Gene Mutation

Classification of Mutations Can Be Made at the: DNA levelDNA level Protein levelProtein level Cellular levelCellular level Organismal levelOrganismal level

Mutation at the DNA Level Change from one allele to a different allele Forward mutation Forward mutation Wild type  mutant Wild type  mutant Reverse mutation Mutant  wild type Mutant  wild type

Quantifying Mutation Mutation rate = number of mutations per unit time per unit time 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 by location.

Mutation at the DNA Level Spontaneous mutationSpontaneous mutation Results from natural processes Induced mutationInduced mutation Results from exposure to environmental chemicals or radiation

Mutation at the Cellular Level Somatic MutationSomatic Mutation –arises in body cells that will not give rise to gametes (not passed to offspring) –can lead to mutant cell population –mutation of proto-oncogenes leads to cancer development Germ-Line MutationGerm-Line Mutation –arises in cells giving rise to gametes –can be passed on to offspring

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

Characteristics of Mutations at the DNA Level Type of Mutation Examples Transition Purine  purine Pyrimidine  pyrimidine AT  GC TA  CG GC  AT CG  TA Transversion Purine  pyrimidine Pyrimidine  purine AT  CG AT  TA GC  TA GC  CG TA  GC TA  AT CG  AT CG  GC Base substitutions: change of one nucleotide into anotherBase substitutions: change of one nucleotide into another

Mutations at the DNA Level Lead to Changes in Protein Composition -A-A-G--T-T-C-lysine Transition-A-G-G--T-C-C-arginine -A-A-G--T-T-C-lysine Transversion-A-C-G--T-G-C-threonine

Characteristics of Mutations at the DNA Level Insertions and DeletionsInsertions and Deletions –addition or removal of one or more nucleotide pairs –cause frameshift mutations –changes in multiples of three cause in-frame deletions or insertions

Characteristics of Mutations at the DNA Level Expanding Trinucleotide RepeatsExpanding Trinucleotide Repeats –may arise as a result of formation of hairpin structures during DNA replication –could also be due to unequal crossing over when repeated regions do not align properly

Effects of Mutations at the Protein Level Silent AGG  CGG Arg Arg Substitution of a Nucleotide Synonymous (Neutral) AAA  AGA Lys Arg Missense AAA  GAA Lys Glu Nonsense CAG  UAG Gln Stop Deletion or Insertion of Nucleotide(s)FrameshiftAA(A)GACUUACCAA Lys-asp-leu-pro  Lys-thr-tyr-gln

Classification of Mutations Based on Protein Function Recessive mutationsRecessive mutations –Loss of function Example: Mutant Tumor Suppressor GenesExample: Mutant Tumor Suppressor Genes Dominant mutationsDominant mutations –Gain of function Example: OncogenesExample: Oncogenes

Applying Your Knowledge Which type of mutation A. can be passed on to offspring? B. represents a loss of protein function? C. involves a pyrimidine being substituted for a purine? 1.Transversion 2.Germ-line mutation 3.Recessive mutation 4.Transition 5.Somatic mutation

Spontaneous Mechanisms of Mutation: Replication Errors Nonstandard base pairings due to flexibility in DNA structure  substitutionsNonstandard base pairings due to flexibility in DNA structure  substitutions

Spontaneous Mechanisms of Mutation: Replication Errors Strand slippage due to looping of one nucleotide strand during replication  insertions or deletionsStrand slippage due to looping of one nucleotide strand during replication  insertions or deletions

Spontaneous Mechanisms of Mutation: Replication Errors Unequal crossing over  insertions or deletionsUnequal crossing over  insertions or deletions

Spontaneous Mechanisms of Mutation: Spontaneous Chemical Changes DepurinationDepurination –Hydrolysis of purine base from the sugar-phosphate backbone

Spontaneous Mechanisms of Mutation: Spontaneous Chemical Changes DepurinationDepurination –Random base inserted opposite the apurinic site during replication can lead to mutation -G-G-C--C-C-G- -G- -C- -C-C-G- -G-G-C--C-C-G- Wild type codes for glycine -G-T-C--C-A-G- Mutant codes for valine -G- -C- -C-A-G-

