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Organic Chemistry with a Biological Emphasis

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Organic Chemistry with a Biological Emphasis

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.

Organic ChemistryChemistry
Author
Tim Soderberg
Publisher
University of Minnesota Morris
Source
LibreTexts
License
CC BY-NC-SA
Language
EN
Category
Basic Sciences
Read online Download PDF (open licence)
Contents· 194 sections
  1. 01: Introduction to Organic Structure and Bonding I
  2. 1.0P: 1.P: Problems for Chapter 1
  3. 1.01: Solutions to selected Chapter 1 problems
  4. 1.01: Prelude to Atoms Electron Configurations and Lewis Structures
  5. 1.02: Drawing organic structures
  6. 1.03: Functional groups and organic nomenclature
  7. 1.04: Structures of some important biomolecules
  8. 1.4.01: Introduction to amino acids and proteins
  9. 1.4.02: Introduction to carbohydrate structure
  10. 1.4.03: Introduction to lipid structure
  11. 1.4.04: Introduction to nucleic acid (DNA and RNA) structure
  12. 1.05: Solutions to Chapter 1 Exercises
  13. 02: Introduction to Organic Structure and Bonding II
  14. 2.0P: 2.P: Problems for Chapter 2
  15. 1.01: Solutions to selected chapter 2 problems
  16. 2.01: Prelude to Organic Structure and Bonding II
  17. 2.02: Valence Bond Theory
  18. 2.03: Molecular orbital theory- conjugation and aromaticity
  19. 2.04: Resonance
  20. 2.05: Non-covalent interactions
  21. 2.06: Physical properties of organic compounds
  22. 2.07: Solutions to Chapter 2 exercises
  23. 03: Conformations and Stereochemistry
  24. 3.0P: 3.P: Problems for Chapter 3
  25. 3.01: Prelude to Conformations and Stereochemistry
  26. 3.02: Conformations of open-chain organic molecules
  27. 3.03: Conformations of cyclic organic molecules
  28. 3.04: Chirality and stereoisomers
  29. 3.05: Naming chiral centers- the R and S system
  30. 3.06: Optical Activity
  31. 3.07: Compounds with multiple chiral centers
  32. 3.08: Meso Compounds
  33. 3.09: Fischer and Haworth projections
  34. 3.10: Stereochemistry of alkenes
  35. 3.11: Stereochemistry in biology and medicine
  36. 3.12: Prochirality
  37. 3.13: Solutions to Chapter 3 exercises
  38. 04: Structure Determination I- UV-Vis and Infrared Spectroscopy Mass Spectrometry
  39. 4.0P: 4.P: Problems for Chapter 4
  40. 4.01: Prelude to Structure Determination I
  41. 4.02: Introduction to molecular spectroscopy
  42. 4.03: Mass Spectrometry
  43. 4.04: Infrared spectroscopy
  44. 4.05: Ultraviolet and visible spectroscopy
  45. 05: Structure Determination Part II - Nuclear Magnetic Resonance Spectroscopy
  46. 5.0E: 5.E: Structure Determination (Exercises)
  47. 5.0S: 5.S: Structure Determination (Summary)
  48. 5.01: Prelude to Structure Determination
  49. 5.02: The Origin of the NMR Signal
  50. 5.03: Chemical Equivalence
  51. 5.04: The 1H-NMR experiment
  52. 5.05: The Basis for Differences in Chemical Shift
  53. 5.06: Spin-Spin Coupling
  54. 5.07: 13C-NMR Spectroscopy
  55. 5.08: Solving Unknown Structures
  56. 5.09: Complex Coupling in Proton Spectra
  57. 5.10: Other Applications of NMR
  58. 06: Overview of Organic Reactivity
  59. 6.0E: 6.E: Overview of Organic Reactivity (Exercises)
  60. 6.0S: 6.S: Overview of Organic Reactivity (Summary)
  61. 6.01: Prelude to Organic Reactivity
  62. 6.02: A First Look at Some Organic Reaction Mechanism
