Karp’s Cell and Molecular Biology: Concepts and Experiments (8th Edition)

Table of contents

Table of contents :
Front Cover
About the Cover
Title Page
Copyright Page
About the Authors
Preface to the Eighth Edition
CONTENTS (with drect page links)
1. Introduction to the Study of Cell and Molecular Biology
1.1 The Discovery of Cells
Microscopy
Cell Theory
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 Mechanical Activities
Cells Are Able to Respond to Stimuli
Cells Are Capable of Self-Regulation
Cells Evolve
1.3 Characteristics That Distinguish Prokaryotic and Eukaryotic Cells
1.4 Types of Prokaryotic Cells
Domain Archaea and Domain Bacteria
Prokaryotic Diversity
1.5 Types of Eukaryotic Cells
Cell Differentiation
Model Organisms
1.6 THE HUMAN PERSPECTIVE: The Prospect of Cell Replacement Therapy
1.7 The Sizes of Cells and Their Components
1.8 Viruses and Viroids
1.9 EXPERIMENTAL PATHWAYS: The Origin of Eukaryotic Cells
Analytic Questions
2. The Chemical Basis of Life
2.1 Covalent Bonds
Polar and Nonpolar Molecules
Ionization
2.2 THE HUMAN PERSPECTIVE: Do Free Radicals Cause Aging?
2.3 Noncovalent Bonds
Ionic Bonds: Attractions between Charged Atoms
Hydrogen Bonds
Hydrophobic Interactions and van der Waals Forces
The Life-Supporting Properties of Water
2.4 Acids, Bases, and Buffers
2.5 The Nature of Biological Molecules
Functional Groups
A Classification of Biological Molecules by Function
2.6 Carbohydrates
The Structure of Simple Sugars
Stereoisomerism
Linking Sugars Together
Polysaccharides
2.7 Lipids
Fats
Steroids
Phospholipids
2.8 Building Blocks of Proteins
The Structures of Amino Acids
The Properties of the Side Chains
2.9 Primary and Secondary Structures of Proteins
Primary Structure
Secondary Structure
2.10 Tertiary Structure of Proteins
Myoglobin: The First Globular Protein Whose Tertiary Structure Was Determined
Tertiary Structure May Reveal Unexpected Similarities between Proteins
Protein Domains
Dynamic Changes within Proteins
2.11 Quaternary Structure of Proteins
The Structure of Hemoglobin
Protein–Protein Interactions
2.12 Protein Folding
Dynamics of Protein Folding
The Role of Molecular Chaperones
2.13 THE HUMAN PERSPECTIVE: Protein Misfolding Can Have Deadly Consequences
2.14 EXPERIMENTAL PATHWAYS: Chaperones—Helping Proteins Reach Their Proper Folded State
2.15 Proteomics and Interactomics
Proteomics
Interactomics
2.16 Protein Engineering
Production of Novel Proteins
Structure-Based Drug Design
2.17 Protein Adaptation and Evolution
2.18 Nucleic Acids
2.19 The Formation of Complex Macromolecular Structures
The Assembly of Tobacco Mosaic Virus Particles
The Assembly of Ribosomal Subunits
Analytic Questions
3. Bioenergetics, Enzymes, and Metabolism
3.1 The Laws of Thermodynamics
The First Law of Thermodynamics
The Second Law of Thermodynamics
3.2 Free Energy
Free-Energy Changes in Chemical Reactions
Free-Energy Changes in Metabolic Reactions
3.3 Coupling Endergonic and Exergonic Reactions
3.4 Equilibrium versus ­Steady-State Metabolism
3.5 Enzymes as Biological Catalysts
The Properties of Enzymes
Overcoming the Activation Energy Barrier
The Active Site
3.6 Mechanisms of Enzyme Catalysis
Substrate Orientation
Changing Substrate Reactivity
Inducing Strain in the Substrate
3.7 Enzyme Kinetics
The Michaelis-Menten Model of Enzyme Kinetics
Enzyme Inhibitors
3.8 THE HUMAN PERSPECTIVE: The Growing Problem of Antibiotic Resistance
3.9 An Overview of Metabolism
