7/28/2019 Chem 4B Midterm 3 Spring 2012 Solutions

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Chemistry 4B Name:___________________________S2012 GSI:_____________________________

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Chemistry 4B, Spring 2012Midterm 3

April 4, 2012(closed book, 50 min.)

Name: GSI:

SID: Section:

Write your name and that of your GSI on all 11 pages of the exam.

In order to maximize your score on the exam: Do the questions you know how to do first. Go back and spend more time on the questions you find more challenging.

Budget your time carefullydon't spend too much time on one problem. Show all work for which you want credit and don't forget to include units.

Question Page Points Score

1 3 10

2 4 10

3 5-6 18

4 6-8 22

_ 5 9-11 20

Total: 80

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Chemistry 4B Name:___________________________S2012 GSI:_____________________________

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Protonated amino acids.

Useful Equations and ConstantsR= 8.314 J / (mol K)

"G = #RTlnK ln[A]

t

[A]0

= #kt1

[B]t

#1

[B]0

= kt

k= Ae#EA

RT v0=

VMax

[S]

KM+ [S]

KM=k#1 + k2

k1

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Chemistry 4B Name:___________________________S2012 GSI:_____________________________

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1. (10 pts) When thinking about amino acid side chains in proteins, we often think ofclosely related chemicals. For example, serine and threonine have similar pKa valuesto alcohols and water. What is the pKa of water? Include in your answer the relevant

equilibrium equations and their relationship to pKa values.

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Chemistry 4B Name:___________________________S2012 GSI:_____________________________

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2. (10 pts total) Multiple choice and short answer.

(i) (2 pts) The only standard amino acid without a stereoisomer is:

a) isoleucine

b) tryptophan

c) proline

d) glycine

e) asparagine

(ii) (2 pts) Water reduces the effective strengths of ion-ion interactions in proteins.Choose the best explanation:

(a) Water competes with polar groups for hydrogen bonds

(b) The dipoles of water molecules screen ions, reducing their effective charge

(c) Both (a) and (b)

(d) The statement is false. Water has no effect on ion pairs.

(iii) Of the following three amino acids, indicate which is most, intermediate, and leastlikely to be in the hydrophobic core of a protein. Also provide the 3-letter code of theamino acid. (2 pts each amino acid)

3-letter code:________ 3-letter code:________ 3-letter code:__________

(Circle one for each):

Most/Intermediate/Least Most/Intermediate/Least Most/Intermediate/Least

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Chemistry 4B Name:___________________________S2012 GSI:_____________________________

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3. (18 pts) You discover a new antibiotic that kills multi-drug resistant Mycobacteriumtuberculosis, which causes TB. You want to test whether this new antibiotic inhibitsprotein synthesis by incorporating the radioactive amino acid [35S]-Met into newlysynthesized proteins made by the bacteria. But you need to make sure you have

enough [

35

S]-Met in lab before starting your experiment.

a) (6 pts) The half-life of [35S]-Met is 87.4 days. What fraction of theradioactivity is left in a batch of [35S]-Met after 3 half-lives. Show your work.

b) (12 pts) For your experiment, you want to grow Mycobacterium smegmatis (aclose relative ofM. tuberculosis, but not pathogenic) in the presence of [35S]-Met, plus and minus the antibiotic, and need to include 10 micro-Curies (!Ci)of radioactivity per reaction. Your lab-mate ordered ~500 !Ci of [35S]-Met onMarch 12th, and the specific activity on Feb 27th (38 days ago) was recordedby the manufacturer as 1.2 Ci/!mol, or 10.5 mCi/mL. What is the minimumvolume of the [35S]-Met that you need to add to each growth condition? Showall of your work. (Hint: You may find the equations given on p. 2 helpful inanswering this question.)

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3. (continued)

b) (extra space, if needed)

4. (22 pts) Papain (from papaya) is a protease that has been used for thousands ofyears. It works as a meat tenderizer by cleaving proteins preferentially C-terminal ofArg or Lys amino acids that are preceded by a hydrophobic amino acid, as illustrated bythe following tripeptides:

---!RX--- or ---!KX---

where ! is any hydrophobic amino acid and X is any amino acid.

a) (8 pts) Draw the products of the cleavage reaction at physiological pH:

7/28/2019 Chem 4B Midterm 3 Spring 2012 Solutions

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4. (continued). Papain follows Michaelis-Menten kinetics (see below), and you find thatit cleaves the model tripeptide FRS with the initial velocities below, rounded to 2significant figures.

! ![S], nM Initial velocity, v (nM/sec)

10 4.830 13100 33300 601000 835000 96

b) (10 pts) What is the Michaelis constant, KM, for this enzyme? Give both amathematical relationship anda graphical representation that allow you toarrive at your answer (These are related to each other.). Be sure to includeunits with your answer.

Chemistry 4B Name:___________________________S2012 GSI:_____________________________

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4. (continued). Papain follows Michaelis-Menten kinetics (see below), and you find thatit cleaves the model tripeptide FRS with the initial velocities below, rounded to 2significant figures.

! ![S], nM Initial velocity, v (nM/sec)

10 4.830 13100 33300 601000 835000 96

b) (10 pts) What is the Michaelis constant, KM, for this enzyme? Give both amathematical relationship anda graphical representation that allow you toarrive at your answer (These are related to each other.). Be sure to includeunits with your answer.

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4. (continued)

c) (4 pts) Circle TRUE or FALSE for the following statements. For each

statement that you mark FALSE, write one sentence explaining why thestatement is false.

(i) You find that certain insects that infest papaya plantations make acompetitive inhibitor of papain. As a competitive inhibitor, this compoundtraps the enzyme-substrate complex in an inactive form. TRUE FALSE

(ii) Enzymes accelerate chemical reactions by favoring the equilibriumtowards product formation. TRUE FALSE

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5. (20 points) You discover a new enzyme that is a DNA topoisomerase(topoisomerases change the topology of DNA) that is very important for certain skincancers.

a) (10 pts) Topoisomerases are metalloenzymes, meaning that they use Mg

2+

orMn2+ to help catalyze the chemical reactions. Indicate which two of thetwenty amino acids are most likely to bind to these metal ions in the enzyme.Explain your reasoning for choosing these two, by making comparisons tochemicals you have used in Chem 4B lab.

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5. (continued)

b) (10 pts) Based on your discovery, you want to look for inhibitors of thistopoisomerase. You propose to look for small molecules (i.e. small organicmolecules of about 500 g/mol in mass or less) that bind to this topoisomerase

and stabilize its folding as a function of temperature, as drawn below. Therationale is that these molecules might serve as competitive inhibitors. Usingour in-class discussions of how enzymes work, explain why this method forlooking for small molecules is potentially useful. Answer by considering therelationship between equilibria and changes in free energy, both in terms ofenzymes and protein folding.

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5. (continued)

b) Extra space if needed.