BIOS 100 FINAL EXAM REVIEW
1. Consider the following reaction, in which glucose undergoes oxidation:C†H•O‚ †+ 6O‚->
6CO‚+ 6H‚O + heat
This reaction has a large negative G, yet glucose is quite stable in aqueous solutions that
contain high concentrations of oxygen. Which of the followinghelps explain the stability of
glucose, despite the large negative G.
A. Random collisions between O‚and glucose are rare.
B. Most random collisions between O‚and glucose do not have sufficientenergy to cause a
reaction.
C. The reaction requires catalysis to occur.
D. The reaction has an unfavorable equilibrium constant.
E. C and D: B. Most random collisions between O‚ and glucose do not have sufficientenergy to
cause a reaction.
2. What would be the effect of a mutation that affects catalysis, but notsubstrate binding?
A. Decreased Vmax
B. Decreased Km
C. Increased Km
D. A and B
E. A and C: A. Decreased Vmax
3. Which of the following can make an important contribution to cooperativebinding of a
ligand?
A. Allostery
B. Competition for binding sites
C. High affinity and specificity in ligand binding
D. Negative feedback
E. Positive feedback: A. Allostery
4. Which of the following is a common mechanism used to increase theaffinity and
specificity of DNA binding proteins?
A. Dimerization
B. Hydrophobic interactions
C. Interactions with the minor groove
D. Negatively charged amino acid side chains
,E. Phosphorylation: A. Dimerization
5. Imagine that you have identified a new transcription factor protein called Slug and you
think that it controls transcription of a gene that controls the ability of slugs to make slime.
You synthesize 10 different pieces of DNA fromthe promoter of the slime gene and you want
to test if any of them bind to theslug protein. Which of the following would be most useful for
testing if Slug binds to any of the DNAs?
A. A gel shift assay
B. A filter binding assay
C. Measure Km for each piece of DNA
D. Measure Vmax for each piece of DNA
E. SDS PAGE: A. A gel shift assay
6. What is a gel shift assay?: Gel shift assay is a technique based on the idea thatprotein:DNA
complexes migrate more slowly than free DNA under non-denaturing electrophoresis or
agarose gel electrophoresis.
7. Eventually you find that Slug binds to the promoter of the slime gene and controls its
transcription. Then you find a second transcription factor called Banana that also binds to the
promoter of the slime gene. The DNA binding sites for Banana and Slug are separated by 4
nucleotides. When you
increase the spacing to 6 or more nucleotides, Banana and Slug can no longer stimulate
transcription of the slime gene. Which hypothesis best explains thisobservation?
A. Binding sites for Banana and Slug are in the major groove of DNA.
B. Banana and Slug bind independently to their sites on DNA.
C. Banana and Slug bind to each other.
D. Banana and Slug induce a conformational change in the DNA that they bindto.
E. Banana and Slug do not undergo cooperative binding to DNA: C. Bananaand Slug bind to
each other.
8. The concentration of transcription factors within cells can be very impor-tant. For
example, increasing the concentration of a specific transcription factor that controls stem cell
differentiation by as little as 2-fold can cause stem cells to differentiate into mesoderm cells.
Which of the following couldmost directly explain this observation?
A. Allostery
B. Changes in Kd
C. Cooperativity
D. Direct reading of DNA sequences
E. Indirect reading of DNA sequences: C. Cooperativity
, 9. Which of the following explain how GTPAases are controlled?
A. Allosteric changes caused by GTP binding.
B. Binding to MAPKKK.
C. Changes in conformation triggered by _binding of Ras_.
D. Cooperative binding of GTP.
E. Phosphorylation of GTPases by kinases.: A. Allosteric changes caused byGTP binding.
10. Which of the following plays the most important role in determining theaffinity of
macromolecular interactions?
A. Cooperativity
B. Hydrogen bonding
C. Hydrophobic interactions
D. Ionic interactions
E. Van der Waals interactions: C. Hydrophobic interactions
11. A protein binds to the DNA sequence AAAAA with a Kd = 10 nM. The sameprotein binds
to the RNA sequence AAUUAU with a Kd = 15 nM, and it binds to a lipid with a Kd = 10
mM. Which of the following statements are true?
A. The protein binds to RNA and DNA with high affinity, but low specificity.
B. The protein binds with low affinity for RNA and DNA, but high specificity.
C. The protein binds with low affinity and low specificity for all three targets.
D. The protein has high specificity for lipids over RNA and DNA.: A. The proteinbinds to RNA
and DNA with high affinity, but low specificity.
12. Enzymes can catalyze cellular reactions through various mechanisms.Which of the
following statements is NOT true regarding enzymes?
A. They accelerate a cellular reaction by destabilizing the transition state.
B. They can form covalent bonds with the substrate during catalysis.
C.They have a higher affinity for the transition state of the substrate than forits stable form.
D. They can provide the chemical groups necessary for simultaneous acid andbase catalysis.
E. They can strain a substrate to force it toward a specific transition state.: A.They accelerate a
cellular reaction by destabilizing the transition state.
13. An enzyme acts on a tyrosine residue on a target protein to create a bindingsite for the SH2
domain. This enzyme is most specifically...
