BI/CH421 Biochemistry I Name: Exam 1

30046_7Exam1A2__2014.pdf

!"#$%&'()!*+,-./*0123)"))45/.6)77777777777777777777777777777777777777)!"#$%&))))))))))89#'9#'8(&))))))))))))))):5;.)))))))))))+<))=)>+15?)@10)<+2)@;)777777777))() Part I: Multiple choice - for each question, circle the choice that best answers the question. Do not write the letter in the margin to indicate your answer, circle it. 3 points each. 1. For a reaction with !H = 10 kJ/mol and !S =10 J/K•mol, at 27°C, the reaction is (directly from problem worked in class) AB spontaneous '( not spontaneous $B at equilibrium. CB It's impossible to determine with the information provided DB None of the above 2. Rank the following bonds in terms of their relative typical strengths 1: Dipole-dipole interaction 2: Ionic interaction 3: London dispersion forces 4: Hydrogen bond a. 4 > 1 > 2 > 3 b. 3 > 2 > 1 >4 c. 2 > 4 > 3 > 1 d. 2> 4 > 1 > 3 3. Which amino acid pairs listed below are some of the major contributors to protein absorbance at 280 nm? a. Tyrosine and proline b. Tryptophan and histidine c. Histidine and proline d. Tyrosine and tryptophan e. All amino acids absorb at 280 nm 4. How many hydrogen bonds can pyridoxal phosphate (shown below) donate to the surrounding water? (similar to Ch2: ?1 in text but not exactly) a. 0 b. 1 c. 2 d. 3 e. >3 5. The pH of a solution containing 1x10-4 M of HCl will be a. 0.004 b. 4 c. -4 d. 10 e. none of the above NOHOHOPOOO

!"#$%&'()!*+,-./*0123)"))45/.6)77777777777777777777777777777777777777)!"#$%&))))))))))89#'9#'8(&))))))))))))))):5;.)))))))))))+<))=)>+15?)@10)<+2)@;)777777777))')6. The molecule drawn below has _______chiral centers. (directly from text Ch 4, #18) a. 0 b. 1 c. 2 d. 3 e. 4 7. Which of the following have the amino acids listed from the largest side chain to the smallest side chain (a question written by your classmate) a. Glycine - Leucine - Methionine - Alanine - Valine b. Valine - Methionine - Leucine - Alanine - Glycine c. Alanine - Glycine - Leucine - Valine - Methionine d. Methionine - Leucine - Valine - Alanine - Glycine e. Valine - - Alanine - Glycine - Methionine - Leucine 8. At a pH of 9.4, roughly 10% of the cysteine side chains are a. in the thiolate form b. protonated c. oxidized d. reduced e. none of the above 9. The side chain of tyrosine has a(n) a. phenol b. sulfur c. primary amine d. imidazole e. none of the above 10. Five graduate students prepare extracts from 5 different tissues. Each student measures the total amount of alcohol dehydrogenase and the total amount of protein in his or her extract. Which extract has the highest specific activity? extract Total protein (mg) Total alcohol dehydrogenase activity (units) A 300 60,000 B 200 80,000 C 3,000 90,000 D 5,000 100,000 E 1,000 200,000 OHCOHH2NCCH3HCHHCHHH

!"#$%&'()!*+,-./*0123)"))45/.6)77777777777777777777777777777777777777)!"#$%&))))))))))89#'9#'8(&))))))))))))))):5;.)))))))))))+<))=)>+15?)@10)<+2)@;)777777777))E) Part II: True False (2 pts each) - Circle T or F below to indicate if the following statement is true or false. 11. T F Liquid water at 0˚C has a greater entropy than ice at 0˚C. (Text, Ch1: 5a) 12. T F A reaction that has a very large and negative Gibbs free energy change will always occur very quickly. (we did a version of this question in lecture with an in class worksheet) 13. T F The equilibrium constant for a process is related to the standard free energy change for that process. 14. T F In the titration of any weak acid with a base, the midpoint of the titration curve occurs at neutral pH (pH = 7). 15. T F There are three amino acid side chains that are capable of forming an isopeptide bond (text Ch4, #27) 16. T F Phosphoserine (serine in which the side chain hydroxyl has been modified by the addition of a phosphate moiety) and methyl serine (where the side chain hydroxyl group of serine is methylated) would have the same isoelectric point since they are derived from the same amino acid. (similar to text Ch4, question26) Part III: Fill in the blank. For the following sentences, fill in the blank with the word(s) that best complete the sentence. (2 pt each) 17. For a process that is enthalpically favored but entropically opposed, it will be spontaneous only when the temperature is (problem worked in class)_____T

