1.
Nitrogen
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Nitrogen is a chemical element with symbol N and atomic number 7. It was first discovered and isolated by Scottish physician Daniel Rutherford in 1772, although Carl Wilhelm Scheele and Henry Cavendish had independently done so at about the same time, Rutherford is generally accorded the credit because his work was published first. Nitrogen is the lightest member of group 15 of the periodic table, the name comes from the Greek πνίγειν to choke, directly referencing nitrogens asphyxiating properties. It is an element in the universe, estimated at about seventh in total abundance in the Milky Way. At standard temperature and pressure, two atoms of the element bind to form dinitrogen, a colourless and odorless diatomic gas with the formula N2, dinitrogen forms about 78% of Earths atmosphere, making it the most abundant uncombined element. Nitrogen occurs in all organisms, primarily in amino acids, in the nucleic acids, the human body contains about 3% nitrogen by mass, the fourth most abundant element in the body after oxygen, carbon, and hydrogen. The nitrogen cycle describes movement of the element from the air, into the biosphere and organic compounds, many industrially important compounds, such as ammonia, nitric acid, organic nitrates, and cyanides, contain nitrogen. The extremely strong bond in elemental nitrogen, the second strongest bond in any diatomic molecule. Synthetically produced ammonia and nitrates are key industrial fertilisers, and fertiliser nitrates are key pollutants in the eutrophication of water systems. Apart from its use in fertilisers and energy-stores, nitrogen is a constituent of organic compounds as diverse as Kevlar used in high-strength fabric, Nitrogen is a constituent of every major pharmacological drug class, including antibiotics. Many notable nitrogen-containing drugs, such as the caffeine and morphine or the synthetic amphetamines. Nitrogen compounds have a long history, ammonium chloride having been known to Herodotus. They were well known by the Middle Ages, alchemists knew nitric acid as aqua fortis, as well as other nitrogen compounds such as ammonium salts and nitrate salts. The mixture of nitric and hydrochloric acids was known as aqua regia, celebrated for its ability to dissolve gold, the discovery of nitrogen is attributed to the Scottish physician Daniel Rutherford in 1772, who called it noxious air. Though he did not recognise it as a different chemical substance, he clearly distinguished it from Joseph Blacks fixed air. The fact that there was a component of air that does not support combustion was clear to Rutherford, Nitrogen was also studied at about the same time by Carl Wilhelm Scheele, Henry Cavendish, and Joseph Priestley, who referred to it as burnt air or phlogisticated air. Nitrogen gas was inert enough that Antoine Lavoisier referred to it as air or azote, from the Greek word άζωτικός. In an atmosphere of nitrogen, animals died and flames were extinguished
2.
Triple bond
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A triple bond in chemistry is a chemical bond between two atoms involving six bonding electrons instead of the usual two in a covalent single bond. The most common triple bond, that between two atoms, can be found in alkynes. Other functional groups containing a triple bond are cyanides and isocyanides, some diatomic molecules, such as dinitrogen and carbon monoxide are also triple bonded. In skeletal formula the triple bond is drawn as three parallel lines between the two connected atoms, triple bonds are stronger and shorter than the equivalent single bonds or double bonds, with a bond order of three. The types of bonding can be explained through in terms of orbital hybridization, in the case of acetylene each carbon atom has two sp orbitals and two p-orbitals. The two sp orbitals are linear with 180° angles and occupy the x-axis, the p-orbitals are perpendicular on the y-axis and the z-axis. When the carbon atoms approach each other the sp orbitals overlap to form a sigma bond. At the same time the approach and together they form a pz-pz pi-bond. Likewise, the pair of py-orbitals form a py-py pi-bond. The result is formation of one bond and two pi bonds. In the bent bond model the triple bond can also formed by the overlapping of three sp3 lobes without the need to invoke a pi-bond
3.
Diatomic molecule
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Diatomic molecules are molecules composed of only two atoms, of the same or different chemical elements. The prefix di- is of Greek origin, meaning two, if a diatomic molecule consists of two atoms of the same element, such as hydrogen or oxygen, then it is said to be homonuclear. Otherwise, if a molecule consists of two different atoms, such as carbon monoxide or nitric oxide, the molecule is said to be heteronuclear. The only chemical elements that form stable homonuclear diatomic molecules at temperature and pressure are the gases hydrogen, nitrogen, oxygen, fluorine. The noble gases are gases at STP, but they are monatomic. The homonuclear diatomic gases and noble gases together are called elemental gases or molecular gases, at slightly elevated temperatures, the halogens bromine and iodine also form diatomic gases. All halogens have been observed as diatomic molecules, except for astatine, other elements form diatomic molecules when evaporated, but these diatomic species repolymerize when cooled. Heating elemental phosphorus gives diphosphorus, P2, dilithium is known in the gas phase. Ditungsten and dimolybdenum form with sextuple bonds in the gas phase, the bond in a homonuclear diatomic molecule is non-polar. All other diatomic molecules are chemical compounds of two different elements, many elements can combine to form heteronuclear diatomic molecules, depending on temperature and pressure. Common examples include the carbon monoxide, nitric oxide. Hundreds of diatomic molecules have been identified in the environment of the Earth, in the laboratory, about 99% of the Earths atmosphere is composed of two species of diatomic molecules, nitrogen and oxygen. The natural abundance of hydrogen in the Earths atmosphere is only of the order of parts per million, the interstellar medium is, indeed, dominated by hydrogen atoms. John Daltons original atomic hypothesis assumed that all elements were monatomic, for example, Dalton assumed waters formula to be HO, giving the atomic weight of oxygen as eight times that of hydrogen, instead of the modern value of about 16. As a consequence, confusion existed regarding atomic weights and molecular formulas for about half a century, at the 1860 Karlsruhe Congress on atomic weights, Cannizzaro resurrected Avogadros ideas and used them to produce a consistent table of atomic weights, which mostly agree with modern values. These weights were an important prerequisite for the discovery of the law by Dmitri Mendeleev. Diatomic molecules are normally in their lowest or ground state, which conventionally is also known as the X state, such excitation can also occur when the gas absorbs light or other electromagnetic radiation. The excited states are unstable and naturally relax back to the ground state, over various short time scales after the excitation, transitions occur from higher to lower electronic states and ultimately to the ground state, and in each transition results a photon is emitted
4.
Biosynthesis
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Biosynthesis is a multi-step, enzyme-catalyzed process where substrates are converted into more complex products in living organisms. In biosynthesis, simple compounds are modified, converted into other compounds and this process often consists of metabolic pathways. Some of these pathways are located within a single cellular organelle, while others involve enzymes that are located within multiple cellular organelles. Examples of these pathways include the production of lipid membrane components. The prerequisite elements for biosynthesis include, precursor compounds, chemical energy and these elements create monomers, the building blocks for macromolecules. Biosynthesis occurs due to a series of chemical reactions, for these reactions to take place, the following elements are necessary, Precursor compounds, these compounds are the starting molecules or substrates in a reaction. These may also be viewed as the reactants in a chemical process. Chemical energy, chemical energy can be found in the form of high energy molecules and these molecules are required for energetically unfavorable reactions. Furthermore, the hydrolysis of these compounds drives a reaction forward, high energy molecules, such as ATP, have three phosphates. Often, the phosphate is split off during hydrolysis and transferred to another molecule. Catalytic enzymes, these molecules are special proteins that catalyze a reaction by increasing the rate of the reaction, coenzymes or cofactors, cofactors are molecules that assist in chemical reactions. These may be metal ions, vitamin derivatives such as NADH and acetyl CoA, in the case of NADH, the molecule transfers a hydrogen, whereas acetyl CoA transfers an acetyl group, and ATP transfers a phosphate. Two examples of type of reaction occur during the formation of nucleic acids. For some of these steps, chemical energy is required, Precursor molecule + ATP ↽ − − ⇀ product AMP + PP i Simple compounds that are converted into other compounds with the assistance of cofactors. For example, the synthesis of phospholipids requires acetyl CoA, while the synthesis of another component, shingolipids. The general equation for these examples is, Precursor molecule + Cofactor → e n z y m e macromolecule Simple compounds that join together to create a macromolecule, for example, fatty acids join together to form phopspholipids. In turn, phospholipids and cholesterol interact noncovalently in order to form the lipid bilayer and this reaction may be depicted as follows, Molecule 1 + Molecule 2 ⟶ macromolecule Many intricate macromolecules are synthesized in a pattern of simple, repeated structures. For example, the simplest structures of lipids are fatty acids, fatty acids are hydrocarbon derivatives, they contain a carboxyl group “head” and a hydrocarbon chain “tail. ”These fatty acids create larger components, which in turn incorporate noncovalent interactions to form the lipid bilayer
5.
Nucleotide
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Nucleotides are organic molecules that serve as the monomer units for forming the nucleic acid polymers DNA and RNA, both of which are essential biomolecules in all life-forms on Earth. Nucleotides are the blocks of nucleic acids, they are composed of three subunit molecules, a nitrogenous base, a five-carbon sugar, and at least one phosphate group. They are also known as phosphate nucleotides, a nucleoside is a nitrogenuous base and a 5-carbon sugar. Thus a nucleoside plus a group yields a nucleotide. Nucleotides also play a role in life-form metabolism at the fundamental. In addition, nucleotides participate in signaling, and are incorporated into important cofactors of enzymatic reactions. In experimental biochemistry, nucleotides can be radiolabeled with radionuclides to yield radionucleotides, a nucleotide is composed of three distinctive chemical sub-units, a five-carbon sugar molecule, a nitrogenous base—which two together are called a nucleoside—and one phosphate group. With all three joined, a nucleotide is also termed a nucleoside monophosphate, thus, the terms nucleoside diphosphate or nucleoside triphosphate may also indicate nucleotides. Nucleotides contain either a purine or a pyrimidine base—i. e, the nitrogenous base molecule, also known as a nucleobase—and are termed ribonucleotides if the sugar is ribose, or deoxyribonucleotides if the sugar is deoxyribose. These chain-joins of sugar and phosphate molecules create a backbone strand for a single- or double helix, in any one strand, the chemical orientation of the chain-joins runs from the 5-end to the 3-end —referring to the five carbon sites on sugar molecules in adjacent nucleotides. Unlike in nucleic acid nucleotides, singular cyclic nucleotides are formed when the group is bound twice to the same sugar molecule. These individual nucleotides function in cell metabolism rather than the nucleic acid structures of long-chain molecules, nucleic acids then are polymeric macromolecules assembled from nucleotides, the monomer-units of nucleic acids. The purine bases adenine and guanine and pyrimidine base cytosine occur in both DNA and RNA, while the pyrimidine bases thymine and uracil in just one, adenine forms a base pair with thymine with two hydrogen bonds, while guanine pairs with cytosine with three hydrogen bonds. Nucleotides can be synthesized by a variety of both in vitro and in vivo. In vivo, nucleotides can be synthesized de novo or recycled through salvage pathways, the components used in de novo nucleotide synthesis are derived from biosynthetic precursors of carbohydrate and amino acid metabolism, and from ammonia and carbon dioxide. The liver is the organ of de novo synthesis of all four nucleotides. De novo synthesis of pyrimidines and purines follows two different pathways, purines, however, are first synthesized from the sugar template onto which the ring synthesis occurs. For reference, the syntheses of the purine and pyrimidine nucleotides are carried out by several enzymes in the cytoplasm of the cell, nucleotides undergo breakdown such that useful parts can be reused in synthesis reactions to create new nucleotides
6.
