Biochemistry and Molecular Biophysics Graduate Group

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BMB 508 - Macromolecular Biophysics: Principles and Methods

Fall, every year

Course Director:

Kim Sharp, Ph.D., sharpk@mail.med.upenn.edu

Time and Place: Mon & Wed, 1:30 - 3:00 p.m. 255 Anatomy-Chemistry Building

This is an introductory course on Macromolecular Biophysics. The first part of the course covers the physical fundamentals underlying the structure and behavior of macromolecules necessary for biological function. The second part of the course covers the interaction of macromolecules with radiation, which underlies many of the methods used to study macromolecules.

The third and final part of the course is student presentations. Each period 2-3 students will present a small set of papers (usually 2 to 3) presenting different sides of an unsolved, possibly controversial topic in macromolecular biophysics. Students can choose from a set of pre-selected topics, or from their own suggestions (with approval from the director). The presentations will emphasize the dynamic, often uncertain dialogue of experiment, interpretation and critique involved in scientific discovery. The presentation will be 'contemporaneously historical', i.e. based on the state of knowledge at the time of the papers. It can use knowledge of earlier literature, but not of research that was unknown at the time. Illustrative examples are listed below. Most typically draw from general journals like Science or Nature. They thus are written to be understood by people outside the specific area of the articles, and without extensive background literature reading, (i.e. BMB508 students!)

Textbooks:Cantor & Schimmel. Vol II, Techniques for the study of biological structure and function. Van Holde: Physical Biochemistry

Grade: Homework: 40%, midterm 30%, Presentations/Participation 30%.

Fall 2014 Course Outline

Date

Topic

Lecturer

Part 1a: The physics of macromolecules:
Energies & Equilbria, Structure & Binding

W sep 3

Molecular Interaction Energies: Bonding, Nonbonding: Nonpolar

C&S Ch5

Sharp

M sep 8

Molecular Interaction Energies: Nonbonding: Polar/Electrostatic

C&S Ch5

Sharp

W sep 10

Equilbria: Folding, Structure and Stability

C&S Ch15,17

Sharp

M sep 15

Equilibria: Binding and Allostery

Sharp

Part 1b: The physics of macromolecules
Forces, Dynamics, Kinetics

W sep 17

Molecular Forces: Fundamentals of Rates and Dynamics

Sharp

M sep 22

Kinetics: Experimental

C&S Ch16

Kohli

W sep 24

Kinetics: Enzymes, Inhibitors and more

C&S Ch16

Kohli

M sep 29

Studying Single Molecules

Goldman

W oct 1

Studying Single Molecules

Goldman

Part 2: Interaction of Molecules and Radiation

 

M oct 6

Scattering: Determination of structure

C&S Ch11,12

K. Gupta

W oct 8

Diffraction 1: Determination of Structure

C&S Ch13

K. Gupta

M oct 13

Diffraction 2: Determination of Structure

C&S Ch13

K. Gupta

W oct 15

Magnetic Resonance 1: Determination of structure and dynamics

C&S Ch9

Wand

M oct 20

Magnetic Resonance 2 “

C&S Ch9

Wand

W oct 22

Magnetic Resonance 3 ”

C&S Ch9

Wand

M oct 27

Absorption: Optical Spectroscopy (UV, Fluorescence, CD)

C&S Ch7

Vinogradov

W oct 29

Absorption: Optical Spectroscopy (UV, Fluorescence, CD)

C&S Ch7

Vinogradov

Part 3: Current Controversies in Biophysics: Student Presentations

M nov 3

See list in separate document

W nov 5

M nov 10

W nov 12

M Nov 17

W nov 19

M nov 24

M dec 1

W dec 3

M dec 8