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| Preface | |
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| Organization and Features of The Cell | |
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| Media and Supplements to Accompany The Cell | |
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| Introduction | |
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| An Overview of Cells and Cell Research | |
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| The Origin and Evolution of Cells | |
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| The First Cell | |
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| The Evolution of Metabolism | |
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| Present-Day Prokaryotes | |
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| Eukaryotic Cells | |
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| The Origin of Eukaryotes | |
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| The Development of Multicellular Organisms | |
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| Cells as Experimental Models | |
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| E. coli | |
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| Yeasts | |
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| Caenorhabditis elegans | |
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| Drosophila melanogaster | |
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| Arabidopsis thaliana | |
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| Vertebrates | |
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| Tools of Cell Biology | |
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| Light Microscopy | |
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| Electron Microscopy | |
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| Subcellular Fractionation | |
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| Growth of Animal Cells in Culture | |
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| Culture of Plant Cells | |
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| Viruses | |
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| Key Experiment: Animal Cell Culture | |
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| Molecular Medicine: Viruses and Cancer | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| The Composition of Cells | |
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| The Molecules of Cells | |
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| Carbohydrates | |
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| Lipids | |
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| Nucleic Acids | |
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| Proteins | |
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| Cell Membranes | |
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| Membrane Lipids | |
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| Membrane Proteins | |
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| Transport across Cell Membranes | |
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| Proteomics: Large-Scale Analysis of Cell Proteins | |
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| Identification of Cell Proteins | |
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| Global Analysis of Protein Localization | |
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| Protein Interactions | |
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| Key Experiment: The Folding of Polypeptide Chains | |
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| Key Experiment: The Structure of Cell Membranes | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| Cell Metabolism | |
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| The Central Role of Enzymes as Biological Catalysts | |
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| The Catalytic Activity of Enzymes | |
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| Mechanisms of Enzymatic Catalysis | |
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| Coenzymes | |
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| Regulation of Enzyme Activity | |
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| Metabolic Energy | |
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| Free Energy and ATP | |
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| The Generation of ATP from Glucose | |
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| The Derivation of Energy from Other Organic Molecules | |
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| Photosynthesis | |
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| The Biosynthesis of Cell Constituents | |
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| Carbohydrates | |
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| Lipids | |
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| Proteins | |
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| Nucleic Acids | |
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| Key Experiment: Antimetabolites and Chemotherapy | |
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| Molecular Medicine: Phenylketonuria | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| Fundamentals of Molecular Biology | |
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| Heredity, Genes, and DNA | |
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| Genes and Chromosomes | |
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| Genes and Enzymes | |
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| Identification of DNA as the Genetic Material | |
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| The Structure of DNA | |
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| Replication of DNA | |
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| Expression of Genetic Information | |
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| Colinearity of Genes and Proteins | |
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| The Role of Messenger RNA | |
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| The Genetic Code | |
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| RNA Viruses and Reverse Transcription | |
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| Recombinant DNA | |
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| Restriction Endonucleases | |
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| Generation of Recombinant DNA Molecules | |
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| Vectors for Recombinant DNA | |
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| DNA Sequencing | |
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| Expression of Cloned Genes | |
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| Detection of Nucleic Acids and Proteins | |
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| Amplification of DNA by the Polymerase Chain Reaction | |
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| Nucleic Acid Hybridization | |
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| Antibodies as Probes for Proteins | |
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| Gene Function in Eukaryotes | |
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| Genetic Analysis in Yeasts | |
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| Gene Transfer in Plants and Animals | |
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| Mutagenesis of Cloned DNAs | |
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| Introducing Mutations into Cellular Genes | |
