It's a very much important notes related to mutation.its types origin and causes

1. MUTATION

2. Mutation
•Mutation: heritable changes in genetic material.
•Mutation
•is the ultimate source of genetic variation
•Provides the raw material for evolution
•Helps in environmental adaptation
•Random and nonadaptive process
•Reversible process
•Somatic or Germinal mutation
•Molecular basis of mutation: Spontaneous or Induced
mutation

3. Somatic mutations
❖ Arise in the somatic cells
❖ Passed on to other cells through the process of
mitosis
❖ Effect of these mutations depends on the type
of the cell in which they occur & the
developmental stage of the organism
❖ If occurs early in development, larger the clone
of the mutated cells

4. Germ line mutations
❖ They occur in the cells that produce gametes
❖ Passed on to future generations
❖ In multicellular organisms, the term mutation is
generally used for germ line mutations

5. Mutagenesis
❖ A process by which the genetic information of an organism is
changed, resulting in a mutation. It may occur spontaneously in
nature, or as a result of exposure to mutagens (Induced).
❖ Removal of an incorrectly inserted base is prevented
❖ Base inserted that tautomerizes and allows a substitution to occur in
subsequent replication
❖ A previously inserted base is chemically altered to a base having
different base pairing specificity
❖ One or more bases are skipped during replication
❖ One or more bases are added during replication
❖ Depurination: loss of purine base to form apurinic site.

6. Spontaneous mutation
❖Spontaneous mutations are naturally occurring mutations and can
arise in any cells.
❖ Occurs in nature without any known cause.
❖ Spontaneous mutations occur infrequently, and their frequencies
vary from gene to gene and from organism to organism
❖The rate of spontaneous mutation for various genes of prokaryotes
range from about 10-5 to 10-7 detectable mutations/ nucleotide pair/
generation.
❖The rate of spontaneous mutation in eukaryotes, ranges from
about 10-4 to 10-7 detectable mutations /nucleotide pair /generation.

7. Spontaneous mutations can be characterized
by the specific change:
❖ Tautomerism – A base is changed by the repositioning of a hydrogen atom,
altering the hydrogen bonding pattern of that base, resulting in
incorrect base pairing during replication.
❖ Depurination – Loss of a purine base (A or G) to form an apurinic site (AP
site).
❖ Deamination – Hydrolysis changes a normal base to an atypical base
containing a keto group in place of the original amine group.
Examples include C → U and A → HX (hypoxanthine), which can be corrected
by DNA repair mechanisms; and 5MeC (5-methylcytosine) → T, which is less
likely to be detected as a mutation because thymine is a normal DNA base.
❖ Slipped strand mispairing – Denaturation of the new strand from the
template during replication, followed by renaturation in a different spot
("slipping"). This can lead to insertions or deletions.

8. Deamination

9. Induced mutation
❖ Induced mutations are those resulting from exposure of
organisms to physical and chemical agents (mutagens) that cause
changes in DNA.
❖ They are Physical Mutagen and Chemical Mutagens.
❖ Hugo de Vries (1900) Coined term and gave Mutation theory.
❖ Muller (1927)working with Drosophila provides proof of mutation
induction by X-rays.
❖ Stadler (1929) described the mutagenic effect of x-rays in Barley.
❖ The rate of induced mutation is 10-3 detectable mutations/
nucleotide pair /generation.

10. Gene mutations
• A gene mutation is a permanent alteration in the DNA sequence that
makes up a gene.
• Change in the nucleotide sequence of a gene
• May only involve a single nucleotide
• May be due to copying errors, chemicals, viruses, etc.
• Based on effect on the structure
➢ Point mutation : single base is involved. One base replaces another.
• Transition
• Transversion
➢ Frameshift mutation
• Insertion/Deletion

12. Sickle cell anemia
• Sickle Cell disease is the result of one nucleotide substitution
• Occurs in the hemoglobin gene

13. Point mutation
Type Description Example Effect
Silent
Mutated codon codes
for the same amino
acid
CAA (glutamine) → CAG (glutamine) none
Missense
Mutated codon codes
for a different amino
acid
CAA (glutamine) → CCA (proline) variable
Nonsense
Mutated codon is a
premature stop codon
CAA (glutamine) → UAA (stop)
usually
serious

14. Frameshift Mutations
• Frameshift is a deletion or insertion of one or more nucleotides that
changes the reading frame of the base sequence.
• Deletions remove nucleotides, and insertions add nucleotides.
• Consider the following sequence of bases in RNA:
AUG-AAU-ACG-GCU = start-asparagine-threonine-alanine
• Now, assume an insertion occurs in this sequence. Let’s say
an A nucleotide is inserted after the start codon AUG:
AUG-AAA-UAC-GGC-U = start-lysine-tyrosine-glycine
• Frameshift mutation can dramatically change how the codons in mRNA
are read. This can have a drastic effect on the protein product.

