BIOL368/F16:Week 9

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BIOL368-01: Bioinformatics Laboratory

Loyola Marymount University

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This journal entry is due on Tuesday, November 1 at midnight PDT (Monday night/Tuesday 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 9" (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/F16" category to the end of your wiki page.

Homework Partners

For your HIV Structure Project, you will be back to working in groups of two. You have the option of working with your partner from the HIV Evolution Project or changing partners. We will take a few moments in class to assemble partners before beginning work this week. Please sit next to your partner in class.

  • Zach, Jordan
  • Colin, Isai
  • Anu, Matt A.
  • Matt O., Will
  • Mia, Avery
  • Shivum, Courtney

Electronic Notebook

Your notebook entry should contain the answers to the questions defining your HIV Structure Research Project and documentation of what you did for the in-class activity. Note that an electronic notebook entry should include the following elements:

  • The purpose: what was the purpose of your investigations?
  • Record your methods and results of what you did. You should document as you work, taking your notes on the wiki as much as possible. Post data, figures, and screenshots. You can post files that are in progress; remember, you can upload a new version of the file and the wiki will automatically link to the new version (while keeping the old).
  • References to data and files should be made within the methods/results section of your notebook.
  • In addition to these inline links, create a Data and Files section of your notebook to make a list of the files generated in this exercise.
    • Remember to back up your files in at least two ways.
  • A scientific conclusion: what was your main finding for today's work?

Although you will have assigned partner, you will need to fill out your own individual journal page with your own work.

Defining Your HIV Structure Research Project

For this project, you can choose to work with the same sequences you used for the HIV Evolution Project, or you may choose different sequences. You will reframe your question from the HIV Evolution Project to make it a structure→function question. Instead of looking at the evolution of variation of the viral DNA sequences, you will look at how variations in the viral amino acid sequences affect the structure and, therefore, function of the virus.

In this week's journal assignment, you will define your research project by answering the following:

  1. What is your question?
  2. Make a prediction about the answer to your question before you begin your analysis.
  3. Which subjects, visits, and clones will you use to answer your question?
    • You should choose a combination of subjects, visits, and clones that will add up to approximately 50 sequences. You will need about that many sequences to answer a reasonably complex question. However, you cannot use more because the multiple sequence alignment tool cannot handle more than that many sequences.
    • Justify why you chose the subjects, visits, and clones you did.

HIV Structure In-class Activity

  1. Convert one of your DNA sequences into protein sequences using either the NCBI Open Reading Frame Finder or the ExPASY Translate tool.
    • How do you know which of the six frames is the correct reading frame (without looking up the answer)?
    • Once you answered the question above, you can check your answer and obtain the rest of the protein sequences from the BEDROCK HIV Problem Space.
  2. Find out what is already known about the HIV gp120 envelope protein in the UniProt Knowledgebase (UniProt KB). UniProt KB has two parts to it, Swis-Prot, which contains entries for proteins that have been manually reviewed, and TrEMBL (which stands for "Translated EMBL"), which are automated translations of all DNA sequences in the EMBL/GenBank/DDBJ databases.
    • If you search on the keywords "HIV" and "gp120", in the main UniProt search field, how many results do you get?
    • Use the entry with accession number "P04578" which corresponds to the reference entry for HIV gp120.
    • What types of information are provided about this protein in this database entry?
  3. We are going to use the PredictProtein server to analyze just the V3 region from Markham et al. (1998).
    • Paste one of the amino acid sequences from Markham et al. (1998) into the input field and submit.
    • Explore the types of information provided. How does this information relate to what is stored in the UniProt database?
  4. Download the structure file for the paper we read in journal club from the NCBI Structure Database.
  5. These files can be opened with the Cn3D software site that is installed on the computers in the lab (this software is free, so you can download it and use it at home, too.) Alternately, you may choose to use the Star Biochem program to do this portion of your work. Answer the following:
    • Find the N-terminus and C-terminus of each polypeptide tertiary structure.
    • Locate all the secondary structure elements. Do these match the predictions made by the PredictProtein server?
    • Locate the V3 region and figure out the location of the Markham et al. (1998) sequences in the structure.

Academic Honesty

As discussed in class, each weekly individual journal assignment needs to conclude with an Acknowledgments and References section.


In this section, you need to acknowledge anyone who assisted you with your assignment, either in person, electronically, or even anonymously without their knowledge (see below).

  1. You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. An appropriate statement could be (but is not limited to) the following:
    • I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
      • Sign this statement with your wiki signature.
  2. Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
  3. If you copied wiki syntax or a particular style from another wiki page, acknowledge that here. Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style. If you need to reference content, use your References section (see below).
  4. You must also include this statement unless otherwise noted: "While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source."


  • In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising. This includes, but is not limited to:
    • data
    • facts
    • images
    • documents, including the scientific literature
  • The references in this section should be accompanied by in text citations on your page that refer to these references.
  • The references should be formatted according to the APA guidelines.
  • For more detailed guidelines, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.

Shared Journal Assignment

  • Store your journal entry in the shared BIOL368/F16:Class Journal Week 9 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/F16" 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.)