2. As we've seen previously, peptide bonds involving the amino acid proline can populate both "trans"and "cis" isomers.trans-Procis-ProThis isomerization reaction can be the rate-limiting step in protein folding. Depending on the proteinsequence, the relative favorability of the trans and cis states can change. For Pro-117 in the proteinstaphylococcal nuclease, the rates of the forward and reverse reactions are: ktrans→cis = 3.1 × 10-2and kcis→trans = 2.5 x 10-3 s-1.(a) What is AG°' for this reaction?(b) A prolyl isomeriase enzyme increases the rate of the forward reaction to kcat.trans->cis = 2.6 s-1.What is the new rate constant for the reverse reaction (kcat,cis→trans)?(c) This prolyl isomerase is a Michaelis-Menten enzyme with kcat = 2.6 s!, KM = 1.9 µuM. Ifyou have 1 nM enzyme, what is Vo for [S]o = 0.7 µM? What about [S]o = 30 µM? For eachcondition, what limits the reaction speed?

Michaelis-Menten model of enzyme kinetics is a very useful model which describe the relationship…

Answered: 2. As we've seen previously, peptide…

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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2. The mature form of TEM-1 ß-lactamase, an enzyme of 290 amino acid residues that hydrolyzes penicillin antibiotics. The protein has the following polar amino acid side chains: 18 Arg; 11 Lys; 6 His; 4 Tyr; 16 Asp; 20 Glu; 8 Asn; 5 Gln. Approximate pKa values 1.5 Arginine 12.5 Lysine 10.0 Histidine 6.5 OD 280nm Tyrosine 10.0 Aspartate or Glutamate 4.0 Terminal NH3+ 8.0 Terminal COOH 4.0 0.0 Α - 0.01 0.10 KCI B Volume (mL) The chromatogram above shows a typical result in the purification of TEM-1 ß-lactamase overex- pressed in E. coli cells. The protein is eluted from an anion exchange column at pH 6.25 with an increasing gradient of KCI. Fraction A is shown to correspond to native enzyme. Since Fraction B has the same amino acid sequence for the first 10 residues, the conclusion is that this fraction represents enzyme in which side chains of glutamine or asparagine residues have been hydrolyzed (deamidated). (a)( ) What is the isoelectric point of the native enzyme? (b)( ) Compared to…
Consider the hypothetical serine protease in the image, which shows the specificity pockets. The S1 pocket is small and hydrophobic, the S2 pocket is deep and hydrophobic, and the S1' pocket has an aspartate residue in the bottom. If the amino acids involved are K, W, and G, which pair is joined by the peptide bond that will be cleaved by the protease? MAKE SURE YOUR CHOICE REFLECTS THE S1-S ORDER DESCRIBED. S1 Rs R1 Ri H. S2 S OGK OKAN OwG IZ IZ
Assume that the 3 polypeptide strands shown below form a parallel B-sheet. Select amino acids AA1, AA2, and AA3 so that the parallel B-sheet is amphipathic and remains stable. Glu-lle-Asn-AA1-Cys-Val Ser-AA2-GIn-Leu-Lys-Phe Lys-Met-Cys-Leu-AA3-Val O AA1 = Pro, AA2 = Leu, AA3 = lle O AA1 = Val, AA2 = Leu, AA3 = Asn O AA1 = Ala, AA2 = Gly, AA3 = Leu AA1 = Phe, AA2 = Arg, AA3 = Ala O O
The diagram to the right illustrates the inter-actions of the amino acid side chains of two a-helical polypeptide strands in a coiled-coil, viewed end-on and projected along the helix axes from the N-terminal to the C-terminal end. Are the macrodipoles of the two a- helices oriented parallel or anti-parallel? For this projec- tion is the positive end of the macro-dipole in the sur- face of the paper or below the surface? f C b g e d a' a d' g b' f'
10. In eukaryotic cells, glycosylation activity of membrane proteins is found in the lumen of the endoplasmic reticulum (ER) and is accomplished by the enzyme oligosaccharyl transferase (OST), which adds oligosaccharides to the amino group of Asn residues of the consensus sequence Asn-X-Thr/Ser. a. The following ER membrane protein construct has a cytosolic N-terminal region and a membrane-spanning variable sequence. The variable sequence is a signal anchor (SA) sequence. Would you expect the C-terminal region of the B subunit to be glycosylated? Why or why not? variable sequence C-terminal region of B-subunit N-terminal region b. An additional transmembrane region is added to the construct prior to the variable sequence, as shown below. The transmembrane is a signal anchor (SA) sequence, while the variable sequence is a stop transfer anchor (STA) sequence. Would you expect the C-terminal region of the B subunit to be glycosylated? Why or why not? C-terminal region of B-subunit…
