2 DNA Replication

Question 1

what do a-helices have to do with protein interaction with DNA?

Answer 1

they can fit into the major groove and interact with the nitrogenous bases

Question 2

when an ORC recognizes an origin site, what happens first?

Answer 2

unzipping of DNA via helicase, establishment of rep fork

Question 3

what class of protein is T-Ag?

Answer 3

helicase

Question 4

is helicase ATp dependent?

Answer 4

yes

Question 5

what are the three major proteins needed to initiate replicaiton?

Answer 5

• helicase (T-ag)
• Humans single stranded binding protein (replication protein A)
• topoisomerase 1

Question 6

what is the function of SSB (RPA)?

Answer 6

required for replication, stabiliizes single stranded DNA

Question 7

what is the cause of blooms disease and what are these patients at risk for?

Answer 7

• deficient in helicase

- risk for malignancies

Question 8

what is the cause of werners syndrome? what are the symptoms?

Answer 8

• gene involved is a helicase

- premature aging, dwarfism, cataracts, scleroderma

Question 9

what polymerase initiates DNA synthesis? how does it do so?

Answer 9

Pol alpha makes RNA/DNA primers

Question 10

what polymerase synthesizes the lagging strand? what is this dependent on?

Answer 10

pol delta, PCNA (proliferating cell nuclear antigen) (clamp) dependent

Question 11

what polymerase synthesizes the leading strand?

Answer 11

pol epsilon, PCNA dependent

Question 12

what type of reaction occurs as nucleotides are added to the DNA chain?

Answer 12

nucleophilic attack, creating a phosphodiester bond

Question 13

what is RF-C’s job in DNA synthesis?

Answer 13

this is a clamp loader, it is responsible for secruing PCNA which then recruits the pol delta or epsilon

Question 14

the pieces of DNA that are synthesized piece meal on the lagging strand are called what?

Answer 14

okazaki fragments

Question 15

what direction exonuclease activity does pol e and d have?

Answer 15

3’ to 5’ because it goes backwards to do this

Question 16

what is necessary to join okazaki fragments?

Answer 16

DNA ligase

Question 17

what is the function of dna pol gama?

Answer 17

mitochondrial DNA synthesis

Question 18

what is the function of DNA pol beta?

Answer 18

repair DNA synthesis

Question 19

what class of molecule do AZT (zidovudine) and acyclovir fall into?

Answer 19

nulceotide anologues, used to treat viral infections due to their lack of a 3’ OH

Question 20

why are the effects of AZT limited?

Answer 20

• very toxic, it inhibits other polymerases

- eventually mutant forms of RT arise that have a lower affinity for the drug

Question 21

at what checkpoint in cell division does p53 function?

Answer 21

G1/S

Question 22

what class of protein is p53?

Answer 22

tumor supressor

Question 23

what happens when you have a mutant p53?

Answer 23

cell growth is not arrested if the DNA is damaged and genetic instability occurs leading to potential malignancies

Question 24

what is the molecular characterization of li fraumeni syndrome?

Answer 24

mutated p53, leading to multiple tumor sites

Question 25

what types of insults to DNA result in base-excision repair?

Answer 25

x rays, oxygen radicals, alkylating agents, spontaneous reactions

Question 26

what sorts of insults lead to nucleotide excision repair?

Answer 26

UV light, polycyclic aromatics, and hydrocarbons leading to PP, bulky adducts, and CPD

Question 27

what sorts of insults lead to recombinational repair?

Answer 27

x rays, anti-tumor agents, leaing to interstrand crosslink and ds breaks

Question 28

what sorts of insults to DNA lead to mismatch repair?

Answer 28

replication errors, leading to A-G or C-T mismatches, insertions, and deletions

Question 29

during mismatch repair in e coli, how is the parent strand recognized?

Answer 29

it is methylated

Question 30

what protein recognizes a mismatch in e coli?

Answer 30

Mut S

Question 31

what is the molecular cause of fragile X?

Answer 31

expansion of over 200 trinucleotide repeats

Question 32

what is the molecular function of myotonic dystrophy?

Answer 32

dramatic expansion of a trinucleotide repeat, over 1000

Question 33

what is the molecular cause of huntingtons

Answer 33

expansion of a trinucleotide repeat

Question 34

what areas of the genome are prone to insertions and deletions?

Answer 34

microsatellites

Question 35

name the basic 4 step process of excision repair and a primary reason it needs to be done?

Answer 35

- incision - excision - resynthesis - ligation - UV light causes thymine dimers to form

Question 36

what is xeroderma pigmentosum caused by?

Answer 36

abnormal excision repair nuclease that is responsible for cleaving DNA near the pyrimidine dimers

Question 37

What enzyme is responsible for removing uracil from DNA when cytosine spontaneously deaminates?

Answer 37

uracil-DNA glycosidase

Question 38

cytosine is deaminated to form what in the presence of HNO2?

Answer 38

uracil

Question 39

Adenine deaminates to form what in the presence of HNO2?

Answer 39

hypoxanthine

Question 40

what does alkylation of N7 of gluanine do to DNA?

Answer 40

causes labilization

Question 41

what is the primary example of a DNA intercolator? why are these a problem?

Answer 41

ethidium bromide | -gives rise to insertions and deletions