Draw Ramachandran plot for: a) regular secondary structure with Φ = 60-65 and Ψ = 60-80
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Draw Ramachandran plot for:
a) regular secondary structure with Φ = 60-65 and Ψ = 60-80
b) regular secondary structure with Φ = -170 and Ψ = 170
c) intrinsically disordered proteins
d) explain why these Ramachsndran plots will be different, and what secondary structures are described in A and in B
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- Let’s consider histidine as a free amino acid in aqueous solution. a) Draw the most likely structure of histidine under biochemical standard state conditions. b) Given that free histidine has the following three pKa values, assign each to its corresponding acidic hydrogen or conjugate base in your structure from part a). pKa1 = 1.7; pKa2 = 6.2; and pKa3 = 9.1 c) For each pKa, give the corresponding expression for the equilibrium constant. It helps to write out the chemical equation for each. d) Create a speciation diagram for histidine by plotting Xi vs pH from pH = 4 to pH = 8 where Xi is the mole fraction of the two histidine species involved in the K2 equilibrium in part c).Before high performance liquid chromatography (HPLC) methods were devised for the separation and analysis of small peptides, electrophoresis on a paper support was frequently used. Separation was affected on the basis of the charge on a peptide at different pH values. a. Calculate the pI (isoelectric point) of the following primary structures of the following protein i.) Lys- Gly- Ala- Glyii.) Lys- Gly-Ala-Gluiii.) His- Gly- Ala- Gluiv.) Glu- Gly- Ala -Gluv.) Gln-Gly-Ala-Lys b.) the migration toward the cathode, the negative pole; A for the migration toward the anode, the positive pole; and O if the peptide remains stationary.A peptide was analyzed with the following results. What is the primary structure of the peptide? State what each experimental result reveals about the structure and indicate your logic. a) Amino acid analysis: R, C (2 equivalents), G, I, H, M, Y, Vb) After one round of Edman degradation, a mixture of glycine and isoleucine were detected. c) Treatment with beta-mercaptoethanol yielded two peptides, a 4-mer and a 5-mer.
- A protein contains three 60-kD polypeptides and six 20-kD polypeptides. Each 60-kD chain is disulfide bonded to two 20-kD chains. The 100-kD units associate noncovalently to form a protein with a molecular mass of 300 kD. Which of the following is correct? a) PAGE shows one single band b) Molecular masses determined by SDS-PAGE with 2-mercaptoethanol are 20kD and 60 kD c) Molecular mass determined by gel filtration is 300 kD d) All answers are correct e) Molecular mass determined by SDS-PAGE without 2-mercaptoethanol is 100 kD can you explain the steps and calculations to solve this question?Kwon Soon-young was asked by his CHEM 160.1 lab instructor to determine the isoelectric pH of an unknown protein sample which is said to be 20% histidine (pI = 7.59), 25% lysine (pI = 9.74), and 55% arginine (pI = 10.76). He plans to perform isoelectric precipitation in order to determine the IpH of the unknown protein sample. From the three buffer solutions below, at which particular buffer system do you think the unknown protein is most likely to precipitate? Explain your reasoning. BUFFER SYSTEM citrate buffer bicarbonate buffer methylamine-methylammonium chloride buffer pH 3.15 7.41 10.46The following proteins were separated by SDS-PAGE in the presence of mercaptoethanol. Sketch the relative positions of the various polypeptides on the gel. Label the positive and negative ends of the gel.Protein A: 40 kDa single polypeptideProtein B: 80 kDa protein, made up of two subunits of molecular weight 20 kDa and 60 kDa, held together by noncovalent interactionsProtein C: 200 kDa protein, made up of four identical subunits (50 kDa each) linked together by disulfide bonds
- The elution of a protein with an isoelectric point of 7.5, is mostly likely to be affected by a change in pH from 7.4 to 6.9 in which type of protein separation technique? a.) size exclusion chromatography b.) SDS-acrylamide gel electrophoresis c.) affinity chromatography d.) ion exchange chromatographyAn ion-exchange chromatographic separation is performed using a diethyl-aminoethyl- (DEAE)-sepharose column to separate proteins in a mixture. The mixture contains Protein A (pl=6.0), B (pl35.0), C (pl=7.5), D (pl =1), and E (pl=4.0). The protein mixture is prepared in a buffer solution pH =5. When the protein mixture is loaded onto the column, and the column is washed with a buffer solution pH 5, which protein(s) will be captured by DEAE-sepharose in the column? O Protein B because it is predominantly in net negative charge form. O Proteins D and E because they have predominately net negative charge in pH 5 solution O Proteins A, C, D and E because they have charges O Proteins A and C because both both predominantly have net positive charges O Proteins Band E because both predominantly have net positive chargeswhich in is the best method for separating proteins A and B that have the properties below: Protein A: a tetramer of identical 80kDa subunits with a pl of 6.4 Protein B: a monomeric protein with a MW of 80kDa and a pl of 9.2 A.) Anion exchange chromatography at pH 11 B.) Gel exclusion chromatography C.) Cation exchange chromatography at pH 4 D. Cation exchange chromatography at pH 11 E.) SDS-PAGE
- Draw the form of histidine (pl = 7.6) that predominates at (i)pH = 7.6 %3D (ii)pH = 10.5 (iii)pH= 5.0 (iv)pH= 1.2In your laboratory, you plan to use ion exchange chromatography to separate the peptide show below from a mixture of different peptides at pH 7.0. Peptide: GDVRWKKFQR A) Draw the structure of the peptide shown above at pH 7. B) Determine the charge of the peptide at pH 7. C) Should you choose a matrix containing DEAE(anion exchange) or CM (cation exchange)? Explain your reasoning in 3-5 sentences. SUBMIT A SINGLE DOCUMENT (PDF) WITH THE THREE REQUIRED ANSWERS. Upload Choose a File1)Ubiquitin is a small protein with a monoisotopic mass of 8560 Da. a) Electrospray ionization of this small protein typically results in major charge states of +8, +9, +10, +11, +12, and +13. Using this information, complete the table below, assuming the charges on each come from protonation. Report mass and m/z values to the ones place. b) Using the data you entered in the table, sketch an expected ESI-MS spectrum for ubiquitin. Label each peak with its charge state. What do you notice about the spacing of peaks along the x-axis. c)The figure shows an experimentally obtained electrospray mass spectrum for ubiquitin. Compare this spectrum to the spectrum you predicted. Are there any differences? If so, what might cause these differences?