The Cell : A Molecular Approach-7판

Table of Contents

PART I. FUNDAMENTALS AND FOUNDATIONS

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 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
Super-resolution light microscopy
Subcellular fractionation
Growth of animal cells in culture
Key Experiment: HeLa Cells
Culture of plant cells
Viruses
Molecular Medicine: Viruses and Cancer

Chapter 2. Molecules and Membranes
The Molecules of Cells
Carbohydrates
Lipids
Nucleic acids
Proteins
Key Experiment: The Folding of Polypeptide Chains
Enzymes as Biological Catalysts
The catalytic activity of enzymes
Mechanisms of enzymatic catalysis
Coenzymes
Regulation of enzyme activity
Cell Membranes
Membrane lipids
Membrane proteins
Key Experiment: The Structure of Cell Membranes
Transport across cell membranes

Chapter 3. Bioenergetics and Metabolism
Metabolic Energy and ATP
Free energy and ATP
Glycolysis and the Krebs cycle
The derivation of energy from lipids
Electron Transport and Oxidative Phosphorylation
The electron transport chain
Chemiosmotic coupling
Key Experiment: The Chemiosmotic Theory
Photosynthesis
Electron transport
ATP synthesis
Synthesis of glucose
The Biosynthesis of Cell Constituents
Carbohydrates
Lipids
Proteins
Key Experiment: Antimetabolites and Chemotherapy
Nucleic acids

Chapter 4. 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
Key Experiment: The DNA Provirus Hypothesis
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
Gene transfer in plants and animals
Mutagenesis of cloned DNAs
Introducing mutations into cellular genes
Genome engineering by the CRISPR/Cas system
Interfering with cellular gene expression
Key Experiment: RNA Interference

Chapter 5. Genomics, Proteomics, and Systems Biology
Genomes and Transcriptomes
The genomes of bacteria and yeast
The genomes of Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana
The human genome
The genomes of other vertebrates
Key Experiment: The Human Genome
Next-generation sequencing and personal genomes
Global analysis of gene expression
Proteomics
Identification of cell proteins
Global analysis of protein localization
Protein interactions
Systems Biology
Systematic screens of gene function
Regulation of gene expression
Networks
Synthetic biology
Molecular Medicine: Malaria and Synthetic Biology

PART II. THE FLOW OF GENETIC INFORMATION

Chapter 6. Genes and Genomes
The Structure of Eukaryotic Genes
Introns and exons
Key Experiment: The Discovery of Introns
Roles of introns
Noncoding Sequences
Key Experiment: The ENCODE Project
Noncoding RNAs
Repetitive sequences
Gene duplication and pseudogenes
Chromosomes and Chromatin
Chromatin
Centromeres
Telomeres

Chapter 7. 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: Maintaining the ends of chromosomes
DNA Repair
Direct reversal of DNA damage
Excision repair
Translesion DNA synthesis
Molecular Medicine: Colon Cancer and DNA Repair
Repair of double-strand breaks
DNA Rearrangements
Yeast mating types
Antibody genes
Key Experiment: Rearrangement of Immunoglobulin Genes
Gene amplification

Chapter 8. RNA Synthesis and Processing
Transcription in Bacteria
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
Key Experiment : Isolation of a Eukaryotic Transcription Factor
Structure and function of transcriptional activators
Eukaryotic repressors
Regulation of elongation
Chromatin and Epigenetics
Histone modifications
Chromatin remodeling factors
Histones and epigenetic inheritance
DNA methylation
Noncoding RNAs
RNA Processing and Turnover
Processing of ribosomal and transfer RNAs
Processing of mRNA in eukaryotes
Splicing mechanisms
Key Experiment: The Discovery of snRNPs
Alternative splicing
RNA editing
RNA degradation

Chapter 9. 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
Protein misfolding diseases
Molecular Medicine: Alzheimer's Disease
Enzymes that catalyze protein folding
Protein cleavage
Glycosylation
Attachment of lipids
Regulation of Protein Function
Regulation by small molecules
Protein phosphorylation and other modifications
Key Experiment: The Discovery of Tyrosine Kinases
Protein-protein interactions
Protein Degradation
The ubiquitin-proteasome pathway
Lysosomal proteolysis

PART III. CELL STRUCTURE AND FUNCTION

Chapter 10. The Nucleus
The Nuclear Envelope and Traffic between the Nucleus and the Cytoplasm
Structure of the nuclear envelope
Molecular Medicine: Nuclear Lamina Diseases
The nuclear pore complex
Selective transport of proteins to and from the nucleus
Key Experiment: Identification of Nuclear Localization Signals
Transport of RNAs
Regulation of nuclear protein import
The Organization of Chromosomes
Chromosome territories
Chromatin localization and transcriptional activity
Replication and transcription factories
Nuclear Bodies
The nucleolus and rRNA
Polycomb bodies: Centers of transcriptional repression
Cajal bodies and speckles: Processing and storage of snRNPs

Chapter 11. 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
Key Experiment: The Signal Hypothesis
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
Molecular Medicine: Gaucher Disease
Endocytosis and lysosome formation
Phagocytosis and autophagy

