BCEM 393 - DNA Repair

Fill in the blank: the chemical agents that alter specific bases within DNA after replication is complete are called ___________.

Mutagens

Fill in the blanks: ___________ are chemical agents that alter DNA bases. DNA bases can be altered through ____________, __________, __________, __________, and _________.

Mutagens, oxidation, deamination, alkylation, UV radiation (and radon gas), x-ray exposure

Explain: guanine oxidation.

• Hydroxyl radical reacts with guanine to form 8-oxoguanine

• 8-oxoguanine base pairs with adenine

• After replication, one strand will have G:C and the other will have A:T

Fill in the blanks: in guanine oxidation, a ____________ reacts with guanine to form ___________, which base pairs with ____________. After replication, one strand will have G:C, and the other will have A:T.

Hydroxyl radical, 8-oxoguanine, adenine

Explain: how does the formation of 8-oxoguanine from guanine oxidation disrupt DNA?

8-oxoguanine base pairs with adenine. Following replication, one strand will have G:C and the other will have A:T

Define: deamination.

The removal of an amino group by reaction with H₂O

True or False: cytosine deamination to uracil happens about 500x per day per cell.

True

Fill in the blanks: in cytosine deamination, cytosine has an ____________ group removed by reaction with ___________, forming ____________, which base pairs with ___________.

Amino, H₂O, uracil, adenine

Fill in the blanks: in adenine deamination, adenine has an ___________ group removed by reaction with _________, forming ____________, which base pairs with ____________.

Amino, H₂O, hypoxanthine, cytosine

Fill in the blanks: cytosine is methylated to 5-methylcytosine to regulate gene transcription. In 5-methylcytosine deamination, 5-methylcytosine has an __________ group removed by reaction with ___________, forming _____________, which base pairs with ____________.

Amino, H₂O, thymine, adenine

Multiple Choice: deamination is unlikely to occur for which of the following bases?

a) Adenine

b) Thymine

c) Cytosine

d) Guanine

b)

Explain: why is deamination unlikely to occur in thymine?

Deamination is the removal of an amino group through reaction with H₂O. Thymine does not have an amino group like adenine, cytosine, and guanine

Define: alkylation.

The addition of a hydrocarbon

Fill in the blanks: aflatoxin B1 is a compound produced by molds that grow on peanuts and other foods. In the body, an enzyme converts this compound into a _______________. This agent reacts with the N-7 atom of ____________ to form a mutagenic adduct that frequently leads to the conversion of a _____ base pair into a _____ base pair.

Highly reactive epoxide (aflatoxin B1 epoxide), guanine, G:C, A:T

Fill in the blanks: UV lights __________ adjacent ____________ along the DNA strand. This results in a ____________ that creates a ___________ in the helix.

Covalently link, pyrimidine residues (e.g., thymine), pyrimidine dimer, bulge

True or False: damage and repair to DNA is occurring constantly, and often, repair will restore the genetic information.

True

Fill in the blanks: the steps for DNA repair are ___________, __________, and ___________.

Recognize, remove, repair

Fill in the blanks: in mismatch repair, a mismatch is recognized by ________. ________ binds and recruits ________, and an exonuclease excises the incorrect region. _________ fills the gap.

MutS, MutL, MutH (an endonuclease), DNA polymerase III

Fill in the blank: in mismatch repair in E. coli, the ____________ is taken to have the correct sequence.

Parental strand (which is methylated)

True or False: mismatch, direct, and nucleotide excision repair are all DNA repair methods used in humans.

False; mismatch and nucleotide excision repair are used in humans, but direct repair is not

Fill in the blanks: direct DNA repair is repair _______________. It can be done through ___________ cleavage of pyrimidine dimers by ____________, which uses energy of visible light to break _____________. This method of DNA repair does not happen in humans.

Without removing fragments of DNA, photochemical, DNA photolyase, cyclobutane ring

Fill in the blanks: nucleotide excision repair recognizes mutations that ____________. ________, an __________, cuts DNA at two sites, then __________ fills the gap and __________ repairs the phosphodiester backbone.

Distort the helix, UvrABC, exinuclease, DNA polymerase I, ligase

Fill in the blanks: in base excision repair, the defective base is flipped into ______________ and undergoes __________ cleavage. ___________ nicks the phosphodiester backbone, and ______________ removes the ___________ unit. __________ inserts the correct nucleotide and __________ seals the strand.

DNA glycosylases active site, glycosidic bond, AP endonuclease, deoxyribosephosphodiesterase, DNA polymerase I, ligase

Multiple Choice: pyrimidine dimers are repaired by (select all that apply):

a) Nucleotide excision repair

b) Base excision repair

c) Mismatch repair

d) Direct repair with photolyase

a), d)

Explain: DNA typically uses thymine instead of uracil, which is found in RNA. Why is that?

Cytosine deaminates to uracil ~500x per cell per day. The methyl group of thymine helps the cell find and detect the product of cytosine deamination (uracil) and distinguish it from thymine

Multiple Choice: oxidation damage is repaired by (select all that apply):

a) Nucleotide excision repair

b) Base excision repair

c) Mismatch repair

d) Direct repair with photolyase

b)

Multiple Choice: deamination damage is repaired by (select all that apply):

a) Nucleotide excision repair

b) Base excision repair

c) Mismatch repair

d) Direct repair with photolyase

b)

Multiple Choice: alkylation damage is repaired by (select all that apply):

a) Nucleotide excision repair

b) Base excision repair

c) Mismatch repair

d) Direct repair with photolyase

b), d)

Multiple Choice: UV radiation damage is repaired by (select all that apply):

a) Nucleotide excision repair

b) Base excision repair

c) Mismatch repair

d) Direct repair with photolyase

a), d)

Multiple Choice: replication errors are repaired by (select all that apply):

a) Nucleotide excision repair

b) Base excision repair

c) Mismatch repair

d) Direct repair with photolyase

c)