Some courses displayed may not be offered every year. For actual course offerings by quarter, please consult the Quarterly Class Search
or GOLD (for current students). To see the historical record of when a particular course has been taught in the past, please visit the Course Enrollment Histories.
BMSE 201A.
Protein Structure and Function
(2)
PLAXCO
Prerequisite: Graduate standing.
Traces the physical interactions by which sequence-specific polypeptides attain a unique, functional native state. Fold design, fold prediction, and protein folding kinetics are also discussed.
BMSE 201B.
Chemistry and Structure of Nuleic Acids
(2)
STAFF
Prerequisite: MCDB 108A-B-C; and, Chemistry 113A or 142A or 142B or 142C.
Primary, seondary, and higher-order structures of DNA and RNA, thermodynamic stability and folding, protein-nucleic acid interactions, ribozymes, applications to gene regulation, RNA world evolution.
BMSE 201C.
Biomembrane Structure and Function
(2)
STAFF
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 quantification of ionic and pH gradients, related special topics in physiology such as the mechanisms of anesthesia.
BMSE 202.
Biomaterials and Biosurfaces
(3)
STAFF
Prerequisite: Consent of instructor.
Recommended Preparation: Prior biochemistry, physical chemistry, or organic chemistry.Enrollment Comments: Same course as Chemical Engineering 202 and Materials 270
Fundamentals of natural and artificial biomaterials and biosurfaces with emphasis on molecular level structure and function and their interactions with the body. Design issues of grafts and biopolymers. Basic biological, biophysical and biochemical systems reviewed for nonbiologists.
BMSE 203.
Protein Engineering and Design
(3)
REICH
Prerequisite: 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.
BMSE 204.
Post-translational Protein Processing
(4)
WAITE
Prerequisite: MCDB 108A or 218A or equivalent.
Structure/function relationships in interesting macromolecules isolated from marine organisms. Focus is on well-characterized pathways from horseshoe crabs, abalones, mussels, and fish as well as others.
BMSE 205A.
Biochemical Techniques
(1)
LEW
Prerequisite: One year of undergraduate biochemistry (e.g., MCDB 108A-B-C) or equivalent.
Enrollment Comments: Quarters usually offered: Fall.
Practical theory and application of basic biochemical techniques. Topics include SDS-PAGE, buffers, centrifugation, antibody methods, spectroscopy and fluorescence techniques.
BMSE 205B.
Strategies in Protein Characterization
(1)
STAFF
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 to be included are amino acid analysis, mass spectrometry, gas-phase sequencing, capillary electrophoresis, and covalent modification chemistry.
BMSE 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.
BMSE 210.
Biochemistry & Molecular Biology Techniques for Physical Scientists
(4)
FYGENSON, DAHLQUIST
Prerequisite: Graduate standing; consent of instructor.
Enrollment Comments: Students must have a cumulative 3.0 for the proceeding 3 quarter(s). Quarters usually offered: Fall.
An intensive laboratory course for physical science and engineering students providing background knowledge and laboratory experience in standard molecular biology and protein purification techniques, as well as techniques for characterizing purified proteins.
BMSE 215.
Biophysical Thermodynamics
(2)
PLAXCO
Prerequisite: Undergraduate course in Physical Chemistry (e.g., Chem 113A-B-C).
An overview of those parts of chemical thermodynamics relevant to the study of biomolecules and biological systems. Topics include fundamental biopolymer structure formation.
BMSE 216B.
Diffraction of Biological Molecules
(2)
STAFF
Prerequisite: MCDB 108A-B-C; and, Chemistry 113A or 142A or 142B or 142C.
Single-crystal macromolecular crystallography methods; crystal growth, geometric and physical basis of diffraction, approaches to phasing and refinement. Xray and neutron solution scattering.
BMSE 217.
Electrostatics of Biopolymers
(2)
PINCUS
Prerequisite: Knowledge of elementary ideas and methods of electrostatics and statisticalmechanics.
Electrostatics of highly charged sufaces in contact with a polar solvent with application to biopolymers (e.g., DNA, f- actin).
BMSE 218A.
Methods and Logic in Molecular Cell Biology I
(3)
STAFF
Recommended Preparation: Undergraduate course(s) in genetics and molecular biology.Enrollment Comments: Quarters usually offered: Fall. Required for MCDB Graduate students.
Repeat Comments: Can be repeated one time if student receives less than a B; graduate students are required to earn a grade of B or better.
Molecular genetics and gene regulation. Experimental design and approaches, and a focus on critical thinking and problem solving, will reveal how fundamental, highly significant biological problems are unraveled using molecular genetic strategies. Reading will be assigned from a mix of classic and current peer-reviewed papers.
BMSE 218B.
