Genetic Change

Module 6 averages about 24 marks a year (2020–2025). Mutation is the single most heavily examined inquiry question in the whole Year 12 course, at about 11 marks a year, so master it first. Genetic technologies (about 7 marks) and biotechnology (about 6) share the rest. School trial papers tend to give this module slightly fewer marks than the HSC does, so do extra practice here.

The syllabus has three inquiry questions:

• Mutation: how mutagens cause mutations; point and chromosomal mutations; somatic and germ-line mutations; coding and non-coding DNA; how mutation, gene flow and genetic drift change the gene pool.
• Biotechnology: past, present and future uses of biotechnology; social and ethical issues; benefits of genetic research; effects on Earth's biodiversity.
• Genetic technologies: reproductive technologies (artificial insemination and pollination), whole-organism and gene cloning, recombinant DNA and transgenic organisms; comparing their processes and outcomes.

A mutation is a permanent change in the DNA sequence. It is the only process that creates completely new alleles; everything else (meiosis, fertilisation, gene flow) shuffles or moves alleles that already exist.

Mutagens

A mutagen is anything that increases the rate of mutation.

• Electromagnetic radiation: UV light causes adjacent thymine bases to bond to each other (thymine dimers), distorting the DNA. Ionising radiation (X-rays, gamma rays) has enough energy to break DNA strands.
• Chemicals: compounds in tobacco smoke, asbestos fibres, some pesticides and mustard gas alter or bind to bases, or insert between them.
• Naturally occurring: uncorrected copying errors during DNA replication, transposons ("jumping genes") that move within the genome, and viruses such as HPV that insert DNA into host cells.

Point mutations

A point mutation changes one base (or a few). Using the real genetic code, here is one mRNA and four mutated versions.

Original mRNA: AUG GCA UGG AAA CAC GGU UAA, which gives Met–Ala–Trp–Lys–His–Gly, then stop.

• A silent substitution works because the code is degenerate: most amino acids have more than one codon.
• A missense substitution swaps one amino acid. The effect depends on where it is. Sickle-cell anaemia comes from one missense change in a haemoglobin gene.
• A nonsense mutation makes a shortened polypeptide, which is usually non-functional.
• An insertion or deletion of one or two bases shifts the reading frame. Deleting the last A of GCA gives AUG GCU GGA AAC ACG GUU…, so every amino acid after the second one changes and the original stop codon is lost. This is why frameshifts usually do more damage than substitutions. Inserting or deleting three bases adds or removes one amino acid without a frameshift.

Chromosomal mutations

These change the structure or number of chromosomes and affect many genes at once.

• Deletion: a section is lost. Duplication: a section is copied.
• Inversion: a section is reversed. Translocation: a section moves to a non-homologous chromosome.
• Aneuploidy: a whole chromosome is gained or lost, usually by non-disjunction (chromosomes failing to separate in meiosis). Trisomy 21 (Down syndrome) is the classic example.
• Polyploidy: whole extra sets of chromosomes; common in plants such as wheat, rare in animals.

Somatic and germ-line mutations

• Somatic mutations occur in body cells. They affect only the individual (and the cells descended from that cell, as in many cancers) and are not inherited.
• Germ-line mutations occur in cells that make gametes, or in the gametes themselves. They can be passed to offspring, appear in every cell of the offspring, and so can change the population's gene pool.

Coding and non-coding DNA

Only a small fraction (about 1–2%) of human DNA codes for proteins (exons). Non-coding DNA includes introns, promoters and other regulatory sequences, and repeated sequences.

• A mutation in an exon can change the polypeptide.
• A mutation in an intron is often harmless, unless it changes how introns are spliced out.
• A mutation in a promoter or regulatory region does not change the protein but can change how much is made, or when and where the gene is switched on.

Changing the gene pool

The gene pool is all the alleles in a population. Its allele frequencies change through:

• Mutation: adds new alleles (germ-line only).
• Natural selection: alleles that improve survival and reproduction become more common.
• Gene flow: individuals or gametes (eg pollen) move between populations, bringing in or removing alleles. It makes neighbouring populations more alike.
• Genetic drift: random changes in allele frequency, strongest in small populations. Alleles can be lost or fixed by chance, regardless of whether they are useful.

Two special cases of drift: a bottleneck (a disaster leaves a few survivors, eg northern elephant seals after hunting) and the founder effect (a few individuals start a new, isolated population).

Worked example: founder effect

On the mainland, allele B makes up 50% of a bird population's gene pool. Five birds colonise an island: one is BB, one is Bb and three are bb. The founders carry 10 alleles, and 2 + 1 = 3 of them are B, so

The island population starts with 30% B instead of 50%, purely by chance. Because it is small, further drift may change it even more, and with little gene flow from the mainland the two populations can diverge.

Reproductive technologies

• Artificial insemination: semen collected from a chosen male is placed into the female. One high-value sire can father many offspring in different places.
• Artificial pollination: pollen from a selected plant is transferred by hand to the stigma of another, often after removing the stamens to prevent self-pollination. Breeders control both parents.

Both are forms of selective breeding: they spread desirable alleles quickly but narrow the gene pool.

Cloning

Whole-organism cloning makes a genetically identical organism. In somatic cell nuclear transfer (Dolly the sheep, born 1996):

1. Remove the nucleus from an egg cell (enucleation).
2. Insert the nucleus from a body cell of the animal to be cloned, then use an electric pulse to fuse them and start division.
3. Implant the embryo in a surrogate mother. The offspring is a clone of the nucleus donor.

Plants are cloned far more easily by cuttings, grafting and tissue culture. Gene cloning makes many copies of one gene, either in bacteria (see recombinant DNA) or by PCR.