Nucleic acid
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Nucleic acids are biopolymers, or large biomolecules, essential to all known forms of life. They are composed of monomers, which are made of three components, a 5-carbon sugar, a phosphate group, and a nitrogenous base. If the sugar is a simple ribose, the polymer is RNA, if the sugar is derived from ribose as deoxyribose, Nucleic acids are arguably the most important of all biomolecules. They are found in abundance in all living things, where they function to create and encode, the encoded information is contained and conveyed via the nucleic acid sequence, which provides the ladder-step ordering of nucleotides within the molecules of RNA and DNA. Using amino acids and the known as protein synthesis, the specific sequencing in DNA of these nucleobase-pairs enables storing and transmitting coded instructions as genes. In RNA, base-pair sequencing provides for manufacturing new proteins that determine the frames and parts, Nucleic acids were discovered by Friedrich Miescher in 1869. In 1889 Richard Altmann discovered that nuclein has acidic properties, and it became called nucleic acid In 1938 Astbury, in 1953 Watson and Crick determined the structure of DNA. The term nucleic acid is the name for DNA and RNA, members of a family of biopolymers. Nucleic acids were named for their initial discovery within the nucleus, all living cells contain both DNA and RNA, while viruses contain either DNA or RNA, but usually not both. The basic component of nucleic acids is the nucleotide, each of which contains a pentose sugar, a phosphate group. Nucleic acids are generated within the laboratory, through the use of enzymes. The chemical methods also enable the generation of altered nucleic acids that are not found in nature, Nucleic acids are generally very large molecules. Indeed, DNA molecules are probably the largest individual molecules known, well-studied biological nucleic acid molecules range in size from 21 nucleotides to large chromosomes. In most cases, naturally occurring DNA molecules are double-stranded and RNA molecules are single-stranded, Nucleic acids are linear polymers of nucleotides. Each nucleotide consists of three components, a purine or pyrimidine nucleobase, a sugar, and a phosphate group. The substructure consisting of a nucleobase plus sugar is termed a nucleoside, Nucleic acid types differ in the structure of the sugar in their nucleotides–DNA contains 2-deoxyribose while RNA contains ribose. Also, the found in the two nucleic acid types are different, adenine, cytosine, and guanine are found in both RNA and DNA, while thymine occurs in DNA and uracil occurs in RNA. The sugars and phosphates in nucleic acids are connected to other in an alternating chain through phosphodiester linkages
7.
Cofactor (biochemistry)
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A cofactor is a non-protein chemical compound or metallic ion that is required for a proteins biological activity to happen. These proteins are enzymes, and cofactors can be considered helper molecules that assist in biochemical transformations. A coenzyme that is tightly or even covalently bound is termed a prosthetic group, the two subcategories under coenzyme are cosubstrates and prosthetic groups. Cosubstrates are transiently bound to the protein and will be released at some point, the prosthetic groups, on the other hand, are bound permanently to the protein. Both of them have the function, which is to facilitate the reaction of enzymes. Additionally, some sources also limit the use of the cofactor to inorganic substances. An inactive enzyme without the cofactor is called an apoenzyme, while the enzyme with cofactor is called a holoenzyme. Some enzymes or enzyme complexes require several cofactors, organic cofactors are often vitamins or made from vitamins. Many contain the nucleotide adenosine monophosphate as part of their structures, such as ATP, coenzyme A, FAD and this common structure may reflect a common evolutionary origin as part of ribozymes in an ancient RNA world. It has been suggested that the AMP part of the molecule can be considered to be a kind of handle by which the enzyme can grasp the coenzyme to switch it between different catalytic centers. Cofactors can be divided into two groups, organic cofactors, such as flavin or heme, and inorganic cofactors, such as the metal ions Mg2+, Cu+, Mn2+. Organic cofactors are sometimes divided into coenzymes and prosthetic groups. The term coenzyme refers specifically to enzymes and, as such, on the other hand, prosthetic group emphasizes the nature of the binding of a cofactor to a protein and, thus, refers to a structural property. Different sources give different definitions of coenzymes, cofactors. It should be noted that terms are often used loosely. However, the author could not arrive at a single all-encompassing definition of a coenzyme, the study of these cofactors falls under the area of bioinorganic chemistry. In nutrition, the list of essential trace elements reflects their role as cofactors, in humans this list commonly includes iron, magnesium, manganese, cobalt, copper, zinc, and molybdenum. Although chromium deficiency causes impaired glucose tolerance, no human enzyme that uses this metal as a cofactor has been identified, iodine is also an essential trace element, but this element is used as part of the structure of thyroid hormones rather than as an enzyme cofactor
8.
Nicotinamide adenine dinucleotide
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Nicotinamide adenine dinucleotide is a coenzyme found in all living cells. The compound is a dinucleotide, because it consists of two nucleotides joined through their phosphate groups, one nucleotide contains an adenine base and the other nicotinamide. Nicotinamide adenine dinucleotide exists in two forms, an oxidized and reduced form abbreviated as NAD+ and NADH respectively, in metabolism, nicotinamide adenine dinucleotide is involved in redox reactions, carrying electrons from one reaction to another. The coenzyme is, therefore, found in two forms in cells, NAD+ is an oxidizing agent – it accepts electrons from other molecules and becomes reduced and this reaction forms NADH, which can then be used as a reducing agent to donate electrons. These electron transfer reactions are the function of NAD. However, it is used in other cellular processes, the most notable one being a substrate of enzymes that add or remove chemical groups from proteins. Because of the importance of these functions, the involved in NAD metabolism are targets for drug discovery. In organisms, NAD can be synthesized from simple building-blocks from the amino acids tryptophan or aspartic acid, in an alternative fashion, more complex components of the coenzymes are taken up from food as the vitamin called niacin. Similar compounds are released by reactions that break down the structure of NAD and these preformed components then pass through a salvage pathway that recycles them back into the active form. Some NAD is also converted into nicotinamide adenine dinucleotide phosphate, the chemistry of this related coenzyme is similar to that of NAD, nicotinamide adenine dinucleotide, like all dinucleotides, consists of two nucleosides joined by a pair of bridging phosphate groups. The nucleosides each contain a ring, one with adenine attached to the first carbon atom. The nicotinamide moiety can be attached in two orientations to this carbon atom. Because of these two structures, the compound exists as two diastereomers. It is the diastereomer of NAD+ that is found in organisms. These nucleotides are joined together by a bridge of two groups through the 5 carbons. In metabolism, the compound accepts or donates electrons in redox reactions, such reactions involve the removal of two hydrogen atoms from the reactant, in the form of a hydride ion, and a proton. The proton is released into solution, while the reductant RH2 is oxidized, the midpoint potential of the NAD+/NADH redox pair is −0.32 volts, which makes NADH a strong reducing agent. The reaction is reversible, when NADH reduces another molecule and is re-oxidized to NAD+
9.
Amino acid
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Amino acids are organic compounds containing amine and carboxyl functional groups, along with a side chain specific to each amino acid. The key elements of an acid are carbon, hydrogen, oxygen. About 500 amino acids are known and can be classified in many ways, in the form of proteins, amino acids comprise the second-largest component of human muscles, cells and other tissues. Outside proteins, amino acids perform critical roles in such as neurotransmitter transport. In biochemistry, amino acids having both the amine and the acid groups attached to the first carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids and they include the 22 proteinogenic amino acids, which combine into peptide chains to form the building-blocks of a vast array of proteins. These are all L-stereoisomers, although a few D-amino acids occur in bacterial envelopes, as a neuromodulator, twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as standard amino acids. The other two are selenocysteine, and pyrrolysine, pyrrolysine and selenocysteine are encoded via variant codons, for example, selenocysteine is encoded by stop codon and SECIS element. N-formylmethionine is generally considered as a form of methionine rather than as a separate proteinogenic amino acid, codon–tRNA combinations not found in nature can also be used to expand the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids. Many important proteinogenic and non-proteinogenic amino acids also play critical roles within the body. Nine proteinogenic amino acids are called essential for humans because they cannot be created from other compounds by the human body, others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also differ between species, because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, and food technology. Industrial uses include the production of drugs, biodegradable plastics, the first few amino acids were discovered in the early 19th century. In 1806, French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that was subsequently named asparagine, cystine was discovered in 1810, although its monomer, cysteine, remained undiscovered until 1884. Glycine and leucine were discovered in 1820, usage of the term amino acid in the English language is from 1898. Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis, in the structure shown at the top of the page, R represents a side chain specific to each amino acid. The carbon atom next to the group is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as amino acids
10.
Protein
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Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, a linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide, short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds, the sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the code specifies 20 standard amino acids, however. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors, proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. Once formed, proteins only exist for a period of time and are then degraded and recycled by the cells machinery through the process of protein turnover. A proteins lifespan is measured in terms of its half-life and covers a wide range and they can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms, many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized, digestion breaks the proteins down for use in the metabolism. Methods commonly used to study structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance. Most proteins consist of linear polymers built from series of up to 20 different L-α-amino acids, all proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, and a variable side chain are bonded. Only proline differs from this structure as it contains an unusual ring to the N-end amine group. The amino acids in a chain are linked by peptide bonds. Once linked in the chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen. The peptide bond has two forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar
11.
Nitrogen cycle
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The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into various chemical forms as it circulates among the atmosphere and terrestrial and marine ecosystems. The conversion of nitrogen can be carried out through both biological and physical processes, important processes in the nitrogen cycle include fixation, ammonification, nitrification, and denitrification. The majority of Earths atmosphere is nitrogen, making it the largest source of nitrogen, however, atmospheric nitrogen has limited availability for biological use, leading to a scarcity of usable nitrogen in many types of ecosystems. The nitrogen cycle is of particular interest to ecologists because nitrogen availability can affect the rate of key ecosystem processes, human activities such as fossil fuel combustion, use of artificial nitrogen fertilizers, and release of nitrogen in wastewater have dramatically altered the global nitrogen cycle. Nitrogen is present in the environment in a variety of chemical forms including organic nitrogen, Ammonium, nitrite, nitrate, nitrous oxide. Organic nitrogen may be in the form of a living organism, the processes of the nitrogen cycle transform nitrogen from one form to another. Many of those processes are carried out by microbes, either in their effort to harvest energy or to accumulate nitrogen in a form needed for their growth, for example, the nitrogenous wastes in animal urine are broken down by nitrifying bacteria in the soil to be used anew. The diagram above shows how these fit together to form the nitrogen cycle. Atmospheric nitrogen must be processed, or fixed, in a form to be taken up by plants. Between 5x1012 and 10x1012 g per year are fixed by lightning strikes and these bacteria have the nitrogenase enzyme that combines gaseous nitrogen with hydrogen to produce ammonia, which is converted by the bacteria into other organic compounds. Most biological nitrogen fixation occurs by the activity of Mo-nitrogenase, found in a variety of bacteria. Mo-nitrogenase is a complex two-component enzyme that has multiple metal-containing prosthetic groups, an example of the free-living bacteria is Azotobacter. Symbiotic nitrogen-fixing bacteria such as Rhizobium usually live in the nodules of legumes. Here they form a relationship with the plant, producing ammonia in exchange for carbohydrates. Because of this relationship, legumes will often increase the content of nitrogen-poor soils. A few non-legumes can also form such symbioses, plants take nitrogen from the soil by absorption through their roots as amino acids, nitrate ions, nitrite ions, or ammonium ions. Most nitrogen obtained by animals can be traced back to the eating of plants at some stage of the food chain. Plants can absorb nitrate or ammonium from the soil via their root hairs, if nitrate is absorbed, it is first reduced to nitrite ions and then ammonium ions for incorporation into amino acids, nucleic acids, and chlorophyll
12.
