Biochemistry Test 2

Name:  _____________________                                                                            March 22, 2017

Possible:  67 pts

pratt2e_prob_05_191.   (3 pts)  On the right is shown the oxygen binding curves of Hb A (dashed line) and of Hb Great Lakes (solid line).  The shape of the oxygen binding curve for Hb A indicates

a)    that Michaelis-Menten kinetics don’t apply.

b)   that a multi-step reaction is occurring.

c)    that multiple intermediates are involved.

d)   that cooperative binding is taking place.

e)    that all of the above are true.

2.   (3 pts)  Using the same figure as in the previous problem, which hemoglobin has a higher affinity for oxygen when pO2 is 20 torr?  (Circle one)

            Hb A               Hb Great Lakes

a)       If the curves were extended, which hemoglobin would have a higher affinity for oxygen when pO2 is 75 torr?  (Circle one)   

            Hb A               Hb Great Lakes

b)      Which hemoglobin is most efficient at delivering oxygen from arterial blood (pO2 =75 torr) to active muscle (pO2 = 20 torr)?  (Circle one)

            Hb A               Hb Great Lakes

3.   (2 pts)  Which one of the following provides the strongest evidence of a common ancestor for homologous proteins?

a)       Invariant residues

b)      Conservatively substituted residues

c)      Variable residues

4.   (2 pt)  Which one of the following is not true of hemoglobin?

a)      When oxygen binds to an iron atom in heme, the iron shifts its position; the heme does not shift.

b)      “Tense” and “relaxed” refer to two states of hemoglobin.

c)      The subunits of hemoglobin “snap” between states.

d)      As oxygen binds to hemoglobin, the oxygen affinity of each subunit changes very gradually.

This Page:  10 pts


 

5.   (3 pts)  The difference between normal hemoglobin and sickle cell hemoglobin is

a)    One amino acid.

b)   Five amino acids.

c)    Normal hemoglobin does have cooperative binding.

d)   Normal hemoglobin binds oxygen more strongly.

e)    Normal hemoglobin has fewer amino acids.

f)    Normal hemoglobin has more amino acids.

6.   (6 pts)  When hemoglobin releases oxygen to tissues, the hemoglobin also tends to absorb a proton, making the blood more basic.  This helps with removing CO2 from the tissues.  This can be explained with two equilibria steps.

      Show the chemical equilibrium between CO2 and H2CO3:    CO2 + H2O H2CO3

      Show the chemical equilibrium between H2CO3 and HCO3-:  H2CO2 HCO3 + H+

7.   (2 pts)  Give the two letters that go with the numbers, such as 2.1.1.13, to identify enzymes. 

EC

8.   (4 pts)  Draw a simple free energy diagram showing how free energy changes on going from substrate to product, both in the absence and in the presence of an enzyme.   

     

9.   (2 pts)  When a substrate binds to an enzyme, the shapes of both the substrate and the enzyme change.  This change in shape is mainly associated with the

a)      induced fit model.

b)      lock and key model.

c)      effect of proximity.

d)      effect of orientation

e)      mechanism of electrostatic catalysis.

This Page:  23 pts

 

 

 

 

10. (20 pts)  Sketch the mechanism by which a serine protease cleaves a peptide bond.  The active site is shown.  (The dashed lines represent hydrogen bonds.)

F06_08

Use arrows to show compounds entering and leaving.

Show protein using “R”s.

Show tetrahedral transition state.

 

 

This Page:  20 pts


 

11. (2 pts)  In the mechanism you just sketched, which step represents covalent catalysis?

Forming a bond to the serine OH.

12. (3 pts)  Serine proteases contain a “tetrahedral hole”.  What is the purpose of this tetrahedral hole?

a)    It stabilizes the transition state, lowering its energy.

b)   It matches the shape of the incoming substrate, ensuring tight binding.

c)    It matches the shape of the product that is about to form, driving the reaction towards product.

d)   It holds water, which is used to solvate the ionic intermediate.

e)    It holds water that has been removed from the ionic intermediate, making it more reactive.

13. (4 pts)  Chymotrypsin is specific for amino acids with large side chains, such as phenylalanine.  Trypsin is specific for amino acids with cationic side chains, such as lysine.  Elastase is specific for small amino acids.  The following figure illustrates the specificity pockets of these proteases.  Which pocket is for which enzyme?

    ________________                __________________                  ___________________

Chymotrypsin                                 trypsin                                     elastase

14. (2 pts)  Which type of evolution is described as species from different parents evolving similar features?

Convergent evolution

15. (3 pts)  What change occurs in a zymogen when it is converted into an active protein?  (A specific example is not required.)

A bond is broken in the zymogen to convert it into an active protein.

This Page:  14 pts