14 - Monday, September 27, 2010 Lecture 14 Reading &...

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Monday, September 27, 2010 Lecture 14 PyMOL: assignment #5, The Protein Data Bank Friday's lecture: Intro to enzymes: EC nomenclature; enzyme specificity Usefulness of Standard State G o . Suppose we specify that all product and reactant concentrations are fixed at 1M. This is the familiar "Standard State". Here is a useful way to think of this Standard State: divide the 1M of each molecule by Avogadro's Number. Now we have exactly one molecule of each. And we notice that there is no consideration now to probabiity (entropy) because that T S term becomes zero. We can now place product and reactant molecules side-by-side, look at each, and write down which is more stable in terms of its atoms and their bonding ( H). This side-by- side comparison of the relative stability of product and reactant molecules is exactly what we mean by G o . Today's lecture P. 104 How do catalysts work? Catalysts speed up a reaction by lowering G o TS in only two possible ways : 1. Bind the transition state and thereby make it more stable (more favorable; lower its free energy; make it more probable). 2. Change the reaction pathway to a new pathway with different intermediates, and different TS having a lower G o TS . Let's consider a very simple example of a catalyst binding a TS: The reaction of hydrogen with ethylene to form ethane, H-H + CH2=CH2 CH 3 CH 3 can occur in the gas phase. The molecules collide, and only a small fraction of the collisions involve the reactants oriented in precisely the right way to allow reaction. But a surface of Ni metal loosely binds both H 2 and CH2=CH2. Each molecule is held above the Ni surface at about the same distance. Now, even though the molecules still move rapidly on the surface, one degree of freedom is removed. The molecules are in the same plane . The chance of orienting in the precise way required for reaction is
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more probable . The TS has been stabilized . The free energy of the TS is lower. The rxn is catalyzed! There are many ways to change the reaction pathway. We will look at a very simple example of a reaction pathway uncatalyzed, and then catalyzed. Our example is ester hydrolysis: addition of water to methyl acetate. At the top of p. 105, for the
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14 - Monday, September 27, 2010 Lecture 14 Reading &...

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