Everything you need to know about jujubes and how to care for your trees!
This section began as a simple info blog about jujubes. But during the dormant winter periods with no live action to write about, I went back to my roots (ha!) to write more on soil, biochemistry, and soil microbiology in general. But I found myself wanting to go deeper still, and so began a new section here:From Soil to Fruit. From Soil to Fruit is my passion project, and is in a more structured book-chapter format than this blog. It is very much a work in progress but will fill out with time.
Photosystem I (PSI) is the second of two photosystems, and the third of four major protein complexes in the thylakoids of cyanobacteria and chloroplasts. (A protein complex is a unit of several protein subunits.)
The other photosystem, photosystem II (PSII), is the first of the four and was described here and here.
Despite being the second photosystem, PSI was the first discovered and hence its name. Both photosystems were discovered in the 1950s but their functions not pieced together until 1961. (By geniuses, in my opinion!)
Another name for photosystem I is plastocyanin–ferredoxin oxidoreductase, and we’ll pick apart the significance of this in the next chapter. But just from the previous chapter, where we discerned the meaning of plastoquinol-plastocyanin reductase, you may have already recognised the ‘-ase’ ending signifies an enzyme (a protein which acts as a catalyst) — and that the ‘oxidoreductase’ part just may have something to do with reduction and oxidation…
Photosystem I (PSI)
As mentioned above, PSI is a protein complex, a structure composed of several protein subunits. Fig. 2 below shows both the protein complex which is PSI (with ‘Psa’ prefixes) and the associated light-harvesting complex (LHC) which collects photon energy (with ‘Lhc’ prefixes):
Comparison with Photosystem II
One interesting comparison between the two photosystems concerns their origins. PSII is only found in oxygenic photosynthesisers — those which can split water, which are all cyanobacteria, algae and plants. This suggests an evolutionary origin of PSII in cyanobacteria, which appeared much later than other photosynthesising bacteria (all anoxygenic photosynthesisers), and which are also believed to be the ancestor of modern chloroplasts.
PSI, on the other hand, has many molecular similarities with the photosystems of the green sulfur bacteria, which are all anoxygenic photosynthesisers. Anoxygenic photosynthesisers all have one photosystem only — perhaps whichever organism branched off and evolved a second one became the ancestor of the first cyanobacterium?
However each came to be, both PSII and PSI are the only two of the four protein complexes in oxygenic photosynthesis which can absorb photons. This makes them the only two of the four which can participate in the so-called light-dependent reactions of photosynthesis — those requiring a photon input.
Both photosystems have a light-harvesting complex (LHC) and a reaction centre. Only PSII has a third component, the oxygen-evolving complex (OEC), which splits water.
As with PSII, PSI also contains photosynthetic pigments able to absorb photons over a range of wavelengths. These are chlorophylls, xanthophylls and carotenes.
The Reaction Centre
Each photosystem contains a reaction centre made of two specialised chlorophyll-protein complexes acting as one unit. The reaction centre of PSII is called P680, and that of PSI is P700. ‘P’ in both instances stands for ‘pigment’, and the number refers to each one’s maximum absorption wavelength: P680 at 680 nm and P700 at 700 nm. Not only does each photosystem harvest photon energy channelled from the antenna complex into the reaction centre, each can also absorb light photons directly: PSII via P680 and PSI via P700.
The photon energy PSII and PSI harvest stimulates an electron in P680 and P700 respectively to a very excited state, which is then ejected. This highly-excited electron initiates a series of electron-transport chain reactions which drive other reactions.
PSII has two roles. One is to harvest photon energy and initiate photosynthesis by ejecting a highly-excited electron which enters an electron-transport chain. The other role is to split water so as to replace the ejected electrons whilst simultaneously freeing up hydrogen ions (protons). These protons go on to enter other reactions which generate energy other cells can use. This energy is called ATP (adenosine triphosphate), and we’ll cover all of this in a later chapter.
PSI has a different purpose. It uses harvested photon energy to transfer the excited electrons originally from PSII across the thylakoid membrane, from the inside of the thylakoid (the lumen) to the outside (the stroma). These electrons are needed to make the energy carrier NADPH (nicotinamide adenine dinucleotide phosphate), and again something to cover in a later chapter.
Further Electron Flow
Photosystem I is the third of four major protein complexes in oxygenic photosynthesis, and yet so far we have only covered the photon energy harvested by both PSII and PSI, with barely a mention of the electrons which have flowed into PSI via PSII and cytochrome b6f complex, nor of the proton production along the way and their role still to come.
Those electrons and protons are about to feature in some very important reactions. The protons must wait for their own chapter, but in the next chapter we will follow the electron flow across the thylakoid membrane, from the lumen to the stroma, via photosystem I.
Anoxygenic photosynthesis was the first to appear on Earth around 3.5 billion years ago, was and is performed solely by several groups of bacteria to this day, and doesn’t produce oxygen. [Hydrogen sulfide (H2S), or ‘rotten egg gas’ is typically produced instead.]
Oxygenic photosynthesis came later, and first appeared around 2 billion years ago. This type does produce oxygen, and was first performed by bacteria known as cyanobacteria, which are also with us to this day.
Oxygenic photosynthesis is by far the most dominant type today, and still performed by cyanobacteria (the only bacteria which can), along with the relatively ‘new’ algae and plants. Oxygenic photosynthesis is completely responsible for the oxygenation of Earth’s modern atmosphere.
In the thylakoid membranes are four major protein complexes essential for oxygenic photosynthesis (Fig. 1) — photosystem II (PSII), cytochrome b6f, photosystem I (PSI), and ATP synthase:
Quick Summary of PSII
(For more detail on PSII’s role in initiating photosynthesis, please go here, and here for more detail on the electron flow within it.)
Photosynthesis begins in PSII, but only in the presence of light, when photon energy activates a complex flow of electrons derived from the splitting of water.
Photon energy begins the process by stimulating an electron in the two chlorophyll-protein complexes in PSII collectively known as P680. That electron becomes highly excited, leaves P680, and is replaced with an electron derived from the splitting of water elsewhere in PSII.
That first highly-excited electron moves to a molecule called pheophytin, and then onto another called plastoquinone.
Plastoquinone’s role is to shunt electrons from the first protein complex, PSII, to the second, the cytochrome b6f complex.
Cytochrome b6f is the second of four protein complexes needed for oxygenic photosynthesis, and the one to receive the electrons sent out of PSII via plastoquinone.
Knowing its other name — plastoquinol-plastocyanin reductase — immediately reveals its role! Whenever you see the ending ‘-ase’ in any of the life sciences, think ‘enzyme’. And whenever you see ‘enzyme’, think also ‘a protein which acts as a catalyst’. And a reductase is a specific enzyme which catalyses a reduction reaction.
Here, cytochrome b6f is catalysing the reduction of plastoquinol to plastocyanin, but let’s back-track a bit to work out what all this means.
Back in PSII, plastoquinone (PQ in Fig. 1 above) is really two molecules: plastoquinone QA and plastoquinone QB. QA transfers two electrons from pheophytin to QB. These two electrons enables plastoquinone QB to acquire two hydrogen ions (H+, also called a proton) from outside the thylakoid membrane (the stroma). QB leaves PSII and enters the thylakoid membrane. In acquiring two electrons, plastoquinone enters a reduced state and is called plastoquinol (PQH2 in Fig. 1 above).
Cytochrome b6f — also in the thylakoid membrane — now catalyses the transfer of those electrons to yet another molecule, plastocyanin (PC in Fig. 1 above). (Plastocyanin is a copper-containing protein, and one reason why copper is an essential plant nutrient.)
Plastocyanin, in receiving electrons, is now reduced in turn. And this is why cytochrome b6f is also called plastoquinol-plastocyanin reductase, as it catalyses the reduction of plastoquinol to plastocyanin. (Enzyme names can be unambiguous and highly descriptive this way!)
In catalysing the movement of two electrons from plastoquinol to plastocyanin, cytochrome b6f additionally pumps the two protons (H+ ions) brought in by plastoquinol from the stroma outside the thylakoid into the lumen inside the thylakoid. These protons have a further role which will be covered in a later chapter.
Further Electron Flow
Biochemistry is the flow of electrons, and biochemical pathways involve complex electron transport chains. Photosynthesis is no exception, and those electrons don’t end with plastocyanin!
Plastocyanin’s role is to move electrons to the third major protein complex in photosynthesis: photosystem I (PSI), and this is the topic of the next chapter.
Chemical reactions involve atoms and molecules, but chemistry at its heart is really the study of the electron flow between those atoms and molecules when these react.
Similarly, biochemistry at its heart is the study of the electron flow within living organisms. A common term in biochemistry for this electron flow is the electron transport chain, of which there are two types: cyclical and non-cyclical.
Electron Flow Requires Energy
Electron transport chains need energy to begin. As energy can neither be created nor destroyed, it must be input from somewhere. In photosynthesis, this energy comes from photons in the visible light spectrum.
The following diagram has been shown previously here and here. It is shown again below (Fig. 1) to make the rest of this chapter easier to follow. Please note that the focus here is only on PSII and the electron flow to cytochrome b6f — everything from cytochrome b6f through to ATP synthase will be covered in other chapters. Electron flow in the diagram below is shown by the blue-dotted lines and ‘e-’ cyan-coloured circles.
One electron in P680 absorbs one photon’s energy (or the accumulated energy of the light-harvesting/antenna complex, enters a highly excited state, and leaves the molecule. P680, in losing this electron, has become oxidised. With the loss of an electron its charge becomes +1 and the P680 molecule is now P680+. This molecule is also now a radical, or a highly reactive compound very much receptive to a replacement electron. (P680+ is sometimes written as P680•+ to make this radical state clearer.)
Radicals can be very important in driving electron flow, as we shall see.
It is the photon energy entering photosystem II which initiates electron flow through the whole of photosynthesis. All electron flows in PSII are non-cyclical, in that electrons are not recycled and reused over and over, but must be continually replaced as they cascade through the transport chain. In the case of photosynthesis, every electron used in that system comes from the continuous splitting of water.
