Table
of Contents
Chapter 1: Introduction to the
Informational Biopolymers.
1.1
Proteins.
1.2 Nucleic
Acids.
1.3
The Roles of the Informational Biopolymers in the Dissemination of
Genetic Information.
1.4
The Cellular Imperative.
Chapter 2: Forces Within and Between
Biopolymers.
2.1
Conformational Potential Energy.
2.2. Dispersion
and Exclusion Effects.
2.3. Ionic
Interactions.
2.4. Dipole
Interactions.
2.5. van der
Waals Forces.
2.6. Hydrogen
Bonds.
2.7. Hydrophobic
Bonds.
2.8. Stacking
Interactions.
2.9. Modeling
Structures by Computational Molecular Mechanics.
Chapter 3: Proteins.
3.1
Amino Acids
3.2 The
Peptide Backbone.
3.3 Secondary Structures..
3.4
Thermodynamics of the a-Helix.
3.5 Tertiary
and Quaternary Structures.
3.6. Protein
Folding.
3.7. Evolutionary Relationships from Primary
Sequences.
Chapter 4: Covalent Features of the
Nucleic Acids.
4.1.
Nucleotide Sugar
4.2. Nucleotide
Base.
4.3. The N-Glycosidic Bond.
4.4. Phosphoester
Bond.
4.5. Pyrimidine
and Nucleotide Cofactors
Chapter 5: Structure, Synthesis and
Function of RNA
5.1.
The Preponderance of Ribosomal, Transfer, and Small Nuclear RNA in Cells.
5.2.
Primary Structures of RNA
5.3. Secondary Structures of RNAs.
5.4. Tertiary Structures of RNAs.
5.5. Protein-RNA Interactions.
5.6 The Biosynthesis of RNAs: Transcription.
5.7. The Participation of RNAs in Protein Synthesis.
Chapter 6: Secondary Structure of
Duplex DNA.
6.1.
Contributions of Fiber Diffraction to Our Knowledge of DNA Structure.
6.2. Prelude to the Watson-Crick Douuble Helix.
6.3. Refined and Archetypal Structures.
6.4. Structural Features Common to All Nucleic Acid Helices.
6.5. Structures From Single-Crystal Diffraction Analysis.
6.6. Structure in Solutions.
6.7.
Hydrogen Bonding in an Aqueous Environment.
6.8. Molecular
Dynamics of DNA.
6.9. Denaturation
and the Thermodynamics of DNA Stability.
6.10. Higher Organization of DNA.
6.11. Macromolecular Structure.
Chapter 7: Primary Sequences of DNA.
7.1. Base
Compositions of Prokaryotic DNAs
7.2. Base Compositions of Eukaryotic DNAs.
7.3. Dinucleotide (Nearest Neighbor) Frequencies
7.4. Sequence Complexity.
7.5. Primary Sequences in Prokaryotes.
7.6. Primary Sequence Elements in Eukaryotes.
7.7. Satellite DNA and Repetitive Sequences.
7.8. Primary
Sequences of Mitochondrial DNA.
7.9. Determining
Evolutionary Relationships from Primary Sequences.
Chapter 8: Interactions of Water
and Cations With DNA, Integral Components of the Native Conformation.
8.1.
The Unusual
Character of Water.
8.2. Hydration of Electrolytes.
8.3. Interactions of Hydrated Ions in Solution
8.4.
Macroscopic
Studies of DNA Hydration.
8.5. Microscopic
Studies of DNA Hydration. Single Crystal Diffraction.
8.6.
Interactions
of Cations with DNA.
Chapter 9: Structures and Functional Interactions of Proteins with DNA.
9.1.
Modes of
Interaction.
9.2 Methods
of Analysis.
9.3.
Principles of Sequence-Specific DNA Binding Proteins.
9.4. DNA-Binding
Proteins of the Structural Class.
9.5. DNA-Binding
Proteins of the Enzymatic Class.
9.6. DNA-Binding
Proteins of the Regulatory Class.
Chapter 10. Cellular Replication of DNA.
10.1 Stages
of Replication.
10.2. Origin Locus of Replication.
10.3. Condensation of dNTP and Elongation of DNA.
10.4. Auxiliary Replicative Processes.
10.5. Replication of the Ends of Linear Eukaryotic DNA by Telomerase.
Chapter 11: Mutations and Unscheduled Decay, Reactivity and Interactions of DNA.
11.1.
Mutations.
11.2. Point Mutations.
11.3. Relative Rates of Point Mutation
11.5. Reactions with
Endogenous Agents.
11.6. Reactions of Exogenous Agents with DNA.
Chapter 12: Repair and Recombination of DNA.
12.1. Enzymes
that Serve Several Functional Roles Including Repair.
12.2. Multiple Pathways for the Repair of Damage Caused by UV Radiation.
12.3. Mismatch Repair.
12.4. Excision Repair.
12.5. Direct Reversal of Certain Lesions.
12.6. The SOS Repair System.
12.7. Recombination and Recombination Repair.
Chapter 13: Prebiotic Origins.
13.1 The Physical
Age of the Universe.
13.2. Formation of Earth.
13.3. Age of
Chemistry.
13.4. Thermodynamic Precepts for Origins and Order. Dissipative Processes.
13.5. Hypercycles.
13.6. Age of Abiotic Chemistry, Synthesis of Alpha and Beta Molecules.
13.7. Synthesis of Gamma Monomeric Units of D-Ribose by Abiotic Means.
13.8. Beta Monomeric Units of Ribose Analogs.
13.9. The Age of Prebiotic Chemistry.
13.10. The RNA World.