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Unit 2 Flashcards

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1
Q

What is a promoter in transcription?

A

The region where RNA Polymerase binds to the DNA to initiate transcription.

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2
Q

What do cis-regulatory elements do?

A

Control whether and how much transcription occurs but are not transcribed themselves.

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3
Q

Define coding strand/sense strand.

A

The strand of DNA whose sequence is identical to the RNA sequence produced during transcription.

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4
Q

What is the function of a terminator?

A

Signals the end of transcription; located downstream of the transcription start site.

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5
Q

What does ‘upstream’ refer to in the context of transcription?

A

Regions of DNA located before the transcription start site on the coding strand.

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6
Q

What does ‘downstream’ refer to in transcription?

A

Regions of DNA located after the transcription start site on the coding strand.

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7
Q

Fill in the blank: The _______ is the template used for RNA synthesis during transcription.

A

[antisense strand]

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8
Q

True or False: The sense strand of DNA is the same as the RNA sequence produced.

A

True

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9
Q

What is the significance of the transcription start site (TSS)?

A

It marks the beginning of transcription on the coding strand.

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10
Q

What are transcription factors?

A

bind to DNA at specific sequences to facilitate or regulate transcription.

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11
Q

What is the first step in the transcription process?

A

Initiation, transcription factors recruit RNA Polymerase and begin process by creating open DNA complex (transcription bubble)

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12
Q

What happens during the elongation phase of transcription?

A

RNA polymerase moves along DNA, copying the template.

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13
Q

What is the final step in the transcription process?

A

The termination process concludes; RNA is released.

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14
Q

What is the -35 sequence?

A

A conserved sequence located upstream of the promoter, typically recognized by RNA polymerase.

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15
Q

What is a promoter?

A

A region of DNA that initiates transcription of a particular gene.

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16
Q

What is the -10 sequence?

A

A conserved sequence known as the Pribnow Box, typically ‘TATAAT’, located at -10.

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17
Q

What is the transcriptional start site?

A

The location where transcription begins, denoted as +1.

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18
Q

What is the Pribnow Box?

A

A conserved sequence located at -10, typically ‘TATAAT’.

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19
Q

What is the template strand?

A

The strand of DNA that is used as a template for RNA synthesis.

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20
Q

What are the promoter elements in prokaryotic transcription?

A

The -10 sequence (Pribnow Box) and the -35 region.

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21
Q

What is the sigma factor?

A

core component of RNA polymerase during initiation; it guides RNA polymerase to the DNA and allows it to bind to the promoter.

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22
Q

What does the RNA polymerase do at the promoter?

A

It opens the DNA to expose the template strand and begins transcription.

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23
Q

What marks the end of the initiation phase in transcription?

A

The release of sigma factor marks the end of initiation.

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24
Q

What happens behind RNA polymerase during elongation?

A

RNA is displaced and DNA strands reanneal.