Oxidation and Reduction: A Matter of Electrons
The Capture and Utilization of Energy
3.10 Glycolysis and Fermentation
ATP Production in Glycolysis
Anaerobic Oxidation of Pyruvate: The Process of Fermentation
3.11 Reducing Power
3.12 Metabolic Regulation
Altering Enzyme Activity by Covalent Modification
Altering Enzyme Activity by Allosteric Modulation
3.13 Separating Catabolic and Anabolic Pathways
3.14 THE HUMAN PERSPECTIVE: Caloric Restriction and Longevity
Analytic Questions
4. The Structure and Function of the Plasma Membrane
4.1 Introduction to the Plasma Membrane
An Overview of Membrane Functions
A Brief History of Studies on Plasma Membrane Structure
4.2 The Lipid Composition of Membranes
Membrane Lipids
The Nature and Importance of the Lipid Bilayer
The Asymmetry of Membrane Lipids
4.3 Membrane Carbohydrates
4.4 Membrane Proteins
Integral Membrane Proteins
Peripheral Membrane Proteins
Lipid-Anchored Membrane Proteins
4.5 Studying the Structure and Properties of Integral Membrane Proteins
Identifying Transmembrane Domains
Experimental Approaches to Identifying Conformational Changes within an Integral Membrane Protein
4.6 Membrane Lipids and Membrane Fluidity
The Importance of Membrane Fluidity
Maintaining Membrane Fluidity
Lipid Rafts
4.7 The Dynamic Nature of the Plasma Membrane
The Diffusion of Membrane Proteins after Cell Fusion
Restrictions on Protein and Lipid Mobility
4.8 The Red Blood Cell: An Example of Plasma Membrane Structure
Integral Proteins of the Erythrocyte Membrane
The Erythrocyte Membrane Skeleton
4.9 Solute Movement across Cell Membranes
The Energetics of Solute Movement
Formation of an Electrochemical Gradient
4.10 Diffusion through the Lipid Bilayer
Diffusion of Substances through Membranes
The Diffusion of Water through Membranes
4.11 The Diffusion of Ions through Membranes
4.12 EXPERIMENTAL PATHWAYS: The Acetylcholine Receptor
4.13 Facilitated Diffusion
4.14 Active Transport
Primary Active Transport: Coupling Transport to ATP Hydrolysis
Other Primary Ion Transport Systems
Using Light Energy to Actively Transport Ions
Secondary Active Transport (or Cotransport): Coupling Transport to Existing Ion Gradients
4.15 THE HUMAN PERSPECTIVE: Defects in Ion Channels and Transporters as a Cause of Inherited Disease
4.16 Membrane Potentials
The Resting Potential
The Action Potential
4.17 Propagation of Action Potentials as an Impulse
4.18 Neurotransmission: Jumping the Synaptic Cleft
Actions of Drugs on Synapses
Synaptic Plasticity
Analytic Questions
5. Aerobic Respiration and the Mitochondrion
5.1 Mitochondrial Structure and Function
Mitochondrial Membranes
The Mitochondrial Matrix
5.2 Aerobic Metabolism in the Mitochondrion
The Tricarboxylic Acid (TCA) Cycle
The Importance of Reduced Coenzymes in the Formation of ATP
5.3 THE HUMAN PERSPECTIVE: The Role of Anaerobic and Aerobic Metabolism in Exercise
5.4 Oxidative Phosphorylation in the Formation of ATP
Oxidation–Reduction Potentials
Electron Transport
Types of Electron Carriers
5.5 Electron-Transport Complexes
Complex I (NADH Dehydrogenase)
Complex II (succinate dehydrogenase)
Complex III (cytochrome bc1)
Complex IV (cytochrome c oxidase)
5.6 Establishment of a Proton-Motive Force
5.7 The Structure of ATP Synthase
5.8 The Binding Change Mechanism of ATP Formation
Components of the Binding Change Hypothesis
Evidence to Support the Binding Change Mechanism and Rotary Catalysis
