Deck 8: Transcriptional Control of Gene Expression

Question 1

Enhancers are considered transcription-control elements that regulate the expression of eukaryotic genes.Which one of the following is true regarding these elements?

A)They are only found upstream of the transcription start site.
B)They are never found more than one kilobase away of the transcription start site.
C)They are only found in introns.
D)They generally range in length from about 50-200 base pairs.

Answer 1

D

Question 2

Define the terms cis-acting DNA sequences and trans-acting proteins.

Answer 2

Cis-acting DNA elements affect only the expression of genes on the same DNA molecule that are linked to the DNA element.In contrast,trans-acting proteins can diffuse through the cell to bind to their target DNA sequence.

Question 3

The TATA box

A)serves as a promoter sequence for genes transcribed by RNA polymerase III.
B)is located approximately 100 base pairs upstream of the start site for mRNAs.
C)is present in all eukaryotic genes.
D)acts to position RNA polymerase II for transcription initiation.

Answer 3

D

Question 4

Describe the similarities and differences between prokaryotic and eukaryotic RNA polymerases.

Question 5

You have identified a transcription factor and hypothesize that it binds to the promoter region of a gene that encodes a protein that causes cells to stop dividing.In order to test the interaction between the transcription factor and the DNA you will need to do a specific assay.Which one of the following would you use to test your hypothesis?

A)fluorescent in situ hybridization
B)chromatin immunoprecipitation
C)immunocytochemistry
D)high-throughput DNA sequencing

Question 6

Sigma factors present in bacteria are proteins required to:

A)allow translation to proceed.
B)terminate DNA replication.
C)initiate transcription.
D)terminate DNA replication and initiate transcription.

Question 7

Which of the following is the correct order of binding of general transcription factors to initiate transcription at RNA polymerase II promoters?

A)TFIID,TFIIB,Pol II,TFIIH
B)PolII,TFIID,TFIIB,TFIIH
C)TFIIB,PolII,TFIIH,TFIID
D)TFIID,TFIIH,TFIIB,PolII

Question 8

Operator constitutive mutants of the lac operon would

A)express the lac repressor constitutively.
B)block the binding of RNA polymerase to the promoter.
C)express β-galactosidase constitutively.
D)prevent the inducer from binding to the repressor.

Question 9

Reporter genes employ fragments of DNA encoding proteins that when translated do not have any obvious effects in the cells and tissues.Which one of the following is NOT a reporter protein?

A)luciferase
B)green fluorescent protein
C) β-galactosidase
D)RNA polymerase 1

Question 10

You are studying the expression of the gene that appears to be under the control of three different transcription-control regions during mouse embryonic development.Which one of the following is the BEST method to use to determine when each of these regions are active in the developing mouse embryo?

A)DNA affinity chromatography
B)polymerase chain reaction
C)reporter gene assay
D)DNAse 1 footprinting

Question 11

The human genome encodes transcription factors that contain an acidic activation domain that is phosphorylated in response to increased levels of the second messenger cAMP.Which one of the following contains one of these activation domains?

A)CBP
B)CDK9
C)CREB
D)CTD

Question 12

All the following elements can function as eukaryotic promoters except

A)a TATA box.
B)an initiator element.
C)CpG islands.
D)an enhancer.

Question 13

Which of the following is a fundamental difference between gene regulation in bacteria compared with eukaryotes?

A)In bacteria,but not eukaryotes,there is a specific sequence that specifies where RNA polymerase binds and initiates transcription.
B)In eukaryotes,but not bacteria,transcription can be influenced by how effectively the DNA sequence of a promoter region interacts with histone octamers.
C)Transcription regulation is the most widespread form of control of gene expression in bacteria but not in eukaryotes.
D)Gene regulation is readily reversible in eukaryotes but not bacteria.

Question 14

How does binding of the lac repressor to the lac operator block transcription initiation?

