An Introduction to Genomes

1. Genomes, Transcriptomes and Proteomes
1. The Human Genome
1.1. DNA
1.2. The Human Genome
1.3. Why is the Human Genome Project Important?
Study Aids For Chapter 1
Further Reading
2. Genome Anatomies
2.1. An Overview of Genome Anatomies
2.2. The Anatomy of the Eukaryotic Genome
2.3. The Anatomy of the Prokaryotic Genome
2.4. The Repetitive DNA Content of Genomes
Study Aids For Chapter 2
Further Reading
3. Transcriptomes and Proteomes
3.1. Genome Expression in Outline
3.2. The RNA Content of the Cell
3.3. The Protein Content of the Cell
Study Aids For Chapter 3
Further Reading
2. Studying Genomes
4. Studying DNA
4.1. Enzymes for DNA Manipulation
4.2. DNA Cloning
4.3. The Polymerase Chain Reaction (PCR)
Study Aids For Chapter 4
Further Reading
5. Mapping Genomes
5.1. Genetic and Physical Maps
5.2. Genetic Mapping
5.3. Physical Mapping
Study Aids For Chapter 5
Further Reading
6. Sequencing Genomes
6.1. The Methodology for DNA Sequencing
6.2. Assembly of a Contiguous DNA Sequence
6.3. The Human Genome Projects
Study Aids For Chapter 6
Further Reading
7. Understanding a Genome Sequence
7.1. Locating the Genes in a Genome Sequence
7.2. Determining the Functions of Individual Genes
7.3. Global Studies of Genome Activity
7.4. Comparative Genomics
Study Aids For Chapter 7
Further Reading
3. How Genomes Function
8. Accessing the Genome
8.1. Inside the Nucleus
8.2. Chromatin Modifications and Genome Expression
Study Aids For Chapter 8
Further Reading
9. Assembly of the Transcription Initiation Complex
9.1. The Importance of DNA-binding Proteins
9.2. DNA-Protein Interactions During Transcription Initiation
9.3. Regulation of Transcription Initiation
Study Aids For Chapter 9
Further Reading
10. Synthesis and Processing of RNA
10.1. Synthesis and Processing of mRNA
10.2. Synthesis and Processing of Non-coding RNAs
10.3. Processing of Pre-RNA by Chemical Modification
10.4. Degradation of mRNAs
10.5. Transport of RNA Within the Eukaryotic Cell
Study Aids For Chapter 10
Further Reading
11. Synthesis and Processing of the Proteome
11.1. The Role of tRNA in Protein Synthesis
11.2. The Role of the Ribosome in Protein Synthesis
11.3. Post-translational Processing of Proteins
11.4. Protein Degradation
Study Aids For Chapter 11
Further Reading
12. Regulation of Genome Activity
12.1. Transient Changes in Genome Activity
12.2. Permanent and Semipermanent Changes in Genome Activity
12.3. Regulation of Genome Activity During Development
Study Aids For Chapter 12
Further Reading
4. How Genomes Replicate and Evolve
13. Genome Replication
13.1. The Topological Problem
13.2. The Replication Process
13.3. Regulation of Eukaryotic Genome Replication
Study Aids For Chapter 13
Further Reading
14. Mutation, Repair and Recombination
14.1. Mutations
14.2. DNA Repair
14.3. Recombination
Study Aids For Chapter 14
Further Reading
15. How Genomes Evolve
15.1. Genomes: the First 10 Billion Years
15.2. Acquisition of New Genes
15.3. Non-coding DNA and Genome Evolution
15.4. The Human Genome: the Last 5 Million Years
Study Aids For Chapter 15
Further Reading
16. Molecular Phylogenetics
16.1. The Origins of Molecular Phylogenetics
16.2. The Reconstruction of DNA-based Phylogenetic Trees
16.3. The Applications of Molecular Phylogenetics
Study Aids For Chapter 16
Further Reading
Keeping up to Date
Keeping up to Date by Reading the Literature
Keeping up to Date Using the Internet

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