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| Interfering with Cellular Gene Expression | |
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| Key Experiment: The DNA Provirus Hypothesis | |
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| Molecular Medicine: HIV and AIDS | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| The Flow of Genetic Information | |
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| The Organization and Sequences of Cellular Genomes | |
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| The Complexity of Eukaryotic Genomes | |
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| Introns and Exons | |
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| Repetitive DNA Sequences | |
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| Gene Duplication and Pseudogenes | |
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| The Composition of Higher Eukaryotic Genomes | |
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| Chromosomes and Chromatin | |
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| Chromatin | |
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| Centromeres | |
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| Telomeres | |
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| The Sequences of Complete Genomes | |
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| Prokaryotic Genomes | |
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| The Yeast Genome | |
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| The Genomes of Caenorhabditis elegans and Drosophila melanogaster | |
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| Plant Genomes | |
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| The Human Genome | |
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| The Genomes of Other Vertebrates | |
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| Bioinformatics and Systems Biology | |
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| Systematic Screens of Gene Function | |
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| Regulation of Gene Expression | |
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| Variation among Individuals and Genomic Medicine | |
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| Key Experiment: The Discovery of Introns | |
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| Key Experiment: The Human Genome | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| Replication, Maintenance, and Rearrangements of Genomic DNA | |
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| DNA Replication | |
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| DNA Polymerases | |
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| The Replication Fork | |
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| The Fidelity of Replication | |
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| Origins and the Initiation of Replication | |
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| Telomeres and Telomerase: Maintaining the Ends of Chromosomes | |
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| DNA Repair | |
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| Direct Reversal of DNA Damage | |
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| Excision Repair | |
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| Translesion DNA Synthesis | |
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| Recombinational Repair | |
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| Recombination between Homologous DNA Sequences | |
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| Models of Homologous Recombination | |
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| Enzymes Involved in Homologous Recombination | |
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| DNA Rearrangements | |
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| Site-Specific Recombination | |
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| Transposition via DNA Intermediates | |
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| Transposition via RNA Intermediates | |
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| Gene Amplification | |
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| Key Experiment: Rearrangement of Immunoglobulin Genes | |
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| Molecular Medicine: Colon Cancer and DNA Repair | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| RNA Synthesis and Processing | |
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| Transcription in Prokaryotes | |
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| RNA Polymerase and Transcription | |
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| Repressors and Negative Control of Transcription | |
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| Positive Control of Transcription | |
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| Eukaryotic RNA Polymerases and General Transcription Factors | |
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| Eukaryotic RNA Polymerases | |
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| General Transcription Factors and Initiation of Transcription by RNA Polymerase II | |
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| Transcription by RNA Polymerases I and III | |
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| Regulation of Transcription in Eukaryotes | |
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| cis-Acting Regulatory Sequences: Promoters and Enhancers | |
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| Transcription Factor Binding Sites | |
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| Transcriptional Regulatory Proteins | |
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| Structure and Function of Transcriptional Activators | |
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| Eukaryotic Repressors | |
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| Relationship of Chromatin Structure to Transcription | |
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| Regulation of Transcription by Noncoding RNAs | |
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| DNA Methylation | |
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| RNA Processing and Turnover | |
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| Processing of Ribosomal and Transfer RNAs | |
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| Processing of mRNA in Eukaryotes | |
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| Splicing Mechanisms | |
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| Alternative Splicing | |
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| RNA Editing | |
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| RNA Degradation | |
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| Key Experiment: Isolation of a Eukaryotic Transcription Factor | |
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| Key Experiment: The Discovery of snRNPs | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| Protein Synthesis, Processing, and Regulation | |
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| Translation of mRNA | |
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| Transfer RNAs | |
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| The Ribosome | |
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| The Organization of mRNAs and the Initiation of Translation | |
