intermediate Filaments 541
Intermediate Filament Assembly and Disassembly 541
Types and Functions of Intermediate Filaments 543
13.8 Microfilaments 544
Microfilament Structure 544
Microfilament Assembly and Disassembly 545
13.9 Myosin: The Molecular Motor of Actin Filaments 547
Conventional (Type II) Myosins 547
Unconventional Myosins 548
13.10 Muscle Contractility 552
Organization of Sarcomeres 552
The Sliding Filament Model of Muscle Contraction 553
13.11 Nonmuscle Motility 557
Actin-Binding Proteins 558
13.12 Cellular Motility 560
13.13 Actin‐Dependent Processes During Development 564
Axonal Outgrowth 564
13.14 The Bacterial Cytoskeleton 567
THE HUMAN PERSPECTIVE 568
The Role of Cilia in Development and Disease 568
EXPERIMENTAL PATHWAYS 569
I. The Step Size of Kinesin 569
II. Studying Actin‐Based Motility without Cells 571
14 Cell Division 578
14.1 The Cell Cycle 579
Phases of the Cell Cycle 579
Cell Cycles in Vivo 580
14.2 Regulation of the Cell Cycle 581
14.3 Control of the Cell Cycle: The Role of Protein Kinases 582
Cyclin Binding 583
Cdk Phosphorylation/Dephosphorylation 583
Cdk Inhibitors 584
Controlled Proteolysis 584
Subcellular Localization 584
14.4 Control of the Cell Cycle: Checkpoints, Cdk Inhibitors, and Cellular Responses 586
14.5 M Phase: Mitosis and Cytokinesis 588
14.6 Prophase 588
Formation of the Mitotic Chromosome 588
Centromeres and Kinetochores 590
Formation of the Mitotic Spindle 591
The Dissolution of the Nuclear Envelope and Partitioning of Cytoplasmic Organelles 594
14.7 Prometaphase 594
14.8 Metaphase 596
14.9 Anaphase 598
The Role of Proteolysis in Progression through Mitosis 598
The Events of Anaphase 600
Forces Required for Chromosome Movements at Anaphase 601
The Spindle Assembly Checkpoint 602
14.10 Telophase and Cytokinesis 603
Motor Proteins Required for Mitotic Movements 603
Cytokinesis 603
Cytokinesis in Plant Cells: Formation of the Cell Plate 607
14.11 Meiosis 608
14.12 The Stages of Meiosis 610
14.13 Genetic Recombination during Meiosis 613
THE HUMAN PERSPECTIVE 615
Meiotic Nondisjunction and Its Consequences 615
EXPERIMENTAL PATHWAYS 616
The Discovery and Characterization of MPF 616
15 Cell Signaling Pathways 624
15.1 The Basic Elements of Cell Signaling Systems 625
15.2 A Survey of Extracellular Messengers and their Receptors 628
15.3 Signal Transduction by G Protein‐Coupled Receptors 629
Receptors 629
G Proteins 630
Termination of the Response 631
Bacterial Toxins 632
15.4 Second Messengers 632
The Discovery of Cyclic AMP 633
Phosphatidylinositol‐Derived Second Messengers 633
Phospholipase C 635
15.5 The Specificity of G Protein‐Coupled Responses 636
15.6 Regulation of Blood Glucose Levels 636
Glucose Mobilization: An Example of a Response Induced by cAMP 637
Signal Amplification 638
Other Aspects of cAMP Signal Transduction Pathways 638
15.7 The Role of GPCRs in Sensory Perception 640
15.8 Protein‐Tyrosine Phosphorylation as a Mechanism for Signal Transduction 641
Receptor Dimerization 641
Protein Kinase Activation 643
Phosphotyrosine‐Dependent Protein–Protein Interactions 643
Activation of Downstream Signaling Pathways 643
Ending the Response 645
15.9 The Ras‐MAP Kinase Pathway 645
Accessory Proteins 645
Adapting the MAP Kinase to Transmit Different Types of Information 647
15.10 Signaling by the Insulin Receptor 648
The Insulin Receptor Is a Protein‐Tyrosine Kinase 648
Insulin Receptor Substrates 1 and 2 649
Glucose Transport 650
Diabetes Mellitus 650
15.11 Signaling Pathways in Plants 651
15.12 The Role of Calcium as an Intracellular Messenger 651
IP3 and Voltage‐Gated Ca2+ Channels 651
Visualizing Cytoplasmic Ca2+ Concentration in Living Cells 651
Ca2+‐Binding Proteins 654
Regulating Calcium Concentrations in Plant Cells 654
15.13 Convergence, Divergence, and Cross‐Talk among Different Signaling Pathways 655
15.14 The Role of NO as an Intercellular Messenger 657
NO as an Activator of Guanylyl Cyclase 658
Inhibiting Phosphodiesterase 658
15.15 Apoptosis (Programmed Cell Death) 659
The Extrinsic Pathway of Apoptosis 660
The Intrinsic Pathway of Apoptosis 661
Necroptosis 662
Signaling Cell Survival 663
THE HUMAN PERSPECTIVE 663
Disorders Associated with G Protein‐Coupled Receptors 663
EXPERIMENTAL PATHWAYS 665
The Discovery and Characterization of GTP‐Binding Proteins 665
16 Cancer 673
16.1 Basic Properties of a Cancer Cell 674
