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Biochemistry

Contacts

Office: Beckman Center, B400
Mail Code: 94305-5307
Phone: (650) 723-6161
Web Site: http://biochem.stanford.edu/

Courses offered by the Department of Biochemistry are listed under the subject code BIOC on the Stanford Bulletin's ExploreCourses web site.

Biochemistry is a department within the School of Medicine, with offices and labs located in the Beckman Center for Molecular and Genetic Medicine at the Stanford Medical Center. Courses offered by the department may be taken by undergraduates as well as graduate and medical school students.

Advanced courses offered in more specialized areas emphasize recent developments in biochemistry, cell biology, and molecular biology. These courses include the physical and chemical principles of biochemistry, enzyme reaction mechanisms, membrane trafficking and biochemistry, molecular motors and the cytoskeleton, mechanisms and regulation of nucleic acid replication and recombination, the biochemistry of bacterial and animal viruses, the molecular basis of morphogenesis, the molecular and cell biology of yeast, and the structure and function of both eukaryotic and prokaryotic chromosomes.

Opportunities exist for directed reading and research in biochemistry and molecular biology, using the most advanced research facilities, including those for light and electron microscopy, chromatography and electrophoresis, protein and nucleic acid purification, rapid kinetic analysis, synthesis and analysis, single molecule analyses using laser light traps, microarray generation and analysis, and computer graphic workstation facilities for protein and nucleic acid structural analysis. Ongoing research uses a variety of organisms from bacteria to animal cells.

 

 

Doctor of Philosophy in Biochemistry

Requirements for the M.S. and Ph.D. degrees are described in the "Graduate Degrees" section of this bulletin. The department does not offer undergraduate degrees.

The Department of Biochemistry offers a Ph.D. program which begins in the Autumn Quarter of each year. The program of study is designed to prepare students for productive careers in biochemistry; its emphasis is training in research, and each student works closely with members of the faculty. In addition to the requirement for a Ph.D. dissertation based on original research, students are required to complete six advanced courses in biochemistry and related areas among the 135 total units required for the Ph.D. Selection of these courses is tailored to fit the background and interests of each student. A second requirement involves the submission of two research proposals which are presented by the student to a small committee of departmental faculty members who are also responsible for monitoring the progress of student curricular and research programs, and a journal club presentation. All Ph.D. students are expected to participate actively in the department's seminar program, and students are encouraged to attend and to present papers at regional and national meetings in cellular biochemistry and molecular biology. Teaching experience is an integral part of the Ph.D. curriculum and is required for the degree.

The Department of Biochemistry offers an M.S. degree only to students already enrolled in the Ph.D. program. Students should contact the Graduate Studies adviser for more details.

Those applying for graduate study should have at least a baccalaureate degree and should have completed work in cell and developmental biology, basic biochemistry and molecular biology, and genetics. Also required are: at least one year of university physics; differential and integral calculus; and organic, inorganic, and physical chemistry. The department is especially interested in those applicants who have research experience in biology or chemistry. Students must submit an application, including transcripts and letters of recommendation, by December for admission in the following Autumn Quarter.

Applications should be submitted at the Office of Graduate Admissions web site. Applicants are notified by March 31 of decisions on their applications. Stanford University requires scores from the Graduate Record Examination (GRE) (verbal, quantitative, and analytical), and applicants are encouraged to submit scores from the GRE Subject Test in biochemistry, biology, or chemistry. Applicants should take the October GRE exam.

All applicants are urged to compete for non-Stanford fellowships or scholarships, and U.S. citizens should complete an application for a National Science Foundation Predoctoral Traineeship. Students are provided with financial support to cover normal living expenses; Stanford tuition costs are paid. Applicants for admission to the department are considered without regard to race, color, creed, religion, sex, age, national origin, or marital status.

Postdoctoral research training is available to graduates who hold a Ph.D. or an M.D. degree. Qualified individuals may write to individual faculty members for further information.

At present, the primary research interests of the department are the structure and function of proteins and nucleic acids, the biochemistry and control of development processes, molecular motors and the cytoskeleton, the trafficking of proteins between membrane-bound organelles, the control and regulation of gene expression, bioinformatics/protein structure design, and the application of microarrays to problems in human health and disease.

