exam 2 Flashcards
Using SDS gel electrophoresis to separate proteins, _________ proteins migrate the fastest in the gel and move farther away from the ___________ because of their _________ charge.
small; anode; negative
large; cathode; positive
large; cathode; negative
small; cathode; negative
large; anode; negative
small; cathode; negative
How is isoelectric focusing used to separate two proteins of equivalent molecular weights, which do not separate using polyacrylamide gel electrophoresis (PAGE)?
Proteins are separated on the basis of ligand affinity; a protein band is formed where the pH = dissociation constant.
Proteins are separated on the basis of overall shape with globular proteins having a lower pI than elliptical proteins.
Proteins are separated on the basis of positive charge; a protein band is formed where the pH = pKa in the gradient.
Proteins are separated on the basis of overall net charge; a protein band is formed where the pH = pI in the gradient.
Proteins are separated on the basis of overall net charge; a protein band is formed where the pH = pI in the gradient.
Which of the TWO following statements about x-ray crystallography are true?
X-ray crystallography is the only technique which can determine the three-dimensional structure of a protein.
Only crystallized proteins can be analyzed.
The basic experimental data are relative intensities and positions of scattered electrons.
The x-ray beam is scattered by the protein sample.
Only crystallized proteins can be analyzed.
The x-ray beam is scattered by the protein sample.
Though oxygen only binds to a particular place in the hemoglobin molecule, the oxy- and deoxy- forms of hemoglobin differ in overall protein conformation. An example of a structural change that does NOT play a role in translating local binding of oxygen to global protein conformational change would be the different ______ in the presence and absence of oxygen binding.
location of the proximal histidine
location of the distal histidine
orientation of the F helix
size of the heme iron
location of the distal histidine
What are the functions of the distal and proximal histidine in mediating oxygen binding to hemoglobin?
The proximal His forms a H-bond with O2; the distal His coordinates with Fe2+
The distal His forms a H-bond with CO; the proximal His coordinates with Fe3+
The distal His forms an ionic bond with H2O; the proximal His coordinates with Fe2+
The distal His forms a H-bond with O2; the proximal His coordinates with Fe2+
The distal His forms a H-bond with O2; the proximal His coordinates with Fe2+.
Although most protein sequencing is now done by mass spectrometry (MS), Edman degradation (ED) is useful if large amounts of a protein can be obtained even if from an uncharacterized species. Answer the True/False questions regarding methods used to sequence a polypeptide fragment and choose the set of all correct answers.
- True / False – Protein sequencing by ED does not require purified protein but sequencing by MS does.
- True / False – The N-terminal residue removed by acid treatment in ED is always a methionine.
- True / False – Trypsin and chymotrypsin treatment often provides identical peptide fragments for ED.
- True / False – Genomic sequences are needed to predict protein sequences by the MS method.
- True / False – Trypsin treatment provides useful sequence information when analyzing data from MS.
(1) False (2) False (3) True (4) True (5) False
(1) False (2) True (3) True (4) False (5) False
(1) True (2) True (3) False (4) False (5) True
(1) False (2) False (3) False (4) True (5) True
(1) True (2) False (3) False (4) True (5) True
(1) False (2) False (3) False (4) True (5) True
When oxygen binds to hemoglobin, which of the following occurs?
His F7 is brought closer to the plane of the porphyrin ring.
The heme group becomes planar.
His E8 is brought closer to the plane of the porphyrin ring.
The atomic radius of the iron is increased.
The heme group becomes planar.
The figure below shows the coordination of heme, O2, and two critical histidine residues in globin proteins. Which of the following steps happens first in the oxygen binding process?
Iron moves into the plane of heme.
O2 binds to the iron of heme.
The F helix moves toward heme.
The proximal histidine moves toward heme.
O2 binds to the iron of heme.
Calculate the purification of the target protein when there is a 30% decrease in activity and a 55% decrease in total protein after centrifugation.
1.8-fold
1.6-fold
0.55-fold
0.64-fold
1.6-fold
The fractional saturation of hemoglobin (Hb) binding to oxygen is illustrated by______________.
[Hb] / [HbO2].
[HbO2] / [Hb].
([HbO2] + [Hb]) / [HbO2].
[HbO2] / ([HbO2] + [Hb]).
