Lecture 18. Thursday, November 2. A simple model of protein folding.

# Lecture 18. Thursday, November 2. A simple model of protein folding.

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Restricted: For students enrolled in Chem130/MCB100A, UC Berkeley, Fall 2006 ONLY 1 John Kuriyan: University of California, Berkeley Chem C130/MCB 100A, Fall 2006, Lecture 18 The net result is that ATP is produced due to the high concentration of B outside. Now let us do some simple book keeping. Consider the interior of the cell as the system. Δ U = q + w (for the system) Here we are follwing the convention that if the system does work then the sign of w is negative.

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Restricted: For students enrolled in Chem130/MCB100A, UC Berkeley, Fall 2006 ONLY 2 Let us make the simplifying assumption that there is no dissipation of heat (q=0). Then: Δ U = w Clearly, the energy of the system has gone up, because ATP has been produced from ADP. Hence Δ U = ( + ) ve . Hence work done = (+)ve i.e., work done on the system by the surroundings. But this is not pressure-expansion work. This is “chemical work.” Now let us relate work (non-expansion) to free energy changes. First look at constant volume conditions. Return to one of the fundamental equations: dU = U S V , N dS + U V S , N dV + U N V , S dN U S = T , U V = P when dN=0: dU = TdS PdV dS = 1 T dU + P T dV when dV=0 (no expansion work) dS = dU T Condition for spontaneous change or equilibrium is: -- dS sys + dS surr 0 dS sys + dU surr T 0
Restricted: For students enrolled in Chem130/MCB100A, UC Berkeley, Fall 2006 ONLY 3 Previously, when we were considering the free energy in the absence of any kind of work being done by the system, we said that: dU surr = dU sys This is true when no expansion work, or any other kind of work, is done. Now let us imagine that the system does some amount of chemical or other non-expansion work. So dq sys = dU sys dw sys where dw sys is non-expansion work. (sign is negative if system does work). Heat transferred to surroundings must come from the system, dq sys = dq surr but dq surr = + dU surr (no expansion work) dq sys = dq surr = dU surr dS surr = dU surr T dS sys + dS surr = dS sys + dU surr T Applying the second law: Substituting dq sys = dU sys dw sys : dU sys dw sys = dU surr or dU surr = ( dU sys dw sys ) Also dS surr = dU surr T = dS sys dU sys dw sys T 0 dS sys dU sys dw sys T TdS sys dU sys dw sys dw sys dU sys TdS sys dw sys dA

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Restricted: For students enrolled in Chem130/MCB100A, UC Berkeley, Fall 2006 ONLY 4 For a spontaneous process, A is negative. If the system does work then dw is negative. Hence In this drawing, w sys is > A but w sys < Δ A Hence, the maximum value of the work done is given by the free energy change.
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## This note was uploaded on 01/12/2010 for the course MCB 100A taught by Professor Kuryian during the Fall '09 term at Berkeley.

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Lecture 18. Thursday, November 2. A simple model of protein folding.

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