Mutations

transcript

Mutation

Definition of a Mutation

• Any change in genetic material.

What are Mutations• Any permanent random chemical change

in either:– the DNA (Gene Mutation)

– or the genetic makeup of a cell (Chromosome Mutation)

Mutations- how often?

• Mutations occur all the time. • In Humans – each gene mutates on average

once in every 1,000,000 to 100,000,000 replications.

• We have about 25,000 genes in each cell• So on average – each person in the room

has one mutated gene (that is one gene that neither of their parents had).

The effects of Mutations

• If a mutation occurs it can cause anything from no effect (silent mutation) to a lethal effect.

• Good or Bad mutations. If the mutation results in a phenotype that is of benefit to the individual, then it will be considered a good mutation.

Mutations and Evolution

• Genetic variation comes from 1 Independent Assortment 2 Crossing over (recombination) 3 Mutations.

• The first two just mix the genes up.

• Only mutations can create new alleles. • All three assist a species to evolve!

Definitions and Terminology

• Microevolution– Changes within populations or species in

gene frequencies and distributions of traits

• Macroevolution– Higher level changes, e.g. generation of

new species or higher–level classification

• Section of a chromosome that encodes the information to build a protein

• Location is known as a “locus”

Allele

• Varieties of the information at a particular locus• Every organism has two alleles (can be same or different) • No limit to the number of alleles in a population

An allele is a viable DNA coding that occupies a given locus (position) on a chromosome.

Genotype

• Genetic information contained at a locus• Which alleles are actually present at a

• Example: – Alleles available: R and W– Possible genotypes:

• RR, RW, WW

Phenotype

• Appearance of an organism

• Results from the underlying genotype

Phenotype

• Example 1:

– Alleles R (red) and W (white), codominance– Genotypes: RR, RW, WW– Phenotypes: Red, Pink, White

Phenotype

• Example 2:

– Alleles R (red) and w (white), simple dominance– Genotypes: RR, Rw, ww– Phenotypes: Red, Red, white

What Are Mutations?What Are Mutations?

• Changes in the nucleotide sequence of DNA

• May occur in somatic cells (aren’t passed to offspring)

• May occur in gametes (eggs & sperm) and be passed to offspring

What Causes Mutations?• There are two ways in which DNA can

become mutated:– Mutations can be inherited.

• Parent to child

– Mutations can be acquired.• Environmental damage• Mistakes when DNA is copied

What are the other factors?

• These factors may include: radiation, chemical exposures, UV light (sunlight)

• Not necessarily harmful!– Dependent on: 1) nature of mutation

2) environment

• Spontaneous– occur randomly throughout genome– rates: 10-6 - 10-4 /gene/cell

• Reversible

• Many mutations are repaired by enzymes

Are Mutations Helpful or Harmful?

• Some type of skin cancers and leukemia result from somatic mutations

• Some mutations may improve an organism’s survival (beneficial)

Significance of Mutations• Most are neutral

• Eye color• Birth marks

• Some are harmful• Sickle Cell Anemia• Down Syndrome

• Some are beneficial• Sickle Cell Anemia to Malaria• Immunity to HIV

Classification of

mutation types

Classification of mutation typesBased on

• Effect on structure

• Effect on function

• Effect on fitness

• By inheritance

• Pattern of inheritance

• By impact on protein sequence

Classification of mutation typesEffect on structure

• The Mutations which alters the structure of the genes

These can be classified as:i. Small-scale mutations Those affecting a small gene in one or a few

nucleotides

ii. Large-scale mutations in chromosomal structure, including

Small-Scale MutationsGene Mutations

• Change in the nucleotide sequence of a gene

• May only involve a single nucleotide

• May be due to copying errors, chemicals, viruses, etc.

Types of Gene Mutations

• Include:

–Point Mutations

–Insertions

–Deletions

–Frameshift

Point Mutation• often caused by

– chemicals or – malfunction of DNA replication, – exchange a single nucleotide for another.

