Biophysical Chemistry I

This course provides a rigorous introduction to the theory underlying widely used biophysical methods, which will be illustrated by practical applications to contemporary biomedical research problems. The course has two equally important goals. The first goal is to explain the fundamental approaches used by physical chemists to understand the behavior of molecules and to develop related analytical tools. The second goal is to prepare students to apply these methods themselves to their own molecular biology research projects. The course will be divided into seven modules: (i) solution thermodynamics with an emphasis on application to analysis of protein structure, folding, and binding interactions; (ii) hydrodynamic methods; (iii) statistical analysis of experimental data; (iv) molecular dynamics calculations; (v) optical spectroscopy with an emphasis on fluorescence; (vi) nuclear magnetic resonance spectroscopy; and (vii) light-scattering and diffraction methods including an overview of cryogenic electron microscopy reconstruction methods. In each module, the underlying physical theories and models will be presented and used to derive the mathematical equations applied to the analysis of experimental data. Weekly recitations will emphasize the analysis of real experimental data and understanding the applications of biophysical experimentation in published research papers. The problem sets emphasize use of PyMOL for analysis of macromolecular structures and use of standard curve-fitting software for analysis of protein binding data; detailed tutorials on the related methods are provided in the recitation sections. The first three modules will be covered in Biophysical Chemistry I during the fall term, while the final three will be covered in Biophysical Chemistry II during the spring term, and treatment of molecular dynamics calculations will be divided between the two terms