Methods and Logic in Molecular Cell Biology II
(5)
STAFF
Recommended Preparation: Undergraduate course(s) in genetics and molecular biology.Enrollment Comments: Quarters usually offered: Winter. Required for MCDB Graduate students.
Repeat Comments: Can be repeated one time if student receives less than a B; graduate students are required to earn a grade of B or better.
Molecular cellular biology in a variety of model systems and contexts from an integrated perspective. A collection of approaches, and a focus on critical thinking and problem solving, will reveal how highly significant biological problems are unraveled using cutting edge technologies. Includes an introduction to bioinformatics, computational, and systems biology. Reading will be assigned from a mix of classic and current peer-reviewed papers.
BMSE 219.
Basic Microscopy for Quantitative Biology
(3)
SEBASTIAN STREICHAN
Prerequisite: Course is limited to 10 students, preference is given to students with interest in applying microscopy methods in their own research.
Fluorescence live imaging is a powerful tool to study dynamics of living matter. This course provides an overview on geometric & Fourier optics, bright field microscopy, and fluorescence & absorption spectroscopy. Practicing these concepts students will construct a light-sheet microscope.
BMSE 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.
BMSE 220B.
Cell Biology - Cytoskeleton & Membrane Trafficking
(2)
MONTELL, MA
Prerequisite: Graduate standing.
Structure and function of the eukaryotic cytoskeleton. Intracellular protein transport and membrane trafficking.
BMSE 220C.
From RNA to Membranes
(2)
KOSIK, MA
Prerequisite: MCDB 108A-B-C or Chemistry 142A-B-C; and 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.
BMSE 222A.
Colloids and Interfaces I
(3)
STAFF
Prerequisite: Consent of instructor.
Enrollment Comments: Same course as Materials 222A and Chemical Engineering 222A.
Introduction to the various intermolecular interactions in solution and in colloidal systems: Van der Waals, electrostatic, hydrophobic, solvation, H-bonding. Introduction to colloidal systems.
BMSE 222B.
Colloids and Interfaces II
(3)
ISRAELACHVILI
Prerequisite: Consent of instructor.
Recommended Preparation: Materials 222A or Chemical Engineering 222A or BMSE 222A.Enrollment Comments: Materials 222A or Chemical Engineering 222A recommended. Same course as Materials 222B or Chemical Engineering 222B.
Continuation of 222A. Interparticle interactions, coagulation, DLVO theory, steric interactions, polymer-coated surfaces, polymers in solution, thin film viscosity. Surfactant and lipid self-assembly: micelles,microemulsions. Surfaces: wetting, contact angles, surface tension. Surfactants on surfaces: langmuir-blodgett films, adsorption, adhesion. Non- equilibrium and dynamic interactions.
BMSE 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 and intracellular set of events that generates a response.
BMSE 224.
Quantitative Biology iQB2 Laboratory Course
(4)
BMSE FACULTY
Prerequisite: For first-year BMSE graduate students only. Grad students from other programs will be considered but they should seek for the approval of the teaching coordinators. Number of participants will be limited to 12 or the number of first-year BMSE students, whichever is smaller.
Recommended Preparation: Undergraduate degree in the life/ physical sciences or an adjacent discipline. General curiosity for how quantitative approaches enable new questions in the life sciences.Enrollment Comments: Quarters usually offered: Fall.
This hands-on research course will integrate investigation of diverse biological phenomena in the lab with quantitative analysis of hypotheses related to the function of living systems. Analysis across different length scales and levels of complexity invokes a synergistic combination of tool building, quantitative data acquisition, complementary theoretical model building. Students will work in subgroups on modules developed by different BMSE faculty to illustrate current research topic in Quantitative Biology.
BMSE 225.
Development
(2)
STAFF
Prerequisite: Graduate standing.
The molecular mechanisms of pattern formation and cellular differentiation that underline developmental processes in a variety of important model systems.
BMSE 229.
Protein Biochemistry
(2)
STAFF
Prerequisite: Graduate standing.
Enrollment Comments: Same course as MCDB 229.
Discussion topics relevant to structure-function relationships in proteins including the chemical reactivity of amino acid side chains, posttranslational modifications, and the covalent and noncovalent interactions of multimeric structures. Case studies involve recent advances in structure-function relationships of mechanoproteins.
BMSE 230.
Gene Regulation
(2)
STAFF
Prerequisite: Graduate standing.
Mechanisms and regulation of transcription and translation in prokaryotic and eukaryotic organisms and their viruses.
BMSE 232.
Bacterial Pathogenesis
(3)
MAHAN
Recommended Preparation: MCDB 101A-B.Enrollment Comments: Not open for credit to students who have completed Biology 228.
