BCH 451 Spring 2005                                   Exam #1                NAME

 

1.         Draw the predominate structures of the following molecules at the pH indicated. Be sure to include all carbon and hydrogen atoms!

 

            a.         (1) A = 2,3-bisphosphoglycerate @ pH = 3.5; B = Tris @ pH = 7.5

 

2.         (7)       D =methionyl-tyrosyl-cysteinyl-valyl-histidyl-prolyl-glutamine@ pH = 11

                        E =asparaginyl-leucyl-lysyl-phenylalanyl-cysteinyl-prolyl-methionine @ pH = 11

 

3.         (0.2 each) Circle and label [name] all of the functional groups or linkages/bonds in your peptide except for the peptide bonds.

 

4.         (0.2 each) Write the pKa by each appropriate functional group in your peptide.

 

5.         (0.3 each) Indicate, using a C for chymotrypsin, B for cyanogen bromide and T for trypsin, the site of cleaveage for these molecules on your peptide: [Use an arrow as well.]

 

6.         (0.3) In your peptide, with what amino acid residue(s) would Sanger’s react?

 

7.         (0.5) Calculate the pI of your peptide: [Show setup for full credit.]

 

8.         (2) What would you expect to happen if your peptide were exposed to iodoacetate? [name or draw any possible product(s).]

 

9.         (2) PUZZLER When your peptide was actually exposed to iodoacetate, no reaction occurred. Based on your previous answer what do you conclude is the reason for the observation. [Give your reasoning.]

 

10.       (2) PUZZLER How would you test your answer to the previous question?

 

11.       (2) How does 2,3-bisphosphoglycerate modify the oxygen affinity of hemoglobin?

 

12.       (2) Describe the immediate environment of the heme ring within the appropriate protein:

 

13.       (2) How is it possible to measure the size of proteins using SDS-PAGE?

 

14.       (1) Definition #1 G = right-handed α-helix, H = parallel β sheet, I = anti-parallel β sheet

 

15.       (1) Define Buffer:

 

16.       Glycine has been used extensively by biochemists as a buffer and thereby acts as a inspiration for this question. To start with, draw the structures (0.3 each) of

 

 

glycine-HCl                                        Glycine                                   sodium glycinate


Going into the laboratory, you find a solution of 2.50 M glycine and 10.0 M sodium hydroxide. (0.5) What would you guess the pH of the glycine solution to be?


(2) Assuming that you wish to make a glycine buffer at pH = 9.2, calculate the number of moles and the volume of sodium hydroxide that you would need to add to 100 mL of the glycine solution to titrate it to the desired pH. [Show your work for full credit.]


(1.5) What would be the net charge on glycine at pH = 9.2? [Show your work for full credit.]


Multiple choice:The dreaded multiple choice: 1.5 points maximum for each question. Circle the SINGLE answer which corresponds to the BEST answer. These questions will be graded with partial credit [both positive and negative values].

 

            a.         One possible interaction in proteins is called a “salt-bridge” because

                        i.         It is the product of an acid and base forming a salt plus water

                        ii.        NaCl can precipitate proteins

                        iii.       Salts contain positive and negative charged ions

                        iv.       Certain salts are found buried inside of proteins

                        v.         Certain salts can form bridges between tertiary structures

 

            b.         The Bohr effect occurs in hemoglobin when

                        i.         Elevated levels of carbon dioxide and protons stabilize the deoxy form

                        ii.        Elevated levels of carbon dioxide and pH stabilize the deoxy form

                        iii.       Elevated levels of carbon dioxide and pH stabilize the oxy form

                        iv.       Elevated levels of carbon dioxide and protons stabilize the oxy form

                        v.         You can’t fool me, it has nothing to do with carbon dioxide

 

            c.         Most protein extractions are performed at cold temperatures because

                        i.         Buffers are more soluble at low temperatures

                        ii.        Gases are more soluble at low temperatures

                        iii.       There are more hydrogen bonds in water at low temperatures

                        iv.       Ammonium sulfate is more soluble at low temperatures

                        v.         You can’t fool me, meat stays fresher at low temperatures

 

            d.         You cannot determine the pI from a titration curve because

                        i.         The titration curve is not accurate enough

                        ii.        It is very difficult to measure the pH of an endpoint

                        iii.       You do not know the concentration of the acid being titrated

                        iv.       You do not know the functional groups being titrated

                        v.         You can’t fool me, it is very easy to do so

 

            e.         Methane is incapable of hydrogen bonding with water because

                        i.         Methane is a symmetrical molecule with tetrahedral structure

                        ii.        Carbon-Hydrogen bonds are almost purely covalent

                        iii.       Methane has no dipole

                        iv.       Methane is hydrophobic

                        v.         You can’t fool me, it certainly can hydrogen bond with water