Organic Chemistry with a Biological Emphasis

by Tim Soderberg

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In this online textbook, a unique approach is taken to the study of organic chemistry. To the greatest extent possible, biological molecules and biochemical reactions are used to explain and illustrate the central concepts of organic chemistry. This approach covers the main organic reaction mechanisms in a biological context. However, earlier chapters on organic structure and spectroscopy also focus as much as possible on examples of interest to students of biology and the health sciences.

Description from LibreTexts.

Publisher
University of Minnesota Morris
Subjects
Chemistry, Organic Chemistry
Licence
CC BY-NC-SA 4.0, as LibreTexts states it. Non-commercial use only.
Who can read
Tweens profiles and older, judged from its title and subjects

Contents

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  1. Front Matter
  2. TitlePage
  3. InfoPage
  4. Table of Contents
  5. Licensing
  6. 1: Introduction to Organic Structure and Bonding I
  7. 1.1: Prelude to Atoms, Electron Configurations, and Lewis Structures
  8. 1.2: Drawing Organic Structures
  9. 1.3: Functional groups and organic nomenclature
  10. 1.4: Structures of some important biomolecules
  11. 1.4.1: Introduction to Amino Acids and Proteins
  12. 1.4.2: Introduction to carbohydrate structure
  13. 1.4.3: Introduction to Lipid Structure
  14. 1.4.4: Introduction to nucleic acid (DNA and RNA) structure
  15. 1.5: Solutions to Chapter 1 Exercises
  16. 1.E: Problems for Chapter 1
  17. 1.1: Solutions to selected Chapter 1 problems
  18. 2: Introduction to Organic Structure and Bonding II
  19. 2.1: Prelude to Organic Structure and Bonding II
  20. 2.2: Valence Bond Theory
  21. 2.3: Molecular orbital theory- conjugation and aromaticity
  22. 2.4: Resonance
  23. 2.5: Non-covalent interactions
  24. 2.6: Physical properties of organic compounds
  25. 2.7: Solutions to Chapter 2 exercises
  26. 2.P: Problems for Chapter 2
  27. 1.1: Solutions to selected chapter 2 problems
  28. 3: Conformations and Stereochemistry
  29. 3.1: Prelude to Conformations and Stereochemistry
  30. 3.2: Conformations of open-chain organic molecules
  31. 3.3: Conformations of cyclic organic molecules
  32. 3.4: Chirality and stereoisomers
  33. 3.5: Naming chiral centers- the R and S system
  34. 3.6: Optical Activity
  35. 3.7: Compounds with multiple chiral centers
  36. 3.8: Meso Compounds
  37. 3.9: Fischer and Haworth projections
  38. 3.P: Problems for Chapter 3
  39. 3.10: Stereochemistry of alkenes
  40. 3.11: Stereochemistry in biology and medicine
  41. 3.12: Prochirality
  42. 3.13: Solutions to Chapter 3 exercises
  43. 4: Structure Determination I- UV-Vis and Infrared Spectroscopy, Mass Spectrometry
  44. 4.1: Prelude to Structure Determination I
  45. 4.2: Introduction to molecular spectroscopy
  46. 4.3: Mass Spectrometry
  47. 4.4: Infrared spectroscopy
  48. 4.5: Ultraviolet and visible spectroscopy
  49. 4.P: Problems for Chapter 4
  50. 5: Structure Determination II - Nuclear Magnetic Resonance Spectroscopy
  51. 5.1: Prelude to Structure Determination
  52. 5.2: The Origin of the NMR Signal
  53. 5.3: Chemical Equivalence
  54. 5.4: The 1H-NMR experiment
  55. 5.5: The Basis for Differences in Chemical Shift
  56. 5.6: Spin-Spin Coupling
  57. 5.7: 13C-NMR Spectroscopy
  58. 5.8: Solving Unknown Structures
  59. 5.9: Complex Coupling in Proton Spectra
  60. 5.E: Structure Determination (Exercises)
