the presentation is about mutations in DNA and all the repair mechanisms involved both in prokaryotes and eukaryotes

2. GroupGroup
Members.Members.
• Manahil Khanam
• Hafiza Iqra Malik
• Minahil Khalid
• Ariba Nameen
• Afra Ejaz
• Aneeqa Sadiq

3. ContentsContents
• Introduction
• Occurrence & causes of Mutations.
• Effect Of Mutagens on DNA Structure.
• What Is DNA Repair?
• Evidences of DNA Repair.
• Repair Mechanisms.
• Photo Reactivation
• Excision Repair

4. ContentsContents
• Recombinational Repair Mechanism
• Repair Of DNA by Homologous Recombination.
• Non homologous repair
• SOS Repair of Damaged DNA.
• Mismatch Repair.

5. IntroductionIntroduction
• Primary function of DNA is to Store information
for Synthesis of Cellular proteins.
• Key aspect of the gene expression process is
that DNA itself does not normally change.
Thus DNA act as permanent storage unit.
• However, rarely mutations can occur.

6.  Mutation
 Heritable change in DNA sequence
that can lead to a change in
phenotype (observable properties of
an organism)
 Mutant
 A strain of any cell or virus differing from
parental strain in genotype (nucleotide
sequence of genome)

7. Occurrence & Causes Of MutatiOccurrence & Causes Of Mutationsons..
• Faithful replication of the genome is necessary for
life
• Mutation rates are generally low in all genomes
and vary from organism to organism
• Most mutations are either neutral or deleterious
• But without the occasional mistake natural selection
has nothing on which to act
• Genetically homogeneous species experience
great peril

8. CONTINUEDCONTINUED
Cells must ;
•Act to replicate DNA faithfully
•Identify mistakes
•Distinguish old (accurate) strand from new (possibly
mutated) strand
•Act to repair mistakes from various sources

9. • Mutation rate is measured as
“ the number of times a mutation
alters the DNA sequence at a
particular locus per replication
cycle or generation.”
• Some factors that impact
mutation rates;
• genome size
• environment
• effectiveness of molecular
repair mechanisms
• life cycle

10. Mutagens Effect on DNA Structure
*CHEMICAL MUTAGENS
1-Nitrous Acid. Deaminates Bases.
2-Nitrogen Mustard. Alkylating agent.
3-Ethyl methane Sulfonate Alkylating agent
4-Proflavin Intercalate with DNA Helix
5- 2 aminopurine, 5 Bromouracil Base Analogue.
*PHYSICAL MUTAGENS
X- Rays Cause base deletion, single
stranded nicks in DNA ,cross
linking & chromosomal breaks.
UV- light Promotes pyrimidine dimer
formation, such as thymine dimers
--To avoid its effect Sunscreen is
used.

11. DNA Repair.DNA Repair.
• “A collection of process by which a cell
identifies & Correct damage to the DNA
molecules that encodes its genome”.
• Most mutations are deleterious, so REPAIR SYSTEMS
ARE VITAL FOR SURVIVAL.
• If repair system did not exist mutations would be so
prevalent, survival of those species would be difficult.

13. Evidences.Evidences.
• The necessity of DNA repair systems
becomes evident when they are
missing.
• No direct evidence in ancient
microbes, for most likely mechanism,
active repair or for the metabolic
activity necessary to sustain it.

14. Evidences.Evidences.
• Up to half million year ago,
strong evidences are found that the
long term survival of bacterial DNA is
closely tied to cellular metabolic
activity & DNA repair,
that over time proves to be superior to
dormancy as a mechanism is
sustaining bacteria viability.

15. DNADNA REPAIRREPAIR
• Bacteria have much higher rate of
mutation, in fact rate is so high that all
these bacterial cells are sometime
called mutator strains.

16. continuedcontinued
• In eukaryotes, especially in humans;
• Only a single DNA repair system,
may have a higher risk of skin cancer.
This higher risk is due to inability to repair UV induced
mutations.
While bacteria have many repair system and also UV
repair mechanism present.

17. What is it’s objective??What is it’s objective??
• DNA repair maintain base
sequence of DNA from one
generation to other.

18. Types of Mechanisms ofTypes of Mechanisms of
repair of damaged DNArepair of damaged DNA
• Photo Reactivation
• Excision Repair
• Recombinational Repair
• Repair of DNA by Homologous
Recombination.
• Non homologous repair
• SOS repair of Damaged DNA.

