Here are the answers to your questions:\n\n1. Factors that can cause damage to DNA include biological agents (viruses), chemicals (mutagens, carcinogens), and physical agents (radiation, UV rays, X-rays).\n\n2. Cigarette smoke contains polyaromatic hydrocarbons like benzo(a)pyrene, which can bind to guanine bases in DNA to form DNA adducts. This can lead to mutations and potentially cancer if unrepaired. \n\n3. Six types of lesions that can occur to DNA are: loss of base, altered base, wrong base, thymine dimers, strand breaks, and deletion-insertion.\n\n4. Dietary contamin

1. DNA Repair
Professor Wan Zurinah Wan Ngah

2. Objectives; At the end of the lectures
the students should be able to
• describe the importance of DNA repair
• Describe factors that can damage DNA
• describe the types of damage that can
occur
• explain base and nucleotide excision
repair processes
• explain the consequences when the
damage is not repaired

3. DNA damage occurs
spontaneously but can increase
by various chemical, biological
and physical factors

4. Factors
• Damage occurs spontaneously eg. 10000
depurinations/d, spontaneous
deamination of C to U (100/d)
• Other factors that can increase DNA
damage:
• Biological agents eg. viruses
• Chemicals eg. mutagens, carcinogens
• Physical agents eg. Radiation, UV, X-rays

5. The lesion that occurs is specific
to the causative factor

6. Types of DNA damage/lesions
DNA Lesions Cause
Loss of base (Depurination) Acid & heat
Altered base Ionizing radiation,
alkylating agents
Wrong base Spontaneous deamination,
C to U, A to HX, 5-
Methyl C to T
Deletion-insertion Intercalating agents eg.
Acridine dyes
Thymine dimers UV
Strand breaks Chemicals, ionizing
radiation

7. Spontaneous changes that require DNA
repair
Spontaneous oxidative damage( red arrows)
Hydrolytic attack (blue arrows)
Uncontrolled methylation by S-Adenosyl Methionine (green arrows)

8. Base Deamination in DNA
Natural bases
Unnatural bases for DNA

9. Most frequent changes causing serious DNA
damage in cells Unnatural base

10. UV light increases the formation
of thymine dimers

11. Thymine dimers
are cyclobutyl
dimer

13. Carcinogens cause damage by
altering bases and DNA structure
Cytotoxic drugs also act by altering
bases and DNA structure

14. Example of a carcinogen from the diet
and environment
Polyaromatic hydrocarbon
group includes
benzo(a)pyrene (cigarette
smoke)
The epoxide can covalently
bind to guanine base in
DNA
Direct or complete
carcinogens
Indirect or incomplete
carcinogens

15. Also a carcinogen from our diet

16. Intercalation chemical into the DNA
double helix
Aromatic
compounds
intercalate in
between base
stacks. Results
in insertion
and addition
of new bases

17. Improper or incomplete DNA
repair can lead to disease
Cells invests heavily in repair
mechanisms

18. Importance of DNA Repair
• DNA damage DNA changes Mutation
• Mutation somatic cells Cancer
• Mutation gamete cells Genetic diseases
(Inborn errors of metabolism)
• Cell invests heavily in repair enzs
• Def in repair enzs lead to diseases eg. Xeroderma
Pigmentosum patients sensitive to UV, skin
lesions---skin cancer etc
• Bloom Syndrome : Helicase/Ligase def, cancer
risk is high

19. Inherited Syndromes with Defects in DNA Repair
NAME PHENOTYPE ENZYME OR PROCESS
AFFECTED
Xeroderma skin cancer, cellular UV nucleotide excision-repair
pigmentosum (XP) sensitivity, neurological
Groups A-G abnormalities
Ataxia-telangiectasia Leukemia, lymphoma, ATM protein, a protein kinase
(AT) cellular -ray sensitivity, activated by double-strand
genome instability breaks, repair by homologous
recombination
BRCA-1 & BRCA-2 breast and ovarian Tumour suppressor gene,
cancer activated by double stranded
DNA breaks
Bloom syndrome Cancer at several sites,
stunted growth, accessory DNA helicase for
genome instability replication/Ligase 1

