Glycolysis, the link reaction and the Krebs cycle

Glycolysis (cytoplasm): glucose is phosphorylated using 2 ATP, making it more reactive, and splits into two triose phosphate molecules. These are oxidised to pyruvate, producing 4 ATP (substrate-level phosphorylation) and 2 reduced NAD. Net yield: 2 ATP. Glycolysis is the same whether or not oxygen is present.

Link reaction (mitochondrial matrix), per pyruvate: decarboxylation (CO₂ removed) and dehydrogenation (NAD reduced) give a 2-carbon acetyl group, which joins coenzyme A → acetyl CoA. It happens twice per glucose.

Krebs cycle (matrix), per turn: acetyl CoA (2C) + oxaloacetate (4C) → citrate (6C); a series of decarboxylations and dehydrogenations regenerates oxaloacetate.

Your turn — carbon dioxide released

Oxidative phosphorylation, anaerobic respiration and RQ

Oxidative phosphorylation (inner mitochondrial membrane): reduced NAD and reduced FAD are oxidised; their electrons pass along the electron transport chain, releasing energy that pumps protons from the matrix into the intermembrane space. The protons then flow back through ATP synthase — chemiosmosis — and the energy released phosphorylates ADP to ATP. Oxygen is the final electron acceptor, combining with electrons and protons to form water. Without oxygen, the chain backs up, no NAD is regenerated, and the Krebs cycle stops.

Anaerobic respiration: only glycolysis can continue, and only if NAD is regenerated.

• Animals: pyruvate + reduced NAD → lactate (lactate dehydrogenase).
• Yeast and plants: pyruvate → ethanal + CO₂ → ethanol.
• Oxygen debt: the extra oxygen needed afterwards to oxidise the accumulated lactate and resynthesise ATP.

A respirometer with soda lime absorbs the CO₂ produced, so any movement of the manometer fluid is caused purely by oxygen uptake. Run it without soda lime and the movement gives the difference between O₂ consumed and CO₂ produced — from which the RQ can be calculated.

Your turn — respiratory quotient

Match the stage to its site and yield

Tap a stage on the left, then its site and main product.

The light-dependent stage and the Z-scheme

Site: the thylakoid membranes.

• Light is absorbed by photosystem II (PSII): chlorophyll is photoactivated and two electrons are excited to a higher energy level and captured by an electron acceptor.
• The electrons pass along an electron transport chain from PSII to PSI. The energy released is used to build a proton gradient across the thylakoid membrane, and protons flowing back through ATP synthase generate ATP: photophosphorylation. This whole path — up, down, up, down — is the Z-scheme.
• The electrons lost from PSII are replaced from the dissociation of water: 2H₂O → 4H⁺ + 4e⁻ + O₂ (photolysis). Oxygen is the waste product.
• Light also photoactivates PSI; its excited electrons are passed to the final acceptor NADP, which, with H⁺ from the water, is reduced to NADPH (reduced NADP).

Products passed on: ATP and reduced NADP.

The Calvin cycle, spectra and limiting factors

Site: the stroma.

• Fixation: CO₂ combines with ribulose bisphosphate (RuBP, 5C), catalysed by rubisco, giving two molecules of glycerate phosphate (GP, 3C).
• Reduction: GP is reduced to triose phosphate (TP, 3C) using NADPH and ATP.
• Regeneration: five-sixths of the TP is used, with more ATP, to regenerate RuBP; the remaining one-sixth is used to make hexose sugars and other compounds.

Pigments (5.2.4): an absorption spectrum shows how much light of each wavelength a pigment absorbs (chlorophyll a and b peak in the blue and red, reflecting green). An action spectrum shows the rate of photosynthesis at each wavelength. The close match between the two is strong evidence that these pigments are the ones actually driving photosynthesis.

Limiting factors (5.2.5): light intensity, CO₂ concentration and temperature. The compensation point is the light intensity at which the rate of photosynthesis exactly equals the rate of respiration, so there is no net gas exchange. Gross photosynthesis is the total fixed; net photosynthesis is what is left after the plant’s own respiration.

Light-dependent or Calvin cycle?

Tap an event, then tap the stage it belongs to.

Your turn — pigment R_f

The genetic code and gene technology

A gene is a sequence of bases coding for a sequence of amino acids. The code is triplet, non-overlapping, degenerate and universal.

Transcription: RNA polymerase reads the DNA template strand and builds a complementary mRNA. In eukaryotes, the primary transcript is spliced: introns are removed and exons joined.

Translation: on the ribosome, each mRNA codon is read by the complementary anticodon of a tRNA carrying a specific amino acid; peptide bonds join them into a polypeptide.

