The unstable genome

Question 1

What is a nucleotide substitution?

Answer 1

Exchanging one base for another (point mutation rather than frameshift)

Question 2

What are nucleotide transitions and transversions?

Answer 2

Transitions - pyrimidine substituted for pyrimidine or purine for purine
Transversion - pyrimidine substituted for purine or vice versa

Question 3

What is a tautomer in genomes?

Answer 3

When hydrogen atoms on bases change position

Question 4

What can amino groups and keto groups tautomerize into?

Answer 4

Amino groups (-NH2) tautomerize to an imino form (=NH)
Keto groups (-C=O) tautomerize to an enol form (=C-OH)

Question 5

What forms are bases in DNA predominantly in?

Answer 5

Their keto and amino tautomeric forms

Question 6

What would an adenine tautomer mispairing with a cytosine cause?

Answer 6

An adenine to guanine transition mutation

Question 7

What happens when base analogues incorporated into DNA?

Answer 7

They can cause mutations eg. a thymine analogue pairs with adenine but the enol tautomer of this thymine analogue pairs with guanine rather than adenine

Question 8

What is base deamination?

Answer 8

Removal of an amino group from a base

Question 9

What is the difference between thymine and uracil?

Answer 9

Thymine has a methyl group on carbon 5 whereas uracil only has a hydrogen
Both can base pair with adenine

Question 10

Why does DNA contain thymine rather than uracil?

Answer 10

• Cytosine can deaminate to produce uracil which base pairs with adenine (rather than guanine)
• Thymine used in DNA so that uracil produced by cytosine deamination can be recognised as base damage and repaired

Question 11

What causes deamination of bases?

Answer 11

Nitrous acid reacting with bases that contain amino groups

Question 12

What is adenine deaminated into and what does this cause?

Answer 12

Into hypoxanthine

Causes an adenine to guanine transition

Question 13

What is depurination of bases?

Answer 13

Hydrolysis of the N-beta-glycosyl bond between the base and pentose sugar

Question 14

Which does dupurination happen to more - purines or pyrimidines?

Answer 14

Purines (adenine and guanine)

Question 15

What is the effect of depurination?

Answer 15

Causes apurinic sites that cannot specify the correct base during DNA replication
(Cells may depurinate bases during base excision repair)

Question 16

What is base akylation?

Answer 16

Transfer of an alkyl molecule such as a methyl group from one molecule to another

Question 17

Which two bases are most likely to be enzymatically methylated?

Answer 17

Cytosine and adenine

Question 18

What is the function of methylating DNA in prokaryotes?

Answer 18

Endogenous DNA methylated to distinguish it from exogenous DNA
Under-methylated DNA destroyed by restriction endonucleases

Question 19

What enzyme methylates adenine residues and what is the function of this process?

Answer 19

DAM methylase (DNA adenine methylation)
Helps distinguish parental DNA strand to remove mismatched base errors that occur during DNA replication

Question 20

In what eukaryotic sequences are cytosine residues most likely to be methylated and what is the function of this?

Answer 20

Cytosine most likely to be methylated in CpG sequences

Promotes formation of Z-form DNA and is involved in repression of gene expression in eukaryotes

Question 21

What endogenous and exogenous agents can damage DNA?

Answer 21

Endogenous - deamination, reactive oxygen species

Exogenous - ionising radiation, UV light, methylating agents

Question 22

What are some pathways involved in repairing DNA damage to avoid mutations?

Answer 22

Base excision repair, nucleotide excision repair, mismatch repair, homologous recombination, DNA end joining

Question 23

What is base excision repair?

Answer 23

Replacing a damaged base with the correct undamaged base
DNA glycosylases remove affected base by cleaving N-glycosidic bond to create apurinic/apyrimidinic site
Site filled in using a DNA polymerase that ultilises the undamaged string as a template

Question 24

What is nucleotide excision repair?

Answer 24

Two phosphodiester bonds from either side of DNA lesion hydrolysed
Short damaged region removed and gap filled by DNA polymerase which uses undamaged strand as a template

Question 25

What are gross chromosomal rearrangements?

Answer 25

Large scale deletions, translocations and insertations

Question 26

What do mutations in genes involved in DNA repair pathways often lead to?

Answer 26

Genome instability and increased cancer risk