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WHAT CAUSES MUTATIONS?
MUPGRET
June 2006
OVERVIEW
 Causes
 Mechanisms
 Life or Progeny?
 Applications
CAUSES
• Spontaneous/Chance
• Induced
•
•
•
Physical
Chemical
Biological
SPONTANEOUS EVENTS
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
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?
MECHANISMS
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DNA Changes
 Base Changes
 Additions, Subtractions
 Insertions, Deletions, Transpositions
Chromosome and Genomic Changes
Epigenetic Changes
 Methylation
 Chromatin Structure
Allele
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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.
A Molecular View
Parents
WW
ww
F1
F2 Progeny
Ww
¼WW ¼Ww ¼wW ¼ww
1: 2 : 1 Genotype = 3: 1 Phenotype
Round vs. wrinkled
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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.
DNA

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Hereditary material.
Contains all information to make
proteins.
Linear polymer of nucleotides.
Each nucleotide has sugar,
phosphate and a base.
Four Bases

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A=Adenine
T=Thymine
C=Cytosine
G=Guanine
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:
AG C T TAG G G TAAAC C CATATA
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.
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
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!
AGCTTAGGGAAAACCCATATAGGGCCATACCCTATCGGTAAG
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
Gene Expression Pathway in Cells
GENE DNA
mRNA copy of gene
mRNA goes to cytoplasm
Focus on the Genetic Code!
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
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
CODON MEANINGS:
into the correct
•A “START PROTEIN” SIGNAL: AUG
amino acid building
•A “STOP PROTEIN” SIGNAL: UAA, UGA, UAG
blocks in the protein
•An amino acid building block of a protein
•Codons identified in the Genetic Code Table chain.
The Universal Genetic Code Table
Name of Building
Block Amino Acid:
Phe=Phenylalanine
Leu=Leucine
Ile=Isoleucine
AUG CODON:
Signal to start
making the protein.
http://anx12.bio.uci.edu/~hudel/bs99a/lecture20/lecture1_6.html
STOP
Codons:
UAA
UAG
UGA
Genetic Code is Written in 3-Letter DNA Words
-TACCTCATGATTATACA- DNA STRAND
AUGGAGUACUAAUAUGU mRNA copied from DNA
mRNA code is “read” in TANDEM CODONS
5’-AUGGAGUACUAAUAUGU mRNA
5’-AUG GAG UAC UAA UAU mRNA
Met-Glu-Tyr-STOP
N Met Glu Tyr C
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
One Gene-One Protein
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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.
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
Spelling Mistake
The DNA “word” TTC is changed to TTT
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
A Mutation is a DNA “Spelling Mistake”
Mutant Genes Encode Defective Proteins:
(1) WILDTYPE
Example: AAA GCT ACC TAT
TTT CGA TGG ATA
Phe Arg Trp Ile
PROTEIN:
WT FUNCTION
(2) MUTANT
AAA GCT ATC TAT
TTT CGA TAG ATA
Phe Arg Stop
UAG
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
Misspelled Genes: 3 Possible Outcomes
DNA
A misspelled gene
Cell may not
be able to
follow
damaged
instruction
Cell does not
make the
protein
OR
X
X
Damaged
protein is
made
Damaged
protein may or
may not be able
to function in
the cell.
OR
Spelling
error may be
harmless
Functional
protein made
by the cell
Xeroderma pigmentosa
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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.
UV damages tissue that
contains molecules that can
absorb light.
Mechanisms of UV damage
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Low penetration into tissues.
Molecular fragmentation—proteins,
enzymes, and nucleic acids contain
double bonds that can be ruptured by UV.
Free radical generation—molecules of
susceptible tissues absorb UV and eject
an electron, which is taken up by oxygen,
then termed superoxide, a free radical.
Free radicals

Are scavenged by superoxide
dismutase, vitamin C, vitamin E,
glutathione peroxidase, carotene.
Lesion mutant in maize
Mutants across organisms
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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.
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.
Mechanisms of Damage
 Penetration depends on type
(some shallow; some deep, no-tracks).
 Ionizations, electron release.
 Breakages, deletions, rearrangements.
Breakage on Purpose
 Studies of development
(cell proliferation and destiny).
 Determination of cell-specific function.
Chemical Mutagens
 Various; mixed mechanisms.
 Interference with DNA replication.
 Interference with cell proliferation.
 Experimental mutagenesis.
 Ethyl methane sulfonate
(single-base changes; “Tilling”).
 Others.
Biological Mutagens
 Transpositions (internal or external).
 Epigenetic changes (internal).
 Methylation.
 Chromatin structural changes.
Transposition on Purpose
 Semi-controllable.
 If the element is molecularly known,
genes in which it is inserted may
be cloned by “fishing”.
Epigenetic Events
 Changes “occur” in predictable
or unpredictable ways.
 Methylation is one known cause.
 Chromatin structural changes
often accompany events.
MAIZE WORKSHOP 2004
Genetics, Genomics, and Bioinformatics
March 7-11, 2004
Twenty-nine graduate students
Eleven instructors
Lecture notes and Exercises
http://shrimp1.zool.iastate.edu/workshop/