Biochemistry: An Organic Chemistry Approach | KitaabNow

Biochemistry: An Organic Chemistry Approach

 31,994
  • Author: Michael B. Smith
  • ISBN: 9780815366454
  • Publisher: CRC Press
  • Edition: 1st
  • Publication Date: May 16, 2020
  • Format: Paperback – 398 pages
  • Language: English


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Description

Reactions in biochemistry can be explained by an understanding of fundamental organic chemistry principles and reactions.  This paradigm is extended to biochemical principles and to myriad biomolecules.

Biochemistry: An Organic Chemistry Approach provides a framework for understanding various topics of biochemistry, including the chemical behavior of biomolecules, enzyme activity, and more. It goes beyond mere memorization. Using several techniques to develop a relational understanding, including homework, this text helps students fully grasp and better correlate the essential organic chemistry concepts with those concepts at the root of biochemistry.  The goal is to better understand the fundamental principles of biochemistry.

Key Features
  • Presents a review chapter of fundamental organic chemistry principles and reactions.
  • Presents and explains the fundamental principles of biochemistry using principles and common reactions of organic chemistry.
  • Discusses enzymes, proteins, fatty acids, lipids, vitamins, hormones, nucleic acids and other biomolecules by comparing and contrasting them with the organic chemistry reactions that constitute the foundation of these classes of biomolecules.
  • Discusses the organic synthesis and reactions of amino acids, carbohydrates, nucleic acids and other biomolecules.
Table of Contents
  1. Preface……………………………………………………………………………………………………………………………..xi
  2. Author…………………………………………………………………………………………………………………………… xiii
  3. Common Abbreviations……………………………………………………………………………………………………..xv
  4. Chapter 1 Fundamental Principles of Organic Chemistry……………………………………………………1
    1. 1.1 Bonding and Orbitals……………………………………………………………………………..1
    2. 1.2 Ionic versus Covalent Chemical Bonds……………………………………………………..2
    3. 1.3 Breaking Covalent Bonds………………………………………………………………………..3
    4. 1.4 Polarized Covalent σ-Bonds…………………………………………………………………….4
    5. 1.5 Reactive Intermediates……………………………………………………………………………5
    6. 1.6 Alkanes and Isomers………………………………………………………………………………7
    7. 1.7 The IUPAC Rules of Nomenclature………………………………………………………….8
    8. 1.8 Rings Made of Carbon: Cyclic Compounds…………………………………………….. 11
    9. 1.9 Hydrocarbon Functional Groups……………………………………………………………. 11
    10. 1.10 Heteroatom Functional Groups……………………………………………………………… 13
    11. 1.10.1 C—X Type Functional Groups………………………………………………….. 13
    12. 1.10.2 C=X Type Functional Groups……………………………………………………. 17
    13. 1.11 Hydrogen-Bonding and Solubility………………………………………………………….. 21
    14. 1.12 Rotamers and Conformation………………………………………………………………….24
    15. 1.13 Conformations with Functional Groups…………………………………………………..30
    16. 1.14 Conformation of Cyclic Molecules………………………………………………………… 31
    17. 1.15 Stereogenic Carbons and Stereoisomers…………………………………………………. 37
    18. 1.16 Absolute Configuration [(R) and (S) Nomenclature]…………………………………. 39
    19. 1.17 Specific Rotation………………………………………………………………………………….44
    20. 1.18 Diastereomers………………………………………………………………………………………46
    21. 1.19 Alkene Stereoisomers: (E) and (Z)-Isomers…………………………………………….. 51
    22. Homework…………………………………………………………………………………………………….54
  5. Chapter 2 The Importance of Water in Biochemical Systems…………………………………………….. 55
    1. 2.1 Hydrogen Bonding……………………………………………………………………………….. 55
    2. 2.2 Solubility……………………………………………………………………………………………. 58
    3. 2.3 Water Molecules in Biological Systems………………………………………………….. 59
    4. 2.4 Acid-Base Equilibria in Water………………………………………………………………. 61