  63. 6.03: A Quick Review of Thermodynamics and Kinetics
  64. 6.04: Catalysis
  65. 6.05: Comparing Biological Reactions to Laboratory Reactions
  66. 07: Acid-base Reactions
  67. 7.0E: 7.E: Acid-base Reactions (Exercises)
  68. 7.0S: 7.S: Acid-base Reactions (Summary)
  69. 7.01: Prelude to Acid-base Reactions
  70. 7.02: Overview of Acid-Base Reactions
  71. 7.03: The Acidity Constant
  72. 7.04: Structural Effects on Acidity and Basicity
  73. 7.05: Acid-base Properties of Phenols
  74. 7.06: Acid-base properties of nitrogen-containing functional groups
  75. 7.07: Carbon Acids
  76. 7.08: Polyprotic Acids
  77. 7.09: Effects of enzyme microenvironment on acidity and basicity
  78. 08: Nucleophilic Substitution Reactions
  79. 8.0E: 8.E: Nucleophilic Substitution Reactions (Exercises)
  80. 8.0S: 8.S: Nucleophilic Substitution Reactions (Summary)
  81. 8.01: Prelude to Nucleophilic Substitution Reactions
  82. 8.02: Two Mechanistic Models for Nucleophilic Substitution
  83. 8.03: Nucleophiles
  84. 8.04: Electrophiles
  85. 8.05: Leaving Groups
  86. 8.06: Regiochemistry of SN1 Reactions with Allylic Electrophiles
  87. 8.07: SN1 or SN2 Predicting the Mechanism
  88. 8.08: Biological Nucleophilic Substitution Reactions
  89. 8.09: Nucleophilic substitution in the Lab
  90. 09: Phosphate Transfer Reactions
  91. 9.0E: 9.E: Phosphate Transfer Reactions (Exercise)
  92. 9.0S: 9.S: Phosphate Transfer Reactions (Summary)
  93. 9.01: Prelude to Phosphate Transfer Reactions
  94. 9.02: Overview of Phosphate Groups
  95. 9.03: Phosphate Transfer Reactions - An Overview
  96. 9.04: ATP The Principal Phosphate Group Donor
  97. 9.05: Phosphorylation of Alcohols
  98. 9.06: Phosphorylation of Carboxylates
  99. 9.07: Hydrolysis of Organic Phosphates
  100. 9.08: Phosphate Diesters in DNA and RNA
  101. 9.09: The Organic Chemistry of Genetic Engineering
  102. 9.10: NMR of phosphorylated compounds
  103. 10: Nucleophilic Carbonyl Addition Reactions
  104. 10.0E: 10.E: Nucleophilic Carbonyl Addition Reactions (Exercises)
  105. 10.0S: 10.S: Nucleophilic Carbonyl Addition Reactions (Summary)
  106. 10.01: Prelude to Nucleophilic Carbonyl Addition Reactions
  107. 10.02: Nucleophilic Additions to Aldehydes and Ketones - An Overview
  108. 10.03: Hemiacetals Hemiketals and Hydrates
  109. 10.04: Acetals and Ketals
  110. 10.05: N-glycosidic Bonds
  111. 10.06: Imines
  112. 10.07: A Look Ahead - Addition of Carbon and Hydride Nucleophiles to Carbonyls
  113. 11: Nucleophilic Acyl Substitution Reactions
  114. 11.0E: 11.E: Nucleophilic Acyl Substitution Reactions (Exercises)
  115. 11.0S: 11.S: Nucleophilic Acyl Substitution Reactions (Summary)
  116. 11.01: Prelude to Nucleophilic Acyl Substitution Reactions
  117. 11.02: Carboxylic Acid Derivatives
  118. 11.03: The Nucleophilic Acyl Substitution Mechanism
  119. 11.04: Acyl Phosphates
  120. 11.04: The Relative Reactivity of Carboxylic Acid Derivatives
  121. 11.06: Acyl Phosphates
  122. 11.07: Hydrolysis of Thioesters Esters and Amides
  123. 11.08: Protein Synthesis on the Ribosome
  124. 11.09: Nucleophilic Substitution at Activated Amides and Carbamides
  125. 11.10: Nucleophilic Acyl Substitution Reactions in the Laboratory
  126. 11.11: A Look Ahead - Acyl Substitution Reactions with a Carbanion or Hydride Ion Nucleophile
  127. 12: Reactions at the -Carbon Part I
  128. 12.0E: 12.E: Reactions at the -Carbon Part I (Exercises)
