Integrated Bioinformatics(Fall 2004)
Questionnaire on notes:Regulatory Proteins
(please press SUBMIT buttonwhen finished)

I. Basic Information andMiscellaneous

A. Your name 
II. Regulatory protein andtranscription of lac
A. How comfortableare you with the role of regulatory protein such as CRP in controllingthe onset of transcription?

B. Do you understand howmutation of specific nucleotides in the sequence upstream from a gene mightaffect the expression of that gene? 

C. How comfortable are youwith how expression of lacZ is regulated?

D. Do you understand whata palindromic DNA sequence is and why they might be preferred as the sitesrecognized by  DNA-binding protein? 

E. Please choose up to threestudy questions that you would most like discussed in class:

SQ1 SQ2 SQ3 SQ4 SQ5 SQ6 SQ7 SQ8
 
Comments for Section II:
III. Regulation of cyanobacterialgenes by environmental nitrogen
A. Do you understandthe basis of this scenario, i.e. how regulation of hetQ may explainhow cyanobacteria differentiate heterocysts in response to nitrogen starvation? 
 
Comments for Section III:
IV. Simulation
A. Can you listat least one reason why DiceRoll might not accurately predict the resultsof rolling a real set of dice? 

B. Can you list several reasonswhy simulating the genome of an organism might not work for some purpose?(Why did I add "for some purpose"?) 

D. Please choose up to threestudy questions that you would most like discussed in class:

SQ9 SQ10
 
Comments for Section IV:
V. Old Business and Miscellaneous
A. How comfortabledo you feel about the process of modifying BlastParser to work onyour data? 

B. How far have you gottenin reaching a satisfying conclusion to the first scenario? Have you modifiedBlastParser to read your file? Does it report only E.coli O157protein that don't match E. coli K12 protein? Have you gonethrough the final list and looked for interesting proteins (those thatmight help us stop this deadly scourge)?

Put here answers to thesequestions and any other concerns you may have.

 

Thanks!

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