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Flashcards in Lecture 7 Deck (42)
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What happens in patients with mutations in genes needed for homologous recombination

Homologous recombination is defective and thus these cells become critically dependant on other pathways for correct DNA repair i.e. base excision and nucleotide excision repair


What chemical modifications can lead to DNA damage

Hydrolysis, oxidation or random uncontrolled methylation


Draw a representation of a heteroduplex structure between two dsDNA molecules 

See image


Explain the process of nucleotide excision repair

An excision endonuclease enzyme cleaves the single strand of the DNA containing the defect by cleaving either side of the dimer etc. This creates a polynucleotide fragment from the DNA molecule that contains the defect which is then removed by DNA helicase. DNA polymerase then extends the primer template junction created to replace the excised sequence. This is followed by resealing of the nick mediated by DNA ligase.


Which base is primarily affected by UV light and more prone to form dimers



How can this defective recombination pathway seen in some cancers be harnessed as a cancer treatment

Combined inactivation of homologous recombination by mutations and the inhibition of base or nucleotide excision repair by anticancer drugs make cells that suffer DNA damage unable to make adequate repairs to their DNA and die. This is known as synthetic lethality.


What happens when cytosine is deaminated and what are the downstream effects of this

Converted to uracil. This will still pair with guanine but during replication the guanine will be replaced with an adenine, leading to a nucleotide substitution from CG-->TA


Homologous recombination is required to mediate genetic recombination and diversity created in meiosis, T or F



How many ways can the Double Holliday Junction be resolved



What is the most frequency types of DNA damage

Hydrolytic depurination and deamination of bases


Pyrimidine dimers can only occur between identical adjacent pyrimidine bases, T or F

F – it can be the same pyrimidine or different ones (i.e. T-C, T-T, C-C)


What are the products of genes encoded by the genes mutated in xeroderma pigmentosum

These genes encode proteins that participate in the nucleotide excision repair pathway


Nucleotide excision repair is only used to repair pyrimidine dimers, T or F

F – it is used to repair a variety of different types of DNA damage including pyrimidine dimers


dsDNA breaks are often caused by non-ionising radiation, T or F

F – they are caused by ionising radiation


What two methods are there of repairing dsDNA breaks

Non-homologous end joining, homologous recombination


Recall the purine bases

Adenine, guanine


What are the four main types of DNA damage

Deamination, depuration, pyrimidine dimers, DNA breaks


Explain how different resolutions of the Double Holliday Junction account for whether homologous recombination occurs or not

If the internal strands are broken and re-joined than the same DNA strands are broken and re-joined at each junction and recombination is not achieved as each chromatid will contain the same sequence of alleles it did prior to cleavage. If external and internal strands are broken and re-joined then different DNA strands are broken and re-joined at each junction. Hence recombination is achieved. This recombination of allelic forms results in chromatids with different combinations of alleles (Ab and aB)


Explain the process of non-homologous end joining

The ends of the double stranded break are rendered flush with loss of bases via degradation from the ends of the strands. These flush ends are then ligated together. However, this leads to a loss of DNA sequence due to the degradation that occurs prior to ligation.


What are pyrimidine dimers and what causes them

Pyrimidine dimers are caused by the covalent linkage of benzene rings in two adjacent pyrimidine bases. This is usually caused by UV light


What is significant about the function of the XP genes

Their function is tightly coupled and targeted to regions of the genome that are highly transcribed. This acts as a surveillance system to signify regions of the genome that are transcribed. RNA polymerase required for transcription is physically coupled to the DNA repair machinery


Xeroderma pigmentosum is a disease caused by defective nucleotide excision repair machinery, what is the effect of this on patients

XP renders patients extremely sensitive to sunlight-induced skin cancer


What does homologous recombination rely on

Using the intact DNA sequence information in the undamaged homologous chromosome


Homologous recombination also isn’t a perfect repair mechanism, T or F

F – homologous recombination provides a perfect repair of dsDNA breaks and is an accurate and preferred method of repair


Uvr genes are homologues of the XP genes found in yeast and are also transcription coupled, T or F



Put these enzymes in the order in which they act in Base Excision repair?

a - DNA polymerase, b - DNA glycosylase, c - phosphodiesterase, d - DNA ligase, e - apurinic/apyrimidinic endonuclease.

b, e, c, a, d


What is the results of the formation of pyrimidine dimers

This arrests DNA replication or can cause mis-reading of the DNA sequence by DNA polymerase


What is meant when we refer to non-homologous end joining being quick and dirty

Non-homologous end joining is a far from optimal repair mechanism. It is carried out quickly but in itself, can induce mutations


Recall the pyrimidine bases

Thymine, cytosine, uracil


Explain the process of depurination

The carbon to nitrogen bond between the carbon position one in the deoxyribose sugar and the nitrogen in the purine ring is hydrolysed. This releases the base and results in the loss of a base pair, nucleotide deletion, in one of the daughter DNA molecules produced during replication