H₂S as a source of electrons for plants

H₂S as a source of electrons for plants

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The first electron source for plants was H2S, but now most modern plants use H2O as an electron source.

What is the advantage of using H2O instead of H2S?

The major reason for this is because H20 can cause hydrogen bonding. Hydrogen bonding is what allows for plants to transport "this electron source" from their roots through their stems an further.

The stronger polarity of H20 also allows for stronger interactions. Such as ionic interactions (not fully bound but 2 polar atoms interacting). This kind of ionic interaction also allows for other types of material interactions such as cohesion and adhesion.

Overall, aside from the discussion of abundance as mentioned above (which is a very good point), it also allowed the plants to grow in directions that were more advantageous (darwinian) for their survival.

Antenna Complexes for Photosynthesis

The capture of light energy for photosynthesis is enhanced by networks of pigments in the chloroplasts arranged in aggregates on the thylakoids. These aggregates are called antennae complexes. Evidence for this kind of picture came from research by Robert Emerson and William Arnold in 1932 when they measured the oxygen released in response to extremely bright flashes of light. They found that some 2500 molecules of chlorophyll was required to produce one molecule of oxygen, and that a minimum of eight photons of light must be absorbed in the process.

The model that emerges is that of some 300 chlorophyll molecules and 40 or so beta carotenes and other accessory pigments acting as a light harvesting antenna surrounding one chlorophyll a molecule that is a part of an action center. A photon is absorbed by one of the pigment molecules and transfers that energy by successive flourescence events to neighboring molecules until it reaches the action center where the energy is used to transfer an energetic electron to an electron acceptor.

The fluorescence model would suggest that each transferred photon has a longer wavelength and lower quantum energy with some energy being lost to heat.

When a photon reaches the chlorophyll a in the reaction center, that chlorophyll can receive the energy because it absorbs photons of longer wavelengths than the other pigments. Two types of chlorophyll centers have been identified, and are associated with two protein complexes identified as Photosystem I and Photosystem II.

H₂S as a source of electrons for plants - Biology

Which statement about carbohydrate biosynthesis during the dark reactions of photosynthesis (i.e. the Calvin cycle reactions) is NOT TRUE?

A. RUBISCO is a an enzyme required for carbon dioxide fixation.
B. NADPH is the source of electrons for glucose biosynthesis.
C. ATP is the energy source for glucose biosynthesis.
D. The reactions occur in the photosynthetic membranes of chloroplasts.
E. Oxygen is not required.

Carbohydrate Biosynthesis

Features of the equation for dark reactions

  • RUBISCO is the CO 2 fixing enzyme for carbohydrate biosynthesis.
  • 6 CO 2 are fixed by RUBISCO per glucose synthesized.
  • Oxygen is not required for carbohydrate biosynthesis.
  • Remainder of reactions used to synthesize glucose and regenerate RuBP.
  • NADPH is used to reduce 3-phosphoglycerate to a 3-carbon sugar. 2 NADPH are required.
  • 3 ATP are required for each RuBP regenerated.

Pathway for carbohydrate biosynthesis

The reactions are catalyzed by soluble enzymes of the chloroplast stroma.

Water oxidation by photosystem II is the primary source of electrons for sustained H 2 photoproduction in nutrient-replete green algae

The unicellular green alga Chlamydomonas reinhardtii is capable of photosynthetic H2 production. H2 evolution occurs under anaerobic conditions and is difficult to sustain due to 1) competition between [FeFe]-hydrogenase (H2ase), the key enzyme responsible for H2 metabolism in algae, and the Calvin-Benson-Bassham (CBB) cycle for photosynthetic reductants and 2) inactivation of H2ase by O2 coevolved in photosynthesis. Recently, we achieved sustainable H2 photoproduction by shifting algae from continuous illumination to a train of short (1 s) light pulses, interrupted by longer (9 s) dark periods. This illumination regime prevents activation of the CBB cycle and redirects photosynthetic electrons to H2ase. Employing membrane-inlet mass spectrometry and [Formula: see text], we now present clear evidence that efficient H2 photoproduction in pulse-illuminated algae depends primarily on direct water biophotolysis, where water oxidation at the donor side of photosystem II (PSII) provides electrons for the reduction of protons by H2ase downstream of photosystem I. This occurs exclusively in the absence of CO2 fixation, while with the activation of the CBB cycle by longer (8 s) light pulses the H2 photoproduction ceases and instead a slow overall H2 uptake is observed. We also demonstrate that the loss of PSII activity in DCMU-treated algae or in PSII-deficient mutant cells can be partly compensated for by the indirect (PSII-independent) H2 photoproduction pathway, but only for a short (<1 h) period. Thus, PSII activity is indispensable for a sustained process, where it is responsible for more than 92% of the final H2 yield.

Keywords: carbon dioxide green algae hydrogen production hydrogenase water splitting.

Copyright © 2020 the Author(s). Published by PNAS.

Conflict of interest statement

The authors declare no competing interest.


H 2 photoproduction ( A…

H 2 photoproduction ( A ) and O 2 exchange ( B )…

The effect of DCMU and the psbA deletion (FuD7) on H 2 (…

Long-term H 2 photoproduction by…

Long-term H 2 photoproduction by pulse-illuminated algae. The cultures of the wild-type (CC-124)…

The release of ambient ( m/z 44) CO 2 and 18 O-labeled (…

The effect of light pulse…

The effect of light pulse duration in the pulse-illumination sequence on CO 2…

H₂S as a source of electrons for plants - Biology

Supplements To Biology 101 Cell Unit

1. Fluorescence In A Chlorophyll Solution

Left: A transparent-green chlorophyll solution of ground up spinach leaves and acetone. Right: Beam of light directed at the chlorophyll solution producing a reddish glow called fluorescence.

A transparent-green chlorophyll solution can be made by grinding up spinach leaves or grass with acetone in a mortar and pestle. The solution is then filtered through cheesecloth and coarse filter paper to remove the impurities and debris. Chlorophyll molecules impart the green color to the solution however, the actual chloroplasts and thylakoid membranes have been dissolved. When a bright beam of light is directed at the chlorophyll solution in the test tube, it gives off a reddish glow. This phenomenon is known as fluorescence. The chlorophyll electrons become excited by the light energy, but have no cytochrome transport system to flow along because the chloroplast thylakoid membranes have been dissolved away. Therefore, the chlorophyll electrons give up their excited energy state by releasing energy in the form of a reddish glow. This is essentially the same phenomenon as a neon light, except the electrons of neon gas molecules in the glass tube become excited and then release their energy as a white glow.

2. Simplified Illustration Of A Mitochondrion

Illustration of a mitochondrion. The inner membrane forms a series of inwardly-projecting folds called cristae. Electrons from glucose are shuttled through a cytochrome transport system along the membranes of the cristae. During this electron transport process, ATP is generated by a complex chemical mechanism known as chemiosmosis. Most of the ATP in animal cells is generated within the mitochondria. Plants can also generate ATP by a similar mechanism along thylakoid membranes of their chloroplasts.

3. ATP Structure & Function

T he structure of adenosine monophosphate, an RNA nucleotide containing the purine base adenine, is very similar to ATP (adenosine triphosphate), except that ATP has three phosphates (PO 4 ) instead of one. ATP is synthesized in all living cells by the addition of a phosphate to ADP (adenosine diphosphate). ATP is the vital energy molecule of all living systems which is absolutely necessary for key biochemical reactions within the cells. The terminal (3rd) phosphate of ATP is transferred to other molecules in the cell, thereby making them more reactive. For example, the monosaccharide glucose is very stable at ordinary body temperatures and would require a great amount of heat (such as from a flame) to break it down into carbon dioxide and water. After receiving a phosphate from ATP (a process called phosphorylation), glucose becomes glucose-phosphate and can be enzymatically broken down within seconds.

M ost of the ATP in eukaryotic cells of animals is made inside cellular organelles called mitochondria from the oxidation of glucose, a process called cellular respiration. Glucose combines with oxygen (oxidation), forming carbon dioxide, water and 38 molecules of ATP. During the oxidation process, electrons from glucose are shuttled through an iron-containing cytochrome enzyme system on the inner mitochondrial membranes (called cristae). The actual synthesis of ATP from the coupling of ADP (adenosine diphosphate) with phosphate is very complicated and involves a mechanism called chemiosmosis. The electron flow generates a higher concentration (charge) of positively-charged hydrogen (H+) ions (or protons) on one side of the membrane. When one side of the membrane is sufficiently "charged," these protons recross the membrane through special channels (pores) containing the enzyme ATP synthetase, as molecules of ATP are produced. The detailed, step-by-step breakdown of glucose during cellular respiration is called the Krebs Cycle or Citric Acid Cycle.

4. Simplified Illustration Of A Chloroplast

Illustration of a chloroplast showing the outer and inner layers of the phospholipid bilayer membrane. Each stack of thylakoid disks represents one granum. The light reactions of photosynthesis occur in the grana. The area between the grana is called the stroma. This is where the dark reactions of photosynthesis occur. In the light reactions, excited electrons from chlorophyll flow through a cytochrome transport system along membranes of the thylakoid disks (thylakoid membranes). During this electron transport process, ATP and NADPH 2 are generated. In the dark reactions of the stroma, CO 2 is gradually converted into glucose through a series of reactions called the Calvin Cycle.

Light Reactions Of Photosynthesis

I n addition to mitochondrial ATP synthesis, plants can also make ATP by a similar process during the light reactions of photosynthesis within their chloroplasts. Electrons flow through a cytochrome transport system on thylakoid membranes in a region of the chloroplast called the grana except that the electrons come from excited (light activated) chlorophyll molecules rather than the break down of glucose. This is an especially vital source of ATP for plants because ATP is also needed for them to synthesize glucose in the first place. Without a photosynthetic source of ATP, plants would be using up their ATP to make glucose, and then using up glucose to make ATP, a "catch-22" situation.

