Molecular Biology of the Cell 1994 by Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts, and James D. Watson.

Transcription

1 Molecular Biology of the Cell 1994 by Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts, and James D. Watson. I. Introduction to the Cell 1. The Evolution of the Cell *. From Molecules to the First Cell *. From Procaryotes to Eucaryotes *. From Single Cells to Multicellular Organisms 2. Small Molecules, Energy, and Biosynthesis -. The Chemical Components of a Cell -. Biological Order and Energy -. Food and the Derivation of Cellular Energy -. Biosynthesis and the Creation of Order -. The Coordination of Catabolism and Biosynthesis 3. Macromolecules: Structure, Shape, and Information -. Molecular Recognition Processes **. Nucleic Acids ***. Protein Structure -. Proteins as Catalysts 4. How Cells Are Studied *. Looking at the Structure of Cells in the Microscope *. Isolating Cells and Growing Them in Culture *. Fractionation of Cells and Analysis of Their Molecules *. Tracing and Assaying Molecules Inside Cells II. Molecular Genetics 5. Protein Function *. Making Machines Out of Proteins **. The Birth, Assembly, and Death of Proteins 6. Basic Genetic Mechanisms **. RNA and Protein Synthesis -. DNA Repair -. DNA Replication -. Genetic Recombination -. Viruses, Plasmids, and Transposable Genetic Elements 7. Recombinant DNA Technology -. The Fragmentation, Separation, and Sequencing of DNA Molecules -. Nucleic Acid Hybridization

2 -. DNA Cloning -. DNA Engineering 8. The Cell Nucleus **. Chromosomal DNA and Its Packaging *. The Global Structure of Chromosomes -. Chromosome Replication **. RNA Synthesis and RNA Processing **. The Organization and Evolution of the Nuclear Genome 9. Control of Gene Expression ***. An Overview of Gene Control *. DNA-binding Motifs in Gene Regulatory Proteins **. How Genetic Switches Work *. Chromatin Structure and the Control of Gene Expression -. The Molecular Genetic Mechanisms That Create Specialized Cell Types *. Posttranscriptional Controls III. Internal Organization of the Cell 10. Membrane Structure **. The Lipid Bilayer **. Membrane Proteins 11. Membrane Transport of Small Molecules and the Ionic Basis of Membrane Excitability -. Principles of Membrane Transport -. Carrier Proteins and Active Membrane Transport, -. Ion Channels and Electrical Properties of Membranes 12. Intracellular Compartments and Protein Sorting *. The Compartmentalization of Higher Cells ***. The Transport of Molecules into and out of the Nucleus **. The Transport of Proteins into Mitochondria and Chloroplasts *. Peroxisomes ***. The Endoplasmic Reticulum 13. Vesicular Traffic in the Secretory and Endocytic Pathways **. Transport from the ER Through the Golgi Apparatus **. Transport from the Trans Golgi Network to Lysosomes **. Transport from the Plasma Membrane via Endosomes: Endocytosis **. Transport from the Trans Golgi Network to the Cell Surface: Exocytosis *. The Molecular Mechanisms of Vesicular Transport and the Maintenance of Compartmental Diversity 14. Energy Conversion: Mitochondria and Chloroplasts *. The Mitochondrion

3 *. The Respiratory Chain and ATP Synthase -. Chloroplasts and Photosynthesis -. The Evolution of Electron-Transport Chains -. The Genomes of Mitochondria and Chloroplasts 15. Cell Signaling *. General Principles of Cell Signaling *. Signaling via G-Protein-linked Cell-Surface Receptors *. Signaling via Enzyme-linked Cell-Surface Receptors *. Target-Cell Adaptation -. The Logic of Intracellular Signaling: Lessons from Computer-based "Neural Networks" 16. The Cytoskeleton **. The Nature of the Cytoskeleton **. Intermediate Filaments ***. Microtubules *. Cilia and Centrioles ***. Actin Filaments ***. Actin-binding Proteins *. Muscle 17. The Cell-Division Cycle **. The General Strategy of the Cell Cycle **. The Early Embryonic Cell Cycle and the Role of MPF *. Yeasts and the Molecular Genetics of Cell-Cycle Control *. Cell-Division Controls in Multicellular Animals 18. The Mechanics of Cell Division *. An Overview of M Phase **. Mitosis *. Cytokinesis IV. Cells in Their Social Context 19. Cell Junctions, Cell Adhesion, and the Extracellular Matrix **. Cell Junctions **. Cell-Cell Adhesion ***. The Extracellular Matrix of Animals **. Extracellular Matrix Receptors on Animal Cells: The Integrins -. The Plant Cell Wall 20. Germ Cells and Fertilization -. The Benefits of Sex *. Meiosis -. Eggs -. Sperm

