COURSE DESCRIPTION & SCHEDULE

Bio 608 Topics in Macromolecular Structure (2 credits)

An advanced course that considers the structural, thermodynamic, electrostatic and dynamic aspects of molecules that direct the folding of proteins and nucleic acids and govern their interactions with each other as well as with small ligands. Students will approach these topics with the aid of state-of-the-art molecular graphics and computational chemistry methods. In addition students use bioinformatics approaches to gain insight into the functions and interrelationships between biological macromolecules.

The course is aimed and increasing the student's understanding of structure-function relationships of biological macromolecules, including how the structures are determined and their dynamical properties. The goal of the course is to provide "hands-on" experience in structure-function and bioinformatics analysis. The course consists of a single class meeting per week (Fridays from 1-5). The lectures will be held in 218 Cooke a Classroom/Laboratory equipped with Macintosh workstations.

Evaluation in this course consists of both subjective and objective measures. The subjective aspect is based on personal observation of the student's progress and interest. The objective measure is comprised of two aspects. First grades on weekly homework that are based on the subject presented. Second, student will prepare a paper and presentation on a topic chosen by the student that uses the methods of computer-aided structural analysis to illustrate a point or answers a question. The ~10 page paper will summarize the conclusions drawn and these conclusions will be presented in an approximately 20 minute presentation during the last two class meetings of the semester.

	Tentative date*	Instructor	Topic
1.	Fri 1/21	KOUDELKA	Introduction to molecular visualization
2.	Fri 1/28	KOUDELKA	Protein structural motifs
3.	Fri 2/4	KOUDELKA	Bioinformatics & Homology Modeling
4.	Fri 2/11	KOUDELKA	Bioinformatics & Homology Modeling II
5.	Fri 2/18	KOUDELKA	Bioinformatics & Homology Modeling III
6	Fri 2/25	KOUDELKA	Small molecule-protein interactions I
7.	Fri 3/4	KOUDELKA	Small molecule-protein interactions II
8.	Fri 3/11	KOUDELKA	DNA structure
9.	Fri 3/18	KOUDELKA	DNA-protein interactions
10.	Fri 3/25	KOUDELKA	Electrostatics
11.	Fri 4/1	-	First round of student presentations
12.	Mon 4/8	-	Second round of student presentations

*PLEASE NOTE: DUE TO POTENTIAL SCHEDULING CONFLICTS, THE SCHEDULED DATES ARE

TO BE CONSIDERED TENTATIVE. THE INSTRUCTOR RESERVES THE RIGHT TO POSTPONE CLASS.

ALL TOPICS WILL BE COVERED, BUT CLASS MAY NOT END ON 4/8