Category Archives: Photosynthesis

Photosynthesis – Light Reactions

The photosynthetic light reactions take place across the thylakoid membrane, an extensive system of membranes extending throughout the chloroplast. This network of membranes is home to a variety of membrane-spanning proteins involved in the interception of light or the transfer of electrons. Working together, these proteins transduce the energy of light into an electrochemical gradient across the thylakoid that ultimately drives ATP synthesis. At the same time, they form a series circuit that removes electrons from water and donates them to an electron acceptor called NADP+, producing NADPH.

Light Harvesting

While there is a variety of pigment molecules involved in photosynthesis, light harvesting and energy transduction are carried out by the chlorophylls. Chlorophylls are closed-ring tetrapyrroles that coordinate a Mg+ in the center of the ring that plays a role in the redox reactions at the core of photosynthesis. In addition, they have a long fatty-acid tail that renders them hydrophobic. Chlorophylls interact with light and show two peaks in their absorption spectra: one in the red range and another in the blue.

Chlorophylls are not freely distributed in the thylakoid membrane, but are found in association with polypeptides. One such class of protein is known as the Light Harvesting Complex, or LHC proteins. These proteins act as antenna complexes, gathering light energy and directing it to the reaction center chlorophylls. In other words, the chlorophylls associated with the antenna complex proteins are not themselves chemically active — that role is reserved for the reaction center chlorophylls. On average, only 1 in 250 chlorophyll molecules is chemically active.

The chlorophylls associated with antenna complex proteins are nonetheless critical to photosynthesis, because as they are struck by photons and excited, they are capable of transmitting that excitation to nearby chlorophylls through resonance energy transfer. Research has shown that this process of energy transfer is an example of quantum coherence, and the network of chlorophylls acts in concert to transfer excitation energy with near 100% efficiency to the reaction center chlorophylls.

Reaction Centers

The LHC proteins surround photosynthetic reaction center proteins. The reaction center proteins also have a number of chlorophylls associated with them that receive the excitation energy from LHC chlorophylls. In addition, each of the 2 reaction center complexes has a set of chlorophylls that are chemically active — they are capable of photochemistry. These chlorophylls, known as the reaction center chlorophylls or special pair, transfer an electron to an electron acceptor upon excitation. When in the ground state, prior to absorbing light energy, the reaction center chlorophyll special pair is both a poor reducing agent and a poor oxidizer. But when excited by energy absorbance, it becomes both a good reducing agent and oxidizer.



Evidence for two photosynthetic reaction centers in plants came from a series of experiments carried out by Robert Emerson. Working with the green alga Chlorella, Emerson used flashes of light at specific wavelengths to drive photosynthesis while measuring the net yield of O2. He observed a particular rate of O2 yield under both 670 nm and 700 nm light. When the culture of algae was excited by both wavelengths simultaneously, however, Emerson measured a rate of O2 yield that was greater than the sum of O2 produced by either wavelength alone. This simple experiment had profound implications, as Emerson and many others would go on to show that photosynthetic electron transport occurred through a series of two reaction centers in series. In other words, electrons passed from one of the reaction centers to the other through a number of intermediaries in and around the thylakoid. The two photosynthetic reaction centers are known as Photosystem II (PS II) and Photosystem I (PS I).


The excitation of the reaction center chlorophyll special pair in PS II raises the energy level of this molecular complex to the point that it becomes energetically favorable for it to lose an electron. As a result, the excited-state chlorophyll reduces a nearby molecule of pheophytin, which is nearly identical in structure to chlorophyll save for the Mg+ at its center. This structural similarity ‘tunes’ the pheophytin to be an efficient electron acceptor from the excited state special pair. The positioning of the primary acceptor pheophytin is important as well, as it is found in the reaction center protein toward the stromal face of the membrane spanning domain. This position results in the charge separation across the thylakoid membrane that underlies the production of an electrochemical gradient.

Photosynthetic Electron Transport Z-scheme
Midpoint potentials of the various redox components in photosynthetic electron transport.

The loss of an electron from the reaction center special pair is known as primary photochemistry, and this leaves the special pair in an unstable, oxidized state. In PS II, the special pair can be re-reduced by a nearby tyrosine amino acid, leaving the tyrosine oxidized. If we follow the trail of redox reactions back to their origin, we find that ultimately, the electrons that re-reduce the special pair are removed from water at a polypeptide closely associated with the lumenal face of the PSII reaction center called the Oxygen Evolving Complex (OEC).

The OEC catalyzes the oxidation of water through a stepwise series of redox intermediate states made possible through its coordination of Mn2+ ions. The OEC thus provides electrons one-at-a-time to the reaction center special pair as they are removed from a cluster of Mn2+ ions. These electrons are eventually replaced on Mn2+ when two water molecules are simultaneously oxidized, releasing four protons (H+) and molecular oxygen (O2). In other words, the oxidizing potential of the reaction center special pair is transferred to the OEC, where it is used to oxidize water.

