RNA World

Question 1

What is the structure of the group 1 intron ribozyme?

Answer 1

A rich bulge
Tetraloop
tetraloop receptor

Question 2

What catalytic mechanism does the ribozyme have?

Answer 2

Either acid/base catalysis or 2 divalent metal ions

Question 3

What catalytic mechanism does the spliceozyme have?

Answer 3

G nucleophilic attack onto the 3’ intron induced by free GTP

Question 4

How does the spliceozyme detect sequence?

Answer 4

Complex coiled shape produces active site by self base pairing

Question 5

Who first observed RNA self splicing?

Answer 5

Tom Cech by removing all protein from solution

Question 6

How long is self splicing RNA?

Answer 6

100s of nucleotides

Question 7

What did Sidney Altman study?

Answer 7

RNase P to determine catalytic component is RNA

Question 8

Who studied the prebiotic soup?

Answer 8

Miller and Urey

Question 9

What did the prebiotic soup experiment show?

Answer 9

Amino acids, nucleotides and oxyribose sugars could be synthesised in basic environment

Question 10

What small molecules are contained in the prebiotic soup?

Answer 10

Water,
Hydrogen
Methane
Ammonia

Question 11

How were the products of the prebiotic soup observed?

Answer 11

Aromatic chromophores

Question 12

Why are polymerases needed?

Answer 12

Natural polymerisation occurs too slowly for sustain organisms with a defined lifespan

Question 13

What does the Hammerhead ribozyme show?

Answer 13

The viriod contains no peptide sequences but can self replicate using 20nt within a 200nt cRNA linear product folded into 3D structure

Question 14

Which virus has the Hammerhead ribozyme?

Answer 14

Cadang Candang virus

Question 15

What can RNA be modified into?

Answer 15

Cofactors

deoxyribose sugars for DNA

Question 16

What are the key catalytic properties of RNA?

Answer 16

U not T
2'OH
Spontaneously forms tertiary structure
Base pairs
Binds metal ions

Question 17

What is the most common ribozyme?

Answer 17

ribosome

Question 18

How are deoxyribonucleotides produced?

Answer 18

Ribonucleotide reductase

Question 19

How does the structure of the ribosome prove the RNA is catalytic?

Answer 19

Positive residues for PO3-

No peptides near peptidyl transferase site

Question 20

How much DNA is transcribed compared to how much codes for proteins?

Answer 20

95% compared to 1%

Question 21

How does RNA act as a regulator?

Answer 21

Forming secondary structures to block RBS or terminate transcription

Question 22

How does RNA interact with ligands?

Answer 22

Riboswitches of mRNA bind ligands to switch translation on/off

Question 23

How have riboswitches been observed?

Answer 23

Xray crystallography

Question 24

Which direct are SELEX oligonucleotides synthesised?

Answer 24

3’ to 5’ on a immobilised support such as biotin/streptavidin to a polystrene bead

Question 25

What is the structure of a SELEX nucleotide?

Answer 25

An aptamer of Primer-random-primer

Question 26

Why is negative selection required for SELEX?

Answer 26

No target sequence so identifies NSB

Question 27

What is the SELEX cycle?

Answer 27

Add library fragments to target/bead complex
Wash to remove fragments
Elute bound ligand
Amplify by PCR

Question 28

How is NextGen sequencing used with SELEX?

Answer 28

To identify RNA aptamers that bind to different parts of the target sequence.
Modification of RNA polymerase for in vitro synthesis

Question 29

What have RNA aptamers been used for?

Answer 29

Administered in vitro to antagonise EFGR receptors to prevent angiogenesis in macular degeneration

Question 30

What is SELEX?

Answer 30

Systematic Evolution of Ligands by Exponential Enhancement