Chem*4520 Metabolic Processes

Fall Semester 2000

Modified Sept 8 2000

schematic view of the enzyme citrate synthase,
with bound acetyl-CoA analog in green

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Lectures: MacKinnon 116
10:30-11:20 am, Mon-Wed-Fri
Course ObjectivesEvaluation
Lecture topicsTextbooks

Contact Dr. Keates

MacNaughton 338, ext 3808

Office Hours:

2:30-4:00 Monday & Wednesday
10:30-12:00 Thursday


The study of chemical and biochemical processes in metabolism. Students will learn to apply the principles of chemical mechanism, thermodynamics and biochemical regulation to understand why particular reactions happen and how metabolism can be directed towards the pathways for synthesis or breakdown.

Chem*4520 builds on and reinforces concepts learned in previous courses:
Basis of chemical and biochemical reactions (Chem*1040, Chem*2580)
Thermodynamics of reactions (Chem*105, Chem*2580)
Fundamental metabolic pathways - glycolysis, TCA cycle, beta-oxidation (Chem*2580)
Gluconeogenesis, pentose phosphate pathway, fatty acid biosynthesis (Chem*3560)
Regulation of enzyme activity, allosteric mechanisms, protein phosphorylation (Chem*3560).

In preparation for this course, make sure you are reasonably conversant with these topics.


Midterm examination35%Tuesday October 24, 7:00-9:00 pm C&M 160
Assignment15%Details to be announced
Final Examination50%Tuesday Dec 12, 8:30-10:30 am.
MacN 113

Sample mid-term examAnswers to 1990 sample mid-term exam

Very brief answers to 1989 sample mid-term exam

new expanded metabolic map (this will be a hand out on the final).

Sample final examVery brief answers to 1990 sample final exam

Lecture Topics

Mon 09-11Bioenergetics, free energy, equilibrium and the direction of reactions.
Wed 09-13Free energy applied to the glycolysis pathway; the aldolase step, the phosphoglycerate kinase step and the pyruvate kinase step
Fri 09-15Chemical mechanisms in biochemical reactions
Mon 09-18,
Wed 09-20
Glucose isomerase, aldolase, glyceraldehyde-3-phosphate dehydrogenase and enolase reaction mechanisms.
Fri 09-22Gluconeogenesis: turning the thermodynamics around
Mon 09-25Monosaccharide interconversions; fructose and galactose entry to glycolysis and synthesis of hexose derivatives; fucose, rhamnose N-acetylglucosamine, glucuronic acid and N-acetylneuraminidate
Wed 09-27Regulation of the TCA cycle
Fri 09-29Regulation of pyruvate use and Glyoxylate cycle
Mon 10-2Mitochondrial membrane transporters
Wed 10-4Relationship of TCA cycle to mitochondrial transport
Fri 10-6Regulation of fatty acid biosynthesis
Wed 10-11Metabolism of unsaturated fatty acids
Fri 10-13Breakdown of unsaturated and odd numbered fatty acids
Mon 10-16Ketone bodies
Wed 10-18Mevalonate to squalene
Fri 10-20Squalene to cholesterol
Mon 10-23Review class
Wed 10-25Regulation of cholesterol synthesis and biosynthesis of steroid hormones
Fri 10-27Synthesis and function of steroid hormones
Mon 10-30Corticosteroids; Biosynthesis of prostanoids
Wed 11-1Function of the prostaglandins
Fri 11-3Leukotrienes
Mon 11-6Amino acid breakdown
Wed 11-8The urea cycle
Fri 11-10Seminar on protein folding by Dr. Wayne Bolen, MBG 337
Mon 11-13Amino acid breakdown pathways
Wed 11-15Branched and aromatic amino acid breakdown
Fri 11-17Aromatic amino acid biosynthesis
Mon 11-20Biologically active amines derived from amino acids
Wed 11-22Pyrimidine biosynthesis
Fri 11-24Purine biosynthesis
Mon 11-27Purine biosynthesis
Wed 11-29Nucleotide interconversions
Fri 12-1Final Review

Problem solutions

Problem set 1 Sept 11-15Problem set 2 Sept 18-22Problem set 3 Sept 25-29
Problem set 4 Oct 2-6Problem set 5 Oct 9-13Problem set 6 Oct 23-27
Problem set 7 Nov 6-13Problem set 8 Nov 14-20


Pick one of the following:
Strongly recommended: Biochemistry, Donald Voet and Judith G. Voet
(2nd Ed.1995, J. Wiley & Sons).
A detailed and comprehensive text, in particular for metabolism and chemical mechanism as covered in this course.
Recommended: Biochemistry, Matthews, Van Holde, Ahern
(3nd Ed.1999, Addison Wesley).
Another comprehensive text, but not quite as detailed for metabolic reaction mechanisms as Voet and Voet. Pick this text if you want a really up to date reference which will help you out in a variety of advanced biochemistry/molecular biology courses.
Also acceptableBiochemistry, Lubert Stryer
(4th Ed. 1995, W.H. Freeman)
Also a good general biochemistry text, unfortunately the coverage of metabolism is not as extensive as Voet and Voet. The main advantage is that everyone who has done Chem*3560 should have Stryer already, but be prepared to visit the Library reserve desk to consult Voet and Voet occasionally.

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