DETAILED CONTENTS 22.4 The Citric Acid Cycle 787 22.5 Biosynthesis of Glucose:Gluconeogenesis 794 SOMETHING EXTRA Influenza Pandemics 802 23 Biomolecules:Lipids and Their Metabolism 805 23.1 Waxes,Fats,and Oils 806 23-2 Soap 809 23-3 Phospholipids 811 23-4 Catabolism of Triacylglycerols:The Fate of Glycerol 23-5 Catabolism of Triacylglycerols:B-Oxidation 816 23-6 Biosynthesis of Fatty Acids 820 237 Prostaglandins and Other Eicosanoids 23.8 Terpenoids 9 23-9 Steroids 23-10 Biosynthesis of Steroids 4 23-11 Some Final Comments on Metabolism SOMETHING EXTRA Statin Drugs 84g 24 Biomolecules:Nucleic Acids and Their Metabolism 852 24-1 Nucleotides and Nucleic Acids 852 24-2 Base Pairing in DNA:The Watson-Crick Model 85 24-3 Replication of DNA 24-4 Transcription of DNA 859 24.5 translation of rna:Protein biosynthesis 24-6 DNA Sequencing 864 24-7 DNA Synthesis 866 24-8 The Polymerase Chain Reaction 869 24-9 Catabolism of Nucleotides 24.10 Biosynthesis of Nucleotides 873 SOMETHING EXTRA DNA Fingerprinting 875
xvi DetaileD Contents 22-4 the citric acid cycle 787 22-5 Biosynthesis of glucose: gluconeogenesis 794 soMetHinG eXtra influenza pandemics 802 23 Biomolecules: lipids and their Metabolism | 805 23-1 waxes, Fats, and oils 806 23-2 soap 809 23-3 phospholipids 811 23-4 catabolism of triacylglycerols: the Fate of glycerol 813 23-5 catabolism of triacylglycerols: b-oxidation 816 23-6 Biosynthesis of Fatty acids 820 23-7 prostaglandins and other Eicosanoids 826 23-8 terpenoids 829 23-9 steroids 837 23-10 Biosynthesis of steroids 842 23-11 some Final comments on Metabolism 848 soMetHinG eXtra statin Drugs 849 24 Biomolecules: nucleic acids and their Metabolism | 852 24-1 nucleotides and nucleic acids 852 24-2 Base pairing in Dna: the watson–crick Model 855 24-3 Replication of Dna 858 24-4 transcription of Dna 859 24-5 translation of Rna: protein Biosynthesis 861 24-6 Dna sequencing 864 24-7 Dna synthesis 866 24-8 the polymerase chain Reaction 869 24-9 catabolism of nucleotides 871 24-10 Biosynthesis of nucleotides 873 soMetHinG eXtra Dna Fingerprinting 875 42912_00_FM_i-xxiv.indd 16 1/16/14 3:00 PM Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it
CONTENTS e25 Secondary Metabolites:An Introduction to Natural Products Chemistry877 25-1 Classifying Natural Products 25-2 Biosynthesis of Pyridoxal Phosphate 87 25-3 Biosynthesis of Morphine 4 25-4 Biosynthesis of Erythromycin 894 SoMETHING EXTRA Bioprospecting:Hunting for Natural Products 903 e26 Orbitals and Organic Chemistry: Pericyclic Reactions 905 26-1 Molecular Orbitals of Conjugated Pi Systems 905 26-2 Electrocyclic Reactions 908 26-3 Stereochemistry of Thermal Electrocyclic Reactions 264 Photochemical Electrocyclic Reactions 78 26-5 Cycloaddition Reactions 913 26-6 Stereochemistry of Cycloadditions 26-7 Sigmatropic Rearrangements 26-8 Some Examples of Sigmatropic Rearrangements 919 26-9 A Summary of Rules for Pericyclic Reactions SOMETHING EXTRA Vitamin D,the Sunshine Vitamin 922 e27 Synthetic Polymers 925 27- Chain-Growth Polymers 926 22.2 Stereochemistry of Polymerization:Ziegler-Natta Catalysts 928 27-3 Copolymers 930 27-4 Step-Growth Polymers 932
Contents xvii To access the following online-only chapters, enter ISBN: 978-1-285-84291-2 at www.cengagebrain.com and visit this book’s companion website. e25 secondary Metabolites: an introduction to natural Products Chemistry | 877 25-1 classifying natural products 878 25-2 Biosynthesis of pyridoxal phosphate 879 25-3 Biosynthesis of Morphine 884 25-4 Biosynthesis of Erythromycin 894 soMetHinG eXtra Bioprospecting: hunting for natural products 903 e26 orbitals and organic Chemistry: Pericyclic reactions | 905 26-1 Molecular orbitals of conjugated pi systems 905 26-2 Electrocyclic Reactions 908 26-3 stereochemistry of thermal Electrocyclic Reactions 910 26-4 photochemical Electrocyclic Reactions 912 26-5 cycloaddition Reactions 913 26-6 stereochemistry of cycloadditions 914 26-7 sigmatropic Rearrangements 917 26-8 some Examples of sigmatropic Rearrangements 919 26-9 a summary of Rules for pericyclic Reactions 921 soMetHinG eXtra Vitamin D, the sunshine Vitamin 922 e27 synthetic Polymers | 925 27-1 chain-growth polymers 926 27-2 stereochemistry of polymerization: Ziegler–natta catalysts 928 27-3 copolymers 930 27-4 step-growth polymers 932 42912_00_FM_i-xxiv.indd 17 1/16/14 3:00 PM Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it
CONTENTS 27-5 Olefin Metathesis Polymerization 934 27.6 Polymer Structure and Physical Properties 936 SOMETHING EXTRA Biodegradable Polymers 940 Appendices A Nomenclature of Polyfunctional Organic Compounds A-1 Acidity Constants for Some Organic Compounds Glossary 9 Answers to In-Text Problems A-3 Index 1-1
