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Molecules and Energetics Block 1 > Transcription > Flashcards

Transcription Flashcards

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Organic Chemistry 101 flashcards
1
Q

What is the ion that is needed to catalyze the enzymatic reaction that catalyzes transcription?

A

Mg+2

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2
Q

What are the 3 main steps of transcription?

A

Initiation, Elongation, and Termination

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3
Q

What direction is RNA synthesized?

A

5’ to 3’

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4
Q

What direction is the template strand of DNA copied? “TEMPLATE Directed”

A

3’ to 5’

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5
Q

Is a primer required in RNA synthesis?

A

No. RNA is synthesized de novo by joining 2 ribonucleotides together to form the first 3’ to 5’ phosphodiester bond.

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6
Q

How many RNA polymerases do prokaryotes have?

A

1

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7
Q

What is the function of the alpha subunit (#2) in the prokaryotic RNA polymerase?

A

Binds regulatory proteins with the “w” subunit

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8
Q

What is the fxn of the B subunit (#1) in the prokaryotic RNA poly?

A

Phosphodiester bond formation AND grasps DNA

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9
Q

What is the fxn of the B’ subunit (#1) in the prokaryotic RNA poly?

A

Grasps DNA template

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10
Q

What is the role of the sigma unit in the prok. RNA poly?

A

Promoter recognition and initiation

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11
Q

The addition of this subunit completes the core enzyme RNA poly and makes it a holoenzyme?

A

Sigma subunit

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12
Q

What is the DNA sequence in the template strand of the gene that binds to the RNA polymerase?

A

Promoter (typically contains 2 consensus sequences)

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13
Q

How is a consensus sequence determined?

A

It’s derived by determining the base found most frequently at each position in the promoter region of the gene

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14
Q

This subunit of RNA polymerase in prokaryotes forms the promoter complex by binding SPECIFICALLY?

A

Sigma subunit

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15
Q

When the first phosphodiester bond is formed during initiation, what is released?

A

The sigma subunit

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16
Q

Once the sigma subunit binds specifically to the consensus sequence, this property of RNA polymerase is activated to form the open promoter complex?

A

Helicase activity in RNA poly unwinds 17 bp of DNA

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17
Q

What is the main fxn of the sigma subunit?

A

1) Directs RNA poly holoenzyme to the promoter due to the high affinity binding btw the sigma subunit and the promoter

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18
Q

What is the specificity of the RNA polymerase for a given promoter is dependent on this subunit?

A

Sigma subunit of the holoenzyme

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19
Q

The sigma70 unit is for what kind of promoter?

A

standard

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20
Q

The sigma32 unit is for what kind of promoter?

A

heat shock

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21
Q

The sigma 54 unit is for what kind of promoter?

A

Nitrogen-starvation genes

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22
Q

What does the transcription bubble consist of?

A

1 )Unwound region: 17 bp of DNA

2) RNA/DNA duplex=12 bp

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23
Q

To prevent positive supercoils from forming in prokaryotes, this topoisomerase creates negative supercoils ahead of the transcription bubble?

A

Gyrase (Type II)

24
Q

As DNA unwinds, negative supercoils are formed. What kind of topoisomerase relaxes negative supercoils behind the transcription bubble?

A

Type I topoisomerase

25
Q

What are the 2 types of template-directed termination of transcription?

A

A) Template-directed Termination

B) Rho-directed Termination

26
Q

What is template-driven termination?

A

Sequence in DNA template strand contains G-C rich repeats (forms hair-pin) followed by A-T rich repeat (loose bc of 2 H-bonds)

27
Q

What is rho-driven termination?

A

Rho protein binds to specific sequences in newly synthesized RNA. Rho protein has ATP-dependent helicase activy that dissociates it from the template strand.

28
Q

What are the products and location of eukaryotic RNA polymerase I?

