Informational Biopolymers of Genes and Gene Expression

Full of novel insights informed by years of research and teaching, R.D. Blake has written a new text that examines the biophysics and biochemistry of nucleic acids and proteins. This book carves out the dynamic interface between chemistry and molecular biology, and provides a detailed picture of nucleic acids and proteins, their structures, biological properties, and origins and evolution. While pitched at a level that is accessible to upper-level undergraduate students of biology, the book will likewise be of keen interest to researchers and graduate students in biology, chemistry and the physical sciences. A broad range of topics accompanied with extensive references, footnotes, boxed asides, chapter ending problems, and detailed illustrations throughout combine to make this an ideal choice for courses on advanced biochemistry, physical biochemistry, nucleic acids and proteins, biophysics and biochemistry, molecular evolution, and protein-nucleic acid interactions.

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 Interaction 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
11.4 Molecular Basis of Mutagenesis
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

About the Author :
R.D.BLAKE was formerly lecturer in the Biochemistry Department at the University of Maine.


Review :
"I am blown away by this book: its scope, its level of detail, its up-to-date coverage. It will be a valuable source to have on one’s shelf to refer to a concise discussion of a topic, with lots of references to the pertinent literature." --Victor Bloomfield, University of Minnesota

"Without doubt, this book will make a useful reference text for the expert and should provide a good text for teaching graduate students." --Philip C. Bevilacqua, University of Pennsylvania

"Written in a detailed but very accessible way, Blake’s book plays down the use of equations and formalisms so they don’t get in the way of the narrative flow of ideas and concepts. The comprehensive array of topics makes it very attractive as both a reference text and a textbook for Physical Biochemistry or Molecular Biology courses. It fills a real unmet need by looking at a whole range of fashionable molecular biology topics with a rigor that has never before been applied to these topics in one volume." --Ken Marx, University of Massachusetts