Biochemistry An Organic Chemistry Approach 1st Edition PDF

Preface.xi
Author xiii
Common Abbreviations. xv
Chapter 1 Fundamental Principles of Organic Chemistry. 1
1.1 Bonding and Orbitals. 1
1.2 Ionic versus Covalent Chemical Bonds. 2
1.3 Breaking Covalent Bonds 3
1.4 Polarized Covalent σ-Bonds 4
1.5 Reactive Intermediates 5
1.6 Alkanes and Isomers. 7
1.7 The IUPAC Rules of Nomenclature 8
1.8 Rings Made of Carbon: Cyclic Compounds 11
1.9 Hydrocarbon Functional Groups. 11
1.10 Heteroatom Functional Groups. 13
1.10.1 C—X Type Functional Groups. 13
1.10.2 C=X Type Functional Groups 17
1.11 Hydrogen-Bonding and Solubility. 21
1.12 Rotamers and Conformation.24
1.13 Conformations with Functional Groups30
1.14 Conformation of Cyclic Molecules. 31
1.15 Stereogenic Carbons and Stereoisomers. 37
1.16 Absolute Confguration [(R) and (S) Nomenclature] 39
1.17 Specifc Rotation.44
1.18 Diastereomers46
1.19 Alkene Stereoisomers: (E) and (Z)-Isomers 51
Homework54
Chapter 2 The Importance of Water in Biochemical Systems 55
2.1 Hydrogen Bonding. 55
2.2 Solubility. 58
2.3 Water Molecules in Biological Systems 59
2.4 Acid-Base Equilibria in Water 61
2.5 Buffers. 65
2.6 Structural Features That Infuence Acid Strength.66
2.7 Acid and Base Character of Alcohols, Thiols, Amines and Carbonyls 67
2.7.1 Acids. 67
2.7.2 Bases. 69
2.8 Elimination Reactions of Alkyl Halides (E2 and E1 Reactions). 71
2.9 Acid-Base Equilibria in Amino Acids 74
2.10 Directionality. 78
Chapter 3 Nucleophiles and Electrophiles83 3.1 Nucleophiles and Bimolecular Substitution (the SN2 Reaction)83 3.2 Nucleophilic Substitution with Alcohols, Ethers, Amines, or Phosphines.85 3.3 Carbocations and the SN1 Reaction.88 3.4 Ethers and Thioethers as Nucleophiles.90 3.5 Chemical Reactions of Carbonyl Groups93 3.6 Biochemical Reactions of Ketones and Aldehydes.96 3.7 Carboxylic Acid Derivatives and Acyl Substitution97 3.8 Biological Hydrolysis. 102 Homework 106 Chapter 4 Radicals 109 4.1 Structure of Radicals.109 4.2 Formation of Radicals in Organic Chemistry. 110 4.3 Reactions of Radicals 111 4.4 Formation of Radicals in Biological Systems. 112 4.5 Radicals in Biological Systems. 114 4.6 Radical Reactions in Biochemical Systems 116 4.7 Radicals and Cancer 118 Homework 119 Chapter 5 Dienes and Conjugated Carbonyl Compounds in Biochemistry 121 5.1 Conjugated Dienes and Conjugated Carbonyl Compounds 121 5.2 Reactions of Conjugated Compounds.124 5.3 Conjugate (Michael) Addition. 127 5.4 Enzyme-Mediated Conjugate Additions. 128 5.5 Sigmatropic Rearrangement Reactions. 129 5.6 Enzyme-Mediated Sigmatropic Rearrangements 132 Homework 133 Chapter 6 Enolates and Enolate Anions 135 6.1 Aldehydes and Ketones Are Weak Acids 135 6.2 Formation of Enolate Anions 136 6.3 The Aldol Condensation137 6.4 Enzyme-Mediated Aldol Condensations. 138 6.5 The Claisen Condensation. 141 6.6 Enzyme-Mediated Claisen Condensation. 142 6.7 Decarboxylation. 143 Homework 144 Chapter 7 Enzymes. 147 7.1 Enzyme Kinetics. 147 7.1.1 Kinetics in Organic Chemistry 147 7.1.2 Catalysts and Catalytic Reactions 149 7.1.3 Enzyme Kinetics 149 7.2 Enzymes and Enzyme Classes 153 7.3 Oxidoreductases (EC 1). 157
