Transcription Flashcards by Kimberly Fender

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

Mg+2

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What are the 3 main steps of transcription?

Initiation, Elongation, and Termination

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What direction is RNA synthesized?

5’ to 3’

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

3’ to 5’

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Is a primer required in RNA synthesis?

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

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How many RNA polymerases do prokaryotes have?

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

Binds regulatory proteins with the “w” subunit

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

Phosphodiester bond formation AND grasps DNA

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

Grasps DNA template

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

Promoter recognition and initiation

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

Sigma subunit

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

Promoter (typically contains 2 consensus sequences)

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How is a consensus sequence determined?

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

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

Sigma subunit

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

The sigma subunit

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

Helicase activity in RNA poly unwinds 17 bp of DNA

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What is the main fxn of the sigma subunit?

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

Sigma subunit of the holoenzyme

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The sigma70 unit is for what kind of promoter?

standard

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The sigma32 unit is for what kind of promoter?

heat shock

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The sigma 54 unit is for what kind of promoter?

Nitrogen-starvation genes

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What does the transcription bubble consist of?

1 )Unwound region: 17 bp of DNA

2) RNA/DNA duplex=12 bp

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

Gyrase (Type II)

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

Type I topoisomerase

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

A) Template-directed Termination | B) Rho-directed Termination

What is template-driven termination?

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)

What is rho-driven termination?

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

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

1) 45 S Pre-rRNA Transcript (5.8S, 18S, 28S rRNAS) | 2) Nucleolus

What are the products/location of eukaryotic RNA polyII?

1) mRNA, miRNA, U1, U2, U4, U5, and snRNA | 2) Nucleus

What are the products/location of eukaryotic RNA polyIII?

1) tRNA, 5 S rRNA, and U6 snRNA | 2) nucleus

What are the products/locatio of mitochondrial RNA poly?

1) All mitochondrial RNAs | 2) mitochondria

What are the 4 components of Eurkaryotic RNA poly?

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

What are general transcription factors?

Proteins required for basal transcription of ALL genes

What are specific transcription factors?

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

What are mediator proteins?

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

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

cis-acting elements

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

trans-acting elements

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

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)

Where is the core promoter of rRNA genes located?

Nontranscribed spacer region of DNA

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

A) 1 TATA-binding protein (TBP) | B) 3 TBP-associated factors (TAFS)

What is the specific transcription factor for eukaryotic poly I?

UBF (Upstream binding factor)

What is the role of UBF?

Stimulates activity of RNA poly I holoenzyme

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

10-12

How many subunits does RNA polyII core enzyme consist of?

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

Contains AA repeats with multiple ser residues that are phosphorylated

What are the general transcription factors for RNA poly II?

TFIID, TFIIB, TFIIF, TFIIE, TFIIH

What is the mediator?

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.

What is the fxn of the mediator?

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

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

TATA Box

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

Initiator sequence

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

TFIIB recognition element (BRE)

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

TFIID

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

TFIIB

What 2 GTFS assemble and stabilize the initiation complex?

TFIIF and TFIIE

What are the 2 main activities of TFIIH?

1) Helicase activity unwinds DNA in the promoter region | 2) Protein kinase activity phosphorylates the C-terminal domain of the core poly II

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

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