DNA replication

Question 1

what does dna repliation require

Answer 1

activated substrated known as dNTPS (deoxyribonucleoside 5/-triphosphates) i.e. dCTP, dATP, dUTP, dGTP

Question 2

double stranded DNA plus dNTPs reacted with polymerases makes

Answer 2

2 double stranded DNA

Question 3

what are the generic four steps that in vivo occur simultaneously during DNA replication

Answer 3

initiation (starting the replication)
priming (primer=rna)
synthesis (replication happens)
termination

Question 4

t/f

eukaryotes have circular chromosomes

Answer 4

false

prokaryotes have circular chromosomes

Question 5

how many start sites for dna replication are there in prokaryotes & what are they called

Answer 5

one.

initiation site

Question 6

t/f

DNA is replication is bidirectional

Answer 6

true

Question 7

t/f

a second round of replication cannot begin until the first is completed

Answer 7

false

second round starts before first is done

Question 8

where does initation of dna replication in prokaryotes start

Answer 8

OriC (origin of replication)

Question 9

what are the OriC recognized by

Answer 9

the initatior protein known as DnaA

Question 10

what type of repeats are adjacent to OriC

Answer 10

AT rich repeats

Question 11

t/f

only in prokaryotes there are AT rich sequences near the replication initiation site

Answer 11

false

this is also true in eukaryotes

Question 12

why are AT rich repeats important

Answer 12

they’re less stable that native DNA so can be used to form the replication bubble

Question 13

what is the helicase in prokaryotes

Answer 13

DnaB

Question 14

what is the role of SS binding proteins

Answer 14

they bind to SS regions of replication bubble and stop it from making secondary structures (bc secondary will hinder replication)

Question 15

t/f

dna polymerase can initatiate new strand synthesis

Answer 15

f

no DNA poly can initiate, it needs to have a primer

Question 16

what is needed to add dNTP DNA polymerases

Answer 16

need a 3’ hydroxyl group at the end of a base paired primer strand

Question 17

in what direction is RNA primer created

Answer 17

5’ to 3’

all of dna synthesis happens in this direction

Question 18

why is a primer needed in each fork i.e. 2

Answer 18

bc synthesis of dna is bidirectional

Question 19

describe rna primer synthesis

Answer 19

primase DnaG is part of the primosome

primosome binds to both strands of the replication bubble –>makes short RNA primer

Question 20

what is the role of DNA poly 1 in prokaryotes

Answer 20

remove the RNA primer (primer excision)

and DNA repair

Question 21

role of dna poly 3 in prokary

Answer 21

replication –> chain elongation during DNA synthesis

and DNA repair

Question 22

diff bn 3’ and 5’ exonucleases

Answer 22

3’ removes prna primers in 3’ to 5’ direction

5’ removes it 5’ to 3’ direction

Question 23

why is dna replication the most accurate process

Answer 23

bc it has proof reading

3/ exonuclease checks it

Question 24

3’ exonucleases are found in which dna polymerases

5’ found in which

Answer 24

poly 1 and 3 have 3’ exonucleases

only poly 1 has 5’ exonucleases

Question 25

what is the processivity of dna poly 1 and 3

Answer 25

poly 1 = low to moderate | poly 3 = high processitivity

Question 26

which polymerase removes rna primer

Answer 26

dna poly 1

Question 27

which poly is involved in replicating dna

Answer 27

dna poly 3

Question 28

what is processivity

Answer 28

measure of how many nucleotides can be added to dna strand as it's growing before it disengages

Question 29

what subunit serves as a sliding clamp that encircles DNA

Answer 29

beta

Question 30

what is the role of the gamma complex

Answer 30

it is a clamp loader so helps get beta (sliding clamp) loaded onto dna

Question 31

which subunit is a structural protein that holds things together

Answer 31

tau

Question 32

what is contained within epsilon

Answer 32

3' exonuclease used for proof reading

Question 33

what is the role of theta

Answer 33

needed for 3' exonuclease activity

Question 34

t/f | each replication fork has one DNA poly 3 holoenzyme

Answer 34

true

Question 35

what charge is the interior of the beta sliding clamp and why

Answer 35

neutral or negative bc for clamp to move on the dna needs to be repulsive -dna is negative

