Preface |
Organization and Features of The Cell |
Media and Supplements to Accompany The Cell |
Introduction / Part I: |
An Overview of Cells and Cell Research / 1: |
The Origin and Evolution of Cells |
The First Cell |
The Evolution of Metabolism |
Present-Day Prokaryotes |
Eukaryotic Cells |
The Origin of Eukaryotes |
The Development of Multicellular Organisms |
Cells as Experimental Models |
E. coli |
Yeasts |
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 |
Key Experiment: Animal Cell Culture |
Molecular Medicine: Viruses and Cancer |
Summary and Key Terms |
Questions |
References and Further Reading |
The Composition of Cells / 2: |
The Molecules of Cells |
Carbohydrates |
Lipids |
Nucleic Acids |
Proteins |
Cell Membranes |
Membrane Lipids |
Membrane Proteins |
Transport across Cell Membranes |
Proteomics: Large-Scale Analysis of Cell Proteins |
Identification of Cell Proteins |
Global Analysis of Protein Localization |
Protein Interactions |
Key Experiment: The Folding of Polypeptide Chains |
Key Experiment: The Structure of Cell Membranes |
Cell Metabolism / 3: |
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 |
Key Experiment: Antimetabolites and Chemotherapy |
Molecular Medicine: Phenylketonuria |
Fundamentals of Molecular Biology / 4: |
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 |
Detection of Nucleic Acids and Proteins |
Amplification of DNA by the Polymerase Chain Reaction |
Nucleic Acid Hybridization |
Antibodies as Probes for Proteins |
Gene Function in Eukaryotes |
Genetic Analysis in Yeasts |
Gene Transfer in Plants and Animals |
Mutagenesis of Cloned DNAs |
Introducing Mutations into Cellular Genes |
Interfering with Cellular Gene Expression |
Key Experiment: The DNA Provirus Hypothesis |
Molecular Medicine: HIV and AIDS |
The Flow of Genetic Information / Part II: |
The Organization and Sequences of Cellular Genomes / 5: |
The Complexity of Eukaryotic Genomes |
Introns and Exons |
Repetitive DNA Sequences |
Gene Duplication and Pseudogenes |
The Composition of Higher Eukaryotic Genomes |
Chromosomes and Chromatin |
Chromatin |
Centromeres |
Telomeres |
The Sequences of Complete Genomes |
Prokaryotic Genomes |
The Yeast Genome |
The Genomes of Caenorhabditis elegans and Drosophila melanogaster |
Plant Genomes |
The Human Genome |
The Genomes of Other Vertebrates |
Bioinformatics and Systems Biology |
Systematic Screens of Gene Function |
Regulation of Gene Expression |
Variation among Individuals and Genomic Medicine |
Key Experiment: The Discovery of Introns |
Key Experiment: The Human Genome |
Replication, Maintenance, and Rearrangements of Genomic DNA / 6: |
DNA Replication |
DNA Polymerases |
The Replication Fork |
The Fidelity of Replication |
Origins and the Initiation of Replication |
Telomeres and Telomerase: Maintaining the Ends of Chromosomes |
DNA Repair |
Direct Reversal of DNA Damage |
Excision Repair |
Translesion DNA Synthesis |
Recombinational Repair |
Recombination between Homologous DNA Sequences |
Models of Homologous Recombination |
Enzymes Involved in Homologous Recombination |
DNA Rearrangements |
Site-Specific Recombination |
Transposition via DNA Intermediates |
Transposition via RNA Intermediates |
Gene Amplification |
Key Experiment: Rearrangement of Immunoglobulin Genes |
Molecular Medicine: Colon Cancer and DNA Repair |
RNA Synthesis and Processing / 7: |
Transcription in Prokaryotes |
RNA Polymerase and Transcription |
Repressors and Negative Control of Transcription |
Positive Control of Transcription |
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 |
Transcription Factor Binding Sites |
Transcriptional Regulatory Proteins |
Structure and Function of Transcriptional Activators |
Eukaryotic Repressors |
Relationship of Chromatin Structure to Transcription |
Regulation of Transcription by Noncoding RNAs |
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 |
Key Experiment: Isolation of a Eukaryotic Transcription Factor |
Key Experiment: The Discovery of snRNPs |
Protein Synthesis, Processing, and Regulation / 8: |
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 that Catalyze 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 |
Key Experiment: Catalytic Role of Ribosomal RNA |
Molecular Medicine: Antibiotic Resistance and the Ribosome |
Cell Structure and Function / Part III: |
The Nucleus / 9: |
The Nuclear Envelope and Traffic between the Nucleus and the 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 |
Sub-Compartments within the Nucleus |
The Nucleolus and rRNA Processing |
Ribosomal RNA Genes and the Organization of the Nucleolus |
Transcription and Processing of rRNA |
Ribosome Assembly |
Key Experiment: Nuclear Lamina Diseases |
Molecular Medicine: Identification of Nuclear Localization Signals |
