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

Info icon This preview shows pages 1–3. Sign up to view the full content.

View Full Document Right Arrow Icon
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.
Image of page 1

Info icon This preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
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:
Image of page 2
Image of page 3
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern