Molecular Biophysics Training Program

To ensure that all our students obtain sufficient breadth in their molecular biophysics training, all students must take courses from the curriculum defined below. In all, seven courses should be taken during the two years a student is funded by the program: four core courses, two elective courses, and a scientific ethics course.

Core Courses (Required)

CHEM209 OR BIOM200 (offered in the FALL)

Chem 209 - Macromolecular Recognition: Professor(s): N. Toor

Structures and functions of nucleic acids, folding and catalysis of nucleic acids, motifs and domains of proteins, principles of protein-protein interactions, chemistry of protein/DNA and protein/RNA interfaces, conformational changes in macromolecular recognition.

BIOM 200 - Molecules to Organisms: Professor(s): Biomedical Sciences Faculty

An in-depth discussion of the molecular processes relating to cell signaling, cell biology, and how drugs interact with different organ systems. The course offers comprehensive coverage of the major pathways in cell signaling from a biochemical perspective.

(Physics students may take either Chem 209 or Chem 219A)

CHEM219A: Special Topics in Biochemistry (offered in the FALL)

Professor(s): U. Muller

This special topics course is designed for first-year graduate students in biochemistry. The course is coordinated with the fall Biochemistry seminar series. Students discuss topics related to the next seminar which recently have included protein processing, the chemical modification of proteins, the biosynthesis and function of glycoproteins, lipid biochemistry and membranes, and systems biology.(BMS students may substitute equivalent course, Physics students may take either Chem 209 or Chem 219A)

PHYS275: Fundamentals of Biological Physics (offered in the FALL, usually taken in 2nd yr)

Professor(s): O. Dudko

This course teaches how quantitative models derived from statistical physics can be used to build quantitative, intuitive understanding of biological phenomena. The organizational thread that links various topics of this course is based upon the underlying physics prospective. The idea of two-state variables and the Gibbs distribution will be employed to investigate ion channel gating, phosphorylation, and ligand-receptor binding and cooperativity.

Physics of random walks will be used to explore the size of a genome and the geography of chromosomes, DNA looping and gene regulation, the emergence of entropic elasticity, and protein folding. We will examine the microscopic and continuum descriptions of diffusion, the Smoluchowski equation, and discuss diffusion as a transport mechanism and a mechanism for delivering ligands to receptors. The theory of rate equations will be applied to the dynamics of ion channels, enzyme kinetics, cytoskeletal assembly, and the dynamics of molecular motors. The propagation of nerve impulses will be discussed as a problem in biological electricity.

CHEM213a/BIOM213a: Structure of Biomolecules and Biomolecular Assemblies (offered in the WINTER)

Professor(s): Kevin Corbett and Elizabeth Komives (and others)

A discussion of structures of nucleic acids and proteins and their larger assemblies. The theoretical basis for nucleic acid and protein structure, as well as methods of structure determination including x-ray crystallography, cryoEM, and computational modeling approaches will be covered.

CHEM213b/BIOM213b: Biophysical Chemistry of Macromolecules (offered in the SPRING every other year)

Professor(s): Elizabeth Komives (and others)

A discussion of the physical principles governing biomolecular structure and function. Experimental and theoretical approaches to understand protein dynamics, enzyme kinetics and mechanisms will be covered.

CHEM291: Molecular Biophysics Seminar

Chem 291- Molecular Biophysics Seminar 

Monthly Journal Club. Held the third Tuesdays of each month, NSB3211, 4:30pm.

 

 

If you have never had undergraduate cell biology, the following is required.

CHEM214D: Molecular and Cellular Biochemistry (offered in the FALL)

Professor(s): G. Ghosh

Recommended for students who have not had a course in cell biology. This course represents a continuation of 114C, or an introductory course for first-year graduate students, and covers topics in molecular and cellular biochemistry. Emphasis will be placed on contemporary approaches to the isolation and characterization of mammalian genes and proteins, and molecular genetic approaches to understanding eukaryotic development and human disease.

Research Ethics (Required)

Take One of the Following Courses

COGS241: Ethics and Survival Skills in Academia, Winter

SOMI226: Scientific Ethics, Spring

CHEM250: Seminar in Chemistry

Professor: Susan Taylor

Regularly scheduled seminars by first-year graduate students provide opportunities for practice in seminar delivery and for the exploration of topics of general interest. (S/U grades only.)

Electives

Take Two of the Following Courses

CHEM204. Introduction to X-ray Crystallography (offered every other year)

Professor(s): P. Ghosh

Analysis of macromecular structures by X-ray diffraction. Topics include symmetry, geometry of diffraction, detection of diffraction, intensity of diffracted waves, phase problem and its solution, heavy atom method, isomorphous replacement, anomalous dispersion phasing methods (MAD), direct methods, molecular replacement.

CHEM207: Modern NMR Methods (offered in the WINTER)

Professor(s): S. Opella

Treats varied pulse sequences, one- and two-dimensional methods, interpretation of relaxation rates, spin-decoupling, multiple quantum filtering, and solvent suppression with application to liquid crystals, membranes, small molecules, proteins, and nucleic acids.

CHEM216: Chemical Biology (offered in the WINTER)

Professor(s): N. Devaraj and P. Dorrestein

A discussion of current topics in chemical biology including mechanistic aspects of enzymes and cofactors, protein design, use of modified enzymes to alter biochemical pathways, chemical intervention in cellular processes, protein modification and natural product discovery.

CHEM217: RNA Structure, Function & Biology (offered in the SPRING)

Professor(s): S. Joseph

Recent discoveries reveal that RNA plays a central role in several cellular functions, ranging from protein synthesis to repairing the ends of chromosomes. This course will focus on several topics in RNA structure and function. Formal lectures will cover the selected topics in-depth with special emphasis on mechanistic studies. Each student will present one research article related to the topic discussed in the lectures. In addition, students will write critiques of the research articles presented in the class. Active participation by the students is strongly encouraged.

CHEM225. Bioinorganic Chemistry (Offered in the SPRING)

Professors: F. A. Tezcan and S. M. Cohen

Metal ions are found in ~50% of all proteins and fulfill numerous essential biological roles. This class will cover the roles of metal ions in biological systems, with emphasis on transition metal ions in enzymes that transfer electrons, bind oxygen, and fix nitrogen. Also included are metal complexes in medicine, toxicity, and metal ion storage and transport.

CHEM265: 3D Electron Microscopy/Macromol (offered in the SPRING)

Professor(s): T. Baker

Biological macromolecules and supramolecular complexes as well as organelles, and small cells are being examined in three-dimensions by modern electron cryo-microscopy and image reconstruction techniques. The basic principles of transmission electron microscopy and 3D image reconstruction are discussed.

CHEM280: Applied Bioinformatics (offered in the WINTER)

Professor(s): W. Wang et al.

Theory and practice of bioinformatics approaches to the structures and functions of nucleic acids, motifs and domains of proteins, principles of protein-protein interactions, chemistry of protein/DNA and protein/RNA interfaces, conformational changes in macromolecular recognition.

CHEM285: Introduction to Computational Chemistry (offered in the SPRING)

Professors R. Amaro and R. Walker

Course in computational methods building on a background in mathematics and physical chemistry. Brief introduction and background in computational theory, molecular mechanics, semi-empirical methods, and ab initio-based methods of increasing elaboration. Emphasis on applications and reliability.