These changes are classified as transitions or transversions• Transition is the exchange of

a purine for a purine (A ↔ G) or

a pyrimidine for a pyrimidine, (C ↔ T). • A transition can be caused by nitrous acid, base mis-pairing, or

mutagenic base analogs.• This is the most common

Point Mutation• often caused by

– chemicals or – malfunction of DNA replication, – exchange a single nucleotide for another.

These changes are classified as transitions or transversions

Less common is a transversion, which exchanges

a purine for a pyrimidine or

a pyrimidine for a purine (C/T ↔ A/G).

Point Mutation

It can be reversed by another point mutation,•in which the nucleotide is changed back to its original state (true reversion) •Point mutations that occur within the protein coding region of a gene may be classified into three kinds:

Silent mutations: which code for the same amino acid.

Missense mutations: which code for a different amino acid.

Nonsense mutations: which code for a stop and can truncate the protein.

Point Mutation

Silent mutations do not result in a change to the amino acid sequence of a protein.

These are also treated as evolutionarily neutral Mutations as they do not alter protein function.

Point Mutation

• a change in a base pair does not result in a change in the sequence of amino acids in a protein

Silent mutations

Point MutationMissense Mutation

in which a single nucleotide is changed, resulting in a codon that codes for a different amino acid.

This renders the resulting protein nonfunctional.

Such mutations are responsible for diseases such as Epidermolysis bullosa, sickle-cell disease.

Point Mutation

Defective protein glycosylation in patients with cutis laxa syndrome

Missense Mutation in Kindler Syndrome

Point MutationNonsense mutation

in which a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA, and in a truncated, incomplete, and usually nonfunctional protein product.

The effect of a nonsense mutation depends on how much of the protein is lost.

Point Mutation• Nonsense Mutation in Kindler Syndrome

(a)Extensive atrophy on the trunk;

(b)Mottled hyperpigmentation in the right axilla;

(c)cigarette-paper-like atrophy on the dorsal aspects of the hands;

(d)mild palmoplantar keratoderma.

• Include:

–Point Mutations

–Insertions

–Deletions

–Frameshift

Gene MutationsSmall-scale mutations

Insertions

• add one or more extra nucleotides into the DNA. • caused by transposable elements,

or errors during replication of repeating elements (e.g. AT repeats).

• Alter reading frame• which can significantly alter the gene product.

Insertions can be reverted by excision of the transposable element.

Insertions

Insertions in Desmoplakin

linical pictures showing the striated keratoderma on (a)palm and (b)sole of the patient and (c)(d) the woolly hair phenotype.

• Include:

–Point Mutations

–Insertions

–Deletions

–Frameshift

Deletions• remove one or more nucleotides from the DNA.

Like insertions, • alter the reading frame of the gene. • irreversible mutations• producing a non-functional protein.

• Deletion of a number of base pairs that is not evenly divisible by three will lead to a frameshift mutation

Deletions

DeletionsReal examples of deletion mutations which cause diseases. (a) Deletion of "T" from the sequence

"TTTTT" in the CFTR gene. (b) Deletion of "AT" from the sequence

"ATAT" in the CFTR gene. (c) Deletion of "TTG" from the sequence

"TTGTTG" in the FIX gene. (d) Deletion of "ATAG" from the sequence

"ATAGATAG" in the APC gene.

Deletions

Deletion Mutation in Keratin 5 Causing the Removal of 5 Amino Acids and Elevated Mutant mRNA Levels in Dowling–Meara Epidermolysis Bullosa Simplex

• Include:

–Point Mutations

–Insertions

–Deletions

–Frameshift

Frameshift Mutation

• Inserting or deleting one or more nucleotides

• Changes the “reading frame” like changing a sentence

• Proteins built incorrectly

Frameshift Mutation

• Original:

–The fat cat ate the wee rat.• Frame Shift (“a” removed):

– The fat caa tet hew eer at.

Frameshift Mutation

A frameshift mutation (framing error) • caused by indels, ie. insertion or deletion of a

number of nucleotides that is not evenly divisible by three from a DNA sequence.

• Resulting in a completely different translation from the original.

• Frameshift mutations frequently result in severe genetic diseases such as Tay-Sachs disease.

