Notes · BiologyUK · A-Levels

Energy transfers in and between organisms

Life is sustained by the capture, transfer and release of energy. This A-level chapter covers photosynthesis (the light-dependent reactions and the Calvin cycle), respiration (glycolysis, the link reaction, the Krebs cycle and oxidative phosphorylation), the flow of energy and biomass through ecosystems, and the recycling of nitrogen and phosphorus.

6 sections~19 min reading time3 competenciesLevel Advanced 6

T·0555 / 8

Exam profile

AO1 · Describe the stages and sites of photosynthesis and respiration and the nutrient cyclesAO2 · Apply net-production, energy-efficiency and biomass calculations and interpret limiting-factor dataAO3 · Analyse experimental data on photosynthesis and respiration and evaluate agricultural and eutrophication data

Operators:describeexplaincalculatecompareanalyseevaluatededuce

basic level

This whole topic is A-level (A2) only; it is not part of the AS qualification.

higher level

The full A-Level requires the biochemical detail of both pathways, their sites, and quantitative work on energy transfer and nutrient cycling.

Depth

Text

Contents · 6 sections

Energy transfers in and between organisms

Photosynthesis: the light-dependent reactions#

AdvancedAQA 7402 3.5.1DfE GCE Biology - photosynthesis

The chloroplast

Fig. 1The light-dependent reactions occur on the thylakoid membranes; the Calvin cycle occurs in the stroma.

Photosynthesis captures light energy and stores it as chemical energy in organic molecules, and it occurs in two stages in the chloroplast. The light-dependent reactions take place on the thylakoid membranes of the grana, where the light-harvesting pigments are held; the light-independent Calvin cycle takes place in the surrounding stroma. Separating the two stages in different compartments, each with the appropriate enzymes and membranes, makes the whole process efficient.

In the light-dependent reactions, light energy absorbed by chlorophyll excites electrons to a higher energy level; these electrons leave the chlorophyll and pass along a chain of electron carriers in the thylakoid membrane. As they pass down the chain they release energy, which is used to move protons into the thylakoid space, creating a proton gradient. The protons then flow back through the enzyme ATP synthase, and this flow drives the synthesis of ATP - a process called photophosphorylation (specifically, chemiosmosis).

The electrons lost from chlorophyll are replaced by the photolysis of water: light energy splits water into protons, electrons and oxygen (

2\text{H}_2\text{O} \rightarrow 4\text{H}^+ + 4e^- + \text{O}_2

). This is the source of the oxygen released by plants and of the protons and electrons used in the reactions. At the end of the chain, the electrons and protons reduce the coenzyme NADP to reduced NADP (NADPH).

The products of the light-dependent stage are therefore ATP, reduced NADP and oxygen. The ATP and reduced NADP are passed to the stroma to power the Calvin cycle, while the oxygen is a by-product that diffuses out. This is why the two stages are linked: the light-independent reactions cannot proceed without the ATP and reduced NADP made in the light, which is one reason the rate of the whole process depends on light.

2\,\text{H}_2\text{O} \rightarrow 4\,\text{H}^+ + 4\,e^- + \text{O}_2

Photolysis of water

Light splits water, providing electrons to replace those lost by chlorophyll, protons for the gradient, and oxygen as a by-product.

The light-dependent reactions

Fig. 2Photolysis replaces electrons; the electron chain drives ATP synthesis (chemiosmosis) and reduces NADP.

Worked example

Linking the two stages

A plant is moved suddenly from light into darkness. Explain what happens to the levels of the products of the light-dependent stage and, in turn, to the Calvin cycle intermediates.

Light-dependent products fall
In darkness there is no light to excite electrons, so ATP and reduced NADP are no longer made and their levels fall.
Effect on the Calvin cycle
The conversion of GP to TP needs ATP and reduced NADP, so it slows; GP accumulates and TP (and RuBP) fall.
Conclude
GP rises while TP and RuBP fall - the classic evidence linking the light-dependent stage to the Calvin cycle.

Result: ATP and reduced NADP fall; GP accumulates while TP and RuBP decrease.

Typical mistakes

Placing the light-dependent reactions in the stroma - they occur on the thylakoid membranes.
Saying the oxygen comes from carbon dioxide - it comes from the photolysis of water.

Active revision

Explain how ATP is synthesised in the light-dependent reactions, referring to the electron transport chain, the proton gradient and ATP synthase.

Active recall

Recall the key points — then reveal.