15. Chromosome Mutations
•Changes the structure of the chromosome.
•Types
•Deletion
•Inversion
•Translocation
•Duplication
•Non-disjunction

16. Deletion
• Due to breakage
• A piece of chromosome is lost.

17. Inversion
• Chromosome segment breaks off Segment flips around
backwards and the segment reattaches

18. Translocation
•Involves two
chromosomes that
aren’t homologous
•Part of one
chromosome is
transferred to another
chromosomes

19. Duplication
•Occurs when a gene sequence is repeated

20. Nondisjunction
•Failure of chromosomes to separate during meiosis
•Causes gamete to have too many or too few chromosomes

21. Making
Connections

22. Induced mutation: Mutagens
• Chemicals
• Base analogues- BU
• Alkylating agents- EMS
• Nitrous acid
• Hydroxylamine
• Intercalating agents
• Oxidative damage
• Radiations

23. ➢ Base analogues- BU
• Base analogs are molecules which have a very similar structure to one of the
four nitrogenous bases which are used in DNA
• An example of a base analog which can be mutagenic is 5-bromouracil which
has a similar structure to Thymine so will form hydrogen bonds with Adenine
in the template strand.
• It can then change shape, so it is complementary to guanine. This means the
base change would be thymine-adenine to guanine-cytosine

24. ➢ Alkylating agents:
• Alkylating agents are chemicals that add
an alkyl group to another molecule.
Alkylation of a base may change the
normal base pairing.
• For example, the alkylating agent EMS
converts guanine to 7-ethylguanine
which pairs with thymine. The mispairing
will lead to mutation. Some alkylating
agents may also cross-link DNA, resulting
in chromosome breaks.

25. ➢ Nitrous acid:
• Nitrous acid deaminates
nitrogenous bases and replaces
the amino group with a –OH
group.
• Nitrous acid acts on adenine,
and cytosine; adenine is
converted to hypoxanthine,
cytosine is converted to uracil.

26. ➢ Hydroxylamine:
• Hydroxylamine is an inorganic compound with the formula NH2OH.

27. ➢ Intercalating agents:
• such as proflavin, acridine and ethidium, that can bind to the major and
minor grooves of DNA and cause addition or deletion of bases during
replication.
• They may result in a frameshift mutation, which can alter the codon
reading frame and result in aberrant DNA transcription and replication.

28. ➢ Oxidative damage:
• DNA oxidation is the process of oxidative damage on Deoxyribonucleic
Acid. It occurs most readily at guanine residues due to the high oxidation
potential of this base relative to cytosine, thymine, and adenine
• An important oxidation product is 8-hydroxyguanine, which mis pairs with
adenine, resulting in G:C to T:A transversions.

29. Radiations:
• Ultraviolet radiation (UV radiation) cross-links adjacent pyrimidines on the same DNA strand,
forming pyrimidine dimers, usually thymine dimers.
• a thymine dimer and illustrates how it interrupts base-pairing between the two DNA strands. These
dimers block DNA replication because the replication machinery cannot tell which bases to insert
opposite the dimer.
Damage by Gamma and X -rays:
• The much more energetic gamma rays and X rays, can interact directly with the DNA molecule. However,
• they damage by ionizing the molecules, especially water, surrounding the DNA.
• This forms free radicals, chemical substances with an unpaired electron. These free radicals, especially
those containing oxygen, are extremely reactive, and they immediately attack neighboring molecules.
• When such a free radical attacks a DNA molecule, it frequently causes a single- or double-stranded break.
• but double-stranded breaks are very difficult to repair properly, so they frequently cause a lasting
mutation. Because ionizing radiation can break chromosomes, it is referred to not only as a mutagen, or
mutation-causing substance, but also as a clastogen, which means “breaker.”

