Deck 13: Regulation of Gene Expression in Bacteria and Bacteriophage

Question 1

Multicellular organisms generally utilize more complex gene regulation than unicellular organisms via mechanisms that include?

A) transcriptional repression and epigenetic modification
B) epigenetic modification
C) polycistronic RNAs and transcriptional repression
D) transcriptional repression
E) polycistronic RNAs

Answer 1

A

Question 2

A region of chromatin has recently become DNAse I hypersensitive. Which enzyme has been activated to cause this change in chromatin structure?

A) kinase
B) histone methyltransferase
C) histone acetylase
D) phosphatase
E) histone deacetylase

Answer 2

C

Question 3

Which of the following is not involved in control of gene expression in eukaryotes?

A) destruction of mRNA
B) change to DNA sequence
C) use of alternative promoters
D) transcriptional repression
E) export of RNA from the nucleus

Answer 3

B

Question 4

Typically, methylation of nucleosome N- terminal tails leads to .

A) tighter packaging of the chromatin and reduced transcription
B) relaxed packaging of the chromatin and increased transcription
C) removal of the protein components of the chromatin from the DNA
D) activation of topoisomerase
E) increased amounts of euchromatin relative to heterochromatin

Question 5

When CpG islands are unmethylated, .

A) chromatin in the promoter region is open, allowing access by transcription factors and RNA polymerase
B) genes downstream of the CpG islands cannot be expressed, because the promoter region is blocked by histones
C) chromatin in the promoter region is closed, preventing transcription factors and RNA polymerase from binding
D) DNAse hypersensitivity in that region of the chromosome is lost
E) chromatin in the enhancer region is closed, so they are unable to bind regulatory proteins to initiate transcription

Question 6

Trans- acting regulators of gene expression include?

A) promoters
B) histone deacetylases
C) introns
D) silencers
E) the TATA box

Question 7

You have identified a mutation in a gene that seems to decrease transcription of another gene 2000 bp away from the mutation site. What regulatory sequence, which may be found within another gene, has likely been mutated in this instance?

A) core promoter
B) enhancer sequence
C) homeodomain motif
D) proximal elements
E) upstream activator sequence

Question 8

If you want to affect chromatin packaging, which amino acid could you mutate to affect both histone acetylation and methylation patterns?

A) asparagine
B) arginine
C) methionine
D) histidine
E) lysine

Question 9

Typically, acetylation of histone tails leads to .

A) increased amounts of euchromatin relative to heterochromatin
B) activation of topoisomerase
C) tighter packaging of the chromatin and reduced transcription
D) relaxed packaging of the chromatin and increased transcription
E) removal of the protein components of the chromatin from the DNA

Question 10

Loss of Xist gene due to mutation leads to defects in which epigenetic process?

A) X- inactivation
B) methylation of CpG islands
C) position effect variegation
D) RNAi
E) genomic imprinting

Question 11

Which protein binds to the silencer sequence and promotes transcriptional silencing in the presence of glucose?

A) Gal10
B) Gal4
C) Mig1
D) Gal2
E) Gal80

Question 12

Prader- Willi syndrome is a genetic disorder involving a partial deletion of chromosome 15q on the paternal chromosome. When both copies of a gene (or chromosome) are functional but only one is expressed, this is an example of _ .

A) genomic imprinting
B) histone acetylation
C) X- inactivation
D) chromatin modifications
E) position effect variegation

Question 13

Chromatin from two tissues, skin and liver, was extracted and analyzed near the gene Twist. The liver chromatin was found to be more DNAse sensitive than the chromatin from skin cells. What might explain this difference?

A) Twist is expressed at the same level in both liver and skin cells.
B) Twist is expressed in skin and not liver.
C) Twist is silenced in skin and not liver.
D) Twist is not expressed in either liver or skin cells
E) Chromatin near Twist in liver cells is heterochromaitic.

Question 14

Chromatin remodeling involves both sliding and relocating of the nucleosomes. Which eukaryotic chromatin remodeling complex is likely involved?

A) Mig1 complex
B) ISWI complex
C) SWR1 complex
D) SWI/SNF complex
E) SHH complex

Question 15

dsRNA is detected and cleaved by?

A) RISC
B) insulator
C) dicer
D) RNA polymerase II
E) miRNA

Question 16

Enhancers and silencers are?

A) are proteins that control gene expression
B) must be transported in to the nucleus after translation
C) are DNA elements where transcription factors bind
D) are cis- acting proteins
E) trans- acting sequences that interact with RNA polymerase

Question 17

For the following gene, MspI and HpaII restriction sites and their positions are indicated here. Recall that HpaII is methylation sensitive, while MspI is not. If this gene is being actively transcribed, how many fragments would you expect from this restrictio digest?

A) 3
B) 5
C) 1
D) 6
E) 4

Question 18

Which of the following would you expect to show the least evolutionary conservation?

A) histone genes
B) intergenic DNA
C) enhancer sequence
D) core promoters
E) coding sequence

Question 19

Molecular biologists can determine experimentally whether a region of DNA contains closed chromatin or open chromatin by assessing the sensitivity of the region to .