Amino Acid Sequence Changed

• By inheritance

Classification of mutation typesEffect on structure

• The Mutations which alters the structure of the genes

These can be classified as:i. Small-scale mutations Those affecting a small gene in one or a few

nucleotides

ii. Large-scale mutations in chromosomal structure, including

• May Involve:– Changing the structure of

a chromosome

– The loss or gain of part of a chromosome

Large-Scale MutationsChromosaome Mutations

Chromosome Mutations

• Five types exist:–Deletion

–Inversion

–Translocation

–Nondisjunction

–Duplication

Deletion

• Due to breakage• A piece of a chromosome is lost

Inversion

• Chromosome segment breaks off

• Segment flips around backwards

• Segment reattaches

Duplication

• Occurs when a gene sequence is repeated

Translocation

• Involves two chromosomes that aren’t homologous

• Part of one chromosome is transferred to another chromosomes

Translocation

Nondisjunction

• Failure of chromosomes to separate during meiosis

• Causes gamete to have too many or too few chromosomes

Chromosome Mutation Animation

• Down Syndrome– Chromosome 21 does

not separate correctly.– They have 47

chromosomes in stead of 46.

– Children with Down Syndrome develop slower, may have heart and stomach illnesses and vary greatly in their degree of inteligence.

• Cri-du-chat– Deletion of material on 5th

chromosome– Characterized by the cat-like

cry made by cri-du-chat babies

– Varied levels of metal handicaps

Sex Chromosome Abnormalities

• Klinefelter’s Syndrome– XXY, XXYY, XXXY– Male– Sterility– Small testicles– Breast enlargement

Sex Chromosome Abnormalities

• XYY Syndrome– Normal male traits– Often tall and thin– Associated with antisocial and behavioral

problems

Sex Chromosome Mutations

• Turner’s Syndrome– X– Female– sex organs don't

mature at adolescence

– sterility– short stature

Sex Chromosome Mutations

• XXX– Trisomy X– Female– Little or no visible differences– tall stature– learning disabilities– limited fertility

• By inheritance

Classification of mutation typesEffect on function

• Loss-of-function mutations

• Gain-of-function mutations

• Dominant negative mutations

• Lethal mutations

• A back mutation or reversion

• Loss-of-function mutations

• results in gene product having less or no function.

• When the allele has a complete loss of function (null allele) it is often called an amorphic mutation.

• Gain-of-function mutations

• changes the gene product such that it gains a new and abnormal function.

• These mutations usually have dominant phenotypes.

• Often called a neomorphic mutation.

Effect on function• Dominant negative mutations

also called antimorphic mutations•have an altered gene product that acts antagonistically to the wild-type allele. •These mutations usually result in an altered molecular function (often inactive.

•In humans, Marfan syndrome is an example• In this the defective glycoprotein product of the

fibrillin gene (FBN1) antagonizes the product of the normal allele.

• Lethal mutations

are mutations that lead to the death of the organisms which carry the mutations

• A back mutation or reversion

is a point mutation that restores the original sequence and hence the original phenotype.

• By inheritance

Classification of mutation typesEffect on fitness

Mutations are either harmful or beneficial

• Harmful mutation

that decreases the fitness of the organism.

• Beneficial mutation

increases fitness of the organism, or which promotes traits that are desirable.

• Neutral mutation:has no harmful or beneficial effect on the organism.

• Deleterious mutation:has a negative effect on the phenotype, and thus decreases the fitness of the organism.

• Advantageous mutation:has a positive effect on the phenotype, and thus increases the fitness of the organism.

• Nearly neutral mutation:may be slightly deleterious or advantageous,

although most nearly neutral mutations are slightly deleterious

• By inheritance

Classification of mutation types

Mutations by inheritance

• inheritable generic in pro-generic tissue or cells on path to be changed to gametes.

• non inheritable somatic (eg, carcinogenic mutation)

• By inheritance

Classification of mutation typesMutations by pattern of inheritanceThe human genome contains two copies of each gene – a paternal and a maternal allele.

Heterozygous mutation: a mutation of only one allele.

Homozygous mutation:an identical mutation of both the paternal and

maternal alleles.