16.2 The Causes of Cancer 677
16.3 The Genetics of Cancer 678
16.4 An Overview of Tumor‐Suppressor Genes and Oncogenes 680
16.5 Tumor‐Suppressor Genes: The RB Gene 681
16.6 Tumor‐Suppressor Genes: The TP53 Gene 684
The Role of p53: Guardian of the Genome 684
The Role of p53 in Promoting Senescence 686
16.7 Other Tumor‐Suppressor Genes 687
16.8 Oncogenes 688
Oncogenes That Encode Growth Factors or Their Receptors 688
Oncogenes That Encode Cytoplasmic Protein Kinases 689
Oncogenes That Encode Transcription Factors 689
Oncogenes That Encode Proteins That Affect the Epigenetic State of Chromatin 689
Oncogenes That Encode Metabolic Enzymes 690
Oncogenes That Encode Products That Affect Apoptosis 690
16.9 The Mutator Phenotype: Mutant Genes Involved in DNA Repair 691
16.10 MicroRNAs: A New Player in the Genetics of Cancer 691
16.11 The Cancer Genome 691
16.12 Gene‐Expression Analysis 694
16.13 Strategies for Combating Cancer 696
16.14 Immunotherapy 696
16.15 Inhibiting the Activity of Cancer‐Promoting Proteins 698
16.16 The Concept of a Cancer Stem Cell 701
16.17 Inhibiting the Formation of New Blood Vessels (Angiogenesis) 701
EXPERIMENTAL PATHWAYS 702
The Discovery of Oncogenes 702
17 Immunity 709
17.1 An Overview of the Immune Response 710
Innate Immune Responses 711
Adaptive Immune Responses 713
17.2 The Clonal Selection Theory as It Applies to B Cells 714
17.3 Vaccination 715
17.4 T Lymphocytes: Activation and Mechanism of Action 717
17.5 The Modular Structure of Antibodies 720
17.6 DNA Rearrangements That Produce Genes Encoding B‐ and T‐Cell Antigen Receptors 723
17.7 Membrane‐Bound Antigen Receptor Complexes 725
17.8 The Major Histocompatibility Complex 726
17.9 Distinguishing Self from Nonself 730
17.10 Lymphocytes Are Activated by Cell‐Surface Signals 731
Activation of Helper T Cells by Professional APCs 731
Activation of B Cells by TH Cells 732
17.11 Signal Transduction Pathways in Lymphocyte Activation 732
THE HUMAN PERSPECTIVE 733
Autoimmune Diseases 733
EXPERIMENTAL PATHWAYS 736
The Role of the Major Histocompatibility Complex in Antigen Presentation 736
18 Techniques in Cell and Molecular Biology 742
18.1 The Light Microscope 743
Resolution 744
Visibility 745
18.2 Bright‐Field and Phase‐Contrast Microscopy 745
Bright‐Field Light Microscopy 745
Phase‐Contrast Microscopy 746
18.3 Fluorescence Microscopy (and Related Fluorescence‐Based Techniques) 746
Laser Scanning Confocal Microscopy 749
Super‐Resolution Fluorescence Microscopy 750
Light Sheet Fluorescence Microscopy 751
18.4 Transmission Electron Microscopy 752
18.5 Specimen Preparation for Electron Microscopy 753
Cryofixation and the Use of Frozen Specimens 754
Negative Staining 755
Shadow Casting 755
Freeze‐Fracture Replication and Freeze Etching 756
18.6 Scanning Electron Microscopy 757
18.7 Atomic Force Microscopy 758
18.8 The Use of Radioisotopes 759
18.9 Cell Culture 760
18.10 The Fractionation of a Cell’s Contents by Differential Centrifugation 762
18.11 Purification and Characterization of Proteins by Liquid Column Chromatography 762
Ion‐Exchange Chromatography 763
Gel Filtration Chromatography 763
Affinity Chromatography 764
18.12 Determining Protein–Protein Interactions 764
18.13 Characterization of Proteins by
Polyacrylamide Gel Electrophoresis 766
SDS–PAGE 767
Two‐Dimensional Gel Electrophoresis 767
18.14 Characterization of Proteins by Spectrometry 767
18.15 Characterization of Proteins by Mass Spectrometry 767
18.16 Determining the Structure of Proteins and Multisubunit Complexes 768
18.17 Fractionation of Nucleic Acids 770
Separation of DNAs by Gel Electrophoresis 770
Separation of Nucleic Acids by Ultracentrifugation 771
18.18 Nucleic Acid Hybridization 773
18.19 Chemical Synthesis of DNA 774
18.20 Recombinant DNA Technology 774
Restriction Endonucleases 774
Formation of Recombinant DNAs 775
DNA Cloning 776
18.21 Enzymatic Amplification of DNA by PCR 778
Process of PCR 778
Applications of PCR 778
18.22 DNA Sequencing 780
18.23 DNA Libraries 782
Genomic Libraries 782
cDNA Libraries 783
18.24 DNA Transfer into Eukaryotic Cells and Mammalian Embryos 783
Transgenic Animals 785
Transgenic Plants 785
18.25 Gene Editing and Silencing 786
In Vitro Mutagenesis 786
Knockout Mice 787
RNA Interference 788
Genome Editing Using Engineered Nucleases 789
18.26 The Use of Antibodies 789
Glossary G-1
Additional Reading A-1
Index I-1
