BIOC 384 EXAM UPDATED ACTUAL QUESTIONS AND
CORRECT ANSWERS
Question:
1. What is believed to be the underlying cause of prion
plaque formation?
Answer:
The PrP^sc proteins are misfolded and aggregated from PrP^c proteins.
Question:
2. Anabolic pathways are most active when the energy
charge is ______ whereas catabolic pathways are most
active when the energy charge is_________. The source of
energy for ____________ pathways is stored fuels whereas the
source of energy for ____________ pathways is abundant
resources from the environment (nutrients or sunlight).
Answer:
high; low; catabolic; anabolic
Question:
3. Why is thymine only in DNA and uracil only in RNA?
Answer:
Uracil can be formed by cytosine deamination so if uracil were normally in DNA
then both spontaneous cytosine deamination and naturally-occurring uracil
would be indistinguishable and G-C to A-T mutations would build up quickly.
Question:
4. Why are A-T rich regions more susceptible to DNA
denaturation than G-C rich regions?
Answer:
G-C rich regions of DNA have more favorable base stacking energy than A-T rich
regions
,Question:
5. Prokaryotic genomic DNA is not found to be packaged
into highly ordered structures such as nucleosomes,
whereas eukaryotic genomic DNA is always packaged
into nucleosomes. What is the best explanation for this
difference?
Answer:
Human DNA is ~1000x longer than bacterial DNA, but eukaryotic cells are only
~10x larger, so ~100x more DNA needs to be packaged into a similar space.
Question:
6. Which of the nucleotide bases (A-E) can most readily
form hydrogen bonds in DNA with the nucleotide base
shown in dotted box?
Answer:
C
Question:
7. If a sample of double-stranded DNA is determined to be
20% thymine, what percent of this DNA sample is purine
nucleotide chemistry?
Answer:
50%
Question:
8. The equilibrium constant Keq for the reaction A<-->B is
1x105 at 25ºC. Calculate the delta Gº' for this reaction.
Answer:
-28.5 kJ/mol
, Question:
9. In the figure below, identify each circled group/atom as a
hydrogen bond donor or hydrogen bond acceptor:
Answer:
1: acceptor 2: donor
3: acceptor 4: donor
Question:
10. The points in the Ramachandran plot are derived by
Answer:
calculating the pi and psi angles of every amino acid in a polypeptide chain as a
measure of rotational freedom on either side of the C-alpha carbon
Question:
11. The polarity of the solvent and other environmental
factors can affect the pKa of an amino acid R group.
Suppose the alpha-amino group of a protein has a pKa of
about 9.0 when it is exposed to H2O on the outside of a
protein. Would you expect the pKa to be higher or lower
than 9.0 if the alpha-amino group were buried in the
hydrophobic interior of the protein and why?
Answer:
The pKa of the alpha-amino group would be lower because the neutral species is
favored.
CORRECT ANSWERS
Question:
1. What is believed to be the underlying cause of prion
plaque formation?
Answer:
The PrP^sc proteins are misfolded and aggregated from PrP^c proteins.
Question:
2. Anabolic pathways are most active when the energy
charge is ______ whereas catabolic pathways are most
active when the energy charge is_________. The source of
energy for ____________ pathways is stored fuels whereas the
source of energy for ____________ pathways is abundant
resources from the environment (nutrients or sunlight).
Answer:
high; low; catabolic; anabolic
Question:
3. Why is thymine only in DNA and uracil only in RNA?
Answer:
Uracil can be formed by cytosine deamination so if uracil were normally in DNA
then both spontaneous cytosine deamination and naturally-occurring uracil
would be indistinguishable and G-C to A-T mutations would build up quickly.
Question:
4. Why are A-T rich regions more susceptible to DNA
denaturation than G-C rich regions?
Answer:
G-C rich regions of DNA have more favorable base stacking energy than A-T rich
regions
,Question:
5. Prokaryotic genomic DNA is not found to be packaged
into highly ordered structures such as nucleosomes,
whereas eukaryotic genomic DNA is always packaged
into nucleosomes. What is the best explanation for this
difference?
Answer:
Human DNA is ~1000x longer than bacterial DNA, but eukaryotic cells are only
~10x larger, so ~100x more DNA needs to be packaged into a similar space.
Question:
6. Which of the nucleotide bases (A-E) can most readily
form hydrogen bonds in DNA with the nucleotide base
shown in dotted box?
Answer:
C
Question:
7. If a sample of double-stranded DNA is determined to be
20% thymine, what percent of this DNA sample is purine
nucleotide chemistry?
Answer:
50%
Question:
8. The equilibrium constant Keq for the reaction A<-->B is
1x105 at 25ºC. Calculate the delta Gº' for this reaction.
Answer:
-28.5 kJ/mol
, Question:
9. In the figure below, identify each circled group/atom as a
hydrogen bond donor or hydrogen bond acceptor:
Answer:
1: acceptor 2: donor
3: acceptor 4: donor
Question:
10. The points in the Ramachandran plot are derived by
Answer:
calculating the pi and psi angles of every amino acid in a polypeptide chain as a
measure of rotational freedom on either side of the C-alpha carbon
Question:
11. The polarity of the solvent and other environmental
factors can affect the pKa of an amino acid R group.
Suppose the alpha-amino group of a protein has a pKa of
about 9.0 when it is exposed to H2O on the outside of a
protein. Would you expect the pKa to be higher or lower
than 9.0 if the alpha-amino group were buried in the
hydrophobic interior of the protein and why?
Answer:
The pKa of the alpha-amino group would be lower because the neutral species is
favored.