5.9 Using the Proton Gradient
The Role of the Fo Portion of ATP Synthase in ATP Synthesis
Other Roles for the Proton-Motive Force in Addition to ATP Synthesis
5.10 Peroxisomes
5.11 THE HUMAN PERSPECTIVE: Diseases that Result from Abnormal Mitochondrial or Peroxisomal Function
Analytic Questions
6. Photosynthesis and the Chloroplast
6.1 The Origin of Photosynthesis
6.2 Chloroplast Structure
6.3 An Overview of Photosynthetic Metabolism
6.4 The Absorption of Light
6.5 Coordinating the Action of Two Different Photosynthetic Systems
6.6 The Operations of Photosystem II and Photosystem I
PSII Operations: Obtaining Electrons by Splitting Water
PSI Operations: The Production of NADPH
6.7 An Overview of Photosynthetic Electron Transport
6.8 Photophosphorylation
6.9 Carbohydrate Synthesis in C3 Plants
Redox Control
Photorespiration
Peroxisomes and Photorespiration
6.10 Carbohydrate Synthesis in C4 and CAM Plants
6.11 THE HUMAN PERSPECTIVE: Global Warming and Carbon Sequestration
Analytic Questions
7. Interactions between Cells and their Environment
7.1 Overview of Extracellular Interactions
7.2 The Extracellular Matrix
7.3 Components of the Extracellular Matrix
Collagen
Proteoglycans
Fibronectin
Laminin
7.4 Dynamic Properties of the Extracellular Matrix
7.5 Integrins
7.6 Anchoring Cells to Their Substratum
Focal Adhesions
Hemidesmosomes
7.7 Interactions of Cells with Other Cells
Selectins
The Immunoglobulin Superfamily
Cadherins
7.8 THE HUMAN PERSPECTIVE: The Role of Cell Adhesion in Inflammation and Metastasis
7.9 Adherens Junctions and Desmosomes
7.10 The Role of Cell-Adhesion Receptors in Transmembrane Signaling
7.11 Tight Junctions: Sealing the Extracellular Space
7.12 Gap Junctions and Plasmodesmata: Mediating Intercellular Communication
Gap Junctions
Plasmodesmata
7.13 EXPERIMENTAL PATHWAYS: The Role of Gap Junctions in Intercellular Communication
7.14 Cell Walls
Analytic Questions
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 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
The Rough Endoplasmic Reticulum
8.4 Functions of the Rough Endoplasmic Reticulum
Synthesis of Proteins on Membrane-Bound versus Free Ribosomes
Synthesis of Secretory, Lysosomal, or Plant Vacuolar Proteins
Processing of Newly Synthesized Proteins in the Endoplasmic Reticulum
Synthesis of Integral Membrane Proteins on ER-Bound Ribosomes
8.5 Membrane Biosynthesis in the Endoplasmic Reticulum
8.6 Glycosylation in the Rough Endoplasmic Reticulum
8.7 Mechanisms That Ensure the Destruction of Misfolded Proteins
8.8 ER to Golgi Vesicular Transport
8.9 The Golgi Complex
Glycosylation in the Golgi Complex
The Movement of Materials through the Golgi Complex
8.10 Types of Vesicle Transport
COPII-Coated Vesicles: Transporting Cargo from the ER to the Golgi Complex
COPI-Coated Vesicles: Transporting Escaped Proteins Back to the ER
8.11 Beyond the Golgi Complex: Sorting Proteins at the TGN
Sorting and Transport of Lysosomal Enzymes
Sorting and Transport of Nonlysosomal Proteins
8.12 THE HUMAN PERSPECTIVE: Disorders Resulting from Defects in Lysosomal Function
8.13 Targeting Vesicles to a Particular Compartment
8.14 Exocytosis
8.15 Lysosomes
8.16 Plant Cell Vacuoles
8.17 Endocytosis
Receptor-Mediated Endocytosis and the Role of Coated Pits
The Role of Phosphoinositides in the Regulation of Coated Vesicles
8.18 EXPERIMENTAL PATHWAYS: Receptor-Mediated Endocytosis
8.19 The Endocytic Pathway
8.20 Phagocytosis