3. The trp repressor is a homodimer with 107 amino acid residues per monomer. The content of proton dissociable groups of each monomer is given below: Side chain pKa number/monomer ZpH 4 ZpH 6 12.5 Arginine Aspartate Glutamate 9. 4.0 4.0 10 Histidine 6.0 2 Lysine Tyrosine -NH3® 10.0 6 9.5 2 7.0 1 -СООН 4.0 1 (a) ( : ) The isoelectric point (pl) of the protein, i.e., the pH at which the overall electrostatic charge on the protein E z = 0, is 5.3. Although the pKa values in the table above are only approximate values generally characteristic of residues with unhindered exposure to solvent, confirm that the overall charge on the protein must pass through zero between pH 4 and pH 6. ) Estimate what must be the average pKa value of all of the residues containing carboxylic (b) ( acid groups using the H-H equation below, assuming that the pka values of the positively charged groups do not change from the values given in the table above: pH pKa log [base]/[acid] + DNA te
2. The diagram to the right shows the change in the structure of the C-terminal portion of each of the ẞ-subu- nits of human hemoglobin (HbA) in the oxyHb to deox- yHb or R-to-T transition. The hydrogen bonding interac- tion of the C-terminal ẞHis 146 residue with the side chain of Asp94, highlighted by the red ellipse, has been shown to be responsible for a major portion of the proton uptake associated with the Bohr effect. Treatment of HbA with the enzyme carboxypeptidase A (CPA) results in loss of the C-terminal ẞHis 146 and ẞTyr145 residues of the ẞ- subunits. (a) ( ) Draw a Hill plot [log(Y/[1-Y]) vs. log(pO2), Y = fraction of heme groups occupied by O2] to compare the values of the Hill coefficient nн and the O2-binding affinity at pH 7.4 of normal HbA before and after treat- ment of with CPA. (b) (' ) How will the plot for CPA-digested HbA change at pH 7.2? (c) 1 Hi5146 HN- ✓ Low PK B-chain. CH2 CH-NH-CO-CH-NH- CH₂ Tyr145 он HbO2 or R state Туг145 CH-CH2- OH co NH CH CH₂ His…
Given the following diagram of how protein AWESOME1 binds to it's target DNA, describe the potential effects of each of the 5 mutations shown below. The wild-type sequence of a helix #1 is also shown in the blue box, and all the mutations are in helix #1 (see numbers for identifying particular residues). a helix #1 R(1)-V-I-L-Y-F-W-I-M-Y-F-S-H-Y-W-R(16) #1 Predict the consequence of the following mutations: 1) Arg(1) to Glu 2) Arg(1) to Ala 3) Phe(6) to lle 4) Trp(7) to Phe 5) Met(9) to Pro in
1. What is the length in AA’s of the LilP protein? Assume fMet is NOT CLEAVED. 2. Write out the sequence of the polypeptide in AA: use the three letter notation, e.g. Met-Ser-Pro-
I. A protein, X, was Isolated from a pathogenlc mlcroorganism. The proteln Is a vlrulence factor whose path0genlclty lies In a heptapeptide of unknown sequence. After trypsin cleavage of the heptapeptide from protein X, the peptlde's compOsition and sequence was determined. The fOllowing were the results of the sequenclng process: 1. When the peptide was treated with dinitrofluorobenzene (DNFB), DNP-asp and a mixture of amino acids were produced. 2. When the same Intact peptide was treated with streptococcal protease, a pentapeptide of composition asp, asN, cys, gly and ser and 2 amlno acids were released. 3. When the heptapeptlde was also treated with hydrOxylamine HCI, a tripeptide and a tetrapeptide were obtained. The C-terminal amino acid of the tripeptide was asN. 1) What is the sequence of the heptapeptide if it is composed of cys, asp, lys, asN, gly and ser only? 2) What is the pl of the heptapeptide?
Consider the hypothetical serine protease, which shows the specificity pockets. The S, pocket has a glutamic acid in the bottom, the S, pocket is small and hydrophobic, and the S,' pocket is deep and hydrophobic. Suggest an amino acid sequence that this protease would cleave. HRY S2 Si Which of the sequences would this protease cleave? O Lys-Ala-Leu O Ala-Lys-Leu Leu-Ala-Lys Ala-Leu-Lys O Leu-Lys-Ala O Lys-Leu-Ala C=O
3. Approximate molecular weight for an unknown protein from gel-filtration experiment is 130 kDa. Thirty six mg of this pure protein was treated with excess of fluorodinitrobenzene. After the reaction and complete acid hydrolysis the mixture was found to contain 356 µg of dinitrobenzene derivative of methionine (free acid) and no other amino acid-dinitrobenzene derivatives. Is this protein consisting of single polypeptide chain or multiple subunits? If it consists of multiple subunits, then how many? From these data, can you calculate the molecular weight of the protein more precisely?

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