DNA Repair and Recombination

Question 1

mutations repaired by mismatch repair

Answer 1

*replication errors; mismatch without damage or modified base; mismatch is recognized by distortion of double helix
*mechanism: mismatched nucleotides in newly synthesized strand are removed and gap is filled and resealed
*occurs predominantly in S phase of cell cycle
*defective in Lynch syndrome (Hereditary nonpolypoposis colorectal cancer)

Question 2

mismatch repair in prokaryotes

Answer 2

-“A” on 5’-GATC-3’ is methylated on parent strand, so we know which is the “correct” strand
-Mut proteins carry out mismatch repair (Mut H, Mut S, and Mut L)
-DNA polymerase fills the gap and DNA ligase seals it together

Question 3

MutH

Answer 3

protein in prokaryotic mismatch repair that binds the GATC site and nicks DNA

Question 4

MutS

Answer 4

protein in prokaryotic mismatch repair that binds the mismatch

Question 5

Mut L

Answer 5

protein in prokaryotic mismatch repair that binds the MutS and MutH together

Question 6

mismatch repair in eukaryotes

Answer 6

-used for single-nucleotide mismatches
-mechanism for recognizing the parent strand is unclear
-Mut homologs (MSH, MLH, and PMS proteins) carry out the mismatch repair

Question 7

mutations repaired by base excision repair

Answer 7

-deaminated bases
-depurinated bases (abasic sites)
-methylated bases

Question 8

steps of base excision repair

Answer 8

1) glycosylase creates an apurinic (AP) site
2) AP endonuclease recognizes AP site and cuts 5’ phosphodiester bond
3) AP lyase cuts 3’ phosphodiester bond
4) DNA polymerase fills gap
5) DNA ligase seals nick

Question 9

glycosylase

Answer 9

an enzyme in base excision repair that cuts the N-glycosidic bond between sugar and base, creating an abasic site

Question 10

AP endonuclease

Answer 10

an enzyme in base excision repair that recognizes the AP site and cuts the 5’ phosphodiester bond

Question 11

AP lyase

Answer 11

an enzyme in base excision repair that removes the sugar by cutting the 3’ phosphodiester bond

Question 12

mutations repaired by nucleotide excision repair

Answer 12

removes a wide variety of lesions, photoproducts, and chemical adducts, especially large adducts like pyrimidine dimers

Question 13

steps of nucleotide excision repair

Answer 13

1) XP proteins recognize lesion (called Uvr in prokaryotes)
2) excision nucleases (excinucleases) make incisions 5’ and 3’ to lesion
3) helicase releases damaged oligomer
4) DNA polymerase fills the gap
5) DNA ligase seals the nick

Question 14

XP proteins (Uvr proteins in prokaryotes)

Answer 14

proteins in nucleotide excision repair that recognize the lesion

Question 15

excision nucleases (excinucleases)

Answer 15

proteins in nucleotide excision repair that make incisions 5’ and 3’ to the lesion so it can be removed by helicase

Question 16

homologous recombination

Answer 16

occurs between 2 homologous chromosomes at meiosis; catalyzed by Rec proteins!

Question 17

non-homologous recombination

Answer 17

site-specific recombination and transposition

Question 18

site-specific recombination

Answer 18

joins 2 DNA segments with short but specific DNA sequences present on both participating DNAs
*recombination only occurs at these sites
*catalyzed by recombinases

Question 19

recombination of immunoglobulin genes - V(D)J recombination

Answer 19

recombinase = RAG
-200 different regions, so it allows for abundant antibody diversity

Question 20

transposons

Answer 20

DNA segments that can move from one DNA molecule to another, or to a different location within the same DNA molecule
*have short, inverted repeats that flank either side of the transposon, which is what gets recognized
*catalyzed by transposases