Chapter 12. Mitochondria, Chloroplasts, and Peroxisomes
Mitochondria
Organization and function of mitochondria
The genetic system of mitochondria
Molecular Medicine: Diseases of Mitochondria: Leber's Hereditary Optic Neuropathy
Protein import and mitochondrial assembly
Mitochondrial lipids
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
Peroxisomes
Functions of peroxisomes
Peroxisome assembly
Molecular Medicine: Peroxisome Biogenesis Disorders

Chapter 13. 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
Microvilli
Cell surface protrusions and cell movement
Myosin Motors
Muscle contraction
Contractile assemblies of actin and myosin in nonmuscle cells
Unconventional myosins
Microtubules
Structure and dynamic organization of microtubules
Assembly of microtubules
Organization of microtubules within cells
Microtubule Motors and Movement
Microtubule motor proteins
Key Experiment: The Isolation of Kinesin
Cargo transport and intracellular organization
Cilia and flagella
Reorganization of microtubules during mitosis
Chromosome movement
Intermediate Filaments
Intermediate filament proteins
Assembly of intermediate filaments
Intracellular organization of intermediate filaments
Functions of intermediate filaments: Keratins and diseases of the skin
Key Experiment: Expression of Mutant Keratin Causes Abnormal Skin Development

Chapter 14. The Plasma Membrane
Structure of the Plasma Membrane
The lipid bilayer
Plasma membrane proteins
Plasma membrane domains
Transport of Small Molecules
Facilitated diffusion and carrier proteins
Ion channels
Active transport driven by ATP hydrolysis
Molecular Medicine: Cystic Fibrosis
Active transport driven by ion gradients
Endocytosis
Phagocytosis
Clathrin-mediated endocytosis
Key Experiment: The LDL Receptor
Clathrin-independent endocytosis

Chapter 15. Cell Walls, the Extracellular Matrix, and Cell Interactions
Cell Walls
Bacterial cell walls
Eukaryotic cell walls
The Extracellular Matrix and Cell-Matrix Interactions
Matrix structural proteins
Matrix polysaccharides
Adhesion proteins
Cell-matrix interactions
Key Experiment: The Characterization of Integrin
Cell-Cell Interactions
Adhesion junctions
Tight junctions
Gap junctions
Molecular Medicine: Gap Junction Diseases
Plasmodesmata

PART IV. CELL REGULATION

Chapter 16. Cell Signaling
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
G Proteins and Cyclic AMP Signaling
G proteins and G protein-coupled receptors
Key Experiment: G Protein-Coupled Receptors and Odor Detection
The cAMP pathway: Second messengers and protein phosphorylation
Cyclic GMP
Tyrosine Kinases and Signaling by MAP Kinase, PI 3-Kinase, and Phospholipase C/Calcium Pathways
Receptor tyrosine kinases
Nonreceptor tyrosine kinases
Molecular Medicine: Cancer: Signal Transduction and the ras Oncogenes
MAP kinase pathways
The PI 3-kinase/Akt and mTOR pathways
Phospholipase C and Ca2+
Receptors Coupled to Transcription Factors
The TGF-?/Smad pathway
NF-?B signaling
The Hedgehog, Wnt, and Notch pathways
Signaling Dynamics and Networks
Feedback loops and signaling dynamics
Networks and crosstalk

Chapter 17. 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
Regulators of Cell Cycle Progression
Protein kinases and cell cycle regulation
Key Experiment: The Discovery of MPF
Key Experiment: The Identification of Cyclin
Families of cyclins and cyclin-dependent kinases
Growth factors and the regulation of G1 Cdk's
S phase and regulation of DNA replication
DNA damage checkpoints
The Events of M Phase
Stages of mitosis
Entry into mitosis
The spindle assembly checkpoint and progression to anaphase
Cytokinesis
Meiosis and Fertilization
The process of meiosis
Regulation of oocyte meiosis
Fertilization

Chapter 18. Cell Death and Cell Renewal
Programmed Cell Death
The events of apoptosis
Key Experiment: Identification of Genes Required for Programmed Cell Death
Caspases: The executioners of apoptosis
Central regulators of apoptosis: The Bcl-2 family
Signaling pathways that regulate apoptosis
Alternative pathways of programmed cell death
Stem Cells and the Maintenance of Adult Tissues
Proliferation of differentiated cells
Stem cells
Medical applications of adult stem cells
Pluripotent Stem Cells, Cellular Reprogramming, and Regenerative Medicine
Embryonic stem cells
Key Experiment: Culture of Embryonic Stem Cells
Somatic cell nuclear transfer
Induced pluripotent stem cells
Transdifferentiation of somatic cells
Chapter 19. 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 and C viruses
Small DNA tumor viruses
Herpesviruses
Retroviruses
Oncogenes
Retroviral oncogenes
Proto-oncogenes
Key Experiment: The Discovery of Proto-Oncogenes
Oncogenes in human cancer
Functions of oncogene products
Tumor Suppressor Genes
Identification of tumor suppressor genes
Functions of tumor suppressor gene products
Cancer genomics
Molecular Approaches to Cancer Treatment
Prevention and early detection
Treatment
Molecular Medicine: Imatinib: Cancer Treatment Targeted against the bcr/abl Oncogene

Answers to Questions
Glossary
Illustration Credits
Index