18-19 DNA replication 2

Question 1

list the components of the OriC region in E. coli

Answer 1

DUE, IHF, R1-5, I1-4, HU proteins, FIS

Question 2

what’s DUE?

Answer 2

DNA unwinding element. tandem repeats of 3*13bp with high AT content

Question 3

what’s IHF

Answer 3

binding site for Integration Host Factor => opens and bends DNA

Question 4

what’s R1-5?

Answer 4

binding sites for DnaA proteins. 5 repeats of a 9bp sequence

Question 5

what’s I1-3?

Answer 5

additional DnaA binding sites

Question 6

what are HU proteins?

Answer 6

histone like proteins that promote DNA bending

Question 7

what’s FIS?

Answer 7

binding site for “factor for inversion stimulation” protein => helps open and bend DNA

Question 8

DnaA proteins coupled with ATP bind to what?

Answer 8

R1-5 and the I1-3 repeats

Question 9

where do IHF and FIS proteins bind and what do they all do?

Answer 9

bind to their respective sites, HU binds nonspecifically. induce DNA to wind around them

Question 10

what happens in the DUE regions when the proteins overwind the other DNA?

Answer 10

Induces UNDERWINDING! opens up a bubble

Question 11

helicase (DnaB) is assembled on what, with the help of what?

Answer 11

assembled on the lagging strands of both small replication forks (melted DUE region), with help of DnaC-ATP protein and hydrolysis of its ATP

Question 12

what other proteins are required for DNA synthesis?

Answer 12

SSB, DNA Pol III, gyrase

Question 13

what happens to DnaA proteins?

Answer 13

ATPases, slowly hydrolyze ATP to ADP. R1-5 bind DnaA-ATP and ADP equally. three I1-3 sites can only bind DnaA-ATP. slowly dissociates and destabilises overwound region.

Question 14

oriC is rich in what sequence?

Answer 14

GATC

Question 15

which base in GATC is methylated?

Answer 15

the A. immediately after replication all GATC is hemimethylated

Question 16

what does hemimethylated oriC do?

Answer 16

binds to plasma membrane, stops new replication process from starting.

Question 17

what enzyme methylates the new GATC? and how long does it take?

Answer 17

Dam methylase, about 20 minutes

Question 18

what is Tus and what does it do?

Answer 18

Terminator Utilization Substance (a protein), binds to ter locus and inhibits helicase

Question 19

what is Ter and what does it do?

Answer 19

several 20bp repeats oriented in opposite directions -> act like traps for the replication forks.

Question 20

how do the two new circular chromosomes unlink?

Answer 20

via topoisomerase type II

Question 21

how many replicator sites do humans have per chromosome?

Answer 21

100-600

Question 22

what do eukaryotic cells not need and why?

Answer 22

don’t need a gyrase because unwinding DNA from histones leaves the helix in an underwound state already

Question 23

what are telomeres and what do they do?

Answer 23

many short simple sequence repeats. stops the chromosomes from growing shorter.

Question 24

what is TELOMERASE?

Answer 24

a protein-RNA complex, “reverse transcriptase” polymerase. actsa to extend parents stand, makes a complementary strand or T-loop which protects the end of telomeres

Question 25

what syntheisizes RNA primers in eukaryotes vs. prokaryotes?

Answer 25

eukaryotes: primase activity of DNA pol alpha, prokaryotes: primase