1. Deamination of Cytosine and 5- methylcytosine -------------------------------------------------------------------------------

2. Chemical Mutagens

3. Intercalating Agents EX, Ethidium bromide, acridine orange EX, Ethidium bromide, acridine orange Can induce frameshift mutations Can induce frameshift mutations

4. Uv Induced Dimers Thymine dimers and T-C dimers Thymine dimers and T-C dimers Replication problems Replication problems Interferes with the ability of the T’s to base pair to the opposite strand, and blocks DNA replication Interferes with the ability of the T’s to base pair to the opposite strand, and blocks DNA replication

5. Other Mutagens Transposable elements—”jumping genes”. Transposable elements—”jumping genes”. Major frameshift mutations Major frameshift mutations Factors in evolution Factors in evolution Mutator genes—mutations increase mutation rate. Four potent mutator genes Mutator genes—mutations increase mutation rate. Four potent mutator genes Mutant DNA pol III 3’  5’ exonuclease activity Mutant DNA pol III 3’  5’ exonuclease activity Mutant methylation enzymes(ex dam) Mutant methylation enzymes(ex dam) Mutant enzymes in excision repair system Mutant enzymes in excision repair system Mutant enzymes in SOS system Mutant enzymes in SOS system

6. Reversions Mutations in an mutant can restore the wild type function (reversion, back mutation, or reverse mutation) Mutations in an mutant can restore the wild type function (reversion, back mutation, or reverse mutation) Spontaneous or induced Spontaneous or induced If mutation occurs at the site of the original=True reversion If mutation occurs at the site of the original=True reversion Wild type restored by mutation at another site= second site mutation Wild type restored by mutation at another site= second site mutation Second site in same gene= intragenic suppression Second site in same gene= intragenic suppression Second site in another gene=intergenic suppression Second site in another gene=intergenic suppression

7. Intragenic Revertant Types Types Same site reversion Same site reversion Second site revertant Second site revertant NOTE: shape of R-groups can also be a factor. EX  NOTE: shape of R-groups can also be a factor. EX 

8. Reversion of Frameshift Mutations For reversion to be successful For reversion to be successful Reversion must be near original site to reduce # of aa altered Reversion must be near original site to reduce # of aa altered Section of polypeptide must be able to withstand alteration without eliminating function Section of polypeptide must be able to withstand alteration without eliminating function

9. Intergenic Suppression Refers to a chnge in another gene which suppresses or eliminates the mutant phenotype. EX Refers to a chnge in another gene which suppresses or eliminates the mutant phenotype. EX Multisubunit proteins—Mutation in one subunit may be masked by mutation in another subunit (ex. restoring hydrophobic patches) Multisubunit proteins—Mutation in one subunit may be masked by mutation in another subunit (ex. restoring hydrophobic patches) Suppression via suppressor tRNAs Suppression via suppressor tRNAs

10. Suppressor tRNA Nonsense mutation- aa codon  “Stop” Nonsense mutation- aa codon  “Stop” Ex. AAG  UAG Ex. AAG  UAG Some bacteria can “read through” these mutations (though protein function may be altered). HOW? Some bacteria can “read through” these mutations (though protein function may be altered). HOW? Mutant tRNA that has an anticodon that recognizes “Stop” as a reading codon. Mutant tRNA that has an anticodon that recognizes “Stop” as a reading codon.  aa encoded depends on which tRNA is mutated  aa encoded depends on which tRNA is mutated Not every suppressor restores normal function Not every suppressor restores normal function

11. Suppressor Mutants (cont’d) EX. UUG (Leu)  UAG (Stop) (AUC anticodon) EX. UUG (Leu)  UAG (Stop) (AUC anticodon) A mutation in a tRNA resulting in “AUC” allows that tRNA to recognize “Stop”. A mutation in a tRNA resulting in “AUC” allows that tRNA to recognize “Stop”.  Can get suppression or partial suppression  Can get suppression or partial suppression NOTE: must be 2 copies of tRNA mutated. Why? NOTE: must be 2 copies of tRNA mutated. Why?  In any cell containing mutator, must also be a wild type  In any cell containing mutator, must also be a wild type Suppressors allow survival, even if sub- optimal Suppressors allow survival, even if sub- optimal

12. Termination of Translation in Suppressor Strains Problem: Must be a means of terminating translation. Problem: Must be a means of terminating translation. HOW? HOW? Release factors still present, will compete for the “Stop “ site Release factors still present, will compete for the “Stop “ site Many genes are double-terminated Many genes are double-terminated EX. UAG-UAA EX. UAG-UAA

13. Photolyase Fig. 20.39 Fig. 20.40 O6-methylguanine methyl transferase Repair by Direct Reversal

14. Excision Repair Most common repair mechanism Most common repair mechanism EX. Uvr system EX. Uvr system NOTE: preferentially repairs dimers in essential regions of genome NOTE: preferentially repairs dimers in essential regions of genome UvRA recognizes damage and binds w/UvrB UvRA recognizes damage and binds w/UvrB UvRA released, UvrC binds UvRA released, UvrC binds UvrC nicks on both sides of damageUvrD unwinds region UvrC nicks on both sides of damageUvrD unwinds region Damaged strand released Damaged strand released DAN pol I DAN pol I Ligase Ligase

15. Recombinational Repair Sister Strand Exchange Sister Strand Exchange

16. Recombinational Repair, aka, Sister Strand Exchange

17. SOS Response Is an inducible system of last resort Is an inducible system of last resort Also called error prone replication because it inactivates the proofreading function of DNA pol III. Also called error prone replication because it inactivates the proofreading function of DNA pol III. Turned on only when DNA damage is extreme Turned on only when DNA damage is extreme Main players: recA and lexA and a battery of inducible enzymes Main players: recA and lexA and a battery of inducible enzymes

18. SOS Response