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43 Cards in this Set

  • Front
  • Back
rules of DNA replication
unwinds helix
lagging formed from okazaki
Untwisting of DNA
bp-ing ensures nucleot are inserted correct positions as new complement strands are synthesized.
semiconservative model
1 from parent, 1 new
meselson and stahl experiment
density and generation
DNA heavy, hybrid, light
density increases L-R
DNA replication= bidirectional
2 replication forks in opp directions
DNA replication=semidiscontinuous
leading strand is continuous
lagging copies is segments that need to be joined
enzymology of DNA replication
DNA polymerase I (Pol I)
needs all four deoxynucleotides a template and a primer, a SS-DNA that pairs with template
DNA polymerases with ecoli
ecoli have several
its Pol I has 3 active sites, is its own editor.
Pol III replicates its chrom, sits at each replication fork
nucleot added 5'-3'
catalyzes 20 cycles before new strand dissociates from template
exonuclease activity with Pol I
3'-5' is proofreading, removes incorrect bases of growing DNA chain
features of replication
helix unwound by helicase
supercoil compensated by gyrase
replication is semidiscontinuous
as helix is unwound during replication the 3-5 strand can be copied continuously by DNA pol proceeding in the 5-3 direction behind the rep fork
replication AGAIN
Pol III uses an RNA primer
primase forms primer
Pol I excises the primer
ligase seals nicks bw fragment
replication fork
duplex unwould by gyrase and helicase, SS's coated with protein, primase primes synthesis on lagging. Pol I and ligase act downstream on lagging to remove RNA primers, replace with DNA and ligate the fragments
10 diff subunits
core enzyme has 3 subs(a,e,t)
theta=holoenzyme assembly
beta=ring around DNA
mechanism of replication
consists of unwinding proteins, priming complex, 2 Pol III
mechanism of replication
DnaA binds to oriC, intitiate separation. DnaB, helicase delivered by DnaC further unwinds. primase binds and contructs RNA primer
mechanism of replication
DnaB helicase unwinds, SSB bind to keep strands separate. Pol replicates each strand
mechanism of replication
the ter locus, rich in G and T, signals end of replication. ter protein is a contrahelicase and prevents unwinding
replication ending of elongation and termination
topoisomerase II (gyrase) releives supercoiling that remains
mitosis intermediates
G1:growth and metabolism
S: DNA replication
G2: growth/prep for division
model for initiation
ORC(after anaphase of G1)
ORC w/ CDc6p (opportunity)
also add MCM (late G1)
activation G1/S
S phase
G2 and up to metaphase
DNA polymerases (greek)
gamma:rep enzyme of mito
delta:3'exo w/ PCNA
PCNA: give delta unlimited processivity and is homo
epsilon:highly processive, no subunit like PCNA
end of chromosomes replicated
telomeres:consist of 5-8bp repeated G-rich nucleot seq
telomere:1-12kbp long, replicated by RNA dependent DNA pol called telomerase
telomere replication
rep of lagging, short RNA primers are added and extended by DNA pol.
synthesis of telomeric DNA by telomerase extends the 5' end
RNA directed DNA Pol
reverse transcriptase
primer required: tRNA that virus captures from host
RT transcribes the RNA into cDNA to form hybrid
RNA genomes replicated
DNA is intermediate in the rep of RNA viruses
viral RNA is template for DNA synthesis
RT activities (3)
RNA directed DNA pol
RNase H activity:degrade RNA in the hybrid
DNA-directed DNA pol:makes duplex after RNase H destroys viral genome
AZT(HIV therapy)inhibits RT
substrate binds to HIV RT. AZTMP blocks chain elongation because 3' cant form phosphodiester with incoming nucleotide
genetic recombination
(proteins:RecA,RecBCD,RuvA,RuvB, and RuvC)
rearranges info, new assoc.
similar DNA=homo
homo acheived by general recom
recomb :need break and reunion
meselson and weigle
ABC is heavy, abc is light
created recombination
progeny bacteriophage
heteroduplex (+and-)--->
(semiconservative DNA rep)
progeny phage of 2 diff geno's
holiday model for homo recomb
+ is 5-3 and - is 3-5
only strands of like polarity exchange DNA during recombination
RecBCD-dependent initiation of recombination
1.bind RecBCd to DNA end,unwind
2.nonspecific cleave, more 3'
3.encounter and cleave
4.displace ssb, bind of RecA enhanced 5' terminal cleavage
5.pair with homo duplex and strand invasion
structure of RecA
352-residue and 38-kD protein
ADP is bound near helices C and D. The filament has 4 turns w/ 6 RecA per turn.
homologous recombination promoted by RecA enzyme
protein aids in invasion of 3'ssDNA into DNA duplex.
forms a d-loop, that is displaced by invasion to form a holiday junction as invastion continues.
site-specific recombination
transposon has inverted nucleotide sequence repeats at the terminal. Creates a staggered cut, ss ends are ligated to transposon. Gaps are filled in and strands are ligated. Transposon insertion generated direct repeats of the target site in host DNA.
can DNA be repaired...?
DNA must be preserved
cells require means for repair
2 principal mechanisms:mismatch repair and reversing chemical damage
mismatch repair
(ie:methyl-directed pathway of e.coli)
scan DNA for mismatched bases, excise the mispaired region and replace it.
Methylation occurs post replication, repair proteins identify methylated strand as parent, remove mismatched bases on the other strand and replace them
UVA irradiation
causes dimerization of adjacent thymine bases. Cyclobutyl ring forms bw C's 5&6 of the pyrimidine rings. Normal base pairing is disrupted by the dimers.
Reversing chemical damage
pyrimidine dimers repaired by photolyase.
excision repair:DNA glycosylase removes dmaged base, get AP site
AP endonuclease cleave backbone, removes serveral residues and gap is repaired by DNA poly and ligase
molecular basis of mutation
point mutations arise by wrong base pairing
can be caused by base anaologs
chemical mutagens react with bases in DNA
insertion and deletion
chemical mutagens
HNO2 converts C to U
nitrosoamines with nitric acid
Hydroxylamine reacts w/ C
alkylation of G
any alkylation agens