Cell Biology

1 Introduction to Cell Biology 1 1.1 The Discovery of Cells 2 1.2 Basic Properties of Cells 3 1.3 Two Fundamentally Different Classes of Cells 7 1.4 Viruses 23 2 The Structure and Functions of Biological Molecules 32 2.1 Covalent Bonds 33 2.2 Noncovalent Bonds 34 2.3 Acids, Bases, and Buffers 39 2.4 The Nature of Biological Molecules 40 2.5 Four Types of Biological Molecules 42 4.5 The Stability of the Genome 140 4.6 Sequencing Genomes: The Footprints of Biological Evolution 145 5 The Path to Gene Expression 160 5.1 The Relationship between Genes, Proteins, and RNAs 161 5.2 An Overview of Transcription in Both Prokaryotic and Eukaryotic Cells 163 5.3 Synthesis and Processing of Eukaryotic Ribosomal and Transfer RNAs 169 5.4 Synthesis and Processing of Eukaryotic Messenger RNAs 175 5.5 Small Regulatory RNAs and RNA Silencing Pathways 189 5.6 Encoding Genetic Information 195 5.7 Decoding the Codons: The Role of Transfer RNAs 198 5.8 Translating Genetic Information 202 6 Controlling Gene Expression 217 6.1 Control of Gene Expression in Bacteria 218 6.2 Control of Gene Expression in Eukaryotes: Structure and Function of the Cell Nucleus 222 6.3 An Overview of Gene Regulation in Eukaryotes 246 6.4 Transcriptional Control 248 6.5 RNA Processing Control 267 6.6 Translational Control 270 6.7 Posttranslational Control: Determining Protein Stability 275 7 Replicating and Repairing DNA 279 7.1 DNA Replication 280 7.2 DNA Repair 298 7.3 Between Replication and Repair 302 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 8.4 The Structure and Functions of Membrane Proteins 316 8.5 Membrane Lipids and Membrane Fluidity 324 8.6 The Dynamic Nature of the Plasma Membrane 326 8.7 The Movement of Substances Across Cell Membranes 333 8.8 Membrane Potentials and Nerve Impulses 350 9 Mitochondrial Structure and Function 364 9.1 Mitochondrial Structure and Function 365 9.2 Oxidative Metabolism in the Mitochondrion 369 9.3 The Role of Mitochondria in the Formation of ATP 375 9.4 Translocation of Protons and the Establishment of a Proton-Motive Force 384 9.5 The Machinery for ATP Formation 385 9.6 Peroxisomes 392 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 10.4 Photosynthetic Units and Reaction Centers 404 10.5 Photophosphorylation 411 10.6 Carbon Dioxide Fixation and the Synthesis of Carbohydrate 412 11 The Extracellular Matrix and Cell Interactions 421 11.1 The Extracellular Space 422 11.2 Interactions of Cells with Extracellular Materials 430 11.3 Interactions of Cells with Other Cells 436 11.4 Tight Junctions: Sealing The Extracellular Space 446 11.5 Gap Junctions and Plasmodesmata: Mediating Intercellular Communication 448 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 12.3 The Endoplasmic Reticulum 465 12.4 The Golgi Complex 476 12.5 Types of Vesicle Transport and Their Functions 481 12.6 Lysosomes 489 12.7 Plant Cell Vacuoles 493 12.8 The Endocytic Pathway: Moving Membrane and Materials into the Cell Interior 494 12.9 Posttranslational Uptake of Proteins by Peroxisomes, Mitochondria, and Chloroplasts 502 13 The Cytoskeleton 510 13.1 Overview of the Major Functions of the Cytoskeleton 511 13.2 The Study of the Cytoskeleton 512 13.3 Microtubules 516 13.4 Intermediate Filaments 540 13.5 Microfilaments 542 13.6 Muscle Contractility 550 13.7 Nonmuscle Motility 557 14 Cell Division 572 14.1 The Cell Cycle 573 14.2 M Phase: Mitosis and Cytokinesis 581 14.3 Meiosis 602 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 15.4 Protein-Tyrosine Phosphorylation as a Mechanism for Signal Transduction 636 15.5 The Role of Calcium as an Intracellular Messenger 648 15.6 Convergence, Divergence, and Cross-Talk Among Different Signaling Pathways 653 15.7 The Role of NO as an Intercellular Messenger 655 15.8 Apoptosis (Programmed Cell Death) 656 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 16.4 New Strategies for Combating Cancer 687 17 Immunity 699 17.1 An Overview of the Immune Response 700 17.2 The Clonal Selection Theory as It Applies to B Cells 704 17.3 T Lymphocytes: Activation and Mechanism of Action 707 17.4 Selected Topics on the Cellular and Molecular Basis of Immunity 710 18 Methods in Cell Biology 732 18.1 The Light Microscope 733 18.10 Nucleic Acid Hybridization 762 18.11 Chemical Synthesis of DNA 764 18.12 Recombinant DNA Technology 764 18.13 Enzymatic Amplification of DNA by PCR 769 18.14 DNA Sequencing 771 18.15 DNA Libraries 773 18.16 DNA Transfer into Eukaryotic Cells and Mammalian Embryos 775 18.17 Determining Eukaryotic Gene Function by Gene Elimination or Silencing 778 18.18 The Use of Antibodies 780 18.2 Transmission Electron Microscopy 740 18.3 Scanning Electron and Atomic Force Microscopy 746 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 18.8 Determining the Structure of Proteins and Multisubunit Complexes 758 18.9 Fractionation of Nucleic Acids 760 Glossary G-1 Additional Readings A-1 Index I-1