It is important for a protease to distinguish between two different proteins so that itonly cleaves its target protein. The target protein has the target sequence glu-asp-ser. What amino acids should line the substrate-binding site (the target proteinbinding site) of the enzyme to help it to recognize its target?Amino acids such as glutamate and aspartate.Amino acids such as glutamine and phenylalanine.Amino acids such as arginine and lysine.Amino acids such as tryptophan and cysteine.Any amino acids would work as long as there are three.

The building blocks of proteins are organic substances called amino acids. They have a side chain (R…

Answered: It is important for a protease to…

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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Many enzymes are switched "on" by attachment of a phosphate group at a specific serine somewhere on the protein (phosphorylation). The basic reaction is: E + ATP2 Ep + ADP Po SERINE PHOSPHO SERINC (Note the "squiggles" before the backone amide and carbonyl indicate the polypeptide chain continues on either side of the serine). For phosphorylation to have this effect, there has to be some equilibrium between inactive and active forms conformations of the enzyme: [Eactive] [Einactive] Einactive 2 Eactive; K* The same basic equilibrium must exist for the phosphorylated protein: [Ep,active] [Ep,inactive] EP,inactive 2 Ep,active; Kp = (a) If phosphorylation increases the measured activity of the enzyme, is K* or K larger? Why? (b) Does the phosphorylation site need to be near the site where the enzyme binds its substrate (e.g. the reactant whose chemistry it catalyzes)? Why or why not?
The tetrapeptide Cys-Trp-Lys-Pro was digested with chymotrypsin and adjusted to pH=0.5 to fully protonate all digestion products. The digestion products were then applied to a strong cation exchange column (sulfonic acid). The products were eluted from the column using a pH gradient from 0.5 to 13. Write the primary amino acid sequence of the products in the order they would elute from the column. Indicate the pH value at which each product elutes from the column
Consider the peptide Asp-Lys-Phe-Glu-Asn-Tyr-Gln-Val-Cys. In a single beaker, you treat this peptide with 2 proteases. One protease cleaves at the N-terminus of aromatic R groups and the other cleaves at the C-terminus of polar, non-ionizable R groups. Following the enzymatic digestion, you want to separate your peptide fragments so that you can identify them. You choose to separate the fragments using an anion exchange column. Beginning at pH=6 you apply your peptide fragments to the column and you gradually decrease the pH of the column stopping the separation when the pH of the column equals 4. Omitting chemical structures, write the amino acid sequence of the peptide fragments that are produced from this digest. Write the order that these fragments will elute from the column (if at all). (Relevant pKa values are: 2.1, 3.8, 4.3, 8.3, 9.6, 10.1, and 10.5)
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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.
Given is a polypepetide in the presence of the enzyme pepsin. N-gly-arg-met-phe-ala-lys-ser-tyr-gly C, What fragments can be formed? choices are below gly-arg-met + phe-ala-lys-ser + tyr-gly gly-arg-met-phe + ala-lys-ser-tyr + gly gly + arg-met-phe-ala + lys-aer-tyr-gly gly-arg + met-phe-ala +lys +ser=tyr=gly
the following is a coenzyme or cofactor involved in enzymatic reaction. identify the biochemical role that S-adenosylmethionine plays within a biochemical tranformation.
Saccharide X, a sugar composed of repeating cellobiose and maltose, is a constituent of a glycoprotein. The saccharide is linked by a(1-2) linkages to three sialic acid residues, then O- linked to the glycoprotein. The glycoprotein is a glucose receptor. Running it through Benedict's Test produced negative results. What are 2 possible amino acids that is able to O-link with the saccharide? Show the part of both saccharide and protein where the bond is formed.
Pro-CHEMBIO peptide is a large peptide sequence with three disulfide bonds (indicated by the lines between cysteine residues). CHEMBIO Protease cleaves amide bonds between two basic amino acid residues to give the final peptide that is active in the body. The products of this protease reaction are: 1. Two chains that make up active CHEMBIO peptide, which contain the N- and C-terminus sections of the original Pro-CHEMBIO molecule 2. A separate inactive peptide What if instead of CHEMBIO Protease, this peptide was cleaved by trypsin? Indicate the cleavage locations on the structure below. asap
When performing his experiments on protein refolding, Christian Anfinsen obtained a quite different result when reduced ribonuclease was reoxidized while it was still in 8 M urea and the preparation was then dialyzed to remove the urea. Ribonuclease reoxidized in this way had only 1% of the enzymatic activity of the native protein. Why were the outcomes so different when reduced ribonuclease was reoxidized in the presence and absence of urea?
The following diagram shows and enzyme (in gray) that has transiently bound cyclic AMP, a signaling molecule (in salmon pink). What kind of bonds/associations are the amino acid side chains in the enzyme (green, blue) forming with the cyclic AMP? Focus only on the bonds/associations indicated by the black arrows. serine CH2 N-H cyclic AMP / (CH2)3 `NH `c=NH, `NH2 serine arginine N CH -Hio threonine CH2 glutamic acid CH2 (B) covalent bonds hydrogen bonds van der Waals forces hydrophobic forces ionic bonds O O O O O
An enzyme that catalyzes disulfide– sulfhydryl exchange reactions, called protein disulfide isomerase (PDI), has been isolated. PDI rapidly converts inactive scrambled ribonuclease into enzymatically active ribonuclease. In contrast, insulin is rapidly inactivated by PDI. What does this important observation imply about the relation between the amino acid sequence of insulin and its threedimensional structure?

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