Mbg Exam 2

Front 1

irreversible state of dormancy for a cell

Back 1

senescence

Front 2

three outcomes of too much DNA damage

Back 2

apoptosis, senescence, unregulated cell division forming a tumor (cancer)

Front 3

unfiltered sunlight causes this damage to dna

Back 3

pyrimidine dimers

Front 4

procarcinogen that intercalates into DNA, covalently bonding to the guanine bases at the N2 position, distorting the DNA

Back 4

benzo[a]pyrene
active form is benzo[a]pyrene diol epoxide

Front 5

base deamination is a type of DNA damage that turns each of these into
Cytidine
Adenine
Guanine
5-methyl cytosine

Back 5

Cytidine to uracil
Adenine to hypoxanthine
Guanine to xanthine
5-methyl cytosine to thymine

Front 6

chemical modification of bases by ROS reactive oxygen species: can turn thymine into

Back 6

thymine glycol

Front 7

normal metabolism leads to this dna modification

Back 7

alkylation

Front 8

normal biological methyl group donor thatreacts accidentally with DNA to produce alkylated bases like 3-methyladenine

Back 8

S-adenosylmethionine

Front 9

three steps of dna repair

Back 9

recognize specific forms of DNA damage, remove damage, and repair it

Front 10

patients with xeroderma pigmentosum lack this form of repair

Back 10

nucleotide excision repair

Front 11

werner syndrome, which produces early aging, has a problem with this part of DNA repair

Back 11

helicase

Front 12

single bases in DNA can be chemically changed, for example by deamination or alkylation, resulting in incorrect base-pairing. base excision repair involves first flipping the mutated base out of the DNA helix and then repairing the base alone.

Back 12

base excision repair

Front 13

this system recognizes bulky modifications of bases, such as uv thymine dimers, which distort the shape of the DNA helix. this system removes a short single stranded dna segment that includes the lesion, creating a single strand gap in the DNA, which is filled by DNA polymerase

Back 13

Nucleotide excision repair

Front 14

these enzymes regconize and repair erroneous insertion, deletion and misincorporation of bases that can arise during DNA replication and recombination.

Back 14

mismatch repair

Front 15

three enzymes essential for Base Excision Repair (BER)

Back 15

DNA glycosylase
AP endonuclease
deoxyribose-phosphate lyase

Front 16

this enzyme in BER removes damanged DNA bases by cleaving the N glycosidic bond between the target base and deoxyribose to create an AP site (apurinic/apyriminic)

Back 16

DNA glycosylase

Front 17

BER enzyme that recognizes the AP site and nicks the damaged DNA on the 5' side (upstream) of the AP site

Back 17

AP endonuclease

Front 18

BER enzyme that removes the single, empty, sugar-phosphate residue. then dna polymerase and dna ligase complete the repair process

Back 18

deoxyribose - phosphate lyase

Front 19

what enzyme in BER has many forms to cut out many different errors?

Back 19

DNA glycoslyase
each recognize different damaged bases, like oxoG (oxidated guanosine) (there are two, one that removes from C and one that removes from A)
also one for uracil, one for thymine to guanine, and others

Front 20

how to fix pyrimidine dimers

Back 20

nucleotide excision repair

Front 21

six steps of NER

Back 21

1. damage recognition
2. binding of a multi-protein complex at the damaged site
3. double incision of the damaged strand several nucleotides away from the damaged site, on both the 5' and 3' sides
4. removal of the damage-containing oligonucleotide from between the two nicks
5. filling in of the resulting gap by DNA polymerase
6. ligation

Front 22

three diseases associated with NER defects

Back 22

Xeroderma pigmentosum
cockayne's syndrome
trichothiodystrophy

Front 23

NER of pyrimidine dimer in e coli:

Back 23

1. uv specific endonuclease uvrABC ase recognizes the dimer, and cleaves the damaged strand at the phosphodiester bonds on both the 5'side and the 3' side of the dimer
2. damaged nucleotide is released, leaving a gap in DNA
3. gap filled by DNA pol I
4. nick sealed by ligase

Front 24

in DNA mismatch repair, how do we know which is right base and which is wrong?

Back 24

strands are hemimethylated; parent strand is methylated, daughter strand is not methylated yet, so we can easily tell

Front 25

dna mismatch repair fixes what issues?

Back 25

erroneous insertion, deletion, and mis incorporation of bases as well as some forms of DNA damage

mismatched bases are G/T, A/C, and base insertion/deletion loops (IDLs)

Front 26

in MMR, what base is methylated, and what bases are considered mismatches when methylated?

Back 26

adenine is methylated
methylated C and G are considered mismatches

Front 27

what do these proteins do
MutS, MutL, Mut...

Back 27

all Mut deal with mismatch repair

Front 28

MMR protein for damage recognition

Back 28

MutS

Front 29

MMR protein that is endonuclease

Back 29

MutH

Front 30

MMR protein DNA helicase

Back 30

MutU

Front 31

what polymerase is used in MMR

Back 31

DNA Pol III

Front 32

in MMR, couples the replicative machinery

Back 32

PCNA

Front 33

lynch syndrome AKA HNPCC is

Back 33

hereditary nonpolyposis colorectal cancer

Front 34

HNPCC is known to be associated with mutations in genes involved in the ...

Back 34

DNA mismatch repair pathway

Front 35

how does cysplatin work

Back 35

binds to the dna strand, forming a bubble that could be cut out by MMR, so it is better if cancer does not have MMR

Front 36

this system uses the enzymes that normally perform genetic recombination between homologous chromosomes during meiosis

Back 36

homologous recombination repair

Front 37

pathway that repairs double strand breaks in DNA, most common for double strand breaks

Back 37

NHEJ - nonhomologous end-joining repair of

Front 38

which dna repair mechanism is the only one that is error prone

Back 38

NHEJ