The Biochemistry and Structural Biology, Cell Biology and Genetics, and Molecular Biology Graduate programs (known collectively as the BCMB programs) offer a joint curriculum in biochemistry, structural, cellular, molecular, and developmental biology. The following courses are offered.

Biochemistry and Structural Biology

This is a two quarter course in structural biology and contemporary biochemistry. The course covers equilibria, bond formation, protein chemistry and structure, nucleic acid chemistry and structure, ligand binding, chemical and enzyme kinetics, enzyme reaction mechanism, principles of macromolecular analysis, principles of protein purification, and principles of macromolecular recognition and specificity. Quarters I and II annually, Drs. Dimitar Nikolov, Min Lu, and staff.

Molecular Genetics

This course is organized around the principles of genetic analysis, with examples chosen from organisms that best illustrate those principles. The course is based on lectures, problem sets, and discussion sections. Topics covered include: the nature of the gene; linkage and physical maps; recombination mechanisms; nature of mutations; mutations as tools to dissect gene function; transposition; epigenetics; cancer genetics; genetic analysis of development and cell-cell signaling. Quarters I and II annually, Dr. Scott Keeney and staff.

Cell and Developmental Biology

This course explores key aspects of cell and developmental biology at a detailed molecular level. The focus is on the integration of structure/function relationships for proteins and signaling pathways within the cell and in the intact organism. Specific topics include: membrane structure; protein biosynthesis and vesicular trafficking; endocytosis; cell architecture and motility; receptor and oncogene mediated signaling; signaling in a developmentally regulated context; and stem cell biology. The course consists of two lectures per week plus one interactive discussion section involving current research papers. Quarters III and IV annually, Drs. Marilyn Resh, Katherine Hajjar, and Mary Baylies.

Gene Structure and Function

A two-quarter course that explores the regulatory mechanisms governing the flow of information in cells from DNA to RNA to protein. The first module of the course deals with DNA replication, recombination and repair, and introduces basic principles of DNA topology and protein-DNA interactions as they apply to these and other processes. In the next module, the fundamentals of gene structure and transcription are presented. Topics to be discussed include: structure and function of transcription factors and RNA polymerases; mechanisms of transcriptional activation and repression; the effects of chromatin on transcription; analysis of transcriptional networks by proteomics and functional genomics; and transcriptional control of the cell cycle. The final module covers post-initiation maturation and processing of mRNA, culminating with its translation into protein. Topics include: mRNA capping, splicing and polyadenylation; regulation of mRNA stability; mechanisms and functions of RNA interference (RNAi); and mechanisms and regulation of translation. Quarters III and IV annually, Drs. Robert Fisher, Beate Schwer, and staff.

Logic and Critical Analysis

This course is designed to promote the critical analysis skills necessary to be a successful scientist. Students read papers from the primary literature and discuss the experiments described. Questions addressed are: what was the hypothesis, what were the experiments designed to test, what other information is necessary to interpret the experiment, do the experiments accomplish their goals, what problems exist in the experiments, and where might you go from here? To develop critical analysis skills, the first group of presentations will emphasize one or two figures only in each paper. Subsequently, two to three papers will be assigned as a thematic group by each instructor and will be discussed sequentially. Quarters III and IV annually, Dr. Andrew Koff, Prasad Jallepalli, Mary Baylies, Amy Lam, and John Petrini.

Graduate Research Seminar

This course represents an opportunity for students in their third year or above to describe their research in formal seminar presentations to the students and faculty of the Biochemistry and Structural Biology, Cell Biology and Genetics, and Molecular Biology Programs. All students from these programs attend the seminars and a small panel of students is designated to lead the discussion following each seminar. Quarters I - IV annually, Dr. Kirk Deitsch.

Developmental Biology

Key concepts in developmental biology are presented and discussed, drawing on research from a number of model systems, including Drosophila, C. elegans, Xenopus, zebrafish, chicken and mouse. The course stresses genetic, cellular, molecular and comparative approaches to problems in development. During the first half, the course concentrates on early embryogenesis and pattern formation in the different model organisms, specifically axis determination, gastrulation and neurulation. This section of the course includes two practical lab sessions, which will provide first hand experience with manipulating and analyzing embryos of different species. The second half of the course focuses on later developmental processes, including growth and patterning of the limbs, development of the nervous system and of sensory structures such as the eye, and the development of muscle, heart and lung. The course meets twice weekly and consists of lectures and interactive group discussions of classic and current research papers. Quarters I and II, every other year, next in 2005. Dr. Ulrike Gaul and staff.

Biophysical Methods

An overview of modern biophysical experimental techniques used in the study of biological systems at the cellular and molecular level. Topics include light microscopy, fluorescence microscopy, Fourier optics and image processing, confocal and multiphoton microscopy, Evanescent Wave Microscopy and Fluorescence Correlations Spectroscopy, phase contrast, electron microscopy, x-ray diffraction, multidimensional NMR, chromophores, calcium measurements, resonance energy transfer, membrane biophysics, ion channels, action potentials, ligand-gated channels, fluctuation analysis, patch-clamping, rapid kinetics, caged compounds, transmitter release, capacitance measurements, amperometry, optical traps, molecular force measurements, and computer modeling. While a basic knowledge of physics and mathematics is helpful, this is an interdisciplinary course designed for students with diverse backgrounds. Quarters I and II, every other year, next in 2005. Dr. Frederick Maxfield and staff.

Focus Groups:

• Cancer Biology
• Cell Structure and Function
• Molecular Biochemistry and Biophysics
• Molecular and Cell Biology of Viruses and Micro-Organisms
• Nucleic Acid Transactions and Genomic Integrity
• Tissue Biology and Development

Each of the above fields of study is covered each semester by 'focus groups' in the format of a student-led journal club focusing in depth on a pre-set theme or topic for a given semester. The specific topic for each focus group is chosen by two faculty members responsible for guiding each group. Groups meet every other week. Material covered typically consists of primary research papers chosen to illustrate key stages in the historical development of the field, as well as recent advances. The groups thus foster an appreciation of the background leading up to the current state of knowledge in the respective fields. Quarters 1-IV annually. Drs. Joan Massague, Frederick Maxfield, Nikola Pavletich, Erik Falck-Pedersen, Stewart Shuman, Katherine Hajjar, and program faculty.