Classification of mutation typesMutations by pattern of inheritanceThe human genome contains two copies of each gene – a paternal and a maternal allele.

Compound heterozygous:comprises two different mutations in the

paternal and maternal alleles.

Wildtype or homozygous non-mutated:organism is one in which neither allele is

mutated. (Just not a mutation)

• By inheritance

Classification of mutation typesMutation by impact on protein sequence

• Frameshift mutation

• Missense mutations

• Neutral mutation

• Nonsense mutation

• Silent mutations

Classification of mutation typesMutation by impact on protein sequence•Frameshift mutation:

is a mutation caused by insertion or deletion of a number of nucleotides that is not evenly divisible by three from a DNA sequence.

Due to the triplet nature of gene expression by codons, the insertion or deletion can disrupt the reading frame, or the grouping of the codons, resulting in a completely different translation from the original.

as a result more altered the protein produced is.

Classification of mutation typesMutation by impact on protein sequence•Missense mutations

mutations are types of point mutations change in single nucleotide is changed to cause

substitution of a different amino acid.

This in turn can render the resulting protein nonfunctional.

these are responsible for diseases such as Epidermolysis bullosa, sickle-cell disease.

Classification of mutation typesMutation by impact on protein sequence•Neutral mutation

occurs in an amino acid codon which results in the use of a different, but chemically similar, amino acid.

This is similar to a silent mutation, where a codon mutation may encode the same amino acid

for example, a change from AUU to AUC will still encode leucine, so no discernible change occurs.

Classification of mutation typesMutation by impact on protein sequence

•Nonsense mutation

is a point mutation in a sequence of DNA that results in

a premature stop codon, or a nonsense codon in the transcribed

and possibly a truncated, and often nonfunctional protein product.

Classification of mutation typesMutation by impact on protein sequence•Silent mutations

do not result in a change to the amino acid sequence of a protein.

may occur in a region that does not code for a protein,

or may occur within a codon in a manner that does not alter the final amino acid sequence.

Classification of mutation typesMutations Based on

• By inheritance

Causes of

mutation

Causes of mutation

Two classes of mutations are

• Spontaneous mutations (molecular decay) and

• Induced mutations caused by mutagens

Causes of mutationSpontaneous mutations (molecular decay)

Spontaneous mutations on the molecular level include:

• Tautomerism

• Depurination

• Deamination

• Transition

• Transversion

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.

The Existence of a molecule in a keto and a enol form is known as tautomerisum.

This is due to a chemical reaction called tautomerization. Commonly this reaction results in the formal migration of a hydrogen atom or proton, accompanied by a switch of a single bond and adjacent double bond.

Depurination

Loss of a purine base (A or G) from the deoxyribose sugar by hydrolysis of the beta-N-glycosidic link between them.

The sugar phosphate backbone remains and the sugar ring has a hydroxyl (-OH) group in the place of the purine.

Studies estimate that as many as 10,000 purines are lost this way each day in a typical human cell,

Depurination

One of the main causes of depurination is the presence of endogenous metabolites in cell undergoing chemical reactions.

Deamination

Deamination is the removal of an amine group from a molecule.

Hydrolysis changes a normal base to an atypical base containing a keto group in place of the original amine group. Example: C → U and A → HX (hypoxanthine), which can be corrected by DNA repair mechanisms;

TransitionTransition is the exchange of

a purine for a purine (A ↔ G) or a pyrimidine for a pyrimidine, (C ↔ T).

A transition can be caused by nitrous acid, base mis-pairing, or mutagenic base analogs.

Transversion

transversion, which exchanges

a purine for a pyrimidine or

a pyrimidine for a purine (C/T ↔ A/G).

Causes of mutation

Induced mutations are mainly caused by mutagens such as

• Chemicals

• Radiations

• Viral infections

Causes of mutationChemical Mutagens –

can be divided into two classes:

Class I Mutagens: which can cause mutations to both replicating and non replicating DNA.

class II mutagens: which affect replicating nucleic acids. molecules look like nucleic acid; hence they are incorporated into the replicating DNA molecule.

