Concepts of Genetics Eighth Edition Klug, Cummings, Spencer

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Concepts of GeneticsEighth EditionKlug,
Cummings, Spencer

• Chapter 15
• Gene Mutation, DNA Repair, and Transposition

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Mutations

• 15.1 Mutations classified in various ways
• Mutation defined as an alteration in DNA
  sequence.
• Consist of single bp substitution, deletion or
  insertion of one or more bp, or major alteration
  in structure of chromosome.
• Extent of changes to characteristics of organism
  depends upon where mutation occurs and degree of
  alteration of gene.
• Occurs in somatic cells (localized cell death,
  altered cellular function or tumours) or germ
  cells (heritable, basis for genetic diversity,
  evolution genetic diseases).

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Mutations

• 15.1.1 Spontaneous, induced and adaptive
• Spontaneous
• Naturally random.
• Linked to normal biological or chemical processes
  in organism.
• Occurs often during DNA replication.
• Induced
• Result from influence of extraneous factor.
• Either natural (UV radiation from sun) or
  artificial (radiation from mineral sources).
• Adaptive
• Organisms may select or direct nature of gene
  mutation to adapt to certain environmental
  pressure.

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Mutations

• Luria-Delbrück fluctuation test (Table 15.1).
• Adaptive mutation
• Little fluctuation in no. of resistant cells in
  same culture.
• Spontaneous
• Great fluctuation occurs in different culture.
• Mutations random.
• Absence of selection.

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Mutations

• 15.1.2 Classification based on location
• Somatic mutations occur in any cell except germ
  cells ? not heritable.
• Germ-line mutations occur in gametes ? inherited.
• Autosomal mutations occur within genes located on
  autosomes.
• X-linked mutations occur within genes located on
  X chromosome.
• Recessive autosomal mutation in somatic cell of
  diploid organism ? unlikely to result in
  detectable phenotype ? masked by wild-type
  allele.

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Mutations

• Inherited dominant autosomal mutations expressed
  phenotypically in first generation.
• X-linked recessive mutations in gametes of
  homogametic (XX) female expressed in hemizygous
  (XY) male offspring provided that male offspring
  receives affected X chromosome.
• Haploinsufficiency ? recessive mutation result in
  visible phenotype when in heterozygous or
  hemizygous state ? wild-type cannot suppress
  expression of mutation ? cause of some human
  diseases.

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Mutations

• 15.1.3 Classification based on type of
  molecular change
• Point mutations ? base substitutions in which one
  bp is altered (Figure 15.1).
• Missense mutations ? change codon (triplet of
  nucleotides) within protein-coding portion of
  gene.
• Nonsense mutation ? changes codon into stop
  codon, resulting in premature termination of
  translation.
• Silent mutation ? alters codon but doesnt result
  in change in amino acid at that position in
  protein (due to degeneracy of genetic code).

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Mutations

• Transition ? if pyrimidine (cytosine, thymine,
  uracil) replaces pyrimidine or purine (adenine,
  guanine) replaces purine.
• Transversion ? if purine and pyrimidine
  interchange.
• Frameshift mutation ? insertion or deletion of
  one or more nucleotides, except triplets, which
  would reestablish initial frame of reading.

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Mutations

• 15.1.4 Classification based on phenotypic effects
• Loss-of-function mutation ? eliminates function
  of gene product ? also known as null mutations or
  knockouts ? dominant or recessive.
• Gain-of-function mutation ? results in gene
  product with new function ? mostly dominant.
• Visible mutation ? affects morphological trait ?
  alter normal/wild-type phenotype.
• Nutritional/biochemical mutation ? sickle-cell
  anemia, hemophilia.
• Behavioural mutation ? affects behaviour pattern.

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Mutations

• Regulatory mutation ? affect regulation of genes.
• Lethal mutation ? interrupt essential process and
  result in death ? Tay-Sachs Huntington disease.
• Conditional mutation ? expression depends on
  environment in which organism finds itself ?
  temperature-sensitive mutations.
• 15.2 Spontaneous mutation rate varies greatly
  among organisms
• Rate of spontaneous mutation low for all
  organisms.
• Rate varies considerably between different
  organisms (Table 15.2).
• Rate varies from gene to gene, even within same
  species.

