Catalytic RNA Flashcards
(27 cards)
What are ribozymes?
RNA molecules that catalyze chemical reactions with essential assistance of proteins
Most ribozymes in nature catalyze ________
Cleavage of the RNA backbone at both sides of phosphate
Catalytic RNAs molecular properties (4):
1) Fold into tertiary structures 2) Binds metal ions 3) Accept and donate protons 4) 2’-OH group
Cleavage initiated by (3):
1) Internal 2’OH attack 2) Hydrolysis 3) Nucleophilic attack
Artificial ribozymes characteristics
Created by in vitro selection (SELEX), not found in nature, less than 100 nt, novel RNA structural motifs, pharma
RNA world hypothesis
RNA genotype and phenotype, RNA as primordial molecule
In vitro selection, types of randomization:
1) Doping 2) Completely random 3) Deep random
In vitro selection techniques
PCR, reverse transcription, affinity binding
Natural ribozyme types (3):
1) Small self-cleaving RNAs 2) Large splicing RNAs 3) Complex catalytic RNAs
Small self-cleaving RNAs examples
Hammerhead, hairpin, hepatitis delta virus (HDV), Varkud satellite (VD), riboswitch, twister, pistol
Large splicing RNAs examples
Group I intron, group II intron, spliceosome
Complex catalytic RNAs examples
Lariat capping, RNase P, ribosome
Viroids characteristics
Smallest known pathogenic agents, hammerhead ribozyme, plants
Reaction and products of hammerhead, hairpin, HDV, VS
Reaction: Self-cleavage by transesterification Products: 5’-hydroxyl and 2’,3’-cyclic phosphate termini
Group I intron common in…..
Nuclear ribosomal DNA of fungi and protists
Model system for _____ and applied in _______
Ribozyme, RNA, horizontal gene transfer studies, mRNA repair therapy
Group I intron 2-step reaction:
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
Group II introns involved in….
Removal of introns, retroelements, full-length circle formation
Spliceosome reaction and products:
Reaction: self-splicing via two coupled transesterification Products: Ligated exons and introns with 5’ lariat end and 3’hydroxyl
Spliceosome and Group II introns thought to be _______
Related
Lariat capping found in….
Eukaryote rRNA introns
Lariat capping reaction and products:
Reaction: self-cleavage by transesterification Products: phosphodiester 5’-lariat end and 3’-hydroxyl
RNase P found in….
All cellular organisms
RNase P reaction and products:
Reaction: hydrolysis in trans Products: 5’-phosphate and 3’-hydroxyl termin Catalytic strategy: Metalloenzyme