A

1) 45 S Pre-rRNA Transcript (5.8S, 18S, 28S rRNAS)

2) Nucleolus

29
Q

What are the products/location of eukaryotic RNA polyII?

A

1) mRNA, miRNA, U1, U2, U4, U5, and snRNA

2) Nucleus

30
Q

What are the products/location of eukaryotic RNA polyIII?

A

1) tRNA, 5 S rRNA, and U6 snRNA

2) nucleus

31
Q

What are the products/locatio of mitochondrial RNA poly?

A

1) All mitochondrial RNAs

2) mitochondria

32
Q

What are the 4 components of Eurkaryotic RNA poly?

A

1) Core RNA Polymerase
2) General transcription factors
3) Specific transcription factors
4) Mediator proteins

33
Q

What are general transcription factors?

A

Proteins required for basal transcription of ALL genes

34
Q

What are specific transcription factors?

A

Proteins that selectively regulate transcription of target genes. Differ in # depending on the gene.

35
Q

What are mediator proteins?

A

Coactivators or corepressors that facilitate interactions btw protein components of the holoenzyme.

36
Q

What are specific sequences of DNA on the same molecule as a gene?

A

cis-acting elements

37
Q

What are the regulatory proteins derived from genes other than target gene?

A

trans-acting elements

38
Q

How many rRNA genes does a human diploid cell have, how many chromosomes, AND how are they arranged?

A

1) 400 rRNA genes
2) Arranged in tandem repeats
3) 5 chromosomes
4) Seperated by nontranscribed spacer DNA (have multiple RNA poly I at once)

39
Q

Where is the core promoter of rRNA genes located?

A

Nontranscribed spacer region of DNA

40
Q

What are the general transcription factors/selectivity factor 1 for eukaryotic RNA poly I?

A

A) 1 TATA-binding protein (TBP)

B) 3 TBP-associated factors (TAFS)

41
Q

What is the specific transcription factor for eukaryotic poly I?

A

UBF (Upstream binding factor)

42
Q

What is the role of UBF?

A

Stimulates activity of RNA poly I holoenzyme

43
Q

The core polymerase for RNA poly I consists of how many subunits?

A

10-12

44
Q

How many subunits does RNA polyII core enzyme consist of?

A

12

45
Q

What is unique about the C-terminal tail domain of RNA poly II?

A

Contains AA repeats with multiple ser residues that are phosphorylated

46
Q

What are the general transcription factors for RNA poly II?

A

TFIID, TFIIB, TFIIF, TFIIE, TFIIH

47
Q

What is the mediator?

A

It is a large coactivator complex (specific transcription factor) that contains 26 proteins that interact with the CTD of core RNA poly II and general transcription factors.

48
Q

What is the fxn of the mediator?

A

Stimulates basal transcription of genes and serves as a link btw general and specific transcription factors

49
Q

This is a consensus cis-acting sequence located -25 to -35 bp upstream of the transcription start site?

A

TATA Box

50
Q

This is a short sequence of 7-8 nucleotides that span the transcription start site? Present in 1/2 promotors.

A

Initiator sequence

51
Q

This is a consensus sequence located around -35 bp upstream of the transcription start site?

A

TFIIB recognition element (BRE)

52
Q

What general transcription factor for RNA poly II directs recruitment of the RNA polymerase II to the TATA box in the core promoter?

A

TFIID

53
Q

What GTF for RNA poly II binds to the BRE element in the core promoter?

A

TFIIB

54
Q

What 2 GTFS assemble and stabilize the initiation complex?

A

TFIIF and TFIIE

55
Q

What are the 2 main activities of TFIIH?

A

1) Helicase activity unwinds DNA in the promoter region

2) Protein kinase activity phosphorylates the C-terminal domain of the core poly II

56
Q

What triggers the elongation step for transcription/RNA poly II?

A

Phosphorylation of CTD by TFIID which releases RNA poly from the core promoter

Molecules and Energetics Block 1 (4 decks)

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