Nature
Education’s Online Biology Textbook TRM
DNA Replication and Repair: A Coordinated Effort
DNA
replication
is
a
precise
process
of
copying
the
genetic
information
within
a
cell
so
that
when
the
cell
divides
each
daughter
cell
will
contain
exact
copies
of
each
gene.
So
how
does
a
cell
go
about
copying
material
as
complicated
as
DNA,
and
how
does
it
makes
sure
the
copy
is
perfect?
By
Padmini
Rangamani
PhD
&
Melanie
Scott,
MD,
PhD
Questions
To
Know
(diagnostic
pre‐assessment
questions)
1. What
is
the
name
of
the
structure
formed
by
DNA?
a. A
knotted
twist
b. A
double
helix
c. A
single
helix
d. Polymeric
strands
2. Which
of
the
following
is
NOT
a
base
found
in
DNA?
a. Thymine
b. Cytosine
c. Guanine
d. Adenine
e. Uracil
1
At
the
end
of
this
module
you
will
have
learned:

The
structure
and
base‐pairing
scheme
of
DNA
allows
each
strand
to
be
used
as
a
template
for
replication
of
the
double
helix

DNA
is
copied
through
a
process
of
semi‐conservative
replication

Many
protein
enzymes
work
together
to
copy
DNA

DNA
replication
begins
at
an
origin
of
replication

DNA
polymerase,
the
main
enzyme
that
copies
DNA,
can
only
copy
in
one
direction
Module:
DNA
replication
In
A
Nutshell
–
(module
overview)
TheResearchMasters.com
3. What
is
the
complementary
strand
of
the
following
DNA
strand:
5’‐GCGTACCGTTA‐3’?
a. 3’‐CGCATGGCAAT‐5’
b. 5’‐CGCATGGCAAT‐3’
c. 3’‐CGCAUGGCAAU‐5’
d. 5’‐
CGCAUGGCAAU‐3’
Nature
Education’s Online Biology Textbook 
TRM
As
DNA
strands
have
opposite
directions,
only
one
strand
(leading
strand)
can
be
copied
as
a
continuous
piece.

