Chem 406 Web Termpapers - Fall 2000
Web Termpaper Assignment
The Assignment:
You are assigned the task of writing a web-based term paper on the enzyme you drew from the hat. This year we will be continuing the theme of last years Web termpapers by looking at the enzymes involved in the citric acid cycle. If you forget 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 plug-in along with embedded JavaScripts buttons. This 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 in evaluating it. Using interactive three-dimensional molecular models produced using the Chime plug-in 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 relationship of your enzyme so that you can communicate this knowledge to others. Specific items that you should include in your term paper include:
- A classification and description of the reaction(s) catalyzed by your enzyme. The application ISIS/Draw can be used to draw out the chemical equation for the reaction catalyzed by your.
- 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 JavaScript buttons.
- 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 as a catalyst how they are able to speed up the reaction.
- A description of any control mechanisms that might exist using Chime and embedded scripts.
- Describe any known metabolic diseases that are linked to your enzyme.
- The ExPASy Enzyme database indicates these.
- The Online Medelian Inheritance of Man database (OMIM) contains a wealth of information on inherited diseases.
Literature Resources:
Your paper should contain 7 to 10 references. Resources for developing a set of references include:
- The NIH's National Center for Biotechnology Information (NCBI) provides free online access to PubMed 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, and the index BIOSIS.
- 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 a 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 this article.
- CAS-Online is the online version of Chemical Abstracts. If you would like to do a CAS-Online search of the literature, see me.
- 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.
- Journal Web Sites
- Other Related Sites
Web Page Development Resources:
Due Dates:
- 31. October, 2000 - Submit list of appropriate PDB files.
- Compare the structures for the pdb files for your enzyme to be sure that they are all for the same protein.
- Identify ligands present as
- Substrate/substrate analogue
- Product/product analogue
- Transition state analogue
- Alosteric effector
- Cofactor
- Solvent component
- Submit your list of ligands along with the list of PDB files.
- 6. November, 2000 - Submit a list of seven referenences for your termpaper. Briefly state the contribution that each makes to knowledge base for your protein.
- 13. November, 2000 - Submit a webpape containing a Chime figure of you enzyme along with three buttons that alter this structure.
- 1. December, 2000 - Web site due. I will have you submit these during our Friday lab meeting.
![[UWEC Web]](../../../../Chem406_F00%20Site/Chem406_F00/Media/smuwec.gif)
[Colleges & Dept's] [Chemistry Dept.] [Chem 406]
Warren Gallagher
Department of Chemistry
(715) 836-5388
wgallagh@uwec.edu
updated: Saturday, December 23, 2000