BIOCHEM320 Exam 1 Practice Questions_updated June 23

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BIOCHEM 320 Exam 1 Practice Questions Here is a list of practice questions. They are not a comprehensive set of study questions, but cover important concepts that you may see on the exam. SHORT ANSWER QUESTIONS 1. Draw the following functional groups indicating any full or partial charges: aldehyde, ketone, phosphate group, hydroxyl, amino, and ester. (These are the most common ones encountered in biochemistry.) 2. Compare and contrast the types of noncovalent interactions. Rank them according to their relative strengths and explain why their strengths differ. 3. Explain why droplets of olive oil will clump together in water. 4. Lipids (fats) are mostly hydrocarbon and absorption occurs in the small intestine and not the stomach. a. Where would a vitamin a supplement more readily be absorbed? Explain your reasoning. b. Draw a picture of what is most likely to happen when vitamin a molecules are mixed with water. Assume vitamin a molecules are completely dispersed in water molecules in the beginning. Then, explain why any changes occur and be sure to discuss any changes in entropy occurring in vitamin a molecules and water molecules. 5. Using your understanding of amino acid ionizable groups, explain why pH can change the structure or function of a protein. 6. Sketch what you predict the titration curve of arginine would look like. (Use class slides and Exam 1 Reference Sheet for p K a s). Indicate all p K a s on the curve. Describe how the protonation states and charges for all the functional groups change as you go from a very acidic pH to a very basic pH. 7. Using a titration curve and the Henderson-Hasselbalch equation, explain why pH = p K a at the midpoint for each ionizable group. 8. Given the following p K a values, rank the acids from strongest to weakest. Then, indicate which one has the smallest K a . Fumaric acid 3.03 Carbonic acid 6.37 Formic acid 3.75 Sulfurous 1.85 9. Explain why lysine is categorized as a basic amino acid. 10. Use the histidine titration curve (end of document) to answer the following questions: a. Describe what is happening in a titration experiment as the pH is increasing from low to high. b. At what point(s) is the R group 100% protonated? c. Draw the structure of the majority of histidine molecules at point E. 11. Each amino acid is unique, however all peptide bonds are identical. Why? 12. Compare and contrast the stabilizing interactions and interacting groups in all four levels of protein structure. 13. Three disulfide bonds are present in a protein that has a single subunit. Based only on this information, what do you know about the protein? 14. Are there any levels of protein structure that are NOT disrupted when a protein denatures? If so, which one(s)? What about when a protein is degraded? 15. Protein structure of the insulin receptor depends on many intramolecular interactions. One of these is an interaction between the R groups of glutamic acid (Glu) and arginine (Arg).

a. Draw and name the interaction that occurs between these two side chains at pH = 7. b. In what pH range would you expect this interaction to occur? c. In what pH range would the interaction be disrupted? 16. Calculate the net charge of the following peptide at pH = 7. Refer to a table of R group p K a s. Lys-Trp-Met-Glu-Phe-Thr-Met-Asp-Val 17. Explain how the hydrophobic effect contributes to protein folding. Which amino acids do you predict to find on the inside? Outside? Active site? 18. Use this word bank to help you fill in the blanks in the following sentences. Word bank: hydrophilic, disulfide bridges, dispersion forces, aqueous, hydrogen bonds, small, polar, hydrophobic, large, nonpolar For a protein that exists in a(n) _______ environment, favorable interactions of _________ amino acid side chains with water lead to the formation of a tightly packed ________ core. This core is stabilized by a __________ number of ________. 19. Use an amino acid table to draw the side chains for valine and alanine. Then, indicate what type of noncovalent interaction(s) is/are most likely to occur between the side chains. Draw an example of each possible noncovalent interaction, being sure to indicate any full or partial charges on the atoms and whether they are temporary or permanent. 20. You are exploring the noncovalent interactions that occur between amino acid R groups in a protein. What type of protein model / visual picture would you use to investigate these interactions? Explain your answer. MULTIPLE CHOICE QUESTIONS 1. Erythromycin and penicillin are drugs used to treat bacterial infections. Both drugs are weak acids with one ionizable hydrogen. Penicillin is a stronger acid compared to erythromycin, therefore penicillin has a _____ Ka and a ______ pKa compared to erythromycin. a. bigger; bigger b. bigger; smaller c. smaller; bigger d. smaller; smaller 2. You have a solution containing one of the 20 standard amino acids and are trying to identify which amino acid is in the solution. At a pH of 3.0, its overall charge is +1. At a pH of 12.0, its overall charge is ‒1. Which of the following amino acids could it be? a. aspartic acid b. glutamine c. phenylalanine d. lysine

