Repair DNA

Question 1

Describe pyrimidine dimers

Answer 1

Can be formed from T or C via photochemical reactions which induce the formation of covanent linkage. Thymine dimers can occur between neighbouring T (CPD). 6-4 photoproduct is an alternative dimer between the carbon at the 6 position of one ring and the carbon at the 4 position of another ring.

Question 2

What is depurination and deamination ?

Answer 2

Depurination is when a purine base is removed from the nucleotide and an apurinic site is left
Deamination can happen to cytosine turning it into uracile. These two reactions are the most common spontaneous reactions creating dangerous DNA damages

Question 3

What can happen if DNA damages are not fixed ?

Answer 3

If DNA damage is not fixed it may be passed on to daughter cells- increased cancer risks and decreased life span.

Question 4

DNA repair mechanisms for single strand breaks

Answer 4

Mismatch repair-deaminated C
Base-excision-replication errors
Nucleotide-excision-pyrimideine dimers.

Question 5

Describe the general steps for excision repair

Answer 5

1. locate damage
2. Excise damage
3. Fill in damage
4. Fix nick with ligase

Question 6

Describe BER

Answer 6

Base excision repair: repairs deaminated C->U. The base is removed with glycosylase. AP site is produced and the sugar-phosphate is removed by AP endonuclease. The gap is filled in with the correct nucleotide (DNA polymeras) and sealed by ligase.

Question 7

Describe MMR

Answer 7

Mismatch repair: Repairs erroneous insertion, deletion and mis-incorporation of bases that can arise during DNA replication. The mismatch is detected and the mispaired nuckeotide and its neighbours are removed. A new correct strand is synthesised by DNA polymerase and sealed in by DNA ligase.

Question 8

Describe NER

Answer 8

Nucleotide-excision repair responds to pyrimidine dimers. Once the damage has been detected, the surrounding DNA is opened to form a bubble. Enzymes cut the damaged region out of the bubble and the damage is repaired by DNA polymerase and sealed by ligase.

Question 9

Double stranded breaks are what and can cause damages how ?

Answer 9

The double stranded breaks are as the name would indicate a damage in both strands. The ds break effectively separates both strands and damage the continuity of the DNA. If the damage is not fixed it will cause the DNA to fragment into smaller pieces and ev. degrade. The DNA won’t follow through when the cell eventually divides.

Question 10

In what ways can ds breaks be repaired ?

Answer 10

Via homolohous recombination the damaged DNA will utilize a “guide” strand to accurately repair the damaged strand. This reparation is to be preferred since it limits the damages to none.
The non-homologous repair works by simply joining the ends together. After processing with DNA nuclease the ends are joined together with DNA ligase. The resulting DNA will have nucleotide loss where the break occured-deletion/mutation

Question 11

Two types of transposons exist

Answer 11

Replicative transposition: the DNA is converted to mRNA. The mRNA codes for two enzymes; revers transcriptase+integrase. RT will convert the mRNA back to DNA and with integrase the fragment will be incorporated into a target DNA. This creates a copy in the genome.
Cut-and-paste transposition: the gene codes for transposase. This enzyme will cut and paste the gene in the target DNA. Every element contains short inverted repeating DNA sequences which are recognized by transposase. No copy is produced, the transposition is conservative.