DEPARTMENT OF MOLECULAR BIOLOGY AND BIOCHEMISTRY
3205 McGaugh Hall; (949) 824-6034
Jerry E. Manning, Department Chair
Faculty
Dana W. Aswad: Regulation of protein function by covalent modification
Hans-Ulrich Bernard: Papillomavirus/cancer
David Camerini: HIV-1 pathogenesis and molecular biology
Paolo Casali: Human immune response to cancer and viral diseases
Melanie Cocco: Structural studies of proteins and DNA using NMR spectroscopy
Michael G. Cumsky: Mitochondrial protein import; regulation of gene expression in yeast
Rowland H. Davis: Regulation of polyamine metabolism in Neurospora crassa
Hung Fan: Molecular biology and pathogenesis of mouse and human retroviruses
David A. Fruman: Signal transduction, immunology, cancer, leukemia, kinase, microarray
Charles G. Glabe: Amyloid Ab peptide in Alzheimer's pathogenesis; gamete recognition
Gale A. Granger (Emeritus): Immunology and pathogenesis: Cell-mediated immunity; tumor immunology; cytokine action
Barbara A. Hamkalo: Molecular basis of differential chromatin condensation
Agnes Henschen-Edman: Protein structure, function, post-translational modification; fibrinogen
Christopher C.W. Hughes: Endothelial cells as initiators and targets of immune responses
Anthony A. James: Malaria parasite development; genetic manipulation of insect vectors
Thomas E. Lane: Molecular/immuno-pathogenic mechanisms of virus-induced demyelinating disease
Hartmut Luecke: Structure-function studies of membrane-associated proteins
Rui (Ray) Luo: Protein structure and noncovalent associations involving proteins
Jerry E. Manning: Major surface proteins and their genes in Trypanosoma cruzi
Alexander McPherson: X-ray and atomic force microscopy analysis of protein, nucleic acid, and virus crystals; structural immunology, structural virology; microgravity research on macromolecular crystal growth
Edward Nelson: Tumor immunology
Timothy F. Osborne: Transcriptional regulation of cholesterol biosynthesis
Thomas L. Poulos: Protein engineering and crystallography
Ingrid Ruf: Mechanisms of viral oncogenesis, maintenance of viral latency and regulation of gene expression
Donald F. Senear: Interactions of proteins and DNA in transcriptional regulation
Andrea J. Tenner: Molecular basis of the enrichment of human leukocyte function
Krishna K. Tewari: Chloroplast DNA: replication and transcription
Shiou-Chuan (Sheryl) Tsai: Structural and chemical biology of multisubunit enzyme complexes that make pharmaceutically important natural products
Luis P. Villarreal: Tissue-specific viral and cellular gene expression; viral vectors
Edward K. Wagner: Herpes simplex virus gene expression during productive and latent infection
Craig M. Walsh: T cell function, development, and homeostasis
Clifford A. Woolfolk: General microbiology; enzymology
The research interests of faculty in the Department of Molecular Biology and Biochemistry include structure and synthesis of nucleic acids and proteins, regulation, virology, biochemical genetics, gene organization, nucleic acids and proteins, cell and developmental biology, molecular genetics, biomedical genetics, and immunology.
The Department offers graduate study in conjunction with the program in Molecular Biology, Genetics, and Biochemistry, which is described in a previous section. Students admitted into the combined program who select a research advisor in the Department begin following the departmental requirements for the Ph.D. at the beginning of their third year. Participation in an advanced topics seminar series and completion of at least one course per year for three years are expected of all students. Students must advance to candidacy in their third year. The normal time for completion of the Ph.D. is five years, and the maximum time permitted is seven years.
Several faculty in the Department also are members of the graduate program in Protein Engineering, which is described in a previous section.
Courses in Molecular Biology and Biochemistry
200A-B-C Research in Molecular Biology and Biochemistry (2 to 12 per quarter) F, W, S. Individual research supervised by a particular professor. See areas of interest listed under Faculty. Prerequisite: consent of instructor.
201A-B-C Seminars in Molecular Biology and Biochemistry (2-2-2) F, W, S. Seminar, two hours. Presentation of research from department laboratories or, when pertinent, of other recent developments. Prerequisite: consent of instructor. Satisfactory/Unsatisfactory only. May be repeated for credit as topics vary.
202A-B-C Tutorial in Molecular Biology and Biochemistry (2-2-2) F, W, S. Tutorials in the area of research of a particular professor which relate current research to the literature. May be conducted as journal clubs. Prerequisite: consent of instructor. May be repeated for credit as topics vary.
