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MBLG1001 Lectures 9 & 10
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COURSE: MBLG1001
Lecturer: Dale Hancock
Lectures 9 & 10
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MBLG1001 Lectures 9 & 10
page 2
DNA Replication.
Reference: Chapter 7 Malacinski, page 119 ….143
Key Concept: This is a very tightly regulated process, carried out once in the life of the cell, just
before cell division. The whole genome is faithfully copied, unlike transcription where only a small
portion of the genome ever gets copied. It is important that this process be as error free as possible as
this is the template for the next generation. Remember the general principles for biopolymer formation
covered in lecture 2.
Terms
•
•
•
•
•
Deoxyribonucleotides are denoted dNTPs, dNDPs or dNMPs
The N refers to any of the 4 bases; it is not specific
The T is tri, D is di and M is mono and refers to the number of phosphates.
The more common ribonucleotides are simply referred to as NTP, NDP or NMP e.g. ATP.
Pi refers to inorganic phosphate (HPO42- at pH 7)
General Biopolymer properties:
•
All biopolymers have a chemically defined and distinguishable beginning and end. DNA
strands “start” with the 5’ phosphate and “finish” with the 3’ –OH.
•
Biopolymer synthesis is an anabolic process (requires energy input). This is provided by the
substrate, dNTPs.
•
All biopolymers are synthesized in one direction only. DNA is ONLY synthesized in the 5’ 3’ direction. The in-coming nucleotide adds to the 3’-OH of the growing nucleic acid chain.
•
Some of the monomer is lost in polymerization, leaving a “residue” incorporated in the
growing chain. The terminal 2 phosphates are cleaved in the polymerization, providing the
energy for phosphodiester bond formation. The two phosphates (termed pyrophosphate)
rapidly cleave in the cell by phosphodiesterase to two phosphates, thus driving the reaction in
the direction of polymerization.
•
The monomer must be “activated” before polymerization. dNTPs are used as substrate. The
dNMPs are activated to the triphosphate level before polymerization.
•
There are three phases to biopolymer formation in vivo (in the cell): Initiation, elongation and
termination.
The general process: (page 127)
dNTP + pNpNpNpN-3’OH pNpNpNpNpN-3’OH + PPi (pyrophosphate rapidly breaks
down to 2Pi in the cell)
MBLG1001 Lectures 9 & 10
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The actual polymerization process is shown below.
BASE
O
-O
P
O
O
O-
H
H
:OH
H
H
O
-O
P
H
O
O
P
O
O
P
O
O-
BASE
O
O-
CH2
O
H
H
OH
H
H
H
BASE
O
-O
P
O
O
O-
H
H
O
H
H
O
-O
P
O-
O
O
P
O-
O-
+
O
H
P
BASE
O
O
O-
H
H
OH
H
H
H
MBLG1001 Lectures 9 & 10
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The best studied model is E. coli and it is the quintessential example of replication. It also illustrates
the main points very well. Eukaryotic replication is more complex but shares the same strategy.
The initiation of DNA replication (page 123) occurs at a defined site called the oriC (C for
chromosomal) site. There are a number of proteins required to be assembled at this site and this
assembly is very tightly regulated. If replication is only going to happen once in the life of the cell,
just prior to cell division you can’t have a basal rate of replication or accidentally start to
replication inappropriately.
The site has a 9 nucleotide sequence which is repeated 4 times over a stretch of 250 nucleotides. The
DnaA protein monomers (50 kDa) bind to this site in a process requiring ATP. The final DNA-protein
complex contains some 15-20 DnaA monomers and covers ~150 base pairs of the DNA. Other
replication proteins (eg DnaB) then assemble onto this complex and an RNA primer is formed.
Replication can now begin.
Elongation.
How is DNA synthesized? Is it conservative, semi-conservative or dispersive? Before the mechanics
of replication could be worked out these questions had to be sorted. Conservative replication results in
one daughter cell containing both parent strands and the other daughter cell containing two newly
synthesized strands of DNA. Semi-conservative replication results in the DNA of both daughter cells
containing one strand from the parent and one newly synthesized strand. The dispersive model has
sections of parental and newly synthesized DNA scattered throughout both strands of the daughter
genome.
