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Mutation and DNA repair mechanism
1. Addis Ababa University
School of Medicine
Department of Biochemistry
Advanced Molecular Biology
Seminar
Mutation and DNA repair Mechanism
by
Ayetenew Abita
Wednesday December 20, 2017GC7/31/2019 1
2. OUTLINE
• Introduction
• Causes of mutation
• Point mutation
• Frame shift mutation
• Abnormal intron removal and exon
splicing
• Summary
• Reference7/31/2019 2
3. INTRODUCTION
• The blue print of genetic information
• The master plan of genetic information
• The genetic database
Is stored in the nucleus as DNA
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4. INTRODUCTION
DNA damage
•Mutation is a permanent
change DNA sequence or
changed in the genetic
message carried by gene.
•Mutagen is an agent that
can bring about a permanent
alteration to the physical
composition of a DNA gene.
•Damaged mRNA lead to
altered polypeptide
sequence.7/31/2019 4
5. CAUSE OF DNA MUTATION
Mutations occur continuously
through endogenous and
exogenous DNA damage.
Examples of endogenous DNA
damage:
Reactive oxygen species (ROS),
DNA replication errors.
Examples of exogenous DNA
damage:
tobacco carcinogens, toxins in
food, pollution, ultraviolet light
from the Sun, gamma and X-
radiation, medications, viruses.
7/31/2019 5
6. TAUTOMERISATION
• The bases of DNA are subject to spontaneous
structural alterations called tautomerisation.
•Some of the hydrogen atoms change their
location producing a tautomer
•An amino group (-NH2) can tautomerise to an
imino form (=NH)
•A keto group (-C=O) can tautomerise to an enol
form (=C-OH)
Ex: Thymine (keto form) shifts to enol form ,
which pairs with guanine.
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8. UV (Ultraviolet)
• UV is normally classified in terms of its wavelength:
UV-C (180-290 nm)--"germicidal"--most energetic and
lethal, it is not found in sunlight because it is absorbed by
the ozone layer.
UV-B (290-320 nm)--major lethal/mutagenic fraction of
sunlight.
UV-A (320 nm visible)"near UV“ also has deleterious
effects primarily because it creates oxygen radicals, but it
produces very few pyrimidine dimers.
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10. Base Analog
Bromouracil (structural analog of Thymine)
Enzyme of nucleotide synthesis and DNA synthesis
treat Bromouracil as thymine and incorporate it
into DNA , where it pairs with adenine.
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11. Alkylation Agent
• Alkylating agents are chemicals that add bulky
chemical groups like methyl (CH3) and ethyl
(CH2-CH3) chains to bases
• Ethyl methansulfonate (EMS) is such an
alkylating agent
• The addition of ethyl group distorts the helix
and leads to incorrect base pairing..
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12. Deaminating agents
Deaminating agents are chemicals that remove
amino groups
• Adenine deamination with nitrous acid produces
hypoxanthine, which can mispair with cytosine,
inducing a TC mutation
7/31/2019 12
14. THE EFFECTS OF MUTATIONS
• Some mutations cannot be passed on to offspring
and do not matter for evolution.
• Somatic mutations occur in non-reproductive cells
and won't be passed onto offspring.
• The only mutations that matter to large-scale
evolution are those that can be passed on to
offspring.
• These occur in reproductive cells like eggs and
sperm and are called germ line mutations.
7/31/2019 14
15. EFFECTS OF GERM LINE MUTATIONS
• A single germ line mutation can have a range of effects
• No change occurs in phenotype.
Some mutations don't have any noticeable effect on
the phenotype of an organism.
• The mutation occurs in a protein-coding region, but
ends up not affecting the amino acid sequence of
the protein.
• Small change occurs in phenotype.
• Big change occurs in phenotype.
Mutations that cause the death of an organism are
called lethals.
• Little mutations with big effects: Mutations to control
genes
7/31/2019 15
18. Point mutation
• A point mutation is a genetic mutation where a
single nucleotide base is changed, inserted or
deleted from a sequence of DNAor DNA.
• Point mutation is a random SNP (single nucleotide
polymorphism ) mutation in the deoxyribonucleic
acid ( DNA) that occurs at one point.
7/31/2019 18
19. Transition/transversion categorization
In 1959, Ernst Freese
• Transition Mutations (Alpha) are due to
replacement of a purine base with another purine
or a pyrimidine with another pyrimidine.