Manganese is crucial in this water-splitting reaction, but it is ‘merely’ a ‘helper’ in this reaction. Splitting water is energy-intensive, and manganese’s role here is to assist in lowering the energy required for the water-splitting to proceed. In other words, manganese doesn’t provide the energy, it helps lower the energy input required. It is not a catalyst (biological catalysts are special proteins called enzymes), but a helper, or cofactor (a non-protein compound or metallic ion required for a catalyst to function).
In PSII, four electrons are released in the oxygen-evolving complex when two water molecules are split into four hydrogen ions (4 H+, also called protons) and two oxygen atoms (2 O, which combine to form oxygen gas, O2): 2H2O → 4H+ + O2 + 4e-
This reaction involves manganese (Mn) in a still not-quite-understood way, but what is clear from this is that manganese is a vital nutrient for plants, for without manganese available to remove electrons from water, oxygenic photosynthesis (by far the most important type today) could never proceed whether photons are present or not.
[The oxygen gas from this reaction leaves as a waste product, but the hydrogen ions (protons) remain for an important role we’ll cover later.]
The Primary Electron Donor and Acceptor in Electron Flow
Driven by energy entering the system via photons, P680 is the first molecule to become excited (sometimes written as P680* to denote this) and donate a high-energy electron in photosynthesis. It is the primary electron donor.
The first molecule accepting that highly-excited electron is pheophytin, also called the primary electron acceptor. It becomes reduced (receives electrons) and negatively-charged, as P680 becomes oxidised (loses electrons) and positively-charged.
(More on reduction-oxidation reactions, which always occur together, is here.)
P680 donates electrons, but P680+ is the strongest biological oxidising agent, or electron acceptor known, and it is this property that makes the oxidation (splitting of) water possible at all in any living organism.
Once it has been energised by photons to donate an electron to pheophytin, P680+ becomes a highly-reactive radical wanting that electron back. P680+ pulls that electron from a tyrosine residue in the surrounding D1 protein.
(Tyrosine is an amino acid. All amino acids share a common structure but each has an additional part unique to them, and which identifies them. That unique, identifiable part is the residue.)
This is where radicals can be important in electron flow, as P680+ by being highly reactive, readily reduces (receives an electron) back to P680. As P680, this molecule is again available for further photon stimulation and oxidation to release a new electron to initiate a new electron flow.
The tyrosine residue meanwhile has become oxidised (loses an electron). It now seeks a new electron, which it obtains from manganese, via manganese’s splitting of water.
This electron flow continues from water to P680 for as long as P680 is stimulated by photons, and is why photosystem II participates in light-dependent reactions of photosynthesis. Photosystem II cannot operate in darkness, and nor can photosynthesis, which begins with PSII.
Pheophytin is a chlorophyll molecule lacking the central magnesium ion (Mg2+) that all chlorophylls otherwise have.
As P680 becomes a positively-charged radical, phaeophytin becomes a negatively-charged radical, and again this is important. The pheophytin radical is likewise highly reactive, and readily passes the additional electron obtained from P680 onto yet another compound: plastoquinone.
Pheophytin’s role is as an intermediary electron carrier, passing the electron from P680 to plastoquinone.
[Fun aside: plastoquinone is very similar in structure to ubiquinone, more commonly known as coenzyme Q10. It is ubiquitous in bacteria and eukaryotes (plants, algae, fungi and animals) — hence its name — and in eukaryotes is found predominantly in the mitochondria. Considering plastoquinone is additionally found in chloroplasts and cyanobacteria, this is still more evidence for the microbial origins of eukaryotes and the endosymbiotic theory.]
Plastoquinone is yet another electron carrier (electron transport chains are called electron transport chains for good reason!) and vital in moving electrons from PSII to the next protein complex in the thylakoid membrane: cytochrome b6f. This will be covered in another chapter.
Oxygenic photosynthesis begins in photosystem II (PSII), which is embedded in, and spans, the thylakoid membranes found only in cyanobacteria, algae, and plants. PSII is the first of four protein complexes in the thylakoid membrane involved in photosynthesis.
A photon inputs energy into the system by stimulating P680, which releases a highly energetic electron and oxidises to the highly reactive P680•+ radical.
This electron moves to pheophytin, which reduces to a highly-reactive pheophytin radical, and then on to plastoquinone.
Plastoquinone acts as an electron carrier through the thylakoid membrane, and the electron enters the second protein complex, cytochrome b6f. We’ll pick up on that electron’s further travels in other chapters.
Meanwhile, the highly reactive P680•+ radical obtains an electron from a tyrosine residue in the surrounding D1 protein and reduces back to P680. The tyrosine residue then obtains an electron from manganese, which removed electrons from water when oxidising water to hydrogen ions and oxygen.
Electrons flow from water to P680 for as long as photons stimulate P680 to drive that electron flow.
Photosystem II in a Nutshell
For each photon input, an electron is released from P680, which then enters an elaborate electron transport chain and drives additional photosynthetic reactions in and on either side of the thylakoid membrane.
For each photon input, an electron is drawn from water to replace that removed from P680.
Every electron used in photosynthetic reactions comes from the splitting of water in PSII.
Photosystem II operates for as long as there are photon and electron inputs into P680.
Photosynthesis as a whole operates for as long as there are photon and electron inputs into P680.
In the cells of plants and algae are structures called chloroplasts(Fig. 1).
(And there is much evidence that these chloroplasts were once independently-living cyanobacteria.)
Chloroplasts have an inner and outer membrane (just like cyanobacteria). Held within the inner membrane is an aqueous liquid called the stroma. Suspended in the stroma are structures called thylakoids, shown as green disk-shaped objects in Fig. 2. These disks are arranged in stacks called grana (plural form of granum).
The dark-green border around each disk in Fig. 2 is the thylakoid’s own membrane, distinct from the chloroplast’s membrane. This membrane keeps the internal part of the thylakoid, called the lumen, together.
Embedded, and spanning, that membrane are four major protein complexes: photosystem II (PSII), cytochrome b6f complex, photosystem I (PSI), and ATP synthase (Fig. 3).
They are called protein complexes as each is a unit of several protein subunits.
Photosynthesis begins with Photosystem II (PSII) in the thylakoid membrane. This is the region where photons are absorbed and where water is split, both actions triggering a cascade of reactions that produces oxygen, energy, and sugar.
Without PSII there can be no photosynthesis — at least in plants, algae and cyanobacteria — and some herbicides such as atrazine work by inhibiting PSII.
Photosystem II (PSII)
Photosystem II is an incredibly complicated structure — Fig. 4 is of the PSII of the cyanobacterium Thermosynechococcus elongatus, and it is a simplified representation at that! The above-mentioned protein subunits this PSII protein complex contains are represented here as simple colour-coded rods, but are themselves highly complicated structures as well. Far more detail is here should you be curious!
Fig. 5 is a more stylised illustration of PSII:
As we pick PSII apart, please do keep in mind that PSII is just one of the four protein complexes in the thylakoid membrane involved in photosynthesis — each of the other three have their own, distinct, roles which will be covered elsewhere.
Breaking It Down
Photosystem II is comprised of three main complexes: a light-harvesting complex, a reaction centre core, and an oxygen-evolving complex.
The Light-Harvesting Complex (LHC)
The light-harvesting complex (LHC), also called the antenna complex, contains the photosynthetic pigments. These are the core photosynthetic pigment chlorophyll a and the additional antennae pigments chlorophyll b, the xanthophylls, and the carotenes. Each has a different peak absorption, and combined they increase the absorbable range of light wavelengths. The xanthophylls and carotenes (collectively called the carotenoids) have additional roles as antioxidants — as they do for us when we ingest them — though in PSII they specifically protect the chlorophylls from photon-induced oxidative stress.
Each LHC contains 250 – 400 of these pigment molecules, and the photon energy they absorb is channelled into the reaction centre of PSII. The CP43 and CP47 proteins at top of Fig. 5 are essential in passing this energy on. These are called the light-harvesting proteins.
The Reaction Centre
The reaction centre is made up of two specialised chlorophyll-protein complexes called D1 and D2. Each contains one chlorophyll a molecule, and this molecule pair is referred to simply as P680. (’P’ for ‘pigment’, and 680 for its maximum absorption at 680 nm.)
P680 both absorbs the photon energy channelled from the light-harvesting complex as well as from photons directly.
P680 is the Photosytem II primary donor, as the photon energy it receives excites an electron into such a high energy state that it becomes unstable. This electron readily moves from (is donated by) P680 to another molecule called pheophytin (Fig. 4, and the ‘Pheo’ in Fig. 5). Pheophytin is the primary electron acceptor in PSII — it is reduced (becoming negatively-charged) and P680 is oxidised to P680+.
(Reduction-oxidation reactions are explained in more detail here.)
Via pheophytin, this electron then transfers to another electron acceptor, plastoquinone QA, then onto plastoquinone QB. This electron flow initiated by P680 continues outside PSII and we’ll follow that in other chapters.
P680+, in losing an electron, becomes the strongest biological oxidising agent known, meaning it very readily uptakes electrons from other substances. This is very important when it comes to the third complex of PSII, the oxygen-evolving complex.
The Oxygen-Evolving Complex (OEC)
Also called the water-splitting complex, this process is found only in chloroplasts and cyanobacteria, and is the sole reason Earth’s atmosphere is 21% oxygen today instead of the original not much, if any, of early Earth.
It is here where water (H2O) is split into oxygen and hydrogen.
How the OEC works is not fully understood, but Bessel Kok’s theory from 1970 is the most accepted and is summarised in Fig. 6 below. Chl a is the chlorophyll a known as P680, TyrZ is a tyrosine residue*, and S0 – 4 represents the five states the OEC can exist in, with S0 the most reduced and S4 the most oxidised. Mn is manganese. Calcium and chloride ions (not shown) are also involved.
(* Tyrosine is an amino acid. All amino acids have an identical structure plus one part unique to each amino acid. That unique part is the residue.)
Two properties of manganese make it an important element in this cycle. Not only can it form bonds with oxygen-containing molecules such as water, but it additionally has four different oxidation states, which enables it to move electrons to and from other substances more readily than other elements. Here manganese is a cofactor, or ‘helper’ in mediating reactions.
