Biochemistry and Molecular Biology
E-mail: bmb-gradasst@lifesci.lscf.ucsb.edu
Web site: http://lifesci.ucsb.edu/BMB/
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Program Chair: Louise Clarke
Roymarie Ballester, Ph.D., Albert Einstein College of Medicine, Assistant Professor (eukaryotic cell microbiology)
Thomas C. Bruice, Ph.D., University of Southern California, Research Professor
John A. Carbon, Ph.D., Northwestern University, American Cancer Society Professor (biochemistry)
Rolf E. Christoffersen, Ph.D., UC Los Angeles, Associate Professor (plant molecular biology)
Louise Clarke, Ph.D., UC Santa Barbara, Professor (biochemistry, genetics)
Dennis O. Clegg, Ph.D., UC Berkeley, Associate Professor (neurobiology)
James B. Cooper, Ph.D., Washington University, Associate Professor (plant molecular biology)
Ellis Englesberg, Ph.D., UC Berkeley, Professor Emeritus
J. Thomas C. Gerig, Ph.D., Brown University, Professor (bo-organic chemistry)
Lori Kohlstaedt, Ph.D., UC Berkeley, Assistant Professor (physical biochemistry)
Nancy L. Lee, Ph.D., University of Pittsburgh, Professor Emeritus (microbiology)
John Lew, Ph.D., University of Calgary, Alberta, Assistant Professor (biochemistry)
Michael J. Mahan, Ph.D., University of Utah, Assistant Professor (microbiology)
Daniel Morse, Ph.D., Albert Einstein College of Medicine, Professor (molecular genetics, biochemistry, marine biology, developmental biology)
Stanley M. Parsons, Ph.D., California Institute of Technology, Professor (biological chemistry)
John J. Perona, Ph.D., Yale University, Assistant Professor (physical biochemistry)
Norbert O. Reich, Ph.D., UC San Francisco, Associate Professor (biological chemistry)
Joel H. Rothman, Ph.D., University of Oregon, Eugene, Associate Professor (developmental biology and genetics)
Cyrus R. Safinya, Ph.D., Massachusetts Institute of Technology, Professor (biomolecular materials)
Charles E. Samuel, Ph.D., UC Berkeley, Professor (virology, molecular biology, biochemistry)
Duane Sears, Ph.D., Columbia University, Professor (biochemistry)
Robert L. Sinsheimer, Ph.D., Massachusetts Institute of Technology, Professor Emeritus (biochemistry)
George Taborsky, Ph.D., Yale University, Professor Emeritus
Edward L. Triplett, Ph.D., Stanford University, Professor Emeritus
Carol A. Vandenberg, Ph.D., UC San Diego, Associate Professor (neurobiology)
Leslie Wilson, Ph.D., Tufts University, Professor
(biochemical pharmacology)
The interdepartmental graduate program in biochemistry and molecular biology offers studies leading to the Ph.D. degree. The program is administered jointly by faculty in the Department of Molecular, Cellular, and Developmental Biology; Chemistry; and Materials. The program provides unique opportunities for intensive research training at the interface between the physical and life sciences in highly interactive and collaborative laboratories. The diverse group of program faculty provide students with an exceptionally broad range of challenging opportunities for multidisciplinary research in biomolecular structure, function, and engineering. Research areas currently under active investigation on campus include kinetics and regulation of enzyme catalysis, chromosome structure and cell cycle regulation, the cytoskeleton and extracellular matrix, mechanisms regulating signal transduction and cellular differentiation, protein structure and structure-function relationships, protein-nucleic acid interactions, biomolecular materials, molecular neurobiology, plant molecular biology, bacterial pathogenesis, and molecular virology and immunology. A complete listing of research interests of the participating faculty can be obtained by writing to the above address, or from the BMB web site at http://lifesci.ucsb.edu/BMB/ (will open in a new browse window).
The program accommodates students with a diversity of backgrounds and career goals who are interested in multidisciplinary research training. Students with undergraduate degrees in one of the life or physical sciences are accepted into the program. In addition to specific program requirements, candidates for graduate degrees must meet all university degree requirements found in the chapter "Graduate Education at UCSB." Highly individualized programs of instruction can be undertaken by a student enrolled in the program after consultation with and approval by the graduate committee and a research mentor. Approximately 22 faculty members from the affiliated departments are available to direct approved research projects under the auspices of the BMB program.
