DNA Replication

Question 1

what is the difference between DNA and RNA structures

Answer 1

RNA has a 2’ OH and 3’ OH where DNA only has a 3’ OH, RNA uses uracil instead of thymine

Question 2

what makes RNA less stable than DNA

Answer 2

the 2’ OH can perform chemistry so RNA can act as a catalyst

Question 3

why can you only add to the 3’ end of a nucleic acid polymer / what does this mean for polymerases

Answer 3

the chemistry of the OH being released when binging with a new dNTP / means that polymerases are directional

Question 4

in what direction do polymerases move

Answer 4

5’-3’ on the primer strand and 3’-5’ on the template strand

Question 5

what do all DNA polymerases need

Answer 5

all DNA polymerases need a primer

Question 6

what can all DNA polymerases not do

Answer 6

they cannot make dimers

Question 7

what is replication on a circular chromosome

Answer 7

bidirectional and semiconservative (keeps one original strand)

Question 8

what is the main origin of replication in EColi

Answer 8

oriC

Question 9

what is DnaA

Answer 9

the initiater protein - it binds to oriC at the 9bp sequence

Question 10

what is DnaB

Answer 10

a helicase that unwinds the helix to expose the template strands (one one each strand) - proceeds away from oriC

Question 11

what is DnaG

Answer 11

a primase that synthesizes RNA primers in the replisome that binds to DnaB to make the RNA primer

Question 12

what is DNA pol III

Answer 12

the major replication enzyme brought by the clamp/clamp loader

Question 13

what is DNA pol I / RNaseH

Answer 13

they replace RNA primer with DNA in okazaki fragments

Question 14

what is DNA ligase

Answer 14

it seals the opening in DNA strands after DNA pol I replaces the primer (connects fragments)

Question 15

what is DNA gyrase

Answer 15

relieves DNA supercoiling - reduces strain from the supercoil during replication

Question 16

what does RNAse H or DNA pol I recognize to replace RNA

Answer 16

recognizes the RNA-DNA hybrid

Question 17

what do topoisomerases in bacteria do

Answer 17

they introduce supercoils to condense DNA - allows it to fit inside the cell - causes stress and tension during replication

Question 18

what do quinolones do / how do they work

Answer 18

they are antibiotics that block the function of DNA gyrase / they would cause too much strain on the DNA which would lead to the double strand breaking - lead to large scale mutation or cell death

Question 19

what do the multiple short terminator sequences do

Answer 19

because bacteria is circular the replisome cannot just run off the chromosome - has to be stopped and that is what the ter clusters do

Question 20

why are there clockwise and counterclockwise sequences

Answer 20

there has to be sequences in both directions or one side will continue to go around and the other will stop

Question 21

what does the protein Tus do

Answer 21

binds to the ter sequences and acts as the orientation-specific counter helicase to stop replication - must be in both directions

Question 22

what are the magicians of replication - they separate the loops

Answer 22

topoisomerase IV and XerC / XerD proteins

Question 23

in slowly growing bacterial cells which is longer, the generation time or the replication time

Answer 23

the generation time is longer than the replication time

Question 24

in rapidly growing cells which is longer, generation time or replication time

Answer 24

the replication time is longer than or equal to the generation time

Question 25

what regulates replication frequency

Answer 25

the concentrations of DnaA and ATP - must be lots of both to replicate