The mechanisms by which bacterial pathogens cause disease. Investigation of the bacterial gene products produced during infection to understand the metabolic, physiological, and genetic factors that contribute to the virulence of bacterial pathogens.
BMSE 232L.
Bacterial Pathogenesis Laboratory
(3)
MAHAN
Prerequisite: BMSE 232 (may be taken concurrently).
Enrollment Comments: Not open for credit to students who have completed Biology 228L.
The latest molecular, biochemical, and genetic techniques available for the identification of microbial gene products that contribute to infection.Study of the regulatory parameters that govern their expression.
BMSE 233.
Cell Biology
(4)
MARTH, MA
Prerequisite: MCDB 1A-AL or MCDB 1B-BL or EEMB 2-2L, or equivalents, or consent of instructor
Enrollment Comments: Not open for credit to students who have completed Biology 237.
Introduction to the structure and function of cell organelles: membranes, nucleus, mitochondria, chloroplasts, endoplasmic reticulum, golgi apparatus, lysosomes, microbodies, microtubules, cilia, centrioles, and microfilaments.
BMSE 235.
Experimental Strategies in Molecular Genetics
(1)
STAFF
Prerequisite: MCDB 101A-B-C and MCDB 108A-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.
BMSE 244.
Informational Macro- and Supra-Molecules
(2)
JAEGER
Prerequisite: Consent of instructor.
Enrollment Comments: 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 and catalytic properties, biopolymer-based materials, special emphasis on cutting-edge technologies.
BMSE 245.
Computational Biochemistry
(3)
PERONA, REICH
Prerequisite: Chemistry 142A-B-C or Biology 108A-B-C and at least two quarters of physicachemistry or equivalent.
Enrollment Comments: 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.
BMSE 246.
Membrane Biochemistry
(3)
PARSONS
Prerequisite: Chemistry 142A-B-C or Biology 108A-B-C or equivalent.
Enrollment Comments: Same course as Chemistry 246.
Introduction to the structures and roles of lipids and their behavior, liposomes, membrane proteins and kinetics, protein sorting, and signal transduction.
BMSE 247.
Quantitative Methods in Biology
(3)
BRIGGS
Recommended Preparation: One year of calculus or consent of instructor.
A review of quantitative methods required to develop models of biological and ecological systems. Topics illustrated through computer exercises.
BMSE 248.
Practical Statistics for Biologists
(4)
MONTELL, MONTELL, KIM
Introduces fundamental concepts in biostatistics such as sources of technical and biological variation, types of statistical tests (ANOVA, non-parametric, linear regression), sampling techniques, power calculations, and how to decide which test is appropriate.
BMSE 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.
BMSE 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.
BMSE 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.
BMSE 255.
Methods in System Biology
(3)
DOYLE
Prerequisite: Prior course work in cellular biology, mathematics; consent of instuctor.
Enrollment Comments: Same course as Chemical Engineering 255.
Fundamentals of dynamic network organization in biology (genes, metabolites). Emphasis on mathematical approaches to model and analyze complex biophysical network systems. Detailed case studies demonstrating successes of systems biology. Basic biological systems reviewed for nonbiologists.
BMSE 257.
Special Topics in Biophysics
(1-4)
STAFF
Enrollment Comments: May be repeated for credit provided topics are different. Same course as Physics 257.
Course varies from year to year according to the currents of the times.
BMSE 258.
Methods in Mechanobiology and Biofabrication
(3)
PRUITT
Prerequisite: The course assumes an engineering background but is structured to be accessible to graduate students in life sciences who have a strong physics and math background, and to engineering graduate students with basic biology knowledge.
Recommended Preparation: Students should have a grounding in Physics/Mechanics, Biology, Differential equations, Linear Algebra, and familiarity with use of a scripting language like MATLAB for analyses.Enrollment Comments: Same course as ME 258.
Cell mechanobiology topics including cell structure, mechanical models, and chemo-mechanical signaling. Review and apply methods for controlling and analyzing the biomechanics of cells using traction force microscopy, AFM, micropatterning and cell stimulation. Practice and theory for the design and application of methods for quantitative cell mechanobiology. Weekly lecture and hands-on laboratory sessions. Final project in the form of a research proposal.
BMSE 259.
Selected Topics in Biological Chemistry
(1-4)
STAFF
Prerequisite: Consent of instructor.
Enrollment Comments: Same course as Chemistry 259. Course may be repeated with a different topic (18 units maximum).
Selected topics from bio-organic, biophysical, or biological chemistry. Thecontent of this course will vary.
BMSE 262.
Research Progress in Biomolecular Science and Engineering
(1)
STAFF
Research presentations by postdoctoral fellows and advanced Ph.D. students of research progress in the department.
BMSE 264.
