Shown below is a substrate for a Trypsin.Draw the mechanism for this serine protease using the artificial substrate. Be sure to draw thecatalytic triad, and show the role of the oxyanion hole. Draw the complete structure of everyintermediate and product and PUSH ARROWS!!!!! Do not abbreviate structures using R and R'H₂N_N_CH.сноCH₂CH₂CH₂NHd=19H₂NH₂OCH-H₂CHNOCH

Trypsin is an enzyme which is normally present in living organism to digest proteins but it is also…

Answered: Shown below is a substrate for a…

Biochemistry

9th Edition

ISBN:9781319114671

Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.

Chapter1: Biochemistry: An Evolving Science

Section: Chapter Questions

Problem 1P

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Using the catalytic mechanism of serine proteases, draw and label a reaction coordinate diagram/graph of the chymotrypsin-catalyzed hydrolysis of a peptide bond.
An active site of a hypothetical serine protease with a peptide substrate bound is shown below: This serine protease has 3 specificity pockets (S1, S2, S1') as shown in the figure above. S1 pocket has a glutamic acid in the bottom, the S2 pocket is small and hydrophobic, and the S1' pocket is deep and hydrophobic. Based on this information you can conclude that R1 is most likely side chain of a. Asp b. Lys c. Lle d. Gly e. Phe
The diagram below shows the substrate binding cleft for a protease, providing the substrate structure, and indicating the residues (using one-letter code) that line the four specificity pockets. 1 M F H₂N K R IZ 2 3 P F S W оо E 4 The protease is known to cleave the amide linkage between W and E residues for substrates containing the WEFD sequence. Using 3-letter code with amino acids linked by a "dash" (ex. GLY-ALA), the N-terminal product is A and the C-terminal product is A
Shown below is a substrate for a Elastase. CH, HN NH NH, Draw the mechanism for this serine protease using the artificial substrate. Be sure to draw the catalytic triad, and show the role of the oxyanion hole. Draw the complete structure of every intermediate and product and PUSH ARROWS!
In serine protease catalytic triad mechanism, the first and second products that leaves the active site are Carboxylic acid and amide respectively Amide and carboxylic acid respectively Ester and amide respectively Carboxylic acid and ester respectively
(c) On the right is a diagram of the ac tive site of E. coli aspartate aminotrans- ferase illustrating the cofactor pyridoxal phosphate (labeled PLP) with the dicar- boxylic acid maleate (labeled MAL) bound in the active site. The structural formula of maleate is shown on the right. Am 194 MAL Arg292 Arg386 Ilx17 Lauf 'coo- H get H Coo- Maleate (c1) Draw the structure of L-aspartate and draw a border around the atoms in the amino acid that maleate simulates. (c2) Identify the active site residues that make hydrogen bonds and electrostatic interac- tions with the oxygen atoms of the carboxylate groups of maleate in the diagram above. Identify the carboxylate groups according to the numbering in the diagram of maleate above. Indicate the hydrogen donor groups of the active site residues. (C3) Compare and draw the structures of L-Arg and L-Lys. On the basis of the diagram why does replacement of an arginine for a lysine have an effect on substrate binding to AspAT? (c4) Of the mutant…
The diagram below shows the substrate binding cleft for a protease, providing the substrate structure, and indicating the residues (using one-letter code) that line the four specificity pockets. F 1 M The protease is known to cleave the amide linkage between W and E residues for substrates containing the WEFD sequence. 1 O Match the specificity pocket (identified by red number) to the residue that occupies it. 3 R Match the specificity pocket (identified by red number) to the residue that occupies it. 4 W 2 1. D 2. E 3. F 4. R 5. W 6. Y
Trypsin uses a nearly identical mechanism as chymotrypsin (including the catalytic triad his57-ser195-asp102. beginning with the enzyme substrate complex draw the complete steps in the trypsin mechanism that occur to release the first product and create the acyl enzyme intermediate in the trypsin active site. The substrate for trypsin to be used is gly-lys-gly-ala
. (a) Explain the biochemical basis for the fact that one can synchro- nize cell populations by treating them with deoxythymidine. (b) Explain the apparent paradox that DATP at low concentrations is an activator of ribonucleotide reductase, whereas at higher concen- trations it becomes inhibitory.
. The mechanism for lysozyme cleavage of its polysaccharide substrate requires Glu35 in its nonionized form, whereas the nearby Asp52 must be ionized (see the figure below). The pK values for the side-chain carboxyl groups on the two amino acids in solution are virtually identical. a) How can one carboxyl group be charged and the other uncharged in the active site of lysozyme? b) The pH optimum for lysozyme is about 5. Why do you suppose that the activity decreases above and below this optimum? Glu3s NAG Asp52 0-H Glu35 -C Asp52 tri-NAG NAG
Briefly describe the induced-fit conformational change when hexokinase binds its substrate.
serine proteases act via a two-step catalytic mechanism. However, as a critical scientist, you may want to see data that supports this claim. One experiment that can provide such evidence is called a 'pre-steady state' kinetics experiment using the chromogenic substrate, N-acetyl- phenylalanine p-nitrophenyl ester. As shown below when this substrate is cleaved, the p-nitrophenylate is a yellow product whose absorbance can be measured in real time using a spectrophotometer. When the chromogenic substrate is rapidly mixed together with a limiting amount of protease enzyme, the accumulation of product is measured right away on fast (millisecond) timescales. In this experiment, one observes two distinct phases of the reaction as shown in the plot below. Based upon what you know about the mechanism of serine proteases, provide a mechanistic interpretation for the observation of these two phases of the reaction. + H₂O N-Acetyl-L-phenylalanine p-nitrophenyl ester p-Nitrophenolate Absorbance…

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