Physiology and Biochemistry

What is photosynthesis and what are the mechanisms of it?

Photosynthesis the process in which electromagnetic energy is converted to chemical energy that can be utilised for various biosynthetic processes. Plants require photons, CO2, and H2O to produce sugar and carbohydrates. Below is the equation to demonstrate photosynthesis:

6CO2 + 6H2O → (Photons and Chlorophyll) C6H12O6 + 6O2

Light-dependent reactions occur in the thylakoid membranes (reaction centres) of the chloroplasts and utilise photons to synthesize ATP and NADPH. The process commences with photosystem II (250-400 pigment molecules) when a chlorophyll molecule gains sufficient energy from the adjacent pigment, which enables photolysis of H2O to occur (breaking of hydrogen and oxygen). This process produces O2 which is expelled and electrons and protons (H+) which are required. This occurs in the granum of the chloroplast or the stacks of thylakoids. Chitnis (1996) states that the H+ are then translocated through the cytochrome which energises and excites H+ to the second stage of light-dependent reactions which is shown in the following stages:

Photosystem II (P680) →Plastoquinone → Cytochrome b6 → Cytochrome f → Plastocyanin → Photosystem I (P700)

Photosystem I activates electrons for transfer to the Fd and finally to NADP+, where the protons from water splitting are exhausted to create NADPH+ H+. To demonstrate the ability to liberate oxygen from water Chitnis, (1996) formulated the following:

The positively charged P800 exerts a strong pull on the H20 molecule, splitting it into H+ and OH- ions. It requires CI- and Mn2+ ions to act as a catalysis:

4H20 → (Mn2+, CI-) → 4 (OH-) + 4H+

OH donates its electron to oxidise P680:

4(OH-) → 4e- →4OH

OH radical obtained forms H20 and liberates oxygen:

4(OH) → H20 → 4H+ → 4e- → 02

Donation of H+ ion from the formation of NADPH is utilised for the Calvin-Benson Cycle. Below is a summary of the differences between the photosystems.

Table 1 Photosystem comparison

The end products are transferred to the light-independent reactions, these reactions occur in the stroma found within the chloroplast between the grana and thylakoid. C02 is delivered to the stroma where they are reduced to ATP and combined with H+ to power the Calvin-Benson Cycle. This process converts ATP into the carbohydrates needed to power the photoautotrophs. The key enzyme of the cycle is RuBisCO. This enzyme fixes C02 to ATP by complex redox reactions to gain the carbohydrates, lipids and proteins which are required for development. Koller (1990) expressed the following equation for this process:

3CO2 + 6NADPH + 5H2O + 9ATP → glyceraldehyde-3-phosphates (G3P) + 2H+ + 6NADP+ + 9ADP + 8Pi

Plants convert photons into chemical energy with a photosynthetic efficiency between 3-6%, however photosynthesis varies with the frequency of light and intensity temperature and proportions of C02, which can vary between 0.1-8% in the atmosphere. Photosynthetic systems store 469 kilojoules of energy and in some cases up to 502 kilojoules. This process is more productive when both photosystems are balanced in their uptake of light. By comparison, solar panels convert photons into electrical energy at an efficiency of 6-20%. This table puts the reactions of photosynthesis into a timescale.

Table 2 Time of Photosynthesis


Photorespiration occurs when the CO2 levels inside a leaf become low. This occurs on hot dry days when a plant is forced to close its stomata to prevent water loss. If the plant continues to fix CO2 when its stomata are closed, the CO2 will get exhausted and the O2 ratio in the leaf will increase relative to CO2 concentrations. When CO2 levels inside the leaf drop to 50ppm, RuBisCO begins to combine O2 with RuBP instead of CO2. Leegood, (1998) suggested that the net outcome of this is that instead of producing 2-3C PGA molecules, only one molecule of PGA is produced and a toxic 2C molecule called Phosphoglycolate. This transaction becomes inefficient and will result in the plant dying from affixation after 24 hours. C3 fixation is greatly affected by this procedure and reduces efficiency of photosynthesis by 25%. This ends up in the plant producing energy which will be utilised to make more energy, resulting in breakthrough (energy not being stored). Photorespiration is expressed as:

RuBP + O2 → Phosphoglycolate + 3-phosphoglycerate + 2H+

Cellular respiration is expressed as:

C6H1206 + 602 + H20 → 6C02 + 12H20 + 673 Kcal

C3 carbon fixation is a metabolic pathway for carbon fixation in photosynthesis. This mechanism converts C02 and RuBP (5 carbon sugar) into 3-phosphoglycerate. This reaction happens in most plants as the first step of the Calvin-Benson Cycle. C4 fixation is a complex process of the more common C3 carbon fixation and is known to have evolved recently (5 million years ago). C4 and CAM overcame the tendency of the enzyme RuBisCO to wastefully fixing oxygen rather than C02 in photorespiration. This is achieved by using an efficient enzyme to fix CO2 in mesophyll cells and shuttling this fixed carbon by the bundle-sheath cells, which surround the vascular network. In these cells, RuBisCO is isolated from oxygen and saturated with the CO2 released by decarboxylation of the bundle-sheath. However, additional energy is required to produce ATP.

This supplementary energy requirement, C4 fixation is able to efficiently fix carbon in arid conditions, with C3 pathways being more efficient in others such as temperate regions. Research conducted by the Horticultural Development Council, (2010) has suggested that photorespiration may be required for assimilating nitrates. A reduction in photorespiration can be achieved by genetic engineering or increasing atmospheric C02 which may not benefit plants that has been proposed in some studies. The overall energy specification of C3 photoautotrophs can be shown as:

6CO2 + 18ATP + 12NADPH + 12H20 → C6H1206 + 18ADP + 18Pi + 12NADPH + 6H+

The overall energy sine qua none of C4 plants can be expressed as:

6CO2 + 30ATP + 12NADPH + 12H20 → C6H1206 + 30ADP + 30Pi + 12NADPH + 18H+

C4 plants have increased C02 assimilation in comparison to C3’s but they consume more energy, they also demonstrate the ability to cope with stress better than C3’s. Refer to the table below for a comparison.

