Organic and Biological Chemistry Book

Part I: ORGANIC CHEMISTRY. 1. Saturated Hydrocarbons Organic and Inorganic Compounds. Bonding Characteristics of the Carbon Atom. Hydrocarbons and Hydrocarbon Derivatives. Alkanes: Acyclic Saturated Hydrocarbons. Structural Formulas. Alkane Isomerism. Conformations of Alkanes. IUPAC Nomenclature for Alkanes. Line-Angle Formulas for Alkanes. Classification of Carbon Atoms. Branched-Chain Alkyl Groups. Cycloalkanes. IUPAC Nomenclature for Cycloalkanes. Isomerism in Cycloalkanes. Sources of Alkanes and Cycloalkanes. Physical Properties of Alkanes and Cycloalkanes. Chemical Properties of Alkanes and Cycloalkanes. Chemistry at a Glance: Properties of Alkanes and Cycloalkanes. Nomenclature and Properties of Halogenated Alkanes. Chemical Connections: The Occurrence of Methane; The Physiological Effects of Alkanes; Chlorofluorocarbons and the Ozone Layer. 2. Unsaturated Hydrocarbons. Unsaturated Hydrocarbons. Characteristics of Alkenes and Cycloalkenes. Names for Alkenes and Cycloalkenes. Line-Angle Formulas for Alkenes. Isomerism in Alkenes. Naturally Occurring Alkenes. Physical Properties of Alkenes. Chemical Reactions of Alkenes. Polymerization of Alkenes: Addition Polymers. Alkynes. Chemistry at a Glance: Chemical Reactions of Alkenes. Chemistry at a Glance: IUPAC Nomenclature for Alkanes, Alkenes, and Alkynes. Aromatic Hydrocarbons. Names for Aromatic Hydrocarbons. Aromatic Hydrocarbons: Physical Properties and Sources. Chemical Reactions of Aromatic Hydrocarbons. Fused-Ring Aromatic Compounds. Chemical Connections: Ethene: A Plant Hormone and High-Volume Industrial Chemical; Cis-Trans Isomerism and Vision; Carotenoids: A Source of Color; Fused-Ring Aromatic Hydrocarbons and Cancer. 3. Alcohols, Phenols, and Ethers Bonding Characteristics of Oxygen Atoms in Organic Compounds. Structural Characteristics of Alcohols. Nomenclature for Alcohols. Isomerism for Alcohols. Important Commonly Encountered Alcohols. Physical Properties of Alcohols. Preparation of Alcohols. Classification of Alcohols. Chemical Reactions of Alcohols. Chemistry at a Glance: Summary of Chemical Reactions Involving Alcohols. Polymeric Alcohols. Structural Characteristics of Phenols. Nomenclature for Phenols. Physical and Chemical Properties of Phenols. Occurrence of and Uses for Phenols. Structural Characteristics of Ethers. Nomenclature for Ethers. Isomerism for Ethers. Physical and Chemical Properties of Ethers. Cyclic Ethers. Sulfur Analogs and Alcohols. Sulfur Analogs of Ethers. Chemical Connections: Menthol: A Useful Naturally Occurring Terpene Alcohol; Ethers as General Anesthetics; Marijuana: The Most Commonly Used Illicit Drug; Garlic and Onions: Odiferous Medicinal Plants. 4. Aldehydes and Ketones. The Carbonyl Group. Structure of Aldehydes and Ketones. Nomenclature for Aldehydes. Nomenclature for Ketones. Isomerism for Aldehydes and Ketones. Selected Common Aldehydes and Ketones. Physical Properties of Aldehydes and Ketones. Preparation of Aldehydes and Ketones. Oxidation and Reduction of Aldehydes and Ketones. Reaction of Aldehydes and Ketones with Alcohols. Chemistry at a Glance: Summary of Chemical Reactions Involving Aldehydes and Ketones. Formaldehyde-Based Polymers. Sulfur-Containing Carbonyl Groups. Chemical Connections: Lachrymatory Aldehydes and Ketones; Melanin: A Hair and Skin Pigment; Diabetes, Aldehyde Oxidation, and Glucose Testing. 5. Carboxylic Acids, Esters, and Other Acid Derivatives. Structure of Carboxylic Acids and Their Derivatives. IUPAC Nomenclature for Carboxylic Acids. Common Names for Carboxylic Acids. Polyfunctional Carboxylic Acids. "Metabolic" Acids. Physical Properties of Carboxylic Acids. Preparation of Carboxylic Acids. Acidity of Carboxylic Acids. Carboxylic Acid Salts. Structure of Esters. Preparation of Esters. Chemistry at a Glance: Summary of the "H Versus R" Relationship for Pairs of Hydrocarbon Derivatives. Nomenclature for Esters. Selected Common Esters. Isomerism for Carboxylic Acids and Esters. Physical Properties of Esters. Chemical Reactions of Esters. Sulfur Analogs of Esters. Polyesters. Chemistry at a Glance: Summary of Chemical Reactions Involving Carboxylic Acids and Esters. Acid Chlorides and Acid Anhydrides. Esters and Anhydrides of Inorganic Acids. Chemical Connections: Nonprescription Pain Relievers Derived from Propanoic Acid; Carboxylic Acids and Skin Care; Aspirin; Nitroglycerin: An Inorganic Triester. 