The
other
strand
(lagging
strand)
has
to
be
copied
in
segments
that
are
joined
together
afterwards.
‐‐
Expand
Your
Knowledge
‐‐
Base
pairing
and
models
of
DNA
replication
over
the
lifetime
of
an
organism,
and
is
carried
out
with
an
astonishingly
high
rate
of
accuracy.
DNA
2
All
cells
must
duplicate
their
DNA
before
cell
division
can
occur.
This
process
occurs
many
times
duplication
also
occurs
at
very
high
rates
‐
about
one
hundred
nucleotide
bases
are
copied
every
second!
Many
scientists
have
devoted
their
research
efforts
to
understanding
the
mechanisms
of
DNA
replication
since
Watson
and
Crick’s
paper
in
1953
laid
out
the
framework
for
the
structure
of
DNA.
In
fact,
Watson
and
Crick
ended
their
first
research
paper
that
outlined
the
DNA
structure
with
the
immediately
suggests
a
possible
copying
mechanism
for
the
genetic
material.”
In
a
follow‐up
scientific
research
paper,
Watson
and
Crick
expanded
their
work
and
outlined
a
possible
mechanism
for
DNA
replication,
where
DNA
strands
act
as
templates
for
duplication.
Watson
and
Crick
said,
“We
imagine
that
prior
to
duplication
the
hydrogen
bonds
[between
bases]
are
broken,
and
the
two
chains
unwind
and
separate.
Each
chain
then
acts
as
a
template
for
the
formation
onto
itself
of
a
new
companion
chain,
so
that
eventually
we
shall
have
two
pairs
of
chains,
where
we
only
had
TheResearchMasters.com
following
statement,
“It
has
not
escaped
our
notice
that
the
specific
[base]
pairing
we
have
postulated
triphosphate
binding
(adenine
with
thymine;
guanine
with
cytosine),
the
complementary
strand
of
any
given
sequence
of
DNA
can
be
easily
worked
out.
Using
this
scheme
each
strand
can
be
copied
to
make
two
new
double‐stranded
DNA
molecules.
So,
if
we
begin
with
a
DNA
double
helix
molecule,
we
will
They
understood
that
as
the
structure
of
DNA
contains
a
base‐pairing
scheme
of
nucleotide
Module:
DNA
replication
one
before.
Moreover,
the
sequence
of
the
pairs
of
bases
will
have
been
duplicated
exactly.”
TRM
Nature
Education’s Online Biology Textbook end
up
with
two
identical
DNA
double
helix
molecules,
each
containing
one
strand
from
the
parent
molecule
and
one
newly
synthesized
strand,
which
complements
the
parent
template
as
illustrated
in
figure
1.
This
hypothesis
about
how
DNA
replicates
is
known
as
the
semi‐conservative
model
of
DNA
replication
as
half
of
the
DNA
from
the
parent
goes
to
each
of
the
two
copies.
[Figure
1:
DNA
structure
and
base
pairing
scheme]
3
Check
your
understanding:
Do
you
know
which
base
pairs
bind
to
each
other?
Can
you
figure
out
TheResearchMasters.com
strand
and
keep
the
new
strand
going.
[Link
to
animation
where
add
base
pairs
in
correct
sequence
to
synthesize
new
strand]
to
see
the
animation.
The
aim
is
to
match
the
correct
bases
to
form
pairs
with
the
template
DNA
Module:
DNA
replication
what
base
pairs
should
be
added
next
in
the
sequence?
Try
this
for
yourselves
by
clicking
on
the
link
Nature
Education’s Online Biology Textbook TRM
It
was
not
until
1958
that
this
mechanism
of
DNA
replication
was
verified
by
Meselson
and
Stahl.
They
conducted
some
very
elegant
experiments
to
determine
which
of
the
three
main
models
of
DNA
replication
was
true.
These
models
were:
1.
the
semi‐conservative
model
of
replication
described
above;
2.
the
conservative
model
of
replication
where
the
parent
DNA
molecule
serves
as
a
template
for
an
entirely
new
double
helix,
resulting
in
an
entirely
new
daughter
DNA
molecule;
3.
