DNA replication

Question 1

key facts about DNA pol 1

6 points

Answer 1

non replicating
requires all dNTPs
not self priming
5'-3' polymerase
3'-5' exonuclease proof reading
5'-3' exonuclease nick translation

Question 2

DNA pol 2 what are the subunits

Answer 2

alpha
beta
episilon

Question 3

what do the DNA pol 2 subunits do

and what doesnt it contain

Answer 3

A = polymerase
B= clamp (DNA N)
E= 3’ exonuclease proof reading
it does not contain 5’-3’ exonuclease

Question 4

what does DNA pol 2 also form so that we can experiment on them
and what kind of mutants does it form

Answer 4

temp sensitive mutants
quick stop
slow stop

Question 5

when U is incorporated into DNA what is the problem

Answer 5

when it is incorporated into GU

Question 6

DNA pol 3 what subunits make the active site

what causes dimerisation

Answer 6

alpha
epsilon
thi
thi 2 responsible for dimerization

Question 7

in pol 3 what clamps the beta clamp whats the loader

Answer 7

Y2, sigma2, phi, X

which uses ATP

Question 8

beta clamp what holds it on DNA

Answer 8

lysine and argenine

Question 9

topoisomerase how many turns for every 10 bp that are replicated

Answer 9

1 turn

Question 10

what does topoisomerase do

Answer 10

relieves superhelical stress that is produced infront and behind the replication fork

Question 11

what happens to the backbone when topoisomerase binds

Answer 11

nicked

and is held together by phosphate tyrosine bonds

Question 12

topo 1 and 3 do what

Answer 12

cuts 1 strand
unwinds DNA
decreases L by 1

Question 13

what does topo-2 and 4 do

Answer 13

cuts both strands
passes 1 strand through another
decreasing L by 2

Question 14

DNA gyrase what does it do

what is its structure

Answer 14

uses ATP to decrease L by 2 everytime
A2 B2
tyrosine of A binds to 5’ phosphate

Question 15

initiation prokaryotes main points

Answer 15

starts at ori c
bidirectionally
has 4 x 9 bp repeats and 3 x 13 bp repeats

Question 16

initiation prokaryotes

DNA A what does it do

Answer 16

specific for repliaction initiation
binds cooperatively to 9bp repeats
requires ATP
which interact with 13bp repeats

Question 17

initiation prokaryotes

DNA B what does it do

Answer 17

moves along the lagging strand

opening fork

Question 18

initiation prokaryotes

what stabalises the opening of the repliaction fork

Answer 18

ss binding proteins

Question 19

initiation prokaryotes 
DNA G (primase) what does it do

Answer 19

associates with DNA B and RNA primer

and the primer is extened by pol 3

Question 20

proof reading how is it done and what happens

Answer 20

3’ only proceeds if correct base is added

if not the 3’ exonuclease activity of pol 3 (DNA Q) removes it

Question 21

mechanism of repilaction fork opening

how does it happen

Answer 21

DNA B
dna dependent ATPase
1 atp for 3bp unwound
stabilised by ssbp

Question 22

ssbp how are they added

Answer 22

as 1 bind the next binds more easily and thus more easily removed

Question 23

synthesis of lagging strand facts

3 sentences

Answer 23

even though it is synthesised discontiuously it is made by pol 3
dimer does not dissociate from the DNA template
lagging strand is looped out before synthesis in the 5’-3’

Question 24

ori c a large number of what

and what is it needed for

Answer 24

GATC sequences
fo DAM
which immediatley after replication will be hemimethylated

Question 25

DAM | what does it do

Answer 25

hemimethylates the DNA

Question 26

termination of replication prokaryotes what is needed 3 answers

Answer 26

6 homologous 23bp sequences 3 sites oriented in each direction binding to protein TUS

Question 27

what does TUS do

Answer 27

prevents fork movement, in only 1 direction

Question 28

termination of replication prokaryotes what happens to the DNA how are the chromosomes seporated

Answer 28

hemi - DNA at ori c has a stong affinity for cell lipid bilayer seporated by topo 4

Question 29

replication in eukaryotes facts 5 facts

Answer 29

``` does not replicated from a single origin 1000s of replication forks from ARS pol is slower okizaki frags are smaller ```

Question 30

what is ARS

Answer 30

autonomously replicating sequence)

Question 31

eukaryotic pols | 5 main types

Answer 31

``` alpha beta y sigma espilon ```

Question 32

eukaryotic pols | pol alpha

Answer 32

has its own primase activity not very processive ass it does not associate with PCNA

Question 33

what is PCNA

Answer 33

proliferating cell nuclear antigen

Question 34

enzyme synthesizing the leading and lagging strand dont do what

Answer 34

they dont associate as a dimer

Question 35

eukaryotic pols dont have | instead they have

Answer 35

5' exonuclease to remove RNA primer | FEN1 (flap) exonuclease

Question 36

eukaryotic pols | pol sigma does what

Answer 36

associates with PCNA and does processive work

Question 37

eukaryotic pols | pol epsilon does what

Answer 37

``` displaces the primer but its not 5'-3' exonuclease rather then degrading primer sigma and epsilon writes over it placing it out FEN1 cuts it out ```

Question 38

telomers | what are they

Answer 38

added repeats at the end of the chromosome | not synthesisted by semi conservative replication

Question 39

telomerase adds telomers what does it add what is it

Answer 39

it adds repeats of TTAGGG 50-100 bp at 3' end ribonucleoprotein acts as a template for synthesis of telomer repeats

Question 40

how is telomer length regulated

Answer 40

by telomer binding proteins | such as TRF1 and TRF2

Question 41

rna replicase | what happens to positive strand

Answer 41

+ve strand is replicated directly to make -ve strand then -ve is used as a template to make +ve no proof reading

Question 42

reverse transcriptase what primer is used how is it degraded

Answer 42

tRNA(lys) rna strand is degraded by RNase H activity before it synthesises another strand