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Cover of The Cell

The Cell, 2nd edition

A Molecular Approach

.

Boston University
Sunderland (MA): Sinauer Associates; .
ISBN-10: 0-87893-106-6

Excerpt

As in the first edition, The Cell is focused on the molecular biology of cells as a unifying theme, with specialized topics discussed throughout the book as examples of more general principles. Aspects of developmental biology, the immune system, the nervous system, and plant biology are thus discussed in their broader biological context in chapters covering areas such as genome structure, gene expression, DNA rearrangements, the plasma membrane, cell signaling, and the cell cycle. Relationships between cell biology and medicine are similarly discussed throughout the text, as well as being highlighted in the Molecular Medicine essays that are included as a special feature in each chapter. These discussions illustrate the striking impact of molecular and cellular biology on human health, and are intended to stimulate as well as inform those students interested in medicine.

Contents

  • Acknowledgments
  • Preface
  • Part I. Introduction
    • Chapter 1. An Overview of Cells and Cell Research
      • The Origin and Evolution of Cells
        • The First Cell
        • The Evolution of Metabolism
        • Present-Day Prokaryotes
        • Eukaryotic Cells
        • The Development of Multicellular Organisms
      • Cells As Experimental Models
        • E. coli
        • Yeasts
        • Dictyostelium discoideum
        • Caenorhabditis elegans
        • Drosophila melanogaster
        • Arabidopsis thaliana
        • Vertebrates
      • Tools of Cell Biology
        • Light Microscopy
        • Electron Microscopy
        • Subcellular Fractionation
        • Growth of Animal Cells in Culture
        • Culture of Plant Cells
        • Viruses
      • Summary
        • THE ORIGIN AND EVOLUTION OF CELLS
        • CELLS AS EXPERIMENTAL MODELS
        • TOOLS OF CELL BIOLOGY
      • Questions
      • References and Further Reading
    • Chapter 2. The Chemistry of Cells
      • The Molecular Composition of Cells
        • Carbohydrates
        • Lipids
        • Nucleic Acids
        • Proteins
      • The Central Role of Enzymes as Biological Catalysts
        • The Catalytic Activity of Enzymes
        • Mechanisms of Enzymatic Catalysis
        • Coenzymes
        • Regulation of Enzyme Activity
      • Metabolic Energy
        • Free Energy and ATP
        • The Generation of ATP from Glucose
        • The Derivation of Energy from Other Organic Molecules
        • Photosynthesis
      • The Biosynthesis of Cell Constituents
        • Carbohydrates
        • Lipids
        • Proteins
        • Nucleic Acids
      • Cell Membranes
        • Membrane Lipids
        • Membrane Proteins
        • Transport across Cell Membranes
      • Summary
        • THE MOLECULAR COMPOSITION OF CELLS
        • THE CENTRAL ROLE OF ENZYMES AS BIOLOGICAL CATALYSTS
        • METABOLIC ENERGY
        • THE BIOSYNTHESIS OF CELL CONSTITUENTS
        • CELL MEMBRANES
      • Questions
      • References and Further Reading
    • Chapter 3. Fundamentals of Molecular Biology
      • Heredity, Genes, and DNA
        • Genes and Chromosomes
        • Genes and Enzymes
        • Identification of DNA as the Genetic Material
        • The Structure of DNA
        • Replication of DNA
      • Expression of Genetic Information
        • Colinearity of Genes and Proteins
        • The Role of Messenger RNA
        • The Genetic Code
        • RNA Viruses and Reverse Transcription
      • Recombinant DNA
        • Restriction Endonucleases
        • Generation of Recombinant DNA Molecules
        • Vectors for Recombinant DNA
        • DNA Sequencing
        • Expression of Cloned Genes
        • Amplification of DNA by the Polymerase Chain Reaction