!"#$%&'()!*+,-./*0123)"))45/.6)77777777777777777777777777777777777777)!"#$%&))))))))))89#'9#'8(&))))))))))))))):5;.)))))))))))+<))=)>+15?)@10)<+2)@;)777777777))&)20. List the four thermodynamic state functions (Question 15, companion CH1) a. _Energy___________ b. _Enthalpy_________ c. _Entropy__________ d. _Gibbs free energy 21. The length of a typical hydrogen bond (from H to Acceptor) is ________. Looking for a number, not a qualitative description 22. Part IV: Short answer and problem solving 23. You are trying to purify an ATP binding protein (protein X) away from 3 other proteins (protein A-C). These proteins have the following properties: Protein pI molecular weight (Da) binds ATP? Protein A 4.5 150,000 Yes Protein B 8.5 35,000 Yes Protein C 4.5 35,000 No Protein X 4.5 35,000 Yes Based on this information, what type of chromatography could you use to separate: a. Protein A from Protein X. Briefly justify your answer. since these proteins differ in size, you would use a size exclusion column. b. Protein B from Protein X. Briefly justify your answer. Since these differ in their pI, you would use an ion exchange column - I would use an anion exchange column since your protein X would stick to the column and protein B would not at neutral pH c. Protein C from Protein X. Briefly justify your answer. You could make some kind of ATP-affinity column since protein A and C are identical in pI and molecular weight, you could use the differential affinity for ATP as a mechanism to separate them.

!"#$%&'()!*+,-./*0123)"))45/.6)77777777777777777777777777777777777777)!"#$%&))))))))))89#'9#'8(&))))))))))))))):5;.)))))))))))+<))=)>+15?)@10)<+2)@;)777777777))F) 24. Tris(hydroxymethyl)aminomethane (commonly called Tris) is a frequently used in biochemistry, however it can be a little tricky since the pH of a Tris-buffered solution is very temperature dependent. a) Based on the information given below, will the pH of a Tris-buffered solution go up or down upon cooling from room temperature down to 4˚C? Briefly justify your answer (a version of Chapter 2: Question 25). !H˚ = 50 kJ/mol pKa = 8.07 at 25˚C The pH would increase. Since !H is positive, this is an enthalpically disfavored reaction. Cooling a solution would therefore shift the equilibrium to the left, towards the acid form of Tris, this would cause the proton concentration to decrease, therefore leading to an increase in pH. b) Use the information given in part A above to determine what range of pHs would Tris be an effective buffer at 25˚C? 7-9 (7.1-9.1) 25. Shown below is a titration curve for glutamic acid. a. Draw the structure of the species that will predominate at the point labeled D below (Companion CH4, Question 20). 5 points HONH2HOOHHONH3HOOHH+

!"#$%&'()!*+,-./*0123)"))45/.6)77777777777777777777777777777777777777)!"#$%&))))))))))89#'9#'8(&))))))))))))))):5;.)))))))))))+<))=)>+15?)@10)<+2)@;)777777777))G) Rubric: 2.5 points for the structure and 1.5 pts for charges (0.5 pt per charge) b. Uh-oh - I forgot to label my axes!!! Please help me finish my graph by writing the correct labels below (2 pt each) X-axis = _____________equivalents of base Y-axis = _____________pH c. This point represents the isoelectric point of glutamate (circle one) A B C D E none of these 26. List two things below that affect the strength of a H-bond. Feel free to make some drawings if this helps you explain. a. (one thing that affects H-bond strength) b. (a second thing that affects H-bond strength) The three things we discussed in class that affect the strength of an H-bond are i) the size of the dipole/ the electronegativity of D and A ii) the length of the bond - the longer the bond, the weaker iii) the angle defined by D-H•••A - these three atoms form a straight line for ideal H-bond, if defines an angle, bond will be weaker. 27. Write out the name of the peptide PERLSTEIN using the 3 letter codes. Write your answer in the blank above each letter (space for second E has X - you don't have to write this one twice). 4 pts _____ - _____ - _____ - _____ - _____ -_____ -__X_ - _____ - _____ P E R L S T E I N __Pro - __Glu_ - _Arg_ - _Leu_ - _Ser_ - Thr - __X_ - _Ile__ - _Asn_ P E R L S T E I N Rubric: 0.5 pt per amino acid name H3NCHCCH2OOCH2COO

