Organic Chemistry
With a Biological Emphasis:
An Option for Second-Semester Organic Chemistry
at the University of Minnesota, Morris
Tim Soderberg
HHMI/AAMC SFFP Report
Competency E4, part 6: Demonstrate knowledge of the chemistry of
carbon-containing compounds relevant to their behavior in an aqueous
environment.
Examples:
• Recognize major types of functional groups and chemical reactions.
• Explain how molecular structure and geometry, including chirality, relate
to chemical reactivity.
• Explain the chemical principles that allow structural inference about bioorganic molecules based on common spectroscopic analyses, such as
NMR, UV/visible/IR absorption, or X-ray diffraction.
• Apply knowledge of the chemistry of covalent carbon compounds to
explain biochemical reactions.
HHMI/AAMC SFFP Report
Competency E4, part 6: Demonstrate knowledge of the chemistry of
carbon-containing compounds relevant to their behavior in an aqueous
environment.
Examples:
• Recognize major types of functional groups and chemical reactions.
• Explain how molecular structure and geometry, including chirality, relate
to chemical reactivity.
• Explain the chemical principles that allow structural inference about bioorganic molecules based on common spectroscopic analyses, such as
NMR, UV/visible/IR absorption, or X-ray diffraction.
• Apply knowledge of the chemistry of covalent carbon compounds to
explain biochemical reactions.
MR5 Committee Recommendations
Chemical and Physical Foundations of Biological Systems
(second of four test sections)
. . . Understanding the mechanical, physical, and biochemical functions of human
tissues, organs, and organ systems is important to the study of medicine. This
section will test the extent to which examinees know the basic chemical and
physical principles that underlie the mechanisms operating in the human body. It
will further test examinees’ ability apply their understanding of these general
principles to living systems.
MR5 Committee Recommendations
Chemical and Physical Foundations of Biological Systems
(second of four test sections)
. . . Understanding the mechanical, physical, and biochemical functions of human
tissues, organs, and organ systems is important to the study of medicine. This
section will test the extent to which examinees know the basic chemical and
physical principles that underlie the mechanisms operating in the human body. It
will further test examinees’ ability apply their understanding of these general
principles to living systems.
The Preview Guide to MCAT2015
Foundational Concept 5: The principles that govern chemical interactions and
reactions form the basis for a broader understanding of the molecular dynamics of
living systems.
The content categories for this foundational concept include:
5A. Unique nature of water and its solutions
5B. Nature of molecules and intermolecular interactions
5C. Separation and purification methods
5D. Structure, function, and reactivity of biologically-relevant molecules
5E. Principles of chemical thermodynamics and kinetics
The Preview Guide to MCAT2015
Foundational Concept 5: The principles that govern chemical interactions and
reactions form the basis for a broader understanding of the molecular dynamics of
living systems.
The content categories for this foundational concept include:
5A. Unique nature of water and its solutions
5B. Nature of molecules and intermolecular interactions
5C. Separation and purification methods
5D. Structure, function, and reactivity of biologically-relevant molecules
5E. Principles of chemical thermodynamics and kinetics
“Leaders in science education say that some of the most important foundational
concepts in the sciences ask students to bring together information from
different disciplines.” (The Preview Guide for MCAT2015, p. 8)
Organic textbooks place a heavy emphasis on lab synthesis – there is a
need for a more biology-focused option.