      • Detection of Nucleic Acids and Proteins
        • Nucleic Acid Hybridization
        • Detection of Small Amounts of DNA or RNA by PCR
        • Antibodies as Probes for Proteins
        • Probes for Screening Recombinant DNA Libraries
      • Gene Function in Eukaryotes
        • Genetic Analysis in Yeasts
        • Gene Transfer in Plants and Animals
        • Mutagenesis of Cloned DNAs
        • Introducing Mutations into Cellular Genes
      • Summary
        • HEREDITY, GENES, AND DNA
        • EXPRESSION OF GENETIC INFORMATION
        • RECOMBINANT DNA
        • DETECTION OF NUCLEIC ACIDS AND PROTEINS
        • GENE FUNCTION IN EUKARYOTES
      • Questions
      • References and Further Reading
  • Part II. The Flow of Genetic Information
    • Chapter 4. The Organization of Cellular Genomes
      • The Complexity of Eukaryotic Genomes
        • Introns and Exons
        • Gene Families and Pseudogenes
        • Repetitive DNA Sequences
        • The Number of Genes in Eukaryotic Cells
      • Chromosomes and Chromatin
        • Chromatin
        • Centromeres
        • Telomeres
      • The Sequences of Complete Genomes
        • Prokaryotic Genomes
        • Sequencing the Yeast Genome
        • The Genomes of Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana
      • The Human Genome
        • Human Gene Mapping
        • Physical Mapping of the Human Genome
      • Summary
        • THE COMPLEXITY OF EUKARYOTIC GENOMES
        • CHROMOSOMES AND CHROMATIN
        • THE SEQUENCES OF COMPLETE GENOMES
        • THE HUMAN GENOME
      • Questions
      • References and Further Reading
    • Chapter 5. Replication, Maintenance, and Rearrangements of Genomic DNA
      • DNA Replication
        • DNA Polymerases
        • The Replication Fork
        • The Fidelity of Replication
        • Origins and the Initiation of Replication
        • Telomeres and Telomerase: Replicating the Ends of Chromosomes
      • DNA Repair
        • Direct Reversal of DNA Damage
        • Excision Repair
        • Postreplication Repair
      • Recombination Between Homologous DNA Sequences
        • DNA Molecules Recombine by Breaking and Rejoining
        • Models of Homologous Recombination
        • Enzymes Involved in Homologous Recombination
      • DNA Rearrangements
        • Site-Specific Recombination
        • Transposition via DNA Intermediates
        • Transposition via RNA Intermediates
        • Gene Amplification
      • Summary
        • DNA REPLICATION
        • DNA REPAIR
        • RECOMBINATION BETWEEN HOMOLOGOUS DNA SEQUENCES
        • DNA REARRANGEMENTS
      • Questions
      • References and Further Reading
    • Chapter 6. RNA Synthesis and Processing
      • Transcription in Prokaryotes
        • RNA Polymerase and Transcription
        • Repressors and Negative Control of Transcription
        • Positive Control of Transcription
        • Transcriptional Attenuation
      • Eukaryotic RNA Polymerases and General Transcription Factors
        • Eukaryotic RNA Polymerases
        • General Transcription Factors and Initiation of Transcription by RNA Polymerase II
        • Transcription by RNA Polymerases I and III
      • Regulation of Transcription in Eukaryotes
        • cis-Acting Regulatory Sequences: Promoters and Enhancers
        • Transcriptional Regulatory Proteins
        • Structure and Function of Transcriptional Activators
        • Eukaryotic Repressors
        • Relationship of Chromatin Structure to Transcription
        • DNA Methylation
      • RNA Processing and Turnover
        • Processing of Ribosomal and Transfer RNAs
        • Processing of mRNA in Eukaryotes
        • Splicing Mechanisms
        • Alternative Splicing
        • RNA Editing
        • RNA Degradation
      • Summary
        • TRANSCRIPTION IN PROKARYOTES
        • EUKARYOTIC RNA POLYMERASES AND GENERAL TRANSCRIPTION FACTORS
