Instructor: Thomas Perkins, tperkins@jila.colorado.edu 303-492-5291
This course provides an overview of the biophysics of enzymes, nucleic acids and the cytoskeleton. Straightforward application of classical Newtonian physics does a poor job of providing insight into biological processes. This course will develop a simple description of the biophysics governing the motion of molecules inside of cells. Topics covered will include diffusion, molecular motors, polymerization of the cytoskeleton and the polymer properties of nucleic acids and microtubules. Each student will give two oral presentations on journal articles along with a critique of the research article. Problem sets will provide a quantitative understanding of the topics discussed. A final paper will be required that addresses a critical question in biophysics and/or outlines a proposed experimental approach to answer the question.
Prereq., CHEM 1131 or 1171, physics 2010, 2020, MCDB 3120, or instructor consent. Recommended prereq., Math 1300 and/or CHEM 3311. Same as MCDB 5550.
Each student will write a 2 page critique on the papers that they present orally to the class (due the second class after their lecture). This summary will be graded and distributed to the class. Prior to a class covering a paper, students will be given a series of questions that can be answered by reading the paper. Students will also provide set of at least three well thought out questions for the student presenter. Students will prepare a final written paper that addresses a critical question in biophysics and outlines a proposed experimental approach to answer the question.
Each student will write a 6-8 page paper (10-12 for graduate students) that either proposes (i) an experiment using biophysical techniques with quantitative estimates, (ii) a critique of a set of papers, or (iii) a topic mutually agreed upon between the student and the instructor.
Each student will give two oral presentations, in teams if necessary, on the primary literature reading assignments. These presentations will be followed by a discussion led by the presenting student(s) to critically analyze the reading material and to review what students have learned from the presentation and the reading material.
20% Weekly critical writings 20% Participation in class discussion 20% Oral presentation 20 % Problem sets 20 % Final written proposal
Mechanics of Motor Proteins and the Cytoskeleton By Jonathon Howard, Sinauer, 2001
Molecular Biology of the Cell (4th Edition, silver cover), By Alberts, et al., 2002 A good, encyclopedic biology text book. Very good for learning vocabulary but a little dry
Biochemistry (5th Edition, green cover), By Berg, Stryer, & Tymoczko, 2002 A great book for learning about biochemistry. Clearly explains lots of topics but not as extensive MBOC. My first choice when I am learning about biochemistry. Older versions of either of these books would be sufficient for this class.
Office: JILA A503 Office Hours: Wednesday 2-3 pm