Mutations and the lac operon

A substitution may be silent (the code is degenerate), missense (a different amino acid) or nonsense (a premature stop codon). An insertion or deletion causes a frameshift, changing every triplet downstream — almost always catastrophic.

The lac operon — the classic example of transcriptional control in a prokaryote. E. coli normally respires glucose. It only makes the enzymes for lactose metabolism when lactose is actually present, because making them otherwise would waste energy.

• The operon consists of a promoter, an operator, and the structural genes lacZ (β-galactosidase, which hydrolyses lactose) and lacY (lactose permease, which transports lactose in).
• A separate regulatory gene continuously produces a repressor protein.
• No lactose: the repressor binds to the operator, physically blocking RNA polymerase from binding to the promoter. The genes are not transcribed.
• Lactose present: lactose binds to the repressor, changing its shape so that it can no longer bind the operator. It detaches, RNA polymerase binds the promoter, and the structural genes are transcribed — the enzymes are made.

Do not say the lactose "switches the gene on". It inactivates the repressor. The gene was always able to be transcribed; it was being blocked. Precision here is worth marks.

Apoptosis and homeobox genes

Apoptosis is programmed cell death: an orderly, controlled sequence in which enzymes break down the cytoskeleton, the cell shrinks, the membrane blebs, chromatin condenses, DNA is fragmented, and the fragments are engulfed by phagocytes without inflammation. Contrast necrosis, which is uncontrolled death after injury, releasing hydrolytic enzymes and causing inflammation.

Apoptosis is essential in development — it is what removes the webbing between the fingers of a developing embryo — and in removing damaged or infected cells. Too little apoptosis allows damaged cells to persist and contributes to cancer; too much contributes to neurodegenerative disease.

Homeobox genes control the body plan: they specify what develops where along the head-to-tail axis. They contain a highly conserved 180-base-pair homeobox sequence, which codes for a 60-amino-acid homeodomain that binds DNA — so their products are transcription factors that switch whole batteries of other genes on or off.

Why the conservation matters: homeobox sequences are strikingly similar in animals, plants and fungi. Such deep conservation across kingdoms is powerful evidence of a common ancestor, and it means that the equivalent gene in a fruit fly can inform us about human development.

The repressor

Dihybrid crosses, linkage and epistasis

Monohybrid: Aa × Aa → 3:1. Dihybrid (two unlinked genes): AaBb × AaBb → 9:3:3:1. A test cross against the homozygous recessive reveals an unknown genotype.

• Codominance — both alleles are expressed in the heterozygote (blood group AB). Multiple alleles — more than two alleles exist in the population (I^A, I^B, I^O), though any individual has only two.
• Sex linkage — a gene on the X chromosome. Males (XY) have a single copy, so a recessive allele is always expressed. Haemophilia and red-green colour blindness are far commoner in males, and a male cannot be a carrier.
• Autosomal linkage — genes on the same chromosome are inherited together unless separated by crossing over. The result is an excess of parental phenotypes and far fewer recombinants than 9:3:3:1 would predict.
• Epistasis — one gene masks or modifies the expression of another at a different locus. If the gene producing a pigment precursor is homozygous recessive, no pigment can be made at all, whatever the second gene says. Look for ratios such as 9:3:4, 9:7 or 12:3:1.

Continuous variation (height, mass) is polygenic: many genes each of small effect, plus a strong environmental contribution, giving a normal distribution. Discontinuous variation is controlled by one or few genes and gives discrete categories.

Your turn — chi-squared

What does χ² = 2.84 mean?

The Hardy-Weinberg principle

Hardy-Weinberg lets you calculate allele frequencies in a population from the phenotypes you can count.

Always start with the recessive phenotype, because it is the only genotype you can identify with certainty. Its frequency is q²; take the square root to get q; then p = 1 − q; then calculate 2pq.

The five assumptions: a large population; random mating; no selection; no mutation; and no migration. If measured frequencies deviate from those predicted, one of these has been violated — which is itself evidence that the population is evolving. In small populations, genetic drift alone can change allele frequencies purely by chance.

