Cell and Molecular Biology: Concepts and Experiments

Cover Page\r......Page 1
Title Page\r......Page 7
Copyright Page\r......Page 8
About the Author\r......Page 9
Dedication\r......Page 10
Acknowledgments\r......Page 12
Brief Contents\r......Page 16
Contents\r......Page 17
1 Introduction to the Study of Cell and Molecular Biology......Page 23
1.1 THE DISCOVERY OF CELLS......Page 24
Cells Are Highly Complex and Organized\r......Page 25
Cells Carry Out a Variety of Chemical Reactions\r......Page 27
Cells Evolve\r......Page 28
1.3 TWO FUNDAMENTALLY DIFFERENT CLASSES OF CELLS......Page 29
Characteristics That Distinguish Prokaryotic and Eukaryotic Cells......Page 30
Types of Prokaryotic Cells......Page 34
Types of Eukaryotic Cells: Cell Specialization......Page 37
The Sizes of Cells and Their Components......Page 38
Synthetic Biology......Page 40
1.4 VIRUSES......Page 43
Viroids......Page 46
2 The Chemical Basis of Life......Page 53
2.1 COVALENT BONDS......Page 54
Ionic Bonds: Attractions Between Charged Atoms......Page 55
Hydrogen Bonds......Page 57
The Life-Supporting Properties of Water......Page 58
2.3 ACIDS, BASES, AND BUFFERS......Page 60
2.4 THE NATURE OF BIOLOGICAL MOLECULES......Page 61
A Classification of Biological Molecules by Function......Page 62
2.5 FOUR TYPES OF BIOLOGICAL MOLECULES......Page 63
Carbohydrates......Page 64
Lipids......Page 68
Proteins......Page 71
Nucleic Acids......Page 96
The Assembly of Tobacco Mosaic Virus Particles and Ribosomal Subunits......Page 98
3 Bioenergetics, Enzymes, and Metabolism......Page 106
The Laws of Thermodynamics and the Concept of Entropy......Page 107
Free Energy......Page 109
3.2 ENZYMES AS BIOLOGICAL CATALYSTS......Page 114
The Properties of Enzymes......Page 115
Overcoming the Activation Energy Barrier......Page 116
The Active Site......Page 117
Mechanisms of Enzyme Catalysis......Page 119
Enzyme Kinetics......Page 122
An Overview of Metabolism......Page 127
Oxidation and Reduction: A Matter of Electrons......Page 128
The Capture and Utilization of Energy......Page 129
Metabolic Regulation......Page 134
4 The Structure of Function of the Plasma Membrane......Page 139
4.1 AN OVERVIEW OF MEMBRANE FUNCTIONS......Page 140
4.2 A BRIEF HISTORY OF STUDIES ON PLASMA MEMBRANE STRUCTURE......Page 141
Membrane Lipids......Page 144
The Asymmetry of Membrane Lipids......Page 147
Membrane Carbohydrates......Page 148
4.4 THE STRUCTURE AND FUNCTIONS OF MEMBRANE PROTEINS......Page 149
Studying the Structure and Properties of Integral Membrane Proteins......Page 150
Peripheral Membrane Proteins......Page 154
4.5 MEMBRANE LIPIDS AND MEMBRANE FLUIDITY......Page 155
The Importance of Membrane Fluidity......Page 156
Lipid Rafts......Page 157
The Diffusion of Membrane Proteins after Cell Fusion......Page 158
Restrictions on Protein and Lipid Mobility......Page 159
The Red Blood Cell: An Example of Plasma Membrane Structure......Page 162
The Energetics of Solute Movement......Page 165
Diffusion of Substances through Membranes......Page 166
Facilitated Diffusion......Page 173
Active Transport......Page 174
The Resting Potential......Page 181
The Action Potential......Page 182
Propagation of Action Potentials as an Impulse......Page 184
Neurotransmission: Jumping the Synaptic Cleft......Page 185
5 Aerobic Respiration and the Mitochondrion......Page 195
5.1 MITOCHONDRIAL STRUCTURE AND FUNCTION......Page 196
Mitochondrial Membranes......Page 197
The Mitochondrial Matrix......Page 198
5.2 OXIDATIVE METABOLISM IN THE MITOCHONDRION......Page 199
The Tricarboxylic Acid (TCA) Cycle......Page 202
The Importance of Reduced Coenzymes in the Formation of ATP......Page 203
Oxidation–Reduction Potentials......Page 204
Types of Electron Carriers......Page 207
5.4 TRANSLOCATION OF PROTONS AND THE ESTABLISHMENT OF A PROTON-MOTIVE FORCE......Page 213
5.5 THE MACHINERY FOR ATP FORMATION......Page 214
The Structure of ATP Synthase......Page 215
The Basis of ATP Formation According to the Binding Change Mechanism......Page 217
