Oct 18

Question 1

What are the agents that deaminate DNA bases?

Answer 1

Nitrous acid

Question 2

Whwere are 5-methylcytosines found in DNA?

Answer 2

Found in CpG island, found in promotor regions to initiate DNA transcription.

Question 3

What happens if Cytosine is deaminated?

Answer 3

It becomes uracil, then CG ->UA ->TA

Question 4

What happens if Guanine becomes deaminated?

Answer 4

It becomes xanthine, it pairs with cytosine so still GC

Question 5

What happens if adenine becomes deaminated?

Answer 5

It becomes hypoxanthine, it pairs with Cytosine so AT becomes GC

Question 6

What site is created when hydrolysis breaks glycosidic bond? What happens after?

Answer 6

It leaves an abasic (apurinic or apyrimidinic site). OH is left on sugar in the place it was bonded to the base. The sugar is then unstable and can form open aldehyde form. THen hydrolysis can attack it and so DNA backbone can break

Question 7

What happens when DNA bases are oxidized by ROS? Where does it happen on bases?

Answer 7

It happens on the double bonds of bases, so especially thymine with C=C bond. A OH is put on each of those carbons, now blocks DNA polymerase.

Question 8

What is the product of an oxidized thymine and guanine by an ROS? What do these product bind to?

Answer 8

Thymine glycol and 8-oxo-guanine. Thymine glycol pairs with A or G. 8-oxo-guanine pairs with A so get GC to TA

Question 9

What parts of DNA bases get alkylated? What type of attack happens?

Answer 9

On the oxygen of C=O, or on the nitrogen not part of glycosidic bond. Nuclophillic attack by an electrophile CH3-

Question 10

What happens when S-adenosylmethionine (SAM) methylates Adenine on DNA?

Answer 10

Get methyl on N6 of adenine, DNA functions like RNA

Question 11

What do sodium nitrate, nitrous acid, and bisulfite HSO3- do to DNA bases? What is left in place of NH2 if it is removed? What happens to the resulting of each base pair?

Answer 11

They deaminate bases ACG. C=O is left in place of CNH2
AT -> hypoxanthine-T -> GC
CG ->UG -> TA
GC -> xanthine-C -> GC

Question 12

Y or N, can multiple chem modifications havppen simultaneously on same base?

Answer 12

Yes

Question 13

What does ionization like UV light do to bases? What is product of thymine and thymine. Can it happen with other bases?

Answer 13

Makes interbase cross links. Especially thymine with another thymine using the double C=C bonds, they make cyclobutane pyrimidine dimer. It happens with TC, CT, or CC base pairs too, they bond with 1 bond not 2 like thymin-thymine

Question 14

What effect does intrastrand crosslinking of bases do to DNA strand?

Answer 14

It induces a kink in the DNA, blocks DNA poly, it stalls

Question 15

What does ionizing radiation do to water (radiolysis)

Answer 15

If forms H2O+, so get OH radicals, then H2O2, O2 radicals.

Question 16

What are intercalating agents? What is the resulting effect on DNA transcription

Answer 16

They are chemicals that mimic base pairs, go between stacked bases. DNA poly will skip these regions and so get indels = shift mutations

Question 17

What is a intercalating agent to remember (hint for SDS page gel staining)

Answer 17

Ethidium bromide

Question 18

What is result of hydroxylamine mutagen on DNA base? What DNA base affects and what is result?

Answer 18

It is NH2 becomes NH(OH). Affects cytosine, so becomes hydroxylaminocytosine, pairs with adenine. Get CG ->HAC-A -> TA

Question 19

What is the analogue of thymine? The keto and enol role and result?

Answer 19

It is 5-bromouracil, it exists in enol and keto form. Keto binds with A so fine, but the enol form pairs with G, so TA becomes CG

Question 20

What is the adenine base analog, what form of it will mispair?

Answer 20

It is 2-amino purine, the NH2 from position 6 moves to 2, and will pair with thymine still. Only when protonated at the N1 will it pair with cytosine so turn AT to GC