Both reaction types occur within the chloroplasts of cyanobacteria, algae, and plants. Fig. 1 shows a simplified diagram of a chloroplast.

Figure 1: A simple representation of a chloroplast
Attribution: Public Domain, https://en.wikipedia.org/w/index.php?curid=10483833

The light-dependent reactions occur in the membranes of the thylakoids within the chloroplasts (the dark green outlines in Fig. 1), but the light-independent reactions occur outside the thylakoids, in the stroma fluid they are suspended in.

The light-independent reactions are also collectively referred to as the Calvin cycle, and can be summarised in one diagram, albeit an involved one (Fig. 2):

Figure 2. The Calvin Cycle
Attribution: Mike Jones, CC BY-SA 3.0 , via Wikimedia Commons

Whilst not clear from this diagram, remember that this is occurring in the stroma of a chloroplast. Thus the Nicotinamide Adenine Dinucleotide Phosphate (NADPH/NADP+) and Adenosine Triphosphate (ATP) shown entering the cycle are the same NADPH and ATP formed by the light-dependent reactions earlier, and which form in the stroma. These molecules then feed into the Calvin cycle to drive it further.

Calvin cycle reactions are called light-independent, as no photon input is required to drive them. However, this is a slightly misleading term, as this part of photosynthesis still requires the presence of light, as the NADPH created is very short-lived and needs to be replenished constantly — via the light-dependent reactions.

The cycle begins with the input of carbon dioxide (CO₂). The carbon in CO₂ is inorganic, but is ‘fixed’ into organic carbon (here, a carbohydrate) via the action of an enzyme, ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO), on another molecule called ribulose 1,5-bisphosphate (RuBP). This creates a very unstable, new molecule which immediately splits into two three-carbon molecules of 3-phosphoglycerate (PGA). One of these enters new metabolic pathways to create other carbohydrates, while the other remains in the cycle to regenerate more RuBP to begin the cycle over — helped with the previously made NADPH and ATP.

NADPH and ATP — formed via the light-dependent reactions — enter the cycle, react, and are converted to NADP⁺ and ADP respectively. NADPH loses two electrons and becomes NADP⁺; ATP loses a phosphate group and becomes adenosine diphosphate (ADP).

These two molecules remain in the stroma and are converted back into NADPH and ATP via the light-dependent reactions. And thus the light independent reactions are coupled to the light-dependent ones in this incredible two billion year old system.

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.

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.

Prokaryotes

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

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.

Eukaryotes

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 + 3P_i→ O₂+ 2H⁺+ 2NADPH + 3ATP
where P_i 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 + 8P_i
where P_i signifies inorganic phosphate and G3P enters other reactions to be converted into glucose.

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:

Figure 1. The thylakoid membrane
Attribution: By Somepics - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=38088695

Overview of Electron Flow From Photosystem II to Cytochrome b₆f and Plastocyanin

Photosystem II (PSII)

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.

Electron Flow in Photosystem I (PSI)

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.

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).

Figure 1. The thylakoid membrane
Attribution: By Somepics - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=38088695

The other photosystem, photosystem II (PSII), is the first of the four and was described here and here.

Despite being the second photosystem, PSI was the first discovered and hence its name. Both photosystems were discovered in the 1950s but their functions not pieced together until 1961. (By geniuses, in my opinion!)

Another name for photosystem I is plastocyanin–ferredoxin oxidoreductase, and we’ll pick apart the significance of this in the next chapter. But just from the previous chapter, where we discerned the meaning of plastoquinol-plastocyanin reductase, you may have already recognised the ‘-ase’ ending signifies an enzyme (a protein which acts as a catalyst) — and that the ‘oxidoreductase’ part just may have something to do with reduction and oxidation…

Photosystem I (PSI)

As mentioned above, PSI is a protein complex, a structure composed of several protein subunits. Fig. 2 below shows both the protein complex which is PSI (with ‘Psa’ prefixes) and the associated light-harvesting complex (LHC) which collects photon energy (with ‘Lhc’ prefixes):

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.

