Biochemistry–

Courses

This information, together with the latest Stanford University time schedule, is also available through Axess at: http://axess.stanford.edu and the Stanford Bulletin at http://www.stanford.edu/dept/registrar/bulletin/61007.htm

There are excellent graduate level courses taught by faculty in other departments in the Medical School as well as by faculty in Biological Sciences and Chemistry. These courses enhance the breadth and depth of graduate education, providing students with an understanding of the multidisciplinary nature of modern biochemistry. Students are also encouraged to come up with areas for courses, which can then be organized in conjunction with one or more member of the faculty.


118Q. Genomics, Bioinformatics and Medicine

Stanford Introductory Seminar. Preference to sophomores. The kind of knowledge gained from sequencing the human genome and the implications of such knowledge for medicine and biomedical research. Novel diagnostic methods and treatment of diseases, including gene therapy and drug design. The ethical implications of genetic information. The use of genome and disease databases to determine the function of genes involved in disease. Recommended: Biological Sciences 42 or Human Biology 2A. http://cmgm.stanford.edu/biochem118/

3 units, Spr (Brutlag)


199. Undergraduate Research

Prerequisite: consent of instructor.

1-18 units, (Staff)


205. Molecular foundation of Medicine

Topics include: DNA structure, replication, repair, and recombination; chromosome structure and function; gene expression including mechanisms for regulating transcription and translation; and methods for manipulating DNA, RNA and proteins. Patient presentations illustrate how molecular biology affects the practice of medicine.

4 units, Aut (Chu, Brown, Krasnow)


210. Advanced Topics in Membrane Biochemistry

The structure, function, and biosynthesis of cellular membranes and organelles. Based on current literature, with extensive student participation. Prerequisites: 200, 203, or equivalents, and consent of instructor.

4 units, Spr (Pfeffer)


214. Physical and Chemical Principles of Biochemistry

Physical chemistry of proteins, nucleic acids and their complexes, and the chemistry underlying biological reactions; principles of enzymatic catalysis. The physical and chemical concepts that are fundamental to biological processes. Appraisal of experimental and conceptual approaches and analysis of classic and current papers in the literature. Areas: interactions involved in protein and nucleic acid structure and folding; energetic, chemical, and structural principles of enzymatic catalysis and control. Prerequisites: 200 and 203 (or equivalent), a course in physical chemistry, and a course in organic chemistry.

3 units, (Herschlag) not given 2003-04


215. Frontiers in Biological Research

(Same as Developmental Biology 215, Genetics 215.) Literature discussion on how to critically evaluate biological research. Held in conjunction with a seminar series, hosted in alternate weeks by Biochemistry, Developmental Biology, and Genetics. Each Wednesday, distinguished investigators present their current work at the frontiers of biological research. Before the seminar, students and course faculty meet and discuss in depth one or more papers from the primary research literature on a related topic. After the seminar, students meet informally with the seminar speaker to discuss their research and future directions. The techniques most commonly used to study problems in biology, and a comparison between the genetic and biochemical approaches in biological research.

1 unit, Aut, Win (Harbury, Kingsley, Baker)


217. Advanced Tutorial in Special Topics

Readings and tutorial in membrane biochemistry, enzyme mechanisms, chromosome structure, biochemical genetics, bacterial and animal viruses, and nucleic acid enzymology. Conducted under the guidance of advanced graduate students and postdoctoral fellows.