Class I Mutagens: • Hydroxylamine

• Nitrous acid

• Alkylating agent

• DNA crosslinkers

• Oxidative damage

• Agents that form DNA adducts

Causes of mutation

• reacts with pyrimidine bases.

• Its effect is strong on cytosine

• It breaks and removes pyrimidine ring of uracil thus producing phosphoribosyl urea and 5' isoxasolone with cytosine,

• finally produces hydroxyl amino (-NOH) derivative, which might be responsible for base pair change (GC-AT pair).

Class I Chemicals Mutagens:Hydroxylamine NH2OH

Causes of mutation

• Mutations induced by hydroxylamine cannot be reversed with hydroxylamine.

Class I Chemicals Mutagens:Hydroxylamine NH2OH

Causes of mutation

• very potent mutagen that acts directly on either replicating or non replicating DNA

• by oxidation or deamination of the bases that contain amino groups (adenine-A, guanine-G and cytosine-C).

• Conversion of the amino groups to keto groups

changes the hydrogen bonding potential of the bases.

Class I Chemicals Mutagens:Nitrous Acid (HNO2)

Causes of mutation

• Adenine is deaminated to hypoxanthine, • Which pairs with cytosine in the place of thymine.

• Since the deamination of adenine leads to AT. GC transition, nitrous acid induces transitions in both directions.

Causes of mutation

• Cytosine is deaminated to uracil, which now pairs with adenine in the place of guanine.

• Deamination of cytosine results in CC. AT transitions,

Causes of mutation

• Deamination of guanine has zero effect, as deaminated guanine also pairs with cytosine.

Causes of mutation

• Nitrous acid also causes interstrand cross-linking of DNA.

• The DNA strands fail to separate and there is no DNA duplication, which is lethal or deleterious.

Causes of mutation

• These agents can mutate both replicating and non-replicating DNA.

• a base analog can only mutate the DNA when the analog is incorporated in replicating the DNA.

• They induce all types of mutations, • transitions, transversions, frameshifts and • even chromosome aberrationsdepending on the specific alkylating agent.

Class I Chemicals Mutagens:Alkylating agent

Causes of mutation

• In mutagenesis,alkylating agents involves the transfer of methyl or ethyl group to the bases such that their base-pairing potentials are altered and transitions result.

Causes of mutation

• carry one, two or more alkyl groups in reactive form• These are capable of being transferred to other

molecules where electron density is high.• They are most powerful mutagens. Examples are:

Causes of mutation

• These chemicals attack different reactive groups. • reactive atoms for alkylation are the N7 of guanine

and the N3 of adenine.

• Alkylation at these positions will distort the double helix. Such distortions can be repaired by an.

• The DNA becomes distorted as a result and the ability of proteins to recognize and bind correctly is hindered.

Causes of mutation

• Alkylation can also occur at oxygen atoms: • O6 of guanine and • O4 of thymine.

This will result in mispairing of base pairs but does not generate major distortions..

O-6-ethylguanine will pair with thymine and O-4-ethylthymine will pair with guanine.

Causes of mutationClass I Chemicals Mutagens:Alkylating agent

• Nitrous acid (HNO2)– causes deamination of A, C, and G– point mutations

• Alkylating agents– EMS (ethyl methane sulfonate),EES (ethyl ethane

sulfonate) mustard gas (sulfur mustard), nitrogen mustard

• cause misspairing and/or depurination• frameshifts

• Nitrous acid

Causes of mutation

• A DNA adduct is a piece of DNA covalently bonded to a (cancer-causing) chemical.

Examples of DNA adducts are:acetaldehyde

(a major component of cigarette smoke)

Etheno adducts

1-Nitropyrene

• This has shown to be the start of a cancerous cell, or carcinogenesis.

Class I Chemicals Mutagens:Agents that form DNA adducts

Causes of mutationClass I Chemicals Mutagens:Agents that form DNA adducts

• Nitrous acid

Causes of mutation

• Chemical agents responsible for crosslinks in DNA

• Crosslinks in DNA occur when various exogenous or endogenous agents react with two different positions in the DNA.

