Organic compound in the context of Isoprenoid

A pigment is a chemical compound that gives a substance or organism color, or is used by humans to add or alter color or change visual appearance. Pigments are completely or nearly insoluble and chemically unreactive in water or another medium; in contrast, dyes are colored substances which are soluble or go into solution at some stage in their use. Dyes are often organic compounds whereas pigments are often inorganic. Pigments of prehistoric and historic value include ochre, charcoal, and lapis lazuli. Biological pigments are compounds produced by living organisms that provide coloration.

Abiogenesis or the origin of life (sometimes called biopoesis) is the natural process by which life arises from non-living matter, such as simple organic compounds. The prevailing scientific hypothesis is that the transition from non-living to living entities on Earth was not a single event, but a process of increasing complexity involving the formation of a habitable planet, the prebiotic synthesis of organic molecules, molecular self-replication, self-assembly, autocatalysis, and the emergence of cell membranes. The transition from non-life to life has not been observed experimentally, but many proposals have been made for different stages of the process.

The study of abiogenesis aims to determine how pre-life chemical reactions gave rise to life under conditions strikingly different from those on Earth today. It uses tools from biology and chemistry, attempting a synthesis of many sciences. Life functions through the chemistry of carbon and water, and builds on four chemical families: lipids for cell membranes, carbohydrates such as sugars, amino acids for protein metabolism, and the nucleic acids DNA and RNA for heredity. A theory of abiogenesis must explain the origins and interactions of these classes of molecules.

A nutrient is a substance used by an organism to survive, grow and reproduce. The requirement for dietary nutrient intake applies to animals, plants, fungi and protists. Nutrients can be incorporated into cells for metabolic purposes or excreted by cells to create non-cellular structures such as hair, scales, feathers, or exoskeletons. Some nutrients can be metabolically converted into smaller molecules in the process of releasing energy such as for carbohydrates, lipids, proteins and fermentation products (ethanol or vinegar) leading to end-products of water and carbon dioxide. All organisms require water. Essential nutrients for animals are the energy sources, some of the amino acids that are combined to create proteins, a subset of fatty acids, vitamins and certain minerals. Plants require more diverse minerals absorbed through roots, plus carbon dioxide and oxygen absorbed through leaves. Fungi live on dead or living organic matter and meet nutrient needs from their host.

Different types of organisms have different essential nutrients. Ascorbic acid (vitamin C) is essential to humans and some animal species but most other animals and many plants are able to synthesize it. Nutrients may be organic or inorganic: organic compounds include most compounds containing carbon, while all other chemicals are inorganic. Inorganic nutrients include nutrients such as iron, selenium, and zinc, while organic nutrients include, protein, fats, sugars and vitamins.

Water pollution (or aquatic pollution) is the contamination of water bodies, with a negative impact on their uses. It is usually a result of human activities. Water bodies include lakes, rivers, oceans, aquifers, reservoirs and groundwater. Water pollution results when contaminants mix with these water bodies. Contaminants can come from one of four main sources. These are sewage discharges, industrial activities, agricultural activities, and urban runoff including stormwater. Water pollution may affect either surface water or groundwater. This form of pollution can lead to many problems. One is the degradation of aquatic ecosystems. Another is spreading water-borne diseases when people use polluted water for drinking or irrigation. Water pollution also reduces the ecosystem services such as drinking water provided by the water resource.

Sources of water pollution are either point sources or non-point sources. Point sources have one identifiable cause, such as a storm drain, a wastewater treatment plant, or an oil spill. Non-point sources are more diffuse. An example is agricultural runoff. Pollution is the result of the cumulative effect over time. Pollution may take many forms. One would is toxic substances such as oil, metals, plastics, pesticides, persistent organic pollutants, and industrial waste products. Another is stressful conditions such as changes of pH, hypoxia or anoxia, increased temperatures, excessive turbidity, or changes of salinity). The introduction of pathogenic organisms is another. Contaminants may include organic and inorganic substances. A common cause of thermal pollution is the use of water as a coolant by power plants and industrial manufacturers.

A fungus (pl.: fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as one of the traditional eukaryotic kingdoms, along with Animalia, Plantae, and either Protista or Protozoa and Chromista.