Gene technology (5.4):

• Restriction enzymes cut DNA at specific palindromic recognition sequences, often leaving sticky ends.
• DNA ligase joins the gene into a plasmid vector cut with the same restriction enzyme, so the sticky ends are complementary — giving recombinant DNA.
• Bacteria take up the plasmid (transformation); marker genes identify the transformed cells.
• PCR amplifies DNA: denature at 95 °C, anneal primers at 50–65 °C, extend with Taq polymerase at 72 °C. Each cycle doubles the DNA.
• Gel electrophoresis separates fragments by size: DNA is negatively charged, so it moves to the anode, and shorter fragments travel further. This underpins genetic fingerprinting.

Inheritance — beyond the simple monohybrid

• Monohybrid — one gene. Heterozygous × heterozygous gives the classic 3:1 phenotypic ratio (Mendel’s law of segregation).
• Dihybrid — two unlinked genes. Double heterozygotes give 9:3:3:1 (Mendel’s law of independent assortment).
• Codominance — both alleles are expressed in the heterozygote (roan cattle; the AB blood group). Note this is not blending.
• Multiple alleles — more than two alleles exist in the population (ABO blood groups: I^A, I^B, I^O).
• Lethal alleles — a genotype that dies before birth, so an expected class is missing: a 3:1 cross becomes 2:1.
• Test cross — cross the unknown dominant phenotype with the homozygous recessive. Any recessive offspring proves the parent was heterozygous.
• Epistasis — one gene masks or modifies the expression of another, distorting the 9:3:3:1 ratio (e.g. to 9:3:4 or 9:7).
• Sex linkage — genes on the X chromosome. Males (XY) are hemizygous, so a single recessive allele is expressed: haemophilia and red-green colour blindness are far more common in males, and a carrier mother passes the allele to half her sons.
• Polygenic inheritance — many genes with small additive effects, plus the environment, give continuous variation.

Sex linkage

Hardy–Weinberg, selection and speciation

The gene pool is the total of all the alleles in a population.

The Hardy–Weinberg principle describes a population at genetic equilibrium, with alleles combining randomly at fertilisation. It only applies if the population is large, mating is random, and there is no mutation, no migration and no selection. If those conditions are broken, allele or genotype frequencies change — and that change in allele frequency is evolution.

Selection (5.6.4): fitness is the set of features allowing an organism to survive and reproduce in its environment. Selection is the differential perpetuation of alleles.

• Stabilising selection favours the modal / intermediate variants (e.g. human birth mass), reducing variation and maintaining the status quo.
• Directional selection favours one extreme, shifting the mean — for example antibiotic resistance in bacteria, or industrial melanism.

Speciation (5.6.5): a species is a group of common ancestry that can normally interbreed to produce fertile offspring. In allopatric speciation a geographical barrier separates two populations; different selection pressures and mutations make them diverge genetically until reproductive isolating mechanisms maintain the divergence even if they meet again. Heterozygotes are important reservoirs of variation, because they carry recessive alleles that selection cannot see.

Your turn — Hardy–Weinberg

Which kind of selection?

Evolutionary trends — moss, fern, angiosperm

The trend from moss to flowering plant is a story of increasing adaptation to life on land.

• Moss — multicellular but not differentiated into true leaves, stem and roots. No cuticle or stomata (except in the spore-producing structures) and no vascular tissue, so support comes only from turgor. Rhizoids attach it but do not penetrate deeply, so mosses are restricted to moist habitats where water is near the surface. Dispersal by spores that need moist conditions to germinate.
• Fern — better adapted to land: well differentiated, with true roots, stems and leaves and a vascular system. It has a waterproof cuticle and fine control over stomata. Support comes from turgor and from lignified xylem. Still dispersed by spores that need moisture.
• Angiosperm (flowering plant) — has all the fern’s water-retention and support features, but more highly evolved: extensive xylem tissue forming wood, and xerophytic adaptations for dry habitats. Crucially, dispersal is by seeds with a tough outer coat that withstands desiccation — so reproduction is no longer tied to water.

Evolutionary trends — Cnidaria, Platyhelminthes, Annelida

• Phylum Cnidaria (hydra, jellyfish) — multicellular and radially symmetrical. Supported by the aqueous medium and by a hydrostatic skeleton formed by the fluid-filled enteron. A single body opening.
• Phylum Platyhelminthes (planarian, liver fluke) — bilaterally symmetrical and flattened dorso-ventrally (which keeps every cell close to the surface, so diffusion suffices). A single opening to the gut. No specialised skeletal system; supported by the body tissue itself.
• Phylum Annelida (earthworm, lugworm) — bilaterally symmetrical and segmented, with a fluid-filled coelom acting as a hydrostatic skeleton against which the circular and longitudinal muscles can work antagonistically. A through-gut with a separate mouth and anus, allowing continuous feeding and regional specialisation of the gut.

The trend to read off: radial → bilateral symmetry; a single gut opening → a through-gut; no skeleton → a hydrostatic skeleton; unsegmented → segmented. Each step supports greater size, greater activity and greater specialisation.

The big ideas to know

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