A transparent-green solution of chlorophyll is made by grinding up spinach or grass leaves in acetone (in a mortar and pestle), and then filtering it through cheesecloth and course filter paper. When a bright beam of light is directed at this chlorophyll solution, a deep red glow is emitted from the test tube. The chlorophyll electrons become excited by the light energy, but have no cytochrome transport system to flow along because the chloroplast thylakoid membranes have been dissolved away. Therefore, the chlorophyll electrons give up their excited energy state by releasing energy in the form of a reddish glow. This phenomenon is known as fluorescence, and is essentially the same principle as a fluorescent light bulb. In a fluorescent light bulb, the electrons of neon gas become excited and then release their energy of activation as a white glow inside the glass tube. In an intact chloroplast with thylakoid membranes, ATP is generated by an electron flow along the cytochrome transport system. Since the electrons are being transported to other "carrier" molecules, their energy is used to generate ATP and no reddish glow is emitted. Leaves generally appear green because wavelengths of light from the red and blue regions of the visible spectrum are necessary to excite the chloroplast electrons, and unused green light is reflected. Thus, we perceive trees, shrubs and grasses as green. During the fall months when chlorophyll production ceases in deciduous trees and shrubs, the leaves turn golden yellow or red due to the presence of other pigments, such as yellow and orange carotenoids and bright red anthocyanins.

A nother important ingredient for photosynthesis is also produced during the light reactions. During these light-dependent reactions of photosynthesis, a chemical called NADP (nicotinamide adenine dinucleotide phosphate) picks up two hydrogen atoms from water molecules forming NADPH 2 , a powerful reducing agent that is used to convert carbon dioxide into glucose during the dark reactions of photosynthesis (also called the Calvin Cycle). When the two atoms of hydrogen join with NADP, oxygen is liberated, and this is the source of oxygen gas in our atmosphere. ATP and NADPH 2 from the light reactions are used in the dark reactions of photosynthesis that take place in the stroma region of the chloroplast.

N ADP (the vital coenzyme required for photosynthesis) is derived from nicotinic acid, a B-vitamin also known as niacin. Niacin prevents pellagra, a disease characterized by severe damage to the tongue, skin and digestive tract. [NAD is another vital coenzyme that carries electrons to the electron transport system in mitochondria.] Nicotine, the alkaloid in tobacco responsible for its highly addictive properties, is also derived from nicotinic acid. Nicotine is a mild stimulant of the central nervous system. In its pure form, nicotine is highly poisonous and is used as an insecticide.

Dark Reactions Of Photosynthesis

I n the dark reactions of photosynthesis (also known as the Calvin Cycle), carbon dioxide (CO 2 ) is converted into glucose through a series of complicated reactions involving ATP (adenosine triphosphate) and NADPH 2 (nicotinamide adenine dinucleotide phosphate), two essential compounds synthesized during the light reactions of daylight. Ordinary C-3 plants form a 3-carbon compound called phosphoglyceric acid (PGA) during the initial steps of the dark reactions. The PGA is converted into another 3-carbon compound called phosphoglyceraldehyde (PGAL). Two PGAL molecules combine to form a 6-carbon glucose molecule. The following equation shows the overall reactants and products of photosynthesis:

S ome plants adapted to hot, arid regions have a different photosynthetic mechanism called CAM photosynthesis. CAM (Crassulacean Acid Metabolism) photosynthesis is found in cacti and succulents, including the crassula family (Crassulaceae). During the hot daylight hours their stomata are tightly closed however they still carry on vital photosynthesis as carbon dioxide gas is converted into simple sugars. During the cooler hours of darkness their stomata are open and CO 2 enters the leaf cells where it combines with PEP (phosphoenolpyruvate) to form 4-carbon organic acids (malic and isocitric acids). The 4-carbon acids are stored in the vacuoles of photosynthetic cells in the leaf. During the daylight hours the 4-carbon acids break down releasing CO 2 for the dark reactions (Calvin cycle) of photosynthesis inside the stroma of chloroplasts. The CO 2 is converted into glucose through a series of complicated reactions involving ATP (adenosine triphosphate) and NADPH 2 (nicotinamide adenine dinucleotide phosphate), the latter two compounds which were synthesized during the light reactions of daylight in the grana of chloroplasts. The adaptive advantage of CAM photosynthesis is that plants in arid regions can keep their stomata closed during the daytime, thereby reducing water loss from the leaves through transpiration however, they can still carry on photosynthesis with a reserve supply of CO 2 that was trapped during the hours of darkness when the stomata were open. The tropical strangler Clusia rosea also has CAM photosynthesis. This unusual tree starts out as an epiphyte on other trees and then completely envelops and shades out its host. In fact, it greatly resembles strangler figs ( Ficus ) of tropical regions of the world.

A nother interesting modification of the photosynthetic pathway is called C-4 Photosynthesis. During C-4 photosynthesis, CO 2 combines with phosphoenolpyruvate (PEP) to form a 4-carbon organic acid (oxaloacetic acid) which migrates (diffuses) to the photosynthetic bundle sheath cells surrounding the vascular bundles (veins) of the leaf. PEP essentially shuttles the CO 2 to the bundle sheath cells where it is released for the dark reactions (Calvin cycle) of photosynthesis. During hot weather the CO 2 level inside leaves is greatly reduced because the leaf stomata are closed. In ordinary C-3 plants which form a 3-carbon compound (PGA) during the initial steps of the dark reactions, photosynthesis in the leaf shuts down without a sufficient supply of CO 2 . C-4 plants have a competitive advantage during hot summer days because they are able to carry on photosynthesis in the bundle sheaths where CO 2 levels are concentrated. Weedy C-4 plants such as Bermuda grass, spurges and purslane grow rapidly during hot summer days, while photosynthesis and growth in C-3 plants shuts down.

Left: Purslane ( Portulaca oleracea ), a European herbin the purslane family (Portulacaceae) that is naturalized throughout southern California. Although it is considered a weed to most gardeners, it actually makes a tasty steamed vegetable. Right: Close-up view of a purslane leaf showing the prominent green veins. Purslane is a classic C-4 plant in which the chloroplasts are concentrated in bundle sheath cells surrounding the veins.

ATP Production In Bacteria

S imilar electron transport systems occur in the membranes of prokaryotic bacteria. Methanogenic bacteria live in marshes, swamps and your gastrointestinal tract. In fact, they are responsible for some intestinal gas, particularly the combustible component of flatulence. They produce methane gas anaerobically (without oxygen) by removing the electrons from hydrogen gas. The electrons and H+ ions from hydrogen gas are used to reduce carbon dioxide to methane. In the reaction, the H+ ions combine with the oxygen from carbon dioxide to form water. During this process, the electrons are shuttled through an anaerobic electron transport system within the bacterial membrane which results in the phosphorylation of ADP (adenosine diphosphate) to form ATP (adenosine triphosphate). This process is much less efficient than aerobic respiration, so only two molecules of ATP (rather than 38) are formed. Desert varnish bacteria make their ATP in a similar fashion, only the electrons are coming from the aerobic oxidation of iron and manganese. A thin coating of iron or manganese oxide is deposited on the surfaces of desert boulders and rocky slopes. During the oxidation process, the electrons are shuttled through an iron-containing cytochrome enzyme system on the inner bacterial membrane. One has only to gaze at the spectacular panoramas of varnish-coated, granitic boulders throughout desert areas of the American southwest to appreciate the magnitude of this bacterial ATP production. The mechanism of ATP synthesis in prokaryotic bacteria is remarkably similar to eukaryotic cells. In addition, the circular DNA molecules of these bacteria are similar to the DNA molecules within some organelles of eukaryotic cells. In fact, some biologists believe that mitochondria and chloroplasts within eukaryotic animal and plant cells may have originated from ancient symbiotic bacteria that were once captured by other cells in the distant geologic past. This fascinating idea is called the "Endosymbiont Theory" (or "Endosymbiont Hypothesis" for those who are more skeptical).

5. Guard Cells & Stomata On Leaves & Stems

The leaf surface of a species of Tradescantia , also known as spiderwort (Commelinaceae), a plant that is commonly grown in hanging baskets. Note the paired guard cells and stoma (opening slit) between them (circled in red). Also note the scattered hairs (trichomes). Each hair arises from a pedestal-like basal cell containing a nucleus.

P lants carry on gas exchange through minute pores called stomata. Carbon dioxide from the atmosphere enters the stomata and oxygen produced by photosynthesis diffuses out of the stomata. Water molecules also escape through the stomata, especially in hot, dry weather. Water loss through the stomata is known as transpiration. If the plant loses too much water it will wilt and eventually die. To cope with this dilemma, plants have evolved paired guard cells on each side of the stoma. When the guard cells are fully turgid or expanded, they have an elongate opening (stoma) between them. The walls adjacent to the stoma are very thin and flexible, while the outer walls on the opposite sides of the stoma are much thicker and more rigid. This differential thickening causes an opening to develop when the guard cells are inflated by internal water pressure (called turgor pressure). When the guard cells lose water on a hot day, they become deflated and push together, thus closing off the stoma. This cleaver strategy prevents the plants from losing excessive water through transpiration. See the following highly magnified view of the paired guard cells:

Photosystem I and Photosystem II

Wait a second. first electrons go through the second photosystem and second they go through the first? That seems really confusing. Why would they name the photosystems that way?

Water molecules are broken down to release electrons. These electrons then move down a gradient, storing energy in ATP in the process. Image by Jina Lee.

Photosystem I and II don't align with the route electrons take through the transport chain because they weren't discovered in that order.

Photosystem I was discovered first. Later, photosystem II was discovered and found to be earlier in the electron transport chain. But it was too late, the name stuck. Electrons first travel through photosystem II and then photosystem I.


Ferredoxins typically carry out a single electron transfer.

However a few bacterial ferredoxins (of the 2[4Fe4S] type) have two iron sulfur clusters and can carry out two electron transfer reactions. Depending on the sequence of the protein, the two transfers can have nearly identical reduction potentials or they may be significantly different. [4] [5]

Ferredoxins are one of the most reducing biological electron carriers. They typically have a mid point potential of -420 mV. [6] The reduction potential of a substance in the cell will differ from its midpoint potential depending on the concentrations of its reduced and oxidized forms. For a one electron reaction, the potential changes by around 60 mV for each power of ten change in the ratio of the concentration. For example, if the ferredoxin pool is around 95% reduced, the reduction potential will be around -500 mV. [7] In comparison, other biological reactions mostly have less reducing potentials: for example the primary biosynthetic reductant of the cell, NADPH has a cellular redox potential of -370 mV ( E
0 = -320 mV).

