Biochemistry Term-Paper Requirement and Format

General Topics:

Choose an enzyme or protein to describe and discuss its biochemical and molecular properties, metabolic function, physiological roles, and potential applications in either (A) human/animal nutrition, health, or disease, or (B) plant production/agricultural applications, such as improvements of yield, resistance to drought or disease, human/animal nutrition, or industrial-use quality.

The Paper must include the following elements:
1. Show the complete DNA sequence of the gene that encodes the protein of your choice. Include the database (i.e. website) from which you obtain the sequence and reference. Use Genbank and NCBI Molecular Biology Resources to search gene/protein sequence (e.g. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed). Describe briefly, if applicable, the gene family, using in a specific organism as an example, such as how many such genes in mouse.
2. Mark the translation start codon and stop codon of the gene; show the deduced amino acid sequence encoded by the gene; describe what is known about posttranslational and/or cotranslational modifications of the protein. Cite the reference from which you get the information.
3. Describe the enzymatic reaction and metabolic function of the protein. Include the specific reaction catalyzed by the enzyme and the metabolic pathway/network that this enzyme is involved in.
4. Describe how the enzyme/protein is regulated, such as long-term, short-term regulation, cofactors, etc.
5. Describe what is known about the cellular and physiological processes that the protein/gene impacts and how it has the effect. Cite the reference from which you get the information.
6. Evaluate critically the gaps of the current knowledge about the regulation and function of the enzyme/protein; what more needs to be learned for a better understanding of the protein and its functions for potential applications.

7. Discuss the potential implication and applications of the above information in/to human nutrition, health, or disease, or in plant growth/agricultural application, such as better yield, more resistance to drought or disease, better nutritional value, or better industrial-use quality.
8. Propose at least one experiment/study that you may use to advance the understanding of the enzyme/protein or test the application of the knowledge for improvements as outlined in 7.

Paper format:
1. Length: The term paper should be approximately, but not exceed 10 (excluding references and large figures), double-spaced, typed pages, with the font size 12 and 1” margin at each side.

2. The format should include:
1) Project summary (<1 page). An abstract of what you’re going to write about.
2) Introduction: (1 page or less). Briefly describe the background and significance that lead to research about the enzyme/topics
3) Main body of the text: describe various aspects (see above) of the enzyme/protein

4) Approaches and methods (1-2 pages). For #8, briefly outline experimental approaches/methods by which you would want to use for your proposed study (NOTE: not the approach about how you find information about writing the paper).
5) References (1-2 pages). Including author’s name, title, journal, vol. page number. Use the format of Journal of Biological Chemistry but include article titles.

Ref examples:
REFERENCES
1. Pappan, K., Zheng, L., Krishnamoorthi, R., and Wang, X. (2004) Evidence for and characterization of Ca2+ binding to the catalytic region of Arabidopsis thaliana phospholipase Dβ. J. Biol. Chem. 279, 47833–47839.

2. Prins, T.W., Tudzynski, P., Von Tiedemann, A.V., Tudzynski, B., ten Have, A., Hansen, M.E., Tenberge, K., and van Kan, J.A.L. (2000) Molecular interactions in fungal pathogenesis. In Fungal Pathology (Kronstad, J.W., eds) pp. 33-64, Kluwer Academic Publishers, Doedrecht, Netherlands

3. protein sequence of xxxx http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=15232671