9 - Lecture 9, September 14, 2011 ANNOUNCEMENTS: 1....

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Lecture 9, September 14, 2011 ANNOUNCEMENTS: 1. Regraded quizzes—how to get them back?! Check the green folder labeled REGRADED. After ~ one week, these also go to the Bio Center Reserve Desk in Stimson 216. 2. Friday 9/16 2:55PM in Comstock B108: New undergrad researchers-- what is expected of you in the lab?! 3. Global health issues-- Cornell Health International general body meeting TODAY 9/14 at 4:30PM in Rockefeller 122. Monday's lecture : Multidomain proteins (within one polypeptide chain) are common. IV structure is common. It is based upon good steric & "chemical fit" of protein surfaces. IV structure can be stable, e.g. hemoglobin, or transient, e.g. the insulin signaling complex. Thermodynamic way of looking at protein stability (folding vs unfolding) Today's lecture: p. 72 We can represent the relationship between the Gibbs Function and the protein structure on a graph. We use the standard state, G o , because the pressure is fixed at 1 atm and because we want concentration to be fixed : G depends on concentration, and we do not want to complicate our discussion now with this dependence. More on conc dependence of G later in the course. The x-axis is termed "structural coordinates". What does that mean?! This is merely a crude way to indicate different structures, with close distance on this axis indicating close in structure . (There is no precise way to use one axis of a graph to indicate all the possible protein structures!). Even though crude, the idea of showing stability this way is useful. To show what is going on, let's first consider the simple case shown on p. 71. Consider poly(Glu), which is in an α -helix at pH 3. For pH > ~4, poly(Glu) has lots of consecutive negative charges, and charge repulsion causes the helix to unfold. A graph of G o vs structural coordinates would show a single dip at the "structural coordinates" that indicate α -helix. This structure has the lowest free energy at pH = 3. And indeed, in the laboratory poly(Glu) is found to exist predominantly in
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an α -helix at pH 3. The location of an α -helix on the structural coordinates axis is arbitrary, but we will mark it with an “X”. But what if we were to elevate the pH to 7? Now our graph shows no dips indicating free energy stability for any particular structure ! The α -helix is no longer any more stable than the many other conformations. Maybe the graph looks like a wavy horizontal line-- who knows? No one structure is more stable than the others, as indicated by the wavy horizontal line.
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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.

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9 - Lecture 9, September 14, 2011 ANNOUNCEMENTS: 1....

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