Depending on the sequence of the supporting protein ferredoxins have reduction potential from around -500mv [6] [8] to -340 mV. [9] A single cell can have multiple types of ferredoxins where each type is tuned to optimally carry out different reactions. [10]

Reduction of ferredoxin Edit

The highly reducing ferredoxins are reduced either by using another strong reducing agent, or by using some source of energy to "boost" electrons from less reducing sources to the ferredoxin. [11]

Direct reduction Edit

Reactions that reduce Fd include the oxidation of aldehydes to acids like the glyceraldehyde to glycerate reaction (-580 mV), the carbon monoxide dehydrogenase reaction (-520 mV), and the 2-oxoacid:Fd Oxidoreductase reactions (-500 mV) [12] [8] like the reaction carried out by pyruvate synthase. [7]

Membrane potential coupled reduction Edit

Ferredoxin can also be reduced by using NADH (-320 mV) or H
2 (-414 mV), but these processes are coupled to the consumption of the membrane potential to power the "boosting" of electrons to the higher energy state. [6] The Rnf complex is a widespread membrane protein in bacteria that reversibly transfers electrons between NADH and ferredoxin while pumping Na +
or H +
ions across the membrane. The chemiosmotic potential of the membrane is consumed to power the unfavorable reduction of Fd
ox by NADH. This reaction is an essential source of Fd −
red in many autotrophic organisms. If the cell is growing on substrates that provide excess Fd −
red , the Rnf complex can transfer these electrons to NAD +
and store the resultant energy in the membrane potential. [13] The energy converting hydrogenases (Ech) are a family of enzymes that reversibly couple the transfer of electrons between Fd and H
2 while pumping H +
ions across the membrane to balance the energy difference. [14]

Electron bifurcation Edit

The unfavourable reduction of Fd from a less reducing electron donor can be coupled simultaneously with the favourable reduction of an oxidising agent through an electron bifurcation reaction. [6] An example of the electron bifurcation reaction is the generation of Fd −
red for nitrogen fixation in certain aerobic diazotrophs. Typically in oxidative phosphorylation the transfer of electrons from NADH to Ubiquinone(Q) is coupled to charging the proton motive force. In Azotobacter the energy released by transferring one electron from NADH to Q is used to simultaneously boost the transfer of one electron from NADH to Fd. [15] [16]

Direct reduction of high potential ferredoxins Edit

Some ferredoxins have a sufficiently high redox potential that they can be directly reduced by NADPH. One such ferredoxin is adrenoxin (-274mV) which takes part in the biosynthesis of many mammalian steroids. [17] The ferredoxin Fd3 in the roots of plants that reduces nitrate and sulfite has a midpoint potential of -337mV and is also reduced by NADPH. [10]

Members of the 2Fe–2S ferredoxin superfamily (InterPro: IPR036010) have a general core structure consisting of beta(2)-alpha-beta(2), which includes putidaredoxin, terpredoxin, and adrenodoxin. [18] [19] [20] [21] They are proteins of around one hundred amino acids with four conserved cysteine residues to which the 2Fe–2S cluster is ligated. This conserved region is also found as a domain in various metabolic enzymes and in multidomain proteins, such as aldehyde oxidoreductase (N-terminal), xanthine oxidase (N-terminal), phthalate dioxygenase reductase (C-terminal), succinate dehydrogenase iron–sulphur protein (N-terminal), and methane monooxygenase reductase (N-terminal).

Plant-type ferredoxins Edit

One group of ferredoxins, originally found in chloroplast membranes, has been termed "chloroplast-type" or "plant-type" (InterPro: IPR010241). Its active center is a [Fe2S2] cluster, where the iron atoms are tetrahedrally coordinated both by inorganic sulfur atoms and by sulfurs of four conserved cysteine (Cys) residues.

In chloroplasts, Fe2S2 ferredoxins function as electron carriers in the photosynthetic electron transport chain and as electron donors to various cellular proteins, such as glutamate synthase, nitrite reductase, sulfite reductase, and the cyclase of chlorophyll biosynthesis. [22] Since the cyclase is a ferredoxin dependent enzyme this may provide a mechanism for coordination between photosynthesis and the chloroplasts need for chlorophyll by linking chlorophyll biosynthesis to the photosynthetic electron transport chain. In hydroxylating bacterial dioxygenase systems, they serve as intermediate electron-transfer carriers between reductase flavoproteins and oxygenase.

Thioredoxin-like ferredoxins Edit

The Fe2S2 ferredoxin from Clostridium pasteurianum (Cp2FeFd P07324 ) has been recognized as distinct protein family on the basis of its amino acid sequence, spectroscopic properties of its iron–sulfur cluster and the unique ligand swapping ability of two cysteine ligands to the [Fe2S2] cluster. Although the physiological role of this ferredoxin remains unclear, a strong and specific interaction of Cp2FeFd with the molybdenum-iron protein of nitrogenase has been revealed. Homologous ferredoxins from Azotobacter vinelandii (Av2FeFdI P82802 ) and Aquifex aeolicus (AaFd O66511 ) have been characterized. The crystal structure of AaFd has been solved. AaFd exists as a dimer. The structure of AaFd monomer is different from other Fe2S2 ferredoxins. The fold belongs to the α+β class, with first four β-strands and two α-helices adopting a variant of the thioredoxin fold. [23] UniProt categorizes these as the "2Fe2S Shethna-type ferredoxin" family. [24]

Adrenodoxin-type ferredoxins Edit

Adrenodoxin (adrenal ferredoxin InterPro: IPR001055), putidaredoxin, and terpredoxin make up a family of soluble Fe2S2 proteins that act as single electron carriers, mainly found in eukaryotic mitochondria and Proteobacteria. The human variant of adrenodoxin is referred to as ferredoxin-1 and ferredoxin-2. In mitochondrial monooxygenase systems, adrenodoxin transfers an electron from NADPH:adrenodoxin reductase to membrane-bound cytochrome P450. In bacteria, putidaredoxin and terpredoxin transfer electrons between corresponding NADH-dependent ferredoxin reductases and soluble P450s. [26] [27] The exact functions of other members of this family are not known, although Escherichia coli Fdx is shown to be involved in biogenesis of Fe–S clusters. [28] Despite low sequence similarity between adrenodoxin-type and plant-type ferredoxins, the two classes have a similar folding topology.

Ferredoxin-1 in humans participates in the synthesis of thyroid hormones. It also transfers electrons from adrenodoxin reductase to CYP11A1, a CYP450 enzyme responsible for cholesterol side chain cleavage. FDX-1 has the capability to bind to metals and proteins. [29] Ferredoxin-2 participates in heme A and iron–sulphur protein synthesis. [30]

The [Fe4S4] ferredoxins may be further subdivided into low-potential (bacterial-type) and high-potential (HiPIP) ferredoxins.

Low- and high-potential ferredoxins are related by the following redox scheme:

The formal oxidation numbers of the iron ions can be [2Fe 3+ , 2Fe 2+ ] or [1Fe 3+ , 3Fe 2+ ] in low-potential ferredoxins. The oxidation numbers of the iron ions in high-potential ferredoxins can be [3Fe 3+ , 1Fe 2+ ] or [2Fe 3+ , 2Fe 2+ ].

Bacterial-type ferredoxins Edit

1bqx A:33-56 1bc6 :33-56 7fd1 A:33-56 6fd1 :33-56 6fdr A:33-56 1frx :33-56 1gao B:33-56 1b0t A:33-56 1b0v A:33-56 1fd2 :33-56 1fdd :33-56 1fer :33-56 1axq :33-56 1g6b A:33-56 2fd2 :33-56 1ff2 A:33-56 1pc5 A:33-56 7fdr A:33-56 1g3o A:33-56 1ftc A:33-56 1frm :33-56 5fd1 :33-56 1a6l :33-56 1frj :33-56 1fdb :33-56 1fri :33-56 1pc4 A:33-56 1f5b A:33-56 1frh :33-56 1d3w A:33-56 1frk :33-56 1f5c A:33-56 1frl :33-56 1fda :33-56 1clf :31-54 1dur A:28-51 1fca :30-53 1fdn :30-53 2fdn :30-53 1xer :77-100 1h7x A:946-969 1gte A:946-969 1h7w B:946-969 1gth A:946-969 1gt8 A:946-969 1gx7 A:28-51 1hfe L:28-51 1blu :2-25 1rgv A:2-25 1kqf B:126-149 1kqg B:126-149 1jb0 C:4-27 1k0t A:4-27 1rof :3-26 1vjw :3-26 1dwl A:2-25 2pda A:738-763 1b0p A:738-763 1kek A:738-763 1c4c A:183-206 1c4a A:183-206 1feh A:183-206 1l0v N:142-165 1kfy N:142-165 1kf6 B:142-165 1jnr B:40-63

A group of Fe4S4 ferredoxins, originally found in bacteria, has been termed "bacterial-type". Bacterial-type ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four cysteine residues that bind to a [Fe4S4] cluster. In Pyrococcus furiosus Fe4S4 ferredoxin, one of the conserved Cys residues is substituted with aspartic acid.

During the evolution of bacterial-type ferredoxins, intrasequence gene duplication, transposition and fusion events occurred, resulting in the appearance of proteins with multiple iron–sulfur centers. In some bacterial ferredoxins, one of the duplicated domains has lost one or more of the four conserved Cys residues. These domains have either lost their iron–sulfur binding property or bind to a [Fe3S4] cluster instead of a [Fe4S4] cluster [31] and dicluster-type. [32]

3-D structures are known for a number of monocluster and dicluster bacterial-type ferredoxins. The fold belongs to the α+β class, with 2-7 α-helices and four β-strands forming a barrel-like structure, and an extruded loop containing three "proximal" Cys ligands of the iron–sulfur cluster.


