Course Syllabus

Biological Chemistry/Chemistry 673: Mechanism & Kinetics of Enzymes - 6311 Med. Sci. I, MWF 10-11

Kinetics for Enzymologists? Hell yeah - Laissez les bons temps rouler!!!

This course delivers an in-depth introduction to the chemical kinetics that describe enzyme action with the goal of developing the skills needed to elucidate enzyme mechanisms. Starting with simple unimolecular reactions, paradigms of increasing complexity are considered along with transient kinetic experiments used to analyze them. This march through key mechanisms reaches a crescendo when we consider catalytic cycles from the point of view of transient kinetics. We then switch viewpoints and analyze steady-state kinetic mechanisms, leaning heavily on Cleland's nomenclature and rules for the analysis of steady-state velocity patterns. Time permitting, we close by considering the complementary information that transient kinetics and steady-state kinetics provide to the mechanistic enzymologist.

While the riveting lectures develop the theory behind kinetic analyses both mathematically and qualitatively, the rubber meets the road in the weekly problem sets. They put the theory into practice with simulations and virtual experiments. An emphasis is placed on learning to design and interpret experiments, analyzing new kinetic situations, and using research-grade software.

It's intense, and it's great fun. Biol. Chem. 673 - the toughest course you'll ever love.

syllabus.pdf

Useful texts:

No textbook adequately covers the topics in this course, and, therefore, none is required. Nonetheless, two books may provide useful alternate perspectives: Alan Fersht, Structure and Mechanism in Protein Science, 1999, W. H. Freeman and Company, New York; Paul F. Cook & W. W. Cleland, Enzyme Kinetics and Mechanism, 2007, Garland Science, London and New York

Software: Many of the exercises in this course will require:

Kaleidagraph, recommended for curve-fitting. A free demo version that is almost fully functional may be obtained at: http://www.synergy.com  The full version is found on the computers of many research groups on campus, or, buy it yourself – it's cheaper than many textbooks.

For simulating mechanisms, we will use Berkeley Madonna, a research-grade program for solving differential equations (and doing other things). Recent operating systems (Mac or Windows) will only run the new (free!) beta java version. Download this at:

http://www.berkeleymadonna.com/jmadonna/jmadrelease.html

Virtual experiments will be performed using webZyme (http://tinyurl.com/webzyme). Your user name will be your unique name, and your default password will be "webzyme", which you may change.

Optional Problem-Solving Sessions:

Weekly problem-solving sessions, scheduled at a mutually convenient time, will cover basic problem-solving skills in kinetics. They will not introduce new course material. Their purpose is to cover the mechanics of using the software required in the course, to discuss basic mathematics, to solve simple kinetics problems (usually much simpler than graded homework), and to discuss data analysis.

Grading:

Grades will be assigned on the basis of problem sets (high-value) and surprise quizzes (low-value).