E-mail: bmbprog@lifesci.ucsb.edu
Website: lifesci.ucsb.edu/BMB  (will open in a new browser window)

Program Chair: Daniel E. Morse

Faculty

Alison Butler, Ph.D., UC San Diego, Professor and Associate Dean of Engineering (bio-inorganic chemistry)

Rolf E. Christoffersen, Ph.D., UC Los Angeles, Associate Professor (plant molecular biology)

Dennis O. Clegg, Ph.D., UC Berkeley, Professor (neurobiology)

James B. Cooper, Ph.D., Washington University, Associate Professor (plant molecular biology)

Patricik S. Daugherty, PhD., University of Texas at Austin, Assistant Professor (protein engineering and design, combinational molecular biology, gene targeting, viral vector engineering)

Timothy Deming, Ph.D., UC Berkeley, Associate Professor (synthetic chemistry, polymerization catalysis, biopolymer synthesis, biocompatible materials)

Deborah K. Fygenson, Ph.D., Princeton University, Assistant Professor (biophysics-experimental)

J. Thomas C. Gerig, Ph.D., Brown University, Professor (bio-organic chemistry)

Jacob Israelachvili, Ph.D., University of Cambridge, Professor (surface and interfacial phenomena, adhesion, colloidal systems, surface forces, bio-adhesion, friction)

John Lew, Ph.D., University of Calgary, Alberta, Assistant Professor (biochemistry)

David Low, Ph.D., UC Irvine, Professor (biochemistry, genetics)

Michael J. Mahan, Ph.D., University of Utah, Associate Professor (microbiology)

Samir Mitragotri, Ph.D., Massachusetts Institute of Technology, Assistant Professor (drug delivery and diagnostics, bio-membrane transport, membrane biophysics, biomedical ultrasound)

Daniel Morse, Ph.D., Albert Einstein College of Medicine, Professor (molecular genetics, biochemistry, marine biology, biomolecular and biomimetic materials)

Stanley M. Parsons, Ph.D., California Institute of Technology, Professor (biological chemistry)

John J. Perona, Ph.D., Yale University, Associate Professor (physical biochemistry)

Philip A. Pincus, Ph.D., UC Berkeley, Professor (polymers, colloids, surfactants, membranes, biomaterials)

Kevin W. Plaxco, Ph.D., California Institute of Technology, Assistant Professor (molecular biology, biochemistry)

Norbert O. Reich, Ph.D., UC San Francisco, Professor (biological chemistry)

Joel H. Rothman, Ph.D., University of Oregon, Eugene, 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)

Galen Stucky, Ph.D., Iowa State University, Professor (biomaterials, surfactants, composites, materials synthesis, porous materials)

Matthew V. Tirrell, PH.D. University of Massachusetts, Auhll Professor and Dean, College of Engineering (bioengineering, polymer science and engineering)

Carol A. Vandenberg, Ph.D., UC San Diego, Associate Professor (neurobiology)

J. Herbert Waite, Ph.D., Duke University, Professor (marine biomolecular materials)

Leslie Wilson, Ph.D., Tufts University, Professor (biochemical pharmacology)

Emeriti Faculty

Thomas C. Bruice, Ph.D., University of Southern California, Research Professor

John A. Carbon, Ph.D., Northwestern University, Research Professor (biochemistry)

Louise Clarke, Ph.D., UC Santa Barbara, Professor Emeritus (biochemistry, genetics)

Ellis Englesberg, Ph.D., UC Berkeley, Professor Emeritus

Nancy L. Lee, Ph.D., University of Pittsburgh, Professor Emeritus (microbiology)

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

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 or engineering disciplines are accepted into the program. In addition to specific program requirements, candidates for graduate degrees must meet all university degree requirements found in the section "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 29 faculty members from the affiliated departments are available to direct approved research projects under the auspices of the BMSE program.

Graduate Program

Admission

In addition to fulfilling the departmental admission requirements outlined below, applicants must also meet the university requirements for admission described in the section "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 target deadline for completed applications is December 15th.

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) general test scores are required of all applicants. One of the following three GRE subject testsbiology; or chemistry; or biochemistry, cell, and molecular biologyis recommended. Applicants whose native language is not English are required to take the Test of English as a Foreign Language (TOEFL). Exceptions to this requirement will be considered for those students who have completed an undergraduate or graduate education at an institution whose primary language of instruction is English. The minimum score for consideration is 630 when taking the paper-based test or 267 when taking the computer-based test, taken within two years of their application to UCSB.