Quantum biology is an emerging field most of the current research is theoretical and subject to questions that require further experimentation. Though the field has only recently received an influx of attention, it has been conceptualized by physicists throughout the 20th century. It has been suggested that quantum biology might play a critical role in the future of the medical world. [5] Early pioneers of quantum physics saw applications of quantum mechanics in biological problems. Erwin Schrödinger's 1944 book What is Life? discussed applications of quantum mechanics in biology. [6] Schrödinger introduced the idea of an "aperiodic crystal" that contained genetic information in its configuration of covalent chemical bonds. He further suggested that mutations are introduced by "quantum leaps". Other pioneers Niels Bohr, Pascual Jordan, and Max Delbruck argued that the quantum idea of complementarity was fundamental to the life sciences. [7] In 1963, Per-Olov Löwdin published proton tunneling as another mechanism for DNA mutation. In his paper, he stated that there is a new field of study called "quantum biology". [8]

Photosynthesis Edit

Organisms that undergo photosynthesis absorb light energy through the process of electron excitation in antennae. These antennae vary among organisms. For example, bacteria use ring-like antennae, while plants use chlorophyll pigments to absorb photons. Photosynthesis creates Frenkel excitons, which provide a separation of charge that cells convert into usable chemical energy. The energy collected in reaction sites must be transferred quickly before it is lost to fluorescence or thermal vibrational motion.

Various structures, such as the FMO complex in green sulfur bacteria, are responsible for transferring energy from antennae to a reaction site. FT electron spectroscopy studies of electron absorption and transfer show an efficiency of above 99%, [9] which cannot be explained by classical mechanical models like the diffusion model. Instead, as early as 1938, scientists theorized that quantum coherence was the mechanism for excitation energy transfer.

Scientists have recently looked for experimental evidence of this proposed energy transfer mechanism. A study published in 2007 claimed the identification of electronic quantum coherence [10] at −196 °C (77 K). Another theoretical study from 2010 provided evidence that quantum coherence lives as long as 300 femtoseconds at biologically relevant temperatures (4 °C or 277 K) . In that same year, experiments conducted on photosynthetic cryptophyte algae using two-dimensional photon echo spectroscopy yielded further confirmation for long-term quantum coherence. [11] These studies suggest that, through evolution, nature has developed a way of protecting quantum coherence to enhance the efficiency of photosynthesis. However, critical follow-up studies question the interpretation of these results. Single molecule spectroscopy now shows the quantum characteristics of photosynthesis without the interference of static disorder, and some studies use this method to assign reported signatures of electronic quantum coherence to nuclear dynamics occurring in chromophores. [12] [13] [14] [15] [16] [17] [18] A number of proposals emerged trying to explain unexpectedly long coherence. According to one proposal, if each site within the complex feels its own environmental noise, the electron will not remain in any local minimum due to both quantum coherence and thermal environment, but proceed to the reaction site via quantum walks. [19] [20] [21] Another proposal is that the rate of quantum coherence and electron tunneling create an energy sink that moves the electron to the reaction site quickly. [22] Other work suggested that geometric symmetries in the complex may favor efficient energy transfer to the reaction center, mirroring perfect state transfer in quantum networks. [23] Furthermore, experiments with artificial dye molecules cast doubts on the interpretation that quantum effects last any longer than one hundred femtoseconds. [24]

In 2017, the first control experiment with the original FMO protein under ambient conditions confirmed that electronic quantum effects are washed out within 60 femtoseconds, while the overall exciton transfer takes a time on the order of a few picoseconds. [25] In 2020 a review based on a wide collection of control experiments and theory concluded that the proposed quantum effects as long lived electronic coherences in the FMO system does not hold. [26] Instead, research investigating transport dynamics suggests that interactions between electronic and vibrational modes of excitation in FMO complexes require a semi-classical, semi-quantum explanation for the transfer of exciton energy. In other words, while quantum coherence dominates in the short-term, a classical description is most accurate to describe long-term behavior of the excitons. [27]

Another process in photosynthesis that has almost 100% efficiency is charge transfer, again suggesting that quantum mechanical phenomena are at play. [18] In 1966, a study on the photosynthetic bacteria Chromatium found that at temperatures below 100 K, cytochrome oxidation is temperature-independent, slow (on the order of milliseconds), and very low in activation energy. The authors, Don DeVault and Britton Chase, postulated that these characteristics of electron transfer are indicative of quantum tunneling, whereby electrons penetrate a potential barrier despite possessing less energy than is classically necessary. [28]

Seth Lloyd is also notable for his contributions to this area of research.

DNA mutation Edit

Deoxyribonucleic acid, DNA, acts as the instructions for making proteins throughout the body. It consists of 4 nucleotides guanine, thymine, cytosine, and adenine. [29] The order of these nucleotides gives the “recipe” for the different proteins.

Whenever a cell reproduces, it must copy these strands of DNA. However, sometimes throughout the process of copying the strand of DNA a mutation, or an error in the DNA code, can occur. A theory for the reasoning behind DNA mutation is explained in the Lowdin DNA mutation model. [30] In this model, a nucleotide may change its form through a process of quantum tunneling. [31] Because of this, the changed nucleotide will lose its ability to pair with its original base pair and consequently changing the structure and order of the DNA strand.

Exposure to ultraviolet lights and other types of radiation can cause DNA mutation and damage. The radiations also can modify the bonds along the DNA strand in the pyrimidines and cause them to bond with themselves creating a dimer. [32]

In many prokaryotes and plants, these bonds are repaired to their original form by a DNA repair enzyme photolyase. As its prefix implies, photolyase is reliant on light in order to repair the strand. Photolyase works with its cofactor FADH, flavin adenine dinucleotide, while repairing the DNA. Photolyase is excited by visible light and transfers an electron to the cofactor FADH-. FADH- now in the possession of an extra electron gives the electron to the dimer to break the bond and repair the DNA. This transfer of the electron is done through the tunneling of the electron from the FADH to the dimer. Although the range of the tunneling is much larger than feasible in a vacuum, the tunneling in this scenario is said to be “superexchange-mediated tunneling,” and is possible due to the protein's ability to boost the tunneling rates of the electron. [30]

Vibration theory of olfaction Edit

Olfaction, the sense of smell, can be broken down into two parts the reception and detection of a chemical, and how that detection is sent to and processed by the brain. This process of detecting an odorant is still under question. One theory named the “shape theory of olfaction” suggests that certain olfactory receptors are triggered by certain shapes of chemicals and those receptors send a specific message to the brain. [33] Another theory (based on quantum phenomena) suggests that the olfactory receptors detect the vibration of the molecules that reach them and the “smell” is due to different vibrational frequencies, this theory is aptly called the “vibration theory of olfaction.”

The vibration theory of olfaction, created in 1938 by Malcolm Dyson [34] but reinvigorated by Luca Turin in 1996, [35] proposes that the mechanism for the sense of smell is due to G-protein receptors that detect molecular vibrations due to inelastic electron tunneling, tunneling where the electron loses energy, across molecules. [35] In this process a molecule would fill a binding site with a G-protein receptor. After the binding of the chemical to the receptor, the chemical would then act as a bridge allowing for the electron to be transferred through the protein. As the electron transfers through and that usually would be a barrier for the electrons and would lose its energy due to the vibration of the molecule recently bound to the receptor, resulting in the ability to smell the molecule. [35] [36]

While the vibration theory has some experimental proof of concept, [37] [38] there have been multiple controversial results in experiments. In some experiments, animals are able to distinguish smells between molecules of different frequencies and same structure, [39] while other experiments show that people are unaware of distinguishing smells due to distinct molecular frequencies. [40] However, it has not been disproven, and has even been shown to be an effect in olfaction of animals other than humans such as flies, bees, and fish. [ citation needed ]

Vision Edit

Vision relies on quantized energy in order to convert light signals to an action potential in a process called phototransduction. In phototransduction, a photon interacts with a chromophore in a light receptor. The chromophore absorbs the photon and undergoes photoisomerization. This change in structure induces a change in the structure of the photo receptor and resulting signal transduction pathways lead to a visual signal. However, the photoisomerization reaction occurs at a rapid rate, in under 200 femtoseconds, [41] with high yield. Models suggest the use of quantum effects in shaping the ground state and excited state potentials in order to achieve this efficiency. [42]

Quantum vision implications Edit

Experiments have shown that the sensors in the retina of human eye is sensitive enough to detect a single photon. [43] Single photon detection could lead to multiple different technologies. One area of development is in quantum communication and cryptography. The idea is to use a biometric system to measure the eye using only a small number of points across the retina with random flashes of photons that “read” the retina and identify the individual. [44] This biometric system would only allow a certain individual with a specific retinal map to decode the message. This message can not be decoded by anyone else unless the eavesdropper were to guess the proper map or could read the retina of the intended recipient of the message. [45]

Enzymatic activity (quantum biochemistry) Edit

Enzymes may use quantum tunneling to transfer electrons long distances. It is possible that protein quaternary architecture may have evolved to enable sustained quantum entanglement and coherence. [46] More specifically, they can increase the percentage of the reaction that occurs through hydrogen tunneling. [47] Tunneling refers to the ability of a small mass particle to travel through energy barriers. This ability is due to the principle of complementarity, which hold that certain objects have pairs of properties that cannot be measured separately without changing the outcome of measurement. Electrons have both wave and particle properties, so they can pass through physical barriers as a wave without violating the laws of physics. Studies show that long distance electron transfers between redox centers through quantum tunneling plays important roles in enzymatic activity of photosynthesis and cellular respiration. [48] [49] For example, studies show that long range electron tunneling on the order of 15–30 Å plays a role in redox reactions in enzymes of cellular respiration. [50] Without quantum tunneling, organisms would not be able to convert energy quickly enough to sustain growth. Even though there are such large separations between redox sites within enzymes, electrons successfully transfer in a generally temperature independent (aside from extreme conditions) and distance dependent manner. [47] This suggests the ability of electrons to tunnel in physiological conditions. Further research is needed to determine whether this specific tunneling is also coherent.

Magnetoreception Edit

Magnetoreception refers to the ability of animals to navigate using the inclination of the magnetic field of the earth. [51] A possible explanation for magnetoreception is the entangled radical pair mechanism. [52] [53] The radical-pair mechanism is well-established in spin chemistry, [54] [55] [56] and was speculated to apply to magnetoreception in 1978 by Schulten et al.. The ratio between singlet and triplet pairs is changed by the interaction of entangled electron pairs with the magnetic field of the earth. [57] In 2000, cryptochrome was proposed as the "magnetic molecule" that could harbor magnetically sensitive radical-pairs. Cryptochrome, a flavoprotein found in the eyes of European robins and other animal species, is the only protein known to form photoinduced radical-pairs in animals. [51] When it interacts with light particles, cryptochrome goes through a redox reaction, which yields radical pairs both during the photo-reduction and the oxidation. The function of cryptochrome is diverse across species, however, the photoinduction of radical-pairs occurs by exposure to blue light, which excites an electron in a chromophore. [57] Magnetoreception is also possible in the dark, so the mechanism must rely more on the radical pairs generated during light-independent oxidation.