!"#$%&'()!*+,-./*0123)"))45/.6)77777777777777777777777777777777777777)!"#$%&))))))))))89#'9#'8(&))))))))))))))):5;.)))))))))))+<))=)>+15?)@10)<+2)@;)777777777))H)28. Shown below is the structure of daptomycin, an antibiotic effective against pathogenic Gram-positive bacteria. a) This medication works by inserting itself into the bacterial cell membrane, ultimately affecting the membrane structural integrity and causing bacterial cell death. Draw a circle around the functional group/portion of daptamycin that is most likely responsible for insertion of this drug into the hydrophobic cell membrane (3 pts) b) What is the relative stereochemistry of the center indicated by the arrow? Please briefly justify your answer (by drawing something that indicates how you figured this out). 5 points The relative configuration of this stereocenter is ___D_____ because: They could write either that it does NOT obey to CO-R-N rule (alpha-H in front, the C=O -> R group -> amine (NH) go counter-clockwise =D). or they could write the fisher projection Rubric: 2 points for blank; 4 points for explanation c) at neutral pH, this molecule would have a ___ charge (circle one) 3 points -3 -2 -1 0 +1 +2 +3 none of these

!"#$%&'()!*+,-./*0123)"))45/.6)77777777777777777777777777777777777777)!"#$%&))))))))))89#'9#'8(&))))))))))))))):5;.)))))))))))+<))=)>+15?)@10)<+2)@;)777777777))I) d) The boxed functional group is ________________(name of moiety boxed, not name of the amino acid). indole 2 points e) Draw a box around the portion of the molecule derived from 3-methyl glutamate. 2 points 29. S-adenosyl methionine (SAM) is shown below bound to an enzyme via several noncovalent bonds with the enzyme's amino acid sidechains - use this picture to complete the chart below Interaction Kind of bond Name of amino acid - use one letter code A Ionic or salt bridge R B Hydrogen bond S C Van der waals or London dispersion or induced dipole induced dipole I NNNNNH2OOHOHSNH3OONHONH2NH2HNNHOHOHNOABC

!"#$%&'()!*+,-./*0123)"))45/.6)77777777777777777777777777777777777777)!"#$%&))))))))))89#'9#'8(&))))))))))))))):5;.)))))))))))+<))=)>+15?)@10)<+2)@;)777777777))9) 30. a. Draw the peptide ARM in the protonation state that would predominate at pH 10.5 b. Estimate the pI of the peptide you drew above - write your answer in the box and show your work for credit. If you did part A above correctly, that should greatly help you with Part B since you should have drawn the neutral form above. You can estimate the pI = (9.4+12.5)/2 = 10.95 or 11. 31. The global market for artificial sweeteners is greater than one billion dollars annually. Therefore, discovering compounds that tightly bind and activate the "sweet" receptors on the tongue can be a lucrative business. The sweet taste is quantified in units of "molar relative sweetness (MRS)" which is a measure that compares the sweetness of sugar substitutes to those of sucrose (table sugar). Saccharin has an MRS of 160, meaning a solution of sucrose has to be 160 times more concentrated than saccharin to have the same amount of perceived sweetness. If the MRS value is directly correlated to the association or binding constant for the interaction of the sweetener with the "sweet" receptor, would you expect the !G˚ for the binding of saccharine to the receptor to be more or less negative than that of sucrose? Briefly explain your answer. H2NCHCCH3OHNCHCCH2OCH2CH2NHCNH2NH2HNCHCCH2OOCH2SCH3H2NCHCCH3OHNCHCCH2OCH2CH2NHCNH2NHHNCHCCH2OOCH2SCH3H2NCHCCH3OHNCHCCH2OCH2CH2NH2CNH2NHHNCHCCH2OOCH2SCH3H3NCHCCH3OHNCHCCH2OCH2CH2NH2CNH2NHHNCHCCH2OOCH2SCH3pKa = 9.4pKa = 12.5net charge = +1net charge = 0net charge = -1

!"#$%&'()!*+,-./*0123)"))45/.6)77777777777777777777777777777777777777)!"#$%&))))))))))89#'9#'8(&))))))))))))))):5;.)))))))))))+<))=)>+15?)@10)<+2)@;)777777777))(8) Keq Sweetener + Receptor ! Sweetener•Receptor complex if the MRS value is directly related to the equilibrium constant for the binding of the sweetener to the receptor, this is related to the !G˚ by the equation: !G˚ = -RT ln Keq and Keq = [complex]/[sweet][receptor] => the larger the Keq, the tighter the binding, the larger and more negative the !G˚. So in this example, you would expect the !G˚ for saccharine to be a more negative number than that of sucrose. This is related to the problem we worked in class relating every factor of 10 in the Keq to be worth ~1.4 kcal/mol of binding energy.

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