Master of Science Biochemistry and Molecular Biology

Degree Requirements

M.S. students may complete their master's degree under either Plan I (thesis) or Plan II (examination). In addition to fulfilling all university requirements for a master's degree, M.S. students must complete a minimum of 12 units of core course modules, all with grades of B or better, and 3 units of BMSE 263 (Research Seminars in Biochemistry and Molecular Biology). Plan I (thesis) students must also successfully complete 18 units of directed reading and research, and must write and defend a master's thesis in consultation with a master's thesis committee.

Plan II (examination) students must complete a minimum of 12 units of core course modules, all with grades of B or better, 3 units of BMSE 263 (Research Seminars in Biochemistry and Molecular Biology), 12 additional units of graduate coursework chosen (with the approval of the graduate advisor) from the course offerings from any of the home departments of BMSE Program faculty, and 6 units of BMSE 295 (Internship in Biotechnology/Pharmacology) or BMSE 596 (Directed Reading and Research). Plan II students must also submit a satisfactory written final report whose content is to be determined in consultation with the master's advisor and two additional BMSE faculty, and is filed with the BMSE graduate program office. This final report must demonstrate an integration of the knowledge acquired in the student's graduate coursework and research studies, and shall satisfy the requirements of a comprehensive examination.

Core module courses in biochemistry-biophysics include BMSE 201A, BMSE 201B, BMSE 201C, BMSE 202, BMSE 205, BMSE 206, BMSE 210, BMSE 211 BMSE 212, BMSE 216, BMSE 217, BMSE 218, BMSE 219, and MCDB/BMSE 229. Core module courses in molecular biology include BMSE 220A, BMSE 220B, BMSE 220C, MCDB 222, BMSE 223, BMSE 226, BMSE 235, BMSE 236, and BMSE 237. Some of these courses are offered in alternate years only; please consult the program for more details.

Doctor of Philosophy Biochemistry and Molecular Biology

Degree Requirements

Ph.D. students in the program are required to demonstrate competency in fundamental areas of biochemistry and molecular biology, normally by the completion of 15 units of core module coursework, and demonstrating a depth of knowledge in at least two advanced topics. Program students will elect a major specialization in either biochemistry-biophysics or molecular biology.

Core module courses in biochemistry-biophysics include BMSE 201A, BMSE 201B, BMSE 201C, BMSE 202, BMSE 205, BMSE 206, BMSE 210, BMSE 211 BMSE 212, BMSE 216, BMSE 217, BMSE 218, BMSE 219, and MCDB/BMSE 229. Core module courses in molecular biology include BMSE 220A, BMSE 220B, BMSE 220C, MCDB 222, BMSE 223, BMSE 226, BMSE 235, BMSE 236, and BMSE 237. Some of these courses are offered in alternate years only; please consult the program for more details.

Competency in the major specialization may be demonstrated by completion of 10 units of modular coursework from the specialization, with grades of B or better. Competency in the minor specialization is normally demonstrated by completion of 5 units of coursework in any of the areas within this minor specialization with grades of B or better. Competency in any area may also be demonstrated by passing written exams administered by the BMSE faculty.

In addition to the course requirements, students are required to complete three laboratory rotations during the first year of study (9 units of BMSE 592) and are expected to rotate through laboratories in more than a single academic department. All BMSE students are required to serve as a Teaching Assistant for at least two quarters, and are expected to attend regularly BMSE 260 (Faculty Research in Biochemistry and Molecular Biology), BMSE 262 (Research Progress in Biochemistry and Molecular Biology), and BMSE 263 (Research Seminars in Biochemistry and Molecular Biology).

BMSE students are required to complete all course requirements before advancement to candidacy, and should complete them before the end of the second year. Ph.D. students advance to candidacy in the Interdepartmental Program according to the current guidelines, by passing two written and oral proposition exams. After advancement to candidacy, Program students are expected to present a formal seminar annually in the Progress in Biochemistry and Molecular Biology Seminar series (BMSE 262), and are required to meet annually with their Ph.D. dissertation committee until completion and defense of the Ph.D. dissertation.

Optional Ph.D. Emphasis in Bioengineering and Biomaterials

The Interdepartmental Graduate Program in Biomolecular Science and Engineering (BMSE) offers an interdisciplinary Ph.D. doctoral emphasis in Bioengineering and Biomaterials. Given the increasing synergy between life sciences and engineering, particularly in areas of biotechnology and biomaterials, program faculty believe that the time has come for the vigorous fusion of engineering and the basic molecular life sciences into a single curriculum. In this new track, barriers to interdisciplinary thinking, training and research at the interface between the life sciences, chemistry, physics and engineering have been removed.

