Gene Mutation. Classification of Mutations Can Be Made at the: DNA levelDNA level Protein...

Gene Mutation Gene Mutation

Classification of Mutations Classification of Mutations Can Be Made at the:Can Be Made at the:

• DNA levelDNA level

• Protein levelProtein level

• Cellular levelCellular level

• Organismal level Organismal level

Mutation at the DNA LevelMutation at the DNA LevelChange from one allele to a different alleleChange from one allele to a different allele

Forward mutationForward mutation

Wild type Wild type mutant mutant

Reverse mutationReverse mutation

Mutant Mutant wild type wild type

Quantifying Mutation Quantifying Mutation

Mutation rate = number of mutationsMutation rate = number of mutations per unit time per unit time

Mutation frequency = frequency of a Mutation frequency = frequency of a specific mutation in a population specific mutation in a population of cells or individuals of cells or individuals

Both are low in value and vary Both are low in value and vary by location.by location.

Mutation at the DNA LevelMutation at the DNA Level

• Spontaneous mutationSpontaneous mutation

Results from natural processesResults from natural processes

• Induced mutationInduced mutation

Results from exposure to Results from exposure to environmental chemicals or radiation environmental chemicals or radiation

Mutation at the Cellular LevelMutation at the Cellular Level• Somatic MutationSomatic Mutation

– arises in body cells that will not give rise to arises in body cells that will not give rise to gametes (not passed to offspring)gametes (not passed to offspring)

– can lead to mutant cell populationcan lead to mutant cell population– mutation of proto-oncogenes leads to cancer mutation of proto-oncogenes leads to cancer

developmentdevelopment

• Germ-Line MutationGerm-Line Mutation– arises in cells giving rise to gametesarises in cells giving rise to gametes– can be passed on to offspringcan be passed on to offspring

Germ-line mutation to X-linked recessive Germ-line mutation to X-linked recessive allele for hemophilia.allele for hemophilia.

Characteristics of Mutations Characteristics of Mutations at the DNA Levelat the DNA Level

Type of MutationType of Mutation ExamplesExamples

TransitionTransitionPurinePurinepurinepurine

PyrimidinePyrimidinepyrimidinepyrimidine

ATATGC TAGC TACGCG

GCGCAT CGAT CGTATA

TransversionTransversionPurinePurinepyrimidinepyrimidine

PyrimidinePyrimidinepurinepurine

ATATCG ATCG ATTATA

GCGCTA GCTA GCCGCG

TATAGC TAGC TAATAT

CGCGAT CGAT CGGCGC

•Base substitutions: change of one nucleotideBase substitutions: change of one nucleotide into another into another

Mutations at the DNA Level Lead to Mutations at the DNA Level Lead to Changes in Protein CompositionChanges in Protein Composition

-A-A-G--A-A-G--T-T-C--T-T-C-

lysinelysine

TransitionTransition

-A-G-G--A-G-G--T-C-C--T-C-C-

argininearginine

-A-A-G--A-A-G--T-T-C--T-T-C-

lysinelysine

TransversionTransversion

-A-C-G--A-C-G--T-G-C--T-G-C-

threoninethreonine

Characteristics of MutationsCharacteristics of Mutations at the DNA Level at the DNA Level

• Insertions and DeletionsInsertions and Deletions– addition or removal of one or more addition or removal of one or more

nucleotide pairsnucleotide pairs– cause frameshift mutations cause frameshift mutations – changes in multiples of three cause changes in multiples of three cause

in-frame deletions or insertionsin-frame deletions or insertions

Characteristics of Mutations at the DNA LevelCharacteristics of Mutations at the DNA Level• Expanding Trinucleotide RepeatsExpanding Trinucleotide Repeats

– may arise as a result of formation of hairpin may arise as a result of formation of hairpin structures during DNA replicationstructures during DNA replication

– could also be due to unequal crossing over when could also be due to unequal crossing over when repeated regions do not align properlyrepeated regions do not align properly

Effects of Mutations Effects of Mutations

at the Protein Levelat the Protein Level SilentSilent AGGAGG CGG CGG

Arg ArgArg Arg

Substitution of Substitution of

a Nucleotidea Nucleotide

SynonymousSynonymous(Neutral)(Neutral)

AAAAAA AGA AGA

Lys ArgLys Arg

MissenseMissense AAAAAA GAA GAA

Lys GluLys Glu

NonsenseNonsense CAGCAG UAG UAG

Gln StopGln Stop

Deletion or Deletion or

Insertion of Insertion of

Nucleotide(s)Nucleotide(s)

