Photosynthesis

Photosynthesis is the conversion of light energy into chemical energy by living organisms. The raw materials are carbon dioxide and water; the energy source is sunlight; and the end-products are oxygen and (energy rich) carbohydrates, for example sucrose, glucose and starch. This process is arguably the most important biochemical pathway,since nearly all life on Earth either directly or indirectly depends on it. It is a complex process occurring in higher plants, phytoplankton, algae, as well as bacteria such as cyanobacteria. Photosynthetic organisms are also referred to as photoautotrophs.

Phototroph

Photoautotroph are organisms that carry out photosynthesis. Using energy from sunlight, carbon dioxide and water are converted into organic materials to be used in cellular functions such as biosynthesis and respiration. In an ecological context, they provide nutrition for all other forms of life (besides other autotrophs such as chemotrophs). In terrestrial environments plants are the predominant variety, while aquatic environments include a range of phototrophic organisms such as algae (e.g. kelp), protists (such as euglena) and bacteria (such as cyanobacteria). One product of this process is starch, which is a storage or reserve form of carbon, which can be used when light conditions are too poor to satisfy the immediate needs of the organism. Photosynthetic bacteria have a substance called bacteriochlorophyll, live in lakes and pools, and use the hydrogen from hydrogen sulfide instead of from water, for the chemical process. (The bacteriochlorophyll pigment absorbs light in the extreme UV and infra-red parts of the spectrum which is outside the range used by normal chlorophyll). Cyanobacteria live in fresh water, seas, soil and lichen, and use a plant-like photosynthesis.

Sunlight

Sunlight, in the broad sense, is the total spectrum of the electromagnetic radiation given off by the Sun. On Earth, sunlight is filtered through the atmosphere, and the solar radiation is obvious as daylight when the Sun is above the horizon. This is usually during the hours known as day. Near the poles in summer, sunlight also occurs during the hours known as night and in the winter at the poles sunlight may not occur at any time. When the direct radiation is not blocked by clouds, it is experienced as sunshine, a combination of bright light and heat. Radiant heat directly produced by the radiation of the sun is different from the increase in atmospheric temperature due to the radiative heating of the atmosphere by the sun's radiation. Sunlight may be recorded using a sunshine recorder. The World Meteorological Organization defines sunshine as direct irradiance from the Sun measured on the ground of at least 120 W·m−2.

Organism

In biology, an organism is an individual living system (such as animal, plant, fungus or micro-organism). In at least some form, all organisms are capable of reacting to stimuli, reproduction, growth and maintenance as a stable whole (after FA An organism may be unicellular or made up, as in humans, of many billions of cells grouped into specialized tissues and organs. The phrase complex organism describes any organism with more than one cell.
The term "organism" first appeared in the English language in 1701 and took on its current definition by 1834 (Oxford English Dictionary).
Based on cell type, organisms may be divided into the prokaryotic and eukaryotic groups. The prokaryotes are generally considered to represent two separate domains, called the Bacteria and Archaea, which are not closer to one another than to the eukaryotes. Eukaryotic organisms, with a membrane-bounded cell nucleus, also contain organelles, namely mitochondria and (in plants) plastids, generally considered to be derived from endosymbiotic bacteria.A similar symbiogenesis hypothesis has been proposed involving the origins of the cell nucleus, it is described as viral eukaryogenesis. Fungi, animals and plants are examples of species that are eukaryotes.

Chemical energy

Chemical energy is the energy due to associations of atoms in molecules and various other kinds of aggregates of matter. It may be defined as a work done by electric forces during re-arrangement of electric charges, electrons and protons, in the process of aggregation. If the chemical energy of a system decreases during a chemical reaction, the difference is transferred to the surroundings in some form (often heat or light); on the other hand if the chemical energy of a system increases as a result of a chemical reaction - the difference then is supplied by from the surroundings (usually again in form of heat or light). For example,

In plants

Plants absorb light primarily using the pigment chlorophyll, which is the reason that most plants have a green color. The function of chlorophyll is often supported by other accessory pigments such as carotenes and xanthophylls. Both chlorophyll and accessory pigments are contained in organelles (compartments within the cell) called chloroplasts. Although all cells in the green parts of a plant have chloroplasts, most of the energy is captured in the leaves. 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 uniformly 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.
Plants convert light in to chemical energy with a maximum photosynthetic efficiency of approximately 6% By comparison solar panels convert light into electric energy at a photosynthetic efficiency of approximately 10-20%. Actual plant's photosynthetic efficiency varies with the frequency of the light being converted, light intensity, temperature and proportion of CO2 in atmosphere.

Xanthophyll

Xanthophylls are yellow pigments from the carotenoid group. Their molecular structure is based on carotenes; contrary to the carotenes, some hydrogen atoms are substituted by hydroxyl groups and/or some pairs of hydrogen atoms are substituted by oxygen atoms. They are found in the leaves of most plants and are synthesized within the plastids. They are involved in photosynthesis along with green chlorophyll, which typically covers up the yellow except in autumn, when the chlorophyll is denatured by the cold.
In plants, xanthophylls are considered accessory pigments, along with anthocyanins, carotenes, and sometimes phycobiliproteins. Xanthophylls, along with carotenic pigments are seen when leaves turn orange in the autumn season.Animals cannot produce xanthophylls, and thus xanthophylls found in animals (e.g. in the eye) come from their food intake. The yellow color of chicken egg yolks also comes from ingested xanthophylls.
Xanthophylls are oxidized derivatives of carotenes. They contain hydroxyl groups and are more polar than carotenes; therefore, carotenes travel further than xanthophylls in paper chromatography.
The group of xanthophylls includes lutein, zeaxanthin, neoxanthin, violaxanthin, and α- and β-cryptoxanthin.
Xanthophyll has a chemical formula of C40H56O2.

Phycocyanin

Phycocyanin is a pigment from the light-harvesting phycobiliprotein family, along with allophycocyanin and phycoerythrin. It is an accessory pigment to chlorophyll. All phycobiliproteins are water soluble and therefore cannot exist within the membrane like carotenoids, but aggregate forming clusters that adhere to the membrane called phycobilisomes. Phycocyanin absorbs orange and red light, particularly near 620 nm (depending on which specific type it is), and emits fluorescence at about 650 nm (also depending on which type it is). Allophycocyanin absorbs and emits at longer wavelengths than Phycocyanin C or Phycocyanin R. Phycocyanins are found in Cyanobacteria (previously called blue-green algae). Phycobiliproteins have fluorescent properties that are used in immunoassay kits. Phycocyanin is from the Greek phyco meaning “algae” and cyanin is from the English word “cyan", which is derived from the Greek “kyanos" and means blue-green. The product Phycocyanin, produced by Spirulina, is used in the food and beverage industry as the colouring agent 'Lima Blue' and is found in sweets and ice cream.

Diatom

Diatoms are a major group of eukaryotic algae, and are one of the most common types of phytoplankton. Most diatoms are unicellular, although they can exist as colonies in the shape of filaments or ribbons (e.g. Fragillaria), fans (Meridion), zigzags (Tabellaria), or stellate colonies (Asterionella). A characteristic feature of diatom cells is that they are encased within a unique cell wall made of silica (hydrated silicon dioxide) called a frustule. These frustules show a wide diversity in form, some quite beautiful and ornate, but usually consist of two asymmetrical sides with a split between them, hence the group name. Fossil evidence suggests that they originated during, or before, the early Jurassic Period. Diatom communities are a popular tool for monitoring environmental conditions, past and present, and are commonly used in studies of water quality.

Microscopy

Microscopy mi·cros·co·py (Pronunciation[mahy-kros-kuh-pee, mahy-kruh-skoh-pee]) is the technical field of using microscopes to view samples or objects. There are three well-known branches of microscopy, optical, electron and scanning probe microscopy.
Optical and electron microscopy involve the diffraction, reflection, or refraction of electromagnetic radiation incident upon the subject of study, and the subsequent collection of this scattered radiation in order to build up an image. This process may be carried out by wide field irradiation of the sample (for example standard light microscopy and transmission electron microscopy) or by scanning of a fine beam over the sample (for example confocal microscopy and scanning electron microscopy). Scanning probe microscopy involves the interaction of a scanning probe with the surface or object of interest. The development of microscopy revolutionized biology and remains an essential tool in that science, along with many others.

In algae and bacteria

Algae come in multiple forms from multicellular organisms like kelp, to microscopic, single-cell organisms. Although they are not as complex as land plants, the biochemical process of photosynthesis is the same. Very much like plants, algae have chloroplasts and chlorophyll, but various accessory pigments are present in some algae such as phycocyanin, carotenes, and xanthophylls in green algae and phycoerythrin in red algae (rhodophytes), resulting in a wide variety of colors. Brown algae and diatoms contain fucoxanthol as their primary pigment. All algae produce oxygen, and many are autotrophic. However, some are heterotrophic, relying on materials produced by other organisms. For example, in coral reefs, there is a mutualistic relationship between zooxanthellae and the coral polyps.
Photosynthetic bacteria do not have chloroplasts (or any membrane-bound organelles). Instead, photosynthesis takes place directly within the cell. Cyanobacteria contain thylakoid membranes very similar to those in chloroplasts and are the only prokaryotes that perform oxygen-generating photosynthesis. In fact, chloroplasts are now considered to have evolved from an endosymbiotic bacterium, which was also an ancestor of and later gave rise to cyanobacterium. The other photosynthetic bacteria have a variety of different pigments, called bacteriochlorophylls, and do not produce oxygen. Some bacteria, such as Chromatium, oxidize hydrogen sulfide instead of water for photosynthesis, producing sulfur as waste.

Photosynthetic reaction centre

A photosynthetic reaction center is a complex of three proteins that is the site where molecular excitations originating from sunlight are transformed into a series of electron-transfer reactions. The reaction center proteins bind functional co-factors, chromophores or pigments such as chlorophyll and pheophytin molecules. These absorb light, promoting an electron to a higher energy level within a pigment. The free energy created is used to reduce a chain of electron acceptors which have subsequently lowered redox-potentials, and is critical for the production of chemical energy during photosynthesis.
Reaction centers are present in all green plants and in many bacteria and algae. Green plants have two reaction centers known as photosystem I and photosystem II and the structures of these centres are complex, involving a multisubunit protein. The reaction centre found in Rhodopseudomonas bacteria is currently better understood since it has fewer proteins than the examples in green plants.

