Molecular Genetics 126:481 FALL 2008
EARLY FINAL EXAM
December 15, 2008
Name ___________________________
Short Essays (short answers that get to the point are more likely to receive full credit)
How is it possible for microRNAs to regulate eukaryotic gene expression by binding to the 3’ untranslated
end of an mRNA? (2 points)
Why is attenuation absent in eukaryotic organisms? (2 points)
What are the differences between activator and coactivator proteins? (3 points)
Explain what a “modification protection assay” is intended to discover and how it is carried out. (3 points)
1
Molecular Genetics 126:481 FALL 2008
EARLY FINAL EXAM
December 15, 2008
How are Caenorhabditis elegans and Drosophila melanogaster good model organisms for development in
higher eukaryotes? (4 points)
How does the anchor cell of C. elegans induce the vulva progenitor cells to differentiate into vulva cells?
Why do the vulva progenitor cells follow different pathways upon receiving the signal from the anchor
cell? (4 points)
The process of excision of a GU-AG intron and splicing of exons is defined as requiring two
transesterification reactions. What does this mean? (4 points)
During sporulation in Bacillus σ and σ are present in both the prespore and mother cells. How is σ
activated in the prespore? (4 points)
E
F
2
F
Molecular Genetics 126:481 FALL 2008
EARLY FINAL EXAM
December 15, 2008
Explain how the iron response protein (IRP) functions to activate expression of Ferritin and at the same
time inhibit expression of Transferrin. (4 points)
Multiple Choice (2 points each)
(1) The attachment site for RNA polymerase in bacteria is called the:
a. Initiator
b. Operator
c. Promoter
d. Start codon
(2) The specificity of bacterial RNA polymerase for their promoters is due to which subunit?
a. α
b. β
c. γ
d. σ
(3) The first protein complex to bind to the core promoter for a protein-coding gene in eukaryotes is;
a. RNA polymerase II
b. General transcription factor TFIIB
c. General transcription factor TFIID
d. General transcription factor TFIIE
(4) Which modification must be made to RNA polymerase II in order to activate the preinitiation complex?
a. Acetylation
b. Methylation
c. Phosphorylation
d. Ubiquitination
(5) What is the name of the DNA sequence that is located near the promoter of the lactose operon, and
which regulates expression of the operon in E. coli?
a. Activator
b. Inducer
c. Operator
d. Repressor
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Molecular Genetics 126:481 FALL 2008
EARLY FINAL EXAM
December 15, 2008
(6) Which of the following types of sequence module enables transcription to respond to general signals
from outside of the cell?
a. Cell-specific modules
b. Developmental modules
c. Repression modules
d. Response modules
(7) Which of the following is NOT a type of activation domain?
a. Acidic domains
b. Glutamine-rich domains
c. Leucine-zipper domains
d. Proline-rich domains
(8) Which of the following is NOT a experiment used to define the site on a DNA molecule to which a
protein binds?
a. Gel retardation assay
b. DNA footprinting assay
c. Modification interference assay
d. Yeast two hybrid assay
(9) Which of the following DNA sequences can increase the rate of transcription initiation of more than one
gene/promoter?
a. Activators
b. Enhancers
c. Silencers
d. Terminators
(10) Approximately how many base pairs form the attachment between the DNA template and RNA
transcript during transcription?
a. 8
b. 12-14
c. 30
d. The entire RNA molecule remains base-paired to the template until transcription is finished.
(11) Which factor is thought to be most important in determining whether a bacterial RNA polymerase
continues or terminates transcription?
a. Nucleotide concentration
b. Structure of the polymerase
c. Methylation of termination sequences
d. Thermodynamic events
(12) What is the role of the Rho protein in termination of transcription?
a. It is a helicase that actively breaks base pairs between the template and transcript.
b. It id s DNA-binding protein that blocks the movement of RNA polymerase along the template.
c. It is a subunit of RNA polymerase that binds to RNA hairpins and stalls transcription.
d. It is a nuclease that degrades the 3’ ends of RNA transcripts.
