Proteins called molecular chaperones assist in the process of protein folding. One class of chaperones found in organismsfrom bacteria to mammals is heat shock protein 90 (Hsp90). All Hsp90 chaperones contain a 10 amino acid signaturesequence that readily allows identification of these proteins in sequence databases.Two representations of the Hsp90 signature sequence are shown here.Y-x-[NQHD]-[KHR]-[DE]-[IVA]-F-[LM]-R-[ED].4YSNKE/FLRE3.7.11 2 3 4 5 6 7 8 9 10CBits At which position(s) are amino acids limited to thoseWhich amino acid(s) are more commonly found at thewith positively charged side chains?01positions limited to amino acids with positively chargedside chains?O K and RO Y onlyO E only4K onlyD onlyH onlyR only8.OF onlyE and D10

Proteins are composed of amino acids, which are bound together by peptide linkage. Amino acids…

Answered: At which position(s) are amino acids…

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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Remembering that the amino acid side chains projecting from each polypeptide backbone in a β sheet point alternately above and below the plane of the sheet, consider the following protein sequence: Leu-Lys-Val-Asp-Ile-Ser-Leu-Arg- Leu-Lys-Ile-Arg-Phe-Glu. Do you find anything remarkable about the arrangement of the amino acids in this sequence when incorporated into a β sheet? Can you make any predictions as to how the β sheet might be arranged in a protein?
A particular protein has the amino acid sequenceN . . . Ala-Pro-His-Trp-Arg-Lys-Gly-Val-Thr . . . Cwithin its primary structure. A geneticist studyingmutations affecting this protein discovered that several of the mutants produced shortened protein molecules that terminated within this region. In one ofthem, the His became the terminal amino acid.a. What DNA single-base change(s) would cause theprotein to terminate at the His residue?b. What other potential sites do you see in the DNAsequence encoding this protein where mutation ofa single base pair would cause premature termination of translation?
A segment of the wild type of DNA sequence coding for the site of N501 mutation is shown below. TGTTGGCTACTAATGGCTATCATCACACGC… identify the correct reading frame, the amino acid sequence in a single letter code, and the charged residues and approximate net charge for this portion of the protein at pH 8 Given the location and type of the mutation, why would scientists potentially be concerned about this variant?
A heptapeptide when treated with trypsin produced two peptides. T1 (D, G, Y) and T2 (K, F, V, A). When the heptapeptide was treated with chymotrypsin, three peptides were produced: CT1 (K,,Y, G), CT2 (F,A, V), and CT3 (D). The sequences of these peptides is not known, however. When the peptide was treated with Sanger’s Reagent and hydrolyzed, DNP-K and DNP-A were recovered. What is the amino acid sequence of the heptapeptide?
You are trying to determine the PTMs on your protein of interest, so you set up a mass spectrometry experiment. You get the following data. Starting sequence: PRTEINSKICKASSDER After Trypsin digest, you get the following major peptides and weights from MS: TEINSKICK/1167 Da ASSDER/664 Da a. Which of these peptides is modified? b. What is the modification?
Proteins called molecular chaperones assist in the process of protein folding. One class of chaperones found in organisms from bacteria to mammals is heat shock protein 90 (Hsp90). All Hsp90 chaperones contain a 10 amino acid “signature sequence” that allows ready identification of these proteins in sequence databases. Two representations of this signature sequence are shown below. (a) In this sequence, which amino acid residues are invariant (conserved across all species)?(b) At which position(s) are amino acids limited to those with positively charged side chains? For each position, which amino acid is more commonly found?(c) At which positions are substitutions restricted to amino acids with negatively charged side chains? For each position, which amino acid predominates?(d) There is one position that can be any amino acid, although one amino acid appears much more often than any other. What position is this, and which amino acid appears most often?
A recent genome sequencing project for the bacterium Burkholderia mallei has identified a new protein with high similarity to the lysylphosphatidylglycerol flippase enzyme. A short section of the new protein sequence is shown below. TVEVNAPGDVQKALSELQQINDGRLDIRI (a) Are any reverse turns likely to be present? Explain your answer. (b) Are any beta-strands likely to be present? Explain your answer. (c) Are any alpha helices likely to be present? Explain your answer. (d) Is any supersecondary structure likely to be present? Explain your answer. (e) Identify two residues that are likely to be buried in the core of the folded protein. Explain your answer. (f) Identify two residues that are likely to be hydrogen bonded to each other. Explain your answer.
A common strategy for identifying distantly relatedhomologous proteins is to search the database using a shortsignature sequence indicative of the particular proteinfunction. Why is it better to search with a short sequencethan with a long sequence? Do you not have more chancesfor a “hit” in the database with a long sequence?
You are studying the toxic protein called ectatomin, a major component of ant venom (specifically from the species Ectatomma tuberculatum), that embeds into cell membranes and creates pores that cause cells to lyse. Ectatomin is a small dimer, meaning the protein is comprised of two polypeptides; the sequences of the two polypeptides are given in the table with single-letter abbreviations. polypeptide sequences of ectatomin monomers polypeptide protein sequence polypeptide 1 GVIPKKIWETVCPTVEPWAKKCSGDIATYIKRECGKL polypeptide 2 WSTIVKLTICPTLKSMAKKCEGSIATMIKKKCDK You could use absorbance at 280?? or colorimetric assays like the Bradford assay or bicinchoninic acid assay (BCA) assay to quantify the amount of ectatomin you have for your experiment. Why might you choose to use a colorimetric method instead of absorbance at 280??? Select the best answer. Measuring absorbance at higher wavelengths, like 595?? or 562??, is more accurate than measuring absorbance at…
why a literature sequence for Mpro includes additional 18 bases on the C-term that can not be found in the nature protein. what is the purpose of these bases?
Imagine a globular protein with a histidine that is involved in a salt bridge to an aspartic acid, in an internal (hydrophobic) region of the protein. What would happen to the pKa of that histidine R group if the protein was mutated, and the aspartic acid was replaced with an alanine? (i.e., would the pKa increase, decrease, or stay the same?). Assume that the location of the histidine stays the same. Explain your answer clearly
A sample of a peptide of unknown sequencewas treated with trypsin; another sample of the same peptide wastreated with chymotrypsin. The sequences (N-terminal to C-terminal)of the smaller peptides produced by trypsin digestion were as follows:

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At which position(s) are amino acids limited to those Which amino acid(s) are more commonly found at the with positively charged side chains? positions limited to amino acids with positively charged 01 side chains? 2 OK and R O Y only 4 O E only O K only D only H only R only 8. OF only E and D 10