1953 article in Nature
Watson and Crick
DNA Replication
AP Biology
2007-2008
Double helix structure of DNA
AP Biology
Directionality of DNA
 You need to
PO4
nucleotide
number the
carbons!

it matters!
N base
5 CH2
O
This will be
IMPORTANT!!
4
“It has not escaped our notice that the specific pairing we have postulated
immediately suggests a possible copying mechanism for the genetic
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material.”
Watson & Crick
The DNA backbone
 Putting the DNA
backbone together

refer to the 3 and 5
ends of the DNA
5
1
C
3
 the last trailing carbon
–O
Sounds trivial, but…
this will be
IMPORTANT!!
base
O
4
O
P O
O
5 CH2
OH
2
Anti-parallel strands
 Nucleotides in DNA
PO4
5 CH2
3
AP Biology
1
ribose
2
backbone are bonded from
phosphate to sugar
between 3 & 5 carbons
5
3
3
5
DNA molecule has
“direction”
 complementary strand runs
in opposite direction

base
O
4
1
2
3
OH
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3
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1
Bonding in DNA
5
Base pairing in DNA
 Purines
hydrogen
bonds
3


adenine (A)
guanine (G)
 Pyrimidines
covalent
phosphodiester
bonds


thymine (T)
cytosine (C)
 Pairing
3
5
….strong or weak bonds?
the bonds fit the mechanism for copying DNA?
AP
Biology
How
do
Copying DNA
 Replication of DNA

A:T

C:G
 2 bonds
 3 bonds
AP Biology
Let’s meet
the team…
DNA Replication
 Large team of enzymes coordinates replication
base pairing allows
each strand to serve
as a template for a
new strand
 new strand is 1/2
parent template &
1/2 new DNA

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Replication: 1st step
 Unwind DNA

Replication: 2nd step
 Build daughter DNA
strand
helicase enzyme
 unwinds part of DNA helix
 stabilized by single-stranded binding proteins
add new
complementary bases
 DNA polymerase III

helicase
DNA
Polymerase III
single-stranded binding proteins
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replication fork
But…
Where’s the
We’re missing
ENERGY
something!
for the bonding!
What?
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2
Energy of Replication
Energy of Replication
 The nucleotides arrive as nucleosides
Where does energy for bonding usually come from?
We come
with our own
energy!
You
remember
ATP!
Are there
otherenergy
ways
other
to
get energy
nucleotides?
out
You of
betit?
!
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ATP
TTP
CTP
3
5
3
5
need “primer” bases to add on to
3
energy
DNA
Polymerase III
can only add
nucleotides to
3 end of a growing
DNA strand
nucleotide to
bond to
energy
no energy
to bond

energy
energy
DNA
Polymerase III
energy
energy
ligase
DNA
Polymerase III
energy
B.Y.O. ENERGY!
The energy rules
the process
energy
energy
DNA
Polymerase III
strand only grows
53
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GTP
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 need a “starter”

DNA bases arrive with their own energy source
for bonding
bonded by enzyme: DNA polymerase III
CMP
TMP
GMP
AMP
ADP
5



modified nucleotide
Replication
 Adding bases
DNA bases with P–P–P
 P-P-P = energy for bonding
energy
energy
And we
leave behind a
nucleotide!
CTP
TTP
GTP
ATP

energy
3
energy
5
3
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5
3
5
Okazaki
Leading & Lagging strands
Replication fork / Replication bubble
Limits of DNA polymerase III

5
3
5
5
5

leading strand
3
5
3
Lagging strand
3
5
3
5
5
5
3
lagging strand
growing
3
replication fork
Leading strand
Lagging strand
Okazaki fragments
joined by ligase
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 “spot

ligase
3

DNA polymerase III
5
3
5
3
5
can only build onto 3 end of
an existing DNA strand
3
5
3
welder” enzyme

3
3
5
DNA polymerase III
continuous synthesis
5
5
leading strand
growing
replication fork 5
3
growing
replication fork
leading strand
3
Leading strand

