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195. Undergraduate Internship in Biotechnology / Pharmacology
(3) Edwards
Prerequisite: consent of instructor.
Research internship in biotechnology or pharmaceutical company laboratory. Placement negotiated on individual basis.
199. Independent Studies in Biomolecular Science and Engineering
(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 BMSE 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.
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) Jaeger
Prerequisite: one year of undergraduate biochemistry (e.g., MCDB 108A-B-C), one quarter of undergraduate physical chemistry (e.g., Chemistry and Biochemistry 142A-B-C, Chemistry and Biochemistry 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 and Biochemistry 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.
202. Biomaterials and Biosurfaces
(3) Israelachvili
Prerequisites: consent of instructor.
Same course as Chemical Engineering 202
Recommended preparation: prior biochemistry, physical chemistry, and organic chemistry.
Fundamentals of natural and artificial biomaterials and biosurfaces with emphasis on molecular level structure and function and the interactions of biomaterials and surfaces with the body. Design issues of grafts and biopolymers. Basic biological and biochemical systems reviewed for nonbiologists.
203. Protein Engineering and Design
(3) Reich, Sagermann
Prerequisites: Consent of Instructor.
Rational design of protein structure, activity and stability.
Current methods and applications of protein engineering including protein evolution, unnatural amino acids and combinatorial methods.
205A. Biochemical Strategies
(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: BMSE 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 and Biochemistry 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 and Biochemistry 142A-B-C, Chemistry and Biochemistry 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.
217. Electrostatics of Biopolymers
(2) Pincus
Prerequisite: knowledge of elementary ideas and methods of electrostatics and statistical mechanics.
Electrostatics of highly charged surfaces in contact with a polar solvent with application to biopolymers (e.g. DNA, f-actin)
220A. Chromosomes and Cell Cycle
(1) Jordan, Wilson
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 and Biochemistry 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.
222A. Colloids and Interfaces I
(3) Israelachvili
Prerequisite: Consent of instructor.
Introduction to the various intermolecular interactions in solution and in colloidal systems: Van der Waals, electrostatic, hydrophobic, solvation, H-bonding. Introduction to colloidal systems: particles, micelles, polymers, etc. Surfaces: wetting, contact angles, surface tensions, etc.
223. Signal Transduction
(2) Feinstein
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) Waite
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.
239. Cellular Microbiology
(4) Cotter
Prerequisites: Graduate standing
Same course as MCDB 239.
Exploration of the mechanisms by which microbes and their eukaryotic hosts interact at the cellular and molecular levels. Focus is on experimental strategies to investigate these interactions and primary literature is discussed.
244. Informational Macro- and Supra- Molecules
(2) Jaeger
Prerequisites: Consent of instructor
Same course as Chemistry 244.
Selected topics at the interface of chemistry and biology: informational molecular coding, molecular machines, self-assembling and self-replicating molecular systems, evolution and selection of molecules with binding of catalytic properties, and biopolymer based materials; special emphasis on cutting-edge technologies.
246. Membrane Biochemistry
(3) Parsons, Reich
Prerequisites: Chemistry and Biochemistry 142A-B-C.
Same course as Chemistry and Biochemistry 246.
Introduction to the structures and roles of lipids and their behavior, lipsomes, membrane proteins and kinetics, protein sorting, and signal transduction.
250. Bionanotechnology
(2) Fygenson
Recommended preparation: background in biochemistry and molecular biology.
Introduction to macromolecular assemblies and force generation strategies. Topics may also include but are not limited to: conformations and behavior of protein polymers; nucleic acid superstructures and membranes; structure, motility and mechanism of linear and rotary motor proteins; and macromolecular switches.
251. Biopharmaceutical Process Engineering
(2) Daugherty
Prerequisite: Mathematics 5A or equivalent; background in biochemistry.
An introduction to the design bioprocess for large-scale production of biopharmaceuticals. Emphasis is placed upon biopharmaceutical products, protein expression systems, host cell optimization, and reactor selection and design.
252. Principles of Bioengineering
(2) Mitragotri
An overview of various aspects of bioengineering including modeling of physiological functions, biomedical devices, drug delivery, and tissue engineering.
253. Analytical Biotechnology
(3) Soh
This course develops fundamental understanding behind modern methods of biotechnology. Topics include theoretical treatment of the double layer, electrophoresis, polymerase chain reaction, modern optics, and fluorescence. In addition, case studies of contemporary emerging trends will be discussed.
254. Drug Design
(3) Reich
Prerequisites: Chemistry and Biochemistry 142A-B-C or MCDB 108A-B-C.
Same course as Chemistry and Biochemistry 262. Lecture, 3 hours.
Rational and Structure-based drug design; pharmacogentetics; combinatorial chemistry and screens; mechanism based drug design; drug metabolism; toxicity; quantitative structure activity relationships; enzyme inhibitors.
256A. Physical Biochemistry
(5) Gerig, Parsons, Perona, Plaxco, Reich
Prerequisites: one year of undergraduate courses in: biochemistry, organic chemistry, and physical chemistry.
Same course as Chemistry and Biochemistry 256A. Lecture, 5 hours; discussion, 1 hour.
Isolation and structural analysis of biomolecules, hydrodynamics, spectroscopy, diffraction, scattering.
256B. Enzyme Kinetics and Mechanisms
(3) Reich
Prerequisites: one year of undergraduate courses in each of the following: biochemistry, organic chemistry, physical chemistry.
Same course as Chemistry and Biochemistry 261. Lecture, 3 hours.
Enzyme kinetic and chemical mechanisms. Theory, experimental design, and data analysis. Enzyme models and non-classical enzymes.
257. Special Topics in Biophysics
(1-4) Staff
May be repeated for credit provided topics are different.
Course varies from year to year according to the currents of the times.
259. Selected Topics in Biological Chemistry
(1-4) Staff
Prerequisite: consent of instructor.
Same course as Chemistry and Biochemistry 259. Course may be repeated with a different topic (18 units maximum). Lecture, 1 to 4 hours.
Selected topics from bio-organic, biophysical, or biological chemistry. The contents of this course will vary.
260. Faculty Research in Biomolecular Science and Engineering
(1) Rothman
Prerequisite: graduate standing.
Same course as MCDB 260.
Seminars on research being conducted by the faculty of the BMSE interdisciplinary program.
262. Research Progress in Biomolecular Science and Engineering
(1) Rothman
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 Biomolecular Science and Engineering
(1) Mahan
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.
290 AA-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.
CE. C. elegans Development: Rothman, J.H.
DN. Developmental Neurobiology: Clegg, D.O.
HW. Marine Structural Proteins: Waite, J.H.
PM. Molecular Plant-Microbe Interactions: Cooper, J.B., Rothman, J.H.
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) Edwards, 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) Edwards, 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 is discussed.
295. Internship in Biotechnology/Pharmacology
(3) Edwards
Prerequisite: acceptance into the B.S./M.S. program in BMSE 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 Biomolecular Science and Engineering
(3) Staff
Prerequisite: enrollment in the BMSE Ph.D. program. Open to first year graduate students only.
May be repeated up to 4 times.
Laboratory rotation project in BMSE faculty laboratories.
596. Directed Reading and Research
(2-12) Staff
Prerequisite: 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 BMSE 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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