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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
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
O 0 Speciﬁcity of endopeptidases. VISUALIZING THE may“ Acylation of the Active Site of Chymotrypsin substrate,
peptide Asp- 1 02 Ser- 1 95
\ hydrophobic pocket
binding site tetrahedral
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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- Fall '07