        • REGULATION OF TRANSCRIPTION IN EUKARYOTES
        • RNA PROCESSING AND TURNOVER
      • Questions
      • References and Further Reading
    • Chapter 7. Protein Synthesis, Processing, and Regulation
      • Translation of mRNA
        • Transfer RNAs
        • The Ribosome
        • The Organization of mRNAs and the Initiation of Translation
        • The Process of Translation
        • Regulation of Translation
      • Protein Folding and Processing
        • Chaperones and Protein Folding
        • Enzymes and Protein Folding
        • Protein Cleavage
        • Glycosylation
        • Attachment of Lipids
      • Regulation of Protein Function
        • Regulation by Small Molecules
        • Protein Phosphorylation
        • Protein-Protein Interactions
      • Protein Degradation
        • The Ubiquitin-Proteasome Pathway
        • Lysosomal Proteolysis
      • Summary
        • TRANSLATION OF mRNA
        • PROTEIN FOLDING AND PROCESSING
        • REGULATION OF PROTEIN FUNCTION
        • PROTEIN DEGRADATION
      • Questions
      • References and Further Reading
  • Part III. Cell Structure and Function
    • Chapter 8. The Nucleus
      • The Nuclear Envelope and Traffic between the Nucleus and Cytoplasm
        • Structure of the Nuclear Envelope
        • The Nuclear Pore Complex
        • Selective Transport of Proteins to and from the Nucleus
        • Regulation of Nuclear Protein Import
        • Transport of RNAs
      • Internal Organization of the Nucleus
        • Chromosomes and Higher-Order Chromatin Structure
        • Functional Domains within the Nucleus
      • The Nucleolus
        • Ribosomal RNA Genes and the Organization of the Nucleolus
        • Transcription and Processing of rRNA
        • Ribosome Assembly
      • The Nucleus during Mitosis
        • Dissolution of the Nuclear Envelope
        • Chromosome Condensation
        • Re-formation of the Interphase Nucleus
      • Summary
        • THE NUCLEAR ENVELOPE AND TRAFFIC BETWEEN THE NUCLEUS AND CYTOPLASM
        • INTERNAL ORGANIZATION OF THE NUCLEUS
        • THE NUCLEOLUS
        • THE NUCLEUS DURING MITOSIS
      • Questions
      • References and Further Reading
    • Chapter 9. Protein Sorting and Transport - The Endoplasmic Reticulum, Golgi Apparatus, and Lysosomes
      • The Endoplasmic Reticulum
        • The Endoplasmic Reticulum and Protein Secretion
        • Targeting Proteins to the Endoplasmic Reticulum
        • Insertion of Proteins into the ER Membrane
        • Protein Folding and Processing in the ER
        • The Smooth ER and Lipid Synthesis
        • Export of Proteins and Lipids from the ER
      • The Golgi Apparatus
        • Organization of the Golgi
        • Protein Glycosylation within the Golgi
        • Lipid and Polysaccharide Metabolism in the Golgi
        • Protein Sorting and Export from the Golgi Apparatus
      • The Mechanism of Vesicular Transport
        • Experimental Approaches to Understanding Vesicular Transport
        • Coat Proteins and Vesicle Budding
        • Vesicle Fusion
      • Lysosomes
        • Lysosomal Acid Hydrolases
        • Endocytosis and Lysosome Formation
        • Phagocytosis and Autophagy
      • Summary
        • THE ENDOPLASMIC RETICULUM
        • THE GOLGI APPARATUS
        • THE MECHANISM OF VESICULAR TRANSPORT
        • LYSOSOMES
      • Questions
      • References and Further Reading
    • Chapter 10. Bioenergetics and Metabolism - Mitochondria, Chloroplasts, and Peroxisomes
      • Mitochondria
        • Organization and Function of Mitochondria
        • The Genetic System of Mitochondria
        • Protein Import and Mitochondrial Assembly
      • The Mechanism of Oxidative Phosphorylation
        • The Electron Transport Chain
        • Chemiosmotic Coupling
        • Transport of Metabolites across the Inner Membrane
