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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Similar questions

From the complete oxidation of glucose (glucose → 6CO2), how many total nucleotide triphosphates are yielded (be sure to deduct payback) as part of substrate level phosphorylation?
ATP synthase is a protein that catalyzes the formation of the energy storage molecule adenosine triphosphate using adenosine diphosphate and inorganic phosphate. Which of the following are true for the protein, ATP synthase? Select all apply A mutation of Asp61 to glutamic acid would have less of a deleterious effect on its ability to synthesize ATP than a mutation of Asp61 to alanine A mutation of Asp61 to alanine would have less of a deleterious effect on its ability to synthesize ATP than a mutation of Asp61 to glutamic acid The F1 subunit is primarily responsible for translocating H+ ions across the inner mitochondrial membrane during ATP synthesis The FO subunit is primarily responsible for translocating H+ ions across the inner mitochondrial membrane during ATP synthesis
The purified OXA-M290 enzyme can now be tested to determine which β-lactamase inhibitor is most effective. This inhibitor could be prescribed in combination with a β-lactam antibiotic to treat the infection caused by the E. coli KGH1 strain. Before testing inhibitors against OXA-M290, the kinetic activity of this enzyme must first be measured. The activity of OXA-M290 is measured using nitrocefin, a chromogenic β-lactam antibiotic. When nitrocefin is hydrolyzed by a β-lactamase, it changes from yellow to red in colour. The nitrocefin hydrolysis product has an extinction coefficient of 20,500 M-1 cm-1 at 486 nm. The hydrolysis of 60 μM nitrocefin by 1 nM OXA-M290 is monitored using a microplate reader. The absorbance of the wells in the plate is measured at 486 nm every 30 seconds. This experiment is carried out with three replicates, generating the following data: Time (min) Absorbance of Replicate 1 Absorbance of Replicate 2 Absorbance of Replicate 3 0.5 0.0984…
You are studying how your Lys-Val-Thr tripep de interacts with another pep de, which places an Asp in close proximity to the Lys on your pep de. How would the presence of an Asp side chain affect the pKa of the Lys side chain? Briefly explain your reasoning. (remember pKas are rela ve, pKa=log([H+][A-]/[HA])
Part B
We learned that three different amino acid transformations of PLP-dependent enzymes canresult from different conformations of the PLP-amino acid imine adduct in the active site.Starting from the PLP adduct of (S)-serine, show mechanisms fora) Decarboxylation of serineb) Racemization of serinec) Conversion of serine to glycine and formaldehyde.
The enzymes GICNAC phosphotrasnferase is a key enzyme involved in the transporting of proteins from the trans-Golgi to the lysozyme. In addition to the catalytic function of the enzyme that involves certain sugars, what is the second critical function of this enzyme? O It recognizes internal signal sequences found on lysozyme-targeted proteins. O It drives the binding of a phosphorylated GlcNac group onto a mannose residue. O It facilitates the reversible binding of specific proteins to the M6P receptor O In is essential for the recruitment of clathrin triskelions to the budding vesicle.
Small molecules are used as inhibitors of protein action - as drugs. They most often do this by blocking the active site within the protein. Potential drugs can be screened computationally to determine if they are strongly bound to the protein. Figure 1 shows a possible conformation of a candidate drug molecule, 4-bromo-2- carboxymethylamide-pyrrole (abbreviation: BCMAP) at the active site of a protein (abbreviation: PR). Figure 2 shows the full protein structure whilst figure 3 shows a known inhibitor of the protein at the site, overlayed with another calculated conformer of BCMAP. (a) Explain what types of interactions, both intermolecular and intramolecular, that a molecular mechanics forcefield must be able to describe in order to be able to accurately determine the geometry of BCMAP in the protein. Identify which interactions will be the most important to describe accurately. Figure 1.4-bromo-2-carboxymethylamide-pyrrole (BCMAP) (C, N, O, and Br atoms in yellow, blue, red, and…
What amino acids can be found in chymotrypsin’s specificity pocket? What would happen if one of those amino acids was changed to lysine? In relation to the amino acid in the specificity pocket, which peptide bond is cleaved; C terminal or N terminal? What is this bond’s proximity to the serine in the active site?
A 65-year-old man with severe atherosclerotic coronary artery disease comes to the emergency department because of a 12-hour history of chest pain. Plasma activity of the MB isozyme of creatine kinase (MB-CK) is markedly increased. Which of the following processes is the most likely explanation for the increased plasma MB-CK? (A) Cell membrane damage (B) Endoplasmic reticulum dilation (C) Mitochondrial swelling (D) Polysome dissociation (E) Sodium pump dysfunction
Some strains of bacteria or microorganisms have developed toxins that can modify the activity of the alpha subunit of G proteins which results in disease. For ex. cholera toxin, produced by Vibrio cholerae, causes ADP ribosylation of the stimulatory Gαs subunit of G proteins. This modification abolishes the GTPase of Gαs, and results in an αs subunit that is always in the “on” or active state. It results in continuous stimulation of adenylyl cyclase (AC). The main cells affected by this are the epithelial cell in gastrointestinal tract. Knowing this altered activity of AC, explain why patients affected by this toxin experience severe diarrhea and dehydration that may result in death.
Based on your understanding of the structure and function of the enzyme chymotrypsin, explain why proteolytic activation by Trypsin in the intestine is required for chymotrypsin to bind its substrates with high affinity. Your answer should include a description of the amino acid residue or residues involved AND a kinetic experiment that suggested this.

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