An elegant series of experiments by Messelson and Stahl proved that DNA
replication was in fact semi conservative. Using the heavy isotope of Nitrogen, 15N and CsCl density
centrifugation they were able to establish that the newly synthesized double stranded DNA contained
one strand from the parent and one new strand. Essentially cells were grown up on the normal “light”
isotope of N, 14N, then the medium was changed to one containing the 15N as sole nitrogen source.
DNA was isolated at various time points after the media change and applied to a CsCl density
gradient. This technique separates by buoyant density and DNA containing 2 light strands (L:L) will
sediment at a different density to a hybrid Heavy:Light (H:L) nucleic acid or the Heavy:Heavy (H:H)
form of DNA.
MBLG1001 Lectures 9 & 10
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If replication was conservative…
The DNA one cell division after medium change would be composed of H:H and L:L in equal
proportions. In the second generation there should be 3 H:H to 1 L:L.
If the replication was semi conservative…..
In the first generation after medium change one would predict the DNA to be composed of solely H:L
if replication was semi conservative. In the next generation you would expect H:L and H:H in a ratio
of 1:1. In the following generation the H:L and H:H would have a ratio of 1:3. In the next generation
it would be 1:7.
If replication was dispersive….
Hybrid H:L DNA would result but if the individual strands were analysed under denaturing conditions
(in CsCl with NaOH to keep the strands apart) they would also have an intermediate density. The
individual DNA strands would always be either H or L in the other models.
The results.
Both single stranded and double stranded densities at each time point confirmed the semi conservative
replication model of replication.
The Statistics
E. coli can, under optimal growth conditions double cell numbers every 20 min. They can take up to
10 h to double in less nutritious circumstances. Despite the variation in doubling time, the replication
fork moves at a constant 1000 NMPs/sec. At this rate it takes 40 min to copy the whole E. coli
genome (4.6 million bases pairs) and another 20 min to separate the cellular components. To double in
less than 60 min means the cell must initiate the next round of replication before the previous one had
finished. This results in multi-forked chromosomes.
Eukaryotes have multiple oriC sites scattered along the chromosomes but these can only be initiated
once in a round of cell division. After they have been accessed by the replication machinery they are
sequestered until the next round of cell division.
Our problems:
1. Replication is bi-directional. The theta model.
2. Bacterial DNA is a closed circle so it will get tangled when it is unwound.
3. DNA polymerases only work in one direction and need primers
MBLG1001 Lectures 9 & 10
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4. The strands must be pulled apart and unwound.
Evidence for bi-directional replication. There are a host of electron micrographs of replicating
bacterial DNA (see your textbook). They show a “theta” where the new strands are peeling from the
parent strand, appearing as a greek theta. The strong evidence is that there are two replication forks,
working in concert in opposite directions from the oriC site. By the time they meet up a complete
second copy of the genome will have been made. This may not seem too amazing until you realize
point 3. If the replication forks are working in opposite directions then the problem of unidirectional
polymerases is interesting.
Enzymes involved in DNA replication
The major player in this whole process is the enzyme DNA polymerase III. What happened to DNA
polymerases I & II you may well ask!!
Another Dale bedtime story. It all started with DNA polymerase I. This enzyme was first discovered
by Arthur Kornberg in 1956 (the enzyme’s isolation is celebrating 50 years this year). There had been
a search for the enzymes responsible for DNA synthesis since the structure of DNA had been solved
(1953). DNA polymerase I seemed to fit the bill. It was a nice little 100 kDa single polypeptide chain
which displayed three activities: 5’ 3’ polymerse activity, 3’ 5’ exonuclease activity and 5’ 3’ exonuclease activity. It did have a couple of problems but these weren’t realized until later. It
certainly was the first of many DNA polymerases to be discovered and it brought molecular biology
to a new era. With this enzyme we could now copy a strand of DNA in a test-tube (in vitro)
There was some doubt among biochemists that DNA pol I (as it was affectionately known) actually
worked fast enough to copy the whole genome. But the main drawback to DNA pol I being the
principal replicative enzyme was a set of mutants produced by John Cairns and Paula DeLucia. These
bacteria possessed a fraction of the DNA polymerase I activity (~1%) of normal cells yet they could
still divide at approximately the same rate as wild type cells. These mutants were more susceptible to
UV damage but otherwise they were fine. Increasingly it became obvious that DNA pol I was not the
major player in this process, although it did turn out to have a critical role, which explained why the
mutants needed some pol I activity to divide. If they had no pol I activity they would not have
survived.
