Table of Contents

1. Introduction to the Study of Cell Biology.1.1 The Discovery of Cells.1.2 Basic Properties of Cells.Cells are Highly Complex and Organized.Cells Possess a Genetic Program and the Means to Use It.Cells Are Capable of Producing More of Themselves.Cells Acquire and Utilize Energy.Cells Carry Out a Variety of Chemical Reactions.Cells Engage in Numerous Mechanical Activities.Cells Are Able to Respond to Stimuli.Cells Are Capable to Self-Regulation 61.3 Two Fundamentally Different Classes of Cells.Characteristics That Distinguish Prokaryotic and Eukaryotic Cells.Types of Prokaryotic Cells.Types of Eukaryotic Cells: Cell Specialization.THE HUMAN PERSPECTIVE: THE PROSPECT FOR CELL REPLACEMENT THERAPY.The Sizes of Cells and Their Components.1.4 Viruses.Viroids.EXPERIMENTAL PATHWAYS: THE ORIGIN OF EUKARYOTIC CELLS.2 The Chemical Basis of Life.2.1 Covalent Bonds.Polar and Nonpolar Molecules.Ionization.THE HUMAN PERSPECTIVE: FREE RADICALS AS A CAUSE OF AGING.2.2 Noncovalent Bonds.Ionic Bonds: Attractions Between Charged Atoms.Hydrogen Bonds.Hydrophobic Interactions and van der Waals Forces.The Life-Supporting Properties of Water.2.3 Acids, Bases, and Buffers.2.4 The Nature of Biological Molecules.Functional Groups.A Classification of Biological Molecules by Function.2.5 Four Types of Biological Molecules.Carbohydrates.Lipids.Proteins.THE HUMAN PERSPECTIVE: PROTEIN FOLDING CAN HAVE DEADLY CONSEQUENCES.Nucleic Acids.2.6 The Formation of Complex Macromolecular Structures.The Assembly of Tobacco Mosaic Virus Particles and Ribosomal Subunits.EXPERIMENTAL PATHWAYS: CHAPERONES: HELPING PROTEINS REACH THEIR PROPER FOLDED STATE.3 Bioenergetics, Enzymes, and Metabolism.3.1 Bioenergetics.The Laws of Thermodynamics and the Concept of Entropy.Free Energy.3.2 Enzymes as Biological Catalysts.The Properties of Enzymes.Overcoming the Activation Energy Barrier.The Active Site and Molecular Specificity.Mechanisms of Enzyme Catalysis.Enzyme Kinetics.THE HUMAN PERSPECTIVE: THE GROWING PROBLEM OF ANTIBIOTIC RESISTANCE.3.3 Metabolism.An Overview of Metabolism.Oxidation and Reduction: A Matter of Electrons.The Capture and Utilization of Energy.Metabolic Regulation.4 The Structure of Function of the Plasma Membrane.4.1 An Overview of Membrane Functions.4.2 A Brief History of Studies on Plasma Membrane Structure.4.3 The Chemical Composition of Membranes.Membrane Lipids.Membrane Carbohydrates.4.4 The Structures and Functions of Membrane Proteins.Integral Membrane Proteins.Studying the Structure and Properties of Integral Membrane Proteins.Peripheral Membrane Proteins.Lipid-Anchored Membrane Proteins.4.5 Membrane Lipids and Membrane Fluidity.The Importance of Membrane Fluidity.Maintaining Membrane Fluidity.The Asymmetry of Membrane Lipids.Lipid Rafts.4.6 The Dynamic Nature of the Plasma Membrane.The Diffusion of Membrane Proteins after Cell Fusion.Restrictions on Protein and Lipid Mobility.The Red Blood Cell: An Example of Plasma Membrane Structure.4.7 The Movement of Substances Across Cell Membranes.The Energetics of Solute Movement.Diffusion of Substances through Membranes.Facilitated Diffusion.Active Transport.THE HUMAN PERSPECTIVE: DEFECTS IN ION CHANNELS AS A CAUSE OF INHERITED DISEASE.4.8 Membrane Potentials and Nerve Impulses.The Resting Potential.The Action Potential.Propagation of Action Potentials as an Impulse.Neurotransmission: Jumping the Synaptic Cleft.