Four electrons are removed by manganese from two water molecules, which oxidises to two oxygen atoms (O) and four hydrogen ions (H+). The two oxygen atoms readily combine to form oxygen gas (O2), which leaves the cell and enters the atmosphere as a waste product. Oxygen is not involved in photosynthesis, it is merely the result of it.
Meanwhile, every time P680 is excited by a photon, it loses an electron to pheophytin. That electron is replaced with an electron from the tyrosine residue, and that electron is replaced by one from the manganese.
This electron flow moves from Photosystem II into the other protein complexes in the thylakoid membrane, to drive reactions there. The hydrogen ions (also called protons) stay in the lumen to drive energy production, also outside Photosystem II. These processes will be covered in separate chapters.
Thylakoids are unique to chloroplasts and their ancestral cyanobacteria, and are where photosynthesis begins for both. This chapter will focus on the thylakoids in chloroplasts, but with references to cyanobacteria where relevant.
The thylakoids in chloroplasts form stacks of disks known as grana (plural form of granum), seen in Fig. 1 below:
(This figure shows the arrangement of thylakoids in cyanobacteria.)
Grana are suspended in an aqueous liquid called the stroma, which fills the entire chloroplast. The individual stacks are joined together by intergranal/stromal thylakoids, also known as stromal lamellae (’stromal plates’), to form a single functioning unit of many. Fig. 2 shows this arrangement:
and Fig. 3 shows a real-life arrangement within a lettuce slice:
Each thylakoid has a membrane surrounding an aqueous lumen (Fig. 4).
ATP is the molecule which stores potential energy to drive further biochemical reactions, and NADPH, together with its oxidised form NADP+, transfer electrons to and from the enzymes needed to build molecules such as carbohydrates.
Light-Dependent Reactions of Photosynthesis
Production of NADPH
Photosystem I and II contain photosynthetic pigments: the carotenes, xanthophylls, phaeophytins, and the predominant chlorophylls which give chloroplasts their green colour.
Photosystem II initiates the light-dependent reactions. A chlorophyll a molecule in PSII absorbs a photon, which excites an electron that was produced elsewhere in PSII by splitting water into oxygen and hydrogen. This electron is at a high energy level, but is very unstable, and thus is transferred to another molecule, and another, resulting in a chain reaction of redox reactions through photosystem II, cytochrome b6f complex, and photosystem I, culminating in the formation of NADPH. These reactions will be explored in more detail in future chapters.
Production of ATP
The molecule adenosine diphosphate (ADP) is converted into ATP via a process known as photophosphorylation during photosynthesis. Cytochrome b6f complex and ATP synthase are the two complexes involved in this reaction.
The net result of all light-dependent reactions in oxidative photosynthesis can be summarised as: 2H2O +2NADP+ +3ADP+3Pi→O2 +2H++2NADPH+3ATP where Pi signifies inorganic phosphorus (P).
Light-Independent Reactions of Photosynthesis
The light-independent reactions of photosynthesis aren’t reactions which occur in the dark or at night — photosynthesis doesn’t occur in these conditions — but rather are reactions which don’t involve a photon input.
Light-independent reactions occur outside the thylakoids, in the surrounding stroma. These take the ATP and NADPH generated by the light-dependent reactions to produce sugar from carbon dioxide and other compounds.
These reactions are also known as the Calvin Cycle, and the net result is: 3CO2 + 6NADPH + 6H+ + 9ATP → glyceraldehyde-3-phosphate (G3P) + 6NADP+ + 9ADP + 3H2O + 8Pi where Pi signifies inorganic phosphorus (P) and G3P enters other reactions to be converted into glucose.
This is the classic textbook equation for photosynthesis. But knowing what we know now, we can see how deceptively simple — and misleading —this equation really is!
The first revelation is that glucose (C6H12O6) isn’t even a product of photosynthesis. The actual sugar product is glyceraldehyde-3-phosphate (G3P), from the light-independent Calvin Cycle reactions of photosynthesis. G3P then enters pathways that are not involved with photosynthesis, to be converted elsewhere into glucose.
The second revelation is that each of the inputs and outputs are from two very different sets of reactions: the light-dependent set and the light-independent set. Carbon dioxide doesn’t really mix with water to produce sugar and oxygen — in fact, each are never in contact with each other, each come from a different set of reactions, and the reactions they enter are in different parts of the chloroplast.
Rather, water is split in the light-dependent photosystem II in the thylakoid membrane to produce highly-excited electrons and oxygen waste. The electrons enter still further light-dependent reactions in the membrane to eventually produce ATP for energy storage and NADPH for electron transport. (This is lithotrophy in action, with water as an inorganic electron donor.)
Meanwhile, the carbon dioxide enters the light-independent Calvin Cycle in the stroma outside the thylakoid membrane. The carbon dioxide is ‘fixed’, with the help of the light-dependent ATP and NADPH products, into a non-glucose sugar and water. (This is autotrophy in action, with carbon dioxide as an inorganic carbon source.)
One other point to make concerns the 12 water molecules on the left, and the six on the right of the ‘photosynthesis equation’. Here it’s implied that only six were used with six spare. But what is really going on is that all 12 water molecules on the left were entering light-dependent reactions while the six on the right are by-products of light independent reactions.
The twelve were split fully in light-dependent reactions, to produce oxygen gas as a waste product and electrons that went on to make ATP and NADPH — there were no spares. Rather, these ’spares’ are in fact six water molecule by-products from carbon dioxide fixation from light-independent reactions of the Calvin Cycle.
Similarities With Cyanobacteria
ATP and NADPH/NADP+ are made and used by all life, though different lifeform groups may use different metabolic pathways to produce these. Here it is worth mentioning that cyanobacteria are the only photosynthesising bacteria with thylakoids, and the only oxygenic photosynthesising bacteria. Further, their thylakoids contain the same four protein complexes (with differences) as found in the thylakoids of chloroplasts. Cyanobacteria are so very similar in structure to chloroplasts, which they predate, that they are regarded as the ancestors of modern chloroplasts.
Prokaryotes (pronounced ‘pro-carry-oats’) comprise the two Domains Bacteria and Archaea. Prokaryotes are defined as unicellular organisms without membrane-bound nuclei, and contain a single circular chromosome.
Cyanobacteria are that one exception, being oxygenic photosynthesising prokaryotes and producing oxygen as a by-product. They are also the only chlorophyll-containing prokaryotes. This is significant, as we’ll see below.
Eukaryotes (pronounced ‘you-carry-oats’) belong to a single Domain, Eukaryota, and are defined as organisms with membrane-bound nuclei. These are ‘everything else’ and include unicellular and multicellular organisms. Yeasts, fungi and protozoa are as much eukaryotes as multicellular plants and animals. (This is why fungal infections are very hard to treat, as their cellular structure is similar to ours, and what kills them has the potential to also kill or severely harm us.)
Eukaryotes have tightly wound chromosomes within their nucleus. There’s no correlation between an organism’s size or complexity and its number of chromosomes. For example, the Australian jack jumper ant (Myrmecia pilosula) has the smallest number of all eukaryotes, with males having one chromosome and females having two. Yet the much smaller (and simpler) protozoan Oxytricha trifallax has the largest number of all organisms, with 16,000 (very short) chromosomes! Humans have 46 and the jujube tree has 24. A species of Adders-tongue fern, Ophioglossum reticulatum, has 1,260!
All eukaryotic cells contain organelles — ‘little organs’, with the nucleus and mitochondrion the two best-known examples. Nuclei and mitochondria are common to all eukaryotes, but only the photosynthesising eukaryotes have the photosynthesising organelles called chloroplasts.
A chloroplast looks like Fig. 1 below (and we’ll be picking this apart in more detail later):
There are typically many chloroplasts per cell (Fig. 2):
Chloroplasts are green as they contain chlorophyll, the actual green pigment which absorbs photons and initiates photosynthesis. Thus any green part of a plant, even if a young branch, both contains chloroplasts and is able to photosynthesise.
Symbiogenesis, or the Endosymbiotic Theory
‘Symbiogenesis’ comes from the Ancient Greek σύν, syn, ‘together’, βίος, bios, ‘life’, and γένεσις, genesis, ‘origin/birth’: ‘life coming together to create new life’).
The theory of symbiogenesis, also known as the endosymbiotic theory, explains the origin of eukaryotic cells from prokaryotic ones. The prefix ‘endo’ in ‘endosymbiotic’, which also comes from Ancient Greek (ἔνδον, éndon, ‘inner; internal’), signifies that this symbiosis involved one organism being completely inside the other.
Also in 1883, Schimper observed that chloroplasts — found only in eukaryotic photosynthesising cells — closely resembled cyanobacteria, and that chloroplasts were also self-replicating. He put forward (in a footnote) the idea that green plants had arisen from a symbiosis of two organisms.
The Russian botanist Konstantin Mereschkowski was influenced by Schimper’s work, and in 1905 proposed further that cell nuclei and chloroplasts descended from a bacterium that had formed a symbiosis with an amoeba.
The French scientist Paul Jules Portier suggested in 1918 that mitochondria also came from a distant symbiosis, and Ivan Emanuel Wallin earned the nickname ‘Mitochondria Man’ from all his work on the subject in the 1920s.
Finally, the electron microscopy work of Hans Ris and especially Lynn Margulis in the 1960s established symbiogenesis as the most accepted theory to this day, as to the origins of both chloroplasts and mitochondria.
One Model for the Theory of Symbiogenesis
Fig. 3 shows one model for the endosymbiotic theory. Here, a prokaryote ancestor first developed a cell membrane around its DNA, thus creating a nucleus and becoming the first eukaryote. This now-ancestor to all eukaryotes then engulfed an aerobic (oxygen-using) prokaryote, which for whatever reason wasn’t digested, but remained inside the eukaryote as an independently-living entity.
It is highly significant that this prokaryote was aerobic, as oxygen is a very strong electron-acceptor. Using oxygen enabled this organism to produce huge amounts of energy compared to what anaerobic prokaryotes could generate from other electron-acceptors such as iron, nitrate, sulfate, and carbon dioxide.
This high energy output enabled the eukaryote host to thrive, and eventually the prokaryotic symbiont became a mitochondrion, still the energy factory of all eukaryotic cells today.
