ATP and chemiosmosis

ATP is the universal energy currency: it is the immediate source of energy for active transport, muscle contraction, protein synthesis and nerve impulses. It is small, soluble, easily transported, and its hydrolysis releases a usefully sized packet of energy — and its phosphate group can be transferred to another molecule to make it more reactive.

Chemiosmosis is how it is made:

• Electrons pass down a chain of carriers, releasing energy at each step.
• That energy drives proton pumps, moving H⁺ across a membrane and creating an electrochemical gradient (a proton motive force).
• Protons flow back down the gradient through ATP synthase, and the energy released drives the phosphorylation of ADP + P_i → ATP.

The elegant point (spec 1(b)): the mitochondrion and the chloroplast do exactly the same thing. Both use an electron transport chain to build a proton gradient across an inner membrane — into the intermembrane space in the mitochondrion, into the thylakoid space in the chloroplast — and both use ATP synthase to cash it in. Learn one mechanism and you have learnt both.

The light-dependent and light-independent reactions

Light-dependent (thylakoid membranes): chlorophyll is photoactivated and loses electrons, which pass along an electron transport chain, pumping protons into the thylakoid space. Chemiosmosis through ATP synthase generates ATP (photophosphorylation). Photolysis of water — 2H₂O → 4H⁺ + 4e⁻ + O₂ — replaces the lost electrons and releases oxygen. NADP is reduced.

Light-independent — the Calvin cycle (stroma):

• Fixation: CO₂ + RuBP (5C), catalysed by rubisco → two molecules of GP (3C).
• Reduction: GP → triose phosphate (3C), using reduced NADP and ATP.
• Regeneration: most of the TP is used to regenerate RuBP; the rest makes hexoses, amino acids and lipids.

Limiting factors: light intensity, CO₂ concentration and temperature. Removing light stops the light-dependent stage, so ATP and reduced NADP run out: GP accumulates and RuBP falls. Removing CO₂ does the opposite: RuBP accumulates and GP falls. Being able to reason this out is worth a great many marks.

Limiting factors

Glycolysis, Krebs and oxidative phosphorylation

Glycolysis (cytoplasm): glucose is phosphorylated using 2 ATP and split into two triose phosphates, which are oxidised to pyruvate, giving 4 ATP (net 2) and 2 reduced NAD. It happens with or without oxygen.

Link reaction (matrix): pyruvate is decarboxylated and dehydrogenated to form acetyl CoA, releasing CO₂ and reduced NAD. Twice per glucose.

Krebs cycle (matrix): acetyl CoA (2C) + oxaloacetate (4C) → citrate (6C). Per turn: 2 CO₂, 3 reduced NAD, 1 reduced FAD, 1 ATP. Two turns per glucose.

Oxidative phosphorylation (inner membrane): the reduced coenzymes are oxidised; electrons pass down the ETC; protons are pumped into the intermembrane space; chemiosmosis through ATP synthase makes the bulk of the ATP. Oxygen is the final electron acceptor, forming water.

Anaerobic: in muscle, pyruvate → lactate; in yeast, pyruvate → ethanal → ethanol + CO₂. In both cases the point is to regenerate NAD so glycolysis can continue. Respiratory substrates: lipids yield most energy per gram (they are the most reduced), then proteins, then carbohydrates.

Where in the cell?

Tap a stage, then tap where it happens.

Your turn — carbon dioxide per glucose

Bacterial growth and aseptic technique

Culturing bacteria needs a suitable nutrient medium (a carbon and a nitrogen source, mineral ions), a suitable temperature and pH, and — for aerobes — oxygen.

Aseptic technique: flame the inoculating loop and the neck of the bottle; work close to a Bunsen flame (the updraught carries airborne microbes away); lift the Petri dish lid as little as possible; tape the lid but do not seal it fully, so that anaerobic pathogens are not favoured; incubate at 25 °C in a school lab, well below body temperature, so that human pathogens are less likely to grow.

The growth curve:

• Lag phase — the bacteria are adapting and synthesising the enzymes they need; there is little division.
• Log (exponential) phase — nutrients are plentiful, so the population doubles at a constant interval (the mean generation time). Plot it on a log scale and it becomes a straight line.
• Stationary phase — nutrients run low and toxic waste accumulates; the death rate equals the reproduction rate.
• Death phase — the death rate exceeds the reproduction rate.

Your turn — bacterial growth

Populations, energy flow and nutrient cycles

Population growth is sigmoid: lag → exponential → stationary at the carrying capacity, where density-dependent factors (competition, predation, disease, waste) limit further growth. Density-independent factors (fire, flood, drought) act regardless of population size.

Energy flow is one-way and lossy: only about 10 % passes between trophic levels, because much is never eaten, some is egested, some excreted, and a lot is lost as heat in respiration.

The nitrogen cycle:

• Nitrogen fixation — Rhizobium (in legume root nodules) and free-living Azotobacter convert N₂ into ammonium.
• Ammonification — saprobiotic bacteria and fungi decompose dead matter and urea, releasing ammonium.
• Nitrification — aerobic nitrifying bacteria oxidise ammonium → nitrite (Nitrosomonas) → nitrate (Nitrobacter).
• Denitrification — anaerobic denitrifying bacteria in waterlogged soil convert nitrate back to N₂.

Your turn — net primary productivity

Your turn — energy transfer

Match the bacterium to the process

Tap the process on the left, then the organism or condition.

Human impact on the environment

• Deforestation — removes habitats, so biodiversity falls; less photosynthesis and the burning of timber both raise atmospheric CO₂; roots no longer bind the soil, so it erodes and leaches, and rivers silt up.
• Eutrophication — fertiliser leaches into water; algae bloom; the bloom blocks the light, so submerged plants die; saprobiotic bacteria decomposing them multiply and their aerobic respiration strips the dissolved oxygen from the water; fish and invertebrates suffocate. Note that the fertiliser does not poison the fish — the bacteria suffocate them.
• Greenhouse gases — CO₂ and CH₄ absorb outgoing long-wave infrared radiation and re-emit it, warming the lower atmosphere. Consequences include shifting species distributions, mismatched life cycles, and rising sea levels.
• Overfishing — removing fish faster than they can reproduce. Managed by quotas, minimum net mesh sizes (so juveniles escape and can breed), and closed seasons and areas.

Sustainability means meeting present needs without compromising the ability of future generations to meet theirs: coppicing and selective felling, crop rotation with legumes, and fish quotas set from population data.

Eutrophication

Why is the ATP yield of anaerobic respiration so low?

The big ideas to know

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