Practice Exam 1 Spr15 - Name CHM 3218 f 5305 Spring 2015...

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Unformatted text preview: Name CHM 3218 f 5305 Spring 2015 Pratice Examination #1 University of Florida Honor Code Statement: "On my honor, I have neither given nor received unauthorized aid in doing this assignment." Student signature Instructions: You would have 2 hours to complete this exam. All books, notes, cell phones, translators and other aids would be prohibited, with the exception of molecular models and calculators. No sharing ofmadeis or 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. Amino acid properties. (Total 28 points). a. Draw the complete structure of a symmetrical dimer made from two copies of the amino acid whose 1 letter code is K. The dimer is formed by connecting the a-amino group of one building block to the a—carboxyl group of the second building block so that a six-membered ring results. All chiral centers should have the (R)-stereochemistry and the predominant ionization state at pH 7 .0 should be shown. (6 points). b. Are the two amino acids in your answer to part a D- or L-arnino acids? Briefly explain your answer. (4 points). Page 1 Name 0. Are the amides in the structure described in part a stable when the compound is dissolved in water? Does hydrolysis occur at significant rates in pure water? Briefly explain your answer. (6 points). d. To determine amino acid composition, the compound described in part a was hydrolyzed under the appropriate conditions, then the pH was adjusted to 9.0 and an excess of phenylisothiocyanate (shown below) was added. Draw the product(s) that would form under these conditions and use curved arrows to show how the reaction proceeds. No stereochemistry needs to be shown in your structures. (8 points). ©N=C=S phenylisothiocyanate Page 2 Name e. Draw the product(s) that would be obtained if the reaction in part d were carried out at pH 11. Briefly explain why the results would be the same or different from the reaction with PITC at pH 9.0 (4 points). Page 3 Name 2. This problem explores the effect of structure on pKa values and buffer behavior. (Total 28 points). a. Of the four diacids shown below, which would you expect to have the lowest pKa value? Briefly explain your answer using words and chemical structures. (4 points). Hozc—cozH HogcvcozH Hozc/‘VCOZH HOZCWCOZH oxalic acid malonic acid succinic acid glutaric acid b. The first pl?a value for compOunds shown in part a are 4.34, 1.23, 4.19 and 2.83 (not in order). Match the pKa value to the corresponding diacid. (1 point each). Oxalic acid Malonic acid Succinic acid Glutaric acid 0. In one of the diacids shown in part a, the le’a values are 2.83 and 5.69. Since both pKa values refer to the same type of functional group, why do they differ? (4 points). Page 4 Name d. Is the diacid described in part c an effective buffer at pH 7 .0? Briefly explain your answer. (4 points). e. At pH 6.0, if the total concentration of the diacid described in part c is 75 mM, what is the concentration of the form with a net charge of -1? (6 points). f. If 1.20 mL of 1 M HCl is added to 250 mL of the solution described in part e, what is the final pH value? (6 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. Show configurations of at! chiral centers explicitly by drawing at! four attached atoms. (2 points each; Total 14 points). One or Three-Letter Code and Side-chain ionizable between Stm‘m pH 3 and 13? (R) f (S) designation (R)-Va.1 No Page 6 Name 4. Oxytocin is a peptide hormone that plays a very important role in childbirth. It has the amino acid sequence Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly. (Total 12 points). a. Draw the complete structure of the peptide as it would exist as pH 7.0. You may neglect stereochemistry in this drawing. (8 points). b. In nature, the side-chains of Cys l and Cys 6 are covalently joined. Show this bond in your structure drawn above and briefly explain how this covalent bond might affect the structural behavior of oxytocin. (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. Note that amino acids are listed in alphabetical order in the data, and no sequence order is implied. (8 points). Total acid hydrolysis: Arg, Asp, Leu (2.0 equivalents), Lys, Met, Ser, Thr ArgC: 2 different products. Each was isolated and hydrolyzed with acid and their amino acid compositions were determined: #1 (Arg, Leu (2.0 equivalents)); #2 (Asp, Lys, Met, Ser, Thr). LysC: No reaction Cyanogen bromide: 2 different products. Each was isolated and hydrolyzed with acid and their amino acid compositions were determined: #1 (Arg, Asp, Leu (2.0 equivalents), Met, Thr); #2 (Lys, Ser). Chymotrypsin: 3 different products. Each was isolated and hydrolyzed with acid and their amino acid compositions were determined: #1 (Lys, Met, Ser, Thr); #2 (Arg, Asp, Leu); #3 (Leu). AspN: No reaction Page 8 Name 6. This problem considers a-helices. (Total 10 points). a. Consider a segment of polypeptide capable of folding into an a-helix. Will it be thermodynamically more likely to do so if the segment is exposed completely to the aqueous surroundings or completely buried in the non-polar interior of a protein. Carefully explain your answer. (4 points). b. The stability of an a-helix is determined no only by the formation of interpeptide hydrogen bonds, but also by the nature of the amino acid side-chains. Predict which of the following amino acid homopolyrners will form stable u—helices and explain why or why not in each case. (2 points each). Polyleucine (Leu)11 at pH 7.0 Polythreonine (Thr)n at pH 7 .0 Polyarginine (Arg)11 at pH 13 Page 9 Name Amino Acid pKa values Name PKEJ PK” PKaB 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 Carb0xypeptidase: Liberates the C-terminal 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, G111 Thermolysin: Cleaves before most hydrophobic residues Trypsin: Cleaves after Lys, Arg Page 10 ...
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