M116 MIDTERM EXAM QUESTIONS
WITH CORRECT ANSWERS
\.Can we predict RNA secondary structures, specifically helices ? - ANSWERS✔-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 - ANSWERS✔-
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 - ANSWERS✔-X-ray
diffraction (i.e. X-ray crystallography) and/or:
• NMR spectroscopy
\.X-ray crystallography of RNA Challenge - ANSWERS✔-Need very homogeneous
preparation,
RNA molecules have a tendency to mis-fold easily.
, (b) RNAs generally make fewer crystal packing contacts than proteins
\.tetraloop - ANSWERS✔-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 - ANSWERS✔-small, self-cleaving ribozyme from
a viroid (a viroid is an infectious RNA molecule),
\.coaxially- stacked helices - ANSWERS✔-Two covalently discontinuous helices, on
the axis of the green line
\.first catalysts - ANSWERS✔-clay minerals such as greigite (Fe5NiS8) or
montmorillonite
\.RNA nucleotides arose (via some sort of catalysis), next problem would be -
ANSWERS✔-polymerization and phosphate addition
\.problems for pre-biotic synthesis - ANSWERS✔-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.
WITH CORRECT ANSWERS
\.Can we predict RNA secondary structures, specifically helices ? - ANSWERS✔-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 - ANSWERS✔-
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 - ANSWERS✔-X-ray
diffraction (i.e. X-ray crystallography) and/or:
• NMR spectroscopy
\.X-ray crystallography of RNA Challenge - ANSWERS✔-Need very homogeneous
preparation,
RNA molecules have a tendency to mis-fold easily.
, (b) RNAs generally make fewer crystal packing contacts than proteins
\.tetraloop - ANSWERS✔-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 - ANSWERS✔-small, self-cleaving ribozyme from
a viroid (a viroid is an infectious RNA molecule),
\.coaxially- stacked helices - ANSWERS✔-Two covalently discontinuous helices, on
the axis of the green line
\.first catalysts - ANSWERS✔-clay minerals such as greigite (Fe5NiS8) or
montmorillonite
\.RNA nucleotides arose (via some sort of catalysis), next problem would be -
ANSWERS✔-polymerization and phosphate addition
\.problems for pre-biotic synthesis - ANSWERS✔-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.
