Molecular Basis of Gene Mutation
In Principle:
    Mutations are changes in the DNA sequences

        mutations in DNA cause substitutions in protein
           Proteins do not mutate!

        spontaneous - 'naturally' occurring through alteration of base pairing
              versus induced - chemical or high-energy radiation mutagenesis
        germline - affecting tissues that produces eggs & sperm
                             heritable meiotically between generations (genetic)
               versus somatic  - affecting other body tissues (multiplies mitotically, e.g. cancer)
                            non-heritable (but gene-based)                            


Molecular mechanisms of DNA mutagenesis

 Nucleotide interchanges are of two types
        transitions   - alternative pyrimidines [ CT ]  or purines [ AG ]
        transversionspurine  pyrimidine [C / T A / G]
        Most mutations are transitions: interchanges of bases of same shape

Spontaneous mutation
       tautomeric shift - spontaneous, transient rearrangement to alternative form [IG1 16.07]
               keto (standard)  enol  (rare) forms of G & T
               amino (standard)  imino (rare) forms of A & C

       Non-standard bases have altered pairing rules :
               modified purine pairs with "wrong" pyrimidine
               modified pyrimidine pairs with "wrong" purine

        T' (enol)     pairs with G (keto)
        C' (imino)  pairs with A (amino)
        G' (enol)    pairs with T (keto)
        A' (imino)  pairs with C (amino)

        A tautomeric shift produces a transition mutation in the complementary strand [see example] [cf IG1 16.12]:

Homework: Based on this diagram, show that tautomeric shifts of the C, G, & T bases also produce transition mutations


Induced mutation - chemical modification of DNA alters base pairing [IG1 16.11, Table16.01]

    alkylation - addition of alkyl group (methyl CH3- or ethyl CH3-CH2-)
          ethyl methane sulfonate (EMS) is a common laboratory mutagen
       6-ethyl G , pairs with T

     deamination - conversion of amino  keto group [IG1 16.13]
           nitrous acid (HNO2) is a common food additive / preservative
       U by loss of NH2, pairs with A
       A hypoxanthine by loss of NH2, pairs with C

     depurination - loss of purine (A or G) base in intact nucleotide
            produces an apurinic  site
                       a common form of damage in 'ancient' DNA
  [IG1 16.16]
            replacement of base may produce transversion
            apyrimidinic sites are similar: loss of C or T

     intercalation - base analogue "wedged" into DNA helix [IG1 16.14]
            acridine dyes resemble 3-ring base pair
            intercalated analogue read as 'extra' base:
           DNAPol "stutters frameshift mutations
                     ethidium bromide is a fluorescent intercalating dye of DNA

    ionizing radiation:  radiochemical damage to DNA    

          Direct effects: formation of thymine dimers  (T^T) [IG1 16.15]
            covalent linkage of adjacent T bases: causes errors in replication

               UV irradiation can cause skin cancer
               photoreactivation or excision repair damage
[IG1 16.19]
                   xeroderma pigmentosum
(OMIM 278700) caused by faulty excision repair

         Indirect effects: oxidative damage within cells
             Radiolysis of H20 produces free radicals:
                H2O   H + OH               [hydroxy radical]
                HO + OH  H2O2           [hydrogen peroxide]
                HOOH  HO2-      [superoxide radical]
           oxidation of bases modifies pairing rules
               8-oxo-7-hydro-deoxyguanosine (GO)
               dG  GO  by oxidation, pairs with   transversion

      Chromosome damage
          double - strand breaks :
                 non-homologue "sticky ends" join end-to-end to form dicentric chromosomes
               226Raradium ingestion by watch dial painters
               cross - linking - different DNA molecules covalently joined
                                       H-bonds converted to covalent bonds


Trinucleotide repeat variation common in human genetic disorders [IG1 20.Tab3]
 
          Slipped-mismatch pairing provides a mechanism

     Huntington Disease  (OMIM citation 143100)
            Neuro-muscular degeneration, 'choreic' movements, typically with late onset

            Huntingtin [sic] (HTT) locus has (CAG)n repeat near 5' end [4p16.3]
                 # copies in affected individuals inversely correlated with severity & age of onset
                        9 ~ 36      unaffected,
                      36 ~ 41     incomplete penetrance
                            >41      adult onset
                            >50      juvenile onset

            huntingtin protein with poly-glutamine (gln)n repeat has been isolated  [IG1 16.10]
                 autosomal dominant inheritance:
                      phenotype is a consequence of presence of modified protein:
                      HD alleles 'dominate' standard alleles

         A genetic counseling ethical dilemma:
              Tiresias' Dilemma: 'It is but sorrow to be wise when wisdom profits not.'

    Fragile-X Syndrome [Martin-Bell Syndrome] (OMIM citation 300624)
            Most common form of inherited predisposition to mental retardation
            (CGG)n repeat occurs upstream from 5' end of FMR-1 gene [Xq28]
                      6 ~   54     unaffected,
                    55 ~ 200    X-linked female carriers, unaffected
                         > 200     affected sons

          X-linked inheritance
                Asymptomatic, hemizygous fathers pass "fragile X" chromosome to daughters
                Heterozygous daughters transmit to 1/2 of sons, who show syndrome &
                                                                              1/2 of daughters are carriers
                     Syndrome becomes more pronounced in successive generations
                     expansion of repeat occurs in female germline
                          Slipped-mismatch provides a hypothesis



Advanced Topics in Molecular Mutagenesis [not on 2250 exam]

Transposable elements - "Jumping Genes"

    The genome is not static: genes move between chromosomes

       Barbara McClintock identified phenomenon in maize in 1930s~40s: Nobel Prize 1983

                    [Keller: "A Feeling for the Organism"]

Suppressor mutations - "Two wrongs make a right" [IG1 16.36]
      mutation in tRNA gene compensates for mutation in coding genes
        mutated anticodon reads nonsense codon as miss-sense:
            phenotypic consequences of genotypic mutation are 'suppressed'

Radiation Genetics & Health Physics -
        an extended discussion of mutation by high-energy ionizing radiation



Optional Homework  See the movies "Blade Runner" and "The World is Not Enough"
       Does Dr Tyrell's discussion of  EMS & Repressor Mutations makes sense? Explain.
       Does Dr Jones' discussion of radiation safety make sense? Explain.


All text material 2013 by Steven M. Carr