Introduction to photosynthesis

This is the first of three lectures on photosynthesis (Slide 1). We begin with a look at how light first engages with photosynthetic matter in flora, initiating the primary processes that will eventually lead to the synthesis of carbohydrates (Slide 2). We refer to processes that occur prior to the charge migration that initiates carbohydrate production as upstream processes; those that ensue are downstream processes.



To understand these processes better we shall first consider the mechanisms for energy transfer and electron transfer, dealing in detail with light absorption and also the decay pathways associated with these processes. Then we shall focus on the structure, nature and role of antenna molecules in biological systems. Most familiar are chlorophyll molecules, but there is a range of ancillary pigment molecules, such as carotenoids, which also play an important part in photosynthesis. Together, these are all held in place in specific positions and orientations by supramolecular structures built from proteins. Last in this lecture we shall examine the molecular orbital descriptions of energy and electron transfer – what we might call upstream processes: those that lead to the initial stages of the photosynthetic reaction.

We begin with an overview of how simple sugars are produced in photosynthesis (Slide 3). The synthetic process begins with the absorption of light. This leads to two half-reactions (although, as we shall see, there is a lot going on between the absorption of light and the start of these processes).


One half-reaction takes place in thylakoid membranes: it involves the absorption of water and the release of oxygen. This is linked by redox reagents adenosine triphosphate (ATP) and reduced nicotinamide adenine dinucleotide phosphate (NADPH) to a second, carbon-based half-reaction promoted by enzymes in the stroma (Slide 4). This leads to the incorporation of carbon dioxide, and hence the production of simple carbohydrate units that we might represent as CH2O – in fact, just a sixth part of the simplest carbohydrate (glucose).


Slide 4 gives an overview of the positioning of the photosynthetic apparatus in green plants. Essentially, plant photosynthesis is supported by chloroplast cells (whose presence in the plant is apparent from the green colour of the chlorophyll they contain, mainly but not exclusively in leaves). Inside these chloroplasts is the stroma, which contains enzymes to assist the carbon-based half-reaction. The stroma surrounds numerous thylakoids, which are structures enclosed by membranes that themselves contain the light-harvesting pigments, principally chlorophyll.

We shall now start to look at the various photosynthetic stages in more detail. Slide 5 is a breakdown summary of the material that is coming up in these three lectures.


3.1 Photon capture

3.1.1 Sunlight

It is appropriate to begin with the arrival of sunlight (Slide 6).When sunlight reaches the Earth’s surface, about 4% of its energy is in ultraviolet radiation. About 43% of the energy falls in the visible range and the rest is in the infrared, where the photons have less energy – certainly not enough to break the chemical bonds in water, for example. In fact, one photon has insufficient energy to achieve such a result even with visible light, whose photons are much more energetic than infrared ones. It is just as well, otherwise we and all living creatures, very largely composed of water, would spontaneously disintegrate in the sunshine.


Certainly, no single photon conveys enough to provide for the complete conversion of carbon dioxide and water into a carbohydrate.

Separating the chemical reaction that produces glucose into six parts, and focusing on the two half-reactions (Slide 7), we find that the mechanism bringing into effect the oxidation of water produces the release of four electrons, and the counterpart half-reaction for the reduction of carbon dioxide consumes four electrons.


Oxidation of water:

Equation 1
Equation 1


Reduction of carbon dioxide:

Equation 2
Equation 2


Each electron event occurs in response to a photon, and so eight photons are consumed in producing each of these carbohydrate units; 48 are needed in total for the synthesis of one molecule of glucose.

These photons must be delivered to the place where the photosynthetic chemistry takes place, which is called a reaction centre. The prospect of even two photons arriving at the same place at the same time is negligible, and so it is crucially important to collect the energy of photons captured in different places and at different times.

To understand this better, a simple calculation of the statistics can be performed (Slide 8). For radiation of frequency ν and intensity I, the number of photons per unit volume is I/hνc. If Vm is the molar volume for the irradiated material, NA is Avogadro’s number, then the volume per molecule is Vm/ NA, and so n-bar ,the mean number of photons within the volume occupied by single molecule, is given by

Equation 3
Equation 3


where λ is the wavelength of the radiation.


Slide 8 Sunlight and photon flux.

The mean intensity of solar radiation at the top of the atmosphere (at normal incidence) is 1.4 kW m–2. If we use Equation 3, sunlight shining on the surface of the sea, using 1.4 kW m–2 as an upper limit for intensity, we find there will be a few million photons in each cubic centimetre of water – nowhere near one photon in any individual water molecule at any given time.

If we ask the question ‘what is the prospect of finding even two photons simultaneously present in a single water molecule?’, the answer is that such an event might be found in about one molecule in a million litres.

This simple calculation affords a nice illustration of the striking effectiveness of the molecular apparatus in photosynthetic organisms, which can not only capture but also gather together the energies of much larger numbers of photons.

