The following data describe the catalysis of cleavage of peptide bonds in small peptides by the enzyme UTSase (the arrow indicates the peptide bond cleaved in each case).| Substrate | \( K_m \) (mM) | \( k_{\text{cat}} \) (s\(^{-1}\)) ||---|---|---|| PAPA\(\downarrow\)G | 4.0 | 26 || PAPA\(\downarrow\)A | 1.5 | 37 || PAPA\(\downarrow\)F | 0.64 | 18 |**Question**: Based on the above data shown for UTSase, what features of the amino acid sequence dictate the specificity of the proteolytic cleavage?**Options**:A. Large hydrophilic R-groups B. Large hydrophobic R-groups C. Neutral R-groups D. Small hydrophilic R-groups E. Large hydrophobic R-groups F. Negatively charged R-groups G. Positively charged R-groups

Peptide bond cleavage is the basic process of hydrolysis of a polypeptide where the peptide bond…

Answered: The following data describe the…

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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Suppose you discover that bacteria that express OmpF have concentrations of <0.1uM of ciprofloxacin in the cytosol but those without this substance have concentrations of up to 50uM in the cytosol by the time they die. What does this tell you about the function of the isolated substance, OmpF, which you suspected from the start was related to quinolone resistance? How is the OmpF structure optimized for this function? Which amino acids in OmpF are suited to each aspect of its function? The structure of ciprofloxacin is shown below for reference.
What would the order of migration be (bottom to top in the gel) in a SDS-PAGE for the following proteins? Concanavalin A (ConA) (a homotetramer of 106 kDa), lysozyme (a monomer of 14.3 kDa) & horse liver alcohol dehydrogenase (ADH) (a homodimer of 80 kDa). a. ADH, ConA, lysozyme b. ConA, ADH, lysozyme c. Lysozyme, ADH, ConA Od. Lysozyme, ConA, ADH
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)
Calculate the energy required, in ATP equivalents, to synthesize a 100-residue protein from free amino acids in E. coli (assume that the Nterminal Met remains attached to the polypeptide and that no ribosomal proofreading occurs).
1. Amino acid analysis of the peptide gave the following residues: Asp Leu Lys Met Phe Tyr. The following facts were observed: Trypsin treatment had no effect. The phenylthiohydantoin released by Edman degradation was C-C-CH2. Brief chymotrypsin treatment yielded several products including a dipeptide and a tetrapeptide. The tetrapeptide contained Leu, Lys and Met is some order. Cyanogen bromide treatment afforded a dipeptide, a tetrapeptide and a free Lys. What is the amino acid sequence for this heptapeptide?
(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…
Given the peptide Val-Ser-Gln-Lys The lateral chain of one of these amino acids can be modified by N-acetylation. Write the semi‐developed form of the lateral chain of this modified amino acid at pH 7 The lateral chain of one of these amino acids can be modified by phosphorylation. Write the semi‐developed form of the lateral chain of this modified amino acid at pH 7.
A family of proteins known as cupredoxins contain a single redoxactive Cu ion coordinated by a Cys, a Met, and two His residues. The reduction potentials of cupredoxins range from about 0.15 V to 0.68 V. What does this information reveal about the role of the protein component of the cupredoxins?
A ribonuclease reaction containing 0.50µM RNASE A will hydrolyze RNA at a maximal rate of 5µM/s in the presence of 40mM RNA at 37°C. What is the turnover number, kcat, for the enzyme (per second).
Assume that a new oxygen transport protein has been discovered in certaininvertebrate animals. X-ray diffraction of the deoxy protein reveals that ithas the dimeric structure shown in panel (a) of the accompanying figure,with a salt bridge between residues histidine 13 and aspartic acid 85. Thetwo monomers interact by salt bridges between the C- and N-termini. TheO2-binding site lies between the two iron atoms shown, which are rigidlylinked to helices A and C (see panel (b)). In the deoxy form, the spacebetween the iron atoms is too small to hold O2, and so the Fe atoms must be forced apart when O2 is bound.Answer the following questions, explaining your answer in each case interms of the structure shown below.(a) Is this molecule likely to show cooperative oxygen binding?(b) Is this molecule likely to exhibit a Bohr effect?(c) Predict the likely effect of a mutation that replaced aspartic acid 85 bya lysine residue.
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
The biosynthetic pathway for the two amino acides E and H is shown schematically in the Figure below: A W E 2 Z H How would this pathway change if C was mutated and non-functional?

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