WHAT CAUSES MUTATIONS?

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WHAT CAUSES MUTATIONS?

• MUPGRET
• June 2006

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OVERVIEW

• Causes
• Mechanisms
• Life or Progeny?
• Applications

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CAUSES

• Spontaneous/Chance
• Induced
• Physical
• Chemical
• Biological

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SPONTANEOUS EVENTS
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INDUCED MUTATION

• Physical Radiation
• Ultraviolet light
• Ionizing X-rays, Gamma rays
• Chemical
• Environmental agents
• Exposures at work and play
• Ethyl methane sulfonate, etc.
• Biological
• Transposable elements
• Epigenetic changes

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LIFE OR PROGENY?

• What organ(s) are affected?
• (skin, flesh, bone, liver, gonads, gametes)
• By which agents?
• How much is too much?
• (organ vs. tissue vs. cell)
• Are there protective measures?
• Are there correctives?
• Are there cures?
• What probability applies? To whom?

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MECHANISMS

• DNA Changes
• Base Changes
• Additions, Subtractions
• Insertions, Deletions, Transpositions
• Chromosome and Genomic Changes
• Epigenetic Changes
• Methylation
• Chromatin Structure

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Allele

• One of two to many alternative forms of the same
  gene (eg., round allele vs. wrinkled allele).
• Alleles have different DNA sequences that cause
  the different appearances we see.

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A Molecular View
Parents
F1
F2 Progeny
WW ww Ww ¼WW ¼Ww ¼wW ¼ww
1 2 1 Genotype 3 1 Phenotype
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Round vs. wrinkled

• The starch-branching enzyme (SBEI) defines the
  round vs. wrinkled phenotype.
• Wrinkled peas result from absence of the branched
  form of starch called amylopectin.
• Dried round peas with amylopectin shrink
  uniformly, and wrinkled do not.

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DNA

• Hereditary material.
• Contains all information to make proteins.
• Linear polymer of nucleotides.
• Each nucleotide has sugar, phosphate and a base.

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Four Bases

• AAdenine
• TThymine
• CCytosine
• GGuanine

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How Does DNA Carry Information?

• To answer this question we must take a closer
  look at DNA.
• DNA is a biopolymer
• Polymers are molecules made of repeating units or
  building blocks
• DNA has four chemical building blocks symbolized
  by the letters A,G,C, T
• The letters of your DNA are in a specific order
  that carries information about you!!
• So, a DNA polymer can be represented as a string
  of letters

A G C T T A G G G T A A A C C C A T A T A
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DNA Carries Information in the Sequence of DNA
Letters
. . .A G C T T A G G G T A A A C C C A T A G . . .
A gene

• A gene is a length of DNA letters that contain
• an instruction for a cell to follow.
• The cell uses specially designed protein
  machines
• to read the information in genes.

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The Order of DNA Letters Encodes the Genetic
Information
The order or sequence of the A, G, C and T
letters in the DNA polymer encodes the actual
genetic information

• Example of the DNA letters in a gene
• AGCTTAGGGTAAACCATATAGGGCCATACCCTATCGGTAAGCTT
• AGCTTAGGGAAAACCCATATAGGGCCATACCCTATCGGTAAG

• The specific order of the DNA letters carries
• the information.
• Changing the order of the DNA letters will
  change the information carried by the gene.
• We will talk about how this happens later!

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Genes Contain Instructions for Building Proteins

• Genes contain instructions for making proteins,
  one of the major types of the molecules of life,
  or biomolecules
• Proteins, like DNA, are polymers
• Protein building blocks are called amino acids
• Amino acids are strung together into long, linear
  polymers by following the instructions in genes
• In general, a gene encodes the instructions for
  one protein
• When a gene is misspelled, the protein made
  from it
• may be made with an incorrect amino acid
• may not work properly

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Gene Expression Pathway in Cells
GENE DNA mRNA copy of gene mRNA goes to
cytoplasm Ribosomes translate genetic
information encoded in the mRNA into protein
building blocks (chains of amino acids) Protein
folds into 3D active structure Protein
functions in cell
Focus on the Genetic Code!
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Genetic Code is Written in 3-Letter DNA Words
(Codons)
-TACCTCATGATTATACA- DNA(DNA strands separated)
-AUGGAGUACUAAUAUGU mRNA (copied from
DNA) 5-AUGGAGUACUAAUAUGU mRNA 5-AUG GAG UAC
UAA UAU mRNA
mRNA code read by ribosome in TANDEM triplets
called codons. Codon adaptors convert RNA
letters into the correct amino acid building
blocks in the protein chain.

