3 of 3A protein was completely digested with trypsin and an internal peptide (i.e. not derivedfrom the N- or C-terminals) was purified. Determine its sequence from the following information:a) amino acid analysis yields one mole of D, T, P, L, Y, F, K, and R per mole of peptide;b) treatment of the intact peptide with FDNB, followed by acid hydrolysis, gives DNP-L and &-DNP-K;c) treatment of the intact peptide with chymotrypsin yields a tripeptide containing K, T, and D; atetrapeptide containing P, L, F, and R, and free tyrosine;d) the tripeptide, in part c, yields DNP-T and ɛ-DNP-K after reaction with FDNB and acid hydrolysis.Note: trypsin will not cleave on the carboxyl side of arginine or lysine if the next amino acid (donating theamino group) is proline.Put your answer here:

Amino Acid analysis or Protein Sequencing is a common method used to determine the sequence of amino…

Answered: A protein was completely digested with…

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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A heptapeptide was found to have an amino acid composition of Asp, Leu, Lys, 2 Met, Phe and Tyr. (a) Trypsin has no effect on the heptapeptide. (b) The phenyl thiohydantoin released by Edman degradation revealed phenylalanine in the N-terminus. (c) Brief chymotrypsin treatment yielded several products including a dipeptide and a tetrapeptide. The amino acid composition of the tetrapeptide was Leu, Lys, and Met. (d) Cyanogen bromide treatment yielded a dipeptide, a tetrapeptide, and free Lys. What is the amino acid sequence of this heptapeptide? Answer Format: (Three letter abbreviation with dash ie., Ala-Gly-…) *
1. A pentapeptide has the sequence of H2N-Glu-His-Leu-Arg-Gly-COOH. a) What is the net charge of the peptide at pH 3, 8, and 11? (Use pka values for side chains and terminal amino and carboxyl groups in the table provided.) peptide. b) Estimate the pl for this pK, values Abbreviation/ symbol pk, M, (-COOH) (-NH5) (R group) pK; pKR Hydropathy Occurrence in index* proteins (%)* Amino acid pl Nonpolar, aliphatic R groups Glycine Alanine Proline Valine 2.34 -0.4 Gly G Ala A Pro P 75 9.60 5.97 7.2 89 115 2.34 9.69 10.96 6.01 6.48 5.97 1.8 1.6 4.2 3.8 4.5 7.8 5.2 1.99 117 131 Val V 2.32 2.36 9.62 9.60 6.6 9.1 Leucine Leu L 5.98 Isoleucine lle I 131 2.36 2.28 9.68 6.02 5.3 Methionine Met M 149 9.21 5.74 1.9 2.3 Aromatic R groups Phenylalanine Tyrosine Tryptophan 2.8 -1.3 3.9 3.2 Phe F 165 1.83 9.13 9.11 9.39 5.48 2.20 Tyr Y Trp W 181 10.07 5.66 204 2.38 5.89 -0.9 1.4 Polar, uncharged R groups Serine Ser S 105 2.21 6.8 9.15 9.62 5.68 5.87 5.07 5.41 5.65 -0.8 Threonine Thr T 119 2.11 -0.7 5.9…
Partial hydrolysis of a protein yielded a number of polypeptides. One of them was purified. Deduce the sequence of amino acids in this polypeptide from the following information: (a) Complete acid hydrolysis yielded ala + arg + 2ser + lys + phe + met + trp + pro (b) Treatment with fluorodinitrobenzene (FDNB, the Sanger reagent) followed by complete acid hydrolysis yielded dinitrophenylalanine (DNP-ala) and a dinitrophenyllysine (e-DNP-lys) as the only DNP derivatives. (c) Neither carboxypeptidase A nor carboxypeptidase B released a C-terminal amino acid. (d) Treatment with cyanogen bromide (CNBr) yielded two peptides: One contained ser + trp + pro. The other contained all the remaining amino acids (including the second ser). (e) Treatment with chymotrypsin yielded three peptides. One contained only ser + pro. Another contained only met + trp. The third contained phe + lys + ser + arg + ala. (f) Treatment with trypsin yielded three peptides. One contained only ala + arg. Another…
You have isolated the following peptide: His-Ser-Arg-Ala-Glu-Leu-Pro-Gly A) Calculate the approximate charge of this peptide at pH 1, pH 3, pH 5, pH8, pH 11, and pH 14. B) What is the PI of this peptide?