Agriculture
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Agriculture is the cultivation and breeding of animals, plants and fungi for food, fiber, biofuel, medicinal plants and other products used to sustain and enhance human life. Agriculture was the key development in the rise of human civilization. The study of agriculture is known as agricultural science, the history of agriculture dates back thousands of years, and its development has been driven and defined by greatly different climates, cultures, and technologies. Industrial agriculture based on large-scale monoculture farming has become the dominant agricultural methodology, genetically modified organisms are an increasing component of agriculture, although they are banned in several countries. Agricultural food production and water management are increasingly becoming global issues that are fostering debate on a number of fronts, the major agricultural products can be broadly grouped into foods, fibers, fuels, and raw materials. Specific foods include cereals, vegetables, fruits, oils, meats, fibers include cotton, wool, hemp, silk and flax. Raw materials include lumber and bamboo, other useful materials are also produced by plants, such as resins, dyes, drugs, perfumes, biofuels and ornamental products such as cut flowers and nursery plants. The word agriculture is a late Middle English adaptation of Latin agricultūra, from ager, field, Agriculture usually refers to human activities, although it is also observed in certain species of ant, termite and ambrosia beetle. To practice agriculture means to use resources to produce commodities which maintain life, including food, fiber, forest products, horticultural crops. This definition includes arable farming or agronomy, and horticulture, all terms for the growing of plants, even then, it is acknowledged that there is a large amount of knowledge transfer and overlap between silviculture and agriculture. In traditional farming, the two are often combined even on small landholdings, leading to the term agroforestry, Agriculture began independently in different parts of the globe, and included a diverse range of taxa. At least 11 separate regions of the Old and New World were involved as independent centers of origin, wild grains were collected and eaten from at least 105,000 years ago. Pigs were domesticated in Mesopotamia around 15,000 years ago, rice was domesticated in China between 13,500 and 8,200 years ago, followed by mung, soy and azuki beans. Sheep were domesticated in Mesopotamia between 13,000 and 11,000 years ago. From around 11,500 years ago, the eight Neolithic founder crops, emmer and einkorn wheat, hulled barley, peas, lentils, bitter vetch, chick peas and flax were cultivated in the Levant. Cattle were domesticated from the aurochs in the areas of modern Turkey. In the Andes of South America, the potato was domesticated between 10,000 and 7,000 years ago, along with beans, coca, llamas, alpacas, sugarcane and some root vegetables were domesticated in New Guinea around 9,000 years ago. Sorghum was domesticated in the Sahel region of Africa by 7,000 years ago, cotton was domesticated in Peru by 5,600 years ago, and was independently domesticated in Eurasia at an unknown time
13.
Fertilizer
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A fertilizer or fertiliser is any material of natural or synthetic origin that is applied to soils or to plant tissues to supply one or more plant nutrients essential to the growth of plants. Fertilizers enhance the growth of plants and this goal is met in two ways, the traditional one being additives that provide nutrients. The second mode by which some fertilizers act is to enhance the effectiveness of the soil by modifying its water retention and aeration and this article, like many on fertilizers, emphasises the nutritional aspect. The nutrients required for plant life are classified according to the elements. Instead compounds containing these elements are the basis of fertilizers, the macronutrients are consumed in larger quantities and are present in plant tissue in quantities from 0. 15% to 6. 0% on a dry matter basis. Plants are made up of four elements, hydrogen, oxygen, carbon. Carbon, hydrogen and oxygen are widely available as water and carbon dioxide, although nitrogen makes up most of the atmosphere, it is in a form that is unavailable to plants. Nitrogen is the most important fertilizer since nitrogen is present in proteins, DNA, to be nutritious to plants, nitrogen must be made available in a fixed form. Only some bacteria and their host plants can fix atmospheric nitrogen by converting it to ammonia, phosphate is required for the production of DNA and ATP, the main energy carrier in cells, as well as certain lipids. Micronutrients are consumed in quantities and are present in plant tissue on the order of parts-per-million, ranging from 0.15 to 400 ppm DM. These elements are present at the active sites of enzymes that carry out the plants metabolism. Because these elements enable catalysts their impact far exceeds their weight percentage, Fertilizers are classified in several ways. They are classified according to whether they provide a single nutrient, multinutrient fertilizers provide two or more nutrients, for example N and P. Fertilizers are also sometimes classified as inorganic versus organic. Inorganic fertilizers exclude carbon-containing materials except ureas, organic fertilizers are usually plant- or animal-derived matter. Inorganic are sometimes called synthetic fertilizers since various chemical treatments are required for their manufacture, the main nitrogen-based straight fertilizer is ammonia or its solutions. Ammonium nitrate is widely used. Urea is another source of nitrogen, having the advantage that it is solid and non-explosive, unlike ammonia and ammonium nitrate. A few percent of the fertilizer market has been met by calcium ammonium nitrate
14.
Soil
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Soil is a mixture of minerals, organic matter, gases, liquids, and countless organisms that together support life on Earth. Soil is called the Skin of the Earth and interfaces with the lithosphere, the hydrosphere, the atmosphere, the term pedolith, used commonly to refer to the soil, literally translates ground stone. Soil consists of a phase of minerals and organic matter, as well as a porous phase that holds gases. Accordingly, soils are often treated as a system of solids, liquids. Soil is a product of the influence of climate, relief, organisms, Soil continually undergoes development by way of numerous physical, chemical and biological processes, which include weathering with associated erosion. Given its complexity and strong internal connectedness soil has been considered as an ecosystem by soil ecologists. Most soils have a dry bulk density between 1.1 and 1.6 g/cm3, while the particle density is much higher. Little of the soil of planet Earth is older than the Pleistocene and none is older than the Cenozoic, Soil science has two basic branches of study, edaphology and pedology. Edaphology is concerned with the influence of soils on living things, pedology is focused on the formation, description, and classification of soils in their natural environment. In engineering terms, soil is referred to as regolith, or loose material that lies above the solid geology. Soil is commonly referred to as earth or dirt, technically, as soil resources serve as a basis for food security, the international community advocates its sustainable and responsible use through different types of soil governance. Soil is a component of the Earths ecosystem. The worlds ecosystems are impacted in far-reaching ways by the carried out in the soil, from ozone depletion and global warming, to rainforest destruction. Following the atmosphere, the soil is the next largest carbon reservoir on Earth, as the planet warms, soils will add carbon dioxide to the atmosphere due to its increased biological activity at higher temperatures. Thus, soil carbon losses likely have a positive feedback response to global warming. Since soil has a range of available niches and habitats. A gram of soil can contain billions of organisms, belonging to thousands of species, mostly microbial, Soil has a mean prokaryotic density of roughly 108 organisms per gram, whereas the ocean has no more than 107 procaryotic organisms per milliliter of seawater. Since plant roots need oxygen, ventilation is an important characteristic of soil and this ventilation can be accomplished via networks of interconnected soil pores, which also absorb and hold rainwater making it readily available for plant uptake
15.
Bacteria
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Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods, Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology, There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants, Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of bodies and bacteria are responsible for the putrefaction stage in this process. In March 2013, data reported by researchers in October 2012, was published and it was suggested that bacteria thrive in the Mariana Trench, which with a depth of up to 11 kilometres is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, You can find microbes everywhere—theyre extremely adaptable to conditions, the vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial particularly in the gut flora. However several species of bacteria are pathogenic and cause diseases, including cholera, syphilis, anthrax, leprosy. The most common fatal diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year. In developed countries, antibiotics are used to treat infections and are also used in farming, making antibiotic resistance a growing problem. Once regarded as constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and these evolutionary domains are called Bacteria and Archaea. The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, for about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. In 2008, fossils of macroorganisms were discovered and named as the Francevillian biota, however, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. Bacteria were also involved in the second great evolutionary divergence, that of the archaea, here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea
16.
Azotobacter
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Azotobacter is a genus of usually motile, oval or spherical bacteria that form thick-walled cysts and may produce large quantities of capsular slime. In addition to being a model organism for studying diazotrophs, it is used by humans for the production of biofertilizers, food additives, the first representative of the genus, Azotobacter chroococcum, was discovered and described in 1901 by the Dutch microbiologist and botanist Martinus Beijerinck. Azotobacter species are Gram-negative bacteria found in neutral and alkaline soils, in water, cells of the genus Azotobacter are relatively large for bacteria. They are usually oval, but may take various forms from rods to spheres, in microscopic preparations, the cells can be dispersed or form irregular clusters or occasionally chains of varying lengths. In fresh cultures, cells are due to the numerous flagella. Later, the cells lose their mobility, become almost spherical, the shape of the cell is affected by the amino acid glycine which is present in the nutrient medium peptone. Under magnification, the cells show inclusions, some of which are colored, in the early 1900s, the colored inclusions were regarded as reproductive grains, or gonidia – a kind of embryo cells. However, it was demonstrated that the granules do not participate in the cell division. The colored grains are composed of volutin, whereas the colorless inclusions are drops of fat, cysts of the genus Azotobacter are more resistant to adverse environmental factors than the vegetative cells, in particular, they are twice as resistant to UV light. They are also resistant to drying, ultrasound and gamma and solar irradiation, the formation of cysts is induced by changes in the concentration of nutrients in the medium and addition of some organic substances such as ethanol, n-butanol, or β-hydroxybutyrate. Cysts are rarely formed in liquid media, the cysts of Azotobacter are spherical and consist of the so-called central body – a reduced copy of vegetative cells with several vacuoles – and the two-layer shell. The inner part of the shell is called intine and has a fibrous structure, the outer part has a hexagonal crystalline structure and is called exine. Exine is partially hydrolyzed by trypsin and is resistant to lysozyme, the central body can be isolated in a viable state by some chelation agents. The main constituents of the shell are alkylresorcinols composed of long aliphatic chains. Alkylresorcinols are also found in bacteria, animals, and plants. During the germination, the cysts sustain damage and release a large vegetative cell, microscopically, the first manifestation of spore germination is the gradual decrease in light refractive by cysts, which is detected with phase contrast microscopy. Germination of cysts, a process, takes about 4–6 h. During germination, the body grows and captures the granules of volutin
17.
