text:
Category: "Photosynthesis"
Posted by kristi on 05 Oct 2021 in Photosynthesis, From Soil to Fruit - How Does Everything Fit Together?, Light-Dependent Reactions
A Summary of Oxygenic Photosynthesis to Date
Oxygenic photosynthesis produces oxygen gas (O2), and is performed by plants, algae and cyanobacteria. (Many other bacteria can photosynthesise, but these are anoxygenic photosynthesisers, typically producing pure sulfur as a product.)
Plants, algae and cyanobacteria are the only organisms with structures known as thylakoids, and it is in the thylakoid membrane that oxygenic photosynthesis occurs.
Fig. 1 below represents the thylakoid membrane, and the four major protein complexes within it that are involved in oxygenic photosynthesis:
Figure 1. The thylakoid membrane
Attribution: By Somepics - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=38088695
So far, we've covered photosystem II (PSII), cytochrome b6f, photosystem I (PSI), and the electron flows through each of PSII and PSI.
This chapter discusses the fourth and final protein complex: ATP synthase.
Let's break down the meaning of 'ATP synthase'. ATP stands for adenosine triphosphate. The -ase ending of 'synthase' tells us that synthase is an enzyme, or protein catalyst. 'Syn' implies 'synthesis', thus ATP synthase is a protein catalyst which synthesises ATP. ATP is the universal molecule of energy storage, as it is found in, and needed by, absolutely every living cell on the planet from the smallest bacterium to the largest trees and animals. Thus ATP synthases (structures differ from group to group) are also found in absolutely every living cell on the planet.
Location in All Life
Where ATP synthase is located in all organisms reveals some interesting support for the endosymbiotic theory of prokaryotic (bacterial and archaeal) cells forming a union with eukaryotic cells (everything else), which paved the way for higher, multicellular life to evolve.
All prokaryotes — the bacteria and archaea — are single-celled organisms. These single cells are bound by a cell membrane, in which their versions of ATP synthase are embedded.
Cyanobacteria, being bacteria, also have ATP synthase in their cell membranes. They are also oxygenic photosynthesisers, which means they further have internal structures called thylakoids. Thylakoids too are membrane-bound, and as can be seen in Fig. 1 above, ATP synthase resides in those membranes too.
All eukaryotes, whether single-celled like yeasts or multicellular like plants and animals, contain mitochondria which have inner and outer membranes. The only place ATP synthase is found in non-photosynthesising eukaryotes is in the inner membranes of their mitochondria, which adds support to the theory that mitochondria were once prokaryotes which formed a symbiosis with eukaryotes. Eukaryotic cells cannot make mitochondria — mitochondria have their own DNA and are self-replicating — and cannot survive without mitochondria synthesising their ATP needs.
Algae and Plants
Algae and plants are the only photosynthesising eukaryotes, and the only eukaryotes to contain chloroplasts. Chloroplasts contain thylakoids, and just as with cyanobacteria, those thylakoid membranes are also the location of ATP synthase. And just as cyanobacteria have ATP synthase in both their cell membrane and thylakoid membranes, so too do plants and algae have ATP synthase in both their mitochondrial and their thylakoid membranes. Plants and algae cannot photosynthesise without chloroplasts, and cannot make their own chloroplasts just as they cannot make their own mitochondria. This ATP synthase connection adds to the evidence that chloroplasts were once cyanobacteria that formed an additional union with (some) eukaryotes that evolved into algae and plants.
ATP Production
ATP (adenosine triphosphate) forms when a phosphate molecule attaches to a molecule called ADP (adenosine diphosphate). This reaction does not occur spontaneously owing to the energy required, and in fact it is the reverse reaction which does occur naturally, in which ATP readily breaks down to ADP and a phosphate group. It is this reverse reaction, of ATP breaking down into ADP, that releases the energy for biochemical pathways to proceed.
Thus all living cells require a constant supply of ATP that breaks down into ADP to release energy, else they die. But as ATP does not form spontaneously, cells need help in overcoming the energy input barrier for it to form at all. They need a catalyst, or a substance which drives a chemical reaction by lowering the energy required. This catalyst is ATP synthase.
The Mechanism of ATP Synthase
As a catalyst, ATP synthase works by lowering the energy required for phosphate to join with ADP to form ATP. It does this by making use of a proton gradient across the membrane it is embedded in. This is the case for all ATP synthases, whether they are in bacterial cell membranes, mitochondrial inner membranes, or the thylakoid membranes of cyanobacteria and chloroplasts.
