RNA Structure

Question 1

Why is RNA almost always a single-strand?

Answer 1

because only one strand of the DNA is usually transcribed for any particular region and therefore there is no complementary RNA strand available

Question 2

What is post-transcriptional modification?

Answer 2

functional RNA rather than mRNA, that chemically modify after synthesis

Question 3

What is an example of post-transcriptional modification?

Answer 3

~10 of the 75~ nucleotides

Question 4

T or F: chemical modifications are usually regulatory and are not permanent

Answer 4

false

Question 5

What is the function of 2’ OH?

Answer 5

1. facilitates a reaction that can break phosphodiester bonds. As a result, RNA is much less stable than
2. allows RNA to form hydrogen bonds more prolifically than DNA, allowing more inter- and intra- molecular interactions

Question 6

T or F? RNA is better for dynamic information

Answer 6

true

Question 7

What does the 2’ OH represent?

Answer 7

RNA favors an A-type helix (when double stranded)

Question 8

Why does the 2’ OH favor an A-type helix?

Answer 8

1. steric hindrance
2. sugar pucker

Question 9

What is a sugar pucker?

Answer 9

buckled conformations in the sugar part of nucleic acid molecules

Question 10

What causes the difference between the sugar pucker found in ribose and deoxyribose?

Answer 10

the 2’OH of ribose causes it to have a different sugar pucker

Question 11

What is the conformation called in ribose?

Answer 11

C3’ endo, which favors the A-type helix

Question 12

What is the conformation called in deoxyribose?

Answer 12

C2’ endo, which favors the B-type helix

Question 13

How do non-coding RNAs often fold into?

Answer 13

molecule-specific, stereotypical, three-dimensional structures

Question 14

What is primary structure?

Answer 14

the base sequence from 5’ to 3’

Question 15

How are secondary structures created?

Answer 15

short (6-8bp) stretches of intra-molecular base-pairing usually with Watson-Crick base-pairing (and G-U), in an antiparallel direction

Question 16

What are ribosomal RNAs made of?

Answer 16

secondary structures called hairpins or stem-loops depending on size of the loop

Question 17

What is tertiary structure?

Answer 17

the overall three-dimensional arrangement of the secondary structures and single stranded regions of the entire RNA

Question 18

What are non-canonical base pairs?

Answer 18

base pairs that involve chemically modified bases, such as methylation (addition of a CH3)

Question 19

What can pairing with modified bases introduce?

Answer 19

structural differences such as kinks

Question 20

Why do RNAs have more base pairing posibilities?

Answer 20

no double strands

Question 21

What is a “wobble” base pair?

Answer 21

uracil pairing with guanine, doubling its chance of pairing

Question 22

What is the benefit of “wobble” base pairing?

Answer 22

allows a single tRNA with uracil in the first position of the anti-codon to recognize two codons differing in the third position

Question 23

How do tertiary structures form?

Answer 23

by folding the stable interaction between short double stranded helices and single-stranded regions driven by hydrophilic and hydrophobic interactions in aqueous environments

Question 24

What do hydrogen bonding of 2’ OH of ribose and unpaired bases in the ss regions allow for?

Answer 24

interactions such as base-triplets and A-minor motifs, which bring three strands together for short stretches

Question 25

What is the affect of the RNA backbone structure on tertiary structure?

Answer 25

the phosphate in the nucleic acid back bone is negatively charged, which electrostatically repulse one another if brought into close proximity (folding)

Question 26

What binds to RNA molecules?

Answer 26

large numbers of cations (like Mg2+) to counteract shielding and neutralizing of the charges

Question 27

Why is searching for potential base-pairing regions false?

Answer 27

because pairing regions tend to be short (as little as 6-8bp)

Question 28

What is phylogenetic analysis?

Answer 28

comparison of sequences between species helps identify true pairing regions, as these are more likely to be conserved during evolution

Question 29

What are co-variations?

Answer 29

Differences that occur between species, yet conserve secondary interactions

Question 30

What can rRNA catalyze?

Answer 30

formation of peptide bonds between amino acids to produce proteins

Question 31

What are highly conserved across species?

Answer 31

rRNA secondary structures

Question 32

What can RNA serve to do?

Answer 32

1. as the genetic material of the phage and viruses 2. structural, catalytic, and regulatory functions like protein

Question 33

What types of enzymatic co-factors are RNA-like molecules?

Answer 33

ATP, NAD

Question 34

RNA likely served as the _ while also performing catalytic functions

Answer 34

primordial genetic material

Question 35

2'OH is reactive, so RNA may have enzymatic activity, however it also _

Answer 35

reduces the stability

Question 36

Why is RNA usually single-stranded?

Answer 36

because it is produced by transcription, which does not usually occur from both strands of the DNA