Oxygen Catastrophe

The Oxygen Catastrophe was a massive environmental change believed to have happened during the Siderian period at the beginning of the Paleoproterozoic era, about 2.4 billion years ago. It is also called the Oxygen Crisis, Oxygen Revolution or The Great Oxidation.
When evolving life forms developed oxyphotosynthesis about 2.7 billion years ago, molecular oxygen was produced in large quantities. The plentiful oxygen eventually caused an ecological crisis, as oxygen was toxic to the anaerobic organisms living at the time.
However, it also provided a new opportunity. Despite recycling, life had remained energetically limited until the widespread availability of oxygen. This breakthrough in metabolic evolution greatly increased the free energy supply to living organisms, having a truly global environmental impactOxygen CatastropheOxygen Catastrophe

Amino acid

In chemistry, an amino acid is a molecule containing both amine and carboxyl functional groups. In biochemistry, this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent.In the alpha amino acids, the amino and carboxylate groups are attached to the same carbon, which is called the α–carbon. The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon. They can vary in size from just a hydrogen atom in glycine through a methyl group in alanine to a large heterocyclic group in tryptophan.
Beyond the amino acids that are found in all forms of life, many non-natural amino acids have vital roles in technology and industry. For example, the chelating agents EDTA and nitrilotriacetic acid are alpha amino acids that are important in the chemical industry.

Hydrogen

Hydrogen is the most abundant of the chemical elements, constituting roughly 75% of the universe's elemental mass.Stars in the main sequence are mainly composed of hydrogen in its plasma state. Elemental hydrogen is relatively rare on Earth, and is industrially produced from hydrocarbons such as methane, after which most elemental hydrogen is used "captively" (meaning locally at the production site), with the largest markets about equally divided between fossil fuel upgrading (e.g., hydrocracking) and ammonia production (mostly for the fertilizer market). Hydrogen may be produced from water using the process of electrolysis, but this process is presently significantly more expensive commercially than hydrogen production from natural gas.

Organic acid

An organic acid is an organic compound with acidic properties. The most common organic acids are the carboxylic acids whose acidity is associated with their carboxyl group -COOH. Sulfonic acids, containing the group OSO3H, are relatively stronger acids. The relative stability of the conjugate base of the acid determines its acidity. Other groups can also confer acidity, usually weakly: -OH, -SH, enol group, and the phenol group. In biological systems organic compounds containing only these groups are not generally referred to as organic acids.

Purple sulfur bacteria

The purple sulfur bacteria are a group of Proteobacteria capable of photosynthesis, collectively referred to as purple bacteria. They are anaerobic or microaerophilic, and are often found in hot springs or stagnant water. Unlike plants , algae, and cyanobacteria, they do not use water as their reducing agent, and so do not produce oxygen. Instead they use hydrogen sulfide, which is oxidized to produce granules of elemental sulfur. This in turn may be oxidized to form sulfuric acid.
The purple sulfur bacteria are divided into two families, the Chromatiaceae and Ectothiorhodospiraceae, which respectively produce internal and external sulfur granules, and show differences in the structure of their internal membranes. They make up the order Chromatiales, included in the gamma subdivision of the Proteobacteria. The genus Halothiobacillus is also included in the Chromatiales, in its own family, but it is not photosynthetic

Evolution

The ability to convert light energy to chemical energy confers a significant evolutionary advantage to living organisms. Early photosynthetic systems, such as those from green and purple sulfur and green and purple non-sulfur bacteria, are thought to have been anoxygenic, using various molecules as electron donors. Green and purple sulfur bacteria are thought to have used hydrogen and sulfur as an electron donor. Green nonsulfur bacteria used various amino and other organic acids. Purple nonsulfur bacteria used a variety of non-specific organic molecules. The use of these molecules is consistent with the geological evidence that the atmosphere was highly reduced at that time.
Fossils of what are thought to be filamentous photosynthetic organisms have been dated at 3.4 billion years old.[
Oxygen in the atmosphere exists due to the evolution of oxygenic photosynthesis, 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 into molecular oxygen by the absorption of a photon by the photosynthetic reaction center

Symbiosis

The term symbiosis (from the Greek: συμ, sym, "with"; and βίοσίς, biosis, "living") commonly describes close and often long-term interactions between different biological species. The term was first used in 1879 by the German mycologist, Heinrich Anton de Bary, who defined it as: "the living together of unlike organisms".
The definition of symbiosis is in flux and the term has been applied to a wide range of biological interactions. The symbiotic relationship may be categorized as being mutualistic, parasitic, or commensal in nature Others define it more narrowly, as only those relationships from which both organisms benefit, in which case it would be synonymous with mutualism.
Symbiotic relationships included those associations in which one organisms lives on another (ectosymbiosis, such as mistletoe), or where one partner lives inside another (endosymbiosis, such as lactobacilli and other bacteria in humans or zooxanthelles in corals). Symbiotic relationships may be either obligate, i.e., necessary to the survival of at least one of the organisms involved, or facultative, where the relationship is beneficial but not essential to survival of the organisms.

Fusion gene

when a fusion gene is expreA fusion gene is a hybrid gene formed from two previously separate genes. It can occur as the result of a translocation, interstitial deletion, or chromosomal inversion. The fusion of two genes is often taken as evidence that these genes have related function.Often, fusion genes are oncogenes; examples include BCR-ABL, FIG-ROS, and TEL-JAK2.
Biologists may also deliberately create fusion genes for research purposes. For example, by creating a fusion gene of a protein of interest and green fluorescent protein, the protein of interest may be observed in cells or tissue using fluorescence microscopy. The protein synthesized ssed is called a fusion protein.