203 Structure and Biosynthesis of Nucleic Acids (4) W. Lecture, three hours. The structure and properties of nucleic acids. The fundamentals of nucleic acid hybridization and recombinant DNA methodology. Replication and rearrangement of DNA. Prerequisites: Biological Sciences 98 and 99 or the equivalent and Chemistry 51A-B-C or the equivalent. (Coordinators, B. Hamkalo and D. Senear)
204 Protein Structure and Function (4) F. Lecture, three hours. The structure and properties of proteins, enzymes, and their kinetic properties. Prerequisites: Biological Sciences 98 and 99 or the equivalent and Chemistry 51C or the equivalent. (Coordinator, Henschen-Edman)
205 Topics in Viral Gene Expression (4) W. Lecture, three hours. Primary research data on the major DNA and RNA viruses emphasizing strategies of regulation of gene expression. Utilization of viruses as molecular biological tools. Graduate-level knowledge of the biochemistry and molecular biology of macromolecules is required. Prerequisites: Molecular Biology 203 and 204 or the equivalent. (Coordinators, E. Wagner and B. Semler)
206 Regulation of Gene Expression (4) W. Lecture, three hours. Aspects of gene expression including the organization of the eukaryotic nucleus in terms of protein-nucleic acid interaction (i.e., chromatin and chromosome structure); comparisons between prokaryotic and eukaryotic gene expression, the enzymology and regulation of RNA transcription in E. Coli and other prokaryotes. Enzymology of transcription in eukaryotes. Prerequisites: Molecular Biology 203, 204, and 205. (Coordinators, R. Sandri-Goldin and C. Greer)
207 Advanced Molecular Genetics (4) W. Lecture, three hours. Introduction to genetic analysis using model organisms such as yeast. Topics include meiosis, DNA repair, cell cycle, cytoskeleton, intracellular sorting (nuclear, endoplasmic, mitochondrial), signaling, prions, and genomewide gene expression analysis. Prerequisite: Molecular Biology and Biochemistry 203. With consent of instructor, may be taken for credit six times. Same as Biological Chemistry 207. (Coordinator, R. Davis)
208 Introduction to Proteomics (3) S. Introduces students to concepts and methods of proteomics including protein identification, expression proteomics, and protein-protein interactions. Prerequisite: Molecular Biology and Biochemistry 204. Same as Physiology and Biophysics 252.
209 Literature in Protein Engineering (1) F, W, S. Seminar, one hour, discussion, half-hour. Students review current papers in the field of protein engineering and present the ideas contained therein to other students and faculty. May be repeated for credit. Same as Physiology 209.
210A-B Basic Medical Biochemistry (10-10) F, W. Lecture, ten hours. Classical and molecular biochemistry, including structure, function, and biosynthesis of macromolecules; metabolic interrelations and control mechanisms; and biochemical genetics. Application of recent advances in knowledge of molecular bases for cellular function to disease states (diagnosis, prevention, and treatment). Prerequisite: consent of instructor.
211 Magnetic Resonance in Biology (4). Lecture, three hours. Basic principles of magnetic resonance. Survey of applications in biology including: protein and nucleic acid structure determination and dynamics, electron paramagnetic resonance and magnetic resonance imaging. Prerequisite: consent of instructor. Concurrent with Biological Sciences 133A.
212 Chromosome Dynamics in Eukaryotes (4) S of even years. Focuses on experimental approaches currently in use to investigate mechanisms by which eukaryotes carry out essential chromosomal functions. A combination of lectures and student presentations focus on these problems from the fields of genetics, cell biology, biochemistry, and molecular biology. Prerequisites: Molecular Biology and Biochemistry 203 and 204.
217A Principles of Cancer Biology I (4) W of even years. Lecture, three hours. Oncogenes and tumor suppressor genes are studied from molecular viewpoints. Also studies their role in cancer; viral carcinogenesis. Designed for graduate students interested in cancer research. Format includes lectures and student-led discussions. Prerequisites: Molecular Biology and Biochemistry 203 and 204.
217B Principles of Cancer Biology II (4) W of odd years. Lecture, three hours. Topics include cancer cell growth and metastasis, chemical carcinogenesis, and cancer genetics and epidemiology. Designed for graduate students interested in cancer research. Format includes lectures and student-led discussions. Prerequisites: Molecular Biology and Biochemistry 203 and 204.
218 Clinical Cancer (3) F of even years. Lecture, two hours. Designed to acquaint students in basic life science with clinical cancer. Restricted to graduate and postdoctoral students. May be repeated for credit. (Coordinator, H. Fan)
219 Fundamental Immunology II (4). Lecture, three hours. Lectures and discussions to achieve a basic understanding of immunoglobulin class switching and somatic hypermutation and response to infections; immunological memory; inherited and acquired immunodeficiencies, mechanisms of allergic reactions; response to self-antigens, tolerance and loss of tolerance, immune response to tumors. Prerequisite: Microbiology and Molecular Genetics 215.