Enter the son, Thomas Kornberg with the discovery of DNA polymerase II and then the next year
(1970) DNA polymerase III. Father Arthur had already been awarded the Nobel Prize in 1959. DNA
pol III is a seriously big enzyme. It has heaps of subunits (over 10 I believe), some of which have a
regulatory role rather than a catalytic function. This type of enzyme is called a holoenzyme. The core
enzyme is the minimum subunits required for activity, while the complete enzyme with regulatory
subunits is known as the holoenzyme. DNA pol III has two activities; the 5’ 3’ polymerase and the
3’ 5’ exonuclease activity. The fully assembled enzyme has a circular clamp which fits around the
DNA template. This circular clamp is assembled in two halves (2 beta subunits) by a clamp loader and
this explains DNA pol III’s ability to remain associated with the template for the entire genome . The
exonuclease activity is responsible for the editing or proof reading role of pol III. If the wrong base
pairs to the template the polymerase stalls long enough for the exonuclease activity to cleave the
nucleotide off and allow another to bind. The enzyme then proceeds.
MBLG1001 Lectures 9 & 10
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Other DNA polymerases
Reverse Transcriptase.
This DNA polymerase, first isolated independently by David Baltimore and Howard Temin, uses
RNA as a template to direct the synthesis of its DNA copy. It is produced by retroviruses, those pesky
little viruses that have an RNA template but, once infected the first thing they do inside the host cell is
make a complementary DNA copy (cDNA) of their template. The notion of having an RNA template
inside a eukaryotic cell is not such a good one for longevity. The most famous retrovirus is HIV.
Because reverse transcriptase is unique to the virus it is targeted by drug therapies such as AZT, an
analog of thymidine.
Klenow Enzyme
Meanwhile back to DNA polymerase I….
***This enzyme has had an important role in molecular biology also. It can be treated briefly with a
proteolytic enzyme to yield two fragments; a ~33kDa and a ~66 kDa polypeptide. The smaller
fragment contains the 5’ 3’ exonuclease activity and the larger peptide has the 3’ 5’ exonuclease
and the 5’ 3’ polymerase activity. The larger fragment is known as the Klenow enzyme and it is
widely used to synthesise DNA from a DNA template. Removing the 5’ 3’ end nibbling improves
the yield of DNA product.
Eukaryotic DNA polymerases
There are at least 5 DNA polymerases in eukaryotes: α, β, δ and ε, while the mitochondria have their
own, DNA pol γ. These are definitely beyond the scope of this course.
Taq polymerase
This is a thermal stabile form of DNA polymerase isolated from the bacterium Thermus aquaticus
which chooses to live in the sulfur springs of Yellowstone National Park. It is used in PCR
(Polymerase Chain Reaction), a technique that enables you to amplify a section of DNA. This
technique is used in crime scene investigations, paternity suits etc. When they want DNA evidence
this is the technique used.
DNA polymerases used in repair.
These enzymes became DNA pols IV and V. They are involved in repair in E. coli and also beyond
the scope of this year’s course!
MBLG1001 Lectures 9 & 10
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In summary:
DNA polymerase III has:
• 5’ to 3’ polymerase activity,
• 3’ to 5’ exonuclease activity,
• It is huge and contains many subunits.
• It is described as a holoenzyme.
DNA polymerase I has:
• 5’ to 3’ polymerase activity,
• 3’ to 5’ exonuclease activity,
• 5’ to 3’ exonuclease activity,
• It is a single 100 000 polypeptide chain
Both DNA pols I and III have important roles in replication. The need for the dual exonuclease
activities was only realized when the role for pol I was established.
After initiation the DNA double helix begins to “melt” under the action of helicase. Replication forks
are set up, moving in each direction around the genome. As the strands are separated, single stranded
binding protein binds to prevent re-annealing. An RNA primer is formed at oriC and DNA
polymerase III then binds and begins the long process of copying the entire genome from each
direction. DNA gyrase and topoisomerases (type I) work their magic in the background to keep the
DNA tangle free and the whole lecture would be really short if it were not for one minor detail…..
DNA polymerases only synthesise DNA in the 5’ 3’ direction!!! The incoming dNTP attaches to
the 3’-OH, releasing pyrophosphate (PPi). How can both strands be synthesised in both directions?
