BIOC 410 Exam
What is the main reason why RNA is particularly labile/unstable? *** The 2' hydroxyl (-OH) group can
react with the phosphate backbone in a transesterification reaction, releasing the next nucleotide down
from it
List the 6 non-coding RNAs commonly investigated and their general function *** a. rRNA (ribosomal
RNA) structured/catalysis
b. tRNA (transfer RNA) protein synthesis
c. snRNA (small nuclear) splicing
d. snoRNA (small nucleolar) processing + modification of rRNA, tRNA and snRNA
e. miRNA / siRNA (micro/short interfering) silencing, translation inhibition
f. lncRNA (long noncoding) telomerase template, X-inactivation, several others
What are the 4 main methods used to detect specific RNA transcripts? *** a. Northern Blot
b. RNAse protection assay
c. RT-PCR
d. Microarray Analysis
What is the main advantage and disadvantage of using a Northern Blot analysis? *** a. +: Can be used if
the size of the RNA is unknown
b. -: RNA must be abundant in sample to get good signal
What is the main advantage and disadvantage of using an RNAse protection assay? *** a. +: Very
sensitive and can detect RNA ends (TSS)
b. -: Size of the RNA cannot be detected
What is the main advantage and disadvantage of using RT-PCR? *** a. +: Very sensitive, can use whole
RNA
,b. -: Size of RNA cannot be detected
What cross-links the RNA transcripts to the membrane in a Northern Blot assay? *** UV radiation
What sort of question are you answering with a Microarray analysis? *** If an RNA transcript is being up
or downregulated compared to the reference condition
How did some researchers come to the conclusion that 50-85% of the RNA transcripts are non-coding?
*** a. Using RNA-seq!
b. They took poly(A) RNA transcripts fragmented them + treated with reverse-transcriptase made cDNA
library made parallel sequencing alignments with reference genome most sequences came from non-
exons
TRUE or FALSE: RNA can fold into anti-parallel AND parallel stranded structures unlike DNA *** TRUE
What are the 3 common tertiary RNA structural motifs? *** a. Two-stem junction (coaxial stack)
b. Pseudoknot
c. Kissing hairpins
What are the 4 common RNA SECONDARY structural motifs? *** a. Double-stranded segment (dsRNA)
b. Bulge
c. Internal Loop (symmetric/asymmetric internal loop)
d. Hairpin (stem-loop)
The A form of dsRNA is a (parallel/anti-parallel) helical structure *** Anti-parallel
,What are the various interactions which help to stabilize RNA secondary/tertiary structures? *** a. H-
bonding
b. Watson/Crick base pairs & non-canonical base pairing
c. Base Stacking
d. Cationic metal (Mg2+, Na+, K+) counterions
What are the structural differences between the A-form of RNA and the B-form of DNA? *** a. A-form
has bases tilted (~20 degrees) from central axis
b. Steric clashing with phosphate + H of C5 cause C3' to be out-of-plane (rather than C2' endo)
c. Phosphates in backbone are closer to each other (7Å vs 5Å)
d. Major groove is narrow/deep = inaccessible for protein binding
If dsRNA is incapable of protein binding due to its major groove being too narrow/deep, how does it
overcome this? *** Non-canonical base pairing within the sequence introduces a kink in the helix,
allowing for proteins to bind
What is the sequence and structure of a tri-loop structure in RNA? *** a. GUGAC (End G and C are
bonded)
b. U and G point outwards while the A nucleotide points in towards the loop and is stabilized by base-
stacking interactions with the GC
In a hairpin triloop, the (helix portion/loop portion) of the loop is often well conserved whereas the
(helix portion/loop portion) of the loop is not *** Loop portion (the 3 nucleotides); helix portion
What are the sequences of the most common tetraloops found in rRNA? *** GNRA & UNCG (N = any
nucleotide, R = purine)
Why is the tetraloop particularly thermodynamically stable? *** a. The first and last bases of the
tetraloop H-bond with each other (non-Watson/Crick)
, b. There is base-stacking between GA pair + CG pair (for GNRA)
What is often the function of the base that sticks out of the loop in hairpins found in RNA? *** To
interact with other parts of the RNA molecule or RNA binding proteins through other stabilizing
interactions (H-bonds, base-stacking, VdW etc.)