[HbO2] / ([HbO2] + [Hb]).
What is the difference between X-ray crystallography and NMR spectroscopy for determining protein structure?
X-ray crystallography collects diffraction data of a protein crystal; NMR spectroscopy collects nuclear spin data of soluble protein.
Incorrect Response
X-ray crystallography collects nuclear spin data of soluble protein; NMR spectroscopy collects diffraction data of a protein crystal.
X-ray crystallography collects diffraction data of molten globules; NMR spectroscopy collects nuclear spin data of membrane proteins.
X-ray crystallography collects graphic data from molecular dynamic calculations; NMR spectroscopy collects nuclear charge data of soluble protein.
X-ray crystallography collects diffraction data of a protein crystal; NMR spectroscopy collects nuclear spin data of soluble protein.
What is the free energy change for transport of glucose from outside the cell to inside the cell at 37ºC when the glucose concentrations are 5 mM outside and 0.1 mM inside?
+1.9 kJ/mol
+10.1 kJ/mol
-10.1 kJ/mol
-1.9kJ/mol
-16.0 kJ/mol
-10.1 kJ/mol
If the histidine on the E helix (His E7) that coordinates the O2 that binds to the heme iron in hemoglobin is mutated to an alanine, what effect would be most likely?
Oxygen binding would not cause the movement of the F helix, since the alanine at E7 cannot coordinate oxygen.
Oxygen binding affinity would increase, since the alanine residue would form strong interaction with the oxygen molecule.
Oxygen binding would take place on the other face of the heme molecule, where the “proximal” histidine would be able to interact with the oxygen.
Oxygen binding would cause hemoglobin polymers to form, due to the introduction of a hydrophobic patch by the addition of this alanine.
Oxygen binding would not cause the movement of the F helix, since the alanine at E7 cannot coordinate oxygen.
The HbS mutation (Glu6 –> Val6) ______________.
results from polymerization of oxyhemoglobin HbS.
results from polymerization of α2βSβ or α2βS2.
results from a mutation that puts a charged amino acid on the β subunit protein surface.
is thought to provide heterozygous individuals protections from malaria
is thought to provide heterozygous individuals protections from malaria
Consider a system where a passive transport channel is available for a neutral molecule X. If RTln(C2/C1) is zero, then
the molecule will move from the area where the concentration is C2 to the area where the concentration is C1.
no net transport will occur.
There is no way to determine if or how transport of X will occur given the information provided.
the molecule will move from the area where the concentration is C1 to the area where the concentration is C2.
no net transport will occur.
A reaction coordinate diagram comparing an uncatalyzed reaction with an enzyme-catalyzed reaction can directly illustrate that the enzyme __________, but will not directly illustrate that the enzyme __________.
stabilizes the transition state; orients the substrates appropriately for the reaction to occur
orients the substrates appropriately for the reaction to occur; provides an alternative path for product formation
stabilizes the transition state; provides an alternative path for product formation
provides an alternative path for product formation; stabilizes the transition state
stabilizes the transition state; orients the substrates appropriately for the reaction to occur
The initial velocity of an enzyme-catalyzed reaction is followed at various substrate concentrations. At very high substrate concentrations it is observed that the initial velocity no longer increases as more substrate is added. The velocity under these conditions is known as_____________.
the ultimate velocity.
the maximum velocity.
optimal velocity.
v[S].
the maximum velocity
A histidine residue at an enzyme’s active site transfers a H+ to an amine group of the substrate as the first step of the reaction. The result is an increase in the rate of release of the product. This is an example of _____________.
entropy reduction mechanism.
general acid catalysis mechanism.
induced fit mechanism.
covalent catalysis mechanism.
general acid catalysis mechanism.
Why does it make sense that small molecules functioning as inactive transition state analogs are the most effect enzyme inhibitors?
Because transition state analogs have structures similar to the substrate and enzymes bind substrates very tightly.
Because the transition state conformation has the most interactions in the active site, and if the analog is inactive, then the enzyme is “stuck.”
Because transition state analogs have structures similar to the product and enzymes bind products very tightly.
Because transition state analogs always contain fluorine atoms, which are highly reactive with the enzyme active site and “kill” the enzyme.
Because the transition state conformation has the most interactions in the active site, and if the analog is inactive, then the enzyme is “stuck.”