      • Chloroplasts and Other Plastids
        • The Structure and Function of Chloroplasts
        • The Chloroplast Genome
        • Import and Sorting of Chloroplast Proteins
        • Other Plastids
      • Photosynthesis
        • Electron Flow through Photosystems I and II
        • Cyclic Electron Flow
        • ATP Synthesis
      • Peroxisomes
        • Functions of Peroxisomes
        • Peroxisome Assembly
      • Summary
        • MITOCHONDRIA
        • THE MECHANISM OF OXIDATIVE PHOSPHORYLATION
        • CHLOROPLASTS AND OTHER PLASTIDS
        • PHOTOSYNTHESIS
        • PEROXISOMES
      • Questions
      • References and Further Reading
    • Chapter 11. The Cytoskeleton and Cell Movement
      • Structure and Organization of Actin Filaments
        • Assembly and Disassembly of Actin Filaments
        • Organization of Actin Filaments
        • Association of Actin Filaments with the Plasma Membrane
        • Protrusions of the Cell Surface
      • Actin, Myosin, and Cell Movement
        • Muscle Contraction
        • Contractile Assemblies of Actin and Myosin in Nonmuscle Cells
        • Unconventional Myosins
        • Cell Crawling
      • Intermediate Filaments
        • Intermediate Filament Proteins
        • Assembly of Intermediate Filaments
        • Intracellular Organization of Intermediate Filaments
        • Functions of Keratins and Neurofilaments: Diseases of the Skin and Nervous System
      • Microtubules
        • Structure, Assembly, and Dynamic Instability of Microtubules
        • The Centrosome and Microtubule Organization
        • Reorganization of Microtubules during Mitosis
        • Stabilization of Microtubules and Cell Polarity
      • Microtubule Motors and Movements
        • Identification of Microtubule Motor Proteins
        • Organelle Transport and Intracellular Organization
        • Separation of Mitotic Chromosomes
        • Cilia and Flagella
      • Summary
        • STRUCTURE AND ORGANIZATION OF ACTIN FILAMENTS
        • ACTIN, MYOSIN, AND CELL MOVEMENT
        • INTERMEDIATE FILAMENTS
        • MICROTUBULES
        • MICROTUBULE MOTORS AND MOVEMENTS
      • Questions
      • References and Further Reading
    • Chapter 12. The Cell Surface
      • Structure of the Plasma Membrane
        • The Phospholipid Bilayer
        • Membrane Proteins
        • Mobility of Membrane Proteins
        • The Glycocalyx
      • Transport of Small Molecules
        • Passive Diffusion
        • Facilitated Diffusion and Carrier Proteins
        • Ion Channels
        • Active Transport Driven by ATP Hydrolysis
        • Active Transport Driven by Ion Gradients
      • Endocytosis
        • Phagocytosis
        • Receptor-Mediated Endocytosis
        • Protein Trafficking in Endocytosis
      • Cell Walls and the Extracellular Matrix
        • Bacterial Cell Walls
        • Plant Cell Walls
        • The Extracellular Matrix
      • Cell-Cell Interactions
        • Cell Adhesion Proteins
        • Tight Junctions
        • Gap Junctions
        • Plant Cell Adhesion and Plasmodesmata
      • Summary
        • STRUCTURE OF THE PLASMA MEMBRANE
        • TRANSPORT OF SMALL MOLECULES
        • ENDOCYTOSIS
        • CELL WALLS AND THE EXTRACELLULAR MATRIX
        • CELL-CELL INTERACTIONS
      • Questions
      • References and Further Reading
  • Part IV. Cell Regulation
    • Chapter 13. Cell Signaling
      • Signaling Molecules and Their Receptors
        • Modes of Cell-Cell Signaling
        • Steroid Hormones and the Steroid Receptor Superfamily
        • Nitric Oxide and Carbon Monoxide
        • Neurotransmitters
        • Peptide Hormones and Growth Factors
        • Eicosanoids
        • Plant Hormones
      • Functions of Cell Surface Receptors
        • G Protein-Coupled Receptors
        • Receptor Protein-Tyrosine Kinases
        • Cytokine Receptors and Nonreceptor Protein-Tyrosine Kinases
