dna replication
DESCRIPTION
Ncert plus two biology surendran aduthilaTRANSCRIPT
![Page 1: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/1.jpg)
2007-2008 AP Biology
DNA Replication
![Page 2: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/2.jpg)
Watson and Crick1953 article in Nature
![Page 3: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/3.jpg)
Double helix structure of DNA
“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” Watson & Crick
![Page 4: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/4.jpg)
Directionality of DNA You need to
number the carbons! it matters!
OH
CH2
O
4
5
3 2
1
PO4
N base
ribose
nucleotide
![Page 5: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/5.jpg)
The DNA backbone Putting the DNA
backbone together refer to the 3 and 5
ends of the DNA the last trailing carbon
OH
O
3
PO4
base
CH2
O
base
OPO
C
O–O
CH2
1
2
4
5
1
2
3
3
4
5
5
![Page 6: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/6.jpg)
Anti-parallel strands Nucleotides in DNA
backbone are bonded from phosphate to sugar between 3 & 5 carbons DNA molecule has
“direction” complementary strand runs
in opposite direction
3
5
5
3
![Page 7: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/7.jpg)
Bonding in DNA
….strong or weak bonds?How do the bonds fit the mechanism for copying DNA?
3
5 3
5
covalentphosphodiester
bonds
hydrogenbonds
![Page 8: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/8.jpg)
Base pairing in DNA Purines
adenine (A) guanine (G)
Pyrimidines thymine (T) cytosine (C)
Pairing A : T
2 bonds C : G
3 bonds
![Page 9: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/9.jpg)
Copying DNA Replication of DNA
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
![Page 10: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/10.jpg)
DNA Replication Large team of enzymes coordinates replication
![Page 11: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/11.jpg)
DNA-pol of eukaryotes
DNA-pol : elongation DNA-pol III
DNA-pol : initiate replication and synthesize primers
DnaG, primase
DNA-pol : replication with low fidelity
DNA-pol : polymerization in mitochondria
DNA-pol : proofreading and filling gap
DNA-pol I
repairing
![Page 12: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/12.jpg)
Replication: 1st step Unwind DNA
helicase enzyme unwinds part of DNA helix stabilized by single-stranded binding proteins
single-stranded binding proteins replication fork
helicase
![Page 13: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/13.jpg)
DNAPolymerase III
Replication: 2nd step Build daughter DNA
strand add new
complementary bases DNA polymerase III
![Page 14: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/14.jpg)
energy
ATPGTPTTPCTP
Energy of ReplicationWhere does energy for bonding usually come from?
ADPAMPGMPTMPCMPmodified nucleotide
energy
We comewith our own
energy!
And weleave behind a
nucleotide!
![Page 15: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/15.jpg)
Energy of Replication The nucleotides arrive as nucleosides
DNA bases with P–P–P P-P-P = energy for bonding
DNA bases arrive with their own energy source for bonding
bonded by enzyme: DNA polymerase III
ATP GTP TTP CTP
![Page 16: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/16.jpg)
§2.2 Primase
• Also called DnaG
• Primase is able to synthesize primers using free NTPs as the substrate and the ssDNA as the template.
• Primers are short RNA fragments of a several decades of nucleotides long.
![Page 17: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/17.jpg)
![Page 18: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/18.jpg)
Limits of DNA polymerase III can only build onto 3 end of
an existing DNA strand
Leading & Lagging strands
5
5
5
5
3
3
3
53
53 3
Leading strand
Lagging strand
Okazaki fragments
ligase
Okazaki
Leading strand continuous synthesis
Lagging strand Okazaki fragments joined by ligase
“spot welder” enzyme
DNA polymerase III
3
5
growing replication fork
![Page 19: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/19.jpg)
DNA polymerase III
Replication fork / Replication bubble
5
3 5
3
leading strand
lagging strand
leading strand
leading strand
5
3
3
5
5
3
5
3
5
3 5
3
growing replication fork
growing replication fork
5
5
5
5
53
3
5
5lagging strand
5 3
![Page 20: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/20.jpg)
DNA polymerase III
RNA primer built by primase serves as starter sequence
for DNA polymerase III
Limits of DNA polymerase III can only build onto 3 end of
an existing DNA strand
Starting DNA synthesis: RNA primers
5
5
5
3
3
3
5
3 53 5 3
growing replication fork
primase
RNA
![Page 21: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/21.jpg)
DNA polymerase I removes sections of RNA
primer and replaces with DNA nucleotides
But DNA polymerase I still can only build onto 3 end of an existing DNA strand
Replacing RNA primers with DNA
5
5
5
5
3
3
3
3
growing replication fork
DNA polymerase I
RNA
ligase
![Page 22: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/22.jpg)
DNA polymerases DNA polymerase III
1000 bases/second! main DNA builder
DNA polymerase I 20 bases/second editing, repair & primer removal
DNA polymerase III enzyme
Arthur Kornberg1959
Roger Kornberg2006
![Page 23: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/23.jpg)
Editing & proofreading DNA 1000 bases/second =
lots of typos!