Other Roles for the Proton-Motive Force in Addition to ATP Synthesis......Page 221
5.6 PEROXISOMES......Page 222
6 Photosynthesis and the Chloroplast......Page 228
6.1 CHLOROPLAST STRUCTURE AND FUNCTION......Page 230
6.2 AN OVERVIEW OF PHOTOSYNTHETIC METABOLISM......Page 231
Photosynthetic Pigments......Page 233
Oxygen Formation: Coordinating the Action of Two Different Photosynthetic Systems......Page 235
Noncyclic Versus Cyclic Photophosphorylation......Page 242
Carbohydrate Synthesis in C3 Plants......Page 243
Carbohydrate Synthesis in C4 Plants......Page 248
Carbohydrate Synthesis in CAM Plants......Page 249
7 Interactions Between Cells and Their Environment......Page 252
7.1 THE EXTRACELLULAR SPACE......Page 253
The Extracellular Matrix......Page 254
Integrins......Page 261
Focal Adhesions and Hemidesmosomes: Anchoring Cells to Their Substratum......Page 264
Selectins......Page 267
Cadherins......Page 271
Adherens Junctions and Desmosomes: Anchoring Cells to Other Cells......Page 272
The Role of Cell-Adhesion Receptors in Transmembrane Signaling......Page 275
7.4 TIGHT JUNCTIONS: SEALING THE EXTRACELLULAR SPACE......Page 276
7.5 GAP JUNCTIONS AND PLASMODESMATA: MEDIATING INTERCELLULAR COMMUNICATION......Page 278
Plasmodesmata......Page 280
7.6 CELL WALLS......Page 282
8 Cytoplasmic Membrane Systems: Structure, Function, and Membrane Trafficking......Page 286
8.1 AN OVERVIEW OF THE ENDOMEMBRANE SYSTEM......Page 287
Insights Gained from the Use of the Green Fluorescent Protein......Page 289
Insights Gained from the Biochemical Analysis of Subcellular Fractions......Page 291
Insights Gained from the Use of Cell-Free Systems......Page 292
Insights Gained from the Study of Mutant Phenotypes......Page 293
Functions of the Rough Endoplasmic Reticulum......Page 295
From the ER to the Golgi Complex: The First Step in Vesicular Transport......Page 305
Glycosylation in the Golgi Complex......Page 306
The Movement of Materials through the Golgi Complex......Page 309
8.5 TYPES OF VESICLE TRANSPORT AND THEIR FUNCTIONS......Page 310
COPII-Coated Vesicles: Transporting Cargo from the ER to the Golgi Complex......Page 311
COPI-Coated Vesicles: Transporting Escaped Proteins Back to the ER......Page 313
Beyond the Golgi Complex: Sorting Proteins at the TGN......Page 314
Targeting Vesicles to a Particular Compartment......Page 316
8.6 LYSOSOMES......Page 319
8.8 THE ENDOCYTIC PATHWAY: MOVING MEMBRANE AND MATERIALS INTO THE CELL INTERIOR......Page 323
Endocytosis......Page 324
Phagocytosis......Page 330
Uptake of Proteins into Mitochondria......Page 331
Uptake of Proteins into Chloroplasts......Page 333
9 The Cytoskeleton and Cell Motility......Page 340
9.1 OVERVIEW OF THE MAJOR FUNCTIONS OF THE CYTOSKELETON......Page 341
The Use of Live-Cell Fluorescence Imaging......Page 342
The Use of In Vitro and In Vivo Single-Molecule Assays......Page 344
The Use of Florescence Imaging Techniques to Monitor the Dynamics of the Cytoskeleton......Page 345
9.3 MICROTUBULES......Page 346
Microtubule-Associated Proteins......Page 347
Microtubules as Structural Supports and Organizers......Page 348
Motor Proteins that Traverse the Microtubular Cytoskeleton......Page 350
Microtubule-Organizing Centers (MTOCs)......Page 355
The Dynamic Properties of Microtubules......Page 357
Cilia and Flagella: Structure and Function......Page 361
9.4 INTERMEDIATE FILAMENTS......Page 369
Intermediate Filament Assembly and Disassembly......Page 370
Types and Functions of Intermediate Filaments......Page 371
9.5 MICROFILAMENTS......Page 373
Microfilament Assembly and Disassembly......Page 374
Myosin: The Molecular Motor of Actin Filaments......Page 376
9.6 MUSCLE CONTRACTILITY......Page 381
The Sliding Filament Model of Muscle Contraction......Page 382
Actin-Binding Proteins......Page 387
Examples of Nonmuscle Motility and Contractility......Page 389
10 The Nature of the Gene and the Genome......Page 401
10.1 THE CONCEPT OF A GENE AS A UNIT OF INHERITANCE......Page 402