The protons, also called hydrogen ions (H+), accumulate in the inner side of a membrane via an electron transport chain. This gradient from a high concentration inside the membrane to a lower concentration outside the membrane creates electrical potential, and it is this energy difference causing protons to move through the membrane which powers ATP synthase and provides the energy needed for ATP to form.
ATP Synthase in Oxygenic Photosynthesis
The conversion of ADP to ATP is known as phosphorylation — whereby a phosphoryl group (an ion containing phosphate and oxygen) becomes attached to another molecule.
Photophosphorylation is the phosphorylation of ADP to ATP using the energy of photons from visible sunlight.
Those photons' role was to initiate photosynthesis by starting an electron flow from photosystem II (PSII), through to cytochrome b6f, and on to photosystem I (PSI), where electron flow ends with the formation of NADPH (nicotinamide adenine dinucleotide phosphate).
Along the way, protons entered the inner side of the thylakoid membrane (called the lumen) — some from the splitting of water in PSII, and some via the actions of cytochrome b6f.
This creates a proton gradient, with a higher concentration in the lumen and a lower concentration on the other side of the thylakoid membrane, in the stroma. Protons are pumped from the lumen to the stroma, and the energy of this electrical potential powers the ATP synthase molecule which spans the membrane.
Where to After ATP Synthase
Up Until Now: Light-Dependent Reactions of Photosynthesis
All chapters on photosynthesis so far have covered the four major protein complexes embedded in the thylakoid membrane: photosystem II (PSII), cytochrome b6f, photosystem I (PSI), the electron flows through each of PSII and PSI, and finally this one on ATP synthase.
All the reactions in all these complexes resulted in the formation of two molecules: NADPH (the universal electron and proton transporter), and ATP (the universal energy storage molecule). All these reactions are collectively called the light-dependent reactions, so-called as they rely on photon input to occur.
These light-dependent reactions of photosynthesis end with electrons in NADPH via PSI, and with the photophosphorylation of ADP to ATP via ATP synthase.
Everything covered so far can be summarised with the following reaction:
2H2O + 2NADP+ + 3ADP + 3Pi → O2 + 2H+ + 2NADPH + 3ATP
where Pi signifies inorganic phosphate.
But photosynthesis is supposedly the production of food via sunlight, and where is that in the above equation?
Enter the light-independent reactions of photosynthesis!
After ATP Synthase: Light-Independent Reactions of Photosynthesis
The light-independent reactions of photosynthesis do not use a photon input, hence the name. Light-dependent reactions occur in the thylakoid membrane, but the light-independent ones occur outside the membrane, in the stroma.
These reactions use the NADPH and ATP made in the stroma via the light-dependent reactions to produce a carbohydrate called glyceraldehyde-3-phosphate (G3P) from carbon dioxide — this is the production of food via sunlight part, and is called the Calvin cycle.
The Calvin cycle will be covered over several more chapters, but for now can be summarised with this equation:
3CO2 + 6NADPH + 6H+ + 9ATP → glyceraldehyde-3-phosphate (G3P) + 6NADP+ + 9ADP + 3H2O + 8Pi
where Pi signifies inorganic phosphate and G3P enters other reactions to be converted into glucose.
Send feedback »
Posted by kristi on 21 Sep 2021 in Photosynthesis, From Soil to Fruit - How Does Everything Fit Together?, Light-Dependent Reactions
Electron Flow
All life is driven by electron flows through incredibly involved pathways called 'electron transport chains'. (That it happens at all is just awe-inspiring!)
All such pathways begin with a primary electron donor and end with a terminal electron acceptor. It is the flow of electrons from the first donor to the last acceptor which drives all aspects of life.
Photosynthesis is just one example of an electron transport chain, of which there are different versions. The electron transport chain which is the oxygenic (oxygenic-producing) photosynthesis of plants, algae and cyanobacteria is very different to those of non-oxygenic photosynthesising bacteria.
Fig. 1 below represents the membrane of a thylakoid, found in all oxygenic photosynthesisers. In it are embedded four major protein complexes, and electrons must flow through the first three for photosynthesis to occur at all.
