Course Description: BIOL448(3) Protein Structure R.H. Kretsinger 15/Dec/02
S/03 9:30 - 10:45 T&R Gilmer 227
(Satisfies the second writing requirement)

The goals of 448 are:
1. To understand the basic characteristics and concepts of the structures of proteins and nucleic acids.
2. To prepare students to evaluate the literature of macromolecular structure critically and creatively.

To realize these goals:
1. Lectures in 448 will explore these concepts and the relevant techniques of structure determination.
2. Students will use programs to visualize and analyze structures in the Protein Data Bank and other online sources.
3. Each student will prepare a paper and will make an oral presentation describing one protein family. S/he assumes the responsibility to teach his classmates about his protein. Lectures by the faculty will be designed to cover other proteins. For this reason no withdrawals will be accepted after 29/Jan.

Prerequisites are introductory chemistry, introductory biology, and either cell biology (Core I), or biochemistry, or (with permission of instructor) both semesters of organic chemistry.

Consistent with the guidelines of the second writing requirement each student will submit by 6/Feb a two page outline of his paper.

Course grades will be based on:
Brief outline 5%
Homework 25%
Main paper 40% date to be established
Oral presentation 30% date to be established

The 448 class WEB site will have:
1. Course outline, Lecture Topics, & Protein or Nucleic Acid Families as Case Studies
2. Instructions for downloading PDB files and for using RIBBONS
3. Lecture notes
4. References
5. Homework exercises (answers, later)

The format of the paper may vary slightly with the subject; please discuss with RHK
double space, 12 font (30 lines/page * 10 words/line ~ 300 words/page)
total MS @ references ~ 15 pages (exclusive of four to eight illustrations).

As a guideline:
Title page:
informative title
student name
BIOL 448
date

Summary:
(two pages maximum)
biological significance of the protein or nucleic acid (family, complex)
important aspects of the structure
relationship of the structure to the function of the protein

Introduction: biological context
(~three pages)

Methods: concise summary:
(~two pages)
preparation (expression) of proteins
structure determination(s) technique(s)
quality and resolution of the resulting structure

Description of the Structure:
(~three pages)
gross anatomy
unique details

Analysis of the Structure:
(~one page)
characteristics (relative to norms of protein structure)
unique details

Relationship of Stucture to Function:
(~five pages)
relate to biological context
unanticipated results or contradictions
outstanding issues and future directions

Literature Cited, one of the standard formats from a leading journal
(four to ten citations)
citation in text (name et al., year)
include title in reference