The Biochemistry of the Nucleic Acids
Published on 30. October 1987
Book
Paperback/Softback
978-94-010-8321-8 (ISBN)
Description
When the first edition of this book was published in 1950, it set out to present an elementary outline of the state of knowledge of nucleic acid biochemistry at that time and it was the first monograph on the subject to appear since Levene's book on Nucleic Acids in 1931. The fact that a tenth edition is required after thirty five years and that virtually nothing of the original book has been retained is some measure of the speed with which knowledge has advanced in this field. As a result of this vast increase in information it becomes increasingly difficult to fulfil the aims of providing an introduction to nucleic acid biochemistry and satisfying the requirements of advanced undergraduates and postgraduates in biochemistry, genetics and molecular biology. We have attempted to achieve these aims by con centrating on those basic aspects not normally covered in the general biochemistry textbooks and by providing copious references so that details of methodology can readily be retrieved by those requiring further information. The first seven editions emerged from the pen of J. N. Davidson who died in September 1972 shortly after completing the seventh edition. The subsequent editions have been produced by various colleagues who have tried to retain something of the character and structure of the earlier editions while at the same time introducing new ideas and concepts and eliminating some of the more out -dated material.
More details
Edition
Softcover reprint of the original 1st ed. 1986
Language
English
Place of publication
Dordrecht
Netherlands
Target group
Professional and scholarly
Dimensions
Height: 28 cm
Width: 21.6 cm
ISBN-13
978-94-010-8321-8 (9789401083218)
DOI
10.1007/978-94-009-4103-8
Other editions
Additional editions
R. L. Adams
The Biochemistry of the Nucleic Acids
E-Book
12/2012
Springer
€74.89
Available for download
James Norman Davidson
The Biochemistry of the Nucleic Acids
Book
10/1986
10th Edition
Chapman and Hall
€89.28
Article exhausted; check different version
Content
1 Introduction.- References.- 2 The structure of the nucleic acids.- 2.1 Monomeric components.- 2.1.1 Pyrimidine bases.- 2.1.2 Purine bases.- 2.1.3 Pentose and deoxypentose sugars.- 2.1.4 Nucleosides.- 2.1.5 Nucleotides.- 2.2 The primary structure of the nucleic acids.- 2.3 Shorthand notation.- 2.4 Base composition analysis of DNA.- 2.5 Molecular weight of DNA.- 2.6 The secondary structure of DNA.- 2.6.1 The basic structures.- 2.6.2 Variations on the B-form of DNA.- 2.6.3 Z-DNA.- 2.6.4 The dynamic structure of DNA.- 2.7 Denaturation and renaturation.- 2.7.1 DNA denaturation: the helix-coil transition.- 2.7.2 The renaturation of DNA: C0t value analysis.- 2.7.3 The buoyant density of DNA.- 2.8 Supercoils, cruciforms and triple-stranded structures.- 2.9 The secondary and tertiary structure of RNA.- 2.10 Chemical reactions of bases, nucleotides and polynucleotides.- 2.10.1 Reactions of ribose and deoxyribose.- 2.10.2 Reactions of the bases.- 2.10.3 Phosphodiester bond cleavage.- 2.10.4 Photochemistry.- References.- 3 Chromosome organization.- 3.1 Introduction.- 3.2 Eukaryote DNA.- 3.2.1 The eukaryote cell cycle.- 3.2.2 Eukaryote chromosomes.- 3.2.3 The allocation of specific genes to specific chromosomes.- 3.2.4 Haploid DNA content (C value).- 3.2.5 Gene frequency.- 3.2.6 Eukaryote gene structure.- 3.3 Chromatin structure.- 3.3.1 Histones and non-histone proteins.- 3.3.2 The nucleosome.- 3.3.3 Nucleosome phasing.- 3.3.4 Higher orders of chromatin structure.- 3.3.5 Loops, matrix and the chromosome scaffold.- 3.3.6 Lampbrush chromosomes.- 3.3.7 Polytene chromosomes.- 3.4 Extranuclear DNA.