Displaying 1 - 72 of 72
Course Units Instructor Prerequisites Description
201A Protein Structure & Function 2

Graduate standing.

Exploration of the relationship between protein sequence, structure, biophysics, and function.

201B Chemistry & Structure of Nucleic Acids 2

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 Biomembranes Structure & Function 2

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 &. Biosurfaces 3

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

Rational design of protein structure, activity, and stability. Current methods and applications of protein engineering including protein evolution, unnatural amino acids, and combinatorial methods.

204 Post-translational Protein Processing 4

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.

205A Biochemical Techniques 1

One year of undergraduate biochemistry (e.g., MCDB 108A-B-C) or equivalent.

Practical theory and application of basic biochemical techniques. Topics include SDS-PAGE, buffers, centrifugation, antibody methods, spectroscopy and fluorescence techniques. 

205B Strategies in Protein Chararacterization 1

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

Undergraduate biochemistry course (e.g., MCDB 108).

Chemical mechanisms of enzyme catalysis. Enzyme models and non-classical enzymes. Theory, experimental design, and data analysis.

210 Biochemistry & Molecular Biology Techniques for Physical Scientists 4

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.

ENGR212 Great Experiments

Consent of instructor.

Introduces students to seminal experiments that introduced pioneering biological engineering methods and experimental analysis. Students will learn the principles of sound experimental design to test a hypothesis, become familiar with techniques using bacterial and stem cell model systems, as well as imaging and analysis methods.

215 Biophysical Thermodynamics 2

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.

216B Diffraction of Biological Molecules 2

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.

217 Electrostatics of Biopolymers 2

Knowledge of elementary ideas and methods of electrostatics and statistical mechanics.

Knowledge of elementary ideas and methods of electrostatics and statistical mechanics.

218A Methods and Logic in Molecular Cell Biology I 3

Undergraduate course(s) in genetics and molecular biology.

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.

218B Methods and Logic in Molecular Cell Biology II 5

Undergraduate course(s) in genetics and molecular biology.

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.

219 Basic Microscopy for Quantitative Biology 3

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.

220A Chromosomes & Cell Cycle 2

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 Cytoskeleton 2

Graduate standing

Structure and function of the eucaryotic cytoskeleton. Structure assembly and function of microtubules, microfilaments, and intermediate filaments.

220C From RNA to Membranes 2

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.

ENGR 220A Molecular Bioengineering 4

Chem 1B/2B, Math 6B, Physics 3

Introduces students to molecular components of biology and application of engineering principles for their analysis. Topics include: molecular components of cells; DNA structure and function, including replication; gene regulation; protein structure, function, and folding; chemical kinetics; signal transduction and mathematical descriptions thereof; and mechanics of biomolecules and subcellular structures (membranes, cytoskeleton).

ENGR 220B Cell and Tissue Bioengineering 4

Engr 220A or consent of Instructor

Introduces students to structural components of cells, tissues, and organ systems, and the application of engineering principles for analysis. Topics include: biomembrane structure, function, and transport; intracellular compartments and trafficking; cell proliferation and death; cell-cell communication; biomaterials and stem cells; quantitative physiology of major organ systems (transport, mechanics, and electrical signaling); and homeostasis.

ENGR 220C Tissue & Systems Bioengineering 4

ENGR 220B or consent of instructor

This course introduces students to tissue and organism- level organization with application of engineering principles for analysis. Topics include: cardiovascular, respiratory, digestive, and central nervous systems, structural components of organisms (bones and muscles), immune system, and of pharmacology.

222A Colloids & Interfaces I 3

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.

222B Colloids and Interfaces II 3

Consent of instructor. Recommended Preparation: Materials 222A or Chemical Engineering 222A or BMSE 222A. 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. Surfactants on surfaces: langmuir- blodgett films, adsorption, adhesion, friction. Biomolecular self-assembly, biological systems.

223 Signal Transduction 2

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.

224 Quantitative Biology iQB2 Laboratory Course 4

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.

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.

