Biochemistry : an organic chemistry approach

Description

Cover Half Title Title Page Copyright Page Table of Contents Preface Author Common Abbreviations 1 Fundamental Principles of Organic Chemistry 1.1 Bonding and Orbitals 1.2 Ionic versus Covalent Chemical Bonds 1.3 Breaking Covalent Bonds 1.4 Polarized Covalent σ-Bonds 1.5 Reactive Intermediates 1.6 Alkanes and Isomers 1.7 The IUPAC Rules of Nomenclature 1.8 Rings Made of Carbon: Cyclic Compounds 1.9 Hydrocarbon Functional Groups 1.10 Heteroatom Functional Groups 1.10.1 C—X Type Functional Groups 1.10.2 C=X Type Functional Groups 1.11 Hydrogen-Bonding and Solubility 1.12 Rotamers and Conformation 1.13 Conformations with Functional Groups 1.14 Conformation of Cyclic Molecules 1.15 Stereogenic Carbons and Stereoisomers 1.16 Absolute Configuration [(R) and (S) Nomenclature] 1.17 Specific Rotation 1.18 Diastereomers 1.19 Alkene Stereoisomers: (E) and (Z)-Isomers Homework 2 The Importance of Water in Biochemical Systems 2.1 Hydrogen Bonding 2.2 Solubility 2.3 Water Molecules in Biological Systems 2.4 Acid-Base Equilibria in Water 2.5 Buffers 2.6 Structural Features That Influence Acid Strength 2.7 Acid and Base Character of Alcohols, Thiols, Amines and Carbonyls 2.7.1 Acids 2.7.2 Bases 2.8 Elimination Reactions of Alkyl Halides (E2 and E1 Reactions) 2.9 Acid-Base Equilibria in Amino Acids 2.10 Directionality Homework 3 Nucleophiles and Electrophiles 3.1 Nucleophiles and Bimolecular Substitution (the SN2 Reaction) 3.2 Nucleophilic Substitution with Alcohols, Ethers, Amines, or Phosphines 3.3 Carbocations and the SN1 Reaction 3.4 Ethers and Thioethers as Nucleophiles 3.5 Chemical Reactions of Carbonyl Groups 3.6 Biochemical Reactions of Ketones and Aldehydes 3.7 Carboxylic Acid Derivatives and Acyl Substitution 3.8 Biological Hydrolysis Homework 4 Radicals 4.1 Structure of Radicals 4.2 Formation of Radicals in Organic Chemistry 4.3 Reactions of Radicals 4.4 Formation of Radicals in Biological Systems 4.5 Radicals in Biological Systems 4.6 Radical Reactions in Biochemical Systems 4.7 Radicals and Cancer Homework 5 Dienes and Conjugated Carbonyl Compounds in Biochemistry 5.1 Conjugated Dienes and Conjugated Carbonyl Compounds 5.2 Reactions of Conjugated Compounds 5.3 Conjugate (Michael) Addition 5.4 Enzyme-Mediated Conjugate Additions 5.5 Sigmatropic Rearrangement Reactions 5.6 Enzyme-Mediated Sigmatropic Rearrangements Homework 6 Enolates and Enolate Anions 6.1 Aldehydes and Ketones Are Weak Acids 6.2 Formation of Enolate Anions 6.3 The Aldol Condensation 6.4 Enzyme-Mediated Aldol Condensations 6.5 The Claisen Condensation 6.6 Enzyme-Mediated Claisen Condensation 6.7 Decarboxylation Homework 7 Enzymes 7.1 Enzyme Kinetics 7.1.1 Kinetics in Organic Chemistry 7.1.2 Catalysts and Catalytic Reactions 7.1.3 Enzyme Kinetics 7.2 Enzymes and Enzyme Classes 7.3 Oxidoreductases (EC 1) 7.3.1 Chemical Oxidation of Alcohols 7.3.2 Oxidases 7.3.3 Chemical Reduction of Carbonyl Compounds 7.3.4 Reductases 7.4 Transferases (EC 2) 7.4.1 Chemical Reactions That Incorporate Methyl, Hydroxyl, Glycosyl or Amino Groups into New Molecules 7.4.2 Methyl, Hydroxyl, Thiol, and Glycosyl Transferases 7.5 Hydrolyases (EC 3) 7.5.1 Chemical Hydrolysis 7.5.2 Esterases 7.5.3 Other Hydrolyases 7.6 Lyases (EC 4) 7.6.1 Bond Cleavage in Organic Chemistry 7.6.1.1 Decarboxylation 7.6.1.2 Enol Formation and the Acid-Catalyzed Aldol 7.6.1.3 Dehydration Reactions 7.6.1.4 [2+2]-Photocycloaddition 7.6.2 Lyase Reactions 7.7 Isomerases (EC 5) 7.7.1 Chemical Isomerization Reactions 7.7.2 Isomerase Reactions 7.8 Ligases (EC 6) 7.8.1 Chemical Methods for Carboxylation and Nucleotide Synthesis 7.8.1.1 Reactions with Carbon Dioxide 7.8.1.2 Synthesis of Polynucleotides and Polynucleosides 7.8.2 Enzymatic Coupling 7.9 Translocases (EC 7) 7.9.1 Enzymatic Transport Reactions 7.9.2 Transport of Organic Materials Homework 8 Lipids 8.1 Carboxylic Acids and Esters 8.2 Nitrate Esters, Sulfate Esters, and Phosphate Esters 8.3 Lipid Classes 8.4 Chemical Synthesis of Esters 8.5 Biosynthesis and Biodegradation of Esters Homework 9 Aromatic Compounds and Heterocyclic Compounds 9.1 Benzene and Aromaticity 9.2 Benzene Is a Carcinogen 9.3 Functionalized Benzene Derivatives 9.4 Electrophilic Aromatic Substitution: The SEAr Reaction 9.5 Enzymatic SEAr Reactions 9.6 Reduction of Aromatic Compounds 9.7 Biological Reduction of Aromatic Rings 9.8 Nucleophilic Aromatic Substitution. The SNAr Reaction 9.9 Enzymatic SNAr Reactions 9.10 Polynuclear Aromatic Hydrocarbons 9.11 Heteroaromatic Compounds: Nitrogen, Oxygen, or Sulfur 9.12 Reactions of Heteroaromatic Compounds 9.13 Enzymatic Reactions That Generate Heterocyclic Compounds 9.14 Reduced Forms of Nitrogen, Oxygen, and Sulfur Heterocycles 9.15 Heteroaromatic Compounds with More Than One Ring Homework 10 Carbon–Metal Bonds, Chelating Agents and Coordination Complexes 10.1 Organometallics 10.2 Organometallics in Organic Chemistry 10.3 Biologically Relevant Metals 10.4 Chelating Agents Homework 11 Amino Acids 11.1 Characteristics of Amino Acids 11.2 Structure of α-Amino Acids Homework 12 Peptides and Proteins 12.1 Reactions and Synthesis of α-Amino Acids 12.2 Amino Acid Biosynthesis 12.3 Peptides Are Poly(amides) of Amino Acid Residues 12.4 Chemical Synthesis of Peptides 12.5 Peptide Biosynthesis 12.6 Proteins and Enzymes Are Poly(peptides) 12.7 Peptide Degradation and End Group Identification 12.8 Peptidases Homework 13 Carbohydrates 13.1 (Poly)hydroxy Carbonyl Compounds 13.2 Monosaccharides 13.3 Mutarotation 13.4 The Anomeric Effect 13.5 Ketose Monosaccharides Homework 14 Glycosides 14.1 Monosaccharides 14.2 Disaccharides, Trisaccharides, Oligosaccharides, and Polysaccharides 14.3 Reactions of Carbohydrates 14.4 Biologically Important Glycosides 14.5 Biosynthesis of Carbohydrates and Glycosides 14.6 Biodegradation of Carbohydrates and Glycosides Homework 15 Nucleic Acids, Nucleosides and Nucleotides 15.1 Nucleosides and Nucleotides 15.2 Polynucleotides 15.3 Chemical Synthesis of Nucleotides 15.4 Biosynthesis of Nucleotides 15.5 Ribozymes 15.6 Hydrolysis of RNA and DNA 15.7 RNA-Mediated Programmable DNA Cleavage 15.8 Restriction Enzymes Homework 16 Answers to Homework Problems Chapter 1 Chapter 2 Chapter 3 Chapter 4 Chapter 5 Chapter 6 Chapter 7 Chapter 8 Chapter 9 Chapter 10 Chapter 11 Chapter 12 Chapter 13 Chapter 14 Chapter 15 Index