Experiments in the lab support the basic theory that radical-pair electrons can be significantly influenced by very weak magnetic fields, i.e. merely the direction of weak magnetic fields can affect radical-pair's reactivity and therefore can "catalyze" the formation of chemical products. Whether this mechanism applies to magnetoreception and/or quantum biology, that is, whether earth's magnetic field "catalyzes" the formation of biochemical products by the aid of radical-pairs, is undetermined for two reasons. The first is that radical-pairs may need not be entangled, the key quantum feature of the radical-pair mechanism, to play a part in these processes. There are entangled and non-entangled radical-pairs. However, researchers found evidence for the radical-pair mechanism of magnetoreception when European robins, cockroaches, and garden warblers, could no longer navigate when exposed to a radio frequency that obstructs magnetic fields [51] and radical-pair chemistry. To empirically suggest the involvement of entanglement, an experiment would need to be devised that could disturb entangled radical-pairs without disturbing other radical-pairs, or vice versa, which would first need to be demonstrated in a laboratory setting before being applied to in vivo radical-pairs.

Other biological applications Edit

Other examples of quantum phenomena in biological systems include the conversion of chemical energy into motion [58] and brownian motors in many cellular processes. [59]


Photosynthetic organisms are photoautotrophs, which means that they are able to synthesize food directly from carbon dioxide and water using energy from light. However, not all organisms use carbon dioxide as a source of carbon atoms to carry out photosynthesis photoheterotrophs use organic compounds, rather than carbon dioxide, as a source of carbon. [4] In plants, algae, and cyanobacteria, photosynthesis releases oxygen. This is called oxygenic photosynthesis and is by far the most common type of photosynthesis used by living organisms. Although there are some differences between oxygenic photosynthesis in plants, algae, and cyanobacteria, the overall process is quite similar in these organisms. There are also many varieties of anoxygenic photosynthesis, used mostly by certain types of bacteria, which consume carbon dioxide but do not release oxygen.

Carbon dioxide is converted into sugars in a process called carbon fixation photosynthesis captures energy from sunlight to convert carbon dioxide into carbohydrate. Carbon fixation is an endothermic redox reaction. In general outline, photosynthesis is the opposite of cellular respiration: while photosynthesis is a process of reduction of carbon dioxide to carbohydrate, cellular respiration is the oxidation of carbohydrate or other nutrients to carbon dioxide. Nutrients used in cellular respiration include carbohydrates, amino acids and fatty acids. These nutrients are oxidized to produce carbon dioxide and water, and to release chemical energy to drive the organism's metabolism. Photosynthesis and cellular respiration are distinct processes, as they take place through different sequences of chemical reactions and in different cellular compartments.

The general equation for photosynthesis as first proposed by Cornelis van Niel is therefore: [14]

CO2 carbon
dioxide + 2H2A electron donor + photons light energy → [CH2O] carbohydrate + 2A oxidized
donor + H2O water

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

CO2 carbon
dioxide + 2H2O water + photons light energy → [CH2O] carbohydrate + O2 oxygen + H2O water

This equation emphasizes that water is both a reactant in the light-dependent reaction and a product of the light-independent reaction, but canceling n water molecules from each side gives the net equation:

CO2 carbon
dioxide + H2O water + photons light energy → [CH2O] carbohydrate + O2 oxygen

Other processes substitute other compounds (such as arsenite) for water in the electron-supply role for example some microbes use sunlight to oxidize arsenite to arsenate: [15] The equation for this reaction is:

CO2 carbon
dioxide + (AsO 3−
3 )
arsenite + photons light energy → (AsO 3−
4 )
arsenate + CO carbon
monoxide (used to build other compounds in subsequent reactions) [16]

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 oxygenic photosynthesis use visible light for the light-dependent reactions, although at least three use shortwave infrared or, more specifically, far-red radiation. [17]

Some organisms employ even more radical variants of photosynthesis. Some archaea use a simpler method that employs a pigment similar to those used for vision in animals. The bacteriorhodopsin changes its configuration in response to sunlight, acting as a proton pump. This produces a proton gradient more directly, which is then converted to chemical energy. The process does not involve carbon dioxide fixation and does not release oxygen, and seems to have evolved separately from the more common types of photosynthesis. [18] [19]

  1. outer membrane
  2. intermembrane space
  3. inner membrane (1+2+3: envelope)
  4. stroma (aqueous fluid)
  5. thylakoid lumen (inside of thylakoid)
  6. thylakoid membrane
  7. granum (stack of thylakoids)
  8. thylakoid (lamella)
  9. starch
  10. ribosome
  11. plastidial DNA
  12. plastoglobule (drop of lipids)

In photosynthetic bacteria, the proteins that gather light for photosynthesis are embedded in cell membranes. In its simplest form, this involves the membrane surrounding the cell itself. [20] However, the membrane may be tightly folded into cylindrical sheets called thylakoids, [21] or bunched up into round vesicles called intracytoplasmic membranes. [22] These structures can fill most of the interior of a cell, giving the membrane a very large surface area and therefore increasing the amount of light that the bacteria can absorb. [21]

In plants and algae, photosynthesis takes place in organelles called chloroplasts. A typical plant cell contains about 10 to 100 chloroplasts. The chloroplast is enclosed by a membrane. This membrane is composed of a phospholipid inner membrane, a phospholipid outer membrane, and an intermembrane space. Enclosed by the membrane is an aqueous fluid called the stroma. Embedded within the stroma are stacks of thylakoids (grana), which are the site of photosynthesis. The thylakoids appear as flattened disks. The thylakoid itself is enclosed by the thylakoid membrane, and within the enclosed volume is a lumen or thylakoid space. Embedded in the thylakoid membrane are integral and peripheral membrane protein complexes of the photosynthetic system.

Plants absorb light primarily using the pigment chlorophyll. The green part of the light spectrum is not absorbed but is reflected which is the reason that most plants have a green color. Besides chlorophyll, plants also use pigments such as carotenes and xanthophylls. [23] Algae also use chlorophyll, but various other pigments are present, such as phycocyanin, carotenes, and xanthophylls in green algae, phycoerythrin in red algae (rhodophytes) and fucoxanthin in brown algae and diatoms resulting in a wide variety of colors.

These pigments are embedded in plants and algae in complexes called antenna proteins. In such proteins, the pigments are arranged to work together. Such a combination of proteins is also called a light-harvesting complex. [24]

Although all cells in the green parts of a plant have chloroplasts, the majority of those are found in specially adapted structures called leaves. Certain species adapted to conditions of strong sunlight and aridity, such as many Euphorbia and cactus species, have their main photosynthetic organs in their stems. The cells in the interior tissues of a leaf, called the mesophyll, can contain between 450,000 and 800,000 chloroplasts for every square millimeter of leaf. The surface of the leaf is coated with a water-resistant waxy cuticle that protects the leaf from excessive evaporation of water and decreases the absorption of ultraviolet or blue light to reduce heating. The transparent epidermis layer allows light to pass through to the palisade mesophyll cells where most of the photosynthesis takes place.

In the light-dependent 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, starting the 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 (energy gradient) across the chloroplast membrane, which is used by ATP synthase in the synthesis of ATP. The chlorophyll molecule ultimately regains the electron it lost when a water molecule is split in a process called photolysis, which releases a dioxygen (O2) molecule as a waste product.

The overall equation for the light-dependent reactions under the conditions of non-cyclic electron flow in green plants is: [25]

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 absorption peaks in violet-blue and red light. In red algae, the action spectrum is blue-green light, which allows these algae to use the blue end of the spectrum to grow in the deeper waters that filter out the longer wavelengths (red light) used by above-ground green plants. The non-absorbed part of the light spectrum is what gives photosynthetic organisms their color (e.g., green plants, red algae, purple bacteria) and is the least effective for photosynthesis in the respective organisms.

Z scheme

In plants, light-dependent reactions occur in the thylakoid membranes of the chloroplasts where they drive the synthesis of ATP and NADPH. The light-dependent reactions are of two forms: cyclic and non-cyclic.

In the non-cyclic reaction, the photons are captured in the light-harvesting antenna complexes of photosystem II by chlorophyll and other accessory pigments (see diagram at right). The absorption of a photon by the antenna complex frees an electron by a process called photoinduced charge separation. The antenna system is at the core of the chlorophyll molecule of the photosystem II reaction center. That freed electron is transferred to the primary electron-acceptor molecule, pheophytin. As the electrons are shuttled through an electron transport chain (the so-called Z-scheme shown in the diagram), it initially functions to generate a chemiosmotic potential by pumping proton cations (H + ) across the membrane and into the thylakoid space. An ATP synthase enzyme uses that chemiosmotic potential to make ATP during photophosphorylation, whereas NADPH is a product of the terminal redox reaction in the Z-scheme. The electron enters a chlorophyll molecule in Photosystem I. There it is further excited by the light absorbed by that photosystem. The electron is then passed along a chain of electron acceptors to which it transfers some of its energy. The energy delivered to the electron acceptors is used to move hydrogen ions across the thylakoid membrane into the lumen. The electron is eventually used to reduce the co-enzyme NADP with a H + to NADPH (which has functions in the light-independent reaction) at that point, the path of that electron ends.

The cyclic reaction is similar to that of the non-cyclic but differs in that it generates only ATP, and no reduced NADP (NADPH) is created. The cyclic reaction takes place only at photosystem I. Once the electron is displaced from the photosystem, the electron is passed down the electron acceptor molecules and returns to photosystem I, from where it was emitted, hence the name cyclic reaction.