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Mutations

• 15.2.1 Deleterious mutations in humans
• Neutral mutations ? vast majority of all
  mutations ? occur in large portions of genome
  that dont contain genes ? have no effects on
  gene products.
• Recent molecular techniques indicate that rate of
  deleterious mutation in humans is high ? at least
  1.6 per individual per generation.

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Mutations

• 15.3 Spontaneous mutations arise from replication
  errors and base modifications
• Many of base modifications that occur during
  spontaneous mutagenesis also occur during induced
  mutagenesis.
• 15.3.1 DNA replication errors
• DNA polymerase occasionally inserts incorrect
  nucleotides ? generally due to mispairing.
• These types of errors predominantly lead to point
  mutations.

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Mutations

• 15.3.2 Replication slippage
• Slippage during replication can lead to small
  insertions or deletions.
• Occurs anywhere in DNA but has preference for
  regions containing repeated sequences.
• Repeat sequences ? hot-spots for DNA mutation ?
  may contribute to hereditary diseases.

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Mutations

• 15.3.3 Tautomeric shifts
• Tautomers ? bases taking alternate chemical
  forms.
• Tautomeric shifts in nucleotides can result in
  mutations due to anomalous base pairing (Figure
  15.2).
• When rare tautomer in template strand pairs with
  noncomplementary base ? mutation occurs during
  DNA replication ? resulting in point mutation
  (Figure 15.3).

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Mutations

• 15.3.4 Depurination and deamination
• DNA base damage by depurination and deamination
  is most common cause of spontaneous mutation.
• Depurination ? loss of one of nitrogenous bases
  in intact DNA double helix ? either guanine or
  adenine ? leads to creation of apurine (AP) site
  on one strand of DNA.
• Deamination ? amino group converted to keto group
  in cytosine and adenine ? cytosine converted to
  uracil and adenine to hypoxanthine ?
  spontaneously or induced by nitrous acid (Figure
  15.4).

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Mutations

• 15.4 Induced mutations arise from DNA damage
  caused by chemicals and radiation
• Mutagens ? natural or artificial agents that
  induce mutations.
• 15.4.1 Base analogs
• Base analogs can substitute for purines and
  pyrimidines during nucleic acid replication
  (Figure 15.5).
• 5-bromouracil (5-BU) behaves as thymine analog ?
  linkage to deoxyribose results in
  bromodeoxyuridine (BrdU).

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Mutations

• 15.4.2 Alkylating agents
• Alkylating agents donate alkyl group (CH3 or
  CH3CH2) to amino or keto groups in nucleotides to
  alter base-paring affinity (Figure 15.6 Table
  15.3).
• 15.4.3 Acridine dyes and frameshift mutations
• Acridine dyes cause frameshift mutations by
  intercalating (wedge) between purines and
  pyrimidines (Figure 15.7).

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Mutations

• 15.4.4 Ultraviolet light and thymine dimers
• Electromagnetic spectrum ? series of
  electromagnetic components of varying wavelength
  (Figure 15.8).
• Purines pyrimidines absorb UV radiation
  intensely at wavelength of 260 nm.
• UV radiation creates pyrimidine dimers (Figure
  15.9) ? distort DNA conformation and inhibit
  normal replication.
• 15.4.5 Ionizing radiation
• Ionizing radiation in form of X rays, gamma rays
  and cosmic rays ? mutagenic (Figure 15.10).

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Mutations

• 15.5 Genomics and gene sequencing have enhanced
  our understanding of mutations in humans
• 15.5.1 ABO blood types
• ABO blood system based on antigenic determinants
  on cells.
• IOIO individuals ? type O blood ? lack
  glycosyltransferase activity ? fail to modify H
  substance to produce A or B antigen.
• IO allele has single base deletion ? results in
  frameshift mutation and truncated protein.