Recombinant DNA: making human insulin

Recombinant DNA joins DNA from two different sources.

1. Get the gene: bacteria cannot remove introns, so the insulin mRNA is turned into intron-free DNA (cDNA) using reverse transcriptase. (Alternatively, the gene is synthesised.)
2. Cut: the same restriction enzyme cuts the gene and a bacterial plasmid, leaving matching sticky ends.
3. Join: the gene and plasmid are mixed and DNA ligase seals them.
4. Transform: bacteria take up the recombinant plasmid.
5. Select: a marker gene (eg antibiotic resistance) identifies bacteria that took up the plasmid.
6. Culture: the bacteria are grown in large fermenters, and the insulin is extracted and purified.

Genetically engineered human insulin was approved in 1982 and replaced insulin from pig and cattle pancreases.

PCR and gel electrophoresis

The polymerase chain reaction copies a target DNA sequence. Each cycle has three temperature steps:

1. Denature (about 95 °C): the strands separate.
2. Anneal (about 50–65 °C): short primers bind either side of the target.
3. Extend (about 72 °C): a heat-stable DNA polymerase (Taq) builds new strands.

The amount of target DNA doubles each cycle, so after $n$ cycles

Worked example. A sample starts with 40 copies of a target sequence. After 20 cycles (assuming perfect doubling):

In practice efficiency falls in later cycles as primers and nucleotides run out, so the real yield is lower.

Gel electrophoresis separates DNA fragments by size. DNA is negatively charged (phosphate groups), so in an electric field it moves towards the positive electrode. Smaller fragments move through the gel more easily and travel further. A ladder of known fragment sizes in one lane lets you estimate the size of unknown bands. In DNA profiling, samples from the same person give lanes with bands in identical positions.

Transgenic organisms

A transgenic organism carries a gene from a different species.

• Agriculture: Bt cotton makes a protein from the bacterium Bacillus thuringiensis that kills certain caterpillar pests, reducing insecticide spraying (most cotton grown in Australia is Bt cotton). Golden rice makes beta-carotene to reduce vitamin A deficiency. Herbicide-tolerant canola lets farmers control weeds.
• Medicine: bacteria or yeast make insulin, human growth hormone and the hepatitis B vaccine; transgenic animals can make human proteins in their milk.

Comparing the technologies

Reproductive technologies and cloning only use alleles already in the species, while recombinant DNA can move a gene between unrelated species, producing combinations that could never arise naturally.

Biotechnology is the use of living organisms or their parts to make products or solve problems.

• Past: fermentation with yeast and bacteria (bread, beer, cheese, yoghurt), selective breeding of crops and livestock, and early vaccines.
• Present: GM crops, recombinant drugs, DNA profiling, IVF, gene sequencing, and CRISPR-Cas9 gene editing (2012), which cuts DNA at a chosen sequence so genes can be altered precisely.
• Future: gene therapy for inherited disorders, personalised medicine based on a person's genome, gene drives to spread a trait through a wild population (for example to suppress malaria mosquitoes), and synthetic biology.

Social and ethical issues

When asked to evaluate, weigh benefits against risks and say whose interests are affected.

• Benefits: more food, fewer pesticides, cheaper and safer medicines, cures for genetic disease.
• Ethical concerns: "designer babies" and germ-line editing, animal welfare in cloning, consent, and genetic privacy (who sees your DNA data).
• Social and economic issues: patents on seeds and genes, the cost of seed for poorer farmers, unequal access to new treatments, and differing cultural and religious views.

Effects on biodiversity

• Reduced diversity: monocultures of one cultivar or clones are genetically uniform, so a single pathogen can destroy a whole crop.
• Gene flow to wild relatives: transgenes (eg herbicide tolerance) can spread by pollen into weeds.
• Resistance: pests and weeds evolve resistance to Bt toxins and herbicides, so refuge crops of non-GM plants are required.
• Possible gains: less land clearing if yields rise, and conservation uses such as storing gametes and cloning endangered species to restore lost diversity.

• Saying a mutagen "causes" a specific mutation every time. It increases the chance of mutation.
• Claiming all mutations are harmful. Many are neutral; some are beneficial and are acted on by selection.
• Stating that somatic mutations can be inherited.
• Mixing up gene flow (movement between populations) with genetic drift (chance).
• Saying DNA moves to the negative electrode, or that larger fragments travel further.
• Forgetting that the same restriction enzyme must cut both the gene and the plasmid.
• Writing that cloning creates new alleles or that PCR makes protein.

• Explain how a mutation affects a protein: follow the chain DNA → mRNA codon → amino acid → protein shape → function. Each link usually earns a mark.
• Distinguish questions need a clear contrast for each feature, not two separate descriptions.
• Evaluate questions (GM crops, cloning, gene editing) need benefits, limitations and a final judgement that follows from them. Use a named example with specific detail.
• Describe a process (recombinant DNA, PCR, SCNT): give the steps in order with the correct enzymes.
• In data questions about allele frequency or mutation rates, describe the trend with numbers from the table, then explain it biologically.
• Distinguish the three agents of change clearly: mutation creates alleles, selection is non-random, drift is random.

• Module 5: mutations change the base sequence that transcription and translation read; meiosis and fertilisation are the other sources of variation; DNA profiling and SNPs depend on the techniques here.
• Module 7: antibiotic resistance spreads by mutation and natural selection; recombinant DNA makes vaccines; gene technologies can make disease-resistant crops.
• Module 8: mutations in proto-oncogenes and tumour-suppressor genes cause cancer; UV is a mutagen behind skin cancer; gene therapy and genetic screening help prevent genetic disease.