Biochemistry 1 Exam 1 Final Answer Key

I. _________________/48 II. _________________/ 4 III. _________________/26 IV. _________________/22 TOTAL ________________/100 Exam I Biochemistry I I. MULTIPLE CHOICE. (48 points; 2 pts each) Choose the BEST answer to the question by circling the appropriate letter. 1. The strength of hydrogen bonds, electrostatic interactions, and the values of the pKas of ionizable amino acid residues could be different in proteins than in aqueous solution because ____. A. B. C. D. 2. Phosphoric acid is tribasic, with pK as of 2.14, 6.86, and 12.4. form that predominates at pH 3.2 is: A. 3. E. B. H2PO4-. C. HPO42-. D. PO43-. the loss of hydrogen bonds the gain of ionic bonds the gain of more van der Waals contacts the spacial arrangement of the assymetrical water molecules as they form the maximum number of hydrogen bonds possible the hydrophobic effect, which is driven by electrostatic interactions In a mixture of the five proteins listed below, which should elute second in size-exclusion (gel filtration) chromatography? A. B. C. D. E. 5. H3PO4. The ionic As the phase changes from water to ice, the decreased density of the water is due to: A. B. C. D. 4. water forms a clathrate structure around proteins proteins are hydrophilic on the inside and hydrophobic on the outside the entropy of the water increases when proteins fold up the microenvironment inside proteins could be different than in solution cytochrome c , M r = 13,000 immunoglobulin G, M r = 145,000 ribonuclease A, M r = 13,700 RNA polymerase, M r = 450,000 serum albumin, M r = 68,500 The pK of the carboxyl group of glycine (pK = 2.3) is less than that for acetic acid (pK =4.8) due to ________. A. B. C. D. E. the the the the the electronegativity of the carbonyl oxygen electrostatic stabilization by the adjacent amino group electronegativity of the nitrogen in the adjacent amino group electronic nature of amino acids fact that acetic acid can be a zwitterion and glycine cannot Page 1 6. Which of the following is not a biological role for amino acids? A. B. C. D. E. 7. Water is generally a good solvent for polar molecules and a poor solvent for nonpolar molecules. These solvent properties are best explained by A. B. C. D. E. 8. increasing decreasing increasing increasing decreasing the the the the the amount of free energy released. amount of free energy released. change in entropy. rate. rate. A student was given a task of identifying the contents of five bottles of amino acids from which the labels had fallen off. Each of the original bottles contained one of the following: R, H, C, P, and W. Which of the following methods could be most readily employed to identify tryptophan? A. B. C. D. E. 10. the high density of liquid water relative to polar solvents the ability to form intermolecular hydrogen bonds the density of solid water being less than the density of liquid water high surface tension high heat of vaporization Enzymes are biological catalysts that affect a reaction by: A. B. C. D. E. 9. components of proteins components of peptide hormones used in the biosynthesis of hormones like thyroxine components of cell walls All of the above are biological uses of amino acids. Electrophoresis Ultraviolet spectroscopy Gel filtration Analytical ultracentrifugation Optical rotation T(°C) pK w 0 14.94 25 14.00 50 13.28 75 12.71 The ion product of liquid water, K w, varies with temperature (T), as indicated by the change in pK w shown in the table above. The definition of neutrality is [H+]=[OH-]. Which of the following is the pH of water at neutrality at 50 °C? A. B. C. D. E. 6.35 6.64 7.00 7.40 13.28 Page 2 11. The term specific activity differs from the term activity in that specific activity: A. B. C. D. E. 12. Of the 20 standard amino acids, only ___________ is not optically active. The reason is that its side chain has ___________. A. B. C. D. E. 13. formed a covalent bond with the amino group. a simple methyl group. an unbranched carbon chain. nothing but a hydrogen atom. a second hydrogen atom. hydrogen bonds van der Waals interactions disulfide bonds between two Cys residues ionic interactions hydrophobic interactions A compound has a pK a of 7.4. To 100 mL of a 1.0 M solution of this compound at pH 8.0 is added 30 mL of 1.0 M hydrochloric acid. The resulting solution is pH: [Note: log 4 = 0.6] A. 15. proline; alanine; glycine; alanine; glycine; The three-dimensional structure of macromolecules is formed and maintained primarily through noncovalent interactions. Which of the following is not considered a noncovalent interaction? A. B. C. D. E. 14. is the activity (enzyme units) per milligram of total protein. is the activity (enzyme units) per a specific protein. is measured only under optimal conditions. refers to proteins other than enzymes. refers only to a purified protein. 