  61. 5.S: Structure Determination (Summary)
  62. 5.10: Other Applications of NMR
  63. 6: Overview of Organic Reactivity
  64. 6.1: Prelude to Organic Reactivity
  65. 6.2: A First Look at Some Organic Reaction Mechanism
  66. 6.3: A Quick Review of Thermodynamics and Kinetics
  67. 6.4: Catalysis
  68. 6.5: Comparing Biological Reactions to Laboratory Reactions
  69. 6.E: Overview of Organic Reactivity (Exercises)
  70. 6.S: Overview of Organic Reactivity (Summary)
  71. 7: Acid-base Reactions
  72. 7.1: Prelude to Acid-base Reactions
  73. 7.2: Overview of Acid-Base Reactions
  74. 7.3: The Acidity Constant
  75. 7.4: Structural Effects on Acidity and Basicity
  76. 7.5: Acid-base Properties of Phenols
  77. 7.6: Acid-base properties of nitrogen-containing functional groups
  78. 7.7: Carbon Acids
  79. 7.8: Polyprotic Acids
  80. 7.9: Effects of enzyme microenvironment on acidity and basicity
  81. 7.E: Acid-base Reactions (Exercises)
  82. 7.S: Acid-base Reactions (Summary)
  83. 8: Nucleophilic Substitution Reactions
  84. 8.1: Prelude to Nucleophilic Substitution Reactions
  85. 8.2: Two Mechanistic Models for Nucleophilic Substitution
  86. 8.3: Nucleophiles
  87. 8.4: Electrophiles
  88. 8.5: Leaving Groups
  89. 8.6: Regiochemistry of SN1 Reactions with Allylic Electrophiles
  90. 8.7: SN1 or SN2? Predicting the Mechanism
  91. 8.8: Biological Nucleophilic Substitution Reactions
  92. 8.9: Nucleophilic substitution in the Lab
  93. 8.E: Nucleophilic Substitution Reactions (Exercises)
  94. 8.S: Nucleophilic Substitution Reactions (Summary)
  95. 9: Phosphate Transfer Reactions
  96. 9.1: Prelude to Phosphate Transfer Reactions
  97. 9.2: Overview of Phosphate Groups
  98. 9.3: Phosphate Transfer Reactions - An Overview
  99. 9.4: ATP, The Principal Phosphate Group Donor
  100. 9.5: Phosphorylation of Alcohols
  101. 9.6: Phosphorylation of Carboxylates
  102. 9.7: Hydrolysis of Organic Phosphates
  103. 9.8: Phosphate Diesters in DNA and RNA
  104. 9.9: The Organic Chemistry of Genetic Engineering
  105. 9.E: Phosphate Transfer Reactions (Exercise)
  106. 9.S: Phosphate Transfer Reactions (Summary)
  107. 9.10: NMR of phosphorylated compounds
  108. 10: Nucleophilic Carbonyl Addition Reactions
  109. 10.1: Prelude to Nucleophilic Carbonyl Addition Reactions
  110. 10.2: Nucleophilic Additions to Aldehydes and Ketones - An Overview
  111. 10.3: Hemiacetals, Hemiketals, and Hydrates
  112. 10.4: Acetals and Ketals
  113. 10.5: N-glycosidic Bonds
  114. 10.6: Imines
  115. 10.7: A Look Ahead - Addition of Carbon and Hydride Nucleophiles to Carbonyls
  116. 10.E: Nucleophilic Carbonyl Addition Reactions (Exercises)
  117. 10.S: Nucleophilic Carbonyl Addition Reactions (Summary)
  118. 11: Nucleophilic Acyl Substitution Reactions
  119. 11.1: Prelude to Nucleophilic Acyl Substitution Reactions
  120. 11.2: Carboxylic Acid Derivatives
  121. 11.3: The Nucleophilic Acyl Substitution Mechanism
  122. 11.4: Acyl Phosphates
  123. 11.4: The Relative Reactivity of Carboxylic Acid Derivatives
  124. 11.6: Acyl Phosphates
  125. 11.7: Hydrolysis of Thioesters, Esters, and Amides
  126. 11.8: Protein Synthesis on the Ribosome
  127. 11.9: Nucleophilic Substitution at Activated Amides and Carbamides
  128. 11.E: Nucleophilic Acyl Substitution Reactions (Exercises)
  129. 11.S: Nucleophilic Acyl Substitution Reactions (Summary)
  130. 11.10: Nucleophilic Acyl Substitution Reactions in the Laboratory
  131. 11.11: A Look Ahead - Acyl Substitution Reactions with a Carbanion or Hydride Ion Nucleophile
