Gene actionGene action

Protein function, and when it Protein function, and when it all goes wrong!all goes wrong!

What do proteins do?What do proteins do?

Structural genes: produce proteins Structural genes: produce proteins that become a part of the structure that become a part of the structure and functioning of the organismand functioning of the organism

Regulatory genes: produce proteins Regulatory genes: produce proteins that switch other genes on or off, and that switch other genes on or off, and the rate at which the protein product the rate at which the protein product is being produced.is being produced.

Case study: thalassaemiaCase study: thalassaemia

Gene locus: chromosome 11Gene locus: chromosome 11 Controls production of the beta chains Controls production of the beta chains

of haemoglobinof haemoglobin About 1600bp make up geneAbout 1600bp make up gene Two possible alleles: normal beta chain Two possible alleles: normal beta chain

development and abnormaldevelopment and abnormal Abnormal beta chains means that red Abnormal beta chains means that red

blood cells do not have functional blood cells do not have functional haemoglobin… and cannot carry haemoglobin… and cannot carry oxygen!oxygen!

Differences in allelesDifferences in alleles

For the thallasaemia gene, there are For the thallasaemia gene, there are two possible alleles. The DNA code two possible alleles. The DNA code for these differ by ONLY ONE base for these differ by ONLY ONE base pair! How is it possible that this pair! How is it possible that this causes so much trouble?!causes so much trouble?!

DNA sequence differencesDNA sequence differencesTemplate DNA code -TGA-CGG-GAC-ACC-CCG-TTC-CAC-TTG-CCA … GTG-

ATTTranscription occurs…

Codon number -12 13 14 15 16 17 18 19 20 … 146 147

Codon sequence -ACU-GCC-CUG-UGG-GGC-AAG-GUG-AAC-GUG… CAC-UAA

Translation occurs…

Amino acid number -12 13 14 15 16 17 18 19 20 … 146 147Amino acid sequence -thr-ala-leu-trp-gly-lys-val-asn-val … his-STOP

NORMAL HBB (thalassaemia) GENE SEQUENCE

ABNORMAL HBB (thalassaemia) GENE SEQUENCE

Template DNA code -TGA-CGG-GAC-ACC-CCG-ATC-CAC-TTG-CCA … GTG-ATT

Transcription occurs…

Codon number -12 13 14 15 16 17 18 19 20 … 146 147

Codon sequence -ACU-GCC-CUG-UGG-GGC-TAG-GUG-AAC-GUG… CAC-UAA

Translation occurs…

Amino acid number -12 13 14 15 16 17 18 19 20 … 146 147Amino acid sequence -thr-ala-leu-trp-gly-STOP …. Uh oh!

Thalassaemia protein product Thalassaemia protein product differencesdifferences

gly lys val

Total: 147 amino acids

Total: 17 amino acids

gly STOP

NORMAL

ABNORMAL

Because of ONE change in the DNA sequence, the polypeptide has been shortened by 130 amino acids!!

MutationsMutations

Changes in the DNA, mRNA or Changes in the DNA, mRNA or resulting polypeptide is called a resulting polypeptide is called a MUTATION.MUTATION.

These mutations are generally only These mutations are generally only significant if they occur during DNA significant if they occur during DNA replication in MEIOSIS (why?)replication in MEIOSIS (why?)

These new DNA sequences that have These new DNA sequences that have arisen are different ALLELES of the arisen are different ALLELES of the genegene

Types of mutationTypes of mutation

Base SUBSTITUTION (a base, or Base SUBSTITUTION (a base, or sequence of bases, is SUBSTITUTED sequence of bases, is SUBSTITUTED for a different base)for a different base)

Base ADDITIONS or INSERTIONS (a Base ADDITIONS or INSERTIONS (a new base or sequence of bases is new base or sequence of bases is added to the code)added to the code)

Base DELETIONS (a base or section Base DELETIONS (a base or section of bases is removed from the code)of bases is removed from the code)

Types of mutationTypes of mutationBase substitution

ATG-CCG-ACC-TAG-TTG …C

Tyr – gly – trp – ile - asn …ser

Base substitutions are USUALLY not too bad. Why?Because the code can usually continue after the changed sequence. In this case, just one amino acid has changed. BUT if it changes a stop or start codon… then you’re in trouble (as we saw before)

Base additions (insertions) and base deletionsATG-CCG-ACC-

TAG-TTG …C TA-GTT-G

…

Base additions and deletions can cause lots of trouble! Why?These are “frame shift mutations” – they change the reading frame, or the triplets. This means that unless a triplet (or multiple of 3) is inserted or deleted, all amino acids after the mutation will be affected.

ATG-CCG-ACC-

TAG-TTG …AGT-TG …

Tyr- gly- trp- ile- asn …asp- gln

Let’s figure out this one… <<

One more type of mutationOne more type of mutation

Trinucleotide repeat mutationsTrinucleotide repeat mutations– The same triplet repeated many timesThe same triplet repeated many times– Result is long, repeating section of DNA. Result is long, repeating section of DNA.

Causes a dangling, fragile region of Causes a dangling, fragile region of chromosomechromosome

Eg. Fragile-X syndrome:Eg. Fragile-X syndrome:

http://4.bp.blogspot.com/_FoiEZNQLqOI/S-6APdSyIII/AAAAAAAABfM/pZLSLHtrpC0/s1600/fragile43.jpg

When does mutation occur?When does mutation occur? ALL THE TIME – just in low frequencies, and ALL THE TIME – just in low frequencies, and

often with little or no consequence. If often with little or no consequence. If anything makes it happen more often, it is anything makes it happen more often, it is called a mutagen.called a mutagen.