19. PHOTO REACTIVATION.PHOTO REACTIVATION.
• What is photo reactivation?
• A DNA repair mechanism.
• Recovery of UV irradiated damaged
of DNA by visible light.
• A method by which cells recover its
DNA after UV exposure.
• UV induce Pyrimidine dimer formation.
• First DNA repair Mechanism
discovered.
• Major finding by AZIZ Sancer.
• (Nobel prize,2015).

20. Photo ReactivationPhoto Reactivation
• Thymine Dimer Formation By UV Light.
• Caused by UV radiations.
• Covalent bonds formation between adjacent
Pyrimidine residues.(TT,CC,TC)
• Thymine dimer is most common.
• Also called “Cyclobutane photo dimer”(CPU).
• T=T dimer formation Cause melanoma.

21. Mechanism of PhotoreactivationMechanism of Photoreactivation..
1. Photolyase binds to thymine dimer
2. FAD- absorbs light
3. FAD get excited
4. Release an electron(e-)
5. Electron interact with dimer
6. Ring splits by cycloreversion
7. connecting Bonds breaks
8. Electron returns to the FAD
9. Phytolyase leaves the DNA.

22. Observations.Observations.
• UV irradiated DNA containing 5bromouracil,
analogue to thymine and incorporated into
replicating DNA replacing thymine.
• It is then resistant to Photoreactivation.
• DNA binds the photolyase enzyme
• But enzyme neither dissociates from dimer & nor
liberate free thymine molecules.

23. Significance Of PhotoreactivationSignificance Of Photoreactivation
• Photoreactivation was the first form DNA repair
Identified.
• Direct Reversal method of DNA repair
• Template Strand is not required.
• No removal of nucleotides involved.
• Photoreactivation is not universal.
• Present in bacteria, plants and many animals.
• Completely absent in Placental animals including
human.
• Human uses nucleotide excision repair NER to remove
thymine dimer.

25. Excision RepairExcision Repair
• “A type of repair system in which one
strand of DNA is directly excised and
then replaced by resynthesis using the
complementary strand as template”
• Also known as Dark repair.

26. General Mechanism of ER.General Mechanism of ER.
• In INCISION step, the damaged
structure is recognized by an
endonuclease that cleaves the DNA
strand on both sides of the damage.
• In the EXISION step, a 5’_3’
exonuclease removes the step of the
damaged strand. Alternatively, a
helicase can displace the damaged
stand, which is subsequently
degraded.

27. General Mechanism of ERGeneral Mechanism of ER
• In the SYNTHESIS step, the resulting single stranded
region serves as a template for a DNA polymerase
to synthesize a replacement for the excised
sequence
.
• Synthesis of the new strand can be associated with
the removal of the old strand, in one coordinated
action.
• Finally, DNA ligase covalently links the 3’end of the
new DNA strand to the original DNA.

29. TypesTypes
• It may be;-
• Base Excision Repair. (BER)
• Nucleotide Excision repair(NER)

30. Base Excision RepairBase Excision Repair
• A pathway of excision repair that recognizes
damage to single bases,
such as deamination or alkylation, and either
repairs;
 The base alone(short-patch repair) or
 Replaces 2–10 nucleotides (long-patch repair).
• Use Glycolyase.
• i.e. in Microcoocusleutus.

31. Story of BER in microbesStory of BER in microbes
• Once upon a time a DNA segment became
damaged.
• DNA glycosylase saw this and thought he could
help so he attached himself to the damaged DNA.

32. • He removed the excised ( damaged) base.
• But there was a gap remain.
• AP endonuclease thought she could fill the
gap.
• She took away backbone pieces and sat in space.

33. • Something still was wrong
• DNA polymerase and ligase
also help them
• Polymerase put right base in
gap
• Ligase sealed base in
The DNA segment lives happily after.

35. Nucleotide Excision Repair (NER)Nucleotide Excision Repair (NER)
• “An excision repair pathway that recognizes
bulky lesions in DNA (such as UV-induced
pyrimidine dimers)”.
 NER is divided into two major sub pathways:
 Transcription-coupled repair (TC-NER), which
repairs damaged in the transcribed strand of
active genes
 Global genome repair (GG-NER), which repairs
damage anywhere in the genome.
 Eukaryotes also Possess it,.

36. Example ofExample of E.coliE.coli in “NER”in “NER”
• The E.coli uvr system repair includes three genes (uvr-
A-B and –C), which codes for the components of a
repair endonucleases.
• MECHANISM;
 DNA is deformed, a Uvr AB dimers recognizes
pyrimidine dimers and other bulky lesions.

