IQ1 Mutation – How does mutation introduce new alleles into a population?

a) Mutagens- Mutations are changes to the genetic material of a cell, which can occur at genome

level, chromosome level, or DNA level. Mutations have a variety of causes and effects.- Some mutations are spontaneous, but most are caused by one of three mutagen types:

o Electromagnetic radiation is emitted by electrically charged particles, and due to its high energy/penetrative ability can travel into the nucleus.

o Chemicals include radioactive agents (see above), carcinogens, and heavy metals which affect DNA repair and cause more errors.

o Biological mutagens include viruses (which put their own DNA into cells which might get into the host’s DNA), and bacteria (which can cause inflammation, leading to heat-based damage or DNA repair errors).

- Electromagnetic radiation exists across a wide spectrum, and only a few are damaging. These are called ionizing radiation and include UV rays, X-rays, and Gamma rays.

- Pyrimidine Dimers occur when T and/or C bases are next to each other and UV radiation can cause them to disconnect from their pair and connect to each other.

- On an average sunny day a person will acquire around 20,000 pyrimidine dimers, and although most are repaired by the cell, some can remain and cause cell death or cancer.

- X-rays and Gamma rays can damage the bases or the sugar-phosphate backbones of DNA directly, or they can ionize water to produce OH- free radicals that do the damage.

- Overall, this interferes with cell division, gene products, and cell metabolism.

- Chemical mutagens typically only affect cells if they are exposed for a long period. They can be ingested, inhaled, or just encountered in the environment.

- Free radicals (see above) are often mutagens, but they can be neutralized with antioxidants which are naturally-occurring in food.

- Some chemicals called base analogues can replace bases in the DNA code, such as acridine orange dyes. Others can create gaps in DNA or change the properties of bases (deamination). Methylation is another chemical effect which changes the DNA’s shape.

- Viruses can insert their own DNA into the host, and bacterial can disrupt host cell DNA and repair systems. Some bacteria also have ‘jumping genes’ which can enter the genome.

- These sequences have the ability to move themselves within the genome due to their inbuilt cut and paste enzymes. They have been known to cause errors in replication and play a role in disruptive the function of certain genes.

- Several biological processes produce free radicals such as detoxification in the liver and the immune response in pathogen destruction.

b) Types of Mutations- DNA mutations are single nucleotide variations which can occur in exons, introns, and

promoter/terminator regions of the genome.- The different types of DNA mutations include substitutions (base is swapped) and

frameshifts (base is inserted/deleted). They have a variety of effects:o Silent – due to the redundancy of the DNA code, the same amino acid is

produced and there is no effect on the gene expression.o Neutral – a different amino acid is coded, but it has the same properties as the

original and no significant effect on the protein.o Missense – a different amino acid is coded, creating a different protein with a

different function (e.g. glutamic acid to valine SC anaemia)o Nonsense – occurs when a stop codon is transcribed. This results in an

incomplete and non-functioning protein.- DNA ‘repair kits’ can fix these small errors, but sometimes they make errors themselves:

for instance, when one strand is longer than the other after an insertion, the base that is removed to put it ‘back to normal’ might be one that was there originally.

- Chromosomal mutations are mutations to large sections of DNA (hundreds to millions of bases) which often occur during crossing-over as chromosomes are being ‘cut up’.

- The different types of chromosome mutations include:o Deletions: part of a chromosome goes missing during crossing-over.o Additions: part/all of a chromosome is duplicated, and/or added to another.o Translocations: crossing-over occurs between non-homologous chromosomeso Inversions: part of a chromosome is cut out and put back in reverse.

- Another type of chromosome mutation is called non-disjunction, where an addition mutation (part of a chromosome is added onto a different one) then induces trisomy.

- Aneuploidy is where a child and parent’s chromosome numbers differ (e.g. trisomy).

- Mutations can be either somatic and hence uninheritable, or germline and heritable.

c) Coding and Non-Coding Mutations- Coding DNA are the genes which are transcribed and translated to form polypeptides,

while non-coding DNA are the parts which are edited out during protein synthesis.- Genes only make up 2-3% of our DNA and are almost completely known by scientists,

but non-coding DNA is mainly unknown – the ‘dark matter’ of the genome.- The ENCODE project is a scientific endeavour currently trying to discover the function of

all this non-coding ‘dark matter’, and currently know more than they don’t.- Non-coding DNA includes promoter and terminator regions for transcription, regulatory

regions that ‘switch on/off’ genes, introns embedded within exons, and RNA coding.- It is essential for cell differentiation, explaining how all cells in the body can have the

same DNA, but be different (e.g. liver cell, bone cell, neuron).

- It can also have mutations, and while (unlike coding DNA) these mutations do not directly affect amino acid sequences, they can affect gene expression and cell function.

- Non-coding DNA mutations have been associated with genetic diseases such as Huntington’s (in SNPs), beta thalassemia, and some forms of cystic fibrosis.

- They can also cause a predisposition towards conditions such as obesity and some infectious diseases such as Hepatitis C.

- Introns are the non-coding sequences of DNA which separate exons (coding sequences) from each other and are removed by the spliceosome enzymes during transcription.