Electron flow — the electron transport chain — of oxygenic photosynthesis is represented by the cyan 'e-' circles:
Overview of Electron Flow From Photosystem II to Cytochrome b6f and Plastocyanin
Electron flow begins in the first major protein complex of photosynthesis: photosystem II (PSII). The high energy of light photons stimulates an electron in a molecule within PSII called P680. This electron reaches such a highly excited state that it is ejected — P680 is thus the primary electron donor.
This electron is replaced with one from the splitting of water elsewhere in PSII. Splitting water produces oxygen gas (O2, hence 'oxygenic photosynthesis').
A highly excited electron is a highly reactive one, and the ejected electron is readily taken up by a molecule called pheophytin. Pheophytin is the first electron acceptor.
Pheophytin, now highly reactive itself, passes that electron to another molecule, plastoquinone (PQ in Fig. 1 above). Pheophytin has become the second electron donor, and plastoquinone is now the second electron acceptor.
And so begins the electron flow from donor to acceptor, to donor, to acceptor, until the final acceptor is reached.
Between PSII and Cytochrome b6f
Plastoquinone, on acquiring a second electron from pheophytin, attracts two protons (hydrogen ions, H+) from outside the thylakoid, and becomes plastoquinol (PQH2 in Fig. 1 above). Plastoquinol leaves PSII, carrying two electrons and two protons, and enters the thylakoid membrane.
Plastoquinol is the means by which electrons move, via the thylakoid membrane, from the first protein complex (PSII) to the second protein complex (cytochrome b6f).
Cytochrome b6f
Cytochrome b6f is an enzyme. An enzyme is a protein which is a catalyst, or something which lowers the activation energy required for a reaction to proceed.
(Many, many biological reactions in all life would never happen at all where it not for catalysts, as more energy is needed than is available to the system. A catalyst lowers the energy required to make a reaction possible.)
Cytochrome b6f has two roles. One is to catalyse the transfer of electrons from plastoquinol to yet another molecule, plastocyanin (PC in Fig. 1 above). Transferring those two electrons releases the two protons acquired earlier by plastoquinol from outside the thylakoid, and cytochrome b6f's second role is to pump these into the inside of the thylakoid. (These protons are now in place to be used by the fourth protein complex, ATP synthase, which we'll cover in a later chapter.)
Between Cytochrome b6f and PSI
Plastocyanin's role is to transfer the two electrons given it via cytochrome b6f to the third major protein complex in photosynthesis: photosystem I (PSI).
Electron Flow in Photosynthesis So Far
So far, we've covered the electron transport chain from PSII to just before photosystem I (PSI). The complex flow of electrons to this point has resulted in three very important events.
One is the splitting of water and production of oxygen gas, the sole means by which Earth's atmosphere changed from 0% to 21% oxygen over two billion years or so, and why all macro-organisms including ourselves exist at all. (Only oxygen can provide the energy needed to sustain the electron transport chains of larger lifeforms.)
The second is the transfer of protons (hydrogen ions, H+) across the thylakoid membrane from the outside stroma to the inside lumen. This is a vital step in the production of energy called adenosine triphosphate (ATP), the universal energy needed by all life for metabolism, and we'll cover this elsewhere.
While these two events are coupled to electron flow, the third involves those very electrons directly.
Those electrons, which were originally released from PSII by photon energy, were transported through the thylakoid membrane via several transport/carrier molecules, and now reside in plastocyanin, en route to PSI. They were carried all this way for one very important reason — to produce the electron-carrier molecule called nicotinamide adenine dinucleotide phosphate (NADPH). NADPH is the terminal electron acceptor in photosynthesis.
Another name for photosystem I (PSI) is plastocyanin–ferredoxin oxidoreductase. Just as we broke down the alternative name for cytochrome b6f, plastoquinol-plastocyanin reductase, so too can we here, and know immediately how PSI functions!
The -ase ending signifies an enzyme, so immediately we know PSI is an enzyme. An oxidoreductase enzyme is one which transfers electrons from a donor (which is oxidised) to an acceptor (which is reduced). With this naming convention, the donor is listed first and the acceptor second. Thus PSI is an enzyme which facilitates the transfer of electrons from plastocyanin the donor, to ferredoxin the acceptor.
Ferredoxins are iron-sulfur proteins and amongst the most reducing of all biological electron carriers. To be reduced means to receive electrons, and it makes sense that such compounds are towards the end of a transport chain.
Let's backtrack a bit and recall that PSII contains a chlorophyll-protein reaction centre called P680, and that PSI contains a reaction centre called P700. 'P' stands for 'pigment, and the number refers to the wavelength of maximum absorption by that pigment.