    5. 2.5 Buffers………………………………………………………………………………………………..65
    6. 2.6 Structural Features That Influence Acid Strength……………………………………..66
    7. 2.7 Acid and Base Character of Alcohols, Thiols, Amines and Carbonyls……….. 67
    8. 2.7.1 Acids………………………………………………………………………………………. 67
    9. 2.7.2 Bases……………………………………………………………………………………….69
    10. 2.8 Elimination Reactions of Alkyl Halides (E2 and E1 Reactions)………………… 71
    11. 2.9 Acid-Base Equilibria in Amino Acids……………………………………………………. 74
    12. 2.10 Directionality………………………………………………………………………………………. 78
    13. Homework…………………………………………………………………………………………………….80
  6. Chapter 3 Nucleophiles and Electrophiles………………………………………………………………………..83
    1. 3.1 Nucleophiles and Bimolecular Substitution (the SN2 Reaction)…………………..83
    2. 3.2 Nucleophilic Substitution with Alcohols, Ethers, Amines, or Phosphines……85
    3. 3.3 Carbocations and the SN1 Reaction…………………………………………………………88
    4. 3.4 Ethers and Thioethers as Nucleophiles……………………………………………………90
    5. 3.5 Chemical Reactions of Carbonyl Groups…………………………………………………93
    6. 3.6 Biochemical Reactions of Ketones and Aldehydes……………………………………96
    7. 3.7 Carboxylic Acid Derivatives and Acyl Substitution…………………………………..97
    8. 3.8 Biological Hydrolysis………………………………………………………………………….. 102
    9. Homework………………………………………………………………………………………………….. 106
  7. Chapter 4 Radicals……………………………………………………………………………………………………… 109
    1. 4.1 Structure of Radicals………………………………………………………………………….. 109
    2. 4.2 Formation of Radicals in Organic Chemistry………………………………………… 110
    3. 4.3 Reactions of Radicals…………………………………………………………………………. 111
    4. 4.4 Formation of Radicals in Biological Systems………………………………………… 112
    5. 4.5 Radicals in Biological Systems……………………………………………………………. 114
    6. 4.6 Radical Reactions in Biochemical Systems…………………………………………… 116
    7. 4.7 Radicals and Cancer…………………………………………………………………………… 118
    8. Homework………………………………………………………………………………………………….. 119
  8. Chapter 5 Dienes and Conjugated Carbonyl Compounds in Biochemistry…………………………. 121
    1. 5.1 Conjugated Dienes and Conjugated Carbonyl Compounds……………………… 121
    2. 5.2 Reactions of Conjugated Compounds……………………………………………………124
    3. 5.3 Conjugate (Michael) Addition……………………………………………………………… 127
    4. 5.4 Enzyme-Mediated Conjugate Additions……………………………………………….. 128
    5. 5.5 Sigmatropic Rearrangement Reactions…………………………………………………. 129
    6. 5.6 Enzyme-Mediated Sigmatropic Rearrangements……………………………………. 132
    7. Homework………………………………………………………………………………………………….. 133
  9. Chapter 6 Enolates and Enolate Anions………………………………………………………………………… 135
    1. 6.1 Aldehydes and Ketones Are Weak Acids………………………………………………. 135
    2. 6.2 Formation of Enolate Anions………………………………………………………………. 136
    3. 6.3 The Aldol Condensation……………………………………………………………………… 137
    4. 6.4 Enzyme-Mediated Aldol Condensations……………………………………………….. 138
    5. 6.5 The Claisen Condensation…………………………………………………………………… 141
    6. 6.6 Enzyme-Mediated Claisen Condensation……………………………………………… 142
    7. 6.7 Decarboxylation………………………………………………………………………………… 143
    8. Homework………………………………………………………………………………………………….. 144
  10. Chapter 7 Enzymes…………………………………………………………………………………………………….. 147
    1. 7.1 Enzyme Kinetics……………………………………………………………………………….. 147
    2. 7.1.1 Kinetics in Organic Chemistry………………………………………………… 147
    3. 7.1.2 Catalysts and Catalytic Reactions…………………………………………….. 149
    4. 7.1.3 Enzyme Kinetics……………………………………………………………………. 149
    5. 7.2 Enzymes and Enzyme Classes…………………………………………………………….. 153
    6. 7.3 Oxidoreductases (EC 1)………………………………………………………………………. 157
    7. 7.3.1 Chemical Oxidation of Alcohols………………………………………………. 157
    8. 7.3.2 Oxidases……………………………………………………………………………….. 159
    9. 7.3.3 Chemical Reduction of Carbonyl Compounds……………………………. 161
