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Department of Biochemistry and Molecular Biology

This is an archived copy of the 2012-13 catalog. To access the most recent version of the catalog, please visit http://catalogs.uchicago.edu.

Chair

  • Tobin R. Sosnick

Professors

  • Francisco Bezanilla
  • Glyn Dawson, Pediatrics
  • Geoffrey Greene, Ben May Department for Cancer Research
  • Stephen B. H. Kent
  • Shohei Koide
  • Anthony A. Kossiakoff
  • Marvin W. Makinen
  • Stephen Meredith, Pathology
  • Keith Moffat
  • Tao Pan
  • Eduardo Perozo
  • Joseph A. Piccirilli
  • Phoebe A. Rice
  • Benoit Roux
  • Nancy B. Schwartz, Pediatrics
  • James A. Shapiro
  • Tobin R. Sosnick

Associate Professors

  • Erin J. Adams
  • Sean D. Crosson
  • Robert J. Keenan
  • David Kovar, Molecular Genetics and Cell Biology
  • Ronald S. Rock
  • Alex Ruthenburg, Molecular Genetics and Cell Biology

Assistant Professors

  • D. Allan Drummond

Emeritus Faculty

  • Wolfgang Epstein
  • Herbert C. Friedmann
  • Alvin Markovitz
  • Theodore L. Steck
  • Donald F. Steiner
  • Edwin W. Taylor
  • Robert B. Uretz
  • John L. Westley
  • Ira G. Wool

The Biochemistry and Molecular Biophysics graduate program is a highly interdisciplinary program that forges a scientific culture of collaboration across the physical and biological sciences disciplines and among diverse laboratories. In this environment, students will have the opportunity to engage in research that aims to understand biological processes at the molecular level. The program is designed to encourage students to pursue research interests at the biological-physical sciences interface using diverse approaches such as structural and chemical biology, molecular and single molecule biophysics, combinatorial mutagenesis, protein engineering and RNA and DNA protein recognition.

Admission

For information about applying to our graduate program, please visit our website at http://molbio.bsd.uchicago.edu/index.php .

Degrees

Doctor of Philosophy

A Ph.D. program requires generally 4 to 6 years of study. The first year is spent in course work and small research projects in several laboratories to become acquainted with the department. Also during the first year there are many opportunities to attend and participate in departmental invited seminars and the Graduate Student Seminar Series. After the preliminary exam at the end of the first year, students choose a research advisor, carry out their Ph.D. research, write and orally defend a thesis.

Each student is required to take a minimum of 9 graded courses; up to two of these classes may be substituted by graded laboratory rotations.  Of the nine courses only the following are required:

BCMB 30400Protein Fundamentals100
BCMB 31600Cell Biology I100
BCMB 31200Molecular Biology-I100
BCMB 32200Biophysics of Biomolecules100

Two additional courses (BCMB 31900 – Introduction to Faculty Research, affectionately called “Faculty All Stars” and BCMB 31800 – Current Seminar Topics in Biochemistry and Molecular Biology) are required. The introduction to faculty research course is not for credit; however, BCMB 31800 is for ½ credit. Each student is required to be a Teaching Assistant for a total of two quarters in their third and fourth years of residence.

The preliminary examination consists of a written research proposal that is prepared and submitted during the summer quarter of the first year. Students will be permitted to take the preliminary examination only after all course and grade requirements have been met. Two outcomes are possible: Pass or Revisions Needed. If revisions are required, the student will have the opportunity to respond to the committee’s concerns and either revise portions of the proposal or re-write the entire proposal as indicated by the committee. Inadequate performance on a second exam is grounds for dismissal from the program. For continuation in the program, students must successfully pass the preliminary exam by the end of the fifth quarter of full-time residence as a graduate student in Biochemistry and Molecular Biophysics.

During the second year, students select a thesis advisor and begin laboratory research. To complete the Ph.D. degree, they must prepare, under the general direction of an appointed doctoral committee, a dissertation based upon their original research. A public seminar describing the results of the dissertation research must be presented and the dissertation must be successfully defended before the doctoral committee.

Biochemistry and Molecular Biology Courses

BCMB 30266. Units.

Equivalent Course(s): IMMU 30266

BCMB 30400. Protein Fundamentals. 100 Units.

The course covers the physical‑chemical phenomena that define protein structure and function.  Topics include:  the principles of protein folding, molecular motion and molecular recognition; protein evolution, design and engineering; enzyme catalysis; regulation of protein function and molecular machines; proteomics and systems biology.  Workshop on X-ray Crystallography: The workshop is an addendum to Protein Fundamentals and is required for all BCMB students. This one week workshop will provide students with an intensive introduction to protein structure determination by x-ray crystallography. In addition to lectures, an extensive laboratory component will give students the opportunity to carry out protein crystallization, data collection (at Argonne), structure determination, refinement, model building and validation.

Instructor(s): Robert Keenan, Shohei Koide, Joseph Piccirilli     Terms Offered: Autumn
Equivalent Course(s): GENE 30400,HGEN 30400,MGCB 30400

BCMB 31000. Fundamentals of Molecular Biology. 100 Units.

This course covers the structure of genetic material, chromatin, replication, DNA repair and transcription, including its regulation, RNA processing, post-transcriptional regulation, and protein synthesis. Third- or fourth-year standing is required for undergraduates; any graduate student may enroll.

Instructor(s): U. Storb, J. Staley     Terms Offered: Winter
Prerequisite(s): Basic knowledge of genetics and biochemistry
Equivalent Course(s): BIOS 21208,GENE 31000,MGCB 31000

BCMB 31100. Evolution of Biological Molecules. 100 Units.

