Name:
Chem 464
Biochemistry- Test 2
Multiple choice (4 points apiece):
1. In hemoglobin, the transition from T state to R state (low to high affinity) is triggered by:
A)
Fe 2+ binding.
B)
heme binding.
C)
oxygen binding.
D)
subunit association.
E)
subunit dissociation.
2. The amino acid substitution of Val for Glu in Hemoglobin S results in aggregation of the
protein because of ___________ interactions between molecules.
A)
covalent
B)
disulfide
C)
hydrogen bonding
D)
hydrophobic
E)
ionic
3. Which of the following statements is false?
A)
A reaction may not occur at a detectable rate even though it has a favorable
equilibrium.
B)
After a reaction, the enzyme involved becomes available to catalyze the reaction
again.
C)
For S 6P, a catalyst shifts the reaction equilibrium to the right.
D)
Lowering the temperature of a reaction will lower the reaction rate.
E)
Substrate binds to an enzyme's active site.
4. Which of these statements about enzyme-catalyzed reactions is false?
A)
At saturating levels of substrate, the rate of an enzyme-catalyzed reaction is
proportional to the enzyme concentration.
B)
If enough substrate is added, the normal Vmax of a reaction can be attained even
in the presence of a competitive inhibitor.
C)
The rate of a reaction decreases steadily with time as substrate is depleted.
D)
The activation energy for the catalyzed reaction is the same as for the uncatalyzed
reaction, but the equilibrium constant is more favorable in the enzyme-catalyzed
reaction.
E)
The Michaelis-Menten constant Km equals the [S] at which V = 1/2 Vmax.
5. To calculate the turnover number of an enzyme, you need to know:
A)
the enzyme concentration.
B)
the initial velocity of the catalyzed reaction at [S] >> Km.
C)
the initial velocity of the catalyzed reaction at low [S].
D)
the Km for the substrate.
E)
both A and B.
6. Which of the following is not a reducing sugar?
A)
Fructose
B)
Glucose
C)
Glyceraldehyde
D)
Ribose
E)
Sucrose
7. From the abbreviated name of the compound Glc( â1 6 4)Gal, we know that:
A)
C-4 of galactose is joined to C-1 of glucose by a glycosidic bond.
B)
the compound is a D-enantiomer.
C)
the glucose residue is at the reducing end.
D)
the galactose is in its pyranose form.
E)
the galactose residue is the â-anomer.
Longer questions
8. This is a REQUIRED question.
Draw the linear structure of D-glucose, the ring structure of â-D glucose, and the linear structure
of D-Galactose. (Galactose is an epimer of Glucose in which the stereochemistry at the C-4
position has been reversed)
Your choice. You may do any six the following seven questions. If you do all seven I will throw
out your worst answer.
9. Define the following terms:
Bohr effect- The effect of pH on the oxygen binding of hemoglobin; As the pH goes
down, hemoglobin releases oxygen, as the pH goes up it binds oxygen more strongly.
Allosteric protein- A protein in which the binding of a ligand at one site affects the
binding at another site
A homotropic interaction The ligand and the modulator are the same.
MWC model - Monod, Wyman and Changeux model of binding. All subunits in an
allosteric protein shift between R and S states simultaneously.
The R-state in Hemoglobin The ‘relaxed’ state of hemoglobin which has a higher affinity
for oxygen and is observed in the oxy-hemoglobin X-ray structure.
10. What is the cause of sickle cell anemia? Since sickle cell anemia is a potentially fatal genetic
problem, why haven’t all the affected individuals died, so the gene can be eliminated from our
gene pool? If I gave you a multi-million dollar grant to cure sickle cell anemia, how would you
propose to cure this disease?
I guess I gave this one away with one of the multiple choice questions. The cause is a mutation
which changes a Glu on the surface of the â subunit of hemoglobin to a Val. This creates a
hydrophobic patch on the hemoglobin surface that allows the hemoglobins in the red blood cell
to aggregate into a fiber that distorts the shape of the red blood cell, so it can no longer pass
through the capillaries. While the homozygous mutation is lethal, the heterozygous individual
can live a fairly normal life, and has an increased resistance to malaria, which is a favorable trait
in certain regions, so this has a positive selection.
11. In Chapter 6 we discussed several ways that enzyme can increase the rate of a reaction.
Name and briefly discuss at least 5 of these methods or principles.
General Principles
Binding energy of the substrate to the enzyme can be used to lower the activation energy
of the reaction. It can do this by creating a binding pocket that specifically stabilizes the
transition state in a reaction.
Entropy reduction. The binding energy can also be used to prevent rotations and
vibrations in the substrate so the substrate is perfectly positioned next to all the catalytic groups
needed to make a reaction ‘go’.