Frameshift Frameshift AA(A)GACUUACCAAAA(A)GACUUACCAA

Lys-asp-leu-pro Lys-asp-leu-pro Lys-thr-tyr-glnLys-thr-tyr-gln

Classification of Mutations Classification of Mutations Based on Protein FunctionBased on Protein Function

• Recessive mutationsRecessive mutations– Loss of functionLoss of function

• Example: Mutant Tumor Example: Mutant Tumor Suppressor GenesSuppressor Genes

• Dominant mutationsDominant mutations– Gain of functionGain of function

• Example: OncogenesExample: Oncogenes

Applying Your KnowledgeApplying Your Knowledge

Which type of mutationWhich type of mutationA. can be passed on to offspring?A. can be passed on to offspring?B. represents a loss of protein function? B. represents a loss of protein function? C. involves a pyrimidine being substituted C. involves a pyrimidine being substituted

for a purine?for a purine?

1.1. TransversionTransversion2.2. Germ-line mutationGerm-line mutation3.3. Recessive mutationRecessive mutation4.4. TransitionTransition5.5. Somatic mutationSomatic mutation

Spontaneous Mechanisms of Mutation: Spontaneous Mechanisms of Mutation:

Replication ErrorsReplication Errors • Nonstandard base pairings due to Nonstandard base pairings due to

flexibility in DNA structure flexibility in DNA structure substitutions substitutions


Replication ErrorsReplication Errors • Strand slippage due to looping of one nucleotide Strand slippage due to looping of one nucleotide

strand during replicationstrand during replicationinsertions or deletionsinsertions or deletions


Replication ErrorsReplication Errors • Unequal crossing overUnequal crossing overinsertions or insertions or

deletionsdeletions

Spontaneous Mechanisms of Mutation: Spontaneous Mechanisms of Mutation: Spontaneous Chemical ChangesSpontaneous Chemical Changes

• DepurinationDepurination– Hydrolysis of purine Hydrolysis of purine

base from the base from the sugar-phosphate sugar-phosphate backbonebackbone


• DepurinationDepurination– Random base inserted opposite the apurinic Random base inserted opposite the apurinic

site during replication can lead to mutation site during replication can lead to mutation

-G-G-C--G-G-C--C-C-G--C-C-G-

-G- -C--G- -C--C-C-G--C-C-G-

-G-G-C--C-C-G--C-C-G-

Wild typeWild typecodes for glycinecodes for glycine

-G-T-C--C-A-G--C-A-G-

Mutant codes Mutant codes for valinefor valine

-G- -C--G- -C--C-A-G-


• Deamination of cytosineDeamination of cytosine– Converts cytosine to uracilConverts cytosine to uracil


Spontaneous Chemical ChangesSpontaneous Chemical Changes

• Deamination of cytosineDeamination of cytosine– DNA replication causes G-C DNA replication causes G-C A-T change A-T change

-C-G-C--C-G-C--G-C-G--G-C-G-

-C-A-C--G-U-G--G-U-G-

-C-G-C--C-G-C--G-C-G-

Wild typeWild typecodes for argininecodes for arginine

-C-A-C--C-A-C---G-T-G--

-C-A-C--G-U-G--G-U-G-

Mutant codes Mutant codes for histidinefor histidineIs this aIs this a

1. transition or1. transition or2. transversion? 2. transversion?

-C-G-C--C-G-C--G-U-G--G-U-G-

Inducing Mutations Inducing Mutations

Mutagens are environmental Mutagens are environmental agents that increase the rate of agents that increase the rate of mutation.mutation.

•ChemicalsChemicals

•Radiation Radiation

Mechanisms of Mutation Due to ChemicalsMechanisms of Mutation Due to ChemicalsCausingCausing Type of MutagenType of Mutagen ExampleExample ChangeChange

SubstitutionsSubstitutions Base analogsBase analogs(incorporated into DNA (incorporated into DNA due to structural due to structural similarities)similarities)

5-bromouracil5-bromouracil(analog of T)(analog of T)

T:AT:AC:GC:G

Mechanisms of Mutation Due to ChemicalsMechanisms of Mutation Due to Chemicals

CausingCausing Type of MutagenType of Mutagen ExampleExample ChangeChange

SubstitutionsSubstitutions Alkylating agentsAlkylating agents(cause mispairing (cause mispairing through chemical through chemical modification of bases)modification of bases)

EMSEMS(ethylmethyl- (ethylmethyl- sulfonate) sulfonate)

C:GC:GT:AT:A



SubstitutionsSubstitutions Deaminating agentsDeaminating agents(chemicals that convert (chemicals that convert cytosine to uracil)cytosine to uracil)