In PS I, the mechanics of photochemistry occur the same as on PS II, but the primary electron acceptor is a modified chlorophyll rather than pheophytin. Rather than having an OEC as a source of electrons, the electron donor for PS I is a small molecule called plastocyanin, which diffuses to the lumenal face of PS I carrying electrons that ultimately came from water via PS II.

Electron Transport

After the oxidation of the PS II reaction center, the lost electron enters a pathway of electron flow through several complexes embedded in the thylakoid membrane. This electron transport pathway includes the protein complexes PS II, cytochrome b6f, and PS I. While it is convenient to represent each of these three components nearby each other, they are actually localized in different parts of the thylakoid membrane. PS II and cytochrome b6f are in the interior portions of thylakoid stack, while PS I is found in regions of the membrane having access to the stroma. Two pools of electron carriers connect each of the three major components, with a small, hydrophobic organic molecule called plastoquinone diffusing between PS II and cytochrome b6f, while a copper-containing protein called plastocyanin links cytochrome b6f with PS I. In other words, PS II reduces plastoquinone, and plastocyanin serves as the electron donor for PS I.

The three major components of the electron transport system do no exist to simply pass electrons along to NADP. Their orientation within the thylakoid is such that, as electrons travel through the various components, their flow enhances the concentration of protons that forms in the lumen due to water oxidation. As described above, the direction of electron movement during photochemistry on PS II is from the lumenal face toward the stromal face of the thylakoid due to the position of the primary electron acceptor. This directional flow allows plastoquinone to gather two protons from the stroma along with the two electrons it receives from PS II. When reduced, plastoquinone leaves PS II and diffuses through the membrane and binds to a cytochrome b6f complex on the lumenal face. As plastoquinone reduces the cytochrome b6f complex, the two protons it was carrying are released into the lumen.

Cytochrome b6f engages in two different processes with the electrons it receives from plastoquinone: non-cyclic transport and cyclic electron transport. When performing non-cyclic transport, the cytochrome b6f complex is reduced by plastoquinone and reduces plastocyanin at the lumenal face. Under certain conditions though, cytochrome b6f passes electrons among several intrinsic electron acceptor sites, each of which can coordinate a quinone molecule. Because this process relies on quinone sites, this has been named the Q cycle. The various quinone binding sites on the cytochrome b6f complex facilitate the flow of electrons toward the stromal face, where they eventually reduce a plastoquinone associated with the cytochrome b6f complex. This plastoquinone is identical to that described above, and once reduced it leaves its binding site at the stromal face of the cytochrome b6f complex and binds at the complex’s lumenal face. The end result of the Q cycle is to further enhance the flow of protons into the lumen.

Once reduced by cytochrome b6f, plastocyanin (a single electron carrier) leaves the complex and diffuses through the lumen to PS I. As the electron donor to PS I, plastocyanin is oxidized by the PS I reaction center special pair when it absorbs a photon of light energy and undergoes photochemistry. The electron that is lost from the reaction center travels to a modified chlorophyll and several intermediate electron acceptors within PS I before reducing ferredoxin, bound to the stromal side of PS I. Ferredoxin is a small protein that coordinates an iron-sulfur complex. When reduced, it provides the reducing power to the enzyme involved in reducing NADP+, called ferredoxin-NADP reductase. It can also participate in cyclic flow of electrons between PS I and the cytochrome b6f complex under certain conditions. The net result of the electron transport pathway is the conservation of light energy in the form of an electrochemical potential gradient across the thylakoid membrane, and the reduction of NADP+ to NADPH.

ATP Synthesis

The energy that is represented by the proton gradient across the thylakoid membrane can be used by ATP synthase to catalyze the addition of a phosphate onto ADP to make ATP. The ATP synthase enzyme is a multimeric molecular machine that converts the gradient of protons into kinetic, rotational energy by permitting protons to flow through its membrane-spanning pore. As protons leave the region of high concentration in the lumen and pass through the pore region, they exit into the stroma, which causes rotation of the membrane-spanning domain. This rotation is propagated by a shaft-like domain called the γ domain to the catalytic domain. Within the catalytic domain, ADP and P(i) are bound, and the rotation of the γ domain causes a conformational change that forces the ADP and P(i) to react and produce ATP.

Here is an animation of ATP synthase.