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Mutations

• 15.5.2 Muscular dystrophy
• Characterized by progressive muscle weakness and
  degeneration ? results from mutation in gene
  encoding dystrophin.
• Two related forms ? Duchenne MD and Becker MD ?
  recessive, X-linked.
• Duchenne MD ? more severe ? result from
  frameshift mutation in dystrophin gene, leading
  to nonfunctional truncated protein ? involves
  heart and lungs ? males lose ability to walk by
  age of 12 and may die in their early 20s ?
  females rarely affected.

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Mutations

• Becker MD ? less severe ? due to alteration of
  protein sequence ? doesnt involve heart and
  lungs ? progresses slowly, from adolescence to
  age of 50 or more.
• 15.5.3 Fragile X syndrome, myotonic dystrophy,
  Huntington disease, spinobulbar muscular
  atrophy
• Genes responsible contain specific trinucleotide
  DNA sequence repeated several times (Table 15.4).

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Mutations

• In several cases, correlation exists between
  number of repeats and age of manifestation of
  mutant phenotypes.
• Greater number of repeats ? earlier disease
  onset.
• In affected individuals ? number of repeats may
  increase in each subsequent generation ?
  phenomenon known as genetic anticipation.
• Fragile X syndrome ? carriers have 54-230 copies
  ? normal but offspring may express syndrome.

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Mutations

• Myotonic dystrophy ? common form of adult MD ?
  atrophy weakness of muscles in face and
  extremities ? cataracts, reduced cognitive
  ability, skin intestinal tumours ? affected
  gene on long arm of chromosome 9.
• Huntington disease ? fatal neurodegenerative
  disease ? inherited as autosomal dominant ?
  affected gene on chromosome 4.
• Spinobulbar muscular atrophy ? Kennedy disease ?
  gene also on chromosome 4.

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Mutations

• 15.6 Genetic techniques, cell cultures and
  pedigree analysis are all used to detect
  mutations
• 15.6.1 Detection in bacteria and fungi
• Nutritional mutations in Neurospora crassa
  detected by growth on complete medium or
  supplemental minimal medium versus no growth on
  minimal medium.
• Prototrophs grow on minimal medium.
• Auxotrophs require specific supplement to minimal
  medium.

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Mutations

• 15.6.2 Detection in plants
• Many genetic mutations in plants detected by
  direct visual observation, by determining plants
  biochemical composition or involves culturing of
  plant cell lines in defined medium.
• 15.6.3 Detection in humans
• Pedigree analysis is used to determine mutational
  basis for human characteristic or disorder
  (Figure 15.11 15.12) ? other methods include in
  vitro culturing or sequencing of DNA and proteins.

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Mutations

• Dominant mutations ? simplest to detect ? if
  X-linked, affected fathers pass trait to all
  their daughters.
• Autosomal dominant mutation for cataracts (Figure
  15.11).
• X-linked recessive mutation for hemophilia in
  descendants of Queen Victoria (Figure 15.12).

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Mutations

• 15.7 Ames test is used to assess mutagenicity of
  compounds
• Concern about possible mutagenic properties of
  any chemical that enters body, whether through
  skin, digestive system or respiratory tract ? air
  water pollution, food preservatives
  additives, artificial sweeteners, herbicides,
  pesticides pharmaceutical products.
• Ames test ? most common test ? involves bacteria.

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Mutations

• Ames test ? involves four strains of bacterium
  Salmonella typhimurium which is sensitive to
  specific types of mutagenesis (Figure 15.13).
• Many carcinogens were shown to be strong
  mutagens.
• 15.8 Organisms use DNA repair systems to
  counteract mutations
• Repair systems counteract many forms of DNA
  damage resulting from internal and external
  agents.

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DNA repair

• 15.8.1 Proofreading and mismatch repair
• Bacterial DNA polymerase III is able to recognize
  and correct errors in replication ? called
  proofreading.
• Mismatch repair corrects errors that remain after
  proofreading ? correct DNA strand is recognized
  based on DNA methylation of parental strand.