the
dispersive
model
of
DNA
replication,
which
proposed
that
the
parent
and
daughter
DNA
molecules
are
a
mixed
combination
of
old
and
new
DNA
strands.
Figure
2
gives
you
a
better
idea
of
the
differences
between
[Figure
2:
DNA
models
of
replication]
Meselson
and
Stahl
realized
that
in
order
to
identify
which
model
was
true,
it
was
necessary
to
distinguish
between
the
original
parent
DNA
molecules
and
the
newly
synthesized
DNA
molecules
after
TheResearchMasters.com
4
the
3
models.
that
incorporates
15N
will
separate
out
in
a
cesium
chloride
density
gradient
at
a
different
level
from
DNA
incorporating
14N.
If
both
14N
and
15N
isotopes
are
incorporated
in
the
DNA,
this
molecule
will
have
an
intermediate
density.
different
densities
(14N
and
15N),
to
incorporate
into
the
DNA
of
Escherichia
coli
(E.coli)
bacteria.
DNA
Module:
DNA
replication
a
round
of
replication.
To
do
this
they
used
two
different
isotopes
of
nitrogen,
which
have
slightly
TRM
Nature
Education’s Online Biology Textbook Meselson
and
Stahl
took
E.coli
bacteria
grown
in
media
containing
15N
and
then
added
these
bacteria
to
media
containing
14N
and
allowed
them
to
grow
and
replicate.
After
one
round
of
replication
they
isolated
DNA
and
separated
the
DNA
according
to
density.
They
found
that
after
only
one
round
of
replication
all
the
DNA
had
an
intermittent
density
between
14N
and
15N.
Therefore
DNA
replication
could
not
occur
by
conservative
replication
as
this
would
lead
to
DNA
molecules
with
either
15N
parent
density,
or
14N
copy
density.
An
outline
of
Meselson
and
Stahl’s
clever
experiment
is
shown
in
Figure
3.
The
experiment
was
continued
to
a
second
round
of
bacterial
replication
in
14N
media.
After
the
second
set
of
replication
the
DNA
molecules
separated
out
at
either
an
intermittent
density,
or
at
14N
copy
density.
This
result
showed
that
replication
could
not
be
occurring
through
dispersive
replication
as
all
the
strands
of
DNA
in
that
model
would
be
of
intermittent
density.
Only
the
semi‐conservative
TheResearchMasters.com
5
[Figure
3:
Meselson
and
Stahl’s
experiment]
Understanding
these
findings
make
it
clear
to
us
now
that
an
organism’s
genome
not
only
contains
all
the
information
required
for
functionality,
but
also
the
DNA
sequence
serves
as
a
template
for
replication.
The
idea
of
matching
up
base‐pair
sequences
is
simple.
However,
while
the
choice
of
nucleotides
for
DNA
replication
is
limited,
the
process
of
replication
itself
is
quite
complex.
There
are
eukaryotic
cells
using
a
variety
of
other
techniques.
Module:
DNA
replication
replication
model
explained
their
findings
and
this
model
has
since
been
shown
to
occur
in
bacteria
and
Nature
Education’s Online Biology Textbook TRM
multiple
enzymes
and
regulatory
processes
that
govern
DNA
duplication
in
order
for
the
duplication
to
be
done
quickly
and,
above
all,
accurately.
Much
of
the
work
in
understanding
DNA
replication
has
been
done
in
bacteria
because
they
are
single‐celled
organisms
that
replicate
rapidly
and
contain
a
relatively
small
genome.
However,
it
has
since
been
shown
by
scientists
that
many
of
the
underlying
principles
of
replication
of
prokaryotic
DNA
apply
in
eukaryotic
cells
as
well.
DNA
replication
occurs
in
a
series
of
coordinated
steps
manner
and
in
the
correct
order
for
DNA
replication
to
begin
and
continue
to
completion.
These
steps
6
The
process
of
DNA
duplication
involves
a
series
of
steps.
Each
step
must
occur
in
a
coordinated

