Respiration

ATP is used as the immediate energy source for almost all cellular processes in all organisms, so it acts as a single, common energy currency.

When energy is needed, ATP is hydrolysed in one step (ATP + H₂O → ADP + Pi + energy), releasing a small, manageable packet of energy that is well matched to the needs of cell reactions, with little wasted as heat.

ATP is also soluble and moves within the cell to where energy is required, and it can be rapidly resynthesised from ADP and inorganic phosphate using energy from respiration, so it is continually recycled rather than stored in bulk.

Glycolysis takes place in the cytoplasm and does not require oxygen. First, glucose (6 carbons) is phosphorylated using 2 ATP, making it more reactive.

The phosphorylated 6-carbon sugar is then split into two molecules of triose phosphate (3 carbons each).

Each triose phosphate is oxidised to pyruvate (3 carbons); the hydrogen removed reduces NAD to reduced NAD, and ATP is produced.

In total 4 ATP are made but 2 were used at the start, so the net yield is 2 ATP, together with 2 reduced NAD and 2 pyruvate per glucose.

NAD and FAD are coenzymes that act as hydrogen (and electron) carriers. During glycolysis, the link reaction and the Krebs cycle they are reduced — they accept hydrogen atoms removed from respiratory substrates, becoming reduced NAD and reduced FAD.

They then carry this hydrogen/reducing power to the electron transport chain on the inner mitochondrial membrane.

There they are oxidised (releasing electrons and protons to the chain) and so are regenerated back to NAD and FAD, ready to pick up more hydrogen. In this way they link the earlier stages of respiration to oxidative phosphorylation.

Oxidative phosphorylation takes place on the inner mitochondrial membrane (cristae). The reduced NAD and reduced FAD made in the earlier stages are oxidised, releasing hydrogen atoms that split into electrons and protons (H⁺).

The electrons are passed along a series of electron carriers (the electron transport chain) embedded in the inner membrane, moving from higher to lower energy levels.

The energy released as the electrons pass down the chain is used to pump protons (H⁺) from the matrix into the intermembrane space, building up a high concentration of H⁺ there — a proton (electrochemical) gradient across the inner membrane.

The protons then diffuse back into the matrix down their gradient through the channel enzyme ATP synthase.

As the protons flow through, ATP synthase catalyses the synthesis of ATP from ADP and inorganic phosphate (Pi); this mechanism is called chemiosmosis.

Finally, the electrons and protons leaving the chain combine with oxygen, the final electron acceptor, to form water (½O₂ + 2H⁺ + 2e⁻ → H₂O); this keeps the chain running by removing the electrons so the carriers can be re-oxidised.

Glycolysis (in the cytoplasm) gives a net 2 ATP by substrate-level phosphorylation, plus 2 reduced NAD.

The link reaction makes no ATP directly but produces 2 reduced NAD (per glucose).

The Krebs cycle (matrix), turning twice per glucose, makes 2 ATP by substrate-level phosphorylation, plus 6 reduced NAD and 2 reduced FAD.

The bulk of the ATP comes from oxidative phosphorylation on the inner membrane: the reduced NAD and reduced FAD from all stages are oxidised, and each reduced NAD yields about 2.5 ATP and each reduced FAD about 1.5 ATP, giving roughly 26–28 ATP.

Adding these together (≈2 + 2 + 28) gives a total of about 32 ATP per glucose; the value is approximate because some ATP is used to transport pyruvate and reduced NAD into the mitochondrion.

In substrate-level phosphorylation, ATP is made by directly transferring a phosphate group from a phosphorylated substrate molecule to ADP, catalysed by an enzyme. It does not require an electron transport chain or oxygen, and it occurs in glycolysis (in the cytoplasm) and in the Krebs cycle (in the mitochondrial matrix).

In oxidative phosphorylation, ATP is not made directly from a substrate; instead the immediate energy source is the flow of protons (H⁺) down an electrochemical gradient through ATP synthase (chemiosmosis). This gradient is built across the inner mitochondrial membrane using energy released as electrons pass down the electron transport chain, and it ultimately depends on oxygen acting as the final electron acceptor.

The two also differ greatly in yield: substrate-level phosphorylation gives only a small number of ATP (a net 2 from glycolysis and 2 from the Krebs cycle per glucose), whereas oxidative phosphorylation produces the large majority of the ATP (about 26–28 per glucose).

A further difference is their dependence on oxygen: substrate-level phosphorylation can still occur without oxygen (so it continues in anaerobic respiration/glycolysis), whereas oxidative phosphorylation stops without oxygen, because the electron transport chain has no final electron acceptor.

In both human muscle and yeast, anaerobic respiration begins with glycolysis in the cytoplasm, producing pyruvate, a net 2 ATP and reduced NAD.

In human muscle (lactate fermentation), the pyruvate is reduced to lactate by accepting hydrogen from reduced NAD (pyruvate + reduced NAD → lactate + NAD). No CO₂ is released, and the lactate can later be oxidised back to pyruvate in the liver when oxygen is available.

In yeast (alcoholic fermentation), the pyruvate is first decarboxylated to release CO₂ and then reduced to ethanol (regenerating NAD). Unlike lactate, ethanol cannot be reconverted and is toxic to yeast at high concentrations.

In both cases the key purpose is to regenerate NAD so that glycolysis can continue to produce ATP.

Both yield far less ATP because, without oxygen, there is no final electron acceptor, so the electron transport chain stops and the link reaction and Krebs cycle cannot run. Respiration therefore stops after glycolysis, giving only the net 2 ATP, and most of the glucose's chemical energy remains locked in the lactate or ethanol rather than being released.

(a) $RQ = \dfrac{\text{CO}_2 \text{ produced}}{\text{O}_2 \text{ consumed}} = \dfrac{216}{240} = 0.90$ (no units).

(b) An RQ of about 0.9 suggests the main substrate is protein (carbohydrate gives an RQ of 1.0 and lipid about 0.7, so 0.9 lies between them and matches protein). More likely, a value near 0.9 indicates a mixture of substrates being respired (mostly carbohydrate with some lipid), but the closest single-substrate match is protein.

(c) An RQ greater than 1.0 (here 1.3) cannot be produced by purely aerobic respiration of any normal substrate, because aerobic respiration never releases more CO₂ than the O₂ it uses. It indicates that the organism is carrying out some anaerobic respiration (e.g. alcoholic fermentation), which releases additional CO₂ without using extra oxygen, so the CO₂:O₂ ratio rises above 1.0.

Oxygen is the final electron acceptor at the end of the electron transport chain. When oxygen is removed, the electrons (and H⁺) have nowhere to go, so the electron transport chain becomes blocked / backs up.

Because the carriers stay reduced, no more H⁺ are pumped across the inner membrane, the proton gradient collapses, and ATP synthase can no longer make ATP by chemiosmosis — so oxidative phosphorylation stops.

With the chain blocked, reduced NAD and reduced FAD cannot be re-oxidised, so there is no supply of NAD/FAD for the Krebs cycle and link reaction, which therefore also stop.

The only stage that can continue is glycolysis, but only if NAD is regenerated by fermentation (lactate, or ethanol + CO₂).

As a result, ATP production falls dramatically to just the net 2 ATP per glucose from glycolysis, instead of the ~32–38 ATP made aerobically.

The germinating seeds are sealed in a tube connected to a capillary tube containing a coloured liquid (manometer). A chemical such as soda lime or potassium hydroxide is placed in the tube to absorb the carbon dioxide produced by the seeds.

Because CO₂ is absorbed but the seeds still take up oxygen, the volume of gas in the sealed tube decreases. This reduced pressure draws the coloured liquid along the capillary tube towards the seeds.

The distance the liquid moves in a measured time, multiplied by the cross-sectional area of the tube, gives the volume of oxygen consumed per unit time — the rate of respiration. The apparatus is kept at a constant temperature in a water bath.

(i) The CO₂ absorber ensures that the only change in gas volume is due to oxygen uptake; if CO₂ were not absorbed, the CO₂ released would offset the O₂ taken up and the liquid would not move accurately.

(ii) The control tube with glass beads (same volume, no living material) experiences the same changes in temperature and atmospheric pressure, so any movement of liquid in the control is subtracted to correct for these abiotic factors, making the results valid.