New: DNA Repair and Recombination

Question 1

holoenzme responsible for the majority of DA synthesis in E.coli

Answer 1

DNA pol 3

Question 2

highly processive polymerase that once it begins catalysis it rarely releases the DNA substrate (due to beta subunit grabbing on)

Answer 2

DNA polymerase 3

Question 3

Okazaki fragments are joined by

Answer 3

DNA polymerase 1 and DNA ligase

Question 4

Okazaki fragments are joined to produce a continuos strand of DNA in these 3 steps:

Answer 4

1. removal of the RNA primer: the 5’ –> 3’ exonuclease activity of DNA pol 1
2. Synthesis of replacement DNA - polymerase activity of DNA pol 1 synthesizes DNA in place of RNA
3. sealing of adjacent DNA fragments - DNA ligase

Question 5

Problem with joining of Okazaki fragments by DNA pol 1 and DNA ligase

Answer 5

after Okazaki fragment synthesis is complete, have a gap between end of Okazaki fragment and RNA primer (need to replace RNA primer)

Question 6

nick translation

Answer 6

When DNA pol 1 extends the Okazaki fragment while its 5’–>3’ exonuclease activity removes the RNA primer

Question 7

DNA ligase binds to the ____ when repairing gaps in DNA

Answer 7

nick

Question 8

DNA ligase then catalyzes the formation of a _______ _______ between 3’ hydroxyl and 5’ phosphate of adjacent Okazaki fragments - then it dissociated from DNA

Answer 8

phosphodiester linkage

Question 9

why cant DNA pol fill in the gap?

Answer 9

no free 3’ end

Question 10

describe eukaryotic chromosomes

Answer 10

large linear, double stranded DNA molecules

Question 11

replication of eukaryotic chromosomes is in what direction

Answer 11

bidirectional

Question 12

compared to E.coli, eukaryotic replication has _____ sets of initiation of DNA synthesis

Answer 12

multiple

Question 13

unique structures at the ends of linear chromosomes (the free end of linear DNA)

Answer 13

telomeres

Question 14

what 2 problems do telomeres have

Answer 14

1. they are susceptible to damage by nucleases

2. due to the nature of DNA synthesis, one strand will shorten upon each round of DNA Synthesis

Question 15

telomeres have the job of

Answer 15

protecting the end from degradation by forming a loop from the guanine rich single stranded DNA - protects end of chromosome from nuclease

Question 16

this enzyme can reverse transcribe DNA from RNA template; has DNA activity but is dependent on RNA

Answer 16

telomerase

Question 17

telomerase unusual hairpin structure forms new primer to make

Answer 17

double stranded DNA

Question 18

_____ of hairpin yields lengthened telomere

Answer 18

cleavage

Question 19

why is telomerase called a reverse transcriptase when it is adding deoxynucleotides?

Answer 19

b/c it is a RNA-dependent DNA polymerase; it has its own RNA template complementary to the telomeric repeat sequence so, it REVERSE transcribes DNA from the RNA template

Question 20

short telomeres cause

Answer 20

premature aging; bone marrow diseases; secondary hit + telomeres cause idiopathic pulmonary fibrosis

Question 21

DNA pol 3 holoenzyme also

Answer 21

fixes mistakes

Question 22

possesses 3’ –> 5’ exonuclease activity - “proofreading”

Answer 22

DNA polymerase 3 holoenzyme

Question 23

pol 3 can catalyze both chain

Answer 23

elongation and degradation

Question 24

exonuclease activity removes mispaired nucleotide before

Answer 24

polymerization continues

Question 25

*most uncorrected replication errors are subsequently corrected by

Answer 25

the DNA repair enzymes

Question 26

____ is the only cellular macromolecule that can be repaired

Answer 26

DNA

Question 27

specific _____ ____ scan DNA to detect any alterations - recognize mismatched bases, modified nucleotides