Water photolysis

Linear electron transport through a photosystem will leave the reaction center of that photosystem oxidized. Elevating another electron will first require re-reduction of the reaction center. The excited electrons lost from the reaction center (P700) of photosystem I are replaced by transfer from plastocyanin, whose electrons come from electron transport through photosystem II. Photosystem II, as the first step of the Z-scheme, requires an external source of electrons to reduce its oxidized chlorophyll a reaction center, called P680. The source of electrons for photosynthesis in green plants and cyanobacteria is water. Two water molecules are oxidized by four successive charge-separation reactions by photosystem II to yield a molecule of diatomic oxygen and four hydrogen ions. The electrons yielded are transferred to a redox-active tyrosine residue that then reduces the oxidized P680. This resets the ability of P680 to absorb another photon and release another photo-dissociated electron. The oxidation of water is catalyzed in photosystem II by a redox-active structure that contains four manganese ions and a calcium ion this oxygen-evolving complex binds two water molecules and contains the four oxidizing equivalents that are used to drive the water-oxidizing reaction (Dolai's S-state diagrams). Photosystem II is the only known biological enzyme that carries out this oxidation of water. The hydrogen ions are released in the thylakoid lumen and therefore contribute to the transmembrane chemiosmotic potential that leads to ATP synthesis. Oxygen is a waste product of light-dependent reactions, but the majority of organisms on Earth use oxygen for cellular respiration, including photosynthetic organisms. [26] [27]

Calvin cycle

In the light-independent (or "dark") reactions, the enzyme RuBisCO captures CO2 from the atmosphere and, in a process called the Calvin cycle, it uses the newly formed NADPH and 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 [25] : 128

Carbon fixation produces the intermediate three-carbon sugar product, which is then converted into the final carbohydrate products. The simple carbon sugars produced by photosynthesis are then used in the forming of other organic compounds, such as the building material cellulose, the 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 is 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, to yield two molecules of a three-carbon compound, glycerate 3-phosphate, also known as 3-phosphoglycerate. Glycerate 3-phosphate, in the presence of ATP and NADPH produced during the light-dependent stages, is reduced to glyceraldehyde 3-phosphate. This product is also referred to as 3-phosphoglyceraldehyde (PGAL) or, more generically, as triose phosphate. Most (5 out of 6 molecules) of the glyceraldehyde 3-phosphate produced is used to regenerate ribulose 1,5-bisphosphate so the process can continue. The triose phosphates not thus "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.

Carbon concentrating mechanisms

On land

In hot and dry conditions, plants close their stomata to prevent water loss. Under these conditions, CO
2 will decrease and oxygen gas, produced by the light reactions of photosynthesis, will increase, 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 CO
2 concentration in the leaves under these conditions. [28]

Plants that use the C4 carbon fixation process chemically fix carbon dioxide in the cells of the mesophyll by adding it to the three-carbon molecule phosphoenolpyruvate (PEP), a reaction catalyzed by an enzyme called PEP carboxylase, creating 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 CO
2 released by decarboxylation of the four-carbon acids is then fixed by RuBisCO activity to the three-carbon 3-phosphoglyceric acids. The physical separation of RuBisCO from the oxygen-generating light reactions reduces photorespiration and increases CO
2 fixation and, thus, the photosynthetic capacity of the leaf. [29] 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 that do not use PEP-carboxylase in carbon fixation are called C3 plants because the primary carboxylation reaction, catalyzed by RuBisCO, produces the three-carbon 3-phosphoglyceric acids directly in the Calvin-Benson cycle. Over 90% of plants use C3 carbon fixation, compared to 3% that use C4 carbon fixation [30] however, the evolution of C4 in over 60 plant lineages makes it a striking example of convergent evolution. [28]

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 spatially separates the CO
2 fixation to PEP from the Calvin cycle, CAM temporally separates these two processes. CAM plants have a different leaf anatomy from C3 plants, and fix the CO
2 at night, when their stomata are open. CAM plants store the CO
2 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 CO
2 inside the leaves, thus allowing carbon fixation to 3-phosphoglycerate by RuBisCO. Sixteen thousand species of plants use CAM. [31]

Calcium oxalate accumulating plants, such as Amaranthus hybridus and Colobanthus quitensis, showed a variation of photosynthesis where calcium oxalate crystals function as dynamic carbon pools, supplying carbon dioxide (CO2) to photosynthetic cells when stomata are partially or totally closed. This process was named Alarm photosynthesis. Under stress conditions (e.g. water deficit) oxalate released from calcium oxalate crystals is converted to CO2 by an oxalate oxidase enzyme and the produced CO2 can support the Calvin cycle reactions. Reactive hydrogen peroxide (H2O2), the byproduct of oxalate oxidase reaction, can be neutralized by catalase. Alarm photosynthesis represents an unknown photosynthetic variation to be added to the already known C4 and CAM pathways. However, alarm photosynthesis, in contrast to these pathways, operates as a biochemical pump that collects carbon from the organ interior (or from the soil) and not from the atmosphere. [32] [33]

In water

Cyanobacteria possess carboxysomes, which increase the concentration of CO
2 around RuBisCO to increase the rate of photosynthesis. An enzyme, carbonic anhydrase, located within the carboxysome releases CO2 from the dissolved hydrocarbonate ions (HCO −
3 ). Before the CO2 diffuses out it is quickly sponged up by RuBisCO, which is concentrated within the carboxysomes. HCO −
3 ions are made from CO2 outside the cell by another carbonic anhydrase and are actively pumped into the cell by a membrane protein. They cannot cross the membrane as they are charged, and within the cytosol they turn back into CO2 very slowly without the help of carbonic anhydrase. This causes the HCO −
3 ions to accumulate within the cell from where they diffuse into the carboxysomes. [34] Pyrenoids in algae and hornworts also act to concentrate CO
2 around RuBisCO. [35]

The overall process of photosynthesis takes place in four stages: [13]

Stage Description Time scale
1 Energy transfer in antenna chlorophyll (thylakoid membranes) femtosecond to picosecond
2 Transfer of electrons in photochemical reactions (thylakoid membranes) picosecond to nanosecond
3 Electron transport chain and ATP synthesis (thylakoid membranes) microsecond to millisecond
4 Carbon fixation and export of stable products millisecond to second

Plants usually convert light into chemical energy with a photosynthetic efficiency of 3–6%. [36] Absorbed light that is unconverted is dissipated primarily as heat, with a small fraction (1–2%) [37] re-emitted as chlorophyll fluorescence at longer (redder) wavelengths. This fact allows measurement of the light reaction of photosynthesis by using chlorophyll fluorometers. [37]

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%. [38] By comparison, solar panels convert light into electric energy at an efficiency of approximately 6–20% for mass-produced panels, and above 40% in laboratory devices.

The efficiency of both light and dark reactions can be measured but the relationship between the two can be complex. [39] For example, the ATP and NADPH energy molecules, created by the light reaction, can be used for carbon fixation or for photorespiration in C3 plants. [39] Electrons may also flow to other electron sinks. [40] [41] [42] For this reason, it is not uncommon for authors to differentiate between work done under non-photorespiratory conditions and under photorespiratory conditions. [43] [44] [45]

Chlorophyll fluorescence of photosystem II can measure the light reaction, and Infrared gas analyzers can measure the dark reaction. [46] It is also possible to investigate both at the same time using an integrated chlorophyll fluorometer and gas exchange system, or by using two separate systems together. [47] Infrared gas analyzers and some moisture sensors are sensitive enough to measure the photosynthetic assimilation of CO2, and of ΔH2O using reliable methods [48] CO2 is commonly measured in μmols/(m 2 /s), parts per million or volume per million and H2O is commonly measured in mmol/(m 2 /s) or in mbars. [48] By measuring CO2 assimilation, ΔH2O, leaf temperature, barometric pressure, leaf area, and photosynthetically active radiation or PAR, it becomes possible to estimate, "A" or carbon assimilation, "E" or transpiration, "gs" or stomatal conductance, and Ci or intracellular CO2. [48] However, it is more common to used chlorophyll fluorescence for plant stress measurement, where appropriate, because the most commonly used measuring parameters FV/FM and Y(II) or F/FM' can be made in a few seconds, allowing the measurement of larger plant populations. [45]

Gas exchange systems that offer control of CO2 levels, above and below ambient, allow the common practice of measurement of A/Ci curves, at different CO2 levels, to characterize a plant's photosynthetic response. [48]

Integrated chlorophyll fluorometer – gas exchange systems allow a more precise measure of photosynthetic response and mechanisms. [46] [47] While standard gas exchange photosynthesis systems can measure Ci, or substomatal CO2 levels, the addition of integrated chlorophyll fluorescence measurements allows a more precise measurement of CC to replace Ci. [47] [49] The estimation of CO2 at the site of carboxylation in the chloroplast, or CC, becomes possible with the measurement of mesophyll conductance or gm using an integrated system. [46] [47] [50]

Photosynthesis measurement systems are not designed to directly measure the amount of light absorbed by the leaf. But analysis of chlorophyll-fluorescence, P700- and P515-absorbance and gas exchange measurements reveal detailed information about e.g. the photosystems, quantum efficiency and the CO2 assimilation rates. With some instruments, even wavelength-dependency of the photosynthetic efficiency can be analyzed. [51]

A phenomenon known as quantum walk increases the efficiency of the energy transport of light significantly. In the photosynthetic cell of an algae, bacterium, or plant, there are light-sensitive molecules called chromophores arranged in an antenna-shaped structure named a photocomplex. When a photon is absorbed by a chromophore, it is converted into a quasiparticle referred to as an exciton, which jumps from chromophore to chromophore towards the reaction center of the photocomplex, a collection of molecules that traps its energy in a chemical form that makes it accessible for the cell's metabolism. The exciton's wave properties enable it to cover a wider area and try out several possible paths simultaneously, allowing it to instantaneously "choose" the most efficient route, where it will have the highest probability of arriving at its destination in the minimum possible time.

Because that quantum walking takes place at temperatures far higher than quantum phenomena usually occur, it is only possible over very short distances, due to obstacles in the form of destructive interference that come into play. These obstacles cause the particle to lose its wave properties for an instant before it regains them once again after it is freed from its locked position through a classic "hop". The movement of the electron towards the photo center is therefore covered in a series of conventional hops and quantum walks. [52] [53] [54]

Early photosynthetic systems, such as those in green and purple sulfur and green and purple nonsulfur bacteria, are thought to have been anoxygenic, and used various other molecules than water as electron donors. Green and purple sulfur bacteria are thought to have used hydrogen and sulfur as electron donors. Green nonsulfur bacteria used various amino and other organic acids as an electron donor. Purple nonsulfur bacteria used a variety of nonspecific organic molecules. The use of these molecules is consistent with the geological evidence that Earth's early atmosphere was highly reducing at that time. [55]

Fossils of what are thought to be filamentous photosynthetic organisms have been dated at 3.4 billion years old. [56] [57] More recent studies, reported in March 2018, also suggest that photosynthesis may have begun about 3.4 billion years ago. [58] [59]

The main source of oxygen in the Earth's atmosphere derives from oxygenic photosynthesis, and its first appearance is sometimes referred to as the oxygen catastrophe. Geological evidence suggests that oxygenic photosynthesis, such as that in cyanobacteria, became important during the Paleoproterozoic era around 2 billion years ago. Modern photosynthesis in plants and most photosynthetic prokaryotes is oxygenic. Oxygenic photosynthesis uses water as an electron donor, which is oxidized to molecular oxygen ( O
2 ) in the photosynthetic reaction center.