Sources: GCE AS and A level subject content for the sciences (Department for Education) · AQA A-level Biology 7402 specification (AQA)

Photosynthesis: the Calvin cycle and limiting factors#

AdvancedAQA 7402 3.5.1DfE GCE Biology - the Calvin cycle

The Calvin cycle

Fig. 3Rubisco fixes CO2 onto RuBP; ATP and reduced NADP reduce GP to TP; most TP regenerates RuBP.

The light-independent reactions (the Calvin cycle) take place in the stroma and use the ATP and reduced NADP from the light-dependent stage to fix carbon dioxide into organic molecules. Carbon dioxide combines with the 5-carbon acceptor ribulose bisphosphate (RuBP), catalysed by the enzyme rubisco, to form two molecules of the 3-carbon glycerate 3-phosphate (GP). Fixing an inorganic gas into an organic molecule is the point at which carbon enters the living world.

GP is then reduced to triose phosphate (TP), a 3-carbon sugar, using the reduced NADP (as a source of hydrogen/electrons) and ATP (as a source of energy) made in the light. Some TP is used to make useful organic products - glucose, and from it starch, cellulose, amino acids and lipids - but most TP must be used to regenerate RuBP so that the cycle can continue, and this regeneration also uses ATP.

The stoichiometry is worth understanding: because RuBP has five carbons and CO2 adds only one, it takes several turns of the cycle to make a hexose sugar. To synthesise one molecule of glucose (6 carbons) the cycle must fix six molecules of CO2, which requires six turns, using 18 ATP and 12 reduced NADP in total. This explains the heavy demand the Calvin cycle places on the products of the light-dependent stage.

The rate of photosynthesis is controlled by limiting factors - the factor in shortest supply limits the rate. Light intensity, carbon dioxide concentration and temperature can each be limiting: at low light, increasing light raises the rate (light limiting); at higher light the rate plateaus because another factor (CO2 or temperature) becomes limiting. Understanding limiting factors is directly applied in commercial glasshouses, where growers raise CO2, light and temperature to increase yield up to the point where a further factor limits.

6\,\text{CO}_2 \rightarrow 1\ \text{glucose}: \ \text{6 turns, 18 ATP, 12 reduced NADP}

Making one hexose

Each turn fixes one CO2; six turns are needed for the six carbons of glucose.

Rate against a limiting factor

Fig. 4Rate rises while the factor is limiting, then plateaus when another factor takes over.

Worked example

Turns of the Calvin cycle

Calculate how many turns of the Calvin cycle, and how much ATP and reduced NADP, are needed to produce two molecules of glucose.

Per glucose
One glucose (6C) needs 6 turns, fixing 6 CO2, using 18 ATP and 12 reduced NADP.
For two glucose
Multiply by two: $6 \times 2 = 12$ turns.
$12\ \text{turns},\ 36\ \text{ATP},\ 24\ \text{reduced NADP}$

Result: 12 turns, 36 ATP and 24 reduced NADP.

Typical mistakes

Saying GP is reduced 'by the light' - it is reduced using reduced NADP and ATP made in the light.
Forgetting that most TP is used to regenerate RuBP, not to make glucose.

Active revision

A glasshouse grower increases light intensity but sees no further rise in the rate of photosynthesis. Explain this result and suggest what the grower should change.

Active recall

Recall the key points — then reveal.

Sources: GCE AS and A level subject content for the sciences (Department for Education) · AQA A-level Biology 7402 specification (AQA)

Respiration: glycolysis and the link reaction#

AdvancedAQA 7402 3.5.2DfE GCE Biology - respiration

Glycolysis and the link reaction

Fig. 5Glycolysis (cytoplasm) gives a net 2 ATP and 2 reduced NAD; the link reaction (matrix) forms acetyl CoA.

Respiration releases the energy stored in organic molecules to make ATP, in a series of stages located in the cytoplasm and the mitochondria. The first stage, glycolysis, takes place in the cytoplasm and does not require oxygen. Glucose (6 carbons) is first phosphorylated using two molecules of ATP (an investment that makes it reactive), then split into two molecules of the 3-carbon triose phosphate.

Each triose phosphate is then oxidised to pyruvate (3 carbons), a step that produces ATP and reduced NAD. In total, glycolysis converts one glucose into two pyruvate molecules, with a net gain of two ATP (four made minus the two used) and two reduced NAD. Because it needs no oxygen, glycolysis is the starting point for both aerobic and anaerobic respiration, and it is common to all living organisms.