20. Types of DNA Repair
• Excision repair
– Repair of thymine-thymine dimers
– Apurinic/apyrimidinic repair
– Removal of uracil
• Direct repair
– Dealkylation of G by G alkyltransferases
• Mismatch repair
• Recombination repair

21. Two types of excision repair are
base excision repair and
nucleotide excision repair

22. Excision repair
• Incision: Enz recognise type of damage. Enz
involved depends on type of damage.
– DNA N-glycosylases--deaminated base, alkylated
or oxidised bases, bases with opened rings
– Depurination--Apurinic-apyrimidinic (AP)
endonuclease;
• Excision of damaged base
• Re-synthesis of new DNA
• Nick is joined by ligase

23. Repair enzymes
• In Prokaryotes-DNA polymerase I (& II)
• In Eukaryotes-DNA polymerase
• Ligase

24. Base excision repair is for small
lesions

27. Nucleotide excision repair is for
large lesions such as thymine
dimers

28. Cyclobutyl/ thymine dimer repair

30. Location on DNA/gene where
mutations can occur
Mutations can occur in the:
• Coding regions or exons
• Intron/exon (splicing)
junction/site
• Regulatory region

31. Class, Group & Type of Mutations
Mutation Group Type
Substitution Synonymous Silent
Non-synonymous Missense
Nonsense
Splice site
Promoter
Deletion Multiple of 3
Not multiple of 3 Frameshift
Large deletion Partial/whole
gene deletion

32. Class, Group & Types of Mutations:
continued
Insertion Multiple of 3
Not multiple of 3 Frameshift
Large insertion Partial/whole gene
duplication
Expansion of Dynamic mutation
trinucleotide repeats

33. missense mutation:non-conservative substitution
a mutation results a change in an amino acid
where the new amino acids has a different property than the
old amino acid. The protein with the new primary structure
may have reduced or no activity. Or qualitative changes with
different characteristics but same biological activity

34. nonsense mutations:
a mutation results in a new stop translation condon
formed before the naturally occuring one.
Translation is stopped prematurely and a shortened
protein with no biological activity is made. mRNA
transcripts degraded by nonsense mediated decay

35. frameshift mutation:
a deletion or insertion of one base results in a change in the
translational reading frame resulting in premature stop codon
downstream. mRNA maybe degraded by nonsense mediated
decay or a truncated protein is produced.

36. Summary
• DNA damage can be increased by
biological, chemicals and physical factors.
• Lesions include loss of base, wrong base,
altered base, thymine dimers, strand
breaks or deletion-insertion.
• Damage is repaired by repair enzymes
• Mechanism of repair include base excision
repair and nucleotide excision repair

37. DNA Repair
A Muslim‟s speech is not exaggerated or affected.
Adbdullah ibn Mas‟ud said:
“By Him besides Whom there is no other god, I never saw
anyone who was harsher on those who exaggerate in their
speech than the Messenger of Allah swt, and I never saw
anyone who was harsher on them after his death than Abu
Bakar, and I think that „Umar feared the most for them of
all people on earth”

38. Okazaki fragments have which
one of the following properties?
A They are double stranded
B They contain covalently linked RNA and
DNA
C They are RNA-RNA hybrids
D They arise from the nicking of the
sugar-phosphate backbone of the
parental DNA chain
E They are removed by nuclease activity
Answer B

39. •Which one of the sequences listed below best
describes the order in which the following
enzymes participate in lagging strand DNA
synthesis in bacteria?
1 DNA polymerase I 2 5’exonuclease
3 DNA polymerase III 4 DNA ligase
5 RNA polymerase
A 5,1,3,2,4
B 3,2,1,5,4 ANSWER D
C 5,3,4,2,1
D 5,3,2,1,4
E 3,2,5,1,4

40. Formation of thymine dimers

41. Questions
• List the factors that can cause damage to
DNA
• How can cigarette smoke cause cancer?
• List 6 types of lesions that can occur to DNA.
• How can dietary contaminants cause
damage to DNA?