The Discovery of Chromosomes......Page 403
Chromosomes as the Carriers of Genetic Information......Page 404
Crossing Over and Recombination......Page 405
Mutagenesis and Giant Chromosomes......Page 407
The Structure of DNA......Page 408
The Watson-Crick Proposal......Page 409
DNA Supercoiling......Page 412
The Complexity of the Genome......Page 415
Whole-Genome Duplication (Polyploidization)......Page 421
Duplication and Modification of DNA Sequences......Page 422
“Jumping Genes” and the Dynamic Nature of the Genome......Page 424
10.6 SEQUENCING GENOMES: THE FOOTPRINTS OF BIOLOGICAL EVOLUTION......Page 427
Comparative Genomics: “If It’s Conserved, It Must Be Important......Page 428
The Genetic Basis of “Being Human”......Page 429
Genetic Variation Within the Human Species Population......Page 430
11 Gene Expression: From Transcription to Translation......Page 441
11.1 THE RELATIONSHIP BETWEEN GENES AND PROTEINS......Page 442
An Overview of the Flow of Information through the Cell......Page 443
11.2 AN OVERVIEW OF TRANSCRIPTION IN BOTH PROKARYOTIC AND EUKARYOTIC CELLS......Page 444
Transcription in Bacteria......Page 447
Transcription and RNA Processing in Eukaryotic Cells......Page 448
11.3 SYNTHESIS AND PROCESSING OF RIBOSOMAL AND TRANSFER RNAs......Page 450
Synthesizing the rRNA Precursor......Page 451
Processing the rRNA Precursor......Page 452
Synthesis and Processing of the 5S rRNA......Page 454
Transfer RNAs......Page 455
11.4 SYNTHESIS AND PROCESSING OF MESSENGER RNAs......Page 456
The Machinery for mRNA Transcription......Page 457
Split Genes: An Unexpected Finding......Page 459
The Processing of Eukaryotic Messenger RNAs......Page 462
Evolutionary Implications of Split Genes and RNA Splicing......Page 469
11.5 SMALL REGULATORY RNAs AND RNA SILENCING PATHWAYS......Page 470
MicroRNAs: Small RNAs that Regulate Gene Expression......Page 474
Other Noncoding RNAs......Page 476
The Properties of the Genetic Code......Page 477
The Structure of tRNAs......Page 479
Initiation......Page 483
Elongation......Page 486
mRNA Surveillance and Quality Control......Page 488
Polyribosomes......Page 489
12 The Cell Nucleus and the Control of Gene Expression......Page 497
The Nuclear Envelope......Page 498
Chromosomes and Chromatin......Page 503
Epigenetics: There’s More to Inheritance than DNA......Page 518
The Nucleus as an Organized Organelle......Page 519
12.2 CONTROL OF GENE EXPRESSION IN BACTERIA......Page 521
The Bacterial Operon......Page 522
12.3 CONTROL OF GENE EXPRESSION IN EUKARYOTES......Page 525
12.4 TRANSCRIPTIONAL-LEVEL CONTROL......Page 527
The Role of Transcription Factors in Regulating Gene Expression......Page 530
The Structure of Transcription Factors......Page 531
DNA Sites Involved in Regulating Transcription......Page 533
Transcriptional Activation: The Role of Enhancers, Promoters, and Coactivators......Page 536
Transcriptional Repression......Page 541
12.5 PROCESSING-LEVEL CONTROL......Page 544
Cytoplasmic Localization of mRNAs......Page 546
The Control of mRNA Translation......Page 547
The Control of mRNA Stability......Page 548
The Role of MicroRNAs in Translational-Level Control......Page 549
12.7 POSTRANSLATIONAL CONTROL: DETERMINING PROTEIN STABILITY......Page 551
13 DNA Replication and Repair......Page 555
Semiconservative Replication......Page 556
Replication in Bacterial Cells......Page 559
 The Structure and Functions of DNA Polymerases......Page 564
Replication in Eukaryotic Cells......Page 568
13.2 DNA REPAIR......Page 574
Nucleotide Excision Repair......Page 575
Mismatch Repair......Page 576
Double-Strand Breakage Repair......Page 577
13.3 BETWEEN REPLICATION AND REPAIR......Page 579
14 Cellular Reproduction......Page 582
14.1 THE CELL CYCLE......Page 583
Control of the Cell Cycle......Page 584
14.2 M PHASE: MITOSIS AND CYTOKINESIS......Page 591
Prophase......Page 593
Prometaphase......Page 598
Metaphase......Page 600
Anaphase......Page 601
Cytokinesis......Page 607
14.3 MEIOSIS......Page 612
The Stages of Meiosis......Page 613
