AQA A Level Biology Topic 5: Energy Transfers in and between Organisms Complete Study Guide

Photosynthesis Processes and Reactions

Photosynthesis occurs in two distinct stages: the light-dependent reaction and the light-independent reaction. The light-dependent reaction takes place within the thylakoid membrane of the chloroplast, while the light-independent reaction, also known as the Calvin cycle, occurs in the stroma of the chloroplast. A critical initial step in the light-dependent reaction is photoionisation. In this process, chlorophyll absorbs light energy, which excites its electrons to a higher energy level. Consequently, electrons are released from the chlorophyll, causing the chlorophyll molecule to become positively charged.

Following photoionisation, the energy from the released electrons is conserved through the production of ATP and reduced NADP, a process described by the chemiosmotic theory. Electrons move along an electron transfer chain consisting of various electron carriers, releasing energy as they progress. This energy is utilized to actively pump protons ($H^+$) from the stroma into the thylakoid space. These protons then move by facilitated diffusion down their electrochemical gradient back into the stroma via the enzyme ATP synthase. The energy generated by this proton movement is used to join inorganic phosphate ($Pi$) to adenosine diphosphate ($ADP$) to form adenosine triphosphate ($ATP$), a process known as photophosphorylation. Additionally, the coenzyme NADP accepts a proton and an electron to become reduced NADP. Another vital component of the light-dependent reaction is the photolysis of water. Water molecules split to produce protons, electrons, and oxygen, according to the equation: $H_2O \rightarrow \frac{1}{2} O_2 + 2e^- + 2H^+$. The electrons generated here replace those lost from the chlorophyll during photoionisation.

The light-independent reaction or Calvin cycle begins when carbon dioxide ($CO_2$) reacts with ribulose bisphosphate ($RuBP$), a reaction catalysed by the enzyme rubisco. This reaction forms two molecules of glycerate 3-phosphate ($GP$). The $GP$ is then reduced to triose phosphate ($TP$) using energy from $ATP$ and the reducing power of reduced NADP, both of which are products of the light-dependent reaction. Some of the resulting triose phosphate is converted into useful organic substances, such as glucose, while the remainder is used to regenerate ribulose bisphosphate ($RuBP$) within the cycle, requiring further energy from $ATP$.

Factors affecting the rate of photosynthesis include temperature, light intensity, and carbon dioxide concentration. As temperature increases, the rate of photosynthesis increases because enzymes like rubisco gain kinetic energy, leading to the formation of more enzyme-substrate ($E-S$) complexes. However, above an optimum temperature, the rate decreases because enzymes denature as hydrogen bonds in their tertiary structure break, reducing the number of $E-S$ complexes. Regarding light intensity, an increase initially leads to a higher rate of photosynthesis because the light-dependent reaction increases, producing more $ATP$ and reduced NADP. This, in turn, boosts the light-independent reaction as more $GP$ is reduced to $TP$ and more $RuBP$ is regenerated. Beyond a certain light intensity, the rate plateaus as another factor, such as temperature or $CO_2$ concentration, becomes limiting. Similarly, increasing $CO_2$ concentration enhances the rate because more $CO_2$ combines with $RuBP$ to form $GP$, leading to more $TP$ and organic substance production. Eventually, the rate stops increasing when another factor becomes limiting.

In agricultural contexts, practices to overcome limiting factors must be evaluated. Such practices should increase the photosynthesis rate to enhance yield, as more glucose allows for faster respiration and more $ATP$ for growth processes like cell division and protein synthesis. However, the profit gained from the extra yield must exceed both monetary and environmental costs.

Required Practical 7: Chromatography of Plant Pigments

Chromatography is used to isolate and investigate pigments from leaves of different plants, such as shade-tolerant versus shade-intolerant varieties. To isolate pigments, leaves are crushed with a solvent. A pencil line is drawn on chromatography paper approximately $1\,cm$ above the bottom. A drop of the pigment extract is added to this line, which serves as the point of origin. The paper is then placed in a boiling tube containing an organic solvent, ensuring the solvent level is below the point of origin. A lid is added, and the solvent moves up the paper, carrying the dissolved pigments. The paper is removed before the solvent reaches the top, and the solvent front is immediately marked with a pencil.

