Guide to Biochemistry

Guide to Biochemistry provides a comprehensive account of the essential aspects of biochemistry. This book discusses a variety of topics, including biological molecules, enzymes, amino acids, nucleic acids, and eukaryotic cellular organizations. Organized into 19 chapters, this book begins with an overview of the construction of macromolecules from building-block molecules. This text then discusses the strengths of some weak acids and bases and explains the interaction of acids and bases involving the transfer of a proton from an acid to a base. Other chapters consider the effectiveness of enzymes, which can be appreciated through the comparison of spontaneous chemical reactions and enzyme-catalyzed reactions. This book discusses as well structure and function of lipids. The final chapter deals with the importance and applications of gene cloning in the fundamental biological research, which lies in the preparation of DNA fragments containing a specific gene. This book is a valuable resource for biochemists and students.

Preface

Acknowledgments

1 Biological Molecules

1.1 Cell Theory

1.2 The Role of Carbon

1.3 Stereochemistry

1.4 The Nature of Macromolecules

1.5 Hybrid Molecules

1.6 The Functions of Macromolecules

1.7 Other Functions of Monomeric Units

2 The Physical Chemistry of Aqueous Systems

2.1 Ionization and Macromolecules

2.2 Hydrogen Bonding in Water

2.3 Ionization of Water

2.4 pH Scale

2.5 Theories of Acids and Bases

2.6 The Relative Strengths of Acids and Bases

2.7 The Interaction of Aqueous Solutions of Monoprotic Acids and Bases

2.8 The Interaction of Polyprotic Weak Acids and Strong Bases

2.9 Buffer Systems

2.10 Summary of Useful Equations in pH Calculations

2.11 Example Calculations

3 Carbohydrates

3.1 The Definition of Carbohydrate

3.2 The Monosaccharides

3.3 The Ring Structures of Monosaccharides

3.4 Derivatives of Monosaccharides

3.5 Oligosaccharides

3.6 Polysaccharides: Homoglycans

3.7 Polysaccharides: Heteroglycans

4 Amino Acids and Proteins

4.1 The Classification of Amino Acids

4.2 Ionic Properties of Amino Acids

4.3 The Major Bonds between Amino Acids in Polypeptide Chains

4.4 The Primary Structure of Proteins

4.5 The Secondary Structure of Proteins

4.6 The Tertiary Structure of Proteins

4.7 The Quaternary Structure of Proteins

5 Enzymes

5.1 Comparison of Chemical and Enzymic Reactions

5.2 Enzyme Architecture

5.3 Enzyme Classification

5.4 Enzyme Catalysis

6 Enzyme Kinetics

6.1 Factors Influencing the Rate of an Enzyme-Catalysed Reaction

6.2 Steady-State Enzyme Kinetics

6.3 Enzyme Inhibition

6.4 Allostery

6.5 Isoenzymes

7 Nucleic Acids

7.1 The Structure of Nucleotides

7.2 Polynucleotide Chains

7.3 The Structure of DNA

7.4 The Structure of RNA

7.5 Some Properties of Nucleic Acids

8 Lipids

8.1 The Classes of Lipids

8.2 Fatty Acids

8.3 Waxes

8.4 Acylglycerols

8.5 Phosphoacylglycerols

8.6 Plasmalogens

8.7 Sphingolipids

8.8 Eicosanoids

8.9 Terpenes

8.10 Steroids

8.11 Circulatory Lipid Complexes

9 Eukaryotic Cellular Organization

9.1 Prokaryotic and Eukaryotic Cells

9.2 The Plasma Membrane: Structure

9.3 The Plasma Membrane: Transport Mechanisms

9.4 Nuclear Structures

9.5 Electron-Transporting Organelles

