Module 03 - Section 02

Question 1

Which type(s) of RNA is/are coding RNA?

Answer 1

mRNA

Question 2

Which type(s) of RNA is/are non-coding RNA?

Answer 2

tRNA and rRNA (both present during translation)

long non-coding RNAs, small nuclear RNAs, Micro RNAs, Small interfering RNAs, small nucleor RNAs, Catalytic RNAs

Question 3

Describe mRNA

Answer 3

• Only type of coding RNA
• Transient molecules
• Transcript copy of a gene that encodes a specific protein
• caries encoded information from the nucleus to the ribosomes where the protein is produced
• coding sequence of mRNA determines amino acid sequence of the protein
• different mRNA adopt different 3D structures depending on what is most energetically favorable

Question 4

What are the 2 main chemical differences between DNA and RNA that results in RNA variability? (that we cover in this course)

Answer 4

(1) Pentose Sugar

(2) Base pairs (uracil instead of thymine

Question 5

How does the difference in pentose sugar aid in RNA’s variability?

Answer 5

Ribose has an extra hydroxyl group on the 2’ carbon qhich allows for hydrogen bonding, which stabilizes the bonding of the polynucleotide

Question 6

What do we mean by non-canonical RNA Base-pairing

Answer 6

RNA does not necessarily follow watson-crick rules. Base-paired segment are often interspersed with a variety of other base pairs, like A-A or G-U

Question 7

What are noncontiguous sequences?

Answer 7

2 sequences that do not share a common border (not next to one another)

Question 8

How is the secondary and 3D shape stabilized in RNA?

Answer 8

Secondary structures include regions of unpaired nucleotide that can interact with noncontiguous sequences - this stabilizes the 3D folding of RNA and produce a compact shape with surfaces that are capable of binding to other molecules

Question 9

Why is RNA sensitive to alkaline conditions?

Answer 9

RNA is hydrolized rapidly under alkaline conditions because of the 2’-hydrozyl group on the ribose sugar

Question 10

Describe the mechanism of hydrolysis of RNA under alkaline condition

Answer 10

(1) Alkaline (basic) pH>7, bases such as -OH can iteract with the 2’hydroxyl on ribose sugar of RNA causing hydrolysis of the phosphodiester bond
(2) Cyclic 2’,3’-monophosphates are the first products of the action of alkali on RNA, which are rapidly hydrolyzed further to yield a mixture of nucleoside 2’ and 3’ monophosphates

Question 11

Why is DNA not easily hydrolyzed under alkaline conditions?

Answer 11

Because it lacks the 2’-OH group that RNA has

Question 12

What is the purpose of the inherent instability of RNA relative to DNA in gene expression?

Answer 12

RNA molecules can be synthesized and degraded many times during the life of a cell, whereas the corresponding DNA is maintained during cell division and during extended periods in non replicating cells

Question 13

What is the secondary structure of RNA?

Answer 13

3D structures due to the ability of RNA to fold back on itself and form intramolecular base pairing - can have many different 3D structures further increasing RNA’s diversity of function

Question 14

What determines RNA’s secondary structure

Answer 14

Intramolecular base pairing that provides the most energetically stable complex

Question 15

What is RNA base stacking?

Answer 15

The local spatial arrangement of an RNA strand, including a description of any intrachain base pairing

Question 16

How is RNA base stacking made favorable?

Answer 16

Burying the hydrophobic bases away from the hydrophilic surroundings

Question 17

Which types of RNA have all their bases stacked even when they aren’t base paired?

Answer 17

tRNA and catalytic RNA

Question 18

What are two example of structural motifs in RNA?

Answer 18

Base-triple interactions and helix-helix packing

Question 19

What are base-triple interactions

Answer 19

3 bases that interact with each other

Question 20

Whata re 3 examples of RNA secondary structure?

Answer 20

Helical structure
Internal Loops
Hairpin Loops

Question 21

Describe the helical structure in RNA

Answer 21

The strand folds back on itself, the “paired strands” (1 strand folded in 2) are antiparallel to one another and from a right-handed helix, dominated by base-stacking interactions

Question 22

Describe the Internal loops structure in RNA

Answer 22

Occur when the double stranded RNA (1 strand folded in 2) separates dued to a lack of Watson-Crick base pairing between 2 strands.

Question 23

What are Bulges in RNA structure?

Answer 23

Special type of internal loop when only one strand contains an unpaired base

Question 24

Describe the Hairpin loops structure in RNA

Answer 24

Occur when a RNA folds back onto itself and there is an unpaired loop of bases at the end of a stem region
Most common type of RNA secondary structure
Nucleotides within the loops are arranged to maximize hydrogen bonding and base stacking, enhancing thermodynamic stability
– often contain specific short sequences such as UUCG or GAAA, which forms energetically favorable loops

Question 25

What specific sequences are often in hairpin loops?

Answer 25

UUCG and GAAA

Question 26

What kind of interactions play a major role in the stability of secondary structures

Answer 26

2’OH is often involved in hydrogen bonding and van der waals interactions, Metal ions also bind to specific sites to help shield the negative charge of the backbone, which allow RNA to tightly pack together

Question 27

Name 4 factors influencing RNA structure stability

Answer 27

(1) Number of GC vs AU (and GU) base pairs
(2) Number of base pairs in stem region
(3) Number of base pairs in a hairpin loop as the formation of loops with more than 10 or less than 5 bases requires more energy
(4) Number of unpaired bases, as unpaired bases decrease the stability of the structure