BIOL 4596
Biophysics of Macromolecules
Section 1 Fall 2007
MW 12.00-13.30 208 Williams
Instructor: Fareed Aboul-ela
Room: 407 Choppin Hall
Tel. 8-2791
Office Hours: M 10-11, Tu 3-4 (or by appt.)
No textbook is required. The following text is recommended:
Principles of Physical Biochemistry: Second Edition
Authors: van Holde, Johnson, and Ho
Pearson Prentice Hall 2006
Class lecture notes can be obtained through BioGrads. Other texts which will provide source material for the course are listed below.
Objective:
Living systems obey the laws of physics and chemistry. The objective of this course is to 1) Gain a basic understanding physical processes in Biology, particularly the physical properties and behavior of biological macromolecules. 2) Gain an understanding of the principles underlying the use of physical methods to study biological systems. Emphasis will be placed on principles and methods commonly used in structure-based drug design.
Tentative Lecture Schedule
Aug. 27 Introduction
Aug. 29 Review of complex numbers, polymer definitions
Sep. 3 Labor Day
Sep. 5 Forces and potentials in macromolecules
Sep. 10 Proteins
Sep. 12 DNA
Sep. 17 Thermodynamics: Helix-coil transitions
Sep. 19 RNA, Dynamics
Sep. 21 Fourier Transforms
Sep. 26 NMR
Sep. 28 Exam I (covering through Fourier Transforms)
Oct. 1 NMR, Mass Spec
Oct. 3 Optical spectroscopy I
Oct. 8 Optical Spectroscopy II
Oct. 10 X-ray diffraction
Oct. 15 Surface Plasmon Resonance, Imaging Methods
Oct. 17 Single Molecule Methods
Oct. 22 Water and Hydration
Oct. 24 Micelle formation, Ion Channels
Oct. 29 Exam 2 (covering through hydration)
Oct. 31 Ion Channels
Nov. 5 Drug Discovery
Nov. 7 Structure Based Drug Design I
Nov. 12 Structure Based Drug Design II
Nov. 14 Presentations
Nov. 19 Presentations
Nov. 21 Presentations
Nov. 26 Presentations
Nov. 28 Presentations
Dec. 3 Presentations
Dec. 5 Prep for Final
Dec. 10 Final Exam, 208 Williams
Grading:
Exam 1: 25%
Exam 2: 25%
Exam 3: 25% (comprehensive)
Term Paper/Presentation 25%
Makeup exams will be offered with an excuse considered valid by the university, on one time and date designated after each exam.
Students will be responsible for the lecture notes and for handouts if specified by the intsructor. The lecture schedule above outlines an approximation of what sections will be covered and when. There will be adjustments to this schedule over the course of the semester. In addition, the lectures will include some modifications from the lecture notes, which will also be posted on Blackboard. Students will be responsible for this material on exams, unless specified otherwise. Students are strongly advised to work example problems which will be posted on Blackboard.
A term paper (5-8 pages, double spaced, + references and figures) on a topic related to Biophysics is required. A set of proposed topics will be distributed by the second week of class. Students can also propose their own topic, which will be subject to approval by the instructor. Topics must be chosen by the 4th week of class, and an outline/summary is required by the middle of the semester. Graduate students are also required to give a short presentation (~20 minutes plus discussion) on their chosen topic.
Blackboard and Online Resources
All students who are enrolled in the course will be enrolled on Blackboard. Any student who does not see the course appear on their course list when they log into blackboard should notify the instructor as soon as possible.
Updated versions of the lectures will be posted on the day of the lecture itself. Exams, and solutions to exams and homeworks from past years will be posted. Students are advised to use these materials as study aids. There will be no homework assignments this term, aside from extra credits, but students may work on homework problems from the text and ask for help with these during office hours. We will also work example problems during the 2nd half of class sessions.
Extra Credit
It will be possible for students to earn up to 5 points (5% of total grade) worth of extra credits by contributing to a discussion forum on Blackboard. Posts can be in the form of a question, a response to another student’s question or comment, or a substantive comment relating course material to the outside world (e. g. medicine, neurology/psychology, pharmaceuticals, etc, some example posts have been contributed by the instructor). The topics of posts on the discussion board must in some way incorporate (but not necessarily be limited to) the course material presented in lectures or in assigned reading from the text. They must contain original words/ideas/questions from students, although they may also refer to articles (for example from newspapers or magazines-properly attributed) or other outside material. Students may contribute as many posts as they choose, but they may obtain no more than one extra credit per week. The instructor reserves the right to judge whether or not a post fits the criteria for extra credit. No more than one extra credit point can be earned within a given week.