Emeriti: (Professors): Robert L. Baldwin, Paul Berg, Douglas L. Brutlag, David S. Hogness, A. Dale Kaiser, I. Robert Lehman

Chair: Mark A. Krasnow

Professors: Philip Beachy, Patrick O. Brown, Gilbert Chu, Ronald W. Davis, James E. Ferrell, Jr., Daniel Herschlag, Mark A. Krasnow, Suzanne R. Pfeffer, James A. Spudich

Associate Professors: Pehr A. B. Harbury, Aaron F. Straight, Julie A. Theriot

Assistant Professors: Rhiju Das

Courtesy Professors: Steven Artandi, Kerwyn C. Huang, Chaitan S. Khosla, Sharon Long, Rajat Rohatgi

Courses

BIOC 109A. The Human Genome and Disease. 3 Units.

The variability of the human genome and the role of genomic information in research, drug discovery, and human health. Concepts and interpretations of genomic markers in medical research and real life applications. Human genomes in diverse populations. Original contributions from thought leaders in academia and industry and interaction between students and guest lecturers. Students with a major, minor or coterm in Biology: 109A/209A or 109B/209B may count toward degree program but not both.
Same as: BIO 109A, BIO 209A, BIOC 209A, HUMBIO 158.

BIOC 109B. The Human Genome and Disease: Genetic Diversity and Personalized Medicine. 3 Units.

Continuation of 109A/209A. Genetic drift: the path of human predecessors out of Africa to Europe and then either through Asia to Australia or through northern Russia to Alaska down to the W. Coast of the Americas. Support for this idea through the histocompatibility genes and genetic sequences that predispose people to diseases. Guest lectures from academia and pharmaceutical companies. Prerequisite: Biology or Human Biology core. Students with a major, minor or coterm in Biology: 109A/209A or 109B/209B may count toward degree program but not both.
Same as: BIO 109B, BIO 209B, BIOC 209B.

BIOC 118Q. Genomics and Medicine. 3 Units.

Preference to sophomores. Knowledge gained from sequencing human genomes and implications for medicine and biomedical research. Novel diagnoses and treatment of diseases, including stem cells, gene therapy and rational drug design. Personal genomics and how it is used to improve health and well being. Social and ethical implications of genetic information such as privacy, discrimination and insurability. Course Webpage: http://biochem118.stanford.edu/.

BIOC 158. Genomics, Bioinformatics and Medicine. 3 Units.

Molecular basis of inherited human disease. Diagnostics approaches: simple Mendelian diseases and complex, multifactorial diseases. Genomics: functional genomics, epigenetics, gene expression, SNPs, copy number and other structural genomic variations involved in disease. Novel therapeutic methods: stem cell therapy, gene therapy and drug developments that depend on the knowledge of genomics. Personal genomics, pharmacogenomics, clinical genomics and their role in the future of preventive medicine. Prerequisites: BIO 41 or HUMBIO 2A or consent of instructor. Those with credit in BIOC 118 not eligible to enroll. Course webpage: http://biochem158.stanford.edu/
Same as: BIOC 258, BIOMEDIN 258, HUMBIO 158G.

BIOC 199. Undergraduate Research. 1-18 Unit.

Students undertake investigations sponsored by individual faculty members. Prerequisite: consent of instructor.

BIOC 200. Applied Biochemistry. 2 Units.

Enrollment limited to MD candidates. Fundamental concepts of biochemistry as applied to clinical medicine. Topics include vitamins and cofactors, metabolism of carbohydrates, lipids, amino acids and nucleotides, and the integration of metabolic pathways. Clinical case studies discussed in small-group, problem-based learning sessions.

BIOC 202. Biochemistry Bootcamp. 1 Unit.

Open to first year Biochemistry students or consent of instructor. Hands-on, five-day immersion in biochemical methods and practice, theory and application of light microscopy, and computational approaches to modern biological problems.

BIOC 205. Molecular Foundations of Medicine. 3 Units.

For medical students. Topics include DNA structure, replication, repair, and recombination; gene expression, including mechanisms for regulating transcription and translation; chromosome structure and function; gene cloning, protein engineering, and genomics. Patient presentations and journal clubs illustrate how molecular biology affects the practice of medicine.

BIOC 209A. The Human Genome and Disease. 3 Units.

The variability of the human genome and the role of genomic information in research, drug discovery, and human health. Concepts and interpretations of genomic markers in medical research and real life applications. Human genomes in diverse populations. Original contributions from thought leaders in academia and industry and interaction between students and guest lecturers. Students with a major, minor or coterm in Biology: 109A/209A or 109B/209B may count toward degree program but not both.
Same as: BIO 109A, BIO 209A, BIOC 109A, HUMBIO 158.