xviii Contents 27-5 olefin Metathesis polymerization 934 27-6 polymer structure and physical properties 936 soMetHinG eXtra Biodegradable polymers 940 appendices a nomenclature of polyfunctional organic compounds a-1 B acidity constants for some organic compounds a-7 c glossary a-9 D answers to in-text problems a-31 index | i-1 42912_00_FM_i-xxiv.indd 18 1/16/14 3:00 PM Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it
PREFACE I've taught o rganic chemistry ma y times for m an hy to sh of the s ect.thinking t出at they would.It didn't take lo though.before I realized what a disc onnect ther oste and real appreciation for the subject,but most seemed to worry getting into medical school.And why not?If a student has a clear caree why shouldn't that person focus his or her efforts toward meeting that goal? All of us who teach organic chemistry know that the large ma jority of our students-90%or more and including many chemistry maiors are inter- ested primarily in medicine,biology,and other life sciences rather than in chem to the lawyer,politician,or business person),why do we continue to teach the way we do?Why do our textbooks and lectures spend so much time discussing iooyWlr rossnchmist but have no conection to the limited amount of ti nore attention to th e organic chemistry of less to the organic chemistry of the research laboratory?Woul ents reach their go than rea e so,and s book nic Ch ing that the time ers v also be h This ie try.Look thr the t of s .e smocpantithataeraewatobobgalcsine阀 ng prin my those that are not Organic chemistry.which began historically as the chemistry of living organisms,is now shifting back in that direction,judging from the increasing amount of biologically oriented research done in many chemistry depart- ments and from the renaming of many departments to include chemical biol- ogy.Shouldn't our teaching reflect that shift? Organization of the Text oscopy that ntial for buildi g furthe orgatanding
P r e f a C e I’ve taught organic chemistry many times for many years. Like most faculty, I began by trying to show 19-year-old students the logic and beauty of the subject, thinking that they would find it as fascinating as I did. It didn’t take long, though, before I realized what a disconnect there was between my own interests and expectations and those of my students. Some students did develop a real appreciation for the subject, but most seemed to worry primarily about getting into medical school. And why not? If a student has a clear career goal, why shouldn’t that person focus his or her efforts toward meeting that goal? All of us who teach organic chemistry know that the large majority of our students—90% or more, and 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, politician, or business person), why do we continue to teach the way we do? Why do our textbooks and lectures spend so much time discussing details of topics that interest professional 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? Wouldn’t it better serve our students if we helped them reach their goals rather than reach goals we set for them? I believe so, and I have written this book, Organic Chemistry with Biological Applications, third edition, to encourage others who might also be thinking that the time has come to do things a bit differently. This is, first and foremost, a textbook on organic chemistry. Look through it and you’ll find that almost all the standard topics are here, although the treatment of some has been attenuated to save space. Nevertheless, my guiding principle in writing this text has been to put a greater emphasis on those organic reactions and topics that are relevant to biological chemistry than on those that are not. Organic chemistry, which began historically as the chemistry of living organisms, is now shifting back in that direction, judging from the increasing amount of biologically oriented research done in many chemistry departments and from the renaming of many departments to include chemical biology. Shouldn’t our teaching reflect that shift? c organization of the text Four distinct groups of chapters are apparent in this text. The first group (Chapters 1–6 and 10–11) covers the traditional principles of organic chemistry and spectroscopy that are essential for building further understanding. xix 42912_00_FM_i-xxiv.indd 19 1/16/14 3:00 PM Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it