Initially there was a long search for 3’ 5’ polymerases, but alas these were never found. It was then
realized that one strand of DNA synthesis is carried out discontinuously. Fragments are made and
these are then joined to form the continuous strand.
Let’s consider the replication fork in detail. There is a leading strand, where the DNA is synthesized
in a continuous fashion from 5’ 3’ by DNA polymerase III, with the sequential addition of dNTPs
onto the growing chain and the release of PPi. This will continue to happen until it meets up with the
other replication fork.
The other players:
DnaB (page 126) or helicase is a hexameric protein (6 subunits) which unwinds double stranded
DNA. This is actually a whole class of enzymes (12 types occur in E. coli alone) present in all cells.
To replicate, repair or transcribe DNA you need access to the middle of the double helix, where the
information is stored. Helicases break the h-bonds (not the covalent phoshpodiester sugar phosphate
MBLG1001 Lectures 9 & 10
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backbone) thus separating the two strands. It requires energy to perform this function, hydrolyzing
NTPs to NDPs + Pi.
Single stranded binding protein (ssbp) prevents the two strands reannealing, as well as
forming intrastrand loops and nuclease attack. The E. coli ssbp is a tetramer which binds to the single
stranded DNA melted by helicase.
DNA ligase (page 136) seals nicks in the sugar phosphate backbone reforming the
phosphodiester bond. To do this it needs a source of energy. In E. coli this is provided by NAD; in
higher organisms ATp is the energy source. DNA pol I can’t join the nick as it relies on the hydrolysis
of pyrophosphate from dNTPs to form the phosphodiester bond.
Primase (page 135) is an RNA polymerase and is part of the primosome complex. It produces
short RNA primers (~11 nt in length) for DNA pol III in the lagging strand.
The replisome is an assembly formed by a dimer of DNA pol III holoenzymes (the complete
package) and the primosome.
Topoisomerases: (page 121 – 123)
These enzymes are responsible for removing the tangles which will inevitably happen when you go to
copy the whole genome. Because the bacterial chromosome is closed circular this is a particular
problem, however the length of eukaryotic chromosomes also cause problems even though they are
linear. There are 2 types of topoisomerases, imaginatively named type I and type II.
Type I topoisomerases cut one strand ahead of the replicating fork. They cut the sugar phosphate
backbone at a phosphodiester bond. With the 2 ends pinned to the enzyme the other strand is allowed
to pass through the gap and the break is reformed. There is a nice picture in your textbook on page
123. Type I topoisomerases do not need an energy source, there is enough energy stored in the
stressed out DNA to fuel the re-formation of the phosphodiester bond.
Type II topoisomerases cut both strands and require an energy source, usually ATP. The most
famous type II enzyme is DNA gyrase. This enzyme works to keep the DNA slightly negatively
supercoiled. DNA gyrase is so crucial to the survival of the bacterial cell that it has become a target
for some antibiotics e.g. nalidixic acid. Gyrase and type I topoisomerases are at work the whole time
keeping the DNA slightly negatively supercoiled. They are particularly important at replication
because the whole genome has to be melted.
What is supercoiling? (see page 38)
If the 2 stands of DNA are both cut and twisted one turn before reforming the DNA becomes
supercoiled. It will make a circular chromosome cross over rather than remain a relaxed circle. The
number of turns of the helix don’t change it is the whole chromosome that crosses over. The more
times it crosses over the more supercoiling it has. This is known as positive supercoiling and has
resulted from twisting in the direction of the helix and tightening it.
If the twisting is in the opposite direction to the turn of the helix then it is described as negative
supercoiling. Most DNA is slightly negatively supercoiled as it makes it easier to locally melt and
copy.
MBLG1001 Lectures 9 & 10
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The replication fork.
The replisome must move in one direction, but the DNA pol only works 5’ to 3’. To copy both strands
one strand has to loop back on itself so the DNA pol III has a 3’-OH from both strands to work.
Helicase and ssbp work together (in front of the replisome) to provide the DNA pol III with a single
stranded DNA template to copy.
The leading strand copies the 3’ to 5’ template strand, producing a continuous 5’ to 3’ complementary
strand.
The lagging strand uses the looped around template strand and forms fragments, known as Okasaki
fragments, extended from RNA primers laid down by primosomes along the other 5’ to 3’ strand. The
fragments are then “nick translated” by DNA pol I and sealed by DNA ligase.
The details will be shown in the lecture….they need pictures.