You have isolated a new protease that cleaves peptide bonds on the carboxyl side of Asp and Glu. Based on the enzyme'sinactivation by DIPF, you suspect that it may utilize a mechanism similar to chymotrypsin.The difference in specificity might be explained by theabsence of the S1 binding pocket.replacement of serine 195 with a positively charged residue.presence of a positively charged residue in the S1 binding pocket.presence of a negatively charged residue in the S1 binding pocket.

In the realm of enzymology, understanding the specificity of proteases is crucial for unraveling…

Answered: You have isolated a new protease that…

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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Diisopropylphosphofluoridate (DIPF) inactivates chymotrypsin by covalently modifying serine 195. Which statement is true of DIPF's inhibitory mechanism? DIPF randomly modifies all serine residues on the protein, and if enough is added, the serine in the active site will eventually be modified. DIPF approaches serine 195 more closely than other substrates. DIPF looks like the substrate for chymotrypsin and binds in the active site as a competitive inhibitor. Serine 195 is in an environment that gives it a higher than normal reactivity with respect to DIPF.
Using the catalytic mechanism of serine proteases, draw and label a reaction coordinate diagram/graph of the chymotrypsin-catalyzed hydrolysis of a peptide bond.
TLCK and TPCK both use Histadine residues in the active site as inhibitors of serine proteases. Why is TLCK specific for trypsin and TPCK is specific for chymotrypsin?
the structures of chymotrypsin and other serine proteases revealed that the active sites of these enzymes shared a particular sterochemical arrangement of residues crucial to their activity. This came to be known as the catalytic triad, as it consisted of the oponyomous serine (Ser) residue, along with a histidine (His) and an aspartate (Asp) residue. Which of the following would result in the greatest decrease in function of the catalytic triad found in serine proteases? O Mutation to Ser, Cys, Asp O Mutation to Ser, His, Asp O Mutation to Cys, His, Asp O Mutation to Ser, His, Glu
Consider, for example, that a particular serine residue is phosphorylated to activate the protein. In the lab, a similar effect is achieved by mutating this residue to either a D (aspartic acid) or E (glutamic acid). What could be the reason?
Some bacteria contain three different forms of aspartokinase, each with its own mode of regulation. Based on the roles of aspartoki- nase, as discussed in the text, propose a regulatory scheme applicable to each form of aspartokinase.
The enzyme aspartate transcarbamoylase catalyzes an early step in pyrimidine biosynthesis. The two states of the multi-subunit enzyme are shown below. Note that the binding of the regulatory molecule CTP (cytosine triphosphate) causes the enzyme complex to be inactive. Is this situation an example of positive or negative regulation? Explain why the use of CTP as the regulatory molecule is logical givén the overall function of this particular enzyme. INACTIVE ENZYME: T STATE catalytic subunits regulatory subunits OFF 6 CTP ON ACTIVE ENZYME: R STATE
Snake venom contains many hydrolase enzymes, including several serine proteases. One such protease (present in high concentrations in snake venom) mimics the action of thrombin to activate fibrin. The venom protease cleaves peptide bonds with a specificity for basic, positively charged amino acids. This enzyme is incubated with a substrate peptide with the sequence SNPDCKVALYMTW. Draw a mechanism for the peptide hydrolysis of this specific peptide catalyzed by this snake venom protease. Include the structure of the active site amino acids of the enzyme and the substrate peptide group (including the full structure of the 2 specific amino acids that contribute to the scissile peptide group in the substrate) in your mechanism. Use the curved arrow convention to illustrate the flow of electrons.
The allosterically regulated enzyme ATCase binds aspartic acid as a substrate and acylates the α–amino group. Succinate acts as a competitiveinhibitor of ATCase because it binds the active site but can’t be acylated.The dependence of v0 on [aspartic acid] for ATCase is shown in panel (a)of the accompanying figure. Panel (b) shows the effect of increasing [succinate] on v0 when [Asp] is held at a low concentration (see thick vertical arrow in panel (a)). Note that in panel (b), v0 is not zero when [succinate] = 0 (see thin horizontal arrow). Explain the shape of the curve in panel (b). Why does v0 increase initially, before decreasing at higher [succinate]?
Which of the following statements are descriptions of metal ion catalysis or examples of metal ion catalysis? Choose all correct answers a Zn²+ cofactor may properly orient the substrate in the active site through ionic interactions. a covalent bond forms between enzyme and substrate lowers the energy or stabilizes the transition state or intermediate catalyst retains its original form after reaction occurs catalysts may participate in oxidation-reduction reactions by changes in the oxidation state
Phosphoglycerate kinase shows induced fit resulting from the binding of both substrates to form the closed catalytic conformation. Maintainence of the closed conformation depends on the formation of a salt bridge between R62 and D200. What would be the effect of the mutation of D200 to the unusual amino acid shown below? Explain.
Serine Proteases, such as chymotrypsin, contain Ser/Asp/His as a catalytic triad (i.e. three collaborating amino acids) of amino acids involved in enzyme catalysis. Why is this? Examine each amino acid of this catalytic triad (schematically detailed below: Ser195/Asp102/His57) and, based on your understanding of amino acid characteristics, predict what the role of each amino acid could be. His57 Ser195 Asp102

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