The OXA-M290 protein is next purified by size exclusion chromatography. To determine the best type of size exclusion resin to use, the size of OXA-M290 must first be determined. Earlier, you determined the amino acid sequence of OXA-M290 (MRVLALSAVFLVASIIGMPAVAKEWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASSAKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYDTKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP). Based on the amino acid sequence, what is the molecular weight of this protein? You can use the free ProtParam tool (https://web.expasy.org/protparam/) to calculate the molecular weights of proteins. Make sure to include units in your answer. Note: The amino acid sequence reported earlier does not include the His-tag that was added to OXA-M290 by the pET-28a vector. However, you do not need to consider the amino acids in the His-tag in your answer to this question. For Context ONLY: For…
The sequence of a 29 aa long peptide can be determined from the following data. a) Treatment of the peptide with dansyl chloride reveals that the amino terminal is Val. b) Trypsin digestion, separation of peptides and Edman degradation give sequences for peptide fragments as follows: Val-Gly-Ala-His-Ala-Gly-Glu-Tyr-Gly-Ala-Glu-Ala-Thr-Glu Ala-Ala-Trp-Gly-Lys Val-Leu-Ser-Pro-Ala-Lys Thr-Asn-Val-Lys c) Chymotrypsin digestion, separation of peptides, and Edman degradation give the following sequences for fragments: Gly-Ala-Glu-Ala-Thr-Glu Gly-Lys-Val-Gly-Ala-His-Ala-Gly-Glu-Tyr Val-Leu-Ser-Pro-Ala-Lys-Thr-Asn-Val-Lys-Ala-Ala-Trp What is the sequence for the peptide?
1a) In MALDI-TOF data, when performing peptide mass mapping search, the number of peptides and the sequence coverage decreases, but protien score increase. Explain b) As the same as part a, the peptide masses and the coverage remain the same, but the protien score increase, explain how this can happen.
A) Based on the mRNA sequence below, provide the corresponding DNA template (5'-3') and protein sequences (N-C terminus) using the single letter abbreviations for each 5' GCA UAU CCU UGU GAU 3' B) Identify the two unique amino acids in the protein sequence above, provide their full names and brief explanation why you chose them C) Draw the two amino acids from 3. connected with a peptide bond to each other (with free amino and carboxy termini) at physiological pH|
a. An oligopeptide ALVGALGATPTPQMWSHSWRGVSIKS was digested with trypsin.Which method would be most appropriate for separating the products: ion exchange or gel filtration chromatography? Explain.b. Suppose that the peptide was digested with cyanogen bromide. What would be the optimal separation technique? Explain
A mixture of Asparagine (pl 5.41), Aspartic Acid (pl 2.98), Histidine (pl 7.59), Lysine (pl 9.74) and Threonine (pl 6.53) are separated by cation exchange chromatography. What is the order of elution of these amino acids if you use gradient buffer system from pH 10 to pH 2: v First 1. Asparagine v Second 2. Aspartic Acid 3. Histidine v Third 4. Lysine v Fourth 5. Threonine v Fifth 6. No separation
A peptide was analyzed with the following results. Whatis the primary sequence of the peptide? Briefly state the conclusions of each experimental result and indicate your logic. a)Mass spectrometry was consistent with a peptide of 7 amino acids containing W,C,D,M,N,K, and I. b)One cycle of Edman degradation of the peptide yielded a single product, the PTH derivative of I c)Cleavage of the peptide with CNBr yielded two products. One contained 5 amino acids, and the other 2. One cycle of Edman degradation yielded the PTH derivatives of Iand N, respectively. d)Treatment of the peptide with trypsin yielded 2 products. One of them had significant light absorbance at 280 nm, and Edman degradation yielded the PTH derivative of I. The other trypsin-generated product contained 4 amino acids, and Edman degradation yielded the PTH derivative of Asp.
Consider the following peptide: Lys-Tyr-Glu-His-Arg-Ala-Asp-Arg-Glu-Tyr-Lys a) What is the net charge of this peptide at pH=1? Show your work. b) What is the net charge of this peptide at pH=14? Show your work.

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