Program Information and Emphases
Staff Graduate Advisor
Juliana SerenaAll students are enrolled in one of two emphases: Biochemistry and Molecular Biology (BCMB) or Biophysics and Bioengineering (BIOPHENG). All students are expected to take the Interdisciplinary Quantitative Biosciences at the Bench (iQB2) in their first quarter (register for both IQB 210 and IQB 224), lab rotations, and a number of core and elective courses, as described below. Students typically join a research group in the Summer of their first year and complete their Doctoral degree within 5-6 years. An important step required of all students is the Advancement to Candidacy Exam that must be taken by the end of the third year of graduate studies.
- Year One Recommended Courses:
Fall Quarter:
- iQB2 course: register for both IQB 210 (4 units) & IQB 224 (4 units). Grade of B or better.
- IQB 262 Research Progress in IPQB (FNS
- MCDB 500 Teaching Assistant Orientation
- MCDB 502 Teaching Assistant Training
Winter Quarter:
- IPQB recommended core lecture courses: IQB 229 (2 units)
- Lab Rotations (register for IQB 592)
- IQB 262 Research Progress in IPQB (FNS
- MCDB 260 Research Strategies in MCDB
- MCDB 501 TAShip
Spring Quarter
- IPQB recommended core lecture courses: IQB 247 (3 units)
- Elective courses towards core unit requirements (sse Appendix … for a list of approved courses*)
- Lab Rotations (register for IQB 592)
- IQB 262 Research Progress in IPQB
- MCDB 260 Research Strategies in MCDB
- iQB2
A signature of the Program is a 10-week immersive course that provides hands-on training at the interface between disciplines, with the goal to equip graduate students with diverse background to tackle biological problems with varied experimental and theoretical approaches and to create a interdisciplinary training environment to foster the pursuit of common biological questions in different systems. Typically, the course features 5 modules of 2 weeks spanning a wide range of topics, from recent advances in Biochemistry to the building of microscopes and the use of optogenetics to study animal behavior. The course aims to be a hands-on collaboration with faculty where students "learn by doing" at the bench.
Courses
| Course Number: | Title: | Units: | Prerequisites: | Description: | Keyword |
|---|---|---|---|---|---|
| 201A | Protein Structure & Function | 2 | Graduate standing. |
Exploration of the relationship between protein sequence, structure, biophysics, and function. |
BIOPHENG |
| 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. |
BCMB |
| 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. |
BCMB |
| 202 | Biomaterials &. Biosurfaces | 3 | Consent of instructor. Same course as Chemical Engineering 202 and Materials 270. 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. |
BIOPHENG |
| 203 | Protein Engineering and Design | 3 | 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. | BIOPHENG |
| 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. |
BCMB |
| 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. |
BCMB |
| 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. |
BCMB |
| 206 | Introduction to Machine Learning for Processing of Biological Images and Structural Biology | 3 | BCMB, BIOPHENG | ||
| 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. |
BCMB |
| 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. |
BCMB, BIOPHENG | |
| 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. |
BIOPHENG |
| 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. |
BIOPHENG |
| 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. |
BIOPHENG |
| 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. |
BCMB |
| 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. |
BCMB |
| 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. |
BIOPHENG |
| 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. |
BCMB, BIOPHENG |
| 220B | Cytoskeleton | 2 | Graduate standing |
Structure and function of the eucaryotic cytoskeleton. Structure assembly and function of microtubules, microfilaments, and intermediate filaments. |
BCMB, BIOPHENG |
| 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. |
BCMB, BIOPHENG |
| 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. |
BIOPHENG |
| 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. |
BIOPHENG |
| 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. |
BCMB |
| 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. |
BCMB, BIOPHENG |
| 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. |
BCMB |
| 230 | Gene Regulation | 2 | Graduate standing. |
Mechanisms and regulation of transcription and translation in prokaryotic and eukaryotic organisms and their viruses. |
|
| 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. |
BCMB | |
| 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. |
BCMB | |
| 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. |
BCMB |
| 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. |
BCMB |
| 239 | Physical Biology of the Cell | 4 | The role of physics in biology through quantitative measurements and modeling, the organization of a cell, and exemplary quantitative results of biological model systems. The physics of biologically relevant macromolecules, including DNA, RNA and mechanisms of transcription and translation; introduction to protein folding and the role of electrostatics in biology. The physics of the cytoskeleton including beam theory, persistence length, molecular motors, instrumentation used to characterize motor properties, as well as the role of active stresses in cell biology. If time permits, a brief introduction to cell motility and the structure of epithelial tissue. PHYS 239 and IQB 239 are the same course. | BCMB | |
| 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. |
BIOPHENG |
| 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. |
BIOPHENG |
| 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. |
BIOPHENG |
| 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. |
BCMB, BIOPHENG | |
| 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. |
BIOPHENG |
| 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. |
BIOPHENG |
| 252 | Principles Bioengineering | 2 | An overview of various aspects of bioengineering including modeling of physiological functions, biomedical devices, drug delivery, and tissue engineering. |
BIOPHENG | |
| 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. |
BIOPHENG |
| 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 | Methods in System Biology | 3 | 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. Same course as Chemical Engineering 255. | BIOPHENG | |
| 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. |
BIOPHENG |
| 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. |
BIOPHENG |
| 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. |
BCMB |
| 262 | BMSE Research Progress in BMSE | 1 | Research presentations by advanced Ph.D. students on research progress in BMSE & MCDB. |
||
| 264 | Literature in Signal Transduction | 1 | Graduate standing. |
Critical reading and presentation of the literature on signal transduction mechanisms t |
BCMB |
| 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. |
|
| 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. |
BIOPHENG | |
| 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). |
BIOPHENG |
| 276B | Biomolecular Materials II | 3 | Consent of instructor. |
Selected topics from bio-organic, biophysical, or biological chemistry. Thecontent of this course will vary. |
