BIOL368/F11:Week 6

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** Don't forget to add the "BIOL368/F11" category to the end of your wiki page.
** Don't forget to add the "BIOL368/F11" category to the end of your wiki page.
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=== Electronic Lab Notebook ===
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=== Star Biochem DNA Glycosylase Exercise ===
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Complete your electronic notebook for this week's project on your individual journal page.  Your notebook entry should contain:
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Today we will prepare for the HIV Structure Project by learning how to use a protein structure viewing program called [http://web.mit.edu/star/biochem/ Star Biochem].
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* Follow the DNA Glycosylase Exercise found [http://web.mit.edu/star/media/uploads/biochem/exercises/version_2-2/guided_exercises/dna_glycosylase_exercise_ver7.pdf here] and record your answers on your Week 6 journal page.
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** For this week only, you just need to record the answers to the questions found in the PDF file, '''''and'''''
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** Capture a screenshot and post it to your page to document your answers for questions 4b, 5a, and 7 (including the ''optional'' part of question 7).
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There is different structure viewing program called Cn3D installed on the computers in Seaver 120This program is also freely available from NCBI at [http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dinstall.shtml this web site].
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* To view the DNA glycosylase enzyme in Cn3D, you need to download the structure file from the [http://www.ncbi.nlm.nih.gov/Structure/index.shtml NCBI Structure database].  To find this file, search for the ID for the structure <code>1ebm</code> and then follow the link to "View in Cn3D" to save the file to your computer's hard drive.
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* Open the structure in Cn3D and use the various menu options to render and color the structure.  Answer the following:
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** Is this structure a tertiary structure or quaternary structure?  Explain your reasoning.
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** How many domains does DNA glycosylase have?  Explain your reasoning.
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** 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?
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** 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.
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** 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 ==
== Shared Journal Assignment ==
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* Store your journal entry in the shared [[BIOL368/F11:Class Journal Week 5]] page.  If this page does not exist yet, go ahead and create it.
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* Store your journal entry in the shared [[BIOL368/F11: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 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.
* Link the shared journal page to this assignment page.
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=== Reflection ===
=== Reflection ===
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Answer these questions on the shared page:
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* Read the [http://www.sciencedaily.com/releases/2011/09/110918144955.htm following article from Science Daily News] about a recent advance (last month!) in solving a protein structure from a virus related to HIV.
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* On the shared reflection page, explain whether you would be interested in playing this game and why or why not? 
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* 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.)

Current revision

BIOL368: Bioinformatics Laboratory

Loyola Marymount University

Home       People        HIV Evolution       HIV Structure       DNA Microarrays       Lionshare       Help  

This journal entry is due on Wednesday, October 12 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.


Contents

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/F11" 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.

  • Follow the DNA Glycosylase Exercise found here and record your answers on your Week 6 journal page.
    • For this week only, you just need to record the answers to the questions found in the PDF file, and
    • Capture a screenshot and post it to your page to document your answers for questions 4b, 5a, and 7 (including the optional part of question 7).

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:
    • Is this structure a tertiary structure or quaternary structure? Explain your reasoning.
    • How many domains does DNA glycosylase have? Explain your reasoning.
    • 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?
    • 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.
    • 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/F11: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/F11" category to the end of the wiki page (if someone has not already done so).

Reflection

  • Read the following article from Science Daily News about a recent advance (last month!) in solving a protein structure from a virus related to HIV.
  • On the shared reflection page, 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.)
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