BNFO 300 
Molecular Biology Through Discovery
Path to class (Thursday, Sep 12) - Hemoglobin and Perutz et al (1965) (Part 2)
(please press SUBMIT button when finished)
Fall 2019  


My advice on the matters for the day (as listed in the calendar):

Protein
  • Hemoglobin Tutorial: If you weren't able to go through this tutorial, go through it now. Section III of the companion should be of help. Parts 2, 3, 4 and beginninf of 5 are the most important parts of the tutorial. Shouldn't be a big time expenditure.
     
  • Perutz et al (1965): Main topic for today (Sections IV through VI). Make sure you're looking at a sufficiently recent version of the companion (9 Sep or later) You'll need to download and run Chimera (a protein visualization program) to do the experiments with protein structure.
     
  • Problem Set 3: You can look over Problems 1 and 2, if you like. We'll work on them in class. If you do look them over, make sure the version of the problem set (upper right corner on first page) is 11 Sep 2019 or later.


I. Basic Information

A. Your name 
II. Old business (no need to repeat anything you've said in a previous questionnaire)

A. Perutz et al (1965) (Sections I and II)

  • Anything further you'd like to discuss regarding the overall questions addressed by the article Perutz et al (1965) and its companion)?
  • Do you understand the connection between Fig. 1 and Table 2?
    

B. Hemoglobin tutorial

  • Anything further you'd like to discuss regarding the tutorial on Hemoglobin Structure? (see also the companion, Section III)
  • Do you understand the basis for alpha helix formation?
  • How hydrophobicity contributes to globin structure?
    

C. Problem Set 2.4 (as a community)

  • Do you have a decent idea how to determine the order of amino acids in a fragment?
  • Do you have a decent idea how to combine the assertions from the tables to get overlaps? (Have you looked at the advice on how to test derived assertions?)
  • Were you finally able to get to the spreadsheet?
  • Any thoughts on your efforts to recreate the work of Sanger & Tuppy?
    
III. Perutz et al (1965) (Sections IV through VI)
  1. Any problems in downloading and running Chimera?

     
  2. How far have you gotten in a productive reading of the article (i.e. doing as you read)?
    You can answer by referring to the last section you read or the last study question you addressed (e.g. SQ12) in the companion.

     
  3. Consider how comfortable you are with the following topics (as defined by the companion to Perutz et al):
    • Were you able to find and bring the whale myoglobin sequence into Chimera?
    • The significance of invariant amino acids in the structure of globin?
    • The significance of prolines in the structure of globin?
    • Particular study questions?
    • Anything else?

    (As always, relate what specific problems you encountered and what you did to try to resolve them)

IV. Miscellaneous
Any other comments, questions, suggestions, or concerns you may have?

Thanks!

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