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DNA Replication DNA Replication ـــــخ ـــــخنَـْس� الـ الـ نَـْس�دنادنا

DNA Replication DNA Replication ـــــخ ـــــخنَـْس� الـ الـ نَـْس�دنادنا

THE MOLECULE BASIS OF INHERITANCE

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1- During DNA replication, base pairing enables 1- During DNA replication, base pairing enables existing DNA strands to serve as templates existing DNA strands to serve as templates

strandsstrandsُمكِّم�لُمكِّم�ل for new complimentary for new complimentaryقالبقالب

• When a cell copies a DNA molecule, each strand serves as a When a cell copies a DNA molecule, each strand serves as a templatetemplate نِّموزج for ordering nucleotides into a new for ordering nucleotides into a new complimentarycomplimentary strandstrand كِّم�لالِّم ..الجانب– Nucleotides line up Nucleotides line up تَـتَـراص along the template strand according to along the template strand according to

the base-pairing rules.the base-pairing rules.

– The nucleotides are linked to form new strands (The nucleotides are linked to form new strands (complementarycomplementary).).

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• Semiconservative replicationSemiconservative replication (the most common and accepted by(the most common and accepted by Watson and Crick). The double helix replicates each of the daughter Watson and Crick). The double helix replicates each of the daughter molecules molecules andand will have one old strand and one newly made strand.will have one old strand and one newly made strand.

• The other two models are the The other two models are the conservativeconservative and the and the dispersivedispersive modelsmodels

Types of DNA replicationTypes of DNA replication

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SemiconservativeSemiconservative DNA Replication DNA Replication ـــــخ ـــــخنَـْس� نَـْس�

1.1. During DNA replication, base pairing During DNA replication, base pairing القواعد enables enables إزدواج

existing DNA strands to serve as existing DNA strands to serve as templatestemplates قالب/ذنِّمو ج for for

new new complimentary strandscomplimentary strands كِّم�لالِّم الجانب

2.2. Several enzymes and other proteins carry out DNA Several enzymes and other proteins carry out DNA

replication:replication: Helicase, Helicase,

Primase, Primase,

Polymerase, Polymerase,

LigaseLigase..

The ends of DNA molecules are replicated by a special The ends of DNA molecules are replicated by a special

mechanism.mechanism.

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• It takes It takes EE. . colicoli less than less than an houran hour to copy each of the 5 million to copy each of the 5 million base pairs in its single chromosome and divide to form two base pairs in its single chromosome and divide to form two identical daughter cells.identical daughter cells.

• A human cell can copy its 6 billion base pairs and divide into A human cell can copy its 6 billion base pairs and divide into daughter cells in only a daughter cells in only a few hoursfew hours..

• This process is remarkably accurate, with only one error per This process is remarkably accurate, with only one error per billion nucleotides.billion nucleotides.

• A A helicase;helicase; untwists untwists لغ� �لغَي اإللتفاف اإللتفاف ييَي and separates the template and separates the template DNA strands at the replication fork.DNA strands at the replication fork.

• Single-strand binding proteins;Single-strand binding proteins; keep the unpaired keep the unpaired template strands template strands apart apart ُمنفصلينُمنفصلين during replicationduring replication..

2. A large team of enzymes and other proteins carries 2. A large team of enzymes and other proteins carries

out DNA replication: out DNA replication: TheThe Replication MechanismReplication Mechanism

• In eukaryotes, there may be In eukaryotes, there may be hundreds or thousands of bubbles hundreds or thousands of bubbles ((each has origin sites for replication) per ) per chromosome. chromosome. – At the origin sites, the DNA strands At the origin sites, the DNA strands

separate forming a replication separate forming a replication “bubble” with replication forks “bubble” with replication forks

النسخ .at each end.at each end شوكة– The replication bubbles elongate The replication bubbles elongate

as the DNA is replicated as the DNA is replicated تستطيلand eventually fuse and eventually fuse بعضها ُمع ..تندُمج

• The replication of a DNA molecule begins at special site called The replication of a DNA molecule begins at special site called

origin of replicationorigin of replication التضاعف التضاعف ُمـنشأ which is a single specific which is a single specific ُمـنشأsequence of nucleotides that is recognized by the replication sequence of nucleotides that is recognized by the replication enzymes.enzymes.