    10. 7.3.4 Reductases…………………………………………………………………………….. 162
    11. 7.4 Transferases (EC 2)……………………………………………………………………………. 163
    12. 7.4.1 Chemical Reactions That Incorporate Methyl, Hydroxyl,
    13. Glycosyl or Amino Groups into New Molecules………………………… 163
    14. 7.4.2 Methyl, Hydroxyl, Thiol, and Glycosyl Transferases…………………… 166
    15. 7.5 Hydrolyases (EC 3)…………………………………………………………………………….. 168
    16. 7.5.1 Chemical Hydrolysis………………………………………………………………. 169
    17. 7.5.2 Esterases……………………………………………………………………………….. 170
    18. 7.5.3 Other Hydrolyases………………………………………………………………….. 171
    19. 7.6 Lyases (EC 4)……………………………………………………………………………………. 174
    20. 7.6.1 Bond Cleavage in Organic Chemistry……………………………………….. 174
    21. 7.6.1.1 Decarboxylation……………………………………………………….. 174
    22. 7.6.1.2 Enol Formation and the Acid-Catalyzed Aldol…………….. 175
    23. 7.6.1.3 Dehydration Reactions………………………………………………. 176
    24. 7.6.1.4 [2+2]-Photocycloaddition…………………………………………… 177
    25. 7.6.2 Lyase Reactions……………………………………………………………………… 178
    26. 7.7 Isomerases (EC 5)……………………………………………………………………………… 180
    27. 7.7.1 Chemical Isomerization Reactions……………………………………………. 181
    28. 7.7.2 Isomerase Reactions……………………………………………………………….. 184
    29. 7.8 Ligases (EC 6)…………………………………………………………………………………… 185
    30. 7.8.1 Chemical Methods for Carboxylation and Nucleotide Synthesis….. 185
    31. 7.8.1.1 Reactions with Carbon Dioxide………………………………….. 185
    32. 7.8.1.2 Synthesis of Polynucleotides and Polynucleosides………… 186
    33. 7.8.2 Enzymatic Coupling……………………………………………………………….. 187
    34. 7.9 Translocases (EC 7)……………………………………………………………………………. 189
    35. 7.9.1 Enzymatic Transport Reactions……………………………………………….. 189
    36. 7.9.2 Transport of Organic Materials………………………………………………… 189
    37. Homework………………………………………………………………………………………………….. 190
  11. Chapter 8 Lipids…………………………………………………………………………………………………………. 193
    1. 8.1 Carboxylic Acids and Esters……………………………………………………………….. 193
    2. 8.2 Nitrate Esters, Sulfate Esters, and Phosphate Esters……………………………….. 196
    3. 8.3 Lipid Classes…………………………………………………………………………………….. 199
    4. 8.4 Chemical Synthesis of Esters……………………………………………………………….203
    5. 8.5 Biosynthesis and Biodegradation of Esters…………………………………………….205
    6. Homework…………………………………………………………………………………………………..209
  12. Chapter 9 Aromatic Compounds and Heterocyclic Compounds……………………………………….. 211
    1. 9.1 Benzene and Aromaticity……………………………………………………………………. 211
    2. 9.2 Benzene Is a Carcinogen…………………………………………………………………….. 213
    3. 9.3 Functionalized Benzene Derivatives…………………………………………………….. 214
    4. 9.4 Electrophilic Aromatic Substitution: The SEAr Reaction………………………… 216
    5. 9.5 Enzymatic SEAr Reactions………………………………………………………………….. 219
    6. 9.6 Reduction of Aromatic Compounds………………………………………………………222
    7. 9.7 Biological Reduction of Aromatic Rings……………………………………………….224
    8. 9.8 Nucleophilic Aromatic Substitution. The SNAr Reaction…………………………225
    9. 9.9 Enzymatic SNAr Reactions…………………………………………………………………..226
    10. 9.10 Polynuclear Aromatic Hydrocarbons…………………………………………………….227
    11. 9.11 Heteroaromatic Compounds: Nitrogen, Oxygen, or Sulfur……………………….230
    12. 9.12 Reactions of Heteroaromatic Compounds……………………………………………… 233
    13. 9.13 Enzymatic Reactions That Generate Heterocyclic Compounds………………..234
    14. 9.14 Reduced Forms of Nitrogen, Oxygen, and Sulfur Heterocycles………………..238
    15. 9.15 Heteroaromatic Compounds with More Than One Ring…………………………. 239
    16. Homework…………………………………………………………………………………………………..240
  13. Chapter 10 Carbon–Metal Bonds, Chelating Agents and Coordination Complexes………………. 243
    1. 10.1 Organometallics………………………………………………………………………………… 243
    2. 10.2 Organometallics in Organic Chemistry………………………………………………… 243
    3. 10.3 Biologically Relevant Metals………………………………………………………………..246
