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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?-Proce.