Course book: Chapter 5 "The structure and versatility of RNA"

Question 1

In what four ways does RNA differ from DNA?

Answer 1

1. Ribose instead of 2’deoxyribose
2. Uracil instead of Thymine
3. If RNA is double-stranded, A-form is preferred over of B-form.
4. RNA is commonly single-stranded, whilst DNA is almost exclusively double-stranded.

Question 2

Why does uracil exist, considering it’s so similar to thymine?

Answer 2

Thymine can be deaminated to uracil spontaneously. The DNA repair machinery is able to repair this via cytosine deaminase, which makes U –> C.

Question 3

Describe how dsRNA is more versatile than dsDNA.

Answer 3

dsRNA is usually the consequence of self-complementarity within a ssRNA. Some regions will anneal, others will repel eachother. There may occur secondary hairpins inside of the major hairpin.

All of the factors above contribute to a intricate 3D structure.

Often, when proteins interact with dsRNA (A-form), the proteins recognize the RNA conforrmation rather than the sequence (as they do for DNA).

Question 4

What’s a strange base pair that can occur in RNA but not in DNA?

Answer 4

U:A:U triple bond.

Question 5

What’s the hammerhead ribozyme? How can it be used in the lab?

Answer 5

The hammerhead enzyme is a ribozyme deriving from viruses infecting plants (viroids).

In alkaline conditions, the 2’ hydroxyl in RNA’s ribose becomes deprotonated, which can then attack the 3’phosphate on the same ribonucleotide. This makes the DNA cyclic.

Lots of proteins use the mechanism above to degrade RNA –> Individual ribonucleotides.

Question 6

In the cell, name an important ribozyme.

Answer 6

The ribozyme in the catalytic core of the ribosomes. You’ll find a ribozyme which catalyses the formation of peptide bonds.