Topic 5 - Energy Flow, Ecosystems and the Environment

Photosynthesis converts light energy into chemical energy. Light energy splits strong bonds in water, the released hydrogen is combined with carbon dioxide to form glucose, and oxygen is released to the atmosphere.

Glucose stores chemical energy in its bonds and can fuel respiration or be converted into other biological molecules. Water supplies hydrogen and oxygen; carbon dioxide supplies carbon, so the overall process is more than “plants take in carbon dioxide”.

A leaf in light can use the products of water splitting and carbon dioxide fixation to build glucose; the oxygen released is a waste product of the photosynthetic pathway, not the source of glucose carbon.

Photophosphorylation uses light-driven electron energy to add inorganic phosphate to ADP and make ATP. ATP hydrolysis then releases a small, usable energy supply for processes such as active transport, synthesis and movement.

ATP is an energy-transfer molecule rather than a long-term store: ADP + Pi can be regenerated to ATP during respiration or photosynthesis, then ATPase-catalysed hydrolysis returns ADP + Pi.

During photosynthesis, ATP made on the thylakoid membrane supplies energy for Calvin-cycle reactions in the stroma. The ATP is not consumed as the carbon skeleton; it powers the chemical steps.

Light excites chlorophyll electrons in the thylakoid membrane. Their movement through electron carriers drives proton pumping and chemiosmosis to make ATP; non-cyclic flow also reduces NADP, while photolysis of water replaces electrons and releases oxygen.

Non-cyclic photophosphorylation uses photosystems II and I and produces ATP, reduced NADP and oxygen. Cyclic photophosphorylation uses photosystem I and returns electrons to the chain, producing ATP but not reduced NADP or oxygen.

In non-cyclic flow, excited electrons leave photosystem II, water supplies replacement electrons, protons accumulate in the thylakoid space, and ATP synthase uses their return flow to phosphorylate ADP.

A fraction of GALP leaves the cycle and forms hexose sugars. Glucose can be respired or joined into starch and cellulose; glucose plus fructose forms sucrose for translocation. Carbon skeletons combined with nitrate-derived nitrogen form amino acids and proteins. Sugar-derived intermediates also contribute to lipids and, with nitrogen and phosphate, nucleotides and nucleic acids.

Products made in a photosynthesising leaf can enter other biomass. For example, sucrose and amino acids move in phloem to roots, where they are respired, stored or polymerised into cell components. Carbon fixed in a leaf is therefore not confined to that leaf.

Chloroplasts organise photosynthesis by separating reactions. The envelope contains the organelle, the stroma provides enzymes for carbon fixation, and thylakoid membranes hold photosystems, electron carriers and ATP synthase.

Grana provide extensive membrane area for absorbing light and building proton gradients, while the small thylakoid space allows a gradient to form quickly. The stroma is the right compartment for the Calvin cycle because its enzymes and substrates are outside the thylakoid lumen.

A defect in ATP synthase would affect ATP production at the thylakoid membrane first; a defect in a stromal Calvin-cycle enzyme would impair carbon fixation even if light absorption continued.

An absorption spectrum shows which wavelengths a pigment absorbs. An action spectrum shows how effective different wavelengths are at driving photosynthesis, usually inferred from oxygen production or another rate measure.

The two spectra answer different questions: absorption describes light capture, whereas action describes the biological response. A peak in action can reflect combined pigments and electron-transfer efficiency rather than one pigment alone.

If photosynthetic rate peaks under blue and red light but falls under green light, the action spectrum indicates effectiveness; a pigment absorption spectrum helps explain why those wavelengths are captured differently.

Paper chromatography separates photosynthetic pigments because they differ in solubility in the solvent and attraction to the paper. Each band can be compared using its Rf value: distance travelled by pigment divided by distance travelled by the solvent front.

Keep the origin above the solvent, mark the solvent front quickly, and compare Rf values only when solvent, paper and conditions are comparable. Different bands indicate different pigments or pigment mixtures.

If a pigment travels 3.0 cm while the solvent front travels 6.0 cm, its Rf is 0.50. A second sample with the same Rf under the same conditions may contain the same pigment, but the result is comparative rather than absolute identification.

1. Cut equal lengths or use equal masses of the same aquatic-plant species and precondition them.
2. Place a shoot cut-end uppermost in a fixed volume and concentration of sodium hydrogencarbonate solution.
3. Allow acclimatisation, then collect oxygen with a photosynthometer, capillary tube or gas syringe for a fixed time.
4. Use at least five levels, repeat each and calculate mean oxygen volume per unit time.
5. Include a dark control where appropriate and plot mean rate against the independent variable.

