Everything from the 4 lessons of this topic on a few pages: the key idea of each lesson, the diagram to remember, the points to learn and the traps examiners set. Read it, cover it, test yourself.
Photosynthesis transfers light energy into chemical energy. In the light-dependent stage, on the thylakoid membranes (stacked into grana), light energy is used to make ATP and reduced NADP. In the light-independent stage (the Calvin cycle) in the stroma, that ATP and reduced NADP are used to turn carbon dioxide into complex organic molecules. Light is absorbed by chloroplast pigments in the thylakoids: chlorophyll a (the primary pigment) and the accessory pigments chlorophyll b, carotene and xanthophyll, which widen the range of wavelengths used. An absorption spectrum shows how much light a pigment absorbs at each wavelength; an action spectrum shows the rate of photosynthesis at each wavelength. The pigments can be separated by chromatography and identified by their Rf values.
Learn the sites exactly: the thylakoids (membranes and spaces, in grana) are the site of the light-dependent stage; the stroma is the site of the light-independent stage. The light-independent stage is not "the dark reaction": it needs a constant supply of products from the light-dependent stage, so it stops soon after the light goes off.
An Rf value only identifies a pigment if it is compared with known values for the same solvent and the same paper or plate. Change the solvent and every Rf changes. Measure both distances from the origin line, not from the bottom of the paper.
The light-dependent stage happens on the thylakoid membranes by photophosphorylation: making ATP using light energy. Light absorbed by a photosystem causes photoactivation of chlorophyll: electrons are excited to a higher energy level and leave it. In non-cyclic photophosphorylation, PSII and PSI are both involved, the oxygen-evolving complex catalyses the photolysis of water to replace the electrons lost from PSII, and both ATP and reduced NADP are made, with oxygen as a by-product. In cyclic photophosphorylation only PSI is involved; electrons return to PSI and only ATP is made. In both, energetic electrons release energy along the electron transport chain; that energy transfers protons into the thylakoid space, and the protons return to the stroma by facilitated diffusion through ATP synthase, providing the energy for ATP synthesis.
Oxygen comes from water, split by photolysis, not from carbon dioxide. And cyclic photophosphorylation makes no reduced NADP and no oxygen: check the counters in the simulator, where only ATP keeps rising.
Protons are pumped into the thylakoid space and flow out to the stroma through ATP synthase, so ATP is made on the stroma side, where the Calvin cycle needs it. Do not mix this up with the mitochondrion, where protons are pumped into the intermembrane space.
The Calvin cycle (light-independent stage) takes place in the stroma and uses the ATP and reduced NADP from the light-dependent stage to make complex organic molecules. It has three main stages. Fixation: the enzyme rubisco combines carbon dioxide with ribulose bisphosphate (RuBP, 5C), giving two molecules of glycerate 3-phosphate (GP, 3C). Reduction: GP is reduced to triose phosphate (TP, 3C) in reactions using reduced NADP and ATP. Regeneration: most of the TP is used to regenerate RuBP, in reactions that use ATP. The remaining TP is used to make carbohydrates, lipids and amino acids, and some GP is used to make amino acids.
Rubisco fixes carbon dioxide; it does not use ATP. ATP and reduced NADP are used in the reduction of GP to TP, and ATP again in regenerating RuBP. Also: RuBP is 5C, GP and TP are both 3C.
In data questions about switching the light off, the first change is in the reduction step: GP rises because it is still being made from RuBP but can no longer be reduced, and RuBP falls because it is not regenerated.
A limiting factor is the factor in shortest supply, which limits the rate of a process; increasing it increases the rate. Light intensity, carbon dioxide concentration and temperature are limiting factors of photosynthesis. More light raises the rate by supplying more ATP and reduced NADP from the light-dependent stage; more carbon dioxide raises the rate of fixation by rubisco; temperature affects the enzyme-controlled light-independent stage most, with a rise up to an optimum and a fall as enzymes denature. The rate stops rising when a different factor becomes limiting. In a chloroplast suspension, electrons from the light-dependent stage reduce a redox indicator such as DCPIP or methylene blue, turning it from blue to colourless, so the time taken measures the rate at different light intensities or wavelengths. In whole plants, such as pondweed in hydrogencarbonate solution, the rate is measured as oxygen given off.
On the plateau, do not say light is limiting. Light is no longer limiting there: increasing it has no effect. Name another factor (carbon dioxide or temperature) and back it up from the graph.
DCPIP is reduced when it turns colourless, not oxidised. It accepts the electrons that would otherwise reduce NADP, so its colour change measures the light-dependent stage only, not the whole of photosynthesis.
Moving the lamp closer also heats the water, so temperature becomes a second independent variable. Use a water bath, an LED lamp or a heat shield (a tank of water between lamp and plant) to control it.