• Replication enzymesReplication enzymes separate the strands, forming a separate the strands, forming a

replication “bubble”replication “bubble” التضاعف التضاعف فقعة ..فقعة– Replication proceeds in both directions until the entire molecule is Replication proceeds in both directions until the entire molecule is

copied. copied.

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• Primer:Primer: بدءيُم ((a short segment of RNA, 10 nucleotides long) is ) is required to start a new chain.required to start a new chain.

• Primase:Primase: ( (an RNA polymerase) ) links ribonucleotides that are links ribonucleotides that are complementary to the DNA complementary to the DNA template into the primer.template into the primer.

• DNA polymerases:DNA polymerases: catalyze the catalyze the elongation of new DNA at a elongation of new DNA at a replication fork. After formation replication fork. After formation of the primer, DNA polymerases of the primer, DNA polymerases can add deoxyribonucleotides to can add deoxyribonucleotides to the 3’ end of the ribonucleotide the 3’ end of the ribonucleotide chain.chain.

• Another DNA polymerase later Another DNA polymerase later replaces the primer replaces the primer ribonucleotides with ribonucleotides with deoxyribonucleotides deoxyribonucleotides complimentary to the template. complimentary to the template.

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• The other parental strand (The other parental strand (5’->3’ into the fork), the ), the lagging strandlagging strand, is copied , is copied away from the fork in short segments away from the fork in short segments ((Okazaki fragments Okazaki fragments صغيرة .(.(قِـطَـع

• Okazaki fragments (Okazaki fragments (each about 100-200 nucleotides) are joined by ) are joined by DNA ligaseDNA ligase

الرابط -to form the sugar-to form the sugar اإلنزَيمphosphate backbone of a single DNA phosphate backbone of a single DNA strand.strand.

• DNA polymerases can only add nucleotides to the free 3’ end of a DNA polymerases can only add nucleotides to the free 3’ end of a growing DNA strand.growing DNA strand.

• A new DNA strand can only elongate in the 5’->3’ direction.A new DNA strand can only elongate in the 5’->3’ direction.

• At the replication fork, one parental strand At the replication fork, one parental strand ( (3’-> 5’ into the fork), the ), the leading strandleading strand, , can be used by polymerases as a template can be used by polymerases as a template for a continuous complimentary for a continuous complimentary strand. strand.

SUMMARY OF DNA REPLICATION SUMMARY OF DNA REPLICATION MECHANISMMECHANISM

Step 1Step 1• Helicases: Enzymes that separate the DNA strandsHelicases: Enzymes that separate the DNA strands• Helicase move along the strands and breaks the hydrogen bonds between the Helicase move along the strands and breaks the hydrogen bonds between the

complimentary nitrogen basescomplimentary nitrogen bases• Replication Fork: the Y shaped region that results from the separation of the Replication Fork: the Y shaped region that results from the separation of the

strandsstrands

Step 2Step 2• DNA Polymerase: enzymes that DNA Polymerase: enzymes that addadd complimentary nucleotides.complimentary nucleotides.• Nucleotides are found floating freely inside the nucleusNucleotides are found floating freely inside the nucleus• Covalent bonds form between the phosphate group of one nucleotide and the Covalent bonds form between the phosphate group of one nucleotide and the

deoxyribose of another deoxyribose of another • Hydrogen bonds form between the complimentary nitrogen basesHydrogen bonds form between the complimentary nitrogen bases

Step 3Step 3• DNA polymerases finish replicating the DNA and fall off.DNA polymerases finish replicating the DNA and fall off.

• The result is two identical DNA molecules that are ready to move to new cells in The result is two identical DNA molecules that are ready to move to new cells in cell division.cell division.

• Semi-Conservative Replication: this type of replication where one strand is from Semi-Conservative Replication: this type of replication where one strand is from the original molecule and the other strand is newthe original molecule and the other strand is new

• Each strand is making its own new strand.Each strand is making its own new strand.• DNA synthesis is occurring in two different directionsDNA synthesis is occurring in two different directions• One strand is being made towards the replication fork and the other One strand is being made towards the replication fork and the other

is being made away from the fork. The strand being made away is being made away from the fork. The strand being made away from the fork has gaps.from the fork has gaps.