Doctor of Philosophy-Biochemistry and Molecular Biology
Admission
In addition to fulfilling the departmental admission requirements outlined below, applicants must also meet the university requirements for admission described in the chapter "Graduate Education at UCSB." The applicants will normally hold a bachelor's degree in chemistry, biochemistry, or another biological science. Undergraduate preparation should include one year each of introductory chemistry, biology and physics, one year of calculus (differential equations recommended), one year of organic chemistry, one year of biochemistry, one course in physical chemistry (one year recommended), one course in molecular genetics or molecular biology and additional specialized electives. The deadline for completed applications is January 1st.
Applicants with strong undergraduate records who lack some of the preparation indicated above may be admitted with the condition that they complete necessary coursework early in their graduate careers.
Transcripts and Graduate Record Exam (GRE) scores are required of all applicants. The GRE general test and one of the following three subject tests-biology; or chemistry; or biochemistry, cell, and molecular biology-are required. In addition, applicants whose native language is not English must receive a score of at least 610 on the Test of English as a Foreign Language (TOEFL), taken within two years of their application to UCSB. Students who have earned a bachelor's or master's degree from a U.S. college or university are exempt from this requirement.
Degree Requirements
Courses: Students in the BMB program must complete two courses, BMB 218A (Nucleic Acids and Proteins) and BMB 256A (Physical Biochemistry), with the grade of B or better. In addition, BMB students must satisfactorily complete two graduate-level elective courses in the 200 series before advancement to candidacy.
Seminars: Each quarter of the student's graduate study, enrollment is also required in BMB 260 (Research Seminar), and BMB 262 (Research Progress in Biochemistry and Molecular Biology). In addition, enrollment in two graduate literature seminars per year in the 260 or 595 series is required until formal advancement to candidacy for the Ph.D.
Examinations: In order to qualify for advancement to doctoral candidacy, students must form a doctoral committee and successfully complete, in addition to the four lecture courses, two qualifying examinations, each consisting of a written research proposition followed by an oral defense of the proposition. The examinations are normally taken at the beginning of the second and third year of graduate study. The topic of the first examination is chosen from an area different from the student' anticipated research; the second examination is based on the students' dissertation research. The final requirement for the Ph.D. degree is a written dissertation and its oral defense, which usually is in the form of a scheduled interdepartmental program seminar.
Research: Students in the BMB program normally complete three one-quarter laboratory rotations during the first year of study, and are expected to begin research for the dissertation by the end of the first calendar year in the program. Research directors may be selected from any of the faculty affiliated with the interdepartmental program.
Biochemistry-Molecular Biology Courses
1FS. Special Topics in Biochemistry and Molecular and
Cellular Biology
(2) Staff
Prerequisites: courses in high school biology and/or
chemistry.
Freshman seminar. Exploration of the biochemical basis
of selected characteristics of living systems. Biological order, specificity
and continuity will be considered in terms of molecular descriptions of
cells and cellular processes, including metabolism, growth and development.
186. Colloquia in Biomedical Research
(1) Samuel, Kohl
Prerequisites: MCDB 5A-AL, MCDB 5B-BL or EEMB 5B-BL,
EEMB 5C-CL, or equivalent with a grade of C or better. May be repeated
for credit in combination with BMB 195 and MCDB 186 to a maximum of 3 units.
Lectures by UCSB faculty from various departments focused
on their current research in a variety of biomedical disciplines.
192AA-ZZ. Special Topics in Biochemistry and Molecular
Biology
(1-4) Staff
Prerequisites: upper-division standing and consent
of instructor. May be repeated for credit to a maximum of 8 units provided
the letter designations are different. Same course as MCDB 192 and EEMB
192.
Special topics of current importance in biochemistry
and molecular biology. Course content will vary. Information may be obtained
in program office.
198. Readings in Biochemistry
(1-5) Staff
Prerequisites: a major in the life or physical sciences
and consent of instructor and program. Students must (1) have attained
upper-division standing; (2) have a minimum 3.0 grade-point average for
the preceding three quarters; (3) have completed at least two upper-division
courses in the sciences. Up to 4 units may apply toward upper-division
major requirements and may be taken in combination with courses numbered
168, 184, 190-199; and BMB courses numbered190-199. Students are limited
to five units per quarter and 30 units total in all 98/99/198/199/199RA
courses combined.
