L4. DNA replication & repair Flashcards
how is DNA replication semi-conservative
- 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
what is the origin of replication
- where replication begins
- DNA is pulled apart at this region
origin of replication - eukaryotes vs bacteria
- eukaryotes: a lot of origins because the DNA is linear
- bacteria: only one because the DNA is circular
what is the replication fork
- place where DNA is being ripped apart
- the forks migrate in opposite directions until they meet with another one
what is DNA polymerase
- 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
leading strand vs lagging stand
- leading: synthesized continuously
- lagging: synthesized discontinuously
why is the lagging strand synthesized discontinuously
the lagging strand is positioned in a 3’ -> 5’ fashion and DNA polymerase only synthesizes 5’ -> 3’
how is the lagging strand synthesized discontinuously
- 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
lagging strand - explain the RNA primers
- 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
explain the problem of chromosome shortening during replication
- 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
shortening of chromosome problem - do bacteria have this problem
no bc their DNA is ciruclar
DNA polymerase - polymerase domain
this domain checks for whether the nucleotide that is added is correct or not
DNA polymerase - exonuclease domain
- 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
explain the unwinding tension problem
when there is unwinding one one end for replication, the other end becomes tangled
how to solve the unwinding tension problem
- helicase
- it unwinds the DNA, but as it unwinds it causes supercoiling on the opposite end
how to solve the helicase supercoiling problem
- topoisomerase
- it runs along and makes little nicks that reduces supercoiling
- then DNA ligase comes in to put them back together
what is telomerase
- 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
explain the depurination
- 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
explain depyrimidation
- hydrolysis of a pyrimidine (C, U, or T)
- less common than depurination bc purines are more susceptible to hydrolysis
explain deamination
- 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)
explain thymine diner mutation
- 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
explain DNA mismatch repair
- 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
nonhomologous end joining
- for double DNA breaks
- ligase glues broken section together
- results in loss of nucleotides at repair site
homologous recombination
- 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
nonhomologous recombination - when can it be used
if one copy of DNA is not broken