If oxygen is available, the pyruvate enters the mitochondrial matrix for the link reaction. Here each pyruvate is oxidised (losing a carbon as CO2, called decarboxylation) and combined with coenzyme A to form acetylcoenzyme A (2 carbons), producing reduced NAD. Because one glucose gives two pyruvate, the link reaction happens twice per glucose, releasing two CO2 and two reduced NAD.

The reduced NAD (and later reduced FAD) produced at each stage is the key link to the final ATP-generating stage. These reduced coenzymes carry the hydrogen atoms (electrons) to the inner mitochondrial membrane, where the bulk of the ATP is made by oxidative phosphorylation. In other words, glycolysis and the link reaction release comparatively little ATP directly; their main role is to strip electrons from glucose onto coenzymes for the electron transport chain.

\text{glucose} \rightarrow 2\ \text{pyruvate} + 2\,\text{ATP (net)} + 2\ \text{reduced NAD}

Net yield of glycolysis

Four ATP are made and two used, a net gain of two; no oxygen is required.

Worked example

Accounting for the products of glycolysis

Starting from one molecule of glucose, state the total number of ATP molecules used and made in glycolysis, the net ATP, and the number of reduced NAD and pyruvate molecules produced.

ATP investment
2 ATP are used to phosphorylate glucose.
ATP made
4 ATP are made as the two triose phosphates are oxidised to pyruvate.
Net and other products
Net ATP = $4 - 2 = 2$ ; also 2 reduced NAD and 2 pyruvate are produced.
$4 - 2 = 2\ \text{ATP net}$

Result: 2 used, 4 made, net 2 ATP, plus 2 reduced NAD and 2 pyruvate.

Typical mistakes

Giving the ATP yield of glycolysis as 4 (the gross) rather than 2 (the net after the initial investment).
Placing glycolysis in the mitochondrion - it occurs in the cytoplasm.

Active revision

Explain why glycolysis can occur in a cell that has no mitochondria and no oxygen, and state what happens to the pyruvate in these conditions.

Active recall

Recall the key points — then reveal.

Sources: GCE AS and A level subject content for the sciences (Department for Education) · AQA A-level Biology 7402 specification (AQA)

Respiration: the Krebs cycle and oxidative phosphorylation#

AdvancedAQA 7402 3.5.2DfE GCE Biology - the Krebs cycle and chemiosmosis

The mitochondrion

Fig. 6The Krebs cycle occurs in the matrix; oxidative phosphorylation on the inner membrane (cristae).

The Krebs cycle takes place in the mitochondrial matrix. The 2-carbon acetyl coenzyme A combines with a 4-carbon acceptor to form a 6-carbon compound (citrate); a series of reactions then regenerates the 4-carbon acceptor, releasing two molecules of carbon dioxide (decarboxylation) and reducing coenzymes (three reduced NAD and one reduced FAD) with one ATP made directly (by substrate-level phosphorylation) per turn. Because one glucose gives two acetyl CoA, the cycle turns twice per glucose.

The main purpose of glycolysis, the link reaction and the Krebs cycle is not the small amount of ATP they make directly, but the reduced coenzymes (reduced NAD and reduced FAD) they produce. These carry pairs of electrons (as hydrogen atoms) to the inner mitochondrial membrane, where the last and most productive stage - oxidative phosphorylation - takes place.

In oxidative phosphorylation the electrons from the reduced coenzymes pass along the electron transport chain, a series of carriers in the inner membrane. As they pass down the chain they release energy, which is used to pump protons from the matrix into the intermembrane space, building a proton gradient. The protons flow back into the matrix through ATP synthase, and this flow drives the synthesis of most of the cell's ATP - the same chemiosmotic mechanism as in photosynthesis.

Oxygen is the final electron acceptor: at the end of the chain it accepts the electrons and protons to form water. This is why oxygen is essential for aerobic respiration - if it is absent, the electron transport chain backs up, the reduced coenzymes cannot be re-oxidised, and the Krebs cycle and link reaction stop. In anaerobic conditions, cells fall back on glycolysis alone, re-oxidising reduced NAD by making lactate (in animals) or ethanol and CO2 (in plants and yeast) so that glycolysis, and its small ATP yield, can continue.

\text{C}_6\text{H}_{12}\text{O}_6 + 6\,\text{O}_2 \rightarrow 6\,\text{CO}_2 + 6\,\text{H}_2\text{O} + \text{ATP}

Overall aerobic respiration

Glucose is fully oxidised; oxygen is the final electron acceptor, forming water.