1-3 units, any quarter (Staff)


218. Computational Molecular Biology

(Same as Biomedical Informatics 231.) For molecular biologists and computer scientists desiring a practical, hands-on approach to computational molecular biology; recommended for molecular biologists and computer scientists desiring to understand the major issues concerning representation and analysis of biological sequences and structure. Existing methods are critically described with the strengths and limitations of each. Future directions for development of new methods. Practical assignments utilizing the tools described. Topics: accessing molecular databases, pattern search, classification of sequence and structure, alignment of sequences, rapid similarity searching, phylogenies, automated pattern learning, representing protein structure, modeling protein structure by homology, protein-protein docking and protein-ligand docking. Final project utilizes or analyzes the methods presented. Lecture/lab. Enrollment limited to 40. Prerequisite: introductory molecular biology at the level of Biological Sciences 42 or consent of instructor. Please note that this course will be offered through the Stanford Overseas Program in Paris in the Fall 2002-03 but will be available on-line as well. http://biochem.stanford.edu/biochem218/

3 units, not given 2005-06 (Brutlag)

220. Chemistry of Biological Processes

(Same as CSB 220.) 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.

4 units, Spr (Wandless, Herschlag, Chen)

221. The Teaching of Biochemistry

To be taken by all teaching assistants in 200, 203, 204, or 217. Emphasizes practical experience in teaching on a one-to-one basis, and problem set design and analysis. Familiarization with current lecture and text materials is expected, along with evaluations of class papers and examinations. Prerequisite: enrollment in the Biochemistry Ph.D. program or consent of instructor.

3 units, any quarter (Staff)

224. Advanced cell Biology

(Same as BIO 214) For PhD 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 undergraduates: BIO 129A,B, and consent of instructor.

2-5 units, Win (Kopito, Theriot, Straight, Pfeffer, Nelson,)


225. Molecular Motor Proteins and the Cytoskeleton

(Same as Developmental Biology 225.) The molecular basis of energy transduction leading to movements generated by microfilament-based and microtubule-based motors. Analysis of forms of myosin, dynein, and kinesin and their roles in the cell, as a model for understanding the structural, biochemical, and functional properties of biological machines in general. Topics: structure of the molecular motors and their accessory proteins; regulation of the function of motile assemblies; functions of molecular motors in cells; spatial and temporal controls on the formation of motile assemblies in cells. Experimental approaches: genetic analysis, DNA cloning and expression, reconstitution of functional assemblies from purified proteins, x-ray diffraction, three-dimensional reconstruction of electron microscope images, spectroscopic methods, and high-resolution light microscopy. Focus is on how a complex cellular process is analyzed at the molecular level by a multifaceted approach using biochemical, biophysical, and genetic techniques. Prerequisites: knowledge of basic biochemistry and cell biology.

3 units, (Spudich) not given 2003-04

228.  Computational Genomic Biology

(Same as BIOMEDIN 228) Application of computational genomics methods to biological problems.  Topics include: assembly of genomic sequences; genome databases; comparative genomics; gene discovery; gene expression analyses including gene clustering by expression, transcription factor binding site discovery, metabolic pathway discovery, functional genomics, and gene and genome ontologies; and medical diagnostics using SNPs and gene expression.  Recent papers from the literature and hands-on use of the methods.  Prerequisites: introductory course in computational molecular biology or genomics such as BIOC 218 or GENE 211.  Via Internet in Winter and Spring.

3 units,  Win (Brutlag)

230. Molecular Interventions in Human Disease

Advanced medical biochemistry focused on an in-depth exploration of specific cases where molecular-level research has led to new medical treatments or profound changes in the understanding of important diseases. There is no textbook; course materials consist of the primary medical and scientific literature on each topic. Students are expected to have a good basic understanding or molecular biology, cell biology, and biochemistry. For each topic, the underlying molecular basis of the disease will be discussed and then two key papers from the primary literature will be examined, one from basic science and one from climical medicine. Students will take turns leading the literature discussions. Specific topics will be used as a starting point to explore general recurring themes in the successes and failures of molecular approaches to the treatment of human diseases. http://cmgm.stanford.edu/biochem/biochem230/

2-3 units, Aut (Harbury, Theriot)

236. Biology by the Numbers

(Same as APPPHYS 136) Skill building in biological quantitative reasoning. Topics include: biological size scales from proteins to ecosystems; biological time scales from enzymatic catalysis and DNA replication to evolution; biological energy, motion, and force from molecular to organismic scales; mechanisms of environmental sensing from bacterial chemotaxis to vision.  Prerequisite: Physics 21, 41, or consent of instructor.  

