1 Introduction to Cell 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 Generic 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 8
Types of Prokaryotic Cells 14
Types of Eukaryotic Cells: Cell Specialization 15
The Sizes of Cells and Their Components 17
Synthetic Biology 17
?? THE HUMAN PERSPECTIVE: The Prospect of Cell Replacement Therapy 20
1.4 Viruses 23
Viroids 26
?? EXPERIMENTAL PATHWAYS: The Origin of Eukaryotic Cells 26
2 The Structure and Functions of Biological Molecules 32
2.1 Covalent Bonds 33
Polar and Nonpolar Molecules 34
Ionizaton 34
2.2 Noncovalent Bonds 34
?? THE HUMAN PERSPECTIVE: Free Radicals as a Cause of Aging 35
Ionic Bonds: Attractions between Charged Atoms 35
Hydrogen Bonds 36
Hydrophobic Interactions and van der Waals Forces 36
The Life-Supporting Properties of Water 37
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 Four Types of Biological Molecules 42
Carbohydrates 43
?? THE HUMAN PERSPECTIVE: Diseases that Result from Expansion of Trinucleotide Repeats 138
4.5 The Stability of the Genome 140
Whole-Genome Duplication (Polyploidization) 140
Duplication and Modification of DNA Sequences 141
Jumping Genes and the Dynamic Nature of the Genome 142
4.6 Sequencing Genomes: The Footprints of Biological Evolution 145
Comparative Genomics: If It s Conserved, It Must Be Important 147
The Genetic Basis of Being Human 148
Genetic Variation Within the Human Species Population 150
?? THE HUMAN PERSPECTIVE: Application of Genomic Analyses to Medicine 151
?? EXPERIMENTAL PATHWAYS: The Chemical Nature of the Gene 154
5 The Path to Gene Expression 160
5.1 The Relationship between Genes, Proteins, and RNAs 161
An Overview of the Flow of Information through the Cell 162
5.2 An Overview of Transcription in Both Prokaryotic and Eukaryotic Cells 163
Transcription in Bacteria 166
Transcription and RNA Processing in Eukaryotic Cells 167
5.3 Synthesis and Processing of Eukaryotic Ribosomal and Transfer RNAs 169
Synthesizing the rRNA Precursor 170
Processing the rRNA Precursor 171
Synthesis and Processing of the 5S rRNA 174
Transfer RNAs 174
5.4 Synthesis and Processing of Eukaryotic Messenger RNAs 175
The Machinery for mRNA Transcription 175
Split Genes: An Unexpected Finding 178
The Processing of Eukaryotic Messenger RNAs 182
Evolutionary Implications of Split Genes and RNA Splicing 188
Creating New Ribozymes in the Laboratory 188
5.5 Small Regulatory RNAs and RNA Silencing Pathways 189
?? THE HUMAN PERSPECTIVE: Clinical Applications of RNA Interference 192
MicroRNAs: Small RNAs that Regulate Gene Expression 193
piRNAs: A Class of Small RNAs that Function in Germ Cells 194
Other Noncoding RNAs 195
5.6 Encoding Genetic Information 195
The Properties of the Genetic Code 195
5.7 Decoding the Codons: The Role of Transfer RNAs 198
The Structure of tRNAs 199
5.8 Translating Genetic Information 202
Initiation 202
Elongation 205
Termination 208
mRNA Surveillance and Quality Control 208
Polyribosomes 209
?? EXPERIMENTAL PATHWAYS: The Role of RNA as a Catalyst 211
6 Controlling Gene Expression 217
6.1 Control of Gene Expression in Bacteria 218
Organization of Bacterial Genomes 218
The Bacterial Operon 218
Riboswitches 221
6.2 Control of Gene Expression in Eukaryotes: Structure and Function of the Cell Nucleus 222
The Nuclear Envelope 222
Chromosomes and Chromatin 227
?? THE HUMAN PERSPECTIVE: Chromosomal Aberrations and Human Disorders 238
Epigenetics: There s More to Inheritance than DNA 243
The Nucleus as an Organized Organelle 244
6.3 An Overview of Gene Regulation in Eukaryotes 246
6.4 Transcriptional Control 248
The Role of Transcription Factors in Regulating Gene Expression 251
The Structure of Transcription Factors 253
DNA Sites Involved in Regulating Transcription 256
Transcriptional Activation: The Role of Enhancers, Promoters, and Coactivators 259
Transcriptional Repression 264
6.5 RNA Processing Control 267
6.6 Translational Control 270
Initiation of Translation 270
Cytoplasmic Localization of mRNAs 271
The Control of mRNA Stability 272
The Role of MicroRNAs in Translational Control 273
6.7 Posttranslational Control: Determining Protein Stability 275
7 Replicating and Repairing DNA 279
7.1 DNA Replication 280
Semiconservative Replication 280
Replication in Bacterial Cells 283
The Structure and Functions of DNA Polymerases 288
Replication in Eukaryotic Cells 292
7.2 DNA Repair 298
Nucleotide Excision Repair 299
Base Excision Repair 300
Mismatch Repair 301
Double-Strand Breakage Repair 301
7.3 Between Replication and Repair 302
?? THE HUMAN PERSPECTIVE: The Consequences of DNA Repair Deficiencies 303
8 Cellular Membranes 306
8.1 An Overview of Membrane Functions 307
8.2 A Brief History of Studies on Plasma Membrane Structure 309
8.3 The Chemical Composition of Membranes 311
Membrane Lipids 311
The Asymmetry of Membrane Lipids 314
Membrane Carbohydrates 315
8.4 The Structure and Functions of Membrane Proteins 316
Integral Membrane Proteins 316
Studying the Structure and Properties of Integral Membrane Proteins 318
Peripheral Membrane Proteins 323
Lipid-Anchored Membrane Proteins 323
8.5 Membrane Lipids and Membrane Fluidity 324
The Importance of Membrane Fluidity 325
Maintaining Membrane Fluidity 325
Lipid Rafts 325
8.6 The Dynamic Nature of the Plasma Membrane 326
The Diffusion of Membrane Proteins after Cell Fusion 327
Restrictions on Protein and Lipid Mobility 328
The Red Blood Cell: An Example of Plasma Membrane Structure 331
8.7 The Movement of Substances Across Cell Membranes 333
The Energetics of Solute Movement 333
Diffusion of Substances through Membranes 335
Facilitated Diffusion 342
Active Transport 343
?? THE HUMAN PERSPECTIVE: Defects in Ion Channels and Transporters as a Cause of Inherited Disease 348
8.8 Membrane Potentials and Nerve Impulses 350
The Resting Potential 350
The Action Potential 351
Propagation of Action Potentials as an Impulse 353
Neurotransmission: Jumping the Synaptic Cleft 354
?? EXPERIMENTAL PATHWAYS: The Acetylcholine Receptor 357
9 Mitochondrial Structure and Function 364
9.1 Mitochondrial Structure and Function 365
Mitochondrial Membranes 366
The Mitochondrial Matrix 368
9.2 Oxidative Metabolism in the Mitochondrion 369
The Tricarboxylic Acid (TCA) Cycle 371
The Importance of Reduced Coenzymes in the Formation of ATP 372
?? THE HUMAN PERSPECTIVE: The Role of Anaerobic and Aerobic Metabolism in Exercise 374
9.3 The Role of Mitochondria in the Formation of ATP 375
Oxidation Reduction Potentials 375
Electron Transport 376
Types of Electron Carriers 377
9.4 Translocation of Protons and the Establishment of a Proton-Motive Force 384
9.5 The Machinery for ATP Formation 385
The Structure of ATP Synthase 386
The Basis of ATP Formation According to the Binding Change Mechanism 387
Other Roles for the Proton-Motive Force in Addition to ATP Synthesis 391
9.6 Peroxisomes 392
?? THE HUMAN PERSPECTIVE: Diseases that Result from Abnormal Mitochondrial or Peroxisomal Function 393
10 Chloroplast Structure and Function 397
10.1 Chloroplast Structure and Function 399
10.2 An Overview of Photosynthetic Metabolism 400
10.3 The Absorption of Light 402
Photosynthetic Pigments 402
10.4 Photosynthetic Units and Reaction Centers 404
Oxygen Formation: Coordinating the Action of Two Different Photosynthetic Systems 404
Killing Weeds by Inhibiting Electron Transport 411
10.5 Photophosphorylation 411
Noncyclic Versus Cyclic Photophosphorylation 412
10.6 Carbon Dioxide Fixation and the Synthesis of Carbohydrate 412
Carbohydrate Synthesis in C3 Plants 412
Carbohydrate Synthesis in C4 Plants 417
Carbohydrate Synthesis in CAM Plants 418
11 The Extracellular Matrix and Cell Interactions 421
11.1 The Extracellular Space 422
The Extracellular Matrix 422
11.2 Interactions of Cells with Extracellular Materials 430
Integrins 430
Focal Adhesions and Hemidesmosomes: Anchoring Cells to Their Substratum 433
11.3 Interactions of Cells with Other Cells 436
Selectins 437
The Immunoglobulin Superfamily 438
Cadherins 439
