429-2009-Q6key

429-2009-Q6key - A as a dimer ( n = 2) and to the promoter...

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580.429 SBE3 2009 Quiz 6 Name: Section meeting time: Section meeting location: Gene regulation. Suppose that a TF named X binds as an n -copy multimer. We model the binding as all-at-once, D + nX ( k on ) n ( k off ) n ! " !! # ! !! DX n with the constraint that the total DNA is constant, D + DX n = D T . Assume that the concentration of TF is sufficiently large that the amount of free TF is effectively unchanged by DNA binding, X ! D T . Note that the kinetic rate constants depend on the number of copies bound. 1. (3 pts) For general n , provide an equation for the fraction of bound DNA at equilibrium, DX n / D T , as a function of n , X , k on , k off . k on n X n ( D T ! D * ) = k off n D * with D * = DX n ( k off n + k on n X n ) D * = k on n X n D T DX n / D T = k on n X n / ( k off n + k on n X n ) or ( k on X / k off ) n / [1 + ( k on X / k off ) n ] 2. (1 pt) Your expression for DX n / D T should be a function of a normalized concentration ( X / K ) , where K depends only on k on and k off . What is K in terms of these parameters? K = k off / k on 3. (4 pts total) Now suppose that X binds to the promoter of gene
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Unformatted text preview: A as a dimer ( n = 2) and to the promoter of gene B as a tetramer ( n = 4). On the axes below, sketch the fraction of bound promoter for each gene (1 pt each). Provide labels for the three tick-marks on the y-axis (2 pts). X 0 K /2 K 2 K 3 K 4 K fraction bound 4. (2 pts) Facebook / Social network. For each possible network project, let me know whether you would (A) opt-in with names; (B) opt-in with anonymous codes; (C) opt-out. 2 pts for all (even blank, assume C-C-C) (i) People in SB3 you phone/text/email at least once/week: A B C (ii) List of Facebook friends in SB3 whose walls you actually read at least once/week: A B C (ii) People in SB3 you eat with at least once/week: A B C 2 pts for axes labels close to 0, 0.5, 1. 1 pt for sigmoidal curves that go through (K,0.5). 1 pt for B steeper than A ....
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This note was uploaded on 03/30/2010 for the course SBE 580.429 taught by Professor Joelbader during the Fall '09 term at Johns Hopkins.

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