37. MECHANISM OF “NER”MECHANISM OF “NER”
 UvrA dissociates &UvrC joins UvrB.
 The UvrBC complex makes an incision on each side:
 UvrD is a helicase that helps to unwind the DNA to
allow the single strand between the two cuts.

39. Long patch & Short patch ERLong patch & Short patch ER
• In almost all cases (99%), the average length of
replaced DNA is ~12 nucleotides. (For this reason, the
process is sometimes described as short-patch repair.
• The remaining 1% of cases involves the replacement
of stretches of DNA mostly ~1500 nucleotide long, but
extending as much as >9000 nucleotides (sometimes
called long-patch repair).
• We do not know why some events trigger the long-
patch rather than short-patch mode.

40. Recombinational Repair MechanismRecombinational Repair Mechanism..
• Recombination repair use activities that
overlap with those involved in genetic
recombination
• Use recombination to replace the double-
stranded region that has been damaged.
• They are also sometimes called “post
replication repair” because they function after
replication.

41. Mechanism.Mechanism.
• DNA polymerase probably proceeds up to or close
to the pyrimidine dimer.
 The polymerase then ceases synthesis of the
corresponding daughter strand.
• Replication restarts some distance farther along.
• This replication may be performed by translation
polymerases, which can replace the main DNA
polymerase at such sites of unrepair damage.

42. Recombination-Repair Systems inRecombination-Repair Systems in E. coliE. coli
• The rec genes of E. coli code for the
principal recombination-repair system.
• The recombination-repair system
functions when replication leaves a
gap in a newly synthesized strand that
is opposite a damaged sequence.

43. InIn E. coliE. coli rec. repair.rec. repair.
• The principle pathway of recombination in E.coli is
identified by the rec genes. In E.coli deficient in
excision repair.
• Mutation of the rec A gene essentially abolishes all
the remaining repair and recovery facilities.
Attempts to replicate DNA in uvr- rec A- cells
produced fragments of DNA.
• Dimers provide a lethal obstacle to replication in
the absence of RecA function. It explain why the
double mutant cannot tolerate>1 to 2 dimers in its
genome.

44. • The single strand of
another duplex is used to
replace the gap (single-
strand exchange).
• The damaged sequence
is then removed and
resynthesized.
•

45. Mismatch repairMismatch repair
• Mismatch=when wrong nucleotides are paired.
ex . T with C
• Repair:
 Special enzymes cut out the mismatched DNA and
replace it with the appropriate base pairs.
• Nuclease (cuts out DNA)
• DNA polymerase(replaces DNA)
• Ligase(seals it with the rest of DNA)

46. Mismatch RepairMismatch Repair..
• Action of DNA polymerase III (including proofreading
exonuclease) results in 1 misincorporation per 108
bases
synthesized.
• Mismatch repair reduces this rate to 1 change in every
1010
or 1011
bases.
• Recognize mis paired bases in DNA, e.g. G-T or A-C
base pairs.
• These do not cause large distortions in the helix: the
mismatch repair system apparently reads the sequence
of bases in the DNA.

48. Role of methylation in discriminatingRole of methylation in discriminating
parental and progeny strandsparental and progeny strands
• dam methylase acts on the A of GATC (note that this
sequence is symmetrical or pseudo palindromic).
• Methylation is delayed for several minutes after
replication.
• Mismatch repair works on the un-methylated strand
(which is newly replicated) so that replication errors
are removed preferentially.
• .

49. Action of Mut S ,Mut L, &Action of Mut S ,Mut L, &
Mut H.Mut H.
• Three gene products (proteins) are involved
• Mut S, Mut L, Mut H
• MutS: recognizes the mismatch (heteroduplex)
• MutL: a dimer; in presence of ATP, binds to MutS-
heteroduplex complex to activate MutH
• MutH: endonuclease that cleaves 5' to the G in an
unmethylated GATC, leaves a nick

50. MutH, L, S action in mismatch repair
#1

51. MutH, L, S action in mismatch repair #2

52. Mismatch repair: Excision of the mis
incorporated nucleotide
Common
in
Eukaryote
s.

54. Proof ReadingProof Reading
• Wrong base is inserted in polynucleotide chain
by mistake.
• DNA polymerase stop it & go one step
backward.
• Incorrect base is removed by exonuclease
activity.
• Polymerase resume normal activity by adding
proper base.
• Thus, Mismatch is proof reading process.