Questions & Discussion

Question: Explain why the origin should be drawn in pencil rather than ink. Answer: Ink is soluble in the solvent and would mix with the pigments, or the ink line itself would move, obscuring results.

Question: Explain why the point of origin should be above the level of the solvent. Answer: Pigments are soluble in the solvent; if submerged, they would dissolve into the solvent in the tube rather than moving up the paper.

Question: Explain why a pigment may not move up the chromatography paper in one solvent. Answer: A pigment may be soluble in one specific solvent but completely insoluble in another.

Question: Describe how pigments can be identified. Answer: This is done by calculating the $R_f$ value using the formula $R_f = \frac{\text{distance moved by spot}}{\text{distance moved by solvent front}}$ and comparing this value to published data.

Question: Explain why the solvent front should be marked quickly once the chromatography paper is removed. Answer: Once the solvent evaporates, the solvent front is no longer visible.

Question: Explain why the centre of each pigment spot should be measured. Answer: This standardises readings because pigment spots often spread out, allowing for more accurate comparisons.

Question: Explain why the obtained $R_f$ values might be similar, but not identical, to published values. Answer: Variations in the specific solvent used, the type of paper, or other running conditions can affect the $R_f$ value.

Question: Explain why $R_f$ values are used instead of the raw distances moved by pigment spots. Answer: The solvent and pigments will move different absolute distances in different runs, but the $R_f$ value remains constant for the same pigment under the same conditions, enabling comparison.

Required Practical 8: Dehydrogenase Activity in Chloroplasts

Dehydrogenase is an enzyme that catalyses the reduction of NADP in the light-dependent reaction, where NADP accepts electrons from the photoionisation of chlorophyll or the photolysis of water. To measure its activity, chloroplasts are extracted from leaves and mixed with DCPIP, a redox indicator dye that acts as an electron acceptor. DCPIP is blue when oxidised and turns colourless when reduced. Four test tubes are typically set up: Tube A (Control 1) contains DCPIP, water, and chloroplasts but is covered in foil to block light; Tube B (Control 2) contains DCPIP, water, and isolation medium but no chloroplasts; Tube C (Standard) contains water and chloroplasts without DCPIP to act as a colour standard; and Tube D (Experiment) contains DCPIP, water, and chloroplasts exposed to light. The time taken for Tube D to turn colourless is recorded.

Questions & Discussion

Question: Give examples of variables that could be controlled in this experiment. Answer: The source of chloroplasts, the volume of the chloroplast suspension, and the volume or concentration of DCPIP.

Question: Explain the purpose of Control 1 (Tube A). Answer: It shows that light is required for DCPIP to decolourise and that chloroplasts alone do not cause the change without light.

Question: Explain why DCPIP in Control 1 stays blue. Answer: In the absence of light, no photoionisation of chlorophyll occurs, so no electrons are released to reduce the DCPIP.

Question: Explain the purpose of Control 2 (Tube B). Answer: It demonstrates that chloroplasts are necessary for DCPIP decolourisation and that light alone does not cause the reduction.

Question: Explain why DCPIP changes from blue to colourless in the experimental tube. Answer: DCPIP is a redox indicator that gets reduced by electrons released during the photoionisation of chlorophyll.

Question: Suggest a limitation with the method and how to overcome it. Answer: The determination of the end point is subjective. This can be improved by using a colorimeter to measure light absorbance at set intervals, zeroing the device against the colour standard (Tube C).

Respiration Stages and Mechanisms

Respiration is essential for producing $ATP$ to release energy for processes like active transport and protein synthesis. Aerobic respiration involves four stages: glycolysis (cytoplasm), the link reaction (mitochondrial matrix), the Krebs cycle (mitochondrial matrix), and oxidative phosphorylation (inner mitochondrial membrane). Glycolysis involves the phosphorylation of glucose to glucose phosphate using two $ATP$ molecules. This is then hydrolysed to two molecules of triose phosphate, which are subsequently oxidised to two molecules of pyruvate. In this process, two NAD molecules are reduced, and four $ATP$ are regenerated, resulting in a net gain of two $ATP$.