Eukaryote

Animals, plants, fungi, and protists are eukaryotes (IPA: /juːˈkærɪɒt/ or IPA: /-oʊt/), organisms whose cells are organized into complex structures enclosed within membranes. The defining membrane-bound structure which differentiates eukaryotic cells from prokaryotic cells is the nucleus. The presence of a nucleus gives these organisms their name, which comes from the Greek ευ, meaning "good/true", and κάρυον, "nut". Many eukaryotic cells contain other membrane-bound organelles such as mitochondria, chloroplasts and Golgi bodies. Eukaryotes often have unique flagella made of microtubules in a 9+2 arrangement.
Cell division in eukaryotes is different from organisms without a nucleus (prokaryotes). It involves separating the duplicated chromosomes, through movements directed by microtubules. There are two types of division processes. In mitosis, one cell divides to produce two genetically-identical cells. In meiosis, which is required in sexual reproduction, one diploid cell (having two instances of each chromosome, one from each parent) undergoes recombination of each pair of parental chromosomes, and then two stages of cell division, resulting in four haploid cells (gametes). Each gamete has just one complement of chromosomes, each a unique mix of the corresponding pair of parental chromosomes.
Eukaryotes appear to be monophyletic, and so make up one of the three domains of life. The two other domains, bacteria and archaea, are prokaryotes, and have none of the above features. But eukaryotes do share some aspects of their biochemistry with archaea, and so are grouped with archaea in the clade Neomura

Mitochondrion

In cell biology, a mitochondrion (plural mitochondria) is a membrane-enclosed organelle found in most eukaryotic cells.These organelles range from 1–10 micrometers (μm) in size. Mitochondria are sometimes described as "cellular power plants" because they generate most of the cell's supply of adenosine triphosphate (ATP), used as a source of chemical energy. In addition to supplying cellular energy, mitochondria are involved in a range of other processes, such as signaling, cellular differentiation, cell death, as well as the control of the cell cycle and cell growth.Mitochondria have been implicated in several human diseases and may play a role in the aging process. The word mitochondrion comes from the Greek μίτος or mitos, thread + χονδρίον or khondrion, granule. Their ancestry is not fully understood, but, according to the endosymbiotic theory, mitochondria are descended from ancient bacteria, which were engulfed by the ancestors of eukaryotic cells more than a billion years ago.

Origin of chloroplasts

with photosynthetic bacteria including a circular chromosome, prokaryotic-type ribosomes, and similar proteins in the photosynthetic reaction center.
The endosymbiotic theory suggests that photosynthetic bacteria were acquired (by endocytosis or gene fusion) by early eukaryotic cells to forIn plants the process of photosynthesis occurs in organelles called chloroplasts. Chloroplasts have many similarities m the first plant cells. In other words, chloroplasts may simply be primitive photosynthetic bacteria adapted to life inside plant cells, whereas plants themselves have not actually evolved photosynthetic processes on their own. Another example of this can be found in complex plants and animals, including humans, whose cells depend upon mitochondria as their energy source; mitochondria are thought to have evolved from endosymbiotic bacteria, related to modern Rickettsia bacteria. Both chloroplasts and mitochondria actually have their own DNA, separate from the nuclear DNA of their animal or plant host cells.
This contention is supported by the finding that the marine molluscs Elysia viridis and Elysia chlorotica seem to maintain a symbiotic relationship with chloroplasts from algae with similar RDA structures that they encounter. However, they do not transfer these chloroplasts to the next generations.

Proterozoic

The geologic record of the Proterozoic is much better than that for the preceding Archean. In contrast to the deep-water deposits of the Archean, the Proterozoic features many strata that were laid down in extensive shallow epicontinental seas; furthermore, many of these rocks are less metamorphosed than Archean-age ones, and plenty are unaltered.Study of these rocks show that the eon featured massive, rapid continental accretion (unique to the Proterozoic), supercontinent cycles, and wholly-modern orogenic activity.
The first known glaciations occurred during the Proterozoic, one began shortly after the beginning of the eon, while there were at least four during the Neoproterozoic, climaxing with the Snowball Earth of the Varangian glaciation

Nitrogen fixation

Nitrogen fixation is the process by which nitrogen is taken from its natural, relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds (such as ammonia, nitrate and nitrogen dioxide)
Nitrogen fixation is performed naturally by a number of different prokaryotes, including bacteria, actinobacteria, and certain types of anaerobic bacteria. Microorganisms that fix nitrogen are called diazotrophs. Some higher plants, and some animals (termites), have formed associations with diazotrophs.
Nitrogen fixation also occurs as a result of non-biological processes. These include lightning, industrially through the Haber-Bosch Process, and combustion.
Biological nitrogen fixation was discovered by the Dutch microbiologist Martinus Beijerinck.

Cyanobacteria and the evolution of photosynthesis

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

Carotenoids

Carotenoids are organic pigments that are naturally occurring in chromoplasts of plants and some other photosynthetic organisms like algae, some types of fungus and some bacteria. There are over 600 known carotenoids; they are split into two classes, xanthophylls and carotenes. They absorb blue light. Carotenoids serve two key roles in plants and algae: they absorb light energy for use in photosynthesis, and they protect chlorophyll from photodamage. In humans, carotenoids such as beta-carotene are a precursor to vitamin A, apigment essential for good vision, and carotenoids can also act as antioxidants.
People consuming diets rich in carotenoids from natural foods, such as fruits and vegetables, are healthier and have lower mortality from a number of chronic illnesses. However, a recent meta-analysis of 68 reliable antioxidant supplementation experiments involving a total of 232,606 individuals concluded that consuming additional beta-carotene from supplements is unlikely to be beneficial and may actually be harmful..

