Bailey_RNA

Question 1

what is the primary difference between RNA and DNA

Answer 1

2’ OH in RNA (makes it ribose) and secondarily we have uridine instead of thymidine

Question 2

what form does RNA take?

Answer 2

A-form, sugar pucker more energetically favorable (3’ endo)

Question 3

T/F. RNA:RNA duplexes are much more stable than DNA:DNA duplexes

Answer 3

True, which is why you often see folded RNA but not folded DNA

Question 4

why is 2’OH group destabilizing?

Answer 4

can be activated as a nucleophile under alkaline conditions or by RNAses

Question 5

RNA secondary structure

Answer 5

commonly stem loops, other 3D elements

Question 6

RNA tertiary structures

Answer 6

long range interactions - like pseudoknots, triple base interactions, ribose zippers, A platforms, tetraloop interactions

Question 7

phylogenetic covariation analysis

Answer 7

align RNAs from members of family to look for concerted changes, often consistent with Watson-Crick basepairing rules

Question 8

what are three edges of bases that can form H-bonds

Answer 8

Hoogsteen, watson-crick, sugar

Question 9

T/F. Metal ions are sometimes necessary for RNA folding.

Answer 9

False, metal ions are required for RNA folding. Metal ions neutralize the electrostatic repulsion between phosphate groups and allow for stacking/folding

Question 10

what is most common hydrated cation used for RNA folding

Answer 10

Mg2+