Standardise plant species, length/mass, cut surface, acclimatisation and timing. Monitor temperature and light rather than assuming the settings are exact; randomise treatment order if plant activity could change over time.

Gross primary productivity (GPP) is the rate at which producers store chemical energy during photosynthesis. Net primary productivity (NPP) is what remains in new plant biomass after respiratory losses: NPP = GPP − R.

Match each value to GPP, NPP or R before calculating, keep area/volume and time units consistent, and rearrange the equation when the unknown is GPP or R.

If GPP is 17,500 kJ m⁻² yr⁻¹ and respiration is 14,000 kJ m⁻² yr⁻¹, NPP is 3,500 kJ m⁻² yr⁻¹. That remainder is the energy available to higher trophic levels.

Only part of the energy or biomass entering a trophic level becomes new tissue. Transfer efficiency is useful output divided by input, multiplied by 100; losses include respiration heat, egestion, excretion and uneaten material.

For energy, first subtract losses to find net productivity. For biomass, use dry mass and ensure intake and transferred biomass share units before applying the percentage formula.

A consumer receives 10,000 kJ m⁻² yr⁻¹ and loses 9,000 kJ, so its net productivity is 1,000 kJ and efficiency is 10%. A dry-mass calculation uses the same ratio logic but a different measured input.

A habitat is where an organism lives; a population is all members of one species there; a community is interacting populations; an ecosystem is the community interacting with the non-living parts of its habitat.

These levels are nested, so the correct term depends on what is included. Ecosystems have energy flow and nutrient cycling, but they are not sealed boxes: organisms and materials can move between them.

A pond’s frogs form a population; frogs, fish and pond plants form a community; adding water chemistry, light and sediment makes the pond an ecosystem.

Biotic factors are effects of living organisms, such as predation, competition, disease and food availability. Abiotic factors are non-living conditions, such as temperature, pH, salinity, light, humidity and oxygen concentration.

A species is abundant only where the combined conditions permit survival and reproduction. One factor can limit a population even when another factor is favourable.

A plant may be restricted to moist, low-salinity soil (abiotic) while herbivory or competition from another plant (biotic) further changes its abundance within that range.

A niche is the role of a species in its habitat: what it uses, where and when it feeds, and how it interacts with other organisms. Distribution and abundance reflect how well that role fits local conditions.

Two species with identical resource use would compete directly. Small differences in feeding time, food or location can reduce overlap and allow coexistence, but similar niches still tend to lower abundance.

Two birds may eat insects in the same tree yet coexist if one feeds in the canopy by day and the other on the trunk at dusk; the distinction is ecological, not just geographical.

1. Use random coordinates or fixed transect intervals to locate quadrats.
2. Keep quadrat area, placement rule and identification method constant.
3. Record count, frequency or percentage cover using a stated rule; use an abundance scale only if justified.
4. At the same positions measure relevant abiotic variables, such as light with a light meter, soil moisture with a calibrated probe, temperature, pH or wind speed.
5. Take enough samples across the habitat, repeat measurements, calculate summaries and plot abundance against position or the abiotic factor.

For a random-quadrat estimate, $\text{estimated population}=\text{mean count per quadrat}\times(\text{total habitat area}/\text{quadrat area})$. Frequency is the percentage of quadrats containing the species. Percentage cover is estimated consistently, for example with a gridded quadrat.

Avoid trampling before measurement, calibrate probes, measure changing abiotic conditions within a short time window and repeat transects where possible. Record confounders because correlation along a gradient does not identify a single cause.

Succession is ecosystem change over time. Pioneer species colonise bare ground, alter soil and microclimate, and are followed by species requiring deeper, more fertile or wetter conditions until a relatively stable community forms.

Each stage changes the abiotic environment and the competition landscape: decomposition builds nutrients, roots stabilise soil, and later vegetation can shade earlier pioneers. Secondary succession starts with soil already present.

On bare rock, lichens and mosses help form soil; grasses and shrubs follow, then trees. Mowing or grazing can hold a stable plagioclimax instead of allowing the expected later community.

Evidence for climate change can come from instrumental temperature and carbon-dioxide records, biological indicators such as pollen, and natural archives such as tree rings. Each proxy measures a different variable and has its own uncertainty.

Agreement among independent records strengthens a conclusion; disagreement may reveal dating, calibration or spatial limits rather than immediately falsifying the trend. Evidence for change is distinct from evidence for a particular cause.

A rising instrumental temperature record alongside higher atmospheric CO2 and a dated shift in pollen composition supports a changing climate, but each record must be aligned in time and location.

Earth’s surface absorbs solar energy and emits infrared radiation. Greenhouse gases absorb some of that outgoing radiation and re-radiate it, reducing heat loss to space; higher concentrations increase the warming influence.