A. an isomerase.
1. Consider the following reaction, in which glucose undergoes oxidation:C†H•O‚ †+ 6O‚->
6CO‚+ 6H‚O + heat
This reaction has a large negative G, yet glucose is quite stable in aqueous solutions that
contain high concentrations of oxygen. Which of the followinghelps explain the stability of
glucose, despite the large negative G.
A. Random collisions between O‚and glucose are rare.
B. Most random collisions between O‚and glucose do not have sufficientenergy to cause a
reaction.
C. The reaction requires catalysis to occur.
D. The reaction has an unfavorable equilibrium constant.
E. C and D: B. Most random collisions between O‚ and glucose do not have sufficientenergy to
cause a reaction.
2. What would be the effect of a mutation that affects catalysis, but notsubstrate binding?
A. Decreased Vmax
B. Decreased Km
C. Increased Km
D. A and B
E. A and C: A. Decreased Vmax
3. Which of the following can make an important contribution to cooperativebinding of a
ligand?
A. Allostery
B. Competition for binding sites
C. High affinity and specificity in ligand binding
D. Negative feedback
E. Positive feedback: A. Allostery
4. Which of the following is a common mechanism used to increase theaffinity and
specificity of DNA binding proteins?
A. Dimerization
B. Hydrophobic interactions
C. Interactions with the minor groove
D. Negatively charged amino acid side chains
,E. Phosphorylation: A. Dimerization
5. Imagine that you have identified a new transcription factor protein called Slug and you
think that it controls transcription of a gene that controls the ability of slugs to make slime.
You synthesize 10 different pieces of DNA fromthe promoter of the slime gene and you want
to test if any of them bind to theslug protein. Which of the following would be most useful for
testing if Slug binds to any of the DNAs?
A. A gel shift assay
B. A filter binding assay
C. Measure Km for each piece of DNA
D. Measure Vmax for each piece of DNA
E. SDS PAGE: A. A gel shift assay
6. What is a gel shift assay?: Gel shift assay is a technique based on the idea thatprotein:DNA
complexes migrate more slowly than free DNA under non-denaturing electrophoresis or
agarose gel electrophoresis.
7. Eventually you find that Slug binds to the promoter of the slime gene and controls its
transcription. Then you find a second transcription factor called Banana that also binds to the
promoter of the slime gene. The DNA binding sites for Banana and Slug are separated by 4
nucleotides. When you
increase the spacing to 6 or more nucleotides, Banana and Slug can no longer stimulate
transcription of the slime gene. Which hypothesis best explains thisobservation?
A. Binding sites for Banana and Slug are in the major groove of DNA.
B. Banana and Slug bind independently to their sites on DNA.
C. Banana and Slug bind to each other.
D. Banana and Slug induce a conformational change in the DNA that they bindto.
E. Banana and Slug do not undergo cooperative binding to DNA: C. Bananaand Slug bind to
each other.
8. The concentration of transcription factors within cells can be very impor-tant. For
example, increasing the concentration of a specific transcription factor that controls stem cell
differentiation by as little as 2-fold can cause stem cells to differentiate into mesoderm cells.
Which of the following couldmost directly explain this observation?
A. Allostery
B. Changes in Kd
C. Cooperativity
D. Direct reading of DNA sequences
E. Indirect reading of DNA sequences: C. Cooperativity
, 9. Which of the following explain how GTPAases are controlled?
A. Allosteric changes caused by GTP binding.
B. Binding to MAPKKK.
C. Changes in conformation triggered by _binding of Ras_.
D. Cooperative binding of GTP.
E. Phosphorylation of GTPases by kinases.: A. Allosteric changes caused byGTP binding.
10. Which of the following plays the most important role in determining theaffinity of
macromolecular interactions?
A. Cooperativity
B. Hydrogen bonding
C. Hydrophobic interactions
D. Ionic interactions
E. Van der Waals interactions: C. Hydrophobic interactions
11. A protein binds to the DNA sequence AAAAA with a Kd = 10 nM. The sameprotein binds
to the RNA sequence AAUUAU with a Kd = 15 nM, and it binds to a lipid with a Kd = 10
mM. Which of the following statements are true?
A. The protein binds to RNA and DNA with high affinity, but low specificity.
B. The protein binds with low affinity for RNA and DNA, but high specificity.
C. The protein binds with low affinity and low specificity for all three targets.
D. The protein has high specificity for lipids over RNA and DNA.: A. The proteinbinds to RNA
and DNA with high affinity, but low specificity.
12. Enzymes can catalyze cellular reactions through various mechanisms.Which of the
following statements is NOT true regarding enzymes?
A. They accelerate a cellular reaction by destabilizing the transition state.
B. They can form covalent bonds with the substrate during catalysis.
C.They have a higher affinity for the transition state of the substrate than forits stable form.
D. They can provide the chemical groups necessary for simultaneous acid andbase catalysis.
E. They can strain a substrate to force it toward a specific transition state.: A.They accelerate a
cellular reaction by destabilizing the transition state.
13. An enzyme acts on a tyrosine residue on a target protein to create a bindingsite for the SH2
domain. This enzyme is most specifically...
A. an isomerase.