220 Structure and Synthesis of Biological Macromolecules Journal Club (2). Seminar, one hour. Advanced topics in macromolecular structure and synthesis as related to biological problems. Satisfactory/Unsatisfactory only. May be repeated for credit as topics vary.
221 Advanced Topics in Immunology (4) F. Lecture, three hours. Literature-based, interactive discussions focused on review of seminal historic and recent immunology literature. Student responsibilities include reading, critical evaluation, and discussion of manuscripts.
221L Advanced Immunology Laboratory (4) S. Laboratory, four hours. An advanced course in immunology for graduate students enrolled in the Biotechnology master's program. Emphasis is placed on learning modern techniques in immunology such as ELISAs, western blotting, immunofluorescent staining assays. Prerequisite: graduate standing. Concurrent with Biological Sciences 121L. Formerly Molecular Biology and Biochemistry 221.
223 Introduction to Computational Biology (4) S. Lecture, three hours; laboratory, two hours. The use of theories and methods based on computer science, mathematics, and physics in molecular biology and biochemistry. Basics in biomolecular modeling. Analysis of sequence and structural data of biomolecules. Analysis of biomolecular functions. Concurrent with Biological Sciences 123A.
224 Virus Engineering Laboratory (4) S. Laboratory, four hours. An advanced laboratory for graduate students enrolled in the Biotechnology master's program. Students learn to engineer recombinant eukuryotic viruses and express genes in mouse tissue. Prerequisite: graduate standing. Concurrent with Biological Sciences 124L.
227 Immunology Journal Club (2) F, W, S. Seminar and discussion, one hour. Advanced topics in immunology as related to an understanding of human disease. Satisfactory/Unsatisfactory only. May be repeated for credit as topics vary.
228 Genetic Engineering and Biotechnology (4) S. An advanced course in genetic engineering and biotechnology for graduate students enrolled in the Biotechnology master's program. Emphasis is placed on learning advanced methods in assembling the gene for expression in bacteria, yeast, and human cells.
229 Research-in-Progress Seminars (1) F, W, S. Seminar and discussion, one hour. Two half-hour presentations by graduate students and postdoctorals to the department on their current research projects. Satisfactory/Unsatisfactory only. May be taken for credit 15 times.
240 Macromolecular Structure, Function, and Interaction (4) W. Lecture, three hours; discussion, one hour. Chemistry of macromolecules; emphasis on proteins. Physical and chemical properties of proteins, forces that maintain protein structure, relationship between structure and function, interactions of proteins with ligands and other macromolecules, and experimental methods to study structure, function, and interactions. Prerequisites: Molecular Biology 203 and 204. Concurrent with Biological Sciences 140. (Coordinators: D. Senear and T. Poulos)
244 Biochemistry of Synaptic Plasticity (4) S. Lecture, two hours; discussion, one hour. Use of the primary literature to explore recent developments in the biochemistry of synaptic transmission that pertain to plasticity, memory, and learning, with a particular emphasis on the role of protein phosphorylation and related signal transduction pathways. Same as Neurobiology and Behavior 244.
250 Recombinant DNA Technology (8) F. Laboratory, eight hours. Individual training in major techniques of recombinant DNA, including extraction and purification of nucleic acids, cloning and subcloning, DNA sequencing, nucleic acid hybridization, and associated procedures. Student must demonstrate accurate documentation of data with laboratory notebook detailing experience. Prerequisite: limited to Biotechnology concentration M.S. students or consent of instructor.
251 Protein Isolation and Characterization (8) W. Laboratory, eight hours. Individual training in major techniques of handling proteins, including isolation, various purification procedures, characterization, and tests for biological or catalytic activity. Student must demonstrate accurate documentation of data with laboratory notebook detailing experience. Prerequisites: Molecular Biology 250; limited to Biotechnology concentration M.S. students or consent of instructor.
254 Protein Crystallography (3) S of even years. Lecture, three hours. Introduces students to the theory and practice of macromolecular crystallography. Covers all aspects, including protein crystallization, space groups, phasing methods, electron density map interpretation, refinement and preparation of results for publication. Corequisite: calculus. Prerequisite: consent of instructor. Same as Physiology and Biophysics 211.
280 Advanced Topics in Biochemistry and Molecular Biology (3) F. Lecture, three hours. Selected topics in specified areas of concentration, e.g., nucleic acids, protein biochemistry, genetic expression, biochemical genetics. Specific topics announced in advance. Prerequisites: Biological Sciences 98 and 99 and consent of instructor. Normally taken with Molecular Biology and Biochemistry 205A. Open to advanced undergraduates.
290A Colloquium in Molecular Biology and Biochemistry (2) F. Colloquium, one and one-half hours. Contemporary research problems in molecular biology and biochemistry. Invited speakers present research and/or review topics. Satisfactory/Unsatisfactory only. May be repeated for credit.
399 University Teaching (4-4-4) F, W, S. Limited to Teaching Assistants.
