Course Syllabus

Biological Chemistry/Chemistry 673: Mechanism & Kinetics of Enzymes  1632 Chemistry, MWF 11:00 - 11:50

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. 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 frequent problem sets. You'll put theory into practice with virtual experiments, and you'll practice your theory with derivations and simulations. 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.

Useful texts:

No textbook adequately covers the topics in this course, and, therefore, none is required. A new book comes closest: Clive Bagshaw, Biomolecular Kinetics: A Step-By-Step Guide, 2017, CRC Press, Taylor & Francis Group, Boca Raton. Also, these two books may provide useful perspectives: Alan Fersht, Structure and Mechanism in Protein Science, 4th ed., 2017, World Scientific Press (essentially the same as the 1999 3rd ed.); and, 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 is recommended for curve-fitting. (No, you can't use Excel instead!! And yes, K'graph is better than Prism.) 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): http://www.berkeleymadonna.com/

We will also have temporary licenses in the last month of the course for KinTek Explorer, a global fitting program with an unusually friendly interface: https://www.kintekexplorer.com  

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.

Grading:

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