exam 3 DNA replication and repair Flashcards
(27 cards)
what are the six problems that need to be solved during DNA replication
- strand polarity - have to synthesize both strands at same times, but polymerase only goes one way
- unzip DNA - separate two strands
- processivity (the idea that you continue to add nucleotides to a polymer without stopping - long molecules - have to make sure polymerase doesn’t fall off DNA
- untangle - two strands are wound around each other - will tangle molecules if pulled apart
- one copy - only make one DNA copy as replicating
- accurate copy - DNA molecule contains genetic info that is accurate
why are there problems during DNA replication
the two strands of DNA are replicated coordinately using different mechanisms but by the same polymerase in the 5’ to 3’ direction
why do eukaryotes have additional complications that prokaryotes don’t
they have a linear genome and the presence of histones
how is DNA replication semi-conservative
for each daughter strand, one is a parental strand, and one is a newly synthesized strand
which way does replication and chain growth occur in
5’ to 3’ direction - new nucleotides are added at the 3’ end
what is DNA replication catalyzed by
DNA polymerase - an enzyme with fingers, palm, and thumb domains
what is the solution to the first problem - strand polarity
okazaki fragments are synthesized on the lagging strand and DNA ligase seals the gap between successive fragments
what is the solution to the second problem - unzip DNA
DNA helicase unzips DNA and uses ATP hydrolysis to drive a rotary engine. unzipped DNA is stabilized by single-stranded binding protein
what is the solution to the third problem - processivity
a sliding clamp holds the DNA polymerase in place, then is loaded on DNA by a clamp loader that uses ATP hydrolysis to lock the clamp around DNA
where do the first three problems occur
at the polymerase complex because they’re all assembled on DNA
what is the fourth problem - the unwinding problem
rapid rotation of DNA is needed ahead of the replication fork - strands are pulled apart, inducing torsional dress on DNA
what relieves torsional stress
topoisomerases
what are the two classes of topoisomerases
nick and swivel mechanism (I) and gating mechanism (II)
what occurs with topoisomerase I
it covalently attaches to a DNA phosphate, breaking a phosphodiester linkage in one DNA strand. now the two ends of the double helix can rotate relative to each other, relieving torsional stress
what is/isn’t required for topI***know!!
- no ATP is required to relieve strain
- a single-stranded nick/break in DNA is required, as is a covalent attachment to the enzyme
what occurs with topoisomerase II
binds to DNA in two places - each other then binds to ATP and induces a double-stranded break in DNA
once topII induces a double-stranded break in DNA, what happens
second DNA helix can be passed through - method cuts DNA, undoes knot, and reseals DNA after - enzyme is gate to let second piece of DNA pass through
what is required to use topII
ATP to untangle DNA and ATP hydrolysis to reseal DNA after
how does topII cut linked rings
topII separates linked rings by cutting DNA and allowing other ring to pass through it - topII is required in bacterial cells to complete replication
how are topI and topII different relieving stress wise
- topI requires that DNA unwinds along its length, which takes time
- topII can relieve stress more rapidly bc it’s making the cut but comes at cost of ATP
why do you need topII any time you have a circular piece of DNA
topI cannot allow two linked rings to pass each other, but topII can - any time you have a circular piece of DNA that’s replicated, need topII
what do enzymes topI and topII have in common
both have nuclease activity
what is the solution for problem 5 (prokaryotic)
prokaryotic origins have a refractory period due to methylation - prevents restarting replication until cell division has happened
what is methylation in prokaryotic cells mediated by
Dam methylase - once original replication is complete, metylase is re-expressed and newly synthesized strand can be methylated and replication can occur again