• Transversions Mutations (Beta) are replacement of
a purine with a pyrimidine or vice versa.
• Transition mutations are about ten times more
common than transversions.
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21. Functional Categorization
1) Nonsense Mutations
a)Stop-gain is a mutation that results in a
premature termination codon (a stop was gained), which
signals the end of translation.
This interruption causes the protein to be abnormally
shortened.
b) Stop-loss is a mutation in the original termination codon (a
stop was lost), resulting in abnormal extension of a protein's
carboxyl terminus.
c)Start-gain creates a TAC start codon upstream of the original
start site.
d) Start-loss is a point mutation in a transcript's TAC start codon,
resulting in the reduction or elimination of protein
production.
7/31/2019 21
22. 1) Nonsense Mutation
Examples of truncated protein formed in nonsense
mutation converts an amino acid codon into a termination
codon.
7/31/2019 22
23. 2)Missense Mutations
Code for a different amino acid. A missense mutation
changes a codon so
that a different protein is created, a non-synonymous
change.
a) Acceptable mutation
Eg: Normal Hemoglobin A molecule ,
67th amino acid in beta chain
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26. 3) Silent mutations
• Since the genetic code are redundant single
nucleotide can change, but the new codon specifies the
same amino acid, resulting in an unmutated protein.
• A silent mutation has no effect on the functioning of
the protein.
• This type of change is called synonymous change, since
the old and new codon code for the same amino acid.
This is possible because 64 codons specify only 20
amino acids.
7/31/2019 26
28. FRAMESHIFT MUTATION
• Inserting or deleting one or more nucleotides
Changes the “reading frame” like changing a sentence
Proteins built incorrectly
• A frameshift mutation is not the same as a
single-nucleotide polymorphism in which a
nucleotide is replaced, rather than inserted
or deleted.
7/31/2019 28
30. Splicing Errors
• Mutation of a splice site resulting in loss of function of that
site.
Results in exposure of a premature stop codon, loss of an exon,
or inclusion of an intron.
• Mutation of a splice site reducing specificity.
May result in variation in the splice location, causing insertion or
deletion of amino acids, or most likely, a disruption of the
reading frame.
• Displacement of a splice site, leading to inclusion or
exclusion of more RNA than expected, resulting in longer or
shorter exons.
• Although many splicing errors are safeguarded by a cellular
quality control mechanism termed nonsense-mediated
mRNA decay (NMD), a number of splicing-related diseases
also exist
.
7/31/2019 30
31. SUMMARY
• Mutations occur continuously through
endogenous and exogenous DNA damage
• Mutation might be point, frame shift, splicing
error.
• lethal mutation: causes the developing organism
to die prematurely.
• loss-of-function mutation: either reduces or
abolishes the activity of the gene.
• gain-of-function mutation: increases the activity
of the gene or makes it active in inappropriate
circumstances .
7/31/2019 31
32. REFERENCE
• Harper’s Review of Biochemistry
• Lehniger’s principle of Biochemistry
• Lippincott’s Illustrated Review of Biochemistry
• Text Book of Biochemistry with clinical
correlations- Devlin TM
• Text Book of Biochemistry by Vasudevan
• Text book of biochemistry, satyanarayana
• Principle of biochemistry, William H. simmons.
7/31/2019 32
DNA repair mechanism
Mismatch repair
Base excision repair
Nucleotide excision repair
Double stranded break repair
Summary
A Mutation occurs when a DNA gene is damaged or changed in such a way as to alter the genetic message carried by that gene.A Mutagen is an agent of substance that can bring about a permanent alteration to the physical composition of a DNA gene such that the genetic message is changed.
Once the gene has been damaged or changed the mRNA transcribed from that gene will now carry an altered message.
The polypeptide made by translating the altered mRNA will now contain a different sequence of amino acids. The function of the protein made by folding this polypeptide will probably be changed or lost. In this example, the enzyme that is catalyzing the production of flower color pigment has been altered in such a way it no longer catalyzes the production of the red pigment.
No product (red pigment) is produced by the altered protein.
In subtle or very obvious ways, the phenotype of the organism carrying the mutation will be changed. In this case the flower, without the pigment is no longer red
Spontaneous tautomeric shifts in the basescontribute to replication errors Ex: Thymine (keto form) shifts to enol form ,which pairs with guanine
Spontaneous tautomeric shifts in the basescontribute to replication errors Ex: Thymine (keto form) shifts to enol form ,which pairs with guanine
The major lethal lesions are pyrimidine dimers in DNA (produced by UV-B and UV-C)--these are the result of a covalent attachment between adjacent pyrimidines in one strand.
