Photosynthesis

• Thylakoids make ATP and reduced NADP from light and water; the stroma spends them fixing CO2. The oxygen comes from water; each CO2 gives two GP; protons are pumped into the thylakoid space.
• Oxygen from water. Protons into the thylakoid space. Two GP per CO2; five TP in six go back to RuBP; 3 ATP : 2 reduced NADP.

• 13.1.1 I can describe — describe the relationship between the structure of chloroplasts, as shown in diagrams and electron micrographs, and their function
• 13.1.2 I can explain — explain that energy transferred as ATP and reduced NADP from the light-dependent stage is used during the light-independent stage (Calvin cycle) of photosynthesis to produce complex organic molecules
• 13.1.3 I can state — state that within a chloroplast, the thylakoids (thylakoid membranes and thylakoid spaces), which occur in stacks called grana, are the site of the light-dependent stage and the stroma is the site of the light-independent stage
• 13.1.4 I can describe — describe the role of chloroplast pigments (chlorophyll a, chlorophyll b, carotene and xanthophyll) in light absorption in thylakoids
• 13.1.5 I can interpret — interpret absorption spectra of chloroplast pigments and action spectra for photosynthesis
• 13.1.6 I can describe — describe and use chromatography to separate and identify chloroplast pigments (reference should be made to Rf values in identification of chloroplast pigments)
• 13.1.7 I can state — state that cyclic photophosphorylation and non-cyclic photophosphorylation occur during the light-dependent stage of photosynthesis
• 13.1.8 I can explain — explain that in cyclic photophosphorylation: • only photosystem I (PSI) is involved • photoactivation of chlorophyll occurs • ATP is synthesised
• 13.1.9 I can explain — explain that in non-cyclic photophosphorylation: • photosystem I (PSI) and photosystem II (PSII) are both involved • photoactivation of chlorophyll occurs • the oxygen-evolving complex catalyses the photolysis of water • ATP and reduced NADP are synthesised
• 13.1.10 I can explain — explain that during photophosphorylation: • energetic electrons release energy as they pass through the electron transport chain (details of carriers are not expected) • the released energy is used to transfer protons across the thylakoid membrane • protons return to the stroma from the thylakoid space by facilitated diffusion through ATP synthase, providing energy for ATP synthesis (details of ATP synthase are not expected)
• 13.1.11 I can outline — outline the three main stages of the Calvin cycle: • rubisco catalyses the fixation of carbon dioxide by combination with a molecule of ribulose bisphosphate (RuBP), a 5C compound, to yield two molecules of glycerate 3-phosphate (GP), a 3C compound • GP is reduced to triose phosphate (TP) in reactions involving reduced NADP and ATP • RuBP is regenerated from TP in reactions that use ATP
• 13.1.12 I can state — state that Calvin cycle intermediates are used to produce other molecules, limited to GP to produce some amino acids and TP to produce carbohydrates, lipids and amino acids
• 13.2.1 I can state — state that light intensity, carbon dioxide concentration and temperature are examples of limiting factors of photosynthesis
• 13.2.2 I can explain — explain the effects of changes in light intensity, carbon dioxide concentration and temperature on the rate of photosynthesis
• 13.2.3 I can describe — describe and carry out investigations using redox indicators, including DCPIP and methylene blue, and a suspension of chloroplasts to determine the effects of light intensity and light wavelength on the rate of photosynthesis
• 13.2.4 I can describe — describe and carry out investigations using whole plants, including aquatic plants, to determine the effects of light intensity, carbon dioxide concentration and temperature on the rate of photosynthesis

Precise vocabulary is part of the biology. Water moves down a water potential gradient; an active site is complementary to its substrate; enzymes are denatured, not killed; ATP releases energy when it is hydrolysed, and respiration never produces energy. Give a calculated answer to the same number of significant figures as the least precise data, or one more, with its unit. A fifth of the qualification is experimental: Papers 3 and 5 test AO3 only, and their questions may be set in contexts outside the syllabus content, so the practical work in this chapter is set out as variables, method, recording, graphs and evaluation rather than as theory.