Your turn — Hardy-Weinberg

PCR, electrophoresis and genetic engineering

PCR amplifies DNA in vitro, doubling it every cycle: denaturation at 95 °C (hydrogen bonds break), annealing at 55–65 °C (primers bind), extension at 72 °C (Taq polymerase, from a thermophile, so it survives the 95 °C step, builds the new strands).

Gel electrophoresis: DNA is negatively charged because of its phosphate groups, so it migrates towards the anode (+). Smaller fragments travel further through the gel. Fragments are therefore separated by length, and compared with a ladder of known sizes.

Genetic engineering: isolate the gene (reverse transcriptase on mRNA gives cDNA, which has no introns — essential, because bacteria cannot splice); cut the gene and a plasmid with the same restriction endonuclease to give complementary sticky ends; join with DNA ligase to form recombinant DNA; transform the bacteria (Ca²⁺ and heat shock); identify the transformed cells with a marker gene (e.g. fluorescence, or antibiotic resistance).

Applications and their issues: gene therapy — somatic (affects only the patient; must be repeated) vs germ line (heritable, and prohibited in humans). DNA profiling uses the highly variable short tandem repeats in non-coding DNA — forensics, paternity, and analysis of relatedness. Sequencing has moved from Sanger chain-termination to high-throughput methods, making whole-genome sequencing routine.

Your turn — mark-release-recapture

Clones, cultures and immobilised enzymes

Natural cloning in plants uses vegetative propagation (runners, bulbs, tubers). Artificial plant cloning uses micropropagation and tissue culture: an explant is taken, sterilised, and grown on a nutrient medium with auxins and cytokinins to form a callus, which is then induced to develop into whole plantlets — thousands of genetically identical plants from one parent, quickly and free of disease.

Animal cloning: artificial twinning (splitting an early embryo) or somatic cell nuclear transfer (the nucleus of a body cell is placed into an enucleated egg, which is stimulated to divide — the Dolly method). Uses: producing genetically identical research animals, and pharming.

Microorganisms in biotechnology — fast reproduction, cheap media (often waste products), no ethical objections, and they can be grown anywhere. Batch culture: a fixed volume, growth follows lag → log → stationary → death phases; used for secondary metabolites such as penicillin. Continuous culture: nutrients added and product removed continuously, so the culture is held in the log phase; used for insulin. Asepsis is essential throughout, or the contaminant will out-compete the culture and may produce toxins.

Immobilised enzymes — trapped in alginate beads, adsorbed onto a surface, or covalently bonded. Advantages: the enzyme is easily recovered and re-used, the product is not contaminated with enzyme, and the enzyme is more stable to changes in temperature and pH. Disadvantage: the rate of reaction is somewhat lower, because the substrate must diffuse to the immobilised active site.

Energy transfer, succession and sustainability

Producers convert only about 1–3% of incident light into biomass. Thereafter, roughly 10% of the energy is transferred between trophic levels; the rest is lost in respiration (as heat), and in the parts not eaten or not digested (egested or excreted).

Succession: pioneer species colonise bare rock; they weather it and, on death and decomposition, add humus to form soil. This makes the habitat less hostile, so new species colonise and out-compete the pioneers. Biomass, soil depth and biodiversity all increase until a stable climax community is reached. Human activity (grazing, mowing, burning) can arrest this, producing a plagioclimax — which is why conservation of a heathland or a chalk grassland means active management, not simply leaving it alone.

Populations: growth is limited by density-dependent factors (competition, predation, disease — these intensify as the population grows) and density-independent factors (fire, flood, extreme temperature). The population settles at the carrying capacity. Conservation is the active management of biodiversity — it can be reconciled with sustainable exploitation (rotational coppicing, selective felling, fishing quotas and mesh-size limits).

Your turn — net primary production

Why short food chains?

Which technique or field?

Tap a statement, then tap where it belongs.

Match the technique

Tap an item on the left, then its partner on the right.

The big ideas to take away

That is the whole of OCR Module 6 — Genetics, evolution and ecosystems. Press Finish to see your score.