407F06_1a.pdf

MBB 694:407, 115:511 Name___________________________ First Test Severinov/Deis Tue. Oct. 3, 2006 Row Leter ____ Seat Number ______ This exam consists of two parts. Part I is multiple choice. Each of these 25 questions is worth two points. Anser the Part I questions on this sheet, below. Answer the Part II questions on the question pages. Please use BLOCK CAPITAL leters like this --- A, B, C, D, E. Not lowercase! 1. ______ 10. ______ 18. ______ 2. ______ 11. ______ 19. ______ 3. ______ 12. ______ 20. ______ 4. ______ 13. ______ 21. ______ 5. ______ 14. ______ 22. ______ 6. ______ 15. ______ 23. ______ 7. ______ 16. ______ 24. ______ 8. ______ 17. ______ 25. ______ 9. ______ GRADE: Part I Total _______ Part II: II-1 _______ II-2 _______ II-3 _______ II-4 _______ II-5 _______ Part II Total _______ Total, I & II _______ MBB First Exam, page 2 Name ________________________ 1. Which sequence represents this peptide: Asp Gly Ser Thr Trp Leu Lys Gln Tyr Asn A. AGSTLGTA D. NYQKLWTSGD B. NSTWKLQYD E. ASHTLGN D. DGSTLN 2. The peptide above is A. Basic B. Acidic C. None of the above 3. The molecular weight of the peptide above is approximately A. 100 Da B. 500 Da C. 1,100 Da D. 10,000 Da 4. ?-helices in proteins form due to A. Hydrogen bond formation betwen amino acid side chains B. Van der Wals interactions within the polypeptide backbone C. Electrostatic forces D. Hydrogen bond formation within the polypeptide backbone 5. Which of the following is false: An ?-helical bundle formed betwen several helices likely forms due to A. Hydrogen bond formation betwen amino acid side chains B. ydrogen bond formation beten polypeptide backbones C. Hydrophobic and Van der Wals interactions betwen the side chains 6. ?-helices and ?-sheets form due to the following interactions in the polypeptide chain: A. Interactions betwen amino acid side-chains B. Interactions beten C ? atoms C. Interactions betwen terminal amino and carbonyl groups of the protein D. None of the above 7. During cation-exchange chromatography, bound proteins are eluted with A. Increasing concentration of salt B. Buffers with decreasing pH C. Decreasing concentration of salt D. Organic solvents MBB First Exam, page 3 Name ________________________ 8. Proteins fold in aqueous solutions mostly due to A. Decrease in free nergy due to formation of salt bridges betwen amino acids of opposite charges B. Formation of hydrogen bonds C. Increase in solute ntropy due to formation of hydrophobic core D. Formation of hydrogen bonds in ? helices and ? sheets 9. Glutamic acid side chain has a pKa of 4.3. At pH of 7.3, approximately how many glutamic acid side chain residues remain not ionized? A. 50% B. 5% C. 0.5% D. 0.05% 10. At physiological conditions, formation of a peptide bond is A. Thermodynamicaly favored B. Not thermodynamicaly favored C. Stabilized by entropic effects of water molecules 11. In the presence of high salt concentrations in the buffer, a basic protein wil bind to A. Cation exchanger B. Anion exchanger C. gel-filtration column D. None of the above 12. During electrophoresis at a pH 2 buffer, peptide LKRPEDKRWP wil migrate towards a A. Positively charged electrode B. Negatively charged electrode C. Wil not migrate at al 13. During electrophoresis at a pH 8 buffer, peptide LKRPEDKRWP wil migrate towards a A. Positively charged electrode B. Negatively charged electrode C. Wil not migrate at al 14. In the previous 2 questions, which condition wil make the peptide migrate the fastest? A. At pH 2 buffer B. In pH 8 buffer C. Migration rate wil not depend on pH MBB First Exam, page 4 Name ________________________ 15. Which of the following statements is true A. Every primary sequence of a polypeptide folds into a defined thre- dimensional structure B. Only evolutionarily related primary sequence can adopt similar three- dimensional structures C. Proteins with unrelated primary sequences can adopt similar thre- dimensional structures 16. Enzyme speed up chemical reactions in the cel by A. Shifting the thermodynamic equilibrium betwen reaction substrates and products B. Increasing the rate of the forward reaction C. Decreasing the rate of a backward reaction D. Increasing the rate of both the forward and backward