• “The oxygen released in photosynthesis comes from carbon dioxide.” Correct It comes from water. The oxygen-evolving complex on PSII catalyses the photolysis of water, 2H2O → 4H+ + 4e− + O2. None of the O2 released comes from the carbon dioxide.
• “Protons are pumped out of the thylakoid into the stroma, then flow back in.” Correct The reverse: pumped from the stroma into the thylakoid space, and back to the stroma through ATP synthase, so ATP is made in the stroma, where the Calvin cycle uses it. Name the compartments: “in” and “out” do not say which side is which.
• “Rubisco fixes one CO2 to make one GP.” Correct One CO2 (1C) + one RuBP (5C) → an unstable 6C compound → two GP (3C each). Count the carbons: 5 + 1 = 6 = 2 × 3.
• “Cyclic photophosphorylation makes ATP and reduced NADP.” Correct Cyclic uses PSI only and makes ATP only: the electrons return to PSI, so none reach NADP, and no water is split.
• “The Calvin cycle is the stage that happens in the dark.” Correct It does not use light directly, but it runs on ATP and reduced NADP from the light-dependent stage, so it stops within seconds of the light going off. It happens in the light, in the stroma.
• “Leaves are green because chlorophyll absorbs green light.” Correct Green is absorbed least; it is reflected or transmitted, and that is the light you see.
• “Reduced NADP supplies the energy for the Calvin cycle and ATP supplies the hydrogen.” Repair The other way round: ATP supplies energy (and phosphate); reduced NADP supplies hydrogen to reduce GP to TP.
• “All the TP made leaves the cycle to make glucose.” Repair Five of every six TP regenerate RuBP; one in six leaves. Three turns fix three CO2 and release one TP.
• “Rubisco combines carbon dioxide with GP.” Repair With RuBP (5C); GP (3C) is the product, two per CO2.
• “Light energy splits water, and the electrons released reduce NADP directly.” Repair The oxygen-evolving complex catalyses photolysis; the electrons from water make good those lost by PSII. NADP is reduced by electrons from PSI.
• “Light gives the electrons in chlorophyll more kinetic energy, so they jump out.” Repair Use the syllabus’s terms: photoactivation raises electrons to a higher energy level, and they are emitted from the chlorophyll as energetic electrons.
• “ATP synthase pumps protons into the thylakoid space.” Repair The electron transport chain, using energy released by the electrons, moves protons in. Protons come out through ATP synthase, by facilitated diffusion, and that is what provides the energy for ATP synthesis.
• “Accessory pigments carry out photosynthesis in wavelengths chlorophyll cannot use.” Repair They absorb those wavelengths and pass the energy to chlorophyll a at the reaction centre; only chlorophyll a there emits the electrons.
• “Rf = distance moved by the solvent ÷ distance moved by the spot = 1.25.” Repair Spot ÷ solvent front, both from the origin, so Rf is never more than 1 and has no unit.
• “The origin line was drawn in ink so that it would be easy to see.” Repair Pencil: ink is a mixture of pigments that would dissolve in the solvent and separate on the paper.
• “Raising the temperature always increases the rate of photosynthesis.” Repair Only while temperature is the limiting factor, and only up to the optimum; above it the Calvin cycle enzymes begin to denature. In dim light, warming changes the rate very little.
• “At the plateau, light is still the limiting factor because the rate has stopped rising.” Repair A plateau on a rate–light graph means light is no longer limiting: raising it has no effect, so another factor (CO2 concentration or temperature) is.
• “DCPIP goes colourless because the chloroplasts make oxygen, which bleaches it.” Repair DCPIP is reduced: it accepts electrons from the light-dependent stage in place of NADP. Reduction, not oxygen, removes the blue.
• “The heat shield is a control.” Repair It is how a standardised variable (temperature) is kept constant. A control is a separate tube — no plant, or no chloroplasts, or kept in the dark — that shows the effect is caused by the independent variable.