Current solution at UMM:
First semester: Two sections, both covering same chapters of Bruice
text
Second semester: two options
a
1: ‘Standard’ o-chem course, continues with Bruice
2: Bio-flavored course, switches to ‘Organic Chemistry With
Biological Emphasis’. Cell Biology prerequisite
Open access textbook:
online (Chemwiki at UC-Davis)
pdf, print (lulu.com)
Mechanistic organization,
biological/medical examples take center
stage
Extensive references/links to primary
literature
NOT a Biochemistry text
Contents of ‘Organic Chemistry
With a Biological Emphasis’ vol II
Chapter 10: Phosphoryl transfer reactions
Chapter 11: Nucleophilic carbonyl addition reactions
Chapter 12: Acyl substitution reactions
Chapters 13/14: Reactions at the a-carbon
Chapter 15: Electrophilic reactions
Chapter 16: Oxidation and reduction reactions
Chapter 17: Radical reactions
(Bio-flavored course at UMM covers chapters 10-17 plus NMR)
Contents of ‘Organic Chemistry
With a Biological Emphasis’ vol II
Chapter 10: Phosphoryl transfer reactions
Chapter 11: Nucleophilic carbonyl addition reactions
Chapter 12: Acyl substitution reactions
Chapters 13/14: Reactions at the a-carbon
Chapter 15: Electrophilic reactions
Chapter 16: Oxidation and reduction reactions
Chapter 17: Radical reactions
(Bio-flavored course at UMM covers chapters 10-17 plus NMR)
Chapter 12: Acyl substitution reactions
Section 1: Introduction to carboxylic acid derivatives and the nucleophilic acyl
substitution reaction
Section 2: Acyl phosphates as activated carboxylic acids
Section 3: Thioesters
Section 4: Esters
Section 5: Nucleophilic acyl substitution reactions involving peptide bonds
Section 6: Activated amide groups
Section 7: A look ahead: acyl substitution reactions with a carbon or hydride
nucleophile
Section 1: Introduction to carboxylic acid derivatives and the nucleophilic acyl
substitution reaction
A: Carboxylic acid derivatives and acyl groups
B: The nucleophilic acyl substitution reaction
C: The relative reactivity of carboxylic acid derivatives
Section 12.2: Acyl phosphates as activated carboxylic acids
A: Glutamine synthetase
B: Asparagine synthetase
C: Glycinamide ribonucleotide synthetase
D: Synthetic parallel - activated carboxylic acids in the lab
Section 12.2: Acyl phosphates as activated carboxylic acids
A: Glutamine synthetase
B: Asparagine synthetase
C: Glycinamide ribonucleotide synthetase
D: Synthetic parallel - activated carboxylic acids in the lab
Section 12.3: Thioesters
A: Introduction to thioesters and Coenzyme A
B: Activation of fatty acids by coenzyme A - a thioesterification reaction
C: Transfer of fatty acyl groups to glycerol: a thioester to ester substitution
D: More transthioesterification reactions
E: Hydrolysis of thioesters
Section 12.3: Thioesters
A: Introduction to thioesters and Coenzyme A
B: Activation of fatty acids by coenzyme A - a thioesterification reaction
C: Transfer of fatty acyl groups to glycerol: a thioester to ester substitution
D: More transthioesterification reactions
E: Hydrolysis of thioesters
Section 12.4: Esters
A: Nonenzymatic esterification: synthesis of ‘banana oil’
B: Nonenzymatic ester hydrolysis and the soap-making process
C: Enzymatic ester hydrolysis: acetylcholinesterase and sarin nerve gas
D: More enzymatic ester hydrolysis: lipase, the resolution of enantiomers, and
dehalogenation
E: Transesterification: the chemistry of aspirin and biodeisel
Section 5: Nucleophilic acyl substitution reactions involving peptide bonds
A: Formation of peptide bonds on the ribosome
B: Hydrolysis of peptide bonds: HIV protease
C: The chemical mechanism of penicillin
Section 12.7: A look ahead: acyl substitution reactions with a carbon or
hydride nucleophile
Other features of OCBE textbook/course
• Chapter on phosphates, phosphoryl transfer reactions
• Emphasis on importance of aldol/Claisen reactions in biological carbon-carbon bond
formation and cleavage
• Eliminations: introduced later (chapter 14), focus on E1cb mechanism
• Sections on thiamine diphosphate and and pyridoxal phosphate coenzyme mechanisms
• Diversity of electrophilic reactions
• Redox: focus on nicotinamide- and flavin-dependent hydrogenation/dehydrogenation
reactions
• Section on disulfide-dithiol redox chemistry, roles of glutathione and lipoamide
My hopes for final versions of the new MCAT and
MCAT preview
• In lists of organic reactions, stress biological relevance, give examples
• Rethink references to purely synthetic chemistry
(emphasize small set of synthetic ‘tools’, understanding of retrosynthetic strategy)
Acknowledgements
University of Minnesota, Morris
Delmar Larsen, Chemwiki project at UC-Davis