Genetic Recombination During Meiosis......Page 619
15 Cell Signaling and Signal Transduction: Communication Between Cells......Page 627
15.1 THE BASIC ELEMENTS OF CELL SIGNALING SYSTEMS......Page 628
15.2 A SURVEY OF EXTRACELLULAR MESSENGERS AND THEIR RECEPTORS......Page 630
15.3 G PROTEIN-COUPLED RECEPTORS AND THEIR SECOND MESSENGERS......Page 631
Signal Transduction by G Protein-Coupled Receptors......Page 632
Second Messengers......Page 636
Regulation of Blood Glucose Levels......Page 640
The Role of GPCRs in Sensory Perception......Page 644
15.4 PROTEIN-TYROSINE PHOSPHORYLATION AS A MECHANISM FOR SIGNAL TRANSDUCTION......Page 645
The Ras-MAP Kinase Pathway......Page 649
Signaling by the Insulin Receptor......Page 653
Signaling Pathways in Plants......Page 655
15.5 THE ROLE OF CALCIUM AS AN INTRACELLULAR MESSENGER......Page 656
15.6 CONVERGENCE, DIVERGENCE, AND CROSSTALK AMONG DIFFERENT SIGNALING PATHWAYS......Page 660
Examples of Convergence, Divergence, and Crosstalk Among Signaling Pathways......Page 661
15.7 THE ROLE OF NO AS AN INTERCELLULAR MESSENGER......Page 662
15.8 APOPTOSIS (PROGRAMMED CELL DEATH)......Page 664
The Extrinsic Pathway of Apoptosis......Page 665
The Intrinsic Pathway of Apoptosis......Page 666
16 Cancer......Page 672
16.1 BASIC PROPERTIES OF A CANCER CELL\r......Page 673
16.2 THE CAUSES OF CANCER......Page 675
16.3 THE GENETICS OF CANCER......Page 676
Tumor-Suppressor Genes and Oncogenes: Brakes and Accelerators......Page 678
The Cancer Genome......Page 689
Gene-Expression Analysis......Page 691
16.4 NEW STRATEGIES FOR COMBATING CANCER......Page 693
Immunotherapy......Page 694
Inhibiting the Activity of Cancer-Promoting Proteins......Page 695
Inhibiting the Formation of New Blood Vessels (Angiogenesis)......Page 697
17 The Immune Response......Page 704
17.1 AN OVERVIEW OF THE IMMUNE RESPONSE......Page 705
Innate Immune Responses......Page 706
Adaptive Immune Responses......Page 708
17.2 THE CLONAL SELECTION THEORY AS IT APPLIES TO B CELLS......Page 709
Vaccination......Page 711
17.3 T LYMPHOCYTES: ACTIVATION AND MECHANISM OF ACTION......Page 712
The Modular Structure of Antibodies......Page 715
DNA Rearrangement of Genes Encoding B- and T-Cell Antigen Receptors......Page 718
The Major Histocompatibility Complex......Page 721
Lymphocytes Are Activated by Cell-Surface Signals......Page 726
Signal Transduction Pathways Used in Lymphocyte Activation......Page 728
18 Techniques in Cell and Molecular Biology......Page 737
Resolution......Page 738
Visibility......Page 739
Phase-Contrast Microscopy......Page 740
Fluorescence Microscopy (and Related Fluorescence-Based Techniques)......Page 741
Laser Scanning Confocal Microscopy......Page 743
18.2 TRANSMISSION ELECTRON MICROSCOPY......Page 744
Specimen Preparation for Electron Microscopy......Page 746
18.3 SCANNING ELECTRON AND ATOMIC FORCE MICROSCOPY......Page 751
18.4 THE USE OF RADIOISOTOPES......Page 752
18.5 CELL CULTURE......Page 753
18.6 THE FRACTIONATION OF A CELL’S CONTENTS BY DIFFERENTIAL CENTRIFUGATION......Page 755
Selective Precipitation......Page 756
Liquid Column Chromatography......Page 757
Polyacrylamide Gel Electrophoresis......Page 759
Protein Measurement and Analysis......Page 761
18.8 DETERMINING THE STRUCTURE OF PROTEINS AND MULTISUBUNIT COMPLEXES......Page 762
Separation of DNAs by Gel Electrophoresis......Page 764
Separation of Nucleic Acids by Ultracentrifugation......Page 765
18.11 NUCLEIC ACID HYBRIDIZATION......Page 767
Restriction Endonucleases......Page 768
DNA Cloning......Page 770
18.14 ENZYMATIC AMPLIFICATION OF DNA BY PCR......Page 773
Applications of PCR......Page 774
18.15 DNA SEQUENCING......Page 775
Genomic Libraries......Page 777
cDNA Libraries......Page 778
18.17 DNA TRANSFER INTO EUKARYOTIC CELLS AND MAMMALIAN EMBRYOS......Page 779
Knockout Mice......Page 782
RNA Interference......Page 784
18.19 THE USE OF ANTIBODIES......Page 785
Glossary......Page 789
Additional Readings......Page 809
Index......Page 815