DNA Repair

Question 1

What may break down DNA molecules?

Answer 1

Thermal degradation

Metabolic byproducts (like oxidation)

Evironmental substances like benzopyrene

Radiation - such as UV light and nuclear

Question 2

What are purines and pyrimidines?

Answer 2

Purines are adenine and guanine

Pyrimidines are cytosine and thymine

They have similarities

Question 3

The similarities between purines and pyrimidines?

Answer 3

Guanine and thymine (remember they are in different groups) but they both have carboxyl groups

Adenine and cytosine both have amine group

Question 4

What exists between base pairs in the DNA double helix?

Answer 4

Hydrogen bonds

There are 3 between C and G

two between A and T

Question 5

What is important to note about thymine and hydrogen bonding?

Answer 5

There is a methyl group which has doesn’t participate in methyl bonding.

Question 6

What happens to cytosine in DNA damage? And how is this caused?

Answer 6

Water can cause cytosine to break down into uracil in a process called hydrolytic attacks

Remember uracil is good for DNA replication but bad in this instance

Question 7

What is the problem when cytosine breaks down to uracil? What structure is uracil similar to?

Answer 7

When a cytosine becomes uracil due to DNA damage, it can no longer make adequate hydrogen bonding to guanine

Uracil is similar to thymine as both have a carboxyl group

Thus if cytosine breaks down to uracil, because its structure is similar to thymine, it binds to free floating adenines instead of guanines.

This leads to mutatuin

Question 8

Cytosine deamination commonality?

Answer 8

Very common

Question 9

What are all of the DNA bases susceptible to?

Answer 9

Oxidative attack or hydrolytic attack by water.

Question 10

Another problem of cytosine becoming uracil?

In reference to new DNA strands

Answer 10

In DNA replication it causes new DNA strands to have an Adenine in the site where there should be a guanine

As the uracil binds to adenine but not guanine

This caused further mutation.

Question 11

What are transition mutations?

Answer 11

When one purine mutates and becomes the other

Or when one pyrimidine mutates to become the other pyrimidine

Question 12

Transversion mutation?

Answer 12

When a purine becomes a pyrimidine or visa versa

Question 13

What is the most likely mutation to occur between the bases? and why?

Answer 13

Transition mutations are more likely

Because substituting one double ring for another double ring structure is more likely than substituting a double structure for a single ring structure

Note purines have a double ring structure and pyrimidines have a single ring structure

Question 14

What is the structure of purines and pyrimidines in terms of ring structures?

Answer 14

Note purines have a double ring structure and pyrimidines have a single ring structure

Question 15

Examples of transition mutations?

Answer 15

A -> G

C -> T

Question 16

Transversion mutation examples:

Answer 16

A —> C or T
G —> C or T
C —> A or G
T —> A or G

Question 17

Failure to repair DNA issues? And an example?

Answer 17

Causes mutations

An example is a frameshift mutation

This is when a purine or pyrimidine is lost from the DNA strand

In the example of DNA replication:

• an adenine may be lost from the template strand
• this means that the new strand doesn’t have a T as the base it binds to is missing
• these cause frameshift mutations

Question 18

What can frameshift mutations cause?

Answer 18

They can lead to missense mutations - this causes different amino acids to be coded for due to changes

Question 19

What is photolytic conversion? What do they involved?

Answer 19

Remember both thymine and cytosine have carbon carbon double bonds. These a pyrimidines remember

These are very vulnerable to light specifically UV light

Everytime you are in sunlight these double carbon bonds breakdown in the pyrmidines.

This causes two pyrimidines like two thymines to bind together and become stuck together.

This distorts the DNA structure affecting DNA rep

Question 20

What is it called when two pyrimidines bind together due to photolytic conversion?

Answer 20

This is called DNA replication

Question 21

What is important to note about DNA constantly under attack?

Answer 21

There is a selection pressure to repair

Question 22

How do you overcome depurination? What is the pathway called and what are the three key enzymes involved?

This is when a cytosine becomes a uracil after losing a amine

Answer 22

You overcome this with the BER pathway

Glycosylase enzyme

• on each DNA strand there is a glycosylase enzyme which is a repair enzyme
• they move along the DNA strand
• if they detect a inappropriate base like uracil then the glycosylase removes a base

Endonuclease / phosphodiesterase

• you then have a phosphodiesterase which removes the DNA backbone
• this causes there to be a gap in the DNA

DNA liberase

• this gap has a small substrate for DNA liberase to bind to
• this allows for insertion of the correct base which isnt uracil

Question 23

How do BER glycosylases work?

Answer 23

• They use a base flipping strategy to identify errors

- they flip the incorrect base out by checking if the base fits its active site. If the base does then it is removed.

Question 24

How are pyrimidine dimers fixed?

Remember these dimers are caused by photolytic conversion from uv light when the carbon carbon double bond of adjacent pyrimidines becomes hydrolysed. This causes pyrimidines like C and T to become bound together.

Answer 24

An excision nuclease comes along and recognises the pyrimidine dimers

These then cut out 12 base pairs of the DNA sequence around the pyrimidine dimers to remove it.

DNA helicase then separates this small double stranded

DNA polymerase plus DNA ligase then synthesises the correct sequence again removing the pyrimidine

This is also called long patch base excision or nucleoside excision repair.

Question 25

What are trans lesional DNA polymerases? When do they come into play? What is the negative impact of these polymerases

Answer 25

There’s are polymerases

These come into play when the standard DNA polymerase comes off of the sliding clamp when it meets aberrant DNA

These trans lesional DNA polymerases are then assembled onto the DNA

However negative impact?

• they allow replication to occur as they sythesise the template strand across the damage aberrant DNA
• however this means replication is incorrect

Question 26

Why are translesional DNA polymerases bad?

Answer 26

This is because they lack precision in template recognition and substrate base choice

They also dont have exoncleotyic proof reading activity - to check what theyve done

But essentially they polymerise over aberrant DNA. Which means incorrect information is replicated

Question 27

What do trans lesional DNA polymerase lead to?

Answer 27

It leads to most base substitution or single nucleotide deletion mutations

It allows DNA to replicate. But this is inaccurate.

This can be good or bad

Question 28

Whats wrong with double strand breaks in DNA?

Answer 28

These are hazardous

Because There is no template for repair

Question 29

What are DNA double strand breaks caused by?

Answer 29

They are caused by ionising radiation

Replication errors - such as when replication forks break

Oxygen radicals

Question 30

What are the two ways to fix chromosome double strand breaks?

Answer 30

Homologous recombination

Non homologous recombination.

Question 31

Describe non homologous ways of repairing a double DNA strand break:

Answer 31

When there is a double strand break, the ends of the DNA molecules are stuck back together

There is a little bit of DNA processing too

However as these strands have broken you may be missing DNA

Thus in joining the DNA sequence there may be missing parts of the sequence

Question 32

So whats the negatives of non homologous end joining in the DNA strand?

Answer 32

The broken strand may have missing genes

Thus when stitching the DNA back together there may be a frameshift change generating a missence amino acid to form

Thus this system is error prone

The end joining also has template specificity

Question 33

Describe the process of homologous recombination:

Answer 33

After the DNA double strand is broken you get processing of this DNA nucleases

This allows DNA to use the template of the homologous chromosome to restore structures that might be lost.!! (Emphasis) this is why this is so accurate

This corrected strand is then cut out and inserted into ANOTHER DNA strand (of another homologous chromosome. )

This means the template strand is replicated

This system is VERY accruate

Question 34

If you lack repair enzymes and thus have damaged DNA what phenotype may you get?

Answer 34

Xeroderma pigmentosa and other human disease.