BIOC 410 EXAM QUESTIONS AND VERIFIED ANSWERS
What is the main reason why RNA is particularly labile/unstable? - answer 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 - answer
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? - answer 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? -
answer 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? -
answer 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? - answer 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? -
answer UV radiation
What sort of question are you answering with a Microarray analysis? - answer 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? - answer 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 - answer TRUE
What are the 3 common tertiary RNA structural motifs? - answer a. Two-stem junction
(coaxial stack)
b. Pseudoknot
c. Kissing hairpins
What are the 4 common RNA SECONDARY structural motifs? - answer 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 - answer Anti-parallel
What are the various interactions which help to stabilize RNA secondary/tertiary
structures? - answer 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? -
answer 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? - answer 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? - answer 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 - answer Loop portion (the 3
nucleotides); helix portion
What are the sequences of the most common tetraloops found in rRNA? - answer GNRA
& UNCG (N = any nucleotide, R = purine)
Why is the tetraloop particularly thermodynamically stable? - answer 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? - answer 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 - answer 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? - answer 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? - answer 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? - answer UNR
What are the 5 types of Bulges/Internal loops for RNA secondary structures? - answer a.
K-turn
b. S-turn
c. Hook-turn
d. Cross-strand purine stack
e. Adenosine platform
What is the difference between an inter- and intra- base stacking interaction? - answer
a. Inter: when two adjacent basePAIRS stack on top of each other/align
b. Intra: when two adjacent INDIVIDUAL nucleotides stack on each other;
K-turns are usually adjacent to what type of structure found within RNA? - answer A
kinked/sharp bend in the helix
What stabilizes hairpin and internal loops/bulges? - answer a. H-bonding between the
base pairings and ribose groups
b. Base stacking
What are the 3 main interactions which help to form the tertiary structural motifs of
RNA? - answer a. Tetraloops + tetraloop receptors
b. A-rich, ssLoop + minor groove of opposing helix
c. Ribose Zipper
What is the main reason why RNA is particularly labile/unstable? - answer 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 - answer
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? - answer 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? -
answer 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? -
answer 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? - answer 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? -
answer UV radiation
What sort of question are you answering with a Microarray analysis? - answer 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? - answer 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 - answer TRUE
What are the 3 common tertiary RNA structural motifs? - answer a. Two-stem junction
(coaxial stack)
b. Pseudoknot
c. Kissing hairpins
What are the 4 common RNA SECONDARY structural motifs? - answer 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 - answer Anti-parallel
What are the various interactions which help to stabilize RNA secondary/tertiary
structures? - answer 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? -
answer 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? - answer 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? - answer 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 - answer Loop portion (the 3
nucleotides); helix portion
What are the sequences of the most common tetraloops found in rRNA? - answer GNRA
& UNCG (N = any nucleotide, R = purine)
Why is the tetraloop particularly thermodynamically stable? - answer 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? - answer 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 - answer 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? - answer 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? - answer 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? - answer UNR
What are the 5 types of Bulges/Internal loops for RNA secondary structures? - answer a.
K-turn
b. S-turn
c. Hook-turn
d. Cross-strand purine stack
e. Adenosine platform
What is the difference between an inter- and intra- base stacking interaction? - answer
a. Inter: when two adjacent basePAIRS stack on top of each other/align
b. Intra: when two adjacent INDIVIDUAL nucleotides stack on each other;
K-turns are usually adjacent to what type of structure found within RNA? - answer A
kinked/sharp bend in the helix
What stabilizes hairpin and internal loops/bulges? - answer a. H-bonding between the
base pairings and ribose groups
b. Base stacking
What are the 3 main interactions which help to form the tertiary structural motifs of
RNA? - answer a. Tetraloops + tetraloop receptors
b. A-rich, ssLoop + minor groove of opposing helix
c. Ribose Zipper