• CODON MEANINGS
• A START PROTEIN SIGNAL AUG
• A STOP PROTEIN SIGNAL UAA, UGA, UAG
• An amino acid building block of a protein
• Codons identified in the Genetic Code Table

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The Universal Genetic Code Table
STOP Codons UAA UAG UGA
Name of Building Block Amino Acid
PhePhenylalanine LeuLeucine IleIsoleucine
AUG CODON Signal to start making the protein.
http//anx12.bio.uci.edu/hudel/bs99a/lecture20/le
cture1_6.html
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Genetic Code is Written in 3-Letter DNA Words
-TACCTCATGATTATACA- DNA STRAND
AUGGAGUACUAAUAUGU mRNA copied from
DNA 5-AUGGAGUACUAAUAUGU mRNA 5-AUG GAG UAC
UAA UAU mRNA Met-Glu-Tyr-STOP
mRNA code is read in TANDEM CODONS
A SHORT PROTEIN IS A PEPTIDE

• CODON MEANINGS
• START PROTEIN HERE AUG (START) Methionine
  (Met)
• STOP PROTEIN HERE UAA, UGA, UAG
• Amino acid building blocks N-Met-Glu-Tyr-C
• Codons are identified in the Genetic Code Table

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One Gene-One Protein

• Archibald Garrod (1902) described alkaptonuria, a
  hereditary disorder, as an inborn error of
  metabolism.
• Proposed that mutations cause specific
  biochemical defects.
• Alkaptonuria defect is dark urine.

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A DNA Spelling Mistake Can Alter the Protein Chain
START
ADD
ADD
ADD
ADD
ADD
ADD
ADD
STOP
ATG TTC AGG CCA AAT TTT GTC GCG UAA GGA ATT
ATG TTT AGG CCA AAT TTT GTC GCG
TTC to TTT spelling change causes a different
protein building block to be inserted in the
second position. That is all it takes.
ADD Codon specifies the amino acid specified by
3-letter word ATG/AUG Codon specifies start
and methionine (met) UAA STOP adding amino
acids to protein chain
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A Mutation is a DNA Spelling Mistake

• Mutant Genes Encode Defective Proteins
• (1) WILDTYPE
  (2) MUTANT
• Example AAA GCT ACC TAT AAA
  GCT ATC TAT
• TTT CGA TGG
  ATA TTT CGA TAG ATA
• Phe Arg Trp
  Ile Phe Arg Stop
• 
  UAG
• PROTEIN WT FUNCTION
  NO FUNCTION
• (1) Normal DNA and amino acid sequence makes a
  wild-type protein.
• (2) Mutation in DNA changes Trp to Stop to make a
  short, mutant protein.
• Mutations in DNA can be Caused by
• Mistakes made when the DNA is replicated (wrong
  base inserted)
• Ultra violet (UV) light and ionizing radiation
  (X-rays) damage DNA
• Environmental chemical carcinogens can damage DNA
• Other factors

DNA Technology The Awesome Skill, I E Alcamo,
Harcourt Academic Press, 2001
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Misspelled Genes 3 Possible Outcomes
DNA
A misspelled gene
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Xeroderma pigmentosa

• Autosomal recessive.
• UV exposure damages DNA.
• Defect in DNA damage repair.
• Risks include cancer, telangiectasia,
  disfigurement.
• Can be diagnosed before birth.
• Take total protection measures from
  sun/fluorescent light.

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UV damages tissue that contains molecules that
can absorb light.
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Mechanisms of UV damage

• Low penetration into tissues.
• Molecular fragmentationproteins, enzymes, and
  nucleic acids contain double bonds that can be
  ruptured by UV.
• Free radical generationmolecules of susceptible
  tissues absorb UV and eject an electron, which is
  taken up by oxygen, then termed superoxide, a
  free radical.

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Free radicals

• Are scavenged by superoxide dismutase, vitamin C,
  vitamin E, glutathione peroxidase, carotene.

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Lesion mutant in maize
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Mutants across organisms

• Sometimes mutations in the same gene in different
  organisms have similar phenotype.
• This allows researchers to choose the organism
  with the best genetic resources to study the
  normal function of that gene.
• This also allows researchers to identify
  prospective genes for a phenotype in one species,
  based on another.

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Ionizing Radiation

• Naturally occurring at low rate
• (cosmic rays radium).
• Deliberate or Accidental releases.
• Isotopes decay at differing rates.
• Elective exposures.
• Health tests.
• Treatments.
• Occupational.

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Mechanisms of Damage

• Penetration depends on type
• (some shallow some deep, no-tracks).
• Ionizations, electron release.
• Breakages, deletions, rearrangements.

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Breakage on Purpose

• Studies of development
• (cell proliferation and destiny).
• Determination of cell-specific function.

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Chemical Mutagens

• Various mixed mechanisms.
• Interference with DNA replication.
• Interference with cell proliferation.
• Experimental mutagenesis.
• Ethyl methane sulfonate
• (single-base changes Tilling).
• Others.

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Biological Mutagens

• Transpositions (internal or external).
• Epigenetic changes (internal).
• Methylation.
• Chromatin structural changes.

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Transposition on Purpose

• Semi-controllable.
• If the element is molecularly known,
• genes in which it is inserted may
• be cloned by fishing.

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Epigenetic Events

• Changes occur in predictable
• or unpredictable ways.
• Methylation is one known cause.
• Chromatin structural changes
• often accompany events.

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MAIZE WORKSHOP 2004
Genetics, Genomics, and Bioinformatics March
7-11, 2004 Twenty-nine graduate students Eleven
instructors Lecture notes and Exercises http//sh
rimp1.zool.iastate.edu/workshop/