Organic Chemistry with a Biological Emphasis Volume II
Tim Soderberg, University of Minnesota, Morris
Copyright Year: 2016
Publisher: University of Minnesota Morris
Conditions of Use
This is a comprehensive textbook with excellent examples for each of the chemical reactions described. The textbook could include a separate chapter or module covering the principles for IUPAC nomenclature of organic compounds. read more
This is a comprehensive textbook with excellent examples for each of the chemical reactions described. The textbook could include a separate chapter or module covering the principles for IUPAC nomenclature of organic compounds.
The content presented is accurate. I am not keen about inclusion of E1 under the "Electrophilic reactions" heading (chapter 14), but this may be a matter of preference.
The examples included in the textbook are those of chemical reactions in biological systems, most of which have been thoroughly studied and understood.
Clear text, adequate terminology; any abbreviation used is described appropriately prior to its first use.
The terminology used throughout the textbook is consistent.
With the exception of spectroscopy (included in volume I) which could represent an independent module and be placed almost anywhere in the textbook, going out of sequence cannot be easily done; however, certain chapters can be skipped if so desired.
Nicely organized textbook!
No interface issues noted.
I have noted a few typos rather than grammatical errors.
I do not find the textbook to be culturally insensitive.
The textbook is an excellent compilation of organic reactions in biological systems. I particularly liked the inclusion of literature references for the examples presented within each chapter, something that you will not find in a typical organic chemistry textbook. The problems included at the end of each chapter are excellent but a larger number would be desirable. A description of general acid/general base catalysis characteristic for biological systems would be beneficial and should be contrasted to the strong acid/base catalyzed reactions.
This textbook covers different material than a traditional Organic Chemistry II course. The material and method of presentation of this textbook sets students up for success in biochemistry and medical based programs. read more
This textbook covers different material than a traditional Organic Chemistry II course. The material and method of presentation of this textbook sets students up for success in biochemistry and medical based programs.
This textbook is scientifically accurate.
The content of this textbook is currently relevant and will likely stay relevant for a very long time.
Overall the text is well written and engaging. There are a few small typos and some places that could be reworded to increase clarity.
The textbook is consistent in terminology and framework
There are a few chapters that can be skipped, but this textbook would not be easily re-ordered.
For the most part the order of this textbook is superior to traditional organic chemistry textbooks
The searchable PDF is great, figures are well done and clear. The examples are fantastic.
Overall the textbook is fantastic. There are one or two typos.
No better or worse than other chemistry textbooks
This is a fantastic book! For pre-medical and biological science students this textbook is far superior to traditional organic texts.
The textbook covers some chapters that are covered in organic chemistry II. It doesn't have a chapter on electrophilic aromatic substitution, aromaticity, amine reactions and ether which are usually covered in org II. read more
The textbook covers some chapters that are covered in organic chemistry II. It doesn't have a chapter on electrophilic aromatic substitution, aromaticity, amine reactions and ether which are usually covered in org II.
The textbook is scientifically accurate.
The textbook is up-to-date with interesting and engaging chapter opening.
Mostly the text is clear. There are certain parts that can be made more clear by providing more examples.
Yes, the text is consistent.
The text can be divisible into smaller reading sections. I am not sure that it can be easily reorganized as the author is referring to reactions in earlier chapters, and that might affect reorganization.
Although the topics are not organized in a typical way of other organic chemistry textbooks, I think the topics in the text are presented in a logical way.
The text is in a pdf format and is free of any interface issues.
There are no grammatical errors in the parts I checked.
Yes, the text has inclusive in the examples used.
The author(s) did a great job explaining organic chemistry in emphasis in biological reactions. I think that it will be well received by the students who find organic chemistry full of dry material and find it hard to relate it to everyday life or to their majors.
Table of Contents
Chapter 9: Phosphate transfer reactions
- Section 1: Overview of phosphate groups
- Section 2: Phosphate transfer reactions - an overview
- Section 3: ATP, the principal phosphate group donor
- Section 4: Phosphorylation of alcohols
- Section 5: Phosphorylation of carboxylates
- Section 6: Hydrolysis of organic phosphates
- Section 7: Phosphate diesters in DNA and RNA
- Section 8: The organic chemistry of genetic engineering
Chapter 10: Nucleophilic carbonyl addition reactions
- Section 1: Nucleophilic additions to aldehydes and ketones: an overview
- Section 2: Hemiacetals, hemiketals, and hydrates
- Section 3: Acetals and ketals
- Section 4: N-glycosidic bonds
- Section 5: Imines
- Section 5: A look ahead: addition of carbon and hydride nucleophiles to carbonyls
Chapter 11: Nucleophilic acyl substitution reactions
- Section 1: Carboxylic acid derivatives
- Section 2: The nucleophilic acyl substitution mechanism
- Section 3: The relative reactivity of carboxylic acid derivatives
- Section 4: Acyl phosphates
- Section 5: Formation of thioesters, esters, and amides
- Section 6: Hydrolysis of thioesters, esters, and amides
- Section 7: Protein synthesis on the ribosome
- Section 8: Nucleophilic substitution at activated amides and carbamides
- Section 9: Nucleophilic acyl substitution reactions in the laboratory
- Section 10: A look ahead: acyl substitution reactions with a carbanion or hydride ion nucleophile
Chapter 12: Reactions at the α-carbon, part I
- Section 1: Review of acidity at the α-carbon
- Section 2: Isomerization at the α-carbon
- Section 3: Aldol addition
- Section 4: α-carbon reactions in the synthesis lab - kinetic vs. thermodynamic alkylation products
Interchapter: Predicting multistep pathways - the retrosynthesis approach
Chapter 13: Reactions at the α-carbon, part II
- Section 1: Decarboxylation
- Section 2: An overview of fatty acid metabolism
- Section 3: Claisen condensation
- Section 4: Conjugate addition and elimination
- Section 5: Carboxylation
Chapter 14: Electrophilic reactions
- Section 1: Electrophilic addition to alkenes
- Section 2: Elimination by the E1 mechanism
- Section 3: Electrophilic isomerization
- Section 4: Electrophilic substitution
- Section 5: Carbocation rearrangements
Chapter 15: Oxidation and reduction reactions
- Section 1: Oxidation and reduction of organic compounds - an overview
- Section 2: Oxidation and reduction in the context of metabolism
- Section 3: Hydrogenation of carbonyl and imine groups
- Section 4: Hydrogenation of alkenes and dehydrogenation of alkanes
- Section 5: Monitoring hydrogenation and dehydrogenation reactions by UV spectroscopy
- Section 6: Redox reactions of thiols and disulfides
- Section 7: Flavin-dependent monooxygenase reactions: hydroxylation, epoxidation, and theBaeyer-Villiger oxidation
- Section 8: Hydrogen peroxide is a harmful 'Reactive Oxygen Species'
Chapter 16: Radical reactions
- Section 1: Overview of single-electron reactions and free radicals
- Section 2: Radical chain reactions
- Section 3: Useful polymers formed by radical chain reactions
- Section 4: Destruction of the ozone layer by a radical chain reaction
- Section 5: Oxidative damage to cells, vitamin C, and scurvy
- Section 6: Flavin as a one-electron carrier
Chapter 17: The organic chemistry of vitamins
- Section 1: Pyridoxal phosphate (Vitamin B6)
- Section 2: Thiamine diphosphate (Vitamin B1)
- Section 3: Thiamine diphosphate, lipoamide and the pyruvate dehydrogenase reaction
- Section 4: Folate
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.