Initiation
of
replication
at
specific
sites

Unwinding
of
the
DNA
double
helix
to
separate
the
strands

Priming
the
start
of
replication
with
a
small
RNA
primer

Addition
of
base
pairs
to
copy
the
template
strand

Removal
of
the
RNA
primer
and
replacement
with
DNA
bases

Proofreading
the
sequence
to
make
sure
it
is
correct
Initiation
of
replication
and
DNA
unwinding
Initiation
of
DNA
replication
begins
at
specific
sites
along
the
DNA
molecule,
called
origins
of
TheResearchMasters.com
involve:
figure
4.
Initiator
proteins
recognize
and
bind
to
the
origin
of
replication.
Replication
of
DNA
then
proceeds
until
the
entire
molecule
is
duplicated.
In
circular
bacterial
DNA,
replication
proceeds
in
both
have
many
origins
of
replication.
The
difference
between
bacteria
and
eukaryotic
cell
origins
is
shown
in
Module:
DNA
replication
replication.
Bacterial
chromosomes
are
circular
and
contain
only
one
origin
of
replication.
Eukaryotes
Nature
Education’s Online Biology Textbook TRM
directions
from
the
origin
site.
In
eukaryotic
chromosomal
DNA,
replication
also
proceeds
in
both
directions
from
each
origin.
7
[Figure
4:
Origins
of
replication]
Initiator
proteins
trigger
the
assembly
of
machinery
required
for
the
DNA
double
helix
to
be
separated
and
then
copied.
The
point
where
the
DNA
molecules
are
being
unwound
forms
a
replication
bubble
and
replication
occurs
at
replication
forks
at
each
end
of
this
bubble.
Figure
5
is
a
representation
of
a
typical
replication
fork,
together
with
some
of
the
proteins
involved
in
DNA
replication.
On
one
side
of
the
fork
is
the
intact
DNA
double
helix.
On
the
other
side
are
the
two
single
strands
of
unwound
DNA.
TheResearchMasters.com
strand
binding
proteins
then
bind
to
the
unwound
single‐strands
of
DNA,
to
prevent
them
from
rejoining.
Since
DNA
molecules
are
twisted
double
helices,
unwinding
can
result
in
torsional
(twisting)
strain
on
the
rest
of
the
wound
helix.
A
family
of
enzymes
called
topoisomerases
work
to
relieve
this
stranded
DNA
molecule
by
breaking
the
hydrogen
bonds
between
the
corresponding
base
pairs.
Single‐
Module:
DNA
replication
The
unwinding
of
DNA
is
catalyzed
by
an
enzyme
called
helicase.
DNA
helicases
unwind
the
double‐
TRM
Nature
Education’s Online Biology Textbook strain
in
the
DNA
molecule
during
replication.
The
unwound
sections
of
DNA
are
now
ready
for
duplication.
8
[Figure
5:
The
replication
fork]
Copying
the
DNA
template:
primers
and
polymerases
In
order
for
replication
to
begin,
the
enzyme
that
does
the
main
copying
of
DNA,
the
DNA
polymerase,
needs
a
short
initial
sequence
of
nucleotides
to
start
it
off.
DNA
polymerases
are
very
good
at
adding
base
pairs
to
a
sequence
that
has
already
started,
but
cannot
initiate
replication
by
themselves.
The
short
initial
sequence
is
made
of
RNA
and
is
called
a
primer.
RNA
primers
are
TheResearchMasters.com
end
of
the
RNA
primer.
RNA
primers
are
ultimately
replaced
by
DNA
nucleotides
as
the
replication
process
continues.
primase
uses
the
DNA
strand
as
a
starting
point
and
the
new
DNA
strand
adds
new
DNA
bases
to
the
3’
Module:
DNA
replication
synthesized
by
an
enzyme
called
a
primase
and
are
usually
between
five
and
10
nucleotides
long.
The
Nature
Education’s Online Biology Textbook TRM
DNA
polymerase
catalyzes
the
polymerization
of
nucleotide
triphosphate
bases
into
the
new
DNA
chain.
DNA
polymerase
was
discovered
by
Nobel
Laureate
Arthur
Kornberg
in
1957
as
a
result
of
his
efforts
to
identify
the
basic
machinery
of
replication
in
E.coli
bacteria.
DNA
polymerase
uses
the
DNA
template
strand
as
a
framework
to
add
complementary
DNA
nucleotides,
starting
at
the
RNA
primer.
The
process,
when
repeated,
results
in
elongation
of
the
new
DNA
strand.
The
rate
of
elongation
is
up
to
500
nucleotides
per
second
in
bacteria
and
about
50
nucleotides
per
second
in
human
cells.
DNA
strands
have
direction!
9
DNA
strands
have
a
5’
end
and
a
3’
end.
The
two
ends
are
different
because
of
the
structural
arrangement
of
the
phosphate
and
sugar
molecules
forming
the
DNA
backbone.
This
means
that
DNA
strands
essentially
can
be
described
as
having
directionality.
As
you
can
see
from
the
illustration
in
figure
6,
each
DNA
strand
of
the
double
helix
is
in
the
opposite
direction
to
the
other
strand.
This
is
Synthesis
of
the
new
DNA
molecule
by
the
DNA
polymerase
can
only
take
place
in
one
direction:
from
the
5’
to
the
3’
end.
This
presents
a
problem
with
replication
as
the
two
strands
of
DNA
in
the
original
double
helix
and
also
in
the
newly
synthesized
strands
are
anti‐parallel.
The
strand
that
is
being
replicated
in
the
5’
to
3’
direction
continues
toward
the
replication
fork
and
is
called
the
leading
strand.
This
strand
is
synthesized
as
a
continuous
strand
of
new
DNA.
The
strand
in
the
3’
to
5’
orientation,
or
TheResearchMasters.com
