Bacterial Transcription 2-21

what is abortive initiation

the RNA is made and then hits the sigma factor getting pushed out, so it makes it again and hits sigma factor again and get pushed out, repeats until sigma factor is knocked loose/falls off

what chalnnel on the RNA polymerase does the sigma factor block

RNA exit channel

at what point durring initiation can the sigma factor fall off

after RNA pol. escapes the promoter - chain is about 10 nucleotides in length

whats ATP- independent melting

the pin does the melting

whats ATP dependent melting

AAA+ protein binds like helicase and binds the DNA and sigma factor together, remodels and opens the DNA (ATP)for and the IHF bends the DNA

when is ATP independent melting used

when there is the -10 promoter region (TATAAT) the A-T rich don’t need extra energy to unwind

when is ATP dependent melting used

when promoter is more stable (C-G rich) needs more energy to break the 3 bonds

what is the RNA polymerase pin and what does it do

melts the DNA

what is AAA+ and what does it do

ATPase, uses atp hydrolysis to apply mechanical force to unwind DNA, bind origin of replication

what is upstream element and what does it do

found before core promoter, between ~100 to 40 bases, enhances efficiency by increasing RNA pol. recruitment

enhancer sequence and what do they do

found upstream/downstream/introns, binds transcriptional activators to boost gene expression, DNA looping to bring enhances in contact with promoter and RNA pol.

what is the IHF and what does it do

Integration host factor, bacterial binding protein that bends DNA

what is kinetic proofreading

wrong base = pol. gets jammed, exonuclease cuts of wrong base and pol is back in place to keep going

what is nucleolytic proofreading of RNA polymerase

makes the wrong base but keeps going, the rest of bases are connected, pol goes backwards and find mistake (where the H-bonds are correct) endonuclease cuts of section and starts over

what is the erroer rate of RNA polymerase

1 in 10K/100K

why is it okay that the error rate of RNA polymerase is higher then the DNA polymerase error rate

because RNA is temporary and degraded after function is fulfilled whereasa DNA is permanent

how does p (RHO) independent termination work

a hairpin is created and kicks RNA pol. so it falls off and RNA is released, most common

why is the hairpin formation at the end of the mRNA important

it tells ends the transcription

what is the difference between the stop codon and the termination sequence of RNA

stop codon - is part of mRNA sequence, end of translation, ribosome recognizes Termination sequence - part of DNA, creates the hairpin or uses the Rho, end of transcription

how does p (Rho) dependent termination work

catches up to pol. and shoves it so it falls of mRNA (uses ATP)

what is Rho

a helicase

what does Rho do to the RNA polymerase

pushes it off