6. Amines and Amides. Bonding Characteristics of Nitrogen Atoms in Organic Compounds. Structure and Classification of Amines. Nomenclature for Amines. Isomerism for Amines. Physical Properties of Amines. Basicity of Amines. Amine Salts. Heterocyclic Amines. Selected Biochemically Important Amines. Alkaloids. Structure and Classification of Amides. Nomenclature for Amides. Selected Amides and Their Uses. Properties of Amides. Preparation of Amides. Hydrolysis of Amides. Polyamides and Polyurethanes. Chemistry at a Glance: Summary of Chemical Reactions Involving Amines and Amides. Chemical Connections: Caffeine: The Most Widely Used Central Nervous System Stimulant; Amphetamines: Central Nervous System Stimulants; Alkaloids Present in Chocolate; Acetaminophen: A Substituted Amide. Part II: BIOLOGICAL CHEMISTRY. 7. Carbohydrates. Biochemistry—An Overview. Occurrence and Functions of Carbohydrates. Classification of Carbohydrates. Chirality: Handedness in Molecules. Stereoisomerism: Enantiomers and Diastereomers. Designating Handedness Using Fischer Projections. Chemistry at a Glance: Constitutional Isomers and Stereoisomers. Properties of Enantiomers. Classification of Monosaccharides. Biochemically Important Monosaccharides. Cyclic Forms of Monosaccharides. Haworth Projection Formulas. Reactions of Monosaccharides. Disaccharides. Chemistry at a Glance: "Sugar Terminology" Associated with Monosaccharides and Their Derivatives. General Characteristics of Polysaccharides. Storage Polysaccharides. Structural Polysaccharides. Chemistry at a Glance: Types of Glycosidic Linkages for Common Glucose-Containing Di- and Polysaccharides. Acidic Polysaccharides. Glycolipids and Glycoproteins. Dietary Considerations and Carbohydrates. Chemical Connections: Blood Types and Monosaccharides; Lactose Intolerance and Galactosemia; Artifical Sweeteners; "Good and Bad Carbs": The Glycemic Index. 8. Lipids. Structure and Classification of Lipids. Fatty Acids: Lipid Building Blocks. Physical Properties of Fatty Acids. Energy-Storage Lipids: Triacylglycerols. Dietary Considerations and Triacylglycerols. Chemical Reactions of Triacylglycerols. Chemistry at a Glance: Classification Schemes for Fatty Acid Residues Present in Triacylglycerols. Membrane Lipids: Phospholipids. Membrane Lipids: Sphingoglycolipids. Chemistry at a Glance: Terminology for and Structural Relationships Among Various Types of Fatty-Acid-Containing Lipids. Membrane Lipids: Cholesterol. Cell Membranes. Emulsification Lipids: Bile Acids. Messenger Lipids: Steroid Hormones. Messenger Lipids: Eicosanoids. Protective-Coating Lipids: Biological Waxes. Chemistry at a Glance: Types of Lipids and How They Function. Chemical Connections: The Fat Content of Tree Nuts and Peanuts; Artificial Fat Substitutes; The Cleansing Action of Soap; Trans Fatty Acids and Blood Cholesterol Levels; Steroid Drugs in Sports; The Mode of Action for Anti-Inflammatory Drugs. 