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Lecture 3 - Lecture 3 Announcements 1 Quiz next Wednesday...

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Lecture 3 August 30, 2006 Announcements: 1. Quiz next Wednesday 9/6. Don’t be late—we start just after 10:10. Be sure to talk to Prof. F. if you have any special problems. 3. Prof. F. would like to meet with any interested students to discuss the topic: “How to Find a Research Lab at Cornell. What are they looking for?! And what do I do when I get there?!” Comstock B106 at 1:25 on Friday 9/1. 4. RasMol office hours + reviews in Carpenter orange computer lab: Sun 1 - 3PM; “review session” in Biotech G01 Tue 4:30 - 5:30PM The first RasMol assignment is the tutorial, pp. 289 - 293 of the LG. There you will find ALL instructions you need. You also need the CD. Go through it systematically. Monday’s lecture: Properties of ionizable groups How to use the Henderson-Hasselbalch Equation to calculate the ratio [unprotonated]/[protonated] Notice that higher pKa means higher affinity for H + . Easy to convert from the ratio [unprotonated]/ [protonated] to the fraction, [unprotonated]/{ [protonated] + [unprotonated]}; e.g. from H-H Equation, find a ratio, which in Monday’s lecture was [COO - ]/[COOH] = 3. Re-write as [COO - ]/[COOH] = 3/1, which means that [COO - ] = 3 and [COOH] = 1, so the total [COO - ] + [COOH] = 4. Then the fraction of carboxyls that are protonated is [COOH]/{ [COO - ] + [COOH]} = 1/4. As another example, H + are sometimes used as "control signals from the outside" to alter a protein's behavior. We find the actual controlled changes in physiological pH to be about 0.4 units, which is enough to change [unprotonated]/[protonated] by a factor of 2.5, which is enough to form or break some ion pair bonds. This is how hemoglobin works! Thus, understanding how to use the H-H equation enables you to understand how pH, pK a , and [unprotonated]/[protonated] are related to each other-- a "mini-pattern" that is important in biochemistry. Today’s lecture : Page 29: Peptides Amino acids are soluble in water, except for the sparingly soluble Tyr. (This is because Tyr crystals are very stable). The structure of amino acids in water is not well-defined, and therefore, not “interesting” to us. The formation of a peptide bond is shown in the middle of p. 29. You see that two amino acids condense, with the loss of one molecule of water per peptide bond.
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Look also at the charges: For each peptide bond formed, two charges are lost: one positive (from the amino group of one residue) and one negative (from the carboxyl group of the other residue). In the example on p. 29, we started out with six charges, and now only two charges are left. The convention for writing peptides is to draw them with the terminal amino on the left and the terminal carboxyl on the right. Always follow this convention! As individual AA, Ala, Val, and Leu are each very soluble in water. However, the tripeptide Ala-Val-Leu is much less soluble in water. Why is this? Because one positive charge and one negative charge are lost for each amino acid, except at the ends. In general, once the peptide bonds form, with the attendant loss of charges of the free AA, THE SIDE CHAINS TAKE OVER THE PROPERTIES OF THE MOLECULE p. 30:
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