Class I Chemicals Mutagens:DNA Crosslinkers

Causes of mutation

• This can either occur in same strand (intrastrand crosslink) or

opposite strands(interstrand crosslink)

• DNA replication is blocked by crosslinks, which causes replication arrest and cell death if the crosslink is not repaired.

Causes of mutation

These are two types: Exogenous Crosslinkers

Endogenous Crosslinkers

Causes of mutation

Exogenous CrosslinkersClass I Chemicals Mutagens:

• Alkylating agents such as1, 3-bis(2-chloroethyl)-1-nitrosourea andNitrogen mustard

which are used in chemotherapy can cross link with DNA at N7 position of guanine on the opposite strands forming interstrand crosslink.

Cisplatin Mostly it acts on the adjacent N-7 guanine forming 1, 2 intrastrand crosslink.

Causes of mutation

Endogenous CrosslinkersClass I Chemicals Mutagens:

• Nitrous acid formed in the stomach dietary source nitrites. It induces formation of interstrand DNA crosslink at aminogroup of guanine at the CG sequences.

• Reactive chemicals such as malondialdehyde which are formed endogenously as the product of lipid peroxidation.

Causes of mutation

• Psoralens are natural compounds (furocoumarins) present in plants.

• These compounds get activated in the presence of UV.

• The crosslinking reaction by Psoralens targets TA sequences in DNA and linking one base of the DNA with the one below it.

• Psoralen adducts cause replication arrest and is used in the treatment of psoriasis and vitiligo.

Causes of mutation

• Aldehydes such as acrolein and crotonaldehyde found in tobacco smoke or automotive exhaust can form DNA interstrand crosslinks in DNA.

• Nitrous acid

Causes of mutationClass I Chemicals Mutagens:

Oxidative damageOxidative damage can be caused by

superoxide radicals, hydrogen peroxide, or hydroxide radicals.

The most important type of oxidative damage is the formation of 8-oxo-guanine which will pair with adenine and generate transversions.

Oxidative damage.

Class II Mutagens: The molecules of class II mutagens look like nucleic

acid; hence they are incorporated into the replicating DNA molecule.

• Base analogs

• Acridine dyes

Causes of mutationClass II- Chemical Mutagens:–

Base analogs

• have a structure similar to the normal bases

• they are metabolized and incorporated into DNA during replication.

• And that they increase the frequency of mis-pairing and thus cause mutation.

Base analogs

• 5-bromo-uracil

• 2-aminopurine

Base analogs

• 5-bromo-uracil

This analogue tautomerizes more readily than thymine. As a result, it will pair with guanine more frequently. The result is a TA -> CG transition.

Base analogs

• 2-aminopurine

This analogue normally pairs with thymine but when it is protonated, it will pair with cytosine. The result is an AT -> GC transition.

Base analogs

• 2-aminopurine

Acridine dyes

• They bind directly to the DNA by using their positive charge.

• Positively charged acridines intercalate or sandwich themselves between the stacked base pairs in DNA.

Acridine dyes • Acridine dyes separate two bases by 6.8 A, thus a

base will be missed.

• Acridine dyes can insert or delete only one base pair in DNA, and thus result in frameshift mutations.

• The examples of this class of mutagens are • nitrous acid (HNO2), • hydroxylamine, • hydrazine, H2O2 etc.

Causes of mutation

• Chemicals

• Radiations

Causes of mutation

• Chemicals

• Radiations

• UV radiation produces pyrimidine problems– bonds form between two adjacent thymines

on one strand • leads to deletion of two bases

– cytosines converted to cytosine hydrate• leads to mispairing of bases

– FRAMESHIFTS

Causes of mutationInduced mutations

Radiations

• Radiation– UV Rays (Sun)

Two nucleotide bases in DNA – cytosine and thymine – are most vulnerable to radiation that can change their properties.

UV light can induce adjacent thymine bases in a DNA strand to pair with each other, as a bulky dimer.

Ionizing Radiation• X-rays, gamma rays, cosmic rays

– induce point mutations – induce gross structural changes in

chromosomes through breakage

Radiations

Mutations

Documents