Enzyme Project for Term Paper

Basic Biochemistry CHEM 351

Fall 2020

Step-3 Report: Introductory Information Report (15 points)

Deadline: Sept 28^th 2020

Each member in your team will explore a different database as instructed below to write the introductory report.

• Team Member-1 (provide your name in the report when you submit your step-3 report for grading; and mention that you explored the Prosite database):
  • Go to the Prosite website (https://prosite.expasy.org/index.html) which is a database for protein/enzyme families.
  • On this site, in the search box, type the name of the enzyme your team chose and click on search. Make sure you have typed the spelling correctly.
  • A new page will come up and when you scroll down, it will list the results of your search.
  • Choose the most suitable one that matches for your enzyme (see the hints I might have given in the enzyme list for some enzymes) and click on it.
  • Review the information provided and write a paragraph In Your Own words describing the following in full sentences like an essay, not question-answer format  (do NOT simply copy and paste for statements form the database! Write your own statements).
    • Name of your enzyme
    • C. Number for the enzyme (share this E.C.Number with your other 2 teammates immediately! They need to search other databases using this same E.C.Number.  They are depending on you to do their part of the work!)
    • In general, what is its function or in what pathways is it involved, and how is it useful in your body (= in humans); or why is this enzyme important, or what roles does it play in the organisms
    • Is the enzyme present only in humans, or present in other organisms also. If so which ones?
    • Is there any “homology” (= similarities) described for different organisms?
    • In which organs/tissues, and in which parts within the cells of these tissues
    • Scroll down on the website to see the list of references. Copy and list these in the current report in the APA style. (Authors, title of the article, journal, volume, year, pages)
    • Also save them on your computer in a folder. You might need these later, to access the full articles, for further steps in the project.
    • For the specific information you are writing in this step-3 report, as mentioned above, Make sure you cite the authors and year, in parenthesis, within the body of the paragraph, when you write the above things,  as you need to give credits to the database sites and the reference articles the database has listed.
    • From the above list of publication references (of the actual scientific articles), choose at least one reference that has published of the introductory information about the enzyme. There will be a “Pubmed ID” active link for each; if you click on it, it will take you to the Pubmed database, where you will see the abstract of this reference article.  Review this abstract and write in your own words, what information you found about this enzyme. (do not simply copy and paste!)
    • In the Pubmed, when you were reviewing the above abstract, on the right side you might find a list of links to other useful articles related to this enzyme. Note them down on your computer, as you might need them again for next steps of the project. And list these references in your current report.
    • Next, check with your other two team members what they found about this enzyme for the aspects you wrote. Write a combined report, all three of you together, combining all the information from the three team members.
    • There will be questions based on the team report, in one of the in-class quizzes
    • Submit the combined report as per the deadline, in the Blackboard Discussions board, under Step-2 Enzyme Project Submissions, to your Professor for grading.  (one report for the whole team, by combining the information form all 3 team members; not separate reports)

• Team-member-2 (Provide your name in the report and mention that you explored the Brenda website):

• First check with your team member who worked on the Prosite website, to see which EC number they had found for the enzyme. Use the same EC number for your work.
• Now Go to Brenda website (http://www.brenda-enzymes.org/). This is also a database for proteins/enzymes.
• On the home page of this website, in the search box, type the name of the enzyme (not the EC number) your team chose (make sure you have spelled it correctly). And click on “search”.
• In the new page that opens up, you will see a Table which lists the number of hits for the enzyme name, and also for the ligand.
• Click on the “hits” link; it will bring up a big list of all the different EC numbers for this enzyme in one column, all the different recommended names and the synonyms.
• First choose the EC number, same as what your team mate had foundwhen she searched the Prosite database and note down recommended name for the enzyme.
• Also, note down at least 3 synonyms (= alternate names) listed.
• Next, click on the EC Number link and in the new page that opens up, it will give a list of organisms to select from. In this pull down menu, choose HomeSapiens (for humans) and click on “submit”.   Wait for a few seconds until the website loads up all the required information.  Note down all the following information:
  • EC number
  • The reaction type it catalyzes
  • Function of the enzyme or the metabolic pathway it is involved?
  • Systematic name of the enzyme
  • Reactants (substrates) it catalyzes, which products are formed. If more substrates /reactions are listed, choose at least first 3 from the list.

(for this Step-3 of the project, no other information required.  You will be visiting this database site again, to get further information later, for step-4 of the project).

• Scroll down further to see the types of organs or tissues or cells the enzyme is found in the humans
• In which part within the cells?
• First when you started this work, you had chosen “home sapiens” in the list of organisms. Now, just go back to the home page of the database,  type your enzyme name. In the new page that opens up, on the left side menu, click on “organism related information” and then,  choose “organism”;  the website will now list all the different organisms in which this enzyme can be found.  Note down a few (based on which ones have literature references associated).

For allof the information you explored in the database, make sure you note down any literature reference number links shown next to the information, in each case (and save them on your computer also.  You will need it later for getting the full articles later on (from Pubmed database) for next part of the project.

• Next, check with your other two team members what they found about this enzyme for the aspects you wrote. Write a combined report, all three of you together, combining all the information from the three team members.
• There will be questions based on the team report, in one of the in-class quizzes
• Submit the combined report as per the deadline, in the Blackboard Discussions board, under Step-2 Enzyme Project Submissions, to your Professor for grading.  (one report for the whole team, by combining the information form all 3 team members; not separate reports)

• Team-member-3: (Mention your name in the report; and mention that you explored the IUBMB database).

• Get the EC number your two teammates had found in common, for the enzyme your team chose.
• Go to the IUBMB website (http://www.sbcs.qmul.ac.uk/iubmb/)
• You will see a Table, where the EC numbers for the Main Class of the enzyme is given. Such as EC1,  EC2,     For your team’s enzyme, look up the first number related to main class information and note that down. Just For example, if the EC number is 2.7.1.11,  then the first number 2 represents the Main Class
• Next, click on that Main Class link. In the new page that opens up, there will be a Table showing the Subclass in bold.   For example, if your enzyme EC number is 2.7.1.11,  then the second number 7  represents the SubClass.  So, look up which subclass your enzyme belongs to.  Note this down.
• Next, under that, look for the 3^rd number, which will be the SubSubClass. Note this down.
• When you have completed the 3^rd number information, you click on the link in the column where it says “separate”.
• A new list opens up, where you can scroll down to find the EC number’s last part.  For example if the EC number was 2.7.1.11,   find the one that has 11 as the last number, which indicates the specific individual enzyme (should be similar to the name of the enzyme of your team).  Note this down.
• Next, click on that link. You will see several details.  Note them down.  For example.
  • Is the EC number shown correctly?
  • The accepted name for this enzyme?
  • The reaction this enzyme catalyzes (reaction equation showing the names of reactants and products).
  • Click on the link to the reaction diagram, copy and paste it into your report. (to do this easily, in your Word document, go to “insert” and choose “textbox” and click on “simple text box”. Then, copy and paste the reaction diagram from the database, to this textbox.  This will enable you to move the textbox wherever you want in the report, and also to resize it).
  • What are the other different names given for the enzyme?
  • What is the systematic name?
  • Are there any other comments or information shown? Note that down.
  • Which are the other databases listed there, you could use in future for looking up other information or references for this enzyme?
  • Are there any references provided on the site for the scientific articles. If so,  note them down.
  • Click on one of those databases listed (DO NOT choose Brenda or Prosite or Expasy or GTD, because these have already been used by your other two team mates). You may choose KEGG, Metacyc, PDB).
  • Any other information from this new database, about your enzyme, note that down, along with new references given.
• Make sure to show your report to your team mates, so you all know what information you all three have found together from all the three databases from the team.
• Submit the combined report to your instructor for grading. There will also be questions on this report, in one of the in-class quizzes