3
5
lagging strand
5
lagging strand
5 5
5
3
5
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3
Starting DNA synthesis: RNA primers


can only build onto 3 end of
an existing DNA strand
5
3
3
Replacing RNA primers with DNA
DNA polymerase I
Limits of DNA polymerase III
5
3
5
3
DNA polymerase I
3
5
5
growing
3
replication fork
5
removes sections of RNA
primer and replaces with
DNA nucleotides
DNA polymerase III
5
3
ligase
growing
3
replication fork
primase
5
RNA 5
RNA primer
RNA
3
3
But DNA polymerase I still
can only build onto 3 end of
an
existing DNA strand
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built by primase
 serves as starter sequence
DNA polymerase III
AP for
Biology

Chromosome erosion
All DNA polymerases can
only add to 3 end of an
existing DNA strand
Houston, we
have a problem!
Telomeres
Repeating, non-coding sequences at the end
of chromosomes = protective cap
DNA polymerase I
5

5
limit to ~50 cell divisions
3
3
3
3
5
5
growing
3
replication fork
5
DNA polymerase III
Loss of bases at 5 ends
in every replication
5


chromosomes get shorter with each replication
number of cell divisions?

AP
Biologyto
 limit
5’
3’
ligase
primase
5’
TTAAGGG TTAAGGG 3
DNA polymerases
 DNA polymerase III

3’

5’
SSB
3’
5’
3’
enzyme extends telomeres
can add DNA bases at 5 end
different level of activity in different cells
 high in stem cells & cancers -- Why?
lagging strand
Okazaki
fragments
5
AP Biology
Replication fork
DNA
polymerase I
telomerase
Telomerase
3
DNA
polymerase III
growing
3
replication fork
5
RNA

5
DNA
polymerase III
Roger Kornberg
2006
 DNA polymerase I

helicase
1000 bases/second!
main DNA builder

20 bases/second
editing, repair & primer removal
DNA polymerase III
enzyme
Arthur Kornberg
1959
leading strand
direction of replication
AP Biology
SSB = single-stranded binding proteins
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4
Editing & proofreading DNA
Fast & accurate!
 It takes E. coli <1 hour to copy
 1000 bases/second =
lots of typos!
5 million base pairs in its single
chromosome
 DNA polymerase I

proofreads & corrects
typos

repairs mismatched bases

removes abnormal bases

divide into daughter cells in only few hours
 repairs damage
throughout life

divide to form 2 identical daughter cells
 Human cell copies its 6 billion bases &
remarkably accurate
only ~1 error per 100 million bases
 ~30 errors per cell cycle


reduces error rate from
1 in 10,000 to
1 in 100 million bases
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What does it really look like?
Any Questions??
1
2
3
4
AP Biology
AP Biology
2007-2008
Energy of Replication
Where does energy for bonding usually come from?
For print version
We come
with our own
energy!
You
remember
ATP!
energy
Are there
other ways
to get energy
out of it?
GTP
TTP
ATP
AP Biology
2007-2008
AP Biology
And we
leave behind a
nucleotide!
TMP
GMP
ADP
AMP
modified nucleotide
5
3
5
Replication
 Adding bases

5
3
5
3
energy
DNA
Polymerase III
no energy
to bond
can only add
nucleotides to
3 end of the
growing DNA strand

 need a primer
nucleotide to
bond to

AP Biology
5
strand grows 53
B.Y.O. ENERGY!
The energy rules
the process
3
5
AP Biology
3
3
5
5
3
Chromosome erosion
DNA polymerases can
only add to 3 end of
an existing DNA strand
5
3
Houston, we
have a problem!
DNA polymerase I
5
3
3
5
5
growing
3
replication fork
DNA polymerase III
5
ligase
Loss of bases at 5 ends
in every replication
energy

AP Biology
3
5
3
3
chromosomes get shorter with each replication
number of cell divisions?
AP
Biologyto
 limit
5
Replication fork
3’
5’
5’
3’
5’
3’
5’
3’
direction of replication
AP Biology
6