2. Chapter 13.1 - 13.4: Transcription basics in prokaryotes part 2

What will do the transcription in prokaryotes?

A holoenzyme

What does a holoenzyme made of?

A Core RNA polymerase and a sigma factor

3 main stages of transcription?

Initiation, Elongation, and termination

When is initiation done?

When the holoenzyme LEAVES the promoter region → elongation is next!

What is a consensus sequence?

A set of most common nucleotides averaged out; usually associated with an important function

How does the promoter work?

There are 2 consensus sequences within the promoter, -35 and -10. these order of nucleotides allow the system to recruit RNA polymerase to that site to start the initiation of elongation (for transcription!)

Anything -1 or below is the what region?

promoter region

briefly describe transcription in prokaryotes:

1. sigma factor + core RNA polymerase creates holoenzyme, binding to the -35 & -10 consensus sequences in the promoter 

2. holoenzyme binds to the promoter and unwinds the double-stranded DNA, where the sigma factor is released, starting the elongation process 

3. RNA nucleotides are added to the 3′ end of the growing RNA strand, and as each nucleotide is added, two phosphate groups are released 

2 types of termination:

Rho-dependent and Rho-independent

What is RUT?

Rho Utilization site

What does RUT do?

A binding site Rho can recognize and attach to

What is Rho?

A helicase enzyme that helps stop transcription by separating the RNA from the DNA template in bacteria

Explain Rho-dependent termination:

Once rho binds to the RNA, it moves toward its 3 end, following the RNA polymerase When RNA polymerase encounters the terminator, it pauses, allowing rho to catch up. The rho factor has helicase activity, which it uses to unwind the DNA–RNA hybrid in the transcription bubble, bringing transcription to an end

What is an inverted repeat?

Inverted repeats are DNA sequences where part of the strand is repeated in the opposite direction further down the same strand — like a mirror image that can fold and pair with itself.

Explain Rho-independent termination:

1. Inverted repeats in DNA → transcribed into RNA → hairpin forms

2. Hairpin causes RNA polymerase to pause

3. String of adenines (A’s) in DNA → transcribed into uracils (U’s) in RNA

4. Weak A–U bonds + hairpin → RNA–DNA hybrid destabilizes

5. RNA transcript detaches, ending transcription