Individual courses one hour every two weeks. Special
readings designed to broaden the outlook of students and to knit into a
cohesive whole the basic principles underlying the major/disciplines of
biochemistry and molecular biology.
199. Independent Studies in Biochemistry.
(1-5) Staff
Prerequisites: a major in the life or physical sciences
and consent of instructor and program. Students must have (1) attained
upper-division standing; (2) have a 3.0 grade-point average for the preceding
three quarter and (3) have completed at least two upper-division courses
in the sciences. Up to 8 units may apply toward upper-division major requirements
and may be taken in combination with courses numbered 168, 169, 184, 190-199,
and BMB courses numbered 195-199, unless otherwise specified by the major.
Students are limited to five units per quarter and 30 units total in all
98/99/198/199/199RA courses combined.
Hours and credit by arrangement with any member of the
staff. Laboratory.
218A. Nucleic Acids and Proteins
(5) Carbon, Kohlstaedt, Perona
Prerequisite: graduate standing in biochemistry-molecular
biology, or chemistry, or consent of instructor. Same course as MCDB 218A.
Properties, structure, and structure-function analysis
of nucleic acid research (synthetic and recombinant DNA, in vitro mutagenesis);
protein dynamics (folding, transport, covalent, and non-covalent structural
adaptations to function). (F)
218B. Molecular and Cellular Biology
(5) Clarke, Clegg, Foltz, Samuel, Wilson
Prerequisite: graduate standing or consent of instructor.
Same course as MCDB 218B.
The cytoskeleton; chromatin and chromosome organization,
structure, and function; mechanisms of gene expression in prokaryotes and
eukaryotes and their viruses; membrane structure, organization, and protein
trafficking; cell-cell and cell-matrix interactions. (W)
218C. Gene Regulation and Development
(5) Staff
Prerequisite: MCDB 218B or BMB 218B. Same course as
MCDB 218C.
Specialized features of plant cells. Regulation of gene
expression during development. Models include prokaryotes (bacteria) and
eukaryotes (plants, yeast, ciliates, C. elegans, Drosophila, sea urchins,
mouse), with emphasis on systems that undergo cellular differentiation
and cellular rearrangement. (S)
218X. Selected Topics in Gene Regulation and Development
(1-4) Staff
Prerequisite: consent of graduate advisor. Same course
as MCDB 218X.
Selected topics in gene regulation and development as
appropriate to fulfill the course requirement of graduate students in biochemistry
and molecular biology.
218Y. Selected Topics in Molecular and Cellular Biology
(1-4) Staff
Prerequisite: consent of graduate advisor. Same course
as MCDB 218Y.
Selected topics in molecular and cellular biology as
appropriate to fulfill the course requirement of graduate students in biochemistry
and molecular biology, and molecular, cellular, and developmental biology.
218Z. Selected Topics in Biochemistry of Nucleic Acids
and Proteins
(1-4) Staff
Prerequisite: consent of graduate advisor. Same course
as MCDB 218Z.
Selected topics in the biochemistry of nucleic acids
and proteins as appropriate to fulfill the course requirement of graduate
students in biochemistry and molecular biology.
221. Preparation and Evaluation of Research Proposals
(1) Foltz
Prerequisites: BMB 218A-B or MCDB 218A-B or consent
of instructor.
Instruction in preparation, writing, and evaluation of
research grant proposals. Students are required to submit a full research
proposal (in Federal funding agency format) at the end of the course.
242. Cellular Growth Control and Oncogenesis
(4) Ballester
Prerequisites: MCDB 108A-B-C and 101A-B, or consent
of instructor.
This course focuses on the molecular mechanism of growth
control in eukaryotes. Topics include: growth factors and their receptors,
intracellular signaling, cell cycle control, oncogenes, tumor suppressor
genes, and cancer. Model system studied will include: mammalian cells,
Xenopus oocytes, C. elegans, Drosophila, and yeast.