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. It is presumed that this is due to the particularly simple body plans and large surface areas of these animals compared to their volumes. [60] 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 (see Kleptoplasty). This allows the mollusks to survive solely by photosynthesis for several months at a time. [61] [62] 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. [63]

An even closer form of symbiosis may explain the origin of chloroplasts. Chloroplasts have many similarities with photosynthetic bacteria, including a circular chromosome, prokaryotic-type ribosome, and similar proteins in the photosynthetic reaction center. [64] [65] The endosymbiotic theory suggests that photosynthetic bacteria were acquired (by endocytosis) by early eukaryotic cells to form the first plant cells. Therefore, chloroplasts may be photosynthetic bacteria that adapted to life inside plant cells. Like mitochondria, chloroplasts possess their own DNA, separate from the nuclear DNA of their plant host cells and the genes in this chloroplast DNA resemble those found in cyanobacteria. [66] DNA in chloroplasts codes for redox proteins such as those found in the photosynthetic reaction centers. The CoRR Hypothesis proposes that this co-location of genes with their gene products is required for redox regulation of gene expression, and accounts for the persistence of DNA in bioenergetic organelles. [67]

Photosynthetic eukaryotic lineages

Symbiotic and kleptoplastic organisms excluded:

  • The glaucophytes and the red and green algae—clade Archaeplastida (unicellular and multicellular)
  • The cryptophytes—clade Cryptista (unicellular)
  • The haptophytes—clade Haptista (unicellular)
  • The dinoflagellates and chromerids in the superphylum Myzozoa—clade Alveolata (unicellular)
  • The ochrophytes—clade Heterokonta (unicellular and multicellular)
  • The chlorarachniophytes and three species of Paulinella in the phylum Cercozoa—clade Rhizaria (unicellular)
  • The euglenids—clade Excavata (unicellular)

Except for the euglenids, which is found within the Excavata, all of them belong to the Diaphoretickes. Archaeplastida and the photosynthetic Paulinella got their plastids— which are surrounded by two membranes, through primary endosymbiosis in two separate events by engulfing a cyanobacterium. The plastids in all the other groups have either a red or green algal origin, and are referred to as the "red lineages" and the "green lineages". In dinoflaggelates and euglenids the plastids are surrounded by three membranes, and in the remaining lines by four. A nucleomorph, remnants of the original algal nucleus located between the inner and outer membranes of the plastid, is present in the cryptophytes (from a red algae) and chlorarachniophytes (from a green algae). [68] Some dinoflaggelates which have lost their photosyntethic ability have later regained it again through new endosymbiotic events with different algae. While able to perform photosynthesis, many of these eukaryotic groups are mixotrophs and practice heterotrophy to various degrees.

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 (formerly called blue-green algae), which are the only prokaryotes performing oxygenic photosynthesis. The geological record indicates that this transforming event took place early in Earth's history, at least 2450–2320 million years ago (Ma), and, it is speculated, much earlier. [69] [70] Because the Earth's atmosphere contained almost no oxygen during the estimated development of photosynthesis, it is believed that the first photosynthetic cyanobacteria did not generate oxygen. [71] 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 Cyanobacteria. Cyanobacteria remained the principal primary producers of oxygen throughout the Proterozoic Eon (2500–543 Ma), in part because the redox structure of the oceans favored photoautotrophs capable of nitrogen fixation. [ citation needed ] Green algae joined cyanobacteria as the major primary producers of oxygen on continental shelves near the end of the Proterozoic, but it was only with the Mesozoic (251–66 Ma) radiations of dinoflagellates, coccolithophorids, and diatoms did the primary production of oxygen in marine shelf waters take modern form. Cyanobacteria remain critical to marine ecosystems as primary producers of oxygen in oceanic gyres, as agents of biological nitrogen fixation, and, in modified form, as the plastids of marine algae. [72]

Although some of the steps in photosynthesis are still not completely understood, the overall photosynthetic equation has been known since the 19th century.

Jan van Helmont began the research of the process in the mid-17th century when he carefully measured the mass of the soil used by a plant and the mass of the plant as it grew. After noticing that the soil mass changed very little, he hypothesized that the mass of the growing plant must come from the water, the only substance he added to the potted plant. His hypothesis was partially accurate – much of the gained mass also comes from carbon dioxide as well as water. However, this was a signaling point to the idea that the bulk of a plant's biomass comes from the inputs of photosynthesis, not the soil itself.

Joseph Priestley, a chemist and minister, discovered that, when he isolated a volume of air under an inverted jar, and burned a candle in it (which gave off CO2), the candle would burn out very quickly, much before it ran out of wax. He further discovered that a mouse could similarly "injure" air. He then showed that the air that had been "injured" by the candle and the mouse could be restored by a plant. [73]

In 1779, Jan Ingenhousz repeated Priestley's experiments. He discovered that it was the influence of sunlight on the plant that could cause it to revive a mouse in a matter of hours. [73] [74]

In 1796, Jean Senebier, a Swiss pastor, botanist, and naturalist, demonstrated that green plants consume carbon dioxide and release oxygen under the influence of light. Soon afterward, Nicolas-Théodore de Saussure showed that the increase in mass of the plant as it grows could not be due only to uptake of CO2 but also to the incorporation of water. Thus, the basic reaction by which photosynthesis is used to produce food (such as glucose) was outlined. [75]

Cornelis Van Niel made key discoveries explaining the chemistry of photosynthesis. By studying purple sulfur bacteria and green bacteria he was the first to demonstrate that photosynthesis is a light-dependent redox reaction, in which hydrogen reduces (donates its – electron to) carbon dioxide.

Robert Emerson discovered two light reactions by testing plant productivity using different wavelengths of light. With the red alone, the light reactions were suppressed. When blue and red were combined, the output was much more substantial. Thus, there were two photosystems, one absorbing up to 600 nm wavelengths, the other up to 700 nm. The former is known as PSII, the latter is PSI. PSI contains only chlorophyll "a", PSII contains primarily chlorophyll "a" with most of the available chlorophyll "b", among other pigments. These include phycobilins, which are the red and blue pigments of red and blue algae respectively, and fucoxanthol for brown algae and diatoms. The process is most productive when the absorption of quanta are equal in both the PSII and PSI, assuring that input energy from the antenna complex is divided between the PSI and PSII system, which in turn powers the photochemistry. [13]

Robert Hill thought that a complex of reactions consisting of an intermediate to cytochrome b6 (now a plastoquinone), another is from cytochrome f to a step in the carbohydrate-generating mechanisms. These are linked by plastoquinone, which does require energy to reduce cytochrome f for it is a sufficient reductant. Further experiments to prove that the oxygen developed during the photosynthesis of green plants came from water, were performed by Hill in 1937 and 1939. He showed that isolated chloroplasts give off oxygen in the presence of unnatural reducing agents like iron oxalate, ferricyanide or benzoquinone after exposure to light. The Hill reaction [76] is as follows:

2 H2O + 2 A + (light, chloroplasts) → 2 AH2 + O2

where A is the electron acceptor. Therefore, in light, the electron acceptor is reduced and oxygen is evolved.

Samuel Ruben and Martin Kamen used radioactive isotopes to determine that the oxygen liberated in photosynthesis came from the water.

Melvin Calvin and Andrew Benson, along with James Bassham, elucidated the path of carbon assimilation (the photosynthetic carbon reduction cycle) in plants. The carbon reduction cycle is known as the Calvin cycle, which ignores the contribution of Bassham and Benson. Many scientists refer to the cycle as the Calvin-Benson Cycle, Benson-Calvin, and some even call it the Calvin-Benson-Bassham (or CBB) Cycle.

Nobel Prize-winning scientist Rudolph A. Marcus was able to discover the function and significance of the electron transport chain.

Otto Heinrich Warburg and Dean Burk discovered the I-quantum photosynthesis reaction that splits the CO2, activated by the respiration. [77]

In 1950, first experimental evidence for the existence of photophosphorylation in vivo was presented by Otto Kandler using intact Chlorella cells and interpreting his findings as light-dependent ATP formation. [78] In 1954, Daniel I. Arnon et al. discovered photophosphorylation in vitro in isolated chloroplasts with the help of P 32 . [79] [80]

Louis N.M. Duysens and Jan Amesz discovered that chlorophyll a will absorb one light, oxidize cytochrome f, chlorophyll a (and other pigments) will absorb another light but will reduce this same oxidized cytochrome, stating the two light reactions are in series.