BIOC 209B. The Human Genome and Disease: Genetic Diversity and Personalized Medicine. 3 Units.

Continuation of 109A/209A. Genetic drift: the path of human predecessors out of Africa to Europe and then either through Asia to Australia or through northern Russia to Alaska down to the W. Coast of the Americas. Support for this idea through the histocompatibility genes and genetic sequences that predispose people to diseases. Guest lectures from academia and pharmaceutical companies. Prerequisite: Biology or Human Biology core. Students with a major, minor or coterm in Biology: 109A/209A or 109B/209B may count toward degree program but not both.
Same as: BIO 109B, BIO 209B, BIOC 109B.

BIOC 210. Advanced Topics in Membrane Trafficking. 3 Units.

The structure, function, and biosynthesis of cellular membranes and organelles. Current literature. Prerequisite: consent of instructor.

BIOC 215. Frontiers in Biological Research. 1 Unit.

Literature discussion in conjunction with the Frontiers in Biological Research seminar series in which investigators present current work. Students and faculty meet beforehand to discuss papers from the speaker's primary research literature. Students meet with the speaker after the seminar to discuss their research and future directions, commonly used techniques to study problems in biology, and comparison between the genetic and biochemical approaches in biological research.
Same as: DBIO 215, GENE 215.

BIOC 218. Computational Molecular Biology. 3 Units.

Practical, hands-on approach to field of computational molecular biology. Recommended for molecular biologists and computer scientists desiring to understand the major issues concerning analysis of genomes, sequences and structures. Various existing methods critically described and strengths and limitations of each. Practical assignments utilizing tools described. Prerequisite: BIO 41 or consent of instructor. All homework and coursework submitted electronically. Course webpage: http://biochem218.stanford.edu/.
Same as: BIOMEDIN 231.

BIOC 220. Chemistry of Biological Processes. 4 Units.

The principles of organic and physical chemistry as applied to biomolecules. Goal is a working knowledge of chemical principles that underlie biological processes, and chemical tools used to study and manipulate biological systems. Prerequisites: organic chemistry and biochemistry, or consent of instructor.
Same as: CSB 220.

BIOC 221. Open Problems in Biology. 1 Unit.

Introduces open problems in biology to those outside the field with quantitative backgrounds (e.g. science, computer science, engineering, and mathematics). Ten different experts cover ten different topics in their respective fields. Focuses on: active areas of biological research, importance of each topic, and why each topic, despite its importance, remains an open problem.
Same as: BIOC 223.

BIOC 221. The Teaching of Biochemistry. 3 Units.

Required for teaching assistants in Biochemistry. Practical experience in teaching on a one-to-one basis, and problem set design and analysis. Familiarization with current lecture and text materials; evaluations of class papers and examinations. Prerequisite: enrollment in the Biochemistry Ph.D. program or consent of instructor.

BIOC 223. Open Problems in Biology. 1 Unit.

Introduces open problems in biology to those outside the field with quantitative backgrounds (e.g. science, computer science, engineering, and mathematics). Ten different experts cover ten different topics in their respective fields. Focuses on: active areas of biological research, importance of each topic, and why each topic, despite its importance, remains an open problem.
Same as: BIOC 221.

BIOC 224. Advanced Cell Biology. 4 Units.

For Ph.D. students. Current research on cell structure, function, and dynamics. Topics include complex cell phenomena such as cell division, apoptosis, compartmentalization, transport and trafficking, motility and adhesion, differentiation, and multicellularity. Current papers from the primary literature. Prerequisite for advanced undergraduates: BIO 129A,B, and consent of instructor.
Same as: BIO 214, MCP 221.

BIOC 226. Interdisciplinary Approaches to Biochemistry: Single Molecule Biophysics to Clinical Outcomes. 3 Units.

Interdisciplinary analyses from basic biochemistry and biophysics to clinical outcomes of disease states and potential therapeutic interventions (translational research). Focus on cardiac system. Cardiomyopathies arise from missense mutations in cardiac muscle proteins, including the cardiac myosin motor. Single molecule biophysics and classical enzyme kinetics and use of induced pluripotent stem cells (iPS cells) and single cell studies lay the foundation for discussions of the effects of cardiomyopathy mutations on heart function. Potential therapeutic approaches discussed, including genetic analysis, DNA cloning, reconstitution of functional assemblies, xray diffraction and 3D reconstruction of electron microscope images, spectroscopic methods, computational approaches, single molecule biophysics, use of induced pluripotent stem cells in research, and other interdisciplinary approaches. Current papers examined. Prerequisites: basic biochemistry.

