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Replication of DNA
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Basic Features of DNA Replication In Vivo
DNA Replication in Prokaryotes
Unique Aspects of Eukaryotic DNA Replication
© John Wiley & Sons, Inc.
Basic Features of DNA Replication In Vivo
DNA replication occurs semiconservatively, is initiated at unique origins, and usually proceeds bidirectionally from each origin of replication.
Synthesis of DNA (RNA,proteins):
1-initiation, 2-extension/elongation, 3-termiantion.
DNA polymerase (protein-enzyme)-essential for conservation of any species 3,000/30,000 nucleotides per minutes
One mistake per billion of nucleotides
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DNA Replication is Semiconservative
Each strand serves as a template
Complementary base pairing determines the sequence of the new strand
Each strand of the parental helix is conserved
Semiconservative=half conserve
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MODEL
Possible Models ofDNA Replication
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The Meselson-Stahl Experiment:DNA Replication in E. coli is Semiconservative
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Bacteria growing with 15N for several generations
Change medium and add 14N
--one generation--two generations--three generations
The Origin of Replication in E. coli
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Replicon: is a sequence of DNA at which DNA replication is initiated on a chromosome, plasmid or virus.
-OriC (245 bp)
-AT-rich region (replication bubble)
-13-mer and 9-mer tandem
Mer=repeating unit=parts
Eukaryotic: ARS(Autonomously Replicating sequences)AT-rich region 11bp
N: any nucleotide
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Bidirectional Replication of the Circular E. coli Chromosome
-Circular DNA (double strand DNA)--Unwind (access and single strand DNA)--Simultaneous semiconservative replication--Swivel (point of break) Topoisomerases--Y-shape structure=replication fork
Topoisomerases: are enzymes that regulate the overwinding or underwinding of DNA.
Bidirectional Replication: The Phage Chromosome
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-Small bacterial virus
-Single stranded DNA (12 bp)
-Cohesive/sticky and complementary ends
-DNA ligase (replication, repair and recombination)
Linear
Circular
replication
• DNA replicates by a semiconservative mechanism: as the two complementary strands of a parental double helix unwind and separate, each serves as a template for the synthesis of a new complementary strand.
• The hydrogen-bonding potentials of the bases in the template strands specify complementary base sequences in the nascent DNA strands.
• Replication is initiated at unique origins and usually proceeds bidirectionally from each origin.
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DNA Replication in Prokaryotes
DNA replication is a complex process, requiring the concerted action of a large number of proteins
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DNA Polymerases and DNA Synthesis In Vitro
Much of what we know about DNA synthesis was deduced from in vitro studies.
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DNA Polymerase I Single polypeptides
5’ to 3’
Triphosphate [dATP]
MgCl2
Free 3’OH group of the DNA strands
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Continuous vs discontinuous--leading and lagging strands
Replicating fork
Bacteriophage T4
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Continuous vs discontinuous--leading and lagging strands
Replicating fork
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Prepriming at oriC in E. coli
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--Replication bubbles
Self aggregation
Why?
DNA helicase: it separates two annealed nucleic acid Strands.
RNA Primers are Used to Initiate DNA Synthesis
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DNA primase: short RNA primerRNA/DNA hybrid(unstable ?)
Perfect conditions for DNA polymerases to work(free 3’OH)
DNA Polymerase I:5'3' Polymerase Activity
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DNA Polymerase I:5'3' Exonuclease Activity
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DNA Polymerase I:3'5' Exonuclease Activity
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DNA Helicase Unwinds the Parental Double Helix
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One of the most important event during DNA replication
Why?
Single-Strand DNA Binding (SSB) Protein
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Access to DNA polymerase
Supercoiling of Unwound DNA
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DNA Topoisomerases I: produce single transient breaks of DNA and remove supercoiling
It blocks DNA replication
DNA Topoisomerases II: produce double transient breaks of DNA and negative supercoiling (DNA gyrase)
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DNA Topoisomerase I Produces Single Strand
Breaks in DNA
Requirements of DNA Polymerases
Primer DNA with free 3'-OH
Template DNA to specify the sequence of the new strand
Substrates: dNTPs
Mg2+
Reaction: nucleophilic attack
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DNA Polymerase III is the True DNA Replicase of E. coli
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DNA Polymerase III:--a 900 KDa multimeric protein--Dimers--Holoenzymes
--High fidelity (error ~1 in a 1 x 1012)
Proofreading mechanism
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Subunits----Prokaryotes
Subunits----Eukaryotes
The Replication Apparatus in E. coli
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Primosome:Initiation of Okazaki fragment during lagging strand
DNA primase and DNA helicase
DnaB and C proteins
Require ATP
DNA helicase:unwinds DNA
DNA primase: synthesis of RNA
Topoisomerase: transient DNA breaks
DNA polymerase III: extend the RNA primers (deoyxribonucleotide). It is holoenzymes
DNA Replication
Synthesis of the leading strand is continuous.
Synthesis of the lagging strand is discontinuous. The new DNA is synthesized in short segments (Okazaki fragment) that are later joined together.