- 3.4.1 Mitochondrial DNA.- 3.4.2 Chloroplast DNA.- 3.4.3 Kinetoplast DNA.- 3.5 Bacteria.- 3.5.1 The bacterial chromosome.- 3.5.2 The bacterial division cycle.- 3.5.3 Bacterial transformation.- 3.6 Viruses.- 3.6.1 Structure.- 3.6.2 Virus classification.- 3.6.3 Life cycle.- 3.6.4 The Hershey-Chase experiment.- 3.6.5 Virus mutants.- 3.6.6 Virus nucleic acids.- 3.6.7 The information content of viral nucleic acids.- 3.6.8 Lysogeny and transduction.- 3.6.9 Tumour viruses and animal cell transformation.- 3.6.10 Viroids.- 3.6.11 Prions.- 3.7 Plasmids and transposons 77.- References.- 4 Degradation and modification of nucleic acids.- 4.1 Introduction and classification of nucleases.- 4.2 Non-specific nucleases.- 4.2.1 Non-specific endonucleases.- 4.2.2 Non-specific exonucleases.- 4.3 Ribonucleases (RNases).- 4.3.1 Endonucleases which form 3?-phosphate groups.- 4.3.2 Endonucleases which form 5?-phosphate groups.- 4.3.3 RNA exonucleases.- 4.3.4 Ribonucleases which act on RNA:DNA hybrids (RNase H).- 4.3.5 Double-stranded RNA-specific ribonucleases.- 4.3.6 Ribonuclease inhibitors.- 4.4 Polynucleotide phosphorylase (PNPase).- 4.5 Deoxy ribonucleases (DNases).- 4.5.1 Endonucleases.- 4.5.2 Exonucleases.- 4.5.3 Restriction endonucleases.- 4.6 Nucleic acid methylation.- 4.6.1 DNA methylation.- 4.6.2 RNA methylation and other RNA nucleotide modifications.- 4.7 Nucleic acid kinases and phosphatases.- 4.7.1 Bacteriophage polynucleotide kinase.- 4.7.2 Eukaryotic DNA and RNA kinases.- 4.8 Base exchange in RNA and DNA.- References.- 5 The metabolism of nucleotides.- 5.1 Anabolic pathways.- 5.2 The biosynthesis of the purines.- 5.3 Preformed purines as precursors.- 5.4 The biosynthesis of the pyrimidines.- 5.5 The biosynthesis of deoxyribonucleotides and its control.- 5.6 The biosynthesis of thymine derivatives.- 5.7 Aminopterin in selective media.- 5.8 Formation of nucleoside triphosphates.- 5.9 General aspects of catabolism.- 5.10 Purine catabolism.- 5.11 Pyrimidine catabolism.- References.- 6 Replication of DNA.- 6.1 Introduction.- 6.2 Semiconservative replication.- 6.3 The replication fork.- 6.3.1 Discontinuous synthesis.- 6.3.2 Okazaki pieces.- 6.3.3 Direction of chain growth.- 6.3.4 Initiation of Okazaki pieces.- 6.3.5 Continuous synthesis.- 6.4 Enzymes of DNA synthesis.- 6.4.1 Introduction.- 6.4.2 DNA polymerases.- 6.4.3 DNA ligases.- 6.4.4 Helix-destabilizing proteins (HD) or single-stranded DNA- binding proteins (ssb).- 6.4.5 DNA unwinding proteins or DNA helicases (DNA-dependent ATPases).- 6.4.6 Topoisomerases.- 6.5 Fidelity of replication.- 6.6 In vitro systems for studying DNA replication.- 6.6.1 dna mutants.- 6.6.2 Permeable cells.- 6.6.3 Cell lysates.- 6.6.4 Soluble extracts.- 6.6.5 Reconstruction experiments.- 6.7 Molecular biology of the replication fork.- 6.7.1 Lagging-strand synthesis.- 6.7.2 Leading-strand synthesis.- 6.7.3 RF replication.- 6.8 Initiation of replication-general.- 6.8.1 Methods of locating the origin and direction of replication.- 6.8.2 Replicons.- 6.8.3 Rate of replication.- 6.8.4 Origin strategies.- 6.8.5 Positive or negative control of initiation.- 6.9 Initiation of replication-specific examples.- 6.9.1 Small single-stranded phage.- 6.9.2 Double-stranded phage.- 6.9.3 Plasmids.- 6.9.4 Bacteria.- 6.9.5 Mitochondria.- 6.9.6 Double-stranded cyclic DNA viruses (SV40 and polyoma).- 6.9.7 Adenoviruses.- 6.9.8 Yeast.- 6.9.9 Higher eukaryotes.- 6.9.10 Retroviruses.- 6.10 Termination of replication.- 6.10.1 Cyclic chromosomes.- 6.10.2 Small linear chromosomes.- 6.10.3 Telomeres.- 6.11 Replication complexes.- 6.12 Chromatin replication.- References.- 7 Repair, recombination and DNA rearrangement.- 7.1 Introduction.- 7.2 Mutations and mutagens.- 7.2.1 Base and nucleoside analogues.- 7.2.2 Alkylating agents.