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25
What is the rut site?
The rut site is a recognition site in RNA where the Rho (p) protein binds and moves toward the 3' end.
26
What is the first way of termination in RNA?
The first way of termination is Rho (p) dependent termination.
27
What happens at the rut site during transcription?
Rho binds to the rut site after it is transcribed, causing the RNA to pause due to the formation of a stem-loop.
28
What role does the stem-loop play in termination?
The stem-loop causes RNA polymerase to pause during transcription.
29
What does Rho (p) protein do after the RNA polymerase pauses?
Rho (p) protein moves down the transcript as a helicase and separates the RNA from the DNA template at the terminator.
30
What is the second mechanism for termination?
Rho independent
31
What is the second mechanism for termination?
Independent/intrinsic termination.
32
What structure causes RNA polymerase to pause?
A stem-loop structure.
33
What follows the stem-loop structure in the termination process?
A terminator sequence.
34
What occurs after RNA polymerase pauses?
Termination occurs as RNA detaches from DNA due to weak interactions.
35
What is the core promoter in eukaryotic transcription?
TATA box
36
What is the conserved sequence of the TATA box?
5'TATAA 3'
37
What are enhancers in eukaryotic transcription?
allow binding of gene-specific transcription factors to increase the amount of transcription.
38
What are silencers in eukaryotic transcription?
allow binding of gene-specific transcription factors to decrease the amount of transcription.
39
What does RNA Polymerase produce?
RNA Polymerase produces all of the ribosomal RNAs.
40
What does RNA Polymerase II produce?
RNA Polymerase II produces all of the mRNAs, small RNAs used for splicing, IncRNA, miRNA (which regulate gene expression), and snRNA used for RNA processing.
41
What does RNA Polymerase III produce?
RNA Polymerase III produces all of the tRNAs.
42
What are trans-acting factors?
Trans-acting factors are proteins that regulate the process of transcription.
43
What are general transcription factors?
General transcription factors are necessary for basal levels of transcription.
44
What is the naming convention for RNA Polymerase transcription factors?
The naming convention includes TF I D for general transcription factors.
45
What is the role of specific transcription factors?
Specific transcription factors refine the amount of transcription to enhance or silence gene expression.
46
What binds to the TATA box?
TFIID binds to the TATA box. TFIID is a complex of proteins that includes the TATA-binding protein (TBP) and several TBP-associated factors (TAFs).
47
What is TFIID?
TFIID is a complex of proteins that includes the TATA-binding protein (TBP) and several TBP-associated factors (TAFs).
48
What binds to TFIID?
TFIIB binds to TFIID.
49
What does TFIIB promote?
TFIIB promotes the binding of RNA polymerase II to the core promoter.
50
What is TFIIF?
TFIIF is bound to RNA polymerase II.
51
What forms a preinitiation complex?
TFIIE and TFIIH bind to RNA polymerase II to form a preinitiation or closed complex.
52
What is the role of TFIIH?
TFIIH acts as a helicase to form an open complex and phosphorylates the CTD of RNA polymerase II.
53
What happens to TFIIB after CTD phosphorylation?
CTD phosphorylation breaks the contact between TFIIB and RNA polymerase II.
54
What is released after TFIIB is no longer in contact with RNA polymerase II?
TFIIB, TFIIE, and TFIIH are released.
55
What is the CTD of RNA polymerase II?
CTD stands for Carboxyl Tail Domain of RNA polymerase II.
56
What is the process of initiation in transcription?
1) TFIID binds to the TATA box. 2) TFIID recruits TFIIB. 3) TFIIB recruits and positions RNA polymerase II, which is brought in by TFIIF. 4) TFIIE and TFIIH bind to complete the pre-initiation complex.
57
How is elongation in eukaryotic transcription similar to prokaryotic transcription?
Eukaryotic elongation is similar to prokaryotic elongation.
58
What binds to the TATA box?
TFIID ## Footnote TFIID is a complex of proteins that includes the TATA-binding protein (TBP) and several TBP-associated factors (TAFs).
59
What does TFIIB promote?
The binding of RNA polymerase II to the core promoter ## Footnote TFIIB is essential for the initiation of transcription in eukaryotes.
60
What is TFIIF bound to?
RNA polymerase II ## Footnote TFIIF is important for stabilizing the interaction between RNA polymerase II and the transcription factors.
61
Which factors bind to RNA polymerase II to form a preinitiation complex?
TFIIE and TFIIH ## Footnote The preinitiation complex is crucial for the initiation of transcription.
62
What role does TFIIH play in transcription?
Acts as a helicase to form an open complex and phosphorylates the CTD of RNA polymerase II ## Footnote This phosphorylation breaks the contact between TFIIB and RNA polymerase II.
63
What happens to TFIIB, TFIIE, and TFIIH after the formation of the open complex?
They are released ## Footnote This release is part of the transition from initiation to elongation in transcription.
64
Fill in the blank: TFIID recruits _______.
TFIIB ## Footnote TFIIB is essential for positioning RNA polymerase II at the core promoter.
65
What does the phosphorylation of the CTD of RNA polymerase II do?
Breaks the contact between TFIIB and RNA polymerase II ## Footnote This is a critical step in the transition to the elongation phase of transcription.
66
True or False: The elongation process in eukaryotes is similar to that in prokaryotes.
True ## Footnote While there are differences in initiation, the overall elongation process shares similarities.
67
What is the role of TFIIB in the transcription process?
Recruits and positions RNA polymerase II ## Footnote TFIIB is key for the assembly of the transcription machinery.
68
Eukaryotic Termination
Happens in conjunction with polydenylation of 3’ end in protein coding transcripts
69
Allosteric model
Termination in eukaryotes in which trans print site it cut at polydenylation site upstream of the terminator, this destabilizes RNA Polymerase and cause it to “falls off off” DNA.
70
Torpedo model
Termination in eukaryotes in which after transcript is cut at poly A site, 5’ exonuclease degrades remaining RNA until it reaches the RNA pol and aides in its removal.
71
What is RNA Processing?
The cleavage of a precursor RNA to create smaller functional RNA units. Preformed by endo and exonuclease.
72
What is splicing?
Splicing is the process that removes segments of RNA and reattaches the remaining RNA segments together.
73
What is a splice site?
A splice site is the location on a transcript where the cut and ligation occurs.
74
What is an intron?
An intron is a segment of RNA that is removed during splicing.
75
What is an exon?
An exon is a segment of RNA that is retained during splicing.
76
What is self-splicing?
Self-splicing is a spontaneous process that does not rely on additional proteins or RNAs.
77
78
What is spliceosomal splicing?
Spliceosomal splicing is mediated by a large protein-RNA complex called the spliceosome.
79
What is an snRNP?
An snRNP (snurp) is an individual unit of the spliceosome made of RNA and protein.

Genetics (2 decks)

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