  129. 12.0S: 12.S: Reactions at the -Carbon Part I (Summary)
  130. 12.01: Prelude to Reactions at the -carbon part I
  131. 12.02: Review of Acidity at the -Carbon
  132. 12.03: Isomerization at the -Carbon
  133. 12.04: Aldol Addition
  134. 12.05: -Carbon Reactions in the Synthesis Lab - Kinetic vs. Thermodynamic Alkylation Products
  135. 13: Reactions at the -Carbon Part II
  136. 13.0E: 13.E: Reactions at the -Carbon Part II (Exercises)
  137. 13.0S: 13.S: Reactions at the -Carbon Part II (Summary)
  138. 13.01: Prelude to Reactions at the -Carbon Part II
  139. 13.02: Decarboxylation
  140. 13.03: An Overview of Fatty Acid Metabolism
  141. 13.04: Claisen Condensation
  142. 13.05: Conjugate Addition and Elimination
  143. 13.06: Carboxylation
  144. 14: Electrophilic Reactions
  145. 14.0E: 14.E: Electrophilic Reactions (Exercises)
  146. 14.0S: 14.S: Electrophilic Reactions (Summary)
  147. 14.01: Prelude to Electrophilic Reactions
  148. 14.02: Electrophilic Addition to Alkenes
  149. 14.03: Elimination by the E1 Mechanism
  150. 14.04: Electrophilic Isomerization
  151. 14.05: Electrophilic Substitution
  152. 14.06: Carbocation Rearrangements
  153. 15: Oxidation and Reduction Reactions
  154. 15.0E: 15.E: Oxidation and Reduction Reactions (Exercises)
  155. 15.0S: 15.S: Oxidation and Reduction Reactions (Summary)
  156. 15.01: Prelude to Oxidation and Reduction Reactions
  157. 15.02: Oxidation and Reduction of Organic Compounds - An Overview
  158. 15.03: Oxidation and Reduction in the Context of Metabolism
  159. 15.04: Hydrogenation of Carbonyl and Imine Groups
  160. 15.05: Hydrogenation of alkenes and Dehydrogenation of Alkanes
  161. 15.06: Monitoring Hydrogenation and Dehydrogenation Reactions by UV Spectroscopy
  162. 15.07: Redox Reactions of Thiols and Disulfides
  163. 15.08: Flavin-Dependent Monooxygenase Reactions - Hydroxylation Epoxidation and the Baeyer-Villiger Oxidation
  164. 15.09: Hydrogen Peroxide is a Harmful - Reactive Oxygen Species
  165. 16: Radical Reactions
  166. 16.0E: 16.E: Radical Reactions (Exercises)
  167. 16.01: Prelude to Radical Reactions
  168. 16.02: Overview of Single-Electron Reactions and Free Radicals
  169. 16.03: Radical Chain Reactions
  170. 16.04: Useful Polymers formed by Radical Chain Reactions
  171. 16.05: Destruction of the Ozone Layer by a Radical Chain Reaction
  172. 16.06: Oxidative Damage to cells Vitamin C and Scurvy
  173. 16.07: Flavin as a One-Electron Carrier
  174. 17: The Organic Chemistry of Vitamins
  175. 17.0E: 17.E: The Oganic Chemistry of Vitamins (Exercises)
  176. 17.0S: 17.S: The Oganic Chemistry of Vitamins (Summary)
  177. 17.01: Prelude to the Organic Chemistry of Vitamins
  178. 17.02: Pyridoxal Phosphate (Vitamin B6)
  179. 17.03: Thiamine Diphosphate (Vitamin B1)
  180. 17.04: Thiamine Diphosphate Lipoamide and the Pyruvate Dehydrogenase Reaction
  181. 17.05: Folate
  182. Appendix I: Index of enzymatic reactions by pathway
  183. Amino acid biosynthesis
  184. Amino acid catabolism
  185. Citric Acid Cycle
  186. Fatty acid metabolism
  187. Glycolysis Gluconeogenesis Fermentation
  188. Isoprenoid biosynthesis
  189. Nucleoside biosynthesis
  190. Nucleotide catabolism
  191. Pentose Phosphate Pathway Calvin Cycle
  192. Appendix II: Review of laboratory synthesis reactions
  193. INTERCHAPTER: Retrosynthetic analysis and metabolic pathway prediction
  194. Pathway prediction practice problems