P680 in PSII absorbs photon energy and kickstarts electron flow in photosynthesis by using that energy to donate an electron to pheophytin.
P700 in PSI also absorbs photon energy, but uses that energy to catalyse the transfer of electrons from plastocyanin to ferredoxin (Fd in Fig. 1 above). These electrons move across the thylakoid membrane, from the inside to the outside. Here, in the aqueous stroma of the chloroplast, those electrons are about to end their journey which began back in PSII.
Here in the stroma, ferredoxin, via the enzyme ferredoxin–NADP+ reductase (FNR in Fig. 1 above) donates those electrons to NADP+, which reduces to NADPH, the terminal electron acceptor in photosynthesis.
NADP+/NADPH
NADPH is the reduced form of NADP+, or nicotinamide adenine dinucleotide phosphate. The two work together to transfer electrons and protons (hydrogen ions, H+) to and from the enzymes needed to drive many anabolic biochemical reactions. This makes each a cofactor, or 'helper molecule'.
(An anabolic reaction is one in which a larger molecule is synthesised from smaller ones — plants building carbohydrates from carbon dioxide is one such example where NADP+/NADPH are involved.)
NADP+/NADPH are universal electron carriers and found in all life.
NADP+ is an electron and proton acceptor (acquires electrons and H+) — accepting electrons and protons converts it into NADPH.
NADPH is an electron and proton donor (loses electrons and H+) — donating electrons and protons converts it into NADP+.
The End Result
Electron flow in photosynthesis (and all biological pathways for that matter) is incredibly involved, and reliant on complex molecules acting in turn to donate and accept electrons.
It is important to realise that this flow would not occur spontaneously in nature as the energy required is too great. Just as paper won't spontaneously ignite, but needs help, electron flow in photosynthesis too requires help, and this is done in two ways.
One is to input energy into the system directly — just as inputting heat energy to paper causes ignition — and in photosynthesis this is done with two photon boosts, one in PSII and one in PSI.
The second form of help is to lower the energy required, and this is done via the enzyme activity within PSII, cytochrome b6f, and PSI.
Electron flow in oxygenic photosynthesis results in the splitting of water to produce oxygen gas as mentioned above. While this is a nice side-benefit for the rest of the planet, this gas production is actually a waste product which doesn't affect the photosynthesiser directly.
The real purpose of electron flow in photosynthesis — from the photosynthesiser's point of view — is to achieve two very important results.
One, as we've seen, is for electrons to end up in NADPH, the universal electron carrier and proton donor. NADPH, along with its NADP+ counterpart, goes on to participate in the Calvin Cycle, the means by which the carbon in carbon dioxide is 'fixed' into the carbon of glucose. (These compounds feature in other biochemical pathways as well.)
The second result of electron flow in photosynthesis is to pump protons (hydrogen ions, H+) across the thylakoid membrane, from the outside stroma to the inside lumen. Here they are available to participate in the second end result of photosynthesis, the generation of the energy molecule ATP. And it is this which we will cover in the next chapter.
Posted by kristi on 24 Aug 2021 in Photosynthesis, From Soil to Fruit - How Does Everything Fit Together?, Light-Dependent Reactions
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 thylakoids are where oxygenic photosynthesis takes place (Fig. 1).
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…
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):
Figure 2. Photosystem I with LHC I (light-harvesting complex I)
A and B are different orientations
'Psa' prefix: Photosystem I proteins
'Lhc' prefix: Light-harvesting complex proteins
Attribution: Эрг, CC BY-SA 4.0 , via Wikimedia Commons
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.
The Light-Harvesting Complex (LHC)
The role of each photosystem's light-harvesting complex (LHC), or antenna complex, is to channel photon energy to each photosystem's reaction centre.
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 electron 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.
Drilling Down
There are two types of photosynthesis: anoxygenic and oxygenic.
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. (Sulfur 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.
All oxygenic photosynthesis occurs in structures known as thylakoids, which are found only in cyanobacteria and the chloroplasts of algae and plants. (There is in fact much evidence that chloroplasts were once cyanobacteria.)
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.
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.
Posted by kristi on 27 Jul 2021 in Photosynthesis, From Soil to Fruit - How Does Everything Fit Together?, Light-Dependent Reactions
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.
