Biol309
Question Bank
Gene Regulation
Multiple Choice
1. Gene regulatory proteins function by:
A. influencing the speed of DNA polymerase.
B. binding to mRNAs and triggering their destruction.
C. activating or blocking the activity of RNA polymerase.
D. binding to the start codon and initiating translation on a ribosome.
2. What is an operon?
A. the regulatory sequence to which a repressor protein will bind.
B. the position near the start of a gene where RNA polymerase binds.
C. a set of genes transcribed as a single mRNA with a single promoter.
D. enhancer and silencer sequences that interact with a distant gene.
3. Homeodomain, zinc finger, and leuzine zipper are examples of:
A. mechanisms proteins use to recognize DNA sequences
B. three types of activator and repressor genes.
C. different types of gene regulatory proteins.
D. eukaryotic promoter sequences.
4. A gene “activator protein” such as the CAP of the lac operon:
A. inhibits gene expression by binding to the operator.
B. strengthens the binding of RNA polymerase to the promoter site.
C. must bind first to lactose in order to function.
D. must bind to a site thousands of bases away from the promoter.
5. Consider a hypothetical operon that regulates leucine synthesis in bacteria. Leucine would most
liking influence expression of this operon by:
A. binding to an enhance sequence.
B. activating the catabolic activator protein.
C. inactivating an operon repressor protein.
D. activating an operon repressor protein.
6. Suppose, instead, that the above operon regulates leucine breakdown. Leucine would most
liking influence expression of this operon by: (select from above choices)
7. Gene ‘enhancers’ and ‘silencers’ are:
A. sites where RNA polymerase binds in prokaryotes.
B. proteins that bind to and regulate RNA polymerase.
C. fundamental components of all nucleic acids.
D. regulatory sites located distant from the gene.
8. Gene transcriptional regulation in eukaryotes differs from prokaryotes in that:
A. general transcription factors are necessary.
B. chromatin remodeling can be used.
C. enhancers and silencers play a role.
D. all of the above are true.
Biol 309
Question Bank
Gene Regulation
Page 1
9. A riboswitch may have all of the following effects, EXCEPT:
A. trigger termination of transcription.
B. alter the pattern of RNA processing.
C. suppress activation of the encoded protein.
D. block ribosome binding sites on the RNA.
10. Which of the following statements correctly describes gene regulation through RNA
interference?
A. RNA molecules cause cleavage of double-stranded DNA of specific genes.
B. siRNAs associated with a RISC enzyme bind to complementary mRNAs.
C. The RISC enzyme binds to and cleaves double-stranded mRNAs.
D. RNAi involves binding of a small RNA to a target gene to inactivate it.
11. In the RNAi regulatory pathway, the DICER enzyme cleaves:
A. RNA polymerase into non-functional pieces.
B. single-stranded DNA into repetitive sequences.
C. double-stranded RNA into short strands.
D. mRNAs of genes to be repressed.
12. RNAi has been suggested to serve all of the following functions, EXCEPT:
A. providing RNA primers during DNA replication
B. suppression of transposable elements
C. control of viral infections
D. repression of normal cellular genes
13. The activity of some genes is affected by where they exist on a chromosome. This so-called
‘position effect’ most likely results from:
A. the inhibitory affect of telomere DNA on gene activity.
B. the presence or absence of nucleosomes in the gene.
C. whether the gene is in heterochromatin or euchromatin.
D. an accumulation of mutations during DNA replication.
True or false
1. Covalent modification of histone proteins is a mechanism of gene regulation.
2. ‘Inducible’ genes are expressed essentially all the time.
3. The lac operon encodes genes required for lactose synthesis.
4. In general, DNA-binding proteins recognize sequences exposed in the minor groove.
5. Operons are common in prokaryotes but rare in eukaryotes.
6. RNAi would be described as ‘transcriptional control’ of gene expression.
7. Regulation of gene expression is not necessary in fully differentiated cell.
8. The ‘dicer’ ribonuclease of the RNAi system cleaves double-stranded RNAs.
Biol 309
Question Bank
Gene Regulation
Page 2
9. An RNA zip-code determines how it will be alternatively spliced.
10. Gene repression occurs in regions of the chromosome with large numbers of methyl-cytosine.
11. Allosteric regulation influences gene expression by effecting the translated protein.
Fill in, etc
1. Genes that are expressed essentially continuously in most cells are called __________________,
whereas those whose expression is turned on or off under different conditions are said to be
_________________________.
2. Name and correctly
place 6 mechanisms of
gene expression along this
pathway from DNA to
protein.