A)lac repressor binding blocks RNA polymerase from interacting with DNA at the start site.
B)lac repressor binding induces a DNase that cleaves the DNA at the transcription start site.
C)lac repressor binding causes a conformational change in RNA polymerase.
D)lac repressor binding induces a protease that degrades the sigma subunit of RNA polymerase.

Question 15

In bacteria,an operon:

A)is a region of DNA that is transcribed as a single mRNA encoding several proteins.
B)encodes for miRNAs.
C)contains a promoter unique for each individual gene in the operator.
D)none of the above

Question 16

Which of the following proteins does not "footprint" the lac operon control region?

A)lac repressor
B)β-galactosidase
C)RNA polymerase
D)cAMP-CAP

Question 17

All of the following statements about the essential carboxy terminal domain (CTD)of RNA polymerase are true except:

A)The CTD is present in RNA polymerase I,II,and III.
B)The CTD can become phosphorylated.
C)The CTD is critical for viability.
D)The CTD of mammals contains more than 50 repeats of a heptapeptide.

Question 18

Describe the structure and function of the carboxy terminal domain (CTD)of RNA polymerase II.

Question 19

You are studying the effects of α-amanitin,a poisonous cyclic octapeptide,on eukaryotic cells and have noticed that following treatment,there is no miRNA transcription.Based on this evidence you conclude that α-amanitin must be inhibiting:

A)RNA polymerase I.
B)RNA polymerase II.
C)RNA polymerase III.
D)RNA polymerase I and RNA polymerase III.

Question 20

Which one of the following terms is used to describe the protein:DNA complex containing several transcription factors bound to a single enhancer?

A)nucleosome
B)chromosome
C)enhanceosome
D)proteasome

Question 21

What is the functional difference between enhancers and promoter proximal elements?

Question 22

A leucine-zipper motif contains

A)a stretch of five leucine residues in a row.
B)a leucine residue at every seventh position.
C)a leucine residue complexed with a zinc ion.
D)an alternating leucine-alanine-proline structure.

Question 23

What is the function of TFIIH in the transcription initiation complex?

A)binding to the TATA box
B)unwinding the DNA duplex
C)catalyzing the synthesis of RNA
D)all of the above

Question 24

Describe the structure and function of a zinc-finger motif.

Question 25

Describe the role of histone deacetylation and hyperacetylation in yeast transcriptional control.

Question 26

Describe the functional properties of TFIID and TFIIH.

Question 27

Which of the following is not a structural motif found in a DNA-binding domain?

A)homeodomain
B)zinc-finger
C)helix-loop-helix
D)random-coil acidic domain

Question 28

What is an enhanceosome?

Question 29

Which of the following is NOT true regarding the chromatin-remodeling SWI/SNF complex?

A)It acts as tumor suppressor.
B)It serves as a co-activator of transcription.
C)It has homology to DNA helicases.
D)It can stabilize DNA-histone interactions.

Question 30

Describe how the electrophoretic mobility shift assay (EMSA)and the DNase I footprinting techniques are used to identify DNA-protein interactions.

Question 31

This serves as the promoter for 70% of eukaryotic genes and typically serves as a control region for genes that are transcribed at relatively low rates.

A)TATA box
B)enhancers
C)CpG islands
D)UAS (upstream activating sequences)

Question 32

All of the following events play a role in yeast-mating type switching except

A)methylation of the silent-mating-type locus.
B)transcription of the gene at the MAT locus.
C)chromatin condensation at the silent mating type locus.
D)a recombination event known as gene conversion.

Question 33

Which of the following is not used in the electrophoretic mobility shift assay (EMSA)?

A)a radiolabeled DNA fragment
B)a polyacrylamide gel
C)a DNA binding protein
D)DNase I

Question 34

An enhancer

A)is a DNA element that stimulates transcription of eukaryotic promoters.
B)binds to RNA polymerase and stimulates transcription.
C)acts as a binding site for RNA polymerase.
D)interacts with repressor proteins to enhance transcriptional repression.

