RNA in prokaryotes

Question 1

What is lnc RNA?

Answer 1

200+ nucleotides, includes riboswitches that regulate molecular biology but they don’t encode aa peptide/ protein.

Question 2

What are CRISPR RNA?

Answer 2

Natural CRISPR-Cas immunity and adaptive immune system in prokaryotes. Transcribed pre-cRNA is then nucleolytically processed to cRNA which provides the immune response.

Question 3

What is sgRNA?

Answer 3

Engineered single guide RNA for CRISPR.

Question 4

What is an R loop?

Answer 4

RNA loop. RNA strand with a certain sequence that is complementary to a DNA strand. Can access the DNA and displace a strand on the DNA so that the single strand forms a loop.

Question 5

What does CRE mean?

Answer 5

R loop formation by lncRNA in cis is an example of CRE. A cis regulatory element. This means that the regulatory element is on the same DNA molecule as the gene it is regulating.

Question 6

What is a riboswitch?

Answer 6

Control gene expression in response to something. Prokaryotic biology. e.g., a metabolite or ion or temperature. Without involvement from a specialized protein receptor. RNA bind small organic molecules via an aptamer domain.

Question 7

What does the aptamer domain do?

Answer 7

Changes its shape. That instructs the second domain called the expression platform that in turn directs the gene expression outcome.

Question 8

How does the riboswitch regulate gene expression?

Answer 8

Altered confirmation on ligand binding. This prevents transcription or translation.

Question 9

What is an example of a riboswitch?

Answer 9

Binding to a metal ion. Could be a 10 mark exam qs!

Question 10

How does a riboswitch function?

Answer 10

Example. Detoxifying magnesium inside bacterial cells. The gene mgtE that encodes Mg2+ transporter. Switches the genes ability to deal with Mg.

Question 11

What is a hypothesis of CRISPR systems and riboswitches?

Answer 11

Anti-Pcas is a glycine sensitive riboswitch. Regulates how the CRISPR system switches on and off. Dont know what binds to it yet.

Question 12

What is the CRISPR site?

Answer 12

The immune system.

Question 13

How does the CRISPR system work?

Answer 13

Protospacer is captured and processed as a prespacer.
Then integrated into a cRISPR array which is a locus of fragments.
- Building of CRISPR immune system.
- Then expression stage.
- Transcribed to ncRNA. Called pre-cRNA.
- CRISPR-Cas effector complex is then transcribed.

Question 14

What is crRNA?

Answer 14

The scaffold to deliver the CRISPR-Cas immune response by immunity proteins and is the basis of gene editing. Digital code for destruction.

Question 15

What is the arrangement of cRNA in prokaryotes?

Answer 15

cRNA is bound to a cascade these then join to Cas3 (nuclease helicase).

Question 16

Why use cognate DNA?

Answer 16

CRISPR RNA is single stranded. but have to base pair it with cognate DNA so it is rigid so xrays work to see the atoms.

Question 17

What are the two main responders used in CRISPR?

Answer 17

cRNA + cascade, Cas3. AND tracrRNA + Cas9. Cas9 is used in gene editing as easier to use however more complicated structure.

Question 18

How does crRNA underpin the immune response?

Answer 18

Forms an R loop at invader DNA. The cascade has a stem loop. Forms an R loop as the crRNA displaces a single strand of one of the double strands. Formation of R loop causes destruction of the virus and immunity.