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The E. coli Replisome
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Replisome: complete replication apparatus
Rolling-Circle Replication
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Replication’s Models-
O-shape
Eye-shape
Y-shape
Rolling-circle (viruses, bacteria , amphibians)
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1- Nick by specific endonucleases
2-parental DNA is intact and functions as template
3-DNA polymerase 5’ to 3’
4- displacement of one of the DNA strand
• DNA replication is complex, requiring the participation of a large number of proteins.
• DNA synthesis is continuous on the progeny strand that is being extended in the overall 5'3' direction, but is discontinuous on the strand growing in the overall 3'5' direction.
© John Wiley & Sons, Inc.
• New DNA chains are initiated by short RNA primers synthesized by DNA primase.
• DNA synthesis is catalyzed by enzymes called DNA polymerases.
• All DNA polymerases require a primer strand, which is extended, and a template strand, which is copied.
© John Wiley & Sons, Inc.
• All DNA polymerases have an absolute requirement for a free 3’-OH on the primer strand, and all DNA synthesis occurs in the 5’ to 3’ direction.
• The 3’ to 5’ exonuclease activities of DNA polymerases proofread nascent strands as they are synthesized, removing any mispaired (match) nucleotides at the 3’ termini of primer strands.
© John Wiley & Sons, Inc.
• The enzymes and DNA-binding proteins involved in replication assembled into a replisome at each replication fork and act in concert as the fork moves along the parental DNA molecule.
© John Wiley & Sons, Inc.
Unique Aspects of Eukaryotic Chromosome Replication
Although the main features of DNA replication are the same
in all organisms, some processes occur only in
eukaryotes.
© John Wiley & Sons, Inc.
DNA Replication in EukaryotesShorter RNA primers and Okazaki fragments
DNA replication only during S phase(bacteria will duplicate DNA only in a rich environment)
Multiple origins of replication(bacteria shows one origins of replication)
Nucleosomes(nucleosomes are not present in bacteria)
Telomeres(telomeres are not present in bacteria)
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Cell Cycle
--check points----S phase----Mitosis
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Replicon: segment of DNAcontaining one Origin (O) andTwo termini (T)
The Eukaryotic Replisome
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SV40 virus: DNA virus (histones)
Bacteria replication
--unwind parental DNA (without histones)
----DNA helicase
----Topoisomerase
----Single -strand DNA binding protein
----DNA polymerase III
Eukaryotic Replication Proteins
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Eukaryotic replication----parental DNA (with histones)
----Polymerases ()
-------Pol initiation of replication (origins) priming of Okazaki fragment complex with DNA primase
-------Pol synthesis of lagging strand
Pol synthesis of leading strand----accessories proteins: PCNA and Rf-C (sliding clamp)
----Pol have exonuclease activity ( 3’to 5”)=proofreading
----Other Pols (pie, lambda, phi, rho, and mu) do not have exonuclease activity ( 5’to 3”)
----Ribonulceases H1 and FEN-1
Produce the RNA/DNA chain
Proliferating Cell Nuclear Antigen: PCNA
Nucleosome Spacing in Replicating Chromatin
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Assembly and disassembly of nucleosomes
Chromatin can have alternative states
Inactive--DNA/histones
Active--Polymerase/TFs
Polymaerase/TFsNO TRANSCRIPTION
HISTONES TRANSCRIPTION
“The addition of either TFs or nucleosomes may form stable structures that can not be changed by modifying the equilibrium with free components”
How is the chromatin structure regulated?
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Chromatin remodeling
The Telomere “extension” Problem
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DNA polymerase can not replicate the terminal DNA---too big ---not enough space ( 3’-OH, primer)
Telomerase(Reverse Transcriptase)
G-rich telomere sequence5’ to 3’
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Aging (early aging….progerias)
Immortality:Cancer and Normal cells
Senescence:normal diploid cells cease to divide, (about 45 to 50 cell divisions).
Telomere Length and Aging Shorter telomeres are
associated with cellular senescence and death.
Diseases causing premature aging are associated with short telomeres.
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Apoptosis (self-destruction):programmed cell death
Telomeres Are Essential for Survival
Figure 28.32
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Dna polymerases classification as follows:
Prokaryotic DNA polymerasesPol I to V
Eukaryotic DNA polymerases
Pol theta, pie, lambda, phi, rho, and mu.
Based on sequence homology
A, B, C, D, X, Y, and RT
bacterial
Since the parental double helix must rotate 360° to unwind each gyre of the helix, during the semi-conservative replication of the bacterial chromosome, some kind of “swivel” must exist. What do geneticists now know that the required swivel is?
a) Topoisomeraseb) Helicasec) A transient single-strand break produced by the action of topoisomerasesd) A transient single-strand break produced by the action of helicasese) A transient single-strand break produced by the action of Ligase
In the E. coli chromosome the origin of replication, called oriC, is characterized as being rich in:
a) A-G base pairsb) A-C base pairsc) C-G base pairsd) C-T base pairse) None of the above