M116 Midterm Questions and Correct Answers
Guaranteed A+!
Can we predict RNA secondary structures, specifically helices ?
Yes, we can predict helical regions by, e.g. 'Free energy minimization'
Computer algorithm searches
However, the above algorithms are not very reliable: There may be many alternate (equally
stable) base-pairing arrangements
How can you determine RNA secondary structure experimentally
co-variation analysis', and by physical probing
How to do the experiment ..(1) 32P end-label (*) the RNA to be examined(2) Incubate with
nuclease under conditions that achieve (on average) just a single hit per RNA molecule (3)
Electrophorese the reaction products in a denaturing gel(4) Autoradiograph the gel
RNA tertiary structure determination, at atomic resolution
X-ray diffraction (i.e. X-ray crystallography) and/or:
• NMR spectroscopy
X-ray crystallography of RNA Challenge
Need very homogeneous preparation,
RNA molecules have a tendency to mis-fold easily.
(b) RNAs generally make fewer crystal packing contacts than proteins
tetraloop
, 4 nt, 5'-GNRA-3', Exceptionally stable, two outside residues of the loop form a non-Watson-
Crick, Base-phosphate and/or base-sugar (2'-OH) hydrogen bonding interactions occur, second
base in the loop may make no base- specific interactions
Core of Hammerhead ribozyme
small, self-cleaving ribozyme from a viroid (a viroid is an infectious RNA molecule),
coaxially- stacked helices
Two covalently discontinuous helices, on the axis of the green line
first catalysts
clay minerals such as greigite (Fe5NiS8) or montmorillonite
RNA nucleotides arose (via some sort of catalysis), next problem would be
polymerization and phosphate addition
problems for pre-biotic synthesis
supply of non-aqueous (organic) solvents• No means for purification/concentration of
intermediates• No activated precursors
• Poor chemical selectivity (mixture of 2'-5 ́ and 3'-5 ́)Plus:• Lack of stereospecificity in the
products (D/L ribose)• Possible instability of key intermediates under "early earth" conditions.
Simplest possible sugar-phosphate backbone
Glycol Nucleic Acid (GNA) Can cross-basepair with RNA
interesting candidates for pre-RNA
Guaranteed A+!
Can we predict RNA secondary structures, specifically helices ?
Yes, we can predict helical regions by, e.g. 'Free energy minimization'
Computer algorithm searches
However, the above algorithms are not very reliable: There may be many alternate (equally
stable) base-pairing arrangements
How can you determine RNA secondary structure experimentally
co-variation analysis', and by physical probing
How to do the experiment ..(1) 32P end-label (*) the RNA to be examined(2) Incubate with
nuclease under conditions that achieve (on average) just a single hit per RNA molecule (3)
Electrophorese the reaction products in a denaturing gel(4) Autoradiograph the gel
RNA tertiary structure determination, at atomic resolution
X-ray diffraction (i.e. X-ray crystallography) and/or:
• NMR spectroscopy
X-ray crystallography of RNA Challenge
Need very homogeneous preparation,
RNA molecules have a tendency to mis-fold easily.
(b) RNAs generally make fewer crystal packing contacts than proteins
tetraloop
, 4 nt, 5'-GNRA-3', Exceptionally stable, two outside residues of the loop form a non-Watson-
Crick, Base-phosphate and/or base-sugar (2'-OH) hydrogen bonding interactions occur, second
base in the loop may make no base- specific interactions
Core of Hammerhead ribozyme
small, self-cleaving ribozyme from a viroid (a viroid is an infectious RNA molecule),
coaxially- stacked helices
Two covalently discontinuous helices, on the axis of the green line
first catalysts
clay minerals such as greigite (Fe5NiS8) or montmorillonite
RNA nucleotides arose (via some sort of catalysis), next problem would be
polymerization and phosphate addition
problems for pre-biotic synthesis
supply of non-aqueous (organic) solvents• No means for purification/concentration of
intermediates• No activated precursors
• Poor chemical selectivity (mixture of 2'-5 ́ and 3'-5 ́)Plus:• Lack of stereospecificity in the
products (D/L ribose)• Possible instability of key intermediates under "early earth" conditions.
Simplest possible sugar-phosphate backbone
Glycol Nucleic Acid (GNA) Can cross-basepair with RNA
interesting candidates for pre-RNA
