BCH3053 Exam 1 Fall 2023 - B - Answer Key

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3053

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Chemistry

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Jan 9, 2024

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Page 1 of 12 Name: Section # BCH 3053 General Biochemistry Exam #1 – B September 19, 2023 Directions: 1. Write your first and last name and section # legibly on top right before you start 2. This exam contains questions that require drawing, short answer responses as well as multiple choice. Follow directions for each question carefully. 3. Only the answers on the front of pages within the bounds of the question will be graded. Page 2 _________ out of 12 points Page 3 _________ out of 12 points Page 4 _________ out of 11 points Page 5 _________ out of 13 points Page 6 _________ out of 19 points Page 7 _________ out of 14 points Page 8 _________ out of 13 points Page 9 _________ out of 6 points Total _________ out of 100 points

Page 2 of 12 1. A buffer contains 0.050 mol of lactic acid (pKa=3.86) and 0.020 mol of sodium lactate per liter. 6 pts (Show your calculations) a. Calculate the pH of the buffer. b. Calculate the new pH of the solution after adding 1.0 mL of 10 M HCl to 1.0 L of the buffer. 2. Which diagram CORRECTLY represents a hydrogen bond? 3 pts a. A and D b. A and C c. C and D d. B and D e. B and C f. 3. What is the concentration of [OH - ] of a solution with a pH of 3.1? 3 pts (Show your calculations)

Page 3 of 12 4. What is the driving force of micelle formation of amphiphilic molecules in water? 3 pts a. The increase in entropy created from removing the water shell that must surround the hydrophobic tails. b. Attraction of polar hydrophilic head groups to outside to form hydrogen bonds with water. c. Van der Waal interactions of the nonpolar tails inside the micelle. d. Polar interaction between neighboring hydrophilic head groups on the outside. e. All of these are true. 5. Identify the binding interactions that might be possible at the specified positions of the following drug. 4 pts. i. ii. iii. iv. a. Van der Waals interactions b. Ionic bonding c. Hydrogen bonding acceptor d. Hydrogen bonding donor 6. What would be the strongest intermolecular interaction between the following two molecules? 2 pts 7. Which substance would make the best buffer at pH of 7.0? 3 pts a. formic acid (pKa=3.8) b. bicarbonate (pKa=6.2) c. acetic acid (pKa=4.8) d. ethylamine (pKa=9.0)

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Page 4 of 12 8. The following molecule was presented to you as a newly discovered amino acid. Would this molecule be considered an amino acid? State specifically how it does or does not meet the criteria to be an amino acid. 4 pts It does not meet the criteria to be an amino acid. An amino acid must have a primary amine group (2-3 hydrogens) and a carboxylate group attached to the same carbon. This molecule has an extra carbon attached the amine which would prevent it from making an amide bond with another amino acid. 9. According to the diagram below, what is the best estimate for the pKa of this amino acid's amino group? 3 pts a. 0.5 b. 1 c. 2 d. 6 e. 11 10. Write the full name for each of the following amino acids. 4 pts

Page 5 of 12 11. Match the following statements with one of the above tripeptides. 6 pts A B C D Pro-His-Asp Ile-Gly-Met Phe-His-Leu Lys-Arg-Ser is most positively charged at pH 7 absorbs UV light MOST likely to be found in the core of protein 12. Draw and provide the name for 1 common amino acid that is considered acidic. 3 pts 13. Draw the amino acid Cysteine (in each box) in its predominate form at a pH of 7 and 9.5. 4 pts pH = 3 pH = 9

Page 6 of 12 14. Using the pKa table provided on the back page determine the pI (isoelectric point) for the amino acid Lysine. Show your calculations. 4 pts 15. Would the following amino acid replacement (Asp → Gly ) in a protein’s amino acid sequence have an effect on the protein’s structure and function? State two reasons why this would be the case. 5 pts Yes, aspartic acid (Asp) is acidic and negatively charged at biological pH, glycine (Gly) is neutral and hydrophobic. Any interaction that would require a negative charge for that amino acid would be lost (ionic, dipole, etc). 16. What term describes a protein’s functional folded conformation? 3 pts Native fold (confirmation) 17. According to the table, ion-exchange chromatography would be the LEAST effective method to separate which protein mixture? 3 pts a. proteins A, C, and E b. proteins A, B, and C c. proteins B, C, and E d. proteins B, E, and F e. All of the answers are correct. 18. Is a parallel or anti-parallel beta pleated sheet considered more stable and state why? 4 pts Anti-parallel beta pleated sheet would be more stable, because all the atoms participating in hydrogen bonding are aligned making the strongest possible interaction. Protein MW pI A 12,500 3.2 B 13,200 5.7 C 13,500 10.5 D 25,200 6.3 E 36,900 5.8 F 78,400 6.1

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Page 7 of 12 19. The following is an example of what type of specific protein confirmation. What type of bonds hold this structure together? 4 pts 20. A sequence of amino acids in a certain protein is found to be -Ser-Gly-Pro-Gly-. The sequence is most probably part of a(n): 3 pts a. antiparallel β sheet. b. parallel α sheet. c. β turn. d. β sheet. e. α helix. 21. What is the primary sequence of a protein and how does it ultimately determine the protein’s final shape and function? 5 pts The primary sequence is the specific order of amino acids in a peptide or protein. The primary sequence leads to shape because each amino acid has a unique side chain. The specific structures / chemistry of these side chains can make particular intramolecular interactions with other amino acids. These interactions are the driving force behind the protein folding and taking shape. The location of each amino acid puts them in position to make these interactions and form the shape. 22. What is the term for a small molecule that binds a protein? 2 pts ligand

Page 8 of 12 23. What happens when a protein is denatured? 3 pts a. It is broken apart into its constituent amino acids. b. Its primary structure is disrupted but its secondary structure remains intact. c. Its secondary and tertiary structure are disrupted but its primary structure remains intact. d. It becomes all α -helix. 24. In one sentence define a chaperone protein and its role in biological systems. 4 pts A chaperone protein is a protein that helps another protein fold correctly into its native state, it can provide the right environment away from other proteins in the cell that may cause it to misfold. 25. Two proteins A and B bind the same ligand, L, with the binding curves to the right. State which protein has the higher binding affinity for the ligand? 3 pts 26. Which statement about protein-ligand binding is CORRECT? 3 pts a. The larger the Ka, the smaller the Kd (dissociation constant). b. The Ka is equal to the concentration of ligand when all of the binding sites are occupied. c. The Ka is independent of such conditions as salt concentration and pH. d. The larger the Ka (association constant), the weaker the affinity. e. The larger the Ka, the faster is the binding.

Page 9 of 12 27. What is the term for the phenomenon that describes how hemoglobin ’s binding affinity for oxygen changes due to changing pH and CO 2 concentration in the blood? 3 pts 28. The binding of oxygen to hemoglobin stabilizes the _____ of the protein due to interactions between _____ residues in the center of the multisubunit complex. 3 pts a. T state; His b. T state; Glu c. R state; His d. R state; Thr e. R state; Glu

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