Oxidative phosphorylation

Fig. 7Electrons from reduced coenzymes drive proton pumping; oxygen is the final electron acceptor.

Worked example

Why blocking oxygen stops respiration

Explain why a cell treated with a chemical that prevents oxygen acting as the final electron acceptor rapidly stops making ATP by oxidative phosphorylation and stops the Krebs cycle.

Electrons cannot be removed
Without oxygen to accept electrons at the end of the chain, electrons cannot flow along it, so no proton gradient is made and ATP synthase stops making ATP.
Coenzymes stay reduced
Reduced NAD and reduced FAD cannot be re-oxidised, so there is no oxidised NAD to accept hydrogen.
Krebs cycle halts
The Krebs cycle and link reaction need oxidised NAD, so without it they stop; only glycolysis (anaerobic) can continue.

Result: Oxidative phosphorylation and the Krebs cycle stop; the cell relies on anaerobic glycolysis alone.

Typical mistakes

Saying most ATP is made in the Krebs cycle - most is made by oxidative phosphorylation on the inner membrane.
Forgetting that anaerobic respiration re-oxidises reduced NAD so that glycolysis can continue.

Active revision

A poison blocks the final electron acceptor in the electron transport chain. Explain the effect this has on ATP production and on the Krebs cycle.

Active recall

Recall the key points — then reveal.

Sources: GCE AS and A level subject content for the sciences (Department for Education) · AQA A-level Biology 7402 specification (AQA)

Energy and biomass transfer through ecosystems#

AdvancedAQA 7402 3.5.3DfE GCE Biology - energy and ecosystems

A pyramid of energy

Fig. 8Energy falls sharply between trophic levels, so the pyramid narrows towards the top.

Biomass is the mass of living material, and it stores chemical energy. It can be measured as the dry mass (after removing water) or, more informatively, as the chemical energy it contains, found by burning a sample in a calorimeter and measuring the heat released. Working in dry mass or energy per unit area per unit time lets us compare productivity fairly between ecosystems.

Plants (producers) capture only a small fraction of the light energy reaching them - most is reflected, transmitted, of the wrong wavelength, or lost as heat. The rate at which they store energy in biomass is the gross primary production (GPP). Plants use some of this stored energy in respiration (R); what is left is the net primary production,

\text{NPP} = \text{GPP} - R

, the energy available to the next trophic level and for the plant's own growth.

Energy is transferred inefficiently from one trophic level to the next: only about 10% of the energy in one level typically becomes biomass in the next. Energy is lost because not all of an organism is eaten or digestible, some is lost as heat from respiration, and some leaves in excretory and egestory products (urine and faeces). The efficiency of transfer is calculated as (energy or biomass transferred / energy or biomass available) x 100.

These losses explain the shape of ecological pyramids and the structure of food chains. Because so much energy is lost at each step, food chains are usually short (rarely more than four or five links) and the biomass or energy at each level falls sharply - giving a pyramid of energy that always narrows towards the top. Farming aims to improve the efficiency of energy transfer to humans, for example by limiting the respiratory and movement losses of livestock or by controlling pests that compete for the crop.

\text{NPP} = \text{GPP} - R

Net primary production

GPP is the total energy fixed; R is the energy lost in respiration; NPP is what remains for growth and the next level.

\text{efficiency} = \dfrac{\text{energy transferred}}{\text{energy available}} \times 100

Energy transfer efficiency

Typically about 10% between animal trophic levels.

Energy transfer efficiency

Fig. 9Only about a tenth of the energy at one level is passed to the next.

Worked example

NPP and transfer efficiency

Producers fix 90 000 kJ m-2 yr-1 (GPP) and respire 30 000 kJ m-2 yr-1. Primary consumers store 6000 kJ m-2 yr-1 in biomass. Calculate the NPP of the producers and the efficiency of energy transfer to the primary consumers.

Net primary production
$\text{NPP} = 90\,000 - 30\,000 = 60\,000$ kJ m-2 yr-1.
Efficiency of transfer
Energy available to the consumers is the NPP; efficiency = (6000 / 60 000) x 100.
$\frac{6000}{60\,000} \times 100 = 10\%$

Result: NPP = 60 000 kJ m-2 yr-1; transfer efficiency = 10%.

Typical mistakes

Confusing GPP (total fixed) with NPP (after respiration), or forgetting to subtract respiration.
Dividing by the wrong figure when calculating efficiency (divide by the energy available at the lower level).