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DNA repair

• 15.8.2 Postreplication repair and SOS repair
  system
• Postreplication repair occurs when DNA
  replication skips over lesion ? requires
  homologous recombination mediated by RecA protein
  (Figure 15.14).
• SOS repair system allows DNA synthesis to become
  error-prone ? SOS repair is mutagenic but may
  allow cell to survive DNA damage that might
  otherwise kill it.

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DNA repair

• 15.8.3 Photoreactivation repair
• Photoreactivation repair removes thymine dimers
  caused by UV light (Figure 15.15).
• Process depends on activity of protein called
  photoreactivation enzyme (PRE).
• 15.8.4 Base and nucleotide excision repair
• Excision repair involves three steps
• Removal of mutation by nuclease.
• Gap filling by DNA polymerase.
• Sealing of nick by DNA ligase.

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DNA repair

• Base excision repair (BER) involves recognition
  of erroneous base by DNA glycosylase and cutting
  of DNA backbone by endonuclease (Figure 15.16).
• Nucleotide excision repair (NER) repairs bulky
  lesions and involves uvr genes (Figure 15.17).

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DNA repair

• 15.8.5 Xeroderma pigmentosum and nucleotide
  excision repair (NER) in humans
• XP is rare recessive genetic disorder ? results
  in severe skin abnormalities may be lethal ?
  exposure to UV radiation in sunlight causes
  reactions ranging from freckling skin
  ulceration to skin cancer (Figure 15.18).
• Individuals with XP ? lost ability to undergo
  nucleotide excision repair.

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DNA repair

• 15.8.6 Double-strand break repair in eukaryotes
• DNA double-strand break (DSB) repair ? activated
  when both DNA strands are cleaved ? is
  responsible for reannealing two strands.
• Homologous recombinational repair fixes DSB by
  digesting back 5 ends of broken helix to leave
  overhanging 3 ends that interact with region of
  undamaged sister chromatid to allow DNA
  polymerase to copy undamaged DNA sequence into
  damaged strand.
• End joining repairs DSBs but doesnt require
  homologous region of DNA during repair.

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Transposition

• 15.9 Transposable elements move within genome
  and may disrupt genetic function
• Transposable elements (transposons or jumping
  genes) ? move within genome and insert
  themselves into various positions within and
  between chromosomes.
• Transposons present in genomes of all organisms
  from bacteria to humans.
• Function is unknown ? apparently useless or
  junk DNA.

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Transposition

• 15.9.1 Insertion sequences
• Insertion sequences (IS elements) move from one
  location to another ? may cause mutations.
• IS elements have transposase gene (cuts into
  chromosomal DNA) and inverted terminal repeats
  (Figure 15.19).
• 15.9.2 Bacterial transposons
• Bacterial transposons (Tn elements) consist of
  protein-encoding genes unrelated to
  transposition.
• Some Tn elements have short inverted repeats and
  transposase gene ? others flanked by two IS
  elements present in opposite orientations (Figure
  15.20).

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Transposition

• 15.9.3 Ac-Ds system in maize
• Maize has two transposable elements ? Activator
  (Ac) Dissociation (Ds) ? expressed in either
  endosperm or aleurone layers (Figure 15.23).
• Ds moves only if Ac is present, but Ac is capable
  of autonomous movement (Figure 15.22).
• 15.9.4 Copia elements in Drosophila
• Copia element in Drosophila consists of long
  direct terminal repeats (DTRs) at each end
  (Figure 15.24).
• Within each DTR is inverted terminal repeat
  (ITR).

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Transposition

• 15.9.5 P element transposons in Drosophila
• P elements in Drosophila ? transposable elements
  with high rates of transposition.
• P elements encode transposase and repressor
  protein that inhibits transposition.
• Transposase gene expressed only in germ line.
• 15.9.6 Transposable elements in humans
• Long interspersed elements (LINES) short
  interspersed elements (SINES) ? major families of
  human transposons ? together account for 34 of
  human genomic DNA.