The Ph.D. degree with an optional emphasis in bioengineering and biomaterials will be awarded upon the successful completion of the following: (1) the core curriculum including seminars, research and advanced coursework; (2) first proposition defense on a topic unrelated to the dissertation research; (3) Ph.D. oral qualifying examination for advancement to candidacy; and (4) submission and successful defense of a research dissertation. (The degree requirements for the optional Ph.D. emphasis in bioengineering and biomaterials replace the degree requirements for the Ph.D. in Biochemistry and Molecular Biology.)

The core curriculum includes the following:

• 218A (or the module of 205, 235, and MCDB 229)

• 218B (or the module of 220A, 220B, 220C, and 230)

• 218C (or the module of 223 and MCDB 225)

• For students entering the program with backgrounds in engineering, physics or mathematics, substitution of specifically designed courses for the above three core requirements may be arranged upon consultation with the program's graduate advisory committee.

• Five units in a minor such as biochemistry and/or molecular biology

• Six units in Advanced Topics, which typically involve seminar presentations by participants in current research topics selected by the faculty

• During each quarter of a student's graduate study, enrollment in the Bioengineering Research Seminar and the Student Research Progress series is required until formal advancement into candidacy for the Ph.D.

In order to qualify for advancement to doctoral candidacy, students must form a doctoral committee and successfully complete, in addition to the required courses, two qualifying examinations each consisting of a written research proposition followed by an oral defense of the proposition. Examinations are normally taken at the beginning of the second and third year of graduate study. The topic of the first examination is chosen by the student and must be different from the anticipated dissertation research. The final requirement for the Ph.D. degree with optional emphasis in bioengineering and biomaterials is a written dissertation and its oral defense, which is usually in the form of a scheduled interdepartmental program seminar.

Laboratory research rotations during the first year of study are available and encouraged. Students 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.

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Biomolecular Science and Engineering Courses

Upper Division

195. Undergraduate Internship in Biotechnology/Pharmacology
(3) Cooper
Prerequisite: consent of instructor.
Research internship in biotechnology or pharmaceutical company laboratory. Placement negotiated on individual basis.

199. Independent Studies in Biochemistry.
(1-5) Staff
Prerequisites: upper-division standing; consent of instructor and department.
Students must have a 3.0 grade-point average for the preceding three quarters. 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 98/99/198/199/199DC/199RA courses combined.
Hours and credit by arrangement with any member of the staff. Laboratory.

Graduate Courses

201A. Protein Structure and Function
(2) Plaxco
Prerequisite: graduate standing.
Exploration of the relationship between protein sequence, structure, biophysics, and function.

201B. Chemistry and Structure of Nucleic Acid
(2) Perona
Prerequisite: one year of undergraduate biochemistry (e.g., MCDB 108A-B-C), one quarter of undergraduate physical chemistry (e.g., Chemistry 142A-B-C, Chemistry 113A).
Primary, secondary, and higher-order structures of DNA and RNA, thermodynamic stability and folding, protein-nucleic acid interactions, ribozymes, applications to gene regulation, RNA world evolution.

201C. Biomembrane Structure and Function
(2) Parsons
Prerequisite: Chemistry 142A-B-C or MCDB 108A-B-C or equivalents.
Lipid diversity, lipid aggregates, dynamics and phase behavior of lipid aggregates, permeabilities of model and cellular bilayers, manipulation and quantitation of ionic and pH gradients, related special topics in physiology such as the mechanisms of anesthesia.

205A. Studies in Protein Purification
(1) Lew
Prerequisite: one year of undergraduate biochemistry (e.g., MCDB 108A-B-C) or equivalent.
A practical approach to purifying and working with proteins in the laboratory. Emphasis is on techniques (mainly qualitative) with a focus on modern methods used in the research literature. Students will have an intuitive sense of protein purification, manipulations, and analysis, and should be able to critically read the primary literature upon successful completion of the course.

205B. Strategies in Protein Characterization
(1) Waite
Prerequisite: a grade of B- or better in MCDB 108A or 208A or the equivalent.
A presentation of traditional and state-of-the-art approaches for characterizing the primary structure of proteins and polysaccharides. Techniques include amino acid analysis, mass spectroscopy, gas-phase sequencing, capillary electrophoresis, and covalent modification chemistry.