  132. 12: Reactions at the α-Carbon, Part I
  133. 12.1: Prelude to Reactions at the α-carbon, part I
  134. 12.2: Review of Acidity at the α-Carbon
  135. 12.3: Isomerization at the α-Carbon
  136. 12.4: Aldol Addition
  137. 12.5: α-Carbon Reactions in the Synthesis Lab - Kinetic vs. Thermodynamic Alkylation Products
  138. 12.E: Reactions at the α-Carbon, Part I (Exercises)
  139. 12.S: Reactions at the α-Carbon, Part I (Summary)
  140. 13: Reactions at the α-Carbon, Part II
  141. 13.1: Prelude to Reactions at the α-Carbon, Part II
  142. 13.2: Decarboxylation
  143. 13.3: An Overview of Fatty Acid Metabolism
  144. 13.4: Claisen Condensation
  145. 13.5: Conjugate Addition and Elimination
  146. 13.6: Carboxylation
  147. 13.E: Reactions at the α-Carbon, Part II (Exercises)
  148. 13.S: Reactions at the α-Carbon, Part II (Summary)
  149. INTERCHAPTER: Retrosynthetic analysis and metabolic pathway prediction
  150. Pathway prediction practice problems
  151. 14: Electrophilic Reactions
  152. 14.1: Prelude to Electrophilic Reactions
  153. 14.2: Electrophilic Addition to Alkenes
  154. 14.3: Elimination by the E1 Mechanism
  155. 14.4: Electrophilic Isomerization
  156. 14.5: Electrophilic Substitution
  157. 14.6: Carbocation Rearrangements
  158. 14.E: Electrophilic Reactions (Exercises)
  159. 14.S: Electrophilic Reactions (Summary)
  160. 15: Oxidation and Reduction Reactions
  161. 15.1: Prelude to Oxidation and Reduction Reactions
  162. 15.2: Oxidation and Reduction of Organic Compounds - An Overview
  163. 15.3: Oxidation and Reduction in the Context of Metabolism
  164. 15.4: Hydrogenation of Carbonyl and Imine Groups
  165. 15.5: Hydrogenation of alkenes and Dehydrogenation of Alkanes
  166. 15.6: Monitoring Hydrogenation and Dehydrogenation Reactions by UV Spectroscopy
  167. 15.7: Redox Reactions of Thiols and Disulfides
  168. 15.8: Flavin-Dependent Monooxygenase Reactions - Hydroxylation, Epoxidation, and the Baeyer-Villiger Oxidation
  169. 15.9: Hydrogen Peroxide is a Harmful - Reactive Oxygen Species
  170. 15.E: Oxidation and Reduction Reactions (Exercises)
  171. 15.S: Oxidation and Reduction Reactions (Summary)
  172. 16: Radical Reactions
  173. 16.1: Prelude to Radical Reactions
  174. 16.2: Overview of Single-Electron Reactions and Free Radicals
  175. 16.3: Radical Chain Reactions
  176. 16.4: Useful Polymers formed by Radical Chain Reactions
  177. 16.5: Destruction of the Ozone Layer by a Radical Chain Reaction
  178. 16.6: Oxidative Damage to cells, Vitamin C, and Scurvy
  179. 16.7: Flavin as a One-Electron Carrier
  180. 16.E: Radical Reactions (Exercises)
  181. 17: The Organic Chemistry of Vitamins
  182. 17.1: Prelude to the Organic Chemistry of Vitamins
  183. 17.2: Pyridoxal Phosphate (Vitamin B6)
  184. 17.3: Thiamine Diphosphate (Vitamin B1)
  185. 17.4: Thiamine Diphosphate, Lipoamide and the Pyruvate Dehydrogenase Reaction
  186. 17.5: Folate
  187. 17.E: The Organic Chemistry of Vitamins (Exercises)
  188. 17.S: The Oganic Chemistry of Vitamins (Summary)
  189. Appendix I: Index of enzymatic reactions by pathway
  190. Amino acid biosynthesis
  191. Amino acid catabolism
  192. Citric Acid Cycle
  193. Fatty acid metabolism
  194. Glycolysis, Gluconeogenesis, Fermentation
  195. Isoprenoid biosynthesis
  196. Nucleoside biosynthesis
  197. Nucleotide catabolism
  198. Pentose Phosphate Pathway, Calvin Cycle
  199. Appendix II: Review of laboratory synthesis reactions
  200. Back Matter
  201. Index
  202. Detailed Licensing