    4. 10.4 Chelating Agents………………………………………………………………………………..248
    5. Homework………………………………………………………………………………………………….. 251
  14. Chapter 11 Amino Acids………………………………………………………………………………………………. 253
    1. 11.1 Characteristics of Amino Acids…………………………………………………………… 253
    2. 11.2 Structure of α-Amino Acids………………………………………………………………… 255
    3. Homework………………………………………………………………………………………………….. 259
  15. Chapter 12 Peptides and Proteins…………………………………………………………………………………… 261
    1. 12.1 Reactions and Synthesis of α-Amino Acids…………………………………………… 261
    2. 12.2 Amino Acid Biosynthesis……………………………………………………………………. 267
    3. 12.3 Peptides Are Poly(amides) of Amino Acid Residues……………………………….268
    4. 12.4 Chemical Synthesis of Peptides……………………………………………………………. 274
    5. 12.5 Peptide Biosynthesis……………………………………………………………………………277
    6. 12.6 Proteins and Enzymes Are Poly(peptides)……………………………………………..280
    7. 12.7 Peptide Degradation and End Group Identification…………………………………280
    8. 12.8 Peptidases………………………………………………………………………………………….284
    9. Homework…………………………………………………………………………………………………..285
  16. Chapter 13 Carbohydrates……………………………………………………………………………………………..287
    1. 13.1 (Poly)hydroxy Carbonyl Compounds…………………………………………………….287
    2. 13.2 Monosaccharides………………………………………………………………………………..288
    3. 13.3 Mutarotation………………………………………………………………………………………293
    4. 13.4 The Anomeric Effect…………………………………………………………………………..294
    5. 13.5 Ketose Monosaccharides……………………………………………………………………..295
    6. Homework…………………………………………………………………………………………………..297
  17. Chapter 14 Glycosides…………………………………………………………………………………………………..299
    1. 14.1 Monosaccharides………………………………………………………………………………..299
    2. 14.2 Disaccharides, Trisaccharides, Oligosaccharides, and Polysaccharides……..300
    3. 14.3 Reactions of Carbohydrates…………………………………………………………………. 301
    4. 14.4 Biologically Important Glycosides………………………………………………………..305
    5. 14.5 Biosynthesis of Carbohydrates and Glycosides……………………………………….308
    6. 14.6 Biodegradation of Carbohydrates and Glycosides………………………………….. 313
    7. Homework………………………………………………………………………………………………….. 316
  18. Chapter 15 Nucleic Acids, Nucleosides and Nucleotides…………………………………………………… 317
    1. 15.1 Nucleosides and Nucleotides……………………………………………………………….. 317
    2. 15.2 Polynucleotides………………………………………………………………………………….. 320
    3. 15.3 Chemical Synthesis of Nucleotides………………………………………………………. 325
    4. Biosynthesis of Nucleotides…………………………………………………………………. 328
    5. Ribozymes………………………………………………………………………………………… 330
    6. Hydrolysis of RNA and DNA………………………………………………………………. 332
    7. RNA-Mediated Programmable DNA Cleavage……………………………………… 333
    8. Restriction Enzymes…………………………………………………………………………… 334
    9. Homework………………………………………………………………………………………………….. 336
  19. Chapter 16 Answers to Homework Problems…………………………………………………………………… 337
    1. Chapter 1……………………………………………………………………………………………………. 337
    2. Chapter 2……………………………………………………………………………………………………. 338
    3. Chapter 3……………………………………………………………………………………………………. 339
    4. Chapter 4……………………………………………………………………………………………………. 341
    5. Chapter 5……………………………………………………………………………………………………. 343
    6. Chapter 6…………………………………………………………………………………………………….344
    7. Chapter 7……………………………………………………………………………………………………. 345
    8. Chapter 8…………………………………………………………………………………………………….349
    9. Chapter 9……………………………………………………………………………………………………. 350
    10. Chapter 10………………………………………………………………………………………………….. 352
    11. Chapter 11………………………………………………………………………………………………….. 353
    12. Chapter 12………………………………………………………………………………………………….. 354
    13. Chapter 13………………………………………………………………………………………………….. 356
    14. Chapter 14………………………………………………………………………………………………….. 358
    15. Chapter 15………………………………………………………………………………………………….. 361
  20. Index…………………………………………………………………………………………………………………………….. 363
Reviews

