DNA REPAIR

Question 1

DNA replication is very precision and so you would think there would be no need for repair. Although there are mechanisms in place to correct errors made in replication such as exonucleases, DNA molecules are not immune from chemical change. What potential damage can be done to DNA?

Answer 1

1. Thermal Degradation (heat/water)
2. Metabolic Byproducts (oxidation)
3. Environmental Substances
4. Radiation (UV, nuclear fission)

Question 2

All molecules are susceptible to chemical damage but why is it important the DNA can be repaired?

Answer 2

Because there are only two molecules of DNA and it contains the information for all other molecules.

Question 3

What are the pyrimidines?

Answer 3

Single C - N ring.

This consists of Cytosine and Thymine and Uracil.

Question 4

What are the purines?

Answer 4

A double C-N ring.

This consists of Adenine and Guanine.

Question 5

Which parts of DNA are vulnerable to attack.

Answer 5

The N=C-NH2 groups on Adenine and Cytosine.

The C=ONH groups on Guanine and Thymine.

Question 6

Cytosine and Guanine form how many bonds?

Answer 6

3 Hydrogen bonds

Question 7

Adenine and Thymine form how many bonds?

Answer 7

2 Hydrogen bonds

Question 8

Why does the Adenine Thymine pair only form 2 hydrogen bonds.

Answer 8

There is an methyl group of the Thymine that does not form hydrogen bonds.

Question 9

Loss of an amino group from Cytosine results in what?

Answer 9

Conversion to a Uracil.

This is called deamination.

Question 10

Thymine and Uracil are very similar in structure. What does this mean?

Answer 10

That Adenine can also bind with Uracil.

Question 11

What is the highest risk with hydrolytic attack?

Answer 11

It more commonly attacks the bond between the base and the phosphodiester backbone. This risks removal of the base completely.

Question 12

Failure to undertake DNA repair results in what?

Answer 12

Mutation.

When replicated, of of the new strands will be different.

Question 13

What types of mutation are there between bases?

Answer 13

Transition

Transversion

Question 14

Which type of mutation is more common?

Answer 14

There are 4 types of transversions and 2 types of transitions.
Despite there being more types of transversion, transition is more likely.

Question 15

Transition mutations are more common, how do this help in mutation?

Answer 15

Transition mutations are also less likely to result in amino acid substitutions. Since more than one codon allows for the same amino acid, most of the alternatives (at least in the 3rd base) are transitional.

Question 16

What is a frameshift mutation?

Answer 16

A mutation which means the triplet codon reading frame is altered. And so, every reading frame after the point of mutation is also altered. This usually generates missense proteins.

Question 17

The pyramidines contain a C=C double bond and are vulnerable to react with light. What does UV light induce?

Answer 17

Photolytic conversion.
UV light induces formation of pyramidine dimers. The C=C bonds react with one another meaning they are no longer free to bind with their complimentary bases.

Question 18

Which pathway seeks to repair depurination/deamination?

Answer 18

The Base Excision Repair Pathway.

Question 19

What is the Base Excision Repair Pathway?

Answer 19

There are a series of repair enzymes called glycosylases, one for each base type.
They use a base flipping method to test if it fits their active site. When an inappropriate base if found, it is cleaved from the DNA creating a hole. A combination of endonucleases and phosphodiesterases cleave the back bone leaving a gap. DNA polymerase can then fill in this gap.

Question 20

Pyrimidine dimers are repaired how?

Answer 20

Excision nucleases recognise the changed structure of the DNA molecule. It cleaves a 12 nucleotide long ssDNA out around the pyramidine dimer. DNA helicase unwinds it from the strands so that DNA polymerase and ligase can fill the gap. This is Nucelotide Exision Repair.

Question 21

Sometimes, replication is taking place before it can be repaired. Normal DNA polymerase cannot carry out replication on damaged DNA. How does replication still take place?

Answer 21

Trans-lesional DNA polymerase can replicate damaged DNA.
The sliding clamp releases normal DNA polymerase from the strand and trans-lesional DNA binds instead to bridge the gap. They do not carry out exonucleolytic proof reading activity and they lack precision. They are the leading cause of substitution and nucleotide deletion but it is a best case scenario and a driver of evolution.

Question 22

Why are double stranded breaks hazardous?

Answer 22

There is no template to facilitate repair.

Question 23

What causes double stranded breaks?

Answer 23

1. Ionising radiation
2. Replication errors
3. Oxygen radicals

Question 24

What are the two mechanisms that exist to repair double stranded breaks?

Answer 24

1. Non- homologous end joining

2. Homologous recombination

Question 25

What happens in non homologous end joining?

Answer 25

When the break occurs, the ends are processed and stuck back together again. Due to processing, some information may be lost, and there is a chance that the wrong strands are rejoined.

Question 26

What happens in homologous recombination?

Answer 26

When the break occurs, nucleases digest the ends of the broken strands and invade the homologous strand as a template for accurate replication.
There is a chance of loss of heterozygosity.

Question 27

What disease can lack of DNA repair enzymes cause?

Answer 27

Xeroderma pigmentosum as well as strong cancer links to any failure in repair systems.