215F07-notes-12-5-07 - Chem 215 F07 Notes — Dr Masato...

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Unformatted text preview: Chem 215 F07 Notes — Dr. Masato Koreeda — Page 1 of 2. Date: December 5, 2007 (7) Peptides (Chapter 23.8, pp 1007—1016) Enzyme: Any of a large class of complex ° primary structure: the order of AAs proteinaceous substances that are produced 0 secondary str: conformation of the peptide by living cells, that are essential to life by - tertiary str: stereo str created by bending acting like catalysts in promoting at the and folding of peptide chains cell temperature, reversible reaction (such 0 quaternary str: stereo str of the complex as hydrolysis and oxidation) Without made of several peptides themselves undergoing marked destruction 153 A in the process, but frequently requiring the single bonds; /' presence of activators (as metal ion) or Stifffiinbonds 110° \ «(,H coenz mes. 0 ( ====:—_—:::::::=======_—_=====::=:==== \fm A \C/C\H Chymotrypsin: a 241—amino acid endoprotease \21“ l 1‘32 6‘ Which shows specificity for cleavage after H c /.\N/,\H mix??? aromatic amino acids (Phe, Try, or Trp). H’ \ W i ::::::::’°““d shaded area represents the plane containing the peptide linkage and the two adjacent carbon atoms :45 ‘1; ”1. A representation of the chymotrypsin molecule showing the placement of histidine, aspartic acid, and serine at the active site. The hydrophobic pocket that binds the peptide residue during cleavage is below and to the right of the serine at position 195. Figure adapted from "A Family of Protein- Cutting Proteins." by Robert M. Stroud. Copyright © 1974 by Scientific American. Inc. All rights reserved. 0— active site é): disulfide bridge Active site Binding site Chem 215 F07 Notes — Dr. Masato Koreeda — Page 2 of 2. Date: December 5, 2007 R O _ - specmc for L-ammo acrds (or D» In a few cases) Peptide—NH k“ NfiLJL NH-peptide ~ usually specific for amino acid preceding cleavage site. 0 R‘ <chymotrypsin Trypsin - cuts after Phe, Tyr, Trp — cuts after Arg, Lys (aromatic sidechains) (basic sidechains) H O H O x/ N N / 3/ N / O H 0 fl Halli O 0 Specificity of endopeptidases. VISUALIZING THE may“ Acylation of the Active Site of Chymotrypsin substrate, protein or peptide Asp- 1 02 Ser- 1 95 \ hydrophobic pocket binding site tetrahedral intermediate acylated serine residue 0iThe use of the HO group as a nucleophile (as its anion) in this reaction is remarkable; the pKa of HOCHZR is about 16 and the pKa of the conjugate acid of histidine base is around 6— 8. This process is made thermodynamically favorable participation of Asp—102 in stabilizing the imidazolium cation of His—57. - The activity of enzymes is a powerful demonstration of the effect that lowering the energy of the transition state can have on the overall rate of the reaction. ...
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