Active revision

A crop has a gross primary production of 25 000 kJ m-2 yr-1 and loses 9000 kJ m-2 yr-1 in respiration. Calculate its net primary production.

Active recall

Recall the key points — then reveal.

Sources: GCE AS and A level subject content for the sciences (Department for Education) · AQA A-level Biology 7402 specification (AQA)

Nutrient cycles and the use of fertilisers#

AdvancedAQA 7402 3.5.4DfE GCE Biology - nutrient cycles

The nitrogen cycle

Fig. 10Four microbial processes move nitrogen between the air, the soil and living organisms.

Unlike energy, which flows through an ecosystem and is lost as heat, nutrients such as nitrogen and phosphorus are recycled. Microorganisms are central to these cycles: saprobionts (decomposers) feed on dead organisms and waste, releasing nutrients back into the soil, and other bacteria carry out the specific conversions of the nitrogen cycle. Mycorrhizae - mutualistic fungi associated with plant roots - greatly increase the surface area for the uptake of water and mineral ions, especially phosphate.

The nitrogen cycle has four microbial processes to know. Nitrogen fixation converts atmospheric nitrogen gas into ammonium (by nitrogen-fixing bacteria, some free-living, some in root nodules); ammonification converts nitrogen in dead organisms and waste into ammonium (by saprobionts); nitrification converts ammonium to nitrite and then nitrate (by nitrifying bacteria, an oxidation needing oxygen); and denitrification converts nitrate back to nitrogen gas (by denitrifying bacteria in anaerobic, waterlogged soils). Plants absorb nitrogen as nitrate and use it to make amino acids and nucleotides.

The phosphorus cycle differs from the nitrogen cycle in that it has no gaseous phase: phosphorus is released from rock by weathering, taken up by plants as phosphate ions, passed along food chains, and returned to the soil by decomposers, with mycorrhizae aiding uptake. Phosphate is a component of DNA, RNA, ATP and phospholipids, so it is essential, and its slow release from rock means it is often a limiting nutrient.

Farmers add fertilisers to replace the nitrogen and phosphorus removed when crops are harvested. Natural fertilisers (manure) and artificial (inorganic) fertilisers both raise productivity, but excess soluble fertiliser can be leached into waterways, causing eutrophication: the nutrients cause algae to grow rapidly (an algal bloom) that blocks light, so plants below die; decomposing bacteria then multiply and use up the dissolved oxygen in respiration, so fish and other aerobic organisms die. Evaluating this trade-off between yield and pollution is a classic assessment task.

Worked example

The sequence of eutrophication

Put the following into the correct causal order and explain: algal bloom, fish die, nitrate leaches into water, plants die, bacteria deplete oxygen.

Nutrient enrichment
Nitrate leaches into the water, providing a surplus of a limiting nutrient.
Bloom and shading
Algae grow rapidly (algal bloom) at the surface, blocking light so that submerged plants cannot photosynthesise and die.
Oxygen depletion
Saprobiotic bacteria decompose the dead plants and algae and multiply, using up the dissolved oxygen in aerobic respiration, so fish and other aerobic organisms die.

Result: Nitrate leaches -> algal bloom -> plants die -> bacteria deplete oxygen -> fish die.

Typical mistakes

Confusing nitrification (ammonium to nitrate, needs oxygen) with denitrification (nitrate to nitrogen gas, in anaerobic soil).
Saying algae 'use up all the oxygen' - it is the decomposing bacteria respiring that deplete the oxygen after the algae die.

Active revision

Explain how the leaching of nitrate fertiliser from a field into a nearby lake can lead to the death of fish in the lake.

Active recall

Recall the key points — then reveal.

Sources: GCE AS and A level subject content for the sciences (Department for Education) · AQA A-level Biology 7402 specification (AQA)

References & sources

Sources

Department for Education

GCE AS and A level subject content for the sciences

AQA

AQA A-level Biology 7402 specification

Energy transfers in and between organisms

6 sections~19 min reading time3 competenciesLevel Advanced 6

Energy transfers in and between organisms

Key points

Linking the two stages

Key points

Turns of the Calvin cycle

Key points

Accounting for the products of glycolysis

Key points

Why blocking oxygen stops respiration

Key points

NPP and transfer efficiency

Key points

The sequence of eutrophication

Sources

Energy transfers in and between organisms

Key points

Linking the two stages

Key points

Turns of the Calvin cycle

Key points

Accounting for the products of glycolysis

Key points

Why blocking oxygen stops respiration

Key points

NPP and transfer efficiency

Key points

The sequence of eutrophication

Sources