BMB/Ch 178 Lecture Notes Fall 2017

Macromolecular Function: Kinetics, Energetics, and Mechanisms

(Links may point to empty files until the real ones are uploaded.)
Date Subject Notes Recommended Reading
1 9/27 Introduction; review of basic thermodynamics; transition state theory PDF link
2 9/29 Transition state theory continued and ramifications; PyMOL tutorial PDF link
3 10/04 Covalent catalysis; General acid/base catalysis PDF link
4 10/06 Metal ions; Electrostatics and hydrogen bonds PDF link
5 10/11 Entropy, intrinsic binding energy and the Circe effect PDF link
6 10/13 Specificity and editing mechanisms; promiscuity and enzyme evolution PDF link
7 10/18 Cooperativity and allostery PDF link
8 10/20 Kinetics 101: rate laws, rate limiting steps PDF link
9 10/25 Steady state kinetics (I) PDF link
10 10/27 Steady state kinetics (II)
Presteady-state kinetics (I)
PDF
PDF
link
11 11/1 Literature Discussion (I) PDF link
12 11/3 Literature discussion (II) - -
13 11/08 Pre-steady state kinetics (II) PDF link
14 11/10 Pre-steady state kinetics (III); Overview of analytical tools PDF link
15 11/15 Kinetics simulations PDF
Berkeley Madonna Short Manual
link
16 11/17 Single molecule kinetics (II) PDF link
17 11/22 Single molecule kinetics (III) PDF link
- 11/24 No class (Thanksgiving) - -
18 11/29 Enzyme design and evolution PDF link
19 12/1 Literature discussion (II) - -
Last modified 29-NOV-2017