207. Enzyme Mechanisms
(2) Reich
Prerequisite: undergraduate biochemistry course (e.g., MCDB 108).
Chemical mechanisms of enzyme catalysis. Enzyme models and non-classical enzymes. Theory, experimental design, and data analysis.

212. Macromolecular Folding
(2) Plaxco
Prerequisites: BMB 201A-B or equivalents.
Focuses on biopolymers as structurally dynamic systems. Exploration of the relationship between biopolymer sequence, the structure that these sequences encode and the kinetic mechanism by which this structure is achieved.

215. Biophysical Thermodynamics
(2) Plaxco
Prerequisite: undergraduate course in physical chemistry (e.g., Chemistry 113A-B-C).
An overview of those parts of chemical thermodynamics relevant to the study of biomolecules and biological systems. Topics include fundamental thermodynamics, experimental and theoretical tools and the thermodynamics of biopolymer structure formation.

216A. Spectroscopy of Biological Molecules
(2) Gerig
Prerequisite: graduate standing.
Introduction to the application of spectroscopic techniques to biological systems, including UV - vis, IR, CD, flurescence, NMR, and ESR.

216B. Diffraction of Biological Molecules
(2) Perona
Prerequisite: one year of undergraduate biochemistry (e.g., MCDB 108A-B-C), one quarter of undergraduate physical chemistry (e.g., Chemistry 142A-B-C, Chemistry 113A).
Single-crystal macromolecular crystallography methods; crystal growth, geometric and physical basis of diffraction, approaches to phasing and refinement. X-ray and neutron solution scattering.

218A. Nucleic Acids and Proteins
(1-5) Staff
Prerequisite: graduate standing in BMB or chemistry.
Same course as MCDB 218A. Not open for credit to students who have completed Biology 218A.
Properties, structure, and structure-function analysis of nucleic acid research (synthetic and recombinant DNA, in vitro mutagenesis); protein dynamics (folding, transport, covalent, an non-covalent structural adaptations to function).

218B. Molecular and Cellular Biology
(1-5) Staff
Prerequisite: graduate standing.
Same course as MCDB 218B. Not open for credit to students who have completed Biology 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.

218C. Gene Regulation and Development
(1-5) Staff
Prerequisite: MCDB 218B or BMB 218B.
Same course as MCDB 218C. Not open for credit to students who have completed Biology 218C.
Specialized features of plant cells. Regulation of gene expression during development. Models include prokaryotes (bacteria) and eukaryotes (plants, yeast, ciliates, C. elegans, drosophilia, sea urchins, mouse), with emphasis on systems that undergo cellular differentiation and cellular rearrangement.

220A. Chromosomes and Cell Cycle
(2) Staff
Prerequisite: graduate standing.
Structure and organization of the nucleus, Chromatin and chromosome structure, organization, and function; DNA replication and replication origins; Eukaryotic cell cycle regulation.

220B. The Cytoskeleton
(2) Wilson
Prerequisite: graduate standing.
Structure and function of the eucaryotic cytoskeleton. Structure assembly and function of microtubules, microfilaments, and intermediate filaments.

220C. Membrane Dynamics and Cell-Cell Interactions
(2) Clegg, Rothman
Prerequisite: undergraduate biochemistry (e.g., MCDB 108A-B-C or Chemistry 142A-B-C) and genetics (e.g., MCDB 101A).
Structure and dynamics of biological membranes and membrane proteins, protein translocation and sorting in the endomembrane system of eukaryotic cells, extracellular matrix protein structure/function, cell-matrix and cell-cell interactions, cell adhesion receptors, transmembrane signaling by cell adhesion receptors.

223. Signal Transduction
(2) Staff
Prerequisite: graduate standing.
A cell's growth is controlled by positive and negative cues from its surroundings. A discussion of the cell's signaling mechanisms that recognize these cues and initiate an intracellular set of events that generates a response.

229. Macromolecular Structure
(2) Staff
Prerequisite: graduate standing.
Properties, structure, and structure-function analysis of nucleic acids and proteins.

230. Gene Regulation
(2) Low, Samuel
Prerequisite: graduate standing.
Mechanisms and regulation of transcription and translation in prokaryotic and eukaryotic organisms and their viruses.

235. Experimental Strategies in Molecular Genetics
(1) Rothman
Prerequisite: undergraduate biochemistry (e.g., MCDB 108A-B-C) and genetics (e.g., MCDB 101A-B-C).
Discussion of experimental strategies used to purify, analyze, and manipulate nucleic acids, isolate molecular clones from complex genomes, physically map genomes, analyze gene expression, and perform reverse genetics.

