Plant Physiology: Key Terms and Glossary

Abscisic acid, the hormone that shuts stomata in the light by opening guard-cell anion channels and letting potassium follow.

The fast part of auxin-driven elongation, in which the wall is acidified and expansins already there loosen it, and which does not account for later growth that needs new transcription.

Gas spaces through a root cortex that let oxygen reach flooded tissue, in maize and rice often opened by ethylene-promoted death of cortical cells.

Air drawn into a water-filled conduit across the widest opening in a pit membrane, which is how a conduit under tension usually embolises.

The living outer layer of a cereal endosperm, which secretes hydrolytic enzymes when gibberellin arrives from the embryo; the starchy endosperm inside is dead and cannot respond.

A plant mitochondrial oxidase that takes electrons from ubiquinol and reduces oxygen without pumping protons, so the energy leaves as heat and cyanide does not stop it.

The continuum outside the plasma membrane, walls and dead xylem included, along which soil solution can move until a seal forces a membrane crossing.

Phloem loading in which sucrose is released into the wall and a sucrose–proton symporter concentrates it in the companion-cell complex.

A protein channel that raises how readily water crosses a membrane, without deciding direction, which remains the water-potential gradient.

The finely branched fungal structure of an arbuscular mycorrhiza, inside a cortical cell wall but outside the cytoplasm, where the plant exchanges carbon for phosphate.

The chloroplast route that clears hydrogen peroxide: ascorbate reduces the peroxide, glutathione reduces the oxidised ascorbate, and NADPH regenerates glutathione.

The differentiated rhizobium, held inside a plant membrane in the nodule, that reduces N2 and returns ammonium while receiving carbon from the host.

The receptor kinase that binds brassinosteroid; without it the plant is a severe dwarf, and gibberellin does not rescue that dwarf.

Crassulacean acid metabolism, in which PEP carboxylase fixes carbon at night into stored malic acid and Rubisco refixes the released CO2 by day behind closed stomata.

The lignified band in the radial and transverse walls of the endodermis that blocks the apoplast, so water and solutes must cross an endodermal membrane before the xylem.

Formation of a vapour cavity in xylem water under tension, after which that conduit no longer carries sap until it is refilled or replaced.

Transcription factors, the CBF/DREB1 group, that during a cold period above freezing induce protective genes so the plant can later survive extracellular ice.

Injury above 0 °C in cold-sensitive plants, when membranes that contain too little unsaturation become rigid and the tissue leaks; it is not damage by ice.

The account of bending in which light or gravity sends auxin to one flank, and that flank then elongates more in a shoot, or is inhibited in a root.

The intercellular CO2 at which photosynthetic uptake balances respiratory release, close to zero in a C4 leaf and clearly higher in a warm C3 leaf.

A block on germination that sits in the covering tissues and is lifted by removing or scarifying them, even though the embryo itself is ready.

The explanation of sap ascent in which evaporation at mesophyll walls pulls a continuous water column, held together by cohesion and by adhesion to the conduit walls.

The F-box protein that, with JA-Ile bound, marks JAZ repressors for destruction so jasmonate-responsive genes are transcribed.

An osmolyte such as proline, glycine betaine, or a sugar alcohol that lowers cytosolic solute potential without poisoning enzymes.

A flavoprotein receptor of blue and UV-A light, related to photolyases but not repairing DNA, that shortens the hypocotyl and helps to set the circadian clock.

The kinase that ethylene receptors keep active when no ethylene is bound, so the ethylene response stays off until the gas removes that restraint.

Movement of electrons from ferredoxin back into the plastoquinone pool and through cytochrome b6f, adding to the proton gradient without making NADPH or O2.

The thylakoid complex that oxidises plastoquinol, passes electrons to plastocyanin, and deposits extra protons in the lumen.

An adenine-derived hormone that promotes cell division, favours shoots when high relative to auxin, and delays leaf senescence.

The change from a dark-grown seedling, long, hooked, and yellow, to a short seedling with an open hook and greening cotyledons.

A protein that holds growth back until gibberellin, bound to GID1, causes the protein to be destroyed. A DELLA that cannot be destroyed, as in *Rht* wheat, keeps the stem short even if gibberellin is supplied.

The gas-filled state of a cavitated xylem conduit, which stops flow in that file.

A germination block that remains after the coat is removed, until after-ripening, cold, light, or a shift in hormones removes it.

An element without which the life cycle cannot be completed, which another element cannot replace, and which acts in metabolism rather than by altering the soil.

Regeneration of NAD+ without oxygen, briefly by lactate and more sustainably in a flooded root by ethanol, so glycolysis can continue when respiration cannot.

The iron–sulphur protein that receives electrons from photosystem I and can pass them to NADP+ or into cyclic flow.

The graft-transmissible signal made in an induced leaf, which is FT protein travelling in the phloem, not the *FT* messenger RNA.

The transcription factor that accumulates in barley aleurone once the DELLA protein is gone and that turns on α-amylase genes.

The assimilation sequence in which glutamine synthetase adds ammonium to glutamate and glutamate synthase regenerates glutamate, the main route for ammonium in the plant.

Liquid xylem sap forced out through hydathodes when root pressure builds and the shoot is not transpiring, distinct from dew condensed from the air.

The primary proton pump of the plant plasma membrane, which acidifies the wall and keeps the cytosol electrically negative so that many solutes can enter with protons.

The ectomycorrhizal hyphae that grow between root cortical cells without entering them, and that, with the mantle, form the surface where minerals are exchanged.

Local cell death, with reactive oxygen, callose, and phytoalexins, after a resistance protein recognises a pathogen effector. It suits a biotroph, which needs a living host, better than a necrotroph, which can use the killed tissue.

The isoleucine conjugate of jasmonic acid, the active form that reports wounding and allows COI1 to destroy JAZ repressors.

The usual C4 arrangement of mesophyll around a thick-walled bundle sheath, so C4 acids can carry CO2 in and it leaks back only slowly. Some C4 species concentrate CO2 without this anatomy.

Disordered proteins, dehydrins among them, induced by drought, cold, and abscisic acid, that accompany desiccation tolerance; no single folding mechanism should be treated as the explanation.

The plant protein of infected nodule cells that holds free oxygen very low, protecting nitrogenase, while still supplying a bacterial oxidase.

The photon flux at which photosynthetic CO2 uptake equals respiratory CO2 release, so net exchange is zero.

An essential element required in large amount relative to a micronutrient; in these notes the set is nitrogen, phosphorus, potassium, calcium, magnesium, and sulphur.

The organic anion made in guard cells via PEP carboxylase, which balances potassium taken up as blue light opens the pore, and which leaves again when abscisic acid closes it.

An essential element required at a much lower level than a macronutrient, whose shortage can still stop the life cycle.

Bulk flow of phloem sap from high turgor where sugar is loaded to lower turgor where sugar is removed.

Unscheduled cell death after acute injury, in which membranes fail early and nutrients are not salvaged into the phloem.

A tonoplast sodium–proton exchanger that, driven by the vacuolar proton gradient, sequesters sodium in the vacuole.

A brief light interruption of a long dark period, read by phytochrome, that can stop a short-day plant from flowering even though the light is useless for photosynthesis.

The bacterial enzyme, which plants do not have, that reduces N2 to ammonia, spends ATP, and is inactivated by oxygen.

The regulator required, with salicylic acid, for pathogenesis-related gene expression during systemic acquired resistance. Which molecule travels from the infected leaf to a distant leaf is a separate question, and it is not settled.

The Mn4Ca cluster on the lumenal side of photosystem II that removes electrons from water, releasing oxygen and protons.

The enzyme that carboxylates phosphoenolpyruvate using bicarbonate and does not react with oxygen, working in C4 mesophyll by day and in CAM leaves at night.

The far-red-absorbing form of phytochrome, produced when Pr absorbs red light, and the form that is active in the reversible responses.

The metabolism of 2-phosphoglycolate made when Rubisco uses oxygen, which releases CO2 and ammonia and returns only three of the four carbons in two such molecules.

A blue-light receptor that activates the guard-cell proton pump so potassium and malate accumulate and the pore opens, and that also redirects auxin efflux so the shoot bends towards the light.

The phytochrome that accumulates while a seedling is in the dark, and that drives de-etiolation under continuous far-red, including responses to a very small dose of light.

The light-stable phytochrome that reads reversible red and far-red treatments, including shade avoidance, where the last flash decides the outcome.

A photoreceptor bearing phytochromobilin, converted by red light from Pr to Pfr and by far-red light back again.

A plasma-membrane protein that lets auxin leave the cell, the face it occupies setting the direction of polar transport.

Shrinkage of the protoplast away from a wall that an external solution is still holding out, which happens in a sufficiently negative bath and not when a leaf simply dries in air.

The copper protein in the thylakoid lumen that carries electrons from cytochrome b6f to photosystem I.

Symplastic phloem loading in which sucrose diffuses in through plasmodesmata and is converted to larger raffinose-family sugars that cannot diffuse back out.

The red-absorbing form of phytochrome, which red light converts into the active Pfr form.

The receptor proteins that bind abscisic acid and then inhibit PP2C phosphatases, releasing the kinases that close stomata and enforce seed responses.

The state of a mature seed that germinates as soon as water, oxygen, and a suitable temperature are supplied, with no further block.

Positive xylem pressure from ion secretion by living root cells, real when transpiration is low, and too small and too poorly timed to be the midday ascent in a tall tree.

The enzyme that adds either CO2 or O2 to ribulose-1,5-bisphosphate, so the same site both feeds the Calvin cycle and starts photorespiration.

The single cotyledon of a grass embryo, lying against the endosperm and absorbing sugars released from the starch.

Ordered dismantling of cells in which chlorophyll, protein, and membranes are broken down and mobile nutrients leave in the phloem while the cell is still coordinated.

A file of living but enucleate phloem elements, maintained by companion cells, that carries a sucrose-rich sap under positive pressure.

An organ that imports sucrose, such as a growing tip, a young leaf, a fruit, a seed, or a storage organ.

The guard-cell anion channel that kinases released by abscisic acid open, so chloride and malate leave and the pore can close.

The plasma-membrane sodium–proton antiporter that a salt-triggered calcium pathway switches on, extruding sodium from the cytosol.

An organ that exports sucrose in the phloem, typically a leaf that has finished expanding.

Iron uptake by dicots and non-grass monocots, as these notes group them: acidify the rhizosphere, reduce Fe3+ to Fe2+, and take up the ferrous ion.

Iron uptake by grasses that release mugineic-acid phytosiderophores and import the Fe3+ chelate.

A carotenoid-derived hormone exported from roots that suppresses shoot branching and stimulates the hyphae of arbuscular mycorrhizal fungi.

The cytosolic enzyme of source mesophyll that makes sucrose phosphate, active when hexose phosphates are high and quiet in the dark.

The cytoplasms joined by plasmodesmata, through which small solutes move without crossing another plasma membrane.

A primed state in leaves distant from an initial infection, dependent on salicylic acid and NPR1, the identity of the mobile signal remaining unsettled.

The F-box auxin receptor that binds AUX/IAA repressors when auxin is present, so those repressors are destroyed and auxin-responsive transcription begins.

The shape of an etiolated seedling in ethylene: a short axis, radial swelling, and an exaggerated apical hook.

Positive hydrostatic pressure of cell contents against the wall, which holds a herbaceous leaf up and falls to zero as the leaf wilts.

Prolonged cold that makes a plant able to flower later, remembered as chromatin state in dividing cells at the apex, not as flowering during the cold and not as freezing tolerance.

Germination of a seed while it is still on the parent, the result when abscisic acid does not impose dormancy.

The chemical potential of water per unit volume, reported as a pressure, which falls as solutes are added or as water is put under tension, and which water flows down.

The series arrangement of two photosystems, one photon-driven step oxidising water and a second raising electrons far enough to reduce NADP+.

The starch-attacking enzyme secreted by cereal aleurone after gibberellin has removed the DELLA repressor and GAMYB has accumulated.

Gravitational potential, the part of water potential that increases with height, negligible across one cell and costly up a tall stem.

Pressure potential, positive when the protoplast presses on the wall and negative when xylem water is under tension.

Solute potential, zero in pure water and negative in any solution.