245. Computational Biochemistry
(3) Perona, Reich, Kohlstaedt
Prerequisites: Chemistry 142A-B-C or MCDB 108A-B-C
and at least two quarters of physical chemistry or equivalent. Same course
as Chemistry 245.
Introduction to molecular modeling and molecular dynamics.
Discussion of practical considerations of energy minimization, solvent
modeling, structure-based drug design. Practical computer graphics experience.
246. Membrane Biochemistry
(3) Reich
Prerequisites: Chemistry 142A-B-C or MCDB 108A-B-C
or equivalent. Same course as Chemistry 246.
Introduction to the structures and roles of lipids and
there behavior, liposomes, membrane proteins and kinetics, protein sorting,
and signal transduction.
254. Drug Design
(3) Reich
Prerequisites: Chemistry 142A-B-C or MCDB 108A-B-C,
or consent of instructor. Same course as Chemistry 262.
Rational drug design. Active site directed and mechanism
based inhibitors. The use of computers and energy calculations in the design
of drugs. Structure based drug design.
256A. Physical Biochemistry
(5) Gerig, Perona, Sears
Prerequisites: one year of undergraduate courses in
each of the following: biochemistry, organic chemistry, physical chemistry
or consent of instructor. Same course as Chemistry 256A.
Isolation and structural analysis of biomolecules. Hydrodynamics
and spectroscopies.
256B. Enzyme Kinetics and Mechanisms
(5) Bruice, Parsons, Reich
Prerequisites: one year of undergraduate courses in
each of the following: biochemistry, organic chemistry, physical chemistry
or consent of instructor. Same course as Chemistry 256B.
Enzyme kinetic and chemical mechanisms. Theory, experimental
design, and data analysis. Enzyme models and nonclassical enzymes.
259. Selected Topics in Biological Chemistry
(1-4) Staff
Prerequisite: consent of instructor. Same course as
Chemistry 259.
Selected topics from bio-organic, biophysical, or biological
chemistry. The content of this course will vary. Course may be repeated
with a different topic (18 units maximum).
260. Research Seminar in Biochemistry-Molecular Biology
(1) J. Cooper
Prerequisite: graduate standing. Same course as MCDB
260.
Seminars on research in progress presented by faculty
of the Department of Chemistry and Department of Molecular, Cellular and
Developmental Biology.
262. Research Progress in Biochemistry and Molecular
Biology
(1) Clarke
Same course as MCDB 262
Research presentations by postdoctoral fellows and advanced
Ph.D. students of research progress in the department.
263. Progress in Biochemistry and Molecular Biology
(1) Staff
Same course as MCDB 263
Research seminars presented by invited speakers on current
research topics.
264. Literature in Signal Transduction
(1) Ballester
Prerequisite: graduate standing.
Critical reading and presentation of the literature on
signal transduction mechanisms that control cell growth and differentiation.
281. Protein Crystallography
(3) Kohlstaedt, Perona
Prerequisite: consent of instructor. Same course as
Chemistry 281.
Introduction to diffraction techniques. Protein crystal
growth and morphology. Data collection and reduction strategies. Approaches
for solving the phase problem. Crystallographic refinement, including molecular
dynamics. Interpretation of crystal structures.
290AA-ZZ. Group Studies
(2) Staff
Prerequisite: consent of instructor.
Presentation and discussion of current research, to be
selected from the following list.
C. Studies in Regulation of Cell Proliferation: Ballester
CC. Centromeres and Chromosomes-Models and Analysis:
Carbon
CS. Advanced Topics in Chromosome Segregation: Clarke
PM. Molecular Plant-Microbe Interactions: J. Cooper
595. Group Studies
(2) Staff
Prerequisite: consent of instructor.
A critical review of research in selected areas of biochemistry-molecular
biology.
596BI. Directed Reading and Research
(2-12) Staff
Prerequisite: consent of instructor. May be repeated
for credit up to half of the graduate units required for the M.A. degree.
Same course as MCDB 596.
Hours and credit by arrangement with faculty.
596CH. Directed Reading and Research.
(2-12) Staff
No more than half the units necessary for the Master's
degree may be taken in Biochemistry-Molecular Biology 596. Same course
as Chemistry 596.
Individual tutorial. Instructor usually is the student's
major professor. A written proposal for each tutorial must be approved
by the department chair. Each faculty member has a unique number designation.