DNA Repair

Question 1

How can damaged be induced?

Answer 1

Spontaneously = depurination and deamination
Mutagen-induced

Question 2

What are the different mutagen0induced DNA damaged?

Answer 2

Pyrimidine dimers
Alklylation
Substitution, deletion, insertion
Frameshift mutations
Double-strand breakd

Question 3

What are the two types of point mutation?

Answer 3

Transition
Transversion

Question 4

What is a transition point mutation?

Answer 4

Purine or pyrimidine is replaced by another of the same kind

Question 5

What is a transversion point mutation?

Answer 5

Purine or pyrimidine is replaced by the other kind

Question 6

What do hydrolytic attacks cause?

Answer 6

Depurination
Deamination

Question 7

What is depurination?

Answer 7

Loss of purine base = A&G from DNA leaving a abasic site

Question 8

What happens if depurination and deamination is left uncorrected?

Answer 8

Lead to deletion or substitution of base pairs during DNA replication

Question 9

What happens in deamination?

Answer 9

Deamination of bases in DNA yields unnatural nucleotides

These unnatural nucleotides, which can be directly recognized and removed by specific DNA glycosylases

Question 10

What does deamination of C produces what?

Answer 10

C&raquo_space;> U which can be repaired by uracil DNA glycosylase

Question 11

What is the role of nitrous acid?

Answer 11

Oxidatively deaminates primary amines = producing transition mutations

Question 12

How is C converted to T?

Answer 12

Cytosine is methylated to 5-methyl cytosine
5-methyl cytosine deaminated to T

Question 13

What can happen when cells are exposed to UV radiation?

Answer 13

Formation of a dimer = between 2 pyrimidine bases

Occurs between two adjacent T or C

Question 14

Name alkylating agents

Answer 14

Nitrogen mustard
EMS
MNNG

Question 15

What are alkylating agents?

Answer 15

Chemical that add an alkyl group to another molecule

Question 16

What problems can nitrogen mustard cause?

Answer 16

N mustard can cross-link w DNA at N7 position of G

Results in chromosome break

Question 17

What happens to guanine bases when exposed to EMS and MNNG?

Answer 17

EMS yiels O6-ethylguanine
MNNG yields O6-methylguanine

Both of which can pair with T (instead of C)

Question 18

What mutations do intercalating agents cause?

Answer 18

Insertion and deletion mutations = frameshift mutations

Question 19

How do intercalating agents work?

Answer 19

They increase the distance between 2 consecutive base pairs

Replication of such DNA generates deletion or insertion of one or more nucleotides int eh newly synthsized DNA

Question 20

Give an example of intercalating agent

Answer 20

Ethidium bromide binds to DNA

Question 21

Missense vs Nonsense mutation

Answer 21

A missense mutation is a type of point mutation in which a single nucleotide change in the DNA sequence leads to the substitution of one amino acid for another in the protein sequence.

A nonsense mutation is a type of point mutation in which a single nucleotide change in the DNA sequence introduces a premature stop codon (nonsense codon) into the mRNA transcript.

Question 22

What does the Ames test assess?

Answer 22

Mutagenicity of compounds

Question 23

How does the Ames test work?

Answer 23

The bacteria is a auxotroph = meaning it cannot make Histidine so needs it to grow

Mix the test compound (potential mutatgent) and bacteria together

If there are colonies growing, the test compound is a mutagen

Need a control to compare basal mutation level

Question 24

Name repair pathways for DNA synthesis error

Answer 24

Proofreading by DNA polymerase (exonuclease)
Mismatch repair (mutSLH)

Question 25

Name repair of DNA modifications

Answer 25

Direct reversal of damage (photoreactivation repair) Excision repair = base or nucleotie By DNA glycosylase or apurinic/apyrimidinic (AP)

Question 26

Name repair of replication fork barriers

Answer 26

Translesion synthesis

Question 27

Name repair of breakd in DNA

Answer 27

Repair double-strand breaks by Homologous recombination Non-homlogous end joining

Question 28

What happens in proofreading?

Answer 28

3' to 5' exonuclease Checks from the newest base added If incorrect, removes it

Question 29

What is the job of midmatch repair?

Answer 29

Correct errors that remain after proofreading

Question 30

How does mismatch repair work in E.coli?

Answer 30

MutH endonuclease makes a nick on 5' side of unmethylated GATC (newly synthesized) UvrD (helicase) and exonuclease removes defective strand Unmethylated strand is corrected by DNAp III

Question 31

What does Dam methylase do?

Answer 31

Enzyme found in bacteria that adds a methyl group to the adenine base in the DNA sequence GATC

Question 32

What does photoreactivation repair do?

Answer 32

Removes pyrimidine dimers = C + T

Question 33

How does photoreactivation repair work?

Answer 33

Occurs only in bacteria PHOTOLYASE = photoreactivation enzyme Cleaves bonds between pyrimidine = light-dependent reaction

Question 34

What enzymes are needed for base excision repair (BER)?

Answer 34

DNA glycosylase cleaves the glycosidic bond = leaving apurinic or apyrimidinic site AP endonuclease cleave the phosphodiester backbone at AP site DNAp I and DNA ligase = restore base

Question 35

What does nucleotide excision repair require to function?

Answer 35

ATP and UvrA-D

Question 36

How does nucleotide excision repair occur?

Answer 36

UvrAB recognize damage UrvBC nicks DNA Urv D unwinds the marked region

Question 37

Why might nucleotide excision repair be needed and what diseases are caused without it?

Answer 37

UV-induced DNA lesions Xeroderma pigmentosum and Cockayne syndrome = unable to repair UV-induced DNA lesions

Question 38

When is translesion DNA synthesis or 'Error-prone repair' used?

Answer 38

When a lesion is encountered during replication = DNAp III is replaced by error-prone translaesion DNAp Pol IV or V

Question 39

What does the translesion DNAp do?

Answer 39

Extend DNA synthesis beyond the T dimer independent of base pairing Has no proofreading exonuclease activity

Question 40

What is non-homologous end joining and how does it work?

Answer 40

Accidental ds-break = loss of nucleotides due to degradation from end joining End recognition by KU heterodimers Deletion of DNA sequence = emergency repair