- 7.2.3 Intercalating agents.- 7.2.4 The effects of ionizing radiation.- 7.2.5 Ultraviolet radiation.- 7.3 Repair mechanisms.- 7.3.1 Reversal of damage.- 7.3.2 Excision repair.- 7.3.3 Mismatch repair.- 7.3.4 Post-replication repair.- 7.4 Recombination.- 7.4.1 E. coli rec system and single-strand invasion.- 7.4.2 Reciprocal recombination between duplex DNA molecules.- 7.4.3 Site-specific recombination.- 7.5 Gene amplification.- 7.5.1 Developmental amplification.- 7.5.2 Amplification by chemical selection.- 7.5.3 Mechanism of amplification.- 7.6 Gene duplication and pseudogenes.- 7.6.1 Multiple related copies of eukaryotic genes.- 7.6.2 Mechanism of tandem gene duplication.- 7.6.3 Pseudogenes.- 7.6.4 Concerted evolution of duplicated genes.- 7.7 Transposition of DNA.- 7.7.1 Transposable elements.- 7.7.2 Transposition in prokaryotes.- 7.7.3 Transposition in eukaryotes.- 7.8 Gene conversion.- 7.8.1 Yeast mating-type locus.- 7.8.2 Variant surface glycoprotein (VSG) genes in trypanosomes.- 7.9 Gene rearrangements.- 7.9.1 Immunoglobulin genes.- 7.9.2 T-cell receptor genes.- 7.9.3 Other gene rearrangements.- 7.10 Chromosomal translocations.- References.- 8 RNA biosynthesis.- 8.1 DNA-dependent RNA polymerases.- 8.1.1 Bacterial DNA-dependent RNA polymerase.- 8.1.2 Eukaryotic DNA-dependent RNA polymerases.- 8.2 Prokaryotic RNA synthesis.- 8.2.1 Prokaryotic initiation of transcription.- 8.2.2 Elongation of RNA transcripts.- 8.2.3 Termination of transcription in prokaryotes.- 8.3 Eukaryotic RNA synthesis.- 8.3.1 Initiation by RNA polymerase II.- 8.3.2 Initiation by RNA polymerase III.- 8.3.3 Initiation by RNA polymerase I.- 8.3.4 Eukaryotic termination.- 8.3.5 Transcription of mitochondrial and chloroplast genes.- 8.4 RNA polymerases and RNA synthesis in DNA viruses.- 8.5 The replication of RNA viruses by RNA-dependent RNA polymerase (Replicase).- 8.5.1 RNA bacteriophage.- 8.5.2 Eukaryotic RNA viruses.- References.- 9 The arrangement of genes, their transcription and processing.- 9.1 Transcription and processing of prokaryotic and bacteriophage mRNA.- 9.2 The organization of eukaryotic protein-encoding genes.- 9.2.1 Genes are often discontinuous.- 9.2.2 Gene families and gene clustering.- 9.3 Transcription and processing of eukaryotic pre-messenger RNA.- 9.3.1 The nature of gene transcripts.- 9.3.2 Caps and 5?-leader sequences of eukaryotic mRNA.- 9.3.3 Poly adenylate tails, 3? -processing and 3? -non-coding sequences of eukaryotic mRNAs.- 9.3.4 Removal of intron transcripts from pre-mRNA.- 9.4 The arrangement of rRNA genes, their transcription and processing.- 9.4.1 The prokaryotic rRNA genes and their processing.- 9.4.2 The rRNA genes of eukaryotes.- 9.4.3 The transcription and processing of eukaryotic ribosomal RNA.- 9.5 The arrangement and expression of tRNA genes.- 9.5.1 tRNA genes.- 9.5.2 The processing of tRNA.- 9.6 The arrangement and expression of mitochondrial and chloroplast genes.- 9.6.1 Protein-encoding genes of mitochondria and chloroplasts.- 9.6.2 Mitochondrial and chloroplast rDNA.- 9.6.3 Mitochondrial and chloroplast tRNA genes.- 9.6.4 The introns of mitochondrial genes and their splicing.- 9.7 A postscript on splicing.- References.- 10 Control of transcription and mRNA processing.- 10.1 The regulation of prokaryotic RNA chain initiation.- 10.1.1 Induction of the lac operon - a negative control system.- 10.1.2 Repression of the trp operon.- 10.1.3 Catabolite repression - a positive control system.- 10.1.4 Other variations in the control of initiation at bacterial operons.- 10.1.5 The repressors of bacteriophage lambda (phage ?).- 10.1.6 The interaction of repressor and activator proteins with DNA.- 10.2 The regulation of the termination of transcription in prokaryotes.- 10.2.1 Attenuation.