Mutagenic component of sunlight Can not penetrate beyond the outer layer ofthe skin and - unable cause germ linemutations. only causes sunburn and skin cancer mainlythrough the formation of pyrimidine dimers
1. Base analog Bromouracil (structural analog of Thymine) Enzyme of nucleotide synthesis and DNA synthesistreat Bromouracil as thymine and incorporate itinto DNA , where it pairs with adenine
printDNA and Mutations :
The effects of mutations
Since all cells in our body contain DNA, there are lots of places for mutations to occur; however, some mutations cannot be passed on to offspring and do not matter for evolution. Somatic mutations occur in non-reproductive cells and won't be passed onto offspring. For example, the golden color on half of this Red Delicious apple was caused by a somatic mutation. Its seeds will not carry the mutation.The only mutations that matter to large-scale evolution are those that can be passed on to offspring. These occur in reproductive cells like eggs and sperm and are called germ line mutations.
Effects of germ line mutationsA single germ line mutation can have a range of effects:
No change occurs in phenotype.Some mutations don't have any noticeable effect on the phenotype of an organism. This can happen in many situations: perhaps the mutation occurs in a stretch of DNA with no function, or perhaps the mutation occurs in a protein-coding region, but ends up not affecting the amino acid sequence of the protein.
Small change occurs in phenotype.A single mutation caused this cat's ears to curl backwards slightly.
Big change occurs in phenotype.Some really important phenotypic changes, like DDT resistance in insects are sometimes caused by single mutations. A single mutation can also have strong negative effects for the organism. Mutations that cause the death of an organism are called lethals — and it doesn't get more negative than that.
Little mutations with big effects: Mutations to control genesMutations are often the victims of bad press — unfairly stereotyped as unimportant or as a cause of genetic disease. While many mutations do indeed have small or negative effects, another sort of mutation gets less airtime. Mutations to control genes can have major (and sometimes positive) effects.
Some regions of DNA control other genes, determining when and where other genes are turned "on". Mutations in these parts of the genome can substantially change the way the organism is built. The difference between a mutation to a control gene and a mutation to a less powerful gene is a bit like the difference between whispering an instruction to the trumpet player in an orchestra versus whispering it to the orchestra's conductor. The impact of changing the conductor's behavior is much bigger and more coordinated than changing the behavior of an individual orchestra member. Similarly, a mutation in a gene "conductor" can cause a cascade of effects in the behavior of genes under its control.
Many organisms have powerful control genes that determine how the body is laid out. For example, Hox genes are found in many animals (including flies and humans) and designate where the head goes and which regions of the body grow appendages. Such master control genes help direct the building of body "units," such as segments, limbs, and eyes. So evolving a major change in basic body layout may not be so unlikely; it may simply require a change in a Hox gene and the favor of natural selection.
lethal mutation: causes the developing organism to die prematurely.conditional mutation: produces its phenotypic effect onlyunder certain conditions, called the restrictive conditions.Under other conditions—the permissive conditions—theeffect is not seen. For a temperature-sensitive mutation, therestrictive condition typically is high temperature, while thepermissive condition is low temperature.loss-of-function mutation: either reduces or abolishes theactivity of the gene. These are the most common class ofmutations. Loss-of-function mutations are usuallyrecessive—the organism can usually function normally as longas it retains at least one normal copy of the affected gene.null mutation: a loss-of-function mutation that completelyabolishes the activity of the gene.gain-of-function mutation: increases the activity of the geneor makes it active in inappropriate circumstances; thesemutations are usually dominant.dominant-negative mutation: dominant-acting mutation thatblocks gene activity, causing a loss-of-function phenotypeeven in the presence of a normal copy of the gene. Thisphenomenon occurs when the mutant gene productinterferes with the function of the normal gene product.suppressor mutation: suppresses the phenotypic effect ofanother mutation, so that the double mutant seems normal.An intragenic suppressor mutation lies within the geneaffected by the first mutation; an extragenic suppressormutation lies in a second gene—often one whose productinteracts directly with the product of the first
the oxygen caring capacity of Hb is lost in this cases.
Codons are redundant
Recall that genetic code is non-overlapping or comma-less