7.58. B. 7.4. C. 7.22. D. 6.8. E. 6.53. Which of the following pairs of molecules could NOT hydrogen bond with each other? (A) (B) (C) (D) (E) Page 3 16. Which of these statements about hydrogen bonds is not true? A. B. C. D. 17. To determine the isoelectric point of a protein using isoelectric focusing, a gel is first established that: A. B. C. D. E. 18. carbohydrates. lipids. nucleic acids. proteins. both A and B. The hydrophobic effect can make important energetic contributions to: A. B. C. D. E. F. 21. be neutral without any charge. show no net charge. have a net positive charge. have positive and negative charges in equal concentration. have a net negative charge. The macromolecules that serve in the storage and transmission of genetic information are: A. B. C. D. E. 20. exhibits a stable pH gradient when ampholytes become distributed in an electric field. contains a denaturing detergent that can distribute uniform negative charges over the protein's surface. relates the unknown protein to a series of protein markers with known molecular weights, M r. is washed with an antibody specific to the protein of interest. neutralizes all ionic groups on a protein by titrating them with strong bases. For amino acids with neutral R-groups, at any pH below the pI of the amino acid, the population of amino acids in solution will: A. B. C. D. E. 19. Individual hydrogen bonds are much weaker than covalent bonds. Hydrogen bonds account for the anomalously high boiling point of water. Individual hydrogen bonds in aqueous water exist for many seconds and sometimes for minutes. In liquid water, the average water molecule forms hydrogen bonds with 3 to 4 other water molecules. membrane structure. folded protein structures. micelles of SDS and protein. enzyme-substrate interactions. oil droplets coming together. all of the above. The properties of water include: A. B. C. D. E. the ability to form hydrophobic interactions with itself a completely disordered structure in the liquid state a low dielectric constant relative to a vacuum being a strong dipole, with a partially negative end at the O atom a diameter of 5 Å Page 4 22. By adding SDS (sodium dodecyl sulfate) for the electrophoresis of proteins through polyacrylamide, it is possible to: A. B. C. D. E. 23. Which of the following amino acids has a sulfur atom in its side chain? A. D. 24. Asn Met B. E. Lys Tyr C. F. Phe Thr The reaction of two amino acids to form a dipeptide is a(n): A. B. C. D. E. II. 25. determine the amino acid composition of the protein. preserve a protein's native structure and biological activity. determine a protein's isoelectric point. separate proteins on the basis of molecular weight. determine an enzyme's specific activity. cleavage. condensation. group transfer. oxidation-reduction. rearrangement. STRUCTURES. (4 points) Draw the structure of Trp-Ala-His (Tryptophanylalanylhistidine) in the ionic form that predominates at pH 7.5. Put an arrow pointing at the group that would become deprotonated after an increase in the pH from 7.5. (4 pts) Page 5 III. SHORT ANSWER. (26 points) Give a brief answer or diagram for each problem or question below. 26. Briefly explain why the amino acids found in naturally occurring proteins are all optically active, with one exception. Are they all the same optical activity? Is this an example of configuration or conformation? (3 pts) 27. A chemist working in a pharmaceutical lab synthesized a new drug as a racemic mixture. Why is it likely that only one enantiomer has biological activity and that it's important that she separate the two enantiomers? (3 pts) 28. Name the three major classes of macromolecules found in biological cells and the precursors or monomers from which they are polymerized. (6 pts) 29. Explain the fact that ethanol (CH3CH2OH) is more soluble in water than is ethane (CH3CH3). (3 pts) 30. (a) Calculate the approximate pI for the peptide ATLDAK. Show your rationale. (b) What is its net charge at pH 7.0? (4 pts) Page 6 31. Circle the one amino acid in each of the following pairs (A-H) that has the higher molecular weight: (4 pts) A Gly/Pro 32. C Trp/Tyr D Asp/His E Glu/Asp MATCHING. A. B. C. D. E. F. G. H. I. J. K. _______12. polysaccharides L. ________3. ________4. H Ser/Thr (22 points) differential centrifugation anion exchange chromatography gel filtration isopycnic centrifugation cation exchange chromatography affinity chromatography hydrophobic interactions salt-bridge Hydrogen bond with water proteins nucleic acids ________2. G Lys/Arg Match the word or phrase on the left with the most appropriate word or phrase on the right. Choices on the right may be used more than once or not at all. (12 