Table 3 Comparison of C3-C4 Pathways

Crassulacean Acid Metabolism is a carbon fixation pathway present in modern plants. These plants fix CO2 during the night, storing it as the four-carbon acid malate. The CO2 is released during the day, where it is concentrated around the enzyme RuBisCO which increases efficiency of photosynthesis. CAM pathways permit stomata to remain closed during the day, reducing evapotranspiration; therefore, it is especially frequent in plants adapted to arid conditions such as Cactaceae.

Table 4 Examples of carbon fixation

Photosynthetically reactive radiation

Photoreceptors are divided into two groups: sensor that absorbs maxmia and trandsue responses to light in the red and blue region. Specialisation of photoreceptors relate to the type of information available during daylight and its application. Absorption of photons by chlorophyll shifts the light transmitted through canopies to lower wavelengths so this section of the spectrum is important for sensing light quality. Blue receptors or cryptochrome is applied by plants as an indicator of sunlight because it is more subject to scattering gradients of light intensity across a short range of tissues.

In aquatic environments blue light takes on greater importance due to natural absorption of red light by H20. Certain cryptochrome can be induced by UV-A radiation. Red light photoreceptors or phytochrome are employed by plants to sense light quality, presence, intensity and duration, phototropism and to sense the direction of light. Phytochrome is synthesised in the inactive form, which has a maximum absorption rate of 660nm. Carotenoid or the third sensor detects light intensity in specific cells. This photoreceptor has been identified in seed plants by a combination of genetic and biochemical research.

Far-red light is enriched in shade, light shifts the balance between the Pr and Pfr forms significantly towards Pr. This is the process of identifying competition, plants utilise these receptors to obtain advantages over their neighbours. Once a plant detects a competitor it can increase growth to gain the ability to sustain light levels.

In nature there will be various frequencies of photons that are absorbed by the two forms of phytochrome. This will result in individual molecules of phytochrome cycling between them. It has been found that the cycling rates can be influenced by light strength and that these cycling speeds can be converted to a signal regulated by adaptations to different photon intensities. The inactivation leads to the inhibition of seed germination in plants that usually thrive in high light levels. When mature plants respond to shade, the disappearance of Pfr signal which prevents stem elongation and stimulates development, leads to increased stature and limited allocation of resources to leaves until shade has been overcome.

Emerson, (1957) measured the efficiency of photosynthesis using a monochromatic light. He witnessed quantum yield (number of 02 evolved per light quanta) and two quanta are needed to transfer one electron. Therefore, eight quanta are required for the evolution of one 02 molecule. Quantum yield decreases sharply towards the far-red light part of the spectrum (680 nm); this region is described as the red drop. Emerson further observed that if the red light of shorter wavelengths was superimposed with far-red the rate of quantum yield would greatly be enhanced; this is referred to as the Emerson Effect. Peavy and Gibbs, (1975) identified that photosynthesis yield was increased by 25% when two lights were supplied simultaneously. They confirmed this by isolating chloroplasts in Spinacia oleracea. The following equation known as The Hill Reaction demonstrates the energy potential:

2H20 (4 Photons, Mn+ (Water splitting enzyme)) → 4H+ + 4e- + 02

Below is a table outlining the different pigmentation involved in light absorption.

Table 1 Pigments distribution in plants and bacteria

In summary, this chapter has focused on the mechanisms and processes involved in photosynthesis and photorespiration. How they are influenced by blue, red and far-red light; how they are required to work for elongation, flowering, budding, surface area expansion and ageing. Several equations were present to establish the efficiency of photosynthesis and photorespiration and how it takes one millisecond to convert photons into starch. An explanation was provided to illustrate how these processes can be developed.

General plant structures and organs

Plant cells are eukaryotic (see glossary for details) cells that differ in several key respects from the cells of other eukaryotic organisms. Their distinctive features include:

  • A large central vacuole, a water-filled volume enclosed by a membrane known as the tonoplast maintains the cell's turgor, controls movement of molecules between the cytosol and sap, stores useful material and digests waste proteins and organelles.

  • A cell wall composed of cellulose and hemicellulose, pectin and in many cases lignin, and secreted by the protoplast on the outside of the cell membrane. This contrasts with the cell walls of fungi, which are made of chitin, and of bacteria, which are made of peptidoglycan.

  • Specialised cell-cell communication pathways known as plasmodesmata, pores in the primary cell wall through which the plasmalemma and endoplasmic reticulum of adjacent cells are continuous.

  • Plastids, notably the chloroplasts which contain chlorophyll and the biochemical systems for light harvesting and photosynthesis, but also amyloplasts specialized for starch storage, elaioplasts specialized for fat storage and chromoplasts specialized for synthesis and storage of pigments. As in mitochondria, which have a genome encoding 37 genes plastids have their own genomes of about 100-120 unique genes and probably arose as prokaryotic endosymbionts living in the cells of an early eukaryotic ancestor of the land plants and algae.

  • Unlike animal cells, plant cells are stationary.

  • Cell division by construction of a phragmoplast as a template for building a cell plate late in cytokinesis is characteristic of land plants and a few groups of algae, notably the Charophytes and the Order Trentepohliales.