The natural greenhouse effect makes Earth habitable. Anthropogenic climate change refers to additional warming linked to human-driven increases in gases such as carbon dioxide and methane from fossil-fuel use, land-use change and agriculture.

Deforestation removes a carbon sink while fossil-fuel combustion adds carbon dioxide. Landfill and ruminants add methane; each pathway changes atmospheric composition through a different mechanism.

Atmospheric carbon dioxide falls only when removal from the atmosphere exceeds additions over the relevant time period. Carbon sinks include forests, soils, peat and oceans, while combustion and land-use change add carbon.

Protecting or restoring a sink changes a flow or storage; it does not make emissions disappear. A strategy should be judged by permanence, scale, leakage and whether it reduces the net atmospheric increase.

Reforestation can increase carbon stored in biomass and soil, but drought, fire or later clearing can return carbon to the atmosphere. Cutting fossil-fuel combustion reduces the source flow directly.

Extrapolating existing data allows models to project how climate variables may change under specified emissions and human-activity scenarios. The output is conditional on the assumptions, not a guaranteed forecast.

Models support planning, such as flood defences or emissions reduction, by showing how outcomes differ between pathways. Uncertainty comes from future behaviour, incomplete processes, feedbacks and possible tipping points.

A high-emissions pathway may produce more warming than rapid mitigation, but the comparison is meaningful only if both scenarios and their assumptions are stated.

Warming changes rainfall, extreme-weather patterns, ocean conditions and seasonal timing. Species may shift poleward or upslope, flower or breed earlier, lose water access, or face extinction when movement or adaptation is too slow.

A climate effect propagates through linked systems: altered temperature or rainfall changes habitat suitability, food timing and competition. Sea level rises through thermal expansion and ice loss, adding a physical pressure to coastal systems.

If plants flower earlier but a migratory bird arrives on its old schedule, the bird may miss peak food availability. A seasonal mismatch is a mechanism, not just a correlation.

The temperature coefficient compares rates 10 °C apart: $Q_{10}=\dfrac{R_{T+10}}{R_T}$. More generally, $Q_{10}=(R_2/R_1)^{10/(T_2-T_1)}$. Use rates measured under otherwise identical conditions and do not apply the relationship across a denaturation region without evidence.

Temperature-dependent enzymes alter photosynthesis, respiration, growth and development in plants and animals, and microbial growth and decomposition. The organism-level result depends on which process becomes limiting and on the species' adaptations, not one universal optimum.

If respiration rate is 3.0 units at 15 °C and 6.6 units at 25 °C, $Q_{10}=6.6/3.0=2.2$. This describes the observed rate change; it does not prove which enzyme caused it.

1. Randomly allocate equal numbers of similar seeds or eggs to replicate containers.
2. Place containers at at least five monitored temperatures in thermostatically controlled conditions and allow equilibration.
3. Keep light, water or salinity, oxygen, pH, food, container volume, starting age and observation interval constant as relevant.
4. Record length at fixed times or count newly hatched organisms without double-counting.
5. Calculate a rate or percentage for each replicate, then mean and spread; plot against actual temperature and identify any optimum.

Use the least sentient suitable organism and the minimum number consistent with reliable evidence. Avoid harmful temperature extremes, minimise handling, maintain appropriate oxygen/salinity/water, define humane endpoints and return or dispose of organisms according to the approved protocol. Plants still require responsible sourcing and disposal.

Variation exists within a population. Random mutation, meiosis and fertilisation create heritable differences; selection pressures then make some phenotypes more likely to survive and reproduce.

Individuals do not evolve because they need to. Selection acts on existing variation: survivors pass advantageous alleles to offspring, so allele frequency changes over generations.

If foxes more often catch visible white rabbits, better-camouflaged brown rabbits leave more offspring and the brown-fur allele becomes more common in the population.

Speciation is the formation of a new species when populations become isolated, gene flow falls, allele frequencies diverge and the populations can no longer produce fertile offspring together.

Geographical barriers produce allopatric speciation. Sympatric speciation occurs without a physical barrier when timing, behaviour or reproductive structures prevent interbreeding.

A mountain range separates two tree populations. Different selection pressures and genetic drift change allele frequencies until hybrids are no longer fertile; this is a mechanism, not a single sudden mutation.

A business exposed to regulation, an environmental group and a government may agree that temperature rose but differ over attribution, acceptable risk or action. Evaluate each claim against the same evidence; a speaker's identity is a reason to inspect incentives, not a reason to dismiss evidence automatically.

Compare strategies using life-cycle greenhouse-gas balance, land and water use, biodiversity, yield, timescale, reversibility, local livelihoods and monitoring evidence. Adaptive management changes limits when population or ecosystem indicators decline.