- EXPERIMENTAL PATHWAYS: THE ACETYLCHOLINE RECEPTOR.5 Aerobic Respiration and the Mitochondrion.5.1 Mitochondrial Structure and Function.Mitochondrial Membranes.The Mitochondrial Matrix.5.2 Oxidative Metabolism in the Mitochondrion.The Tricarboxylic Acid (TCA) Cycle.The Importance of Reduced Coenzymes in the Formation of ATP.THE HUMAN PERSPECTIVE: THE ROLE OF ANAEROBIC AND AEROBIC METABOLISMIN EXERCISE.5.3 The Role of Mitochondria in the Formation of ATP.Oxidation-Reduction Potentials.Electron Transport.Types of Electron Carriers.5.4 Translocation of Protons and the Establishment of a Proton-motive Force.5.5 The Machinery for ATP Formation.The Structure of ATP Synthase.The Basis of ATP Formation According to the Binding Change Mechanism.Other Roles for the Proton-motive Force in Addition to ATP Synthesis.5.6 Peroxisomes.THE HUMAN PERSPECTIVE: DISEASES THAT RESULT FROM ABNORMAL MITOCHRONDRIAL OR PEROXISOMAL FUNCTION.6 Photosynthesis and the Chloroplast.6.1 Chloroplast Structure and Function.6.2 An Overview of Photosynthetic Metabolism.6.3 The Absorption of Light.Photosynthetic Pigments.6.4 Photosynthetic Units and Reaction Centers.Oxygen Formation: Coordinating the Action of Two Different Photosynthetic Systems.Killing Weeds by Inhibiting Electron Transport.6.5 Photophosphorylation.Noncyclic Versus Cyclic Photophosphorylation.6.6 Carbon Dioxide Fixation and the Synthesis of Carbohydrate.Carbohydrate Synthesis in C3 Plants.Carbohydrate Synthesis in C4 Plants.Carbohydrate Synthesis in CAM Plants.7 Interactions Between Cells and Their Environment.7.1 The Extracellular Space.The Extracellular Matrix.7.2 Interactions of Cells with Extracellular Materials.Integrins.Focal Adhesions and Hemidesmosomes: Anchoring Cells to Their Substratum.7.3 Interactions of Cells with Other Cells.Selectins.Immunoglobulins and Integrins.Cadherins.THE HUMAN PERSPECTIVE: THE ROLE OF CELL ADHESION IN INFLAMMATIONAND METASTASIS.Adherens Junctions and Desmosomes: Anchoring Cells to Other Cells.The Role of Cell-Adhesion Receptors in Transmembrane Signaling.7.4 Tight Junctions: Sealing the Extracellular Space.7.5 Gap Junctions and Plasmodesmata: Mediating Intercellular Communication.Plasmodesmata.7.6 Cell Walls.8 Cytoplasmic Membrane Systems: Structure, Function, and Membrane Trafficking.8.1 An Overview of the Endomembrane System.8.2 A Few Approaches to the Study of Endomembranes.Insights Gained from Autoradiography.Insights Gained from the Use of the Green Fluorescent Protein.Insights Gained from the Biochemical Analysis of Subcellular Fractions.Insights Gained from the Use of Cell-Free Systems.Insights Gained from the Study of Genetic Mutants.8.3 The Endoplasmic Reticulum.The Smooth Endoplasmic Reticulum.Functions of the Rough Endoplasmic Reticulum.From the ER to the Golgi Complex: The First Step in Vesicular Transport.8.4 The Golgi Complex.Glycosylation in the Golgi Complex.The Movement of Materials