Discovering the structure of DNA

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Discovering the structure of DNA

• DNA Deoxyribose nucleic acid

• Made out of sugars (deoxyribose), phosphates
  
• and nitrogen bases

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Discovering the structure of DNA

• Structure was discovered in 1953 by James
• Watson and Francis Crick

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Discovering the structure of DNA
Rosalind Franklins DNA image
Chargoffs rule A T C G
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Cell division and DNA replication

• Cells divide

?Growth, Repair, Replacement

• Before cells divide they have to double cell
  
• structures, organelles and their genetic
• information

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DNA replication
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Site and function of nucleic acids

• DNA
• RNA
• site of DNA
• IN eukaryoytes cellsDNA is found in the
  nucleus(chromosomes) and in the mitochondria.
• In prokaryotes there is a single chromosome
  which contain DNA .There may be also a non
  chromosomal DNA in the form of plasmid.
• Functions of DNA replications(cell division)
• expression of genetic information and protein
  synthesis(through RNAs)

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Site of RNAs

• 1. RNAs that synthesized in the mitochondria
  remain within this organelle.
• 2. RNAs that synthesized in the nucleus perform
  their function in the cytoplasm.
• Function of RNAs
• 1. RNAs participate in the process of expression
  of genetic information that stored in DNA
  (protein synthesis).
• Some viruses use RNA in their its single or
  double stranded form as a genetic material i.e
  RNA is used instead of DNA.

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Steps of DNA replication

• Replication folk
• chain elongation reverse transcriptase
• DNA repair
• regulation of DNA synthesis
• inhibitor of replication.

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Semiconservative

• The process by which DNA is copied is called
  semiconservative. This mean that after
  replication ,each of daughter DNA mol. Will of
  daughter DNA mol. Will contain
• 1. one old strand one parental strand is
  conserved.
• 2.one new strand which is synthesized from free
  nucleotide present in the nucleus.

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Cont.

• During replication , the double strand DNA
  mol.I(duplex) that is to be copied is separated
  into two strands and each is used as a template
  for the synthesis of a new complementary strand.

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In prokaryotes

• DNA polymerase I catalyzes DNA repair.
• DNA polymerases II is unknown function.
• DNA polymerases III catalyses mostly replication
  of DNA.

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In eukaryotes

• DNA pol- alpha catalyses replication of nuclear
  DNA.
• DNA pol beta catalyses replication DNA repair.
• DNA pol gamma catalyses replication of
  mtochondria DNA.
• DNA pol delta responsible for leading strand of
  DNA replication.

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Cont.

• DNA pol e responsible for synthesis of lagging
  strand and repair.

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A. Strand separation

• For replication strands of DNA separated,
  polymerase use only single stranded DNA as
  template.
• IN prokaryotes.E.coli ORIC initiation of
  replication.
• IN eukaryotes multiple site for replication
  along the DNA helix.

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Replication folk

• As strands unwind and separate , they form the
  V shape where synthesis occur.This region is
  called repliction folk.
• 1. RF moves along the DNA mol. As synthesis
  occur.
• 2. replication of double stranded DNA is
  bidirectional.

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Proteins responsible

• A. helix destabilizing (HD) proteins they bind
  nonenzymatically to a single stranded DNA,without
  interfering with the ability of the nucleotides
  serve as a template
• Functions
• 1wo strands separated.
• Protect DNA from nuclease enzyme that cleave
  single stranded DNA.

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Cont.

• B. Helix unwinding proteins also called
  helicase.or rep proteins.
• 1. bind single stranded DNA near the replication
  fork and then move into the neighbouring double
  stranded region.
• 2.Requires energy. 2ATP mol. Are consumed to
  separate each base pair.
• 3. once the strand separated destabilizing
  proteins binds.

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Topo I and II

• Swivels
• Prevents formation of supertwinsting and rotation
  of the entire chromosome ahead of replication
  folk. Super twisting makes further separation
  more difficult and entire chromosome consume more
  energy.

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Topoisomerase I (DNA swivelases

• They cut and rejoin a single of double helix .
• This process does not require ATP as the energy
  released from the cleavage (cutting ) of
  phosphodiester bond is reused to reseal (rejoin)
  the strand.
• By creating transient nickthe DNA helix on
  either side of the nick is allowed to rotate at
  the phosphodiester bond opposite the nick ,thus
  relieving accumulated supertwiste.

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Topoisomerase II (DNA gyrase)

• It binds to both strand of the DNA and make
  transient breaks in both strands of DNA helix to
  pass through the break and finally reseal the
  break .
• A negative supertwists can be introduced that
  allow the break unwinding of the DNA double helix.

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Formation of RNA primer

• 1. polymerase III is unable to assemble the first
  few nucleotides of a new strand using the parent
  DNA strand as a template.
• 2.This assembly require RNA primer
• A. a short fragment of RNA . 10 nucleotides.
• B.Complementary and antiparallel to the DNA
  strand.

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Cont.

• C. free -OH group at 3end . This Oh serves as a
  the acceptor of the first nucleotide from DNA
  polymerase III.
• 3.synthesis of RNA primer requires primosome
  which is a complex of an protein called RNA pol
  and protein called DNA B protein.
• Primosome binds with single stranded DNA and
  enable the initiation of synthesis of RNA primer.
  

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Cont.

• RNA primer is later removed.

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Synthesis of new DNA

• The substrate of DNA are dATP,dGTP,dTTp,and
  dCTP. If one of four nucleotide is not available
  , DNA synthesis will blocked.
• Using the free 3ÓH group of the RNA primer as the
  acceptor of the first nucleotide , DNA polymerase
  III begins to add subsequent nucleotide.