In anaerobic conditions, pyruvate is converted to lactate in animals and some bacteria, or ethanol and $CO_2$ in plants and yeast. This conversion oxidises reduced NAD back to NAD, allowing glycolysis to continue and produce a small amount of $ATP$. Anaerobic respiration produces much less $ATP$ per glucose molecule than aerobic respiration because it only involves glycolysis (2 $ATP$) and lacks oxidative phosphorylation, which accounts for approximately 34 $ATP$ molecules.

In aerobic respiration, pyruvate is actively transported into the mitochondrial matrix for the link reaction. Pyruvate is oxidised and decarboxylated to acetate, producing $CO_2$ and reduced NAD. Acetate then combines with coenzyme A to form Acetyl Coenzyme A. For every glucose molecule, the link reaction produces two Acetyl Coenzyme A, two $CO_2$, and two reduced NAD. In the Krebs cycle, Acetyl Coenzyme A (2C) reacts with a 4C molecule to produce a 6C molecule, releasing coenzyme A. Through a series of redox reactions, the 4C molecule is regenerated, losing two $CO_2$ and reducing NAD and FAD. One $ATP$ is produced per cycle via substrate-level phosphorylation. Total products per glucose in the Krebs cycle are six reduced NAD, two reduced FAD, two $ATP$, and four $CO_2$.

Oxidative phosphorylation involves reduced NAD and FAD being oxidised to release hydrogen atoms, which split into protons ($H^+$) and electrons ($e^-$). Electrons move down the electron transfer chain (ETC) via redox reactions, releasing energy. This energy is used by electron carriers to actively pump protons from the matrix into the intermembrane space. Protons then diffuse back into the matrix through ATP synthase, synthesising $ATP$ from $ADP$ and $Pi$. Oxygen acts as the final electron acceptor at the end of the ETC, combining with protons and electrons to form water. Other respiratory substrates include breakdown products of lipids (fatty acids converted to Acetyl CoA) and proteins (amino acids converted to Krebs cycle intermediates).

Required Practical 9: Measuring Respiration Rates

A respirometer measures oxygen ($O_2$) uptake to determine the rate of aerobic respiration. A known mass of an organism, such as yeast, is added to a substrate like glucose. A buffer maintains pH, and a chemical like sodium hydroxide ($NaOH$) absorbs released $CO_2$. As the organism respires, it consumes $O_2$, and because the $CO_2$ is absorbed, the gas volume and pressure decrease, causing a coloured liquid in a capillary tube to move toward the organism. The apparatus must be airtight to prevent pressure changes from external air and is left for 10 minutes to equilibrate and allow the respiration rate to stabilise.

Respiration rate can be calculated by determining the volume of gas consumed: $\text{Volume} = \pi r^2 \times \text{distance moved by liquid}$. This volume is then divided by the mass of the organism and the time taken, with units such as $cm^3\,min^{-1}\,g^{-1}$. To measure anaerobic respiration, the $CO_2$-absorbing chemical is removed, and conditions are made anaerobic by adding a layer of liquid paraffin or using an $O_2$-absorber. In this case, the liquid moves away from the organism as $CO_2$ is released, increasing pressure.

Redox indicators like methylene blue can also measure respiration. These dyes take up hydrogens (electrons) and become reduced instead of NAD or FAD. Methylene blue turns from blue to colourless when reduced. The rate is calculated as $Rate (s^{-1}) = \frac{1}{\text{time taken for colour to disappear}}$. Key controls include maintaining a constant temperature with a water bath and pH with a buffer. Tubes must not be shaken as this would introduce oxygen, re-oxidising the methylene blue back to its blue state.

