L4. DNA replication & repair

Question 1

how is DNA replication semi-conservative

Answer 1

• the parental strand is broken apart by certain enzymes
• each of those strands are used as a template
• this results in each daughter strand of DNA having one new and one conserved strand of DNA

Question 2

what is the origin of replication

Answer 2

• where replication begins
• DNA is pulled apart at this region

Question 3

origin of replication - eukaryotes vs bacteria

Answer 3

• eukaryotes: a lot of origins because the DNA is linear
• bacteria: only one because the DNA is circular

Question 4

what is the replication fork

Answer 4

• place where DNA is being ripped apart
• the forks migrate in opposite directions until they meet with another one

Question 5

what is DNA polymerase

Answer 5

• DNA polymerase carries out DNA replication
• it uses the parental strand as a template and adds nucleotides to grow the new strand
• 2 phosphates are hydrolyzed off and that generates energy to add a nucleotide to the growing strand

Question 6

leading strand vs lagging stand

Answer 6

• leading: synthesized continuously
• lagging: synthesized discontinuously

Question 7

why is the lagging strand synthesized discontinuously

Answer 7

the lagging strand is positioned in a 3’ -> 5’ fashion and DNA polymerase only synthesizes 5’ -> 3’

Question 8

how is the lagging strand synthesized discontinuously

Answer 8

• enzymes grabs and flip the DNA to replicate it 5’ -> 3’ while still moving in the opposite direction
• once finished with one fragment, it lets go and does it again with another fragment
• RNA primers are then added towards the end of each fragment
• DNA ligase then seals the fragments together

Question 9

lagging strand - explain the RNA primers

Answer 9

• primers have a hydroxyl group at the end that will allow another nucleotide to join
• DNA polymerase will use the primers to add another nucleotide onto the hydroxyl group

Question 10

explain the problem of chromosome shortening during replication

Answer 10

• when a primer is cleaved off, there’s no hydroxyl group at the end of the lagging strand
• so after many rounds of replication, DNA gets shorter
• this is part of why we age bc shortening can impact our coding DNA

Question 11

shortening of chromosome problem - do bacteria have this problem

Answer 11

no bc their DNA is ciruclar

Question 12

DNA polymerase - polymerase domain

Answer 12

this domain checks for whether the nucleotide that is added is correct or not

Question 13

DNA polymerase - exonuclease domain

Answer 13

• this domain has exonuclease activity
• it is where the wrong nucleotide goes
• the domain exposes the previous nucleotide hydroxyl group which allows the wrong nucleotide to be cleaved off

Question 14

explain the unwinding tension problem

Answer 14

when there is unwinding one one end for replication, the other end becomes tangled

Question 15

how to solve the unwinding tension problem

Answer 15

• helicase
• it unwinds the DNA, but as it unwinds it causes supercoiling on the opposite end

Question 16

how to solve the helicase supercoiling problem

Answer 16

• topoisomerase
• it runs along and makes little nicks that reduces supercoiling
• then DNA ligase comes in to put them back together

Question 17

what is telomerase

Answer 17

• it makes long non-coding DNA sequences using RNA primers to extend the end of the chromosomes (telomeres)
• counteracts the shortening chromosome problem
• they are always in heterochromatin (even in interphase) form bc they have no coding info

Question 18

explain the depurination

Answer 18

• frameshift mutation that is caused by hydrolysis of a purine group (G or A)
• purine is hydrolyzed off and only has a sugar backbone
• in the next round of replication, there will be a loss of information in that region

Question 19

explain depyrimidation

Answer 19

• hydrolysis of a pyrimidine (C, U, or T)
• less common than depurination bc purines are more susceptible to hydrolysis

Question 20

explain deamination

Answer 20

• mutation caused by a loss of a nitrogen group (C will instead be a U)
• results in a mismatched base pair
• if not corrected, the next round of replication will have one correct strand and one strand with a mismatch (A instead of a G)

Question 21

explain thymine diner mutation

Answer 21

• caused by UV damage creating a covalent link between pyrimidine bases (C, U, or T)
• creates a kink in DNA and the DNA cannot function properly

Question 22

explain DNA mismatch repair

Answer 22

• enzymes with endonuclease activity will see a bulge when the bases are not binding properly
• they will be able to see which is the parental strand by seeing which is methylated and take out the incorrect nucleotide
• DNA polymerase then adds in the correct one

Question 23

nonhomologous end joining

Answer 23

• for double DNA breaks
• ligase glues broken section together
• results in loss of nucleotides at repair site

Question 24

homologous recombination

Answer 24

• for double DNA breaks
• an enzyme chews up broken sections and opens up the broken DNA
• it will line the broken DNA with the nonbroken one and use the nonbroken one as a template
• the broken DNA strand, now filled with DNA, is put back and is used as a template for the other broken strand
• ligase then seals everything up

Question 25

nonhomologous recombination - when can it be used

Answer 25

if one copy of DNA is not broken