RNA Structure Flashcards
Why is RNA almost always a single-strand?
because only one strand of the DNA is usually transcribed for any particular region and therefore there is no complementary RNA strand available
What is post-transcriptional modification?
functional RNA rather than mRNA, that chemically modify after synthesis
What is an example of post-transcriptional modification?
~10 of the 75~ nucleotides
T or F: chemical modifications are usually regulatory and are not permanent
false
What is the function of 2’ OH?
- facilitates a reaction that can break phosphodiester bonds. As a result, RNA is much less stable than
- allows RNA to form hydrogen bonds more prolifically than DNA, allowing more inter- and intra- molecular interactions
T or F? RNA is better for dynamic information
true
What does the 2’ OH represent?
RNA favors an A-type helix (when double stranded)
Why does the 2’ OH favor an A-type helix?
- steric hindrance
- sugar pucker
What is a sugar pucker?
buckled conformations in the sugar part of nucleic acid molecules
What causes the difference between the sugar pucker found in ribose and deoxyribose?
the 2’OH of ribose causes it to have a different sugar pucker
What is the conformation called in ribose?
C3’ endo, which favors the A-type helix
What is the conformation called in deoxyribose?
C2’ endo, which favors the B-type helix
How do non-coding RNAs often fold into?
molecule-specific, stereotypical, three-dimensional structures
What is primary structure?
the base sequence from 5’ to 3’
How are secondary structures created?
short (6-8bp) stretches of intra-molecular base-pairing usually with Watson-Crick base-pairing (and G-U), in an antiparallel direction
What are ribosomal RNAs made of?
secondary structures called hairpins or stem-loops depending on size of the loop
What is tertiary structure?
the overall three-dimensional arrangement of the secondary structures and single stranded regions of the entire RNA
What are non-canonical base pairs?
base pairs that involve chemically modified bases, such as methylation (addition of a CH3)
What can pairing with modified bases introduce?
structural differences such as kinks
Why do RNAs have more base pairing posibilities?
no double strands
What is a “wobble” base pair?
uracil pairing with guanine, doubling its chance of pairing
What is the benefit of “wobble” base pairing?
allows a single tRNA with uracil in the first position of the anti-codon to recognize two codons differing in the third position
How do tertiary structures form?
by folding the stable interaction between short double stranded helices and single-stranded regions driven by hydrophilic and hydrophobic interactions in aqueous environments
What do hydrogen bonding of 2’ OH of ribose and unpaired bases in the ss regions allow for?
interactions such as base-triplets and A-minor motifs, which bring three strands together for short stretches
What is the affect of the RNA backbone structure on tertiary structure?
the phosphate in the nucleic acid back bone is negatively charged, which electrostatically repulse one another if brought into close proximity (folding)
What binds to RNA molecules?
large numbers of cations (like Mg2+) to counteract shielding and neutralizing of the charges
Why is searching for potential base-pairing regions false?
because pairing regions tend to be short (as little as 6-8bp)
What is phylogenetic analysis?
comparison of sequences between species helps identify true pairing regions, as these are more likely to be conserved during evolution
What are co-variations?
Differences that occur between species, yet conserve secondary interactions
What can rRNA catalyze?
formation of peptide bonds between amino acids to produce proteins
What are highly conserved across species?
rRNA secondary structures
What can RNA serve to do?
- as the genetic material of the phage and viruses
- structural, catalytic, and regulatory functions like protein
What types of enzymatic co-factors are RNA-like molecules?
ATP, NAD
RNA likely served as the _ while also performing catalytic functions
primordial genetic material
2’OH is reactive, so RNA may have enzymatic activity, however it also _
reduces the stability
Why is RNA usually single-stranded?
because it is produced by transcription, which does not usually occur from both strands of the DNA