Spontaneous Mechanisms of Mutation: Spontaneous Chemical Changes Deamination of cytosineDeamination of cytosine –Converts cytosine to uracil

Spontaneous Mechanisms of Mutation: Spontaneous Chemical Changes Deamination of cytosineDeamination of cytosine –DNA replication causes G-C  A-T change -C-G-C--G-C-G- -C-A-C--G-U-G- -C-G-C- -G-C-G- Wild type codes for arginine -C-A-C- -- -G-T-G- -C-A-C--G-U-G- Mutant codes for histidine Is this a 1. transition or 2. transversion? -C-G-C--G-U-G-

Inducing Mutations Mutagens are environmental agents that increase the rate of mutation. ChemicalsChemicals RadiationRadiation

Mechanisms of Mutation Due to Chemicals Causing Type of Mutagen ExampleChange Substitutions Base analogs (incorporated into DNA due to structural similarities) 5-bromouracil (analog of T) T:A  C:G

Mechanisms of Mutation Due to Chemicals Causing Type of Mutagen ExampleChange Substitutions Alkylating agents (cause mispairing through chemical modification of bases) EMS (ethylmethyl- sulfonate) C:G  T:A

Mechanisms of Mutation Due to Chemicals Causing Type of Mutagen ExampleChange Substitutions Deaminating agents (chemicals that convert cytosine to uracil) Nitrous Acid C:G  T:A A:T  G:C

Mechanisms of Mutation Due to Chemicals Causing Type of Mutagen ExampleChange Substitutions Hydroxylating agents (adds a hydroxyl group to cytosine, causing C to A pairing) Hydroxylamine C:G  T:A

Mechanisms of Mutation Due to Chemicals Causing Type of Reaction ExampleChange Substitutions Oxidative reaction (oxidative changes to bases that cause mispairing) Hydrogen peroxide or Oxygen radicals G:C  T:A

Mechanisms of Mutation Due to Chemicals Causing Type of Mutagen Examples Deletions or Insertions Intercalating agents (insert between adjacent DNA bases) Acridine Orange Ethidium Bromide

Mechanisms of Mutation Due to Radiation Formation of Pyrimidine dimersFormation of Pyrimidine dimers –Ultraviolet radiation produces dimers from adjacent thymines (thymine-thymine dimers) –Dimers interfere with DNA function

Applying Your Knowledge Which type of mutation is caused by A. intercalating agents like acridine orange? B. ultraviolet light? C. alkylating agents like EMS? 1.Substitution 2.Deletion or Insertion 3.Pyrimidine Dimer Formation

Repair Mechanisms Type of Repair Directed at Mismatch Repair (methyl-directed in bacteria) Mispaired bases Portion of new DNA strand with mismatch is removed Mismatch is recognized along with nearby methyl-A DNA polymerase restores missing nucleotides

Repair Mechanisms Type of Repair Directed at Photoreactivation (Type of direct repair) Thymine-Thymine Dimers In Bacterial Cells

Repair Mechanisms Type of Repair Directed at Direct Repair: restores original structure O 6 -Methylguanine which pairs with adenine

Repair Mechanisms Type of Repair Directed at Base-Excision Repair: Base removed then entire nucleotide replaced Modified bases such as uracil product of cytosine deamination Removes damaged base Cleaves backbone removes sugar Seals gap in backbone Adds new nucleotide to exposed 3’-OH group

Repair Mechanisms Type of Repair Directed at Nucleotide Excision Repair Thymine-Thymine Dimers (eukaryotes) Other large distortions in helix

Uses of Mutants Genetic dissection: Genetic dissection: understanding how normal biological processes work understanding how normal biological processes work Fruit Fly mutants used to study developmental processes AntennapediaBithorax

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

Applying Your Knowledge Which mechanism A. is used to reverse Thymine-Thymine dimers in bacteria? B. identifies an old DNA strand based on methylation of bases? C. is used to remove chemically modified bases? 1.Mismatch Repair 2.Photoreactivation 3.Direct Repair 4. Base Excision Repair 5. Nucleotide Excision Repair