  • The sperm of bryophytes have flagellae similar to those in animals, but higher plants, including Gymnosperms (please refer to the glossary for details) and flowering plants lack the flagellae and centriolees that are present in animal cells

  • Parenchyma cells are living cells that have diverse functions ranging from storage and support to photosynthesis and phloem loading (transfer cells). Apart from the xylem and phloem in its vascular bundles, leaves are mainly composed of parenchyma cells. Some parenchyma cells, as in the epidermis, are specialized for light penetration and focusing or regulation of gas exchange, but others are among the least specialized cells in plant tissue, and may remain totipotent, capable of dividing to produce new populations of undifferentiated cells, throughout their lives. Parenchyma cells have thin, permeable primary walls enabling the transport of small molecules between them, and their cytoplasm is responsible for a wide range of biochemical functions such as nectar secretion, or the manufacture of secondary products that discourage herbivory. Parenchyma cells which contain many chloroplasts and are concerned primarily with photosynthesis are called chlorenchyma cells. Others, such as the majority of the parenchyma cells in potato tubers and the seed cotyledons of legumes have a storage function.

  • Collenchyma cells - collenchyma cells are alive at maturity and have only a primary wall and a secondary wall. These cells mature from meristem derivatives that initially resemble parenchyma, but differences quickly become apparent. Plastids do not develop and the secretary apparatus (ER and Golgi) proliferates to secrete additional primary wall. The wall is most commonly thickest at the corners, where three or more cells come in contact and thinnest where only two cells come in contact, though other arrangements of the wall thickening are possible.

Pectin and hemicellulose are the dominant constituents of collenchyma cell walls of dicotyledon angiosperms which may contain as little as 20% of cellulose in Petasites. Collenchyma cells are typically quite elongated, and may divide transversely to give a septet appearance. The role of this cell type is to support the plant in axes still growing in length, and to confer flexibility and tensile strength on tissues. The primary wall lacks lignin that would make it tough and rigid, so this cell type provides what could be called plastic support. Support that can hold a young stem or petiole into the air, but in cells that can be stretched as the cells around them elongate. Stretchable support is a good way to describe what collenchyma does. Parts of the strings in celery are collenchyma.

  • Sclerenchyma cells - Sclerenchyma cells are hard and tough cells with a function in mechanical support. They are of two broad types – sclereids or stone cells and fibres. The cells develop an extensive secondary cell wall that is laid down on the inside of the primary cell wall. The secondary wall is impregnated with lignin, making it hard and impermeable to water. Thus, these cells cannot survive for long as they cannot exchange sufficient material to maintain active metabolism. Sclerenchyma cells are typically dead at functional maturity, and the cytoplasm is missing, leaving an empty central cavity.

Functions for sclereid cells (hard cells that give leaves or fruits a gritty texture) include discouraging herbivory, by damaging digestive passages in small insect larval stages, and physical protection (a solid tissue of hard sclereid cells form the pit wall in a peach and many other fruits). Functions of fibres include provision of load-bearing support and tensile strength to the leaves and stems of herbaceous plants. Sclerenchyma fibres are not involved in conduction, either of water and nutrients or of carbon compounds but it are likely that they may have evolved as modifications of xylem and phloem initials in early land plants.

Types of plant tissues

The major classes of cells differentiate from undifferentiated meristematic cells to form the tissue structures of roots, stems, leaves, flowers and reproductive structures.

Xylem cells are elongated cells with lignified secondary thickening of the cell walls. Xylem cells are specialised for conduction of water, and first appeared in plants during their transition to land in the Silurian period more than 425 million years ago. The possession of xylem defines the vascular plants or Tracheophytes. Xylem tracheids are pointed, elongated xylem cells, the simplest of which have continuous primary cell walls and lignified secondary wall thickenings in the form of rings, hoops or reticulate networks. More complex tracheids with valve-like perforations called bordered pits characterise the gymnosperms. The ferns and other pteridophytes and the gymnosperms only have xylem tracheids, while the angiosperms also have xylem vessels. Vessel members are hollow xylem cells aligned end-to-end, without end walls that are assembled into long continuous tubes. The bryophytes lack true xylem cells, but their sporophyte have a water conducting tissue known as the hydrome that is composed of elongated cells of simpler construction.

Phloem is a specialised tissue for food conduction in higher plants. The conduction of food is a complex process which is carried in the plant with the help of special cell called phloem cells. These cells conduct inter and intra cellular fluid (food: - proteins and other essential element required by the plant for its metabolism) through the process of osmosis. This phenomenon is called as ascent of sap in plants. Phloem consists of two cell types, the sieve tubes and the intimately-associated companion cells. The sieve tube elements lack nuclei and ribosomes, and their metabolism and functions are regulated by the adjacent nucleate companion cells. Sieve tubes are joined end to end with perforate end-plates between known as sieve plates, which allow transport of photosynthetic between the sieve elements. The companion cells, connected to the sieve tubes via plasmodesmata, are responsible for loading the phloem with sugars. The bryophytes lack phloem, but moss sporophyte has a simpler tissue with analogous function known as the leptome.

Plant epidermal cells are specialised parenchyma cells covering the external surfaces of leaves, stems and roots. The epidermal cells of aerial organs arise from the superficial layer of cells known as the tunica that covers the plant shoot apex, whereas the cortex and vascular tissues arise from innermost layer of the shoot apex known as the corpus. The epidermis of roots originates from the layer of cells immediately beneath the root cap.

The epidermis of all aerial organs, but not roots, is covered with a cuticle made of waxes and the polyester cutin. Several cell types may be present in the epidermis. Notable among these are the stomata guard cells, glandular and clothing hairs or trichomes, and the root hairs of primary roots. In the shoot epidermis of most plants, only the guard cells have chloroplasts. The epidermal cells of the primary shoot are thought to be the only plant cells with the biochemical capacity to synthesize cutin.

Root systems: an overview

In vascular plants, the root is the organ of a plant that typically lies below the surface of the soil. This is not always the case, however, since a root can also be aerial or aerating (growing up above the ground or especially above water). Furthermore, a stem normally occurring below ground is not exceptional either. So, it is better to define root as a part of a plant body that bears no leaves, and therefore also lacks nodes. There are also important internal structural differences between stems and roots.