what
is
meant
by
the
term
anti‐parallel.
strand
is
therefore
produced
in
short
segments
which
are
ultimately
joined
together
to
form
the
whole
DNA
lagging
strand.
polymerase
must
work
in
the
opposite
direction
moving
away
from
the
replication
fork.
The
lagging
Module:
DNA
replication
lagging
strand,
has
to
be
turned
by
the
DNA
polymerase
to
the
correct
5’
to
3’
orientation
and
the
TRM
Nature
Education’s Online Biology Textbook Check
your
understanding:
So,
we’ve
just
learned
that
DNA
strands
in
a
double
helix
have
different
structures
at
each
end
to
give
them
a
5’
end
and
a
3’
end,
and
that
these
differences
at
the
ends
of
DNA
give
the
strand
a
direction.
We
also
now
know
that
DNA
can
only
be
synthesized
in
one
direction,
the
5’
end
of
a
new
base
to
the
3’
end
of
an
existing
base.
Do
you
think
you
could
add
the
TheResearchMasters.com
10
[Figure
6:
Schematic
of
the
leading
strand
and
the
lagging
strand
directions
of
replication]
to
animation
where
add
base
pairs
in
correct
sequence
and
in
correct
5’
to
3’
direction
to
synthesize
new
strand]
the
animation.
Add
the
correct
base
in
the
correct
orientation
to
keep
your
new
strand
going.
[Link
Module:
DNA
replication
correct
base
in
the
right
orientation
to
elongate
a
new
DNA
strand?
Try
it
out
by
clicking
the
link
to
TRM
Nature
Education’s Online Biology Textbook Copying
leading
and
lagging
strands
The
leading
strand
is
elongated
in
the
direction
of
the
replication
fork
and
in
the
direction
of
the
unwinding
DNA.
As
shown
in
figure
7,
the
leading
strand
is
elongated
as
a
continuous
strand
as
the
bases
are
being
added
in
the
correct
5’
to
3’
direction.
This
means
that
the
DNA
polymerase
only
needs
one
RNA
primer
at
the
origin
of
replication.
The
polymerase
is
able
to
continue
adding
DNA
bases
until
it
reaches
an
RNA
primer
at
another
origin
of
replication
or
the
end
of
the
DNA
strand.
For
circular
bacterial
DNA
this
means
that
the
leading
strand
is
synthesized
in
one
continuous
strand
of
new
DNA
still
contain
many
RNA
primers
corresponding
to
the
number
of
replication
origins
in
each
DNA
double
11
that
has
only
one
RNA
primer
at
the
single
origin
of
replication.
Leading
strands
in
eukaryotic
cells
will
helix
being
copied.
The
lagging
strand
of
DNA
is
not
in
the
correct
orientation
for
DNA
replication
and
therefore
needs
to
be
replicated
in
segments
moving
away
from
the
replication
fork,
as
shown
in
figure
8.
The
new
DNA
strand
is
therefore
discontinuous.
The
segments
of
DNA
replicated
in
the
lagging
strand
are
known
as
Okazaki
fragments.
Each
of
these
fragments
requires
a
separate
RNA
primer
in
order
to
Module:
DNA
replication
TheResearchMasters.com
[Figure
7:
Synthesis
of
the
leading
strand
of
DNA]
TRM
Nature
Education’s Online Biology Textbook initiate
DNA
strand
elongation
by
DNA
polymerase.
The
RNA
primers
are
removed
by
a
separate
enzyme
(DNA
polymerase
I
in
bacteria)
and
replaced
with
DNA
nucleotides.
The
fragments
are
then
joined
together
by
DNA
ligase.
12
[Figure
8:
Synthesis
of
the
lagging
strand
of
DNA]
Table
1:
Main
components
of
the
DNA
replication
machinery
Protein
Function
Helicase
Unwinds
the
DNA
double
helix
Single‐strand
binding
proteins
Prevent
unwound
single
strand
DNA
from
rejoining
Topoisomerase
Relieves
torsional
strain
on
helix
during
strand
unwinding
Primase
Synthesizes
RNA
primers
Polymerase
Elongates
DNA
strands
Ligase
Ligates
(joins)
Okazaki
fragments
together
Module:
DNA
replication
role
each
one
plays
during
replication.
Table
1
summarizes
the
main
protein
enzymes
involved
in
DNA
replication
with
an
outline
of
the
TheResearchMasters.com
Nature
Education’s Online Biology Textbook TRM
Check
your
understanding:
We
have
now
learned
that
there
are
many
different
proteins
and
enzymes
that
are
needed
to
replicate
DNA.
All
these
proteins
have
specific
functions
and
carry
out
these
functions
at
specific
points
in
the
replication
process.
Can
you
put
all
the
information
together
to
decide
which
protein
or
enzyme
you
need
to
use
in
the
right
order
to
replicate
DNA?
Give
it
a
try!
It’s
not
as
hard
as
you
think!
Click
on
the
animation
and
drag
the
right
protein
or
enzyme
to
the
replicating
DNA
strand
in
the
right
order
to
keep
the
replication
going.
[Link
to
animation
where
13
choose
correct
protein
or
enzyme
to
perform
the
next
required
function
in
the
sequence
to
replicate
DNA]
Protecting
the
ends
of
genes
with
telomeres
Replication
of
the
ends
of
linear
genes,
such
as
eukaryotic
chromosomal
DNA,
represents
a
clear
problem
for
the
DNA
replication
machinery.
DNA
polymerases
can
only
replicate
DNA
in
a
5’
to
3’
five
to
10
bases
at
the
end
cannot
be
replicated
by
a
polymerase
as
there
is
no
3’
end
exposed
to
allow
a
DNA
base
to
be
added.
This
represents
a
problem
for
the
cell,
as
with
each
cellular
replication
the
DNA
length
gets
