Download MBBS DNA Damages and Repair Lecture PPT

DNA DAMAGES AND REPAIR.

DNA is subjected to lots of stress and strain during

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replication and cell division.

Also it is exposed to many chemical, physical, and

biological agents which enters the cell from

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environment.

All such agents inflict a variety of damages on DNA

molecule.

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Maintenance of the integrity of DNA is vital for the

survival and continuation of species, Hence DNA repair
mechanisms to take care of these damages.

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CAUSES OF DNA DAMAGE.

Replication error----
normally errors are repaired by

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the proof reading mechanisms of DNA replication and
are not transmitted. But when they are increases or are
not repaired properly, they can give rise to disease.
CHEMICALS.

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A wide variety of chemicals are present in

environment to which all of us are exposed .

Examples are ?

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Insecticide and pesticides.
Pollutants including gases.
Oxidising agents, alkylating agents.
Industrials wastes
Food adulteration and preservative.

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All the chemicals causes modification of bases,

Bulky adduct formation between bases, alteration

of bases by deamination, etc and lead to DNA

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damage.
DEAMINATION OF BASES.

Cytosine and adenine undergo deamination

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spontaneous or chemically induced to form uracil and
hypoxanthine . The original sequence is thus changed.
Thymus Dimers by UV Light.

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UV light radiations induce the condensation of adjacent thymine

bases in DNA strand forming thymine- thymine dimers.

CHAIN BREAKS BY IONIZING RADIATION.

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X-rays and

gamma rays can cause DNA strand in the backbone in single
strand or in both the strands.

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DAMAGE BY OXYGEN RADICALS.

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ADDUCT FORMATION.
MECHANISM OF DNA REPAIR.

BASE EXCISION REPAIR- modified and altered bases

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are repaired by base excision repair mechanism.


NUCLEOTIDE EXICION REPAIR- The repair mechanism

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involves called Excinuclease. Exinuclease cuts nucleotide,

The gap is filed by DNA polymerase.

DIRECT THYMINE DIMER REPAIR- DNA photolyase

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catalyse the removal of bonds forming thymine dimers

and converting them to back to normal in prokaryotes.

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MISMATCH REPAIR ? specific endonucleases identify the

wrong base in newly synthesized strand.
TRANSCRIPTION.

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Transcription-
cellular process in which RNA synthesized

using DNA template known transcription.

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ROLE OF DNA --- only one strand used.

-Template strand/non ?coding strand.

-non template strand/coding strand.

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Transcription.
ROLES OF DNA AND RNA.

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DNA is the MASTER PLAN.

RNA is the BLUPRINT of the Master plan.

Transcription---

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process in which RNA is synthesized from

DNA.

DNA express through RNA.

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Synthesis of RNA occurs in 5'-3' direction.
Nucleotide ATP, GTP,CTP,UTP ARE NECESSORY.
Enzyme and factors.

Eukaryotes

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prokaryotes

RNA POLYMERASE

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RNA POLYMERASE

RNA polymerase I

Only one type of RNA polymerase

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RNA polymerase II

Sigma factor.

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RNA polymerase III
DIFFERENCE BETWEEN REPLICATION
ANDTRANSCRIPTION

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REPLICATION

TRANSCRIPTON

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TEMPLATE

BOTH STRAND

SINGLE STRAND

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PRIMER

YES

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NO

ENZYME

DNA POLYMERASE

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RNA POLYMERASE

PRODUCT

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Ds DNA

ssRNA

BASE PAIR

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A -T, G-C,

A-U, T-A, G-C

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PROOF READING

YES

NO

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DNA dependent RNA polymerase.

RNA polymerase main enzyme responsible for

transcription.

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Five core unit and sixth sigma factor to make

holoenzyme.

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Beta subunit has polymerisation activity.

RNAP reads the template strand in 3'-5' direction

and synthesize new RNA in 5'-3' direction and does

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not require a RNA primer.


RNA polymearase.

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RNA polymerase.
STEPS OF TRANSCRIPTION.

Initiation.

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Elongation.
Termination.

Initiation----
RNAP binds to a region of gene DNA called

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promoter with the help of sigma factor.

RNA polymerase binds to DNA promoter.
Initiation require special DNA sequence.

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Recognise DNA strand.

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Transcription.
INITIATION OF TRANSCRIPTION.

RNAP binding?
initiation begins with the binding of

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RNAP to the promoters of the DNA to form pre
initiation complex.

RNAP has an associated unbinding activity.

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Binding is followed by a change in RNAP conformation.

This places Beta subunit of RNAP on the first
nucleotide of the initiation site.

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The RNAP then catalyzes polymerisation of the first

nucleotide with the second nucleotide according to the
template strand sequence.

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Promoter region.
Elongation.

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The RNA polymerase core enzyme progresses along DNA

molecule to continue elongation.

The elongation continues till the termination signals are

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encountered.

TERMINATION--
Two types of termination signals are

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present.

Rho- factor dependent signals...............
Rho- factor independent signals.............