The first root that comes from a plant is called the radicle. The three major functions of roots are: 1absorption of water and inorganic nutrients, 2 anchoring of the plant body to the ground and 3 storage of food and nutrients. In response to the concentration of nutrients, roots also synthesis cytokinins, which acts as a signal as to how fast the shoots can grow. Roots often function in storage of food and nutrients. The roots of most vascular plant species enter into symbiosis with certain fungi to form mycorrhizal, and a large range of other organisms including bacteria also closely associate with roots. The parts of a root are the xylem, the epidermis, the cortex, the root cap, the root hairs, the phloem, and the cambium.

Early root growth is one of the functions of the apical meristem located near the tip of the root. The meristem cells more or less continuously divide, producing more meristem, root cap cells (these are sacrificed to protect the meristem), and undifferentiated root cells. The latter become the primary tissues of the root, first undergoing elongation, a process that pushes the root tip forward in the growing medium. Gradually these cells differentiate and mature into specialized cells of the root tissues.

Complexities of the root

  • Adventitious roots arise out-of-sequence from the more usual root formation of branches of a primary root, and instead originate from the stem, branches, leaves, or old woody roots. They commonly occur in monocots and pteridophytes, but also in many dicots, such as: Trifolium, Hedera, Fragaria and Salix. Most aerial roots and stilt roots are adventitious. In some conifers adventitious roots can form the largest part of the root system.

  • Aerating roots: roots raising above the ground, especially above water such as in some mangrove genera, Avicenna, Sonneratia. In some plants like Avicenna the erect roots have a large number of breathing pores for exchange of gases.

  • Aerial roots: roots entirely above the ground, such as in Hedera or in epiphytic orchids. They function as prop roots, as in maize or anchor roots or as the trunk in strangler fig.

  • Contractile roots: they pull bulbs or corms of monocots, such as hyacinth and lily, and some taproots, such as dandelion, deeper in the soil through expanding radically and contracting longitudinally. They have a wrinkled surface.

  • Coarse roots: Roots that have undergone secondary thickening and have a woody structure. These roots have some ability to absorb water and nutrients, but their main function is transport and to provide a structure to connect the smaller diameter, fine roots to the rest of the plant.

  • Fine roots: Primary roots usually <2 mm diameter that have the function of water and nutrient uptake. They are often heavily branched and support mycorrhizal. These roots may be short lived, but are replaced by the plant in an ongoing process of root 'turnover'.

  • Haustorial roots: roots of parasitic plants that can absorb water and nutrients from another plant, such as in Viscum album and dodder.

  • Propagative roots: roots that form adventitious buds that develop into aboveground shoots, termed suckers, which form new plants, as in Canada thistle, cherry and many others.

  • Proteoid roots or cluster roots: dense clusters of rootlets of limited growth that develop under low phosphate or low iron conditions in Proteaceae and some plants from the following families Betulaceae, Casuarinaceae, Elaeagnaceae, Moraceae, Fabaceae and Myricaceae.

  • Stilt roots: these are adventitious support roots, common among mangroves. They grow down from lateral branches, branching in the soil.

  • Storage roots: these roots are modified for storage of food or water, such as carrots and beets. They include some taproots and tuberous roots.

  • Structural roots: large roots that have undergone considerable secondary thickening and provide mechanical support to woody plants and trees.

  • Surface roots: These proliferate close below the soil surface, exploiting water and easily available nutrients. Where conditions are close to optimum in the surface layers of soil, the growth of surface roots is encouraged and they commonly become the dominant roots.

  • Tuberous roots: A portion of a root swells for food or water storage, e.g. sweet potato. A type of storage root distinct from taproot

Phloem tissue consists of less specialized and nucleate parenchyma cells, sieve-tube cells, and companion cells.

Sieve tubes and elements

The sieve-tube cells lack a nucleus, have very few vacuoles, but contain other organelles such as ribosomes. The sieve tube is an elongated rank of individual cells, called sieve-tube members, arranged end to end. The endoplasmic reticulum is concentrated at the lateral walls. Sieve-tube members are joined end to end to form a tube that conducts food materials throughout the plant. The end walls of these cells have many small pores and are called sieve plates and have enlarged plasmodesmata.

Companion cells and carbon uptake

The survival of sieve-tube members depends on a close association with the companion cells. All of the cellular functions of a sieve-tube element are carried out by the companion cell, a typical plant cell, except the companion cell usually has a larger number of ribosomes and mitochondria. This is because the companion cell is more metabolically active than a 'typical' plant cell. The cytoplasm of a companion cell is connected to the sieve-tube element by plasmodesmata.

There are three types of companion cell.

  1. Ordinary companions cells - which have smooth walls and few or no plasmodesmata connections to cells other than the sieve tube.

  2. Transfer cells - which have much folded walls that are adjacent to non-sieve cells, allowing for larger areas of transfer. They are specialised in scavenging solutes from those in the cell walls that are actively pumped requiring energy.

  3. Intermediary cells - which have smooth walls and numerous plasmodesmata connecting them to other cells.

The first two types of cell collect solutes through apoplastic (cell wall) transfers, whilst the third type can collect solutes via the symplast through the plasmodesmata connections

The process of osmosis is circuital for a plants survival

Osmosis may occur when there is a partially permeable membrane, such as a cell membrane. When a cell is submerged in water, the water molecules pass through the cell membrane from an area of low solute concentration to one of high solute concentration (inside the cell); this is called osmosis. The cell membrane is selectively permeable, so only necessary materials are let into the cell and wastes are left out.

When the membrane has a volume of pure water on both sides, water molecules pass in and out in each direction at the exact same rate; there is no net flow of water through the membrane.

