Karp's Cell and Molecular Biology

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 1.3 Two Fundamentally Different Classes of Cells 8 1.4 Viruses and Viroids 26 1.5 Green Cells: Volvox, an Experiment in Multicellularity 35 1.6 Engineering Linkage: Tissue Engineering 36 2 The Chemical Basis of Life 39 2.1 Covalent Bonds 40 2.2 Engineering Linkage: Radionuclides for Imaging and Treatment 43 2.3 Noncovalent Bonds 44 2.4 Acids, Bases, and Buffers 48 2.5 The Nature of Biological Molecules 49 2.6 Green Cells: Chemical Fertilizers 52 2.7 Four Types of Biological Molecules 53 2.8 The Formation of Complex Macromolecular Structures 95 3 Bioenergetics, Enzymes, and Metabolism 99 3.1 Bioenergetics 100 3.2 Enzymes as Biological Catalysts 108 3.3 Metabolism 123 3.4 Green Cells: Regulation of Metabolism by the Light/Dark Cycle 134 3.5 Engineering Linkage: Using Metabolism to Image Tumors 135 4 The Structure and Function of the Plasma Membrane 137 4.1 Introduction to the Plasma Membrane 138 4.2 The Chemical Composition of Membranes 142 4.3 Membrane Proteins 148 4.4 Membrane Lipids and Membrane Fluidity 156 4.5 The Dynamic Nature of the Plasma Membrane 159 4.6 The Movement of Substances across Cell Membranes 166 4.7 Membrane Potentials and Nerve Impulses 189 4.8 Green Cells: Electrical Signaling in Plants 198 4.9 Engineering Linkage: Neurotechnology 199 5 Aerobic Respiration and the Mitochondrion 203 5.1 Mitochondrial Structure and Function 204 5.2 Aerobic Metabolism in the Mitochondrion 209 5.3 The Role of Mitochondria in the Formation of ATP 215 5.4 Engineering Linkage: Measuring Blood Oxygen 224 5.5 Establishment of a Proton-Motive Force 225 5.6 The Machinery for ATP Formation 226 5.7 Peroxisomes 233 5.8 Green Cells: Glyoxysomes 237 6 Photosynthesis and the Chloroplast 239 6.1 The Origin of Photosynthesis 240 6.2 Chloroplast Structure 241 6.3 An Overview of Photosynthetic Metabolism 243 6.4 The Absorption of Light 244 6.5 Green Cells: Chromoplasts 246 6.6 Photosynthetic Units and Reaction Centers 247 6.7 Photophosphorylation 255 6.8 Carbon Dioxide Fixation and the Synthesis of Carbohydrate 256 6.9 Engineering Linkage: Photodynamic Therapy 264 7 Interactions Between Cells and Their Environment 267 7.1 Extracellular Interactions 268 7.2 Engineering Linkage: Organoids 277 7.3 Interactions of Cells with Extracellular Materials 278 7.4 Interactions of Cells with Other Cells 284 7.5 Tight Junctions: Sealing the Extracellular Space 294 7.6 Intercellular Communication 296 7.7 Cell Walls 303 7.8 Green Cells: Cell Walls and Plant Terrestrialization 306 8 Cytoplasmic Membrane Systems: Structure, Function, and Membrane Trafficking 307 8.1 An Overview of the Endomembrane System 308 8.2 A Few Approaches to the Study of Endomembranes 311 8.3 The Endoplasmic Reticulum 317 8.4 The Golgi Complex 330 8.5 Types of Vesicle Transport 335 8.6 Engineering Linkage: Extracellular Vesicles for Drug Delivery 347 8.7 Lysosomes 348 8.8 Green Cells: Plant Cell Vacuoles 350 8.9 The Endocytic Pathway: Moving Membrane and Materials into the Cell Interior 351 8.10 Posttranslational Uptake of Proteins by Peroxisomes, Mitochondria, and Chloroplasts 363 9 The Cytoskeleton and Cell Motility 369 9.1 Overview of the Major Functions of the Cytoskeleton 370 9.2 Structure and Function of Microtubules 372 9.3 Green Cells: Why the Woodbine Twineth 376 9.4 Motor Proteins: Kinesins and Dyneins 377 9.5 Microtubule-Organizing Centers (MTOCs) 383 9.6 Structure and Function of Cilia and Flagella 390 9.7 Intermediate Filaments 398 9.8 Actin and Myosin 402 9.9 Muscle Organization and Contraction 410 9.10 Engineering Linkage: Muscle Biomechanics 416 9.11 Actin-Binding Proteins 417 9.12 Cellular Motility 420 9.13 The Bacterial Cytoskeleton 430 10 The Nature of the Gene and the Genome 433 10.1 The Concept of a Gene as a Unit of Inheritance 434 10.2 The Discovery of Chromosomes 435 10.3 Chromosomes as the Carriers of Genetic Information 436 10.4 The Chemical Nature of the Gene 441 10.5 The Complexity of the Genome 452 10.6 The Stability of the Genome 458 10.7 Sequencing Genomes: The Footprints of Biological Evolution 464 10.8 Engineering Linkage: Engineering Genomes 467 10.9 The