5 - Lecture 5 Friday September 2 2011 Announcements 1 Quiz...

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Lecture 5 Friday, September 2, 2011 Announcements: 1. Quiz Wed 9/7. More info at the end of today's lecture PyMOL exercise next week (for second quiz): #2, Secondary Structure. 2. No office hours or reviews on Monday, Labor Day. Office hours and review session on Tuesday 9/6 at the usual times. PyMOL reviews on Sunday 9/4 and on Tu 9/6. 3. Today, Friday, Comstock B108 at 2:55PM: info session for transfer students and other interested students, “How to succeed at this place”. 4. Health careers “orientations” all at 4:35PM, for those applying in 2012: HUMEC: TU 9/6 IN 153 MVR CALS: WED 9/7 IN 145 WARREN ARTS: TH 9/8 IN KAUFMAN AUD ENG: MON 9/12 IN UPSON LOUNGE 5. Prof is getting requests to publicize sports clubs and charities. Please confine requests for publicity to activities for Cornell students in science, education, or health. Friday’s class : Role of the Mb heme group and the holoprotein What to do with an AA sequence without the 3-d structure? a. Compare the new AA sequence to a data bank of all previously-determined AA sequences, and look for matches with proteins of known function. b. Evolutionary relationships: Look at the big picture, how lifeforms are connected, by studying protein sequences. c. Special sequences: Find short stretches of AA sequence that match "special sequences" that have known function: e.g. target of a kinase; import into nucleus d. Predict protein folding? (some success for very small proteins, but not from "first principles" of chemistry and physics) e. History of x-ray diffraction; basics of the diffraction experiment Today's lecture: An example of part of the Mb crystal x-ray diffraction pattern is given at the left top of p. 43 in the LG. The actual amount of “spot data” needed is greater than the ~600 spots shown; about 10,000 spots were needed to find the structure of Mb, a part of which is represented as the "electron density map" in the upper right on p. 43. 1. In the center of that picture, on a diagonal, is the heme group. 2. The surrounding (black) protein electron density consists of different AA parts of Mb. 3. Close to either flat side of the heme is a His, each His sidechain extending from a helix.
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Refer to the middle/bottom of p. 43: The upper left picture shows what PyMOL terms a "sticks" model. This representation is useful when you can zoom in, since each atom of each AA, as well as the heme, is clearly shown. Proceeding clockwise, next see the Mb "ribbon", which shows the path of the main chain. This means simply that no AA side chains are shown. Next the "cartoon" representation (PyMOL terminology) clearly reveals the predominance of alpha-helices, of which there are eight, labeled as helices A-H.
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5 - Lecture 5 Friday September 2 2011 Announcements 1 Quiz...

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