Classification and biodiversity

Classification is hierarchical: domain, kingdom, phylum, class, order, family, genus, species, with a binomial name for each species. Modern classification is phylogenetic — it aims to reflect evolutionary relationships, and is increasingly based on molecular evidence (DNA and rRNA sequences, protein comparison, immunology) rather than appearance, which can mislead through convergent evolution.

The three-domain system (Bacteria, Archaea, Eukarya) replaced the five-kingdom system when ribosomal RNA sequencing revealed that the archaea are as different from bacteria as either is from us.

Biodiversity can be assessed at three levels: within a habitat (species richness and diversity indices), within a species (the proportion of polymorphic loci — the variety of alleles in the gene pool), and at the molecular level (DNA fingerprinting and sequencing).

Your turn — Simpson’s Diversity Index

DNA replication and mitosis

Semi-conservative replication: DNA helicase unwinds the helix and breaks the hydrogen bonds; free nucleotides pair with the exposed bases; DNA polymerase forms the phosphodiester bonds, always working 5′→3′. Each daughter molecule keeps one parental strand.

The cell cycle: interphase (G1 → S, where DNA replicates → G2), then mitosis, then cytokinesis.

• Prophase — chromosomes condense and become visible as two sister chromatids; the nuclear envelope breaks down; the spindle forms.
• Metaphase — chromosomes align on the equator.
• Anaphase — centromeres divide and the chromatids are pulled to opposite poles.
• Telophase — nuclear envelopes re-form; chromosomes decondense.

Cancer is a failure of the controls on this cycle: mutations in proto-oncogenes (making them oncogenes) or tumour suppressor genes allow uncontrolled mitosis. Carcinogens and mutagens increase the mutation rate and so the risk.

Meiosis and sexual reproduction in humans and plants

Meiosis halves the chromosome number and generates variation. Two divisions produce four haploid, genetically different cells.

• Crossing over (prophase I) — homologous chromosomes pair; chiasmata form and sections of non-sister chromatids are exchanged, creating new allele combinations.
• Independent assortment (metaphase I) — each homologous pair aligns independently: 2ⁿ combinations for n pairs.
• Random fertilisation — any sperm may fuse with any egg.

In humans: spermatogenesis produces four small motile sperm from each primary spermatocyte and runs continuously from puberty; oogenesis produces one large ovum plus polar bodies, and is arrested part-way until ovulation. Fertilisation: the acrosome reaction digests a path through the zona pellucida; the membranes fuse; the cortical reaction then hardens the zona pellucida to prevent polyspermy; the haploid nuclei fuse to give a diploid zygote.

In flowering plants: the anther makes pollen; the ovule contains the embryo sac. Pollination is followed by the growth of the pollen tube down the style, and then by double fertilisation — one male nucleus fuses with the egg cell to form the diploid zygote, and the other fuses with two polar nuclei to form the triploid endosperm, the food store for the embryo.

Mitosis or meiosis?

Tap a statement, then tap the process it describes.

Monohybrid, dihybrid, linkage and sex linkage

• Monohybrid — one gene. Heterozygous × heterozygous gives a 3:1 phenotypic ratio.
• Codominance — both alleles are expressed in the heterozygote (e.g. the AB blood group; roan cattle). Heterozygous × heterozygous gives 1:2:1.
• Dihybrid — two unlinked genes. Double heterozygotes give 9:3:3:1.
• Linkage — genes on the same chromosome are inherited together, so the parental combinations are far more common than expected and the recombinants are rare (they only arise by crossing over). A dihybrid cross that gives a strongly non-9:3:3:1 ratio is the classic sign of linkage.
• Sex linkage — genes on the X chromosome. Males are XY and so hemizygous: a single recessive allele is expressed. Haemophilia and Duchenne muscular dystrophy are therefore far more common in males, and a carrier mother passes the allele to half of her sons.

Mutation (spec 5(f)): a gene mutation can be a single base substitution — in sickle cell anaemia, one base change substitutes valine for glutamic acid in the β-globin chain, so the haemoglobin polymerises and distorts the red cell. A chromosome mutation such as the non-disjunction that gives three copies of chromosome 21 causes Down’s syndrome.

Testing your genetic ratios

1. Null hypothesis: there is no significant difference between the observed and expected results — any difference is due to chance.
2. Work out the expected numbers from the predicted ratio.
3. Calculate χ².
4. Compare with the critical value at p = 0.05 for the correct degrees of freedom.
5. Below the critical value → accept the null hypothesis. At or above it → reject it: the difference is significant, so something else (such as linkage) is operating.

p = 0.05 means that a difference this large would arise by chance alone in fewer than 1 in 20 experiments. It is the conventional threshold in biology — not a natural law.

Your turn — chi-squared

Interpreting your χ²

Natural selection, Hardy–Weinberg and speciation

Variation is continuous (polygenic, strongly influenced by the environment — height, mass) or discontinuous (controlled by one or a few genes — blood group). Its ultimate source is mutation; sexual reproduction shuffles it.

Natural selection: variation → selection pressure → the better-adapted individuals survive and reproduce → the frequency of the advantageous allele increases. Stabilising selection favours the intermediate; directional selection favours one extreme; disruptive selection favours both extremes.

The Hardy–Weinberg principle applies only if the population is large, mating is random, and there is no mutation, no migration and no selection. If observed frequencies differ from predicted, one of those conditions is broken — the population is evolving.

Speciation: allopatric — a geographical barrier prevents gene flow; the two populations diverge under different selection pressures until they are reproductively isolated. Sympatric — reproductive isolation arises without a physical barrier (polyploidy, a change in flowering time, a behavioural change). Genetic drift — chance changes in allele frequency — has a far larger effect in small populations.

Your turn — Hardy–Weinberg

Where does the variation come from?

Tap a source of variation, then when it happens.

DNA profiling, PCR and genetic engineering

PCR amplifies DNA: denature (95 °C) → anneal primers (50–65 °C) → extend with Taq polymerase (72 °C). Each cycle doubles the amount of DNA, so n cycles gives 2ⁿ copies.

Gel electrophoresis: DNA is negatively charged, so all fragments move towards the anode; the gel sieves them, so shorter fragments travel further. Comparing the pattern of bands from short tandem repeats gives a DNA profile, used in forensics, paternity testing and in establishing evolutionary relationships.

Genetic engineering: the gene is cut out with a restriction enzyme (leaving sticky ends), joined into a plasmid vector cut with the same enzyme using DNA ligase, and taken up by a host cell (transformation). Marker genes identify the transformed cells. This is how human insulin is made.

Applications and ethics: gene therapy, genetically modified crops (pest resistance, higher yield, Golden Rice), and stem cell therapy. The debate is real and you must be able to argue both sides: benefits to health and food security against the escape of transgenes, the loss of biodiversity, the welfare of GM animals, and questions about the destruction of embryos and about who controls and profits from the technology.

Your turn — PCR

Reading a DNA profile

The big ideas to know

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