shorter.
This
means
that
important
sequencing
areas
of
the
genetic
code
could
be
lost
too.
Module:
DNA
replication
even
if
an
Okazaki
fragment
starts
from
an
RNA
primer
placed
right
at
the
end
of
the
DNA
strand,
those
particularly
difficult
in
the
lagging
strand
with
multiple
Okazaki
fragments.
As
you
can
see
in
figure
9,
TheResearchMasters.com
direction,
and
they
also
need
to
continue
from
a
previously
existing
primer
or
base.
The
problem
is
TRM
Nature
Education’s Online Biology Textbook One
mechanism
cells
have
devised
to
protect
the
ends
of
genes,
is
to
add
repeating
sequences
of
non‐coding
DNA
base‐pairs
to
the
ends
of
each
strand
of
DNA.
These
non‐coding
short
repeat
sequences
are
known
as
telomeres.
The
idea
is
that
parts
of
the
telomere
are
lost
during
replication,
so
protecting
important
genetic
information
near
the
gene.
Telomeres
can
TheResearchMasters.com
14
[Figure
9:
Linear
ends
of
DNA
get
shortened
during
replication]
do
not
make
telomerase
except
during
embryological
development.
That
means
that
ultimately,
as
cells
age,
there
is
a
higher
chance
that
vital
parts
of
the
genetic
code
can
be
lost
during
replication
events.
required
to
add
telomeres
to
DNA
strands
is
called
telomerase.
Interestingly,
most
human
cells
Module:
DNA
replication
be
labeled
in
cells
and
can
be
seen
at
the
ends
of
condensed
chromosomes.
The
enzyme
TRM
Nature
Education’s Online Biology Textbook 15
[Photo
1:
Image
of
telomeres
on
chromosomes]
Proofreading
and
repair
The
base
pair
specificity
alone
is
not
enough
to
ensure
accurate
replication
of
the
original
DNA
molecule.
During
elongation,
incorrect
nucleotides
are
incorporated
at
an
error
rate
of
about
1
in
100,000
nucleotides.
DNA
polymerases
proofread
the
nucleotides
as
they
are
added
to
the
growing
repair
is
illustrated
in
figure
10,
which
shows
removal
of
nucleotides
damaged
by
ultraviolet
light.
Defects
in
the
proofreading
and
error
repair
machinery
have
been
associated
with
diseases
caused
by
DNA
mutations,
such
as
cancer.
Module:
DNA
replication
to
ensure
correct
and
accurate
DNA
replication
of
the
parent
template.
The
sequence
of
events
in
DNA
the
mismatch
error
is
not
identified
by
DNA
polymerase,
special
enzymes
help
catalyze
mismatch
repair,
TheResearchMasters.com
chain
and
in
the
event
of
a
mismatch,
the
polymerases
remove
the
incorrect
nucleotide.
In
cases
where
TRM
Nature
Education’s Online Biology Textbook 16
[Figure
10:
Mismatch
repair]
Applications
in
science:
polymerase
chain
reaction
(PCR)
cells,
but
also
to
understand
how
these
principles
can
be
used
in
a
laboratory
setting,
often
as
a
research
tool.
One
such
tool
that
has
been
developed
through
wonderful
findings
from
many
different
scientists
is
the
polymerase
chain
reaction
(PCR).
PCR
is
used
in
many
ways
by
scientists
to
help
them
examine
both
gene
structure
and
gene
expression.
A
key
discovery
was
made
by
Thomas
Brock
in
1969
when
he
identified
Thermus
aquaticus
TheResearchMasters.com
The
main
principles
of
DNA
replication
are
important
not
just
to
understand
what
happens
in
stability
of
Taq
DNA
polymerase
at
high
temperatures
led
directly
to
thermal
cycling
as
a
way
of
elongating
and
producing
double
strand
DNA
using
small
DNA
primers
to
initiate
the
process.
Kary
Mullis
was
the
first
to
identify
the
usefulness
of
the
thermal
cycling
process
in
1983,
and
put
it
together
is
able
to
replicate
DNA
even
at
high
temperatures
that
would
normally
degrade
other
enzymes.
This
Module:
DNA
replication
(Taq),
a
bacterium
able
to
thrive
in
high
temperature
water
of
hot
springs.
The
DNA
polymerase
in
Taq
TRM
Nature
Education’s Online Biology Textbook as
the
PCR
technique,
which
heralded
a
new
era
in
cell
and
molecular
biology
research.
The
method
uses
repeated
cycles
of
heating
and
cooling
for
DNA
melting
and
enzymatic
DNA
replication
and
an
overview
of
how
this
works
is
shown
in
figure
11.
DNA
primers
along
with
thermally‐stable
DNA
polymerase
are
used
to
exponentially
amplify
a
given
portion
of
a
DNA
sample
flanked
by
the
primers.
PCR
is
a
vital
technique
used
extensively
in
genetic
cloning,
as
well
as
other
genetic
manipulations.
PCR
is
also
useful
in
identifying
gene
expression
through
a
mechanism
of
reverse
transcription,
which
copies
the
messenger
RNA
in
a
cell
into
DNA.
TheResearchMasters.com
17
[Figure
11:
Overview
of
PCR]
replication
have
provided
insight
into
cell
division,
how
genetic
information
is
handled
in
cells
and
explanation
of
the
consequences
of
aberrant
DNA
replication.
In
the
next
module,
we
will
continue
our
exploration
of
DNA
by
exploring
the
world
of
DNA
packaging
into
chromosomes.
The
extensive
scientific
research
performed
over
the
last
few
decades
investigating
DNA
Module:
DNA
replication
Nature
Education’s Online Biology Textbook TRM
Bringing
It
Al
l
Together:
(Summary)

