Molecular biology : principles of genome function / Nancy L. Craig [and five others] ; with end of chapter questions by Deborah Zies and Claire Burns.

Preceded by Molecular biology : principles of genome function / Nancy L. Craig ... [et al.]. 1st ed. 2010.

Includes bibliographical references and index.

Machine generated contents note: 1.Genomes and the 1low of biological information -- Introduction -- 1.1.The roots of biology -- 1.2.The genome: a working blueprint for life -- 1.3.Bringing genes to life: gene expression -- 1.4.Regulating gene expression -- 1.5.Cellular infrastructure and gene expression -- 1.6.Expression of the genome -- 1.7.Evolution of the genome and the tree of life -- 2.Biological molecules -- Introduction -- 2.1.Atoms, molecules, and chemical bonds -- 2.2.Life in aqueous solution -- 2.3.Non-covalent interactions -- 2.4.Nucleotides and nucleic acids -- 2.5.The structure of DNA -- 2.6.Chemical properties of RNA -- 2.7.RNA folding and structure -- 2.8.The RNA world and its role in the evolution of modern-day life -- 2.9.Fundamentals of protein structure -- 2.10.Protein folding -- 2.11.Protein folds -- 2.12.Protein-DNA interactions -- 2.13.Sugars and carbohydrates -- 2.14.Lipids -- 2.15.Chemical modification in biological regulation --

Contents note continued: 3.The chemical basis of life -- Introduction -- 3.1.Thermodynamic rules In biological systems -- 3.2.Binding equilibria and kinetics -- 3.3.Binding processes in biology -- 3.4.Enzyme catalysis -- 3.5.Enzyme kinetics -- 4.Chromosome structure and function -- Introduction -- 4.1.Organization of chromosomes -- 4.2.The cell cycle and chromosome dynamics -- 4.3.Packaging chromosomal DNA -- 4.4.Variation in chromatin structure -- 4.5.Covalent modifications of histones -- 4.6.Nucleosome-remodeling complexes -- 4.7.DNA methylation -- 4.8.The separation of chromatin domains by boundary elements -- 4.9.Elements required for chromosome function -- 4.10.The centromere -- 4.11.The telomere -- 4.12.Chromosome architecture in the nucleus -- 5.The cell cycle -- Introduction -- 5.1.Steps in the eukaryotic cell cycle -- 5.2.Cyclins and Cdks -- 5.3.Regulation of Cdk activity -- 5.4.Cell cycle regulation by Cdks -- 5.5.Regulation of proteolysis by Cdks --

Contents note continued: 5.6.Checkpoints: Intrinsic pathways that can halt the cell cycle -- 5.7.Extrinsic regulators of cell cycle progression -- 5.8.The cell cycle and cancer -- 5.9.The bacterial cell cycle -- 6.DNA replication -- Introduction -- 6.1.Overview of DNA replication -- 6.2.DNA polymerases: structure and function -- 6.3.DNA polymerases: fidelity and processivity -- 6.4.Specialized polymerases -- 6.5.DNA helicases: unwinding of the double helix -- 6.6.The sliding clamp and clamp loader -- 6.7.Origins and initiation of DNA replication -- 6.8.Leading and lagging strand synthesis -- 6.9.The replication fork -- 6.10.Termination of DNA replication -- 6.11.The end-replication problem and telomerase -- 6.12.Chromatin replication -- 6.13.Regulation of initiation of replication In E. coli -- 6.14.Regulation of replication initiation in eukaryotes -- 7.Chromosome segregation -- Introduction -- 7.1.The stages of mitosis -- 7.2.Chromosome condensation and cohesion --

Contents note continued: 7.3.The mitotic spindle -- 7.4.Prometaphase and metaphase -- 7.5.Anaphase: an irreversible step in chromosome segregation -- 7.6.The completion of mitosis and cytokinesis -- 7.7.Meiosis: generating haploid gametes from diploid calls -- 7.8.Chromosome segregation in bacteria -- 8.Transcription -- Introduction -- 8.1.Overview of transcription -- 8.2.RNA polymerase core enzyme -- 8.3.Promoter recognition in bacteria and eukaryotes -- 8.4.Initiation of transcription and transition to an elongating complex -- 8.5.Transcription elongation -- 8.6.Transcription termination -- 9.Regulation of transcription -- Introduction -- 9.1.Principles of transcription regulation -- 9.2.DNA-binding domains in proteins that regulate transcription -- 9.3.Mechanisms for regulating transcription initiation in bacteria -- 9.4.Competition between cl and Cro and control of the fate of bacteriophage lambda -- 9.5.Regulation of transcription termination in bacteria --

Contents note continued: 9.6.Regulation of transcription initiation and elongation in eukaryotes -- 9.7.Combinatorial regulation of eukaryotic transcription -- 9.8.The role of signaling cascades in the regulation of transcription -- 9.9.Gene silencing -- 10.RNA processing -- Introduction -- 10.1.Overview of RNA processing -- 10.2.tRNA and rRNA processing -- 10.3.tRNA and rRNA nucleotide modifications -- 10.4.mRNA capping and polyadenylation -- 10.5.RNA splicing -- 10.6.Eukaryotic mRNA splicing by the spliceosome -- 10.7.Exon definition and alternative splicing -- 10.8.RNA editing -- 10.9.Degradation of normal RNAs -- 10.10.Degradation of foreign and defective RNAs -- 10.11.RNA-binding domains in proteins -- 11.Translation -- Introduction -- 11.1.Overview of translation -- 11.2.tRNA and the genetic code -- 11.3.Aminoacyl-tRNA synthetases -- 11.4.Structure of the ribosome -- 11.5.The translation cycle: the ribosome in action --

