The diagram below shows the substrate binding cleft for a protease, providing thesubstrate structure, and indicating the residues (using one-letter code) that line thefour specificity pockets.1 MFH₂NKRIZ23 PFSWооE 4The protease is known to cleave the amide linkage between W and E residues forsubstrates containing the WEFD sequence.Using 3-letter code with amino acids linked by a "dash" (ex. GLY-ALA), the N-terminalproduct isA and the C-terminal product isA

Proteases are enzymes which digest the proteins by cleaving the peptide bonds at specific locations.…

Answered: The diagram below shows the substrate…

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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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?
Which strategies listed does this enzyme use to facilitate cleavage of α-galactoside? Choice 1 of 6:Dehydration synthesis Choice 2 of 6:acid base catalysis Choice 3 of 6:covalent catalysis Choice 4 of 6:metal ion catalysis Choice 5 of 6:stabilizing the transition state Choice 6 of 6:binding with high affinity to the product
Match the enzymatic activity with the proper description within the ubiquitin-proteasome pathway. Drag and drop options on the right-hand side and submit. For keyboard navigation... SHOW MORE ✓ E1 E2 E3 Proteasome = ||| = ||| = ||| Degradation Ubiquitin-activating enzymes Ubiquitin-conjugating enzymes. Ubiquitin ligases
To answer this question, please reference the Problem Solving Video: pH and pK, of an Amino Acid. Proteases are enzymes that cleave peptide bonds using general acid-base catalysis. General acid-base catalysis relies on a protor donor or acceptor other than water. Proteases rely on proton transfer to create strong nucleophiles from active-site amino acid residues. In the protease chymotrypsin, an active-site serine is a potent nucleophile. A nearby residue, His 57, interacts with serine to increase its reactivity. A schematic of chymotrypsin's active site illustrates the active site Ser 195 and His 57 R groups. The Asp 102 residue helps position the His 57 residue via hydrogen bonding. Asp 102 [His] [His+] His 57 6.0 -H-N Chymotrypsin is a digestive enzyme with a catalytic optimum between pH 7.8 and 8.0. However, due to the presence of gastric juice, chymotrypsin often functions in an environment of pH 5.5-7.0. Incorrect The imidazole group of free histidine has a pK₂ of 6.0. Use the…
Consider the metabolic pathway show below that converts substrate A to B with the enzyme A-ase, B to C with B-ase(I), and so forth. Acety/A-ase Acetate - A-ase Deacetylase A-ase Protease & C-ase B-ase ABCD What is the mechanism of regulation of B-ase? Positive allostery Reversible Covalent modification Isoenzymes Proteolytic Activation Feedback Inhibition 1
1. Please fully explain (use illustrate where appropriate) the Modes of Enzyme Catalysis exemplified by the serine protease: Chymotrypsin. In your answer discuss employing the illustration whenever possible: the overall reaction mechanism, stability of the reaction transition state, proximity and orientation effects, acid-base catalysis, and covalent catalysis. (c) (0) Ap Asp Toe His Asp 10 C-N bond cleavage HN Ho Ser Ger Binding of substi 196 Ser Gly alto video LBHB NH Sere HAR Proton donation by H (h) Fel of amino product yest OHN Hig Ser Ap (0) Formation of covalent (ES) Alp Me complex Serios
10. Chymotrypsin is a serine protease enzyme. The Km for the reaction of chymotrypsin with N-acetylvaline ethyl ester is 8.8*102, and the Km for the reaction of chymotrypsin with N- acetyltyrosine ethyl ester is 6.6*10“ M. catalytic triad Ser 195 His 57 Gly 193 N-H OH R-N- Ca N-H O-C- Asp 102 N-acetyl valine N-acetyl tyrosine Chymotrypsin Active Site a. What is the nucleophile here and how is it activated? b. Which substrate has an apparent higher affinity for the enzyme. c. Propose a reason for the difference in affinity based on the shape of each of the substrates (see active site figure, cleaves on the C-side of aromatic residues).
Changing which pairs of the amino acids is most likely to directly lead to the most severe problems with substrate (Blue) binding by the protein depicted by the red ribbon.
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…
The last residue of the protein (tail) is Tryptophan, and the first residue (head) is labeled with IAEDANS acceptor. Estimate the length of the protein (head to tail) if the efficiency of RET measures at 0.01 Please show step by step and how to get the 34.014 number
Answer the following using the picture attached: A. How does pepsin differ from chymotrypsin in terms of its active site residues and mechanism? B. How do these changes permit pepsin to operate at such a low pH?
The figure below shows the dependence of the enzyme's rate, v (in µM/min), as a function of substrate concentration, S (in mM). Also shown is the dependence of the rate in the presence of an inhibitor, present at a concentration of 0.2 mM. Based on this information, which of the following does this inhibitor most likely interact with? 1/v 1- 05 1/[S) O A. Michaelis complex O B. [E O C. free enzyme O D. free substrate O E. Both "A" and "B."

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