Deck 11: Transcription in Eukaryotes

Question 1

Transcription of protein-coding genes in eukaryotes is carried out by

A) RNA polymerase I
B) RNA polymerase II
C) RNA polymerase III
D) RNA polymerase; there is only one type of RNA polymerase in eukaryotes.

Answer 1

RNA polymerase II

Question 2

Gene regulatory elements are

A) trans-acting transcription factors
B) cis-acting transcription factors
C) trans-acting DNA sequences
D) cis-acting DNA sequences

Answer 2

cis-acting DNA sequences

Question 3

Which of the following is involved in transcription in prokaryotes, but not in eukaryotic transcription?

A) regulatory proteins
B) RNA polymerase
C) promoters
D) operators

Answer 3

operators

Question 4

In order to be highly transcribed, a eukaryotic protein-coding gene may

A) be transcribed by RNA Polymerase III
B) leave its chromosome territory to associate with a transcription factory
C) become dimethylated on Lys9 of histone H3
D) become covalently attached to the nuclear matrix

Question 5

Eukaryotic core promoter elements have all of the following characteristics, except:

A) They serve as the recruitment site for RNA polymerase II.
B) They serve as the recognition site for general transcription factors.
C) They all contain a TATA box.
D) They become nonfunctional when moved even a short distance from the start oftranscription.

Question 6

What types of proteins bind to promoter-proximal elements?

A) the TATA-binding proteins (TBP)
B) general transcription factors plus RNA polymerase
C) general transcription factors
D) regulatory transcription factors

Question 7

The primary difference between an enhancer and a promoter-proximal element is that:

A) Enhancers are transcription factors; promoter-proximal elements are DNA sequences.
B) Enhancers enhance transcription; promoter proximal-elements inhibit transcription.
C) Enhancers are part of the core promoter; promoter-proximal elements are regulatory sequences distinct from the core promoter.
D) Enhancers are at considerable distances from the core promoter; promoter-proximal elements are close to the core promoter.

Question 8

Which of the following statements about silencers is correct?

A) They contain a consensus sequence called a TATA box.
B) They are found in a variety of locations and are functional in any orientation.
C) They are located only in introns.
D) They are located only in 5?-flanking regions.

Question 9

If the DNA double helix were inflexible, which of the following forms of transcriptional regulation would be most strongly affected?

A) The ability of the TATA-binding protein (TBP) to recognize the promoter.
B) The ability of RNA polymerase II to associate with the general transcription factors.
C) The ability of RNA polymerase II to initiate transcription.
D) The ability of enhancers to influence transcription.

Question 10

A long-range regulatory element that marks the border between regions of heterochromatin and euchromatin is called a(n)

A) enhancer
B) insulator
C) locus control region
D) matrix attachment region

Question 11

Which of the following would not likely improve the expression of a transgene that integrated into a heterochromatic region of the genome?

A) inclusion of matrix attachment regions (MARs)
B) inclusion of insulator elements
C) inclusion of a strong promoter
D) inclusion of a G-less cassette

Question 12

Patients with "Hispanic thalassemia" have a deletion of the ________ of the beta-globin gene cluster that results in silencing of the genes.

A) locus control region
B) coding region
C) matrix attachment region
D) promoter

Question 13

Which regulatory sequences must maintain their orientation with respect to the gene transcription start site to function?

A) promoter and silencer
B) promoter and enhancer
C) promoter and locus control region
D) silencer and enhancer

Question 14

What is the key property of DNase I that makes it useful for determining whether chromatin is in a closed (tightly condensed) or open (loosely packed) configuration?

A) DNase I is an enzyme.
B) DNase I will digest DNAs from all species equally effectively.
C) DNase I preferentially digests DNA not associated with protein.
D) DNase I cuts at specific DNA recognition sequences.

Question 15

Imagine you're assaying the DNase I sensitivity of the promoter regions of the beta-globin and vitellogenin genes in chicken liver, instead of in chick embryo erythroblasts. In this case you expect to find that:

A) The beta-globin and vitellogenin promoters are equally sensitive to DNase I treatment.
B) The beta-globin and vitellogenin promoters are equally resistant to DNase I treatment.
C) The beta-globin promoter is much more sensitive to DNase I treatment.
D) The vitellogenin promoter is much more sensitive to DNase I treatment.