Roles

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.

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:

Figure 1. The thylakoid membrane
Attribution: By Somepics - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=38088695

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

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 Q_A and plastoquinone Q_B. Q_A transfers two electrons from pheophytin to Q_B. These two electrons enables plastoquinone Q_B to acquire two hydrogen ions (H⁺, also called a proton) from outside the thylakoid membrane (the stroma). Q_B leaves PSII and enters the thylakoid membrane. In acquiring two electrons, plastoquinone enters a reduced state and is called plastoquinol (PQH₂ in Fig. 1 above).

Cytochrome b₆f — also in the thylakoid membrane — now catalyses the transfer of those electrons to yet another molecule, plastocyanin (PC in Fig. 1 above). (Plastocyanin is a copper-containing protein, and one reason why copper is an essential plant nutrient.)

Plastocyanin, in receiving electrons, is now reduced in turn. And this is why cytochrome b₆f is also called plastoquinol-plastocyanin reductase, as it catalyses the reduction of plastoquinol to plastocyanin. (Enzyme names can be unambiguous and highly descriptive this way!)

In catalysing the movement of two electrons from plastoquinol to plastocyanin, cytochrome b₆f additionally pumps the two protons (H⁺ ions) brought in by plastoquinol from the stroma outside the thylakoid into the lumen inside the thylakoid. These protons have a further role which will be covered in a later chapter.

Further Electron Flow

Biochemistry is the flow of electrons, and biochemical pathways involve complex electron transport chains. Photosynthesis is no exception, and those electrons don’t end with plastocyanin!

Plastocyanin’s role is to move electrons to the third major protein complex in photosynthesis: photosystem I (PSI), and this is the topic of the next chapter.

Chemical reactions involve atoms and molecules, but chemistry at its heart is really the study of the electron flow between those atoms and molecules when these react.

Similarly, biochemistry at its heart is the study of the electron flow within living organisms. A common term in biochemistry for this electron flow is the electron transport chain, of which there are two types: cyclical and non-cyclical.

Electron Flow Requires Energy

Electron transport chains need energy to begin. As energy can neither be created nor destroyed, it must be input from somewhere. In photosynthesis, this energy comes from photons in the visible light spectrum.

Electron Flow in Photosystem II (PSII)

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.

Figure 1. The thylakoid membrane
Attribution: By Somepics - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=38088695

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.

Electron Flow

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).

Figure 3. The thylakoid membrane
Attribution: By Somepics - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=38088695

They are called protein complexes as each is a unit of several protein subunits.

Photosynthesis begins with Photosystem II (PSII) in the thylakoid membrane. This is the region where photons are absorbed and where water is split, both actions triggering a cascade of reactions that produces oxygen, energy, and sugar.

Without PSII there can be no photosynthesis — at least in plants, algae and cyanobacteria — and some herbicides such as atrazine work by inhibiting PSII.

Photosystem II (PSII)

Photosystem II is an incredibly complicated structure — Fig. 4 is of the PSII of the cyanobacterium Thermosynechococcus elongatus, and it is a simplified representation at that! The above-mentioned protein subunits this PSII protein complex contains are represented here as simple colour-coded rods, but are themselves highly complicated structures as well. Far more detail is here should you be curious!

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)

The light-harvesting complex (LHC), also called the antenna complex, contains the photosynthetic pigments. These are the core photosynthetic pigment chlorophyll a and the additional antennae pigments chlorophyll b, the xanthophylls, and the carotenes. Each has a different peak absorption, and combined they increase the absorbable range of light wavelengths. The xanthophylls and carotenes (collectively called the carotenoids) have additional roles as antioxidants — as they do for us when we ingest them — though in PSII they specifically protect the chlorophylls from photon-induced oxidative stress.

Each LHC contains 250 – 400 of these pigment molecules, and the photon energy they absorb is channelled into the reaction centre of PSII. The CP43 and CP47 proteins at top of Fig. 5 are essential in passing this energy on. These are called the light-harvesting proteins.