4 -. Fertilization 21. Cellular Mechanisms of Development *. Morphogenetic Movements and the Shaping of the Body Plan *. Cell Diversification in the Early Animal Embryo, *. Cell Memory, Cell Determination, and the Concept of Positional Values *. The Nematode Worm: Developmental Control Genes and the Rules of * Cell Behavior -. Drosophila and the Molecular Genetics of Pattern Formation. I. Genesis of the Body Plan -. Drosophila and the Molecular Genetics of Pattern Formation. II. Homeotic Selector Genes and the Patterning of Body Parts, -. Plant Development -. Neural Development 22. Differentiated Cells and the Maintenance of Tissues *. Maintenance of the Differentiated State *. Tissues with Permanent Cells *. Renewal by Simple Duplication *. Renewal by Stem Cells: Epidermis, *. Renewal by Pluripotent Stem Cells: Blood Cell Formation, *. Genesis, Modulation, and Regeneration of Skeletal Muscle -. Fibroblasts and Their Transformations: The Connective-Tissue Cell Family 23. The Immune System -. The Cellular Basis of Immunity -. The Functional Properties of Antibodies -. The Fine Structure of Antibodies -. The Generation of Antibody Diversity -. T Cell Receptors and Subclasses -. MHC Molecules and Antigen Presentation to T Cells -. Cytotoxic T Cells -. Helper T Cells and T Cell Activation -. Selection of the T Cell Repertoire 24. Cancer -. Cancer as a Microevolutionary Process -. The Molecular Genetics of Cancer

5 Molecular Cell Biology - Lodish 1. The Dynamic Cell * 1.1. Evolution: At the Core of Molecular Change * 1.2. The Molecules of Life * 1.3. The Architecture of Cells * 1.4. The Life Cycle of Cells * 1.5. Cells into Tissues * 1.6. Molecular Cell Biology: An Integrated View of Cells at Work 2. Chemical Foundations Covalent Bonds Noncovalent Bonds Chemical Equilibrium Biochemical Energetics Activation Energy and Reaction Rate 3. Protein Structure and Function * 3.1. Hierarchical Structure of Proteins ** 3.2. Folding, Modification, and Degradation of Proteins ** 3.3. Functional Design of Proteins ** 3.4. Membrane Proteins * 3.5. Purifying, Detecting, and Characterizing Proteins 4. Nucleic Acids, the Genetic Code, and the Synthesis of Macromolecules Structure of Nucleic Acids * 4.2. Synthesis of Biopolymers: Rules of Macromolecular Carpentry * 4.3. Nucleic Acid Synthesis *** 4.4. The Three Roles of RNA in Protein Synthesis Stepwise Formation of Proteins on Ribosomes 5. Biomembranes and the Subcellular Organization of Eukaryotic Cells * 5.1. Microscopy and Cell Architecture * 5.2. Purification of Cells and Their Parts ** 5.3. Biomembranes: Structural Organization and Basic Functions ** 5.4. Organelles of the Eukaryotic Cell 6. Manipulating Cells and Viruses in Culture Growth of Microorganisms in Culture Growth of Animal Cells in Culture Viruses: Structure, Function, and Uses 7. Recombinant DNA and Genomics DNA Cloning with Plasmid Vectors Constructing DNA Libraries with λ Phage and Other Cloning Vectors Identifying, Analyzing, and Sequencing Cloned DNA Bioinformatics Analyzing Specific Nucleic Acids in Complex Mixtures Producing High Levels of Proteins from Cloned cdnas Polymerase Chain Reaction: An Alternative to Cloning DNA Microarrays: Analyzing Genome-Wide Expression 8. Genetic Analysis in Cell Biology * 8.1. Mutations: Types and Causes

6 Isolation and Analysis of Mutants Genetic Mapping of Mutations Molecular Cloning of Genes Defined by Mutations Gene Replacement and Transgenic Animals 9. Molecular Structure of Genes and Chromosomes ** 9.1. Molecular Definition of a Gene * 9.2. Chromosomal Organization of Genes and Noncoding DNA Mobile DNA Functional Rearrangements in Chromosomal DNA ** 9.5. Organizing Cellular DNA into Chromosomes ** 9.6. Morphology and Functional Elements of Eukaryotic Chromosomes * 9.7. Organelle DNAs 10. Regulation of Transcription Initiation *** Bacterial Gene Control: The Jacob-Monod Model Bacterial Transcription Initiation * Eukaryotic Gene Control: Purposes and General Principles * Regulatory Sequences in Eukaryotic Protein-Coding Genes Eukaryotic Transcription Activators and Repressors RNA Polymerase II Transcription-Initiation Complex * Molecular Mechanisms of Eukaryotic Transcriptional Control Other Transcription Systems 11. RNA Processing, Nuclear Transport, and Post-Transcriptional Control Transcription Termination * Processing of Eukaryotic mrna Regulation of mrna Processing ** Signal-Mediated Transport through Nuclear Pore Complexes * Other Mechanisms of Post-Transcriptional Control * Processing of rrna and trna 12. DNA Replication, Repair, and Recombination General Features of Chromosomal Replication The DNA Replication Machinery The Role of Topoisomerases in DNA Replication DNA Damage and Repair and Their Role in Carcinogenesis Recombination between Homologous DNA Sites 13. Regulation of the Eukaryotic Cell Cycle *** Overview of the Cell Cycle and Its Control ** Biochemical Studies with Oocytes, Eggs, and Early Embryos * Genetic Studies with S. pombe ** Molecular Mechanisms for Regulating Mitotic Events Genetic Studies with S. cerevisiae * Cell-Cycle Control in Mammalian Cells ** Checkpoints in Cell-Cycle Regulation 14. Gene Control in Development Cell-Type Specification and Mating-Type Conversion in Yeast ** Cell-Type Specification in Animals * Anteroposterior Specification during Embryogenesis Specification of Floral-Organ Identity in Arabidopsis