        • Receptors Linked to Other Enzymatic Activities
      • Pathways of Intracellular Signal Transduction
        • The cAMP Pathway: Second Messengers and Protein Phosphorylation
        • Cyclic GMP
        • Phospholipids and Ca2+
        • Ras, Raf, and the MAP Kinase Pathway
        • The JAK/STAT Pathway
      • Signal Transduction and the Cytoskeleton
        • Integrins and Signal Transduction
        • Regulation of the Actin Cytoskeleton
      • Signaling in Development and Differentiation
        • The Receptor Tyrosine Kinase/Ras/MAP Kinase Pathway in Drosophila and C. elegans
        • Hedgehog and Wingless
        • Notch Signaling
      • Regulation of Programmed Cell Death
        • Caspases and Apoptosis
        • Cell Death Receptors and Caspase Activation
        • Signaling Cell Survival
      • Summary
        • SIGNALING MOLECULES AND THEIR RECEPTORS
        • FUNCTIONS OF CELL SURFACE RECEPTORS
        • PATHWAYS OF INTRACELLULAR SIGNAL TRANSDUCTION
        • SIGNAL TRANSDUCTION AND THE CYTOSKELETON
        • SIGNALING IN DEVELOPMENT AND DIFFERENTIATION
        • REGULATION OF PROGRAMMED CELL DEATH
      • Questions
      • References and Further Reading
    • Chapter 14. The Cell Cycle
      • The Eukaryotic Cell Cycle
        • Phases of the Cell Cycle
        • Regulation of the Cell Cycle by Cell Growth and Extracellular Signals
        • Cell Cycle Checkpoints
        • Coupling of S Phase to M Phase
      • Regulators of Cell Cycle Progression
        • MPF: A Dimer of Cdc2 and Cyclin
        • Families of Cyclins and Cyclin-Dependent Kinases
        • Growth Factors and the D-Type Cyclins
        • Inhibitors of Cell Cycle Progression
      • The Events of M Phase
        • Stages of Mitosis
        • MPF and Progression to Metaphase
        • Proteolysis and the Inactivation of MPF: Anaphase and Telophase
        • Cytokinesis
      • Meiosis and Fertilization
        • The Process of Meiosis
        • Regulation of Oocyte Meiosis
        • Fertilization
      • Cell Proliferation in Development and Differentiation
        • Proliferation of Differentiated Cells
        • Stem Cells
      • Summary
        • THE EUKARYOTIC CELL CYCLE
        • REGULATORS OF CELL CYCLE PROGRESSION
        • THE EVENTS OF M PHASE
        • MEIOSIS AND FERTILIZATION
        • CELL PROLIFERATION IN DEVELOPMENT AND DIFFERENTIATION
      • Questions
      • References and Further Reading
    • Chapter 15. Cancer
      • The Development and Causes of Cancer
        • Types of Cancer
        • The Development of Cancer
        • Causes of Cancer
        • Properties of Cancer Cells
        • Transformation of Cells in Culture
      • Tumor Viruses
        • Hepatitis B Viruses
        • SV40 and Polyomavirus
        • Papillomaviruses
        • Adenoviruses
        • Herpesviruses
        • Retroviruses
      • Oncogenes
        • Retroviral Oncogenes
        • Proto-Oncogenes
        • Oncogenes in Human Cancer
        • Functions of Oncogene Products
      • Tumor Suppressor Genes
        • Identification of Tumor Suppressor Genes
        • Functions of Tumor Suppressor Gene Products
        • Roles of Oncogenes and Tumor Suppressor Genes in Tumor Development
      • Applications of Molecular Biology to Cancer Prevention and Treatment
        • Prevention and Early Detection
        • Molecular Diagnosis
        • Treatment
      • Summary
        • THE DEVELOPMENT AND CAUSES OF CANCER
        • TUMOR VIRUSES
        • ONCOGENES
        • TUMOR SUPPRESSOR GENES
        • APPLICATIONS OF MOLECULAR BIOLOGY TO CANCER PREVENTION AND TREATMENT
      • Questions
      • References and Further Reading
  • Glossary

By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed.

Copyright © 2000, Geoffrey M Cooper.
Bookshelf ID: NBK9839

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