Catalytic RNA

Question 1

What are ribozymes?

Answer 1

RNA molecules that catalyze chemical reactions with essential assistance of proteins

Question 2

Most ribozymes in nature catalyze ________

Answer 2

Cleavage of the RNA backbone at both sides of phosphate

Question 3

Catalytic RNAs molecular properties (4):

Answer 3

1) Fold into tertiary structures 2) Binds metal ions 3) Accept and donate protons 4) 2’-OH group

Question 4

Cleavage initiated by (3):

Answer 4

1) Internal 2’OH attack 2) Hydrolysis 3) Nucleophilic attack

Question 5

Artificial ribozymes characteristics

Answer 5

Created by in vitro selection (SELEX), not found in nature, less than 100 nt, novel RNA structural motifs, pharma

Question 6

RNA world hypothesis

Answer 6

RNA genotype and phenotype, RNA as primordial molecule

Question 7

In vitro selection, types of randomization:

Answer 7

1) Doping 2) Completely random 3) Deep random

Question 8

In vitro selection techniques

Answer 8

PCR, reverse transcription, affinity binding

Question 9

Natural ribozyme types (3):

Answer 9

1) Small self-cleaving RNAs 2) Large splicing RNAs 3) Complex catalytic RNAs

Question 10

Small self-cleaving RNAs examples

Answer 10

Hammerhead, hairpin, hepatitis delta virus (HDV), Varkud satellite (VD), riboswitch, twister, pistol

Question 11

Large splicing RNAs examples

Answer 11

Group I intron, group II intron, spliceosome

Question 12

Complex catalytic RNAs examples

Answer 12

Lariat capping, RNase P, ribosome

Question 13

Viroids characteristics

Answer 13

Smallest known pathogenic agents, hammerhead ribozyme, plants

Question 14

Reaction and products of hammerhead, hairpin, HDV, VS

Answer 14

Reaction: Self-cleavage by transesterification Products: 5’-hydroxyl and 2’,3’-cyclic phosphate termini

Question 15

Group I intron common in…..

Answer 15

Nuclear ribosomal DNA of fungi and protists

Question 16

Model system for _____ and applied in _______

Answer 16

Ribozyme, RNA, horizontal gene transfer studies, mRNA repair therapy

Question 17

Group I intron 2-step reaction:

Answer 17

1) Guanosine cofactor binds to active site, nucleophilic attack at 5’ site and cleavage 2) 3’OH of upstream exon attaches to 3’ splice site, two exons ligated and intron released

Question 18

Group II introns involved in….

Answer 18

Removal of introns, retroelements, full-length circle formation

Question 19

Spliceosome reaction and products:

Answer 19

Reaction: self-splicing via two coupled transesterification Products: Ligated exons and introns with 5’ lariat end and 3’hydroxyl

Question 20

Spliceosome and Group II introns thought to be _______

Answer 20

Related

Question 21

Lariat capping found in….

Answer 21

Eukaryote rRNA introns

Question 22

Lariat capping reaction and products:

Answer 22

Reaction: self-cleavage by transesterification Products: phosphodiester 5’-lariat end and 3’-hydroxyl

Question 23

RNase P found in….

Answer 23

All cellular organisms

Question 24

RNase P reaction and products:

Answer 24

Reaction: hydrolysis in trans Products: 5’-phosphate and 3’-hydroxyl termin Catalytic strategy: Metalloenzyme

Question 25

Ribosome found in….

Answer 25

All cellular organisms

Question 26

Ribosome reaction and products:

Answer 26

Reaction: peptidyl transfer Products: amide bond

Question 27

Ribozyme application example

Answer 27

Self-splicing group I ribozymes in mRNA reprogramming