Chem 406 Web Termpapers - Fall 1999
Web Termpaper Assignment
The Assignment:
You are hereby assigned the task of writing a web-based term paper on the enzyme that you drew from the hat. The enzymes are all involved in either glycolysis, gluconeogenesis or lactic acid fermentation. If you have forgotten which enzyme you drew, click here. The term paper should be a minireview that deals with the structure-function relationships of the enzyme. The primary reasoning behind making this term paper a web-based one is that it provides you with the ability to illustrate your term paper with interactive three-dimensional molecular models using the Chime plugin along embedded scripts. Also, it will allow us to publish your efforts for world-wide consumption, instead of having them collect dust in the dark reaches of my office. Keep in mind, the content of your paper will be the primary factor used to evaluate it. Using the interactive three-dimensional molecular models produced using the Chime plugin 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 your enzyme, 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) catalyzed by your enzyme. ISIS/Draw can be used to draw out the reaction.
- A description of the bioenergetics for the reaction: is it reversible or irreversible under physiological conditions.
- A description of the tertiary/quaternary structure of you enzyme using Chime and embedded scripts.
- Describe the fold of the polypeptide.
- Describe any cofactors that the enzyme requires
- A description of the active site and its catalytic strategy using Chime and embedded scripts.
- Desribe which amino acid sidechains and cofactors are involved and explain how they are able to speed up the reaction.
- A description of any control mechanisms that might exist using Chime and embedded scripts.
Literature Resources:
Your paper should contain 7 to 10 references. Resources for developing a set of references include:
- 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. 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 in McIntyre library.
- The NIH's National Center for Biotechnology Information provides free online access to Medline, which you can use to do a key word searchs of the scientific literature.
- 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 other articles that refer to the article the originally reported 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.
- Journal Web Sites
- Other Related Sites
Web Page Development Resources:
Due Dates:
- Please submit a preliminary list of your references by November 18.
- Submit a draft version of an interactive Chime for your enzyme by November 19.
- Submit your completed web term paper by December 3. A drop-box will be set up on the BMB Server for this purpose.
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[Webpaper_F99] [Chem 406]
Warren Gallagher
Department of Chemistry
(715) 836-5388
wgallagh@uwec.edu
updated: Tuesday, December 19, 2000