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. + (H ) 3 H 3 (H ) 3 H 2 (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. 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 acid to the RIS conjugate base. d. Is the equilibrium constant you have just defined the same as the acid dissociation constant Ka? e. he pk a of RIS is 8.3. If the concentration of protonated RIS is 10 mm in a solution of ph 7.3, what is the concentration (in mm) of the conjugate base at the same ph?

2 2. Pictured below is the small molecule thromboxane. his molecule plays a very important role in the process of blood clotting. H pka = 5 hromboxane H H 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? d. How many geometric isomers does this molecule have? e. Using the pk a values provided above, draw the dominant form of thromboxane at the indicated ph. i) ph = 3 ii) ph = 9

3 3. he molecule shown below is Rarvone (R)carvone a. Draw the enantiomer of R arvone b. Briefly describe one way you could distinguish these enantiomers from one another c. Write the correct molecular formula for arvone 4. Shown below are two arrowpushing mechanisms. Please provide the products. a. R H 2 H 3 I b. S R S R'

4 5. riplestranded D was first observed in Scientists later discovered that the formation of triplestranded D involves a type of base pairing called Hoogsteen pairing, which differs from the Watsonrick base pairing observed in normal doublestranded D. Below is an example of a Hoogsteen base pair. 1 H 2 D H 2 D a. Identify each of these bases by name. 1 = 2 = b. Redraw these two base pairs showing all lone pair electrons. c. Draw the hydrogen bond interactions expected for this Hoogsteen 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 Hoogsteen base pairing. Show how two thymines and an adenine could interact with each other to form a base trio by using both Watsonrick and Hoogsteen base pairing.

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' 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

7 7. Shown below are three amino acids with the pk a values of their respective groups. ~9.8 +H 3 H H ~3.9 ~2.1 ~9.2 H +H 3 H H ~1.8 ~9.0 H +H 3 H H H ~6.5 2 H + 3 ~10.5 (a) (b) (c) H ~2.2 a. Identify each of the amino acids (a) through (c). b. 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 ph of the surrounding solution? + H 3 H + H 3 H H + H 3 H H 3 + (1) between 3 and 4 (2) between 7 and 8 (3) between 10 and 11

8 8. Shown below is a picture of a protein. he major interactions that hold the protein in its properly folded conformation are highlighted in yellow. 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? c. Label each of the amino acid side chains with the full name, three letter abbreviation and one letter code.

9 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. 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.

10 9. Proteins and B bind to each other as shown at physiological ph (7.0): H 2 H Protein H 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 ph 7? b. What would you expect to happen to the strength of the interaction as the ph is slowly increased from 7 to 14? c. What would you expect to happen to the strength of the interaction as the ph is slowly decreased from 7 to 1?