Biochemistry

PrefaceAcknowledgments1 The Scene of Action A. The Simplest Living Things B. Eukaryotic Cells C. The Evolution of Complex Organisms D. The Kingdom Protista E. Multicellular Organisms F. The Regulation of Cell Chemistry References Study Questions2 The Molecules from Which We Are Made A. Structural Principles for Small Molecules B. The Proteins C. Sugars and Polysaccharides D. Nucleic Acids E. The Lipids F. Some Important Small Molecules and Ions G. The Chemical Composition of Cells H. How We Have Learned the Structures References Study Questions3 Energetics of Biochemical Reactions A. Thermodynamics B. Tables of ΔG° Values for Biochemical Compounds C. Electrode Potentials and Free Energy Changes for Oxidation-Reduction Reactions D. Thermodynamics and Life Processes E. Linear Free Energy Relationships References Study Questions4 How Molecules Stick Together A. Principle of Complementarity B Forces Acting between Molecules C The Quantitative Measurement of Binding D. How Macromolecules Pack Together E. Cooperative Changes in Conformation F. Muscle G. Self-Assembly of Macromolecular Structures References Study Questions5 Membranes and Cell Coats A. The Structure of Membranes B. Membrane Metabolism and Function C. Cell Surface Antigens and Receptors D. Structure of Bacterial Cell Walls E. Plant Cell Walls References Study Questions6 Enzymes: The Protein Catalysts of Cells A. Primer on Enzyme Kinetics B. Inhibition and Activation of Enzymes C. Growth Rates of Cells D. Specificity of Enzymatic Action E. Mechanisms of Catalysis F. The Regulation of Enzymatic Activity G. Classification of Enzymes References Study Questions7 The Kinds of Reactions Catalyzed by Enzymes A. a Preview of Some Metabolic Pathways B. Classifying Enzymatic Reactions C. Nucleophilic Displacement Reactions (Reaction Type 1) D. Displacement Reactions on Carbonyl Groups E. Displacement on a Phosphorus Atom F. Multiple Displacement Reactions and the Coupling of ATP Cleavage to Endergonic Processes G. Transfer of Sulfate H. Addition and Elimination Reactions I. Enolic Intermediates in Isomerization Reactions J. Beta Cleavage and Condensation K. Some Isomerization and Rearrangement Reactions References Study Questions8 Coenzymes—Nature's Special Reagents A. ATP and the Nucleotide "Handles" B. Coenzyme a and Phosphopantetheine C. Bound Biotin as a Prosthetic Group D. Thiamine Diphosphate E. Pyridoxal Phosphate F. Keto Acids and Other Unusual Electrophilic Centers G. Hydrogen Transfer Coenzymes H. Pyridine Nucleotide Coenzymes and Dehydrogenases I. The Flavin Coenzymes J. Lipoic Acid and the Oxidative Decarboxylation of α-Keto Acids K. Tetrahydrofolic Acid and Other Pterin Coenzymes L. Vitamin B12 Coenzymes References Study Questions9 Organization of Metabolism: Catabolic Pathways A. The Oxidation of Fatty Acids B. The Citric Acid Cycle C. Oxidative Pathways Related to the Citric Acid Cycle D. Catabolism of Propionyl Coenzyme a and Propionate E. Catabolism of Sugars F. Fermentation: "Life Without Oxygen" References Study Questions10 How Oxygen Meets the Electrons with Generation of ATP and Other Stories A. Historical Notes B. Heme Protiens C. Nonheme Iron Proteins D. Quinones as Hydrogen Carriers E. The Electron Transport Chain and Oxidative Phosphorylation E. Energy from Inorganic Reactions G. Oxygenases and Hydroxylases References Study Questions11 Biosynthesis: How New Molecules Are Put Together A. Metabolic Loops and Biosynthetic Families B. Harnessing the Energy of ATP C. Reducing Agents for Biosynthesis D. Assembling the Monomer Units E. Biosynthesis and Modification of Polymers F. Regulation of Biosynthetic Pathways References Study Questions12 Some Specific Pathways of Metabolism of Carbohydrates and Lipids A. Interconversions of Monosaccharides B. Synthesis and Utilization of Oligosaccharides C. Synthesis of Polysaccharides D. The Intracellular Breakdown of Polysaccharides and Glycolipids E. Specific Aspects of Fatty Acid Metabolism F. Metabolism of Triglycerides, Phospholipids, and Glycolipids G. The Polyketides H. Polyprenyl (Isoprenoid) Compounds I. Steroid Compounds References Study Questions13 Light in Biology A. Properties of Light B. Absorption of Light by Matter C. Fluorescence and Phosphorescence D. Photochemistry E. Photosynthesis F. Vision G. Other Light Responses H. Bioluminescence References Study Questions14 The Metabolism of Nitrogen-Containing Compounds A. Fixation of N2 and Other Reactions of Inorganic Nitrogen Compounds B. Incorporation of NH3 into Amino Acids and Proteins C. Synthesis and Catabolism of the Glutamic Acid Family of Compounds D. Compounds Derived from Aspartate E. Alanine and the Branched Chain Amino Acids F. Serine and Glycine G. Cysteine and Sulfur Metabolism H. Metabolism of Aromatic Compounds I. The Metabolism of Tryptophan and the Synthesis of NAD J. The Metabolism of Histidine K. The Metabolism of Pyrimidines and Purines L. Folic Acid, Flavins, and Dimethylbenzimidazole References Study Questions15 Biochemical Genetics and the Synthesis of Nucleic Acids and Proteins A. How the Present Concepts Emerged B. The Transcription of RNA Molecules C. Translation of the Genetic Message: Protein Synthesis D. Genetic Methods E. Replication of DNA F. Restriction and Modification of DNA G. Recombination, Integration, and Excision H. Mutations, Cancer and Genetic Engineering I. The Eukaryotic Chromosome and Its Control References Study Questions16 Growth, Differentiation, and Chemical Communication between Cells A. The Hormones B. Neurochemistry C. Differentiation and Developmental Biology D. Ecological Matters (Author's Personal Postscript References Study QuestionsAppendix. The Construction of Molecular Model A. Ball-and-Stick Models B. Space-Filling Models C. Cardboard ModelsSubject Index