7 - Friday September 9 2011 Lecture 7 Announcements 1 Mean score for each quiz Quiz 1A 23.3 sd 6.6 Quiz 1B 23.1 sd 5.7 Quiz 1C 21.8 sd 7.6 2

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Friday, September 9, 2011 Lecture 7 Announcements 1. Mean score for each quiz, Quiz 1A 23.3 sd 6.6 Quiz 1B 23.1 sd 5.7 Quiz 1C 21.8 sd 7.6 2. Regrade policy: submit written ( WRITTEN , NOT ORAL ) argument, attached to quiz. Place in purple Re-Grade Folder at front of classroom. You will have one week after the quizzes are returned to submit a quiz for re-grading. 3. If you do not pick up your quiz today at the end of lecture, you can find your quiz at the Reserve Desk of the Bio Center, 2 nd floor of Stimson. 4. Quiz 2 on Wed 9/14 will cover lectures 5, 6, and 7. Policy reminder: If you missed Quiz 1 (or if you miss any quiz for any reason) you are eligible to take the make-up quiz on Wed 11/30 (which will cover the lectures from 11/14 – 11/21). 5. No graphing calculators are allowed during quizzes and other exams in this course. If you are using one during the quiz, you will receive a score of 0, and you cannot drop that score. 6. PyMOL assignment #2: Secondary Structures. 7. Watch two videos: " Steric Hindrance of a Polypeptide Chain " and " Secondary Structures in Proteins " 8. Any interested students: Today, Friday 9/9 at 2:55PM in Comstock B108, "Should I apply to medical school this year?!” Wednesday's lecture: Ramachandran Maps; every point within these maps is a φ , ψ value. Most φ , ψ values can never be observed because of steric hindrance; Characteristics of the α -helix, including amphipathic helices Today's lecture: BETA SHEET : (p. 53) 1. The allowed regions of rotation occur within the range φ -60 to -150 and ˚ ˚ ψ +90 to +180 . These angles make the polypeptide chain in a ˚ ˚ β -sheet relatively extended, in contrast to the more compact α -helix structure. 2. Repetition of these φ , ψ values leads to a structure with an average length of the sheet found in proteins of approximately 6 residues, or about 20 Angstroms in length. 3. All possible hydrogen bonds are made, but for the beta sheet these H-bonds are always between neighboring strands, not within one strand . 4. In representations of protein structure, a strand of β -sheet is indicated by an arrow, pointing from amino toward carboxyl direction of this piece of polypeptide. ANTIPARALLEL : The side-by-side β -sheet strands “run in opposite directions” with one strand having the direction “amino carboxyl” and the strand next to it “carboxyl amino”. Hydrogen bonds are formed between C=O and NH of peptide bonds on neighboring strands .
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PARALLEL : The side-by-side strands both run in the same direction. The two strands cannot be a continuous run of AAs in the sequence, because in the parallel β -sheet each side-by-side strand runs in the same direction. Think about this and see the Powerpoint lecture!
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This note was uploaded on 01/01/2012 for the course BIOMG 3310 taught by Professor Feigenson during the Fall '11 term at Cornell University (Engineering School).

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7 - Friday September 9 2011 Lecture 7 Announcements 1 Mean score for each quiz Quiz 1A 23.3 sd 6.6 Quiz 1B 23.1 sd 5.7 Quiz 1C 21.8 sd 7.6 2

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