what causes mutations? mupgret june 2006. overview causes mechanisms life or progeny? ...

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

DNA Changes Base Changes Additions, Subtractions Insertions, Deletions, Transpositions

Chromosome and Genomic Changes Epigenetic Changes

Methylation Chromatin Structure

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.

A Molecular View

Parents F1 F2 Progeny

WW ww Ww ¼WW ¼Ww ¼wW ¼ww

1: 2 : 1 Genotype = 3: 1 Phenotype

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.

DNA

Hereditary material. Contains all information to make

proteins. Linear polymer of nucleotides. Each nucleotide has sugar,

phosphate and a base.

Four Bases 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:

A G C T T A G G G T A A A C C C A T A T A

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

Example of the DNA letters in a gene:

AGCTTAGGGTAAACCATATAGGGCCATACCCTATCGGTAAGCTT

AGCTTAGGGAAAACCCATATAGGGCCATACCCTATCGGTAAG

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

The specific order of the DNA letters carriesthe information.

• Changing the order of the DNA letters will change the information carried by the gene.

• We will talk about how this happens later!

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

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!

Genetic Code is Written in 3-Letter DNA Words (Codons)

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

-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.

http://anx12.bio.uci.edu/~hudel/bs99a/lecture20/lecture1_6.html

The Universal Genetic Code Table

Name of Building Block Amino Acid: Phe=PhenylalanineLeu=LeucineIle=Isoleucine

AUG CODON: Signal to start making the protein.

STOP Codons:UAAUAGUGA

Genetic Code is Written in 3-Letter DNA Words

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

-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

Met Glu TyrN C

A SHORT PROTEIN IS A PEPTIDE

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.

A DNA Spelling Mistake Can Alter the Protein Chain

ATG TTC AGG CCA AAT TTT GTC GCG UAA GGA ATTSTART ADD ADD ADDADD ADDADD ADD STOP

TTC to TTT spelling change causes a different protein building block to be inserted in the second position. That is all it takes.

Spelling Mistake The DNA “word” TTC is changed to TTT

ATG TTT AGG CCA AAT TTT GTC GCG

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

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

A Mutation is a DNA “Spelling Mistake”

DNA Technology: The Awesome Skill, I E Alcamo, Harcourt Academic Press, 2001

Misspelled Genes: 3 Possible Outcomes

A misspelled gene

DNA

Cell may not be able to

follow damaged

instruction

Cell does not make the

protein

X

X

OR Spelling error may be harmless

Functional protein made

by the cell

OR Damaged protein is made

Damaged protein may or

may not be able to function in

the cell.

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.

UV damages tissue that contains molecules that can absorb light.

Mechanisms of UV damage

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 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 maybe cloned by “fishing”.

Changes “occur” in predictable or unpredictable ways.

Methylation is one known cause. Chromatin structural changes

often accompany events.

Epigenetic Events

Genetics, Genomics, and BioinformaticsMarch 7-11, 2004Twenty-nine graduate studentsEleven instructorsLecture notes and Exercises

http://shrimp1.zool.iastate.edu/workshop/

MAIZE WORKSHOP 2004