Some time later a eukaryote-with-prokaryote ancestor similarly engulfed a cyanobacterium, and that cell became the ancestor of all plants and algae, with the cyanobacterium symbiont becoming the ancestor of all chloroplasts. (Animal cells have mitochondria only, while plant and algae cells have both mitochondria and chloroplasts.)
Evidence That Chloroplasts Were Originally Cyanobacteria
Fig. 4 shows the similarities between a modern chloroplast and cyanobacterium, which have in common:
a double membrane,
ribosomes (where mRNA is translated into amino acid sequences),
thylakoids (where chlorophyll is found and the light-dependent reactions of photosynthesis occur)
Going further, cyanobacteria are the only photosynthesising prokaryotes with thylakoids, and by association, the only prokaryotes with chlorophyll. Similarly, chloroplasts are the only organelles with thylakoids and chlorophyll.
There is further evidence that chloroplasts evolved from a cyanobacterial ancestor, and much of this evidence also supports mitochondria evolving from an aerobic prokaryotic ancestor.
Chloroplasts (and mitochondria) are about the size of bacteria: 1 – 10 μm.
Not only do chloroplasts (and mitochondria) have their own DNA molecules, but these molecules are circular as is found in prokaryotes and not eukaryotes. (Chloroplast DNA is written ctDNA and mitochondrial DNA is written mtDNA.)
Another major piece of evidence is that chloroplasts (and mitochondria) reproduce themselves, and by binary fission, or cell division, just as prokaryotes do. If chloroplasts (and mitochondria) are removed from a cell, that cell cannot generate new chloroplasts (or mitochondria).
There is a close relationship between the chloroplast and cyanobacterial genomes. (Similarly, there is a close relationship between mitochondria and the bacterial genus Rikettsia.)
Many bacterial genes are missing in chloroplasts (and mitochondria). Some of these genes may have been lost over millenia, but the remainder are found in the nuclear chromosomes of their host eukaryote. This is indicative of a gene transfer having taken place.
Chloroplast (and mitochondrial) ribosomes are more like the ribosomes of bacteria than the ribosomes of eukaryotes.
Chloroplasts (and mitochondria) additionally have porins, proteins which aid in the transport of molecules across a cell membrane. Porins are only found elsewhere in some bacterial groups, including the cyanobacteria.
When Did the Chloroplast First Appear?
Cyanobacteria are believed to have first appeared around 2 – 2.4 billion years ago, when oxygen levels began to rise in the atmosphere from their photosynthetic activity.
The fossil record shows that eukaryotes had appeared by at least 1.5 billion years ago, and the symbiosis of a cyanobacterium with a eukaryote is believed to have occurred between 1 – 2 billion years ago.
The first photosynthesising eukaryotes were the red and brown algae, which first appeared 1.2 billion years ago. This suggests that the endosymbiont cyanobacterium had evolved into a chloroplast by this time.
The Significance of Endosymbiosis
All life needs an energy source. Those organisms which obtain theirs from the photons in sunlight are phototrophs. Those which obtain theirs by breaking chemical bonds are chemotrophs. Some, like plants, can do both!
This energy is converted into potential energy which is stored in a molecule called adenosine triphosphate (ATP). All life, without exception, no matter its evolutionary age or size, stores potential energy as ATP.
All life additionally needs an electron source (also called an electron donor). Some, the lithotrophs obtain theirs from inorganic materials such as hydrogen sulfide or ammonia. The organotrophs obtain theirs from organic materials such as carbohydrates and fats. Some, like plants again, can do both.
Those electrons move from the electron donor (ammonia, carbohydrate) to an electron acceptor, and this initiates chemical reactions to generate ATP.
Anaerobic Electron Acceptors
All life prior to the appearance of cyanobacteria was microbial and anaerobic (not requiring oxygen), as there was very little oxygen gas present in Earth’s atmosphere at the time. These are the anaerobes. Such organisms used (and still use) iron, nitrate, sulfate, sulfur, manganese, carbon dioxide and other substances as electron acceptors.
These elements and compounds, however, have low affinities for electrons compared to oxygen, and this limits the generation of ATP molecules. Anaerobic organisms can never generate enough potential energy to be anything other than single-celled organisms.
The arrival of cyanobacteria changed the course of evolution drastically. These were the first phototrophs to use water as an electron source, which was split into hydrogen and oxygen ions. These oxygen ions readily formed oxygen gas. This production of oxygen as a by-product of cyanobacterial photosynthesis led to the eventual oxygenation of Earth, and cyanobacteria are the sole reason Earth’s atmosphere changed from less than 1% oxygen to 21% today.
This increase in oxygen led to the arrival of aerobes able to take advantage of it. Oxygen is a very strong electron acceptor and enables much larger quantities of ATP to be generated. The numbers differ depending on the specific metabolic pathway, but as an example, an anaerobe can only generate two molecules of ATP for every molecule of glucose, while an aerobe can generate 30 – 32 molecules. (The theoretical yield calculates as 38, but there are real-life losses to do with movement of intermediate molecules along the way.)
The Rise of Aerobes
Where it not for cyanobacteria, life may well have remained fully anaerobic — and microscopic — to this day. Instead, somewhere along the way, an aerobic prokaryote became engulfed by an early eukaryote, which itself was probably anaerobic. The union proved advantageous in that the prokaryote survived, and the eukaryote became better able to survive in an ever-increasingly oxygenated world. (Oxygen is toxic for many anaerobes.) The eukaryote became aerobic and the prokaryote became assimilated over time to become the first mitochondrion.
When a second prokaryote — a cyanobacterium — also became engulfed and assimilated to be the first chloroplast, the beginnings of macro life could begin in earnest, all fuelled by mitochondrial ATP and chloroplastic chlorophyll. And this is the world we are part of today, all because one cyanobacterium one day long ago was not digested!
‘Photons’ are commonly thought of as the particles of light, but they are actually the particles of radiation, of which light is just one form.
Radio waves, microwaves, infrared waves, visible light waves, ultraviolet waves, x-rays and gamma rays are all forms of radiation, each of which can be defined by either their wave frequency or their wavelength.
The wave frequency is the number of times a wave cycles per second. ‘One cycle per second’ is a unit of measurement called the hertz (Hz). The wavelength is the distance between two peaks or troughs of a wave, and the shorter the wavelength, the higher the energy.
These frequencies and wavelengths form a continuum called the electromagnetic spectrum (Fig. 1):
At one end of this spectrum are the very long radio wave photons, with a frequency of 3 Hz and a wavelength of 100,000 km — longer than the Earth’s diameter — and beyond. At the other end are the very short gamma ray photons, with a frequency of 300 exahertz (EHz, 1018 Hz) and a wavelength of 1 picometre (pm, 10-12 m).
Fig. 2 is a good summary of the electromagnetic spectrum’s properties:
What we call ‘visible light’, also known as the ‘visible spectrum’, occupies a very thin band of the electromagnetic spectrum, and is defined as the range of wavelengths a typical human eye can detect (though some people may be able to see slightly either side of this defined range). We see this entire band as white light collectively, and ‘the colours of the rainbow’ when separated into still smaller bands.
It’s worth noting that this ‘visible light’ is nothing more than an arbitrary range that our eyes can detect — for example, many, if not all birds readily see in the ultraviolet range, which is part of their ‘visible light spectrum’ but not ours.
Photons within our visible spectrum range from frequencies of 400 – 790 terahertz (THz, 1012 Hz) and wavelengths of 380 – 700 nanometres (nm, 10-9 m).
Our eyes detect the lower frequency/longer-wavelength end of the visible spectrum as red light, and the higher frequency/shorter-wavelength end as violet light. Infrared (‘below-red’) radiation sits below visible red and ultraviolet (‘beyond-violet’) radiation sits above visible violet.
Just as our eyes are optimised for a specific range of frequencies within the electromagnetic spectrum, so too are the photosynthetic pigments.
A pigment is a substance which absorbs visible light. What isn’t absorbed is reflected, and it is the reflected wavelengths we see as colour. A substance which does not absorb any wavelength within the visible light spectrum reflects each one back, and we see it as white. Conversely, a substance which does absorb all wavelengths within this spectrum reflects none back, and we see it as black.
There are several photosynthetic pigments, spanning a range of colours, the colour of each dependent on the particular molecule and wavelengths it reflects.
Anoxygenic Photosynthetic Pigments
Anoxygenic photosynthetic pigments are called bacteriochlorophylls, of which there are eight known: bacteriochlorophylls a, b, c, cs, d, e, f, and g. These molecules are found only in phototrophic bacteria and archaea, most of which are anoxygenic photosynthesisers.* As anoxygenic photosynthesisers were the first photosynthesisers to appear on Earth, it’s possible that these bacteriochlorophylls are representative of the first photosynthetic pigments to ever appear on Earth.
* Some bacteriochlorophyll-containing microbes are phototrophs, but not autotrophs, and thus not photosynthesisers. There are no photosynthesising archaea.
No phototrophic microbe has all eight bacteriochlorophyll versions, but two or three at most.
Bacteriochlorophylls absorb wavelengths not absorbed by the oxygenic photosynthesisers, which may be a carry-over from the environment of early Earth. Bacteriochlorophyll g absorbs wavelengths at 670 and 788 nm, on either side of the red-infrared boundary of 700 nm. The other bacteriochlorophylls absorb even longer wavelengths, all in the infrared range of 788 nm – 1 mm, and the bacteriochlorophyll b of the purple bacteria can absorb even longer wavelengths into the microwave spectrum — but only just! Microwave wavelengths range from 1 mm – 1 m, and bacteriochlorophyll b absorbs those from 1020 – 1040 nm (1.02 – 1.04 mm).
Oxygenic Photosynthetic Pigments
These are the pigments found in plants, algae and cyanobacteria, though carotenes, xanthophylls and phaeophytins can also be found in some bacteria.
Carotenes are a group of related pigments responsible for the orange colour of carrots. We see them as orange hues as they absorb ultraviolet, violet, and blue light while reflecting orange, red and yellow light.
Xanthophylls are a group of yellow pigments which absorb and reflect similar wavelengths as the carotenes — xanthophylls and carotenes are very similar in structure and together make a larger group called the carotenoids.
Phaeophytin a is a grey-brown pigment and phaeophytin b is yellow-brown.
Chlorophylls are the best-known of all the photosynthesising pigments, and there are several versions as with the bacteriochlorophylls: chlorophyll a, b, c1, c2, d, and f.
Chlorophyll a is the most common and found in all oxygenic photosynthesisers, b is mostly in plants, c1 and c2 are in algae, and d and f are in the cyanobacteria. As cyanobacteria were the first oxygenic photosynthesisers, it’s possible that chlorophyll d and/or f are representative of the first chlorophyll molecules to have ever appeared on Earth.
Each chlorophyll molecule absorbs a range of wavelengths specific to it: chlorophyll a, for example, absorbs blue light from 400 – 450 nm and red light from 650 – 700 nm, while chlorophyll b absorbs blue light from 450 – 500 nm and red light from 600 – 650 nm.
The chlorophylls d and f specific to cyanobacteria hint at the evolution of cyanobacteria from the anoxygenic photosynthesisers, as these are the only oxygenic pigments capable of absorbing in the infrared range. Both absorb just outside visible red light, at around 710 nm.
The carotene, xanthophyll and phaeophytin pigments reveal themselves in autumn leaves when deciduous trees break down the chlorophyll so as to reabsorb its components from their leaves before shedding them. These non-green pigments were always there, but outnumbered and obscured by the amount of chlorophyll present.
Why Aren’t Leaves Black?
As we’ve seen, each oxygenic photosynthetic pigment type has its own wavelength range at which absorption is most efficient. The presence of several different pigments increases the total amount of visible light which can be absorbed.
Green and yellow light are the most abundant wavelengths in sunlight — the most amount of the sun’s energy is in the green region of 483 – 520 nm — and yet none of the photosynthetic pigments absorb in the green-yellow range. It is, after all, these wavelengths reflecting back which are responsible for the mass of green we see in nature.
Why are the most abundant wavelengths, in a sense, ‘wasted’ by oxygenic photosynthesisers? Why isn’t every wavelength made use of, which would make cyanobacteria, algae and plants black?
It turns out that there is no definitive answer to this, but quite a few theories!
One is that there is more sunshine than photosynthesisers know what to do with. The chemical reactions driven by photosynthesis only require so much energy, and absorbing the most energetic part of the visible spectrum would only lead to overheating. Not absorbing this high energy possibly protects against a plant version of sunburn.
On a similar note, absorbing too much energy may lead to the production of too many loose electrons, causing a phenomenon known as photoinhibition, and the production of tissue-damaging free radicals.
Another possibility is that, for plants especially, being able to respond to different levels of blue and red light as the seasons change could aid in growth, preparation for dormancy, or timing flowering correctly.
Another theory concerns evolution never resulting in optimal solutions, but rather in ‘good enough’ solutions. These pigments ‘just work’ and have done so for millions of years with no need for drastic changes. An offshoot of this concerns the probable water environment plants first developed in, where blue light is the most available. When plants moved onto land they then possibly developed the means to absorb red light which is more abundant in that environment.
My favourite theory, for what it’s worth, involves the cyanobacteria and chloroplasts. Cyanobacteria were the first oxygenic photosynthesisers to appear on Earth, and cyanobacteria, unlike the anoxygenic bacteria, contain chlorophyll. Chloroplasts are the chlorophyll-containing organelles in plant cells in which photosynthesis occurs.
There is much evidence to suggest that the first chloroplast was originally a cyanobacterium engulfed by another cell. (Similarly there is much evidence to suggest that the first mitochondrion was a bacterium engulfed by a cell. Topics to be covered elsewhere in this book!)
For whatever reason, perhaps from one or some of the ones above, cyanobacteria evolved green-reflecting chlorophyll pigments. If a cell did engulf a cyanobacterium, this only happened the once in all of evolution, as evidenced by the structural similarities of chloroplasts in all plants and algae. If so, then this cyanobacterium-chloroplast became the common ancestor of all plants and algae to come, all of which would take on the same green appearance ‘fixed’ in evolution as a ‘good enough’ solution.
Photosynthesis (from the Ancient Greek combining form φωτω-, phōtō-, from φῶς, phôs, ‘light’, and σύνθεσις, synthesis, ‘a putting together’: ‘a putting together with light’) is the process by which plants, algae, cyanobacteria, and a few other bacterial species convert the light energy of photons and the carbon from carbon dioxide into the chemical energy of carbohydrates. These carbohydrates (sugars) are stored as a food source — in short, photosynthesisers make their own food with the help of sunlight.
There are other organisms which are phototrophs, and others again which are autotrophs, but only photosynthesising organisms are both (and can be called photoautotrophs).
The Two Types of Photosynthesis
There are two types of photosynthesis: anoxygenic (not producing oxygen), and oxygenic (producing oxygen).
All anoxygenic photosynthesisers are bacterial, and believed to be amongst the first life on Earth appearing at least 3.5 billion years ago. These microbes are with us to this day, and include the green sulfur bacteria and the purple bacteria.
These were the only photosynthesisers in existence for about 1.5 billion years, until cyanobacteria appeared some 2 billion years ago. These organisms, also still with us to this day, were the first to produce oxygen as a by-product of photosynthesis. This led to the gradual oxygenation of Earth’s atmosphere during a period known as the Great Oxygen Event (or Oxygen Catastrophe depending on your point of view).
The atmosphere prior to their appearance was nothing like today’s. It was predominately nitrogen gas (N2) and carbon dioxide (CO2), with traces of water (H2O), methane (CH4), carbon monoxide (CO) and hydrogen gas (H2). Cyanobacterial activity was the sole means by which this atmosphere slowly became oxygenated, driving both a mass extinction of many anaerobic lifeforms (those which grow in the absence of oxygen) and the evolution of multicellular life (impossible without oxygen, owing to the amount of energy required).
Oxygenic photosynthesis is by far the dominant form today, and performed by all cyanobacteria, algae and plants.
The Formula for Photosynthesis
All photosynthesis, whether anoxygenic or oxygenic, can be written with the basic formula: CO2 + 2H2A + photons → [CH2O]n + H2O + 2A
where: 1. A is typically S (sulfur) in anoxygenic, and always O (oxygen) in oxygenic photosynthesis; and 2. [CH2O]n is a carbohydrate.
With reference to the Metabolic Classifications chapter, this formula shows us that: 1. the carbon from CO2, an inorganic molecule, is converted into carbohydrate, an organic molecule. Here, inorganic carbon is the carbon source, making this an example of autotrophy; 2. the A atoms are oxidised from ionic form to elemental form. (Please read Understanding Redox (Reduction-Oxidation) Reactions for a deeper explanation of this process). Here, A ions are losing electrons, making the H2A compound the electron donor. A is typically sulfur or oxygen, which are both inorganic, making this an example of lithotrophy; 3. photons are present. These are the energy source, making this an example of phototrophy.
Anoxygenic photosynthesis typically involves sulfur, and substituting S for A into the basic formula above gives: CO2 + 2H2S + photons → [CH2O]n + H2O + 2S
The carbohydrate is glucose, which to fit the above equation can be written as [CH2O]6, but is more commonly written as C6H12O6. Thus we have: CO2 + 2H2S + photons → C6H12O6 + H2O + 2S
Both sides of a chemical formula must balance, therefore: 6CO2 + 12H2S + photons → C6H12O6 + 6H2O + 12S
H2S is hydrogen sulfide, or ‘rotten-egg gas’. Thus we see that some of life’s first photosynthesisers were — and still are — using the energy from light and the electrons from sulfide (S2-) ions to convert carbon dioxide into glucose food, whilst producing pure (elemental) sulfur (S) as a by-product!
Other anoxygenic photosynthesisers make use of hydrogen gas (A = null), ferrous (Fe2+) iron ions (A = Fe), and even arsenic salts (A = HAsO42-) as electron donors in their conversion of carbon dioxide to carbohydrate.
Today this is the most widespread form of photosynthesis, simply because of the sheer biomass these organisms comprise. Unlike anoxygenic photosynthesisers, which are all bacterial, oxygenic photosynthesisers include microbial cyanobacteria, unicellular algae, and multicellular algae and plants. Cyanobacteria are the only bacterial representatives of this group.
All oxygenic photosynthesisers use water as their electron source, thus substituting O for A in the above basic formula gives: 6CO2 + 12H2O + photons → C6H12O6 + 6H2O + 6O2
The Law of Conservation of Energy states that energy can neither be created nor destroyed. It can only be transformed or transferred from one form to another.
In other words, living things cannot make their own energy, but must acquire it somehow. Each organism must continuously input energy into its system from somewhere, so as to drive that system.
For photosynthesisers — and all phototrophs for that matter — that ’somewhere’ is sunlight.
Sunlight constantly bathes and warms the Earth, but it is not bestowing some ‘life-force’ to the planet whilst doing so. Rather, phototrophs are constantly extracting energy from its photons, which then drives metabolic pathways for their growth and reproduction. They are the sole means by which photon energy is converted into the chemical energy all other organisms can then access by either eating those phototrophs, or organisms which have eaten phototrophs, or both.
Phototrophs are the ones to continuously pump external solar energy into the greater system that is Life on Earth — should they cease to be, then so too will that energy input come to an end and the vast bulk of life disappear.
[Not all life necessarily, but certainly all terrestrial and aquatic macroorganisms would die off. Many microbial species would also become extinct, but many more would be unaffected so long as the sun and Earth’s atmosphere are still present. The micro and macro life around ocean floor hydrothermal vents will persist for as long as the water remains and those vents continue to pump out heat and minerals. (This is a completely different ecological system worth exploring later.)]
As a Food Input via Autotrophy
The Law of Conservation of Mass states that the quantity of mass in a closed system must remain constant over time. This means that mass can neither be created nor destroyed. It can only be rearranged/converted into new forms, with no net loss or gain.
In other words, living things cannot create from nothing the carbohydrates, lipids and proteins they need to live, grow and reproduce — they must continually obtain a source of carbon (and other elements) from which to synthesise these. These carbon (and other) atoms must enter the organism in a form the organism can make use of.
Photosynthesisers — and all autotrophs for that matter — obtain their carbon from carbon dioxide. (Photoautotrophs use photon energy while chemoautotrophs use chemical energy to do this). That carbon goes into the carbohydrates autotrophs can then use as food, and those carbohydrates, along with the autotrophs themselves, become food in turn for other organisms — that food becomes their carbon source. Those organisms in turn become the carbon source for still others, and so on.
Autotrophs are the sole means by which inorganic carbon is converted into organic forms all organisms can use. Without autotrophs, there is no mechanism by which otherwise inaccessible carbon in carbon dioxide becomes the accessible carbon all life needs.
As an Input of Inorganic Materials via Lithotrophy
Anoxygenic photosynthesisers — and all lithotrophs for that matter — use inorganic substances such as hydrogen gas, iron and sulfides as their electron donor sources. This makes the hydrogen, iron and sulfur atoms available in forms other organisms can use, and contributes to nutrient cycling within their environments.
The oxygenic photosynthesisers use water as their inorganic electron donor. Here, the oxygen atoms in water are oxidised to oxygen gas, the one gas essential for all macro life, and which makes it possible at all. (Another topic to explore later!)
A Bridge Between Inorganic and Organic
Life is organic, but all life can be traced back to organisms which convert at least one inorganic material into an organic one.
For example, many food chains begin with phototrophs converting light energy into the chemical energy of organic carbohydrates. (Many, but not all, as people learn at school. Some food chains, as with deep sea hydrothermal vent ecosystems, begin with chemotrophs converting the chemical energy of inorganic minerals rather than light. But it’s still inorganic in origin.)
Food chains also begin with autotrophs converting inorganic carbon dioxide into organic carbohydrates. And the electrons which drove their manufacture most likely came from inorganic materials such as sulfur and water. (Most autotrophs are also lithotrophs, though there are organoautotrophs which use organic compounds as electron donors.)
Photosynthesisers are a unique all-in-one package of phototroph, lithotroph and autotroph, and in a way are the complete bridge between inorganic materials and organic life.
Below is the same photo of the young Ta-Jan mentioned back on 1st September 2020 in this post.
The photo below was taken today, 15th September. This tree has not seen soil since July, as part of a little experiment to a) show how tough these trees are, and b) show how much energy is contained in the roots and trunk to sustain any particular one through and post-dormancy. It has been, and still is, kept cool and moist in wood shavings, but without having seen soil, or much sunlight, all this time.
This tree is approximately 560 mm long from trunk tip to root tip in a vertical line, ignoring the bends in the roots. Approximately 360 mm is trunk (including the graft), and the root section, if straightened, would measure approximately 300 mm.
Can you see the new leaves growing about 30 mm from the top, on the left? These are about 8 mm long and were barely an open bud back on September 1st.
Let’s zoom in on that trunk now. (Note that the first photos date from the 6th, not 1st September.)
Can you see that the very tip is heavily reddish-brown, and that the buds and nodes are also noticeably reddish-brown against the more grey wood? And that the grey wood itself has (faint) reddish-brown streaks along it?
The other side of the trunk happens to be mostly reddish-brown with grey streaks, and with a very green tip:
These are the colours jujube wood cycles through as it ages: green for the newest growth, reddish-brown for the next, and grey for the oldest.
The two pictures below, taken last summer 2019 along a Li trunk, show this well:
The newest growth is a vivid green, transitioning to a reddish-brown as it ages during a season, transitioning again to grey as it ages more. It is very easy to age jujube wood by its colour (and texture, from very smooth green to ever roughening grey with each passing year). Last year’s wood is grey and rough, while a current year’s growth always begins a vivid green that has turned reddish-brown by the following autumn. Only the very newest growth remains green by summer’s end.
As a jujube tree enters dormancy, all its wood, regardless of colour and age, dulls to the same grey tones. This colour change may subconsciously register to make these trees look even more lifeless than they are throughout winter. But these colours return in a gentle flush come spring, as shown by the Ta-Jan above. It too was completely grey over winter, but has now picked up where it left off last season. In time that green tip will become reddish-brown over this season, and the reddish-brown will transition to grey during this season.
Nothing says ’spring’ to me more than seeing the first red flushes around the buds and nodes, and watching them gradually extend along the trunk and branches!
These days it’s ‘just known’ that we/animals take in oxygen to survive (exhaling carbon dioxide as a waste product), while plants take in carbon dioxide to survive (releasing oxygen as a waste product).
Three years later to the month, in August 1774, Priestley discovered ‘dephlogisticated air’; we would call it oxygen gas (O2).
The Dutch scientist Jan Ingenhousz became interested in the gaseous exchange of plants after meeting Priestley in 1771, and in 1779 made two very important discoveries.
One was that plants, when submerged, produced bubbles around their leaves when exposed to light, but ceased this bubble production when in the dark. He identified the bubble gas as oxygen and further observed that only a plant’s green parts ever produced this gas — Ingenhousz had discovered photosynthesis.
His second discovery was that plants give off carbon dioxide in the dark — in other words, they can respire just as animals do.
Even today, 241 years later, most people don’t realise this, that plants both photosynthesise and respire. And understandably so, as high school level botany is quite rudimentary at best! It’s fair to say that most people would assume that photosynthesis is to a plant what breathing is to us.
And yet both are very different, though complementary, processes. Let’s explore these now!
Photosynthesis is a two-stage process that converts the energy in light photons into the chemical energy of carbon molecule bonds which can be later used for food and other cellular functions. It occurs in the chloroplasts of plant cells and in the cell membranes of photosynthetic bacteria.
In the first stage, light energy is stored in adenosine triphosphate (ATP) (the ‘energy currency’ of cells) and another compound, nicotinamide adenine dinucleotide phosphate (NADPH). It goes without saying that this step is light-dependent!
These two molecules then feature in the second stage, whereby the energy stored within them is used to take the carbon out of air (specifically, out of inorganic carbon dioxide) and ‘fix’ it into organic three-carbon molecules. This stage is called the Calvin Cycle and is light-independent.
These three-carbon molecules are 3-phosphoglycerate and D-glyceraldehyde 3-phosphate (G3P). Two are needed to make the six-carbon glucose molecule (though the biochemical pathways involved are far more complex than this casual statement may imply!). Other combinations make more complex carbohydrates such as sucrose, starch and cellulose. Starch can be stored as an energy reserve (’food’), and cellulose is an important structural material that reinforces cell walls (we know it as ‘fibre’).
Photosynthesis is how a plant makes its own food, but to use that food, a different process altogether is required: cellular respiration.
The word ‘respiration’ when commonly used means to inhale and exhale air, or to breathe. But in biochemistry there is much more to ‘respiration’ than simply breathing. Respiration — more accurately cellular respiration — is a series of reactions occurring at the cellular level in which organic molecules are converted into carbon dioxide and water, releasing energy along the way that can then be used by the cell.
Cellular respiration is undertaken by every single living cell on the planet - in every cell in multicellular organisms such as plants, and in every unicellular bacterium.
Respiration is the sole means by which all cells obtain energy, and, like photosynthesis, cellular respiration is a two-stage process.
The first stage occurs in a cell’s cytoplasm, and involves the splitting of glucose to ultimately produce two molecules of pyruvate and two molecules of adenosine triphosphate (ATP), the ‘energy currency’ of cells. These products then enter further reactions in the second stage to generate still more ATP again.
Aerobic respiration uses oxygen as an electron acceptor, and occurs in all eukaryotic organisms (all plants, animals and fungi) and the aerobic prokaryotes (bacteria and archae).
Anaerobic respiration does not require oxygen, but is less efficient than aerobic respiration, as oxygen is by far the strongest electron acceptor. It is for this reason that anaerobic respiration only occurs in anaerobic prokayotes — the energy obtained isn’t enough to sustain multicellular organisms.
Electron acceptors in anaerobic respiration include sulfate (SO42-), nitrate (NO3-) and even elemental sulfur (S) — and this has significant consequences in soil microbiology generally, including the nitrogen cycle and the release of nutrients to plants.
In aerobic respiration, the second stage takes place in the mitochondria of eukaoryotic cells, and in either the cytoplasm or cell membrane of aerobic prokaryotes, and is called the Krebs cycle or the citric acid cycle.
In anaerobic respiration, the second stage takes place in the cytoplasm or cell membrane of anaerobic prokaryotes. There is no one common process like the Krebs cycle, owing to the different possible electron acceptors determining different chemical reactions. Anaerobic pathways are shorter and less complex than aerobic ones. And some result in delicious foodstuffs such as alcohol, vinegar, and Emmental cheese!
Some microbes are capable of both aerobic and anaerobic respiration, and these are called facultative anaerobes. Again this can be significant in soil microbiology if the presence of oxygen drives some reactions and its absence drives others. Denitrification — the return of nitrogen gas to the atmosphere during the nitrogen cycle — is only done anaerobically by facultative anerobes, for example.
Fun facts: mitochondria are, believe it or not, prokaryotes our eukaryotic ancestors (probably themselves prokaryotes) long ago engulfed and formed a beneficial relationship with. Thus cellular respiration is a prokaryotic creation no eukaryote ever independently developed for itself. All eukaryotes to this day literally cannot exist without prokaryotes, though prokaryotes certainly don’t need eukaryotes.
Chloroplasts are also prokaryotic in origin, meaning plant cells contain two prokaryotes: a chloroplast and a mitochondrion.
Putting it All Together
People are familiar with the concept of a simple food chain, with, say, grass at the bottom, a herbivore next, and a carnivore at the top.
But what isn’t as well-known is that for each level up the food chain, from grass to herbivore to carnivore, up to 90% of the energy is ‘lost’ as heat each time from biochemical processes!
As energy cannot be created from nothing, it must be continually input from some external source to keep that food chain going.
That external source is light photons, and the mechanism by which it enters a food chain as usable energy is via photosynthesis.
Photosynthesis only occurs during daylight, converting light energy into ATP and NADPH chemical energy, which then enter the Calvin cycle to ‘fix’ the carbon in carbon dioxide into carbohydrates.
These carbohydrates are ‘food’, both for the plant and for anything that eats it. Either way, the carbohydrates end up in cellular respiration to produce usable energy via the Krebs cycle. (Organisms higher up the food chain also extract energy from their food via cellular respiration and the Krebs cycle.)
A plant can simultaneously photosynthesise and undergo cellular respiration in the daytime — the two processes are not mutually exclusive and in fact complement each other. Photosynthesis makes the food the plant needs to grow and develop, and the energy for that growth and development can only come from breaking down that food via cellular respiration.
Growth and development are more likely to occur during daylight, partly because of the carbohydrate production going on at the same time that can fuel that, and partly because temperatures are warmer, which speeds up enzymatic reactions.
Cellular respiration still occurs during the night when photosynthesis stops, as discovered by Ingenhousz in 1779, but here the plant is more likely to undergo maintenance respiration in repairing/replacing the DNA, proteins and injured tissues needed to maintain a healthy living state rather than actively growing.
In the Context of Deciduous Trees and Dormancy
With jujube trees now beginning to bud and come back to life, it’s fitting to draw on all of the above and return to last week’s post and the recent topic dealing with winter dormancy to put everything in context.
It might be clearer now how a tree leaving dormancy is able to feed itself, via cellular respiration, with the stem and root reserves it laid down during dormancy induction. And despite its lifeless appearance throughout winter, low-level cellular respiration — maintenance respiration — was in play to keep that tree going throughout endodormancy and ecodormancy.
Cellular respiration ramps up after exiting dormancy to produce new leaves and the chloroplasts needed for photosynthesis. (Even now that little Ta-Jan continues to develop leaves with no signs of ill-health and with its roots yet to meet soil again — not that I suggest for a moment anyone else ever do this. This is my little experiment.)
Once photosynthesis is restored, a tree can again produce its carbohydrate food source instead of drawing on depleting reserves. It will continue to fuel its own growth and development this way, until shortening days once again signal the approach of winter.
When this signal comes, the tree will delegate more carbohydrates to storage than to growth, until photosynthesis stops completely and all leaves are dropped. Cellular respiration slows to a subsistence level as the tree settles into dormancy, and the cycle begins anew.
We covered the three stages of dormancy here, wrapping up with a description of the internal changes during the last stage which prepare a tree for spring. These changes are invisible externally, but set in motion the changes that do become visible externally.
Depending on your location, late August/early September through to late September/early October is the time of year jujube trees begin to show those visible changes that mark them ready for spring. Let’s explore what is happening.
At the end of the final stage of dormancy, ecodormancy, growth-suppressing hormones are switched off, growth-inducing hormone production increases, and cell-to-cell communications within the tree are restored.
The restored communications means that phloem (sap) can flow again, bringing the food reserves that were laid down in the roots and stems prior to dormancy to the buds. It is vital that the tree has good reserves of nutrients stored away to sustain bud growth, as it cannot yet photosynthesise to make its own food.
Phloem also delivers the growth hormones to the buds, which signal their time to grow and develop.
The tree is fully heterotrophic at this stage — it is as wholly reliant on its stored organic compounds (sugars and starches) to get it into spring as an animal is reliant on its stored organic compounds (fats, mostly) to get it through a winter.
The root on this little Ta-Jan might not look like much, but it is packing a lot of energy.
This particular tree has been in a box, in the dark, covered with moist wood shavings, since early August and whilst still in ecodormancy. It’s still in that box, and it is only the stored energy in the Ta-Jan’s root and trunk now fuelling this new green growth at the top in preparation for spring:
Back in early August, the trunk was the typical grey colour all jujube wood is during dormancy. The photo below is of a similarly-aged, but still sleepy, Redlands trunk showing this colour. Sleepy, but awakening — if you look very closely you may just make out the red flush returning to the trunk (distinct from the shadow along right hand edge), and the active buds:
It is only once buds grow and produce leaves that a tree can become autotrophic and make its own organic compounds again. This it does via inorganic carbon dioxide and photosynthesis.
Photosynthesis also requires water, which is transported by the xylem from the roots to the leaves. This is a passive process, driven by capillary action and transpiration, whereby water evaporating from the leaves creates a water potential difference which draws water up from further down the plant.
Xylem becomes blocked during endodormancy by air bubbles formed from a freeze-thaw cycle as temperatures drop over winter. These air bubbles are removed during ecodormancy, when the xylem is repaired. While there are no leaves as yet to drive photosynthesis and transpiration, the xylem is ready to move water immediately it is needed.
Water can still reach the buds, where it is needed for growth, via the phloem.
The carbohydrate reserves in the roots also go into new root growth, seeking out the water and nutrients needed when phtosynthetic and growth processes return and replace those reserves.
In time enough foliage will develop that the tree is once again able to produce enough carbohydrates via photosynthesis (called photosynthates) that it can feed itself, grow, develop and reproduce, and subsequently build up new carbohydrate reserves in preparation for the next period of dormancy.
And the little Ta-Jan? I’ve become quite attached to this little fellow that packs quite a punch for his (lack of) height, and will make him the feature blogging tree for the 2020-21 year!
All living things need energy to fuel the biochemical pathways that enable them to grow, reproduce and move.
The Law of Conservation of Energy states that energy can neither be created nor destroyed. It can only be transformed or transferred from one form to another.
In other words, living things cannot make their own energy, but must acquire it somehow. They must continually input energy into their systems, where it can then drive those systems.
For some organisms, their energy source comes directly from the sun, via light photons. Other organisms must break the chemical bonds in molecules to release — and use — the energy stored within.
This energy, whether released from photons or bonds, is then stored as potential energy in adenosine triphosphate (ATP), carbohydrates, lipids (a more accurate word than ‘fats’), and proteins until needed for living, growth and reproduction.
An organism will die without an energy source.
All organisms are made of carbohydrates, lipids and proteins, which are needed for growth, reproduction and movement. These molecules all contain carbon, making them organic molecules.
The Law of Conservation of Mass states that the quantity of mass in a closed system must remain constant over time. This means that mass can neither be created nor destroyed. It can only be rearranged/converted into new forms, with no net loss or gain.
In other words, living things cannot create from nothing the carbohydrates, lipids and proteins they need to live, grow and reproduce — they must continually obtain a source of carbon (and other elements) from which to synthesise these. These carbon (and other) atoms must enter the organism in a form the organism can make use of, where, through biochemical pathways they ultimately end up in other carbon molecules the organism then uses for life or expels as waste.
Some organisms use the carbon in an inorganic carbon source (carbon dioxide, or CO2) to make their carbohydrates, lipids and proteins. Other organisms use the carbon in organic carbon sources (carbohydrates, lipids and proteins) to make their own particular carbohydrates, lipids and proteins.
An organism will eventually die if a usable carbon source is not available.
The suffix ‘-troph’ is from the Ancient Greek word τροφή (trophḗ, or ‘nourishment’).
The words this suffix is appended to tells us the energy and carbon sources a particular group of organisms uses, or its metabolism.
Classification by Energy Source
The prefixes ‘photo-’ and ‘chemo-’ define the energy source:
‘Nourishment from light’. From the Ancient Greek combining form φωτω- (phōtō-, from φῶς, phôs, ‘light’) + τροφή (trophḗ, or ‘nourishment’).
‘Nourishment from chemicals’. From the combining word chemo- (‘chemical’) + τροφή (trophḗ, or ‘nourishment’).
Chemotrophs release energy by breaking the bonds of chemical compounds, which is converted into the chemical potential energy of adenosine triphosphate (ATP), carbohydrates, lipids and proteins.
Classification by Carbon Source
The prefixes ‘auto-’ and ‘hetero-’ define the carbon source:
‘Self-nourishment’. From the Ancient Greek combining form αὐτο- (auto-, from αὐτός, autós, ‘self’) + τροφή (trophḗ, or ‘nourishment’).
An autotroph is an organism that uses inorganic carbon (carbon dioxide) as its carbon source. Think plants.
The take-home message is that it does not need a (once-)living (organic) carbon source (such as carbohydrates, lipids and proteins) to make its own carbohydrates, fats and proteins.
Autotrophs are also known as primary producers, as they produce the food source (eg grass, leaves) at the beginning of all food chains and webs.
‘Nourishment from other (source)’. From the Ancient Greek ἕτερος (héteros, ‘other, another, different’) + τροφή (trophḗ, or ‘nourishment’).
A heterotroph is an organism that uses organic compounds as its carbon source. Think animals.
The take-home message is that it does need a (once-)living (organic) carbon source (such as carbohydrates, fats and proteins) to make its own carbohydrates, fats and proteins.
Heterotrophs are also known as primary, secondary, tertiary and quarternary consumers as they are consumers of autotrophs (primary consumers) and/or other heterotrophs (secondary, tertiary and quarternary consumers).
The flowchart below shows how the energy source and carbon source classifications combine:
We can be even more precise when considering a third aspect of metabolism:
Classification by Electron Donor Source
The subject of electron donors is a very technical subject at the heart of all biochemistry, as electron donors are the means by which energy is released from the energy source. Without electron donors there can be no biochemistry.
This is beyond the scope of this post, but it’s still worth mentioning ever so briefly here.
The prefixes ‘organo-’ and ‘litho-’ define the source of electrons needed to release energy from the energy source:
‘Nourishment from organic (materials)’. From the combining word organo- (‘organic’) + τροφή (trophḗ, or ‘nourishment’).
Organotrophs use organic compounds as electron donors.
‘Nourishment from rock (inorganic materials)’. From the Ancient Greek λίθος (líthos, ‘stone’) + τροφή (trophḗ, or ‘nourishment’).
Lithotrophs use inorganic compounds as electron donors.
Putting it All Together: In Order, Classification by Energy Source, Electron Donor Source, and Carbon Source
Combining all three defines a particular metabolism precisely. Writing this in the order by which energy enters and moves through an organism, from energy source, to electron donor, to carbon source, we have all these possible metabolisms:
Plants are photolithoautotrophs, as they obtain energy from photons (photo), use water as the electron donor (litho), and obtain carbon from carbon dioxide (auto). The simpler words autotroph and phototroph can also be used: in fact autotroph is the word usually taught in high school ecology classes for ‘plants’.
