Biological Regulatory Mechanisms
Biochemistry 201A
WINTER QUARTER, 2004 (4 units)
Prerequisites:Genetics 200AandBiochemistry 200A(Macromolecules)

OVERVIEW OF COURSE

COURSE SCHEDULE

LECTURES: All lectures will be held from 10:00AM-12:00noon. Handouts and reference lists will be provided. References with three stars indicate the discussion paper for the week, references with two stars (one per lecture) indicate required reading, and references with one star (a maximum of five per lecture) indicate interesting but optional reading. PDF files will be available for all required papers on the Web site, and copies of the optional papers will be placed in the student's lounge (MBGH) the afternoon of each lecture. Please make copies and leave the originals in the folders.

REVIEW SESSIONS:
The TAs will hold weekly review sessions at 6:30-8:30PM on Mondays (or occasionally on Tuesdays), with snacks provided. They will answer questions, give examples of the types of questions you might expect on the final exam, and help guide your choice of topics for the final proposal. Students have found this sort of information extremely valuable in the past and, though not mandatory, you are strongly encouraged to take advantage of the sessions. Joachim will hold an additional review session on Thursday, January 8 at 5pm in MBGH S261, focused on techniques. Again, students have found this session very valuable.

FINAL EXAM: The final will be a one-hour oral exam given by two faculty members. The format is similar to a qualifying exam, with questions pertaining to a research proposal (approximately 2/3 of the exam) followed by questions concerning general course material. The exam schedule will be posted on this web site on March 10.

2004 FINAL EXAM PROPOSALS: The final will be a one-hour oral exam, given by two faculty members. The format is much like a qualifying exam, with questions pertaining to a research proposal (~2/3 of the exam) followed by questions concerning general course material. The ability to reason through problems and experimental approaches will be emphasized more than the ability to recall specific details. Students are asked to write a one-page research proposal on a BioReg-related topic that should be well-focused and based on a clear, testable hypothesis. As a general guideline, the proposal should cover a body of work that a team of two scientists could complete in 2-3 years; that is, you can propose more than one line of experimentation, and an experiment, if successful, can be followed up with additional experiments. It is important that you be able to explain how the results of the experiments will answer the questions you posed. Sample proposals will be handed out later in the course.

Students are encouraged to run possible ideas for proposals (and early drafts) past the faculty and the TA's as the course proceeds and not to wait until the last minute. It is strongly recommended that you submit a written abstract to TAs and faculty members at least a week in advance of the proposal due date to allow time to refine your ideas. Written proposals (10 copies) must be handed in by noon on Tuesday, March 9 to Alan's assistant, Jude Hawley, S372A (neighborhood 3E), Mission Bay; (jhawley@biochem.ucsf.edu). Or to Laura Baxter at the Parnassus Campus,
HSE 901D. An exam schedule will be posted on the Web site by noon on Wednesday, March 10 The faculty will review proposals and contact students if there appear to be any general problems or questions (very unlikely if you've discussed your ideas ahead of time). Exams will be given over four days (Mar 15-18). You will not know which faculty members are on your exam and should not expect the "obvious" ones based on your research topic. It may be hard to believe, but these exams can be quite fun when approached constructively, and students generally find them very valuable in preparing for future exams.

GRADES: Grades will be assigned after all finals are completed, and a list will be posted on the Web Site the morning of ______indicating which faculty member you should see to receive your grades and feedback on your final exam. You will be given one grade for the final itself and an overall course grade. The final will account for 75% of the course grade, and the problem sets and participation in discussion sections will account for the rest.

DISCUSSION SECTIONS
Four sections will be assigned, two from 1:30-3:00 and two from 3:30-5:00 on Fridays. Assignments will be posted on the Web site during the first week of the course. Papers selected for discussion will be indicated on the Monday handouts and a set of questions to help guide your thinking will be provided on the Web site, along with the PDF version of the paper.
Discussion Section Assignments


PROBLEM SETS:
There will be three problem sets designed to help you assess your understanding of the material as the course proceeds. Problems will be based in part on the required (two starred) papers from each section of the course. There will be no problem set for the translation lectures, but material in the required papers should be considered fair game for the oral exam. The TAs will grade the problems and provide critical feedback.

Problem Set 1-- word version
Distributed 1/20/04
-- Due 1/27/04
Problem Set 2 -- Distributed 2/5/04
-- Due 2/13/04
Problem Set 3-- Distributed 2/19/04
-- Due 2/27/04


Sample exam questions