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

By:

Craig, Nancy Lynn, 1952- [author.]

Material type: Text

TextPublisher: Oxford, United Kingdom ; New York, NY, United States of America : Oxford University Press, [2014]Edition: Second editionDescription: xxxi, 912 pages : illustrations (chiefly color) ; 28 cmContent type:

text

Media type:

unmediated

Carrier type:

volume

ISBN:

9780198705970 (hbk.)
0198705972 (hbk.)
9780199658572 (pbk.)
0199658579 (pbk.)

Subject(s):

DDC classification:

572.8 23 C.N.M

LOC classification:

QH506 .M6628 2014

Contents:

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.

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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.

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