DETAILED CONTENTS 17.6 Carbonyl Condensations:The Aldol Reaction 715 17.7 Dehydration of Aldol Products 719 Intramolecular Aldol Reactions 722 17.9 The Claisen Condensation Reaction 723 17.10 Intramolecular Claisen Condensations 726 17.11 Conjugate Carbonyl Additions:The Michael Reaction 78 17.12 Carbonyl Condensations with Enamines:The Stork Reaction 730 17.13 Biological Carbonyl Condensation Reactions 733 Summary 35 Summary of Reactions 736 Lagniappe-X-Ray Crystallography 38 Exercises 739 18 Amines and Heterocycles 749 18.1 Naming Amines 750 18.2 Properties of Amines 752 183 Basicity of Amines 754 18.4 Basicity of Arylamines 757 18.5 Biological Amines and the Henderson-Hasselbalch Equation 758 18.6 Synthesis of Amines 759 18.7 Reactions of Amines 764 18.8 Heterocyclic Amines 769 18.9 Fused-Ring Heterocycles 773 18.10 Spectroscopy of Amines7 Summary 778 Summary of Reactions 779 Lagniappe-Green Chemistry ll:lonic Liquids 780 Exercises 782 19 Biomolecules:Amino Acids,Peptides, and Proteins 79 19.1 Structures of Amino Acids 792 19.2 Amino Acids and the Henderson-Hasselbalch Equation:Isoelectric Points 797 19.3 Synthesis of Amino Acids 800 194 Peptides and Proteins 802 19.5 Amino Acid Analysis of Peptides 4
xiv detailed contents 17.6 Carbonyl Condensations: The Aldol Reaction 715 17.7 Dehydration of Aldol Products 719 17.8 Intramolecular Aldol Reactions 722 17.9 The Claisen Condensation Reaction 723 17.10 Intramolecular Claisen Condensations 726 17.11 Conjugate Carbonyl Additions: The Michael Reaction 728 17.12 Carbonyl Condensations with Enamines: The Stork Reaction 730 17.13 Biological Carbonyl Condensation Reactions 733 Summary 735 Summary of Reactions 736 Lagniappe—X-Ray Crystallography 738 Exercises 739 Amines and Heterocycles 749 18.1 Naming Amines 750 18.2 Properties of Amines 752 18.3 Basicity of Amines 754 18.4 Basicity of Arylamines 757 18.5 Biological Amines and the Henderson–Hasselbalch Equation 758 18.6 Synthesis of Amines 759 18.7 Reactions of Amines 764 18.8 Heterocyclic Amines 769 18.9 Fused-Ring Heterocycles 773 18.10 Spectroscopy of Amines 776 Summary 778 Summary of Reactions 779 Lagniappe—Green Chemistry II: Ionic Liquids 780 Exercises 782 Biomolecules: Amino Acids, Peptides, and Proteins 791 19.1 Structures of Amino Acids 792 19.2 Amino Acids and the Henderson–Hasselbalch Equation: Isoelectric Points 797 19.3 Synthesis of Amino Acids 800 19.4 Peptides and Proteins 802 19.5 Amino Acid Analysis of Peptides 804 18 19 39144_ FM_i-xxiv.indd xiv 8/26/09 10:48:50 AM
DETAILED CONTENTS 199 Peptide Sequencing:The Edman Degradation 805 Peptide Synthesis 807 9 Protein Structure 812 Enzymes and Coenzymes 814 How Do Enzymes Work?Citrate Synthase 818 Summary 821 Summary of Reactions 822 Lagniappe-The Protein Data Bank 823 Exercises 824 Amino Acid Metabolism 832 20 20.1 An Overview of Metabolism and Biochemical Energy 833 20.2 Catabolism of Amino Acids:Deamination 836 20.3 The Urea Cycle 841 204 Catabolism of Amino Acids:The Carbon Chains 845 20.5 Biosynthesis of Amino Acids 850 Summary 854 Lagniappe-Visualizing Enzyme Structures 855 Exercises 857 Biomolecules:Carbohydrates 862 21 21.1 Classification of Carbohydrates 863 21.2 Depicting Carbohydrate Stereochemistry:Fischer Projections84 21.3 D,L Sugars 868 21.4 Configurations of the Aldoses 870 21.5 Cyclic Structures of Monosaccharides:Anomers 872 21.6 Reactions of Monosaccharides 876 21.7 The Eight Essential Monosaccharides 882 21.8 Disaccharides 883 21.9 Polysaccharides and Their Synthesis 886 21.10 Cell-Surface Carbohydrates and Carbohydrate Vaccines Summary 890 Summary of Reactions 891 Lagniappe-Sweetness 892 Exercises 893