In a solution, the concentration of water is diluted by the presence of solute particles. If there is a solution on one side, and pure water on the other, there will be a higher concentration of water molecules on the pure water side of the membrane. Therefore, water molecules pass through the membrane from the pure water side toward the solution side more frequently than from the solution side going to the pure water side. This will result in a net flow of water to the side with the solution. Assuming the membrane does not break, this net flow will slow and finally stop as the pressure on the solution side becomes such that the movement in each direction is equal: dynamic equilibrium. This could either be due to the water potential on both sides of the membrane being the same, or due to osmosis being inhibited by factors such as pressure potential or osmotic pressure.

Osmosis can also be explained using the notion of entropy, from statistical mechanics. Suppose a permeable membrane separates equal amounts of pure solvent and a solution. Since a solution possesses more entropy than pure solvent, the second law of thermodynamics states that solvent molecules will flow into the solution until the entropy of the combined system is maximized. Notice that, as this happens, the solvent loses entropy while the solution gains entropy. Equilibrium, hence maximum entropy, is achieved when the entropy gradient becomes zero, and dissolution takes place.

Pure water is more ordered than water in a solution; thus, from an entropic standpoint it takes some net energy to move a water molecule from a disordered solution and "pack it in" with pure water. This is the same explanation as to why the disordered air does not spontaneously separate and order into oxygen and nitrogen; it would take energy for this to happen. Additionally, particle size has no bearing on osmotic pressure, as this is the fundamental postulate of colligative properties.

A plant's Immuno responses and system

By means of cells that behave like nerves, plants receive and distribute within their systems information about incident light intensity and quality. Incident light which stimulates a chemical reaction in one leaf will cause a chain reaction of signals to the entire plant via a type of cell termed a "bundle sheath cell". Researchers from the Warsaw University of Life Sciences in Poland found that plants have a specific memory for varying light conditions which prepares their immune systems against seasonal pathogens.

The processes that govern photosynthesis

Photosynthesis is a process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight. Photosynthesis occurs in plants, algae, and many species of bacteria, but not in archaea. Photosynthetic organisms are called photoautotrophs, since they can create their own food. In plants, algae, and cyanobacteria, photosynthesis uses carbon dioxide and water, releasing oxygen as a waste product. Photosynthesis is vital for life on Earth. As well as maintaining the normal level of oxygen in the atmosphere, nearly all life either depends on it directly as a source of energy, or indirectly as the ultimate source of the energy in their food. The amount of energy trapped by photosynthesis is immense, approximately 100 terawatts which is about six times larger than the power consumption of human civilization. As well as energy, photosynthesis is also the source of the carbon in all the organic compounds within organisms' bodies. In all, photosynthetic organisms convert around 100,000,000,000 tonnes of carbon into biomass per year.

Although photosynthesis can happen in different ways in different species, some features are always the same. For example, the process always begins when energy from light is absorbed by proteins called photosynthetic reaction centers that contain chlorophylls. In plants, these proteins are held inside organelles called chloroplasts, while in bacteria they are embedded in the plasma membrane. Some of the light energy gathered by chlorophylls is stored in the form of adenosine triphosphate (ATP). The rest of the energy is used to remove electrons from a substance such as water. These electrons are then used in the reactions that turn carbon dioxide into organic compounds. In plants, algae and cyanobacteria, this is done by a sequence of reactions called the Calvin cycle, but different sets of reactions are found in some bacteria, such as the reverse Krebs cycle in Chlorobium. Many photosynthetic organisms have adaptations that concentrate or store carbon dioxide. This helps reduce a wasteful process called photorespiration that can consume part of the sugar produced during photosynthesis.

Overview of cycle between autotrophs and heterotrophs. Photosynthesis is the main means by which plants, algae and many bacteria produce organic compounds and oxygen from carbon dioxide and water (green arrow).

Photosynthesis evolved early in the evolutionary history of life, when all forms of life on Earth were microorganisms and the atmosphere had much more carbon dioxide. The first photosynthetic organisms probably evolved about 3,500 million years ago, and used hydrogen or hydrogen sulphide as sources of electrons, rather than water. Cyanobacteria appeared later, around 3,000 million years ago, and drastically changed the Earth when they began to oxygenate the atmosphere, beginning about 2,400 million years ago. This new atmosphere allowed the evolution of complex life such as protists. Eventually, no later than a billion years ago, one of these protists formed a symbiotic relationship with a cyanobacterium, producing the ancestor of many plants and algae. The chloroplasts in modern plants are the descendants of these ancient symbiotic cyanobacteria.

The general equation for photosynthesis is therefore:

2n CO2 + 2n H2O + photons → 2(CH2O) n + n O2 + 2n A

Carbon dioxide + electron donor + light energy → carbohydrate + oxygen + oxidized electron donor

Since water is used as the electron donor in oxygenic photosynthesis, the equation for this process is:

2n CO2 + 2n H2O + photons → 2(CH2O) n + 2n O2

Carbon dioxide + water + light energy → carbohydrate + oxygen

Other processes substitute other compounds (such as arsenite) for water in the electron-supply role; the microbes use sunlight to oxidize arsenite to arsenates; the equation for this reaction is:

(AsO33-) + CO2 + photons → CO + (AsO43-)

Carbon dioxide + arsenite + light energy → arsenate + carbon monoxide (used to build other compounds in subsequent reactions)

Photosynthesis occurs in two stages.

In the first stage, light-dependent reactions or light reactions capture the energy of light and use it to make the energy-storage molecules ATP and NADPH. During the second stage, the light-independent reactions use these products to capture and reduce carbon dioxide.