Action Spectrum

An action spectrum is the rate of a physiological activity plotted against wavelength of light. It shows which wavelength of light is most effectively used in a specific chemical reaction. Some reactants are able to use specific wavelengths of light more effectively to complete their reactions. For example, chlorophyll is much more efficient at using the red and blue spectrums of light to carry out photosynthesis. Therefore, the action spectrum graph would show spikes above the wavelengths representing the colors red and blue.

wavelength

In physics wavelength is the distance between repeating units of a propagating wave of a given frequency. It is commonly designated by the Greek letter lambda Examples of wave-like phenomena are light, water waves, and sound waves.

Light to chemical energy

The light energy is converted to chemical energy using the light-dependent reactions. This chemical energy production is about 5-6% efficient, with the majority of the light that strikes a plant reflected and not absorbed.However, of the energy that is absorbed, approximately 30-50% is captured as chemical energy.The products of the light-dependent reactions are ATP from photophosphorylation and NADPH from photoreduction. Both are then utilized as an energy source for the light-independent reactions.
Not all wavelengths of light can support photosynthesis. The photosynthetic action spectrum depends on the type of accessory pigments present. For example, in green plants, the action spectrum resembles the absorption spectrum for chlorophylls and carotenoids with peaks for violet-blue and red light. In red algae, the action spectrum overlaps with the absorption spectrum of phycobilins for blue-green light, which allows these algae to grow in deeper waters that filter out the longer wavelengths used by green plants. The non-absorbed part of the light spectrum is what gives photosynthetic organisms their color (e.g., green plants, red algae, purple bacteria) and is the least effective for photosynthesis in the respective organisms.

antenna complex

molecules to oxygen, protons and electrons.The light-harvesting (or antenna) complex of plants is an array of protein and chlorophyll molecules embedded in the thylakoid membrane which transfer light energy to one chlorophyll a molecule at the reaction center of a photosystem.
The antenna pigments are predominantly chlorophyll a, chlorophyll b and carotenoids. Their absorption spectra are non-overlapping in order to broaden the range of light that can be absorbed in photosynthesis. The carotenoids have another role as an antioxidant to prevent photo-oxidative damage of chlorophyll molecules. Each antenna complex has between 250 and 400 pigment molecules and the energy they absorb is shuttled by resonance energy transfer to a specialized chlorophyll-protein complex known as the reaction center of each photosystem. The reaction center initiates a complex series of chemical reactions that capture energy in the form of chemical bonds.
For photosystem II, when either of the two chorophyll a molecules at the reaction center absorb energy, an electron is excited and transferred to an electron acceptor molecule, phaeophytin, leaving the chlorophyll a in an oxidized state. The oxidised chlorophyll a replaces the electrons by photolysis that involves the reduction of water

thylakoid

The thylakoid membrane is the site of the light-dependent reactions of photosynthesis with the photosynthetic pigments embedded directly in the membrane. It is an alternating pattern of dark and light bands mesasuring each 0.001 μm.The thylakoid lipid bilayer shares characteristic features with prokaryotic membranes and the inner chloroplast membrane. For example, acidic lipids can be found in thylakoid membranes, cyanobacteria and other photosynthetic bacteria and are involved in the functional integrity of the photosystems.The thylakoid membranes of higher plants are composed primarily of phospholipids and galactolipids that are asymmetrically arranged along and across the membranes.The lipids for the thylakoid membranes are synthesized in a complex pathway involving exchange of lipid precursors between the endoplasmic reticulum and inner membrane of the plastid envelope and transported from the inner membrane to the thylakoids via vesicles.

z-scheme

In plants, light-dependent reactions occur in the thylakoid membranes of the chloroplasts and use light energy to synthesize ATP and NADPH. The light-dependent reaction has two forms; cyclic and non-cyclic reaction. 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). When a chlorophyll molecule at the core of the photosystem II reaction center obtains sufficient excitation energy from the adjacent antenna pigments, an electron is transferred to the primary electron-acceptor molecule, Pheophytin, through a process called Photoinduced charge separation. These electrons are shuttled through an electron transport chain, the so called Z-scheme shown in the diagram, that initially functions to generate a chemiosmotic potential across the membrane. An ATP synthase enzyme uses the chemiosmotic potential to make ATP during photophosphorylation, whereas NADPH is a product of the terminal redox reaction in the Z-scheme. The electron enters the Photosystem I molecule. The electron is excited due to the light absorbed by the photosystem. A second electron carrier accepts the electron, which again is passed down lowering energies of electron acceptors. The energy created by the electron acceptors is used to move hydrogen ions across the thylakoid membrane into the lumen. The electron is used to reduce the co-enzyme NADP, which has functions in the light-independent reaction. The cyclic reaction is similar to that of the non-cyclic, but differs in the form 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 back to photosystem I, from where it was emitted, hence the name cyclic reaction.