Contents note continued: 11.6.Protein factors critical to the translation cycle -- 11.7.Translation initiation -- shared features in bacteria and eukaryotes -- 11.8.Bacterial translation initiation -- 11.9.Eukaryotic translation initiation -- 11.10.Translation elongation: decoding, peptide bond formation, and translocation -- 11.11.Translation termination, recycling, and reinitiation -- 11.12.Ribosome rescue in bacteria and eukaryotes -- 11.13.Recoding: program med stop codon read-through and frameshifting -- 11.14.Antibiotics that target the ribosome -- 12.Regulation of translation -- Introduction -- 12.1.Global regulation of initiation in bacteria and eukaryotes -- 12.2.Regulation of initiation by cis acting sequences in the 5' untranslated region in bacteria and eukaryotes -- 12.3.Regulation of translation through cis acting sequences in the 3' UTR in eukaryotes -- 12.4.Viral corruption of the translational machinery -- 13.Regulatory RNAs -- Introduction --

Contents note continued: 13.1.Overview of regulatory RNAs -- 13.2.Bacterial base-pairing sRNAs -- 13.3.Eukaryotic sRNAs: miRNAs, siRNAs, and rasiRNAs -- 13.4.Processing of eukaryotic sRNAs -- 13.5.Loading of Argonaute family proteins with eukaryotic sRNAs -- 13.6.Gene silencing by small eukaryotic RNAs -- 13.7.Viral defense role of bacterial, archaeal, and eukaryotic sRNAs -- 13.8.RNA-mediated regulation in cis -- 13.9.Protein-binding regulatory RNAs -- 13.10.Long intergenic non-coding RNAs -- 14.Protein modification and targeting -- Introduction -- 14.1.Chaperone-assisted protein folding -- 14.2.Targeting of proteins throughout the cell -- 14.3.Post-translational cleavage of the polypeptide chain -- 14.4.Lipid modification of proteins -- 14.5.Glycosylation of proteins -- 14.6.Protein phosphorylation, acetylation, and methylation -- 14.7.Protein modification by nucleotides -- 14.8.Direct chemical modification of proteins -- 14.9.Ubiquitination and sumoylation of proteins --

Contents note continued: 14.10.Protein degradation -- 15.Cellular responses to DNA damage -- Introduction -- 15.1.Types of DNA damage -- 15.2.Post-replication mismatch repair -- 15.3.Repair of DNA damage by direct reversal -- 15.4.Repair of DNA damage by base excision repair -- 15.5.Nucleotide excision repair of bulky lesions -- 15.6.Translesion DNA synthesis -- 15.7.The DNA damage response -- 15.8.The DNA damage response in bacteria -- 15.9.The DNA damage response in eukaryotes -- 15.10.DNA damage and cell death in mammalian cells -- 16.Repair of DNA double-strand breaks and homologous recombination -- Introduction -- 16.1.An overview of DNA double-strand break repair and homologous recombination -- 16.2.Double-strand break repair by NHEJ -- 16.3.Homology-directed repair of double-strand breaks -- 16.4.Generation of single-stranded DNA by helicases and nucleases -- 16.5.The mechanism of DNA strand pairing and exchange -- 16.6.Gene conversion through homology-directed repair --

Contents note continued: 16.7.Repair of damaged replication forks by homology-directed repair -- 16.8.Homologous recombination -- 16.9.Chromosome rearrangements during aberrant repair and recombination -- 17.Mobile DNA -- Introduction -- 17.1.Transposable elements: overview -- 17.2.An overview of DNA-only transposons -- 17.3.DNA-only cut-and-paste transposition -- 17.4.DNA-only nick-and-paste transposition -- 17.5.DNA cut-and-paste transposition in adaptive immunity -- 17.6.Retrotransposons -- 17.7.LTR retrotransposons -- 17.8.Non-LTR retrotransposons -- 17.9.Control of transposition -- 17.10.CSSR: overview -- 17.11.CSSR systems that control gene expression -- 17.12.CSSR conversion of DNA dimers to monomers -- 17.13.Bacteriophage lambda Integration and excision -- 18.Genomics and genetic variation -- Introduction -- 18.1.Genome sequences and sequencing projects -- 18.2.Finding functions in a genome -- 18.3.Functional genomics -- 18.4.The ENCODE project --

Contents note continued: 18.5.The evolving genome: evolutionary forces -- 18.6.The evolving genome: mechanisms of variation -- 18.7.Gene duplication and divergence of gene function -- 18.8.Changes In chromosome structure and copy number variation -- 18.9.Epigenetics and imprinting -- 18.10.Human genetic diseases: finding disease loci -- 18.11.Human genetics: impacts and implications -- 19.Tools and techniques in molecular biology -- Introduction -- 19.1.Model organisms -- 19.2.Cultured cells and viruses -- 19.3.Amplification of DNA and RNA sequences -- 19.4.DNA cloning -- 19.5.Genome manipulation -- 19.6.Detection of biological molecules -- 19.7.Separation and isolation of biological molecules -- 19.8.Identifying the composition of biological molecules -- 19.9.Detection of specific DNA sequences -- 19.10.Detection of specific RNA molecules -- 19.11.Detection of specific proteins -- 19.12.Detection of interactions between molecules -- 19.13.Imaging cells and molecules --

Contents note continued: 19.14.Molecular structure determination -- 19.15.Obtaining and analyzing a complete genome sequence.