Gene action

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 • 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 • Controls production of the beta chains of haemoglobin • About 1600bp make up gene • 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!

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?!

5. DNA sequence differences NORMAL HBB (thalassaemia) GENE SEQUENCE ABNORMAL HBB (thalassaemia) GENE SEQUENCE

6. Total: 147 amino acids gly lys val gly STOP Thalassaemia protein product differences NORMAL Total: 17 amino acids 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. • 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

8. Types of mutation • 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 DELETIONS (a base or section of bases is removed from the code)

9. Types of mutation Base substitution 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) ATG-CCG-ACC-TAG-TTG … C Tyr – gly – trp – ile - asn … ser Base additions (insertions) and base deletions Base additions and deletions can cause lots of trouble! Why? ATG-CCG-ACC- TAG-TTG … C TA-GTT-G … Tyr- gly- trp- ile- asn … asp- gln 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- T AGT-TG … AG-TTG … Let’s figure out this one… <<

10. One more type of mutation • 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.jpg

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. • 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.

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

14. Thalidomide • 1950s – pregnant women took Thalidomide drug to prevent morning sickness • 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. • 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. • Sometimes new alleles are good! • Mutation is the basis of evolution. • 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

17. All the alleles! • 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)

18. Human Genome Project • 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)

19. Comparative Genomics • 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!

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

21. Identifying active genes • 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) • 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.