DNA Replication and Repair1C part 1

Question 1

What were the three models of DNA replication that researchers thought of?

Answer 1

1. Semiconservative Replication
2. Conservative Replication
3. Dispersive Replication

Question 2

Semi-conservative Replication+ configration

Answer 2

Each daughter strand remains paired with its complimentary parental strand.

one strand daughter, one strand parent

Question 3

Conservative

Answer 3

after replication, both daughter strands pair up parent strand stay together

Question 4

Dispersion

Answer 4

Daughter strand will have a mixture of parental and newly synthesized DNA

Question 5

Meselsin Stahl Experiment tell me the procedure (3)

Answer 5

1. Took normal coli cell DNA and made them divide in heavy nitrogen (N15) so all the DNA were heavy.
2. DNA switched to light nitrogen and dna made after the switch would have to be made up of N14 as this would have been the only nitrogen available for DNA synthesis.
3. measured the density of the DNA (and, indirectly, N14/N15) using density gradient centrifugation.

Question 6

generation 0 meselson-Stahl (3)

• contents
  -Band
  -time

Answer 6

• All heavy N15 E coli DNA
• before the switch to light nitrogen
  -produced a single band after centrifugation.

Question 7

Generation 1 Meselson Stahl (3)

content
band
fit/reject

Answer 7

• 100% hybrid of light and heavy nitrogen
  -fits with dispersive and semi conservative but not conservative
  -single band middle

Question 8

Generation 2 Meselson Stahl

Answer 8

• Two bands, 1 middle and 1 light band
• Know that it was conservative as in dispersive replication, all the molecules should have bits of old and new DNA, making it impossible to get a “purely light” molecule.
• 2 hybrid, 2 light

Question 9

what do you expect over Generation 3/4 of the Meselson Stahl experiment?

Answer 9

over the third and fourth generations, we’d expect the hybrid band to become progressively fainter (because it would represent a smaller fraction of the total DNA) and the light band to become progressively stronger (because it would represent a larger fraction).

Question 10

Why is the buffer important in the Meselson and Stahl experiment and what is it? (2)

Answer 10

Caesium Chloride solution forms a density gradient when centrifuged, the Cs ions will form an increasing concentration going down the tube and the DNA molecules will float to the density zones that match their own density. This allows separating similar molecules with small differences in density.

Since proteins are heavier they sediment in the heaviest, bottom-most layer while RNA being lighter is present at the topmost layer with the lowest density

Question 11

spacing btwn the possible bands are

Answer 11

equal

Question 12

Nucleotides can only be added to the new strand at the____ and thus DNA is

Answer 12

3’-OH end and thus, Dna is synthesized in a 5’-3’ direction

Question 13

What end of the daughter cell is growing?

Answer 13

3’ end of daughter strand is growing

Question 14

What provides energy for the formation of new phosphodiester bond

Answer 14

hydrolysis of pyrophosphate provides energy for the formation of new phosphodiester bond

During strand elongation, two phosphates are cleaved from the incoming nucleotide triphosphate and the resulting nucleotide monophosphate is added to the DNA strand.

Question 15

pyrophosphate (1)

Answer 15

is just two phosphates (POP)

Question 16

DNPT (4)

Name

type

what

dna

Answer 16

Deoxyribose nucleoside Triphosphate

DCTP
DGTP
DATP
DTTP

contains deoxyribose with 3 phosphate groups

lose 2 phosphate during DNA replication incorporation

Question 17

DNA polymerases (5)

Answer 17

synthesizes daughter in 5’-3’

can only add bases on the 3’ OH end

reads template in a 3’-5’ end

cannot synthesize from scratch, it required a RNA primer that has a 3-OH group end untouched for DNA polymerases to bind and replicate.

Is an enzyme so it has an active site. Active site can catalyze 4 different reactions with the different DNTP. It binds to whatever the complimentary base is as that is the most energetically favoured.

Question 18

Replisome (9)

Answer 18

1. helicase
2. primase
3. single stranded binding protein
4. DNA topoisomerase/Gyrase
5. DNA Pol 3
6. DNA Pol 1
7. Sliding Camp
8. Ligase
9. molecular machines of enzymes that replicate DNA

Question 19

Helicase

Answer 19

Unwinds the Double Helix by breaking hydrogen bonds btwn the 2 parental strands

Question 20

Primase (2)

Answer 20

Synthesizes RNA primers for DNA polymerase
-provides the hydroxyl group

Question 21

Single Stranded binding proteins

Answer 21

stabilizes single stranded DNA before replication (as single stranded can break) by preventing reannealing so that the strands can serve as template

Question 22

DNA Topoisomerase/gyrase+ how it does this

Answer 22

removes supercoils that form ahead of the replication fork, relives torque of mainly circular DNA

does this by either making single stranded cuts or cutting both double strands and rehealing it.

Question 23

DNA polymerase 3

Answer 23

synthesizes DNA by adding nucleotides to the new DNA strand

Question 24

DNA polymerase 1

Answer 24

removes RNA primer and fills in the gap between with DNA

Question 25

Sliding clamp (2)

Answer 25

attaches DNA pol 3 to DNA template to prevent it from dissociating. Without it, DNA poly 3 would synthesize a short segment before falling off

pushes DNA polymerase 3 to go faster and increase replication speed

Question 26

Ligase+ present in… (2)

Answer 26

Joins the ends of DNA segments that DNA pol 1 synthesized after removing the RNA primer by forming phosphodiester bonds.

present in leading strand and in lagging strand.

Question 27

How are the two strands different in DNA Replication?

Answer 27

one strand is synthesized continuously (leading)

one strand is synthesized discontinuously (lagging) in small DNA fragments

Question 28

Why is there a lagging strand?

Answer 28

Because DNA polymerase can only synthesize in 5’-3’ direction

Question 29

DNA replication steps (7)

Answer 29

1. DNA helices unwinds double helix
2. RNA primate lay down RNA primer
3. Topoisomerase prevents dna twisting ahead of replication fork during unwinding
4. dna poly 3 extends rna primer
5. dna helicase continue to unwind resulting in leading and lagging strands synthesis by dna pol 3
6. dna pol 1 removes rna primer of ozakaki fragments and fills in gaps with dNTPs
7. DNA ligase seals nicks by reforming the phophodiester bond