Literature in Signal Transduction
(1)
BALLESTER, LEW
Prerequisite: Graduate standing.
Critical reading and presentation of the literature on signal transduction mechanisms that control cell growth and differentiation.
BMSE 265.
BMSE Seminar Discussion Group
(1)
STAFF
A weekly seminar discussion group to review, in advance, relevant literature of participating BMSE seminar guests.
BMSE 272.
Mechanical Force and Biomolecules
(2)
SALEH
Explores single-molecule biophysics and the role of mechanical force in biomolecular behavior. Emphasis is placed on modern experimental techniques and the effects of mechanical stress on DNA conformation, protein unfolding, and force-generation by motor proteins. Recent literature is used throughout.
BMSE 276A.
Biomolecular Materials I: Structure and Function
(3)
SAFINYA
Repeat Comments: Same course as Materials 276A.
Survey of classes of biomolecules (lipids, carbohydrates, proteins, nucleic acids). Structure and function of molecular machines (enzymes for biosynthesis, motors, pumps).
BMSE 276B.
Biomolecular Materials II: Applications
(3)
SAFINYA
Prerequisite: Materials/BMSE 276A.
Repeat Comments: Same course as Materials 276B.
Interactions and self assembly in biomolecular materials. Chemical and drug delivery systems. Tissue engineering. Protein synthesis using recombinant nucleic acid methods: advanced materials development. Nonviral gene therapy.
BMSE 290AAZZ.
Group Studies
(2)
STAFF
Prerequisite: Consent of instructor.
Presentation and discussion of current research, to be selected from the following list: A. Biomolecular Materials Synthesis; B. Biomineralization; BP. Bacterial Pathogenesis; CE. C. elegans Development; DN. Developmental Neurobiology; HW. Marine Structural Proteins; PM. Molecular Plant-Microbe Interactions; PR. Protein-Nucleic Acid Interactions; S. Molecular Virology and Interferon Action.
BMSE 290A.
Group Studies: Biomolecular Materials Synthesis
BMSE 290B.
Group Studies: Biomineralization
BMSE 290BP.
Group Studies: Bacterial Pathogenesis
BMSE 290C.
Group Studies
BMSE 290CC.
Group Studies
BMSE 290CE.
Group Studies: C. elegans Development
BMSE 290CS.
Group Studies
BMSE 290D.
Group Studies
BMSE 290DN.
Group Studies: Developmental Neurobiology
BMSE 290HW.
Group Studies: Marine Structural Proteins
BMSE 290LK.
Group Studies
BMSE 290PM.
Group Studies: Molecular Plant-Microbe Interactions
BMSE 290PR.
Group Studies: Protein-Nucleic Acid Interactions
BMSE 290S.
Group Studies: Molecular Virology and Interferon Action
BMSE 293.
Computational Methods in Biochemistry-Molecular Biology
(1)
STAFF
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. Emphaisis is on utilizing accessible software tools that are designed for non-programmers.
BMSE 294B.
Bioengineering: Career and Development Opportunities at the Interface between Biotechnology and Engineering
(2)
CLEGG
Prerequisite: Consent of instructor.
Enrollment Comments: Same as MCDB 294B and CH E 294B
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.
BMSE 592.
Laboratory Research Rotation in Biochemistry
(1-4)
STAFF
Prerequisite: Enrollment in the BMSE Ph.D. program; open to first year graduate students only.
Enrollment Comments: May be repeated up to 4 times.
Laboratory rotation project in BMSE faculty laboratories.
BMSE 595.
Biochemistry/Molecular Biology Literature Seminar
(2)
STAFF
Prerequisite: Consent of instructor; graduate standing.
A critical review of research in selected areas of biochemistry-molecular biology.
BMSE 595BG.
Bacterial Genetics
(2)
LOW
Prerequisite: Consent of instructor.
Enrollment Comments: Same course as MCDB 595BG. May be repeated for credit in combination with Biology 595AA-ZZ and EEMB 595AA-ZZ to a maximum of 8 units. Individual letter designations may be repeated for credit to a maximum of 4 units.
A critical review of research in selected fields of biology.
BMSE 596.
Directed Reading and Research
(2-12)
STAFF
Prerequisite: Graduate standing; consent of instructor.
Enrollment Comments: May be repeated for credit up to half of the graduate units required for the M.S. degree. Same course as Chemistry 596.
Individual tutorial. Instructor is usually the student's major research advisor. Each faculty member has a unique number designation.
BMSE 599.
Ph.D. Dissertation Preparation
(2-12)
STAFF
Prerequisite: Graduate standing as a Ph.D. student and advancement to Doctoral Candidacy.
Enrollment Comments: Instructor should be the chair of the student's doctoral committee.
Writing of the Ph.D. dissertation.