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BIOL 415 > Exam 3: Eukaryotic Transcription > Flashcards

Exam 3: Eukaryotic Transcription Flashcards

1
Q

In Eukaryotic transcription, the general transcription apparatus binds to the________

A

Promoter

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2
Q

What is the nucleolus?

A

A spherical compartment in the nucleus for rRNA synthesis.

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3
Q

What is the gene product of RNA polymerase I? Where is this product synthesized?

A

rRNA synthesized in the nucleolus

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4
Q

What is the gene product of RNA polymerase II and where is it synthesized?

A

mRNA/miRNA synthesized in the nucleoplasm.

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5
Q

What is the product of RNA polymerase III and where is it synthesized?

A

5S rRNA (component of the ribosome), tRNA, snRNA synthesized in the nucleoplasm

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6
Q

What do the terms upstream and downstream refer to?

A

Upstream refers to components towards the 5’ end and downstream refers to components located toward the 3’ end

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7
Q

How many RNA polymerases are in prokaryotes?

A

Three

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8
Q

True or false: all promoters contain sets of short sequences that are regulated by the appropriate class of factors

A

True

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9
Q

Name the three eukaryotic RNA polymerases and explain a unique feature of each one’s promoter

A
  1. RNA polymerase I: promoters are bipartite (contain two parts)
  2. RNA polymerase II: Promoters are complicated and contain 5’ regulatory elements (upstream) and downstream regulatory elements.
  3. RNA polymerase III: promoters are often internal to the gene
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10
Q

RNA polymerase I is bipartite. What are the two components?

A

RNA polymerase I includes two components: the core promoter (allows for initiation) and the upstream promoter element.

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11
Q

True or false: RNA polymerase III only uses upstream promoters?

A

RNA polymerase III uses both downstream and upstream promoters.

The promoters for 5S and tRNA genes are internal and lie downstream of the start point.

The promoters for snRNA gene lie upstream of the start point.

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12
Q

True or false: there is only one type of RNA polymerase III

A

False: there are three types of RNA polymerase III that are recognized in different ways.

Type 1 and 2: promoter for RNA poly III consists of bipartite sequences downstream of the start point (box A separated from box B or C).

Type 3: promoter for RNA poly III consists of separated sequences upstream of the start point (Oct, TATA, PSE)

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13
Q

Describe the stages of reaction at type 2 internal RNA poly III promoters used for tRNA genes.

A

TFIIIC binds to both Box A and Box B. The allows TFIIIB to bind at the start point. At the point, the RNA polymerase III can bind.

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14
Q

Describe the stages of reaction for type I RNA poly III promoters.

A

TFIIIA binds at box A, which allows TFIIIC to bind at box B. This allows TFIIIB to bind at the start point, which allows RNA polymerase III to bind.

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15
Q

Define basal transcription factor

A

A transcription factor required by RNA polymerase II to form the initiation complex at all promoters. These factors are identified as TFIIX where X is a letter and the I, II, or III signifies the polymerase.

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16
Q

Define core promoter

A

A minimal sequence at which the basal transcription apparatus assembles. Site where initiation occurs. About 40 bp long and includes the lnR and either a TATA box or DPE (downstream promoter element).

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17
Q

Define initiator (lnR)

A

The sequence of a poly II promoter between -3 and +5 with the general sequence Py2CAPY5

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18
Q

Define TATA box

A

A conserved A:T rich element found upstream from the start site that helps position RNA polymerase II for initiation.

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19
Q

Define TATA-less promoter

A

Promoter that lacks the TATA box site

20
Q

What is DPE?

A

Downstream promoter element: a common regulatory sequence in TATA-less promoters.

21
Q

What is the start point

A

The position on the DNA corresponding to the first base incorporated into RNA. A purine (A/G) typically A

22
Q

What are the RNA polymerase II core promoter elements?

A

A TATA box or DPE and InR.

23
Q

What are the common regulatory regions of RNA polymerase II?

A

TATA box located at -25

CAAT box located upstream and responsible for controlling frequency of initiation.

GC box located at variable positions upstream and responsible for controlling frequency of initiation.

24
Q

Define TFIID

A

A transcription factor that binds to the TATA sequence upstream of the start point of RNA poly II promoters. It is composed of TBP (TATA binding protein) and up to 11 TAFs (TBP associated factors).