8.21 Posttranslational Uptake of Proteins by Peroxisomes, Mitochondria, and Chloroplasts
Uptake of Proteins into Peroxisomes
Uptake of Proteins into Mitochondria
Uptake of Proteins into Chloroplasts
Analytic Questions
9. The Cytoskeleton and Cell Motility
9.1 Overview of the Major Functions of the Cytoskeleton
9.2 Structure and Function of Microtubules
Structure and Composition of Microtubules
Microtubule-Associated Proteins
Microtubules as Structural Supports and Organizers
Microtubules as Agents of Intracellular Motility
9.3 Motor Proteins: Kinesins and Dyneins
Motor Proteins Traverse the Microtubular Cytoskeleton
Kinesins
Cytoplasmic Dynein
9.4 EXPERIMENTAL PATHWAY: The Step Size of Kinesin
9.5 Microtubule-Organizing Centers (MTOCs)
Centrosomes
Basal Bodies and Other MTOCs
Microtubule Nucleation
9.6 Microtubule Dynamics
The Dynamic Properties of Microtubules
The Underlying Basis of Microtubule Dynamics
9.7 Structure and Function of Cilia and Flagella
Structure of Cilia and Flagella
Growth by Intraflagellar Transport
The Mechanism of Ciliary and Flagellar Locomotion
9.8 THE HUMAN PERSPECTIVE: The Role of Cilia in Development and Disease
9.9 Intermediate Filaments
Intermediate Filament Assembly and Disassembly
Types and Functions of Intermediate Filaments
9.10 Actin
Actin Structure
Actin Filament Assembly and Disassembly
9.11 Myosin: The Molecular Motor of Actin
Conventional (Type II) Myosins
Unconventional Myosins
9.12 Muscle Organization and Contraction
Organization of Sarcomeres
The Sliding Filament Model of Muscle Contraction
9.13 Actin-Binding Proteins
9.14 Cellular Motility
9.15 EXPERIMENTAL PATHWAY: Studying Actin-Based Motility without Cells
9.16 Actin-dependent Processes During Development
Axonal Outgrowth
9.17 The Bacterial Cytoskeleton
Analytic Questions
10. The Nature of the Gene and the Genome
10.1 The Concept of a Gene as a Unit of Inheritance
10.2 The Discovery of Chromosomes
10.3 Chromosomes as the Carriers of Genetic Information
10.4 Genetic Analysis in Drosophila
Crossing Over and Recombination
Mutagenesis and Giant Chromosomes
10.5 The Structure of DNA
The Watson-Crick Proposal
The Importance of the Watson-Crick Proposal
10.6 EXPERIMENTAL PATHWAYS: The Chemical Nature of the Gene
10.7 DNA Supercoiling
10.8 The Complexity of the Genome
DNA Denaturation
DNA Renaturation
10.9 THE HUMAN PERSPECTIVE: Diseases That Result from Expansion of Trinucleotide Repeats
10.10 The Stability of the Genome: Duplication
Whole-Genome Duplication (Polyploidization)
Duplication and Modification of DNA Sequences
Evolution of Globin Genes
10.11 The Dynamic Nature of the Genome: “Jumping Genes”
Transposons
The Role of Mobile Genetic Elements in Genome Evolution
10.12 Sequencing Genomes: The Footprints of Biological Evolution
10.13 Comparative Genomics: “If It’s Conserved, It Must Be Important”
10.14 The Genetic Basis of “Being Human”
10.15 Genetic Variation within the Human Species Population
DNA Sequence Variation
Structural Variation
Copy Number Variation
10.16 THE HUMAN PERSPECTIVE: Application of Genomic Analyses to Medicine
Analytic Questions
11. The Central Dogma: DNA to RNA to Protein
11.1 The Relationship between Genes, Proteins, and RNAs
Evidence That DNA Is the Genetic Material
An Overview of the Flow of Information through the Cell
11.2 The Role of RNA Polymerases in Transcription
11.3 An Overview of Transcription in Both Prokaryotic and Eukaryotic Cells