Through the Golgi Complex.8.5 Types of Vesicle Transport and Their Functions.COPII-Coated Vesicles: Transporting Cargo from the ER to the Golgi Complex.COPI-Coated Vesicles: Transporting Escaped Proteins Back to the ER.Beyond the Golgi Complex: Sorting Proteins at the TGN.Targeting Vesicles to a Particular Compartment.8.6 Lysosomes.THE HUMAN PERSPECTIVE: DISORDERS RESULTING FROM DEFECTSIN LYSOSOMAL FUNCTION.8.7 Plant Cell Vacuoles.Endocytosis.8.8 The Endocytic Pathway: Moving Membrane and Materials into the Cell Interior.Phagocytosis.8.9 Posttranslational Uptake of Proteins by Peroxisomes, Mitochondria,and Chloroplasts.Uptake of Proteins into Peroxisomes.Uptake of Proteins into Mitochondrial.Uptake of Proteins into Chloroplasts.EXPERIMENTAL PATHWAYS: RECEPTOR-MEDIATED ENDOCYTOSIS.9 The Cytoskeleton and Cell Motility.9.1 Overview of the Major Functions of the Cytoskeleton.9.2 The Study of the Cytoskeleton.The Use of Fluorescence Microscopy.The Use of Video Microscopy and Laser Beams for In Vitro Motility Assays.The Use of Cells with Altered Gene Expression.9.3 Microtubules.Structure and Composition.Microtubule-Associated Proteins.Microtubules as Structural Supports and Organizers.Microtubules as Agents of Intracellular Motility.Motor Proteins That Traverse the Microtubular Cytoskeleton.Microtubule-Organizing Centers (MTOCs).The Dynamic Properties of Microtubules.THE HUMAN PERSPECTIVE: THE ROLE OF CILIA IN DEVELOPMENT AND DISEASE.Cilia and Flagella: Structure and Function.The Structure of Cilia and Flagella.9.4 Intermediate Filaments.Intermediate Filament Assembly and Disassembly.Types and Functions of Intermediate Filaments.9.5 Microfilaments.Microfilament Assembly and Disassembly.Myosin: The Molecular Motor for Actin Filaments.9.6 Muscle Contractility.The Sliding Filament Model of Muscle Contraction.9.7 Nonmuscle Motility.Actin-Binding Proteins.Examples of Nonmuscle Motility and Contractility.10 The Nature of the Gene and the Genome.10.1 The Concept of a Gene as a Unit of Inheritance.10.2 Chromosomes: The Physical Carriers of the Genes.The Discovery of Chromosomes.Chromosomes as the Carriers of Genetic Information.Genetic Analysis in Drosophila.Crossing Over and Recombination.Mutagenesis and Giant Chromosomes.10.3 The Chemical Nature of the Gene.The Structure of DNA.The Watson-Crick Proposal.10.4 The Structure of the Genome.The Complexity of the Genome.THE HUMAN PERSPECTIVE: DISEASES THAT RESULT FROM EXPANSION OFTRINUCLEOTIDE REPEATS.10.5 The Stability of the Genome.Whole-Genome Duplication (Polyploidization).Duplication and Modification of DNA Sequences."Jumping Genes" and the Dynamic Nature of the Genome.10.6 Sequencing Genomes: The Genetic Basis of Being Human.Comparative Genomics: "If It's Conserved, It Must Be Important.THE HUMAN PERSPECTIVE: APPLICATION OF GENOMIC ANALYSES TO MEDICINE.EXPERIMENTAL PATHWAYS: THE CHEMICAL NATURE OF THE GENE.11 Expression of Genetic Material: From Transcription to Translation.11.1 The Relationship Between Genes and Proteins.An Overview of the Flow of Information Through the Cell.11.2 An Overview of Transcription in Both Prokaryotic and Eukaryotic Cells.Transcription in