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| The Process of Translation | |
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| Regulation of Translation | |
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| Protein Folding and Processing | |
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| Chaperones and Protein Folding | |
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| Enzymes that Catalyze Protein Folding | |
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| Protein Cleavage | |
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| Glycosylation | |
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| Attachment of Lipids | |
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| Regulation of Protein Function | |
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| Regulation by Small Molecules | |
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| Protein Phosphorylation | |
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| Protein-Protein Interactions | |
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| Protein Degradation | |
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| The Ubiquitin-Proteasome Pathway | |
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| Lysosomal Proteolysis | |
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| Key Experiment: Catalytic Role of Ribosomal RNA | |
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| Molecular Medicine: Antibiotic Resistance and the Ribosome | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| Cell Structure and Function | |
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| The Nucleus | |
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| The Nuclear Envelope and Traffic between the Nucleus and the Cytoplasm | |
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| Structure of the Nuclear Envelope | |
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| The Nuclear Pore Complex | |
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| Selective Transport of Proteins to and from the Nucleus | |
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| Regulation of Nuclear Protein Import | |
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| Transport of RNAs | |
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| Internal Organization of the Nucleus | |
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| Chromosomes and Higher-Order Chromatin Structure | |
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| Sub-Compartments within the Nucleus | |
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| The Nucleolus and rRNA Processing | |
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| Ribosomal RNA Genes and the Organization of the Nucleolus | |
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| Transcription and Processing of rRNA | |
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| Ribosome Assembly | |
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| Key Experiment: Nuclear Lamina Diseases | |
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| Molecular Medicine: Identification of Nuclear Localization Signals | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| Protein Sorting and Transport: The Endoplasmic Reticulum, Golgi Apparatus, and Lysosomes | |
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| The Endoplasmic Reticulum | |
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| The Endoplasmic Reticulum and Protein Secretion | |
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| Targeting Proteins to the Endoplasmic Reticulum | |
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| Insertion of Proteins into the ER Membrane | |
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| Protein Folding and Processing in the ER | |
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| Quality Control in the ER | |
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| The Smooth ER and Lipid Synthesis | |
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| Export of Proteins and Lipids from the ER | |
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| The Golgi Apparatus | |
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| Organization of the Golgi | |
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| Protein Glycosylation within the Golgi | |
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| Lipid and Polysaccharide Metabolism in the Golgi | |
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| Protein Sorting and Export from the Golgi Apparatus | |
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| The Mechanism of Vesicular Transport | |
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| Experimental Approaches to Understanding Vesicular Transport | |
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| Cargo Selection, Coat Proteins, and Vesicle Budding | |
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| Vesicle Fusion | |
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| Lysosomes | |
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| Lysosomal Acid Hydrolases | |
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| Endocytosis and Lysosome Formation | |
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| Phagocytosis and Autophagy | |
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| Key Experiment: The Signal Hypothesis | |
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| Molecular Medicine: Gaucher Disease | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| Bioenergetics and Metabolism: Mitochondria, Chloroplasts, and Peroxisomes | |
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| Mitochondria | |
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| Organization and Function of Mitochondria | |
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| The Genetic System of Mitochondria | |
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| Protein Import and Mitochondrial Assembly | |
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| The Mechanism of Oxidative Phosphorylation | |
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| The Electron Transport Chain | |
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| Chemiosmotic Coupling | |
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| Transport of Metabolites across the Inner Membrane | |
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| Chloroplasts and Other Plastids | |
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| The Structure and Function of Chloroplasts | |
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| The Chloroplast Genome | |
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| Import and Sorting of Chloroplast Proteins | |
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| Other Plastids | |
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| Photosynthesis | |
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| Electron Flow through Photosystems I and II | |
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| Cyclic Electron Flow | |
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| ATP Synthesis | |
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| Peroxisomes | |
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| Functions of Peroxisomes | |
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| Peroxisome Assembly | |
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| Key Experiment: The Chemiosmotic Theory | |