9.6 Organelles Associated with Protein Synthesis

9.7 Lysosomes and Microbodies

9.8 The Cytoskeleton

10 Principles of Cellular Metabolism

10.1 Biological Energetics

10.2 Equilibrium Thermodynamics

10.3 Coupled Reactions

10.4 The Role of ATP

10.5 Metabolic Pathways

10.6 Intracellular Control of Metabolism

10.7 Extracellular Control of Metabolism

11 Carbohydrate Metabolism

11.1 The Pathways of Carbohydrate Metabolism

11.2 The Reactions of Glycolysis

11.3 NAD+ and Glycolysis

11.4 The Role of Glycogen

11.5 Glycogenesis and Glycogenolysis

11.6 The Role of Gluconeogenesis

11.7 The Reactions of Gluconeogenesis

11.8 The Role of the Pentose Phosphate Pathway

11.9 The Reactions of the Pentose Phosphate Pathway

11.10 The Energetics of Carbohydrate Metabolism

11.11 The Regulation of Carbohydrate Metabolism

12 The Tricarboxylate Cycle

12.1 Role in Metabolism

12.2 Entry of Pyruvate into the Mitochondrion

12.3 The Oxidative Decarboxylation of Pyruvate

12.4 The Reactions of the Tricarboxylate Cycle

12.5 The Energetics of the Cycle

12.6 Anaplerosis

12.7 The Regulation of the Cycle

12.8 The Glyoxylate Cycle

13 Mitochondrial Oxidative Phosphorylation

13.1 The Role of Oxidative Phosphorylation

13.2 The Structure of Electron-Transport Assemblies

13.3 Oxidation-Reduction Reactions

13.4 The Sequence of Electron-Transport Carriers

13.5 The Synthesis of ATP

13.6 Mechanisms of Coupling Electron Transport to ATP Synthesis

13.7 Inhibitors of Oxidative Phosphorylation

14 Photosynthesis

14.1 The Role of Photosynthesis

14.2 The Thylakoid Photosystems

14.3 The Light Reactions: Electronic Excitation

14.4 The Light Reactions: Electron Transport

14.5 The Dark Reactions: The Calvin Cycle

14.6 The Dark Reactions: Carbohydrate Synthesis

15 The Metabolism of Lipids

15.1 Fatty Acids as Energy Sources

15.2 The β-Oxidation Pathway

15.3 Ketone Body Metabolism

15.4 The Synthesis of Fatty Acids

15.5 The Synthesis of Triacylglycerols

15.6 The Synthesis of Eicosanoids

15.7 The Synthesis of Cholesterol

15.8 The Metabolism of Steroid Hormones

16 Nitrogen Metabolism

16.1 The Biosynthesis of Amino Acids in Plants and Microorganisms

16.2 The Biosynthesis of Amino Acids in Mammals and Humans

16.3 The Degradation of Amino Acids

16.4 The Disposal of Amino Nitrogen in the Animal Kingdom

16.5 The Urea Cycle

16.6 The Biosynthesis of Heterocyclic Compounds

16.7 The Hybridoma Technique

16.8 The Degradation of Heterocyclic Compounds

17 Gene Expression

17.1 The Central Dogma

17.2 Transcription: Initiation and Elongation

17.3 Transcription: Termination

17.4 Translation: The Role of Amino-Acid-TRNA Ligases

17.5 Translation: The Genetic Code

17.6 Translation: The Mechanism of Protein Biosynthesis

17.7 Mutation

17.8 Control of Gene Expression

18 The Replication of Deoxyribonucleic Acid

18.1 Semiconservative Replication

18.2 An Overview of DNA Replication

18.3 The Enzymology of DNA Replication in Prokaryotes

18.4 DNA Repair

19 Gene Cloning

19.1 Applications of Gene Cloning

19.2 Outline of Gene Cloning Methodology

19.3 Vectors Employed in E. Coli

19.4 Restriction Endonucleases

19.5 The Transport of Recombinant DNA Molecules into a Host Bacterium

19.6 Selection of Recombinant DNA

19.7 DNA-Sequencing Techniques

Index