PREFACE The second group (Chapters 7-9 and 12-18)covers the comm reactions found in all texts.As each laboratory reaction is discussed,however a biological example is also shown to make the material more interesting and meaningful to students.For instance,trans fatty acids are described at the same time that catalytic hydrogenation is discussed(Section 8-5):biological methylations with S-adenosylmethionine are covered with SN2 reactions (Section 12-11):and biological reductions with NADH are introduced along with laboratory NaBH4 reductions(Section 13-3). The third group of chapters(19-24)is unique to this text in its depth of coverage.These chapters deal exclusively with the main classes of biomol- ecules -amino acids and proteins,carbohydrates,lipids,and nucleic acids and show how thoroughly organic chemistry permeates biological chemistry Following an introduction to each class,major metabolic pathways for that ciass ard finally.for om mhe perspecnve of mecdanisnc organic chemistry those faculty who want a f natur and pericyclic reactions 山e book ends with a fo and had-copy vote o tho se topics.This opte What's New Text content has been revised substantially for this 3rd edition as a result of user feedback.Most noticeably.two new chapters have been made available for those who want them:Chapter 26 on Pericyclic Reactions and Chapter 27 on Synthetic Polvmers.Other changes include Every chapter ends with a brief Something Extra essay that has been repo- sitioned to follow im ediately after the last text section where it is more likely to be noticed and read The problems at the ends of chapters are now organized by topic to make it easier for students to find questions on specific subjects. New problems have been added in every chapter,164 in all. t refe TABLES a called out in color move more en te and art All figure captions have a boldfaced title,and the captions themselves use colored text to make it easier to focus on specific features in the fig ure art New topics in this 3rd edition include: .A new Something Extra,"Organic Foods:Risk versus Benefit."in Chapter 1 A new Something Extra,"Alkaloids:From Cocaine to Dental Anesthet- ics,"in Chapter 2 New coverage of bridged bicyclic molecules in Section 4-9 ·New coverage of mercu New coverage of alcohol to alkyl fluoride conversions in Section 12-3 A new section 12-5."Organometallic Coupling reactions."covering both organocopper reactions and the palladium-catalyzed Suzuki-Miyaura reaction
xx PrefaCe 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 and meaningful to students. For instance, trans fatty acids are described at the same time that catalytic hydrogenation is discussed (Section 8-5); biological methylations with S-adenosylmethionine are covered with SN2 reactions (Section 12-11); and biological reductions with NADH are introduced along with laboratory NaBH4 reductions (Section 13-3). The third group of chapters (19–24) is unique to this text in its depth of coverage. These chapters deal exclusively with the main classes of biomolecules—amino acids and proteins, carbohydrates, lipids, and nucleic acids— and show how thoroughly organic chemistry permeates biological chemistry. Following an introduction to each class, major metabolic pathways for that class are discussed from the perspective of mechanistic organic chemistry. And finally, for those faculty who want additional coverage of natural products, polymers, and pericyclic reactions, the book ends with a fourth group of chapters (25–27) devoted to those topics. This final group is available in both electronic and hard-copy formats at the request of the adopter. c What’s new Text content has been revised substantially for this 3rd edition as a result of user feedback. Most noticeably, two new chapters have been made available for those who want them: Chapter 26 on Pericyclic Reactions and Chapter 27 on Synthetic Polymers. Other changes include: • Every chapter ends with a brief Something Extra essay that has been repositioned to follow immediately after the last text section where it is more likely to be noticed and read. • The problems at the ends of chapters are now organized by topic to make it easier for students to find questions on specific subjects. • New problems have been added in every chapter, 164 in all. • Text references to all numbered fiGUres and taBles are called out in color to help students move more easily between text and art. • All figure captions have a boldfaced title, and the captions themselves use colored text to make it easier to focus on specific features in the figure art. new topics in this 3rd edition include: • A new Something Extra, “Organic Foods: Risk versus Benefit,” in Chapter 1 • A new Something Extra, “Alkaloids: From Cocaine to Dental Anesthetics,” in Chapter 2 • New coverage of bridged bicyclic molecules in Section 4-9 • New coverage of mercury-catalyzed alkyne hydration in Section 8-15 • New coverage of aromatic fluorination and fluorinated drugs in Section 9-6 • New coverage of alcohol to alkyl fluoride conversions in Section 12-3 • A new Section 12-5, “Organometallic Coupling Reactions,” covering both organocopper reactions and the palladium-catalyzed Suzuki–Miyaura reaction 42912_00_FM_i-xxiv.indd 20 1/16/14 3:00 PM Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s). Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it