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Organic Chemistry with a Biological Emphasis (SUNY Oneonta)

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Organic Chemistry with a Biological Emphasis (SUNY Oneonta)

Chemistry
Author
Jacqueline Bennett
Publisher
SUNY Oneonta
Source
LibreTexts
Language
EN
Category
Basic Sciences
Read online Download PDF (open licence)
Contents· 194 sections
  1. 01: Introduction to Organic Structure and Bonding I
  2. 1.01: Prelude to Atoms Electron Configurations and Lewis Structures
  3. 1.02: Drawing Organic Structures
  4. 1.03: Functional groups and organic nomenclature
  5. 1.04: Structures of some important biomolecules
  6. 1.4.01: Introduction to Amino Acids and Proteins
  7. 1.4.02: Introduction to carbohydrate structure
  8. 1.4.03: Introduction to Lipid Structure
  9. 1.4.04: Introduction to nucleic acid (DNA and RNA) structure
  10. 1.05: Solutions to Chapter 1 Exercises
  11. 1.E: Problems for Chapter 1
  12. 1.01: Solutions to selected Chapter 1 problems
  13. 02: Introduction to Organic Structure and Bonding II
  14. 2.01: Prelude to Organic Structure and Bonding II
  15. 2.02: Valence Bond Theory
  16. 2.03: Molecular orbital theory- conjugation and aromaticity
  17. 2.04: Resonance
  18. 2.05: Non-covalent interactions
  19. 2.06: Physical properties of organic compounds
  20. 2.07: Solutions to Chapter 2 exercises
  21. 2.P: Problems for Chapter 2
  22. 1.01: Solutions to selected chapter 2 problems
  23. 03: Conformations and Stereochemistry
  24. 3.01: Prelude to Conformations and Stereochemistry
  25. 3.02: Conformations of open-chain organic molecules
  26. 3.03: Conformations of cyclic organic molecules
  27. 3.04: Chirality and stereoisomers
  28. 3.05: Naming chiral centers- the R and S system
  29. 3.06: Optical Activity
  30. 3.07: Compounds with multiple chiral centers
  31. 3.08: Meso Compounds
  32. 3.09: Fischer and Haworth projections
  33. 3.10: Stereochemistry of alkenes
  34. 3.11: Stereochemistry in biology and medicine
  35. 3.12: Prochirality
  36. 3.13: Solutions to Chapter 3 exercises
  37. 3.P: Problems for Chapter 3
  38. 04: Structure Determination I- UV-Vis and Infrared Spectroscopy Mass Spectrometry
  39. 4.01: Prelude to Structure Determination I
  40. 4.02: Introduction to molecular spectroscopy
  41. 4.03: Mass Spectrometry
  42. 4.04: Infrared spectroscopy
  43. 4.05: Ultraviolet and visible spectroscopy
  44. 4.P: Problems for Chapter 4
  45. 05: Structure Determination II - Nuclear Magnetic Resonance Spectroscopy
  46. 5.01: Prelude to Structure Determination
  47. 5.02: The Origin of the NMR Signal
  48. 5.03: Chemical Equivalence
  49. 5.04: The 1H-NMR experiment
  50. 5.05: The Basis for Differences in Chemical Shift
  51. 5.06: Spin-Spin Coupling
  52. 5.07: 13C-NMR Spectroscopy
  53. 5.08: Solving Unknown Structures
  54. 5.09: Complex Coupling in Proton Spectra
  55. 5.10: Other Applications of NMR
  56. 5.E: Structure Determination (Exercises)
  57. 5.S: Structure Determination (Summary)
  58. 06: Overview of Organic Reactivity
  59. 6.01: Prelude to Organic Reactivity
  60. 6.02: A First Look at Some Organic Reaction Mechanism
  61. 6.03: A Quick Review of Thermodynamics and Kinetics
  62. 6.04: Catalysis
  63. 6.05: Comparing Biological Reactions to Laboratory Reactions
  64. 6.E: Overview of Organic Reactivity (Exercises)
