Michael B. Smith

Biochemistry (eBook, ePUB)

An Organic Chemistry Approach

• Format: ePub

Produktbeschreibung

Organic Chemistry and Biochemical Applications provides a framework for understanding various topics of organic chemistry, as well as the behavior of biomolecules, enzyme activity, and more.

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Produktdetails

• Verlag: Taylor & Francis
• Seitenzahl: 472
• Erscheinungstermin: 27. April 2020
• Englisch
• ISBN-13: 9781351258067
• Artikelnr.: 59315177

Autorenporträt

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.

Inhaltsangabe

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