Question 36

t/f both strands of the replication fork are synthesized simultaneously

Answer 36

true

Question 37

what is the difference bn how the leading and lagging strands are synthesized

Answer 37

the leading strand synthesized continuously | lagging synthesized discontinuously

Question 38

in what direction in relation to the fork is dna synthesis occuring in the lagging strand

Answer 38

its being synthesized away from the fork

Question 39

what is special of the backbone on the lagging strand

Answer 39

it has a nick on it

Question 40

okozaki fragments are made on which strand of the replication fork

Answer 40

lagging strand

Question 41

t/f | for the leading strand the fork has to open before new synthesis can be initiated

Answer 41

false | the LAGGING strand needs the fork to be open

Question 42

since both strands are made simultaneously how do both strands become in the same orientation

Answer 42

a loop is added on the lagging strand which puts the 2nd okozaki fragment in same orientation as the leading strand so the polymerase can move smoothly

Question 43

as the DS helix is being opened, helical tension is formed and ___ is needed to regulate it

Answer 43

topoisomerase

Question 44

dna poly 3 can recognize

Answer 44

mismatched base pairs (aka AG or CT)

Question 45

what is the role of epsilon subunit

Answer 45

removes mismatched pairs with it's 3' to 5' exonuclease activity

Question 46

how is the chain extended after epsilon subunits remove mismatched base pairs

Answer 46

extended by dna poly 3

Question 47

where is the termination region in relation to OriC

Answer 47

180 degrees from it

Question 48

what are ter sites

Answer 48

termination sites in prokaryotes | has 6 sites oriented in opposite directions on either side of the 180 degree point

Question 49

why is the ter orientation in opp dir's on either side of the 180 degrees

Answer 49

bc binds to the TUS protein

Question 50

in how many directions can the TUS protein go

Answer 50

one | the fork can pass right past it but can't pass it in other direction

Question 51

what is the process of rna primers being removed by dna poly 1 called

Answer 51

nick translation

Question 52

how does nick translation work

Answer 52

dna poly 1 5' exonuclease hydrolyses the RNA primers | simultaneously the 3' end of the okazaki fragment (DNA) is extended by the incorporation of deoxyribonucleotides

Question 53

role of dna ligase

Answer 53

seals the nick

Question 54

what is the last step in termination of dna synthesis in prokaryotes

Answer 54

type 2 topoisomerase separated the 2 interlinking strands of the replicated circles and refolds the dna into supercoils

Question 55

what are the 4 similarities bn pro and euk dna replication

Answer 55

1. semi conservative 2. bidirectional 3. short RNA primers req'd to initiate new strand synthesis 4. leading strand made continuously lagging made discontinuously

Question 56

in eukaryotes | what is te role of dna poly gamma

Answer 56

replication of mitochondrial dna

Question 57

in euk | whats role of dna poly delta and epsilon

Answer 57

poly delta replicated the lagging strand | poly epsilon replicates the leading strand

