Transcription in Prokaryotes

rRNA

ribosomal RNA, makes up ribosomes

DNA-directed RNA polymerase

synthesizes RNA from a DNA template, only one in prokaryotes, at least three in eukaryotes

E. Coli RNA polymerase

pentamer core enzyme with 4 types of subunits (a, B, B’, w) bound to a sigma factor

a subunit of RNA Pol in E. Coli

performs enzyme assembly and initiation

B subunit or RNA pol in E. Coli

binds Nucleotides and performs initiation and elongation

B’ subunit of RNA pol in E. Coli

binds the DNA template strand

w subunit of RNA pol in E. coli

stabilizes the enzyme and assists in folding

sigma factor of RNA Polymerase in E.Coli

a protein that binds the core enzyme of RNA polymerase to form the holoenzyme, changes the DNA binding properties of RNA polymerase and increases affinity to bind specific sequences

+1 site

first nucleotide to be transcribed, initiation site

-1 site

the last nucleotide to not be transcribed

Promotor

initiation site (+1), pribnow region (-10 region), -35 region

pribnow region

a highly conserved region of DNA in the -10 region, TATAAT, which interacts with the sigma factor to allow RNA polymerase to bind

-35 region

a highly conserved region of DNA, TTGACA, which interacts with the sigma factor to allow RNA polymerase to bind

step one of transcription

nonspecific binding of holoenzyme and migration to the promotor

step two of transcription

formation of a closed-promotor complex when DNA polymerase recognizes promotor sequence

step three of transcription

formation of an open-promotor complex, DNA ‘unzips’

step four of transcription

initiation of mRNA synthesis, usually with a purine

abortive initiations

only 2-9 nucleotides are transcribed and then it falls off, most initiations!

step 5 of transcription

elongation of mRNA by about 8 more nucleotides

step 6 of transcription

release of sigma factor as RNA polymerase proceeds

Coding Strand

the non-template DNA strand, RNA pol moves along in the 5’-3’ direction of this strand; mRNA is identical with U for T

Non coding strand

template DNA strand, RNA pol moves in 3’-5’ direction, mRNA is complementary to this strand

Rate of transcription

sequence dependent, slower than replication (slows in GC rich areas), 20-50 nucleotides per second

DNA:RNA double helix

about 8 bp region that forms a hybrid double helix as mRNA is transcribed

error rate of transcription

about 1 in 10⁴, much more error filled than DNA replication

p-dependent termination

rho factor binds to a C rich region of transcript (rho utilization site), rho factor advances in the 5’-3’ direction towards replication bubble, rho factor catalyzes unwinding of hybrid double helix, when it catches up to RNA polymerase transcription is terminated

rho factor (p)

a hexameric helicase, made up of 6 identical structures

p-independent termination

termination occurs at a palindromic GC-rich region followed by an AT rich region, GC-rich palindrome forms hairpin structure causing RNA pol to pause, following AT-rich region has weak RNA:DNA hybrid bonding so the mRNA is released

palindrome

5’-3’ sequence on one strand is the same as the 5’-3’ sequence on the complementary strand

transcription in prokaryotes

transcription and translation occur in the cytoplasm, mRNA can be translated as it is still being transcribed

transcription in eukaryotes

transcription occurs in the nucleus while translation occurs in the cytoplasm, pre-mRNA must be processed by splicing, 5’cap and poly-A tail

plus-sense, single stranded RNA virus

the RNA virus can be translated immediately to form proteins and also replicated to make more RNA

minus-sense, single stranded RNA virus

the RNA virus must be first translated to mRNA so it can be translated to form proteins, and can also be replicated to form more RNA

double stranded RNA viruses

the RNA must first be transcribed to plus-sense mRNA which is then replicated or translated

RNA-dependent RNA polymerase

a protein that is able to transcribe RNA from other RNA molecules, lacks proof reading, mistake prone

Retroviruses

infects cells with viral RNA and reverse transcriptase, which integrates the viral RNA into the Cells genome, the viral DNA codes for all materials needed for more viruses to be produced in the cell