10 - Lecture 10 Friday, September 17, 2010 Announcements 1....

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Lecture 10 Friday, September 17, 2010 Announcements 1. Quiz 2A 23.3 Quiz 2B 24.5 Quiz 2C 23.9 2. We do not assign letter grades at this time (in fact, not until the end of the semester). To give you a very rough idea of where you stand: divide your raw score by the mean to find your normalized score ("NS"); use this very rough guide: mid-range for grade of A, NS = 1.2; mid-range for grade of B+, NS = 1.0; mid-range for grade of C, NS = 0.80. This is a rough guide . 3. Three Wednesdays when there will NOT be a quiz: 10/13 (day of return from Fall Break) 10/20 (day before the midterm exam) 11/24 (day when Thanksgiving recess begins) 4. Meet today with any interested transfer students to discuss How to succeed at this place. 2:55 PM in B108 Comstock. 5. Regraded quizzes are placed in a green folder at the front of the lecture hall. After about one week, they are brought over to the Reserve Desk of the Bio Center in Stimson. Wednesday's lecture: Thermodynamic treatment of protein folding/unfolding and representation of stability using a graph of G o vs “structural coordinates”. ALL information for the fold structure is in the AA sequence. However, that fact that proteins can fold so much faster than seems possible (sec to min) is not understood. Today's lecture: p. 78 Do proteins exist that speed up folding? Yes, with 3 categories known. Although no “protein machines” speed up the “search” through φ , ψ values, there are 3 classes of proteins that are present in every cell, required for folding: 1. Disulfide isomerases 2. Prolyl isomerases 3. Molecular chaperones 1. In proteins with multiple disulfides, the wrong ones can form! The process of making and breaking disulfides is speeded up by the enzyme disulfide isomerase , so that in just minutes the correct disulfides can be formed.
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p. 78, top left, shows a diagram of disulfide bonds forming, then exchanging (breaking and re-forming). The diagram shows 4 Cys, labeled A, B, C, and D. In a real protein with disulfides, as it folds, sometimes the "right" disulfides form, sometimes the wrong ones. Eventually, all the right ones form, and the protein can then reach its final lowest free energy structure. To speed up the breaking- and-reforming process, all cells have the enzyme disulfide isomerase. 2. [note that LG print of cis Pro has an NH inserted by mistake; see ppt file in Blackboard for the correct structure] In some proteins, at one or a very few positions, the angle of the peptide C-N bond, the bond with partial double bond character (whether cis or trans ), is 0 o ( cis ) rather than the 180 o ( trans ) as in the vast majority of peptide bonds. These few exceptions all involve a Pro side chain. Since the polypeptide is synthesized on the ribosome always with 180 o angles for this bond, it must isomerize for these few cases where a cis peptide bond occurs in the structure, in order that the protein can achieve its most stable final structure. But, with an energy barrier of about 80kJ/mol for this
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10 - Lecture 10 Friday, September 17, 2010 Announcements 1....

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