?? THE HUMAN PERSPECTIVE: The Role of Cell Adhesion in Inflammation and Metastasis 441
Adherens Junctions and Desmosomes: Anchoring Cells to Other Cells 443
The Role of Cell-Adhesion Receptors in Transmembrane Signaling 445
11.4 Tight Junctions: Sealing The Extracellular Space 446
11.5 Gap Junctions and Plasmodesmata: Mediating Intercellular Communication 448
Plasmodesmata 451
11.6 Cell Walls 452
12 Cellular Organelles and Membrane Trafficking 456
12.1 An Overview of the Endomembrane System 457
12.2 A Few Approaches to the Study of Endomembranes 459
Insights Gained from Autoradiography 459
Insights Gained from the Use of the Green Fluorescent Protein 459
Insights Gained from the Biochemical Analysis of Subcellular Fractions 461
Insights Gained from the Use of Cell-Free Systems 462
Insights Gained from the Study of Mutant Phenotypes 463
12.3 The Endoplasmic Reticulum 465
The Smooth Endoplasmic Reticulum 466
Functions of the Rough Endoplasmic Reticulum 466
From the ER to the Golgi Complex: The First Step in Vesicular Transport 475
12.4 The Golgi Complex 476
Glycosylation in the Golgi Complex 478
The Movement of Materials through the Golgi Complex 478
12.5 Types of Vesicle Transport and Their Functions 481
COPII-Coated Vesicles: Transporting Cargo from the ER to the Golgi Complex 482
COPI-Coated Vesicles: Transporting Escaped Proteins Back to the ER 484
Beyond the Golgi Complex: Sorting Proteins at the TGN 484
Targeting Vesicles to a Particular Compartment 486
12.6 Lysosomes 489
Autophagy 490
?? THE HUMAN PERSPECTIVE: Disorders Resulting from Defects in Lysosomal Function 492
12.7 Plant Cell Vacuoles 493
12.8 The Endocytic Pathway: Moving Membrane and Materials into the Cell Interior 494
Endocytosis 494
Phagocytosis 501
12.9 Posttranslational Uptake of Proteins by Peroxisomes, Mitochondria, and Chloroplasts 502
Uptake of Proteins into Peroxisomes 502
Uptake of Proteins into Mitochondria 502
Uptake of Proteins into Chloroplasts 504
?? EXPERIMENTAL PATHWAYS: Receptor-Mediated Endocytosis 505
13 The Cytoskeleton 510
13.1 Overview of the Major Functions of the Cytoskeleton 511
13.2 The Study of the Cytoskeleton 512
The Use of Live-Cell Fluorescence Imaging 512
The Use of In Vitro and In Vivo Single-Molecule Assays 513
The Use of Fluorescence Imaging Techniques to Monitor the Dynamics of the Cytoskeleton 515
13.3 Microtubules 516
Structure and Composition 516
Microtubule-Associated Proteins 517
Microtubules as Structural Supports and Organizers 518
Microtubules as Agents of Intracellular Motility 519
Motor Proteins that Traverse the Microtubular Cytoskeleton 520
Microtubule-Organizing Centers (MTOCs) 525
The Dynamic Properties of Microtubules 527
Cilia and Flagella: Structure and Function 531
?? THE HUMAN PERSPECTIVE: The Role of Cilia in Development and Disease 535
13.4 Intermediate Filaments 540
Intermediate Filament Assembly and Disassembly 540
Types and Functions of Intermediate Filaments 542
13.5 Microfilaments 542
Microfilament Assembly and Disassembly 544
Myosin: The Molecular Motor of Actin Filaments 546
13.6 Muscle Contractility 550
The Sliding Filament Model of Muscle Contraction 552
13.7 Nonmuscle Motility 557
Actin-Binding Proteins 558
Examples of Nonmuscle Motility and Contractility 560
14 Cell Division 572
14.1 The Cell Cycle 573
Cell Cycles in Vivo 574
Control of the Cell Cycle 574
14.2 M Phase: Mitosis and Cytokinesis 581
Prophase 583
Prometaphase 588
Metaphase 590
Anaphase 592
Telophase 597
Motor Proteins Required for Mitotic Movements 597
Cytokinesis 597
14.3 Meiosis 602
The Stages of Meiosis 603
?? THE HUMAN PERSPECTIVE: Meiotic Nondisjunction and Its Consequences 608
Genetic Recombination During Meiosis 610
?? EXPERIMENTAL PATHWAYS: The Discovery and Characterization of MPF 611
15 Cell Signaling Pathways 617
15.1 The Basic Elements of Cell Signaling Systems 618
15.2 A Survey of Extracellular Messengers and Their Receptors 621
15.3 G Protein-Coupled Receptors and Their Second Messengers 621
Signal Transduction by G Protein-Coupled Receptors 622
?? THE HUMAN PERSPECTIVE: Disorders Associated with G Protein-Coupled Receptors 625
Second Messengers 627
The Specificity of G Protein-Coupled Responses 630
Regulation of Blood Glucose Levels 631
The Role of GPCRs in Sensory Perception 634
15.4 Protein-Tyrosine Phosphorylation as a Mechanism for Signal Transduction 636
The Ras-MAP Kinase Pathway 640
Signaling by the Insulin Receptor 644
?? THE HUMAN PERSPECTIVE: Signaling Pathways and Human Longevity 647
Signaling Pathways in Plants 648
15.5 The Role of Calcium as an Intracellular Messenger 648
Regulating Calcium Concentrations in Plant Cells 652
15.6 Convergence, Divergence, and Cross-Talk Among Different Signaling Pathways 653
Examples of Convergence, Divergence, and Cross-Talk Among Signaling Pathways 654
15.7 The Role of NO as an Intercellular Messenger 655
15.8 Apoptosis (Programmed Cell Death) 656
The Extrinsic Pathway of Apoptosis 658
The Intrinsic Pathway of Apoptosis 659
16 Cancer 664
16.1 Basic Properties of a Cancer Cell 665
16.2 The Causes of Cancer 667
16.3 The Genetics of Cancer 669
Tumor-Suppressor Genes and Oncogenes: Brakes and Accelerators 671
The Cancer Genome 683
Gene-Expression Analysis 685
16.4 New Strategies for Combating Cancer 687
Immunotherapy 688
Inhibiting the Activity of Cancer-Promoting Proteins 689
Inhibiting the Formation of New Blood Vessels (Angiogenesis) 692
?? EXPERIMENTAL PATHWAYS: The Discovery of Oncogenes 694
17 Immunity 699
17.1 An Overview of the Immune Response 700
Innate Immune Responses 700
Adaptive Immune Responses 703
17.2 The Clonal Selection Theory as It Applies to B Cells 704
Vaccination 706
17.3 T Lymphocytes: Activation and Mechanism of Action 707
17.4 Selected Topics on the Cellular and Molecular Basis of Immunity 710
The Modular Structure of Antibodies 710
DNA Rearrangements that Produce Genes Encoding B- and T-Cell Antigen Receptors 713
Membrane-Bound Antigen Receptor Complexes 716
The Major Histocompatibility Complex 716
Distinguishing Self from Nonself 721
Lymphocytes Are Activated by Cell-Surface Signals 722
Signal Transduction Pathways in Lymphocyte Activation 723
?? THE HUMAN PERSPECTIVE: Autoimmune Diseases 724
?? EXPERIMENTAL PATHWAYS: The Role of the Major Histocompatibility Complex in Antigen Presentation 727
18 Methods in Cell Biology 732
18.1 The Light Microscope 733
Resolution 733
Visibility 734
Preparation of Specimens for Bright-Field Light Microscopy 735
Phase-Contrast Microscopy 735
Fluorescence Microscopy (and Related Fluorescence-Based Techniques) 736
Video Microscopy and Image Processing 738
Laser Scanning Confocal Microscopy 739
Super-Resolution Fluorescence Microscopy 740
18.2 Transmission Electron Microscopy 740
Specimen Preparation for Electron Microscopy 742
18.3 Scanning Electron and Atomic Force Microscopy 746
Atomic Force Microscopy 748
18.4 The Use of Radioisotopes 748
18.5 Cell Culture 749
18.6 The Fractionation of a Cell s Contents by Differential Centrifugation 752
18.7 Isolation, Purification, and Fractionation of Proteins 752
Selective Precipitation 752
Liquid Column Chromatography 753
Polyacrylamide Gel Electrophoresis 756
Protein Measurement and Analysis 757
18.8 Determining the Structure of Proteins and Multisubunit Complexes 758
18.9 Fractionation of Nucleic Acids 760
Separation of DNAs by Gel Electrophoresis 760
Separation of Nucleic Acids by Ultracentrifugation 760
18.10 Nucleic Acid Hybridization 762
18.11 Chemical Synthesis of DNA 764
18.12 Recombinant DNA Technology 764
Restriction Endonucleases 764
Formation of Recombinant DNAs 766
DNA Cloning 766
18.13 Enzymatic Amplification of DNA by PCR 769
Applications of PCR 770
18.14 DNA Sequencing 771
18.15 DNA Libraries 773
Genomic Libraries 773
cDNA Libraries 774
18.16 DNA Transfer into Eukaryotic Cells and Mammalian Embryos 775
18.17 Determining Eukaryotic Gene Function by Gene Elimination or Silencing 778
In Vitro Mutagenesis 778
Knockout Mice 778
RNA Interference 780
18.18 The Use of Antibodies 780
Glossary G-1
Additional Readings A-1
Index I-1
