7.2 DNA Replication
adapted from John Burrell http://click4biology.
DNA replication has been outlined in section 3.4.1 which should be reviewed before tackling this section.
This HL section provides more detail on the process of DNA replication which takes place during the S
section of the Interphase. The models of DNA replication are based on some prokaryotic organisms
such as E.coli. The diversity of this group however would suggest that we should be cautious in
extrapolating the mechanism to the whole group. Eukaryotic organisms have more complex mechanism
although share the same broad mechanism. Students should pay close attention to the orientation of the
nucleotides when the DNA chain is polymerized.
7.2.1 State that DNA replication occurs in a 5 prime to 3 prime direction. The 5’ end of the free DNA
nucleotide is added to the 3’ end of the chain of nucleotides that is already synthesized
At each replication fork the DNA is replicated in the 5' to 3' direction
The 5' end of a free nucleotide adds to the 3' end of the new polynucleotide chain.
This replication can occur at either end of a replication bubble!
7.2.3 State that DNA replication is initiated at many points in eukaryotic chromosomes.
Prokaryotic DNA polymerase can work at around 1000 bases per second which means the whole
circular (loop) can replicated between 20 and 40 minutes.
The eukaryotic DNA polymerase works much slower around 50 bases per second. With as many as 80
million bases to replicate the job is achieved in about one hour by having many replication forks
7.2.2 Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase,
DNA polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside
triphosphates. The explanation of Okazaki fragments in relation to the direction of DNA polymerase III
action is required. DNA polymerase III adds nucleotides in the 5 prime to 3 prime directions. DNA
polymerase I excises the RNA primers and replaces them with DNA.
The diagram shows the loop DNA of a prokaryotic organism.
Ori is the point of origin (start) for DNA replication. Ter is the point at which the
replication will finish.
The DNA replication takes place under the control of a number of different
proteins and enzymes here indicated as replication complex.
In E. coli five such polymerases have been identified with DNA polymerase III
being associated with most polymerization of the pentose-phosphate
backbone. Humans have as many as fourteen polymerases.
Compare these:
Eukaryotic DNA: Forms Nucleosomes; made of Linear Chromosomes, includes Many Replication Forks
Prokaryotic DNA: No Nucleosomes/ no histones, is a Circular DNA, No Replication Fork/ Single point
In this model of DNA replication note the following:
New DNA on the Leading strand forms in the
direction stated 5' to 3'. This is a single complete
new strand.
On the lagging strand the new DNA still forms in
the stated direction but this time is in small
fragments (Okazaki) that will later be joined
together as one DNA polymer
A larger diagram the needs some additions.
Add the enzymes and label the diagrams using the terms below
a)
Parental DNA
The original DNA molecule in front of the replication fork
b)
DNA Helicase
Enzyme that breaks the hydrogen bonds between the
polynucleotide base pairings. This opens up the double helix.
c)
DNA Polymerase III
Adds Nucleotides in a 5' to 3' direction on this strand it
moves alongside the helicase enzyme.
d)
New DNA molecule
Newly replicated DNA the blue strand is the original the red
the newly synthesized. This shows the semi-conservative
replication.
e)
RNA Primase
Adds a few RNA nucleotides on the lagging strand and
allows the DNA polymerase to add nucleotides.
f)
DNA Polymerase III
Adds Nucleotides to the lagging strand forming short
sections of DNA the so called Okazaki fragments
g)
DNA Polymerase I
Replaces the RNA fragments with DNA but the sugarphosphate backbone is not complete.
h)
DNA Ligase
Joins the sugar phosphate backbone to complete the
polynucleotide and therefore the other DNA molecule.
Summary: This diagram is the usual version
used to describe the process of leading and
lagging strand polymerase activity.
( p) shows the orientation of the DNA helix (with
helicase) for the diagram below.
(q) Note the position of the replication fork with
the DNA helicase opening the DNA chain.
(r) The leading strand forming with DNA
polymerase III
On the lagging strand (top) the new strand is
presented as a number of Okazaki fragments.
(s) The DNA polymerase III on this strand has to
work from the beginning of each fragment
towards the 3' free end of the lagging strand
(away from the replication fork).
DNA ligase is the enzyme that joins the
fragments.
Remember always think about the action of the
DNA polymerase III adding the 5' of the free
nucleotide to the 3' of the already established
new strand.
This single fact allows the process to be tracked
and alternative diagrams to be interpreted.
Primers provide the 3’ OH group that is needed to synthesize a new strand.
All polymerization both leading and lagging strands begin with the addition of 'priming' RNA nucleotides.
(u) RNA nucleotides (yellow) attach to the first few bases on the template through the action of a
Primase (RNA primer) enzyme.
DNA polymerase III then adds DNA nucleotides to the Primer (v).
Later the RNA primer is broken down and removed by DNA polymerase I
DNA nucleotides are added to replaced the removed RNA nucleotides.
The Pentose -phosphate backbone is joined by DNA ligase.
2. Below is a diagram of a DNA molecule that is undergoing bidirectional replication. On
the diagram label primers, Okazaki fragments, and the site of action of the enzymes DNA
polymerase I, DNA polymerase III, ligase, and helicase. Show the polarities (5' to 3') of
the daughter strands. Be sure to label where replication is continuous or discontinuous.