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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