Mutations and Examples

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CHAPTERCHAPTERCHAPTERCHAPTERWhat Genes Are and What They DoWhat Genes Are and What They DoPART IIIPART III

OUTLINEOUTLINE

Anatomy and Function of a Gene:

Dissection Through Mutation

3.1 Mutations: Primary Tools of Genetic Analysis3.2 What Mutations Tell Us About Gene Function3.4 Examples found in eukaryotic gene regulation lecture

Types of mutations in the coding sequence Types of mutations in the coding sequence of genesof genes

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Hartwell et al., 4th edition, Chapter 8

Fig. 8.28a

Mutations in the coding sequence of a gene Mutations in the coding sequence of a gene can alter the gene productcan alter the gene product

Missense mutations replace one amino acid with another

• Conservative – chemical properties of mutant amino acid are similar to the original amino acid

e.g. aspartic acid [(-)charged] glutamic acid [(-)charged]

• Nonconservative – chemical properties of mutant amino acid are different from original amino acid

e.g. aspartic acid [(-)charged] alanine (uncharged)

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Mutations in the coding sequence of a gene Mutations in the coding sequence of a gene can alter the gene product (cont)can alter the gene product (cont)

Nonsense mutations change codon that encodes an amino acid to a stop codon (UGA, UAG, or UAA)

Frameshift mutations result from insertion or deletion of nucleotides with the coding region

No frameshift if multiples of three are inserted or deleted

Silent mutations do not alter the amino acid sequence

Degenerate genetic code – most amino acids have >1 codon

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A nonsense mutation in a protein-coding gene A nonsense mutation in a protein-coding gene creates a truncated, nonfunctional proteincreates a truncated, nonfunctional protein



Fig 8.32a

Nonsense suppressionNonsense suppression

A second, nonsense suppressing mutation in the anticodon of a tRNA gene allows production of a (mutant) full-length polypeptide



Fig 8.32b

Mutations classified by their effect on DNAMutations classified by their effect on DNA

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Fig. 7.2a - c


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Mutations classified by their effect on DNA Mutations classified by their effect on DNA (cont)(cont)

Fig. 7.2d


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Mutations classified by their effect on DNA Mutations classified by their effect on DNA (cont)(cont)

Fig. 7.2e

How natural processes can change How natural processes can change the information stored in DNAthe information stored in DNA

Depurination

• 1000/hr in every cell

Deamination of C

• C changed to U

• Normal C-G A-T after replication


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Fig. 7.6a, b

How natural processes can change the How natural processes can change the information stored in DNA (cont)information stored in DNA (cont)

X-rays break the sugar − phosphate backbone of DNA

Ultraviolet (UV) light causes adjacent thymines to form abnormal covalent bonds (thymine dimers)


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Fig. 7.6c, d

How natural processes can change the How natural processes can change the information stored in DNA (cont)information stored in DNA (cont)

Irradiation causes formation of free radicals (e.g. reactive oxygen) that can alter individual bases

• 8-oxodG mispairs with A

• Normal G-C mutant T-A after replication


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Fig. 7.6e

Mistakes during DNA replication Mistakes during DNA replication

Incorporation of incorrect bases by DNA polymerase is exceedingly rare (< 10-9 in bacteria and humans)

Two ways that replication machinery minimizes mistakes

• Proofreading function of DNA polymerase (Fig 7.7)

3'-to-5' exonuclease recognizes and excises mismatches

• Methyl-directed mismatch repair (later in this chapter)

Corrects errors in newly replicated DNA


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DNA polymerase’s proofreading functionDNA polymerase’s proofreading function

Mispaired base is recognized and excised by 3'-to-5' exonuclease of DNA polymerase

Improves fidelity of replication 100-fold


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Fig. 7.7

Rates of spontaneous mutationRates of spontaneous mutation

Rates of recessive forward mutations at five coat color genes in mice

11 mutations per gene every 106 gametes

Mutation rates in other organisms 2 – 12 mutations per gene every 106 gametes


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Fig. 7.3b

Different genes, different mutation ratesDifferent genes, different mutation rates

Mutation rates are <10-9 to >10-3 per gene per gamete

• Differences in gene size

• Susceptibility of particular genes to various mutagenic mechanisms

Average mutation rate in gamete-producing eukaryotes is higher than that of prokaryotes

• Many cell divisions take place between zygote formation and meiosis in germ cells

More chance to accumulate mutations

• Can diploid organisms tolerate more mutations than haploid organisms?

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Hartwell et al., 4th ed., Chapter 716

Unequal crossing-over can occur Unequal crossing-over can occur between homologous chromosomesbetween homologous chromosomes

Pairing between homologs during meiosis can be out of register

Unequal crossing-over results in a deletion on one homolog and a duplication on the other homolog


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Fig. 7.8a

Transposable elements (TEs) move Transposable elements (TEs) move around the genomearound the genome

TEs can "jump" into a gene and disrupt its function

Two mechanisms of TE movement (transposition)


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Fig. 7.8b

How mutagens alter DNA:How mutagens alter DNA:Chemical action of mutagenChemical action of mutagen

Replace a base: Base analogs - chemical structure almost identical to normal base


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Fig. 7.10a

How mutagens alter DNA:How mutagens alter DNA:Chemical action of mutagenChemical action of mutagen


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Alter base structure and properties: Hydroxylating agents add an –OH group

Fig. 7.10b

How mutagens alter DNA:How mutagens alter DNA:Chemical action of mutagen (cont)Chemical action of mutagen (cont)

Alter base structure and properties (cont): Alkylating agents add ethyl or methyl groups


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Fig. 7.10b

How mutagens alter DNA:How mutagens alter DNA:Chemical action of mutagen (cont)Chemical action of mutagen (cont)

Alter base structure and properties (cont): Deaminating agents remove amine (-NH2) groups


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Fig. 7.10b

How mutagens alter DNA:How mutagens alter DNA:Chemical action of mutagen (cont.)Chemical action of mutagen (cont.)

Insert between bases: Intercalating agents


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Fig. 7.10c

Mutations outside the coding sequence Mutations outside the coding sequence can disrupt gene expressioncan disrupt gene expression



Fig. 8.28b

Mutations classified by their effects Mutations classified by their effects on protein functionon protein function



Table 8.2

DNA repair mechanisms that are very accurateDNA repair mechanisms that are very accurate

Reversal of DNA base alterations

• Alkyltransferase – removes alkyl groups

• Photolyase – splits covalent bond of thymine dimers

Homology-dependent repair of damaged bases or nucleotides

• Base excision repair (Fig 7.11)

• Nucleotide excision repair (Fig 7.12)

Correction of DNA replication errors

• Methyl-directed mismatch repair (Fig 7.13)


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Base excision repair Base excision repair removes removes

damaged basesdamaged bases

Different glycosylases cleave specific damaged bases

Particularly important for removing uracil (created by cytosine deamination) from DNA


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Fig. 7.11

Nucleotide excision repair corrects Nucleotide excision repair corrects damaged nucleotidesdamaged nucleotides

UvrA – UvrB complex scans for distortions to double helix (e.g. thymine dimers)

UvrB – UvrC complex nicks the damaged DNA

4 nt to one side of damage

7 nt to the other side of damage


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Fig. 7.12

Mutations and Examples

Documents

gene productmissense

types of mutations

deletedsilent mutations

proteincoding gene

aspartic acid

trna gene

gene function3

amino acids