Answer 27

repair enzymes

Question 28

repair that does not require breaking the phosphodiester backbone of DNA

Answer 28

direct repair

Question 29

mechanisms that do involve breaking the DNA backbone to repair

Answer 29

mismatch; base-excision; and nucleotide-excision

Question 30

repair of thymine dimers is done by

Answer 30

DNA photolyase - photoreactivation

Question 31

double-helical DNA is very sensitive to damage by

Answer 31

UV light; dimerization of adjacent pyrimidines in a DNA strand is common

Question 32

repair after photodimerization is _____ repair

Answer 32

direct

Question 33

mismatch-repair system corrects errors that

Answer 33

were not corrected by proofreading that cannot be directly repaired

Question 34

in Ecoli, MutS recongnizes the error, MutL reruits MutH to

Answer 34

cleave the DNA and the exonuclease activity of MutH excises the bases MISMATCH-REPAIR

Question 35

parent strand may be marked by methylation or adenines so that repair machinery can

Answer 35

recognize the correct base

Question 36

_______ synthesizes new strand in mismatch repair and ____ ligates the pieces together

Answer 36

DNA pol 3; DNA ligase

Question 37

nucleotide deamination

Answer 37

*hydrolytic deamination* of C to U or G to A; DNA glycosylases hydrolyze base-sugar N glycosidic bonds; deaminated bases are then removed and replaced

Question 38

AlkA glycosylase does what?

Answer 38

hydrolyzes the glycosidic bond leaving an AP site | base -excision repair

Question 39

AP endonuclease detects AP site and

Answer 39

nicks the sugar-phosphate backbone (base excision repair)

Question 40

deoxyribose phosphodiesterase excises the

Answer 40

deoxyribose phosphate (base-excision repair)

Question 41

DNA pol 1 fills gap and DNA ligase

Answer 41

seals the nick

Question 42

what happens when excision repair does not function?

Answer 42

extreme sensitivity to the sun, greater risk of skin cancer, cancer growth, xeroderma pigmentosum

Question 43

carcinogens are detected using bacteria via what test

Answer 43

ames test

Question 44

simple, sensitive means of determining if a chemical is mutagenic

Answer 44

Ames test

Question 45

3 steps of the Ames test

Answer 45

1. Salmonella bacteria that require histidine because of a mutation in its biosynthetic pathway are treated with the chemicals 2. salmonella are plated on a plate lacking histidine 3. salmonella growth suggest that the chemical caused a mutation which restored histidine synthesis

Question 46

exchange or transfer of pieces of DNA from on chromosome to another or within a chromosome

Answer 46

recombination

Question 47

occurs between pieces of DNA tat have closely related sequences (exchange between paired chromosomes during meiosis)

Answer 47

homologous recombination

Question 48

non-homologous recombination occurs between

Answer 48

unrelated sequences

Question 49

site specific recombination

Answer 49

recombination at a specific location

Question 50

why is recombination needed?

Answer 50

mutation gives new genetic variation; recombination created different combinations of mutations within a genome.

Question 51

recombination also plays an important role in the

Answer 51

repair of DNA

Question 52

how can recombination be used in repair

Answer 52

severe lesions in DNA can be repaired by strand exchange from intact daughter chromosome to defective daughter

Question 53

RAD51

Answer 53

key protein in double strand breaks repaired by recombination

Question 54

know steps of double strand breaks repaired by recombination!

Answer 54

1. break recognized, 5' end digested, single-strand regions are bound by RAD51 2. strand inversion occurs-single strand form damaged DNA replaces a strand in undamaged DNA. This 3 stranded structure is called a DISPLACEMENT LOOP 3. DNA synthesis occurs, using the undamaed DNA as a template 4. a second strand invasion occurs to complete the repair, forming a HOLLIDAY JUNCTION 5 cleavage and ligation yield two intact helices

Question 55

what happens when ds break repair doesn't function?

Answer 55

human BRACA1 and BRACA2 - human breast cancer genes BRC repeats of BRACA2 interact directly with Rad51 BRCA2 may serve to deliver Rad51 to the site of DNA damage conserved C-terminus appears to bind ssDNA and dsDNA