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Chain elongation

• DNA pol lII moves along the template strand ,
  substrate nucleotide pair with the pairing rule.
  AT, GC,thus complementary to the parent strand.
• New strand runs in 5-3 direction while template
  strand runs 3-5. The daughter strand chain must
  grow in opposite directions, one towards
  replication fork and the other away from it.

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Cont.

• Leading strand is the strand that being copied in
  the direction towards replication fork . It is
  synthesized almost continuously
• Lagging strand is the strand being copied in
  the direction away from replication fork . It is
  synthesized discontinuously by forming small
  fragment of DNA called OKAZAKI fragments.
• They are joined to become a single , continuous
  strand.

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Excision of RNA primers and their replacement
with DNA

• 1. DNA polymerase III continues to synthesize DNA
  un till it is blocked by a fragment of the RNA
  primer.
• 2.The RNA primer is excised by DNA polymerase I
• 3. Gaps resulting from the excised RNA primers
  are filled by DNA pol I.
• 4. Nicks are sealed by DNA ligase.
• 5. final phosphodiester linkage between the 5
  phosphate group on the DNA chain synthesized by
  DNA polymerase III and 3 hydroxyl group on the
  chain made by DNA polymerase I is catalyzed by
  DNA ligase .The energy required for this joint is
  provided by cleavage of ATP tp AMP and Ppi.

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Reverse transcriptase

• Also called RNA dependent DNA polymerase
• DNA RNA - protein
• Retroviruses has a mechanism for reversing the
  first step in this flow form RNA to DNA.
• The retrovirus contain ss RNA nucleic acid and a
  viral enzyme called reverse transcriptase.

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Mechanism of replication

• 1.Ss RNA ? ds DNA
• 2.This enzyme synthesize a DNA RNA hybride mol.
  Using
• A) RNA genome as template.
• B) dATP ,dGTP and dCTP gTTP as substrates.
• 3. RNA degraded by Rnase H .
• The remaining DNA strand in turn serve as a
  template to form a double stranded genome of the
  virus.
• The newly synthesized viral double stranded DNA
  enters the nucleus of the infected cell and can
  integrate by recombination into host chromosome.
• Eg HIV(AIDS) ,hepatitis A virus and some tumor
  viruse.
• RT are important in recombinant DNA technolongy.

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DNA repair

• A)Causes of DNA damage
• Physical agent e.g x-ray , ultraviolet light.
• Chemical agent e.g alkylating agent
• Ionizing radiation
• B) single base alteration
• 1. depurination i.e removal of purine.
• 2.deamination of cytosine to uracil
• 3. deamination of adenine to hypoxathine.
• 4.Alkylation of base i.e addition of alkyl group.
• 5. Insertion or deletion of nucleotide.
• Base analog incorporation.

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Two base alteration

• a. formation of thymine thymine dimer by
  ultraviolet light

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Cont.

• Chain break e.g phosphodiester bonds can be
  broken.
• Cross linkage
• A. between bases in same or opposite strands.
• B. between DNA and protein molecule e.g histones

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fate of damaged DNA

• 1.Repaired
• 2. Replaced by DNA recombination
• 3. Retained retention leads to mutation and
  cell death.

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Mechanism of DNA repair

• Excision repair damaged only one strand eg
  thymine dimers and missing base.
• Repair of pyrimidine-pyrimidine dimer
• The dimers result form covalent joining of two
  adjacent pyrimidine.
• Caused by uv rays
• Thymine dimers prevent DNA pol from replicating
  the DNA strand beyond the site of dimer
  formation.
• Dimer is excised and repair
• Uv specific endonuclease recognises the dimer
  and makes a nick near it ,at 5 end
• gap is filled by polymerase I ,in the direction
  of 5 to 3.Other strand acts as template.
• Thymine dimer region is excised by the 5-3
  exonuclease activity of DNA pol I and sealed by
  DNA ligase.

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Xeroderma pigmentosum

• It is an autosomal recessive disease, is an e.g
  of a defective mechanism for the repair of
  pyrimidine dimers in DNA.
• Absence of uv specific endonucleases require for
  the recognition of the dimers is the cause of
  this disease.
• Individuals are sensitive to uv light which
  causes extensive accumulation of thymine dimers
  in skin cells with malignant transformation.

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Some of the most common symptoms are An
unusually severe sunburn after a short sun
exposure. The sunburn may last for several weeks.
The sunburn usually occurs during a childs first
sun exposure. development of many freckles at an
early age. Irregular dark spots. Thin skin.
Excessive dryness. Rough-surfaced growths
(solar keratoses), and skin cancers. Eyes that
are painfully sensitive to the sun and may easily
become irritated, bloodshot, and clouded.
Blistering or freckling on minimum sun exposure.
Premature aging of skin, lips, eyes, mouth and
tongue
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Repair of cytosine deamination to uracil

• Abnormal uracil is recognized by glycosylase that
  cleaves the base .
• Endonuclease cuts the phosphodiester bond on
  5side.
• DNA pol I fills the gap.
• DNA ligase seals the breaks.

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Photoreactivation or light repair

• Thymine repair
• Use visible light (300-600nm) for activating
  specific enzyme called photoactivating enzyme
  which directly cleave and correct the dimer in
  its place.

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Recombination repair(sister strand exchange)

• In prokaryotes (E.coli) , the cell deal with DNA
  replication at the dimer and reinitiating it on
  the other side of the dimer . This leaves gap in
  the newly synthesized strand b.
• By sister strand exchange , the unmutated single
  stranded segment from homologous DNA excised form
  good strand (d strand) and inserted into the gap
  present in b strand opposite the dimer.
• The gap in d strand is next filled by polymerase
  I.