(Plants are actually phototrophic during the day when sunlight is present and they are photosynthesising, but switch to heterotrophy at night to utilise the carbon compounds they made during the day.)
Animals are chemoorganoheterotrophs, as they obtain energy from organic compounds (chemo), use organic compounds as electron donors (organo), and obtain carbon from organic compounds (hetero). The simpler words chemotroph and heterotroph can also be used, and heterotroph is the word learnt in high school for ‘animals’.
Bacteria and/or archaea (similar to bacteria but with enough significant differences to justify their own domain) are found in all of the above groups. Some of these groups play important roles in soil formation (pedogenesis) and making essential nutrients available to plants.
For example, the photolithotrophic cyanobacteria were the very organisms to oxygenate the planet two billion years ago and make multicellular life possible. To this day some have roles in nitrogen fixation and soil stabilisation through the production of polysaccharides that bind sand particles together and absorb water.
Exploring the metabolisms of soil bacteria reveals a lot of useful information about pedogenesis and nutrient availability, and these are topics well worth exploring in future posts.
Ecodormancy is the third and last stage of dormancy. It is a ‘less dormant’ state in which a tree becomes more responsive to external environmental factors, but is prevented from growth because of response to those factors, such as the still present very cold temperatures. A tree in ecodormancy is slowly preparing for spring and becomes less and less cold-tolerant as spring (and bud burst) approaches.
Expression of the DORMANCY-ASSOCIATED MADS-BOX (DAM) genes — growth suppressors — is less and less as ecodormancy progresses. Buds begin to accumulate starch reserves in readiness for new growth and development.
Callose plugs elsewhere throughout the tree now begin to degrade, which now opens up whole-tree communications. These callose deposits were laid down in the phloem during dormancy induction, and removal of these enables phloem sap to flow again. Phloem sap is a water-based fluid in which hormones, minerals and sugars are dissolved, and it is only when these growth-restoring components (including the water) can reach the buds will those be able to grow at all.
Production of the phytohormone (plant hormone) abscisic acid — which blocks phloem transport and cellular communications — declines and production of growth phytohormones such as auxins and gibberellin increases.
Xylem is the tissue that transports water from roots to the rest of a plant via capillary action. It is driven by transpiration, a passive process whereby water removed from leaves as a by-product of photosynthesis creates a water potential difference which draws water up from further down the plant. Xylem is non-functional throughout endodormancy, from both a lack of leaves driving that transpiration, as well as from air bubble blockages caused by repeated freeze-thaw cycles as winter progressed.
These blockages are removed during ecodormancy when the xylem is repaired. Starch in surrounding cells is broken down into sugars, which then move into the xylem cells. The increased sugar concentration creates an osmotic potential which drives (and eventually restores) water movement.
Expression of SHORT VEGETATIVE PHASE (SVP) genes increases during early spring — these are growth inhibitors which keep premature growth suppressed until bud break.
The tree is now ready for spring and a new growth and reproduction cycle.
Endodormancy is the second, and true stage of dormancy. During endodormancy the tree is in such a deep state of rest that it cannot respond to favourable environmental factors even if it wanted to. This probably protects it from responding to brief, unseasonal warm spells in the middle of winter.
This deep state of dormancy also makes study of the deep state of dormancy quite difficult! More is known on how green annual plants respond to temperature than how deciduous woody perennials do.
But what is known is that continuous chilling exposure throughout endodormancy (’chilling hours’) leads to the formation of proteins belonging to the glycoside hydrolase family 17 (GH17) group of enzymes. These enzymes gradually break down the callose (formed during onset of dormancy induction) in shoot meristems. This unblocks the plasmodesmata and restores cell-to-cell communications in the meristems. Restoration of communications helps buds maintain an inactive state and remain resistant to freezing.
Callose deposits in the phloem remain undisturbed, and this together with air bubbles in the xylem (caused by reduced transpiration and a freeze-thaw cycle as temperatures get colder) prevents any sap flow through the tree whatsoever.
Continual production of the phytohormone (plant hormone) abscisic acid during dormancy appears to maintain bud dormancy, and reducing absisic acid levels appears to release a tree from dormancy.
Another phytohormone, gibberellic acid, appears to act in reverse. It is at low levels during dormancy, as it enters catabolic (breakdown) pathways that maintain bud dormancy, while increasing levels of the hormone help bring about dormancy release.
Expression of the DORMANCY-ASSOCIATED MADS-BOX (DAM) genes are high during endodormancy but become repressed as chilling exposure increases. These genes appear to be epigenetically regulated in response to temperature changes, and factor in bud dormancy release and dormancy release in general.
The carbohydrates stored within the plant during dormancy induction become important in preventing freezing damage to tissues throughout endodormancy. A cell full of water will burst when frozen; a cell full of sugars will not. (Sugar added to water lowers the freezing point by preventing water molecules forming hydrogen bonds and solidifying and expanding — the water has to become even colder before these bonds can form.)
Abscisic acid causes a rise in dehydrins, a family of plant proteins produced in response to cold and drought stress. These further prevent injury by regulating the concentrations of salts and sugars in cells. (This regulation is known as osmotic regulation or osmoregulation.) Dehydrins also maintain a very low rate of plant metabolism.
As temperatures slowly rise again, and chilling exposure is reduced, carbohydrate metabolism begins to increase. This leads to an increase in free radicals and a condition known as ‘oxidative stress’. Free radicals are highly unstable and very reactive molecules (often of oxygen, •O2-) produced as waste products of metabolic reactions in all living organisms, including plants. These are not removed from an organism, but rather ‘hang around’ until they encounter a molecule to react with. Their highly reactive nature makes them very destructive, and in humans are responsible for faulty DNA repair, tissue damage, degenerative diseases, wrinkling, and aging in general. (Unfortunately this free radical battle is a very natural and unavoidable part of life — oxygen gives us life while it slowly oxidises us to death.)
Oxidative stress is a normal state of all organisms, and comes from an imbalance of free radicals and the means to counter them. (A diet full of antioxidants is one way we control free radicals, and reduce our oxidative stress effects, for example.)
As metabolism increases in a tree, so does free radical production, and oxidative stress. This increase of free radicals is possibly another mechanism which signals a tree to leave dormancy. Similarly, as callose degrades and unblocks the plasmodesmata in meristem tissue, oxygen levels can rise to kickstart cell metabolism, leading to increased free radicals and another dormancy release signal.
Next week we’ll examine the processes in a tree after it receives these dormancy release signals and enters the third and final stage of dormancy: ecodormancy!
Before Getting Started: This and the next two posts will be referring to genes and the proteins they code for. Writing the two can be confusing, as they often have the same name! This becomes even more confusing when the qualifying terms ‘protein’ and ‘gene’ are not written alongside the names, as is common in scientific papers written for an expert audience.
For example, the insulin like growth factor 1 (IGF1) protein in humans is encoded by the insulin like growth factor 1 (IGF1) gene. Here is where nomenclature becomes very important, as if I hadn’t used the words ‘protein’ and ‘gene’ you would have had to know that the uppercase, non-italicised ‘IGF1’ denotes the protein, and the uppercase, italicised ‘IGF1’ denotes the gene, in order to be able to follow along.
Crops such as maize and rice are extensively studied, and it’s understandable that nomenclature standards have evolved within those fields for researchers to communicate unambiguously with each other. But there’s no standard that covers ‘all plants’ — many species haven’t even been genotyped much less studied — and here I’ll simply be using the nomenclature as reported in the literature. You may see uppercase, lowercase, or both.
It is standard to use italics for genes and non-italics for proteins regardless, and please read those as such wherever they occur. I will also use ‘gene’ and ‘protein’ everywhere appropriate for extra clarity!
The lower temperatures of autumn are detected by the whole plant and helps it develop cold hardiness (cold acclimation) well ahead of the very cold temperatures that are coming. Proteins and lipids become less fluid as temperatures fall, which creates rigidity in the cell membranes. These stiffened membranes enable an influx of calcium ions (Ca2+) into the cells as calcium channels are activated. This has flow-on effects to do with hormone and enzyme processes that further affect growth and transpiration.
As plants can’t regulate their temperature, plant metabolism slows as temperature-dependent enzyme reactions also slow or cease as temperatures drop.
Increasing levels of cytokine and decreasing levels of the auxin indole-3-acetic acid (both phytohormones) towards the end of the growing season results in the production of callose, a polysaccharide (a long chain carbohydrate polymer). This begins depositing in the plasmodesmata in response to increasing levels of abscisic acid (another phytohormone), which blocks phloem transport and cell-to-cell communications. Abscisic acid inhibits DNA replication, and is a growth inhibitor and storage promoter.
Phytochromes are photoreceptors in leaves which are sensitive to the red and far-red (just before infra-red) end of the visible light spectrum. These wavelengths are longer than those at the blue/ultraviolet end of the spectrum. The sun’s highest point in the sky becomes lower and lower as the winter solstice approaches, and these longer red wavelengths scatter less through the atmosphere than the blue wavelengths. The phytochromes thus detect more red/far-red light than blue as winter advances.
This detection of change in light stimuli make phytochromes a molecular switch — genetic regulators which trigger the reduced expression of the CONSTANS (CO)/FLOWERING LOCUS T (FT) gene module, which regulates flowering. The CO protein becomes less stable in shorter days, and this leads to decreased FT gene expression. The reduced production of the FT protein in turn decreases production of gibberellin synthesis. These lower amounts of gibberellin set in motion physiological changes within the plant that enable bud formation. The FT protein moves through the phloem to the apices of shoots where the formation of bud scales and embryonic shoots develops.
Leaf senescence and leaf fall ends transpiration, causing xylem flow to come to a halt.
During the growing season, carbohydrates produced in the leaves via photosynthesis were regularly transported from the leaves to ’sinks’ such as stems, fruit and roots. This production slows gradually through autumn and winter until leaf fall, when it ceases altogether. Prior to leaf fall though, nitrogen is removed from the leaves and relocated to the main storage organs — the stems and roots in this case — which reach maximum storage capacity just before leaf fall.
With all these processes in place, the tree is now ready for the endodormancy stage, the subject of our next post!