DNA polymerase I proofreads & corrects
typos repairs mismatched bases removes abnormal bases
repairs damage throughout life
reduces error rate from 1 in 10,000 to 1 in 100 million bases
![Page 24: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/24.jpg)
Fast & accurate! It takes E. coli <1 hour to copy
5 million base pairs in its single chromosome divide to form 2 identical daughter cells
Human cell copies its 6 billion bases & divide into daughter cells in only few hours remarkably accurate only ~1 error per 100 million bases ~30 errors per cell cycle
![Page 25: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/25.jpg)
1
2
3
4
What does it really look like?
![Page 26: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/26.jpg)
Characteristics of replication
Semi-conservative replication
Bidirectional replication
Semi-continuous replication
High fidelity
![Page 27: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/27.jpg)
§1.1 Semi-Conservative Replication
![Page 28: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/28.jpg)
Semiconservative replication
Half of the parental DNA molecule is conserved in each new double helix, paired with a newly synthesized complementary strand. This is called semiconservative replication
![Page 29: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/29.jpg)
Semiconservative replication
![Page 30: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/30.jpg)
Experiment of DNA semiconservative replication
"Heavy" DNA(15N)
grow in 14N medium
The first generation
grow in 14N medium
The second generation
![Page 31: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/31.jpg)
Significance
The genetic information is ensured to be transferred from one generation to the next generation with a high fidelity.
![Page 32: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/32.jpg)
Bidirectional Replication
• Replication starts from unwinding the dsDNA at a particular point (called origin), followed by the synthesis on each strand.
• The parental dsDNA and two newly formed dsDNA form a Y-shape structure called replication fork.
![Page 33: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/33.jpg)
3'
5'
5'
3'
5'
3'
5'3'
direction of replication
Replication fork
![Page 34: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/34.jpg)
Bidirectional replication
• Once the dsDNA is opened at the origin, two replication forks are formed spontaneously.
• These two replication forks move in opposite directions as the syntheses continue.
![Page 35: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/35.jpg)
Bidirectional replication
![Page 36: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/36.jpg)
Replication of prokaryotes
The replication process starts from the origin, and proceeds in two opposite directions. It is named replication.
![Page 37: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/37.jpg)
Replication of eukaryotes
• Chromosomes of eukaryotes have multiple origins.
• The space between two adjacent origins is called the replicon, a functional unit of replication.
![Page 38: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/38.jpg)
origins of DNA replication (every ~150 kb)
![Page 39: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/39.jpg)
Semi-continuous Replication
The daughter strands on two template strands are synthesized differently since the replication process obeys the principle that DNA is synthesized from the 5´ end to the 3´end.
![Page 40: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/40.jpg)
5'
3'
3'
5'
5'
direction of unwinding3'
On the template having the 3´- end, the daughter strand is synthesized continuously in the 5’-3’ direction. This strand is referred to as the leading strand.
Leading strand
![Page 41: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/41.jpg)
Semi-continuous replication
3'
5'
5'3'
replication direction
Okazaki fragment
3'
5'
leading strand
3'
5'
3'
5'replication fork
![Page 42: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/42.jpg)
• Many DNA fragments are synthesized sequentially on the DNA template strand having the 5´- end. These DNA fragments are called Okazaki fragments. They are 1000 – 2000 nt long for prokaryotes and 100-150 nt long for eukaryotes.
• The daughter strand consisting of Okazaki fragments is called the lagging strand.
Okazaki fragments
![Page 43: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/43.jpg)
Continuous synthesis of the leading strand and discontinuous synthesis of the lagging strand represent a unique feature of DNA replication. It is referred to as the semi-continuous replication.
Semi-continuous replication
![Page 44: Dna replication](https://reader033.vdocuments.net/reader033/viewer/2022060108/55503189b4c9058f2f8b4f38/html5/thumbnails/44.jpg)
2007-2008 AP Biology
Any Questions??