A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists is chitin in their cell walls. Fungi, like animals, are heterotrophs; they acquire their food by absorbing dissolved organic molecules, typically by secreting digestive enzymes into their environment. Fungi do not photosynthesize. Growth is their means of mobility, except for spores (a few of which are flagellated), which may travel through the air or water. Fungi are the principal decomposers in ecological systems. These and other differences place fungi in a single group of related organisms, named the Eumycota (true fungi or Eumycetes), that share a common ancestor (i.e. they form a monophyletic group), an interpretation that is also strongly supported by molecular phylogenetics. This fungal group is distinct from the structurally similar myxomycetes (slime molds) and oomycetes (water molds). The discipline of biology devoted to the study of fungi is known as mycology (from the Greek μύκης, mykes 'mushroom'). In the past, mycology was regarded as a branch of botany, although it is now known that fungi are genetically more closely related to animals than to plants.

Photosynthesis (/ˌfoʊtəˈsɪnθəsɪs/ FOH-tə-SINTH-ə-sis) is a system of biological processes by which photopigment-bearing autotrophic organisms, such as most plants, algae and cyanobacteria, convert light energy — typically from sunlight — into the chemical energy necessary to fuel their metabolism. The term photosynthesis usually refers to oxygenic photosynthesis, a process that releases oxygen as a byproduct of water splitting. Photosynthetic organisms store the converted chemical energy within the bonds of intracellular organic compounds (complex compounds containing carbon), typically carbohydrates like sugars (mainly glucose, fructose and sucrose), starches, phytoglycogen and cellulose. When needing to use this stored energy, an organism's cells then metabolize the organic compounds through cellular respiration. Photosynthesis plays a critical role in producing and maintaining the oxygen content of the Earth's atmosphere, and it supplies most of the biological energy necessary for complex life on Earth.

Some organisms also perform anoxygenic photosynthesis, which does not produce oxygen. Some bacteria (e.g. purple bacteria) uses bacteriochlorophyll to split hydrogen sulfide as a reductant instead of water, releasing sulfur instead of oxygen, which was a dominant form of photosynthesis in the euxinic Canfield oceans during the Boring Billion. Archaea such as Halobacterium also perform a type of non-carbon-fixing anoxygenic photosynthesis, where the simpler photopigment retinal and its microbial rhodopsin derivatives are used to absorb green light and produce a proton (hydron) gradient across the cell membrane, and the subsequent ion movement powers transmembrane proton pumps to directly synthesize adenosine triphosphate (ATP), the "energy currency" of cells. Such archaeal photosynthesis might have been the earliest form of photosynthesis that evolved on Earth, as far back as the Paleoarchean, preceding that of cyanobacteria (see Purple Earth hypothesis).

Lithification (from the Ancient Greek word lithos meaning 'rock' and the Latin-derived suffix -ific) is the process in which sediments compact under pressure, expel connate fluids, and gradually become solid rock. Essentially, lithification is a process of porosity destruction through compaction and cementation. Lithification includes all the processes which convert unconsolidated sediments into sedimentary rocks. Petrifaction, though often used as a synonym, is more specifically used to describe the replacement of organic material by silica in the formation of fossils.

A biogeochemical cycle, or more generally a cycle of matter, is the movement and transformation of chemical elements and compounds between living organisms, the atmosphere, and the Earth's crust. Major biogeochemical cycles include the carbon cycle, the nitrogen cycle and the water cycle. In each cycle, the chemical element or molecule is transformed and cycled by living organisms and through various geological forms and reservoirs, including the atmosphere, the soil and the oceans. It can be thought of as the pathway by which a chemical substance cycles (is turned over or moves through) the biotic compartment and the abiotic compartments of Earth. The biotic compartment is the biosphere and the abiotic compartments are the atmosphere, lithosphere and hydrosphere.

