Proteins: The RNA World Flashcards
Why is it thought that RNA is key to the beginning of life?
Believed that a self-replicating RNA ribozyme is key to splicing process. Therefore splicing is RNA dependent and requires a guanine nucleotide and covalent metal ions.
How would a ribozyme be formed?
1) RNA molecules linear sequence folds up into a complex structure generating an active site with a guanine nucleotide in
2) The 3’-OH is the critical thing from the sugar residue performs a nucleophilic attack on a phosphodiester
3) Cleavage then generates a free 3’-OH which undergoes nucleophilic attack to a specific site on the RNA.
4) A covalent bond forms between the 3’ end and of the first exon and the 5’ end of the third exon to give a mature RNA product.
What do ribozymes catalytic properties depend on?
That they contain uridine not thymidine, they contain a 2’ ribose, they fold spontaneously into complex 3D structures, they’re base pairing and they bind metal ions.
Why do eukaryotic gene breaks simple co-linearity?
As the have the process of placing exons and removing introns.
What are ribozymes able to do?
They have catalytic activity and can be substrates for carrying genetic information.
Who did an experiment to recreate the origins of life?
Miller and Urey.
How did they do the experiment to recreate the origins of life?
A flask with water in which was heated by a spark chamber and gases above that get exposed to these elements. The water is then sampled for living organisms.
What did Miller and Urey find?
Nucleotides, amino acids and ribose sugars, suggesting that very early atmospheric chemistry could have generated the precursors of the modern biological polymers that are in the central dogma which were RNA not DNA as 2’ deoxy ribose could not be made.
What chemistry suggests that RNA is at the base of all life?
That many modern enzymes have cofactors that ate ribonucleotide derivatives as they have 2’ hydroxy which is essential for cellular activities.
What does the self splicing intron tell us about how likely it is that RNA is at the base of life?
The self-splicing intron is 100s of nucleotides long which is unlikely to be made but short RNA catalysts are probable. For example viroids that contain no proteins encoding for genes but are self splicing with a hammerhead ribozyme.
What converts ribonucleotides to 2’deoxyribonucleotides?
Ribonucleotide reductase
What is SELEX?
Systematic evolution of ligands by exponential enrichment: a method to produce single-stranded oligonucleotides of RNA or DNA which specifically bind to a target ligand/s.
How does SELEX work?
Starts with the synthesis of a very large oligonucleotide library of randomly generated sequences if a fixed kebabs flanked by constant 5’ and 3’ ends as primers. The sequences are exposed to the target ligand (a protein or small organic compound) and those that do not bind are removed by affinity chromatography. The bound sequences are eluted and amplified using PCR and the method is repeated.