Most organisms that utilize photosynthesis to produce oxygen use visible light to do so, although at least three use infrared radiation

In the light reactions, one molecule of the pigment chlorophyll absorbs one photon and loses one electron. This electron is passed to a modified form of chlorophyll called pheophytin, which passes the electron to a quinone molecule, allowing the start of a flow of electrons down an electron transport chain that leads to the ultimate reduction of NADP to NADPH. In addition, this creates a proton gradient across the chloroplast membrane; its dissipation is used by ATP synthase for the concomitant synthesis of ATP. The chlorophyll molecule regains the lost electron from a water molecule through a process called photolysis, which releases a dioxygen (O2) molecule. The overall equation for the light-dependent reactions under the conditions of non-cyclic electron flow in green plants is…

2 H2O + 2 NADP+ + 3 ADP + 3 Pi + light → 2 NADPH + 2 H+ + 3 ATP + O2

Not all wavelengths of light can support photosynthesis. The photosynthetic action spectrum depends on the type of accessory pigments present. For example, in green plants, the action spectrum resembles the absorption spectrum for chlorophylls and carotenoids with peaks for violet-blue and red light. In red algae, the action spectrum overlaps with the absorption spectrum of phycobilins for blue-green light, which allows these algae to grow in deeper waters that filter out the longer wavelengths used by green plants. The non-absorbed part of the light spectrum is what gives photosynthetic organisms their colour and is the least effective for photosynthesis in the respective organisms.

The Calvin-Benson Cycle

In the Light-independent or dark reactions the enzyme RuBisCO captures CO2 from the atmosphere and in a process that requires the newly formed NADPH, called the Calvin-Benson Cycle, releases three-carbon sugars, which are later combined to form sucrose and starch. The overall equation for the light-independent reactions in green plants is:

3 CO2 + 9 ATP + 6 NADPH + 6 H+ → C3H6O3-phosphate + 9 ADP + 8 Pi + 6 NADP+ + 3 H2

To be more specific, carbon fixation produces an intermediate product, which is then converted to the final carbohydrate products. The carbon skeletons produced by photosynthesis are then variously used to form other organic compounds, such as the building material cellulose, as precursors for lipid and amino acid biosynthesis, or as a fuel in cellular respiration. The latter occurs not only in plants but also in animals when the energy from plants gets passed through a food chain.

The fixation or reduction of carbon dioxide is a process in which carbon dioxide combines with a five-carbon sugar, ribulose 1, 5-bisphosphate (RuBP), to yield two molecules of a three-carbon compound, glycerate 3-phosphate (GP), also known as 3-phosphoglycerate (PGA). GP, in the presence of ATP and NADPH from the light-dependent stages, is reduced to glyceraldehyde 3-phosphate (G3P). This product is also referred to as 3-phosphoglyceraldehyde (PGAL) or even as triose phosphate. Triose is a 3-carbon sugar. Most of the G3P produced is used to regenerate RuBP so the process can continue. The 1 out of 6 molecules of the triose phosphates not "recycled" often condense to form hexose phosphates, which ultimately yield sucrose, starch and cellulose. The sugars produced during carbon metabolism yield carbon skeletons that can be used for other metabolic reactions like the production of amino acids and lipids.

C4 and C3 carbon-fixing and CAM plants

In hot and dry conditions, plants will close their stomata to prevent loss of water. Under these conditions, CO2 will decrease, and oxygen gas, produced by the light reactions of photosynthesis, will decrease in the stem, not leaves, causing an increase of photorespiration by the oxygenase activity of ribulose-1, 5-bisphosphate carboxylase/oxygenase and decrease in carbon fixation. Some plants have evolved mechanisms to increase the CO2 concentration in the leaves under these conditions.

C4 plants chemically fix carbon dioxide in the cells of the mesophyll by adding it to the three-carbon molecule phosphoenolpyruvate or (PEP), a reaction catalyzed by an enzyme called PEP carboxylase and which creates the four-carbon organic acid, oxaloacetic acid. Oxaloacetic acid or malate synthesized by this process is then translocated to specialized bundle sheath cells where the enzyme, rubisco, and other Calvin cycle enzymes are located, and where CO2 released by decarboxylation of the four-carbon acids is then fixed by rubisco activity to the three-carbon sugar 3-phosphoglyceric acids. The physical separation of rubisco from the oxygen-generating light reactions reduces photorespiration and increases CO2 fixation and thus photosynthetic capacity of the leaf. C4 plants can produce more sugar than C3 plants in conditions of high light and temperature. Many important crop plants are C4 plants, including maize, sorghum, sugarcane, and millet. Plants lacking PEP-carboxylase are called C3 plants because the primary carboxylation reaction, catalyzed by rubisco, produces the three-carbon sugar 3-phosphoglyceric acids directly in the Calvin-Benson cycle.

Xerophytes, such as cacti and most succulents, also use PEP carboxylase to capture carbon dioxide in a process called Crassulacean acid metabolism (CAM). In contrast to C4 metabolism, which physically separates the CO2 fixation to PEP from the Calvin cycle, CAM only temporally separates these two processes. CAM plants have a different leaf anatomy from C4 plants, and fix the CO2 at night, when their stomata are open. CAM plants store the CO2 mostly in the form of malic acid via carboxylation of phosphoenolpyruvate to oxaloacetate, which is then reduced to malate. Decarboxylation of malate during the day releases CO2 inside the leaves, thus allowing carbon fixation to 3-phosphoglycerate by rubisco.

Plants usually convert light into chemical energy with a photosynthetic efficiency of 3-6%. Actual plants' photosynthetic efficiency varies with the frequency of the light being converted, light intensity, temperature and proportion of carbon dioxide in the atmosphere, and can vary from 0.1% to 8%. By comparison, solar panels convert light into electric energy at a photosynthetic efficiency of approximately 6-20% for mass-produced panels, and up to 41% in a research laboratory.