For example, in the carbon cycle, atmospheric carbon dioxide is absorbed by plants through photosynthesis, which converts it into organic compounds that are used by organisms for energy and growth. Carbon is then released back into the atmosphere through respiration and decomposition. Additionally, carbon is stored in fossil fuels and is released into the atmosphere through human activities such as burning fossil fuels. In the nitrogen cycle, atmospheric nitrogen gas is converted by plants into usable forms such as ammonia and nitrates through the process of nitrogen fixation. These compounds can be used by other organisms, and nitrogen is returned to the atmosphere through denitrification and other processes. In the water cycle, the universal solvent water evaporates from land and oceans to form clouds in the atmosphere, and then precipitates back to different parts of the planet. Precipitation can seep into the ground and become part of groundwater systems used by plants and other organisms, or can runoff the surface to form lakes and rivers. Subterranean water can then seep into the ocean along with river discharges, rich with dissolved and particulate organic matter and other nutrients.

In geology and mineralogy, a mineral or mineral species is, broadly speaking, a solid substance with a fairly well-defined chemical composition and a specific crystal structure that occurs naturally in pure form.

The geological definition of mineral normally excludes compounds that occur only in living organisms. However, some minerals are often biogenic (such as calcite) or organic compounds in the sense of chemistry (such as mellite). Moreover, living organisms often synthesize inorganic minerals (such as hydroxylapatite) that also occur in rocks.

Carbon (from Latin carbo 'coal') is a chemical element; it has symbol C and atomic number 6. It is nonmetallic and tetravalent—meaning that its atoms are able to form up to four covalent bonds due to its valence shell exhibiting 4 electrons. It belongs to group 14 of the periodic table. Carbon makes up about 0.025 percent of Earth's crust. Three isotopes occur naturally, C and C being stable, while C is a radionuclide, decaying with a half-life of 5,700 years. Carbon is one of the few elements known since antiquity.

Carbon is the 15th most abundant element in the Earth's crust, and the fourth most abundant element in the universe by mass after hydrogen, helium, and oxygen. Carbon's abundance, its unique diversity of organic compounds, and its unusual ability to form polymers at the temperatures commonly encountered on Earth, enables this element to serve as a common element of all known life. It is the second most abundant element in the human body by mass (about 18.5%) after oxygen.

Hydrogen is a chemical element; it has the symbol H and atomic number 1. It is the lightest and most abundant chemical element in the universe, constituting about 75% of all normal matter. Under standard conditions, hydrogen is a gas of diatomic molecules with the formula H₂, called dihydrogen, or sometimes hydrogen gas, molecular hydrogen, or simply hydrogen. Dihydrogen is colorless, odorless, non-toxic, and highly combustible. Stars, including the Sun, mainly consist of hydrogen in a plasma state, while on Earth, hydrogen is found as the gas H₂ (dihydrogen) and in molecules, such as in water and organic compounds. The most common isotope of hydrogen, H, consists of one proton, one electron, and no neutrons.

Hydrogen gas was first produced artificially in the 17th century by the reaction of acids with metals. Henry Cavendish, in 1766–1781, identified hydrogen gas as a distinct substance and discovered its property of producing water when burned: this is the origin of hydrogen's name, which means 'water-former' (from Ancient Greek: ὕδωρ, romanized: húdōr, lit. 'water', and γεννάω, gennáō, 'I bring forth'). Understanding the colors of light absorbed and emitted by hydrogen was a crucial part of the development of quantum mechanics.

Waxes are a diverse class of organic compounds that are lipophilic solids that are malleable near ambient temperatures. They include higher alkanes and lipids, typically with melting points above about 40 °C (104 °F), melting to give low viscosity liquids. Waxes are insoluble in water but soluble in nonpolar organic solvents such as hexane, benzene and chloroform. Natural waxes of various types are produced by plants and animals and occur in petroleum.

Cyanobacteria (/saɪˌænoʊbækˈtɪəriə/ sy-AN-oh-bak-TEER-ee-ə) are a group of autotrophic gram-negative bacteria of the phylum Cyanobacteriota that can obtain biological energy via oxygenic photosynthesis. The name "cyanobacteria" (from Ancient Greek κύανος (kúanos) 'blue') refers to their bluish green (cyan) color, which forms the basis of cyanobacteria's informal common name, blue-green algae.