Transcription in Bacteria
Transcription and RNA Processing in Eukaryotic Cells
11.4 Synthesis and Processing of Eukaryotic Ribosomal and Transfer RNAs
Synthesis and Processing of the rRNA Precursor
The Role of snoRNAs in the Processing of Pre-rRNA
Synthesis and Processing of the 5S rRNA
Transfer RNAs
11.5 Synthesis and Structure of Eukaryotic Messenger RNAs
The Formation of Heterogeneous Nuclear RNA (hnRNA)
The Machinery for mRNA Transcription
The Structure of mRNAs
11.6 Split Genes: An Unexpected Finding
11.7 The Processing of Eukaryotic Messenger RNAs
5′ Caps and 3′ Poly(A) Tails
RNA Splicing: Removal of Introns from a Pre-RNA
11.8 Evolutionary Implications of Split Genes and RNA Splicing
11.9 Creating New Ribozymes in the Laboratory
11.10 RNA Interference
11.11 THE HUMAN PERSPECTIVE: Clinical Applications of RNA Interference
11.12 Small RNAs: miRNAs and piRNAs
miRNAs: A Class of Small RNAs that Regulate Gene Expression
piRNAs: A Class of Small RNAs that Function in Germ Cells
11.13 CRISPR and other Noncoding RNAs
CRISPR: Noncoding RNA in Bacteria
Other Noncoding RNAs
11.14 Encoding Genetic Information
The Properties of the Genetic Code
Identifying the Codons
11.15 Decoding the Codons: The Role of Transfer RNAs
The Structure of tRNAs
tRNA Charging
11.16 Translating Genetic Information: Initiation
Initiation of Translation in Prokaryotes
Initiation of Translation in Eukaryotes
The Role of the Ribosome
11.17 Translating Genetic Information: Elongation and Termination
Elongation Step 1: Aminoacyl-tRNA Selection
Elongation Step 2: Peptide Bond Formation
Elongation Step 3: Translocation
Elongation Step 4: Releasing the Deacylated tRNA
Termination
11.18 mRNA Surveillance and Quality Control
11.19 Polyribosomes
11.20 EXPERIMENTAL PATHWAYS: The Role of RNA as a Catalyst
Analytic Questions
12. Control of Gene Expression
12.1 Control of Gene Expression in Bacteria
Organization of Bacterial Genomes
The Bacterial Operon
Riboswitches
12.2 Structure of the Nuclear Envelope
The Nuclear Pore Complex and Its Role in Nucleocytoplasmic Trafficking
RNA Transport
12.3 Packaging the Eukaryotic Genome
Nucleosomes: The Lowest Level of Chromosome Organization
Higher Levels of Chromatin Structure
12.4 Heterochromatin
X Chromosome Inactivation
The Histone Code and Formation of Heterochromatin
12.5 The Structure of a Mitotic Chromosome
Telomeres
Centromeres
12.6 THE HUMAN PERSPECTIVE: Chromosomal Aberrations and Human Disorders
12.7 Epigenetics: There’s More to Inheritance than DNA
12.8 The Nucleus as an Organized Organelle
12.9 An Overview of Gene Regulation in Eukaryotes
12.10 Profiling Gene Activity
DNA Microarrays
RNA Sequencing
12.11 The Role of Transcription Factors in Regulating Gene Expression
12.12 The Structure of Transcription Factors
The Zinc-Finger Motif
The Helix–Loop–Helix (HLH) Motif
The Leucine Zipper Motif
12.13 DNA Sites Involved in Regulating Transcription
12.14 An Example of Transcriptional Activation: The Glucocorticoid Receptor
12.15 Transcriptional Activation: The Role of Enhancers, Promoters, and Coactivators
Coactivators That Interact with the Basal Transcription Machinery
Coactivators That Alter Chromatin Structure
12.16 Transcriptional Activation from Paused Polymerases
12.17 Transcriptional Repression
DNA Methylation
Genomic Imprinting
Long Noncoding RNAs (lncRNAs) as Transcriptional Repressors
12.18 RNA Processing Control
12.19 Translational Control
