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, a cell biology course, an elective course and a scientific ethics course. Some useful workshops and minicourses related to molecular biophysics are listed here as well.


CHEM219A:  Special Topics in Biochemistry
Professor: T. Nakagawa, Fall
This special topics course is designed for first-year graduate students in biochemistry. Topics presented in recent years have included protein processing, the chemical modification of proteins, the biosynthesis and function of glycoproteins, lipid biochemistry and membrane structure, and bioenergetics.

CHEM209:  Macromolecular Recognition
Professor: P. Ghosh, Fall
 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.

CHEM280:  Applied Bioinformatics
Professor: L. Weinberger, W. Wang, Winter
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.

CHEM213:  Chemistry and Biochemistry of Macromolecules
Professor: P. Jennings, P. Wolynes, Spring
A discussion of the structural principles governing biological macromolecules, the techniques used in their study, and how their functional properties depend on three-dimensional structure.

A CELL BIOLOGY COURSE IS REQUIRED (Choose one of the following)

CHEM214: Molecular and Cellular Biochemistry
Professor: D. Donoghue, Fall
(Conjoined with Chem. 114D.) This course represents a continuation of 114C, or an introductory course for first- and second-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.

CHEM221:Signal Transduction
Professor: Alexander Hoffmann, Winter
The aim of this course is to develop an appreciation for a variety of topics in signal transduction. We will discuss several historical developments while the focus will be on current issues. Both experimental approaches and results will be included in our discussions. Topics may vary from year to year.

BGGN222:  Advanced Cell Biology
Professor: D. Forbes, Winter
A coverage of modern cell biology for first year graduate students.

 

TAKE ONE OF THE FOLLOWING COURSES

COGS241:  Ethics and Survival Skills in Academia, Winter
Course Website:  http://ethics.ucsd.edu/courses/survival/index.html

**Register for COGS241 on the ethics website here AND on TritonLink (like any other class) to receive units for this course.**

SOMI266:  Scientific Ethics, Spring
Course Website:  http://ethics.ucsd.edu/courses/ethics/index.html

**Register for SOMI266 on the ethics website here AND on TritonLink (like any other class) to receive units for this course.**

PHAR219:  Ethics in Scientific Research, Spring

**This is a one week ethics course taught by Dr. Palmer Taylor.  Register for it on TritonLink.**

 

TAKE ONE OF THE FOLLOWING COURSES

CHEM216:  Chemical Biology
Professor: E. Komives, M. Burkart, Fall
A discussion of current topics in chemical biology including mechanistic aspects of enzymes and cofactors, use of modified enzymes to alter biochemical pathways, chemical intervention in cellular processes, and natural product discovery.

PHY239: (special topics) Quantitative Molecular Biology
Professor: T. Hwa, Fall
A discussion of gene networks and systems in Molecular Biology
 
PHYS272: Biophysics of Molecules, Winter
Professor: O. Dudko
Physical concepts and techniques used to study the structure and function of biological molecules, the thermodynamics and kinetics of biological activity, and physical descriptions of biological processes. Examples from enzyme action, protein folding, photobiology, and molecular motors.

CHEM232:  Statistical Mechanics of Chemical Systems
Professor: P. Wolynes, Fall
Equilibrium statistical mechanics, distribution functions, and partition functions. Boltzman, Bose, and Fermi statistics. The different ensembles; ensemble averages and QM expectation values; derivation of thermodynamic properties of simple systems.

CHEM207: Modern NMR Methods
Professor: S. Opella, Winter
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.

PHARM231:  Contemporary Topics in the Pharmacological Sciences
Professors: R. Tsien and P. Taylor, Spring
The course presents the basic principles of fluorescence, looking in more detail at steady-state fluorescence instrumentation and microscopy as well as time-resolved fluorescence and the use of fluorescent tools in research.  In this course, students must also select a paper on the techniques of fluorescent tools in studying cellular or molecular function.

 

Molecular Biophysics Workshops and Minicourses