DNA mutation and repair

Question 1

What helps keep the fidelity of DNA replication

Answer 1

Relatively low error rate of DNA polymerase
3’->5’ exonuclease proofreading
Cells have repair systems that increases error rat 1000x fold

Question 2

Sources of DNA Damage

Answer 2

DNA replication errors
Reactive cellular metabolites
Chemicals
High energy radiation
Mobile genetic elements

All lead to a premutational damage where a few things can happen to the damaged DNA

1. nothing-> cancer
2. chop out messed up DNA and replace
3. reverse the damage
4. just accept the base pair

Question 3

Major sources of DNA mutation

Answer 3

1. Mis-incorporation of nucleotides during DNA replication
2. Inherent chemical instability of bases
   (nonenzymatic) Deamination of C–> U
   Hydrolysis of N-gylycocsidic linkage-depurination
3. Environmental mutagens
   Deaminatig agents (c->u or g->x)
   alkylating agents (puts bulky group on the nt)
4. ionizing radiation
   UV light -> pyrimidine dimers

Question 4

Misincorporation of nucleotide during DNA replication

Answer 4

Its supposed to be A-T and G-C

but sometimes adenine undergoes a tautamer that makes it want to bind to G

Question 5

Inherent chemical instability of bases (nonenzymatic)

Answer 5

randomly a C will turn to a U or
A hydrolysis will just randomly occur and drop the purine (de purination)
so youll have the backbone without the actual nucleotides

Question 6

Environmental mutagens

Answer 6

Chemical mutagens: deaminating agents (c-> U or a g-> X) nitrous acid precursors can lead to deamination

Alkylating agents can put bulky groups DNA
DMS-> OMG (that leads to G-T pairing)

Question 7

Ionizing radiation

Answer 7

UV light can cause pyrimidine dimers which need photolyase repair (via bacteria

Question 8

Intercalating agents

Answer 8

Lead to insertion/ deleltion of base which causes frameshift mutations

Question 9

What has to happen so that damaged DNA can be repaired

Answer 9

Cell must:
sense the damage done
activate appropriate changes in the cell environment (ie cell cycle, apop)
activate repair mechanisms
Prioritize which damage to repair first (you would want to repair proliferating cells but it doesnt matter if theres a cell that is going to die)

Question 10

Types of Repair of DNA damage

Answer 10

1. Mismatch repair (fixes mismatches)
2. Base excision repair (remove bad bases)
3. Nucleotide excision repair (remove large structural damages (thymidine dimers)
4. Direct repair: OMG and photolyase
5. Recombinational repair (uses sister chromosome)

Question 11

DNA methylation and mismatch repair

Answer 11

• As DNA gets synthesized, it is unmethylated for a period of time, but the template strand is still methylated from before “hemimethylated DNA”
• When DNA has a mismatch mut S and mut L come in a complex and Mut H comes in and nicks the new strand of DNA (unmethylated)
• Exonuclease comes in and dissolves the unmethylated DNA until the nick, DNA polymerase, ssbinding proteins and ligase refill the segment

Question 12

Base excision Repair

Answer 12

Deamination of C-> U
DNA Glycosylase/ glycosidase recognizes the uracil, Ap endonuclease cleaves the phophodiester back bone and DNAP 1 uses 5’>3’ exonuclease activity and replases the repair and ligase seals the nick

Question 13

Nucleotide (BASE) excision repair

Answer 13

Xeroderma pigmentosum (deficiet in excision repare)

use an excinucluease, DNA helicase polymerase e, and ligase

UVR a b (bind) c (cut) and D scans for thymidine dimers, causing a nick, D will take out the messed up polymerase and ligase

Question 14

Direct repair

Answer 14

when the damages is enzymatically reversed

g-> OMG is reversed with MGMT (can be targeted for Cancer)

Question 15

Recombination repair

Answer 15

Things linke double strand damage need to be repaired from the a separate chromosome. the lesions come from the ionizing radiation and oxidative reactions

Homologous recombination repair (occurs in late S or early G2 phase)

Non homologous occurs in G1 phase