Protein Sorting and Transport: The Endoplasmic Reticulum, Golgi Apparatus, and Lysosomes / 10: |
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 |
Quality Control 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 |
Cargo Selection, Coat Proteins, and Vesicle Budding |
Vesicle Fusion |
Lysosomes |
Lysosomal Acid Hydrolases |
Endocytosis and Lysosome Formation |
Phagocytosis and Autophagy |
Key Experiment: The Signal Hypothesis |
Molecular Medicine: Gaucher Disease |
Bioenergetics and Metabolism: Mitochondria, Chloroplasts, and Peroxisomes / 11: |
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 |
Electron Flow through Photosystems I and II |
Cyclic Electron Flow |
ATP Synthesis |
Peroxisomes |
Functions of Peroxisomes |
Peroxisome Assembly |
Key Experiment: The Chemiosmotic Theory |
Molecular Medicine: Diseases of Mitochondria: Leber's Hereditary Optic Neuropathy |
The Cytoskeleton and Cell Movement / 12: |
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 |
Nonmuscle Myosins |
Formation of Protrusions and Cell Movement |
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 and Dynamic Organization of Microtubules |
Assembly of Microtubules |
Organization of Microtubules within Cells |
Microtubule Motors and Movement |
Identification of Microtubule Motor Proteins |
Cargo Transport and Intracellular Organization |
Cilia and Flagella |
Reorganization of Microtubules during Mitosis |
Chromosome Movement |
Key Experiment: Expression of Mutant Keratin Causes Abnormal Skin Development |
Key Experiment The Isolation of Kinesin |
The Plasma Membrane / 13: |
Structure of the Plasma Membrane |
The Phospholipid Bilayer |
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 |
Key Experiment: The LDL Receptor |
Molecular Medicine: Cystic Fibrosis |
Cell Walls, the Extracellular Matrix, and Cell Interactions / 14: |
Cell Wall |
Bacterial Cell Walls |
Eukaryotic Cell Walls |
The Extracellular Matrix and Cell-Matrix Interactions |
Matrix Structural Proteins |
Matrix Polysaccharides |
Matrix Adhesion Proteins |
Cell-Matrix Interactions |
Cell-Cell Interactions |
Adhesion Junctions |
Tight Junctions |
Gap Junctions |
Plasmodesmata |
Key Experiment: The Characterization of Integrin |
Molecular Medicine: Gap Junction Diseases |
Cell Regulation / Part IV: |
Cell Signaling / 15: |
Signaling Molecules and Their Receptors |
Modes of Cell-Cell Signaling |
Steroid Hormones and the Nuclear 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 Ca[superscript 2+] |
The PI 3-Kinase/Akt and mTOR Pathways |
MAP Kinase Pathways |
The JAK/STAT and TGF-[beta]/Smad Pathways |
NF-[kappa]B Signaling |
The Hedgehog, Wnt, and Notch Pathways |
Signal Transduction and the Cytoskeleton |
Integrins and Signal Transduction |
Regulation of the Actin Cytoskeleton |
Signaling Networks |
Feedback and Crosstalk |
Networks of Cellular Signal Transduction |
Key Experiment: The Src Protein-Tyrosine Kinase |
Molecular Medicine: Cancer: Signal Transduction and the ras Oncogenes |
The Cell Cycle / 16: |
The Eukaryotic Cell Cycle |
Phases of the Cell Cycle |
Regulation of the Cell Cycle by Cell Growth and Extracellular Signals |
Cell Cycle Checkpoints |
Restricting DNA Replication to Once per Cell Cycle |
Regulators of Cell Cycle Progression |
Protein Kinases and Cell Cycle Regulation |
Families of Cyclins and Cyclin-Dependent Kinases |
Growth Factors and the Regulation of G[subscript 1] Cdk's |
DNA Damage Checkpoints |
The Events of M Phase |
Stages of Mitosis |
Cdk1/Cyclin B and Progression to Metaphase |
The Spindle Assembly Checkpoint and Progression to Anaphase |
Cytokinesis |
Meiosis and Fertilization |
The Process of Meiosis |
Regulation of Oocyte Meiosis |
Fertilization |
Key Experiment: The Discovery of MPF |
Key Experiment: The Identification of Cyclin |
Cell Death and Cell Renewal / 17: |
Programmed Cell Death |
The Events of Apoptosis |
Caspases: The Executioners of Apoptosis |
Central Regulators of Apoptosis: The Bcl-2 Family |
Signaling Pathways that Regulate Apoptosis |
Stem Cells and the Maintenance of Adult Tissues |
Proliferation of Differentiated Cells |
Stem Cells |
Medical Applications of Adult Stem Cells |
Embryonic Stem Cells and Therapeutic Cloning |
Embryonic Stem Cells |
Somatic Cell Nuclear Transfer |
Key Experiment: Identification of Genes Required for Programmed Cell Death |
Key Experiment: Culture of Embryonic Stem Cells |
Cancer / 18: |
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 and C 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 |
Molecular Approaches to Cancer Treatment |
Prevention and Early Detection |
Molecular Diagnosis |
Treatment |
Key Experiment: The Discovery of Proto-Oncogenes |
Molecular Medicine STI-571: Cancer Treatment Targeted against the bcr/abl Oncogene |
Answers to Questions |
Glossary |
Index |