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Molecular Genetics 126:481 FALL 2008
EARLY FINAL EXAM
December 15, 2008
(13) Antitermination is involved in regulation of which of the following?
a. Operons encoding enzymes involved in the biosynthesis of amino acids with regulation dependent
on the concentration of the amino acids.
b. Operons encoding enzymes involved in the degradation of metabolites, regulation dependent on the
presence of the metabolite
c. Genes present in the upstream region of the operon
d. Genes present in the downstream region of the operon.
(14) What is the major transcriptional change that occurs during the Stringent Response in E. coli?
a. Transcription rates are increased for most genes.
b. Transcription rates are increased only for the amino acid biosynthesis operons.
c. Transcription rates are decreased for most genes.
d. Transcription rates are decreased only for the amino acid biosynthesis operons.
(15) Which of the following is necessary for the RNA endonuclease activity of RNA polymerase that
occurs when RNA polymerase is stalled during transcription?
a. Rho
b. RelA
c. GreA
d. RNAse H
(16) How is the lariat structure formed during splicing of a GU-AG intron?
a. After cleavage of the 5’ splice site, a new phosphodiester bond is formed between the 5’ nucleotide
and the 2’ carbon of the nucleotide at the 3’ splice site.
b. After cleavage of the 5’ splice site, a new phosphodiester bond is formed between the 5’ nucleotide
and the 2’ carbon of an internal adenosine.
c. After cleavage of the 5’ splice site, a new phosphodiester bond is formed between the 5’ nucleotide
and the 2’ carbon of the nucleotide at the 5’ splice site.
d. After cleavage of the 3’ splice site, a new phosphodiester bond is formed between the 5’ nucleotide
and the 2’ carbon of an internal adenosine.
(17) What are cryptic splice sites?
a. These are splice sites that are used in some cells, but not in others.
b. These are splice sites that are always used.
c. These are splice sites that are involved in alternative splicing, resulting in the removal of exons
from some mRNA molecules.
d. These are sequences within exons or introns that resemble consensus splicing signals, but are not
true splice sites.
(18) What statement correctly describes trans-splicing?
a. The order of exons within an mRNA transcript is rearranged to yield a different mRNA sequence.
b. Exons are deleted from some mRNA transcripts but not others.
c. Intron sequences are not removed from RNA transcripts and are translated into proteins.
d. Exons from different RNA transcripts are joined together.
(19) The chemical modification of eukaryotic rRNA molecules takes place in the:
a. Cytoplasm.
b. Endoplasmic reticulum.
c. Nuclear envelope.
d. Nucleolus.
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Molecular Genetics 126:481 FALL 2008
EARLY FINAL EXAM
December 15, 2008
(20) Which of the following is an example of RNA editing?
a. Removal of introns from an RNA transcript.
b. Degradation of an RNA molecule by nucleases.
c. Alteration of the nucleotide sequence of an RNA molecule.
d. Capping of the 5’ end of an RNA transcript.
(21) Nonsense-mediated RNA decay (NMD) is a system for the degradation of eukaryotic mRNA
molecules with what features?
a. NMD degrades mRNA molecules with stop codons at incorrect positions.
b. NMD degrades mRNA molecules that encode nonfunctional proteins.
c. NMD degrades mRNA molecules that lack a start codon.
d. NMD degrades mRNA molecules that lack a stop codon.
(22) Which of the following describes RNA interference?
a. Antisense RNA molecules block translation of mRNA molecules.
b. Double-stranded RNA molecules are bound by proteins that block their translation.
c. Double-stranded RNA molecules are cleaved by a nuclease into short interfering RNA molecules.
d. Short interfering RNA molecules bind to the ribosome to prevent the translation of viral mRNAs.
(23) How are RNA molecules transported out of the nucleus?
a. Passive diffusion through the membrane.
b. Through the membrane pores in an energy-dependent process.
c. Through membrane pores in an energy independent process.
d. Through a channel in the membrane that leads to the endoplasmic reticulum.