Symbiosis
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Symbiosis is any type of a close and long-term biological interaction between two different species, be it mutualistic, commensalistic, or parasitic. In 1879, Heinrich Anton de Bary defined it as the living together of unlike organisms, Symbiosis can be obligatory, which means that one or both of the symbionts entirely depend on each other for survival, or facultative when they can generally live independently. When one organism lives on another such as mistletoe, it is called ectosymbiosis, or endosymbiosis when one partner lives inside the tissues of another, as in Symbiodinium in corals. In 1877, Albert Bernhard Frank used the term symbiosis which previously had used to depict people living together in community to describe the mutualistic relationship in lichens. In 1879, the German mycologist Heinrich Anton de Bary defined it as the living together of unlike organisms, symbiotic relationships can be obligate, meaning that one or both of the symbionts entirely depend on each other for survival. For example, in lichens, which consist of fungal and photosynthetic symbionts, the algal or cyanobacterial symbionts in lichens, such as Trentepohlia, can generally live independently, and their symbiosis is, therefore, facultative. Endosymbiosis is any relationship in which one symbiont lives within the tissues of the other, either within the cells or extracellularly. Mutualism or interspecies reciprocal altruism is a relationship between individuals of different species where both individuals benefit, in general, only lifelong interactions involving close physical and biochemical contact can properly be considered symbiotic. Mutualistic relationships may be either obligate for both species, obligate for one but facultative for the other, or facultative for both, a large percentage of herbivores have mutualistic gut flora to help them digest plant matter, which is more difficult to digest than animal prey. This gut flora is made up of cellulose-digesting protozoans or bacteria living in the herbivores intestines, coral reefs are the result of mutualisms between coral organisms and various types of algae which live inside them. Most land plants and land ecosystems rely on mutualisms between the plants, which fix carbon from the air, and mycorrhyzal fungi, which help in extracting water, an example of mutual symbiosis is the relationship between the ocellaris clownfish that dwell among the tentacles of Ritteri sea anemones. The territorial fish protects the anemone from anemone-eating fish, and in turn the stinging tentacles of the anemone protect the clownfish from its predators, a special mucus on the clownfish protects it from the stinging tentacles. A further example is the fish, which sometimes lives together with a shrimp. The shrimp digs and cleans up a burrow in the sand in which both the shrimp and the fish live. The shrimp is almost blind, leaving it vulnerable to predators when outside its burrow, in case of danger the goby fish touches the shrimp with its tail to warn it. When that happens both the shrimp and goby fish quickly retreat into the burrow, different species of gobies also exhibit mutualistic behavior through cleaning up ectoparasites in other fish. Another non-obligate symbiosis is known from encrusting bryozoans and hermit crabs, the bryozoan colony develops a cirumrotatory growth and offers the crab a helicospiral-tubular extension of its living chamber that initially was situated within a gastropod shell. A spectacular examples of mutualism is between the siboglinid tube worms and symbiotic bacteria that live at hydrothermal vents and cold seeps
18.
Plant
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Plants are mainly multicellular, predominantly photosynthetic eukaryotes of the kingdom Plantae. The term is generally limited to the green plants, which form an unranked clade Viridiplantae. This includes the plants, conifers and other gymnosperms, ferns, clubmosses, hornworts, liverworts, mosses and the green algae. Green plants have cell walls containing cellulose and obtain most of their energy from sunlight via photosynthesis by primary chloroplasts and their chloroplasts contain chlorophylls a and b, which gives them their green color. Some plants are parasitic and have lost the ability to produce amounts of chlorophyll or to photosynthesize. Plants are characterized by sexual reproduction and alternation of generations, although reproduction is also common. There are about 300–315 thousand species of plants, of which the great majority, green plants provide most of the worlds molecular oxygen and are the basis of most of Earths ecologies, especially on land. Plants that produce grains, fruits and vegetables form humankinds basic foodstuffs, Plants play many roles in culture. They are used as ornaments and, until recently and in variety, they have served as the source of most medicines. The scientific study of plants is known as botany, a branch of biology, Plants are one of the two groups into which all living things were traditionally divided, the other is animals. The division goes back at least as far as Aristotle, who distinguished between plants, which generally do not move, and animals, which often are mobile to catch their food. Much later, when Linnaeus created the basis of the system of scientific classification. Since then, it has become clear that the plant kingdom as originally defined included several unrelated groups, however, these organisms are still often considered plants, particularly in popular contexts. When the name Plantae or plant is applied to a group of organisms or taxon. The evolutionary history of plants is not yet settled. Those which have been called plants are in bold, the way in which the groups of green algae are combined and named varies considerably between authors. Algae comprise several different groups of organisms which produce energy through photosynthesis, most conspicuous among the algae are the seaweeds, multicellular algae that may roughly resemble land plants, but are classified among the brown, red and green algae. Each of these groups also includes various microscopic and single-celled organisms
19.
Legume
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A legume is a plant or its fruit or seed in the family Fabaceae. Legumes are grown agriculturally, primarily for their grain seed called pulse, for forage and silage. Well-known legumes include alfalfa, clover, peas, beans, lentils, lupin bean, mesquite, carob, soybeans, peanuts, Fabaceae is the most common family found in tropical rainforests and in dry forests in the Americas and Africa. A legume fruit is a dry fruit that develops from a simple carpel. A common name for type of fruit is a pod, although the term pod is also applied to a number of other fruit types, such as that of vanilla. Legumes are notable in that most of them have symbiotic nitrogen-fixing bacteria in structures called root nodules, for that reason, they play a key role in crop rotation. The term pulse, as used by the United Nations Food and this excludes green beans and green peas, which are considered vegetable crops. Also excluded are seeds that are grown for oil extraction. However, in usage, these distinctions are not always clearly made. Some Fabaceae, such as Scotch broom and other Genisteae, are leguminous but are not called legumes by farmers. Farmed legumes can belong to many classes, including forage, grain, blooms, pharmaceutical/industrial, fallow/green manure. Most commercially farmed species fill two or more roles simultaneously, depending upon their degree of maturity when harvested, grain legumes are cultivated for their seeds. The seeds are used for human and animal consumption or for the production of oils for industrial uses, grain legumes include beans, lentils, lupins, peas, and peanuts. Like other plant-based foods, pulses contain no cholesterol and little fat or sodium, Legumes are also an excellent source of resistant starch which is broken down by bacteria in the large intestine to produce short-chain fatty acids used by intestinal cells for food energy. Preliminary studies in humans include the potential for regular consumption of legumes in a diet to affect metabolic syndrome. There is evidence that a portion of pulses in a diet may lower blood pressure and reduce LDL cholesterol levels. Some, like alfalfa, clover, vetch, stylo, or Arachis, are sown in pasture, other forage legumes such as Leucaena or Albizia are woody shrub or tree species that are either broken down by livestock or regularly cut by humans to provide livestock feed. Legume species grown for their flowers include lupins, which are farmed commercially for their blooms as well as being popular in gardens worldwide, industrially farmed legumes include Indigofera and Acacia species, which are cultivated for dye and natural gum production, respectively
20.
Rice
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Rice is the seed of the grass species Oryza sativa or Oryza glaberrima. As a cereal grain, it is the most widely consumed staple food for a part of the worlds human population. It is the agricultural commodity with the third-highest worldwide production, after sugarcane and maize, wild rice, from which the crop was developed, may have its native range in Australia. Chinese legends attribute the domestication of rice to Shennong, the emperor of China. Genetic evidence has shown that rice originates from a single domestication 8, previously, archaeological evidence had suggested that rice was domesticated in the Yangtze River valley region in China. From East Asia, rice was spread to Southeast and South Asia, Rice was introduced to Europe through Western Asia, and to the Americas through European colonization. There are many varieties of rice and culinary preferences tend to vary regionally, in some areas such as the Far East or Spain, there is a preference for softer and stickier varieties. Rice, a monocot, is grown as an annual plant, although in tropical areas it can survive as a perennial. The rice plant can grow to 1–1.8 m tall, occasionally more depending on the variety and it has long, slender leaves 50–100 cm long and 2–2.5 cm broad. The small wind-pollinated flowers are produced in a branched arching to pendulous inflorescence 30–50 cm long, the edible seed is a grain 5–12 mm long and 2–3 mm thick. Rice cultivation is well-suited to countries and regions with low costs and high rainfall, as it is labor-intensive to cultivate. However, rice can be grown practically anywhere, even on a hill or mountain area with the use of water-controlling terrace systems. Although its parent species are native to Asia and certain parts of Africa, centuries of trade, the traditional method for cultivating rice is flooding the fields while, or after, setting the young seedlings. The name wild rice is used for species of the genera Zizania and Porteresia. The Greek word is the source of all European words, the origin of the Greek word is unclear. It is sometimes held to be from the Tamil word அரிசி, however, Krishnamurti disagrees with the notion that Old Tamil arici is the source of the Greek term, and proposes that it was borrowed from descendants of Proto-Dravidian *wariñci instead. The varieties of rice are typically classified as long-, medium-, the grains of long-grain rice tend to remain intact after cooking, medium-grain rice becomes more sticky. Medium-grain rice is used for dishes, for risotto in Italy
21.
Lightning
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Lightning is a sudden electrostatic discharge that occurs during a thunder storm. This discharge occurs between electrically charged regions of a cloud, between two clouds, or between a cloud and the ground. The charged regions in the atmosphere temporarily equalize themselves through this discharge referred to as an if it hits an object on the ground. Lightning causes light in the form of plasma, and sound in the form of thunder, Lightning may be seen and not heard when it occurs at a distance too great for the sound to carry as far as the light from the strike or flash. This article incorporates public domain material from the National Oceanic and Atmospheric Administration document Understanding Lightning, the details of the charging process are still being studied by scientists, but there is general agreement on some of the basic concepts of thunderstorm electrification. The main charging area in a thunderstorm occurs in the part of the storm where air is moving upward rapidly and temperatures range from -15 to -25 Celsius. At that place, the combination of temperature and rapid upward air movement produces a mixture of super-cooled cloud droplets, small ice crystals, the updraft carries the super-cooled cloud droplets and very small ice crystals upward. At the same time, the graupel, which is larger and denser. The differences in the movement of the precipitation cause collisions to occur, when the rising ice crystals collide with graupel, the ice crystals become positively charged and the graupel becomes negatively charged. The updraft carries the positively charged ice crystals upward toward the top of the storm cloud, the larger and denser graupel is either suspended in the middle of the thunderstorm cloud or falls toward the lower part of the storm. The result is that the part of the thunderstorm cloud becomes positively charged while the middle to lower part of the thunderstorm cloud becomes negatively charged. This part of the cloud is called the anvil. While this is the charging process for the thunderstorm cloud. In addition, there is a small but important positive charge buildup near the bottom of the cloud due to the precipitation. Many factors affect the frequency, distribution, strength and physical properties of a lightning flash in a particular region of the world. These factors include ground elevation, latitude, prevailing wind currents, relative humidity, proximity to warm and cold bodies of water, to a certain degree, the ratio between IC, CC and CG lightning may also vary by season in middle latitudes. Lightnings relative unpredictability limits a complete explanation of how or why it occurs, the actual discharge is the final stage of a very complex process. At its peak, a thunderstorm produces three or more strikes to the Earth per minute
22.
Metalloprotein
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Metalloprotein is a generic term for a protein that contains a metal ion cofactor. A large number of all proteins are part of this category and it is estimated that approximately half of all proteins contain a metal. In another estimate, about one quarter to one third of all proteins are proposed to require metals to carry out their functions, thus, metalloproteins have many different functions in cells, such as storage and transport of proteins, enzymes and signal transduction proteins. The role of ions in infectious diseases has been reviewed. In metalloproteins, metal ions are coordinated by nitrogen, oxygen or sulfur centers belonging to amino acid residues of the protein. These donor groups are provided by side-chains on the amino acid residues. Especially important are the imidazole substituent in histidine residues, thiolate substituents in cysteine residues, given the diversity of the metalloproteome, virtually all amino acid residues have been shown to bind metal centers. The peptide backbone also provides donor groups, these include deprotonated amides, in addition to donor groups that are provided by amino acid residues, a large number of organic cofactors function as ligands. Perhaps most famous are the tetradentate N4 macrocyclic ligands incorporated into the heme protein, inorganic ligands such as sulfide and oxide are also common. The sixth coordination site contains a water molecule or a dioxygen molecule, by contrast the protein myoglobin, found in muscle cells, has only one such unit. The active site is located in an hydrophobic pocket and this is important as without it the iron would be irreversibly oxidized to iron. The equilibrium constant for the formation of HbO2 is such that oxygen is taken up or released depending on the pressure of oxygen in the lungs or in muscle. In hemoglobin the four subunits show a cooperativity effect that allows for easy oxygen transfer from hemoglobin to myoglobin, in both hemoglobin and myoglobin it is sometimes incorrectly stated that the oxygenated species contains iron. It is now known that the nature of these species is because the iron atom is in the low-spin state. In oxyhemoglobin the iron atom is located in the plane of the porphyrin ring and this change in spin state is a cooperative effect due to the higher crystal field splitting and smaller ionic radius of Fe2+ in the oxyhemoglobin moiety. Hemerythrin is another iron-containing oxygen carrier, the oxygen binding site is a binuclear iron center. The iron atoms are coordinated to the protein through the side chains of a glutamate and aspartate. The uptake of O2 by hemerythrin is accompanied by oxidation of the reduced binuclear center to produce bound peroxide
23.