The
unique
structure
of
DNA,
and
its
base
pairs,
allows
DNA
replication
to
occur
through
the
coordinated
effort
of
multiple
protein
enzymes

Replication
starts
at
an
origin
and
produces
separate
copies
of
each
strand
though
a
process
of
semi‐conservative
replication

Bacteria
use
one
origin
to
replicate
their
DNA,
but
eukaryotes
use
many
origins,
which
helps
speed
up
the
replication
process
for
large
genes
Bacteria
and
eukaryotes
use
similar
enzymes
to
carry
out
replication,
but
the
process
is
best
understood
by
scientists
in
the
simpler
bacterial
system

New
DNA
strands
are
synthesized
at
the
replication
fork

The
leading
strand
has
a
5’
to
3’
direction
and
is
produced
as
a
continuous
new
segment
18

of
replicated
DNA
toward
the
replication
fork

The
lagging
strand
has
a
3’
to
5’
direction
and
is
produced
in
discontinuous
segments

New
DNA
is
proofread
for
copy
accuracy
and
repaired
as
it
is
being
copied
Module:
DNA
replication
Fragments
are
ligated
to
form
continuous
DNA
strands

TheResearchMasters.com
(Okazaki
fragments)
that
form
in
a
direction
away
from
the
replication
fork
Nature
Education’s Online Biology Textbook TRM
Test
Your
Understanding:
1. DNA
replicates
through
a
process
known
as
a. Conservative
replication
b. Liberal
replication
c. Semi‐conservative
replication
d. Dispersive
replication
2. Which
enzyme
unwinds
DNA
to
separate
the
two
strands
during
replication?
a. DNA
polymerase
b. DNA
peptidase
c. DNA
helicase
d. RNA
primer
3. Okazaki
fragments
a. are
formed
in
the
leading
strand
b. are
formed
in
the
lagging
strand
c. are
synthesized
by
an
RNA
primer
d. fill
in
the
gaps
left
by
primers
19
2. DNA
mutations
often
occur
at
G‐C
sequences.
This
is
because
cytosine
can
be
methylated
to
form
5‐methylcytosine
and
then
is
easily
deaminated
to
form
which
other
base?
a. Thymine
b. Adenine
c. Guanine
d. Cytosine
3. Which
of
the
following
helps
to
explain
why
human
cells
are
quicker
at
DNA
replication
than
bacterial
cells?
a. There
are
more
replication
origins
in
human
cells
compared
with
bacteria
b. Bacterial
DNA
polymerase
add
bases
more
slowly
than
human
DNA
polymerase
c. Human
DNA
polymerase
adds
bases
much
faster
than
bacterial
DNA
polymerase
Module:
DNA
replication
1. You
are
using
a
strain
of
bacteria
that
has
a
mutated,
non‐functional
DNA
polymerase
I.
You
would
expect
that
DNA
replication
in
these
bacteria
a. would
not
be
possible
as
there
is
nothing
to
add
nucleotides
to
the
template
b. would
not
be
possible
as
no
primer
will
be
formed
to
start
replication
in
the
DNA
c. would
produce
a
leading
strand
with
an
intact
RNA
primer
d. would
result
in
only
one
strand
of
DNA
being
replicated
at
a
time
TheResearchMasters.com
Apply
Your
Knowledge:
Nature
Education’s Online Biology Textbook TRM
Instructor
Supplements
Test
question
bank:
1. In
order
to
remove
RNA
primers,
DNA
polymerase
I
acts
as
a
a. 3’
to
5’
polymerase
b. 5’
to
3’
exonuclease
c. 5’
to
3’
polymerase
d. 5’
to
3’
ligase
e. 3’
to
5’
endonuclease
2. The
enzyme
that
helps
to
relieve
the
tension
in
the
DNA
ahead
of
the
replication
fork
by
breaking
and
twisting
the
DNA
is
called
a. Helicase
b. Topoisomerase
c. Polymerase
d. Primase
20
3. The
enzyme
that
connects
Okazaki
fragments
together
is
called
a. DNA
polymerase
b. RNA
polymerase
c. Primase
d. DNA
ligase
5. Telomeres
are
important
in
DNA
replication
because
a. They
produce
the
template
for
replication
b. They
start
replication
off
at
specific
points
on
the
DNA
c. They
allow
Okazaki
fragments
to
be
formed
d. They
protect
the
end
of
the
DNA
strand
during
replication
6. Telomeres
a. Can
reach
15,000
base
pairs
in
length
b. Lose
some
length
during
each
DNA
replication
c. Prevent
base
pair
sequences
being
lost
at
the
ends
of
DNA
d. Prevents
ends
of
DNA
strands
from
fusing
back
together
e. All
the
above
Module:
DNA
replication
4. Which
is
a
major
difference
between
DNA
replication
in
prokaryotes
and
eukaryotes?
a. Prokaryotes
use
DNA
gyrase
instead
of
DNA
helicase
b. There
is
only
one
origin
of
replication
in
prokaryotes
c. Prokaryotes
use
conservative
replication
d. Prokaryotes
do
not
use
DNA
polymerase
TheResearchMasters.com
Nature
Education’s Online Biology Textbook TRM
7. The
enzyme
that
add
the
sequence
TTAGGG
to
the
end
of
existing
chromosomes
is
called
a. Exonuclease
b. Endonuclease
c. Chromophore
d. Telomerase
8. An
enzyme
that
is
able
to
transcribe
RNA
back
to
DNA
is
called
a. Reverse
transcriptase
b. RNA
polymerase
c. DNA
polymerase
d. Restriction
enzyme
9. An
enzyme
that
cuts
DNA
only
at
specific
base
sequences
is
called
a. Reverse
transcriptase
b. DNA
ligase
c. Restriction
enzyme
d. Topoisomerase
21
10. Bacterial
transformation
involves
a. Formation
of
new
DNA
from
RNA
b. Formation
of
new
RNA
from
DNA
c. Infection
of
the
bacterium
by
a
phage
d. Assimilation
of
external
DNA
into
the
bacterial
genome
12. Which
mode
of
DNA
replication
could
Meselson
and
Stahl
eliminate
based
on
their
experimental
findings
after
just
one
round
of
replication?
a. Conservative
replication
b. Semi‐conservative
replication
c. Dispersive
replication
d. None
of
the
above
Module:
DNA
