chapter 5.3

Question 1

colon cancer

Answer 1

mismatch repair

Question 2

skin cancer

Answer 2

nucleotide excision repair

Question 3

what are two most frequent spontaneous chemical reactions that cause serious DNA damage in cells

Answer 3

depurination and deamination

Question 4

deamination of adenine

Answer 4

hypoxathine

Question 5

deamination of guanine

Answer 5

xanthine

Question 6

deamination of cytosine

Answer 6

uracil

Question 7

deamination of thymine

Answer 7

NONE

Question 8

what is deamination (for dummies)

Answer 8

the removal of an amine group from a base

note: if the normal C is paired with a G and is then deaminated, it will become a U. then, this U will be replicated and paired with an A and then this sequence is mutated

Question 9

is deamination spontaneous

Answer 9

yes!

note: it is estimated to occur 100 times per day in every human cell

Question 10

deamination can lead to……

Answer 10

point mutations if not corrected

Question 11

how is deamination fixed

Answer 11

base-excision repair

Question 12

what is depurination (for dummies)

Answer 12

the loss of a purine base (A or G)

the A or G is cleaved out at AP (apurinic) sites

Question 13

what usually happens as a result of depurination

Answer 13

transversions! the missing base is normally replaced with a T

Question 14

is depurination spontaneous

Answer 14

yes!

Question 15

when does base excision repair occur

Answer 15

prior to DNA replication

Question 16

when does mismatch excision repair occur

Answer 16

mainly post DNA replication

Question 17

when does nucleotide excision repair occur

Answer 17

prior to DNA replication

Question 18

when does proofreading by DNA polymerase occur

Answer 18

during DNA replication

Question 19

what does non-homologous end joining and homologous recombination fix

Answer 19

double stranded DNA breaks

Question 20

what are the main enzymes in base excision repair

Answer 20

DNA glycosylase - cut out wrong base (chop it out)
APEI endonuclease + AP lyase- cut out backbone
DNA Pol Beta + DNA ligase - add the correct base back in and repair the backbone (sew everything back up together and make it look cute again)

Question 21

what enzyme recognizes the unusual nucleotides and how does it do this

Answer 21

DNA glycosylases and base flipping

Question 22

what is base flipping (for dummies)

Answer 22

DNA glycosylase flips a base completely out of the double helix to check it out when it thinks it’s the wrong base paired into the helix

Question 23

what does mismatch excision repair fix

Answer 23

errors that remain in DNA after proofreading by DNA polymerase

Question 24

what are the steps of mismatch excision repair

Answer 24

1. removal of the mutation by a nuclease
2. gap filling by DNA polymerase
3. sealing of the nick by DNA ligase

Question 25

what kind of damage does UV radiation cause

Answer 25

pyrimidine dimers

Question 26

what are thymine dimers + how do they happen (for dummies)

Answer 26

UV radiation gets thymine overly excited and makes it want to bond with its friends so it creates a C-C bond between itself and an adjacent thymine (its friend)

Question 27

what do T-T dimers interfere with

Answer 27

replication and transcription

Question 28

what mechanism fixes T-T dimers

Answer 28

excision repair

Question 29

what does nucleotide excision repair fix

Answer 29

DNA regions containing chemically modified bases that distort the normal shape of DNA

Question 30

how does DNA synthesis get around DNA lesions

Answer 30

DNA lesions cause DNA replication to stall so DNA polymerase delta or epsilon are momentarily switched out for an error-prone DNA polymerase that simply *overlooks* the bump in the DNA and moves right along and the lesion is bypassed! after, the polymerases switch back this is called translesion synthesis

Question 31

what is the difference between base excision repair and nucleotide excision repair

Answer 31

BER - one single base NER - often chunks of the backbone to fix pyrimidine dimers

Question 32

nonhomologous end joining

Answer 32

1. synapse forms at the broken ends of the double-stranded break by DNAPK 2. nucleases remove bases from the DNA ends 3. the two molecules are ligated together with several base pairs missing note: error prone because base loss causes genetic mutation and incorrect rejoining can cause chromosomal rearrangment

Question 33

nonhomologous end joining (for dummies)

Answer 33

at the double stranded break, DNAPK ("dna pick") comes and PICKS the two molecules up, cuts the torn ends so they line up, and sews them together without caring what is cut off (error prone)

Question 34

homologous recombination

Answer 34

genetic exchange at equivalent positions along two chromosomes with substantial DNA sequence homology

Question 35

how does homologous recombination fix DNA damage

Answer 35

causing the exchange of large regions of chromosomes between the maternal and paternal pair of homologous chromosomes