Chem 406: Biophysical Chemistry, Fall 1998
Term Paper Assignment

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The Assignment:

You are hereby assigned the task of writing a web-based term paper. The term paper will be a minireview that deals with the structure-function relationships of an enzyme. The primary reasoning behind making this term paper a web-based one is the ability to illustrate your term paper with interactive three-dimensional molecular models using the Chime plugin and embedded scripts. Keep in mind that content will be the primary factor used when evaluating your term paper, . Using the interactive three-dimensional molecular models that are available on the web is currently one of the best ways of communicating information about macromolecular structures. During the construction of your web term paper, you will inevitably be forced to learn something about the structure-function aspects of you chosen system, in order to communicate this knowledge to others. Specific items that you should include in your term paper include:

• A description of the reaction(s) that is catalyzed by your enzyme.
• A description of the biological source and cellular location of your enzyme.
• A description of the biological significance of the enzyme and the reaction it catalyzes.
• A description of the tertiary/quaternary structure of you enzyme using Chime and embedded scripts.
• A description of the active site and its catalytic strategy using Chime and embedded scripts.
• A description of any control mechanisms that might exist using Chime and embedded scripts.

Literature Resources:

• Macromolecular Structures: This is an index that comes out once a year that summarizes the structures of biological macromolecules that were reported in the literature during the previous year. This is an excellent resource for choosing an enzyme. Each entry gives a brief description of the biological significance of the protein along with a description of its structure. It also provides you with good references for a Science Citation Index search. Copies of the 1991, 1992, 1993, 1995 and 1996 volumes can be found P426.
• Structure: This journal reports on the structure of biological macromolecules. Each article also provides a section that discusses the biological significance of the molecule being discussed. Most of the issues contain minireview articles that can be used as an example of what a minireview contains. Unfortunately, McIntyre library does not subscribe to this journal. Some old copies of the journal can be found in P426. Structure has a website where you can see the abstracts of articles at no cost.
• Entrez: The NIH's National Center for Biotechnology Information provides free online access to Medline, which you can use to do a key word search of scientific journals.
• The Science & Engineering subject guide listing at the McIntyre library web page provides links to the full text of The American Chemical Society Journals, which includes Biochemistry, the index BIOSIS and the Wilson's General Science Abstracts.
• CAS-Online is the online version of Chemical Abstracts. If you would like to do a CAS-Online search of the literature, see me.
• Science Citation Index: This extremely useful research tool that allows you to find scientific articles which have cited a particular article of interest. For example, the PDB file for a protein provides the reference for the article in which the structure was first reported in the literature. You can use that citation in a Science Citation Index search to find articles that refer to the structure of that protein. McIntyre library has the hard copy volumes of Science Citation Index up through 1992, when the subscription was canceled. To do an online search of Science Citation Index from 1992 to present see the reference librarian. I strongly urge you to make use of this resource.

Web Page Development Resources:

• The 1996 and 1997 Chem406 Web term papers.
• An example of using Chime with embedded scripts to describe the structure-function relationships of oxymyoglobin, which you may use as a template.
• Some elaborate examples produced by Charles Grisham at the University of Virginia of using Chime with embedded scripts to describe structure-function relationships in biological macromolecules.
• The Rasmol/Chime site at the University of Massachusetts.

Due Dates:

• After selecting an enzyme, check with me. I want to be sure that you have chosen a doable system and that none of your classmates has chosent the same system.
• Your final paper should contain seven to ten references. Please submit a list of your references by November 6.
• Submit a draft version of an interactive Chime for your chosen enzyme by November 23.
• Submit your completed web term paper by December 11.

Warren Gallagher
Department of Chemistry
(715) 836-5388
wgallagh@uwec.edu

updated: Friday, December 18, 1998