Practice Exam 1 Fall08 - Name CHM 3218 Fall 2008 Practice...

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Unformatted text preview: Name CHM 3218 Fall 2008 Practice Examination #1 University of Florida Honor Code Statement: ”On my honor, I have neither given nor received unauthorized did in doing this assignment. " Student signature Instructions: You would have .two hours in which to complete this exam. All books, notes and other aids would be prohibited, with the exception of molecular models and calculators. Be sure to budget your time and answer questions briefly but completely. To receive partial credit for incorrect answers, be sure to show your work, particularly in problems involving calculations. Write your name on each page. 1. Consider amino acid derivative 1 and its hydrolysis products for the questions in this section. (Total 20 points). a. Assign correct (R) i (S) designations to each asymmetric center in structure 1. (4 points). b. Which of the compounds shown below in their Fischer projection forms (2 — 5) corresponds to the hydrolysis product of 1? Is the correct structure a D- or L-amino acid? (4 points). CO2H COZH COZH COZH N N 2 3 4 5 c. What is the name and one-letter code for the hydrolysis product of 1? (3 points). d. If 1 is added to water that is initially at neutral pH and the hydrolysis is allowed to proceed to completion in the absence of a buffer, will the final pH of the solution be acidic, neutral or basic? Show the relevant equilibrium (or equilibria) to support your answer. (4 points). Page 1 Name e. Consider the four graphs shown below (Curves A — D). Which of these corresponds to the titration behavior expected for the complete aqueous hydrolysis product of 1? Briefly explain your answer, indicating the places on your chosen curve from which pKa values can be determined (and the approximate values). (5 points). 12 — 12 — Curve A Curve B 10 10 8 8 PH 6 pH 6 4 4 2 2 0 0 I I I I I I 0.0 0.5 1.0 1.5 2.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 Equivalents of NaOH S Equivalents of NaOH 12 Curve D 10 8 pH 6 4 2 0 I I I I I I 0 I I I I I 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 Equivalents of NaOH Equivalents of NaOH Page 2 Name Page 3 Name 2. This problem explores the effect of structure on pKa values using alanine and homopeptides of alanine (Table 1) as examples. (Total 20 points). Table 1. Ionization behavior of alanine and alanine homopeptides. Ammo acid or peptide ' Ala-Ala-Ala-Ala-Ala-Ala a. Draw the structure of Ala-Ala in its predominant ionization state at pH 7.0 (you may neglect stereochemistry). Identify the functional groups associated with pK1 and ng. (4 points). 2 b. Why does the value of pK1 increase With each addition of an Ala residue to the Ala oligopeptide? (4 points). 0. Why does the value of pKz decrease with each addition of an Ala residue to the Ala oligopeptide? (4 points). d. What is the concentration of the form of Ala With no net charge at pH 9.0 if the total concentration of Ala is 25 mM? (4 points). Page 4 Name e. What volume of 5 M NaOH must be added to 20 mL of the buffer solution described in part d to increase its pH to 10.00? (4 points). Page 5 Name 3. Fill in the missing information in the table. You should draw the predominant species at pH 7, paying attention to stereochemistry. (2 points each; Total 16 points). One 01' Three—Letter Code and Structure Side—chain ionizable over the pH range 3 — 10?* + (R) I (S) designation Page 6 Name 4. Delta sleep inducing peptide (DSIP) has been investigated for its clinical potential in treating insomnia, pain and withdrawal. Its linear sequence is Trp-Ala—Gly-Gly-Asp-Ala-Ser-Gly- Glu. (Total 10 points). a. Draw the complete structure of DSIP as it would exist as pH 8.0. You may neglect stereochemistry in this drawing. (6 points). b. What is the net charge of DSIP at pH 8.0? Briefly explain your answer. (4 points). Page 7 Name 5. Using the following information, deduce the sequence of the original octapeptide. Be sure to consult the list of peptide cleavage reagents on the last page of the exam. (Total 10 points). Total acid hydrolysis: Arg, Asp, Ile, Met, Phe, Pro, Tyr, Val Trypsin cleaves the octapeptide to yield a dipeptide containing Asp and Arg, and a hexapeptide with all the remaining amino acids. CNBr cleavage of the octapeptide yields a dipeptide containing Phe and Pro and a hexapeptide with all the remaining amino acids. Chymotrypsin cleaves the octapeptide into two tetrapeptides. Complete hydrolysis and amino acid composition analysis yielded the following data: #1 (Arg, Asp, Tyr, Val); #2 (He, Met, Phe, Pro). Carboxypeptidase treatment of the octapeptide gives Phe. Page 8 Name 6. To identify amino acids, they are first derivatized with phenyisothiocyanate (PITC) in the reaction shown below. (Total 14 points) H H HZN COZH NTN COZH +6” ~C\ pH9.0 O 3 ‘37)- H2 NHZ a. Use curved arrows to show a reasonable chemical mechanism for this reaction. Note that the ionization state of th e functional groups in Lys may not be correct for pH 9. 0. You must write the correct ionization state as part of your mechanism (10 points). b. Lysine contains two amino groups, but reaction with PITC occurs almost exclusively on the a-amino group under the reaction conditions shown above. Briefly explain why the side- chain amino group does not react with PITC. (4 points). Page 9 Name 7. This problem describes a method that can be used to determine the number of polypeptide chains in proteins suspected to possess quaternary structure. (Total 10 points). a. A sample (660 mg) of a protein with total molecular weight 132,000 g / mole was treated with an excess of l-fluoro-2,4-dinitrobenzene under slightly alkaline conditions until the reaction was complete. This reagent reacts specifically with free (it-amino groups in polypeptide chains. The peptide bonds were then completely hydrolyzed by heating in 6 M HCl. Amino acid analysis gave 5.5 mg of the following compound whose molecular weight is 281 g / mole: H 0W1 OQN CH3 CH3 If no other labeled amino acids were detected, calculate the number of polypeptide chains in the original protein. (6 points). b. What can you deduce from the data in part a about the sequence of amino acids in the chain(s) found in the original protein? (4 points). Page 10 Name Amino Acid pKa values Name pK a,1 pKasz pKagy, Alanine 2.34 9.69 Arginine 2.17 9.04 12.48 Asparagine 2.02 8.80 Aspartate 1.88 9.60 3.65 Cysteine 1.96 10.28 8.18 Glutamate 2.19 9.67 4. 25 Glutamine 2.17 9.13 Glycine 2.34 9.60 Histidine 1.82 9.17 6. 00 Isoleucine 2.36 9.68 Leucine 2.36 9.60 Lysine 2.18 8.95 10.53 Methionine 2.28 9.21 Phenylalanine 1.83 9.13 Proline 1.99 10.96 Serine 2.21 9.15 Threonine 2.11 9.62 Tryptophan 2.38 9.39 Tyrosine 2.20 9.11 10.07 Valine 2.32 9.62 Reagents for peptide cleavage ArgC: Cleaves after Arg AspN: Cleaves before Asp Carboxypeptidase: Liberates the C-terrninal amino acid as long as this residue is not Pro. If the C-terminal residue is Pro, there is no reaction Chymotrypsin: Cleaves after Leu, Phe, Trp, Tyr CNBr: Cleaves after Met LysC: Cleaves after Lys Staphylococcus aureus V8: Cleaves after Asp, Glu Therrnolysin: Cleaves before most hydrophobic residues Trypsin: Cleaves after Lys, Arg Page 11 ...
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