cellular respiration

Cellular respiration describes the metabolic reactions and processes that take place in a cell or across the cell membrane to get biochemical energy from fuel molecules and the release of the cells' waste products. Energy can be released by the oxidation of multiple fuel molecules and is stored as "high-energy" carriers. The reactions involved in respiration are catabolic reactions in metabolism.
Fuel molecules commonly used by cells in respiration include glucose, amino acids and fatty acids, and a common oxidizing agent (electron acceptor) is molecular oxygen (O2). There are organisms, however, that can respire using other organic molecules as electron acceptors instead of oxygen. Organisms that use oxygen as a final electron acceptor in respiration are described as aerobic, while those that do not are referred to as anaerobic.
The energy released in respiration is used to synthesize molecules that act as a chemical storage of this energy. One of the most widely used compounds in a cell is adenosine triphosphate (ATP) and its stored chemical energy can be used for many processes requiring energy, including biosynthesis, locomotion or transportation of molecules across cell membranes. Because of its ubiquitous nature, ATP is also known as the "universal energy currency", since the amount of it in a cell indicates how much energy is available for energy-consuming processes.

enzymes

Enzymes are biomolecules that catalyze.chemical reactions. Almost all enzymes are proteins. In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, the products. Almost all processes in a biological cell need enzymes in order to occur at significant rates. Since enzymes are extremely selective for their substrates and speed up only a few reactions from among many possibilities, the set of enzymes made in a cell determines which metabolic pathways occur in that cell.

tyrosine

Aside from being a proteogenic amino acid, tyrosine has a special role by virtue of the phenol functionality. It occurs in proteins that are part of signal transduction processes. It functions as a receiver of phosphate groups that are transferred by way of protein kinases (so-called receptor tyrosine kinases). Phosphorylation of the hydroxyl group changes the activity of the target protein.
A tyrosine residue also plays an important role in photosynthesis. In chloroplasts (photosystem II), it acts as an electron donor in the reduction of oxidized chlorophyll. In this process, it undergoes deprotonation of its phenolic OH-group. This radical is subsequently reduced in the photosystem II by the four core manganese cluster.

oxygen

Oxygen is the element with atomic number 8 and represented by the symbol O. It is a member of the chalcogen group on the periodic table, and is a highly reactive nonmetallic period 2 element that readily forms compound(notably oxides) with almost all other elements. At standard temperature and pressure two atoms of the element bind to form dioxygen, a colorless, odorless, tasteless diatomic gas with the formula O2. Oxygen is the third most abundant element in the universe by mass after hydrogen and heli and the most abundant element by mass in the Earth's crust. Oxygen constitutes 88.8% of the mass of water and 20.9% of the volume of air.
All major classes of structural molecules in living organisms, such as proteins, carbohydrates, and fats, contain oxygen, as do the major inorganic compounds that comprise animal shells, teeth, and bone. Oxygen in the form of O2 is produced from water by cyanobacteria, algae and plants during photosynthesis and is used in cellular respiration for all complex life. Oxygen is toxic to anaerobic organisms, which were the dominant form of early life on Earth until O2 began to accumulate in the atmosphere 2.5 billion years ago. Another form (allotrope) of oxygen, ozone (O3), helps protect the biosphere from ultraviolet radiation with the high-altitude ozone layer, but is a pollutant near the surface where it is a by-product of smog.

photosystems 1

Photosystems protein complexes involved in photosynthesis. They are found in the thylakoid membranes of plants, algae and cyanobacteria (in plants and algae these are located in the chloroplasts), or in the cytoplasmic membrane of photosynthetic bacteria. A photosystem (or Reaction Center) is an enzyme which uses light to reduce molecules. This membrane protein complex is made of several subunits and contains numerous cofactors. In the photosynthetic membranes, reaction centers provide the driving force for the bioenergetic electron and proton transfer chain. When light is absorbed by a reaction center (either directly or passed by neighbouring pigment-antennae), a series of oxido-reduction reactions is initiated, leading to the reduction of a terminal acceptor. Two families of photosystems exist: type I reaction centers (like photosystem I (P700) in chloroplasts and in green-sulphur bacteria) and type II reaction centers (like photosystem II (P680) in chloroplasts and in non-sulphur purple bacteria). Each photosystem can be identified by the wavelength of light to which it is most reactive (700 and 680 nanometers, respectively for PSI and PSII in chloroplasts), and the type of terminal electron acceptor. Type I photosystems use ferredoxin-like iron-sulfur cluster proteins as terminal electron acceptors, while type II photosystems ultimately shuttle electrons to a quinone terminal electron acceptor. One has to note that both reaction center types are present in chloroplasts and cyanobacteria, working together to form a unique photosynthetic chain able to extract electrons from water, creating oxygen as a byproduct.

water photolysis

The NADPH is the main reducing agent in chloroplasts, providing a source of energetic electrons to other reactions. Its production leaves chlorophyll with a deficit of electrons (oxidized), which must be obtained from some other reducing agent. The excited electrons lost from chlorophyll in photosystem I are replaced from the electron transport chain by plastocyanin. However, since photosystem II includes the first steps of the Z-scheme, an external source of electrons is required to reduce its oxidized chlorophyll a molecules. The source of electrons in green-plant and cyanobacterial photosynthesis 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 electron yielded in each step is transferred to a redox-active tyrosine residue that then reduces the photoxidized paired-chlorophyll a species called P680 that serves as the primary (light-driven) electron donor in the photosystem II reaction center. The oxidation of water is catalyzed in photosystem II by a redox-active structure that contains four manganese ions; this oxygen-evolving complex binds two water molecules and stores the four oxidizing equivalents that are required to drive the water-oxidizing reaction. Photosystem II is the only known biological enzyme that carries out this oxidation of water. The hydrogen ions contribute to the transmembrane chemiosmotic potential that leads to ATP synthesis. Oxygen is a waste product of light-independent reactions, but the majority of organisms on Earth use oxygen for cellular respiration, including photosynthetic organisms.

