Qiao 2

Question 0

What are transition and transversion mutations?

Answer 0

Transition: purine -> purine or pyr -> pyr
Transversion: pur pyr

Question 1

What is required for ligase to anneal a “nick?”

Answer 1

3’ OH end, 5’ phosphate end, dsDNA, ATP

Question 2

What are the main sources of DNA damage?

Answer 2

DNA replication errors (endogenous), spontaneous mutations (endogenous), environmental mutagens e.g. UV, IR, chemicals (exogenous)

Question 3

What are the two types of spontaneous mutation?

Answer 3

1. Base loss (depurination): water cleaves A/G base from backbone, leaves empty space
2. Deamination: cytosine deaminated to uracil and ultimately becomes thymine (C:G -> U:A -> T:A)

Question 4

Dietary nitrites react with stomach acid, forming ____, which causes _____.

Answer 4

Nitrous acid (HNO2), oxidative deamination (C to U, ultimately C to T)

Question 5

What are the products of cellular respiration that can cause oxidative DNA damage?

Answer 5

Reactive oxygen species (ROS) such as oxygen radicals, superoxide, and hydrogen peroxide

Question 6

When exposed to ______, two neighboring pyrimidine bases can form ______.

Answer 6

UV-B light (~260nm); cyclobutane pyrimidine dimers (CPD)

• They are usually thymine dimers but it can be any pair of pyrimidines.
• UV can also produce 6-4 pyrimidine pyrimidones, aka 6-4 photoproducts (6-4PPs).

Question 7

Polycyclic aromatic hydrocarbons (PAH), carcinogens found in cigarette smoke, lead to ________ mutations that cause lung cancer by disrupting ________ gene function.

Answer 7

G to T transversion; p53 tumor suppressor

Question 8

How does the Ames Test assess mutagenicity?

Answer 8

Mix the potential mutagenic compound with histidine-dependent bacteria and incubate in a histidine-free medium. If bacteria colonizes, that means the bacteria mutated and gained the ability to grow without histidine.

Question 9

What are the different cellular responses to DNA damage?

Answer 9

• Repair: direct reversal, excision (BER, NER, MMR), recombinational repair (HR, EJ)
• Checkpoint activation (transcriptional regulation, cell cycle arrest)
• Apoptosis
• Tolerance (polymerase does nothing)

Question 10

Direct reversal of DNA damage caused by UV light (thymine dimers, 6-4 PPs) is carried out by _____, which is NOT present in ______.

Answer 10

Photolyase; humans (use nucleotide excision repair for UV damage)

Question 11

Guanine can undergo ______ at its ___ position, resulting in a G:C to A:T transition mutation.

Answer 11

Alkylation (methylation); O6

Question 12

The DNA repair protein _________ repairs O6meG (O6alkG) by transferring the methyl group to its own _______ residue. This is an example of ____ repair.

Answer 12

O6-alkylguanine-DNA alkyltransferase (AGT); cysteine; direct

Question 13

Mismatch repair (MMR) is a type of excision repair that utilizes ___ proteins. When mutated, they cause _____.

Answer 13

Mut; hereditary nonpolyposis colorectal cancer (HNPCC) aka Lynch syndrome

Question 14

If ___ is abundant in a cell, it can remove O6meG quickly (direct repair). If it escapes direct repair, ____ proteins will deal with O6meG – T as a mismatch, but they cannot remove O6meG. This causes a ____ of pyrimidine removal/addition and generates ______ that result in _____.

Answer 14

AGT; MMR; futile cycle; ss- and dsDNA breaks; cell death

Question 15

In BER, incorrect bases are removed from the DNA backbone by _____, creating an _____. The mutated strand is nicked (phosphodiester bond is broken, still dsDNA) by ______, and then ____ cleaves deoxyribose, creating a free 3’ OH that DNA Pol and DNA ligase can use to finish the repair.

Answer 15

DNA-N-glycosylases; apyrimidinic (AP) site; AP endonuclease; deoxyribose-phosphate lyase

Question 16

The ___ gene recognizes the 8-OXOGuanine:A mismatch. Mutations in this gene lead to mutations in ___, a tumor suppressor gene for colorectal cancer.

Answer 16

MutY; APC

Question 17

A total of about 25 proteins are involved in _____, where double nicks in damaged DNA remove big chunks of DNA (usually caused by UV damage).

Answer 17

Nucleotide excision repair (NER)

Question 18

Deficiencies in nucleotide excision repair (NER) can cause ________ (diseases). NER is critical for repairing UV-induced damage because humans cannot do ____ since we don’t have ______.

Answer 18

Xeroderma pigmentosum, Cockayne’s syndrome, trichothiodystrophy; direct repair of photoproducts; photolyase

Question 19

Double-strand breaks (DSB) can be repaired through _______ (perfect repair) using undamaged _____ as a template. Error-prone repair can be done through _______, which uses _____, ____ and ____.

Answer 19

Homologous recombination (HR); sister chromatids; non-homologous end-joining (NHEJ); Ku heterodimer; DNA-activated protein kinase; ligase