MCDB224 in place of BMSE225 Signal Transduction and Development in Multicellular Systems 2

Graduate standing.

Cellular and organismal growth and other responses are controlled by positive and negative cues from both internal and external sources. We discuss the signaling mechanisms that recognize these cues and initiate an intracellular set of events that generates a response. We also discuss the molecular mechanisms of pattern formation and cellular differentiation that underlie developmental processes in a variety of important multicellular model systems.

229 Protein Biochemistry 2

Graduate standing.

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.

230 Gene Regulation 2

Graduate standing.

Mechanisms and regulation of transcription and translation in prokaryotic and eukaryotic organisms and their viruses.

ENGR230 Bioengineering Student Seminar 1

Designed for majors. Quarters usually offered: Winter, Spring, Fall. Designed for graduate students with a bioengineering emphasis

Seminar series where students present their original thesis research and also review journal articles that critically analyze contemporary bioengineering research. Three quarters of ENGR 230 are required for the optional BioE graduate emphasis. Presentations will be evaluated and feedback provided.

ENGR230 Bioengineering Student Seminar 1

Designed for graduate students with a bioengineering emphasis

Seminar series where students present their original thesis research and also review journal articles that critically analyze contemporary bioengineering research. Three quarters of ENGR 230 are required for the optional BioE graduate emphasis. Presentations will be evaluated and feedback provided.

232 Bacterial Pathogenesis 3

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.

232L Bacterial Pathogenesis Lab 3

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.

233 Cell Biology 4

Same as MCDB 203, Consent of Instructor.

Introduction to the structure and function of cell organelles: membranes, nucleus, mitochondria, chloroplasts, endoplasmic reticulum, golgi apparatus, lysosomes, microbodies, microtubules, cilia, centrioles, and microfilaments.

235 Experimental Strategies in Molecular Genetics 1

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

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

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 technologie.

246 Membrane Biochem 4

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.

MCDB246 Stem Cell Biology in Health and Disease

Basic biology of embryonic and adult stem cells and nuclear transfer, with emphasis on latest findings from the current literature.

ME246 Molecular and Cellular Biomechanics 3

Course introduces fundamental concepts in molecular and cellular biomechanics. Will consider the role of physical, thermal and chemical forces, examine their influence on cell strength and elasticity, and explore the properties of enzymatically-active materials.

247 Quantitative Methods in Biology 3

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.

248 Practical Statistics for Biologists 4

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.

250 Bionanotechnology 2

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.

BIOE250AA Tissue Engineering and Regenerative Medicine 2-4

An introduction to the principles of tissue engineering: interplay and design of cells, biomaterials, and bioactive molecules to assist the body in the repair of damaged tissues. This includes concepts such as examining material fabrication approaches, engineering cells and their behavior, studying tissue microenvironments from diverse organ systems, the role of the extracellular matrix in repair, in vitro approaches to tissue engineering, and delivery of bioactive molecules (growth factors, extracellular vesicles, etc.), among others. By the end of this course, students will be able to design and evaluate tissue engineered constructs to repair a specific organ system.

251 Biopharm Process Engineering 2

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 Bioengineering 2

An overview of various aspects of bioengineering including modeling of physiological functions, biomedical devices, drug delivery, and tissue engineering.

253 Analytical Biotechnology 3

Graduate standing. Effective Date changed to S05 per Grad Div (5/3/05). ME 291A.

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 are discussed.

254 Drug Design 3

Chemistry 142A-B-C or Biology 108A-B-C.

Rational and structure-based drug design; pharmacogenetics; combinatorial chemistry and screens; mechanism-based drug design; drug metabolism; toxicity; quantitative structure activity relationships; enzyme inhibitors.

255 Systems Biology 3

Prior course work in cellular biology, mathematics; consent of instuctor.

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.

257 Special Topics in Bio Physics 1 to 4

May be repeated for credit provided topics are different.

Course varies from year to year according to the currents of the times.

258 Methods in Mechanobiology and Biofabrication 3

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.

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.

