Biochemistry Problem Set
Q1) Using the identity-based scoring system and the Blosum-62 substitution matrix to calculate the alignment score for the alignment of the following two sequences:
(1) ASNFLDKAGK and (2) ATDYLEKAGK
Now randomly rearrange the second sequence and recalculate the alignment scores. What do these results tell you about the quality of the original alignment? How do the ID-based score and Blosum-62 score compare?
Q2) A comparison of the aligned amino acid sequences of two proteins each consisting of 150 amino acids reveals them to be only 8% identical. However, their three-dimensional structures are very similar. Are these two proteins related evolutionarily? Explain.
Q3) Does myoglobin exhibit a Bohr effect? Why or why not?
Q4) Lampreys are primitive organisms whose ancestors diverged from the ancestors of fish and mammals approximately 400 million years ago. Lamprey blood contains a hemoglobin related to mammalian hemoglobin. However, lamprey hemoglobin is monomeric in the oxygenated state. Oxygen-binding data for lamprey hemoglobin are as follows (Y = fractional saturation):
|
pO2
|
Y
|
pO2
|
y
|
pO2
|
Y
|
|
0.1
|
.0060
|
2.0
|
.112
|
50.0
|
.889
|
|
0.2
|
.0124
|
3.0
|
.170
|
60.0
|
.905
|
|
0.3
|
.0190
|
4.0
|
.227
|
70.0
|
.917
|
|
0.4
|
.0245
|
5.0
|
.283
|
80.0
|
.927
|
|
0.5
|
.0307
|
7.5
|
.420
|
90.0
|
.935
|
|
0.6
|
.0380
|
10.0
|
.500
|
100
|
.941
|
|
0.7
|
.0430
|
15.0
|
.640
|
150
|
.960
|
|
0.8
|
.0481
|
20.0
|
.721
|
200
|
.970
|
|
0.9
|
.0530
|
30.0
|
.812
|
|
|
|
1.0
|
.0591
|
40.0
|
.865
|
|
|
a) Plot these data to produce an oxygen-binding curve. You can use MS Excel or Googlesheets for graphing. At what oxygen partial pressure is this hemoglobin half-saturated? On the basis of the appearance of this curve, does oxygen binding seem to be cooperative?
b) Further studies revealed that lamprey hemoglobin forms oligomers, primarily dimers, in the deoxygenated state. Propose a model to explain any observed cooperativity in oxygen binding by lamprey hemoglobin. How would this change the curve you plotted in part (a)?
Q5) The reaction of the hydrolysis of glucose 6-phosphate to give glucose and phosphate has a ΔGo′ = -13.8 kJ/mol. The reaction takes place at 25oC. Initially, the concentration of glucose 6-phosphate is 10-5 M, that of glucose is 10-1 M, and that of phosphate is 10-1 M.
(a) What is equilibrium constant for the reaction?
(b) What is the ΔG for this reaction under the initial conditions?
(c) Under the initial conditions, in which direction will the reaction proceed? Why?
(d) Under standard conditions, in which direction will the reaction proceed? Why?
Q6) An enzyme has a KM value of 0.5mM.
a) At what substrate concentration will the velocity of the enzyme reach ¼ of the Vmax?
b) Sketch a Michaelis-Menten plot of the reaction kinetics in (a). Label the axes. Indicate the positions of KM and the substrate concentration, S, at ¼Vmax.