Transcription Part I

Front 1

First Step of Transcription

Back 1

Initiation

Hint 1

sigma subunit binds to consensus sequence - RNA Polymerase helicase unwinds 17 bp to form open promoter

Front 2

Second Step of Transcription

Back 2

Elongation

Hint 2

-RNA Polymerase generates transcription bubble (17 bp unwound, 12 bp RNA/DNA duplex)
-topoisomerases prevent supercoiling

Front 3

What supercoiling is caused by unwinding DNA? How is it prevented?

Back 3

positive supercoiling; prevented by negative supercoiling ahead of transcription bubble by Topo II

Hint 3

Negative supercoiling behind transcription bubble is relaxed by Topo I

Front 4

Significance of sigma subunits

Back 4

sigma subunits give specificity, create high affinity binding that directs poly holoenzyme to promoter

Hint 4

bind preferentially to a consensus sequence in the promoter of a certain gene

Front 5

Protein subunits of prokaryotics RNA polymerase

Back 5

alpha - binds regulatory proteins with omega subunit
beta - phosphodiester bond formation, grasps DNA
beta prime - grasps DNA template
sigma - promoter recognition and initiation

Front 6

closed promoter complex

Back 6

RNA polymerase searches for promoter site by sliding along double stranded DNA; sigma subunit binds specifically to promoter sequences to form closed promoter complex

Hint 6

consensus sequences are derived by determining the base found most frequently at each position in the promoter region of the gene

Front 7

open promoter complex

Back 7

RNA polymerase unwinds 17 bp of DNA around initiation site to form the open promoter complex

Hint 7

first phosphodiester bond is formed during initiation; sigma subunit is released upon completion of the initiation step --> elongation by core RNA polymerase

Front 8

RNA polymerase I

Back 8

rRNA in nucleolus

Front 9

RNA polymerase II

Back 9

mRNA in nucleus (also miRNA)

Front 10

RNA polymerase III

Back 10

tRNA, 5 S rRNA, U6 snRNA in nucleus

Front 11

How does RNA polymerase I function in production of ribosomes?

Back 11

RNA Poly I transcribes tandem repeats of rRNA genes to generate 45 S pre-rRNA; multiple RNA Poly I enzymes transcribe each gene

Hint 11

Components:
Core Polymerase I: 10-12 subunites
General Transcription Factors (Selectivity Factor I): 1 TATA binding protein (TBP); 3 TBP associated factors (TAFs)
Specific Transcription Factor: Upstream Binding Factor (UBF) stimulates activity of holoenzyme (recognize and recruit)

Front 12

Components of Poly II Holoenzyme

Back 12

Core RNA polymerase: C-terminal tail domain contains multiple Ser residues that are phosphorylated
General Transcription Factors: TFIID, TFIIB, TFIIF, TFIIE, TFIIH
Specific Transcription Factors: Activator proteins, repressor proteins, coactivators and corepressors that regulate specific gene transcription
Mediator: Large, 26 protein complex that interacts with CTD and GTFs

Front 13

cis-Acting Elements

Back 13

SEQUENCES of DNA on the same molecule as the gene

Hint 13

Core promoter; proximal promoter elements, enhancers, silencers

Front 14

trans-Acting Factors

Back 14

PROTEINS derived from genes other than the target gene

Hint 14

General and Specific transcription factors, mediators

Front 15

RNA Poly I General Transcription Factors

Back 15

Selectivity Factor 1; 1 TATA-binding protein (TBP); 3 TBP-associated Facts (TAFs)

Hint 15

POLY I produces 45 S Pre-rRna Transcript in nucleolus

Front 16

RNA Poly I Specific Transcription Factors

Back 16

Upstream Binding Factor (UBF) stimulates activity of Poly I holoenzyme

Hint 16

UBF is a trans-acting factor, which bind the cis-acting Promoter Sequence

Front 17

RNA Poly II General Transcription Factors

Back 17

TFs:
TFIID (TBP + TAFs) - General transcription factor that directs recruitment of RNA Poly II to the TATA box (TBP binds directly to TATA box)
TFIIH - Helicase activity unwinds DNA in promoter region; protein kinase phosphorylates C-terminal domain of the Core Poly II)
TFIIB, TFIIF, TFIIE

Hint 17

Phosphorylation of CTD by TFIIH releases Poly II from promoter so it can transcribe DNA template during elongation phase

Front 18

RNA Poly II Specific Transcription Factors

Back 18

Activator Proteins, Repressor proteins, coactivators and corepressors

Hint 18

POLY II produces mRNA, miRNA, U1, U2, U4, U5 snRNA transcripts in nucleus

Front 19

TATA Box

Back 19

Consensus cis-acting sequences located 25-30 bp upstream of the transcription start site

Hint 19

TBP (TATA Binding Protein) binds directly to TATA box; Element of Core Promoter, recruits Poly II holoenzyme

Front 20

BRE

Back 20

TFIIB Recognition Element - Consensus Sequence located 35 bp upstream of transcription start site

Hint 20

Element of Core Promoter; recruits Poly II holoenzyme

Front 21

TFIID

Back 21

complex of:
TATA Binding Protein (TBP) binds directy to TATA box in core promoter
TBP-Associated Factors (TAFs) modify TBP binding, assist in TBP recognition of core promoters

Hint 21

General transcription factors that directs recruitment of Poly II to TATA box in core promoter

Front 22

TFIIH

Back 22

Helicase activity unwinds DNA in promoter region

Protein Kinase activity phosphorylates C-terminal Domain (CTD) of Core RNA Poly II

Hint 22

Phosphorylation of CTD by TFIIH release RNA Poly II from core promoter to transcribe DNA template during elongation

Front 23

TFIIB

Back 23

Binds to BRE (TFIIB Recognition Element) in Core Promoter - also binds to TBP, TFIIF, and TFIIE

Front 24

Mediator

Back 24

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