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1. What will happen if there is a change in the configuration of a protein molecule? Provide an example.
2. Give the IUPAC name for Ala-Gly-Leu
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- 2. Consider the peptide Trp-Arg-Glu-Cys-Gly-Tyr. For the drawings requested below, please show in zig-zag style, from amino to carboxy terminus, with correct stereochemistry a. Draw the predominant form at pH = 2 b. Draw the predominant form at pH = 5 c. Draw the predominant form at pH = 7 d. Draw the predominant form at pH = 124. A. Draw the structure of the following peptide sequence at pH 2.0: ASP-ALA-THR-LYS-GLY B. What is the net charge of this pentapeptide at pH 2.0?3a) The 3° structure of a protein refers to the protein's overall, 3-dimensional shape in space. This will incorporate any 2° structure the protein has, but is predominantly the result of side-group interactions. Name the type of interaction, if any, that you would expect to see under physiological conditions (an aqueous solution at pH 7.0-7.5) between the following pairs of amino acid side groups. Serine and asparagine: Methionine and lysine: Glutamate and aspartic acid: Alanine and phenylalanine:
- 1. To determine the sequence of amino acids in protein, partial hydrolyses at different points are made and then compared to other sets of partial hydrolyses For example: Complete hydrolysis gave: Phenylalanine-1 Histidine-2 Glutamic acid-1 Leucine - 4 Asparagine-1 Cystine -2 Glutamine-1 Glycine - 2 The Partial Hydrolyses yielded the following: 1st Hydrolysis : 4 polypeptides ● . IA: phe-val-asn-gln-his-leu IB: IC: leu-tyr-leu-val ID: val-cys-gly 2nd Hydrolysis: 3 polypeptides IIA: phe-val-asn-gIn-his-leu-cys-gly-ser-his-leu IIB: val-glu-ala-leu-tyr-leu IIC: val-cys-gly Write down the primary structure of this polypeptide by finding the overlaps of the amino acids therein: Serine-1 Valine-3 Alanine-1 tyrosine-1 cys-gly-ser-his-leu-val-glu-ala4) For various amino acid pairs (for example: F to A, E to R, D to N, V to L, S to W), ask yourself: a) Based on what you know about the chemical properties of the side chains, what effect would you expect on the stability of the protein if you mutated one residue of the pair into the other in the interior of the protein? What forces might have an impact on this change (ie: what types of interactions would you expect that amino acid to be involved in?) How would your answer change if the amino acid were located on the surface of the protein? b) c)A peptide has the sequence Glu-His–Trp–Ser-Gly–Leu-Arg-Pro–Gly The pK, values for the peptide's side chains, terminal amino groups, and carboxyl groups are provided in the table. Amino acid Amino pKa Carboxyl pKa Side-chain pKa glutamate 9.60 2.34 4.25 histidine 9.17 1.82 6.00 tryptophan 9.39 2.38 serine 9.15 2.21 glycine 9.60 2.34 leucine 9.60 2.36 arginine 9.04 2.17 12.48 proline 10.96 1.99 Calculate the net charge of the molecule at pH 3. net charge at pH 3:
- 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 = 12Two peptide segments are shown below. Predict which one would have the most negative AG when going from an unfolded to a folded structure. Justify your choice. (i) Gly-Ala-Asn-lle-Val-Trp-Leu-Glu-Met-Phe-Val-Pro OR (ii) Ala-Gly-Lys-lle-Arg-Tyr-Thr-Cys-Val-Glu-Met-Ser1. Cysteine is an important amino acid that stabilizes the structure of peptides and proteins by the formation of disulfide bond with another cysteine residue. Illustrate the titrimetric profile of cysteine and calculate its isoelectric pH. [Hint: The sulfhydryl group is titratable] 2. The tripeptide Glu-Pro-Arg (EPR) which is a product of Lactobacillus casei fermentation of milk was found to have potent blood pressure lowering properties. Draw the structure of the tripeptide, give its systematic name, show its titration profile, and determine its isoelectric pH.
- A peptide has the sequence Glu-His-Trp-Ser-Gly-Leu-Arg-Pro-Gly The pK₁ values for the peptide's side chains, terminal amino groups, and carboxyl groups are provided in the table. Amino acid Amino pKa Carboxyl pKa Side-chain pKa glutamate 9.60 2.34 4.25 histidine 9.17 1.82 6.00 9.39 2.38 9.15 2.21 9.60 2.34 9.60 2.36 9.04 2.17 10.96 1.99 tryptophan serine glycine leucine arginine proline Calculate the net charge of the molecule at pH 3. Calculate the net charge of the molecule at pH 8. 12.48 net charge at pH 3: net charge at pH 8:27. Draw palmitic acid, identify a, B and w carbons, write out its short hand notation 28. Examine the peptide sequence below and then answer the questions: H2N-Gly- Leu- Ala-Asp-Cys-Asn-Trp-lle-Ser-Phe-Lys-Cys-Arg-Pro-coOH a. Circle the asparagine residue b. A possible intramolecular disulfide bond can be formed within this peptide between which two residues? c. Circle one residue which has a positively charged side chain under pH 7.4 d. Circle one residue which has a negatively charged side chain under pH 7.4 e. Circle the residue which can be phosphorylatedA mixture of Aspartic Acid (pl 2.98), Histidine (pl 7.59), Lysine (pl 9.74), Phenylalanine (pl 5.48) 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. Aspartic Acid v Second 2. Histidine v Third 3. Lysine 4. Phenylalanine v Fourth 5. Threonine v Fifth 6. No separation