Chapter 4: Questions.
1. Draw and label a single RNA that has the following features:
a. 9 bp stem
b. 5 base loop
c. 2 base bulge
Draw out both the primary sequence and the secondary structure.
2. What is the main chemical difference between deoxyribose and ribose? How does the
difference affect the structures DNA and RNA form?
3. Name 5 cellular functions of RNAs? Why are these functions important? For the
functions you’ve chosen, name the RNA(s) that can either perform or play a role in that
function (Note: there can be multiple RNAs that can perform a function).
4. Please match each type of RNA to its appropriate function.
a. tRNA
b. mRNA
c. snoRNA
d. miRNA
e. rRNA
f. snRNA
5. Please state which 5 RNAs that function in gene expression. Please state their
functions within the process of gene expression.
6. Please state 5 roles for RNA in the cell.
7. In order for RNA to form secondary structure, there must be base pairing.
a. Please state the canonical base pairs that are found in RNA.
b. Please state which is the most common non-canonical base pair found in RNA.
c. Why is non-canonical base pairing important in allowing secondary structure to form?
8. Are non-canonical base pairs stronger or weaker than canonical base pairs in RNA?
Why? If non-canonical base pairing is weaker, please state how this is compensated for?
9. What type of secondary structure does RNA adopt? Please describe this structure in
detail.
10. Below is the structure of a t-RNA. On the diagram, please show where each of the
loops is present. Also, please show where the amino acid acceptor site is. Are the loops
in tRNA loops? Please explain your answer.
11. Please state which bases are 5’ and 3’ to the anticodon. Please state how these bases
interact with each other. Why is this interaction important?
12. Please state the sequence that is at the end of the amino acid acceptor site.
13. Please explain how tertiary structure for RNA are formed.
14. Please name and describe 5 possible tertiary structures for RNA.
15. Please define the term misfolded RNA. How does misfolding affect function of an
RNA.
4. Below is the structure of the L-shaped structure. For the L shaped structure, properly
label the 5’ and 3’ ends. Also, properly label the 3 stems on the model. What function
does each stem have? Label the location of where the amino acid is attached. Which
nucleotides are directly 5’ and 3’ to the anti-codon? What experiment tells us that the Lshaped structure is the correct one? How does the structure relate to its function?
5. Name 3 types of RNA tertiary structure. Explain the mechanism of how these
structures form.
Pseudoknot Motif: A single-stranded loop base pairs with complementary
sequence outside the loop. This results in folding into a 3-dimensional
structure by co-axial stacking.
A-minor Motif: Single-stranded adenines make tertiary contacts with the
minor grooves of RNA double helices by hydrogen bonding with phosphatesugar backbone, or the bases neighboring the groove
Tetra-loop Motif: Stem-loop with the loop motif having the sequence UUUU.
Base stacking interactions stabilize the tetra-loop structure.
Ribose-Zipper Motif: Helix-helix interactions involving hydrogen bonding
between the 2’ OH of a ribose in one helix and the 2-oxygen of a pyrimidine
base, or the 3-nitrogen of a purine base of the other helix between their
respective minor groove surfaces
Kink-Turn Motif: This motif has a sharp bend in the phosphodiester
backbone of a three nucleotide bulge
6. (Matching) Determine the function for the types of RNAs listed below.
a. mRNA
b. tRNA
c. snRNA
d. miRNA
e. rRNA
f. snoRNA
a.
Controls translation and Stability of mRNA
b.
Functions as a translation template. Also, can function as a scaffold.
c.
Functions in translation to bring an amino acid to the ribosome
d.
Functions as part of the ribosome structure
e.
Functions in Ribosomal RNA processing
f.
Functions in splicing of pre-mRNA
7. Explain the structure of the double stranded RNA double helix? How does the
structure of this helix differ from the typical DNA structure? If a protein were to bind,
where on this helix will a protein most likely bind? Why is it most likely that a protein
would bind at that spot?
1. RNA forms an A-type double-stranded double helix.
This type of helix has a
deep, narrow major groove, and a shallow, broad minor groove. The 2’ OH groups
from the ribose stick out into the minor groove. 2. DNA can form three different
types of double helices A-type, B-type and a Z-type, with the predominant form in
vivo being the B-type helix. The 2’OH group from the ribose, in the RNA double
helix, hinders formation of the B-type. 3. If a protein were to bind the RNA double
helix, it would most likely bind at the minor groove, 4. due to the fact that the
minor groove is shallow, broad and includes the ribose 2’OH groups, which are very
accessible for H-bonding.