30. DNA repair mechanisms:
In order to maintain the integrity of information contained in it, the DNA has
various repair mechanisms.
1. Direct Repair:
• Damage is reversed by a repair enzyme which is called photoreactivation.
• This mechanism involves a light dependent enzyme called DNA photolyase.
• It uses energy from the absorbed light to cleave the C-C bond of cyclobutyl ring
of the thymine dimers. In this way thymine dimers are monomerized.

31. 2.Excision repair (dark repair):
A light-independent repair mechanism that involves three steps:
(i) recognition, binding, and removal of damaged DNA
(ii) repair synthesis of excised region by DNA polymerase
(iii) ligation by DNA ligase to seal the break
There are two major types of excision repair:
➢Base excision repair:
• Involves DNA glycosylases, enzymes that recognize abnormal bases.
• It cleave the glycosidic bond between the base and the deoxyribose sugar, leaving an
apurinic or apyrimidinic site (AP site)
• That in turn recognized by an AP endonuclease that clips out the sugar-phosphate group.
• DNA polymerase beta fills in the missing nucleotide and DNA ligase seals the nick. There
are at least two ligating enzymes – both use ATP to provide the needed energy.
• Base excision repair is involved in repairing bases altered by alkylation (addition of methyl
and ethyl groups) and deamination (removal of amine groups)

32. Base excision repair

33. ➢ Nucleotide excision repair:
• Nucleotide excision repair involves removal of larger lesions (e.g., thymine-thymine dimers)
• Utilizes a special enzyme called an excinuclease that cuts on either side of the damage and
excises an oligonucleotide containing the damage.
• The damage is recognized by one or more protein factors that assemble at the damage
location and the damaged area removed
• DNA polymerases delta or epsilon fills in the correct nucleotides using the intact (opposite)
strand as a template, followed by ligation (ligase)

34. Nucleotide excision repair

35. 3. Mismatch repair:
• Provides a “backup” to the replicative proofreading carried out by most DNA
polymerases during DNA replication.
• Occurs after DNA synthesis, so must have some way to determine which of a
mismatched base pair (e.g., an A-G base pair) is the correct one. Correct
determination of the template strand in prokaryotes occurs on the basis the of
methylation state. Adenine bases are methylated in E. coli, whereas cytosine
bases are methylated in eukaryotes.
• The appropriate enzyme (a GATC-specific endonuclease) makes a “nick” in the
unmethylated strand at GATC sites either 5’ or 3’ to the mismatch.
• The incision site can be ≥ 1,000 nucleotides from the mismatch. If the damage
is 5’ to the mismatch, a 5’→3’ exonuclease is required. Alternatively, if the
damage is 3’ to the mismatch, a 3’→5’ exonuclease is required.
• DNA polymerase delta fills in the gap and DNA ligase seals the nick.

36. 4a. REPAIRING STRAND BREAKS
• Ionizing radiation and certain chemicals can generate both single-strand
and double-strand breaks in the DNA backbone
• Single-strand breaks: Repaired using the same enzyme systems
(polymerase and ligase) used in base-excision repair
• Double-strand breaks:
• Direct joining of the broken ends. This requires proteins that recognize and
bind to the exposed ends and bring them together for ligating.
• Homologous recombination – this requires information on the intact sister
chromatid (available after chromosome duplication). The process is not yet
well understood.
• Two of the proteins used in homologous recombination in humans are
encoded by BRCA1 and BRCA2. Inherited mutations in these genes
predispose women to breast and ovarisn cancers.

37. REPAIRING STRAND BREAKS

38. 4b. REPAIRING EXTENSIVE DAMAGE
• Postreplication (recombination) repair:
• Occurs after DNA synthesis and when damage (e.g., thymine dimers) were
not removed prior to DNA replication. What happens is that DNA
polymerase “jumps over” the damage (e.g., a thymine dimer) and restarts
DNA synthesis somewhere past the damage.
• A recombination protein (RecA in E. coli) stimulates recombination and
exchange of single strands between the strand with the UV-dimers and gap
and the sister double helix.
• The resulting gap in the sister double helix is filled in by DNA polymerase
and sealed by DNA ligase.
• The “original” strand with the UV-dimer now has a complete “other”
strand and the UVdimer can now be removed by “normal” mechanisms.

39. 5. Error-Prone (SOS) repair system:
• Sometimes the replicating machinery is unable to repair the damaged
portion and bypasses the damaged site, known as translesion
synthesis also called bypass system and is emergency repair system.
• This mechanism is catalyzed by a special class of DNA polymerases
called Y-family of DNA polymerases which synthesized DNA directly
across the damaged portion.