CHM376_Fa22_PS4

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Jan 9, 2024

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CHM376 Biochemistry I Fall 2022 Problem Set #4: Amino Acids, Peptides and Hormones 1. Draw the generic structure of an -amino acid. Circle the atoms that correspond to the backbone and the side-chain. Why do we not draw the backbone structure with an NH 2 or a COOH group? ( Note that on an exam, drawing the amino acids in their correct protonation state is absolutely critical. If an amino acid is drawn in the incorrect protonation state for a given pH it is not considered correct ). Next, look at the structure of the beta amino acid beta alanine. Can you “find” this structure as part of the much larger molecule as described in the Biothermodynamics PowerPoint? ( Hint: look at the structure of acetyl-coA ). We don’t draw the back-bone structure with NH2 or COOH because at physiological PH: 7 the amide group exists in protonated form while the carboxylic acid group exists in the deprotonated state. Beta-alanine isn’t normally used in peptide synthesis however they are components of carnosine which is a molecule within muscles that acts as a buffer. 2. Are there any biologically important beta amino acids ? Name one molecule that is composed, in part, of a beta amino acid. 3. The ingestion of what amino acid causes Jamaican vomiting sickness ? he primary cause is Hypoglycin that is
found in unrippended fruit of the Ackee tree, the hypoglycin if consumed from these fruits gets metabolized into a compound that can disrupt the movement of fatty acids into the mitochondira thus disrupting metabolism. he primary cause is Hypoglycin that is
found in unrippended fruit of the Ackee tree, the hypoglycin if consumed from these fruits gets metabolized into a compound that can disrupt the movement of fatty acids into the mitochondira thus disrupting metabolism. 4. What is the structural difference between arginine and canavanine ? Suggest a reason why canavanine consumption may be toxic for herbivores. ( Note: the answer to this question is not in the notes; you are being asked to infer an answer on the basis of the structure of these two amino acids ). 5. Why should you not consume ink cap mushrooms and alcohol together? How is the consumption of ink cap mushrooms similar to a common therapeutic approach to alcoholism?
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6. Name some of the ways we can classify amino acids. 7. Explain the meaning of the term essential , non-essential and semi essential amino acids. ( Note: you are responsible for understanding the meaning of these terms, but not which amino acids belong in each category ). 8. Are all of the 20 major (genetically encoded) amino acids chiral? 9. What is hippuric acid ? From what amino acid is hippuric acid derived? 10. What metabolite, excreted in the urine, is produced upon consumption of aspirin or PeptoBismol TM ? What amino acid is required for the synthesis of this metabolite? 11. What is skatole ? What amino acid is broken down to give skatole ? 12. What amino acids taste sweet ? 13. Given the structure of cinnamic acid and cinnamoyl-coA, identify all the organic functional groups in each of these two molecules. 14. Draw the amino acid isoleucine and label the backbone and side chain atoms. How many enantiomers of isoleucine are possible? How many chiral centers are found in each of the 20 ‘standard’ amino acids? 15. Identify and give the L/D stereochemistry of the amino acid shown below. 16. Agree or disagree with the following statement: only the L-amino acids are biologically important. Provide evidence for your statement . 17. What is the isoelectric point ? What is an ampholyte ? What is a zwitterion ? 18. Calculate the pI of all 20 of the genetically encoded amino acids. You work must include a structure of all possible charge states and the actual calculation of the pI . ( Note: on an exam if you perform the calculation without showing the correct structures you will obtain little credit ).
19. Use the H-H equation to calculate the fraction of histidine that has a protonated side chain at pH 7.3. ( Note: do not confuse fraction and ratio on an exam. The H-H equation directly gives you the ratio; you must convert this to the fraction . Also note the wording of this question; for pI calculations, and the calculation of the charge on a peptide, you may use the 1-pH unit rule. Since this question asked for the fraction, you must give the exact number. Because of approximations, the results of these two approaches will not always be the same.) 20. A slightly trickier version of Question 19. The side chain of an amino acid is 40% deprotonated, 60% protonated at pH = 5.82. What amino acid is this? You must show all your work . 21. What is the unique optical property of the aromatic amino acids ? 22. What amino acid derivative may be responsible, in part, for the health benefits of intense exercise? 23. Draw the amino acid proline at pH = 7. Note the number of hydrogen atoms on the backbone nitrogen at pH 7 . (Note that if on an exam, you are asked to draw proline – either the free amino acid or as part of a peptide, you must draw the correct number of protons on the nitrogen or the entire amino acid is incorrect.) 24. The molar extinction coefficient ( or e) of tryptophan is 5690 cm -1 M -1 at = 280 nm. A solution of tryptophan is placed in a 1 cm wide cuvette and the measured absorbance is 0.2. What is the concentration of the tryptophan in molar units ? ( Note: the extinction coefficients of the amino acids, , are found in the Fact Sheet. These are in units of M -1 cm -1 . You will have these values on an exam, but the units, and the Beer- Lambert law is something you are expected to know ). 25. What is the inductive effect? What is the evidence for an inductive effect in the amino acid backbone? 26. What is the meaning of the term post-translational modification? Draw the known post -translational modifications that are formed in proteins. What amino acids are modified in each of these post-translational modifications? What is the thermodynamic driving force for AMPylation? What cofactor usually contributes the ADP-Ribose group for ADP-Ribosylation? 27. How does disulfide bond formation alter the titration properties of cysteine? 28. Given the structure of each molecule, identify the amino acid precursors for histamine , epinephrine , GABA , and serotonin . 29. Name three biochemical functions for the amino acid glycine .
30. Describe two genetic disorders of amino acid metabolism. 31. What is the most significant similarity between typical organic polymers and proteins? What are two significant differences between typical organic polymers and proteins? 32. Draw all possible peptides formed from the amino acids L-alanine and glycine. 33. Draw both major resonance structures of the peptide bond and explain why the peptide bond is largely planar . Is the bond predominantly cis or trans , and why? 34. Draw the following peptides at the pH shown. Calculate the charge on the peptide and record the charge in the third column of the table. ( Re cal l that oxidized refers to the disulfide bonded peptide whereas reduced has cysteine that is not disulfide bonded. Also note that you are not required to draw the stereochemistry of the amino acids were this question to appear on an exam ). 35. Explain how most biologically active peptides are produced. 36. What is the ‘ love peptide ’ and what are some if its biological effects? 37. Explain the process for the conversion of pro-insulin to insulin. How many N- and C- termini are found in pro-insulin and insulin? 38. What is the role of desmosine in the peptide elastin? What amino acids give rise to desmosine ? 39. What amino acids would you expect to find in excess in the antimicrobial peptides. 40. What is the meaning of the term ‘ non-ribosomal peptide’ ? How can non-ribosomal peptides be distinguished from other peptides? 41. 1.0g of a protein is dissolved in 100 mL of distilled water at 25 o C. The resulting solution has an osmotic pressure of .001 atm. What is the molecular weight of the protein? Use R = .0821 L atm -1 mol -1 . ( Hint: use the Morse equation and solve for the molarity of the protein.) Sequence pH Charge Ala-Val-Thr-Leu 7 Ile-Tyr-His-Glu-Gln-Phe 12 Asp-Ala-Asn-Ser-Cys 12 Glu-Pro-Gly-Lys-Ser 1 Ala-His-Arg-Met 4 Oxidized (Ala-Cys-Leu) 2 12 Reduced Ala-Cys-Leu 12
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