Symbiosis and the origin of chloroplasts

Several groups of animals have formed symbiotic relationships with photosynthetic algae. These are most common in corals, sponges and sea anemones, possibly due to these animals having particularly simple body plans and large surface areas compared to their volumes. In addition, a few marine mollusks Elysia viridis and Elysia chlorotica also maintain a symbiotic relationship with chloroplasts they capture from the algae in their diet and then store in their bodies. This allows the mollusks to survive solely by photosynthesis for several months at a time. Some of the genes from the plant cell nucleus have even been transferred to the slugs, so that the chloroplasts can be supplied with proteins that they need to survive.

Cyanobacteria and the evolution of photosynthesis

The biochemical capacity to use water as the source for electrons in photosynthesis evolved once, in a common ancestor of extant cyanobacteria. The geological record indicates that this transforming event took place early in Earth's history, at least 2450-2320 million years ago (Ma), and possibly much earlier. Available evidence from geobiological studies of Archean (>2500 Ma) sedimentary rocks indicates that life existed 3500 Ma, but the question of when oxygenic photosynthesis evolved is still unanswered. A clear paleontological window on cyanobacterial evolution opened about 2000 Ma, revealing an already-diverse biota of blue-greens. Cyanobacteria remained principal primary producers throughout the Proterozoic Eon (2500-543 Ma), in part because the redox structure of the oceans favored photoautotrophs capable of nitrogen fixation. Green algae joined blue-greens as major primary producers on continental shelves near the end of the Proterozoic, but only with the Mesozoic (251-65 Ma) radiations of dinoflagellates, coccolithophorids, and diatoms did primary production in marine shelf waters take modern form. Cyanobacteria remain critical to marine ecosystems as primary producers in oceanic gyres, as agents of biological nitrogen fixation, and, in modified form, as the plastids of marine algae.

Carbon dioxide levels and photorespiration (C2)

As carbon dioxide concentrations rise, the rate at which sugars are made by the light-independent reactions increases until limited by other factors. RuBisCO, the enzyme that captures carbon dioxide in the light-independent reactions, has a binding affinity for both carbon dioxide and oxygen. When the concentration of carbon dioxide is high, RuBisCO will fix carbon dioxide. However, if the carbon dioxide concentration is low, RuBisCO will bind oxygen instead of carbon dioxide. This process, called photorespiration, uses energy, but does not produce sugars.

RuBisCO oxygenase activity is disadvantageous to plants for several reasons:

  1. One product of oxygenase activity is phosphoglycolate (2 carbon) instead of 3-phosphoglycerate (3 carbon). Phosphoglycolate cannot be metabolized by the Calvin-Benson cycle and represents carbon lost from the cycle. A high oxygenase activity, therefore, drains the sugars that are required to recycle ribulose 5-bisphosphate and for the continuation of the Calvin-Benson cycle.

  2. Phosphoglycolate is quickly metabolized to glycolate that is toxic to a plant at a high concentration; it inhibits photosynthesis.

  3. Salvaging glycolate is an energetically expensive process that uses the glycolate pathway and only 75% of the carbon is returned to the Calvin-Benson cycle as 3-phosphoglycerate. The reactions also produce ammonia (NH3) which is able to diffuse out of the plant leading to a loss of nitrogen.

A highly simplified summary is:

2 glycolate + ATP → 3-phosphoglycerate + carbon dioxide + ADP +NH3

Transpirational Pull

Is the results ultimately from the evaporation of water from the surfaces of cells in the interior of the leaves. This evaporation causes the surface of the water to recess into the pores of the cell wall. Inside the pores, the water forms a concave meniscus. The high surface tension of water pulls the concavity outwards, generating enough force to lift water as high as a hundred meters from ground level to a tree's highest branches. Transpirational pull only works because the vessels transporting the water are very small in diameter, otherwise cavitation would break the water column. And as water evaporates from leaves, more is drawn up through the plant to replace it. When the water pressure within the xylem reaches extreme levels due to low water input from the roots, then the gases come out of solution and form a bubble - an embolism form, which will spread quickly to other adjacent cells, unless bordered pits are present.

The Cohesion Tension Theory

The Cohesion Tension Theory is a theory of intermolecular attraction commonly observed in the process of water traveling upwards (against the force of gravity) through the xylem of plants which was put forward by John Joly and Henry Horatio Dixon.

Water is a polar molecule due to the high electro-negativity of the oxygen atom, which is an uncommon molecular configuration whereby the oxygen atom has two lone pairs of electrons. When two water molecules approach one another they form a hydrogen bond. The negatively charged oxygen atom of one water molecule forms a hydrogen bond with a positively charged hydrogen atom in another water molecule. This attractive force has several manifestations. Firstly, it causes water to be liquid at room temperature, while other lightweight molecules would be in a gaseous phase. Secondly, it is one of the principal factors responsible for the occurrence of surface tension in liquid water. This attractive force between molecules allows plants to draw water from the root and then through the xylem to the leaf where photosynthesis converts water and carbon dioxide into glucose.

Water is constantly lost by transpiration in the leaf. When one water molecule is lost another is pulled along by the processes of cohesion and adhesion. Transpiration pull, utilizing capillary action and the inherent surface tension of water, is the primary mechanism of water movement in plants. However, it is not the only mechanism involved. Any use of water in leaves produces forces water to move into them.

Biological nitrogen fixation

Occurs when atmospheric nitrogen is converted to ammonia by an enzyme called nitrogenase. The formula for BNF is:

N2 + 6 H+ + 6 e → 2 NH3

The process is coupled to the hydrolysis of 16 equivalents of ATP and is accompanied by the co-formation of one molecule of H2. In free-living diazotrophs, the nitrogenase-generated ammonium is assimilated into glutamate through the glutamine synthetase/glutamate synthase pathway.

Enzymes responsible for nitrogenase action are very susceptible to destruction by oxygen. Many nitrogen-fixing organisms exist only in anaerobic conditions, respiring to draw down oxygen levels, or binding the oxygen with a protein such as Leghemoglobin.