detailed contents xv 19.6 Peptide Sequencing: The Edman Degradation 805 19.7 Peptide Synthesis 807 19.8 Protein Structure 812 19.9 Enzymes and Coenzymes 814 19.10 How Do Enzymes Work? Citrate Synthase 818 Summary 821 Summary of Reactions 822 Lagniappe—The Protein Data Bank 823 Exercises 824 Amino Acid Metabolism 832 20.1 An Overview of Metabolism and Biochemical Energy 833 20.2 Catabolism of Amino Acids: Deamination 836 20.3 The Urea Cycle 841 20.4 Catabolism of Amino Acids: The Carbon Chains 845 20.5 Biosynthesis of Amino Acids 850 Summary 854 Lagniappe—Visualizing Enzyme Structures 855 Exercises 857 Biomolecules: Carbohydrates 862 21.1 Classification of Carbohydrates 863 21.2 Depicting Carbohydrate Stereochemistry: Fischer Projections 864 21.3 d,l Sugars 868 21.4 Configurations of the Aldoses 870 21.5 Cyclic Structures of Monosaccharides: Anomers 872 21.6 Reactions of Monosaccharides 876 21.7 The Eight Essential Monosaccharides 882 21.8 Disaccharides 883 21.9 Polysaccharides and Their Synthesis 886 21.10 Cell-Surface Carbohydrates and Carbohydrate Vaccines 889 Summary 890 Summary of Reactions 891 Lagniappe—Sweetness 892 Exercises 893 20 21 39144_ FM_i-xxiv.indd xv 8/26/09 10:48:51 AM
DETAILED CONTENTS 22 Carbohydrate Metabolism 901 22.1 Hydrolysis of Complex Carbohydrates 902 222 Catabolism of Glucose:Glycolysis4 22.3 Conversion of Pyruvate to Acetyl CoA9 22.4 The Citric Acid Cycle 915 22.5 Biosynthesis of Glucose:Gluconeogenesis 921 Summary 929 Lagniappe-Influenza Pandemics 99 Exercises 931 23 Biomolecules:Lipids and Their Metabolism 936 231 Waxes,Fats,and Oils937 23.2 Soap 940 23.3 Phospholipids 942 23.4 Catabolism of Triacylglycerols:The Fate of Glycerol943 23.5 Catabolism of Triacylglycerols:B-Oxidation 947 23.6 Biosynthesis of Fatty Acids 951 237 Terpenoids 23.8 Steroids 965 23.9 Biosynthesis of Steroids 969 23.10 Some Final Comments on Metabolism 975 Summary 978 Lagniappe-Saturated Fats,Cholesterol,and Heart Disease97 Exercises 979 24 Biomolecules:Nucleic Acids and Their Metabolism 987 24.7 Nucleotides and Nucleic Acids 987 24.2 Base Pairing in DNA:The Watson-Crick Model990 24.3 Replication of DNA 992 24.4 Transcription of DNA994 24.5 Translation of RNA:Protein Biosynthesis 99 24.6 DNA Sequencing 999 247 DNA Synthesis 1000 24.8 The Polymerase Chain Reaction 1004 24.9 Catabolism of Nucleotides 1005 24.10 Biosynthesis of Nucleotides 1008 Summary 1009 Lagniappe-DNA Fingerprinting 1010 Exercises 1011
xvi detailed contents Carbohydrate Metabolism 901 22.1 Hydrolysis of Complex Carbohydrates 902 22.2 Catabolism of Glucose: Glycolysis 904 22.3 Conversion of Pyruvate to Acetyl CoA 911 22.4 The Citric Acid Cycle 915 22.5 Biosynthesis of Glucose: Gluconeogenesis 921 Summary 929 Lagniappe—Influenza Pandemics 929 Exercises 931 Biomolecules: Lipids and Their Metabolism 936 23.1 Waxes, Fats, and Oils 937 23.2 Soap 940 23.3 Phospholipids 942 23.4 Catabolism of Triacylglycerols: The Fate of Glycerol 943 23.5 Catabolism of Triacylglycerols: -Oxidation 947 23.6 Biosynthesis of Fatty Acids 951 23.7 Terpenoids 956 23.8 Steroids 965 23.9 Biosynthesis of Steroids 969 23.10 Some Final Comments on Metabolism 975 Summary 978 Lagniappe—Saturated Fats, Cholesterol, and Heart Disease 978 Exercises 979 Biomolecules: Nucleic Acids and Their Metabolism 987 24.1 Nucleotides and Nucleic Acids 987 24.2 Base Pairing in DNA: The Watson–Crick Model 990 24.3 Replication of DNA 992 24.4 Transcription of DNA 994 24.5 Translation of RNA: Protein Biosynthesis 996 24.6 DNA Sequencing 999 24.7 DNA Synthesis 1000 24.8 The Polymerase Chain Reaction 1004 24.9 Catabolism of Nucleotides 1005 24.10 Biosynthesis of Nucleotides 1008 Summary 1009 Lagniappe—DNA Fingerprinting 1010 Exercises 1011 22 23 24 39144_ FM_i-xxiv.indd xvi 8/26/09 10:48:51 AM
DETAILED CONTENTS xvii Secondary Metabolites:An Introduction 25 to Natural Products Chemistry 101s 25.1 Classification of Natural Products 1016 25.2 Biosynthesis of Pyridoxal Phosphate 1017 25.3 Biosynthesis of Morphine 1022 25.4 Biosynthesis of Erythromycin 1031 Summary 1040 Lagniappe-Bioprospecting:Hunting for Natural Products 1041 Exercises 1041 Appendices Nomenclature of Polyfunctional Organic Compounds A-1 Acidity of Constants for Some Organic Compounds A7 Glossary A-9 D Answers to In-Text Problems A-28 Index 1-1
detailed contents xvii Secondary Metabolites: An Introduction to Natural Products Chemistry 1015 25.1 Classification of Natural Products 1016 25.2 Biosynthesis of Pyridoxal Phosphate 1017 25.3 Biosynthesis of Morphine 1022 25.4 Biosynthesis of Erythromycin 1031 Summary 1040 Lagniappe—Bioprospecting: Hunting for Natural Products 1041 Exercises 1041 Appendices A Nomenclature of Polyfunctional Organic Compounds A-1 B Acidity of Constants for Some Organic Compounds A-7 C Glossary A-9 D Answers to In-Text Problems A-28 Index I-1 25 39144_ FM_i-xxiv.indd xvii 8/26/09 10:48:51 AM
