prokaryotic RNA regulation

Question 1

what kind of ribosomoal concensus sequence do euk use?

Answer 1

Kozak concenus sequence

Question 2

what kind of ribosomoal concensus sequence do prok use?

Answer 2

Shine-Dalgarno sequence on the mRNA is the ribosomal binding site

and is complementary to the anti-SD to the 16S small ribosomal subunit

Question 3

what is the point of having the Ribosomal binding site?

Answer 3

the RNA-RNA (mRNA and ribosome) interactions allow for proper alignment of the ribosome on the mRNA molecule at the open reading frame

Question 4

how can the ribosomal binding site regulate translation initiation in prokary?

Answer 4

having a strong concensus sequence will allow efficient pairing of ribosome
will be recruited quicker so quicker translation

also the DISTANCE of the RBS to the start codon can also influence stenght of interaction as the AUG can sit perfectly within the ribosomoe decoding site (no need for scanning)

Question 5

what is a concensus sequence

Answer 5

series of highly frequent nucleotides or amino acids, conserved across different species

Question 6

what are riboswitches?

Answer 6

sections of a RNA molecule with an extensive folded secondary strucuture and can act as on/off switches

areas of d.s RNA and s.s DNA

Question 7

Which organisms can riboswitches be found?

Answer 7

they are wide spread in bacteria

very rare in Euk

Question 8

what is the function of riboswitches

Answer 8

they can act as sensors for the environment (heat, temp, salt, metal ions) and can regulate translation

regulate gene expression

Question 9

describe a way (general) how riboswitches can control translation initiation

Answer 9

riboswitches can change the accessbility to the Shine-D (RibosomalBS) in response to a metabolite

through conformational change (d.s DNA or s.s DNA)

Question 10

name an example of a riboswitch controlling a riboswitch

Answer 10

adenosyl methionine synthase can be controlled by a riboswitch

Question 11

name an example of a thermometer (riboswitch)

Answer 11

Listeria uses a riboswitch to control expression of its virulance genes

at high temp the transcriptional activator for the virulance genes is able to be transcribed

Question 12

how does a temperature sensing riboswitch work?

Answer 12

thermometers have weakly complementary regions at low temperatures and blocks the RBS, preventing translation initiation

at higher temp, this unstable secondary structure unfolds and exposes the RBS allowing ribosomal recruitment

Question 13

what is attenutation?

Answer 13

• reduce the force/ effect of something

in genetics, translation can feedback on transcription leading to premature transcription terminiation

Question 14

in the trp operon, what happens if there is low amounts of tryptophan in the environment?

Answer 14

as there is not enough charged trp-tRNA molecules
ribosome gets stalled

so region 2-3 stem loop form creating antitermination strucutre ALLOWING translation elongation

Question 15

in the trp operon, what happens if there is high amounts of tryptophan in the environment?

Answer 15

translation of region 1 and region 2 of leader peptide occurs quickly
region 3+4 complementary base pair creating termination structure

translation is terminated, operon is repressed and energy resources are conserved

Question 16

describe the trp operon

Answer 16

encodes 5 protein coding genes needed for tryptophan synthesis

regulatory elements including promoter, operator region (which can be bound to a trp repressor protein) and leader region

Question 17

describe the leader region of the trp operon

Answer 17

made up of 4 regions and can create different stem loop structure depending on rate of ribosomal activity

region 1 encoded a 14aa long leader peptide with 2 trp codons - can respond to levels of translation

Question 18

what is the main difference between E and P in RNA processig

Answer 18

Pro do not have RNA-processing
transcript+translate occur simultaneously so there is no need for nuclear export
And in sane location