Initiation of Translation
Cytoplasmic Localization of mRNAs
The Control of mRNA Stability
12.20 The Role of MicroRNAs in Translational Control
12.21 Posttranslational Control: Determining Protein Stability
Analytic Questions
13. DNA Replication and Repair
13.1 DNA Replication
13.2 DNA Replication in Bacterial Cells
Replication Forks and Bidirectional Replication
Unwinding the Duplex and Separating the Strands
The Properties of DNA Polymerases
Semidiscontinuous Replication
13.3 The Machinery Operating at the Replication Fork
13.4 The Structure and Functions of DNA Polymerases
Exonuclease Activities of DNA Polymerases
Ensuring High Fidelity during DNA Replication
13.5 Replication in Viruses
13.6 DNA Replication in Eukaryotic Cells
Initiation of Replication in Eukaryotic Cells
Restricting Replication to Once Per Cell Cycle
The Eukaryotic Replication Fork
Replication and Nuclear Structure
13.7 Chromatin Structure and Replication
13.8 DNA Repair
Nucleotide Excision Repair
Base Excision Repair
Mismatch Repair
Double-Strand Breakage Repair
13.9 Between Replication and Repair
13.10 THE HUMAN PERSPECTIVE: Consequences of DNA Repair Deficiencies
Analytic Questions
14. Cell Division
14.1 The Cell Cycle
Phases of the Cell Cycle
Cell Cycles in Vivo
14.2 Regulation of the Cell Cycle
14.3 EXPERIMENTAL PATHWAYS: The Discovery and Characterization of MPF
14.4 Control of the Cell Cycle: The Role of Protein Kinases
Cyclin Binding
Cdk Phosphorylation/Dephosphorylation
Cdk Inhibitors
Controlled Proteolysis
Subcellular Localization
14.5 Control of the Cell Cycle: Checkpoints, Cdk Inhibitors, and Cellular Responses
14.6 Overview of M Phase: Mitosis and Cytokinesis
14.7 Prophase
Formation of the Mitotic Chromosome
Centromeres and Kinetochores
Formation of the Mitotic Spindle
The Dissolution of the Nuclear Envelope and Partitioning of Cytoplasmic Organelles
14.8 Prometaphase
14.9 Metaphase
14.10 Anaphase
The Role of Proteolysis in Progression through Mitosis
The Events of Anaphase
Forces Required for Chromosome Movements at Anaphase
The Spindle Assembly Checkpoint
14.11 Telophase and Cytokinesis
Motor Proteins Required for Mitotic Movements
Cytokinesis
Cytokinesis in Plant Cells: Formation of the Cell Plate
14.12 Overview of Meiosis
14.13 The Stages of Meiosis
14.14 THE HUMAN PERSPECTIVE: Meiotic Nondisjunction and Its Consequences
14.15 Genetic Recombination during Meiosis
Analytic Questions
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 Signal Transduction by G Protein-Coupled Receptors
Receptors
G Proteins
Termination of the Response
Bacterial Toxins
15.4 EXPERIMENTAL PATHWAYS: The Discovery and Characterization of GTP-Binding Proteins
15.5 THE HUMAN PERSPECTIVE: Disorders Associated with G Protein-Coupled Receptors
15.6 Second Messengers
The Discovery of Cyclic AMP
Phosphatidylinositol-Derived Second Messengers
Phospholipase C
15.7 The Specificity of G Protein-Coupled Responses
15.8 Regulation of Blood Glucose Levels
Glucose Mobilization: An Example of a Response Induced by cAMP
Signal Amplification
Other Aspects of cAMP Signal Transduction Pathways
15.9 The Role of GPCRs in Sensory Perception
15.10 Protein-Tyrosine Phosphorylation as a Mechanism for Signal Transduction
Receptor Dimerization
Protein Kinase Activation
Phosphotyrosine-Dependent ­Protein–Protein Interactions
Activation of Downstream Signaling Pathways
Ending the Response
15.11 The Ras-MAP Kinase Pathway
Accessory Proteins
