Exam 4 Quiz 1 Flashcards
Semiconservative DNA replication
2 strands make up chromosome, one old, one new
deoxynucleoside triphosphates (dNTPs)
-triphosphates used for energy
-dATP, dTTP, dCTP, dGTP
DNA replication is synthesized in the…
5’ to 3’ direction
one strands 3’ end attaches to the other strands 5’ end. this requires
removal of 2 phosphates
pyrophosphate
2 phosphates
construction of the replisome occurs at
the origin of replication
origin of replication
-starting point around 250 base pairs
-higher in A:T [ ] bc there is only 2 H bonds
Identification done by
DNA A proteins
DNA A
-up to 40 proteins
-add tension to H bonds so they’re easier to break (via helicase)
helicase
breaks apart the hydrogen bonds between nitrogenous bases
pulling apart is done by
DNA B (helicase)
DNA B
-pull back/ break apart bonds between nitrogenous bases
what does helicase use to help
DNA C
DNA C
helps with loading onto the strands
what mode of energy is used when strands are pulled apart
ATP hydrolysis
ATP hydrolysis immediately requires
-topoisomerase
-single-stranded binding proteins
topoisomerase
relieve supercoiling tension
single stranded binding proteins
stabilize the single strands
what synthesizing machinery is needed
DNA polymerase 3 and primase
DNA polymerase 3
-1000 bases/sec
-synthesizes 5’-3’
-use dNTPs
-require template (DNA)
-require primase
what family of DNA polymerase 3 does bacteria use
family C
primase
-adds primer
-complimentary
-RNA based
-10 bases long
why is primase needed?
DNA polymerase can NOT start de novo, requires a free OH group
DNA polymerase 3 proofreading capabilities
exonuclease activity that works in the 3’-5’ direction can can go back to cut out
5 total DNA polymerases, what do they do?
-2 for DNA replication
-3 for DNA repair
DNA replication fork
-lagging strand and leading strand
-lagging strand
-discontinuous
-Okazaki fragments
Okazaki fragments
-1000-2000 in bacteria
-100 in eukaryotes
leading strand
continuous
replication is ___________
bi directional from the replication fork
how does bi-directional replication work?
as you move further away from the origin of replication, chromosomes will fold down into theta structure
Repairing the strands
DNA polymerase I and DNA ligase
DNA polymerase I
-facilitator
-exonuclease activity in 5’-3’
-remove RNA polymerases and fill them back in
DNA ligase
performs the last phosphodiester linkage
Termination of replication
Ter sites/Tus protein
Ter site
-termination site
-opposite of origin of replicaiton
-bound by tus protein
tus protein
-blocker for when replication forks come through
-prevent messing up
-soften ending component
termination of replication ends with _______________________ so we need ____________________
2 interlocking chromosomes, topoisomerase IV (to unlink chromosomes)
MukBEF
pulls the unlinked chromosomes to opposite poles
how can E coli replicate faster than their allotted replication time?
-multiple levels of replication occurring
-replication is a constant process
Bacteria # of replication origins
1
eukarya # of replication origins
many
archaea # of replication origins
few
bacteria direction of origin
bidirectional
eukarya dirention of origin
bidirectional
archaea direction of origin
bidirectional
bacteria composition of DNA polymerase
DNA polymerase C
eukarya composition of DNA polymerase
DNA polymerase B
archaea composition of DNA polymerase
DNA polymerase B
bacteria all other components
unique replisome
eukarya all other components
conserved replication of proteins
archaea all other components
conserved replication of proteins
bacteria end of replication
Ter/Tus and topoisomerase IV
Archaea end of replication
unknown
Eukarya end of replication
telomerase
Plasmids
extrachromosomal DNA found in cytoplasm
-double stranded
-circular
-in bacteria and archaea
-non essential for normal growth
-less than 5% of chromosome size
-copy numbers
copy number
number of plasmids, different amounts of different plasmids (can be between 1-100s)
advantages plasmids have for bacteria
-carry antibiotic resistance genes
-virulence factors
-bacteriocins against closely related proteins
resistance genes
usually several different genes against several different antibiotics
virulence factors
helps bacteria establish an infection via attachment proteins and toxins that damage the host tissue
plasmids do not have to…
follow normal binary fission methods, replication methods separate from chromosomes
rolling circle method
-one strand gets nicked leaving a free 3’ OH group and free 5’ phosphate group , DNA polymerase extends from 3’ OH group and works itself around the plasmid and dispenses the 5’ end (dangles) where complimentary strand synthesis occurs