By similar methods (Slide 9) it is possible to calculate the number of photons arriving in a chlorophyll molecule per second,

Equation 4
Equation 4


where σ is the effective area of the molecule; it turns out to be about one photon per second, once we take account of the typical reduction of intensity due to cloud cover, etc.


The intensity of full sunlight in the spectral region of 400–700 nm corresponds to an intensity of around 103 photons nm–2 s–1. Taking into account cloud cover, canopies, etc, this becomes approximately 1 photon molecule–1 s–1.

3.1.2 Absorbing photons

For the efficient harvesting of sunlight, to have any prospect of bringing several photon energies together, we need antenna complexes – that is, a variety of light-absorbing molecules (chromophores), strongly absorbing at different wavelengths, and oriented at various angles with respect to the incident light.

We also need to enable the energy of several photons, once captured, to be moved towards a common location – the reaction centre. This involves a succession of chromophores, as we shall see. However, some chromophores act in another capacity, as photoprotectors – absorbers that remove excess energy, preventing system overload under intense light conditions.

Slide 10 summarises what happens when a photon is absorbed. In most forms of photosynthesis, chlorophyll molecules (or bacteriochlorophyll molecules in the case of photosynthetic bacteria) are the molecules that absorb light. A single chlorophyll molecule (represented as Chl on Slide 10) absorbs a single quantum of light, at the appropriate wavelength, giving rise to an electronically excited state (the S1 state – the first excited singlet state).


Once a chlorophyll molecule enters the excited state, several different things may occur. The first is that the excited state may directly decay. This involves the excited state undergoing relaxation back to the ground state, indicated here by the vertical scale energy positioning of the red dot signifying an electron. During this process the excess energy must be ‘returned’. This occurs either by dissipation through molecular vibrations (heating) or by giving off light (i.e. fluorescence).

The second process that can occur from an electronically excited state of a chlorophyll molecule is resonance energy transfer (RET) to a neighbouring chlorophyll molecule (see Lecture 4 for details). This involves the transfer of the excited state energy from one chlorophyll molecule to another via the exchange of a virtual photon. Here, two electrons are involved, distinguished on the slide by different colours: red and black.

Finally, the excited state energy of the chlorophyll molecule can be given up to initiate a charge-transfer reaction, again involving two electrons. This is shown in the third pathway on Slide 10, where the electron donor is depicted in blue and the electron acceptor in yellow. The excited state chlorophyll molecule is in green. Effectively, the donor transfers an electron to the ground state of the chlorophyll molecule, while the excited state electron is simultaneously transferred to the electron acceptor. The net result is a hole remaining in the donor level and an additional electron moving into the acceptor, giving rise to an overall charge-separated state.

3.1.3 Light-absorbing molecules

Chlorophyll molecules (Slide 11) are the main type of pigment molecule in the antenna complexes of photosynthetic organisms. Although there are a number of different chlorophyll molecules (i.e. slightly different chemical structure), they all share the same basic structure. They are squarish planar molecules about 1 nm on a side. There is a magnesium atom in the centre, coordinated to four nitrogens. The nitrogens are part of a pyrrole ring (a five-membered ring with four carbons and one nitrogen). Importantly, a delocalised π-system (a molecular orbital extending over a molecule with sufficient double bond character) extends over the molecule. The chlorophyll molecules also have a phytol tail (side-chain).


The electronic spectra of the chlorophyll molecules display two major absorption bands: one in the blue (or near-UV) region and one in the red (or near-IR) region. The lack of absorption in the green region of the visible range gives the chlorophylls their characteristic green colour.

It is interesting to note that the significantly different spectra of chlorophyll a and chlorophyll b result from one small change in the molecular structure, viz. changing the methyl group at the top of the ring structure to an aldehyde group.

A second important class of molecules found in antenna systems of photosynthetic organisms is the carotenoid molecules (Slide 12). There are many hundreds of distinct carotenoid molecules; the name denotes a connection with carrots, because it is one of these chemical structures that gives those root vegetables their distinctive orange colour. All such molecules have some common structural features: they are extended linear molecules with a delocalised π-system.


Carotenoids have several important functions in photosynthetic antenna systems. Firstly, they are accessory pigments in the collection of light. They can absorb light and transfer the energy to carotenoid-type pigment molecules.

Secondly, it is often the carotenoids that function as photoprotectors. That is, they rapidly quench triplet excited states of chlorophyll molecules before the latter have time to react with oxygen to form excited-state singlet oxygen molecules – a form of molecular oxygen that is highly reactive and destructive to biological systems. (Molecular oxygen in its natural form exists in an electronic state of triplet character – an illustration of Hund’s rule.) The carotenoids also quench (electronically deactivate) singlet oxygen when it is formed.