Adapting the MAP Kinase to Transmit Different Types of Information
15.12 Signaling by the Insulin Receptor
The Insulin Receptor Is a Protein-Tyrosine Kinase
Insulin Receptor Substrates 1 and 2
Glucose Transport
Diabetes Mellitus
15.13 Signaling Pathways in Plants
15.14 The Role of Calcium as an Intracellular Messenger
IP3 and Voltage-Gated Ca2+ Channels
Visualizing Cytoplasmic Ca2+ Concentration in Living Cells
Ca2+-Binding Proteins
Regulating Calcium Concentrations in Plant Cells
15.15 Convergence, Divergence, and Cross-Talk among Different Signaling Pathways
15.16 The Role of NO as an Intercellular Messenger
NO as an Activator of Guanylyl Cyclase
Inhibiting Phosphodiesterase
15.17 Apoptosis (Programmed Cell Death)
The Extrinsic Pathway of Apoptosis
The Intrinsic Pathway of Apoptosis
Necroptosis
Signaling Cell Survival
Analytic Questions
16. Cancer
16.1 Basic Properties of a Cancer Cell
16.2 The Causes of Cancer
16.3 EXPERIMENTAL PATHWAYS: The Discovery of Oncogenes
16.4 Cancer: A Genetic Disorder
16.5 An Overview of Tumor-Suppressor Genes and Oncogenes
16.6 Tumor-Suppressor Genes: The RB Gene
16.7 Tumor-Suppressor Genes: The TP53 Gene
The Role of p53: Guardian of the Genome
The Role of p53 in Promoting Senescence
16.8 Other Tumor-Suppressor Genes
16.9 Oncogenes
Oncogenes That Encode Growth Factors or Their Receptors
Oncogenes That Encode Cytoplasmic Protein Kinases
Oncogenes That Encode Transcription Factors
Oncogenes That Encode Proteins That Affect the Epigenetic State of Chromatin
Oncogenes That Encode Metabolic Enzymes
Oncogenes That Encode Products That Affect Apoptosis
16.10 The Mutator Phenotype: Mutant Genes Involved in DNA Repair
16.11 MicroRNAs: A New Player in the Genetics of Cancer
16.12 The Cancer Genome
16.13 Gene-Expression Analysis
16.14 Strategies for Combating Cancer
16.15 Immunotherapy
16.16 Inhibiting the Activity of Cancer-Promoting Proteins
16.17 The Concept of a Cancer Stem Cell
16.18 Inhibiting the Formation of New Blood Vessels (Angiogenesis)
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
17.3 THE HUMAN PERSPECTIVE: Autoimmune Diseases
17.4 Vaccination
17.5 EXPERIMENTAL PATHWAYS: The Role of the Major Histocompatibility Complex in Antigen Presentation
17.6 T Lymphocytes: Activation and Mechanism of Action
17.7 The Modular Structure of Antibodies
17.8 DNA Rearrangements That Produce Genes Encoding B- and T-Cell Antigen Receptors
17.9 Membrane-Bound Antigen Receptor Complexes
17.10 The Major Histocompatibility Complex
17.11 Distinguishing Self from Nonself
17.12 Lymphocytes Are Activated by Cell-Surface Signals
Activation of Helper T Cells by Professional APCs
Activation of B Cells by TH Cells
17.13 Signal Transduction Pathways in Lymphocyte Activation
18. Techniques in Cell and Molecular Biology
18.1 The Light Microscope
Resolution
Visibility
18.2 Bright-Field and Phase-Contrast Microscopy
Bright-Field Light Microscopy
Phase-Contrast Microscopy
18.3 Fluorescence Microscopy (and Related Fluorescence-Based Techniques)
Laser Scanning Confocal Microscopy
Super-Resolution Fluorescence Microscopy
Light Sheet Fluorescence Microscopy
18.4 Transmission Electron Microscopy
18.5 Specimen Preparation for Electron Microscopy
Cryofixation and the Use of Frozen Specimens
Negative Staining
Shadow Casting
Freeze-Fracture Replication and Freeze Etching
18.6 Scanning Electron Microscopy
18.7 Atomic Force Microscopy
18.8 The Use of Radioisotopes