7.3.1 Chemical Oxidation of Alcohols 157 7.3.2 Oxidases. 159 7.3.3 Chemical Reduction of Carbonyl Compounds. 161 7.3.4 Reductases 162 7.4 Transferases (EC 2). 163 7.4.1 Chemical Reactions That Incorporate Methyl, Hydroxyl, Glycosyl or Amino Groups into New Molecules. 163 7.4.2 Methyl, Hydroxyl, Thiol, and Glycosyl Transferases. 166 7.5 Hydrolyases (EC 3) 168 7.5.1 Chemical Hydrolysis 169 7.5.2 Esterases. 170 7.5.3 Other Hydrolyases 171 7.6 Lyases (EC 4). 174 7.6.1 Bond Cleavage in Organic Chemistry 174 7.6.1.1 Decarboxylation 174 7.6.1.2 Enol Formation and the Acid-Catalyzed Aldol 175 7.6.1.3 Dehydration Reactions 176 7.6.1.4 [2+2]-Photocycloaddition 177 7.6.2 Lyase Reactions 178 7.7 Isomerases (EC 5). 180 7.7.1 Chemical Isomerization Reactions. 181 7.7.2 Isomerase Reactions.184 7.8 Ligases (EC 6). 185 7.8.1 Chemical Methods for Carboxylation and Nucleotide Synthesis 185 7.8.1.1 Reactions with Carbon Dioxide 185 7.8.1.2 Synthesis of Polynucleotides and Polynucleosides. 186 7.8.2 Enzymatic Coupling. 187 7.9 Translocases (EC 7). 189 7.9.1 Enzymatic Transport Reactions. 189 7.9.2 Transport of Organic Materials 189 Homework 190 Chapter 8 Lipids 193 8.1 Carboxylic Acids and Esters. 193 8.2 Nitrate Esters, Sulfate Esters, and Phosphate Esters.196 8.3 Lipid Classes 199 8.4 Chemical Synthesis of Esters203 8.5 Biosynthesis and Biodegradation of Esters.205 Homework209 Chapter 9 Aromatic Compounds and Heterocyclic Compounds 211 9.1 Benzene and Aromaticity 211 9.2 Benzene Is a Carcinogen. 213 9.3 Functionalized Benzene Derivatives. 214 9.4 Electrophilic Aromatic Substitution: The SEAr Reaction. 216 9.5 Enzymatic SEAr Reactions 219 9.6 Reduction of Aromatic Compounds222 9.7 Biological Reduction of Aromatic Rings224 9.8 Nucleophilic Aromatic Substitution. The SNAr Reaction.225
9.9 Enzymatic SNAr Reactions226 9.10 Polynuclear Aromatic Hydrocarbons227 9.11 Heteroaromatic Compounds: Nitrogen, Oxygen, or Sulfur.230 9.12 Reactions of Heteroaromatic Compounds. 233 9.13 Enzymatic Reactions That Generate Heterocyclic Compounds.234 9.14 Reduced Forms of Nitrogen, Oxygen, and Sulfur Heterocycles.238 9.15 Heteroaromatic Compounds with More Than One Ring239 Homework240 Chapter 10 Carbon–Metal Bonds, Chelating Agents and Coordination Complexes243 10.1 Organometallics243 10.2 Organometallics in Organic Chemistry243 10.3 Biologically Relevant Metals.246 10.4 Chelating Agents.248 Homework 251 Chapter 11 Amino Acids 253 11.1 Characteristics of Amino Acids 253 11.2 Structure of α-Amino Acids255 Homework259 Chapter 12 Peptides and Proteins. 261 12.1 Reactions and Synthesis of α-Amino Acids261 12.2 Amino Acid Biosynthesis267 12.3 Peptides Are Poly(amides) of Amino Acid Residues268 12.4 Chemical Synthesis of Peptides. 274 12.5 Peptide Biosynthesis277 12.6 Proteins and Enzymes Are Poly(peptides)280 12.7 Peptide Degradation and End Group Identifcation280 12.8 Peptidases284 Homework285 Chapter 13 Carbohydrates.287 13.1 (Poly)hydroxy Carbonyl Compounds287 13.2 Monosaccharides.288 13.3 Mutarotation293 13.4 The Anomeric Effect.294 13.5 Ketose Monosaccharides.295 Homework297 Chapter 14 Glycosides299 14.1 Monosaccharides.299 14.2 Disaccharides, Trisaccharides, Oligosaccharides, and Polysaccharides.300 14.3 Reactions of Carbohydrates. 301 14.4 Biologically Important Glycosides305
14.5 Biosynthesis of Carbohydrates and Glycosides.308 14.6 Biodegradation of Carbohydrates and Glycosides. 313 Homework 316 Chapter 15 Nucleic Acids, Nucleosides and Nucleotides. 317 15.1 Nucleosides and Nucleotides. 317 15.2 Polynucleotides320 15.3 Chemical Synthesis of Nucleotides. 325 15.4 Biosynthesis of Nucleotides. 328 15.5 Ribozymes.330 15.6 Hydrolysis of RNA and DNA332 15.7 RNA-Mediated Programmable DNA Cleavage 333 15.8 Restriction Enzymes 334 Homework 336 Chapter 16 Answers to Homework Problems.337 Chapter 1 337 Chapter 2 338 Chapter 3 339 Chapter 4 341 Chapter 5 343 Chapter 6344 Chapter 7345 Chapter 8349 Chapter 9 350 Chapter 10 352 Chapter 11 353 Chapter 12 354 Chapter 13 356 Chapter 14 358 Chapter 15 361 Index363
Biochemistry An Organic Chemistry Approach 1st Edition PDF Ebook

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.