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BISC 320 > RNA Structure > Flashcards

RNA Structure Flashcards

1
Q

Why is RNA almost always a single-strand?

A

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

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2
Q

What is post-transcriptional modification?

A

functional RNA rather than mRNA, that chemically modify after synthesis

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3
Q

What is an example of post-transcriptional modification?

A

~10 of the 75~ nucleotides

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4
Q

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

A

false

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5
Q

What is the function of 2’ OH?

A
  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
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6
Q

T or F? RNA is better for dynamic information

A

true

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7
Q

What does the 2’ OH represent?

A

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

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8
Q

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

A
  1. steric hindrance
  2. sugar pucker
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9
Q

What is a sugar pucker?

A

buckled conformations in the sugar part of nucleic acid molecules

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10
Q

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

A

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

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11
Q

What is the conformation called in ribose?

A

C3’ endo, which favors the A-type helix

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12
Q

What is the conformation called in deoxyribose?

A

C2’ endo, which favors the B-type helix

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13
Q

How do non-coding RNAs often fold into?

A

molecule-specific, stereotypical, three-dimensional structures

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14
Q

What is primary structure?

A

the base sequence from 5’ to 3’

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15
Q

How are secondary structures created?

A

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

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16
Q

What are ribosomal RNAs made of?

A

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

17
Q

What is tertiary structure?

A

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

18
Q

What are non-canonical base pairs?

A

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

19
Q

What can pairing with modified bases introduce?

A

structural differences such as kinks

20
Q

Why do RNAs have more base pairing posibilities?

A

no double strands

21
Q

What is a “wobble” base pair?

A

uracil pairing with guanine, doubling its chance of pairing

22
Q

What is the benefit of “wobble” base pairing?

A

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

23
Q

How do tertiary structures form?

A

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

24
Q

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

A

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

25
Q

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

A

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

26
Q

What binds to RNA molecules?

A

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

27
Q

Why is searching for potential base-pairing regions false?

A

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

28
Q

What is phylogenetic analysis?

A

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

29
Q

What are co-variations?

A

Differences that occur between species, yet conserve secondary interactions

30
Q

What can rRNA catalyze?

A

formation of peptide bonds between amino acids to produce proteins

31
Q

What are highly conserved across species?

A

rRNA secondary structures

32
Q

What can RNA serve to do?

A
  1. as the genetic material of the phage and viruses
  2. structural, catalytic, and regulatory functions like protein
33
Q

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

A

ATP, NAD

34
Q

RNA likely served as the _ while also performing catalytic functions

A

primordial genetic material

35
Q

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

A

reduces the stability

36
Q

Why is RNA usually single-stranded?

A

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

BISC 320 (20 decks)

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