LS1a Midterm Exam 1 Review Session Problems

Transcription

1 LS1a Midterm Exam 1 Review Session Problems 1. n aqueous mixture of a weak acid and its conjugate base is often used in the laboratory to prepare solutions referred to as buffers. ne commonly used acid is called RIS, which has the chemical formula shown below. + ( ) 3 3 ( ) 3 (acid) (conjugate base) a. Draw the chemical structures for both the acid and conjugate base forms of RIS. You may use any drawing convention you wish, but you MUS include all lone pairs of electrons and any net formal charges. cid onjugate Base b. Write the chemical reaction for the deprotonation of RIS acid to its conjugate base using the chemical formulae provided above. ( ) ( ) c. Write an expression for the equilibrium constant for the deprotonation reaction of the RIS conjugate base to RIS acid. K eq = [( ) 3 ] [+] [( ) ] d. Is the equilibrium constant you have just defined the same as the acid dissociation constant Ka? Yes e. he pk a of RIS is 8.3. If the concentration of protonated RIS is 10 mm in a solution of p 7.3, what is the concentration (in mm) of the conjugate base at the same p? he concentration of ris base is 1 mm.

2 2. Pictured below is the small molecule thromboxane. his molecule plays a very important role in the process of blood clotting. pka = 5 cis hromboxane trans 3 pka = 15 a. ircle the chiral centers in the molecule. b. Identify and label any cis or trans double bonds in the molecule. c. Ignoring geometric isomers, how many different stereoisomers are possible for this molecule? 2 5 = 32 d. ow many geometric isomers does this molecule have? 2 2 = 4 e. Using the pk a values provided above, draw the dominant form of thromboxane at the indicated p. i) p = 3 ii) p = 9 3 3

3 3. he molecule shown below is Rarvone (R)carvone a. Draw the enantiomer of R arvone (L)carvone or b. Briefly describe one way you could distinguish these enantiomers from one another By different interactions with another chiral molecule. [r by rotation of planepolarized light] c. Write the correct molecular formula for arvone Shown below are two arrowpushing mechanisms. Please provide the products. a. R 2 3 I R I b. S R S R' R' S R S

4 5. riplestranded D was first observed in Scientists later discovered that the formation of triplestranded D involves a type of base pairing called oogsteen pairing, which differs from the Watsonrick base pairing observed in normal doublestranded D. Below is an example of a oogsteen base pair. 1 2 D 2 D a. Identify each of these bases by name. 1 = denine 2 = hymine b. Redraw these two base pairs showing all lone pair electrons. 1 D 2 D c. Draw the hydrogen bond interactions expected for this oogsteen base pair.

5 d. Formation of a triple helix requires three bases to interact with each other to form a base trio rather than a base pair. ne way in which this threeway interaction can take place is for the three bases to engage in both Watsonrick base pairing and oogsteen base pairing. Show how two thymines and an adenine could interact with each other to form a base trio by using both Watsonrick and oogsteen base pairing. D D D

6 6. onsider a D polymerization step during PR: 3' 5' 3' D polymerase dp, dp, dp,dp 72 o 5' a. Would the following reaction proceed? Why or why not? 3' 5' 3' 5' 5' D polymerase dp, dp, dp, dp 72 o 3' 5' 3' o, because D synthesis occurs in a 5 to 3 direction and requires a free 3' group as well as a template following the 3' group. t the 3 ends of both red and blue strands, no remaining template exists for the polymerase to continue synthesizing D.

7 b. onsider the reaction below; what would the result be if you forgot to add dp to the reaction mixture? Draw the resulting product (be sure to label the 3 and 5 end of your products). 3' 5' 5' 3' D polymerase dp, dp, dp? 72 o 5 3

8 7. Shown below are three amino acids with the pk a values of their respective groups. ~ ~3.9 ~2.1 ~ ~1.8 ~ ~ (a) (b) (c) ~10.5 ~2.2 b. Identify each of the amino acids (a) through (c). a = spartic cid b = istidine c = Lysine c. Based on the structures shown below and the pk a values of the corresponding groups from above, what is the most likely range of the p of the surrounding solution? (1) between 3 and 4 (2) between 7 and 8 (3) between 10 and 11

9 8. Shown below is a picture of a protein. he major interactions that hold the protein in its properly folded conformation are highlighted. f a c e b d a. Briefly describe each interaction ae b. Which of these interactions would be most affected if the protein were placed in reducing conditions? d, disulfide bond would be broken. c. Label each of the amino acid side chains with the full name, three letter abbreviation and one letter code. Serine, Ser, S; Valine, Val, V; Leucine, Leu, L; Lysine, Lys, K; ysteine, ys, ;

10 d. If you were to subject a dilute solution of this protein to denaturing conditions, and then remove the denaturant, would you expect the protein to refold into the conformation shown above? Discuss the thermodynamic factors that contribute to your answer. Yes, the folded protein is thermodynamically more stable. he entropic driving force is the release of ordered water from solvation shells around hydrophobic side chains ( S positive). his offsets the entropic penalty paid by restricting the conformational freedom of the protein ( S negative). Enthalpic contributors are the formation of electrostatic, hydrogen bonding, and Van der Waals interactions within the protein ( negative). Enthalpic detractors are the loss of hydrogen bonding interactions with water around the polar side chains and backbone atoms. e. If were you were to subject a concentrated solution of protein to denaturing conditions, and then remove the denaturant, would you expect the protein to refold into the conformation shown above? Discuss the thermodynamic factors that contribute to your answer. o, protein will aggregate. Release of ordered water is still the entropic driving force. If a single molecule of protein is in a dilute solution, the only way it can release this ordered water is have its hydrophobic side chains associate with one another away from water in the interior of the protein (i.e. the hydrophobic effect drives the protein to fold). owever, if another molecule of protein is nearby, hydrophobic side chains on the two different molecules of protein can interact with each other to accomplish the same thing. herefore, if the concentration is high enough, protein molecules can achieve the same favorable S by interacting with each other rather than by folding correctly. In addition, because the protein does not have to adopt a specific properly folded conformation, there is less of an entropic penalty to aggregation than there is to folding. Enthalpically, aggregation is similar to folding because all of the same types of interactions can be formed/broken.

11 9. Proteins and B bind to each other as shown at physiological p (7.0): 2 Protein 2 Protein B lutamate sidechain pka = ~ 4 rginine sidechain pka = ~ 12 a. What types of interactions exist between the lu and rg side chains at p 7? Ionic interaction between +/ charges; 2 hydrogen bonds between lu oxygen lone pairs and rg protons. b. What would you expect to happen to the strength of the interaction as the p is slowly increased from 7 to 14? s the p increases from 7 to 12, an increasing fraction of the arginine side chains on protein B become deprotonated and therefore neutral. hus, at p >12, the ionic interaction is lost. he hydrogen bonding interactions remain, although the overall strength of interaction is now weakened. c. What would you expect to happen to the strength of the interaction as the p is slowly decreased from 7 to 1? s the p decreases from 7 to 4, an increasing fraction of the glutamate side chains on protein become protonated and therefore neutral. t p < 4, the ionic interaction is lost. he hydrogen bonding interactions remain, although they are weaker because neutral oxygen is less electronegative than negatively charged oxygen.