pts) ________1. ________2. ________3. ________4. ________5. ________6. ________7. ________8. ________9. _______10. _______11. ________1. F Leu/Val You have recently purified a protein preparation by differential centrifugation to get your crude extract, then ammonium sulfate precipitation (2S), and two different types of ion-exchange chromatography (cation & anion). You determined the specific activities of the preparation at the various steps (crude, 2S, cation, anion) as 0.1; 5; 500; and 500 U/mg, respectively. Do you think that your protein is relatively pure (>95%)? Explain. How would you determine if it were pure or not? Which step did not increase the purity? (4 pts) IV. 33. B Asp/Ser M. N. O. 34. polymer of nucleotides polymer of simple sugars polymer of L-amino acids polymer of D-amino acids Ile "interacting" with Val Asp interacting with Glu His interacting with Glu Ser interacting with Glu Water interacting with air Water interacting with water separation of negatively charged proteins separation of positively charged proteins separation based on density separation based on binding separation based on size For the bonds or interactions on the left, indicate THREE (3) of the characteristics on the right that are most appropriate. Items on right can be used more than once.(10pt) Charge-charge electrostatic interactions A. Has an energy of around 0.2-0.5 kcal/mole per ___________________________ bond or group Hydrogen bond B. Has an energy between 3 and 7 kcal/mole per ___________________________ bond or group van der Waals interactions C. Is optimal at or near the van der Waals contact ___________________________ distance Hydrophobic interactions D. Requires nonpolar species ___________________________ E. Is also called a salt-bridge or ion-pair F. Involves any atom G. Involves uncharged O and H, or N and H atoms H. Requires polar or charged species I. Exists only in water J. Involves charged species only Page 7 No. on Test Correct Answer 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 D B D B B E B D B B A E C B D C A C C F D D D B 25 The peptide must have an amino-terminal Trp residue, a carboxyl-terminal His residue. The imidazole side chain is mostly deprotonated because the pH is above the pK a. 26 The a carbon of nineteen of the twenty amino acids found in proteins is asymmetric because it is bonded to four different groups. (Glycine alone is not optically active because its a carbon is bonded to two hydrogen atoms and is thus symmetric.) They are all L-amino acids. This is an example of configuration. 27 Biomolecules are stereospecific. Therefore, each of the two enantiomers of the drug may have very different effects on an organism by binding in a complementary way to a target protein in the cell, therefore, in a stereospecific way. One may be beneficial, the other toxic or ineffective and its presence would reduce the efficacy of the other enantiomer. _ Page 1 No. on Test Correct Answer 28 Proteins-amino acids Nucleic acids-nucleotides Polysaccharides-monosaccharides 29 Ethanol can form hydrogen bonds with water molecules, but ethane cannot. When ethanol dissolves, the decrease in the system's entropy that results from formation of ordered arrays of water around the CH3CH2- group is partly compensated by the favorable interactions (hydrogen bonds) of the hydroxyl group of ethanol with water molecules. Ethane cannot form such hydrogen bonds and, in fact, there is an increase in the system's entropy when ethane molecules stay together rather than "disolve" in water. 30 O = O = O = = O = O + H3N-CH-C-NH-CH-C-NH-CH-C-NH-CH-C-NH-CH-C-NH-CH-COOCH3 H-C-OH CH2 CH3 H-C- CH3 CH3 CH2 (CH2)4 COO- NH + 3 CH3 Ala(A) Thr(T) Leu(L) Asp(D) Ala(A) Lys(K) (a) pI is about from 6-7; C-term and D have pK ~4-5 and ~3, respectively; Nterm and K have pK ~8-9 and ~11, respectively. The pI is midway between the pK's of the ionizations involving the neutral species; (4+8)/2 = 6 or at other extreme; (9+5)/2 = 7 (b) zero; at 7 both C-term and D are negative and both N-term and K are positive. Although, it might be slightly negative due to some N-term deprotonation and loss of plus charge. 31 A Pro; B Asp; C Trp; D His; E Glu; F Leu; G Arg; H Thr 32 Best answer is YES because after two steps there is no further increase in specific activity. In addition, there is a 5000-fold purification, which is substantial. If there is a NO answer there must be mention of the second ion exchange chromatography step having no effective purification, i.e., not working. Either answer could be confirmed by SDS-gel electrophoresis. Page 2 No. on Test Correct Answer 33 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 34 O K O M L N E G J C A B 1. B, E, J (C) 2. B, G, H 3. A, C, F (G) 4. B, D, I [Note: letters in () are correct or partially correct, but if missing not counted as wrong] Page 3