Prokaryotes.Transcription and RNA Processing in Eukaryotic Cells.11.3 Synthesis and Processing of Ribosomal and Transfer RNAs.Synthesizing the rRNA Precursor.Processing the rRNA Precursor.Synthesis and Processing of the 5S rRNA.Transfer RNAs.11.4 Synthesis and Processing of Messenger RNAs.The Machinery for mRNA Transcription.Split Genes: An Unexpected Finding.The Processing of Eukaryotic Messenger RNAs.Evolutionary Implications of Split Genes and RNA Splicing.Creating New Ribozymes in the Laboratory.11.5 Small Noncoding RNAs and RNA Interference.MicroRNAs: Hundreds of RNAs of Unknown Function.THE HUMAN PERSPECTIVE: POTENTIAL CLINICAL APPLICATIONSOF RNA INTERFERENCE.11.6 Encoding Genetic Information.The Properties of the Genetic Code.11.7 Decoding the Codons: The Role of Transfer RNAs.The Structure of tRNAs.11.8 Translating Genetic Information.Initiation.Elongation.Termination.mRNA Surveillance: No Nonsense Allowed.EXPERIMENTAL PATHWAYS: THE ROLE OF RNA AS A CATALYST.12 The Cell Nucleus and the Control of Gene Expression.12.1 The Nucleus of a Eukaryotic Cell.The Nuclear Envelope.Chromosomes and Chromatin.THE HUMAN PERSPECTIVE: CHROMOSOMAL ABERRATIONS.Epigenetics: There's More to Inheritance than DNA Sequence.The Nucleus as an Organized Organelle.12.2 Control of Gene Expression in Prokaryotes.The Bacterial Operon.12.3 Control of Gene Expression in Eukaryotes.12.4 Transcriptional-Level Control.The Role of Transcription Factors in Regulating Gene Expression.The Structure of Transcription Factors.DNA Sites Involved in Regulating Transcription.Transcriptional Activation: The Role of Enhancers, Promoters, and Coactivators.Transcriptional Repression.12.5 Processing-Level Control.12.6 Translational-Level Control.Cytoplasmic Localization of mRNAs.The Control of mRNA Translation.The Control of mRNA Stability.12.7 Postranslational Control: Determining Protein Stability.13 DNA Replication and Repair.13.1 DNA Replication.Semiconservative Replication.Replication in Bacterial Cells.The Structure and Functions of DNA Polymerases.Replication in Eukaryotic Cells.13.2 DNA Repair.Nucleotide Excision Repair.Base Excision Repair.Mismatch Repair.Double-Strand Breakage Repair.THE HUMAN PERSPECTIVE: THE CONSEQUENCES OF DNA REPAIR DEFICIENCIES.13.3 Between Replication and Repair.14 Cellular Reproduction.14.1 The Cell Cycle.Cell Cycles in Vivo.Control of the Cell Cycle.14.2 M Phase: Mitosis and Cytokinesis.Prophase.Prometaphase.Metaphase.Anaphase.Telophase.Forces Required for Mitotic Movements.Cytokinesis.14.3 Meiosis.The Stages of Meiosis.THE HUMAN PERSPECTIVE: MEIOTIC NONDISJUNCTION AND ITS CONSEQUENCES.Genetic Recombination During Meiosis.EXPERIMENTAL PATHWAYS: THE DISCOVERY AND CHARACTERIZATION OF MPF.15 Cell Signaling and Signal Transduction: Communication Between Cells.15.1 The Basic Elements of Cell Signaling Systems.15.2 A Survey of Extracellular Messengers and Their Receptors.15.3 G Protein-Coupled Receptors and Their Second Messengers.Signal Transduction by G Protein-Coupled Receptors.THE HUMAN PERSPECTIVE: DISORDERS ASSOCIATED WITH G PROTEIN-COUPLEDRECEPTORS.The Discovery of a Second Messenger: Cyclic AMP.Lipid-Derived Second Messengers.The