1. Gene action Protein function, and when it all goes wrong!

2. What do proteins do? Structural genes: produce proteins that become a part of the structure and functioning of the organism Structural genes: produce proteins that become a part of the structure and functioning of the organism Regulatory genes: produce proteins that switch other genes on or off, and the rate at which the protein product is being produced. Regulatory genes: produce proteins that switch other genes on or off, and the rate at which the protein product is being produced.

3. Case study: thalassaemia Gene locus: chromosome 11 Gene locus: chromosome 11 Controls production of the beta chains of haemoglobin Controls production of the beta chains of haemoglobin About 1600bp make up gene About 1600bp make up gene Two possible alleles: normal beta chain development and abnormal Two possible alleles: normal beta chain development and abnormal Abnormal beta chains means that red blood cells do not have functional haemoglobin… and cannot carry oxygen! Abnormal beta chains means that red blood cells do not have functional haemoglobin… and cannot carry oxygen!

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

5. DNA sequence differences Template DNA code -TGA-CGG-GAC-ACC-CCG-TTC-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-AAG-GUG-AAC-GUG… CAC-UAA Translation occurs… Amino acid number -12 13 14 15 16 17 18 19 20 … 146 147 Amino 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 … 146 147 Amino acid sequence -thr-ala-leu-trp-gly-STOP …. Uh oh!

6. Thalassaemia protein product differences glylysval 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!!

7. Mutations Changes in the DNA, mRNA or resulting polypeptide is called a MUTATION. Changes in the DNA, mRNA or resulting polypeptide is called a MUTATION. These mutations are generally only significant if they occur during DNA replication in MEIOSIS (why?) These mutations are generally only significant if they occur during DNA replication in MEIOSIS (why?) These new DNA sequences that have arisen are different ALLELES of the gene These new DNA sequences that have arisen are different ALLELES of the gene

8. Types of mutation Base SUBSTITUTION (a base, or sequence of bases, is SUBSTITUTED for a different base) Base SUBSTITUTION (a base, or sequence of bases, is SUBSTITUTED for a different base) Base ADDITIONS or INSERTIONS (a new base or sequence of bases is added to the code) Base ADDITIONS or INSERTIONS (a new base or sequence of bases is added to the code) Base DELETIONS (a base or section of bases is removed from the code) Base DELETIONS (a base or section of bases is removed from the code)

9. Types of mutation Base 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 deletions ATG-CCG-ACC-TAG-TTG …CTA-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… <<

10. One more type of mutation Trinucleotide repeat mutations Trinucleotide repeat mutations –The same triplet repeated many times –Result is long, repeating section of DNA. Causes a dangling, fragile region of chromosome Eg. Fragile-X syndrome: http://4.bp.blogspot.com/_FoiEZNQLqOI/S- 6APdSyIII/AAAAAAAABfM/pZLSLHtrpC0/s1600/fragile43.j pg

11. When does mutation occur? ALL THE TIME – just in low frequencies, and often with little or no consequence. If anything makes it happen more often, it is called a mutagen. ALL THE TIME – just in low frequencies, and often with little or no consequence. If anything makes it happen more often, it is called a mutagen. If a mutation occurs in a somatic cell, it only affects that cell and any daughter cells produced by MITOSIS. This is the case with cancers. If a mutation occurs in a somatic cell, it only affects that cell and any daughter cells produced by MITOSIS. This is the case with cancers. If a mutation occurs in a germline cell (gamete- producing), then the mutation can be passed on to ALL cells of the next generation. This is how new alleles arise. If a mutation occurs in a germline cell (gamete- producing), then the mutation can be passed on to ALL cells of the next generation. This is how new alleles arise.

12. How does mutation occur? - INDUCED MUTATION – when a causative agent is identified (eg. Cancer- causing UV). Agent is called a MUTAGEN –SPONTANEOUS MUTATION – no causative agent identified. Ie. A mistake made during replication

13. Known mutagens Mustard gas: causes cancers (carcinogenic) Mustard gas: causes cancers (carcinogenic) Peanut oil: fumes cause lung cancer Peanut oil: fumes cause lung cancer UV radiation: causes cancers (especially skin cancer) UV radiation: causes cancers (especially skin cancer) Nuclear radiation: causes large nucleotide deletions, which can lead to cell death and/or cancers Nuclear radiation: causes large nucleotide deletions, which can lead to cell death and/or cancers Some chemicals and drugs (eg. Thalidomide) Some chemicals and drugs (eg. Thalidomide)

14. Thalidomide 1950s – pregnant women took Thalidomide drug to prevent morning sickness 1950s – pregnant women took Thalidomide drug to prevent morning sickness Caused germline mutations which meant that offspring were often born with horrific deformities Caused germline mutations which meant that offspring were often born with horrific deformities Continued to be prescribed for many years after the effects were suspected. Continued to be prescribed for many years after the effects were suspected. Still used to treat symptoms of illnesses such as AIDS Still used to treat symptoms of illnesses such as AIDS

15. The horror of Thalidomide The 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 impaired http://images.theage.com.au/2011/06/26/2453630/thalidomide-thumb-169-408x264.jpg

16. OH NO! MUTATION SUCKS!! Not true – in fact mutation means that new alleles arise. Not true – in fact mutation means that new 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 it is DOMINANT, it can be eradicated easily. If a negative (deleterious) allele arises, and it is DOMINANT, it can be eradicated easily. If it’s recessive, though, it can hide throughout generations and be integrated into the gene pool of the population If it’s recessive, though, it can hide throughout generations and be integrated into the gene pool of the population

17. All the alleles! All the genetic code in an organism is the GENOME All the genetic code in an organism is the GENOME Comparing genomes can lead us to understand where new alleles have arisen from (eg. What kind of mutation has caused them) Comparing genomes can lead us to understand where new alleles have arisen from (eg. What kind of mutation has caused them)

18. Human Genome Project The whole human genome has been sequenced The whole human genome has been sequenced So, we know the code, but we’re still finding out which sections code for what (all the gene loci) So, we know the code, but we’re still finding out which sections code for what (all the gene loci)

19. Comparative Genomics General idea: the closer the relationship between two species, the more similar their DNA code will be General idea: the closer the relationship between two species, the more similar their DNA code will be Therefore, by finding out the genome of many species, we can not only work out relationships, but also identify the rise of different alleles! Therefore, by finding out the genome of many species, we can not only work out relationships, but also identify the rise of different alleles!

20. Why don’t all our genes show in every cell? All our cells have our whole genome in them… but not all the proteins coded are produced by every cell. All our cells have our whole genome in them… but not all the proteins coded are produced by every cell. Genes are turned on and off, usually via the action of other genes. Genes are turned on and off, usually via the action of other genes. Sometimes genes are turned on or off with mutagens Sometimes genes are turned on or off with mutagens An “active gene” is one that is being transcribed and translated within a particular cell or tissue An “active gene” is one that is being transcribed and translated within a particular cell or tissue

21. Identifying active genes Microarrays Microarrays –Plates with strands of DNA which are “marked” at known genes –These markers can be fluorescent (so they can be identified again) –Markers can be used to identify genes that are “turned on” in particular cells

22. Switching genes off We can switch off deleterious mutant genes (sometimes) We can switch off deleterious mutant genes (sometimes) RNA interference: introduce double stranded RNA to cell, coding for a particular gene. This can act to “turn off” the translation process. RNA interference: introduce double stranded RNA to cell, coding for a particular gene. This can act to “turn off” the translation process. –This process is not fully understood, but its potential is exciting.