Assignment:

You are assigned the task of writing a web-based term termpaper that focusses on a description of transcription in eukaryotes. Your termpaper should include the following components:

• An overview of the transcription process
• A comparison of prokaryotic and eukaryotic transcription which is illustrated with 3-dimensional, interactive, molecular models.
• A detailed description of eukaryotic transcription which is illustrated with 3-dimensional, interactive, molecular models.
• A description of the effects of the deadly amanitin toxin from the poisonous Amanita phalloides mushroom which is illustrated with 3-dimensional, interactive, molecular models.
• A discussion of the contributions that Kornberg's work is expected to make to the area of stem-cell research.
• A discussion of the contributions that Kornberg's work is expected to make to another area biology of your choosing.

Your termpaper should be a scholarly review of the original literature. You may use sources such Chapter 29 from Stryer's Biochemistry to help you with accessing and organizing your sources, but the narative of your termpaper should cite the original literature and do this within the body of the narative. You should use hyperlinks to link your citations to the reference section of your termpaper. The references listed in the reference section of your termpaper should be linked to the PubMed entry for each reference. Your reference section should also list any PDB files that you used to create your 3-dimensional models. These references should be linked to their corresponding entry in the Protein Data Bank.

Resources:

• Protein Data Bank
• Narated Tutorial on how to use the Protein Databank
• Chapter 29 - RNA Synthesis and Processing, from Stryer's Biochemistry, 6^th Ed.
• The NIH's National Center for Biotechnology Information (NCBI) provides free online access to PubMed which you can use to do a key word search of the scientific literature.
• Science Citation Index: This extremely useful research tool 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 for other articles that refer to this article.
• Journal Web Sites
  • Biochemistry (full text available online and at McIntyre)
  • Science Magazine (full text available online and at McIntyre)
  • Cell (full text available online and at McIntyre)
  • Nature (full text available online and at McIntyre)
  • Nature, Structural and Molecular Biology (full text available online)
  • Biophysical Journal (full text available online for articles published over a year ago)
  • Journal of Biological Chemistry (McIntyre and full text available online for articles published over a year ago )
  • Journal of Molecular Biology (abstracts online and full text available at McIntyre)
  • PNAS (Proceedings of the National Academy of Science, USA) (fultext available online or in McIntyre)
  • Proteins: Structure, Function, and Genetics (abstracts online, order articles through Interlibrary Loan )
  • Protein Science (full text available online)
  • Structure
  • Stryer's Biochemistry, 5^th Ed.
• For articles that you cannot obtain online or in McIntyre Library, there is always Interlibrary Loan .

Due Date:

Wednesday, 13. December, 2006 - Submit the your complete site.