Desolvation - As the substrate enters the active site water molecules that could get in the
way of the reaction are striped away so the reaction can become more efficient.
Induced fit - Sometime the binding of the substrate induces a conformational change in
the enzyme that only activates the enzyme to do the reaction after other interfering chemicals
(like water) have been excluded from the active site.
Specific catalytic groups
General Acid/base catalysis - when amino acids in the enzyme act as acids or bases
Specific Acid/base catalysis when the enzyme creates H+ or OH- in an active site to act as
an acid or a base
Metal Ion catalysis - when a metal ion that is bound to the enzyme takes part in the
chemical reaction
Covalent catalysis - When a covalent bond between the substrate and the enzyme is
formed as part of the reaction pathway.
12. Below is a proposed mechanism for RNase A (An enzyme that clips RNA molecules)
(8 points)Tell me about the different types of catalysis you see occurring in this mechanism.
In step 1 His 12 is acting as a general base to remove a proton from the 2' OH of the
ribose, and His 119 is acitng as a general acid to donate its proton to the phosphate group
between the two ribose sugars. In step 2 the roles are reversed at His 119 now becomes a general
base to remove a proton from water and His 12 now becomes an acid to donate a proton to the 2'3' cyclic phosphate. Note that since Hiss 119 removed a proton from water, the remaining OHbecomes a specific base that can now also attach the 2'-3' cyclic phosphate.
(2 points) Tell me why this enzyme will degrade RNA but not DNA,
(Yes, I know this question is a Chapter 8 question, but I think you can figure it out)
This mechanism cleverly uses the 2'OH as part of the reaction pathway. Since this OH
does not exist in the deoxyribose sugar of DNA, DNA cannot be degraded by this mechanism
and this enzyme.
13. In this chapter we discussed several different ways that enzyme activity is regulated in the
cell. Discuss at least three different ways in which enzyme activity is regulated. (Note: your
discussion may NOT include inhibitors)
Non-covalent, reversible binding of allosteric effectors - The binding of small molecules,
including the substrate, can be used to alter the KM, and/or the Vmax of the enzyme. Typically the
enzyme is a multi-subunit enzyme and the binding of the effector molecules induces a
conformational change in she unit in which it is bound, and this, in turn, alters the conformation
of the other subunits to create the change in enzyme activity.
Covalent, reversible modification of enzymes. There are over 50 different ways in which
enzymes can be covalently modified to change their activity. Usually this change is associated
with a second pair of enzymes, one that adds the modification, and a second that removes it.
Typically this second set of proteins are somewhat promiscuous, and can modify a number of
different proteins in the same manner, so as to create a complex interplay regulatory forces
Covalent, irreversible modification of enzymes. The most common irreversible change
is proteolytic cleavage, in which one or more peptide bonds are cleaved so pieces of the protein
can be removed. Typically this kind of control is used to keep an enzyme from being active when
it is first synthesized, but then to activate it when it is in the proper place in the cell or the
organism.
A given enzyme may not have any regulatory controls, or can have any or all of the above
controls used to modify its activity. The cell is a wonderfully complicated place to live.
14. Compare and contrast cellular location, function and structure of proteoglycans with
glycoproteins
Proteoglycans - Macromolecules of the cell surface or extracellular matrix composed of
one or more sulfated glycosaminoglycan chains covalently bound to protein. Typically they are
mostly carbohydrate and do not contain that much protein. The carbohyrate portion is rich in
information and can be used to bind other molecules, or other molecules, will bind to specific
proteoglycans. Proteoglycans are the major component of the extracellular matrix.
Glycoproteins have one or more oligosaccharide joined to the protein. The are found in at
the cell surface, in the extracelluar matric, and in specific cellular organelles. Glycoproteins
usually contain more protein than carbohydrate, although in some cases they can be up to 80%
carbohydrate. Typically the carbohydrate portion contains more branch points and is structurally
more complicated than that of proteoglycans, making the carbohydrate even richer in
information. Hence the carbohydrate portions of glycoproteins are the usual targets of lectins.
15. What are lectins. Give at least three examples of how lectins are used in your body.
Lectins are proteins that bind carbohydrates with high specificity and affinity. They serve
a wide variety of functions including cell-cell recognition, cell adhesion, and intracellular
targeting of newly synthesized proteins.
Examples
Lectins used to identify and remove old red blood cells that have lost the terminal sialic
acids from their surface glycopoteins
Lectins are used to identify and remove old peptide hormones whose attached
carbohydrates have been degraded.
The lectins P-selectin and Integrin are used to signal a leukocyte in the bloodstream to
enter an area of inflamation
A variety of lectins are used to mediate inflamatory responses in your body.
Viruses, bacteria and parasites all can use lectins to identify and bind to their target host
cell.
There are lots more....