3. Which of the following, if any, describes a similar property between covalent and noncovalent bonds? a. The interacting atoms in both types of bonds are always different in size. b. The interacting atoms in both types of bonds are always located in the same molecule. c. The interacting atoms in both types of bonds always share electrons equally. d. None of the above describes a similar property. 4. You are studying a protein and observe that it has a single disulfide bond. Based only on this information, what must be true about the protein? a. It has more than one cysteine. b. It has more than one polypeptide chain. c. The disulfide bond is important for stabilizing the secondary structure. d. All of the above must be true. 5. The p K a of lysine’s R-group is 10.53; therefore, at a pH of 7, the R-group will be a. protonated and positively charged. b. protonated and uncharged. c. deprotonated and negatively charged. d. deprotonated and uncharged. 6. Look at the image of the common structure of an amino acid (right). What type of bond is the arrow pointing to? a. Polar covalent bond b. Nonpolar covalent bond c. Amide bond d. Dipole-dipole bond 7. Thinking also about this same bond from the previous question (#6). Fill in the blanks with the words that most appropriately complete this sentence. Electrons participating in this bond spend most of their time around the ________ atom because this atom has a _______ attraction for the bonding electrons. a. nitrogen; weaker b. nitrogen; stronger c. carbon; weaker d. carbon; stronger 8. What are the most important factors for determining protein charge? a. pH of environment and α-carboxyl p K a b. hydrophobicity and R group p K a c. pH of environment and R group p K a d. hydrophobicity and α- carboxyl p K a

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9. Which term describes all types of noncovalent bonds? a. hydrophobic b. electrostatic c. intermolecular d. intramolecular 10. What characteristic of an atom determines magnitude and duration of a charge? a. size b. weight c. density d. electronegativity e. all of the above 11. Name the noncovalent interaction that would occur between the groups inside the red box. a. ionic b. dipole-dipole c. ion-dipole d. dispersion forces 12. Lipids (fats) are mostly hydrocarbon and absorption occurs in the small intestine and not the stomach. Therefore, a vitamin a supplement would be absorbed more readily in the a. stomach because vitamin a is mostly hydrophobic. b. stomach because vitamin a is mostly hydrophilic. c. small intestine because vitamin a is mostly hydrophobic. d. small intestine because vitamin a is mostly hydrophilic. 13. Consider functional groups in the side chain of an amino acid. Which of the following statements, if any, is/are TRUE? a. The weak/conjugate acid form of an amine group has a charge of +1. b. The acid form of a carboxylic acid has a charge of 0. c. Both A and B are correct statements. d. Neither A or B is a correct statement.

14. You have a solution with an unknown amino acid. Given the following observations, what amino acid could be present? -average α-amino group pKa is ~9.5 -R group is ionizable -charge of the R group can be -1 a. tyrosine b. arginine c. threonine d. The solution could be A or B, but not C. 15. At which point on the curve, if any, would the amino acid R groups be mostly deprotonated? a. Point 1 b. Point 3 c. Point 5 d. None of the above 16. If an amino acid was substituted for leucine, which do you predict would have the SMALLEST effect on protein structure? a. aspartic acid b. glutamine c. valine d. lysine 17. Lysine is categorized as a basic amino acid. Which of the following arguments explains this categorization? a. The R group contains an amine functional group that can ionize. b. The alpha-carboxylic acid group can ionize. c. The alpha-amino group can ionize. d. A and C, but not B explain this categorization. e. A, B, and C explain this categorization. 18. The protein below is made from four polypeptide chains. Which statement must be true?

a. This protein has quaternary structure, but not tertiary structure b. This protein has disulfide bonds c. This protein has tertiary structure, but not quaternary structure d. A and B only e. None of the above 19. Complete the sentence below. London dispersion forces are attractive forces that arise due to ________. a. infinitesimal dipoles generated by the constant random motion of electrons b. ion pairing between oppositely charged functional groups c. permanent dipoles of molecules containing covalent bonds between atoms of very different electronegativities d. the hydrophobic effect 20. Which of the following describes a difference between covalent and noncovalent bonds? a. Covalent bonds always occur between atoms in the same molecule, but noncovalent bonds do not. b. Atoms in covalent bonds always share electrons, but atoms in noncovalent bonds do not. c. Atoms in a covalent bond always have permanent, partial charges, but atoms in a noncovalent bond do not. d. All of the above correctly describe a difference. 21. When hydrogen is covalently bound to ______, the electronegativity difference is not large enough for it to serve as a strong hydrogen-bond ______. a. nitrogen; donor b. carbon; donor c. nitrogen; acceptor d. carbon; acceptor 22. The amino acid to the right belongs in the ______category. Its R group is drawn in the _______ form. a. acidic; conjugate base b. acidic; acid c. basic; conjugate acid d. basic; acid

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23. The amino acid to the right belongs in the _______category. Based on the way its R group is drawn, the pH of the solution could be _______. a. basic; above 13 b. basic; below 7 c. acidic; above 7 d. acidic; below 13 24. Which of the phrases correctly compares the term ‘protein’ with the term ‘polypeptide’? a. The term protein means the same as the term polypeptide. b. A protein can be one or more polypeptides. c. A polypeptide is always a protein. d. B and C, but not A. e. A, B and C are all correct. 25. The image to the right depicts a specific amino acid at pH = 7. It belongs in the same group as a. proline. b. threonine. c. arginine. d. glutamic acid.

BIOCHEM320 Exam 1 Practice Questions_updated June 23

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