- 10.2.2 Antiterminators of transcription.- 10.3 Modification of prokaryotic RNA polymerase.- 10.3.1 Diversity in sigma factor.- 10.3.2 Bacteriophage T4 modulation of host RNA polymerase.- 10.4 Control of gene expression in eukaryotes.- 10.4.1 Promotors.- 10.4.2 Cis-acting control elements.- 10.4.3 Trans-acting factors.- 10.4.4 The nature of active chromatin.- 10.4.5 Multiple gene copies, amplification and gene rearrangement.- 10.5 Regulation of gene expression by RNA.- 10.5.1 Antisense RNA.- 10.5.2 Identifiers.- 10.6 The control of pre-mRNA processing.- 10.6.1 3?-Processing and poly-adenylation.- 10.6.2 Splicing of pre-mRNA.- 10.6.3 Control of the rate of processing and nuclear transport of mRNA.- References.- 11 The translation of mRNA: protein synthesis.- 11.1 The structure of tRNA.- 11.2 The genetic code.- 11.2.1 The codon as a nucleotide triplet.- 11.2.2 Assignment of amino acid codons.- 11.2.3 Assignment of termination codons.- 11.2.4 Assignment of initiation codons.- 11.2.5 The degeneracy of the genetic code.- 11.2.6 Variations in the code and codon usage.- 11.3 Aminoacylation of tRNA.- 11.4 General aspects of polypeptide formation.- 11.5 The events on the bacterial ribosome.- 11.5.1 Chain initiation.- 11.5.2 Chain elongation.- 11.5.3 Chain termination.- 11.6 The events on the eukaryotic ribosome.- 11.6.1 Chain initiation.- 11.6.2 Chain elongation.- 11.6.3 Chain termination.- 11.7 The control of the cellular location of the products of translation.- 11.7.1 Secreted proteins.- 11.7.2 Membrane proteins.- 11.7.3 Organelle proteins.- 11.8 The ribosome.- 11.8.1 Structure of the components.- 11.8.2 Organization of components in the ribosome.- 11.8.3 Functional domains in the ribosome.- 11.9 Other protein-synthesizing systems.- 11.9.1 Archaebacteria.- 11.9.2 Mitochondria.- 11.9.3 Chloroplasts.- 11.10 The regulation of translation in prokaryotes.- 11.10.1 Control of the translation of bacteriophage mRNA.- 11.10.2 Autogenous control of ribosomal protein synthesis.- 11.10.3 Codon usage and translational control.- 11.11 The regulation of translation in eukaryotes.- 11.11.1 The role of mRNA structure.- 11.11.2 The role of protein phosphorylation.- 11.11.3 Regulation in cells infected with viruses.- 11.11.4 Translationally inactive mRNA.- 11.12 The coupling of transcription and translation.- 11.13 Translational accuracy and misreading.- 11.13.1 Ribosomal optimization of translational accuracy.- 11.13.2 Suppression.- References.- Appendix: methods of studying nucleic acids.- A. 1 Occurrence and chemical analysis.- A. 1.1 Chemical determination of nucleic acids in tissues 459.- A. 1.2 Analysis of base composition and nearest-neighbour frequency.- A. 1.3 Estimation of the molecular weight of DNA.- A.2 Isolation and separation of nucleic acids.- A.2.1 Isolation and separation of DNA.- A.2.2 Isolation and separation of RNA.- A. 3 Hybridization of nucleic acids.- A.4 Methods of labelling nucleic acids.- A. 4.1 General labelling methods.- A.4.2 End-labelling methods.- A.5 Determination of nucleic acid sequences.- A. 5.1 Determination of DNA sequences.- A.5.2 Determination of RNA sequences.- A.6 Restriction mapping of DNA.- A.7 Cloning DNA.- A.7.1 The principles 480.- A.7.2 The construction of recombinants and their introduction into bacteria.- A.7.3 The identification of recombinant DNA clones.- A. 8 Analysis and manipulation of cloned DNA.- A. 8.1 Mapping of RNA transcripts 491.- A.8.2 Identification of regions of DNA that interact with proteins.- A.8.3 Allocation of cloned genes to specific chromosomes.- A.8.4 Expression in eukaryotic cells.- A.9 Chemical synthesis of oligonucleotides.- A.10 Cell-free systems for transcription ana translation.- A.11 The use of inhibitors in the study of gene expression.- References.