• Read the command word before you decide how much to write. This syllabus has seventeen, and its own meanings for them are: assess — make an informed judgement; calculate — work out from given facts, figures or information; comment — give an informed opinion; compare — identify/comment on similarities and/or differences; contrast — identify/comment on differences; define — give a precise meaning; describe — state the points of a topic / give characteristics and main features; determine — establish an answer using the information available; discuss — write about issue(s) or topic(s) in depth in a structured way; explain — set out purposes or reasons / make the relationships between things clear / say why and/or how and support with relevant evidence; give — produce an answer from a given source or recall/memory; identify — name/select/recognise; outline — set out the main points; predict — suggest what may happen based on available information; sketch — make a simple freehand drawing showing the key features; state — express in clear terms; suggest — apply knowledge and understanding to situations where there are a range of valid responses to make proposals / put forward considerations. In this topic the gap that matters is between outline the Calvin cycle (the three stages) and explain photophosphorylation (the reasons each step happens).
• Interleave with the chapters that use this one. Topic 14 is the one later topic that builds on this one: its outcomes on the stomata say that opening and closing them balances the need for carbon dioxide uptake against water loss. When you reach them, re-answer “explain how a fall in CO2 concentration inside the leaf changes the rate of photosynthesis” (13.2.2). And whenever you revise chapter 12, redo the mitochondrion-and-chloroplast chemiosmosis table from memory. Recalling a topic inside a new context is worth more than another pass over this chapter on its own; at A Level, Paper 4 assumes the whole of the AS content, so nothing here is ever finished with.

• Cambridge International AS & A Level Biology 9700 has five components. Topic 13 is A Level content, so it is examined in Papers 4 and 5. A Level content: examined in Paper 4 (A Level structured, which also requires the AS content) and, as practical context, Paper 5. AS Level candidates take Papers 1, 2 and 3; A Level candidates take all five, either staged over two years (Papers 1–3 in year one, Papers 4 and 5 in year two) or together in one series. Examinations are available in the June and November series, and in March in India.
• Across both the AS Level and the A Level the assessment objectives are weighted AO1 40% (knowledge and understanding), AO2 40% (handling, applying and evaluating information) and AO3 20% (experimental skills and investigations). AS candidates are graded a–e; A Level candidates A*–E. There is no data booklet in Biology. At A Level, the statistical formulae (Hardy–Weinberg, the Lincoln index, Simpson’s index, standard deviation, standard error, 95% confidence intervals, the χ² test, the t-test, and Pearson’s and Spearman’s correlation) are printed in a question when it needs them, and so are the tables of critical values; degrees of freedom you must work out yourself. Everything else — magnification, surface area to volume, RQ, Rf, rates — you must recall, and this chapter says which is which.
• There is no multiple-choice paper on A Level content. The outcomes of this topic, examined in Paper 4, require you to state where each stage happens, explain cyclic and non-cyclic photophosphorylation, outline the three stages of the Calvin cycle, explain how a change in light, CO2 or temperature changes the rate, and use Rf values to identify pigments. Counting molecules through the Calvin cycle is how you check an outline of it.
• An electron micrograph of a chloroplast to label and relate to function; absorption and action spectra to read and interpret; a chromatogram to measure; rate curves at different CO2 concentrations and temperatures to read for which factor limits where. The numbers you must recall: Rf = spot ÷ solvent front, rate = 1/time, and a capillary volume πr2l. A question supplies light intensity ∝ 1/d2, pigment wavelengths and reference Rf values.
• Two named investigations. With a chloroplast suspension: independent variable lamp distance (or filter colour), dependent variable time for DCPIP to decolourise, controls in the dark and without chloroplasts. With Cabomba or Elodea: independent variable light intensity, CO2 concentration (sodium hydrogencarbonate) or temperature, dependent variable volume of gas per minute; temperature standardised with a water bath and a heat shield; main error, oxygen that dissolves or is respired and never collected.
• Read the command word before you decide how much to write. This syllabus has seventeen, and its own meanings for them are: assess — make an informed judgement; calculate — work out from given facts, figures or information; comment — give an informed opinion; compare — identify/comment on similarities and/or differences; contrast — identify/comment on differences; define — give a precise meaning; describe — state the points of a topic / give characteristics and main features; determine — establish an answer using the information available; discuss — write about issue(s) or topic(s) in depth in a structured way; explain — set out purposes or reasons / make the relationships between things clear / say why and/or how and support with relevant evidence; give — produce an answer from a given source or recall/memory; identify — name/select/recognise; outline — set out the main points; predict — suggest what may happen based on available information; sketch — make a simple freehand drawing showing the key features; state — express in clear terms; suggest — apply knowledge and understanding to situations where there are a range of valid responses to make proposals / put forward considerations. In this topic the gap that matters is between outline the Calvin cycle (the three stages) and explain photophosphorylation (the reasons each step happens).