Exam 4 Quiz 1 Flashcards by Bella Forster

Semiconservative DNA replication

2 strands make up chromosome, one old, one new

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deoxynucleoside triphosphates (dNTPs)

-triphosphates used for energy
-dATP, dTTP, dCTP, dGTP

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DNA replication is synthesized in the…

5’ to 3’ direction

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one strands 3’ end attaches to the other strands 5’ end. this requires

removal of 2 phosphates

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pyrophosphate

2 phosphates

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construction of the replisome occurs at

the origin of replication

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origin of replication

-starting point around 250 base pairs
-higher in A:T [ ] bc there is only 2 H bonds

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Identification done by

DNA A proteins

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DNA A

-up to 40 proteins
-add tension to H bonds so they’re easier to break (via helicase)

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helicase

breaks apart the hydrogen bonds between nitrogenous bases

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pulling apart is done by

DNA B (helicase)

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DNA B

-pull back/ break apart bonds between nitrogenous bases

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what does helicase use to help

DNA C

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DNA C

helps with loading onto the strands

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what mode of energy is used when strands are pulled apart

ATP hydrolysis

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ATP hydrolysis immediately requires

-topoisomerase
-single-stranded binding proteins

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topoisomerase

relieve supercoiling tension

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single stranded binding proteins

stabilize the single strands

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what synthesizing machinery is needed

DNA polymerase 3 and primase

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DNA polymerase 3

-1000 bases/sec
-synthesizes 5’-3’
-use dNTPs
-require template (DNA)
-require primase

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what family of DNA polymerase 3 does bacteria use

family C

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primase

-adds primer
-complimentary
-RNA based
-10 bases long

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why is primase needed?

DNA polymerase can NOT start de novo, requires a free OH group

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DNA polymerase 3 proofreading capabilities

exonuclease activity that works in the 3’-5’ direction can can go back to cut out

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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

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