3 rna chain termination 4 rna chain termination

help protect the growing RNA chains from degradation by nucleases.
3) RNA chain termination 4) RNA chain termination
Occurs when RNA polymerase encounters a termination signal
The transcription complex dissociates releasing the nascent RNA molecule
There are two types of transcription terminators in E. coli
Rho-dependent terminators – req. protein factor (ρ) and rut (rho utilization) seq. on transc.
RNA
Rho-independent terminators – req. inverted repeats on complementary strand, form
hairpin, RNA poly. Falls off a 6A’s seq.
1. Cleavage of endonuclease usually occurs 30 nucleotides downstream from a conserved
polyadenylation signal (consensus AAUAAA), and upstream from a GU- rich sequence
2. Addition of poly(A) tail by poly(A) polymerase.
The actual transcription termination events often occur at multiple sites that are located 1000
to 2000 nucleotides downstream from the site that will become the 3’ end of the mature
transcript transcription proceeds beyond the site that will become the 3’ terminus
Rho-Dependent Termination Rho-Independent Termination
The mechanism by which rho-dependent termination of transcription occurs is
similar to that of rho-independent termination (i.e. both involve the formation of
hairpin structures upstream from the site of termination as hairpins impede the
movement of RNA polymerase, causing it to pause).
Rho-dependent terminators also contain additional sequences:
1) These sequences are ~50 to 90 bps upstream from the inverted repeats.
2) Rho protein binding site called rut (for rho utilization) near the 3’ end
of the transcript.
The presence of the rho protein indicates the presence of a termination signal.
When RNA polymerase encounters this signal, the transcription complex pauses
and allows the rho protein to unwind the DNA/RNA base pairing and releasing
the nascent RNA molecule.
Rho protein binds to the rut sequence in the transcript and moves 5’ to
3’following RNA polymerase.
When polymerase encounters the hairpin, it pauses, allowing rho to catch up, pass
through the hairpin, and use its helicase activity to unwind the DNA/RNA base-
pairing at the terminus and release the RNA transcript.
Rho-independent terminators contain a GC-rich region containing inverted
repeats followed by six or more AT base pairs, with the A’s present in the
template strand.
1) Transcription of inverted repeats (on complementary strand)
Sequences of nucleotides in each DNA strand that are inverted and
complementary.

2) Formation of a hairpin structure on the nascent RNA that impedes
transcription
When transcribed, these inverted repeat regions produce single- stranded RNA
sequences that can base- pair and form hairpin structures.
3) RNA Pol pauses and falls off at the ‘AAAAAA’ sequence
RNA hairpin structures form immediately after the synthesis of the
participating regions of the RNA chain and retard the movement of RNA
polymerase molecules along the DNA, causing pauses in chain extension.
AU base-pairing is weak and therefore requires less energy to separate
In prokaryotes, a mutation that deletes the region from -10 to -35 will seriously
down-regulate transcription of that gene.