Molecular Bio (Exam 2): Bacterial Transcription

RNA transcript is complementary to what strand?

template strand.

The DNA strand with the same sequence as an mRNA is what strand?

coding (sense) strand.

What is the initial product of transcription; original unmodified RNA product?

primary transcript.

What is the region of DNA where RNA polymerase binds to initiate transcription?

promoter.

What is the sequence of DNA that causes RNA polymerase to terminate transription?

terminator.

What is the DNA sequence from promoter to terminator?

transcription unit.

What is the position on DNA corresponding to the first base incorporated into RNA?

startpoint (+1).

What is the DNA sequence after the sequence of interest?

downstream.

What is the DNA sequence before the sequence of interest?

upstream.

What occurs through base pairing in a bubble of unpaired DNA?

transcription.

What stage of transcription is when the promoter is recognized, and the open complex is formed?

initiation.

What is the process in which short DNA is released until elongation starts?

abortive transcription.D

RNA polymerase does not move during which transcription stage?

initiation.

What is the stage where the transcription bubble moves along DNA and the RNA chain is extended in the 5’ to 3 direction?

elongation.

What is the stage where RNA polymerase dissociates and RNA is released?

termination.

RNA polymerase achieves what by starting elongation after abortive transcription?

promoter clearance.

Bacterial RNA polymerase consists of what two parts?

core enzyme and sigma factor.

Core enzyme in bacterial RNA polymerase is required for what?

polymerization activity.

The complete holoenzyme of the bacterial RNA polymerase is required for initiation of transcription by what?

binding to promoter.

What is the function of the 2 alpha units in bacterial RNA polymerase core enzyme?

regulation of promoter binding.

What is the function of the 1B and 1B’ units in bacterial RNA polymerase core enzyme?

polymerization.

What is the function of the sigma factor in bacterial RNA polymerase holoenzyme?

promoter recognition.

How many kinds of RNA polymerase are there in E coli?

only one.

Sigma factor is only required for what?

initiation (promoter recognition).

Sigma factor changes DNA-binding properties of RNA polymerase so that its affinity for general DNA is __________ and its affinity for promoters is __________.

reduced; increased.

Although sigma factor is required for promoter binding of RNA polymerase, it does not bind __________ by itself.

promoters.

Sigma factor is responsible for stable __________ of holoenzyme and promoter, having a half-life of several hours.

stable.

The half-life of core enzyme and any DNA complex is 1 hour, and sigma factor __________ it to <1 second.

reduces.

RNA polymerase binds to the promoter as a __________ complex.

closed.

After binding to the promoter, RNA polymerase separates DNA strands to form what?

open complex.

RNA polymerase incorporates how many nucleotides in de novo synthesis?

first two.

What makes up a ternary complex that grows RNA without polymerase movement?

RNA polymerase + DNA + RNA.

There may be cycles of __________ __________ before RNA polymerase leaves promoter.

abortive initiations.

When does RNA polymerase leave promoter and start elongation?

promoter clearance.

After promoter clearance, another RNA polymerase can initiate transcription at the same __________.

promoter.

Sigma factor controls binding to what?

promoters.

Sigma factor may be released from RNA polymerase core enzyme when the __________ RNA is elongated.

nascent.

Sigma factor association MAY be modified in a way to allow what?

promoter clearance.

Sigma factor is not required for what?

elongation.

What is an RNA chain that is still being synthesized, so that the 3’ end is paired with DNA where RNA polymerase is elongating?

nascent RNA.

What is mRNA that encodes one protein?

monocistronic mRNA.

A bacterial mRNA may be what in having several coding regions?

polycistronic.

Promoter recognition depends on what sequences?

consensus sequences.

What are sequences that represent nucleotides or amino acids most often present at a particular position?

consensus sequences.

What are sequences in which many examples of a particular nucleic acid or protein are compared, and the same individual bases or amino acids are always found at particular locations?

conserved sequences.

-35 element, -10 element, and purine at +1 are examples of what sequences?

promoter consensus sequences.

The promoter consensus sequences consist of a purine where?

at startpoint.

The promoter consensus sequences consist of a purine at start point, and what other two elements?

-10 and -35 elements.

Pribnow box is another name for?

-10 element.

Individual promoters usually differ from the __________ at one or more positions.

consensus.

Promoter efficiency can be affected by?

additional elements.

What mutations decrease promoter efficiency, and usually decrease conformity to consensus sequences?

down mutations.

What mutations increase promoter efficiency and usually increases conformity to the consensus sequences?

up mutations.

Mutations in what element can affect initial binding of RNA polymerase (i.e. closed complex)?

-35 element.

Mutations in what element does not affect the rate of open complex formation?

-35 element.

Mutations in what element affect formation of closed complex or open complex, or both?

-10 element.

-10 and -35 elements interact with?

sigma factor.

Which element is crucial for melting?

-10 element.

E coli responds to environmental changes by activating specific what?

sigma factors.

Multiple regions in RNA polymerase directly contact __________ DNA.

promoter.

Sigma70 changes its structure to expose its DNA-binding regions when it associates with __________ __________.

core enzyme.

In sigma70, what region masks DNA-binding domains (DBDs).

N-terminal.

DNA-binding domains (DBDs) in sigma70 are exposed upon binding to __________ __________.

core enzyme.

What region of alpha subunit binds UP elements.

CTD (C-terminal domain).

What is the DNA sequence that ends transcription?

terminator (t).

Actual signal for transcription termination often lies in RNA and t is located before the last __________ in the RNA

nucleotide.

What is the most common termination signal in the RNA product?

hairpin.

Which terminator depends on the hairpin structure in RNA product for release of RNA polymerase?

intrinsic terminator.

Intrinsic terminators do not require additional what?

protein factors.

Intrinsic terminators have hairpin rich in __________, followed by a region rich in __________.

G-C; U.

Which region in RNA product from intrinsic termination destabilizes RNA-DNA hybrid when RNA polymerase pauses at the hairpin?

U-rich.

The efficacy of termination depends on what 2 things?

hairpin structures (sequence), and length of U-run.

What is a terminator protein and hexameric helicase?

Rho factor.

Rho binds to __________ site on a nascent RNA.

rut.

Rho binds to rut site on a what?

nascent RNA.

Rut sequence is upstream of what?

termination site.