Specificity of G Protein-Coupled Responses.Regulation of Blood Glucose Levels.The Role of GPCRs in Sensory Perception.15.4 Protein-Tyrosine Phosphorylation as a Mechanism for Signal Transduction.The Ras-MAP Kinase Pathway.Signaling by the Insulin Receptor.Signaling Pathways in Plants.15.5 The Role of Calcium as an Intracellular Messenger.Regulating Calcium Concentrations in Plant Cells.15.6 Convergence, Divergence, and Crosstalk Among Different Signaling Pathways.Examples of Convergence, Divergence, and Crosstalk Among Signaling Pathways.15.7 The Role of NO as an Intercellular Messenger.15.8 Apoptosis (Programmed Cell Death).The Extensive Pathway of Apoptosis.The Intrinsic Pathway of Apoptosis.16 Cancer.16.1 Basic Properties of a Cancer Cell.16.2 The Causes of Cancer.16.3 The Genetics of Cancer.Tumor-Suppressor Genes and Oncogenes: Brakes and Accelerators.16.4 New Strategies for Combating Cancer.Immunotherapy.Gene Therapy.Inhibiting the Activity of Cancer-Promoting Proteins.Inhibiting the Formation of New Blood Vessels (Angiogenesis).EXPERIMENTAL PATHWAYS: THE DISCOVERY OF ONCOGENES.17 The Immune Response.17.1 An Overview of the Immune Response.Innate Immune Responses.Adaptive Immune Responses.17.2 The Clonal Selection Theory as It Applies to B Cells.Vaccination.17.3 T Lymphocytes: Activation and Mechanism of Action.17.4 Selected Topics on the Cellular and Molecular Basis of Immunity.The Molecular Structure of Antibodies.DNA Rearrangement of Genes Encoding B- and T-Cell Antigen Receptors.Membrane-Bound Antigen Receptor Complexes.The Major Histocompatibility Complex.Distinguishing Self from Nonself.Lymphocytes Are Activated by Cell-Surface Signals.Signal Transduction Pathways Used in Lymphocyte Activation.THE HUMAN PERSPECTIVE: AUTOIMMUNE DISEASES.EXPERIMENTAL PATHWAYS: THE ROLEOF THE MAJOR HISTOCOMPATIBILITYCOMPLEX IN ANTIGEN PRESENTATION.18 Techniques in Cell and Molecular Biology.18.1 The Light Microscope.Resolution.Visibility.Phase-Contrast Microscopy.Fluorescence Microscopy (and Related Fluorescence-Based Techniques).Video Microscopy and Image Processing.Confocal Scanning Light Microscopy.Preparation of Specimens for Light Microscopy.18.2 Transmission Electron Microscopy.Specimen Preparation for Electron Microscopy.18.3 Scanning Electron Microscopy.18.4 The Use of Radioisotopes.18.5 Cell Culture.18.6 The Fractionation of a Cell's Contents by Differential Centrifugation.18.7 Isolation, Purification, and Fractionation of Proteins.Selective Precipitation.Liquid Column Chromatography.Polyacrylamide Gel Electrophoresis.18.8 Determination of Protein Structure.18.9 Purification and Fractionation of Nucleic Acids.Separation of DNAs by Gel Electrophoresis.18.10 Measurement of Protein and Nucleic Acid Concentration.18.11 Ultracentrifugation.Sedimentation Behavior of Nucleic Acids.18.12 Nucleic Acid Hybridization.18.13 Recombinant DNA Technology.Restriction Endonucleases.Formation of Recombinant DNAs.DNA Cloning.Chemical Synthesis and Site-Directed Mutagenesis.Gene Transfer into Eukaryotic Cells and Mammalian Embryos.Enzymatic Amplification of DNA by PCR.DNA Sequencing.18.14 The Use of Antibodies.Glossary.Index.