If a mutation occurs in a somatic cell, it only If a mutation occurs in a somatic cell, it only affects that cell and any daughter cells affects that cell and any daughter cells produced by MITOSIS. This is the case with produced by MITOSIS. This is the case with cancers.cancers.

If a mutation occurs in a germline cell If a mutation occurs in a germline cell (gamete-producing), then the mutation can (gamete-producing), then the mutation can be passed on to ALL cells of the next be passed on to ALL cells of the next generation. This is how new alleles arise.generation. This is how new alleles arise.

How does mutation occur?How does mutation occur?

- INDUCED MUTATION – when a - INDUCED MUTATION – when a causative agent is identified (eg. causative agent is identified (eg. Cancer-causing UV). Agent is called a Cancer-causing UV). Agent is called a MUTAGENMUTAGEN– SPONTANEOUS MUTATION – no SPONTANEOUS MUTATION – no

causative agent identified. Ie. A mistake causative agent identified. Ie. A mistake made during replicationmade during replication

Known mutagensKnown mutagens

Mustard gas: causes cancers (carcinogenic)Mustard gas: causes cancers (carcinogenic) Peanut oil: fumes cause lung cancerPeanut oil: fumes cause lung cancer UV radiation: causes cancers (especially UV radiation: causes cancers (especially

skin cancer)skin cancer) Nuclear radiation: causes large nucleotide Nuclear radiation: causes large nucleotide

deletions, which can lead to cell death deletions, which can lead to cell death and/or cancersand/or cancers

Some chemicals and drugs (eg. Some chemicals and drugs (eg. Thalidomide)Thalidomide)

ThalidomideThalidomide

1950s – pregnant women took 1950s – pregnant women took Thalidomide drug to prevent morning Thalidomide drug to prevent morning sicknesssickness

Caused germline mutations which meant Caused germline mutations which meant that offspring were often born with horrific that offspring were often born with horrific deformitiesdeformities

Continued to be prescribed for many years Continued to be prescribed for many years after the effects were suspected.after the effects were suspected.

Still used to treat symptoms of illnesses Still used to treat symptoms of illnesses such as AIDSsuch as AIDS

The horror of ThalidomideThe horror of ThalidomideThe effects of Thalidomide were unpredictable and often devastating. Often offspring of a Thalidomide taking mother were born missing limbs, while others were developmentally impaired or had other physical defects. Previous animal tests had not shown these effects, as the drug is not a mutagen to all species.

Recently, Australian families have launched a class action against the inventor of the drug, a German man. The children who were affected are now in their 50s and 60s. The photo is of a patient born with no arms or legs, but is not mentally impairedhttp://images.theage.com.au/2011/06/26/2453630/thalidomide-thumb-169-408x264.jpg

OH NO! MUTATION SUCKS!!OH NO! MUTATION SUCKS!! Not true – in fact mutation means that new Not true – in fact mutation means that new

alleles arise.alleles arise. Sometimes new alleles are good!Sometimes new alleles are good! Mutation is the basis of evolution.Mutation is the basis of evolution.

If a negative (deleterious) allele arises, and If a negative (deleterious) allele arises, and it is DOMINANT, it can be eradicated easily.it is DOMINANT, it can be eradicated easily.

If it’s recessive, though, it can hide If it’s recessive, though, it can hide throughout generations and be integrated throughout generations and be integrated into the gene pool of the populationinto the gene pool of the population

All the alleles!All the alleles!

All the genetic code in an organism is All the genetic code in an organism is the GENOMEthe GENOME

Comparing genomes can lead us to Comparing genomes can lead us to understand where new alleles have understand where new alleles have arisen from (eg. What kind of arisen from (eg. What kind of mutation has caused them)mutation has caused them)

Human Genome ProjectHuman Genome Project

The whole human genome has been The whole human genome has been sequencedsequenced

So, we know the code, but we’re still So, we know the code, but we’re still finding out which sections code for finding out which sections code for what (all the gene loci)what (all the gene loci)

Comparative GenomicsComparative Genomics

General idea: the closer the General idea: the closer the relationship between two species, relationship between two species, the more similar their DNA code will the more similar their DNA code will bebe

Therefore, by finding out the genome Therefore, by finding out the genome of many species, we can not only of many species, we can not only work out relationships, but also work out relationships, but also identify the rise of different alleles!identify the rise of different alleles!

Why don’t all our genes show Why don’t all our genes show in every cell?in every cell?

All our cells have our whole genome in All our cells have our whole genome in them… but not all the proteins coded are them… but not all the proteins coded are produced by every cell.produced by every cell.

Genes are turned on and off, usually via Genes are turned on and off, usually via the action of other genes.the action of other genes.

Sometimes genes are turned on or off with Sometimes genes are turned on or off with mutagensmutagens

An “active gene” is one that is being An “active gene” is one that is being transcribed and translated within a transcribed and translated within a particular cell or tissueparticular cell or tissue

Identifying active genesIdentifying active genes

MicroarraysMicroarrays– Plates with strands of DNA which are Plates with strands of DNA which are

“marked” at known genes“marked” at known genes– These markers can be fluorescent (so These markers can be fluorescent (so

they can be identified again)they can be identified again)– Markers can be used to identify genes Markers can be used to identify genes

that are “turned on” in particular cellsthat are “turned on” in particular cells

Switching genes offSwitching genes off

We can switch off deleterious mutant We can switch off deleterious mutant genes (sometimes)genes (sometimes)

RNA interference: introduce double RNA interference: introduce double stranded RNA to cell, coding for a stranded RNA to cell, coding for a particular gene. This can act to “turn particular gene. This can act to “turn off” the translation process.off” the translation process.– This process is not fully understood, but This process is not fully understood, but

its potential is exciting.its potential is exciting.