DNA Replication Flashcards
Three fundamental rules of DNA replication
1) DNA replication is semi-conservative
2) Replication begins at an origin and proceeds bidirectionally
3) DNA synthesis proceeds in a 5’-> 3’ direction and is semidiscontinuous
Which drug can target viral DNA polymerases specifically, such as in herpes simplex, whose structure resembles a guanine attached to an incomplete ribose ring
Acyclovir
What sort of sequences are good as origins of replication and why?
AT base pair rich sequences because they only form two bonds and therefore are easier to melt into ssDNA.
True or false: DNA replication is only bidirectional in prokaryotes
False
Protein which forces DNA strands apart to create origin of replication
DnaA
Enzyme which couples energy from ATP cleavage to produce a conformational change in DnaA, thus forcing the strands apart
AAA+ ATPase
Creates phosphodiester bonds to seal nicks in the DNA strand
DNA Ligase
Enzyme responsible for strand elongation, requiring ssDNA template and an RNA primer
DNA Polymerase
Unwind DNA double strands in helix
Helicase
Responsible for sythesizing RNA complementary to the template DNA strand to start DNA synthesis
Primase
Enzymes which adjust the supercoiling of DNA double helices
topoisomerase
Type I Topoisomerase
cleave one of the strands of the double helix
Type II Topoisomerase
cleave both strands to perform its function
binds to the single-stranded portion of each
DNA strand, preventing the strands from reannealing and protecting them from degradation
by nucleases
Single-stranded DNA binding protein (SSB)
What do we call the Type II topoisomerase which alleviates positive supercoiling imposed by strand unwinding
DNA gyrase
Three aspects of genome fidelity
1) geometry of the active site of DNA Polymerase (purine-pyrimidine pairing)
2) Proofreading (3’->5’ exonuclease activity)
3) mismatch repair and DNA methylation
How does DNA methylation factor into mismatch repair?
Methylation marks the parent strand so repair functions know which side to fix
Three prokaryotic DNA Polymerases involved just in DNA repair
DNA Polymerase II, IV, and V
Prokaryotic DNA polymerase involved in DNA repair and also removes RNA primers during replication
DNA Polymerase I
Prokaryotic DNA polymerase responsible for synthesizing most of the DNA during replication. High proccessivity
DNA Polymerase III
Which prokaryotic DNA Pol(s) have 5’->3’ exonuclease activity?
DNA Polymerase I
Which prokaryotic DNA Pol(s) have 3’->5’ exonuclease activity?
DNA Polymerase I and III
3 major causes of mtDNA depletion
1) Issues with mitochondrial fusion / fission
2) Availability (rather lack) of nucleotides
3) Presence of machinery to replicate
A given cell contains multiple types of mitochondrial DNA, with varying levels of each from one cell to the next.
heteroplasmy
Mitochondrial DNA Maintenance Defects affect which three groups the most?
1) children
2) those treated for HIV-1 and hepatitis B virus infections
3) young adults
Why do MDMDs exhibit autosomal inheritance patterns?
Most mitochondrial proteins are nuclear-encoded and all known mutations occur there.
Eukaryotic DNA Polymerase containing primase and initiating DNA synthesis
Pol alpha
Eukaryotic DNA Polymerase whose function is repair
Pol beta
Eukaryotic DNA Polymerase responsible for replicating mtDNA
Pol gamma
Eukaryotic DNA Polymerase thought to elongate Okazaki fragments of the lagging strand
Pol delta
Eukaryotic DNA Polymerase thought to elongate the leading strand
Pol epsilon
Which eukaryotic DNA polymerases have 3’ -> 5’ exonuclease/proofreading activity
Polymerase gamma, delta, and epsilon
Are eukaryotic origins of replication specific or non-specific?
Non-specific. They’re just AT rich and occurs ~30-300 kbp
Which is faster: eukaryotic or prokaryotic DNA synthesis?
prokaryotic
What type of enzyme is telomerase a special type of?
Reverse Transcriptase