Question 16

Small eukaryotic proteins that are known to add specificity to polymerase-dependent RNA synthesis are known as

A) general transcription factors
B) mediators
C) histones
D) elongation factors

Question 17

The unwinding of DNA during the initiation of transcription is mediated by
The helicase activity of

A) TFIID
B) THIIE
C) TFIIF
D) TFIIH

Question 18

Reinitiation of transcription requires

A) phosphorylation of the RNA polymerase II (RNA pol II) C-terminal domain (CTD).
B) dephosphorylation of the RNA pol II CTD.
C) acetylation of the RNA pol II CTD.
D) deacetylation of the RNA pol II CTD.

Question 19

TAFs and TBP are together known as

A) TFIID
B) TFIIE
C) TFIIF
D) TFIIH

Question 20

RNA polymerase II is only responsive to the presence of transcriptional activators in the presence of which protein complex?

A) spliceosome
B) enhancer
C) Mediator
D) SWI/SNF

Question 21

In an in vitro transcription assay, a G-less cassette could be used to do which of the following?

A) generate an RNA product of defined length
B) pause RNA polymerase at a defined site in a template
C) induce RNA polymerase backtracking
D) A and B

Question 22

Fundamentally, what makes one cell different from another in a multicellular eukaryote?

A) The different cells contain different sets of enhancers and promoter-proximal elements.
B) The different cells contain different sets of transcription factors.
C) The different cells contain different sets of cell-type-specific genes.

Question 23

The basic leucine zipper (bZIP) motif has all of the following characteristics, except:

A) it is a DNA-binding domain that directly contacts DNA in the major groove
B) is a stretch of amino acids that fold into a long alpha-helix with leucines in every seventh position
C) it facilitates dimerization of two similar polypeptide chains
D) it is not as common as the zinc finger motif

Question 24

Which is not a common DNA binding motif?

A) chromodomain
B) zinc finger
C) helix-turn-helix
D) basic helix-loop-helix

Question 25

You create a chimeric protein that contains the DNA binding domain of the Fork head transcription factor and the transactivation domain of the Sp1 transcription factor. Which of the following predictions would you make concerning the activity of your chimeric protein?

A) It would activate the transcription of genes normally activated by Fork head.
B) It would activate the transcription of genes normally activated by Sp1.
C) It would activate the transcription of genes normally activated by both Fork head and Sp1.
D) It would not activate the transcription of any genes.

Question 26

Which assay would allow you to determine whether two transcription factors with nearby binding sites in a promoter sequence bind to the sequence synergistically?

A) in vitro run-off assay
B) fluorescence recovery after photobleaching (FRAP)
C) X-ray crystallography
D) electromobility shift assay (EMSA)

Question 27

Which of the following is not true of Hox family genes?

A) Each Hox gene has a 180 base pair sequence called the homeobox.
B) In both fruit flies and mammals, the order of the Hox genes on the chromosomecorrelates with where they are expressed in embryos.
C) In fruit flies the order of Hox genes on the chromosome correlates with where they are expressed in embryos; in mammals there is no correlation.
D) The expression of the Hox genes is sequential, moving in order along the chromosome.

Question 28

Histone acetyl transferases exert their effect on gene activity at least in part by:

A) neutralizing positive charges on lysines of histones
B) increasing the negative charge on glutamic acids of histones
C) modifying the base sequence of the promoter
D) adding bulky methyl groups to lysines and arginines of histones

Question 29

Which of the following is not true of regulatory proteins that are classified as coactivators?

A) Many coactivators function as chromatin modification complexes.
B) Many coactivators function as chromatin remodeling complexes.
C) All coactivators increase transcriptional activity.
D) All coactivators bind DNA directly.

Question 30

Which statement best describes the key difference between the "enhanceosome" and "hit and run" models for transcriptional activation?