7 15. Transport across Cell Membranes * Diffusion of Small Molecules across Phospholipid Bilayers * Overview of Membrane Transport Proteins * Uniporter-Catalyzed Transport * Intracellular Ion Environment and Membrane Electric Potential * Active Transport by ATP-Powered Pumps * Cotransport by Symporters and Antiporters * Transport across Epithelia * Osmosis, Water Channels, and the Regulation of Cell Volume 16. Cellular Energetics: Glycolysis, Aerobic Oxidation, and Photosynthesis Oxidation of Glucose and Fatty Acids to CO Electron Transport and Oxidative Phosphorylation Photosynthetic Stages and Light-Absorbing Pigments Molecular Analysis of Photosystems CO2 Metabolism during Photosynthesis 17. Protein Sorting: Organelle Biogenesis and Protein Secretion ** Synthesis and Targeting of Mitochondrial and Chloroplast Proteins * Synthesis and Targeting of Peroxisomal Proteins *** Overview of the Secretory Pathway ** Translocation of Secretory Proteins across the ER Membrane ** Insertion of Membrane Proteins into the ER Membrane * Post-Translational Modifications and Quality Control in the Rough ER ** Protein Glycosylation in the ER and Golgi Complex * Golgi and Post-Golgi Protein Sorting and Proteolytic Processing ** Receptor-Mediated Endocytosis and the Sorting of Internalized Proteins * Molecular Mechanisms of Vesicular Traffic 18. Cell Motility and Shape I: Microfilaments *** The Actin Cytoskeleton ** The Dynamics of Actin Assembly * Myosin: The Actin Motor Protein ** Muscle: A Specialized Contractile Machine * Actin and Myosin in Nonmuscle Cells * Cell Locomotion 19. Cell Motility and Shape II: Microtubules and Intermediate Filaments *** Microtubule Structures ** Microtubule Dynamics and Associated Proteins ** Kinesin, Dynein, and Intracellular Transport * Cilia and Flagella: Structure and Movement ** Microtubule Dynamics and Motor Proteins during Mitosis ** Intermediate Filaments 20. Cell-to-Cell Signaling: Hormones and Receptors *** Overview of Extracellular Signaling Identification and Purification of Cell-Surface Receptors ** G Protein Coupled Receptors and Their Effectors *** Receptor Tyrosine Kinases and Ras ** MAP Kinase Pathways * Second Messengers

8 * Interaction and Regulation of Signaling Pathways ** From Plasma Membrane to Nucleus 21. Nerve Cells Overview of Neuron Structure and Function The Action Potential and Conduction of Electric Impulses Molecular Properties of Voltage-Gated Ion Channels Neurotransmitters, Synapses, and Impulse Transmission Neurotransmitter Receptors Sensory Transduction Learning and Memory 22. Integrating Cells into Tissues *** Cell-Cell Adhesion and Communication ** Cell-Matrix Adhesion ** Collagen: The Fibrous Proteins of the Matrix ** Noncollagen Components of the Extracellular Matrix The Dynamic Plant Cell Wall 23. Cell Interactions in Development Dorsoventral Patterning by TGFβ-Superfamily Proteins Tissue Patterning by Hedgehog and Wingless Molecular Mechanisms of Responses to Morphogens Reciprocal and Lateral Inductive Interactions Overview of Neuronal Outgrowth Directional Control of Neuronal Outgrowth Formation of Topographic Maps and Synapses Cell Death and Its Regulation 24. Cancer * Tumor Cells and the Onset of Cancer * Proto-Oncogenes and Tumor-Suppressor Genes Oncogenic Mutations Affecting Cell Proliferation Mutations Causing Loss of Cell-Cycle Control Mutations Affecting Genome Stability