Cell and Molecular Biology. Concepts and Experiments

Cover
Title Page
Copyright page
About the Author
Preface
Acknowledgments
Contents
Chapter 1: Introduction to the Study of Cell and Molecular Biology
	1.1 The Discovery of Cells
	1.2 Basic Properties of Cells
		Cells Are Highly Complex and Organized
		Cells Possess a Generic 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 Mechanical Activities
		Cells Are Able to Respond to Stimuli
		Cells Are Capable of Self-Regulation
		Cells Evolve
	1.3 Two Fundamentally Different Classes of Cells
		Characteristics That Distinguish Prokaryotic and Eukaryotic Cells
		Types of Prokaryotic Cells
		Types of Eukaryotic Cells: Cell Specialization
		The Sizes of Cells and Their Components
		Synthetic Biology
		THE HUMAN PERSPECTIVE: The Prospect of Cell Replacement Therapy
	1.4 Viruses
		Viroids
		EXPERIMENTAL PATHWAYS: The Origin of Eukaryotic Cells
Chapter 2: The Chemical Basis of Life
	2.1 Covalent Bonds
		Polar and Nonpolar Molecules
		Ionizaton
	2.2 Noncovalent Bonds
		THE HUMAN PERSPECTIVE: Free Radicals as a Cause of Aging
		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 Misfolding 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
Chapter 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
		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
Chapter 4: The Structure and 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
		The Asymmetry of Membrane Lipids
		Membrane Carbohydrates
	4.4 The Structure 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
		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 and Transporters 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
Chapter 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 Metabolism in 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 Mitochondrial or Peroxisomal Function
Chapter 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
Chapter 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
		The Immunoglobulin Superfamily
		Cadherins
		• THE HUMAN PERSPECTIVE: The Role of Cell Adhesion in Inflammation and 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
Chapter 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 Mutant Phenotypes
	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
		Autophagy
		THE HUMAN PERSPECTIVE: Disorders Resulting from Defects in Lysosomal Function
	8.7 Plant Cell Vacuoles
	8.8 The Endocytic Pathway: Moving Membrane and Materials into the Cell Interior
		Endocytosis
		Phagocytosis
	8.9 Posttranslational Uptake of Proteins by Peroxisomes, Mitochondria, and Chloroplasts
		Uptake of Proteins into Peroxisomes
		Uptake of Proteins into Mitochondria
		Uptake of Proteins into Chloroplasts
		EXPERIMENTAL PATHWAYS: Receptor-Mediated Endocytosis
Chapter 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 Live-Cell Fluorescence Imaging
		The Use of In Vitro and In Vivo Single-Molecule Assays
		The Use of Fluorescence Imaging Techniques to Monitor the Dynamics of the Cytoskeleton
	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
		Cilia and Flagella: Structure and Function
		THE HUMAN PERSPECTIVE: The Role of Cilia in Development and Disease
	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 of 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
Chapter 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
		DNA Supercoiling
	10.4 The Structure of the Genome
		The Complexity of the Genome
		THE HUMAN PERSPECTIVE: Diseases that Result from Expansion of Trinucleotide 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 Footprints of Biological Evolution
		Comparative Genomics: "If It's Conserved, It Must Be Important"
		The Genetic Basis of "Being Human"
		Genetic Variation Within the Human Species Population
		THE HUMAN PERSPECTIVE: Application of Genomic Analyses to Medicine
		EXPERIMENTAL PATHWAYS: The Chemical Nature of the Gene
Chapter 11: Gene Expression: From Transcription to Translation
	11.1 The Relationship between Genes, Proteins, and RNAs
		An Overview of the Flow of Information through the Cell
	11.2 An Overview of Transcription in Both Prokaryotic and Eukaryotic Cells
		Transcription in Bacteria
		Transcription and RNA Processing in Eukaryotic Cells