Quantum coherence

In quantum mechanics, all objects have wave-like properties (see de Broglie waves). For instance, in Young's double-slit experiment electrons can be used in the place of light waves. Each electron can go through either slit and hence has two paths that it can take to a particular final position. In quantum mechanics these two paths interfere. If there is destructive interference, the electron never arrives at that particular positionQuantum coherenc Quantum coherence. This ability to interfere is called quantum coherence.

The quantum description of perfectly coherent paths is called a pure state, in which the two paths are combined in a superposition. The correlation between the two particles exceeds what would be predicted for classical correlation alone (see Bell's inequalities). If this two-particle system is decohered (which would occur in a measurement via Einselection), then there is no longer any phase relationship between the two states. The quantum description of imperfectly coherent paths is called a mixed state, described by a density matrix and is entirely analogous to a classical system of mixed probabilities (the correlations are classical).

Quantum mechanical effects

Through photosynthesis, sunlight energy is transferred to molecular reaction centers for conversion into chemical energy with nearly 100-percent efficiency. The transfer of the solar energy takes place almost instantaneously, so little energy is wasted as heat. However, only 43% of the total solar incident radiation can be used (only light in the range 400-700 nm), 20% of light is blocked by canopy, and plant respiration requires about 33% of the stored energy, which brings down the actual efficiency of photosynthesis to about 6.6%.
A study led by researchers with the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California at Berkeley suggests that long-lived wavelike electronic quantum coherence plays an important part in this instantaneous transfer of energy by allowing the photosynthetic system to simultaneously try each potential energy pathway and choose the most efficient option. Results of the study are presented in the April 12, 2007 issue of the journal Nature.

halophiles

Halophiles are extremophiles that thrive in environments with very high concentrations of salt (at least 2 M, approximately ten times the salt level of ocean water). The name comes from Greek for "salt-loving". Some halophiles are classified into the Archaea domain, but there are also bacterial halophiles and some eukaryota, such as the alga Dunaliella salina. Some well-known species give off a red color from carotenoid compounds. Such species contain the photosynthetic pigment bacteriorhodopsin. Halophiles are categorized slight, moderate or extreme, by the extent of their halotolerance.High salinity represents an extreme environment that relatively few organisms have been able to adapt to and occupy. Most halophilic and all halotolerant organisms expend energy to exclude salt from their cytoplasm to avoid protein aggregation (‘salting out’). In order to survive the high salinities, halophiles employ two differing strategies to prevent desiccation through osmotic movement of water out of their cytoplasm. Both strategies work by increasing the internal osmolarity of the cell. In the first, that employed by the majority of Bacteria, some Archaea, yeasts, algae and fungi, organic compounds are accumulated in the cytoplasm – these are known as compatible solutes. These can be synthesised again or accumulated from the environment[1]. The most common compatible solutes are neutral or zwitterionic and include amino acids, sugars, polyols, betaines and ectoines, as well as derivatives of some of these compounds

cyanobacteria

Cyanobacteria, also known as blue-green algae, blue-green bacteria or Cyanophyta, is a phylum of bacteria that obtain their energy through photosynthesis. The name "cyanobacteria" comes from the color of the bacteria. They are a significant component of the marine nitrogen cycle and an important primary producer in many areas of the ocean, but are also found on land.
Stromatolites of fossilized oxygen-producing cyanobacteria have been found from 2.8 billion years ago.The ability of cyanobacteria to perform oxygenic photosynthesis is thought to have converted the early reducing atmosphere into an oxidizing one, which dramatically changed the life forms on Earth and provoked an explosion of biodiversity. Chloroplasts in plants and eukaryotic algae have evolved from cyanobacteria.

photosystems

Photosystems are protein complexes involved in photosynthesis. They are found in the thylakoid membranes of plants, algae and cyanobacteria (in plants and algae these are located in the chloroplasts), or in the cytoplasmic membrane of photosynthetic bacteria. A photosystem (or Reaction Center) is an enzyme which uses light to reduce molecules. This membrane protein complex is made of several subunits and contains numerous cofactors. In the photosynthetic membranes, reaction centers provide the driving force for the bioenergetic electron and proton transfer chain. When light is absorbed by a reaction center (either directly or passed by neighbouring pigment-antennae), a series of oxido-reduction reactions is initiated, leading to the reduction of a terminal acceptor. Two families of photosystems exist: type I reaction centers (like photosystem I (P700) in chloroplasts and in green-sulphur bacteria) and type II reaction centers (like photosystem II (P680) in chloroplasts and in non-sulphur purple bacteria). Each photosystem can be identified by the wavelength of light to which it is most reactive (700 and 680 nanometers, respectively for PSI and PSII in chloroplasts), and the type of terminal electron acceptor. Type I photosystems use ferredoxin-like iron-sulfur cluster proteins as terminal electron acceptors, while type II photosystems ultimately shuttle electrons to a quinone terminal electron acceptor. One has to note that both reaction center types are present in chloroplasts and cyanobacteria, working together to form a unique photosynthetic chain able to extract electrons from water, creating oxygen as a byproduct.