A) The "enhanceosome" model requires the involvement of both promoter proximal elements and the core promoter, whereas the "hit and run" model only involves promoter proximal elements.
B) The "enhanceosome" model requires that a stable transcriptional activation complex assembles in an ordered fashion, whereas the "hit and run" model suggests that such complexes are formed stochastically.
C) The "enhanceosome" model requires synergy between multiple transcriptional (co)activators, whereas the "hit and run" model allows that each transcriptional regulatory protein may function independently.
D) The "enhanceosome" model only applies to genes that undergo developmental regulation, whereas the "hit and run" model only applies to genes that undergo dynamic regulation even in a terminally differentiated cell.

Question 31

Chromatin remodeling by the SWR1 family results in:

A) nucleosome sliding
B) replacement of a core histone with a variant histone
C) nucleosome displacement
D) remodeled nucleosomes

Question 32

Which is the correct order of recruitment of transcriptional regulatory proteins to a gene promoter?

A) SWI/SNF, histone acetyltransferase (HAT) complex, preinitiation complex
B) HAT complex, SWI/SNF, preinitiation complex
C) preinitiation complex, SWI/SNF, HAT complex
D) the order of recruitment is gene-specific.

Question 33

Which protein or protein complex helps RNA polymerase to traverse nucleosomes?

A) FACT
B) SWI/SNF
C) Sonic hedgehog
D) Polycomb

Question 34

Which method was most instrumental in the development of the current model for transcript elongation by RNA Polymerase II?

A) in vitro run-off assay
B) fluorescence recovery after photobleaching (FRAP)
C) X-ray crystallography
D) electromobility shift assay (EMSA)

Question 35

Familial dysautonomia is a rare autosomal recessive disorder characterized by a mutation in a gene the plays a role in

A) promoter clearance
B) transcript elongation
C) proofreading and backtracking
D) nucleotide translocation

Question 36

Which of the following factors plays a role in RNA cleavage during polymerase backtracking?

A) TFIIS
B) FACT
C) HDAC
D) Elongator

Question 37

Which of following events is not true about the nuclear import of proteins?

A) The nuclear localization sequence of the protein to be imported binds to importin.
B) The nuclear localization sequence of the protein is removed once the protein enters the nucleus.
C) The energy for import is provided by the small GTPase Ran.
D) Import may occur against a concentration gradient.

Question 38

Nuclear import and export of proteins

A) occurs by diffusion through the nuclear envelope.
B) is mediated by structures embedded in the nuclear envelope called nuclear pore complexes.
C) is mediated by structures embedded in the nuclear envelope called nuclear localization sequences.
D) occurs by active transport through phospholipid-lined channels in the nuclear envelope.

Question 39

During nuclear transport, RanGTP

A) causes disassembly of import complexes, but is required for the assembly of export complexes.
B) causes assembly of import complexes, but is required for the disassembly of export complexes.
C) is present in equal concentrations in the nucleus and cytoplasm.
D) is required to provide energy for cargo recognition and docking.

Question 40

RanGAP stimulates the conversion of

A) GTP to GDP
B) GDP to GTP
C) GDP to GMP
D) GMP to GDP

Question 41

Steroid hormones, such as glucocorticoids, bind to receptors inside the cell. The hormone-receptor complex is transported into the nucleus, where it can directly affect gene expression. To get from the location where the receptor binds the hormone to its site of action:

A) the receptor-hormone dimer must dissociate to form a monomer.
B) the receptor-hormone complex must become water soluble by binding to a carrier molecule.
C) the receptor-hormone complex must be transported through the nuclear pore complex.
D) the receptor-hormone complex must be activated by a signaling cascade.

Question 42

List the major types of RNA polymerases in eukaryotes and the types of genes they are responsible for transcribing.

Question 43

How has in situ hybridization (FISH) evidence supported the chromosome territories and transcription factories hypotheses?

Question 44

Diagram the structure of a "typical" eukaryotic protein-coding gene, including all potential
regulatory regions. Indicate where the RNA polymerase II preinitiation complex interacts.

Question 45

Draw a diagram of a RNA polymerase II promoter, showing all of the types of elements it could have. Exact sequences are not necessary.

Question 46

Compare and contrast the key characteristics of proximal promoter elements, enhancers, and locus control regions.