	11.3 Synthesis and Processing of Eukaryotic 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 Eukaryotic 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 Regulatory RNAs and RNA Silencing Pathways
		THE HUMAN PERSPECTIVE: Clinical Applications of RNA Interference
		MicroRNAs: Small RNAs that Regulate Gene Expression
		piRNAs: A Class of Small RNAs that Function in Germ Cells
		Other Noncoding RNAs
	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 and Quality Control
		Polyribosomes
		EXPERIMENTAL PATHWAYS: The Role of RNA as a Catalyst
Chapter 12: Control of Gene Expression
	12.1 Control of Gene Expression in Bacteria
		Organization of Bacterial Genomes
		The Bacterial Operon
		Riboswitches
	12.2 Control of Gene Expression in Eukaryotes: Structure and Function of the Cell Nucleus
		The Nuclear Envelope
		Chromosomes and Chromatin
		THE HUMAN PERSPECTIVE: Chromosomal Aberrations and Human Disorders
		Epigenetics: There's More to Inheritance than DNA
		The Nucleus as an Organized Organelle
	12.3 An Overview of Gene Regulation in Eukaryotes
	12.4 Transcriptional 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 RNA Processing Control
	12.6 Translational Control
		Initiation of Translation
		Cytoplasmic Localization of mRNAs
		The Control of mRNA Stability
		The Role of MicroRNAs in Translational Control
	12.7 Posttranslational Control: Determining Protein Stability
Chapter 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
	13.3 Between Replication and Repair
		THE HUMAN PERSPECTIVE: The Consequences of DNA Repair Deficiencies
Chapter 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
		Motor Proteins 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
Chapter 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-Coupled Receptors
		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
		THE HUMAN PERSPECTIVE: Signaling Pathways and Human Longevity
		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 Cross-Talk Among Different Signaling Pathways
		Examples of Convergence, Divergence, and Cross-Talk Among Signaling Pathways
	15.7 The Role of NO as an Intercellular Messenger
	15.8 Apoptosis (Programmed Cell Death)
		The Extrinsic Pathway of Apoptosis
		The Intrinsic Pathway of Apoptosis
Chapter 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
		The Cancer Genome
		Gene-Expression Analysis
	16.4 New Strategies for Combating Cancer
		Immunotherapy
		Inhibiting the Activity of Cancer-Promoting Proteins
		Inhibiting the Formation of New Blood Vessels (Angiogenesis)
		EXPERIMENTAL PATHWAYS: The Discovery of Oncogenes
Chapter 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 Modular Structure of Antibodies
		DNA Rearrangements that Produce 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 in Lymphocyte Activation
		THE HUMAN PERSPECTIVE: Autoimmune Diseases
		• EXPERIMENTAL PATHWAYS: The Role of the Major Histocompatibility Complex in Antigen Presentation
Chapter 18: Techniques in Cell and Molecular Biology
	18.1 The Light Microscope
		Resolution
		Visibility
		Preparation of Specimens for Bright-Field Light Microscopy
		Phase-Contrast Microscopy
		Fluorescence Microscopy (and Related Fluorescence-Based Techniques)
		Video Microscopy and Image Processing
		Laser Scanning Confocal Microscopy
		Super-Resolution Fluorescence Microscopy
	18.2 Transmission Electron Microscopy
		Specimen Preparation for Electron Microscopy
	18.3 Scanning Electron and Atomic Force Microscopy
		Atomic Force 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
		Protein Measurement and Analysis
	18.8 Determining the Structure of Proteins and Multisubunit Complexes
	18.9 Fractionation of Nucleic Acids
		Separation of DNAs by Gel Electrophoresis
		Separation of Nucleic Acids by Ultracentrifugation
	18.10 Nucleic Acid Hybridization
	18.11 Chemical Synthesis of DNA
	18.12 Recombinant DNA Technology
		Restriction Endonucleases
		Formation of Recombinant DNAs
		DNA Cloning
	18.13 Enzymatic Amplification of DNA by PCR
		Applications of PCR
	18.14 DNA Sequencing
	18.15 DNA Libraries
		Genomic Libraries
		cDNA Libraries
	18.16 DNA Transfer into Eukaryotic Cells and Mammalian Embryos
	18.17 Determining Eukaryotic Gene Function by Gene Elimination or Silencing
		In Vitro Mutagenesis
		Knockout Mice
		RNA Interference
	18.18 The Use of Antibodies
Glossary
Additional Readings
Index