  65. 6.S: Overview of Organic Reactivity (Summary)
  66. 07: Acid-base Reactions
  67. 7.01: Prelude to Acid-base Reactions
  68. 7.02: Overview of Acid-Base Reactions
  69. 7.03: The Acidity Constant
  70. 7.04: Structural Effects on Acidity and Basicity
  71. 7.05: Acid-base Properties of Phenols
  72. 7.06: Acid-base properties of nitrogen-containing functional groups
  73. 7.07: Carbon Acids
  74. 7.08: Polyprotic Acids
  75. 7.09: Effects of enzyme microenvironment on acidity and basicity
  76. 7.E: Acid-base Reactions (Exercises)
  77. 7.S: Acid-base Reactions (Summary)
  78. 08: Nucleophilic Substitution Reactions
  79. 8.01: Prelude to Nucleophilic Substitution Reactions
  80. 8.02: Two Mechanistic Models for Nucleophilic Substitution
  81. 8.03: Nucleophiles
  82. 8.04: Electrophiles
  83. 8.05: Leaving Groups
  84. 8.06: Regiochemistry of SN1 Reactions with Allylic Electrophiles
  85. 8.07: SN1 or SN2 Predicting the Mechanism
  86. 8.08: Biological Nucleophilic Substitution Reactions
  87. 8.09: Nucleophilic substitution in the Lab
  88. 8.E: Nucleophilic Substitution Reactions (Exercises)
  89. 8.S: Nucleophilic Substitution Reactions (Summary)
  90. 09: Phosphate Transfer Reactions
  91. 9.01: Prelude to Phosphate Transfer Reactions
  92. 9.02: Overview of Phosphate Groups
  93. 9.03: Phosphate Transfer Reactions - An Overview
  94. 9.04: ATP The Principal Phosphate Group Donor
  95. 9.05: Phosphorylation of Alcohols
  96. 9.06: Phosphorylation of Carboxylates
  97. 9.07: Hydrolysis of Organic Phosphates
  98. 9.08: Phosphate Diesters in DNA and RNA
  99. 9.09: The Organic Chemistry of Genetic Engineering
  100. 9.10: NMR of phosphorylated compounds
  101. 9.E: Phosphate Transfer Reactions (Exercise)
  102. 9.S: Phosphate Transfer Reactions (Summary)
  103. 10: Nucleophilic Carbonyl Addition Reactions
  104. 10.01: Prelude to Nucleophilic Carbonyl Addition Reactions
  105. 10.02: Nucleophilic Additions to Aldehydes and Ketones - An Overview
  106. 10.03: Hemiacetals Hemiketals and Hydrates
  107. 10.04: Acetals and Ketals
  108. 10.05: N-glycosidic Bonds
  109. 10.06: Imines
  110. 10.07: A Look Ahead - Addition of Carbon and Hydride Nucleophiles to Carbonyls
  111. 10.E: Nucleophilic Carbonyl Addition Reactions (Exercises)
  112. 10.S: Nucleophilic Carbonyl Addition Reactions (Summary)
  113. 11: Nucleophilic Acyl Substitution Reactions
  114. 11.01: Prelude to Nucleophilic Acyl Substitution Reactions
  115. 11.02: Carboxylic Acid Derivatives
  116. 11.03: The Nucleophilic Acyl Substitution Mechanism
  117. 11.04: Acyl Phosphates
  118. 11.05: The Relative Reactivity of Carboxylic Acid Derivatives
  119. 11.06: Acyl Phosphates
  120. 11.07: Hydrolysis of Thioesters Esters and Amides
  121. 11.08: Protein Synthesis on the Ribosome
  122. 11.09: Nucleophilic Substitution at Activated Amides and Carbamides
  123. 11.10: Nucleophilic Acyl Substitution Reactions in the Laboratory
  124. 11.11: A Look Ahead - Acyl Substitution Reactions with a Carbanion or Hydride Ion Nucleophile
  125. 11.E: Nucleophilic Acyl Substitution Reactions (Exercises)
  126. 11.S: Nucleophilic Acyl Substitution Reactions (Summary)
  127. 12: Reactions at the -Carbon Part I
  128. 12.01: Prelude to Reactions at the -carbon part I
  129. 12.02: Review of Acidity at the -Carbon
  130. 12.03: Isomerization at the -Carbon
