A biotechnology company focused on peptide therapeutics is investigating theproperties of several peptides for a variety of applications. Their sequences aregiven below:Pep A: NGSLGAAGRGPep B: KKALLAHALHPep C: LVQAIFPTPSa. What is the net charge of each sequence at pH 7 (to the nearest 0.1 chargeunit)?b. Which peptide sequence would be most likely to be part of an intrinsicallyordered domain in a protein? Explain.c.Which peptide would likely be best suited as part of a pH-sensitive drug carrierthat is designed to change its charge between neutral pH and endosomal pH(which is between 5 and 6)? Explain.d. Which peptide sequence would be most likely to be buried in the interior of aprotein? Explain.

First thing one must observe while studying any peptide sequence is to look at the nature of the…

Answered: A biotechnology company focused on…

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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2q Which of the peptide sequences below best matches the hydropathy plot shown? 5 10 Residue Number RAFLILFMTYFLILFLI ILYYAGSREDHSGYLIL LHGDQNRERDGHSQERD EQSDTERNQHGALIYLI 3q Which of the peptide sequences below best matches the hydropathy plot shown? 5 10 Residue Number Hydropathy value -4 -2 0 2 4 Hydropathy value -4 -2 ILYYAGSREDHSGYLIL EQSDTERNQHGALIYLI LIFLAIFPAGSTSEDRR RAFLILFMTYFLILFLI L 15 15
Which of the peptide sequences below best matches the hydropathy plot shown? L 10 Residue Number 4 2 Hydropathy value -2 0 セー RAFLILFMTYFLILFLI ILYYAGSREDHSGYLIL OLHGDQNRERDGHSQERD EQSDTERNQHGALIYLI 01 5 15
Which of the peptide sequences below best matches the hydropathy plot shown? 5 10 15 Residue Number ILYYAGSREDHSGYLIL EQSDTERNQHGALIYLI LIFLAIFPAGSTSEDRR RAFLILFMTYFLILFLI LHGDQNRERDGHSQERD 2 Hydropathy value 0 -4 -2
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?
A researcher has synthesized two peptides and needs to confirm whether the peptides were synthesized with the correct sequence using mass spectrometry. What is the sequence of the b4 and y7 ions for peptide GAMECHANGER? The peptide SLISRAEFLAGVRVGV is digested with trypsin. Then the products of the digestion are subjected to ESI TOF-MS in positive ion mode with the peptides in a pH 2 solution. What peptide fragments will result and what are their m/z?
Draw the structure of peptides TGPNLHGLFGR and ELAGAPPEPA, and calculate m/z values of their an, bn, and yn sequence ions.
The amino acid sequence of three peptide fragments are shown below. Peptide 1: QAMGRAGDLKYLGLHSV Peptide 2: ALMALFMVMALVLVSVLFIA Peptide 3: MVEDLLKQIARYLISE (a) Circle all of the charged residues in peptide 1 (assume pH =7.0). Box all of the aromatic residues in peptide 2. Underline all of the nonpolar residues in peptide 3. (b) Determine the net charge of the predominant form of each of the peptides at pH 4.5 and pH 11.5. Assume the ionizable groups have the pKa values listen in Table 2.1 of your text. (c) Which of these peptides would be most likely to be found as an alpha helix in a soluble (cytoplasmic) protein? Which would be most likely to be found as an alpha helix in a transmembrane protein? Which would be least likely to form an alpha helix of any kind?
Identify and briefly describe the different PEGylation strategies you can use to PEGylate this peptide and draw the chemical structure of the resulting mPEG peptide conjugates.
"Regarding resolution of mass spectrometers and various ways mass of peptides can be represented, which is or are true? " "A larger peptides will have a smaller difference between the monoisotopic and average masses, compared to smaller peptides, because the contribution of 13C is greater. " Higher resolution allows investigators to distinguish between monoisotopic masses and other masses of otherwise identical peptides. "Average mass size is always smaller than monoisotopic mass, because 13C and 15N contribute to monoisotopic mass. " "Monoisotopic mass is calculated as if there are no heavy isotopes within the peptide, and so is always smaller than the average observed mass."
A peptide has the following amino acid composition: 2 Met, 2 Phe, 2 Glu, 1 Arg, 1 Lys, 1 Val, 1 Leu, 1 Gly, 1 Ser Reaction of the intact peptide with dansyl chloride followed by acid hydrolysis creates a derivative of Met. A specific cleavage of the intact peptide produces fragments with the following sequences: Fragment A: Glu-Gly-Lys-Phe Fragment B: Met-Ser-Leu-Arg Fragment C: Met-Val-Glu-Phe Which reagent was used for the specific cleavage? Cyanogen bromide Carboxypeptidase A Trypsin Chymotrypsin
A peptide has the following amino acid composition: 2 Met, 2 Phe, 2 Glu, 1 Arg, 1 Lys, 1 Val, 1 Leu, 1 Gly, 1 Ser Reaction of the intact peptide with dansyl chloride followed by acid hydrolysis creates a derivative of Met. A specific cleavage of the intact peptide produces fragments with the following sequences: Fragment A: Glu-Gly-Lys-Phe Fragment B: Met-Ser-Leu-Arg Fragment C: Met-Val-Glu-Phe What information do this result give about the sequence of the peptide? Explain how you arrived on you answer.
A peptide with 19 amino acid residues was digested with trypsin and generated the following fragments: • GGIR SFLG WAAPK AEEGLR A similar peptide was treated with chymotrypsin and generated the following fragments: • LG AEEGLRW AAPKGGIRSF Elucidate the correct sequence of the peptide.

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