Plants that contribute to nitrogen fixation include the legume family – Fabaceae – with taxa such as clover, soybeans, alfalfa, lupines, peanuts, and rooibos. They contain symbiotic bacteria called Rhizobia within nodules in their root systems, producing nitrogen compounds that help the plant to grow and compete with other plants. When the plant dies, the fixed nitrogen is released; making it available to other plants and this helps to fertilize the soil. The great majority of legumes have this association, but a few genera do not. In many traditional and organic farming practices, fields are rotated through various types of crops, which usually includes one consisting mainly or entirely of clover or buckwheat (family Polygonaceae), which were often referred to as green manure.


Also known as monocots, are one of two major groups of flowering plants (or angiosperms) that are traditionally recognized, the other being dicotyledons, or dicots. Monocot seedlings typically have one cotyledon, in contrast to the two cotyledons typical of dicots. Monocots evolved from a single ancestor, and are younger than dicots, from which they probably branched off, as recent genetic research has shown. They evolved 100-120 million years ago, shortly after the flowering plant explosion. Monocots have a distinctive arrangement of vascular tissue known as an atactostele in which the vascular tissue is scattered rather than arranged in concentric rings. Many monocots are herbaceous and do not have the ability to increase the width of a stem via the same kind of vascular cambium found in non-monocot woody plants.


Also known as dicots, is a name for a group of flowering plants whose seed typically has two embryonic leaves or cotyledons. There are around 199,350 species within this group. Flowering plants that are not dicotyledons are monocotyledons, typically having one embryonic leaf. Seeds: The embryo of the monocot has one cotyledon or seed leaf, while the embryo of the dicot has two. Contrasts to monocots…

Flowers: The flower parts in monocots are multiples of three, while in dicots are multiples of four or five.

Stems: In monocots, the stem vascular bundles are scattered, while in dicots they are in a ring.

Secondary growth: In monocots, stems rarely show secondary growth; in dicots, stems frequently have secondary growth.

Pollen: In monocots, pollen has one furrow or pore, while in dicots it has three.

Roots: The roots are adventitious in monocots, while in dicots they develop from the radicle.

Leaves: In monocots, the major leaf veins are parallel, while in dicots they are reticulated and branched.

Secondary Thickening

In many vascular plants, secondary growth is the result of the activity of the vascular cambium. The latter is a meristem that divides to produce secondary xylem cells on the inside of the meristem and secondary phloem cells on the outside. This growth increases the girth of the plant root or stem, rather than its length, hence the phrase "secondary thickening". As long as the vascular cambium continues to produce new cells, the stem or root will continue to grow in diameter. In woody plants, this process produces wood.

Secondary growth results in an increase in diameter. Obstructions, both foreign objects such as this metal post, and parts of the plant, such as stubs of limbs, can be "swallowed" by continued growth.

Because this growth usually ruptures the epidermis of the stem or roots, plants with secondary growth usually also develop a cork cambium. The cork cambium gives rise to thickened cork cells to protect the surface of the plant and reduce water loss. If this is kept up over many years, this process may produce a layer of cork. In the case of the cork oak it will yield harvestable cork.

Secondary growth also occurs in many non-woody plants, e.g. tomato, potato tuber, carrot taproot and sweet potato tuberous root. A few long-lived leaves also have secondary growth.

Primary growth in roots and stems is growth in length and occurs in all vascular plants. Secondary growth occurs mainly in many dicots and gymnosperms. Monocots usually lack secondary growth. If they do have secondary growth, it differs from that described above.

Types of pigments

Among the most important molecules for plant function are the pigments. Plant pigments include a variety of different kinds of molecules, including porphyrins, carotenoids, and anthocyamins. All biological pigments selectively absorb certain wavelengths of light while reflecting others. The light that is absorbed may be used by the plant to power chemical reactions, while the reflected wavelengths of light determine the colour the pigment will appear to the eye.

Chlorophyll is the primary pigment in plants; it is a porphyrins that absorbs red and blue wavelengths of light while reflecting green. It is the presence and relative abundance of chlorophyll that gives plants their green color. All land plants and green algae possess two forms of this pigment: chlorophyll a and chlorophyll b. Kelps, diatoms and other photosynthetic heterokonts contain chlorophyll c instead of b, while red algae possess only chlorophyll a. All chlorophylls serve as the primary means plants use to intercept light in order to fuel photosynthesis.

Carotenoids are red, orange, or yellow tetraterpenoids. They function as accessory pigments in plants, helping to fuel photosynthesis by gathering wavelengths of light not readily absorbed by chlorophyll. The most familiar carotenoids are carotene (an orange pigment found in carrots), lutein (a yellow pigment found in fruits and vegetables), and lycopene (the red pigment responsible for the colour of tomatoes). Carotenoids have been shown to act as antioxidants and to promote healthy eyesight in humans.

Anthocyanins (literally "flower blue") are water-soluble flavonoid pigments that appear red to blue, according to pH. They occur in all tissues of higher plants, providing colour in leaves stems, roots, flowers, and fruits, though not always in sufficient quantities to be noticeable. Anthocyanins are most visible in the petals of flowers, where they may make up as much as 30% of the dry weight of the tissue. They are also responsible for the purple color seen on the underside of tropical shade plants such as Tradescantia zebrina; in these plants, the anthocyanin catches light that has passed through the leaf and reflects it back towards regions bearing chlorophyll, in order to maximize the use of available light.

Betalains are red or yellow pigments. Like anthocyanins they are water-soluble, but unlike anthocyanins they are indole-derived compounds synthesized from tyrosine. This class of pigments is found only in the Caryophyllales (including cactus and amaranth), and never co-occur in plants with anthocyanins. Betalains are responsible for the deep red color of beets, and are used commercially as food-coloring agents. Plant physiologists are uncertain of the function that betalains have in plants which possess them, but there is some preliminary evidence that they may have fungicidal properties.

Driagram of major elements of plant physiology