Question 35

All the following statements about heterochromatin are true except:

A)DNA dyes stain heterochromatin more darkly than euchromatin.
B)The DNA of heterochromatin is more highly condensed than that of euchromatin.
C)Heterochromatin is associated with inactive genes.
D)Heterochromatin is more susceptible to DNaseI than is euchromatin.

Question 36

The mediator complex

A)can form a molecular bridge between activators of transcription and DNA replication machinery.
B)can function to maintain a promoter in a hypoacetylated state.
C)has histone acetylase activity.
D)none of the above

Question 37

Describe the structure of the RNA polymerase II transcription initiation complex.

Question 38

How can transcription factors be purified using sequence-specific DNA-affinity chromatography?

Question 39

Transcriptionally inactive genes

A)are always located within euchromatin.
B)are not located within nucleosomes.
C)often are methylated.
D)are not resistant to DNase I.

Question 40

Bromodomains are found in chromosome-associated proteins that contribute to transcriptional activation.To facilitate this activation,the bromodomains bind to histones,specifically their lysine residues that have been post-translationally modified by:

A)methylation.
B)acetylation.
C)phosphorylation.
D)ubiquitination.

Question 41

Describe how lipid soluble hormones,glucocorticoid for example,regulate gene transcription acting through nuclear hormone receptors.

Question 42

Which one of the following techniques would be best suited to follow how a thyroxine-bound receptor translocates from the cytoplasm to its DNA response element?

A)in situ hybridization and a radioactive fragment of the DNA response element
B)fluorescence microscopy and a GFP-tagged receptor fusion protein
C)pulse-chase radiolabeling
D)none of the above

Question 43

Lipid soluble hormones activate transcription by

A)binding to specific cell-surface receptors.
B)phosphorylating a protein kinase.
C)binding to a nuclear receptor.
D)inhibiting a histone deacetylase.

Question 44

Which protein domains are found in nuclear-receptor family members?

A)variable region,DNA-binding domain,ligand-binding domain
B)acetylase domain,DNA-binding domain,ligand-binding domain
C)variable region,acetylase domain,ligand-binding domain
D)variable region,DNA-binding domain,acetylase domain

Question 45

Regulation of transcription by steroid hormones

A)involves hormone receptors only found in the nucleus.
B)involves cytoplasmic hormone receptors that can move to the nucleus.
C)involves two ligase domains.
D)always activates transcription.

Question 46

Which of the following statement(s)regarding transcription initiation and RNA Pol III is (are)true?

A)ATP hydrolysis is not required for initiation.
B)Pol III is responsible for synthesizing tRNAs and 5S-rRNA.
C)The promoter elements of tRNA genes lie entirely within the transcribed sequence.
D)all of the above

Question 47

Describe the mechanism of transcriptional control for the heat shock genes.What advantage does this type of control impart to the cell?

Question 48

What family of proteins plays an essential role in the repression of genes that help to direct the formation of specific tissues and organs in a developing embryo?

A)Retinoblastoma
B)Trithorax
C)Polycomb
D)Pax

Question 49

The nuclear-receptor superfamily consists of several proteins that bind to consensus sequences of DNA response elements.Which of the following is NOT considered a member of this superfamily?

A)retinoic acid receptor
B)acetylcholine receptor
C)glucocorticoid receptor
D)progesterone receptor

Question 50

Epigenetics marks refer to modifications to DNA and proteins that in turn regulate gene expression.Which statement is true regarding these specific types of modifications?

A)They have the ability to both silence and activate genes.
B)They can involve the methylation of cytosine bases.
C)They are linked to the acetylation of histones.
D)All of the above

Question 51

X chromosome inactivation in mammals is mediated by

A)micro RNAs (miRNA).
B)long non-coding RNAs (ncRNA).
C)messenger RNA (mRNA).
D)short RNA-directed methylation of histones and DNA.