Organic Chemistry with a Biological Emphasis Volume I


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Organic Chemistry with a Biological Emphasis Volume I, Is a textbook written by Tim Soderberg 

About the Book

The traditional approach to teaching Organic Chemistry, taken by most of the textbooks that are currently available, is to focus primarily on the reactions of laboratory synthesis, with much less discussion – in the central chapters, at least – of biological molecules and reactions. This is despite the fact that, in many classrooms, a majority of students are majoring in Biology or Health Sciences rather than in Chemistry, and are presumably taking the course in order to learn about the chemistry that takes place in living things.
In an effort to address this disconnect, I have developed a textbook for a two-semester, sophomore-level course in Organic Chemistry in which biological chemistry takes center stage. For the most part, the text covers the core concepts of organic structure, structure determination, and reactivity in the standard order. What is different is the context: biological chemistry is fully integrated into the explanation of central principles, and as much as possible the in-chapter and end-of-chapter problems are taken from the biochemical literature. Many laboratory synthesis reactions are also covered, generally in parallel with their biochemical counterparts – but it is intentionally the biological chemistry that comes first.

About the Contributors


Tim Soderberg teaches Organic and Bioorganic Chemistry at UMM, as well as General Chemistry labs. He received a B.A. in English from Amherst College in 1987, and a California teaching credential from San Francisco State University in 1989. After teaching English as a Second Language in Tokyo, Japan for about five years, he returned to the United States and enrolled at Sonoma State University where he completed all of the undergraduate Chemistry, Calculus, and Physics courses necessary to enter a graduate Chemistry program. He came to UMM in the Fall of 2000 after receiving his Ph.D. in Biological Chemistry from the University of Utah under the direction of Professor C. Dale Poulter. His graduate research focused on the enzymology of two prenyltransferase enzymes: one that modifies tRNA, and one that is involved in the early biosynthesis of ether-linked membrane lipids in archaea. His research at UMM focused on characterization of enzymes in the pentose phosphate pathway in Archaea.

Table of Contents

Chapter 1: Introduction to organic structure and bonding, part I

  • Section 1: Drawing organic structures
  • Section 2: Functional groups and organic nomenclature
  • Section 3: Structures of some important classes of biological molecules

Chapter 2: Introduction to organic structure and bonding, part II

  • Section 1: Covalent bonding in organic molecules
  • Section 2: Molecular orbital theory
  • Section 3: Resonance
  • Section 4: Non-covalent interactions
  • Section 5: Physical properties of organic compounds

Chapter 3: Conformation and Stereochemistry

  • Section 1: Conformations of open-chain organic molecules
  • Section 2: Conformations of cyclic organic molecules
  • Section 3: Chirality and stereoisomers
  • Section 4: Labeling chiral centers
  • Section 5: Optical activity
  • Section 6: Compounds with multiple chiral centers
  • Section 7: Meso compounds
  • Section 8: Fischer and Haworth projections
  • Section 9: Stereochemistry of alkenes
  • Section 10: Stereochemistry in biology and medicine
  • Section 11: Prochirality

Chapter 4: Structure determination part I – Infrared spectroscopy, UV-visible spectroscopy, and mass spectrometry

  • Section 1: Mass Spectrometry
  • Section 2: Introduction to molecular spectroscopy
  • Section 3: Infrared spectroscopy
  • Section 4: Ultraviolet and visible spectroscopy

Chapter 5: Structure determination part II – Nuclear magnetic resonancespectroscopy

  • Section 1: The origin of the NMR signal
  • Section 2: Chemical equivalence
  • Section 3: The 1H-NMR experiment
  • Section 4: The basis for differences in chemical shift
  • Section 5: Spin-spin coupling
  • Section 6: 13C-NMR spectroscopy
  • Section 7: Solving unknown structures
  • Section 8: Complex coupling in 1H-NMR spectra
  • Section 9: Other applications of NMR

Chapter 6: Overview of organic reactivity

  • Section 1: A first look at some organic reaction mechanisms
  • Section 2: A quick review of thermodynamics and kinetics
  • Section 3: Catalysis
  • Section 4: Comparing biological reactions to laboratory reactions

Chapter 7: Acid-base reactions

  • Section 1: Acid-base reactions
  • Section 2: Comparing the acidity and basicity of organic functional groups– the acidityconstant
  • Section 3: Structural effects on acidity and basicity
  • Section 4: Acid-base properties of phenols
  • Section 5: Acid-base properties of nitrogen-containing functional groups
  • Section 6: Carbon acids
  • Section 7: Polyprotic acids
  • Section 8: Effects of enzyme microenvironment on acidity and basicity

Chapter 8: Nucleophilic substitution reactions

  • Section 1: Two mechanistic models for nucleophilic substitution
  • Section 2: Nucleophiles
  • Section 3: Electrophiles
  • Section 4: Leaving groups
  • Section 5: SN1 reactions with allylic electrophiles
  • Section 6: SN1 or SN2? Predicting the mechanism
  • Section 7: Biological nucleophilic substitution reactions
  • Section 8: Nucleophilic substitution in the lab


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Additional information


Tim Soderberg, University of Minnesota, Morris


University of Minnesota Morris






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