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| Molecular Medicine: Diseases of Mitochondria: Leber's Hereditary Optic Neuropathy | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| The Cytoskeleton and Cell Movement | |
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| Structure and Organization of Actin Filaments | |
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| Assembly and Disassembly of Actin Filaments | |
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| Organization of Actin Filaments | |
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| Association of Actin Filaments with the Plasma Membrane | |
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| Protrusions of the Cell Surface | |
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| Actin, Myosin, and Cell Movement | |
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| Muscle Contraction | |
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| Contractile Assemblies of Actin and Myosin in Nonmuscle Cells | |
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| Nonmuscle Myosins | |
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| Formation of Protrusions and Cell Movement | |
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| Intermediate Filaments | |
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| Intermediate Filament Proteins | |
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| Assembly of Intermediate Filaments | |
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| Intracellular Organization of Intermediate Filaments | |
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| Functions of Keratins and Neurofilaments: Diseases of the Skin and Nervous System | |
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| Microtubules | |
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| Structure and Dynamic Organization of Microtubules | |
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| Assembly of Microtubules | |
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| Organization of Microtubules within Cells | |
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| Microtubule Motors and Movement | |
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| Identification of Microtubule Motor Proteins | |
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| Cargo Transport and Intracellular Organization | |
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| Cilia and Flagella | |
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| Reorganization of Microtubules during Mitosis | |
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| Chromosome Movement | |
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| Key Experiment: Expression of Mutant Keratin Causes Abnormal Skin Development | |
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| Key Experiment The Isolation of Kinesin | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| The Plasma Membrane | |
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| Structure of the Plasma Membrane | |
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| The Phospholipid Bilayer | |
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| Membrane Proteins | |
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| Mobility of Membrane Proteins | |
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| The Glycocalyx | |
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| Transport of Small Molecules | |
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| Passive Diffusion | |
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| Facilitated Diffusion and Carrier Proteins | |
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| Ion Channels | |
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| Active Transport Driven by ATP Hydrolysis | |
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| Active Transport Driven by Ion Gradients | |
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| Endocytosis | |
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| Phagocytosis | |
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| Receptor-Mediated Endocytosis | |
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| Protein Trafficking in Endocytosis | |
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| Key Experiment: The LDL Receptor | |
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| Molecular Medicine: Cystic Fibrosis | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| Cell Walls, the Extracellular Matrix, and Cell Interactions | |
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| Cell Wall | |
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| Bacterial Cell Walls | |
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| Eukaryotic Cell Walls | |
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| The Extracellular Matrix and Cell-Matrix Interactions | |
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| Matrix Structural Proteins | |
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| Matrix Polysaccharides | |
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| Matrix Adhesion Proteins | |
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| Cell-Matrix Interactions | |
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| Cell-Cell Interactions | |
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| Adhesion Junctions | |
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| Tight Junctions | |
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| Gap Junctions | |
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| Plasmodesmata | |
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| Key Experiment: The Characterization of Integrin | |
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| Molecular Medicine: Gap Junction Diseases | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| Cell Regulation | |
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| Cell Signaling | |
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| Signaling Molecules and Their Receptors | |
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| Modes of Cell-Cell Signaling | |
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| Steroid Hormones and the Nuclear Receptor Superfamily | |
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| Nitric Oxide and Carbon Monoxide | |
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| Neurotransmitters | |
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| Peptide Hormones and Growth Factors | |
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| Eicosanoids | |
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| Plant Hormones | |
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| Functions of Cell Surface Receptors | |
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| G Protein-Coupled Receptors | |
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| Receptor Protein-Tyrosine Kinases | |
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| Cytokine Receptors and Nonreceptor Protein-Tyrosine Kinases | |
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| Receptors Linked to Other Enzymatic Activities | |
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| Pathways of Intracellular Signal Transduction | |
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| The cAMP Pathway: Second Messengers and Protein Phosphorylation | |
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| Cyclic GMP | |
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| Phospholipids and Ca[superscript 2+] | |
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| The PI 3-Kinase/Akt and mTOR Pathways | |