Finally, carotenoids are now known to be involved in the regulation of energy transfer in antenna complexes (Slide 13). All chlorophyll-based photosynthetic organisms contain antenna complexes. These are huge supramolecular structures with the chlorophyll and carotenoid molecules embedded within the surrounding protein matrix, and the helical structure of the protein matrix spans the membrane.


Slide 14 shows some more examples of antenna systems. The top image of the PSII supercomplex shows schematically how energy can be transferred from the point at which the photon is absorbed to the reaction centre where charge separation occurs.


3.1.4 Molecular orbital representation

The mechanism for the transfer of energy in antenna complexes will be discussed in detail in Lecture 4. However, we can begin to understand some features by looking at a molecular orbital (MO) representation (Slide 15), which is a very intuitive way of thinking about the energy-transfer process.


In Slide 15 we have two molecular species: a donor D and an acceptor A. Initially D is in the excited state. This can be described by an electron being promoted from the HOMO (highest occupied molecular orbital) to the LUMO (lowest unoccupied molecular orbital), after the molecular species has absorbed a photon.

Energy transfer involves the excited state being ‘relocated’ from D to A, as a result of Coulombic interactions (here labelled V; more details of how this electronic coupling works will be given in Lecture 4 of this topic: ‘Molecular energy transfer and photobiology’. There are two ways to think about this within the MO picture.

The upper left panel portrays the energy transfer process as de-excitation of D followed by (almost simultaneous) excitation of A. In effect, the energy gain by the de-excitation of D is given up to allow the excitation of A.

A second way to think about the energy transfer process is a double electron-transfer-type process (lower left). An electron is transferred from the HOMO of A to the HOMO of D, while the electron in the LUMO of D is transferred to the LUMO of A.

In both cases the final result is that the excited state is transferred from D to A, as displayed in the panel on the right.

3.2 Electron transfer

3.2.1 Molecular orbital picture

Once solar energy has been trapped by an antenna and relocated to the reaction centre via the energy-transfer process, the energy must be temporarily stored until it can be utilised for long-term storage (i.e. food production). This is achieved through a series of electron-transfer reactions. The first major aim of the reaction centre is to get the positive and negative charges as far away from one another as possible so that charge recombination can’t occur. See Slide 16.


The molecular orbital picture can also be used to describe the electron-transfer process (Slide 17). In the energy-transfer process discussed before, there is no net change in the number of electrons in D or A. In the case of electron transfer there is a net change in the number of electrons of each molecular species.


The electron-transfer process first involves the absorption of a photon (first window in Slide 17) to give rise to an excited state. In the second window we see that an electron has been promoted from the donor HOMO to the donor LUMO. Now electron transfer can occur from the donor LUMO to the acceptor LUMO (which is lower in energy). The final window shows the final charge-transfer state.

There is a net loss of one electron from the donor (making it positively charged) and a net gain of one electron for the acceptor (making it negatively charged).

3.2.2 In the reaction centre

Some of the photosynthetic systems that have been most completely characterised come from photosynthetic bacteria, which deploy a similar strategy to that of green plants, but often in more symmetric and therefore more easily determined structures. Electron transfer in the photosynthetic bacterial reaction centre occurs in several steps (Slide 18). The charge-transfer process occurs initially in the bacteriochlorophyll ‘special pair’ (the protruding groups in the structure coloured orange) where the electron transfers to the accessory bacteriochlorophyll within about 3 ps. The electron is then transferred from the accessory bacteriochlorophyll, through the bacteriopheophytin to the menaquinone, in 200 ps and finally to the ubiquinone in 100 ms.


It is essential to get the positive and negative charge as far from each other as possible to ensure that recombination does not occur. This energy storage by charge separation is similar to that of a capacitor.

Slide 19 gives a schematic representation of the charge-separation process that occurs in the photosynthetic reaction centre. Typically, a chlorophyll molecule is excited away from the reaction centre (where the charge-transfer process occurs). The chlorophyll molecule enters an excited state and this excitation is transferred, via the resonance energy-transfer mechanism, towards the reaction centre. This is shown schematically as transfer occurring from Chl1 to Chl2. However, many successive such steps generally occur.


Here we see the distinct types of successive stages in the process leading towards carbohydrate production:

  1. One chlorophyll molecule is excited by the absorption of light.
  2. Energy hops from one chlorophyll to another.
  3. This results in electron transfer to an acceptor A.
  4. The resulting vacancy in P is filled by transfer of an electron from a donor D.

In consequence, D acquires a positive charge while A has a negative charge. This is the point at which photosynthetic chemistry begins.

3.2.3 Lecture summary

Slide 20 summarises the main points for upstream processes in photosynthesis covered in this lecture. The following two lectures will focus on the energy-transfer process (Lecture 4) and the electron-transfer process (Lecture 5).