  131. 12.04: Aldol Addition
  132. 12.05: -Carbon Reactions in the Synthesis Lab - Kinetic vs. Thermodynamic Alkylation Products
  133. 12.E: Reactions at the -Carbon Part I (Exercises)
  134. 12.S: Reactions at the -Carbon Part I (Summary)
  135. 13: Reactions at the -Carbon Part II
  136. 13.01: Prelude to Reactions at the -Carbon Part II
  137. 13.02: Decarboxylation
  138. 13.03: An Overview of Fatty Acid Metabolism
  139. 13.04: Claisen Condensation
  140. 13.05: Conjugate Addition and Elimination
  141. 13.06: Carboxylation
  142. 13.E: Reactions at the -Carbon Part II (Exercises)
  143. 13.S: Reactions at the -Carbon Part II (Summary)
  144. 14: INTERCHAPTER- Retrosynthetic analysis and metabolic pathway prediction
  145. 14.01: Pathway prediction practice problems
  146. 15: Electrophilic Reactions
  147. 15.01: Prelude to Electrophilic Reactions
  148. 15.02: Electrophilic Addition to Alkenes
  149. 15.03: Elimination by the E1 Mechanism
  150. 15.04: Electrophilic Isomerization
  151. 15.05: Electrophilic Substitution
  152. 15.06: Carbocation Rearrangements
  153. 15.E: Electrophilic Reactions (Exercises)
  154. 15.S: Electrophilic Reactions (Summary)
  155. 16: Oxidation and Reduction Reactions
  156. 16.01: Prelude to Oxidation and Reduction Reactions
  157. 16.02: Oxidation and Reduction of Organic Compounds - An Overview
  158. 16.03: Oxidation and Reduction in the Context of Metabolism
  159. 16.04: Hydrogenation of Carbonyl and Imine Groups
  160. 16.05: Hydrogenation of alkenes and Dehydrogenation of Alkanes
  161. 16.06: Monitoring Hydrogenation and Dehydrogenation Reactions by UV Spectroscopy
  162. 16.07: Redox Reactions of Thiols and Disulfides
  163. 16.08: Flavin-Dependent Monooxygenase Reactions - Hydroxylation Epoxidation and the Baeyer-Villiger Oxidation
  164. 16.09: Hydrogen Peroxide is a Harmful - Reactive Oxygen Species
  165. 16.E: Oxidation and Reduction Reactions (Exercises)
  166. 16.S: Oxidation and Reduction Reactions (Summary)
  167. 17: Radical Reactions
  168. 17.01: Prelude to Radical Reactions
  169. 17.02: Overview of Single-Electron Reactions and Free Radicals
  170. 17.03: Radical Chain Reactions
  171. 17.04: Useful Polymers formed by Radical Chain Reactions
  172. 17.05: Destruction of the Ozone Layer by a Radical Chain Reaction
  173. 17.06: Oxidative Damage to cells Vitamin C and Scurvy
  174. 17.07: Flavin as a One-Electron Carrier
  175. 17.E: Radical Reactions (Exercises)
  176. 18: The Organic Chemistry of Vitamins
  177. 18.01: Prelude to the Organic Chemistry of Vitamins
  178. 18.02: Pyridoxal Phosphate (Vitamin B6)
  179. 18.03: Thiamine Diphosphate (Vitamin B1)
  180. 18.04: Thiamine Diphosphate Lipoamide and the Pyruvate Dehydrogenase Reaction
  181. 18.05: Folate
  182. 18.E: The Organic Chemistry of Vitamins (Exercises)
  183. 18.S: The Oganic Chemistry of Vitamins (Summary)
  184. 19: Appendix I- Index of enzymatic reactions by pathway
  185. 19.01: Amino acid biosynthesis
  186. 19.02: Amino acid catabolism
  187. 19.03: Citric Acid Cycle
  188. 19.04: Fatty acid metabolism
  189. 19.05: Glycolysis Gluconeogenesis Fermentation
  190. 19.06: Isoprenoid biosynthesis
  191. 19.07: Nucleoside biosynthesis
  192. 19.08: Nucleotide catabolism
  193. 19.09: Pentose Phosphate Pathway Calvin Cycle
  194. 20: Appendix II- Review of laboratory synthesis reactions