The Reaction Centre

The reaction centre is made up of two specialised chlorophyll-protein complexes called D1 and D2. Each contains one chlorophyll a molecule, and this molecule pair is referred to simply as P680. (’P’ for ‘pigment’, and 680 for its maximum absorption at 680 nm.)

P680 both absorbs the photon energy channelled from the light-harvesting complex as well as from photons directly.

P680 is the Photosytem II primary donor, as the photon energy it receives excites an electron into such a high energy state that it becomes unstable. This electron readily moves from (is donated by) P680 to another molecule called pheophytin (Fig. 4, and the ‘Pheo’ in Fig. 5). Pheophytin is the primary electron acceptor in PSII — it is reduced (becoming negatively-charged) and P680 is oxidised to P680⁺.

(Reduction-oxidation reactions are explained in more detail here.)

Via pheophytin, this electron then transfers to another electron acceptor, plastoquinone Q_A, then onto plastoquinone Q_B. 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, Tyr_Z is a tyrosine residue*, and S_0 – 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, which extracted it from a water molecule.

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.

Figure 1. Chloroplasts in the cells of the moss Bryum capillare
Attribution: Des_Callaghan, CC BY-SA 4.0 , via Wikimedia Commons

Chloroplasts contain structures called thylakoids, which are suspended in a fluid called the stroma. (Stacks of thylakoids are called grana — a singular stack is called a granum).
A simple representation of a chloroplast is shown in Fig. 2.

Figure 2. The arrangement of grana within a chloroplast
Attribution: Public Domain, https://en.wikipedia.org/w/index.php?curid=10483833

The light-dependent reactions are named not so much because they occur in the light (although they do), but because they are driven by the energy of photons within the visible light spectrum. 

The light-dependent reactions occur within the thylakoid membranes, represented by the dark-green borders in Fig. 2. The thylakoid membrane is distinct from the chloroplast’s membrane, and keeps the internal part of the thylakoid, called the lumen, together. Thylakoid lumens are represented by the fluorescent-green ovals in Fig. 2.

Embedded, and spanning, the thylakoid membrane are four major protein complexes: photosystem II (PSII), cytochrome b6f complex, photosystem I (PSI), and ATP synthase (Fig. 3). The ‘chloroplast stroma’ and ‘thylakoid lumen’ labels mark the external and internal sides of the thylakoid membrane respectively.

Figure 3. The thylakoid membrane
Attribution: By Somepics - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=38088695

These four are called protein complexes as each is made of several protein subunits. All four will be covered in detail in the following pages, and we will see Fig. 3 many more times yet!

But here in this overview we can summarise the light-dependent reactions of photosynthesis as two processes:

1. a flow of electrons is kickstarted by photon energy striking photosystems II and I. These electrons move through the thylakoid membrane and end in a molecule called Nicotinamide Adenine Dinucleotide Phosphate (NADPH/NADP+) in the chloroplast stroma. NADP⁺/NADPH, as the universal electron (e^-) and proton (H⁺) carrier in life, then goes on to participate as an important cofactor in many biochemical reactions; and
2. an accumulation of protons (H⁺ ions) arises in the thylakoid lumen. These H⁺ ions come from the splitting of water by photosystem II in the lumen, and via the cytochrome b6f complex pumping still more across the membrane from the stroma to the lumen. These H⁺ ions create a gradient of high (in the lumen) to low concentration (in the stroma) across the membrane, which in turn creates enough electrical potential to generate Adenosine Triphosphate (ATP), also in the stroma. ATP is the universal storage of energy in life, and vital for biochemical processes to occur at all.

A cyanobacterium, alga or plant — having produced NADP⁺/NADPH and ATP via photon energy — can now use these molecules to make carbohydrates from carbon dioxide. This part, the making of carbohydrate food, involves the light-independent reactions and will be covered more thoroughly in that section.

Please keep reading for a breakdown of how each of the components involved in the light-dependent reactions of photosynthesis just work — the beauty and complexity of life never ceases to amaze me!