3 units, Aut (Theriot, Fisher)

238. Computational Proteomic Biology

(Same as BIOMEDIN 238) Application of computational protein analysis to biological problems.  Topics include: protein sequence analysis and comparison including protein sequence databases, amino acid composition, protein alignment, protein motifs, protein families and probabilistic models of families; protein structure including structure comparison, superposition methods, structural motifs, and structure and domain databases; protein structure prediction including secondary structure, homology modeling, threading and ab initio structure prediction; protein-protein interaction databases and protein-protein interaction prediction; and protein-DNA interaction motifs and protein-ligand docking.  Prerequisites: BIOC 218 or SBIO/BIOPHYS 228.  Via Internet in Spring.

3 units, not given 2008-09 (Brutlag)

241. Biological Macromolecules

(Same as BIOPHYS 241, SBIO 241.)  The physical and chemical basis of macromolecular function.  Forces that stabilize biopolymers with three-dimensional structures and their functional implications.  Thermodynamics, molecular forces, and kinetics of enzymatic and diffusional processes, and relationship to their practical application in experimental design and interpretation. Biological function and the level of individual molecular interactions and at the level of complex processes.  Case studies.  Prerequisite: introductory biochemistry and physical chemistry or concent of instructor.

3-5 units, Aut (Puglisi, Block, Herschlag, Ferrell, Garcia, Weis)


257. Currents in Biochemistry

This course will be comprised of a series of seminars by the faculty of the Biochemistry Department on the subject of their ongoing research. Students will be given preprints and recent reprints in preparation for each session. Presentations will include the broad background of the research topics, current advances (and retreats), general significance and an open discussion of research directions being taken tactically and strategically. Requirements will include participation in the discussion and critical written reviews of each of two topics presented in the course.

1 unit, (Spudich)

278. Systems Biology

(Same as BIOE 310, CS 278, CSB 278) Complex biological behaviors through the integration of computational modeling and molecular biology.  Topics: reconstructing biological networks from high-throughput data and knowledge bases.  Network properties.  Computational modeling of network behaviors at the small and large scale.  Using model predictions to guide an experimental program.  Robustness, noise, and cellular variation.

3 units, Aut (Covert, Dill, Brutlag, Ferrell)

298. Biochemistry Consulting Service

Students are presented with requests for advice from faculty and students in the biological sciences and Medical School encountering experimental and analytical problems in their research.  Students work with the instructor and other biochemistry faculty to propose solutions.  May be repeated for credit.

3 units, Aut, Win, Spr, Sum (Brown)

299. Directed Reading

Prerequisite: consent of instructor.

1-18 units, any quarter (Staff)


399. Research and Special Advanced Work

Register by section numbers by arrangement with faculty. Prerequisite: consent of instructor.

1-18 units, any quarter (Staff)


459. Frontiers in Interdisciplinary Biosciences

(Cross-listed in multiple departments in the schools of Humanities and Sciences, Engineering, and Medicine; students should enroll directly through their affiliated department, otherwise enroll in ChE 459.) An introduction to cutting-edge research involving interdisciplinary approaches to bioscience and biotechnology; for specialists and non-specialists. Organized and sponsored by the Stanford BioX Program. Three seminars each quarter address a broad set of scientific and technical themes related to interdisciplinary approaches to important issues in bioengineering, medicine, and the chemical, physical, and biological sciences. Leading investigators from Stanford and throughout the world present the latest breakthroughs and endeavors that cut broadly across many core disciplines. Pre-seminars introduce basic concepts and provide background for non-experts. Registered students attend all pre-seminars in advance of the primary seminars, others welcome. Prerequisite: keen interest in all of science, engineering, and medicine with particular interest in life itself. Recommended: basic knowledge of mathematics, biology, chemistry, and physics.

1 unit, Aut, Win, Spr (Robertson)

Stanford Medicine Resources:

Footer Links: