Title: InkBiology / Photosynthesis and primary productivity
On every note of this deck, unless a note says otherwise:
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Front: DEFINE
Define: Photoionisation.
Back: The loss of an electron from a chlorophyll molecule after it absorbs light energy, leaving the molecule positively charged.

Front: DEFINE
Define: Thylakoid.
Back: A flattened, membrane-bound sac inside a chloroplast; the membrane holds the pigments, the electron carriers and ATP synthase.

Front: DEFINE
Define: Compensation point.
Back: The light intensity at which the rate of photosynthesis exactly equals the rate of respiration, so there is no net exchange of carbon dioxide or oxygen.

Front: DEFINE
Define: Granum.
Back: A stack of thylakoids, giving a large area of membrane within a small volume.

Front: SPOT THE ERROR
Say what is wrong with this claim:
The light-independent stage does not need light, which is why it is called the dark stage and why it carries on all night.
Back: No step absorbs a photon, and the cycle still stops in the dark. Every turn spends ATP and reduced NADP, both made only in the light-dependent stage and neither stored in quantity, so the cycle stalls within seconds of the light going.

Front: DEFINE
Define: Photosystem.
Back: A cluster of pigment molecules held in a thylakoid membrane, funnelling absorbed energy to a single chlorophyll a molecule at its reaction centre.

Front: CHECK YOURSELF
A student illuminates isolated chloroplasts in a buffer containing a blue dye that turns colourless when it is reduced. The dye loses its colour in the light and stays blue in the dark. Explain these observations, and predict what would happen if the thylakoid membranes were first punctured.
Back: In the light, photosystem II absorbs energy and electrons are lost from chlorophyll. Those electrons pass along the carriers in the thylakoid membrane, and the dye intercepts them, acting in place of NADP as the final electron acceptor. Gaining electrons is reduction, so the dye is reduced and loses its colour.
In the dark no electrons are excited, so nothing is passed along the chain, nothing reduces the dye and it stays blue. The reaction needs light directly, which is what makes it part of the light-dependent stage.
Puncturing the thylakoids would leave the dye still losing its colour, because the carriers are in the membrane and can still pass electrons to it. What would stop is ATP synthesis: protons pumped into the thylakoid space would leak straight back out, no gradient could build, and there would be nothing to drive ATP synthase.
That last part is the discriminating one. It separates the electron chain, which needs an intact membrane only as a scaffold, from chemiosmosis, which needs an intact membrane as a barrier.

Front: DEFINE
Define: RuBP.
Back: Ribulose bisphosphate, a five-carbon compound; the molecule that accepts carbon dioxide.

Front: DEFINE
Define: Photophosphorylation.
Back: The synthesis of ATP from ADP and inorganic phosphate using energy that originally came from light.

Front: CHECK YOURSELF
A grower measures the rate of photosynthesis of a tomato crop through a clear spring day. The rate rises through the morning, levels off from about 11 am to 3 pm despite the light continuing to brighten until 1 pm, and then falls through the afternoon. Explain the shape of this curve, and suggest one change the grower could make to raise the midday part of it.
Back: Through the morning the rate rises because light intensity is increasing and light is the limiting factor: more light means more photoionisation, more ATP and reduced NADP, and a faster Calvin cycle.
From about 11 am the rate levels off even though the light is still brightening, so light has stopped being limiting. Something else has taken over, most likely the carbon dioxide concentration around the leaves, which the crop itself has been depleting all morning, or the temperature if it is high enough to be closing stomata.
The afternoon fall follows the light back down: once the intensity drops far enough, light becomes limiting again and the rate falls with it.
To raise the middle of the curve the grower should increase the factor that is limiting there, which means carbon dioxide, enriching the air to about 0.10 per cent. Adding more light during the plateau would change nothing at all, which is precisely why a grower identifies the limiting factor before spending money on it.

Front: DEFINE
Define: Chemiosmosis.
Back: The movement of protons down a concentration gradient through ATP synthase, driving the synthesis of ATP.

Front: CHECK YOURSELF
In an experiment, algae photosynthesising in bright light were given carbon dioxide labelled with the isotope carbon-14. Samples were killed at intervals of a few seconds and their compounds separated. After five seconds the label was found almost entirely in GP; after thirty seconds it was in GP, TP and RuBP; after two minutes it was also in glucose and starch. Explain this sequence.
Back: Labelled carbon dioxide is fixed by rubisco onto RuBP, and the six-carbon product splits at once into two molecules of GP. GP is therefore the first compound the label can possibly appear in, which is why after five seconds it is almost the only one labelled.
By thirty seconds the labelled GP has been reduced to TP using reduced NADP and ATP, so the label appears in TP. Some of that labelled TP has then been used to regenerate RuBP, so the label reaches RuBP as well, and that also shows RuBP is rebuilt from TP rather than supplied from outside.
By two minutes, some labelled TP has left the cycle. Two TP condense into a hexose, and hexoses are polymerised into starch, so the label finally turns up in the products the plant stores.
The order of appearance is the evidence for the order of the pathway, which is how the cycle was worked out in the first place. Notice how long the label takes to reach glucose compared with GP: most of the TP never leaves the cycle at all.

Front: DEFINE
Define: TP.
Back: Triose phosphate, a three-carbon sugar phosphate; the product of reducing GP, and the molecule that either leaves the cycle or rebuilds RuBP.

Front: DEFINE
Define: Photolysis.
Back: The splitting of water using light energy, giving electrons, protons and oxygen.

Front: DEFINE
Define: Stroma.
Back: The fluid surrounding the thylakoids, containing the enzymes of the light-independent stage, along with DNA and 70S ribosomes.

Front: DEFINE
Define: Limiting factor.
Back: The factor, of all those a process requires, whose shortage is holding the rate back at that moment.

Front: SPOT THE ERROR
Say what is wrong with this claim:
Plants photosynthesise during the day and respire at night.
Back: Every living plant cell respires day and night, and root cells never see light at all. What changes with the light is photosynthesis, which in daylight usually outruns respiration, so the apparent switch is a net figure rather than a switch.

Front: DEFINE
Define: Rubisco.
Back: RuBP carboxylase, the enzyme that joins carbon dioxide to RuBP. Slow, easily out-competed by oxygen, and probably the most abundant protein on Earth.

Front: DEFINE
Define: Plateau.
Back: The region of a rate graph where increasing the factor on the horizontal axis no longer increases the rate, because something else has become limiting.

Front: DEFINE
Define: GP.
Back: Glycerate 3-phosphate, a three-carbon compound; the first stable product of fixation.

Front: SPOT THE ERROR
Say what is wrong with this claim:
Chlorophyll absorbs green light, and that is why leaves are green.
Back: Exactly backwards. Chlorophyll absorbs strongly in the blue and the red and takes almost nothing from the green band between them, so green light is reflected and transmitted. A leaf is green because green is the light chlorophyll has no use for.

Front: DEFINE
Define: Compensation period.
Back: The time taken from first light for a plant to reach its compensation point. The term appears on some specifications rather than all; check whether your board uses it.