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Termination

Eukaryotes

Prokaryotes

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Polyadenylation signal(AAUAAA)

Rho-factor dependent.......

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transcribed.
Reaches to -35 bp downstream

Rho- factor independent......

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RNA transcript released.
INITIATION.

INITIATION.

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The process of RNA synthesis in

bacteria begins with the binding of RNA polymerase
molecule on the DNA.. RNAP recognises the
transcription start site on the template strand of DNA

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with the help of certain specific region on the DNA
known as promoter element.

PE region identified in bacteria---

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1.Pribnow box

2.The `-35' sequence
ELONGATION.

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ELONGATION---The elongation of the RNA molecule

occurs from the 5' to its 3' end, antiparallel to the
template strand. RNAP assembles ribonucleotides in a
complementary sequence to the tepmlate strand by

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watson ? crick base pairing rule.
TERMINATION.

TERMINATION--
Two type of such signals are are

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identified in prokaryotes.

1.Rho factor? it is a protein that binds either to

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the growing RNA or template strand of DNA and
dissociate the the RNAP from DNA, thus
terminating the synthesis of RNA. The released
RNAP associates with the sigma factor( which was
released earlier during initiation) and is recycled.

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TRANSCIRIPTION IN EUKARYOTES.

Much more complicated.

Three different RNA polymerase.

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Required many transcription factor protein.

Transcription initiation needs promoter and upstream

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regulatory regions.

Enhancer /silencer --are DNA sequences that regulate

the rate of initiation of transcription by RNA

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polymerase II.


PROMOTERS.
TRANSCRIPTION IN EUKARYOTES.

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Eukaryotes transcription is more complex compound to

that of prokaryotes. There exist three distinct RNA
polymerases transcribing different type of RNAs

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compared to the single RNAP in prokaryote.

RNAP I ----for r RNA.

RNAP II ---for m RNA.

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RNAP III--- for t RNA and small r RNA.


INITIATION---

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Transcription starts with the RNAP

recognising the promoter site.

TATA box---similar to the pribnow box in prokaryotes a

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highly conserved nucleotide base sequence ( TATAAA)

occurs about -25 bp upstream to the TIS in eukaryotes. This

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sequences is also called as Goldberg- Hogness box.

ENHANCER SEQUENCE-- increases the rate of

transcription.

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SILENCER SEQUENCE--- Decreases the rate of

transcription.

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HORMONE RESPONSE ELEMENT-- are the sites used by

the hormones to regulate the transcription.

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INITIATION COMPLEX.

CAAT box--Further upstream to the TIS (-70 bp ),

there occurs another sequence (GGCCAATCT)

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known as CAAT box.

PRE-INITIATION COMPLEX ?

RNA polymerase of

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eukaryotes (e.g RNAP II ) can not recognise TATA and
CAAT boxes directly. A group of protein factor play a
role in recognising the promoter regions of DNA and
called as transcription factor. TF bind to the promoter

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on DNA sequentially along with the enzyme to form a
pre-initiation complex.
TRANSCRIPTION IN EUKARYOTES.

ELONGATION--

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Elongation of the nascent m RNA occurs

similar to that of prokaryotes.

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TERMINATION? once transcription is completed , it is

terminated and RNAP-II is dephosphorylated.

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POST-TRANSCRIPTIONAL
MODIFICATIONS.

The mRNA in prokaryotes is fully functional as soon as it is

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synthesised. on the contrary , eukaryotic RNA produced by
transcription as primary transcript are non-functional. They
undergo extensive structural alteration to produce the
mature functional molecule.
Messenger RNA.

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The primary transcript of mRNA synthesised by RNA

polymerase II in eukaryotes is often called
heterogeneous nuclear RNA. hn RNA is subjected to

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extensive processing in the nucleus to produce mature
mRNA, which then enters the cytoplasm to take part in
protein synthesis.
Messenger RNA processing.

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The cap-
The 5' terminal of mRNA is

crowned with a 7-methylguanosine cap.

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The tail-

The 3' end of mRNA is attached by a number of

adenylate residues .This is known as poly-A tail.

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Splicing-

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During processing introns are removed and exons are

spliced together to form mature RNA.

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MICRO RNAs(miRNA) AND SMALL INTERFERING
RNA(siRNA).

Micro RNA and small interfering RNA are a class of small RNA involved

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in gene silencing.

They form complimentary hybrid with the target DNA and lead to either

its degradation or inhibition of translation.

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Micro RNA- Long single stranded precursor RNAs.
INSIDE the nucleus, primary miRNA transcript is

first processed by a nuclease called DROSHA to produce a smaller

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double stranded hairpin loop like pre-miRNA.

This is exported out of the nucleus to cytoplasm and trimmed by

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nuclease enzyme DICER to produce double stranded miRNA duplex.

Duplex miRNA unbound and one of the strand is selected, The selected

miRNA is loaded into the RNA induced silencing complex(RISC) to form

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a mature functional mi RNA.

It is used to silence silence target mRNA-------TRANSLATIONAL ARREST.