55. Homologous Recombination Repair (HR)Homologous Recombination Repair (HR)
• Introduction;-
• HR allows for proper chromosome segregation during
meiosis, promoting genomic integrity between
generations.
• Represents the highest fidelity repair mechanism for
DNA breaks.
• Diploid human cell maintains ~6x109
bp of DNA.

56. HR.HR.
• Highly regulated process, as too much HR can lead
to large chromosomal rearrangements.
• Common in Mammals as Double stand break repair
, but also seen in bacteria

57. HOMOLOGOUS REPAIRHOMOLOGOUS REPAIR

62. SOS repair of damaged DNA.SOS repair of damaged DNA.
• Most complicated process.
• Damage inflicted on DNA by mutagenic agents
induce a complex series of changes which are
collectively known as SOS response.
• Leads to increased capacity to repair damaged
DNA.
• Most effective process.

63. What is SOS?What is SOS?
• SOS means” SAVE OUR SOULS”.
• Cause it is last resort to repair DNA damaged.
• Very large lesions in DNA that interferes in
damaging & Mutations.
• Lesions may be caused by oxidative stress &
radiations, needs stalling which is lethal.
• Then SOS repair actives.

64. Effective proteins.Effective proteins.
• Two effective proteins interact in SOS response.
• 1- Rec A
• 2-Lex A
 Rec A protein is product of recA gene.
• In addition to recombinational repair it also
have protease function.
 Lex A protein act as repressor for number of
gene.
• If SOS is not needed , these genes remain
repressed by Lex repressor.

65. RecA & Lec A controlRecA & Lec A control
recA lexA target gene
LexA
RecA
LexA
LexA
e.g. recA, lexA, uvrA, uvrB, umuC
Repressed
SOS response is controlled by LexA and RecA
OFF
ON
recA lexA target gene
LexA
e.g. RecA, UvrA, UvrB, UmuC
de-repressed
RecA is activated in the presence of damaged DNA. It serves as a co-protease to activate a latent,
self-cleaving proteolytic activity in LexA, thereby removing the repressor from SOS inducible genes.
RecARecA RecA
RecA
+ cleaved LexA
active proteins

66. MechanismMechanism
• Rec A protease activity induced by DNA damage.
• Activation of RecA occurs within few minutes after
damage.
• The protease activity catalysis cleavage of Lex A
repressor, making it inactive.
• SOS genes now expressed to produce enzyme
required for DNA repair.

68. High Rate of Mutations.High Rate of Mutations.
• SOS response is an emergency measure to repair
mutational damage.
• Cell survive after SOS otherwise they have been
lethal.
• Possibility of new mutations increases in DNA repair.
• Cause SOS repair system allows DNA synthesis
Bypassing the damaged site, in a process “Error
prone repair”.

69. Error-prone repairError-prone repair
• When repair has not occurred prior to
replication. How does the polymerase copy
across a non-pairing, mutated base, or an
apyrimidinic/apurinic site?
o DNA polymerase III usually dissociates at a nick or a
lesion.
o But replication can occur past these lesions,
especially during the SOS response

71. Mechanism Protein/Enzyme used
Photoreactivation Photolyase
Base Excision Repair Glycosylase, AP Endonuclease , Pol,
Ligase
Nucleotide Excision Repair UvrA , UvrB , UvrC , Uvr D
Recombination Repair rec genes
Mismatch Repair Mut S, Mut L, Mut H
Homologous Repair ATM Kinase , MRN complex, Polymerase
sigma and epsilon
Non- homologous repair Ku ,DNA- PKcs , Artemis

72. Conclusions.Conclusions.
• DNA Damage is very Harmful & lethal in both
prokaryotes & Eukaryotes.
• In Humans it can cause many Syndromes.
• DNA damage is a natural process which have
many repair Mechanisms.
• Photo reactivation was First process of DNA
repair in prokaryotes which was discovered.
• SOS repair is most efficient very important for
microbes.

73. References;-References;-
• Microbiology & Immunology by Ajit kr. &
Nirmala.
• Lewin’s GENES XI by Elliot & Stephen.
• Molecular biology of gene.
• Genetic Analysis & Principles by Robert
J .Booker.
• Evidence of DNA repair in bacteria
(Sarah Stewart & Martin B)
• www. easybiologyclass.com
• www.GoogleScholar.com

74. •DO u
have any
Questions
please???
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