Development of the concept

In 1893, Charles Reid Barnes proposed two terms, photosyntax and photosynthesis, for the biological process of synthesis of complex carbon compounds out of carbonic acid, in the presence of chlorophyll, under the influence of light. Over time, the term photosynthesis came into common usage as the term of choice. Later discovery of anoxygenic photosynthetic bacteria and photophosphorylation necessitated redefinition of the term. [81]

C3 : C4 photosynthesis research

After WWII at late 1940 at the University of California, Berkeley, the details of photosynthetic carbon metabolism were sorted out by the chemists Melvin Calvin, Andrew Benson, James Bassham and a score of students and researchers utilizing the carbon-14 isotope and paper chromatography techniques. [82] The pathway of CO2 fixation by the algae Chlorella in a fraction of a second in light resulted in a 3 carbon molecule called phosphoglyceric acid (PGA). For that original and ground-breaking work, a Nobel Prize in Chemistry was awarded to Melvin Calvin in 1961. In parallel, plant physiologists studied leaf gas exchanges using the new method of infrared gas analysis and a leaf chamber where the net photosynthetic rates ranged from 10 to 13 μmol CO2·m −2 ·s −1 , with the conclusion that all terrestrial plants having the same photosynthetic capacities that were light saturated at less than 50% of sunlight. [83] [84]

Later in 1958–1963 at Cornell University, field grown maize was reported to have much greater leaf photosynthetic rates of 40 μmol CO2·m −2 ·s −1 and was not saturated at near full sunlight. [85] [86] This higher rate in maize was almost double those observed in other species such as wheat and soybean, indicating that large differences in photosynthesis exist among higher plants. At the University of Arizona, detailed gas exchange research on more than 15 species of monocot and dicot uncovered for the first time that differences in leaf anatomy are crucial factors in differentiating photosynthetic capacities among species. [87] [88] In tropical grasses, including maize, sorghum, sugarcane, Bermuda grass and in the dicot amaranthus, leaf photosynthetic rates were around 38−40 μmol CO2·m −2 ·s −1 , and the leaves have two types of green cells, i. e. outer layer of mesophyll cells surrounding a tightly packed cholorophyllous vascular bundle sheath cells. This type of anatomy was termed Kranz anatomy in the 19th century by the botanist Gottlieb Haberlandt while studying leaf anatomy of sugarcane. [89] Plant species with the greatest photosynthetic rates and Kranz anatomy showed no apparent photorespiration, very low CO2 compensation point, high optimum temperature, high stomatal resistances and lower mesophyll resistances for gas diffusion and rates never saturated at full sun light. [90] The research at Arizona was designated Citation Classic by the ISI 1986. [88] These species was later termed C4 plants as the first stable compound of CO2 fixation in light has 4 carbon as malate and aspartate. [91] [92] [93] Other species that lack Kranz anatomy were termed C3 type such as cotton and sunflower, as the first stable carbon compound is the 3-carbon PGA. At 1000 ppm CO2 in measuring air, both the C3 and C4 plants had similar leaf photosynthetic rates around 60 μmol CO2·m −2 ·s −1 indicating the suppression of photorespiration in C3 plants. [87] [88]

There are three main factors affecting photosynthesis [ clarification needed ] and several corollary factors. The three main are: [ citation needed ]

Total photosynthesis is limited by a range of environmental factors. These include the amount of light available, the amount of leaf area a plant has to capture light (shading by other plants is a major limitation of photosynthesis), rate at which carbon dioxide can be supplied to the chloroplasts to support photosynthesis, the availability of water, and the availability of suitable temperatures for carrying out photosynthesis. [94]

Light intensity (irradiance), wavelength and temperature

The process of photosynthesis provides the main input of free energy into the biosphere, and is one of four main ways in which radiation is important for plant life. [95]

The radiation climate within plant communities is extremely variable, with both time and space.

In the early 20th century, Frederick Blackman and Gabrielle Matthaei investigated the effects of light intensity (irradiance) and temperature on the rate of carbon assimilation.

  • At constant temperature, the rate of carbon assimilation varies with irradiance, increasing as the irradiance increases, but reaching a plateau at higher irradiance.
  • At low irradiance, increasing the temperature has little influence on the rate of carbon assimilation. At constant high irradiance, the rate of carbon assimilation increases as the temperature is increased.

These two experiments illustrate several important points: First, it is known that, in general, photochemical reactions are not affected by temperature. However, these experiments clearly show that temperature affects the rate of carbon assimilation, so there must be two sets of reactions in the full process of carbon assimilation. These are the light-dependent 'photochemical' temperature-independent stage, and the light-independent, temperature-dependent stage. Second, Blackman's experiments illustrate the concept of limiting factors. Another limiting factor is the wavelength of light. Cyanobacteria, which reside several meters underwater, cannot receive the correct wavelengths required to cause photoinduced charge separation in conventional photosynthetic pigments. To combat this problem, a series of proteins with different pigments surround the reaction center. This unit is called a phycobilisome. [ clarification needed ]

Carbon dioxide levels and photorespiration

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.

The salvaging pathway for the products of RuBisCO oxygenase activity is more commonly known as photorespiration, since it is characterized by light-dependent oxygen consumption and the release of carbon dioxide.

Step 1: Glycolysis

When glucose is transported into the cytoplasm of cells, it is broken down into two molecules of pyruvate (Figure (PageIndex<2>)). This process is called glycolysis (glyco- for glucose and -lysis, meaning to break apart). Glycolysis involves the coordinated action of many different enzymes. As these enzymes start to break the glucose molecule apart, an initial input of energy is required. This initial energy is donated by molecules of ATP.

Figure (PageIndex<2>): In glycolysis, glucose (represented by a ring of six carbons) is converted to fructose-1,6-bisphosphate (labeled fructose diphosphate). This consumes 2 ATP, releasing 2 ADP. Fructose-1,6-bisphosphate is broken into two glyceraldehyde-3-phosphate molecules. Each is represented by a chain of three carbons attached to a phosphate (Pi). The phosphate is removed from each of the two glyceraldehyde-3-phosphate molecules, producing 2 pyruvates, 2 NADH, and 4 ATP. Overall, glycolysis consumes 2 ATP, but it then generates 4 ATP and 2 NADH. Image by OpenStax (CC-BY). Access for free at

Though two molecules of ATP are used to get glycolysis going, four more molecules of ATP are produced during the reaction, resulting in the net production of two ATP per molecule of glucose. In addition to ATP, two molecules of nicotinamide adenine dinucleotide (NAD + ) are reduced to form NADH (Figure (PageIndex<3>)). When NAD + is reduced to NADH, two high energy electrons derived from breaking the bonds of glucose are added to it. One of those negatively charged electrons is balanced by the positive charge (+) on NAD + . The other is balanced by adding a proton (H + ) to the molecule.

Figure (PageIndex<3>): When NAD + is reduced to NADH, it gains one proton (H + ) and two electrons (e - ). The reverse reaction (oxidation) can also occur. The chemical structure of NAD + is a modified version of two nucleotides attached together. It is represented by ADP (adenosine diphosphate) attached to ribose (rib, a five-carbon sugar), attached to a ring of carbon and nitrogen.

Photosynthesis Stage I: The Light Reactions

An overview of photosynthesis is available at

Chloroplasts Capture Sunlight

Every second, the sun fuses over 600 million tons of hydrogen into 596 tons of helium, converting over 4 tons of helium (4.3 billion kg) into light and heat energy. Countless tiny packets of that light energy travel 93 million miles (150 million km) through space, and about 1% of the light which reaches the Earth&rsquos surface participates in photosynthesis. Light is the source of energy for photosynthesis, and the first set of reactions which begin the process requires light &ndash thus the name, light reactions, or light-dependent reactions.

When light strikes chlorophyll (or an accessory pigment) within the chloroplast, it energizes electrons within that molecule. These electrons jump up to higher energy levels they have absorbed or captured, and now carry, that energy. High-energy electrons are &ldquoexcited.&rdquo Who wouldn&rsquot be excited to hold the energy for life?

The excited electrons leave chlorophyll to participate in further reactions, leaving the chlorophyll &ldquoat a loss&rdquo eventually they must be replaced. That replacement process also requires light, working with an enzyme complex to split water molecules. In this process ofphotolysis (&ldquosplitting by light&rdquo), H2O molecules are broken into hydrogen ions, electrons, and oxygen atoms. The electrons replace those originally lost from chlorophyll. Hydrogen ions and the high-energy electrons from chlorophyll will carry on the energy transformation drama after the light reactions are over.

The oxygen atoms, however, form oxygen gas, which is a waste product of photosynthesis. The oxygen given off supplies most of the oxygen in our atmosphere. Before photosynthesis evolved, Earth&rsquos atmosphere lacked oxygen altogether, and this highly reactive gas was toxic to the many organisms living at the time. Something had to change! Most contemporary organisms rely on oxygen for efficient respiration. So plants don&rsquot just &ldquorestore&rdquo the air, they also had a major role in creating it!

To summarize, chloroplasts &ldquocapture&rdquo sunlight energy in two ways. Light &lsquo&lsquoexcites&rsquo&rsquo electrons in pigment molecules, and light provides the energy to split water molecules, providing more electrons as well as hydrogen ions.

Light Energy to Chemical Energy

Excited electrons that have absorbed light energy are unstable. However, the highly organized electron carrier molecules embedded in chloroplast membranes order the flow of these electrons, directing them through electron transport chains (ETCs). At each transfer, small amounts of energy released by the electrons are captured and put to work or stored. Some is also lost as heat with each transfer, but overall the light reactions are extremely efficient at capturing light energy and transforming it into chemical energy.

Two sequential transport chains harvest the energy of excited electrons, as shown in Figure below.

(1) First, they pass down an ETC, which captures their energy and uses it to pump hydrogen ions by active transport into the thylakoids. These concentrated ions store potential energy by forming a chemiosmotic or electrochemical gradient &ndash a higher concentration of both positive charge and hydrogen inside the thylakoid than outside. (The gradient formed by the H + ions is known as a chemiosmotic gradient.) Picture this energy buildup of H + as a dam holding back a waterfall. Like water flowing through a hole in the dam, hydrogen ions &ldquoslide down&rdquo their concentration gradient through a membrane protein which acts as both ion channel and enzyme. As they flow, the ion channel/enzyme ATP synthase uses their energy to chemically bond a phosphate group to ADP, making ATP.

(2) Light re-energizes the electrons, and they travel down a second electron transport chain (ETC), eventually bonding hydrogen ions to NADP + to form a more stable energy storage molecule, NADPH. NADPH is sometimes called &ldquohot hydrogen,&rdquo and its energy and hydrogen atoms will be used to help build sugar in the second stage of photosynthesis.

Membrane architecture: The large colored carrier molecules form electron transport chains which capture small amounts of energy from excited electrons in order to store it in ATP and NADPH. Follow the energy pathways: light &rarr electrons &rarr NADPH (blue line) and light &rarr electrons &rarr concentrated H + &rarr ATP (red line). Note the intricate organization of the chloroplast.

NADPH and ATP molecules now store the energy from excited electrons &ndash energy which was originally sunlight &ndash in chemical bonds. Thus chloroplasts, with their orderly arrangement of pigments, enzymes, and electron transport chains, transform light energy into chemical energy. The first stage of photosynthesis &ndash light-dependent reactions or simply light reactions &ndash is complete.

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