Nitrogenase
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Nitrogenases are enzymes that are produced by certain bacteria, such as cyanobacteria. These enzymes are responsible for the reduction of nitrogen to ammonia, nitrogenases are the only family of enzymes known to catalyze this reaction, which is a key step in the process of nitrogen fixation. Nitrogen fixation is required for all forms of life, with nitrogen being essential for the biosynthesis of molecules that create plants, animals, the equilibrium formation of ammonia from molecular hydrogen and nitrogen has an overall negative enthalpy of reaction, the activation energy is very high. Nitrogenase acts as a catalyst, reducing this energy barrier such that the reaction can take place at ambient temperatures, the nitrogenase complex consists of two proteins, The homodimeric Fe protein, a reductase which has a high reducing power and is responsible for the supply of electrons. The heterotetrameric MoFe protein, a nitrogenase which uses the electrons provided to reduce N2 to NH3, the Fe protein is a dimer of identical subunits which contains one cluster and weighs approximately 60-64kDa. The function of the Fe protein is to transfer electrons from a reducing agent, the transfer of electrons requires an input of chemical energy which comes from the binding and hydrolysis of ATP. The hydrolysis of ATP also causes a change within the nitrogenase complex, bringing the Fe protein. The MoFe protein is a heterotetramer consisting of two α subunits and two β subunits, weighing approximately 240-250kDa. The MoFe protein also contains two clusters, known as P-clusters, located at the interface between the α and β subunits and two FeMo cofactors, within the α subunits. The core of the P-cluster takes the form of two linked by a central sulfur atom. Each P-cluster is covalently linked to the MoFe protein by six cysteine residues, each FeMo cofactor consists of two non-identical clusters, and, which are linked by three sulfide ions. Each FeMo cofactor is covalently linked to the α subunit of the protein by one cysteine residue, electrons from the Fe protein enter the MoFe protein at the P-clusters, which then transfer the electrons to the FeMo cofactors. Each FeMo cofactor then acts as a site for nitrogen fixation, nitrogenase is an enzyme responsible for catalyzing nitrogen fixation, which is the reduction of nitrogen to ammonia and a process vital to sustaining life on Earth. There are three types of nitrogenase found in various nitrogen-fixing bacteria, molybdenum nitrogenase, vanadium nitrogenase, molybdenum nitrogenase, which can be found in diazotrophs and legumes, is the nitrogenase that has been studied the most extensively and thus is the most well characterized. Figures 1-2 display the structure and key catalytic components of molybdenum nitrogenase extracted from Azotobacter vinelandii. Vanadium nitrogenase and iron-only nitrogenase can both be found in species of Azotobacter as an alternative nitrogenase. Equations 1 and 2 show the reactions of nitrogen fixation in molybdenum nitrogenase. Component I is a MoFe protein in molybdenum nitrogenase, a VFe protein in vanadium nitrogenase, Component II is a Fe protein that contains the Fe-S cluster, which transfers electrons to Component I
24.
Iron
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Iron is a chemical element with symbol Fe and atomic number 26. It is a metal in the first transition series and it is by mass the most common element on Earth, forming much of Earths outer and inner core. It is the fourth most common element in the Earths crust, like the other group 8 elements, ruthenium and osmium, iron exists in a wide range of oxidation states, −2 to +6, although +2 and +3 are the most common. Elemental iron occurs in meteoroids and other low oxygen environments, but is reactive to oxygen, fresh iron surfaces appear lustrous silvery-gray, but oxidize in normal air to give hydrated iron oxides, commonly known as rust. Unlike the metals that form passivating oxide layers, iron oxides occupy more volume than the metal and thus flake off, Iron metal has been used since ancient times, although copper alloys, which have lower melting temperatures, were used even earlier in human history. Pure iron is soft, but is unobtainable by smelting because it is significantly hardened and strengthened by impurities, in particular carbon. A certain proportion of carbon steel, which may be up to 1000 times harder than pure iron. Crude iron metal is produced in blast furnaces, where ore is reduced by coke to pig iron, further refinement with oxygen reduces the carbon content to the correct proportion to make steel. Steels and iron alloys formed with metals are by far the most common industrial metals because they have a great range of desirable properties. Iron chemical compounds have many uses, Iron oxide mixed with aluminium powder can be ignited to create a thermite reaction, used in welding and purifying ores. Iron forms binary compounds with the halogens and the chalcogens, among its organometallic compounds is ferrocene, the first sandwich compound discovered. Iron plays an important role in biology, forming complexes with oxygen in hemoglobin and myoglobin. Iron is also the metal at the site of many important redox enzymes dealing with cellular respiration and oxidation and reduction in plants. A human male of average height has about 4 grams of iron in his body and this iron is distributed throughout the body in hemoglobin, tissues, muscles, bone marrow, blood proteins, enzymes, ferritin, hemosiderin, and transport in plasma. The mechanical properties of iron and its alloys can be evaluated using a variety of tests, including the Brinell test, Rockwell test, the data on iron is so consistent that it is often used to calibrate measurements or to compare tests. An increase in the content will cause a significant increase in the hardness. Maximum hardness of 65 Rc is achieved with a 0. 6% carbon content, because of the softness of iron, it is much easier to work with than its heavier congeners ruthenium and osmium. Because of its significance for planetary cores, the properties of iron at high pressures and temperatures have also been studied extensively
25.
Molybdenum
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Molybdenum is a chemical element with symbol Mo and atomic number 42. The name is from Neo-Latin molybdaenum, from Ancient Greek Μόλυβδος molybdos, meaning lead, molybdenum minerals have been known throughout history, but the element was discovered in 1778 by Carl Wilhelm Scheele. The metal was first isolated in 1781 by Peter Jacob Hjelm, molybdenum does not occur naturally as a free metal on Earth, it is found only in various oxidation states in minerals. The free element, a metal with a gray cast, has the sixth-highest melting point of any element. It readily forms hard, stable carbides in alloys, and for this reason most of production of the element is used in steel alloys. Most molybdenum compounds have low solubility in water, but when molybdenum-bearing minerals contact oxygen and water, industrially, molybdenum compounds are used in high-pressure and high-temperature applications as pigments and catalysts. Molybdenum-bearing enzymes are by far the most common catalysts for breaking the chemical bond in atmospheric molecular nitrogen in the process of biological nitrogen fixation. At least 50 molybdenum enzymes are now known in bacteria and animals and these nitrogenases contain molybdenum in a form different from other molybdenum enzymes, which all contain fully oxidized molybdenum in a molybdenum cofactor. These various molybdenum cofactor enzymes are vital to the organisms, and molybdenum is an element for life in all higher eukaryote organisms. In its pure form, molybdenum is a metal with a Mohs hardness of 5.5. It has a point of 2,623 °C, of the naturally occurring elements, only tantalum, osmium, rhenium, tungsten. Weak oxidation of molybdenum starts at 300 °C and it has one of the lowest coefficients of thermal expansion among commercially used metals. The tensile strength of molybdenum wires increases about 3 times, from about 10 to 30 GPa, there are 35 known isotopes of molybdenum, ranging in atomic mass from 83 to 117, as well as four metastable nuclear isomers. Seven isotopes occur naturally, with masses of 92,94,95,96,97,98. Of these naturally occurring isotopes, only molybdenum-100 is unstable, molybdenum-98 is the most abundant isotope, comprising 24. 14% of all molybdenum. Molybdenum-100 has a half-life of about 1019 y and undergoes double beta decay into ruthenium-100, molybdenum isotopes with mass numbers from 111 to 117 all have half-lives of approximately 150 ns. All unstable isotopes of molybdenum decay into isotopes of niobium, technetium, as also noted below, the most common isotopic molybdenum application involves molybdenum-99, which is a fission product. It is a parent radioisotope to the short-lived gamma-emitting daughter radioisotope technetium-99m, in 2008, the Delft University of Technology applied for a patent on the molybdenum-98-based production of molybdenum-99
26.
Vanadium
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Vanadium is a chemical element with symbol V and atomic number 23. It is a hard, silvery grey, ductile, and malleable transition metal, the elemental metal is rarely found in nature, but once isolated artificially, the formation of an oxide layer stabilizes the free metal somewhat against further oxidation. Four years later, however, he was convinced by other scientists that erythronium was identical to chromium, both names were attributed to the wide range of colors found in vanadium compounds. Del Rios lead mineral was later renamed vanadinite for its vanadium content, in 1867 Henry Enfield Roscoe obtained the pure element. Vanadium occurs naturally in about 65 different minerals and in fossil fuel deposits and it is produced in China and Russia from steel smelter slag, other countries produce it either from the flue dust of heavy oil, or as a byproduct of uranium mining. It is mainly used to produce specialty steel alloys such as high-speed tool steels, the most important industrial vanadium compound, vanadium pentoxide, is used as a catalyst for the production of sulfuric acid. Large amounts of ions are found in a few organisms. The oxide and some salts of vanadium have moderate toxicity. Particularly in the ocean, vanadium is used by life forms as an active center of enzymes. Vanadium was discovered by Andrés Manuel del Río, a Spanish-Mexican mineralogist, Del Río extracted the element from a sample of Mexican brown lead ore, later named vanadinite. He found that its salts exhibit a variety of colors. Later, Del Río renamed the element erythronium because most of the salts turned red upon heating, Del Río accepted Collet-Descotils statement and retracted his claim. In 1831, the Swedish chemist Nils Gabriel Sefström rediscovered the element in a new oxide he found working with iron ores. Later that same year, Friedrich Wöhler confirmed del Ríos earlier work, Sefström chose a name beginning with V, which had not been assigned to any element yet. He called the element vanadium after Old Norse Vanadís, because of the many beautifully colored chemical compounds it produces, in 1831, the geologist George William Featherstonhaugh suggested that vanadium should be renamed rionium after del Río, but this suggestion was not followed. The isolation of vanadium metal proved difficult, in 1831, Berzelius reported the production of the metal, but Henry Enfield Roscoe showed that Berzelius had in fact produced the nitride, vanadium nitride. Roscoe eventually produced the metal in 1867 by reduction of chloride, VCl2. In 1927, pure vanadium was produced by reducing vanadium pentoxide with calcium, the first large-scale industrial use of vanadium was in the steel alloy chassis of the Ford Model T, inspired by French race cars
27.
