BNFO 301 
Introduction to Bioinformatics
Questionnaire on Gene Regulation and Bacteriophage and Madsen tour
(please press SUBMIT button when finished)
(and please don't use quotation marks in your answers. They break the questionnaire program!)
Spring 2013 

I. Basic Information

A. Your name 
II. Lifestyles of bacteriophage
  1. How far did you get in the tour entitled Gene Regulation and Bacteriophage?  
  2. Do you understand what lysogeny is and why it might serve the bacteriophage?
  3. Do you understand the need for a general repressor in lysogenic phage?
  4. Anything other phage-related issues?
     

Do you have any favorite study questions (SQ1-SQ5) you think need discussion?  

III. Gene regulation
  1. Do you understand the different levels of gene regulation?
  2. Do you understand the relationship between transcriptional proteins (like RNA polymerase and repressors) and specific DNA sequences?
  3. Can you recognize sequences to which lambda repressor binds?
  4. Do you understand the power of regulatory feedback loops?
  5. Do you understand how the interplay between the lambda repressor and Cro protein might achieve a stable decision of lysogeny vs lysis?
  6. Anything other regulation-related issues?
     

Do you have any favorite study questions (SQ6-SQ21) you think need discussion?  

IV. Madsen et al (1999)
  1. How far did you get in the tour entitled Gene Regulation and Bacteriophage?  
  2. Did you have any trouble obtaining the article?
  3. Do you have an idea how to assess whether an article might be useful in answering your specific question?
  4. Do you feel comfortable in interpretting Figure 1?
  5. Do you understand the significance of beta-galactosidase activity measurements?
  6. Do you feel comfortable in interpretting Figure 3?
  7. Do you understand the principle behind primer extension experiments?
  8. Were you able to find the sequence between ORF4 and ORF5 in the genome sequence of TP901-1?
  9. Are you able to argue persuasively based on experimental data and your own observations whether ORF4 is or is not a general repressor of lytic function?
  10. Anything other issues related to the article?
     

Do you have any favorite study questions you think need discussion?  

V. Miscellaneous
Any question from the exam you'd like to discuss? If so, what about it?
     
Any miscellaneous comments, questions, suggestions, concerns?
     

Thanks!

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