Match protein/RNA with its function (answers can be used more than once or not at all)
(24). spliceosome
a. small nuclear ribonucleoproteins (snRNP)
(25). microRNAs
b. guanylyl transferase
(26). mRNA capping
c. ribozyme
(27). autocatalytic RNA splicing
d. dicer
e. poly-A polymerase
Match protein with its function (answers can be used more than once or not at all)
(28). JAK
a. G-protein
(29). Glucocorticoid receptor
b. Endonuclease
(30). RAS
c. DNA-binding protein
(31). IF-2
d. RNA binding protein
e. Kinase
Match lambda gene with its function (answers can be used more than once or not at all)
(32). cI
a. Anti-termination
(33). N
b. Transcriptional repressor
(34). CRO
c. Transcriptional activator
(35). cII
d. Transcriptional terminator
e. Translation factor
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Answers to practice exam #3
How is it possible for microRNAs to regulate eukaryotic gene expression by binding to the 3’ untranslated end of an
mRNA?
Binding to the 3’-UTR initiates an RNA cleavage event that removes the polyA tail and begins the mRNA
degradation process
Why is attenuation absent in eukaryotic organisms?
Attenuation is the mechanism whereby amino acid biosynthesis operons are regulated by the cellular
concentration of the amino acid that is the product of the genes in the operon by transcription termination. The
attenuation mechanism requires that translation by ribosomes and transcription occur in the same subcellular
compartment. In eukaryotes transcription and translation are carried out in different compartments, so
attenuation would not be possible in eukaryotes.
What are the differences between activator and coactivator proteins?
An activator is a DNA binding protein that stabilizes construction of the RNA polymerase II transcription initiation
complex. A coactivator is a protein that stimulates transcription initiation by binding nonspecifically to DNA or via
protein-protein interactions.
Explain what a “modification protection assay” is intended to discover and how it is carried out.
Modification protection is a technique used to identify nucleotides involved in interactions with a DNA-binding
protein
How are Caenorhabditis elegans and Drosophila melanogaster good model organisms for development in higher
eukaryotes?
Developmental pathways in animals utilize similar regulators, therefore discovery of regulators in lower animals
can reveal how development is controlled in higher animals.
How does the anchor cell of C. elegans induce the vulva progenitor cells to differentiate into vulva cells? Why do
the vulva progenitor cells follow different pathways upon receiving the signal from the anchor cell?
The anchor cell produces a diffusible signal that stimulates differentiation of vulva cells. Different vulva cells
undergo different differentiation pathways because they are exposed to differing concentrations of the signal
molecule, and the vulva cells themselves produce secondary signaling molecules that control differentiation in
nearby vulva cells.
The process of excision of a GU-AG intron and splicing of exons is defined as requiring two transesterification
reactions. What does this mean?
A transesterification reaction is the simultaneous cleavage and reformation of a phosphodiester bond. During
intron splicing the donor site phosphodiester bond is cleaved and then reformed with the branchpoint nucleotide
within the intron, forming a lariat structure. In the second transesterification, the branch point phospodiester
bond I cleaved and simultaneously formed between the donor and acceptor sites. The net effect is that there is no
change in the number of phosphodiester bonds.
During sporulation in Bacillus σE and σF are present in both the prespore and mother cells. How is σF activated in
the prespore?
Sigma F is activated in the prespore by when it is released from protein-protein interaction with AB. Sigma F is
inactive when it is bound to AB.
Explain how the iron response protein (IRP) functions to activate expression of Ferritin and at the same time inhibit
expression of Transferrin.
The iron response protein can bind to iron response elements in RNA only when it is not bound to iron. In the case
of ferritin, binding of IRP to the 5’-IRE blocks translation of the ferritin mRNA, so when it is not bound ferritin
protein is produced. In the case of transferrin, binding to the 3’-IRE blocks degradation of the transferrin mRNA
thereby increasing half life of the mRNA and stimulating transferrin protein production.
1=c, 2=c, 3=c, 4=c, 5=c, 6=d, 7=c, 8=d, 9=b, 10=b, 11=d, 12=a, 13=a, 14=c, 15=c, 16=b, 17=d, 18=d, 19=d, 20=c,
21=a, 22=c, 23=b, 24=a, 25=d, 26=b, 27=c, 28=e, 29=c, 30=a, 31=d, 32=b and c, 33=a, 34=c, 35=c