Question 58

which strand does dna poly alpha replicate

Answer 58

both leading and lagging

Question 59

what is the inherent processivity of all 5 eukaryotic dna polymerases

Answer 59

``` alpha-moderate beta-low gamma-high delta-low epsilon-high ```

Question 60

which eukaryotic dna poly has high processivity with PCNA

Answer 60

delta

Question 61

in the tertiary structure, where are nucleosome dissociated and where are they reassembled

Answer 61

dissociated ahead of the replication fork | reassembled on newly synthesized DNA

Question 62

what is the speed and size of the tertiary structure in replication

Answer 62

10 times slower | size of genome is massive

Question 63

what are present to accomodate the large size of the genome

Answer 63

multiple initation sites of replication known as ARS

Question 64

what are the highly repetitive sequences at the ends of linear chromosomes that protect the chromosome from being damaged

Answer 64

telomeres

Question 65

what is the origin of replication | in prok and euk

Answer 65

pro: OriC Euk: ARS

Question 66

what is the bind origin of replication (i.e. what protein recognizes the origin of replication in each) in prok and euk

Answer 66

pro: DnaA complex euk: ORC

Question 67

what is the helicase | in prok and euk

Answer 67

pro: DnaB/C complex euk: MCM

Question 68

what is used to stabilize SS DNA | in prok and euk

Answer 68

pro: SSBs Euk: RPA

Question 69

what is used to increase processivity | in prok and euk

Answer 69

pro: Beta-subunit poly 3 euk: PCNA for DNA poly delta

Question 70

what is the clamp loader | in prok and euk

Answer 70

pro: gamma complexx euk: RFC (replication factor C)

Question 71

what makes RNA primer | in prok and euk

Answer 71

Pro: DnaG euk: DNA poly alpha

Question 72

what synthesizes DNA | in prok and euk

Answer 72

pro: DNA poly 3 Euk: DNA poly epsilon (leading strand) DNA poly delta (lagging strand) DNA poly gamma (mitochondria)

Question 73

what is used for the removal of RNA primers | in prok and euk

Answer 73

pro: DNA poly 1 (nick translation) euk: RNAse H and Fen1 (flap endonuclease 1)

Question 74

what does RNAse H do

Answer 74

destroys DNA/RNA hybrids and removes the RNA from it

Question 75

diff bn exonuclease and endo

Answer 75

exo cuts from the ends | endo makes cut from within

Question 76

what genetic defect causes Aicardi-goutieres syndrome

Answer 76

RNAse H which acts on RNA/DNA hybrids and is involved in removal of RNA primers in eukaryotic replication

Question 77

during eukaryotic replication, a pre-replication complex (pre-RC) assembles on what

Answer 77

on the ARS which includes ORC(origin of replication), MCMs (inactive helicases) and other proteins

Question 78

how are helicases activated

Answer 78

by the addition of addtl proteins | -thats when it can start unwinding the DNA bc it;s active

Question 79

what is ARS rich in and what does that allow it to do

Answer 79

ARS is AT rich --> helps it open up inititial replication bubble

Question 80

t/f | more pre-RC are assembled (licensing) than used (firing)

Answer 80

true

Question 81

in order for replication in eukaryotes to start the helicase needs to be

Answer 81

activated so it can unwind the dna

Question 82

what keeps things regulated during eukaryotic replication

Answer 82

topoisomerase | -which work ahead of the replication fork to keep the DNA untangled

Question 83

what makes the leading and lagging strand into the same orientation

Answer 83

a loop

Question 84

what is RNaseH / FEN 1 doing during eukaryotic replication

Answer 84

taking out RNA primers

Question 85

what causes meier-gorlin syndrome (failure in growth)

Answer 85

mutations in genes that encode the proteins needed for the Pre-RC complex including: ORC -bc of impaired replication licensing (aka assembly)

Question 86

what are the highly repetitive seq's at the 3' ends of linear chromosomes

Answer 86

telomeres

Question 87

what are telomeres added by

Answer 87

telomerase

Question 88

what is the protein compnent enzyme and the RNA component of telomerase

Answer 88

protein: hTERT = human telomerase reverse transcriptase RNA: hTR = human telomerase RNA

Question 89

what does the telomerase use it's rna component (hTR) for

Answer 89

to add repeats | -telomerase repositions itself to add each repeat

Question 90

how is the daughter strand synthesized

Answer 90

by unsing complementary base pairing by DNA poly alpha (puts RNA primer to synthesize the DNA)

Question 91

what is left when telomerase moves away

Answer 91

a single stranded 3' overhang

Question 92

the telomere ends are protected by loops that are stabilized by binding of telomere-binding proteins called

Answer 92

TRF1 and TRF2

Question 93

telomere length is maintained by

Answer 93

telomerase

Question 94

what would happen in a dividing cell with little or no telomerase

Answer 94

not much short term telomeres would shorten after rounds of replication cells would die cells would stop dividing

Question 95

telomeres shorten with each round of dna replication unless maintained by

Answer 95

telomerase

Question 96

what mutation causes Dyskeratosis congenita (which worsens with successive generations)

Answer 96

mutations in the catalytic domain (hTERT) or rna component of telomerase (hTR)

Question 97

diseases of telomere shortening show anticipation because

Answer 97

loss or partial loss of telomerase function leads to telomere shortening n the germ cells