Preface any times for years and it has ofter the he te nd thei ts and expecta tudents e the l d ty nd I that feeling to oths V,d into medical school.That may be an ex ation but there is also a lot of truth in it.All of us who teach orga nic chemistry know that the large maiority of our students-90%or more.including many chemistry maior are interested primarily in medicine.biologv.and other life sciences rather than in pure chemistry. But if we are primarily teaching future physicians,biologists,biochem- ists,and others in the life sciences(not to mention the occasional lawyer and businessperson),why do we continue to teach the way we do?Why do we spend so much time discussing details of topics that interest research chem- ists but have no connection to biology?Wouldn't the limited amount of time we have be better spent paying more attention to the organic chemistry of liv ing organisms and less to the organic chemistry of the research laboratory?I believe so,and I have written this book,Organic Chemistry with Biological Applications,to encourage others who might also be thinking that the time has come to try doing things a bit differently. oremost,a textbook on organic chemis will at almo all o ard topics ar ere.Neve text Organization of the Text When looking through the text,three distinct grou uns of chanters are ent.The first gr (Chapters 1-6 and 10-11) ers the traditio ples of organic chemistry that are essential for building the background up (Chapters 7-9 and ratory reaction is discussed.however,a biological example is also shown to make the material more interesting to students.As an example,trans fatty xvili acids are described at the same time that catalytic hydrogenation is discussed
xviii I’ve taught organic chemistry many times for many years, and it has often struck me what a disconnect there is between the interests and expectations of me—the teacher—and the interests and expectations of those being taught— my students. I love the logic and beauty of organic chemistry, and I want to pass that feeling on to others. My students, however, seem to worry primarily about getting into medical school. That may be an exaggeration, but there is also a lot of truth in it. All of us who teach organic chemistry know that the large majority of our students—90% or more, including many chemistry majors—are interested primarily in medicine, biology, and other life sciences rather than in pure chemistry. But if we are primarily teaching future physicians, biologists, biochemists, and others in the life sciences (not to mention the occasional lawyer and businessperson), why do we continue to teach the way we do? Why do we spend so much time discussing details of topics that interest research chemists but have no connection to biology? Wouldn’t the limited amount of time we have be better spent paying more attention to the organic chemistry of living organisms and less to the organic chemistry of the research laboratory? I believe so, and I have written this book, Organic Chemistry with Biological Applications, to encourage others who might also be thinking that the time has come to try doing things a bit differently. This is, first and foremost, a textbook on organic chemistry, and you will find that almost all of the standard topics are here. Nevertheless, my guiding principle in writing this text has been to emphasize organic reactions and topics that are relevant to biological chemistry. Organization of the Text When looking through the text, three distinct groups of chapters are apparent. The first group (Chapters 1–6 and 10–11) covers the traditional principles of organic chemistry that are essential for building the background necessary to further understanding. The second group (Chapters 7–9 and 12–18) covers the common organic reactions found in all texts. As each laboratory reaction is discussed, however, a biological example is also shown to make the material more interesting to students. As an example, trans fatty acids are described at the same time that catalytic hydrogenation is discussed Preface 39144_ FM_i-xxiv.indd xviii 8/26/09 10:48:51 AM