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Lilly Zhang Section 101b Wed 9am Chem27 Section Handout Thurs 8-9pm Greenhouse Section Handout 2 • • • Problem set 1 graded, answer key posted, see me if you have any questions Attendance counts towards your grade Memorize all mechanisms, reagents, and protecting groups Protein Folding †Hydrophobic effect – enthalpically disfavored, entropically favored, entropy is the driving force. †Alpha helices † Beta sheets † Beta turns Edman Degradation † Practice writing out the mechanism of the reaction and know the main “intermediates” and “products” of the transformation † Know how to reassemble the starting material by looking at the amino acid part of PTH † Practice identifying unnatural amino acids in the degradation chain, and untangling branched and/or cyclic starting compounds (i.e. cyclosporin) Overall transformation: Cyanogen bromide cleavage Overall transformation: Practice Questions 1) Draw the extended conformation of the sequence Leu-Glu-Phe-Ser in a polypeptide chain, accounting for stereochemistry. How might be β sheet be stabilized? 2) Researchers isolated the novel peptide antibiotic from Streptococcus. In order to characterize the structure of the peptide, researchers decide to use cyanogens bromide cleavage followed by Edman degradation. O +NH2 H N +H3N N H N H O S O NH2 NH OH H N O H N O -O N H OH O O a) Draw the full product of cyanogen bromide cleavage of this peptide (try not to draw out the entire mechanism – it’s incredibly time consuming!) b) How many rounds of Edman degradation would you require to fully sequence the peptide resulting from the cyanogen bromide treatment? 3) A novel peptidic natural product (PNP) is analyzed by three rounds of Edman degradation. The product obtained in steps one and two was used as the substrate in the next round. Substrate First Round PNP Second Round PTH A Third Round PTH B D D N=C=S D Reagent Ph-NCS Ph-NCS Product PTH A ….. D D ….. a) Draw the structure of the starting peptide b) Why did the researchers use the perdeuterated phenyl isothiocynate in the third step?