25
Q

Define TAF

A

The subunits of TFIID that assist TBP in binding to DNA. They also provide points of contact for other components of the transcription apparatus.

26
Q

Define TBP

A

TATA-binding protein: the subunit of transcription factor TFIID that binds to the TATA box in the promoter and is positioned at the promoters that do not contain a TATA box by other factors.

A component of the positioning factor that is required for each type of RNA polymerase to bind to its promoter.

27
Q

True or false: TBP is a universal factor for all 3 RNA polymerases

A

True

28
Q

True or false: TBP is not involved whin the absence of a TATA box DNA element.

A

False: the TBP is still involved in the absence of the TATA box DNA element

29
Q

What are the positioning factors for each RNA polymerase?

A

RNA polymerase III: TFIIIB
RNA polymerase I: SL1
RNA polymerase II: TFIID

30
Q

Where does TBP bind when there is a TATA box?

A

The minor groove of DNA at the TATA box

31
Q

True or false: binding of TBP to the DNA causes the DNA strand to bend by 80 degrees

A

True, this forms the saddle structure

32
Q

True or false: TBP alone is sufficient for transcription

A

False: TBP is not sufficient for transcription. Transcription requires both TBP and TAF

33
Q

Define Kinase

A

Enzymes that catalyze transfer of phosphate group to substrate (phosphorylate)

34
Q

Define CTD

A

Carboxy-terminal domain: The domain of the largest subunit of eukaryotic RNA polymerase II that is phosphorylated at initiation and is involved in coordinating several activities with transcription.

35
Q

Define Preinitiation complex

A

The assembly of transcription factors at the promoter before RNA polymerase binds in eukaryotic transcription. It directs the binding of RNA polymerase

36
Q

What are the steps of the pre-initiation complex of RNA polymerase II?

A
  • RNA polymerase II does not bind DNA by itself.
  • Initiation requires the basal transcription factors to act in a defined order to build a complex that is joined by RNA polymerase.
  • Initiation complex is assembled at promoters for RNA polymerase II by an ordered sequence of association of transcription factors.
    1. TFIID binds
    2. Remaining TFs bind in a defined order
    3. RNA polymerase II binds to the complex and initiated transcription
37
Q

What is the role of TFIIB in RNA polymerase II attachement?

A

TFIIB binds to DNA and contacts RNA polymerase near the RNA exit site and at the active center and orients it on the DNA strand. TFIIB determines the path of the DNA where it contacts the factors TFIIE, F, and H.

38
Q

What general transcription factor consists of 6 subunits with multiple roles? What are some of these roles?

A

TFHII has 6 subunits with multiple enzymatic activity.

  1. Provides kinase at initiation
  2. Provides a repair complex (complex of repair enzymes) for damaged DNA at elongation
39
Q

Phosphorylation of _____ is required for ______ to begin

A

CTD, elongation

40
Q

What is the role of CTD during and after transcription?

A
  • During transcription, CTD is modified through phosphorylation
  • CTD coordinates processing of RNA after transcription
41
Q

True or false: CTD is required for capping mRNA

A

True: the capping enzyme binds to the phosphorylated CTD Ser. This allows the cap structure to be added to the 5’ end of the newly synthesized mRNA.

42
Q

What is the importance of the interaction of SCAFs and CTD?

A

SCAFs (scaffolding proteins) bind to the CTD and recruit splicing factors to the RNA complex. Splicing factors then bind to SCAFS

43
Q

Define enhancer

A

A cis-acting regulatory sequence that increases the utilization of most eukaryotic promoters and can function in either orientation in any location relative to the promoter.

Short regulatory sequences that increase the transcription of target genes. This occurs by increasing the activity of a promoter

44
Q

True or false: enhancers can only activate promoters located downstream from the enhancer location

A

False: An enhancer activates the promoter closest to itself and can be any distance either upstream or downstream of the promoter.

45
Q

True or false: enhancers can interact with promoters on separate circular DNAs

A

False: an enhancer can only interact with a promoter of the enhancer is located on the same circular DNA or if the DNA with the promoter and the DNA with the enhancer are interlocked (circles are overlapping).

BIOL 415 (7 decks)

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