Name:
2 points
Chem 465
Biochemistry II
Multiple choice (4 points apiece):
1. The role of the Dam methylase is to:
A)
add a methyl group to uracil, converting it to thymine.
B)
modify the template strand for recognition by repair systems.
C)
remove a methyl group from thymine.
D)
remove a mismatched nucleotide from the template strand.
E)
replace a mismatched nucleotide with the correct one.
2. The ABC excinuclease is essential in:
A)
base-excision repair.
B)
methyl-directed repair.
C)
mismatch repair.
D)
nucleotide-excision repair.
E)
SOS repair.
3. In homologous recombination in E. coli, the protein that assembles into long, helical
filaments that coat a region of DNA is:
A)
DNA methylase.
B)
DNA polymerase.
C)
histone.
D)
RecA protein.
E)
RecBCD enzyme.
4. Which of the following statements about E. coli RNA polymerase (core enzyme) is
false?
A)
In the absence of the subunit, core polymerase has little specificity for
where initiation begins.
B)
The core enzyme contains several different subunits.
C)
The core enzyme has no polymerizing activity until the ó subunit is
bound.
D)
The RNA chain grows in a 5' 63' direction.
E)
The RNA product is complementary to the DNA template.
5. Which one of the following statements about eukaryotic RNA polymerases is correct?
A)
All three eukaryotic RNA polymerases recognize the same promoters as
prokaryotic polymerases.
B)
None of the eukaryotic RNA polymerases recognizes prokaryotic
promoters.
C)
Only eukaryotic RNA polymerase I recognizes prokaryotic promoters.
D)
Only eukaryotic RNA polymerase II recognizes prokaryotic promoters.
E)
Only eukaryotic RNA polymerase III recognizes prokaryotic promoters.
6. A branched ("lariat") structure is formed during:
A)
attachment of a 5' cap to mRNA.
B)
attachment of poly(A) tails to mRNA.
C)
processing of preribosomal RNA.
D)
splicing of all classes of introns.
E)
splicing of group II introns.
7. Reverse transcriptase:
A)
can utilize only RNA templates.
B)
has a 3' 6 5' proofreading exonuclease but not a 5' 6 3' exonuclease.
C)
is activated by AZT.
D)
is encoded by retroviruses.
E)
synthesizes DNA with the same fidelity as a typical DNA polymerase.
Pick 5 any five of questions 8 - 13.
8. (14 points) Give me a brief description of Mismatch, Base Excision, Nucleotide
Excision, and Direct repair mechanisms in e. coli cells.
Mismatch - Figures like 25-23 or 25-24. MutL and MutS hydrolyze ATP and bind to
mismatch. MutH hydrolyzes ATP and binds to MutL. DNA on both sides of mismatch
are threaded though complex creating a loop. This continues until the MutL protein
finds a hemi-methylated GATC site. MutL nicks the unmethylated side of the hemimethylated site. If the site is on the 5' side of the mismatch the unmethylated DNA
strand is unwound (using Helicase II) and degraded in the 3'65' direction (by
Exonuclease I or X) from the nick through the mismatch. If the site is on the 3' side of
the mismatch the unmethylated DNA strand is unwound (using Helicase II) and
degraded in the 5'63' direction (by Exonuclease VII or RecJ nuclease) from the nick
through the mismatch. In both cases the single stranded DNA is stabilized by SSB until
the missing DNA can be replaced by DNA polymerase III.
Base Excision - Figure like 25-25. DNA glycosylases recognize specific damaged DNA
bases and removed just the base for the DNA double helix, creating an AP or abasic
site. An AP endo nuclease then recognizes a site that is missing a base, and nick the
DNA at that spot. A small segment of DNA is then removed and replaced with DNA
polymerase I. Once the polymerase stops, a ligase is required to seal the translated
nick.
Nucleotide Excision - a figure like 25-26. A multi-subunit exinuclease recognizes a large
DNA lesion and nicks 5 bonds away on the 3' side and 8 bonds away on the 5' side to
generate a 12-13 residue fragment. The fragment is unwound (DNA helicase), removed
and the DNA replaced by DNA Polymerase I with the help of ligase (as above).
Direct Repair - A photolyase binds to a pyrimidine dimer and uses UV light energy to
unlink the two linked bases from each other.
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9. (14 points) What is a recombinase and how does it work?
A recombinase is and enzyme that catalyzes recombination. What I was looking
for was a discussion of the enzyme that does site specific recombination and a diagram
like figure 25-40. But I did not specifically say site-specific recombination, so I may give
some lee-way in your answer.
There are two classes of site-specific recombinases one that have ser and ones
that have tyr at the active site. In general these proteins work as a tetramer, with each
monomer binding a specific site on the DNA. Two of the monomers first cut the DNA at
the binding site and attach themselves the cut site by their tyrosine (or serine). They
then attach the DNA they are bound to with the free end of the other piece of DNA.
Making a Holliday structure. The other monomers taht exchange their DNA with one
of the monomers that has not clipped its DNA and attach their DNA to the other strand
as it gets clipped. Freeing up the enzyme
10. (14 points) Explain how a prokaryotic RNA polymerase chooses where to start
transcribing DNA into RNA, and what makes it stop.
11. (14 points) Tell me about the synthesis and processing of r-RNA in the Eukaryotic
cell.
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12. (14 points)
A. Describe the life cycle of a retrovirus
B. Explain why a retrotransposon resembles a retrovirus
13. (14 points) Compare a DNA polymerase with an RNA polymerase with a reverse
transcriptase
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1B
2D 3D 4C 5B 6E 7D
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