This introductory graduate-level course connects evolutionary changes in genes and genomes with the structure, function and behavior of the protein and RNA molecules they encode.  Our central themes will be the mechanisms and dynamics by which molecular structure and function evolve, how protein/RNA architecture shapes evolutionary trajectories, and how patterns in present-day sequences can be interpreted to reveal the interplay data of evolutionary history and molecular properties.  We will teach core concepts in both macromolecular biochemistry (folding and stability of proteins and RNA, structure-function relationships, kinetics, catalysis) and molecular evolution (selection, mutation, drift, epistasis, effective population size, phylogenetics) and specifically explore the interplay between them. Students will derive and simulate evolution using molecular-level models; analyze empirical structure, function and sequence data in an evolutionary framework; and, through discussion and reading of classic and recent literature, trace the development of key ideas in molecular evolution up to the present day.

Instructor(s): D. Allan Drummond, Joseph Thornton     Terms Offered: Winter
Prerequisite(s): Comfort with basic computer programming (course will use Python and R); undergraduate biology, chemistry, calculus, and introductory statistics.
Equivalent Course(s): HGEN 31100,ECEV 31100

BCMB 31200. Molecular Biology-I. 100 Units.

Nucleic acid structure and DNA topology; methodology; nucleic-acid protein interactions; mechanisms and regulation of transcription in eubacteria, and of replication in eubacteria and eukaryotes; mechanisms of genome and plasmid segregation in eubacteria.

Instructor(s): L. Rothman-Denes     Terms Offered: Winter Quarter
Equivalent Course(s): MGCB 31200,DVBI 31200

BCMB 31300. Molecular Biology-II. 100 Units.

The content of this course covers the mechanisms and regulation of eukaryotic gene expression at the transcriptional and post-transcriptional levels. Our goal is to explore research frontiers and evolving methodologies. Rather than focusing on the elemental aspects of a topic, the lectures and discussions highlight the most significant recent developments, their implications and future directions.

Instructor(s): J. Staley, J. Holaska, A. Ruthenburg     Terms Offered: Spring Quarter
Equivalent Course(s): MGCB 31300,DVBI 31300

BCMB 31358. Simulation, Modeling, and Computation in Biophysics. 100 Units.

This course develops skills for modeling biomolecular systems.  Fundamental knowledge covers basic statistical mechanics, free energy, and kinetic concepts.  Tools include molecular dynamics and Monte Carlo simulations, random walk and diffusion equations, and methods to generate random Gaussian and Poisson distributors.  A term project involves writing a small program that simulates a process.  Familiarity with a programming language or Mathlab would be valuable.

Instructor(s): B. Roux     Terms Offered: Spring
Prerequisite(s): BIOS 20200 and Bios 26210-26212, or consent from instructor
Equivalent Course(s): BIOS 21358,CPNS 31358

BCMB 31400. Genetic Analysis of Model Organisms. 100 Units.

Fundamental principles of genetics discussed in the context of current approaches to mapping and functional characterization of genes.  The relative strengths and weaknesses of leading model organisms are emphasized via problem-solving and critical reading of original literature.

Instructor(s): A. Palmer, D. Bishop, E. Ferguson, J. Malamy     Terms Offered: Autumn
Equivalent Course(s): DVBI 31400,HGEN 31400,MGCB 31400

BCMB 31600. Cell Biology I. 100 Units.

Eukaryotic protein traffic and related topics, including molecular motors and cytoskeletal dynamics, organelle architecture and biogenesis, protein translocation and sorting, compartmentalization in the secretory pathway, endocytosis and exocytosis,and mechanisms and regulation of membrane fusion.

Instructor(s): A. Turkewitz, B. Glick     Terms Offered: Autumn Quarter
Equivalent Course(s): MGCB 31600,DVBI 31600

BCMB 31800. Current Seminar Topics in Biochemistry & Molecular Biology. 50 Units.

Lectures on current research by departmental faculty and other invited speakers. A required course for all first-year graduate students.

Equivalent Course(s): BPHS 31800

BCMB 31900. Introduction to Research. 100 Units.

Lectures on current research by departmental faculty and other invited speakers. A required course for all first-year graduate students

Instructor(s): Staff     Terms Offered: Autumn, Winter Quarters
Equivalent Course(s): MGCB 31900,DVBI 31900,GENE 31900,HGEN 31900

BCMB 32200. Biophysics of Biomolecules. 100 Units.

This course covers the properties of proteins, RNA, and DNA, as well as their interactions. We emphasize the interplay between structure, thermodynamics, folding, and function at the molecular level. Topics include cooperativity, linked equilibrium, hydrogen exchange, electrostatics, diffusion, and binding.

Instructor(s): T. Sosnick     Terms Offered: Spring
Prerequisite(s): Consent of instructor
Equivalent Course(s): BIOS 21328,BPHS 31000

BCMB 32300. Macromolecular Function. 100 Units.

This course will be an in depth assessment of the structure and function of biological membranes. In addition to lectures, directed discussions of papers from the literature will be used. The main topics of the courses are: (1) Energetic and thermodynamic principles associated with membrane formation, stability and solute transport (2) membrane protein structure, (3) lipid-protein interactions, (4) bioenergetics and transmembrane transportmechanisms, and (5) specific examples of membrane protein systems and their function (channels, transporters, pumps, receptors). Emphasis will be placed on biophysical approaches in these areas. The primary literature will be the main source of reading.

Equivalent Course(s): MGCB 32300

BCMB 32500. Bioorganic Chemistry. 100 Units.

A goal of this course is to relate chemical phenomena with biological activities. We cover two main areas: (1) chemical modifications of biological macromolecules and their potential effects; and (2) the application of spectroscopic methods to elucidate the structure and dynamics of biologically relevant molecules.  Not offered in 2012-13.

Equivalent Course(s): CHEM 32500