EXAM 3 BCH 441 QUESTIONS AND ANSWERS WITH COMPLETE
SOLUTIONS GRADED A++
Large km infer that
the affinity for substrate is lower since
km=
(k-1 + kcat (aka k2))/k1
A small km implies k1 and kcat are
either small or the rate of reversibility is high or some combination of the two.
If the rates of formation and product generation are high, the value of km
will be higher but the substrate will not have a high affinity for the enzyme as it quickly
either forms and/or dissociates
Catalytic efficiency =
kcat(k2)/km
A higher catalytic efficiency would mean higher rate of product formation
(k2 or kcat) than km(km= (k1 + kcat (aka k2))/k-1) or substrate affinity
Lower affinity does not necessarily mean
lower efficiency if kcat is large
Based on the structure of the active site, provide an explanation for how
chorismate mutase lowers the energy required to place the substrate into a
conformation resembling the proposed "near attack complex"?
The near attack complex (NAC) is a reactive confirmation of the ground state that is
directly converted into the transition state this can help predict the magnitude of the
, catalytic event. The NAC of chorismate mutase uses 2 carbon atoms that pie orbitals
point to eachother (within the distance of Van Der Waals interactions about 3.7
angstroms) to form a bond. Chorismate mutase lowers the energy needed to place the
substrate, chorismate, into a confirmation that already resembles the NAC. By having
an active site that specifically positions the substrates functional groups through
electrostatic interactions and hydrogen bonds, effectively preorganizing the molecule
into a strained confirmation that is more like the transition state. This in return reduces
the energy barrier to reach the NAC.
Within the active site of an enzyme, pKa values of side chains can be dramatically
different from the values you are familiar with. Explain what type of environment
would lead to increasing the pKa of glutamic acid by 3 or 4 pH units. Explain how
the pKa of lysine could be lowered by 3-4 pH units
Raising the pKa of Glu is essentially increasing the affinity for the proton. When
deprotonated, Glu is ionized. Therefore, if having a negative charge was energetically
unfavorable, then the pKa could effectively increase to avoid having a charge. This
could occur in an active site or buried nonpolar regions of a protein. It can also be due
to positioning and interactions with other groups. Think about the LBHB in the serine
protease mechanism between Asp and His. In a LBHB the proton is shared equally
between atoms (you can decide if they are donors or acceptors). To be equally shared,
the strength of the bonds must be similar. If we are talking about a proton that is
essentially pKa. The same argument can be made for Lys except it is lowering the pKa
to avoid being charged
SOLUTIONS GRADED A++
Large km infer that
the affinity for substrate is lower since
km=
(k-1 + kcat (aka k2))/k1
A small km implies k1 and kcat are
either small or the rate of reversibility is high or some combination of the two.
If the rates of formation and product generation are high, the value of km
will be higher but the substrate will not have a high affinity for the enzyme as it quickly
either forms and/or dissociates
Catalytic efficiency =
kcat(k2)/km
A higher catalytic efficiency would mean higher rate of product formation
(k2 or kcat) than km(km= (k1 + kcat (aka k2))/k-1) or substrate affinity
Lower affinity does not necessarily mean
lower efficiency if kcat is large
Based on the structure of the active site, provide an explanation for how
chorismate mutase lowers the energy required to place the substrate into a
conformation resembling the proposed "near attack complex"?
The near attack complex (NAC) is a reactive confirmation of the ground state that is
directly converted into the transition state this can help predict the magnitude of the
, catalytic event. The NAC of chorismate mutase uses 2 carbon atoms that pie orbitals
point to eachother (within the distance of Van Der Waals interactions about 3.7
angstroms) to form a bond. Chorismate mutase lowers the energy needed to place the
substrate, chorismate, into a confirmation that already resembles the NAC. By having
an active site that specifically positions the substrates functional groups through
electrostatic interactions and hydrogen bonds, effectively preorganizing the molecule
into a strained confirmation that is more like the transition state. This in return reduces
the energy barrier to reach the NAC.
Within the active site of an enzyme, pKa values of side chains can be dramatically
different from the values you are familiar with. Explain what type of environment
would lead to increasing the pKa of glutamic acid by 3 or 4 pH units. Explain how
the pKa of lysine could be lowered by 3-4 pH units
Raising the pKa of Glu is essentially increasing the affinity for the proton. When
deprotonated, Glu is ionized. Therefore, if having a negative charge was energetically
unfavorable, then the pKa could effectively increase to avoid having a charge. This
could occur in an active site or buried nonpolar regions of a protein. It can also be due
to positioning and interactions with other groups. Think about the LBHB in the serine
protease mechanism between Asp and His. In a LBHB the proton is shared equally
between atoms (you can decide if they are donors or acceptors). To be equally shared,
the strength of the bonds must be similar. If we are talking about a proton that is
essentially pKa. The same argument can be made for Lys except it is lowering the pKa
to avoid being charged