Prokaryote
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A prokaryote is a unicellular organism that lacks a membrane-bound nucleus, mitochondria, or any other membrane-bound organelle. The word prokaryote comes from the Greek πρό before and καρυόν nut or kernel, prokaryotes can be divided into two domains, Archaea and bacteria. In contrast, species with nuclei and organelles are placed in the domain Eukaryota, in the prokaryotes, all the intracellular water-soluble components are located together in the cytoplasm enclosed by the cell membrane, rather than in separate cellular compartments. Bacteria, however, do possess protein-based bacterial microcompartments, which are thought to act as primitive organelles enclosed in protein shells, some prokaryotes, such as cyanobacteria may form large colonies. Others, such as myxobacteria, have multicellular stages in their life cycles, molecular studies have provided insight into the evolution and interrelationships of the three domains of biological species. Eukaryotes are organisms, including humans, whose cells have a well defined membrane-bound nucleus, the division between prokaryotes and eukaryotes reflects the existence of two very different levels of cellular organization. Distinctive types of prokaryotes include extremophiles and methanogens, these are common in extreme environments. Prokaryotes have a cytoskeleton, albeit more primitive than that of the eukaryotes. At least some also contain intracellular structures that can be seen as primitive organelles. Membranous organelles are known in some groups of prokaryotes, such as vacuoles or membrane systems devoted to special metabolic properties, in addition, some species also contain carbohydrate-enclosed microcompartments, which have distinct physiological roles. Most prokaryotes are between 1 µm and 10 µm, but they can vary in size from 0.2 µm to 750 µm, Bacteria and archaea reproduce through asexual reproduction, usually by binary fission. DNA transfer between prokaryotic cells occurs in bacteria and archaea, although it has mainly studied in bacteria. In bacteria, gene transfer occurs by three processes and these are bacterial virus -mediated transduction, plasmid-mediated conjugation, and natural transformation. Transduction of bacterial genes by bacteriophage appears to reflect an occasional error during intracellular assembly of virus particles, the transfer of bacterial DNA is under the control of the bacteriophage’s genes rather than bacterial genes. Conjugation in the well-studied E. coli system is controlled by plasmid genes, infrequently during this process, a plasmid may integrate into the host bacterial chromosome, and subsequently transfer part of the host bacterial DNA to another bacterium. Plasmid mediated transfer of host bacterial DNA also appears to be a process rather than a bacterial adaptation. Natural bacterial transformation involves the transfer of DNA from one bacterium to another through the intervening medium, for a bacterium to bind, take up and recombine donor DNA into its own chromosome, it must first enter a special physiological state called competence. About 40 genes are required in Bacillus subtilis for the development of competence, the length of DNA transferred during B. subtilis transformation can be as much as a third to the whole chromosome
28.
Archaea
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The Archaea constitute a domain and kingdom of single-celled microorganisms. These microbes are prokaryotes, meaning that they have no cell nucleus or any other membrane-bound organelles in their cells, Archaea were initially classified as bacteria, receiving the name archaebacteria, but this classification is outdated. Archaeal cells have unique properties separating them from the two domains of life, Bacteria and Eukaryota. The Archaea are further divided into multiple recognized phyla, classification is difficult because the majority have not been isolated in the laboratory and have only been detected by analysis of their nucleic acids in samples from their environment. Archaea and bacteria are generally similar in size and shape, although a few archaea have very strange shapes, such as the flat, other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, including archaeols. Archaea use more energy sources than eukaryotes, these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea use sunlight as a source, and other species of archaea fix carbon, however, unlike plants and cyanobacteria. Archaea reproduce asexually by fission, fragmentation, or budding, unlike bacteria and eukaryotes. They are also found in the colon, oral cavity. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet, Archaea are a major part of Earths life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, one example is the methanogens that inhabit human and ruminant guts, where their vast numbers aid digestion. Methanogens are also used in production and sewage treatment, and enzymes from extremophile archaea that can endure high temperatures. For much of the 20th century, prokaryotes were regarded as a group of organisms and classified based on their biochemistry, morphology. For example, microbiologists tried to classify based on the structures of their cell walls, their shapes. In 1965, Emile Zuckerkandl and Linus Pauling proposed instead using the sequences of the genes in different prokaryotes to work out how they are related to each other and this approach, known as phylogenetics, is the main method used today. Archaea were first classified as a group of prokaryotes in 1977 by Carl Woese. These two groups were named the Archaebacteria and Eubacteria and treated as kingdoms or subkingdoms, which Woese. Woese argued that group of prokaryotes is a fundamentally different sort of life
29.
Termite
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Termites are eusocial insects that are classified at the taxonomic rank of infraorder Isoptera, or as epifamily Termitoidae within the cockroach order Blattodea. Termites were once classified in an order from cockroaches. However, the first termites emerged during the Permian or even the Carboniferous. About 3,106 species are described, with a few hundred more left to be described. Although these insects are called white ants, they are not ants. Like ants and some bees and wasps from the separate order Hymenoptera, all colonies have fertile males called kings and one or more fertile females called queens. Termites mostly feed on plant material and cellulose, generally in the form of wood, leaf litter, soil. Termites are major detritivores, particularly in the subtropical and tropical regions, Termites are among the most successful groups of insects on Earth, colonising most landmasses except for Antarctica. Their colonies range in size from a few hundred individuals to enormous societies with several million individuals, Termite queens have the longest lifespan of any insect in the world, with some queens reportedly living up to 30 to 50 years. Unlike ants, which undergo a metamorphosis, each individual termite goes through an incomplete metamorphosis that proceeds through egg, nymph. Colonies are described as superorganisms because the termites form part of a self-regulating entity, Termites are a delicacy in the diet of some human cultures and are used in many traditional medicines. Several hundred species are significant as pests that can cause serious damage to buildings, crops. Some species, such as the West Indian drywood termite, are regarded as invasive species, the infraorder name Isoptera is derived from the Greek words iso and ptera, which refers to the nearly equal size of the fore and hind wings. Termite derives from the Latin and Late Latin word termes, altered by the influence of Latin terere from the earlier word tarmes, Termite nests were commonly known as terminarium or termitaria. In early English, termites were known as wood ants or white ants, the modern term was first used in 1781. DNA analysis from 16S rRNA sequences has supported a hypothesis, originally suggested by Cleveland and colleagues in 1934 and this earlier conclusion had been based on the similarity of the symbiotic gut flagellates in the wood-eating cockroaches to those in certain species of termites regarded as living fossils. In the 1960s additional evidence supporting that hypothesis emerged when F. A. McKittrick noted similar morphological characteristics between some termites and Cryptocercus nymphs. These similarities have led some authors to propose that termites be reclassified as a family, the Termitidae, within the order Blattodea
30.
Nitrate
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Nitrate is a polyatomic ion with the molecular formula NO−3 and a molecular mass of 62.0049 g/mol. Nitrates also describe the functional group RONO2. These nitrate esters are a class of explosives. The anion is the base of nitric acid, consisting of one central nitrogen atom surrounded by three identically bonded oxygen atoms in a trigonal planar arrangement. The nitrate ion carries a charge of −1. This arrangement is used as an example of resonance. Like the isoelectronic carbonate ion, the ion can be represented by resonance structures. A common example of a nitrate salt is potassium nitrate. A rich source of nitrate in the human body comes from diets rich in leafy green foods, such as spinach. NO3- is the active component within beetroot juice and other vegetables. Nitrite and water are converted in the body to nitric oxide, nitrate salts are found naturally on earth as large deposits, particularly of nitratine, a major source of sodium nitrate. Nitrates are found in man-made fertilizers, as a byproduct of lightning strikes in earths nitrogen-oxygen rich atmosphere, nitric acid is produced when nitrogen dioxide reacts with water vapor. Nitrates are mainly produced for use as fertilizers in agriculture because of their solubility and biodegradability. The main nitrate fertilizers are ammonium, sodium, potassium, several million kilograms are produced annually for this purpose. The second major application of nitrates is as oxidizing agents, most notably in explosives where the oxidation of carbon compounds liberates large volumes of gases. Sodium nitrate is used to air bubbles from molten glass. Mixtures of the salt are used to harden some metals. Explosives and table tennis balls are made from celluloid, although nitrites are the nitrogen compound chiefly used in meat curing, nitrates are used in certain specialty curing processes where a long release of nitrite from parent nitrate stores is needed
31.
Hermann Hellriegel
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Hermann Hellriegel was a German agricultural chemist who discovered that leguminous plants assimilate the free nitrogen of the atmosphere. He was born at Mausitz, in Saxony, from 1873 to 1882, he was Wanderlehrer at Bernburg. The question of the ability of plants to use the nitrogen of the air had long been one of inquiry. The important parts of experiments he published in Untersuchungen über die Stickstoffnahrung der Gramineen und Leguminosen. This article incorporates text from a now in the public domain, Gilman. Thurston, H. T. Colby, F. M. eds and this work in turn cites, Römer, Hermann Hellriegel, Nachruf Works by or about Hermann Hellriegel at Internet Archive
32.
Martinus Beijerinck
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Martinus Willem Beijerinck was a Dutch microbiologist and botanist. He is often considered one of the founders of virology and environmental microbiology, in spite of his numerous pioneering and seminal contributions to science in general, he was never awarded the Nobel Prize. Born in Amsterdam, Beijerinck studied at the Technical School of Delft and he obtained his Doctor of Science degree from the University of Leiden in 1877. At the time, Delft, then a Polytechnic, did not have the right to confer doctorates and he became a teacher in microbiology at the Agricultural School in Wageningen and later at the Polytechnische Hogeschool Delft. He established the Delft School of Microbiology and his studies of agricultural and industrial microbiology yielded fundamental discoveries in the field of biology. His achievements have been perhaps unfairly overshadowed by those of his contemporaries, Robert Koch and Louis Pasteur, because unlike them, in 1885 he became member of the Royal Netherlands Academy of Arts and Sciences. He is considered one of the founders of virology, in 1898, he published results on the filtration experiments demonstrating that tobacco mosaic disease is caused by an infectious agent smaller than a bacterium. His results were in accordance with the observation made by Dmitri Ivanovsky in 1892. He named the new pathogen virus to indicate its non-bacterial nature, Beijerinck asserted that the virus was somewhat liquid in nature, calling it contagium vivum fluidum. Beijerinck also discovered nitrogen fixation, the process by which diatomic nitrogen gas is converted to ammonium ions, bacteria perform nitrogen fixation, dwelling inside root nodules of certain plants. In addition to having discovered a biochemical reaction vital to soil fertility and agriculture, Beijerinck discovered the phenomenon of bacterial sulfate reduction, a form of anaerobic respiration. He learned bacteria could use sulfate as an electron acceptor. This discovery has had an important impact on our current understanding of biogeochemical cycles, spirillum desulfuricans, now known as Desulfovibrio desulfuricans, the first known sulfate-reducing bacterium, was isolated and described by Beijerinck. Beijerinck invented the enrichment culture, a method of studying microbes from the environment. He is often credited with framing the microbial ecology idea that everything is everywhere, but, the environment selects. Beijerinck was an eccentric figure. He was verbally abusive to students, never married, and had few professional collaborations and he was also known for his ascetic lifestyle and his view of science and marriage being incompatible. His low popularity with his students periodically depressed him, as he very much loved spreading his enthusiasm for biology in the classroom, beijerinckia, Beijerinckiaceae, and Beijerinck are named after him
33.