replication
11. Which
of
the
following
about
transposons
is
NOT
true?
a. They
are
DNA
sequences
that
were
first
observed
in
maize
b. They
are
DNA
sequences
that
move
around
the
genomes
of
adjacent
cells
c. They
are
DNA
sequences
that
move
around
the
genome
of
individual
cells
d. They
can
cause
genetic
mutations
TheResearchMasters.com
Nature
Education’s Online Biology Textbook TRM
Discussion
Starters
5. RNA
viruses
need
to
convert
their
RNA
genetic
information
into
DNA
in
order
to
use
the
cell’s
own
DNA
replication
enzymes
to
proliferate.
How
do
you
think
they
can
do
this?
22
4. How
does
a
cell
that
has
already
replicated
DNA
during
S‐phase
and
is
now
in
G2
of
the
cell
cycle
prevent
DNA
replication
from
occurring
again?
TheResearchMasters.com
3. How
does
PCR
use
what
we
know
about
DNA
replication
to
amplify
DNA
sequences?
Module:
DNA
replication
2. Why
does
DNA
polymerase
only
increase
the
length
of
DNA
during
replication
in
a
5’
to
3’
direction?
1. What
is
the
importance
of
complementary
base
pairs
in
conservation
of
base
sequence
during
DNA
replication?
Nature
Education’s Online Biology Textbook TRM
Links
embedded
in
text
(pink
highlighted
boxes)
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
Cell
division
–
link
to
modules
on
cell
division
and
mitosis
S‐phase
of
cell
cycle
–
link
to
modules
on
cell
division
and
mitosis
DNA
double
helix
–
link
to
module
on
DNA
structure
Structure
of
DNA
–
link
to
module
on
DNA
structure
Base‐pairing
scheme
–
link
to
module
on
DNA
structure
Nucleotide
triphosphate
bases
–
link
to
module
on
DNA
structure
DNA
backbone
–
link
to
module
on
DNA
structure
Condensed
chromosomes
–
link
to
modules
on
chromosomes
and
mitosis
Genetic
cloning
–
link
to
modules
on
DNA
cloning
and
DNA
technology
Reverse
transcription
–
link
to
modules
on
viruses
and
DNA
technology
DNA
packaging
into
chromosomes
–
link
to
module
on
chromosomes
23
Module:
DNA
replication
1. Semi‐conservative
DNA
replication:
DNA
replication
that
produces
two
helices
each
containing
an
original
template
strand
and
a
new
copy
strand
2. Helicase:
enzyme
responsible
for
unwinding
the
DNA
double
helix
3. Topoisomerase:
enzyme
that
helps
prevent
torsional
strain
as
DNA
is
being
unwound
4. Single‐strand
binding
protein:
bind
to
single‐strand
DNA
to
prevent
rejoining
5. Primase:
enzyme
that
makes
RNA
primers
to
initiate
replication
6. DNA
polymerase:
enzyme
that
adds
bases
in
a
5’
to
3’
direction
to
elongate
DNA
strands
7. DNA
ligase:
enzyme
that
joins
together
DNA
fragments
produced
during
replication
8. Conservative
model
of
DNA
replication:
DNA
replication
that
produces
a
completely
new
double
helix
copy
of
the
original
parent
helix
9. Dispersive
model
of
DNA
replication:
DNA
replication
that
produces
copies
of
DNA
and
mixes
new
DNA
with
parent
DNA
in
each
strand
10. Isotopes:
different
forms
of
a
chemical
element
that
contain
the
same
number
of
protons
in
their
nuclei
but
have
different
numbers
of
neutrons
11. Prokaryotes:
organisms
with
no
nucleus
or
organelles
that
have
circular
or
looped
DNA
e.g.
bacteria
12. Eukaryotes:
organisms
with
cells
containing
a
nucleus
and
ordered
DNA
structure
as
chromosomes
that
divide
primarily
by
mitosis
13. Origins
of
replication:
initiation
sites
of
DNA
replication
14. Chromosomes:
Packaging
units
of
DNA
15. Replication
bubble:
Separated
strands
of
the
DNA
parent
double
helix
that
is
being
actively
replicated
16. Replication
fork:
Site
of
DNA
replication
where
the
double
helix
is
being
unwound
17. Primer:
Small
sequence
of
nucleotides
that
allow
strand
elongation
by
DNA
polymerase
18. Directionality
of
DNA:
the
orientation
of
DNA
bases
to
produce
a
strand
that
has
different
5’
and
3’
ends
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boxes)
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
31.
32.
33.
Antiparallel
strands:
DNA
strands
that
point
in
the
opposite
direction
Leading
strand:
the
5’
to
3’
newly
synthesized
strand
of
DNA
Lagging
strand:
the
3’
to
5’
newly
synthesized
strand
of
DNA
Continuous
strand:
the
leading
strand
formed
with
minimal
RNA
primers
Discontinuous
strand:
the
lagging
strand
formed
from
segments
of
newly
synthesized
DNA
Okazaki
fragment:
segment
of
newly
synthesized
DNA
on
the
lagging
strand
DNA
polymerase
I:
enzyme
in
bacteria
that
removes
RNA
primers
and
replaces
them
with
DNA
nucleotides
Telomeres:
protective
repeated
non‐coding
DNA
sequences
at
the
end
of
linear
chromosomal
DNA
Telomerase:
enzyme
that
adds
telomeres
to
the
ends
of
DNA
Error
rate:
the
rate
of
wrongly
matched
DNA
base‐pairs
Mismatch
error:
Incorrect
matching
of
base
pairs
(e.g.
T
with
G
or
C
instead
of
A)
Mismatch
repair:
the
process
of
removing
wrong
base
pairs
or
damaged
DNA
and
replacing
with
correct
nucleotides
DNA
mutations:
mismatches
of
DNA
within
a
gene
that
can
affect
the
gene
product
Thermus
aquaticus
(Taq):
heat‐stable
bacteria
found
in
hot‐springs
Thermal
cycling:
the
process
of
heating
and
cooling
to
elongate
and
amplify
DNA
segments
during
PCR
TRM
24
Nature
Education’s Online Biology Textbook Module:
DNA
replication
TheResearchMasters.com