242. Cellular Growth Control and Oncogenesis
(4) Staff
Prerequisites: MCDB 108A-B-C and 101A-B.
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.

256A. Physical Biochemistry
(5) Gerig, Perona, Plaxco
Prerequisites: one year of undergraduate courses in biochemistry, organic chemistry, and physical chemistry.
Same course as Chemistry 256A.
Isolation and structural analysis of biomolecules; hydrodynamics, spectroscopy, diffraction, scattering.

260. Faculty Research in Biochemistry-Molecular Biology
(1) Mahan
Prerequisite: graduate standing.
Same course as MCDB 260.
Seminars on research being conducted by the faculty of the BMB interdisciplinary program.

262. Research Progress in Biochemistry and Molecular Biology
(1) Staff
Same course as MCDB 262.
Research presentations by postdoctoral fellows and advanced Ph.D. students of research progress in the department.

263. Research Seminars in Biochemistry-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) Lew
Prerequisite: graduate standing.
Critical reading and presentation of the literature on signal transduction mechanisms that control cell growth and differentiation.

290AA-ZZ. Group Studies
(2) Staff
Prerequisite: consent of instructor.
Presentation and discussion of current research, to be selected from the following list.
A. Molecular Marine Biology: Morse, D.E.
B. Biomineralization: Stucky, G.D.
BP. Bacterial Pathogensis: Mahan, M.J.
C. Studies in Regulation of Cell Proliferation: Ballester
CE. C. elegans Development: Rothman
DN. Developmental Neurobiology: Clegg, D.O.
HW. Marine Structural Proteins: Waite, J.H.
PM. Molecular Plant-Microbe Interactions: J. Cooper
PR. Protein-Nucleic Acid Interactions: Perona, J.J.
S. Molecular Virology and Interferon Action: Samuel, C.E.

291. Research Ethics
(1) Cooper
Prerequisite: consent of instructor.
Discussion of ethical issues in biochemistry-molecular-biology research.

293. Computational Methods in Biochemistry-Molecular Biology
(1) Christoffersen
Prerequisite: graduate standing.
Survey of computational methods in molecular biology. Topics include analysis and presentation of data, database searching, quantitative image analysis, and protein homology modeling. Emphasis is on utilizing accessible software tools that are designed for non-programmers.

294A. Workshop on Biotechnology Project Management
(2) Morse
Prerequisite: consent of instructor.
Based on presentations by faculty and invited speakers from the biotechnology and pharmaceutical industries. Discussion topics cover all aspects on biotechnology project management including drug discovery and development, scale up and process development, QC/QA, formulation and delivery, clinical development, and regulatory issues.

294B. Bioengineering: Career and Development Opportunities at the Interface between Biotechnology and Engineering
(2) Morse
Prerequisite: consent of instructor.
Based on presentations by experts from the bioengineering industry. Presenters describe their companies' technologies and developments, including biosensors, therapeutics, tissue engineering, quantum dots, and advanced instrumentation. Training and educational requirements for different career tracks are discussed.

295. Internship in Biotechnology/Pharmacology
(3) Staff
Prerequisite: acceptance into the B.S./M.S. program in BMB and consent of instructor (who is M.S. program faculty advisor).
Research internship in biotechnology or pharmaceutical company laboratory. Placement negotiated on individual basis.

592. Laboratory Research Rotation in Biochemistry
(3) Staff
Prerequisite: enrollment in the BMB Ph.D. program. Open to first year graduate students only.
May be repeated up to 4 times.
Laboratory rotation project in BMB faculty laboratories.

595. Biochemistry/Molecular Biology Seminar
(2) Staff
Prerequisites: graduate standing and consent of instructor.
A critical review of research in selected areas of biochemistry and molecular biology.

596. Directed Reading and Research
(2-12) Staff
Prerequisites: graduate standing and consent of instructor.
May be repeated for credit up to half of the graduate units required for the M.S. degree. Instructor should be student's major professor.
Hours and credit by arrangement with faculty.

598. Masters Thesis Research and Preparation
(2-12) Staff
Prerequisite: graduate standing as an M.S. student in the BMB program.
No unit credit allowed toward the M.S. degree. Instructor should be student's major professor or chair of committee.
Preparation of the thesis and writing the thesis.

599. Ph.D. Dissertation Preparation
(2-12) Staff
Prerequisite: graduate standing as a Ph.D. student and advancement to doctoral candidacy.
Instructor should be the chair of the student's doctoral committee.
Writing the Ph.D. dissertation.

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