259 Special Topics Biochemistry 1 to 4

Consent of instructor.

Selected topics from bio-organic, biophysical, or biological chemistry. The content of this course will vary.

MCDB260 Research Strategies in Molecular, Cellular and Developmental Biology 2

seminar counts as BMSE265

A review and critique of relevant literature in advance of the weekly MCBD Biology research seminar. Includes illustrating the significance, identifying the key findings, evaluating data and conclusions, and proposing further directions and questions. Practice of presentation skills. Weekly meeting with seminar speakers.

262 BMSE Research Progress in BMSE 1

Research presentations by advanced Ph.D. students on research progress in BMSE & MCDB.

CHEM262A Drug Design 3

Sources for new drugs. Biochemistry of diseases. Target validation techniques. Mechanism of action of enzymes and receptors. Enzyme inhibition and receptor binding studies. Structure base drug design: conformational analysis, docking and binding affinity calculations. Course also teaches proposal writing skills.

CHEM262B Drug Design

Medicinal chemistry for lead optimization, combinatorial synthesis, quantitative structure-activity relationships, pharmacokinetics, drug metabolism and toxicity, pharmacogenomics. Drugs that interact with DNA and Protein drugs. Clinical trials, intellectual property in drug design. Students develop their own drug design project.

264 Literature in Signal Transduction 1

Graduate standing.

Critical reading and presentation of the literature on signal transduction mechanisms t

265 BMSE Sem Discussion Group 1

None; intended for non-advanced BMSE graduate students only.

A weekly seminar discussion group to review, in advance, relevant literature of participating BMSE seminar guests.

Chem 271 Bioinorganic Chemistry 3

Chemistry 173A-B or the equivalent.

Selected topics in bioinorganic chemistry and metal-lobiochemistry with a major focus on recent developments. Topics will include discussions of metalloproteins and corresponding model compound investigations. Emphasis will be on reaction mechanisms and spectroscopic properties of metal sites.

MATRL271B Structure and Characterization of Complex Fluids 3

Structure, phase behavior, and phase transitions in complex fluids. Characterization techniques including x-ray and neutron scattering, and light and microscopy methods. Systems include colloidal and surfactant dispersions (e.g., polyballs, microemulsions, and micells), polymeric solutions and biomolecular materials (e.g., lyotropic liquid crystals).

272 Mechanical Force and Biomolecules 3

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.

276A Biomolecular Materials I: Structure and Function 3

Consent of instructor. Concurrently offered with Mat 276A.

Survey of classes of biomolecules (lipids, carbohydrates, proteins, nucleic acids). Structure and function of molecular machines (enzymes for biosynthesis, motors, pumps).

276B Biomolecular Materials II 3

Consent of instructor.

Selected topics from bio-organic, biophysical, or biological chemistry. Thecontent of this course will vary.

290XX Group Studies 2

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.

293 Computational Methods Biochemistry & Molecular Biology 1

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.

EEMB509 Levels of Biological Organization II: Communities and Ecosystems 4

Graduate standing.

This is the second in a set of advanced courses in ecology and evolution, and includes modules on the origins of diversity, species interactions and coexistence, the causes and consequences of food-web complexity, and ecosystem level processes.

592 BMSE Lab Rotation 4

Enrollment in the BMSE Ph.D. program; open to first year graduate students only.

Laboratory rotation project in BMSE faculty laboratories.

595 Biochemistry & Molecular Biology Literature Seminar 2

Consent of instructor; graduate standing.

A critical review of research in selected areas of biochemistry-molecular biology.

595XX Critical Review of Selected Literature 2

Consent of instructor.

A critical review of literature in specified research areas.

596 Directed Reading Research 2 to 12

Graduate standing; consent of instructor.

Individual tutorial. Instructor is usually the student's major research advisor. Each faculty member has a unique number designation.

599 PhD Dissert preparation 3 to 12

Graduate standing as a Ph.D. student and advancement to Doctoral Candidacy.

Writing of the Ph.D. dissertation.