A) DNAse
B) nucleosomes
C) histone deacetylase
D) methyltransferase
E) RNA polymerase II

Question 20

Gene regulation in eukaryotes often involves which of the following, which are not also used by prokaryotes?

A) coupled transcription and translation
B) transcription factors
C) formyl- methionine
D) histone modification
E) promoters

Question 21

A transcription factor that binds to a gene first and facilitates the binding of other transcription factors is called a .

Question 22

Eukaryotes use these highly specialized enhancer elements, which regulate the transcription of multiple genes packaged in complexes of closely related genes (e.g., fi- globin).

Question 23

Which protein complex directs DNA bending into loops that contact RNA polymerase and transcription factors bound at the core promoter or with protein complexes bound to proximal promoter elements?

Question 24

What effect does methylation of CpG islands have on human promoters?

Question 25

Enzymes that create epigenetic marks are sometimes referred to as writers, whereas enzymes that eliminate epigenetic marks are called .

Question 26

Which molecules bind regulatory sequences of DNA to encourage positive regulation of transcription?

Question 27

Gal80 is mutated such that it cannot interact with Gal3. What effect would you expect to see in the presence of galactose?

Question 28

In the GAL gene system, which protein binds to the activation domain of the activator protein, ultimately blocking transcription in the absence of galactose?

Question 29

RNA polymerase can bind to _ to generate different mRNAs from the same gene.

Question 30

Many types of cancer are known to overexpress the receptor protein tyrosine kinase. Which molecular technique can be used to reduce expression of tyrosine kinase in cell culture?

A) PCR
B) DNAse sensitivity assay
C) western blotting
D) RNAi
E) southern blotting

Question 31

For the following gene, which mutant likely has lost its enhancer?

Question 32

What are the protein- binding sequences that direct enhancers to interact with the intended promoter and that block communication between enhancers and other promoters?

Question 33

Inherited traits that can change without affecting the sequence of DNA are examples of what?

Question 34

What are three proteins or groups of proteins you would expect to find bound to the core promoter region in eukaryotes?

Question 35

What are the three mechanisms by which chromatin remodelers can move nucleosomes?

Question 36

If you block histone deacetylase, what effect would you expect to see on transcriptional activity?

Question 37

In the GAL gene system, which protein acts as an activator protein through its transcription- initiating effect?

Question 38

Gal4 is mutated such that it still binds to the DNA but cannot interact with Gal80. What effect would you expect to see in the absence of galactose?

Question 39

For the following gene, you notice the following results. What type of sequence has been mutated in mutant 4?

Question 40

During RNAi, what do miRNAs target for destruction?

A) CpG islands
B) histones
C) ribosomes
D) heterochromatic regions of DNA
E) mRNAs

Question 41

What gene is critical for establishment of X- inactivation in mammals?

Question 42

Scientists can create transgenic organisms by inserting foreign DNA randomly into the chromosomes of a host. A scientist might do this in order to express genes carried in the foreign DNA and in this case the foreign DNA is often engineered to include insulator sequences at the ends of the foreign sequence. Explain why insulators would be useful in this context.

Question 43

How does transcription inhibition differ between prokaryotes and eukaryotes? Describe the two mechanisms used by eukaryotes to direct the enhancers toward certain promoters and away from others.

Question 44

Explain how genomic imprinting can effect gene expression in mammalian embryos?

Question 45

Which enzyme cuts dsRNA into 21- 25 bp fragments during RNAi?

Question 46

What role do chromatin remodelers play in eukaryotic gene expression?

Question 47

In the GAL gene system, are cis- acting regulatory elements, and protein is a trans- acting regulatory protein.

Question 48

Demethylation and acetylation lead to open chromatin structure and are associated with
regions of genomes.

Question 49

The enhancers that are present near a gene are present in every cell in an organism, yet these enhancers can have tissue- specific effects on gene expression. Explain how enhancers could have tissue- specific effects on gene expression.

Question 50

binds to siRNAs and then either blocks translation or destroys mRNA that is complementary to the siRNA.

Question 51

in Drosophila results from the movement of the transcriptionally active w+ allele into the centromeric heterochromatin region of the fruit- fly X chromosome.

Question 52

Viruses with dsRNA genomes evolved a long time ago and can be found in parasitic relationships with species from a variety of taxa. What mechanism do eukaryotes use to combat such viruses?

Question 53

Which protein complex binds dsRNA fragments to generate ssRNAs for RNAi?

Question 54

The gene encoding coat color is X- linked, and male cats have a single copy of the X chromosome. They can therefore express either the O or o allele, resulting in orange or black coat, respectively. Female cats, on the other hand, have two copies of the X chromosome. Thus, they can be heterozygous and express either orange or black pattern called tortoiseshell. Using this information, list the possible genotypes for these individuals:
• orange male
• orange female
• black male
• black female
• tortoiseshell

Question 55

Histone deacetylase (HDAC) inhibitors are commonly used as mood stabilizers or in the treatment of neurodegenerative diseases. What effect would a HDAC inhibitor have on the target cells?