TRUE or FALSE: Although the helix of the hairpin loop does help to stabilize the structure, the individual
loops would still be able to exist without them *** FALSE. The stability from the loops is the ONLY thing
keeping those loops together. The structure of the loop itself is actually thermodynamically UNfavorable
What are the 3 major contributing forces/interactions that stabilize the RNA secondary structures? ***
a. H-bonding (W-C, non-WC, w/ ribose, w/ phosphate)
b. Base stacking (inter + intra)
c. Bulges and loops w/ each other
What are the structural characteristics of a Uridine/U-turn? *** a. A sharp phosphate turn within the
backbone of an RNA molecule consisting of a UNR consensus sequence where other nucleotides present
within the loop are forced facing outward
b. Uridine 2'OH H-bonds with N7 of R residue
c. P-O backbone between U and N residues is turned 120 deg from standard helical conformation
d. Often found in many tRNA anti-codon loop
What is the consensus sequence for a U-Turn Motif/Uridine Turn? *** UNR
What are the 5 types of Bulges/Internal loops for RNA secondary structures? *** a. K-turn
b. S-turn
c. Hook-turn
d. Cross-strand purine stack
What is the main reason why RNA is particularly labile/unstable? *** The 2' hydroxyl (-OH) group can
react with the phosphate backbone in a transesterification reaction, releasing the next nucleotide down
from it
List the 6 non-coding RNAs commonly investigated and their general function *** a. rRNA (ribosomal
RNA) structured/catalysis
b. tRNA (transfer RNA) protein synthesis
c. snRNA (small nuclear) splicing
d. snoRNA (small nucleolar) processing + modification of rRNA, tRNA and snRNA
e. miRNA / siRNA (micro/short interfering) silencing, translation inhibition
f. lncRNA (long noncoding) telomerase template, X-inactivation, several others
What are the 4 main methods used to detect specific RNA transcripts? *** a. Northern Blot
b. RNAse protection assay
c. RT-PCR
d. Microarray Analysis
What is the main advantage and disadvantage of using a Northern Blot analysis? *** a. +: Can be used if
the size of the RNA is unknown
b. -: RNA must be abundant in sample to get good signal
What is the main advantage and disadvantage of using an RNAse protection assay? *** a. +: Very
sensitive and can detect RNA ends (TSS)
b. -: Size of the RNA cannot be detected
What is the main advantage and disadvantage of using RT-PCR? *** a. +: Very sensitive, can use whole
RNA
,b. -: Size of RNA cannot be detected
What cross-links the RNA transcripts to the membrane in a Northern Blot assay? *** UV radiation
What sort of question are you answering with a Microarray analysis? *** If an RNA transcript is being up
or downregulated compared to the reference condition
How did some researchers come to the conclusion that 50-85% of the RNA transcripts are non-coding?
*** a. Using RNA-seq!
b. They took poly(A) RNA transcripts fragmented them + treated with reverse-transcriptase made cDNA
library made parallel sequencing alignments with reference genome most sequences came from non-
exons
TRUE or FALSE: RNA can fold into anti-parallel AND parallel stranded structures unlike DNA *** TRUE
What are the 3 common tertiary RNA structural motifs? *** a. Two-stem junction (coaxial stack)
b. Pseudoknot
c. Kissing hairpins
What are the 4 common RNA SECONDARY structural motifs? *** a. Double-stranded segment (dsRNA)
b. Bulge
c. Internal Loop (symmetric/asymmetric internal loop)
d. Hairpin (stem-loop)
The A form of dsRNA is a (parallel/anti-parallel) helical structure *** Anti-parallel
,What are the various interactions which help to stabilize RNA secondary/tertiary structures? *** a. H-
bonding
b. Watson/Crick base pairs & non-canonical base pairing
c. Base Stacking
d. Cationic metal (Mg2+, Na+, K+) counterions
What are the structural differences between the A-form of RNA and the B-form of DNA? *** a. A-form
has bases tilted (~20 degrees) from central axis
b. Steric clashing with phosphate + H of C5 cause C3' to be out-of-plane (rather than C2' endo)
c. Phosphates in backbone are closer to each other (7Å vs 5Å)
d. Major groove is narrow/deep = inaccessible for protein binding
If dsRNA is incapable of protein binding due to its major groove being too narrow/deep, how does it
overcome this? *** Non-canonical base pairing within the sequence introduces a kink in the helix,
allowing for proteins to bind
What is the sequence and structure of a tri-loop structure in RNA? *** a. GUGAC (End G and C are
bonded)
b. U and G point outwards while the A nucleotide points in towards the loop and is stabilized by base-
stacking interactions with the GC
In a hairpin triloop, the (helix portion/loop portion) of the loop is often well conserved whereas the
(helix portion/loop portion) of the loop is not *** Loop portion (the 3 nucleotides); helix portion
What are the sequences of the most common tetraloops found in rRNA? *** GNRA & UNCG (N = any
nucleotide, R = purine)
Why is the tetraloop particularly thermodynamically stable? *** a. The first and last bases of the
tetraloop H-bond with each other (non-Watson/Crick)
, b. There is base-stacking between GA pair + CG pair (for GNRA)
What is often the function of the base that sticks out of the loop in hairpins found in RNA? *** To
interact with other parts of the RNA molecule or RNA binding proteins through other stabilizing
interactions (H-bonds, base-stacking, VdW etc.)
TRUE or FALSE: Although the helix of the hairpin loop does help to stabilize the structure, the individual
loops would still be able to exist without them *** FALSE. The stability from the loops is the ONLY thing
keeping those loops together. The structure of the loop itself is actually thermodynamically UNfavorable
What are the 3 major contributing forces/interactions that stabilize the RNA secondary structures? ***
a. H-bonding (W-C, non-WC, w/ ribose, w/ phosphate)
b. Base stacking (inter + intra)
c. Bulges and loops w/ each other
What are the structural characteristics of a Uridine/U-turn? *** a. A sharp phosphate turn within the
backbone of an RNA molecule consisting of a UNR consensus sequence where other nucleotides present
within the loop are forced facing outward
b. Uridine 2'OH H-bonds with N7 of R residue
c. P-O backbone between U and N residues is turned 120 deg from standard helical conformation
d. Often found in many tRNA anti-codon loop
What is the consensus sequence for a U-Turn Motif/Uridine Turn? *** UNR
What are the 5 types of Bulges/Internal loops for RNA secondary structures? *** a. K-turn
b. S-turn
c. Hook-turn
d. Cross-strand purine stack