Photosynthesis Overview

What we call ‘photosynthesis’ is a collection of events that uses the energy contained in light and reducing CO2. A simplified net reaction is shown below:

H2O + CO2 + light → (CH2O)n + O2

On an annual basis, this collection of processes is responsible for fixing 7 × 1013 kg of CO2. To help put this value in perspective, that is equal to 1% of all known fossil fuel reserves on the planet and roughly 10× the annual global energy consumption. In addition, photosynthesis also releases oxygen at a rate that replaces all O2 in the atmosphere every 2000 years.

Photosynthesis consists of 2 interdependent processes known as the light reactions and the carbon reactions. For our purposes, we will further disassemble the light reactions into the processes of photochemistry and electron transport. Both of these parts of the light reactions take place across the system of membranes found within chloroplasts, known as the thylakoid membrane system.

As we will discuss in more detail elsewhere, light results in the polarization of this membrane due to the formation of a H+ gradient. This proton gradient is used to by ATP synthase to combine ADP and Pi to form ATP, which is one of the key products of the light reactions. The other major product of the light reactions is an energy carrier called NADPH. All together, the light reactions can be thought of as a series of oxidation-reduction reactions powered by light energy, with electrons supplied by H2O and ultimately reducing NADP+ to NADPH.

In the carbon reactions, the energy from the light reactions, represented by ATP and NADPH, is used to reduce atmospheric CO2 to carbohydrates. This takes place in a series of enzyme-mediated reactions that takes place in the stroma of the chloroplast. The series of reactions represents an example of a biochemical cycle, with the initial reactant regenerated by the pathway. The products of the cycle are excess molecules that are “exported” from the pathway.

It is fairly obvious from the above descriptions that the carbon reactions are dependent upon the light reactions for ATP and NADPH. But it is important to keep in mind that the ADP and NADP+ produced by the carbon reactions are absolutely essential for the light reactions to continue. Without the return of these substrates to the light reactions, the cell would experience significant damage due to continued exposure to light energy.

Overview of Light

Light is one form of electromagnetic radiation. As such, it occupies a small slice of the electromagnetic spectrum, which also includes forms of radiation having greater energy than visible light, such as gamma rays and x-rays, and other forms having less energy than light, such as infrared radiation and microwaves. Each of these is characterized by two physical parameters that describe the quality of radiation: wavelength (λ) and frequency (ν). Visible light includes radiation having a wavelength between approximately 400 nm and 700 nm. Because the speed of radiation, c, is a universal constant, wavelength and frequency always vary inversely with each other and their product is equal to c.


A diagram of the Milton spectrum, showing the type, wavelength (with examples), frequency, the black body emission temperature.

By Inductiveload, NASA [GFDL ( or CC-BY-SA-3.0 (, via Wikimedia Commons

Because light is a form of energy, and because we are interested in understanding how light energy is transduced into chemical energy, it is important to understand the relation between light quality and energy. Comparing blue light (450nm < λ < 475nm) with red light (620nm < λ < 730nm) for example, note that blue light has a smaller wavelength and therefore a greater frequency than red light. Even though the speed of light is a constant, the energy is not — energy varies in direct relation to frequency. So in the above example, blue light contains greater energy than red light of a given fluence rate.


In addition to being described in terms of its wave-like properties, the energy in light exists in discrete packets (called photons) rather than as a continuous stream. Photons are measurable down to the individual one, known as a quantum. As we will see next, the fact that light travels in photons, each having a predictable quantum of energy, helps us understand the events surrounding light absorbance by molecules and the transduction of energy into a chemical form.

Light Interacts with Molecules

As you look around the world, you see objects of all different colors. The production of those colors, and in fact our ability to perceive them, both rest on the fact that visible light can interact with matter in specific, predictable ways. Whether a particular frequency of radiation interacts with a particular molecule depends on the structure of the molecule — the arrangement of atoms in space. In the same way an aerial antenna depends on the precise spacing of its elements to intercept radio waves (another form of electromagnetic radiation) of specific frequencies, so too are biological molecules ‘tuned’ to specific frequencies of light to maximize energy transduction. In the case of the photosynthetic pigments known as chlorophylls, their molecular structure allows them to absorb blue and red wavelengths, but not yellow, green, or orange. While most plants have pigments that absorb yellow and orange, green light goes unused by the plant, being either transmitted or reflected.

When a pigment molecule intercepts a photon for which it is receptive, the energy of the photon is conserved by a rearrangement of electrons in the molecule. This rearrangement results in the boosting of an electron from the ground state to an excited state. Sometimes, the excited state is dissipated through the re-emission of light energy, known as fluorescence. Other times, if there are like molecules in close proximity, the excited state can be passed among them through resonant energy transfer. Under certain highly specialized circumstances, the excited state can represent the first step toward a photochemical reaction in which the electron departs the excited state molecule and reduces a nearby electron acceptor. Finally, the excited state may be dissipated through a process called radiationless decay, which releases heat to the surroundings. Each one of these processes plays an important role in photosynthesis.