• Gaps are later joined by another enzyme, DNA ligaseGaps are later joined by another enzyme, DNA ligase

• The strands in the double helix are The strands in the double helix are antiparallelantiparallel اإلتجاه فى ُمتضادَين و ..ُمتوازَيين

• The sugar-phosphate backbones run in The sugar-phosphate backbones run in opposite directions.opposite directions.– Each DNA strand Each DNA strand has a 3’has a 3’ end with a end with a free OHfree OH

group attached to deoxyribose and group attached to deoxyribose and a 5’ enda 5’ end with a with a free phosphatefree phosphate group attached to group attached to deoxyribose.deoxyribose.

– The The 5’ -> 3’5’ -> 3’ direction of one strand runs direction of one strand runs counter to counter to لـ لـ ُمعاكس the the 3’ -> 53’ -> 5’ direction of ’ direction of ُمعاكسthe other strand. the other strand.

SUMMARY OF DNA REPLICATION MECHANISMSUMMARY OF DNA REPLICATION MECHANISM

The two DNA-strands separate forming replication bubbles.The two DNA-strands separate forming replication bubbles.

Each strand functions as a template for synthesizing new Each strand functions as a template for synthesizing new complementary & lagging strands complementary & lagging strands viavia primers,primers, polymerase and ligasepolymerase and ligase..

G C TA AT G

GT ATA CC

GT ATA CC

G C TA AT G

Templates

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PolymerasePolymeraseComplementary (leading) strand

Lagging strand (complementary)

PrimerPrimer

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Okazaki fragments

LigaseLigase

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Fig. 16.15, Page 298

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البَــــْد�البَــــْد�ءء

اإلستطاإلستطالةالة

• Helicase:Helicase: untwists the double helix to untwists the double helix to separateseparate the DNA strands by forming the DNA strands by forming replication bubbles. replication bubbles.

• Replication enzymes:Replication enzymes: separates DNA strands, forming a separates DNA strands, forming a replication “bubble”replication “bubble”..

• Replication bubble:Replication bubble: formed at the origin sites of replication as DNA strands formed at the origin sites of replication as DNA strands separate, and hence, replication forks formed at each end. separate, and hence, replication forks formed at each end.

• Replication site:Replication site: it is also called it is also called origin of replicationorigin of replication which is a single specific which is a single specific sequence of nucleotides that is recognized by the replication enzymes sequence of nucleotides that is recognized by the replication enzymes and at which replication starts. and at which replication starts.

• Primer:Primer: is a short piece of RNA (10 nucleotide long) which is synthesised is a short piece of RNA (10 nucleotide long) which is synthesised by by primaseprimase and used to initiate the leading strands of the new DNA. and used to initiate the leading strands of the new DNA.

• DNA-polymerase:DNA-polymerase: builds up the new DNA strand by adding nucleotides to builds up the new DNA strand by adding nucleotides to the primer (from 5’ to 3’ end). the primer (from 5’ to 3’ end).

• Leading strand:Leading strand: the elongation strand ( the elongation strand (5’ 3’ into the fork5’ 3’ into the fork)) that initiate the that initiate the new DNA after recognizing the sequence of the primer by special proteins. new DNA after recognizing the sequence of the primer by special proteins.

• Lagging strand: Lagging strand: IsIs the other parental strand ( the other parental strand (5’ 3’ into the fork5’ 3’ into the fork), is copied), is copied away from the fork in short segments (Okazaki fragments). away from the fork in short segments (Okazaki fragments).

• Okazaki fragments:Okazaki fragments: the newly formed segments (the newly formed segments (5’ 3’, away from the fork5’ 3’, away from the fork)) then, form the lagging strand when connected by ligase then, form the lagging strand when connected by ligase towards the fork. towards the fork.

• DNA-ligase:DNA-ligase: joins the Okazaki fragments of the newly formed bases to form joins the Okazaki fragments of the newly formed bases to form the new lagging DNA strand. the new lagging DNA strand.

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