Cyanobacteria are probably the most numerous taxon to have ever existed on Earth and the first organisms known to have produced oxygen, having appeared in the middle Archean eon and apparently originated in a freshwater or terrestrial environment. Their photopigments can absorb the red- and blue-spectrum frequencies of sunlight (thus reflecting a greenish color) to split water molecules into hydrogen ions and oxygen. The hydrogen ions are used to react with carbon dioxide to produce complex organic compounds such as carbohydrates (a process known as carbon fixation), and the oxygen is released as a byproduct. By continuously producing and releasing oxygen over billions of years, cyanobacteria are thought to have converted the early Earth's anoxic, weakly reducing prebiotic atmosphere, into an oxidizing one with free gaseous oxygen (which previously would have been immediately removed by various surface reductants), resulting in the Great Oxidation Event and the "rusting of the Earth" during the early Proterozoic, dramatically changing the composition of life forms on Earth. The subsequent adaptation of early single-celled organisms to survive in oxygenous environments likely led to endosymbiosis between anaerobes and aerobes, and hence the evolution of eukaryotes during the Paleoproterozoic.

In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. Hydrocarbons are examples of group 14 hydrides. Hydrocarbons are generally colourless and hydrophobic; their odor is usually faint, and may be similar to that of gasoline or lighter fluid. They occur in a diverse range of molecular structures and phases: they can be gases (such as methane and propane), liquids (such as hexane and benzene), low melting solids (such as paraffin wax and naphthalene) or polymers (such as polyethylene and polystyrene).

In the fossil fuel industries, hydrocarbon refers to naturally occurring petroleum, natural gas and coal, or their hydrocarbon derivatives and purified forms. Combustion of hydrocarbons is the main source of the world's energy. Petroleum is the dominant raw-material source for organic commodity chemicals such as solvents and polymers. Most anthropogenic (human-generated) emissions of greenhouse gases are either carbon dioxide released by the burning of fossil fuels, or methane released from the handling of natural gas or from agriculture.

A solvent (from the Latin solvō, "loosen, untie, solve") is a substance that dissolves a solute, resulting in a solution. A solvent is usually a liquid but can also be a solid, a gas, or a supercritical fluid. Water is a solvent for polar molecules, and the most common solvent used by living things; all the ions and proteins in a cell are dissolved in water within the cell.

Major uses of solvents are in paints, paint removers, inks, and dry cleaning. Specific uses for organic solvents are in dry cleaning (e.g. tetrachloroethylene); as paint thinners (toluene, turpentine); as nail polish removers and solvents of glue (acetone, methyl acetate, ethyl acetate); in spot removers (hexane, petrol ether); in detergents (citrus terpenes); and in perfumes (ethanol). Solvents find various applications in chemical, pharmaceutical, oil, and gas industries, including in chemical syntheses and purification processes

Fallow is a farming technique in which arable land is left without sowing for one or more vegetative cycles. The goal of fallowing is to allow the land to recover and store organic matter while retaining moisture and disrupting pest life cycles and soil borne pathogens by temporarily removing their hosts. Crop rotation systems typically called for some of a farmer's fields to be left fallow each year.

The increase in intensive farming, including the use of cover crops in lieu of fallow practices, has caused a loss of acreage of fallow land, as well as field margins, hedges, and wasteland. This has reduced biodiversity; fallows have been the primary habitat for farmland bird populations.

Oil shale is an organic-rich fine-grained sedimentary rock containing kerogen (a solid mixture of organic chemical compounds) from which liquid hydrocarbons can be produced. In addition to kerogen, general composition of oil shales constitutes inorganic substance and bitumens. Based on their deposition environment, oil shales are classified as marine, lacustrine and terrestrial oil shales. Oil shales differ from oil-bearing shales, shale deposits that contain petroleum (tight oil) that is sometimes produced from drilled wells. Examples of oil-bearing shales are the Bakken Formation, Pierre Shale, Niobrara Formation, and Eagle Ford Formation. Accordingly, shale oil produced from oil shale should not be confused with tight oil, which is also frequently called shale oil.

A 2016 estimate of global deposits set the total world resources of oil shale equivalent of 6.05 trillion barrels (962 billion cubic metres) of oil in place. Oil shale has gained attention as a potential abundant source of oil. However, the various attempts to develop oil shale deposits have had limited success. Only Estonia and China have well-established oil shale industries, and Brazil, Germany, and Russia utilize oil shale to some extent.