Transcription in Prokaryotes and Eukaryotes

cytoplasm

transcription location in prokaryotes

Nucleus

transcription location in eukaryotes

RNA polymerase

what is the main enzymes that synthesizes cellular rna (prokaryotes)

transcription

Process in which enzymes uses one of the strands of DNA within a gene as a template to

produce a messenger RNA

initiation

what is the first step of transcription

RNA polymerase and transcription factors find to promoter region

how does initiation begin

the two DNA strands are pried apart

what happens when RNA polymerase and transcription factors bind to promoter?

pair of Mg ions

active center of RNA polymerase

enzyme

one Mg ion is tightly bounds to the

nucleoside triphosphate

one Mg ion comes in with the ____ ____ and leaves with pyrophosphate

alpha, beta, beta prime and omega

what are the subunits of RNA polymerase

sigma factor

co-factor of RNA polymerase

alpha

subunits that is part of assembly and activation of enzymes

beta

subunit that binds to DNA

beta prime

subunit that binds to NTPS and interacts with sigma

omega

subunit that helps in maintaining the plasticity of the active site of RNA

polymerase

sigma

subunit that recognizes promoter sequences on DNA

Holoenzyme

when the sigma factor binds to RNA polymerase what does it become

it is released

what happens to the sigma factor when transcription begins

consensus sequence

bases appearing with the highest frequency

at each position when a series of sequences with a common function

it positions RNA polymerase correct to ensure accurate initiation of transcription

why is the consensus sequence important

promoter sites

RNA polymerase binds to _____ _____ on the DNA template to initiate transcription

Pribnow box (TATAAT) and TTGACA

what are the two consensus sequences of promoter sites in prokaryotes

TATAAT (Pribnow box)

-10 consensus sequence (prokaryotes)

TTGACA

-35 consensus sequence (prokaryotes)

Basal promoter sequence

controls the frequency of transcription initiation at promoter sequences

sense strand

what strand has the same sequence of mRNA (except T is U)

antisense/template strand

what strand generate the mRNA

forms phosphodiester bond

how does elongation of prokaryotic RNA synthesis begin

5' to 3'

what direction if RNA synthesized

3 to 5

What direction is DNA read?

RNA polymerase synthesizes a 10 nucleotide long polynucleotide

what has to happen for the RNA polymerase to stay bound to the DNA strand

reaches the stop signal: Palindromic

GC region followed by AT region

what determines where transcription is terminated

hairpin loop

Palindromic regions forms what type of loop

pauses

what does RNA polymerase do at the hairpin loop

its unstable due to rnaU-dnaA base pair

what is the effect of the hairpin loop on the RNA-DNA hybrid helix

rho factor

ATP- dependent helicase that binds the nascent RNA chain and pulls it away from RNA polymerase and the DNA template.

Rifampicin

inhibits initiation by binding to the polymerase and blocking the

exit of the nascent RNA.

Actinomycin

intercalates between the bases of the DNA double helix, preventing the DNA from being used as a template.

closely coupled

Transcription and translation in prokaryotes are

spatially and temporally separate

Transcription and translation in eukaryotes are

nuclear membrane

separates the site of RNA synthesis from that

of protein synthesis (eukaryotes)

23s, 16s, and 5s

what are the sedimentation coefficients in prokaryotes

28s, 18s, 5.8s

what are the sedimentation coefficients in eukaryotes

three

eukaryotes have ____ DNA polymerases compared to prokaryotes one

located in nucleolus and synthesizes rRNA (18, 18, 5,8)

DNA Polymerase I

located in nucleoplasm and synthesizes mRNA

DNA Polymerase II

located in nucleoplasm and makes tRNA and 5s rRNA

DNA Polymerase III

α-amanitin

Eukaryotic RNA polymerases differ in sensitivity to

the toxin

Insensitive

α-amanitin: DNA poly I

inhibited

α-amanitin: DNA poly II

inhibited at high concentrations

α-amanitin: DNA poly III

Ribosomal initiator element (rInr) + Upstream promoter element (UPE)

what is the promoter regions for DNA Poly I

Enhancer element + Ribosomal initiator element (rInr) + TATA box

OR

Enhancer element + Ribosomal initiator element (rInr) + Downstream promoter element (DPE)

what is the promoter regions for DNA Poly II

5s rRNA (type I) - A and C block

tRNA (type II) - A and B block

what is the promoter regions for DNA Poly III

TATA box

consensus sequence Located between positions -30 and -100 bp upstream of the initiation site in eukaryotes

Initiator element (Inr),

located between -3 and +5 bp and often paired with the

TATA box.

Downstream core promoter element (DPE)

- Located between +28 and +35 bp,

which works in cooperation with Inr when the TATA box is absent.

CAAT box and GC box

- Located between -40 and -150 bp upstream. The GC box is

common in genes that are continuously expressed.

transcription factors

RNA Polymerase need ___ ________ to interact with promoters

Transcription factor II D (TFIID)

recognizes TATA box and initiates assembly of active transcription complex

TATA binding protein (TBP)

component of TFIID that is bound to TATA box

TFIIA, B, D, E, F, and H

H helps RNA Polymerase II to bind to form

basal transcription complex

TFIIH

helicase transcription factor that opens the DNA double helix

phosphorylates

TFIHH also has kinases which ___ the carboxyl terminal domain

CstF and CPSF

what factors contribute to the addition of the poly A tail

polyA tail

Polyadenylation of a primary transcript at 3' end

• Helps maintain the stability of mRNA molecules.

• Help move mRNA out of the nucleus

• Protects the mRNA from exonuclease digestion

PolyA tail function

no

does mature-mRNA contain introns

splicing

the process of removing introns and reconnecting exons in a pre-mRNA

introns

Noncoding segments of nucleic acid that lie between coding sequences.

there are two consensus sequences on the 5' and 3' end

how do you identify splice sites

AGGUAGGGU - begins at first GU

consensus sequence of intron at 5'

10C/Us X CAG

consensus sequence of intron at 3' end

branch site

internal site location between 5' and 3' region of intron

two transesterification

what type of reactions does splicing involve

precursor to transesterification reactions

2'OH attacks phosphate between exon and 5' intron.

transesterification 1

2'—5' - phosphodiester bond is

formed between A residue and 5'-

phosphate

free 3' OH group on exon 1

what is generated at the end of transesterification 1

transesterification 2

3'OH group attacks phosphodiester bond between intron and exon 2

lariat form

after exons are joined what type of intron is released

5' cap

guanosine triphosphate is reacted with guanylyl transferase that forms a modified guanonsine nucelotide on 5' end of mRNA

5' cap

Methylation of 7 position of guanine nucleotide located at the 5'-end of eukaryotic pre-mRNAs forms the

protects form nucleases, enhance translation, and enhanced transport

5' cap functions

Ribozymes

RNA molecules that can catalyze chemical reactions,

Tetrahymena with guanosine cofactor

what is an example of a riboenzyme

intron is releases and splices itself twice to form a linear RNA

how does Tetrahymena work