18.9 Cell Culture
18.10 The Fractionation of a Cell’s Contents by Differential Centrifugation
18.11 Purification and Characterization of Proteins by Liquid Column Chromatography
Ion-Exchange Chromatography
Gel Filtration Chromatography
Affinity Chromatography
18.12 Determining Protein–Protein Interactions
18.13 Characterization of Proteins by Polyacrylamide Gel Electrophoresis
SDS–PAGE
Two-Dimensional Gel Electrophoresis
18.14 Characterization of Proteins by Spectrometry
18.15 Characterization of Proteins by Mass Spectrometry
18.16 Determining the Structure of Proteins and Multisubunit Complexes
18.17 Fractionation of Nucleic Acids
Separation of DNAs by Gel Electrophoresis
Separation of Nucleic Acids by Ultracentrifugation
18.18 Nucleic Acid Hybridization
18.19 Chemical Synthesis of DNA
18.20 Recombinant DNA Technology
Restriction Endonucleases
Formation of Recombinant DNAs
DNA Cloning
18.21 Enzymatic Amplification of DNA by PCR
Process of PCR
Applications of PCR
18.22 DNA Sequencing
18.23 DNA Libraries
Genomic Libraries
cDNA Libraries
18.24 DNA Transfer into Eukaryotic Cells and Mammalian Embryos
Transgenic Animals
Transgenic Plants
18.25 Gene Editing and Silencing
In Vitro Mutagenesis
Knockout Mice
RNA Interference
Genome Editing Using Engineered Nucleases
18.26 The Use of Antibodies
Glossary
A
B
C
D
E
F – G
H
I
K – L
M
N
O – P
Q – R
S
T
U
V – W – X – Y
Additional Reading
INDEX
A
B
C
D
E
F
G
H
I
J – K – L
M
N
O
P
Q – R
S
T
U
V
W
X – Y – Z
Nobel Prizes Awarded for Research in Cell and Molecular Biology Since 1958
Topics of Human Interest
Experimental Pathways (WEB)
ch05 Coupling Oxidation to Phosphorylation
ch09 The Molecular Motor That Drives Fast Axonal Transport
ch12 Genes That Control Embryonic Development
ch13 The Role of Human NER Deficiencies in DNA Repair Research
Clinical Case Studies (WEB)
ch01
Why don’t antibiotics cure my cold?
ch02
Defects in Hemoglobin Structure and Function
Protein Conformational Diseases
Good vs. Bad Fats?
ch03
MeOH Poisoning: Drunken Cure
Anaerobic Respiration: Sore Muscles or make me some beer.
ch04
Heartburn – Treat it or Prevent it
Commonly Prescribed Anti-Depressants
ch05
Cyanide Poisoning: Winter of Frozen Dreams
Mitochondrial Diseases
Peroxisomal Import Diseases
ch06
Can Plants Get Cancer?
ch07
Collagen Disorders
Proteoglycans: Dietary Supplements or Snake-oil treatments?
Sticky Cells: Cell Connections, Metastasis and Cancer
ch08
Lysosomal Storage Disease
High Cholesterol
Unique Sugars Create our Blood Types
ch09
Microtubules and Disease
Intermediate Filaments and Skin Blisters
Actin Dynamics and Cell Motility
ch10
Models for Human Genetic Disease
Chromosomal Translocations and Leukemia
Transposons and Antibiotic Resistance
ch11
Transcription-linked DNA Repair
Thalassemias and Defective mRNA Splicing
Targeting the Protein Synthesis Machinery
ch12
Telomeres: Fountain of Youth
Blocking the Estrogen Receptor to Block Cancer
ch13
Bacterial DNA Replication Machinery as an Antibiotic Target
DNA Repair and Cancer
ch14
Checkpoints, Cancer, and Proliferation
Meiosis, Infertility, and Miscarriages
ch15
Cannabis Physiology through G-protein Mediated Signaling
EGF Receptor Signaling and Cancer
Male Sexual Enhancement: NO Signaling and Viagra
ch16
Generation of Cancer Cell Culture Models to Mimic the Disease State
ch17
Vaccine Development
Viral Destruction of the Immune System
The Boy in the Bubble and the Promise of Gene Therapy