Practice Exam 1 Summer11 - Name CHM 3218 f 5305 Summer 201...

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Unformatted text preview: Name CHM 3218 f 5305 Summer 201 1 Practice 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 and other aids would be prohibited, with the exception of molecular models and calculators. N0 sharing ofmodeis 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. A portion of the Escherichia coii cell wall is shown below. (Total 15 points). GG_ G D _ 9H3 H CO: H D g”! a ”Mgr W" A _ O . N _ N ”Y H H 6°: 0 CH; D co," Portion of E. coll cell wall EH: a. Assign correct (R) or (S) designations to each of the three stereocenters marked with arrows. (2 points each). h. Hydrolysis of the cell wall peptide yields several amino acids, including the one shown below. Draw the correct Fischer representation and correctly label the chiral center using the DEL system (4 points). co; H3; Menz— Page 1 Name 0. The cell wall peptide shown above is exposed to water. Is it stable with respect to hydrolysis? Briefly explain your answer. (5 points). Page 2 Name 2. This problem explores the effect of structure on pIt‘a values and buffer behavior. (Total 24 points). a. Draw the complete structure of the amino acid whose one letter code is D in its fillly protonated form and label the fimctional groups with the corresponding pKa values. You can ignore stereochernistry in your drawing and a complete table of amino acid pIr’a values can be found on the last page of the exam. (4 points). b. Why do the side-chain and main-chain pKa values differ for the same type of fimctional group in the structure drawn in part a? Your answer should explain both why they are different and why one is larger than the other. (4 points). 0. What is the isoelectric point for the amino acid with a one letter code of D? (4 points). Page 3 Name d. What is the concentration of the amino acid with a one letter code of D having a net charge of -1 at pH 10.40 if the total concentration is 30 mM? (6 points). 6. What volume of 2.5 M HCl must he added to 300 mL of the buffer solution described in part d to decrease its pH to 9.80? (6 points). Page 4 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 10 points). One or Three-Letter Code and Side-chain ionizable between Structure pH 3 and 13? (R) I (S) designation No + _ H N CO 3 >6, 2 H / HS Page 5 Name 4. Melanocyte stimulating hormone is part of a group of peptide hormones that causes skin darkening. It has the sequence Ac-Cys-Glu-His-Phe-Arg—Trp-Cys-Lys-ProMal-NH; with a disulfide bridge between the two Cys residues. (Total 19 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). 0 A Ar: = CH3 attached to N-terminus NH; = C—terminal OH replaced by NH; b. Can the peptide whose structure is shown in part a be sequenced by the Edman degradation method discussed during lecture? Briefly explain your answer. (3 points). 0. Use curved arrows to show a chemical mechanism for reducing the disulfide bond of the peptide shown in part a with excess B-mercaptoethanol (structure shown below). You can abbreviate the peptide structure with “R” groups. (8 points). ”WSH [S-merca ptoeth an ol Page 6 Page 7 Name 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, Cys, Lys, Met (2 equivalents), Phe, Ser, Tyr Cyanogen Bromide: 2 different products. Each was isolated and hydrolyzed with acid and their amino acid compositions were determined: #1 (Lys, Met, Phe, Ser); #2 (Arg, Cys, Met, Tyr). Carboxypeptidase: Met Chymotrypsin: 3 different products. Each was isolated and hydrolyzed with acid and their amino acid compositions were determined: #1 (Tyr); #2 (Lys, Met, Ser); #3 (Arg, Cys, Met, Phe). Trypsin: 3 different products. Each was isolated and hydrolyzed with acid and their amino acid compositions were determined: #1 (Arg, Tyr); #2 (Met, Ser); #3 (Cys, Lys, Met, Phe). Page 8 Name 6. Peptide and protein conformation and properties. (Total 14 points). a. Draw the complete structure of the peptide Glu-His-Ser in the form that predominates at pH 7.0. Indicate all C-C and C-N bonds that are freely rotatable by marking each one with “Rot”. (6 points). b. Use words and chemical structures to explain why some bonds in the peptide drawn in part a are not freely rotatable. (4 points). 0. What is the pI of the peptide shown in part a? A table of amino acid pKa values appears on the last page of the test; you may assume that these values can also be used for groups within peptides. (4 points). Page 9 Name 7. To test whether proteins stabilized by disulfide bonds are nevertheless in their minimum energy conformations, three proteins were treated with excess B-mercaptoethanol in the presence of 8 M urea. These reagents were gradually removed to allow the proteins to refold and re-form disulfide bonds. The data obtained are shown below. (Total 10 points). Calculated recovery of Number of biological activity with disulfide bonds random disulfide bond formation Experimentally- observed recovery of biological activity Ribonuclease Lysozyme Insulin a. Do the data for ribonuclease and lysozyme support, or contradict the hypothesis that disulfide-stabilized proteins exist in their minimum-energy conformation? Briefly explain your answer. (6 points). b. Based on the data shown above, what can you conclude about the structure of insulin? (4 points). Page 10 Name Amino Acid pKa values Name PKaJ PKaQ PKHB 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 10.01If Valine 2.32 9.62 Reagents for peptide cleavage ArgC: Cleaves after Arg AspN: Cleaves before Asp Carboxypeptidase: 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 afier Asp, Glu Thermolysin: Cleaves before most hydrophobic residues Trypsin: Cleaves afier Lys, Arg Page 11 ...
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