Biochemistry

Biochemistry

An Organic Chemistry Approach

Smith, Michael B.

Taylor & Francis Inc

05/2020

472

Dura

Inglês

9780815367130

15 a 20 dias

993

Descrição não disponível.
Contents

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 ?-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 Groups...........................................................30

1.14 Conformation of Cyclic Molecules.................................................................. 31

1.15 Stereogenic Carbons and Stereoisomers.......................................................... 37

1.16 Absolute Configuration [(R) and (S) Nomenclature]........................................ 39

1.17 Specific Rotation..............................................................................................44

1.18 Diastereomers...................................................................................................46

1.19 Alkene Stereoisomers: (E) and (Z)-Isomers..................................................... 51

Homework...................................................................................................................54

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 Influence 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

Homework...................................................................................................................80

Chapter 3 Nucleophiles and Electrophiles...................................................................................83

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 Groups.........................................................93

3.6 Biochemical Reactions of Ketones and Aldehydes..........................................96

3.7 Carboxylic Acid Derivatives and Acyl Substitution.........................................97

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 Condensation................................................................................. 137

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 Esters.........................................................................203

8.5 Biosynthesis and Biodegradation of Esters....................................................205

Homework.................................................................................................................209

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 Compounds...............................................................222

9.7 Biological Reduction of Aromatic Rings.......................................................224

9.8 Nucleophilic Aromatic Substitution. The SNAr Reaction..............................225

9.9 Enzymatic SNAr Reactions.............................................................................226

9.10 Polynuclear Aromatic Hydrocarbons.............................................................227

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 Ring............................... 239

Homework.................................................................................................................240

Chapter 10 Carbon-Metal Bonds, Chelating Agents and Coordination Complexes................... 243

10.1 Organometallics............................................................................................. 243

10.2 Organometallics in Organic Chemistry......................................................... 243

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 ?-Amino Acids........................................................................... 255

Homework................................................................................................................. 259

Chapter 12 Peptides and Proteins................................................................................................ 261

12.1 Reactions and Synthesis of ?-Amino Acids................................................... 261

12.2 Amino Acid Biosynthesis............................................................................... 267

12.3 Peptides Are Poly(amides) of Amino Acid Residues.....................................268

12.4 Chemical Synthesis of Peptides...................................................................... 274

12.5 Peptide Biosynthesis.......................................................................................277

12.6 Proteins and Enzymes Are Poly(peptides).....................................................280

12.7 Peptide Degradation and End Group Identification.......................................280

12.8 Peptidases.......................................................................................................284

Homework.................................................................................................................285

Chapter 13 Carbohydrates...........................................................................................................287

13.1 (Poly)hydroxy Carbonyl Compounds.............................................................287

13.2 Monosaccharides............................................................................................288

13.3 Mutarotation...................................................................................................293

13.4 The Anomeric Effect......................................................................................294

13.5 Ketose Monosaccharides................................................................................295

Homework.................................................................................................................297

Chapter 14 Glycosides.................................................................................................................299

14.1 Monosaccharides............................................................................................299

14.2 Disaccharides, Trisaccharides, Oligosaccharides, and Polysaccharides........300

14.3 Reactions of Carbohydrates............................................................................ 301

14.4 Biologically Important Glycosides.................................................................305

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 Polynucleotides............................................................................................... 320

15.3 Chemical Synthesis of Nucleotides................................................................ 325

15.4 Biosynthesis of Nucleotides............................................................................ 328

15.5 Ribozymes...................................................................................................... 330

15.6 Hydrolysis of RNA and DNA......................................................................... 332

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 6...................................................................................................................344

Chapter 7................................................................................................................... 345

Chapter 8...................................................................................................................349

Chapter 9................................................................................................................... 350

Chapter 10................................................................................................................. 352

Chapter 11................................................................................................................. 353

Chapter 12................................................................................................................. 354

Chapter 13................................................................................................................. 356

Chapter 14................................................................................................................. 358

Chapter 15................................................................................................................. 361

Index............................................................................................................................................... 363
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Acyl Carrier Protein;Formylglycinamide Ribotide Amidotransfer Ase;Metabolism reactions;Acetyl Co-A;UV spectroscopy in biochemistry;Acetyl CoA;Carbonyl chemistry;C2 C3 Bond;Essential oils;American Chemical Society;Anti-cancer agents;National Academy;Biotransformation;Tetrahedral Intermediate;amino acid reaction;Enolate Anion;electrophiles;Grignard Reagent;organic chemistry;Anomeric Carbon;nucleophiles;Stereogenic Center;biochemistry reactions;IUPAC Nomenclature;Acid Base Reaction;Amine Unit;Oxocarbenium Ion;Metal EDTA Complex;Organolithium Reagents;Arenium Ion;Electrophilic Aromatic Substitution;Claisen Condensation;Stereogenic Carbon;Transition Metals;Sigmatropic Rearrangements;Formylglycinamide Ribotide Amidotransferase