reaction 17. For an enzymatic reaction characterized by a low Km for substrate the following is true: A. The maximal velocity of the reaction is high B. The maxial velocity of the reaction is low C. The maximal velocity of the reaction is reached at low substrate concentrations D. The substrate has a high affinity for the enzyme 18. Which of the following applies for an enzyme with a high k cat value A. The enzyme binds its substrate wel B. Large aounts of enzyme-substrate complex are formed in the reaction C. The maximal velocity of the reaction is high D. The enzye-substrate complex tends to efficiently disociate with the formation of the reaction product 19. A protein that interacts with nucleic acids A. Is likely to have many ?-helices B. Could be rich in D and E amino acids C. Wil migrate to the negatively charged elctrode during elctrophoresis in a pH 7.5 buffer D. Wil elute late from a gel-filtration column. 20. Amino acid G is often found in A. Paralel ?-sheets B. Antiparalel ?-sheets C. ?-turns D. Hydrophobic core of proteins 21. Isoelectrofocusing separates proteins A. By charge only B. By charge and mas C. By affinity D. By mas only MBB First Exam, page 5 Name ________________________ 22. Benzoic Acid (?-COOH) is most soluble at A. Low temperatures B. Low pH C. Neutral pH D. High pH 23. Disolving salt (NaCl crystals) in water breaks many ionic "bonds." What favors the proces of of disolving? A. Enthalpy B. Bond energy C. The entropy term (T?S) is positive D. The entropy term (T?S) is negative 24. LUCA, the last comon ancestor, would be A. aerobic B. multicelular C. an RNA World type cel D. anaerobic and single celed 25. After this exam I wil A. laugh B. cry C. drink D. cannot tel from data given MBB First Exam, page 6 Name ________________________ Answer the following questions on the question pages: 1. a. Draw a structural formula of a GRV tripeptide. (5) b. "MALDI-TOF MS" is an acronym. What do the leters stand for? Briefly define what happens when a protein is put through MALDI-TOF MS. (5) MBB First Exam, page 7 Name ________________________ 2. a. Using structural formulae ilustrate al potentiometric equilibria for aminoacid E. Indicate pKa values for each equilibrium. In other words draw the charge forms observed for "E" in aqueous solution, using 2, 4 and 9.5 as the pKa's. (4) b. Calculate the pI or isoelectric point for amino acid "E" and then state the Henderson Haselbalch equation. Which two charge forms are present at pH=7 and what is the ratio of their concentrations? (6) MBB First Exam, page 8 Name ________________________ 3. The alignment below shows sequences of related enzymes that perform identical biochemical functions in different organisms. Based on the information available, which two organisms are most similar to each other? Which organisms are furthest apart? Aongst ainoacid positions underlined in the alignment, which is likely the most important for the protein function? Which one is least important? Explain your reasoning. (10) Organism A KLMTKGRTVGIIFWYRTINEDASSI D KLITKGKTVGFIFWYRTVNEDASTK B KLITKRRTVAIIFWYRTIQEDASSI C KLMSKGRTVGIIFWYRTINEDASSI MBB First Exam, page 9 Name ________________________ 4. a. An enzymatic reaction is characterized by a K M value of .5 mM in the presence of 50 mM salt in the buffer. In the presence of 300 mM salt a K M value of 5 mM. Explain this observation. What inferences can you draw about the nature of interactions that are required for substrate-enzyme complex formation. (5) b. If S = 9.5 mM and Vmax = 80, with Km = 0.5 mM, calculate the initial rate for this enzyme in the absence of inhibitors. State quation, show work, circle answer. (5) MBB First Exam, page 10 Name ________________________ 5. a. The standard free energy change for the reaction [A] + [B] ? [C] is 8 kJ/mol. If the concentrations observed are [A] = 2 M, [B] = 3 M, and [C] = 10 M, calculate 1) the equilibrium constant for this reaction and 2) the actual free nergy change. State quations, show work, circle both answers. R = 8.3 J/mol deg, and T = 300 K. (5) b. Diagram Stanley Miler's apparatus, tel what he used as his "primordial atmosphere" and what he got as products. Critique the experiment briefly. (5) deis Microsoft Word - 407F06_1a.doc