Mechanism Of DNA Repair

Question 1

The main DNA damaging agents are

Answer 1

UV light, Xrays, replication errors

Question 2

The main mechanisms if DNA repair Are?

Answer 2

Base excision repair, nucleotide excision repair, recombinational repair, mismatch repair

Question 3

Explain mismatch repair in E.coli

Answer 3

1- the MutS travels in a 5’-3’ direction when it is reading the 5’-3’ strand.
2- the area with the error will not be smooth like the rest of the DNA molecule and so the MutS recognises it and clamps together.
3- it uses ATP and recruits MutL(for the 3’-5’) and MutH(for the 5’-3’)
4- an endonuclease cuts away the damages portion
5- the DNA polymerase retranscribes it

Question 4

How does E.coli know which strand to repair

Answer 4

There is and enzyme DAM methylase, which methylated the A in a 5’- GATC-3’ sequence.
When a new DNA is formed it is for a brief period of time unmethylated, and the MutH only acts on unmethylated strands

Question 5

Detail mismatch repair in eukaryotes

Answer 5

There are MutS and MutL (MLH or PMS) homologues, there are many MutS as they are specific for different kinds of mutations. There is no DAM methylase nor any MutH

Question 6

How do eukaryotes know which strand to repair

Answer 6

For the lagging strand: the nicks between the okazaki fragments are equivalent to the single strand breaks formed by the MutH in E.coli
For the leading strand: there are ribonucleotides present here that act like nicks

Question 7

Explain microsatellite instability

Answer 7

Dinucleitide repeats are highly unstable, and present in Lynch syndrome (hereditary non polyposis colorectal carcinoma), is caused by defects in mismatch repair system

Question 8

Explain translesion synthesis

Answer 8

There is the polymerase switch for the leading strand, and the template switch for the lagging strand. It is a DNA damage tolerance process that allows the completion of DNA replication despite the presence of errors

Question 9

insertions and deletions are treated by

Answer 9

mismatch repair

Question 10

mismatch repair defects are associated with

Answer 10

cancer

Question 11

list the mechanisms of DNA repair in eukaryotes

Answer 11

~Nucleotide excision repair
~Base excision repair
~double stranded break repair (NHEJ or HR)

Question 12

explain the polymerase switch

Answer 12

there is a group of DNA pol named Z-K, that are dedicated to ease replicative stress, these enzymes can temporarily replace DNA pol alpha as it has a greater flexibility to accept non conventional base pairing. This is error prone

Question 13

the low fidelity of DNA polymerases

Answer 13

is responsible for a large fraction of point mutations induced by DNA damage

Question 14

what is nucleotide excision repair

Answer 14

the repair of damages causing a distortion of the double helix, they interfere with base pairing and they block transcription and replication. Are used when lesions are caused by exogenous agents

Question 15

Base excision repairs

Answer 15

are more specifically devoted to repair small chemical changes. Are used when lesions are caused by endogenous genotoxic agents

Question 16

the 2 subclasses of NER are

Answer 16

~global genome NER which checks the entire genome

~transcription coupled repair which repairs damages that block RNA polymerase

Question 17

the 2 helices are separated by

Answer 17

XPB and XPD which are subunits of the TFII H with helicase activity, then they are cut by XPF and XPG

Question 18

defects in the NER result in which 3 syndromes

Answer 18

~xeroderma pigmentosum
~cockayne syndrome
~trichothiodystrophy

Question 19

explain the process of base excision repair

Answer 19

a DNA glycosylase removes the modified base, an AP endonuclease recognizes the AP site and cuts at the 5’ end, a phosphodiesterase removes the sugar phosphate, a DNA BETA inserts the lacking nucleotide

Question 20

there are no diseases due to

Answer 20

BER genes

Question 21

when there is a DNA double strand break what are the 2 ways in which it is fixed

Answer 21

~ by End joining in the G1 pase where a second copy is not available–error prone
~by Homologous recombination in the S and G2 phase when DNA has been duplicated –error free

Question 22

non homologous end joining

Answer 22

~the KU complex recognizes the 2 broken ends are binds to them
~the KU-DNA complex recruits DNA-KPc proteins
~the 2 protein complexes join the ends and allow the entering of DNA ligase IV