Energy Input
Oxygenic photosynthesis begins in photosystem II (PSII), a protein complex embedded in, and spanning, the thylakoid membranes of chloroplasts and cyanobacteria. Here, photon energy is transferred to the two chlorophyll-protein complexes in PSII collectively known as P680.
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+
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
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
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.
To Summarise
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).
Figure 1. Chloroplasts in the cells of the moss Bryum capillare
Attribution: Des_Callaghan, CC BY-SA 4.0 , via Wikimedia Commons
(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).
Figure 2. The arrangement of grana within a chloroplast
Attribution: Public Domain, https://en.wikipedia.org/w/index.php?curid=10483833
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 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!
Figure 4. Cyanobacterial photosystem II, Monomer, Protein Data Bank Entry 2AXT (PDB 2AXT)
Attribution: Neveu,Curtis (C31004), CC BY-SA 3.0, via Wikimedia Commons
Fig. 5 is a more stylised illustration of PSII:
Figure 5. Schematic of PSII, highlighting electron transfer
Attribution: Kaidor, CC BY-SA 4.0 , via Wikimedia Commons
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), 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 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.)
Figure 6. The Kok cycle. The oxidation state of the manganese centres is subject to debate.
Attribution: Yikrazuul, Public domain, via Wikimedia Commons
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.
The Thylakoid
Posted by kristi on 29 Jun 2021 in Photosynthesis, From Soil to Fruit - How Does Everything Fit Together?, The Chloroplast
What Are Thylakoids?
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:
Figure 1. The structure of a chloroplast
Attribution: Kelvinsong, CC BY 3.0 , via Wikimedia Commons
(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:
Figure 3. Slice of a lettuce chloroplast showing grana arrangement.
(Top) 10-nm-thick scanning transmission electron microscopy (STEM) tomographic slice of a lettuce chloroplast. Grana stacks are interconnected by unstacked stromal thylakoids, called "stroma lamellae". Round inclusions associated with the thylakoids are plastoglobules. Scalebar = 200 nm.
(Bottom) Large-scale 3D model generated from segmentation of tomographic reconstructions by STEM. grana = yellow; stroma lamellae = green; plastoglobules = purple; chloroplast envelope = blue.
Attribution: By Yuv345 - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=93345039
Thylakoid Structure
Each thylakoid has a membrane surrounding an aqueous lumen (Fig. 4).
Figure 4. Thylakoid structures
Attribution: http://en.wikipedia.org/wiki/Image:Granum.png, CC BY-SA 3.0 , via Wikimedia Commons
Embedded in the membranes are four major protein complexes: photosystem II (PSII), cytochrome b6f complex, photosystem I (PSI), and ATP synthase (Fig. 5). These four complexes participate in a series of reactions called the light-dependent reactions of oxygenic photosynthesis, to produce two molecules: adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH).
ATP is the molecule which stores potential energy to drive further biochemical reactions, and NADPH, together with its oxidised form NADP+, transfer electrons and protons (hydrogen ions, H+) 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.
Net Reaction
The net result of all light-dependent reactions in oxidative photosynthesis can be summarised as:
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:
Photosynthesis as a Whole
All the reactions of both the light-dependent and light-independent reactions can in turn be summed up with one net reaction for oxygenic photosynthesis overall:
6CO2 + 12H2O + photons → C6H12O6 + 6H2O + 6O2
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 source.)
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.)
(To complete the picture, we know photons are the energy source, which is phototrophy. Altogether we have photolithoautotrophy in play.)
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.
Endosymbiotic Origin
Backstory: Of Prokaryotes and Eukaryotes
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.
Many prokaryotes can photosynthesise via compounds known as bacteriochlorophylls. They are all, with one exception, anoxygenic photosynthesisers, in that they do not produce oxygen as a by-product.
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.
Development of the Theory
Hugo von Mohl was the first to describe chloroplasts in 1837, though he called these Chlorophyllkörnen ('grain of chlorophyll'). Andreas Franz Wilhelm Schimper named these Chloroplastiden ('chloroplastids') in 1883, and Eduard Adolf Strasburger named these Chloroplasten ('chloroplasts') in 1884.
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.)
Figure 3. One model for the symbiogenesis theory
Attribution: Kelvinsong, CC BY-SA 3.0 , via Wikimedia Commons
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)
Figure 4. Comparison of a chloroplast with a cyanobacterium
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.
Electron Source
All life additionally needs an electron source (also called an electron donor source). 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!