3. Complete the following sentences with the appropriate words. A cluster of genes coordinately
regulated is called a(n) ______________. The _________________ is the site where RNA
polymerase will bind. The __________ is the regulatory sequence to which a repressor protein
can bind.
4. The passing of traits between generations by non-genetic means is called
___________________. What are three such mechanisms by which gene regulatory states can be
passed during cell replication:
1.
2.
3.
5. In the regulation of the lac operon, the catabolic activator protein (CAP) binds to the DNA when
the level of ____________ (glucose/lactose) in the cell is ______ (low/high). The ability of the
CAP to bind to its regulator site is determined by its association with the small molecule called
_________, which ________ (increases/decreases) in concentration when glucose decreases.
6. Expression of some genes can be regulated by special sequences in the mRNA untranslated
region (UTR). Some of these, called a ____________________ found in the ____ (3’/5’) UTR can
cause transcription to prematurely terminate. In contrast, sequences called a __________________
found in the ____ (3’/5’) UTR influence where in the cell the RNA will be translated.
Biol 309
Question Bank
Gene Regulation
Page 3
7. Refer to this diagram of the lac operon when answering this question.
A. Identify the parts of the lac operon labeled in this figure and explain the function of each
regulatory element the proteins that interact with it.
B. Will the operon be activated or repressed under each of the following conditions? Explain.
a) both lactose and glucose are present
b) neither lactose nor glucose are present
c) only lactose is present.
d) only glucose is present.
C. In a strain of E. coli that carries a mutation in the regulation of the lac operon, the following
pattern of b-galactosidase (one of the lac operon structural genes) production was observed:
Conditions
Level of b-galactosidase
a) both lactose and glucose are present
Low
b) neither lactose nor glucose are present
High
c) only lactose is present.
High
d) only glucose is present.
Low
A. In which condition(s) is gene expression abnormal?
B. Does the mutation appear to inactivate the repressor protein or the CAP?
Explain.
8. Complete these sentences using the word options given below.
In the first stage of RNA interference, a ___________________ RNA precursor is cleaved
by the ____________ enzyme The cleaved molecules are approximately _____ (insert
number) bases in length and are called __RNA if the RNA originated from a virus or
__RNA if the RNA was of endogenous origin (if the RNA precursor was produced
artificially, it s called __RNA). The cleaved RNA is then separated into
__________________ RNA, which then binds to the ribonuclease complex called
_____________. The short RNA molecules can then target the complex to __RNA with a
__________________ sequence, which is then cut at that site.
RNAi
mi
m
RISC
sh
Biol 309
complementary
si
r
Dicer
Double-stranded
Question Bank
identical
hp
t
Single-stranded
Gene Regulation
Page 4
9. Affinity of the Lac operon repressor protein for the operator site decreases in the presence
lactose, yet the affinity of Trp operon repressor protein for the operator increases in the presence of
tryptophan.
A. Why does this make sense considering the functions of the genes in these operons?
B. In general terms, explain how the presence of lactose or tryptophan causes the change in
the behavior of these proteins.
10. Some bacteria possess a fascinating system for combatting viral infections called CRISPR
(Clustered Regularly Interspersed Short Palindromic Repeats). The genetic elements of the
CRISPR locus (region) of the bacterial chromosome are arranged like this:
The spacer DNAs are actually sequences
from viral genomes, that were copied and
placed between the palindromic repeats
during a viral infection. Through the
action of the Cas enzymes, the viral
sequences can be used to target viral
RNA or DNA for destruction, as shown
in the figure to the right. DNA sequences
from different viruses are retained and
can be used as a defense against the
viruses in the future.
A. Which steps in the CRISPR
mechanism are most similar to the Dicer and RISC steps of the iRNA process of eukaryotes?
B. Describe three similarities between the functions or mechanisms of the RNAi and the
CRISPR. (e.g., “ In both CRISPR and iRNA…”)
C. Other than the specific enzymes involved, identify three differences between the RNAi and
the CRISPR mechanisms. (e.g., “ In CRISPR …, whereas in iRNA…”)
D. Explain the function of the palindromic repeats in the CISPR mechanism?
Biol 309
Question Bank
Gene Regulation
Page 5