Hydrolysis
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Hydrolysis usually means the cleavage of chemical bonds by the addition of water. When a carbohydrate is broken into its component sugar molecules by hydrolysis, generally, hydrolysis or saccharification is a step in the degradation of a substance. Hydrolysis can be the reverse of a reaction in which two molecules join together into a larger one and eject a water molecule. Thus hydrolysis adds water to break down, whereas condensation builds up by removing water, usually hydrolysis is a chemical process in which a molecule of water is added to a substance. Sometimes this addition causes both substance and water molecule to split into two parts, in such reactions, one fragment of the target molecule gains a hydrogen ion. A common kind of hydrolysis occurs when a salt of an acid or weak base is dissolved in water. Water spontaneously ionizes into hydroxide anions and hydronium cations, the salt also dissociates into its constituent anions and cations. For example, sodium acetate dissociates in water into sodium and acetate ions, sodium ions react very little with the hydroxide ions whereas the acetate ions combine with hydronium ions to produce acetic acid. In this case the net result is an excess of hydroxide ions. For example, dissolving sulfuric acid in water is accompanied by hydrolysis to give hydronium and bisulfate, for a more technical discussion of what occurs during such a hydrolysis, see Brønsted–Lowry acid–base theory. Acid–base-catalysed hydrolyses are very common, one example is the hydrolysis of amides or esters and their hydrolysis occurs when the nucleophile attacks the carbon of the carbonyl group of the ester or amide. In an aqueous base, hydroxyl ions are better nucleophiles than polar molecules such as water, in acids, the carbonyl group becomes protonated, and this leads to a much easier nucleophilic attack. The products for both hydrolyses are compounds with carboxylic acid groups, perhaps the oldest commercially practiced example of ester hydrolysis is saponification. It is the hydrolysis of a triglyceride with a base such as sodium hydroxide. During the process, glycerol is formed, and the fatty acids react with the base and these salts are called soaps, commonly used in households. In addition, in living systems, most biochemical reactions take place during the catalysis of enzymes, the catalytic action of enzymes allows the hydrolysis of proteins, fats, oils, and carbohydrates. As an example, one may consider proteases and they catalyse the hydrolysis of interior peptide bonds in peptide chains, as opposed to exopeptidases. However, proteases do not catalyse the hydrolysis of all kinds of proteins and their action is stereo-selective, Only proteins with a certain tertiary structure are targeted as some kind of orienting force is needed to place the amide group in the proper position for catalysis
34.
Adenosine triphosphate
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Adenosine triphosphate is a nucleotide, also called a nucleoside triphosphate, is a small molecule used in cells as a coenzyme. It is often referred to as the unit of currency of intracellular energy transfer. ATP transports chemical energy within cells for metabolism, most cellular functions need energy in order to be carried out, synthesis of proteins, synthesis of membranes, movement of the cell, cellular division, transport of various solutes etc. The ATP is the molecule that carries energy to the place where the energy is needed, when ATP breaks into ADP and Pi, the breakdown of the last covalent link of phosphate liberates energy that is used in reactions where it is needed. Substrate-level phosphorylation, oxidative phosphorylation in cellular respiration, and photophosphorylation in photosynthesis are three mechanisms of ATP biosynthesis. Metabolic processes that use ATP as an energy source convert it back into its precursors, ATP is therefore continuously recycled in organisms, the human body, which on average contains only 250 grams of ATP, turns over its own body weight equivalent in ATP each day. ATP is used as a substrate in signal transduction pathways by kinases that phosphorylate proteins and it is also used by adenylate cyclase, which uses ATP to produce the second messenger molecule cyclic AMP. The ratio between ATP and AMP is used as a way for a cell to sense how much energy is available and control the metabolic pathways that produce and consume ATP. Apart from its roles in signaling and energy metabolism, ATP is also incorporated into nucleic acids by polymerases in the process of transcription, ATP is the neurotransmitter believed to signal the sense of taste. The structure of this consists of a purine base attached by the 9′ nitrogen atom to the 1′ carbon atom of a pentose sugar. Three phosphate groups are attached at the 5′ carbon atom of the pentose sugar and it is the addition and removal of these phosphate groups that inter-convert ATP, ADP and AMP. When ATP is used in DNA synthesis, the sugar is first converted to deoxyribose by ribonucleotide reductase. ATP was discovered in 1929 by Karl Lohmann, and independently by Cyrus Fiske and Yellapragada Subbarow of Harvard Medical School and it was proposed to be the intermediary molecule between energy-yielding and energy-requiring reactions in cells by Fritz Albert Lipmann in 1941. It was first artificially synthesized by Alexander Todd in 1948, ATP consists of adenosine – composed of an adenine ring and a ribose sugar – and three phosphate groups. The phosphoryl groups, starting with the group closest to the ribose, are referred to as the alpha, beta, consequently, it is closely related to the adenosine nucleotide, a monomer of RNA. ATP is highly soluble in water and is stable in solutions between pH6.8 and 7.4, but is rapidly hydrolysed at extreme pH. Consequently, ATP is best stored as an anhydrous salt, ATP is an unstable molecule in unbuffered water, in which it hydrolyses to ADP and phosphate. This is because the strength of the bonds between the groups in ATP is less than the strength of the hydrogen bonds, between its products, and water
35.
Metal cluster
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In chemistry, a cluster is an ensemble of bound atoms or molecules that is intermediate in size between a molecule and a bulk solid. Clusters exist of diverse stoichiometries and nuclearities, for example, carbon and boron atoms form fullerene and borane clusters, respectively. Transition metals and main group elements form especially robust clusters, clusters can also consist solely of a certain kind of molecules, such as water clusters. The phrase cluster was coined by F. A, Cotton in the early 1960s to refer to compounds containing metal–metal bonds. In another definition a cluster contains a group of two or more metal atoms where direct and substantial metal bonding is present. The prefixed terms nuclear and metallic are used and imply different meanings, for example, polynuclear refers to a cluster with more than one metal atom, regardless of the elemental identities. Heteronuclear refers to a cluster with at least two different metal elements, the main cluster types are naked clusters and those with ligands. For transition metal clusters, typical stabilizing ligands include carbon monoxide, halides, isocyanides, alkenes, for main group elements, typical clusters are stabilized by hydride ligands. Transition metal clusters are composed of refractory metal atoms. In general metal centers with extended d-orbitals form stable clusters because of overlap of valence orbitals. Thus, metals with a low state for the later metals. Polynuclear metal carbonyls are generally found in transition metals with low formal oxidation states. The polyhedral skeletal electron pair theory or Wades electron counting rules predict trends in the stability, jemmis mno rules have provided additional insight into the relative stability of metal clusters. The development of cluster chemistry occurred contemporaneously along several independent lines, the first synthetic metal cluster was probably calomel, which was known in India already in the 12th century. The existence of a mercury to mercury bond in this compound was established in the beginning of the 20th century, atomic clusters can be either pure, formed from a single atomic species, or mixed, formed from a mixed atomic species. Atomic and molecular clusters are aggregates of 5-105 atomic or molecular units, quantum many-body mechanisms are also important. And yet the clusters exhibit physical and chemical properties specific only to their configuration space, many of their properties are due to the fact that a large fraction of their component atoms is found at their surface. With increasing size, the number of atoms at the cluster surface will scale approximately as N−1/3
36.
FeMoco
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FeMoco is the primary cofactor of nitrogenase. Nitrogenase is the enzyme catalyzes the conversion of atmospheric N2 into ammonia. Containing iron and molybdenum, the cofactor is called FeMoco, the FeMo cofactor is a cluster with composition Fe7MoS9C. This large cluster can be viewed as two subunits composed of one Fe4S3 cluster and one MoFe3S3 cluster, the two clusters are linked by three sulfide ligands. The unique Fe is anchored to the protein by a cysteine and it is also bound to three sulfides, resulting in tetrahedral molecular geometry. The additional six Fe centers in the cluster are each bonded to three sulfides and these six internal Fe centers define a trigonal prismatic arrangement around a central carbide center. The molybdenum is attached to three sulfides and is anchored to the protein by the group of a histidine residue. Also bound to Mo is a bidentate homocitrate cofactor, leading to octahedral geometry, crystallographic analysis of the MoFe protein initially proposed the geometry of FeMoco, which was confirmed by extended X-ray absorption fine-structure studies. Distances for Fe-S, Fe-Fe and Fe-Mo distances were determined to be 2.32,2.64, according to the analysis by electron paramagnetic resonance spectroscopy, the resting state of the FeMo cofactor has a spin state of S=3/2. Upon one-electron reduction, the cofactor becomes EPR silent, understanding the process in which an electron is transferred in the protein adduct shows a more precise kinetic model of the FeMo cofactor. The formal oxidation state is MoIV-2FeII-5FeIII-C4−-H+, including the cysteine proton, biosynthesis of FeMoco is a complicated process that requires nifS, nifQ, nifB, nifE, nifN, nifV, nifH, nifD, and nifK gene products. FeMoco assembly is proposed to be initiated by NifS and NifU which mobilize Fe and these fragments are transferred to the NifB scaffold and arranged into a Fe7MoS9C cluster before transfer to the NifEN protein and rearranged before delivery to the MoFe protein. Several other factors participate in the biosynthesis, for example, NifV is the homocitrate synthase that supplies homocitrate to FeMoco. NifV, a factor, is proposed to be involved in the storage and/or mobilization of Mo. Fe protein is the electron donor for MoFe protein6. These biosynthetic factors have been elucidated and characterized with the functions and sequence confirmed by biochemical, spectroscopic. Isolation of the FeMo cofactor from nitrogenase is done through centrifugal sedimentation of nitrogenase into the MoFe protein, the FeMo cofactor is extracted by treating the MoFe protein with acids5. The first extraction is done with N, N-dimethylformamide and the second by a mixture of N-methylformamide, the three proteins that play a direct role in the M-cluster synthesis are NifH, NifEN, and NifB. The NifB protein is responsible for the assembly of the Fe-S core of the cofactor, NifB belongs to the SAM enzyme superfamily
37.
Active site
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In biology, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of residues that form bonds with the substrate. The active site is usually a groove or pocket of the enzyme which can be located in a tunnel within the enzyme. An active site can catalyse a reaction repeatedly as its residues are not altered at the end of the reaction, usually, an enzyme molecule has only one active site, and the active site fits with one specific type of substrate. An active site contains a site that binds the substrate. Residues in the site form hydrogen bonds, hydrophobic interactions. In order to function, the site needs to be in a specific conformation. A tighter fit between a site and the substrate molecule is believed to increase efficiency of a reaction. Most enzymes have deeply buried active sites, which can be accessed by a substrate via access channels, there are two proposed models of how enzymes fit to their specific substrate, the lock and key model and the induced fit model. Emil Fischers lock and key model assumes that the site is a perfect fit for a specific substrate. Daniel Koshlands theory of enzyme-substrate binding is that the active site, the induced fit model is a development of the lock-and-key model and assumes that an active site is flexible and it changes shape until the substrate is completely bound. The substrate is thought to induce a change in the shape of the active site, the hypothesis also predicts that the presence of certain residues in the active site will encourage the enzyme to locate the correct substrate. Conformational changes may occur as the substrate is bound. After the products of the move away from the enzyme. Once the substrate is bound and oriented in the active site, the residues of the catalytic site are typically very close to the binding site, and some residues can have dual-roles in both binding and catalysis. Catalytic residues of the site interact with the substrate to lower the energy of a reaction. They do this by a number of different mechanisms, firstly, they can act as donors or acceptors of protons or other groups on the substrate to facilitate the reaction. They can also form electrostatic interactions to stabilise charge buildup on the state or leaving group
38.
