PCB 4524- Exam 1

Promoter

region of DNA where RNA polymerase binds to initiate transcription

Terminator

sequence of DNA that causes RNA polymerase to terminate transcription.

Start point (Start site)

the position on DNA corresponding to the first base incorporated into RNA

transcription unit

the sequence between a site of initiation and termination by RNA polymerase; may include more than one gene

UP element

increases strength of interaction between RNA pol and bacterial promoter

directly upstream of -35 element (around -40 to -60)

Upstream

identifies sequences in the opposite direction from expression;

for example, the bacterial promoter is upstream of the transcription unit, the initiation codon is upstream of the coding region

Downstream

identifies sequences proceeding farther in the direction of expression;

for example, the coding region is downstream of the initiation codon

primary transcript

the original unmodified RNA product corresponding to a transcription unit.

Sigma factor (σ)

• Confers RNAPol with promoter specificity

• Promotes isomerization (DNA melting)

• part of holoenzyme

Regulon

genes (bacteria) under the coordinated control of a single regulatory mechanism

Holoenzyme

Formed when the core enzyme binds to a helper protein called a sigma (σ) factor.

This complete complex targets specific promoter sequences on DNA to start transcription accurately.

Once transcription begins, the sigma factor usually falls off, leaving the core enzyme to finish the job

Pyrophosphorolytic editing

Removes single misincorporated nucleotide using PPi

Hydrolytic editing

Backtracking and hydrolysis of several nucleotides

DNA footprinting

identify the exact binding sites of proteins (like transcription factors) on a specific DNA sequence

When a protein binds to a specific region on a DNA fragment, it protects that underlying sequence from being cut by an added enzyme or chemical

EMSA

test used to detect interactions between proteins and nucleic acids like DNA or RNA

based on observation that DNA fragments migrate quicker through polyacrylamide gel than the same fragment that’s binded to a protein

Transcription in-vitro Assay

synthesize RNA molecules from DNA in a test tube

ChiP sequencing

Transcription Factors

any DNA binding protein playing a role in transcription, activators, repressors

Needed for initiation in eukaryotes

GTFs (General Transcription Factors)

RNAPol 2 requires 6 GTFs: TFIIA, B, D, E, F, H

TBP

-monomeric

TATA box

highly conserved promoter in eukaryotic DNA

Initiator element (Inr)

DPE (downstream promoter element)

TFIID

TFIIA

TFIIB

TFIIH

TFIIE

TAFs

TBP-associated factors

SP1

Activators