Visible Light and Photosynthetic Pigments
Posted by kristi on 01 Jun 2021 in Photosynthesis, From Soil to Fruit - How Does Everything Fit Together?, Photosynthesis in Plants
Photons and the Electromagnetic Spectrum
'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):
Figure 1. Frequencies and wavelengths along the electromagnetic spectrum
Attribution: !Original: PenubagVector: Victor Blacus, CC BY-SA 3.0 , via Wikimedia Commons
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:
Figure 2. Electromagnetic spectrum properties
Attribution: Inductiveload, NASA, CC BY-SA 3.0 , via Wikimedia Commons
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.
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
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
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.
Phaeophytins
Phaeophytin a is a grey-brown pigment and phaeophytin b is yellow-brown.
Chlorophylls
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: An Overview
Posted by kristi on 05 May 2021 in Photosynthesis, From Soil to Fruit - How Does Everything Fit Together?, Photosynthesis in Plants, Photosynthesis in Bacteria
What is Photosynthesis?
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.
Metabolically, all photosynthesisers are both phototrophs, with their energy source coming from photons, and autotrophs, with their carbon source coming from inorganic carbon.
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
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.
Photosynthesisers are not only photoautotrophs, they are also photolithoautotrophs.
Anoxygenic Photosynthesis
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.
Oxygenic Photosynthesis
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:
There is far more going on behind the scenes than this deceptively simple formula implies, but nonetheless, this formula is the reason why Earth's atmosphere is 21% oxygen gas today.
The Importance of Photosynthesisers
As an Energy Input via Phototrophy
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.
Photosynthesis and Cellular Respiration
Posted by kristi on 08 Sep 2020 in The Essentials For Life (As We Know It), Agricultural Chemistry, Photosynthesis, Dormancy, Biochemical Pathways, Life of a Ta-Jan
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).
Yet right up into the early 1770s not much was known about 'air' and its components, except that it was regarded as a "a simple elementary substance, indestructible and unalterable", and that it might have contained 'phlogiston'.
The English scientist Joseph Priestley charted a new field of discovery into 'the airs' (gases) with his famous experiment with a bell jar, mint plant and mouse. This experiment, performed in August 1771, established that "…plants, instead of affecting the air in the same manner with animal respiration, reverse the effects of breathing, and tend to keep the atmosphere sweet and wholesome…" (link to a PDF).
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.
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.
A Crash Course in Photosynthesis
Posted by kristi on 31 Dec 2019 in Jujube Botany, The Essentials For Life (As We Know It), Photosynthesis, Leaves
Photosynthesis is the process by which plants, algae, cyanobacteria, and a few other bacterial species convert light energy into chemical energy, which is stored as a food source. Photosynthetic organisms thus produce their own food, and are called autotrophs ('self-nourishment'). Those that must take in food, such as us, are heterotrophs ('other/different nourishment').
Photosynthesis is a truly amazing process without which we and all other multicellular organisms would never have come to be. And the photosynthesis we are most interested in — oxygenic photosynthesis which occurs in plants, algae and cyanobacteria, as opposed to the anoxygenic photosynthesis in some bacteria — would never have developed at all, were it not for water.
Early Earth (believed to have formed over 4.5 billion years ago) had virtually no oxygen in its atmosphere, and the first life did not appear until at least 3.5 billion years ago. The first photosynthetic organisms probably appeared around this time, and performed anoxygenic photosynthesis, photosynthesis which does not produce oxygen.
It wasn't until cyanobacteria evolved around two billion years ago that oxygen was produced from photosynthesis (oxygenic photosynthesis), leading to the oxygenation of Earth's atmosphere. This Great Oxygen Event (or Oxygen Catastrophe depending on your point of view) would have made extinct most of the organisms of the time, which were all unicellular and anaerobic (not requiring oxygen for growth; oxygen in this case would have been poisonous for them). This oxygenation however is directly responsible for the evolution of all multicellular life that has ever existed on Earth.
Oxygenic photosynthesis is the most common today. It is a very complex process, but can be summarised in words as:
carbon dioxide + water + photons (particles of light, light energy) → glucose + oxygen + water
and chemically as:
6CO2 + 12H2O + photons → C6H12O6 + 6O2 + 6H2O
You could say more long-windedly that the input of light energy causes six molecules of carbon dioxide to react with twelve molecules of water, to form one molecule of glucose (a simple carbohydrate which the plant stores as food/chemical energy), six molecules of oxygen gas which is released into the air that we and many other organisms then breathe, and six molecules of water.
