DNA & Genomics

Question 1

What is the difference between ribose and deoxyribose?

Answer 1

A hydrogen atom is attached to the 2’ carbon atom of deoxyribose whereas a -OH group is attached to the 2’ carbon atom of ribose

Question 2

Why is the RNA molecule more reactive than DNA?

Answer 2

The ribose sugar in RNA contains a -OH group which is polar and reactive.

Question 3

Describe the formation of a nucleotide.

Answer 3

A nitrogenous base is attached to the 1’ carbon atom of the pentose sugar via a condensation reaction forming a nucleoside and a glycosidic bond.
A phosphate group is attached to the 5’ carbon atom of the pentose sugar via a condensation reaction, forming a nucleotide and a phosphoester bond.

Question 4

What contributes to the stability of the DNA molecule?

Answer 4

Hydrogen bonds between the nitrogenous bases of opposite DNA strands by complementary base pairing and hydrophobic interactions between stacked nitrogenous bases

Question 5

Why does DNA polymerase only add new nucleotides to the 3’ end of the growing strand?

Answer 5

The active site of DNA polymerase is only specific to the 3’ end of a deoxyribonucleotide

Question 6

In what direction is the parental DNA strand being read in DNA replication?

Answer 6

3’ to 5’

Question 7

In what direction is the daughter DNA strand being synthesised in during DNA replication?

Answer 7

5’ to 3’

Question 8

What is the role of DNA polymerase I?

Answer 8

DNA polymerase I hydrolyses the RNA primer and replaces it with deoxyribonucleotides complementary to the DNA template strand

Question 9

Why are the daughter strand synthesised continuously as a leading strand and the other synthesised discontinuously as a lagging strand?

Answer 9

The parental stands of DNA have an antiparallel arrangement

Question 10

What is the role of DNA ligase?

Answer 10

DNA ligase catalyses the formation of phosphodiester bond between two okazaki fragments so that the gap between the two fragments are sealed.
It requires the free 3’ OH group of one DNA strand and a 5’ phosphate group of another DNA strand.

Question 11

What is the difference in DNA replication in prokaryotic cells and eukaryotic cells?

Answer 11

Prokaryotic genome are small in size and therefore would only require one origin of replication.
Eukaryotic genome is very large so many origins of replication is present, forming many short daughter stands at each replication bubble which eventually link together to form a continuous daughter DNA strand

Question 12

Explain the end-replication problem.

Answer 12

At the 5’ end of the newly synthesised daughter strand, RNA primer is hydrolysed which leaves a gap that should be filled.
The DNA polymerase I is unable to add deoxyribonucleotides to fill the gap at the 5’ end of the lagging strand.
This is due to the absence of an existing 3’ OH group.
Repeated rounds of replication leads to the shortening of DNA molecules.

Question 13

What is a gene?

Answer 13

A gene is a specific nucleotide sequence within DNA which codes for a specific sequence of amino acids in a polypeptide molecules or a functional RNA molecule

Question 14

What are the 5 features of the genetic code?

Answer 14

It is a triplet code (3 bases in 1 codon which codes for one amino acid)
It is degenerate as one amino acid can be coded by many codons
It is punctuated (presence of 4 codons - 1 start and 3 stop, signal the start and ends of translation)
It is non-overlapping, nucleotides of the genetic code are always read in triplets and read only once
It is universal as the codons which codes for a specific amino acid is used across all organisms

Question 15

What is transcription?

Answer 15

Transcription is a process in which a sequence of DNA bases of a gene are read to form a complementary sequence of bases in a RNA molecule

Question 16

Describe the transcription process in eukaryotic cells

Answer 16

Proteins called transcription factors bind to the promoter to facilitate the binding of DNA polymerase to the promoter, forming the transcription initiation complex.
The binding of DNA polymerase causes the DNA double helix to unwind and unzip.
One of the DNA strand is used as a template strand and the other will be a non-template strand.
The RNA polymerase reads the template strand in the 3’ to 5’ direction while the RNA strand is synthesised in the 5’ to 3’ direction.
RNA polymerase catalyses the formation of phosphodiester bonds between adjacent ribonucleotides added to the growing RNA strand.
RNA polymerase transcribes a terminator sequence
RNA and RNA polymerase dissociate from DNA molecule which reforms the double helix

Question 17

What is the difference in the effect of adding a 5’ modified guanosine cap and the polyadenylation of the 3’ end?

Answer 17

The 5’ modified guanosine cap is not recognised by exonuclease so the 5’ end is not degraded by exonucleases, but exonucleases can still recognise the poly-A tail but it will take a longer time for exonuclease to degrade the poly-A tail due to its greater length

Question 18

Why is post-transcriptional modification important?

Answer 18

The 5’ cap and 3’ polyA tail assist in the export of mRNA out of the nucleus
The 5’ cap and the 3’ polyA tail protect mRNA from degradation
The 5’ cap and 3’ polyA tail are involved in the initiation of translation.

Question 19

What is the role of aminoacyl-tRNA synthetase?

Answer 19

Aminoacyl-tRNA synthetase has a specific active site which binds one specific type of amino acid to its tRNA molecule