Department of Biochemistry
and Molecular Biophysics
2801 North Bldg.
Pre-requisites: General Biochemistry, Physical Chemistry (thermodynamics and kinetics), Calculus, Differential equations
All biological processes require the interaction of a number of macromolecules with each other as well as with small ligand effectors in order to function in a precise, controlled manner. In some cases, these interactions are long-lived; however, in most cases, transient interactions are essential for proper control of biological function. Even “isolated” ligand-macromolecule interactions and/or conformational transitions are linked to other binding and/or conformational transitions, hence all macromolecular interactions involve multiple equilibria. The focus of this course is to introduce you to the quantitative approaches and logic needed to define these multiple equilibrium processes and to begin to dissect them in order to understand the forces involved in stabilizing and regulating the function of these macromolecules. This requires investigations of the energetics, thermodynamics (stabilities, affinities), kinetics and mechanism of binding and enzyme catalysis, including both steady state and transient (pre-steady state) approaches.
This course will discuss the theoretical principles, logic and approaches used to study these processes from a quantitative perspective. Topics will include thermodynamics, multiple binding equilibria, analysis of binding isotherms, Wyman linkage relationships, cooperativity, allostery, macromolecular assembly, enzyme catalysis and mechanism, steady-state and pre-steady state kinetics, as well as single molecule approaches. Some techniques used to study binding processes will also be discussed. The student will also learn to use computer simulation and non-linear least squares methods to aid in the analysis of equilibrium binding and kinetic studies.
The following books, as well as original research articles, will supplement the lectures.
- Introduction to Macromolecular Binding Equilibria – C. P. Woodbury (CRC Press)
- Binding and Linkage-Jeffries Wyman and Stanley J. Gill – (University Science Books)
- Kinetics for the Life Sciences – H. Gutfreund (Cambridge University Press)
Course grades will be based on three exams (80%). Problem sets will be given every 1-2 weeks and will be graded (20%).