Week 3

Question 1

What is a pro of genome instability?

Answer 1

Mutation and genetic variation is essential for evolution

Question 2

What is a con of genome instability?

Answer 2

Cna lead to cancer karyotype

Question 3

What are some factors that decrease genome stability?

Answer 3

DNA damage
Mistakes when copying DNA

Question 4

What are some methods used to try to maintain stability?

Answer 4

Avoid errors (replication)
correct errors (replication)
repair DNA damage

Question 5

What causes DNA damage generally?

Answer 5

Intrinsic and extrinsic factors (It’s pretty inert however it is still a chemical so can have chemical interactions)

Question 6

Define mutation

Answer 6

A permanent change to the DNA sequence of the genome

Question 7

Does DNA damage always result in mutation?

Answer 7

No.
If DNA damage goes unnoticed during replication, the mistake will be passed on and the sequence will be changed

Question 8

How can cell death be caused by damage to DNA?

Answer 8

1. Damage or lesion to DNA
2. DNA replication and transcription are blocked
3. Cell death

Question 9

What are the two forms of intrinsic DNA damage?

Answer 9

Spontaneooud hydrolytic damage
Adding bonds

Question 10

What are the two forms spontaneoud hydrolytic damage??

Answer 10

Depurination
Deamination

Question 11

Describe depurination

Answer 11

N glycosyl bond breaks leaving an abasic site
Loss of G and A is most common
(around 20,000 per human cell per day)

Question 12

Describe deamination

Answer 12

Deaminated cytosine becoems a uracil.
Deaminated 5-methyl cytosine becomes thymine which is harder to be found. CpG sequences are common hotspots for mutation. (500 per human cell per day)

Question 13

What are the two forms adding bonds?

Answer 13

oxidative damage, alykylation

Question 14

Describe alykylation

Answer 14

Alkylating agents transfer methyl or ethyl groups to DNA base.
Eg. methylation of O in guanine becomes O6 methylguanine which base pairs with thymine

Question 15

Describe oxidative damage

Answer 15

many ways that oxygen can damage…
eg. 8-oxo-guanine is one of the msot common.
base pairs ambiguosly with cytosine or adenine

Question 16

What are the three types of ectrinsic DNA damage?

Answer 16

Carcinogens
UV light
Cancer treatments

Question 17

Describe how carcinogens cause extrinsic DNA damage

Answer 17

Benzopyrene foound in coal tar and cigarette smoke, is metabolised and modifies guanine blocking DNA replication and transcription

Question 18

Describe how UV light cause extrinsic DNA damage

Answer 18

Most comon= Cyclobutane pyrimidine dimer (CPD)
Blocks transcription/ translation
Linked to skin cancer

Question 19

Describe how cancer treatment cause extrinsic DNA damage

Answer 19

Cisplatin binds to 2 guanine cuasing intrastrand crosslinking
Blocks replication
Treats a range of cancers

Question 20

What are the two types of DNA repairs that involve direct reversal?

Answer 20

DNA photolyases
DNA Alkyltrasferases

Question 21

Describe how DNA photolyases repair DNA

Answer 21

NOT PRESENT IN HUMANS
repairs UV induced photoproducts
energy derived from visible light is used to break cyclobutane ring structure, transferring energy to FADH-

Question 22

Describe how DNA Alkyltransferases repair DNA

Answer 22

PRESENT IN HUMANS
Catalytic cysteine acts as the acceptor for the alkylation group. Alkyltransferases becomes alkylated then dies

Question 23

WHat is the most common type of DNA lesion in normal cells?

Answer 23

Abasic sites

Question 24

What is the most common form of DNA lesion caused by UV light?

Answer 24

Cyclopryrimidine dimers

Question 25

What unusual feature of DNA Alkyltransferases is taken as an indication of the strong evolutionary pressure to repair DNA?

Answer 25

It is not a true catalyst

Question 26

Describe the general strategy of DNA exision repair

Answer 26

1. Find DNA damage 2. DNA glycosylase cleaves Nglycosyl bond, releasing base 3. cut on either side of the damage 4. AP endonuclease cleaves the backbone on the 5' side on abasic side 5. DNA polymerase inserts a single nucleotide to fill the gap 6. dRP lyase cleaves the backbone on 3' side releasing damged flap 7. Damaged section is removed 8. Copy undamaged strand 9. Ligase seals the nick

Question 27

How can DNA glycosylase access a faulty base in dsDNA?

Answer 27

base flipping enzyme can put faulty base into active site whihc has hi specificty

Question 28

Describe nucleotide exision repair in bacteria

Answer 28

1. UvrA2 detects distrotability of DNA 2. UvrA2 gets UvrB2 to double check that there is damage 3. UvrA2 dissociates 4. UvrB2 remians, recruits UvrC 5.UvrC cleaves 4/5th bond upstream of lesion, and 8th bond downstream 6. UvrD displaces faulty section 7. gap filling, ligation

Question 29

Base vs nucleotide excision pathway Whats the difference between their substrates?

Answer 29

BER= non bulky lesions, mostly intrinsic NER= bulky lesions, mostly extrinsic

Question 30

Base vs nucleotide excision pathway What are some examples of their substrates?

Answer 30

BER= U, TandG, 8oxoG, methylated A NER= CPDs, large alykylating products, cisplatin

Question 31

Base vs nucleotide excision pathway Whats the difference between their damage recognition?

Answer 31

BER= specific, unique ezymes NER= not as specific

Question 32

Base vs nucleotide excision pathway Whats the difference between their DNA cleavage?

Answer 32

No difference- DNA is cut either side of damage

Question 33

Base vs nucleotide excision pathway Whats the difference between their repair patches?

Answer 33

BER= 1 nucleotide long NER= e.coli- 12-13 nt humans- 24-32 nt long

Question 34

What is caused by mutations in DNA exision repair?

Answer 34

Xeroderma Pigmnetosum

Question 35

What dsDNA breaks happen accidentally?

Answer 35

Ionizing radiation DNA damaging agents dessication (spores) Weird nucelase activity Replication past DNA nick

Question 36

What dsDNA breaks happen on purpose?

Answer 36

Meiotic recomb VDJ recomb

Question 37

How are single ended dsDNA breaks created?

Answer 37

replication over a ssDNA break

Question 38

What are the three basic steps to non homologous end joining?

Answer 38

1. Ku70/80 binds to each end 2. DNA Pkcs binds 3. Complex containing ligase binds DNA and joins the end

Question 39

Why is NHEJ subject to errors?

Answer 39

-no requirement for homologous donor -can occur at any stage in cell cycle