3. Double helix structure of DNA
âIt 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.â
Watson & Crick
4. Directionality of DNA
ď§ You need to
PO
number the
carbons!
ďľ
nucleotide
4
it matters!
N base
5ⲠCH2
This will be
IMPORTANT!!
4â˛
O
3â˛
AP Biology
1â˛
ribose
OH
2â˛
5. The DNA backbone
ď§ Putting the DNA
backbone together
ďľ
refer to the 3Ⲡand 5â˛
ends of the DNA
ď§ the last trailing carbon
Sounds trivial, butâŚ
this will be
IMPORTANT!!
5â˛
PO4
5ⲠCH2
4â˛
base
O
1â˛
C
3â˛
O
â
O P O
O
5ⲠCH2
2â˛
base
O
4â˛
1â˛
2â˛
3â˛
OH
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3â˛
6. Anti-parallel strands
ď§ Nucleotides in DNA
backbone are bonded from
phosphate to sugar
between 3Ⲡ& 5Ⲡcarbons
5â˛
3â˛
3â˛
5â˛
DNA molecule has
âdirectionâ
ďľ complementary strand runs
in opposite direction
ďľ
AP Biology
8. Base pairing in DNA
ď§ Purines
adenine (A)
ďľ guanine (G)
ďľ
ď§ Pyrimidines
thymine (T)
ďľ cytosine (C)
ďľ
ď§ Pairing
ďľ
A:T
ď§ 2 bonds
ďľ
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C:G
ď§ 3 bonds
9. Copying DNA
ď§ Replication of DNA
base pairing allows
each strand to serve
as a template for a
new strand
ďľ new strand is 1/2
parent template &
1/2 new DNA
ďľ
ď§ semi-conservative
copy process
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11. Replication: 1st step
ď§ Unwind DNA
ďľ
Iâd love to be
helicase & unzip
your genesâŚ
helicase enzyme
ď§ unwinds part of DNA helix
ď§ stabilized by single-stranded binding proteins
helicase
single-stranded binding proteins
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replication fork
12. Replication: 2nd step
ď§ Build daughter DNA
strand
add new
complementary bases
ďľ DNA polymerase III
ďľ
DNA
Polymerase III
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ButâŚ
Whereâs the
Weâre missing
ENERGY
something!
for the bonding!
What?
13. Energy of Replication
Where does energy for bonding usually come from?
We come
with our own
energy!
You
remember
ATP!
Are there
other ways
other energy
to get energy
nucleotides?
out of it?
You bet!
CTP
GTP
TTP
ATP
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modified nucleotide
And we
leave behind a
nucleotide!
energy
energy
CMP
TMP
GMP
AMP
ADP
14. Energy of Replication
ď§ The nucleotides arrive as nucleosides
ďľ
DNA bases with PâPâP
ď§ P-P-P = energy for bonding
ďľ
ďľ
DNA bases arrive with their own energy source
for bonding
bonded by enzyme: DNA polymerase III
ATP
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GTP
TTP
CTP
15. 5â˛
Replication
ď§ Adding bases
ďľ
can only add
nucleotides to
3Ⲡend of a growing
DNA strand
ď§ need a âstarterâ
nucleotide to
bond to
ďľ
strand only grows
5â˛â3â˛
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B.Y.O. ENERGY!