Nitrous AcidNitrous Acid C:GC:GT:AT:A

A:TA:TG:CG:C



SubstitutionsSubstitutions Hydroxylating agentsHydroxylating agents(adds a hydroxyl group (adds a hydroxyl group to cytosine, causing C to to cytosine, causing C to A pairing)A pairing)

HydroxylamineHydroxylamine C:GC:GT:AT:A


CausingCausing Type of ReactionType of Reaction ExampleExample ChangeChange

SubstitutionsSubstitutions Oxidative reactionOxidative reaction(oxidative changes to (oxidative changes to bases that cause bases that cause mispairing)mispairing)

Hydrogen Hydrogen peroxide or peroxide or Oxygen radicalsOxygen radicals

G:CG:CT:AT:A


CausingCausing Type of MutagenType of Mutagen ExamplesExamples

Deletions or Deletions or InsertionsInsertions

Intercalating agentsIntercalating agents(insert between adjacent (insert between adjacent DNA bases)DNA bases)

Acridine OrangeAcridine OrangeEthidium BromideEthidium Bromide

Mechanisms of Mutation Mechanisms of Mutation

Due to RadiationDue to Radiation

• Formation of Pyrimidine dimersFormation of Pyrimidine dimers– Ultraviolet radiation produces dimers from Ultraviolet radiation produces dimers from

adjacent thymines adjacent thymines (thymine-thymine dimers)(thymine-thymine dimers)

– Dimers interfere with DNA functionDimers interfere with DNA function


Which type of mutation is caused by Which type of mutation is caused by A. intercalating agents like acridine A. intercalating agents like acridine

orange?orange?B. ultraviolet light? B. ultraviolet light? C. alkylating agents like EMS?C. alkylating agents like EMS?

1.1. SubstitutionSubstitution2.2. Deletion or InsertionDeletion or Insertion3.3. Pyrimidine Dimer FormationPyrimidine Dimer Formation

Repair MechanismsRepair MechanismsType of RepairType of Repair Directed atDirected at

Mismatch RepairMismatch Repair

(methyl-directed in bacteria) (methyl-directed in bacteria)

Mispaired basesMispaired bases

Portion of new DNA

strand with mismatch

is removed

Mismatch is recognized along with

nearby methyl-A

DNA polymerase

restores missing

nucleotides


PhotoreactivationPhotoreactivation(Type of direct repair)(Type of direct repair)

Thymine-Thymine DimersThymine-Thymine Dimers

In Bacterial Cells

Repair MechanismsRepair Mechanisms

Type of RepairType of Repair Directed atDirected at

Direct Repair: Direct Repair: restores original restores original structurestructure

OO66-Methylguanine which pairs -Methylguanine which pairs with adeninewith adenine


Base-Excision Repair:Base-Excision Repair:

Base removed thenBase removed thenentire nucleotide replacedentire nucleotide replaced

Modified bases such as Modified bases such as uracil product of cytosine uracil product of cytosine deaminationdeamination

Removes damaged base

Cleaves backboneremoves sugar

Seals gap in backbone

Adds new nucleotide to exposed 3’-OH group

Repair MechanismsRepair Mechanisms

Type of RepairType of Repair Directed atDirected at

Nucleotide Excision Nucleotide Excision RepairRepair

Thymine-Thymine Dimers (eukaryotes) Thymine-Thymine Dimers (eukaryotes) Other large distortions in helix Other large distortions in helix

Uses of Mutants Uses of Mutants • Genetic dissection: Genetic dissection: understanding how normal biological understanding how normal biological processes work processes work

Fruit Fly mutants used to study developmental processesFruit Fly mutants used to study developmental processes

AntennapediaAntennapedia BithoraxBithorax

Uses of Mutants Uses of Mutants • Mutation breeding: Mutation breeding: selection of traits induced by a mutagenselection of traits induced by a mutagen


Which mechanismWhich mechanismA. is used to reverse Thymine-Thymine dimers in A. is used to reverse Thymine-Thymine dimers in

bacteria?bacteria?B. identifies an old DNA strand based on B. identifies an old DNA strand based on

methylation of bases? methylation of bases? C. is used to remove chemically modified bases?C. is used to remove chemically modified bases?

1.1. Mismatch RepairMismatch Repair2.2. PhotoreactivationPhotoreactivation3.3. Direct RepairDirect Repair4. Base Excision Repair4. Base Excision Repair5. Nucleotide Excision Repair5. Nucleotide Excision Repair

Gene Mutation. Classification of Mutations Can Be Made at the: DNA levelDNA level Protein...

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