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| MAP Kinase Pathways | |
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| The JAK/STAT and TGF-[beta]/Smad Pathways | |
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| NF-[kappa]B Signaling | |
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| The Hedgehog, Wnt, and Notch Pathways | |
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| Signal Transduction and the Cytoskeleton | |
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| Integrins and Signal Transduction | |
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| Regulation of the Actin Cytoskeleton | |
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| Signaling Networks | |
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| Feedback and Crosstalk | |
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| Networks of Cellular Signal Transduction | |
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| Key Experiment: The Src Protein-Tyrosine Kinase | |
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| Molecular Medicine: Cancer: Signal Transduction and the ras Oncogenes | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| The Cell Cycle | |
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| The Eukaryotic Cell Cycle | |
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| Phases of the Cell Cycle | |
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| Regulation of the Cell Cycle by Cell Growth and Extracellular Signals | |
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| Cell Cycle Checkpoints | |
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| Restricting DNA Replication to Once per Cell Cycle | |
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| Regulators of Cell Cycle Progression | |
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| Protein Kinases and Cell Cycle Regulation | |
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| Families of Cyclins and Cyclin-Dependent Kinases | |
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| Growth Factors and the Regulation of G[subscript 1] Cdk's | |
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| DNA Damage Checkpoints | |
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| The Events of M Phase | |
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| Stages of Mitosis | |
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| Cdk1/Cyclin B and Progression to Metaphase | |
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| The Spindle Assembly Checkpoint and Progression to Anaphase | |
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| Cytokinesis | |
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| Meiosis and Fertilization | |
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| The Process of Meiosis | |
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| Regulation of Oocyte Meiosis | |
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| Fertilization | |
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| Key Experiment: The Discovery of MPF | |
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| Key Experiment: The Identification of Cyclin | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| Cell Death and Cell Renewal | |
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| Programmed Cell Death | |
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| The Events of Apoptosis | |
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| Caspases: The Executioners of Apoptosis | |
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| Central Regulators of Apoptosis: The Bcl-2 Family | |
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| Signaling Pathways that Regulate Apoptosis | |
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| Stem Cells and the Maintenance of Adult Tissues | |
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| Proliferation of Differentiated Cells | |
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| Stem Cells | |
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| Medical Applications of Adult Stem Cells | |
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| Embryonic Stem Cells and Therapeutic Cloning | |
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| Embryonic Stem Cells | |
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| Somatic Cell Nuclear Transfer | |
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| Key Experiment: Identification of Genes Required for Programmed Cell Death | |
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| Key Experiment: Culture of Embryonic Stem Cells | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| Cancer | |
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| The Development and Causes of Cancer | |
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| Types of Cancer | |
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| The Development of Cancer | |
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| Causes of Cancer | |
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| Properties of Cancer Cells | |
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| Transformation of Cells in Culture | |
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| Tumor Viruses | |
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| Hepatitis B and C Viruses | |
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| SV40 and Polyomavirus | |
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| Papillomaviruses | |
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| Adenoviruses | |
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| Herpesviruses | |
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| Retroviruses | |
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| Oncogenes | |
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| Retroviral Oncogenes | |
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| Proto-Oncogenes | |
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| Oncogenes in Human Cancer | |
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| Functions of Oncogene Products | |
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| Tumor Suppressor Genes | |
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| Identification of Tumor Suppressor Genes | |
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| Functions of Tumor Suppressor Gene Products | |
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| Roles of Oncogenes and Tumor Suppressor Genes in Tumor Development | |
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| Molecular Approaches to Cancer Treatment | |
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| Prevention and Early Detection | |
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| Molecular Diagnosis | |
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| Treatment | |
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| Key Experiment: The Discovery of Proto-Oncogenes | |
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| Molecular Medicine STI-571: Cancer Treatment Targeted against the bcr/abl Oncogene | |
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| Summary and Key Terms | |
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| Questions | |
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| References and Further Reading | |
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| Answers to Questions | |
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| Glossary | |
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| Index | |