Genetic Basis of “Being Human” 468 10.10 Green Cells: Gene Transfer by Agrobacterium tumefaciens 475 11 The Central Dogma: DNA to RNA to Protein 477 11.1 The Relationships among Genes, Proteins, and RNAs 478 11.2 An Overview of Transcription in Both Prokaryotic and Eukaryotic Cells 483 11.3 Synthesis and Processing of Eukaryotic Ribosomal and Transfer RNAs 487 11.4 Synthesis and Structure of Eukaryotic Messenger RNAs 491 11.5 Small Regulatory RNAs and RNA Silencing Pathways 507 11.6 Green Cells: Long-Range siRNA Movement 512 11.7 CRISPR and Other Noncoding RNAs 513 11.8 Encoding Genetic Information 514 11.9 Decoding the Codons: The Role of Transfer RNAs 517 11.10 Translating Genetic Information 520 11.11 Engineering Linkage: DNA Origami 534 12 Control of Gene Expression 537 12.1 Control of Gene Expression in Bacteria 538 12.2 Engineering Linkage: Building Digital Logic with Genes 542 12.3 Structure of the Nuclear Envelope 543 12.4 Chromosomes and Chromatin 550 12.5 The Nucleus as an Organized Organelle 567 12.6 An Overview of Gene Regulation in Eukaryotes 570 12.7 Transcriptional Control 571 12.8 Green Cells: The ABC Model and MADS Domain Transcription Factors 592 12.9 RNA Processing Control 593 12.10 Translational Control 594 12.11 Posttranslational Control: Determining Protein Stability 601 13 DNA Replication and Repair 605 13.1 DNA Replication 606 13.2 DNA Replication in Bacterial Cells 610 13.3 The Structure and Functions of DNA Polymerases 617 13.4 Replication in Viruses 621 13.5 Engineering Linkage: Storing Data in DNA 621 13.6 DNA Replication in Eukaryotic Cells 622 13.7 DNA Repair 628 13.8 Green Cells: Gamma Gardens 632 13.9 Between Replication and Repair 633 14 Cell Division 637 14.1 The Cell Cycle 638 14.2 M Phase: Mitosis and Cytokinesis 651 14.3 Engineering Linkage: The Role of Membrane Tension in Cell Division 672 14.4 Green Cells: Unique Aspects of Plant Cell Division 673 14.5 Meiosis 673 15 Cell Signaling and Signal Transduction: Communication between Cells 685 15.1 The Basic Elements of Cell Signaling Systems 686 15.2 A Survey of Extracellular Messengers and Their Receptors 689 15.3 G Protein-Coupled Receptors and Their Second Messengers 690 15.4 Engineering Linkage: Biosensors in Medicine and Biology 709 15.5 Protein-Tyrosine Phosphorylation as a Mechanism for Signal Transduction 710 15.6 Green Cells: Auxin Signaling 721 15.7 The Role of Calcium as an Intracellular Messenger 721 15.8 Convergence, Divergence, and Cross-Talk among Different Signaling Pathways 726 15.9 The Role of NO as an Intracellular Messenger 729 15.10 Apoptosis (Programmed Cell Death) 731 16 Cancer 737 16.1 Basic Properties of a Cancer Cell 738 16.2 The Causes of Cancer 741 16.3 Cancer: A Genetic Disorder 747 16.4 Engineering Linkage: Therapeutic Radiation 767 16.5 Green Cells: Plant-Based Chemotherapies 767 16.6 Strategies for Combating Cancer 768 17 The Immune Response 775 17.1 An Overview of the Immune Response 776 17.2 Green Cells: The Plant Immune System 780 17.3 The Clonal Selection Theory as It Applies to B Cells 781 17.4 T Lymphocytes: Activation and Mechanism of Action 787 17.5 Selected Topics on the Cellular and Molecular Basis of Immunity 790 17.6 Engineering Linkage: Adoptive T-cell Therapy 808 17.7 Signal Transduction Pathways in Lymphocyte Activation 809 18 Techniques in Cell and Molecular Biology 811 18.1 The Light Microscope 812 18.2 Transmission Electron Microscopy 822 18.3 Scanning Electron and Atomic Force Microscopy 828 18.4 The Use of Radioisotopes 830 18.5 Cell Culture 831 18.6 The Fractionation of a Cell’s Contents by Differential Centrifugation 833 18.7 Isolation, Purification, and Fractionation of Proteins 834 18.8 Determining the Structure of Proteins and Multisubunit Complexes 840 18.9 Fractionation of Nucleic Acids 842 18.10 Nucleic Acid Hybridization 845 18.11 Chemical Synthesis of DNA 846 18.12 Recombinant DNA Technology 847 18.13 Enzymatic Amplification of DNA by PCR 851 18.14 DNA Sequencing 853 18.15 DNA Libraries 855 18.16 DNA Transfer into Eukaryotic Cells and Mammalian Embryos 857 18.17 Gene Editing and Silencing 860 18.18 The Use of Antibodies 864 Additional Readings A-1 Glossary G-1 Index I-1