Thank you very much as your assistance is greatly appreciated. Our growing understanding of how proteins fold allows researchers to make predictions about protein structure based on aminoacid sequence data. Consider the amino acid sequence.123459.10Ile – Ala - HisThr – Tyr – Gly –Pro –Phe – Glu – Ala11121314151617181920Ala -Met – Cys – Lys – Trp – Glu – Ala – Gln –Pro – Asp –2122232425262728Gly – Met – Glu – Cys – Ala –Phe – His – ArgWhere might bends or ß turns occur?Where might intrachain disulfide cross-linkages form?residues 14 and 16between residues 4 and 18residues 7 and 19between residues 12 and 22residues 9 and 19between residues 13 and 24between residues 14 and 16residues 10 and 11 Suppose that the sequence is part of a larger globular protein.Consider the probable location, either on the external surfaceWhich statements correctly describe the probableor the interior of the protein, of each of the aminolocations of the amino acids?acid residues.Ala is located on the external surface of the proteinbecause it is polar.The table gives the hydropathy index values for selectedamino acids in the peptide.Thr is polar and can be located on the externalsurface or in the interior of the protein.Amino acidHydropathy indexAsp is located on the external surface of the proteinbecause it is charged.alanine1.8isoleucine4.5Gln is located in the interior of the protein because itis uncharged.Ile and Lys are located in the interior of the proteinbecause they are not polar.threonine-0.7glutamine-3.5lysine-3.9aspartate-3.5

The proteins are composed of twenty standard amino acids that differ from each other on the basis of…

Our growing understanding of how proteins fold allows researchers to make predictions about protein structure based on amino acid sequence data. Consider the amino acid sequence. 1 2 3 4 6. 7 8 9. 10 lle – Ala - His - Thr – Tyr – Gly –Pro –Phe - Glu – Ala 11 12 13 14 15 16 17 18 19 20 Ala – Met – Cys – Lys – Trp – Glu – Ala – Gln – Pro – Asp – | 21 22 23 24 25 26 27 28 Gly –Met – Glu – Cys – Ala -Phe – His – Arg

Our growing understanding of how proteins fold allows researchers to make predictions about protein structure based on amino acid sequence data. Consider the amino acid sequence. 1 2 3 4 6. 7 8 9. 10 lle – Ala - His - Thr – Tyr – Gly –Pro –Phe - Glu – Ala 11 12 13 14 15 16 17 18 19 20 Ala – Met – Cys – Lys – Trp – Glu – Ala – Gln – Pro – Asp – | 21 22 23 24 25 26 27 28 Gly –Met – Glu – Cys – Ala -Phe – His – Arg

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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Treatment of a polypeptide with 2-mercaptoethanol yields two polypeptides 1. Ile—Val—Cys—Arg—Thr—Gly—Cys—Lys—Asn—Phe—Leu2. Trp—Lys—Cys—Phe—Arg—His—Thr—Lys—Cys—SerTreatment of the intact polypeptide with trypsin yields fragments with the following aminoacid compositions(Arg, Cys2, Ile, Ser, Val)(Arg, Cys2, Gly, Lys, Thr, Phe)(Asn, Leu, Phe)(His, Lys, Thr)(Lys, Trp)Edmands chemistry reveal the following PTH derivatives in equal quantity after cycle 1• PTH--Ile and PTH--Trp a) Rewrite the intact polypeptide, by indicating the positions of the disulfide bonds(Indicate your reasoning) b) How many products do you expect after chymotrypsin cleavage of the intactpolypeptide? c) You are performing an isoelectric focusing experiment (IEF) on a gel with a pH range of 2to 14. Indicate on the diagram below at what point along the gel will peptide 1 abovefocus, in the presence (X) and absence (Y) of DTT. (also show your calculations)
Calculate the overall net charge of the following polypeptide at pH = 2.0Gly-Pro-Glu-Asp-Leu-His-Ile-Gln-Asn-Phe A) +1.76 B) -1.76 C) +0.24 D) -0.24
Ala Leu Glu Glu Asn Ala represent the following amino acid in its predominant form at pH= 7
Treatment of a polypeptide by 2-mercaptoethanol yields two polypeptides that have the following amino acid sequences: Ala-Phe-Cys-Met-Tyr-Cys-Leu-Trp-Cys-Asn Val-Cys-Trp-Val-Ile-Phe-Gly-Cys-Lys Chymotrypsin-catalyzed hydrolysis of the intact polypeptide yields polypeptide fragments with the following amino acid compositions: (Ala, Phe) (Asn, Cys2, Met,Tyr) (Cys, Gly, Lys) (Cys2, Leu,Trp2,Val) (Ile, Phe,Val) Indicate the positions of the disulfide bonds in the original polypeptide.
Treatment of a polypeptide by 2-mercaptoethanol yields two polypeptides that have the following amino acid sequences: Ala-Phe-Cys-Met-Tyr-Cys-Leu-Trp-Cys-Asn Val-Cys-Trp-Val-Ile-Phe-Gly-Cys-Lys Chymotrypsin-catalyzed hydrolysis of the intact polypeptide yields polypeptide fragments with the following amino acid compositions: (Ala, Phe) (Asn, Cys2, Met,Tyr) (Cys, Gly, Lys) (Cys2, Leu,Trp2,Val) (Ile, Phe,Val) Indicate the positions of the disulfide bonds in the original polypeptide. I don't understand how the order of amino acids in Step 2 was arranged. Please explain. Thank you.
Identify and encircle the peptide bonds in this polypeptide (Asp-Sec-Leu-Cys-Glu).
Ile-Ala-His-Thr-Tyr-Gly-Pro-Phe-Glu-Ala-Ala-Met-Cys-Lys-Trp-Glu-Ala-Gln-Pro-Asp-Gly-Met-Glu-Cys-Ala-Phe-His-Arg What will be the secondary structure formed from this sequence?
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?
Consider the peptide Trp-Arg-Glu-Cys-Gly-Tyr. For the drawings requested below, please show them in zig-zag style, from amino to carboxy terminus, with correct stereochemistry Draw the predominant form at pH = 2 Draw the predominant form at pH = 5 Draw the predominant form at pH = 7 Draw the predominant form at pH = 12
Write the one letter code for the oligopeptide Ser-Cys-Ile-Glu-Asn-Cys-Glu and calculate the total charge on it at pH 4.5.
Ala-Arg-Val-His-Asp-Gln Given the polypeptide chain above Estimate the net charge of the polypeptide chain at physiological pH (7.4) and at pH 5.0 . How many peptide bonds are there? What kind of polypeptide is it?
The following are sequences from three different alpha helices found inhuman proteins: hBak(72-87): GQVGRQLAIIGDDINR hCB1(196-210): VTASFTASVGSLFLT hCB2(248-262): LVLAVLLICWFPVL Classify each of these three helices as either a) mostly hydrophobic, b)mostly hydrophilic, or c) amphipathic. Use the helical wheel to explainyour answers. Given the character of these helices, in which part of the protein wouldyou expect them to reside?