17 - Monday, October 3, 2011, Lecture 17 Announcements: 1....

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Monday, October 3, 2011, Lecture 17 Announcements: 1. Reading and problem assignments for this week, as in LG plus reading in text 220- 2. PyMOL assignment # 6, Chymotrypsin. This is the one and only PyMOL assignment that will appear on the midterm exam. Note: no office hrs or reviews for this PyMOL until Sun 10/16! 3. Conflict for the midterm exam Th 10/20 7:30PM ? e-mail prof before Fall Break to describe your conflict. Meet briefly after class on Wed 10/5 to set the day and time. Day will probably be Sat 10/22 or Sun 10/23. Check your calendar now so that you can be ready on Wed to give your input re the make-up date. Friday's lecture: turnover number, and the concept of enzyme "efficiency" in lowering G o of TS use of pH to "inhibit" enzyme activity and find ionizable residues that might be involved in catalysis. competitive and non-competitive inhibition irreversible enzyme inhibition Today's lecture: p. 126 Some conventions for talking about enzyme mechanisms: Each drawn structure of substrate, intermediates, and products, has “some” stability, hence can be drawn as a low point on a G o vs progress of rxn diagram curve. Notice that these structures are each at the “bottom” of portion of the curve. The significance of being at these “local free energy minima” is that a small change in its structure moves the free energy higher, so the structure tends to come back to that same structure-- a measure of stability. (In contrast, a structure at a high point on the G o vs progress of rxn curve is unstable: a small change in its structure leads to a lower energy, so the structure moves in that direction, which means the structure changes-- the definition of unstable). Between the intermediates are higher free energy states, the transitions states between intermediates. The highest free energy state is the overall TS of the rxn. Catalysis happens between the intermediate states. A convention is to show the electron flows on a diagram in order to represent what is going to happen in the next step, leading to the next intermediate. Chymotrypsin mechanism, step-by-step In the discussion that follows, refer to LG pp. 126-136. Note p. 127, which shows the difficulty of drawing 3-dimensional binding on a 2-dimensional page: upper left, Ser 195 seems to be located in two places at once! However, this is merely the limitation of the simple drawings. Bottom right, see a better, pseudo-3D image of the same binding event.
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P. 128 shows all steps, and names the product of each step.
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This note was uploaded on 01/01/2012 for the course BIOMG 3310 taught by Professor Feigenson during the Fall '11 term at Cornell University (Engineering School).

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17 - Monday, October 3, 2011, Lecture 17 Announcements: 1....

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