# 3 - Lecture 3 September 2 2009 Announcements 1 Quiz next...

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

Lecture 3 September 2, 2009 Announcements: 1. Quiz next Wednesday 9/9. 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 B108 at 3:25 on Friday 9/4. 4. PyMOL: ** If you cannot run PyMOL because you have a new Windows computer that operates with a 64-bit Vista system, we are working on a fix. Send e-mail to Bertheleau at bmn27, and he will get back to you about the fix. Office hours + reviews for PyMOL will normally happen in two places: Carpenter red computer lab: Sundays 3 - 5PM; “review session” in Malott Hall room 253 Tuesdays 4:30 - 6PM The first PyMOL assignment is the tutorial, pp. 300-309 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 : p. 25 At the top left are the two "sulfur-containing" amino acids. These two have VERY different properties: The Cys SH group is ionizable. It interacts favorably with water. The S - is a very powerful nucleophile, i.e. it is highly chemically reactive.

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

View Full Document
If two CysSH are physically close, they can oxidize to form Cys-S-S-Cys: the two Cys are joined by a disulfide bond, which is a covalent bond. Cys-S-S-Cys is very nonpolar.
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

### What students are saying

• 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.

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

• 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.

Dana University of Pennsylvania ‘17, Course Hero Intern

• 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.

Jill Tulane University ‘16, Course Hero Intern