BIOL368/F14:Week 6

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BIOL368: Bioinformatics Laboratory

Loyola Marymount University

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This journal entry is due on Wednesday, October 8 at midnight PDT (Tuesday night/Wednesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

Individual Journal Assignment

  • Store this journal entry as "username Week 6" (i.e., this is the text to place between the square brackets when you link to this page).
  • Create the following set of links. These links should all be in your personal template; then use the template on your journal entry.
    • Link to your journal entry from your user page.
    • Link back from your journal entry to your user page.
    • Link to this assignment from your journal entry.
    • Don't forget to add the "BIOL368/F14" category to the end of your wiki page.

Star Biochem DNA Glycosylase Exercise

Today we will prepare for the HIV Structure Project by learning how to use a protein structure viewing program called Star Biochem.

  1. Follow the DNA Glycosylase Exercise found here and record your answers on your Week 6 journal page.
    • For your electronic notebook, combine your methods and results. You can copy your method from the DNA Glycosylase Exercise wiki page, changing the wording and/or tense as appropriate to indicate that this is what you did. Be sure to record the answers to each of the questions found in the exercise, and
    • Capture a screenshot and post it to your electronic notebook page to document your answers for questions 4b, 5a, and 7 (including the optional part of question 7).
  2. There is different structure viewing program called Cn3D installed on the computers in Seaver 120. This program is also freely available from NCBI at this web site.
    • To view the DNA glycosylase enzyme in Cn3D, you need to download the structure file from the NCBI Structure database. To find this file, search for the ID for the structure 1ebm and then follow the link to "View in Cn3D" to save the file to your computer's hard drive.
    • Open the structure in Cn3D and use the various menu options to render and color the structure. Answer the following:
      1. Is this structure a tertiary structure or quaternary structure? Explain your reasoning.
      2. How many domains does DNA glycosylase have? Explain your reasoning.
      3. Can you view the same things in the structure using this program as you did when you were using Star Biochem? Why or why not?
      4. Capture at least one screenshot that is a similar a view to one of your previous screenshots as possible and post it to your page.
      5. Which program do you prefer to use to view this structure? Why? You will choose to use one (or both) of these programs for your HIV Structure Project.

Shared Journal Assignment

  • Store your journal entry in the shared BIOL368/F14:Class Journal Week 6 page. If this page does not exist yet, go ahead and create it.
  • Link to the shared journal entry from your user page; this should be part of your template.
  • Link the shared journal page to this assignment page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "BIOL368/F14" category to the end of the wiki page (if someone has not already done so).


  1. Did you learn anything that deepened your understanding of protein structure from this assignment? If so, what?
  2. What is not (yet) clear?
  3. Read the following article from Science Daily News about a relatively recent advance in solving a protein structure from a virus related to HIV.
    • Explain whether you would be interested in playing this game and why or why not?
    • Do you think that games like this could assist you in learning about protein structure? (I'm not asking you to play it, per se, although you can if you want; I just want you to comment based on reading the article.)