BMB/Ch 178 Course Description Fall 2017

Macromolecular Function: Kinetics, Energetics, and Mechanisms

Course content: Energetic principles and molecular mechanisms that underlie macromolecular function. Allostery, enzyme evolution, and computational enzyme design. Practical kinetics sections discuss how to infer molecular mechanisms from rate/equilibrium measurements and their application to more complex biological systems, and include steady-state and pre-steady-state kinetics, and kinetic simulations.

Prerequisites for course: Bi/Ch 110a (biochemistry) or equivalent. BMB/Ch 178 is intended for graduate students or advanced undergraduates majoring in biology or chemistry. Permission from Shu-ou is required for undergraduates other than seniors to take this course.

Reading material: Most of the lectures will be based on literature, which will be provided on the course website. Structure and Mechanism in Protein Science by A. Fersht, 3rd Edition (2000) or later (ISBN 0716732688) is a great reference if you get lost in class. An electronic copy of this book is freely available on Copies of the print book are also on reserve in Millikan.

Class web page:

Homework: There will be three problem sets, downloadable from the course website. You may consult with others on the problem sets, but the written work must be done independently by each student. Copying other's work is not allowed and will be reported to the Honor court. Problem sets are due at the end of lecture on the specified dates. Late homework will not be accepted without a medical excuse.

Ideally, each student will get a chance to present at least one article during literature discussion at the end of the quarter. Students not presenting articles during the particular literature discussion will be graded based on participation.

Final: The final will be an open book, open note take home test. Details for the final will be uploaded as we approach the finals day. Final is due December 8th, at 5 pm, in a dropbox in front of Braun 109.

Grading: The course is offered for letter grade only. The problem sets will be worth 60% of the grade, literature presentations 10%, and the final 30%.

Computer facilities: Pymol will be used to assist the students in viewing and analyzing structures. The educational version of Pymol can be downloaded from:
Berkeley Madonna for kinetic simulations is needed near the end of this course. The software can be downloaded from: The user manual for Berkeley Madonna can be found at:

Email: E-mail is the best way for students to reach the professors, TAs or David Mathog. If you are enrolled in the BMB178 class please send mail from a campus account. Please get an account from IMSS if you don't already have one and give your e-mail address to the TAs before the end of the first week of class so that we can set up an e-mail distribution list.

Last modified 21-Sep-2017