Replication - Part 2 Flashcards
- always at the same position on a DNA molecule
- “origin of replication”
initiation
origin of replication in prokaryotes, viruses
oriC
how many origin of replications are there in prokaryotes and viruses
single origin
how many origin of replications are there in eukaryotes
multiple
no. of replication origin in yeast
300 origins
no. of replication origin in humans
20,000 origins
- segment of DNA that replicates from a single origin of replication
- genome is divided into
replicons
origin of replication in E.coli
oriC
no. of base pairs in oriC
~245 bp
two parts of the oriC
- 13-nuc repeat motif
- 9-nuc repeat motif
- repeated 3x
- consensus seq: 5’GATCTNTTNTTTT3’
13-nuc repeat motif
how many times is the 13-nuc repeat motif repeated
3
- repeated 5x
- consensus seq: (di ma type kapoi)
9-nuc repeat motif
how many times is the 9-nuc repeat motif repeated
5
what is formed in the 13 nucleotide repeat motif once dnaA is present
melted region
binds to 9-nuc repeat of oriC
DnaA
what does the dnaA do
tortional stress on DNA
what happens at 13-nuc repeat of oriC
melting of helix
attaches to the melted region
dnaBC
later detaches
dnaC
what is formed after dnaC detaches
pre-priming complex
what does dnaB do
unwinds more DNA
releases tension during the unwinding of dnaB
DNA topoisomerase
attaches to ssDNA
SSB
primase that attaches to DNA
DnaG
initial assembly of the complex that initiates primer synthesis
primosome
dimer that binds after RNA primer is synthesized
DNA pol III
enhances binding of DNA pol III
sliding clamp
large protein complex that carries out DNA replication, starting at the replication origin
replisome
Detaches SSB once DNA pol III arrrives to copy template
replication mediator protein (RMP)
proofreads and replaces primers
DNA pol I
seals nicks
DNA ligase
what happens after DNA ligase seals nicks
termination of replication
replication fork in 3D:
the DNA on the lagging strand is __
folded
termination of replication
genetically determined
hypotheses of termination of replication
- secondary structure hinders progress of replication fork
- terminus destablizes components of replication machinery
- protein binds terminus and modifies binding or action of replisome
hinders progress of replication fork
secondary structure
destablizies components at replication machinery
terminus
binds terminus and modifies binding or action of replisome
protein
- defined termination sequence
- 23bp consensus sequence
- binding site of ter protein which has contra-helicase activity
ter element
what binds to ter element
ter protein
what does the ter protein have
contra-helicase activity
replication models for circular DNA
- theta model
- rolling circle model
DNA in theta model
- bacterial DNA
- λ DNA
DNA in rolling circle model
- F factor
- ø X 174 DNA
- λ DNA
products of theta replication
two circular DNA molecules
where continuous DNA synthesis begin in rolling-circle model
3’ end of broken nucleotide strand
how is replication initiated in rolling circle model
break in one of nucleotide strands
what is released in rolling circle model
- ss linear DNA
- ds circular DNA
creates a nick in rolling circular model
endonuclease
origin of replication for yeast
ARS (autonomously replicating sequence)
ARS subdomains
- A and B1 = ORS
- B2
- B3
A and B1
ORS
function of ORS
binding site of ORC
ORC
origin replicating complex
ORS
origin replication sequence
function of B2
melting
function of B3
binding site of ABF
- tortional stress on DNA
ABF
ARS binding factor 1 protein
- tightly bound
- cooperates in the synthesis of the first few nucleotides of the new polynucleotide
eukaryotic primase and DNA pol α
synthesizes an RNA primer
primase
no. of nucleotides of RNA in RNA primer
8-12
extends the RNA primer by adding ~20 nucs of DNA
DNA pol α
how many nucs does DNA pol α add to extend RNA primer
~20 nucs
elongates RNA
DNA pol δ
how many eukaryotic DNA polymerases are there
10
for primer synthesis in eukaryotes
DNA pol α
for mitochondrial DNA replication
DNA pol γ
main elongating enzyme
DNA pol δ
works with DNA pol δ by increasing its processivity
Proliferating cell nuclear antigen (PCNA)
removes RNA primers in eukaryotes
RNase H, FEN1
accuracy of DNA replication
- specificity of base pairing
- pre-synthetic error control
- proof-reading ability of DNA polymerase
before the nucleotide is covalently added to the growing chain
pre-synthetic error control
what does DNA pol undergo during pre-synthetic error contrl
conformational change
what does the DNA pol do during pre-synthetic error control
double-checks exact base pair geometry
DNA repair mechanisms to correct replication errors
proof-reading ability (3’-5’ exonuclease)
