Your assignment is to write a review paper on one enzyme.

The first challenge is to choose an enzyme that will be the target of your study for the semester. Enzyme nomenclature has always been based on the reaction catalyzed by the enzyme, the activity, but classically there were few "rules" for systematically naming enzymes. The Enzyme Commission was formed in the mid-1950's as a committee of the International Union of Biochemistry to address this problem, and they published their report on the problem in 1961 (a longer history). The Enzyme Commission built an ordered hierarchy of enzymes, by activity, and introducted a numbering method for enzyme activities (the "E.C." in the number of each enzyme refers to the Enzyme Commission). Updates are made to the hierarchy at regular intervals (typical 2 or more times anually) as new enzymes are characterized and existing enteries are revised. The E.C. number scheme involves assigning four numbers to each enzyme. The first number is the most inclusive; the final number is the most specific. The following table illustrates the highest level of organization.

1.*	Oxidoreductases	Enzymes that catalyze redox reactions
2.*	Transferases	Enyzmes that catalyze group transfer reactions
3.*	Hydrolases	Enzymes that catalyze bond breakage by the addition of an equivalent of water
4.*	Lyases	Enzymes that catalyze bond breakage by mechanisms other than hydrolysis or redox mechanisms
5.*	Isomerases	Enzymes that catalyze the change in structure of one molecule
6.*	Ligases	Enzymes that catalyze bond formation using ATP as an energy source
7.*	Translocases	Enzymes that assist in moving another molecule, usually across a membrane

Further classifications are made by substrates, cofactors or products. These classifications ultimately group enzyme into a large hierarchy of categories based on the details of the reaction they catalyze. This hiearchy is published electronically in several forms (some of which you will be using). I have taken one of these sources and prepared it for your use. The enzyme hierarchy currently contains 8405 enzyme records. Of those records, 6896 enzymes are available for your selection. Begin your search for an enzyme by browsing an enzyme class above or searching for an enzyme by name below. Feel free to explore a variety of enzymes before selecting one.

With an enzyme, the next question is what, exactly, is a review paper? A review is a paper that does not report original research findings, but instead summarizes what is known about a topic, in this case your enzyme. A review paper may be very broad in that it discusses a little bit about a wide variety of aspects of the topic, or it may be very focused describing just one aspect of the topic in great detail. For your enzyme paper, the choice is up to you; you may write your review paper at any level. While you have some choice with regard to focus, there are some things which must be characteristic of your paper. They are:

• Your paper must have a title. The title "Enzyme Name" is not sufficient. The title should give a clear indication of the theme and content of your paper.
• Your paper must have an abstract. An abstract is short description of your paper that is included in an index database. The abstract summarizes your paper in about 250 words.
• Your paper needs to address the basic chemistry of the reaction catalyzed the enzyme. This would include identifying the substrate(s), product(s), reaction and cofactor(s), if applicable. These details are included in each enzyme record; the basics should be easy to find. The method you use to address this doesn't matter. You may do it all in prose, or it may be a figure or table in your paper.
• The written portion of your paper must be longer than six pages (common/typical text font at 12 points, double spaced, one inch margins on all four sides and text on one side of the page). The abstract counts toward the minimum length.
• Your paper must cite at least twelve sources. These may be either journal articles, electronic databases or analysis tools. Format your citations according to the style of Biochemistry. In short, in-text citations are numbered and appear superscripted at the end of a cited idea, outside the punctuation.1, 2 In the reference section, format journal articles as follows:
  
  1. Wegner, A. (1979) Equilibrium study of the actin-tropomyosin interaction, J. Mol. Biol. 131, 839-853.
  
  Format citations to electronic resources as follows:
  
  2. Author (if any). Resource/Tool name. URL (date accessed).
  
  The reference section should follow the text of your paper and appear before any tables or figures that you might use.

Since the requirements are few, you may be left wondering what to actually write about in your paper. Ultimately, that depends on your interests and your enzyme. The following may help you to start your research. It is not necessary that you do or consider each of these things, they are simply suggestions to help you with your research.

• One consideration to keep in mind is that one E.C. number may or may not represent one enzyme by name. For example, if you were to choose E.C. 1.1.1.1, alcohol dehydrogenase, that enzyme is found in a wide variety of organisms and is always alcohol dehydrogenase. Discussion of a sequence or kinetic parameters for alcohol dehydrogenase should mention a particular organism or species. Conversely, if you were to choose E.C. 4.6.1.24, ribonuclease T1, that enzyme is only found in the fungus Aspergillus oryzae used for fermenting rice wine (sake). The one caveat is that there are many other enzymes with the same (not identical, but very similar) structure and activity from other organisms. These are the many links to specific proteins with different names under the listing for RNase T1. Please be sure that you identify the situation for your enzyme choice and remain concious of that while you research and write.
• Enzymes with EC numbers in the form of *.*.*.n* are enzymes with preliminary EC numbers. Choosing one of these enzymes shouldn't cause too many problems; watch out for database queries by EC number, they might work better by enzyme name.
• In thinking about the activity of your enzyme, you may want to identify the range of substrates. Some enzymes only act on one substrate, others may act on a wide variety of related substrates. See the KEGG or Rhea database.
• You may wish to investigate the steady-state kinetic parameters for your enzyme. Remember that these numbers are measured under well defined conditions, which need to be reported as well. Also, don't forget the units; they are necessary for interpretation and may be reported differently between authors. These values are listed in the BRENDA database.
• Are there known inhibitors of your enzyme? How do they function? Check the BRENDA database.
• You may wish to ask about the biological role of your enzyme. Is it part of a metabolic pathway? See the BRENDA, KEGG or MetaCyc databases.
• From what organisms and tissues is your enzyme found? See BRENDA.
• Is your enzyme involved in any disease conditions? See BRENDA or PubMed.
• Is your enzyme used in any commerical, industrial or research applications? See BRENDA.
• Is your enzyme used as a model system to study something other than activity? See BRENDA.
• What is the sequence? See Protein @ NCBI or Swiss-Prot.
• Is the sequence similar to other proteins? Use BLAST.
• Is the structure of your enzyme known? See BRENDA, Swiss-Prot or EC→PDB.
• What methods have been used to study the enzyme? See PubMed.

Your paper is due (upload below) on or before 7 November, 2025.