- The spliceosome is made up of snRNP units and bind to three points on the introns – the 5’ junction, the 3’ junction, and the branch point – in order to remove them.

- If a mutation occurs at one of these binding points, the intron may not be removed, which has a detrimental effect on translation.

d) Effects of Mutation, Genetic Drift- Population genetics is the study of how a population changes over time, leading to

species evolving. It includes quantitative studies analysing the distribution of variations.- The distribution is affected by selection pressure, mutation, gene flow, and genetic drift.- Gene flow is the change of allele frequency due to individuals entering and leaving a

population. Humans can use artificial insemination/pollination to induce this.

- Genetic drift occurs when chance events cause unpredictable changes in allele frequency (not determined by selection). It can eliminate even favourable alleles.

- It can be caused by natural/human-made disasters or isolating events.- The effect of genetic drift is much more pronounced in small populations, but affects all.- The two types of genetic drift are called the founder effect and the bottleneck effect:

o Founder Effect: A small group of individuals is removed from the original population to start a new one, which now has a more limited gene pool.

o Bottleneck Effect: A large group of individuals is removed from the original population via death/infertility, limiting the original gene pool.

IQ2 Biotechnology – How do genetic techniques affect Earth’s biodiversity?

- Biotechnology involves the use of living systems, organisms, or parts of organisms to manipulate natural processes and develop products, systems, or environments to benefit people: it is “the use of biological and biochemical systems to better the existence of humanity”.

a) History of Biotechnology- Ancient biotechnology began with the first farming around 10,000 years ago in

Mesopotamia. It aimed to provide a more reliable food source by growing plants and domesticating animals rather than hunting and gathering.

- Domestication of dogs, sheep, and goats as well as rice, barley, and wheat was the first step towards selective breeding: animals which were friendly and could co-exist with humans had access to greater food and safety, and as such this trait became evolutionarily desirable.

- Humans went on to domesticate more animals and these were later selectively bred for other traits such as endurance or food yield. Corn is a major example of this – between 5000 BC and 1500 BC, corn was bred to have more kernels and be 5 times larger than the wild form.

- Fermentation is the process that many microorganisms (yeast, moulds, bacteria) use to convert sugars into energy, and it produces products that are necessary in making food – e.g. carbon dioxide in bread and lactic acid in yogurt. This property was discovered in China in about 4000 BC, probably by accident, and is still used today!

- Traditional medicine was typically plant-based, taking advantage of the chemicals naturally produced by these organisms. Other bio-medicine included honey as a natural antibiotic for respiratory infections/wounds (used by ancient Egyptians), and mouldy soybean curds (China) or mouldy cheese (Ukraine) to treat infected wounds due to the mould releasing natural antibiotics.

- Contemporary Aboriginals still use traditional medical and agricultural technology, as well as aquaculture. There is evidence of 6000-year-old canal systems to trap fish/eels in river systems in Victoria/NSW, and the freshwater yabby was also farmed by transporting individuals in net wrappings to stock other billabongs and creeks.

- Classical biotechnology is generally considered to have started in 1800s with the advent of modern scientific thought. The invention of microscopes by Leeuwenhoek started a revolution in biotechnology as microbes could be identified for the first time.

- Gay-Lussac discovered that microbes were responsible for the gas in beer froth, and Pasteur explained that the fermentation process was biological not chemical – proposing that microbes were responsible for lactic acid fermentation and identifying yeast and bacteria in bread, cheese, yoghurt and alcohol production.

- Mendel pioneered plant hybridization and artificial pollination, leading to agricultural development. Through this he also discovered the principles of heredity, improving selective breeding procedures.

- The discovery of antibiotics in the early 20th century was the greatest discovery of classical biomedicine, paving the way for contemporary scientists to develop modern pharmaceutical drugs.

- Modern biotechnology embraces genetic modification and generally involves genetic engineering techniques that modify DNA. It is considered to have begun in the 1950s after the discovery of DNA. It includes:

o Recombinant DNA – transgenic DNA made up of genes from multiple species.o Gene Probes – short fluorescent-tagged DNA strands that attach to matching

strands, allowing that specific gene to be isolated.o Gene Sequencing – determining the order of bases in a strand of DNA in order to

‘read the code’, e.g. in the Human Genome Project.o Monoclonal Antibodies – lab-manufactured synthetic antibodies made from

cloned immune cells (e.g. from mice) to fight diseases such as cancer.o RNA Interference – gene silencing caused by strands of RNAi which disrupt

mRNA. This happens naturally but can also be replicated synthetically.o Marker Assisted Breeding – detection of desirable genetic traits using SNPs or

other DNA markers instead of searching for the expressed trait.o Gene Drive – altering allele frequency by attaching strands of non-coding DNA

which cause that allele to replace different alleles of the same gene.o Stem Cell Research – using non-differentiated cells to study the development of

the body, create new organs, and heal untreatable injuries (e.g. spinal cord).o ELIZA – Enzyme-Linked Immunosorbent Assay which uses natural antibodies to

locate antigens in a sample and diagnose illness precisely.