BIOC 236. Biology by the Numbers: Evolution. 3 Units.

Topics in biology from a quantitative perspective. Subjects vary. 2012-13 focus: evolution, from basic principles of evolutionary dynamics to fundamental quantitative questions that are far from being answered; from early life, metabolic processes, and molding of earth by microbes to spread of human epidemics; from analysis of genomes and molecular phylogenies to aspects of multi-cellular development. Prerequisite: familiarity with ordinary differential equations and probability. Biology background not required.
Same as: APPPHYS 236.

BIOC 241. Biological Macromolecules. 3-5 Units.

The physical and chemical basis of macromolecular function. Topics include: forces that stabilize macromolecular structure and their complexes; thermodynamics and statistical mechanics of macromolecular folding, binding, and allostery; diffusional processes; kinetics of enzymatic processes; the relationship of these principles to practical application in experimental design and interpretation. The class emphasizes interactive learning, and is divided equally among lectures, in-class group problem solving, and discussion of current and classical literature. Enrollment limited to 50. Prerequisites: Background in biochemistry and physical chemistry recommended but material available for those with deficiency in these areas; undergraduates with consent of instructor only.
Same as: BIOPHYS 241, SBIO 241.

BIOC 257. Currents in Biochemistry. 1 Unit.

Seminars by Biochemistry faculty on their ongoing research. Background, current advances and retreats, general significance, and tactical and strategic research directions.

BIOC 258. Genomics, Bioinformatics and Medicine. 3 Units.

Molecular basis of inherited human disease. Diagnostics approaches: simple Mendelian diseases and complex, multifactorial diseases. Genomics: functional genomics, epigenetics, gene expression, SNPs, copy number and other structural genomic variations involved in disease. Novel therapeutic methods: stem cell therapy, gene therapy and drug developments that depend on the knowledge of genomics. Personal genomics, pharmacogenomics, clinical genomics and their role in the future of preventive medicine. Prerequisites: BIO 41 or HUMBIO 2A or consent of instructor. Those with credit in BIOC 118 not eligible to enroll. Course webpage: http://biochem158.stanford.edu/
Same as: BIOC 158, BIOMEDIN 258, HUMBIO 158G.

BIOC 299. Directed Reading in Biochemistry. 1-18 Unit.

Prerequisite: consent of instructor.

BIOC 350. Development of Thesis Research. 2 Units.

Biochemistry 2nd year PhD students with permission of instructor only. Students place their thesis research into a broader scientific perspective, identify important questions to ask, and learn to communicate these clearly. The course includes a series of roundtable discussions with students and faculty about the students' proposed research topics. The initial focus is on developing the equivalent of a specific aims page for a research grant.

BIOC 360. Developing an Original Research Proposal. 1 Unit.

Biochemistry 3rd year PhD students with permission of instructor only. Students develop new research directions. Topics well outside of student's research topic must be chosen. Series of discussion groups with faculty and students. Students present possible outside research topics followed by presentation of important questions and approaches to answer these questions. Focus is on developing the equivalent of specific aims for research grants.

BIOC 370. Medical Scholars Research. 4-18 Units.

Provides an opportunity for student and faculty interaction, as well as academic credit and financial support, to medical students who undertake original research. Enrollment is limited to students with approved projects.

BIOC 399. Graduate Research and Special Advanced Work. 1-18 Unit.

Allows for qualified students to undertake investigations sponsored by individual faculty members.

BIOC 459. Frontiers in Interdisciplinary Biosciences. 1 Unit.

Students register through their affiliated department; otherwise register for CHEMENG 459. For specialists and non-specialists. Sponsored by the Stanford BioX Program. Three seminars per quarter address scientific and technical themes related to interdisciplinary approaches in bioengineering, medicine, and the chemical, physical, and biological sciences. Leading investigators from Stanford and the world present breakthroughs and endeavors that cut across core disciplines. Pre-seminars introduce basic concepts and background for non-experts. Registered students attend all pre-seminars; others welcome. See http://biox.stanford.edu/courses/459.html. Recommended: basic mathematics, biology, chemistry, and physics.
Same as: BIO 459, BIOE 459, CHEM 459, CHEMENG 459, PSYCH 459.

BIOC 801. TGR Project. 0 Units.

BIOC 802. TGR Dissertation. 0 Units.