Integrated Bioinformatics (Fall 2012)
Questionnaire on notes: Modeling - Tour of Eisenthal & Cornish-Bowdin and program
(please press SUBMIT button when finished)

I. Basic Information

A. Your name 
II. Retrospective/prospective on glycolysis and rate equations
How do you feel about Friday's whirlwind tour of glycolysis and simple reaction kinetics?
 
A.  Do you feel comfortable regarding the logic of glycolysis and the problems it confronts and solves?
 
B.  Can you recognize the elements of glycolysis (as represented by the pathway displayed in the presentation) whose sources or fates remain not fully described by the pathway?
 
C.  Given the chemical equation of an uncatalyzed reaction, can you write the rate equation?
 
D.  Do you feel comfortable simulating a simple reaction, such as the spontaneous degradation of ADP-As?
 
E.  Do you feel you understand critical differences between simulations based on differential equations (such as ADP-As.pl) and analytical equations (such as the extra column you added in Excel)?
 
F.  Do you understand how knowing the rate equation for a metabolite (never mind how complicated it may be) enables you to calculate (very simply) the concentration for that metabolite over time?
 
G.  Anything else you want to mention?
 
Responses to issues A-G:

We barely touched enzyme kinetics (and in recognition of this, I made up something extra that I've posted online), but from what you've seen thus far:
 
H.  Do you understand what Vmax and Km mean?
 
I.  Do you understand the basis for determining Vmax and Km?
 
J.  Do you understand how the Michaelis-Menton equation is derived from first principles?
 
K.  Anything else you want to mention?
 
Responses to issues H-K:

III. Tour of Eisenthal & Cornish-Bowdin
A.  Do you see how to interpret Table I in light of Figure 1?
 
B.  Do you see how to combine the information in Table I with Equation 2?
 
C.  Anything else?
 
Responses to questions in Section III:


Please choose up to four study questions from the notes that you would most like discussed in class:
SQ1  SQ2  SQ3  SQ4  SQ5  SQ6  SQ7  SQ8  SQ9  SQ10  SQ11  SQ12 
IV. Glycolysis, the program
A.  Can you equate elements of the process of modeling with segments of the program Glycolysis.pl?
 
B.  Have you run Glycolysis.pl and plotted the results in Excel?
 
C.  How far along are you in changing Glycolysis.pl to acknowledge the high amount of blood glucose?
 
D.  Do you understand the output of Glycolysis.pl?
 
Responses to questions in Section IV:


Please choose up to four study questions from the notes that you would most like discussed in class:
SQ13  SQ14  SQ15  SQ16  SQ17  SQ18  SQ19  SQ20  SQ21  SQ22 
V. Miscellaneous

A. I notice that Paul raised the question of whether we should meet on Wednesday, November 21. I'll be here, willing and able.
    What are your thoughts on the matter?

B.Any miscellaneous comments, questions, suggestions, concerns?

Thanks!

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