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Lecture 14 - Monday Lecture 14 Reading problem assignments...

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Monday, September 25, 2006 Lecture 14 Reading & problem assignments for this week as in LG RasMol: assignment #4, The Protein Data Bank Do something about hepatitis B? Info session Wed 9/27 Rockefeller 132, 5:30-6:15PM Grad school info: OUB Open House Tu 9/26 Stimson 216, 7-9PM; also big day: Grad School Day, Wed 9/27 Barton Hall 11AM – 2:30PM Friday's lecture: The IV structure of Hb is different with and without oxygen bound. Without oxygen, Hb IV structure is stabilized by (potentially) ~8 ion pairs between AA, and (potentially) ~5 ion pairs between AA and BPG, none of which are present in oxygenated Hb. Binding of oxygen at one site has an effect at a distant site: an allosteric effect, switching the IV. The IV that has low affinity for oxygen is the T or Tense State , and the IV with high oxygen binding affinity the R or Relaxed State. The Bohr Effect is the acid-induced release of oxygen by hemoglobin. The underlying cause is the protonation of some His and terminal amino groups, thereby forming more ion pairs from among the "potential ion pairs" in the T-state of Hb. Fetal Hb has higher affinity for oxygen than does adult Hb, because of the mutation of a His to a Ser, resulting in loss of (approximately) two ion pairs with BPG. Also, oxygen transfers across the placenta because of the slightly higher oxygen pressure on the maternal side. Two models can explain Hb behavior: the Sequential Model and the 2-State Model. Intro to enzymes: EC nomenclature; enzyme specificity Today's lecture By now we know how to study enzyme structure, but how do we find out how an enzyme works? By measuring reaction rates (reaction kinetics), we can get information that we can use to find out how enzymes work. At the top of page 97 is one possible general type of reaction, wherein two molecules collide: A + B C + D (Note that the equations will be different if the reaction is of some other general type, such as A + B C or A B + C )
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We define the rxn rate = rxn velocity = V = d [C]/ dt = d [D]/ dt = - d [A]/ dt The units of V are conc/time for example, (M x sec -1 ) or (microM x min -1 ) Suppose we begin with substrates only. At first, there is no C and no D (the products). Now the reaction rate is defined as the initial rxn velocity V in = k 1 [A]x[B] The units of k 1 are (conc) -1 x (time) -1 for out reaction above, A + B C + D Now let's go to equilibrium , where the forward and the reverse rxns are going at equal rates, k 1 [A] eq x[B] eq = k -1 [C] eq x[D] eq and K eq = k 1 /k -1 = [C] eq x[D] eq /[A] eq x[B] eq The general case,
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