Question 47

You have made a transgenic mouse using a cDNA coding for a human protein under
control of a heterologous promoter. In most of the transgenic mice, you observe position-dependent expression of the human protein. Define the term "position-dependent" and
give examples of regulatory regions that you could link to the promoter-human
cDNA construct that might confer position-independent expression. Explain your choice of regulatory regions.

Question 48

Imagine you're assaying the DNase I sensitivity of the promoter regions of the beta-globin and vitellogenin genes in chicken liver, instead of in chick embryo erythroblasts. Show sample results from assay.

Question 49

Describe a model for transcriptional regulation by matrix attachment regions (MARs).

Question 50

Explain the underlying genetic defect leading to Hutchinson-Gilford progeria.

Question 51

Draw a rough diagram of the structure of yeast RNA polymerase II. Show where the DNA lies and show the location of the active site. What is the structure of the CTD?

Question 52

Does RNA polymerase II bind directly to the core promoter by itself to initiate transcription? Explain your answer.

Question 53

Promoter clearance requires what post-translational modification of RNA polymerase II? Where does this post-translational modification occur?

Question 54

List in order the proteins that assemble to form an RNA polymerase II preinitiation complex.

Question 55

What shape does TBP have? What is the geometry of the interaction between TBP, the TATA box, and the DNA double helix? Does TBP interact with the major or minor groove?

Question 56

Describe the G-less cassette transcription assay that led to the discovery of Mediator. Include a graph illustrating the effect of Mediator on activated versus basal transcription

Question 57

Explain why transcription factors are called "modular" proteins. How is this exploited in a yeast two-hybrid assay?

Question 58

Compare and contrast four different classes of DNA-binding domains found in eukaryotic transcription factors.

Question 59

Describe the structure and function of the homeodomain. What other protein domain does it most resemble?

Question 60

Explain what is meant by the term "colinear expression" as it describes Hox genes in Drosophila.

Question 61

Describe a model for how Polycomb group proteins silence homeobox genes.

Question 62

What does "Sonic the Hedgehog" have to do with zinc fingers?

Question 63

Explain how the disease Greig cephalopolysyndactyly syndrome is related to the zinc-finger DNA binding domain.

Question 64

Draw a detailed diagram of a basic leucine zipper (bZIP). Illustrate the interaction of this motif with another polypeptide and with DNA. Point out the leucine zipper and the basic DNA-binding domain.

Question 65

Describe a common motif found in transactivation domains.

Question 66

Do coactivators and corepressors bind DNA directly? Explain your

Question 67

Could the Polycomb-group protein complexes PRC1 and PRC2 be considered co-repressors? Why or why not?

Question 68

Compare and contrast the structure and function of six post-translational modifications of histone N-terminal tails.

Question 69

What roles are histone acetyltransferases (HATs), histone deacetylases (HDACs), histone methyltransferases (HMTs) thought to play in activation and repression of transcription?

Question 70

Define the "histone code" hypothesis and discuss evidence for and against it.

Question 71

Explain how the same type of chemical modification of nucleosomes,

Question 72

Discuss the role of the variant linker histone H1b in muscle progenitor cell differentiation.

Question 73

Describe four different ways in which chromatin structure can be altered by chromatin remodeling complexes. What role does chromatin remodeling play in activation and repression of gene transcription?

Question 74

Which is recruited first to a gene, the preinitiation complex, histone acetyltransferases (HATs), or SWI/SNF? Explain your answer.

Question 75

Compare and contrast the "enhanceosome" and the "hit and run" model for transcription complex assembly.

Question 76

Explain how fluorescence recovery after photobleaching (FRAP) experiments may differentially support either the "hit and run" model or the "enhanceosome" models of transcriptional activation.

Question 77

Describe X-ray crystallographic evidence for a four step cycle of RNA synthesis during RNA polymerase II transcription.

Question 78

RNA polymerase has a single active site that switches between RNA synthesis and cleavage. Describe a model for this "tunable" RNA polymerase active site. How does this compare with the structure and function of DNA polymerase active sites?

Question 79

What is the proposed function of TFIIS in RNA polymerase II-mediate transcription?

Question 80

After initiation of transcription, how does RNA polymerase II move through nucleosomes?