Hydrogenation
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Hydrogenation – to treat with hydrogen – is a chemical reaction between molecular hydrogen and another compound or element, usually in the presence of a catalyst such as nickel, palladium or platinum. The process is employed to reduce or saturate organic compounds. Hydrogenation typically constitutes the addition of pairs of atoms to a molecule. Catalysts are required for the reaction to be usable, non-catalytic hydrogenation takes place only at high temperatures. Hydrogenation reduces double and triple bonds in hydrocarbons and it has three components, the unsaturated substrate, the hydrogen and, invariably, a catalyst. The reduction reaction is carried out at different temperatures and pressures depending upon the substrate, the same catalysts and conditions that are used for hydrogenation reactions can also lead to isomerization of the alkenes from cis to trans. This process is of great interest because hydrogenation technology generates most of the fat in foods. A reaction where bonds are broken while hydrogen is added is called hydrogenolysis, some hydrogenations of polar bonds are accompanied by hydrogenolysis. For hydrogenation, the source of hydrogen is H2 gas itself. The hydrogenation process often uses greater than 1 atmosphere of H2, usually conveyed from the cylinders, gaseous hydrogen is produced industrially from hydrocarbons by the process known as steam reforming. For many applications, hydrogen is transferred from donor molecules such as acid, isopropanol. These hydrogen donors undergo dehydrogenation to, respectively, carbon dioxide, acetone and these processes are called transfer hydrogenations. Typical substrates are listed in the table With rare exceptions, H2 is unreactive toward organic compounds in the absence of metal catalysts, the unsaturated substrate is chemisorbed onto the catalyst, with most sites covered by the substrate. In heterogeneous catalysts, hydrogen forms surface hydrides from which hydrogens can be transferred to the chemisorbed substrate, platinum, palladium, rhodium, and ruthenium form highly active catalysts, which operate at lower temperatures and lower pressures of H2. Non-precious metal catalysts, especially based on nickel have also been developed as economical alternatives. The trade-off is activity vs. cost of the catalyst and cost of the apparatus required for use of high pressures, notice that the Raney-nickel catalysed hydrogenations require high pressures, Catalysts are usually classified into two broad classes, homogeneous catalysts and heterogeneous catalysts. Homogeneous catalysts dissolve in the solvent that contains the unsaturated substrate, heterogeneous catalysts are solids that are suspended in the same solvent with the substrate or are treated with gaseous substrate. Some well known homogeneous catalysts are indicated below and these are coordination complexes that activate both the unsaturated substrate and the H2
39.
Glutamic acid
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Glutamic acid is an α-amino acid with formula C 5H 9O 4N. It is usually abbreviated as Glu or E in biochemistry and its molecular structure could be idealized as HOOC-CH-2-COOH, with two carboxyl groups -COOH and one amino group -NH2. However, in the state and mildly acid water solutions. Glutamic acid is used by almost all living beings in the biosynthesis of proteins and it is non-essential in humans, meaning the body can synthesize it. The acid can lose one proton from second carboxyl group to form the conjugate base and this form of the compound is prevalent in neutral solutions. The glutamate neurotransmitter plays the role in neural activation. This anion is also responsible for the flavor of certain foods. In highly alkaline solutions the doubly negative anion −OOC-CH-2-COO− prevails, the radical corresponding to glutamate is called glutamyl. When glutamic acid is dissolved in water, the group may gain a proton, and/or the carboxyl groups may lose protons. In sufficiently acid environments, the group gains a proton. At pH values between about 2.5 and 4.1, the carboxylic acid closer to the amine generally loses a proton, and the acid becomes the neutral zwitterion −OOC-CH-2-COOH. This is also the form of the compound in the solid state. The switchover is gradual, the two forms are in equal concentrations at pH2.10, at even higher pH, the other carboxyl loses its proton and the acid exists almost entirely as the glutamate anion −OOC-CH-2-COO−, with a single negative charge. The switchover occurs at pH4.07, the latter is the case, in particular, in the physiological pH range. At even higher pH, the group loses the extra proton. The switchover occurs at pH9.47, the carbon atom adjacent to the amino group is chiral, so glutamic acid can exist in two optical isomers, D and L. The L form is the one most widely occurring in nature, but the D form occurs in special contexts, such as the cell walls of the bacterium Escherichia coli. Although they occur naturally in foods, the flavor contributions made by glutamic acid
40.
Glutamine synthetase
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The amide group of glutamate is a nitrogen source for the synthesis of glutamine pathway metabolites. Other reactions may take place via GS, competition between ammonium ion and water, their binding affinities, and the concentration of ammonium ion, influences glutamine synthesis and glutamine hydrolysis. Glutamine is formed if an ammonium ion attacks the acyl-phosphate intermediate, ammonium ion binds more strongly than water to GS due to electrostatic forces between a cation and a negatively charged pocket. Another possible reaction is upon NH2OH binding to GS, rather than NH4+, glutamine Synthetase can be composed of 8,10, or 12 identical subunits separated into two face-to-face rings. Bacterial GS are dodecamers with 12 active sites between each monomer, each active site creates a ‘tunnel’ which is the site of three distinct substrate binding sites, nucleotide, ammonium ion, and amino acid. ATP binds to the top of the bifunnel that opens to the surface of GS. Glutamate binds at the bottom of the active site, the middle of the bifunnel contains two sites in which divalent cations bind. One cation binding site is involved in transfer of ATP to glutamate, while the second stabilizes active GS. Hydrogen bonding and hydrophobic interactions hold the two rings of GS together, each subunit possesses a C-terminus and an N-terminus in its sequence. The C-terminus stabilizes the GS structure by inserting into the region of the subunit across in the other ring. The N-terminus is exposed to the solvent, in addition, the central channel is formed via six four-stranded β-sheets composed of anti-parallel loops from the twelve subunits. GS catalyzes the ATP-dependent condensation of glutamate with ammonia to yield glutamine, the hydrolysis of ATP drives the first step of a two-part, concerted mechanism. ATP phosphorylates glutamate to form ADP and an intermediate, γ-glutamyl phosphate. ADP and Pi do not dissociate until ammonia binds and glutamine is released, ATP binds first to the top of the active site near a cation binding site, while glutamate binds near the second cation binding site at the bottom of the active site. The presence of ADP causes a shift in GS that stabilizes the γ-glutamyl phosphate moiety. Ammonium binds strongly to GS only if the intermediate is present. Ammonium, rather than ammonia, binds to GS because the site is polar. In the second step, deprotonation of ammonium allows ammonia to attack the intermediate from its site to form glutamine
41.
Anaerobic organism
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An anaerobic organism or anaerobe is any organism that does not require oxygen for growth. It may react negatively or even die if oxygen is present, an anaerobic organism may be unicellular or multicellular. Van Leeuwenhoek sealed one of the tubes by using a flame. In 1913 Martinus Beijerinck repeated Van Leeuwenhoeks experiment and identified Clostridium butyricum as a prominent anaerobic bacterium in the sealed pepper infusion tube liquid. That Leeuwenhoek, one hundred years before the discovery of oxygen, for practical purposes, there are three categories of anaerobe, Obligate anaerobes, which are harmed by the presence of oxygen. Aerotolerant organisms, which use oxygen for growth, but tolerate its presence. Facultative anaerobes, which can grow without oxygen but use oxygen if it is present, some obligate anaerobes use fermentation, while others use anaerobic respiration. In the presence of oxygen, facultative anaerobes use aerobic respiration, without oxygen, some of them ferment, there are many anaerobic fermentative reactions. This is only 5% of the energy per molecule that the typical aerobic reaction generates. Since normal microbial culturing occurs in air, which is an aerobic environment. Hydrogen then reacts with oxygen gas on a palladium catalyst to more water. The issue with the Gaspak method is that a reaction can take place where the bacteria may die. The thioglycollate supplies a medium mimicking that of a dicot, thus providing not only an anaerobic environment, complex multicellular life that does not need oxygen is said to be rare, however there are examples of such organisms. Some organisms metabolise primarily using glycogen, for example the Nereid s and some polychaetes, or the juvenile Trichinella spiralis parasites. )
42.
Leghemoglobin
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Leghemoglobin is a nitrogen or oxygen carrier and hemoprotein found in the nitrogen-fixing root nodules of leguminous plants. Leghemoglobin has close chemical and structural similarities to hemoglobin, and, the holoprotein is widely believed to be a product of both plant and the bacterium in which the apoprotein is produced by the plant and the heme is produced by the bacterium. There is some evidence, however, that suggests that the heme moiety is also produced by the plant, leghemoglobin buffers the concentration of free oxygen in the cytoplasm of infected plant cells to ensure the proper function of root nodules. Leghemoglobin has an affinity for oxygen, about ten times higher than the β chain of human hemoglobin. This allows an oxygen concentration that is low enough to allow nitrogenase to function, although leghemoglobin was once thought to provide a buffer for nodule oxygen, recent studies indicate that it stores only enough oxygen to support nodule respiration for a few seconds. Its function is to provide oxygen to the respiring symbiotic bacterial cells in a manner analogous to hemoglobin transporting oxygen to respiring tissues in animals. Other plants, like Casuarina sp which is an actinorhizal plant, hemoglobin Myoglobin Phytoglobin Virtanen, A. I. Sunderland, MA, Sinauwr Associates, Inc. p.269
43.
Cyanobacteria
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The name cyanobacteria comes from the color of the bacteria. Sometimes, they are called blue-green algae, and incorrectly so, because cyanobacteria are prokaryotes, like other prokaryotes, cyanobacteria have no membrane-sheathed organelles. Photosynthesis is performed in distinctive folds in the membrane of the cell. Biologists commonly agree that chloroplasts found in eukaryotes have their ancestry in cyanobacteria, via a process called endosymbiosis, Cyanobacteria are a group of photosynthetic, nitrogen fixing bacteria that live in a wide variety of habitats such as moist soils and in water. They may be free-living or form relationships with plants or with lichen-forming fungi as in the lichen genus Peltigera. They range from unicellular to filamentous and include colonial species, colonies may form filaments, sheets, or even hollow balls. Cyanobacteria can fix nitrogen in anaerobic conditions by means of specialized cells called heterocysts. Heterocysts may also form under the environmental conditions when fixed nitrogen is scarce. Free-living cyanobacteria are present in the column in rice paddies, and cyanobacteria can be found growing as epiphytes on the surfaces of the green alga, Chara. Cyanobacteria such as, can provide rice plantations with biofertilizer, many cyanobacteria form motile filaments of cells, called hormogonia, that travel away from the main biomass to bud and form new colonies elsewhere. The cells in a hormogonium are often thinner than in the state. To break away from the parent colony, a hormogonium often must tear apart a weaker cell in a filament, each individual cell of a cyanobacterium typically has a thick, gelatinous cell wall. They lack flagella, but hormogonia of some species can move about by gliding along surfaces, many of the multicellular filamentous forms of Oscillatoria are capable of a waving motion, the filament oscillates back and forth. In water columns, some cyanobacteria float by forming gas vesicles and these vesicles are not organelles as such. They are not bounded by membranes, but by a protein sheath. Cyanobacteria can be found in almost every terrestrial and aquatic habitat—oceans, fresh water, damp soil, temporarily moistened rocks in deserts, bare rock and soil and they can occur as planktonic cells or form phototrophic biofilms. They are found in almost every endolithic ecosystem, a few are endosymbionts in lichens, plants, various protists, or sponges and provide energy for the host. Some live in the fur of sloths, providing a form of camouflage, aquatic cyanobacteria are known for their extensive and highly visible blooms that can form in both freshwater and marine environments
. PMID 23289741.