“There is a continuing demand for up to date organic & bio-organic chemistry undergraduate textbooks. This well planned text builds upon a successful existing work and adds content relevant to biomolecules and biological activity”. – Professor Philip Page, Emeritus Professor, School of Chemistry University of East Anglia, UK

“Introduces the key concepts of organic chemistry in a succinct and clear way”. – Andre Cobb, KCL, UK

Author Biography

Professor Michael B. Smith was born in Detroit, Michigan, and moved to Madison Heights, Virginia, in 1957. He graduated from Amherst County High School in 1964. He worked at Old Dominion Box Factory for a year after graduation and then started college at Ferrum Jr. College in 1965. He graduated in 1967 with an A.A. and began studies at Virginia Tech later that year, graduating with a B.S. in Chemistry in 1969. He worked as a chemist at the Newport News Shipbuilding & Dry Dock Co, Newport News, Virginia, from 1969 until 1972. In 1972 he began studies in graduate school at Purdue University in West Lafayette, Indiana, working with Prof. Joseph Wolinsky. He graduated in 1977 with a Ph.D. in Organic Chemistry. He took a postdoctoral position at Arizona State University in Tempe, Arizona, working on the isolation of anti-cancer agents from marine animals with Professor Bob Pettit. After one year, he took another postdoctoral position at MIT in Cambridge, Massachusetts, working on the synthesis of the anti-cancer drug bleomycin with Professor Sidney Hecht. Professor Smith began his independent career as an assistant professor in the Chemistry department at the University of Connecticut, Storrs, Connecticut, in 1979.

He received tenure in 1986, and spent six months on sabbatical in Belgium, with Professor Leon Ghosez at the Universite Catholique de Louvain in Louvain la Neuve, Belgium. He was promoted to full professor in 1994 and spent his entire career at UCONN. Prof. Smith’s research involved the synthesis of biologically interesting molecules. His most recent work involved the preparation of functionalized indocyanine dyes for the detection of hypoxic cancerous tumors (breast cancer). Another project involved the synthesis of inflammatory lipids derived from the dental pathogen, Porphyromonas gingivalis. He has published 26 books, including Organic Chemistry: An Acid-Base Approach, 2nd edition (Taylor & Francis), the 5th–8th editions of March’s Advanced Organic Chemistry (Wiley), and Organic Synthesis, 4th edition (Elsevier), winner of a 2018 Texty Award. Prof. Smith published 96 peer-reviewed research papers and retired from UCONN in January of 2017.

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