9. Proteins Characteristics of Proteins. Amino Acids: The Building Blocks for Proteins. Chirality and Amino Acids. Acid-Base Properties of Amino Acids. Cysteine: A Chemically Unique Amino Acid. Peptide Formation. Biochemically Important Small Peptides. General Structural Characteristics of Proteins. Primary Structure of Proteins. Secondary Structure of Proteins. Tertiary Structure of Proteins. Quaternary Structure of Proteins. Fibrous and Globular Proteins. Chemistry at a Glance: Protein Structure. Protein Hydrolysis. Protein Denaturation. Glycoproteins. Lipoproteins. Chemical Connections: The Essential Amino Acids; Substitutes for Human Insulin; Protein Structure and the Color of Meat; Denaturation and Human Hair; Cyclosporine: An Antirejection Drug; Lipoproteins and Heart Attack Risk. 10. Enzymes and Vitamins. General Characteristics of Enzymes. Nomenclature and Classification of Enzymes. Enzyme Structure. Models of Enzyme Action. Enzyme Specificity. Factors That Affect Enzyme Activity. Chemistry at a Glance: Enzyme Activity. Enzyme Inhibition. Regulation of Enzyme Activity: Allosteric Enzymes. Chemistry at a Glance: Enzyme Inhibition. Regulation of Enzyme Activity: Zymogens. Antibiotics That Inhibit Enzyme Activity. Medical Uses of Enzymes. Vitamins. Water-Soluble Vitamins. Fat-Soluble Vitamins. Chemical Connections: H. pylori and Stomach Ulcers; Enzymatic Browning: Discoloration of Fruits and Vegetables; Heart Attacks and Enzyme Analysis. 11. Nucleic Acids. Types of Nucleic Acids. Nucleotides: Building Blocks of Nucleic Acids. Primary Nucleic Acid Structure. The DNA Double Helix. Replication of DNA Molecules. Overview of Protein Synthesis. Ribonucleic Acids. Chemistry at a Glance: DNA Replication. Transcription: RNA Synthesis. The Genetic Code. Anticodons and tRNA Molecules. Translation: Protein Synthesis. Mutations. Chemistry at a Glance: Protein Synthesis. Nucleic Acids and Viruses. Recombinant DNA and Genetic Engineering. The Polymerase Chain Reaction. DNA Sequencing. Chemical Connections: Use of Synthetic Nucleic Acid Bases in Medicine; Antibiotics That Inhibit Bacterial Protein Synthesis. 12. Biochemical Energy Production. Metabolism. Metabolism and Cell Structure. Important Intermediate Compounds in Metabolic Pathways. High-Energy Phosphate Compounds. An Overview of Biochemical Energy Production. The Citric Acid Cycle. Chemistry at a Glance: Simplified Summary of the Four Stages of Biochemical Energy Production. Chemistry at a Glance: Summary of the Reactions of the Citric Acid Cycle. The Electron Transport Chain. Chemistry at a Glance: Summary of the Flow of Electrons Through the Four Complexes of the Electron Transport Chain. Oxidative Phosphorylation. Chemistry at a Glance: Summary of the Common Metabolic Pathway. ATP Production for the Common Metabolic Pathway. The Importance of ATP. Non-ETC Oxygen-Consuming Reactions. Chemical Connections: Cyanide Poisoning; Brown Fat, Newborn Babies, and Hibernating Animals; Flavonoids: An Important Class of Dietary Antioxidants. 13. Carbohydrate Metabolism. Digestion and Absorption of Carbohydrates. Glycolysis. Fates of Pyruvate. ATP Production for the Complete Oxidation of Glucose. Glycogen Synthesis and Degradation. Gluconeogenesis and the Cori Cycle. Terminology for Glucose Metabolic Pathways. The Pentose Phosphate Pathway. Chemistry at a Glance: Glucose Metabolism. Hormonal Control of Carbohydrate Metabolism. Chemical Connections: Lactate Accumulation; Diabetes Mellitus. 14. Lipid Metabolism. Digestion and Absorption of Lipids. Triacylglycerol Storage and Mobilization. Glycerol Metabolism. Oxidation of Fatty Acids. ATP Production from Fatty Acid Oxidation. Ketone Bodies. Biosynthesis of Fatty Acids: Lipogenesis. Biosynthesis of Cholesterol. Chemistry at a Glance: Interrelationships Between Carbohydrate and Lipid Metabolism. Relationships Between Lipid and Carbohydrate Metabolism. Chemical Connections: High-Intensity Versus Low-Intensity Workouts; Statins: Drugs That Lower Plasma Levels of Cholesterol. 15. Protein Metabolism Protein Digestion and Absorption. Amino Acid Utilization. ransamination and Oxidative Deamination. The Urea Cycle. Amino Acid Carbon Skeletons. Amino Acid Biosynthesis. Hemoglobin Catabolism. Chemistry at a Glance: Interrelationships Among Lipid, Carbohydrate, and Protein Metabolism. Interrelationships Among Metabolic Pathways. Chemical Connections: The Chemical Composition of Urine. Arginine, Citrulline, and the Chemical Messenger Nitric Oxide.