bacteria variation

The concept that oxygen production is not directly associated with the fixation of carbon dioxide was first proposed by Cornelis Van Niel in the 1930s, who studied photosynthetic bacteria. Aside from the cyanobacteria, bacteria only have one photosystem and use reducing agents other than water. They get electrons from a variety of different inorganic chemicals including sulfide or hydrogen, so for most of these bacteria oxygen is not produced.
Others, such as the halophiles (an Archaea), produced so-called purple membranes where the bacteriorhodopsin could harvest light and produce energy. The purple membranes was one of the first to be used to demonstrate the chemiosmotic theory: light hit the membranes and the pH of the solution that contained the purple membranes dropped as protons were pumping out of the membrane.

metabolism

Metabolism is the set of chemical reactions that occur in living organisms in order to maintain life. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories. Catabolism breaks down large molecules, for example to harvest energy in cellular respiration. Anabolism, on the other hand, uses energy to construct components of cells such as proteins and nucleic acids.
The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed into another by a sequence of enzymes. Enzymes are crucial to metabolism because they allow organisms to drive desirable but thermodynamically unfavorable reactions by coupling them to favorable ones. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or signals from other cells

Protein

Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by a gene and encoded in the genetic code. Although this genetic code specifies 20 "standard" amino acids plus selenocysteine and - in certain archaea - pyrrolysine, the residues in a protein are sometimes chemically altered in post-translational modification: either before the protein can function in the cell, or as part of control mechanisms. Proteins can also work together to achieve a particular function, and they often associate to form stable complexes

Carbohydrates

Carbohydrates (from 'hydrates of carbon') or saccharides (Greek σάκχαρον meaning "sugar") are the most abundant of the four major classes of biomolecules, which also include proteins, lipids and nucleic acids. They fill numerous roles in living things, such as the storage and transport of energy (starch, glycogen) and structural components (cellulose in plants, chitin in animals). Additionally, carbohydrates and their derivatives play major roles in the working process of the immune system, fertilization, pathogenesis, blood clotting, and development.
Chemically, carbohydrates are simple organic compounds that are aldehydes or ketones with many hydroxyl groups added, usually one on each carbon atom that is not part of the aldehyde or ketone functional group. The basic carbohydrate units are called monosaccharides, such as glucose, galactose, and fructose. The general stoichiometric formula of an unmodified monosaccharide is (C·H2O)n, where n is any number of three or greater; however, many molecules with formulae that differ slightly from this are still called carbohydrates and other compounds that possess formulae that agree with this general rule may not be in fact carbohydrates (eg formaldehyde). Despite the inexactness of the term, "carbohydrate" remains a useful descriptive name and with a little experience even a novice will soon become aware of what is, and is not, a carbohydrate. Monosaccharides can be linked together in almost limitless ways. Many carbohydrates contain one or more modified monosaccharide units that have had one or more groups replaced or removed. For example, deoxyribose, a component of DNA, is a modified version of ribose; chitin is composed of repeating units of N-acetylglucosamine, a nitrogen-containing form of glucose. The names of carbohydrates often end in the suffix -ose.

Carbon fixation

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

xerophyte

A xerophyte or xerophytic organism is a plant which is able to survive in an ecosystem with little available water or moisture, usually in environments where potential evapotranspiration exceeds precipitation for all or part of the growing season. Plants like the cactus and other succulents are typically found in deserts where low rainfall amounts are the norm, but xerophytes such as the bromeliads can also be found in moist habitats such as tropical forests, exploiting niches where water supplies are limited or too intermittent for mesophytic plants. Plants that live under arctic conditions may also have a need for xerophytic adaptations, as water is unavailable for uptake when the ground is frozen.
Adaptations of xerophytes include reduced permeability of the epidermal layer, stomata and cuticle to maintain optimal amounts of water in the tissues by reducing transpiration, adaptations of the root system to acquire water from deep underground sources or directly from humid atmospheres (as in epiphytic orchids), and succulence, or storage of water in swollen stems, leaves or root tissues. The typical morphological consequences of these adaptations are collectively called xeromorphisms.

Photorespiration

Photorespiration(or "photo-respiration")is the alternate pathway for production of glyceraldehyde 3-phosphate (G3P) by RuBisCO, the main enzyme of the light-independent reactions of photosynthesis (also known as the Calvin cycle or the Primary Carbon Reduction (PCR) cycle). Although RuBisCO favors carbon dioxide to oxygen,(approximately 3 carboxylations per oxygenation), oxygenation of RuBisCO occurs frequently, producing a glycolate and a glycerate. This usually occurs when oxygen levels are high; for example, when the stomata (tiny pores on the leaf) are closed to prevent water loss on dry days. It involves three cellular organelles: chloroplasts, peroxisomes, and mitochondria

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 oxygen concentration is high, RuBisCO will bind oxygen instead of carbon dioxide. This process, called photorespiration, uses energy, but does not make sugar.
RuBisCO oxygenase activity is disadvantageous to plants for several reasons:
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.
Phosphoglycolate is quickly metabolized to glycolate that is toxic to a plant at a high concentration; it inhibits photosynthesis.
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.
A highly-simplified summary is:
2 glycolate + ATP → 3-phophoglycerate + carbon dioxide + ADP +NH3
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.