Energy Transfer and Ecosystems

Biomass is the mass of living material, measured as the mass of carbon or the dry mass of tissue per given area. Dry mass is determined by drying a sample in an oven at $100^{\circ}C$ and weighing it repeatedly until the mass remains constant, indicating all water has evaporated. Chemical energy in biomass is estimated using calorimetry, where a known mass of dry biomass is burnt to heat a known volume of water. The temperature increase is used to calculate the energy. Valid calorimetry requires a stirrer for even heat distribution and insulation to minimize heat exchange with the environment.

Gross Primary Production ($GPP$) is the total chemical energy store in plant biomass in a given area and time. Net Primary Production ($NPP$) is the energy remaining after respiratory losses ($R$) are subtracted: $NPP = GPP - R$. $NPP$ is the energy available for plant growth, reproduction, and higher trophic levels. Productivity is measured in $kJ\,ha^{-1}\,year^{-1}$, which accounts for varying environment sizes and seasonal variations. For consumers, net production ($N$) is calculated as $N = I - (F + R)$, where $I$ is ingested energy and $F$ is energy lost in faeces and urine. Energy transfer is inefficient due to reflection of light, respiratory heat loss, and parts of organisms not being consumed or digested.

Farming practices increase efficiency by reducing losses. Crop farming uses herbicides to reduce competition, pesticides to prevent biomass loss to insects, and fertilisers to provide nutrients. Livestock farming restricts animal movement and keeps them warm to minimize respiratory heat loss, slaughters animals while they are young and growing rapidly, and uses selective breeding for higher growth rates.

Nutrient Cycles and Fertilisers

Saprobionts play a vital role in recycling elements by decomposing organic matter through extracellular digestion, releasing inorganic ions. Mycorrhizae are symbiotic fungi that increase the surface area of plant roots, enhancing water and ion uptake in exchange for organic compounds. The nitrogen cycle involves several bacterial processes: nitrogen fixation ($N_2 \rightarrow NH_3/NH_4^+$), ammonification (organic nitrogen compounds decomposed to $NH_4^+$ by saprobionts), nitrification (oxidation of $NH_4^+ \rightarrow NO_2^- \rightarrow NO_3^-$ by nitrifying bacteria in aerobic conditions), and denitrification (reduction of $NO_3^- \rightarrow N_2$ by denitrifying bacteria in anaerobic conditions). Aerating soil through ploughing increases fertility by promoting nitrification and inhibiting denitrification.

The phosphorus cycle involves phosphate ions being released from rocks by weathering, taken up by producers, transferred through food chains, and returned to the soil via excretion and decomposition by saprobionts. Fertilisers are used to replace nutrients lost during harvest. Natural fertilisers (manure, compost) release ions slowly via decomposition and are less likely to cause leaching. Artificial fertilisers contain inorganic compounds of N, P, and K. Excessive fertiliser use can lead to leaching and eutrophication. This involves an algal bloom blocking light, causing submerged plants to die. Saprobionts then decompose the dead plants using up oxygen through aerobic respiration, which results in the death of fish due to lack of oxygen.

Exam Insight: Common Pitfalls

Misconception: Chloroplasts absorb light energy. Correction: Specifically, chlorophyll absorbs light energy. Misconception: NAD is used in photosynthesis. Correction: NADP is used in photosynthesis; NAD and FAD are used in respiration. Misconception: $GP$ stands for glucose phosphate. Correction: $GP$ stands for glycerate 3-phosphate. Misconception: Using 'TP' in an exam. Correction: Triose phosphate must be written in full at least once as 'TP' is not an official specification abbreviation. Misconception: Respiration 'uses' energy. Correction: Respiration releases energy from substrates; energy is not 'used' by the process itself. Misconception: Faeces is an excretory product. Correction: Faeces is undigested food and is not a product of metabolism; therefore, it is not an excretory product. Misconception: Nitrogen-fixing bacteria convert $N_2$ directly to nitrates. Correction: They convert $N_2$ into ammonia or ammonium ions. Misconception: All lipids contain phosphorus. Correction: Only phospholipids contain phosphorus.