- CRISPR-Cas9 is a very precise gene-editing tool that finds genes using a strand of guide RNA that you create, then cuts the DNA using the Cas9 enzyme.

- Gene editing is used in agriculture to increase the nutritional value of foods (Golden Rice vitamin A, low-cholesterol margarine, RNAi edited low-fat cottonseed), or to enable crops to survive in tough conditions (disease-resistant Bt wheat/corn/tomatoes, cold-resistant extra-large ‘super salmon’, Australian salt-tolerant wheat).

- Medicine has been advanced not only by directly manipulating diseased human DNA (gene therapy), but also by using transgenic organisms to produce proteins, vaccines, hormones, and blood clotting/thinning agents (biopharming) such as HPV vaccines in potatoes and insulin in E. coli.

- Biotech is also used in industry to produce bio-plastics from plants and corn-starch, paper and textiles from potato starch, biofuels (e.g. biodiesel/ethanol/methane), and for bacterial bioremediation to process contaminants (e.g. heavy metals, toxic chemicals).

- In the future, biotechnology will advance further and become even more important!- Cellulosic biofuel – made from the cellulose in wood, grasses, or the non-edible parts of

plants (e.g. cornstalks) – emits 85% less greenhouse gas than petroleum-based fuels.- Versatile, biodegradable plastics from renewable sources reduce use of petrochemicals.- Complex/synthetic transgenic species with non-naturally-occurring traits or traits

controlled by multiple rather than singular genes allow greater adaptation to abiotic stresses (drought, salinity), increase nutritional value (vitamins and micronutrients), and eliminate allergens, improve shelf life of fruits/vegetables.

- Personalized medicine where medication is tailored to the individual patient’s genetic content to ensure optimal drug metabolism.

- Genomic studies which help researchers improve enzymes using DNA probes to find genes that produce specific enzymes for industrial use.

- Bioengineering which combines disciplines of bio such as genetics, molecular biology etc. and is driven by student contests such as iGEN and BioMod.

- ‘Backyard biotech’ and open-source genetics opening innovations to the masses.

b) Assessing the Impacts- Biotechnology has a wide range of positive social and ethical implications, helping to

extend our lives, prevent our illnesses, and meet UN Sustainable Development Goals for availability of clean water and food, production of green energy, and decreasing poverty.

- However, biotechnology (specifically DNA manipulation) is also controversial as it can pose risks, impact on religious, philosophical, or cultural beliefs, and raise social issues.

- Risks include everything from transgenic crops causing allergies or outcompeting natural plants, to artificial microbes becoming zoonotic diseases, to outright bio-terrorism.

- Genetic pollution is gene flow of artificial genes into the wild.- Ethical questions range from whether vegetarians can eat plants that have animal genes

or Jews can eat food with pig genes, to whether altering human DNA is ‘playing God’.- Social and economic issues include ownership (e.g. gene patenting) and intellectual

property rights, commercial monopolies, and government regulations.

IQ3 Genetic Technologies – Could artificial DNA manipulation change populations forever?

a) Review of Technologies- Artificial pollination is where pollen (or whole anthers/stamen) are removed from one

parent flower and applied to the stigma of the other parent flower. It is used in agriculture and hybridisation and plant conservation.

- Artificial insemination is a reproductive technology that involves the deliberate introduction of male sperm into the reproductive tract of selected females. It became widely-used in the 1980s due to more effective transport/storage of sperm. It is used on both animals and humans: animal husbandry/agriculture, wildlife conservation, and human reproduction/genetic screening (IVF).

- Whole organism cloning is creating a genetically identical organism using somatic cells from a mature donor organism. It is asexual reproduction/reproductive technology.

- Plants can be cloned through cuttings and tissue culture, but animals must be cloned either by dividing an already-formed embryo (embryo cloning) or putting the nucleus of a somatic cell instead of sperm into an egg cell (adult cloning). Both types of animal clone must then be grown in a surrogate.

- Gene cloning occurs at the cellular level. The target gene located in an organism using genetic sequencing, then produced by getting intron-free cDNA from mRNA using reverse transcriptase and using PCR to amplify it.

- It is then treated with a restrictor enzyme that makes the ends sticky and connects them to a plasmid which contains regulatory DNA. The damaged backbone is repaired with ligase and the plasmid is placed in bacteria to be replicated.

- This is used to create transgenic species (e.g. bacteria that produces insulin proteins) or in gene therapy to replace a human’s disease-causing genes with a healthy copy.

- It is then placed in the target organism via inserting recombinant plasmids or using a retrovirus/a microscopic glass needle.

b) Biodiversity- Biodiversity is critical in maintaining healthy ecosystems and sustaining plant and animal

life on Earth. It is essential for the long term survival of a wide range of species and to feed and maintain the health of a growing human population.

- The use of modern biotechnology in agriculture gives humans the ability to alter the course of evolution by combining the traits of different species (transgenic organisms) and cloning individuals with desirable traits.

- These technologies may initially increase biodiversity in the short term due to new genetic combinations that are not produced naturally.

- In the long term, biodiversity may be reduced due to selectively breeding desired gene combinations.