The energy rules
the process
3â˛
energy
DNA
Polymerase III
energy
DNA
Polymerase III
energy
DNA
Polymerase III
DNA
Polymerase III
energy
3â˛
5â˛
16. 5â˛
3â˛
5â˛
need âprimerâ bases to add on to
3â˛
energy
no energy
to bond
ďť
energy
energy
energy
energy
ligase
energy
energy
3â˛
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5â˛
3â˛
5â˛
17. Okazaki
Leading & Lagging strands
Limits of DNA polymerase III
can only build onto 3Ⲡend of
an existing DNA strand
ďľ
ents
fragm
ki
Okaza
3â˛
5â˛
3â˛
5â˛
5â˛
5â˛
3â˛
ligase
growing
3â˛
replication fork
5â˛
5â˛
Lagging strand
Leading strand
ďź
3â˛
Lagging strand
ďľ
ďľ
Okazaki fragments
joined by ligase
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ď§ âspot
welderâ enzyme
ďť
3â˛
5â˛
3â˛
DNA polymerase III
Leading strand
ďľ
continuous synthesis
18. Replication fork / Replication bubble
3â˛
5â˛
5â˛
3â˛
DNA polymerase III
leading strand
5â˛
3â˛
5â˛
3â˛
3â˛
5â˛
5â˛
5â˛
3â˛
lagging strand
3â˛
5â˛
3â˛
5â˛
lagging strand
5â˛
5â˛
leading strand
3â˛
growing
replication fork
3â˛
leading strand
lagging strand
5Ⲡ5â˛
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growing
replication fork 5â˛
5â˛
5â˛
3â˛
19. Starting DNA synthesis: RNA primers
Limits of DNA polymerase III
can only build onto 3Ⲡend of
an existing DNA strand
ďľ
5â˛
3â˛
3â˛
5â˛
5â˛
3â˛
5â˛
3â˛
5â˛
growing
3â˛
replication fork
DNA polymerase III
primase
RNA 5â˛
RNA primer
built by primase
ďľ serves as starter sequence
AP for DNA polymerase III
Biology
ďľ
3â˛
20. Replacing RNA primers with DNA
DNA polymerase I
removes sections of RNA
primer and replaces with
DNA nucleotides
ďľ
3â˛
5â˛
DNA polymerase I
5â˛
5â˛
3â˛
ligase
growing
3â˛
replication fork
RNA
5â˛
3â˛
But DNA polymerase I still
can only build onto 3Ⲡend of
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AP existing DNA strand
21. Chromosome erosion
All DNA polymerases can
only add to 3Ⲡend of an
existing DNA strand
Houston, we
have a problem!
DNA polymerase I
5â˛
3â˛
3â˛
5â˛
5â˛
growing
3â˛
replication fork
DNA polymerase III
RNA
Loss of bases at 5Ⲡends
in every replication
chromosomes get shorter with each replication
AP limit to number of cell divisions?
ďľ Biology
ďľ
5â˛
3â˛
22. Telomeres
Repeating, non-coding sequences at the end
of chromosomes = protective cap
5â˛
limit to ~50 cell divisions
ďľ
3â˛
3â˛
5â˛
growing
3â˛
replication fork
5â˛
telomerase
Telomerase
ďľ
ďľ
ďľ
TTAAGGG TTAAGGG TTAAGGG
enzyme extends telomeres
can add DNA bases at 5Ⲡend
different level of activity in different cells
AP Biology
ď§
high in stem cells & cancers -- Why?
5â˛
3â˛
23. Replication fork
DNA
polymerase I
5â
3â
DNA
polymerase III
ligase
lagging strand
primase
Okazaki
fragments
5â
3â
5â
SSB
3â
helicase
DNA
polymerase III
5â
3â
leading strand
direction of replication
AP Biology
SSB = single-stranded binding proteins
24. DNA polymerases
ď§ DNA polymerase III
1000 bases/second!
ďľ main DNA builder
ďľ
Thomas Kornberg
??
ď§ DNA polymerase I
20 bases/second
ďľ editing, repair & primer removal
ďľ
DNA polymerase III
enzyme
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Arthur Kornberg
1959
25. Editing & proofreading DNA
ď§ 1000 bases/second =
lots of typos!
ď§ DNA polymerase I
ďľ
proofreads & corrects
typos
ďľ
repairs mismatched bases
ďľ
removes abnormal bases
ď§ repairs damage
throughout life
ďľ
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reduces error rate from
1 in 10,000 to
1 in 100 million bases
26. Fast & accurate!
ď§ It takes E. coli <1 hour to copy
5 million base pairs in its single
chromosome
ďľ
divide to form 2 identical daughter cells
ď§ Human cell copies its 6 billion bases &
divide into daughter cells in only few hours
remarkably accurate
ďľ only ~1 error per 100 million bases
ďľ ~30 errors per cell cycle
ďľ
AP Biology
27. What does it really look like?
1
2
3
4
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Enzymes
more than a dozen enzymes & other proteins participate in DNA replication
The energy rules the process.
In 1953, Kornberg was appointed head of the Department of Microbiology in the Washington University School of Medicine in St. Louis. It was here that he isolated DNA polymerase I and showed that life (DNA) can be made in a test tube. In 1959, Kornberg shared the Nobel Prize for Physiology or Medicine with Severo Ochoa â Kornberg for the enzymatic synthesis of DNA, Ochoa for the enzymatic synthesis of RNA.