(This equation doesn't really occur. Carbon dioxide doesn't react with water during photosynthesis, and glucose isn't even the product. Rather, this equation is used in textbooks as a 'good enough' summary of the inputs and outputs of photosynthesis. In reality there are two very different sets of reactions going on, and these are described in this site's From Soil to Fruit book chapter.)
As you can see here, oxygenic photosynthesis requires water, and produces oxygen. Anoxygenic photosynthesis does not require water, and does not produce oxygen. To this present day, many anoxygenic photosynthetic bacteria utilise hydrogen sulfide ('rotten egg gas') instead of water to form glucose, and produce solid sulfur instead of oxygen as a by-product!
We (multicellular organisms) literally would not be here today were it not for the presence of water and those early cyanobacteria (or some similar organism that may have evolved had they not) producing the oxygen that kickstarted the whole process. And we won't be here tomorrow should oxygenic photosynthesis cease to exist.
As plants are our special interest here, let's now discuss photosynthesis as it directly relates to plants.
For starters, plants are the only photosynthetic organisms with specialised equipment dedicated to photosynthesis — leaves. (Though there are plants, for example cacti, that don't have leaves and instead photosynthesise via other body parts such as the stems.)
In the leaves are special structures called chloroplasts, which contain chlorophyll a and chlorophyll b. These absorb red and blue light the most, and the green and near-green wavelengths the least. These green and near-green wavelengths are reflected back, and we see the leaves as green.
Carbon dioxide enters the leaves via pores called stomata (plural form of stoma), and water enters via the xylem. Xylem is a transport tissue, whose purpose is to conduct water from the roots to stems and leaves via capillary action for various biochemical processes including photosynthesis. (Note to self: these could be subjects for future posts.)
With carbon dioxide and water in place, what happens next in the chloroplast is incredibly involved and perhaps the subject of future posts if I run out of things to write about in winter!
(Update: please refer to the Photosynthesis section of the From Soil to Fruit book for those posts!)
But to gloss over all that, very simply, water molecules are split in the chloroplast into hydrogen and oxygen. Electrons are released, which are excited by the photons absorbed by chlorophyll a. This triggers a chain reaction of electron flow which ultimately produces energy (stored as adenosine triphosphate (ATP) and sugars.
The oxygen from the water-splitting is a by-product not used by the plant, and exits the chloroplast to be released via the stomata into the atmosphere. The hydrogen stays in the chloroplast, where it combines with carbon dioxide to form sugar.
We can infer factors that affect photosynthesis and hence plant growth. Light intensity is an obvious one — not too much photosynthesis occurs at night! Latitude and altitude will also play into how much light is received during the day and over a year, and structures or other vegetation that cast shadows for long hours will affect sun-loving plants.
The wavelengths of light received influence photosynthesis. Plants grown commercially under cover often require special lightbulbs for optimum growth — your reading light just won't cut it!
Photosynthesis increases when carbon dioxide levels increase, and it is routine to pump this gas into commercial greenhouses for increased growth.
Photosynthesis, like all other biological processes, requires enzymes to drive reactions (this is part of the complexity not shown and deliberately skipped over in this post). Enzymes are biological catalysts, and each one has its optimum temperature at which full operation occurs. Just a few degrees above or below this optimum is enough to slow the rate of operation, while lower or higher again will halt enzyme activity altogether.
Extremely high temperatures will denature enzymes, and in very extreme cases (such as a lack of water needed for its coolant and solvent properties) cause a plant to shut down and even die. (Likewise, a fever-induced high body temperature in a person is potentially dangerous — a body must keep a fine line between a slightly higher than normal temperature that kills invasive bacteria or viruses, and a too high temperature that shuts down biochemical reactions and leads to a body breaking down.)
Water, the miracle molecule, and photosynthesis, the miracle process by which light is converted into food, are the very backbone of life on this planet. Had oxygenic photosynthesis not appeared around two billion years ago, anoxygenic photosynthetic life would in all likelihood still be around, but would remain as simpler unicellular life to the present day.
It is oxygenic photosynthesis producing oxygen that enabled multicellular organisms such as jujube trees and people to evolve at all.
Next week I'll cover a process even more important than photosynthesis — the nitrogen cycle. For if not for the nitrogen cycle there'd be no such thing as a plant in the first place.