Biochemistry

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Posted by kaori 03/17/2009 @ 23:10

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Biochemistry

The general structure of an α-amino acid, with the amino group on the left and the carboxyl group on the right.

Biochemistry is the study of the chemical processes in living organisms. It deals with the structure and function of cellular components such as proteins, carbohydrates, lipids, nucleic acids and other biomolecules.

Although there are a vast number of different biomolecules many are complex and large molecules (called polymers) that are composed of similar repeating subunits (called monomers). Each class of polymeric biomolecule has a different set of subunit types. For example, a protein is a polymer whose subunits are selected from a set of 20 or more amino acids. Biochemistry studies the chemical properties of important biological molecules, like proteins, in particular the chemistry of enzyme-catalyzed reactions.

The biochemistry of cell metabolism and the endocrine system has been extensively described. Other areas of biochemistry include the genetic code (DNA, RNA), protein synthesis, cell membrane transport, and signal transduction.

Since all known life forms that are still alive today are descended from the same common ancestor, they have similar biochemistries, even for matters that seem to be essentially arbitrary, such as handedness of various biomolecules. It is unknown whether alternative biochemistries are possible or practical.

Originally, it was generally believed that life was not subject to the laws of science the way non-life was. It was thought that only living beings could produce the molecules of life (from other, previously existing biomolecules). Then, in 1828, Friedrich Wöhler published a paper on the synthesis of urea, proving that organic compounds can be created artificially.

The dawn of biochemistry may have been the discovery of the first enzyme, diastase (today called amylase), in 1833 by Anselme Payen. Eduard Buchner contributed the first demonstration of a complex biochemical process outside of a cell in 1896: alcoholic fermentation in cell extracts of yeast. Although the term “biochemistry” seems to have been first used in 1882, it is generally accepted that the formal coinage of biochemistry occurred in 1903 by Carl Neuberg, a German chemist. Previously, this area would have been referred to as physiological chemistry. Since then, biochemistry has advanced, especially since the mid-20th century, with the development of new techniques such as chromatography, X-ray diffraction, NMR spectroscopy, radioisotopic labeling, electron microscopy and molecular dynamics simulations. These techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle (citric acid cycle).

Today, there are three main types of biochemistry as established by Michael E. Sugar. Plant biochemistry involves the study of the biochemistry of autotrophic organisms such as photosynthesis and other plant specific biochemical processes. General biochemistry encompasses both plant and animal biochemistry. Human/medical/medicinal biochemistry focuses on the biochemistry of humans and medical illnesses.

Monomers and polymers are a structural basis in which the four main macromolecules (Carbohydrates, lipids, proteins, and nucleic acids), or biopolymers, of biochemistry are based on. Monomers are smaller micromolecules that are put together to make macromolecules. Polymers are those macromolecules that are created when monomers are synthesized together. When they are synthesized, the two molecules undergo a process called dehydration synthesis.

Carbohydrates have monomers called monosaccharides. Some of these monosaccharides include glucose (C6H12O6), fructose (C6H12O6), and deoxyribose (C5H10O4). When two monosaccharides undergo dehydration synthesis, water is produced, as two hydrogen atoms and one oxygen atom are lost from the two monosaccharides' carboxyl group.

Lipids are usually made up of a molecule of glycerol and other molecules. In triglycerides, or the main lipid, there is one molecule of glycerol, and three fatty acids. Fatty acids are considered the monomer in that case, and could be saturated or unsaturated. Lipids, especially phospholipids, are also used in different pharmaceutical products, either as co-solubilisers e.g. in Parenteral infusions or else as drug carrier components (e.g. in a Liposome or Transfersome).

Proteins are large molecules, and have monomers of amino acids. There are 20 different known kinds of amino acids, and they contain a carboxyl group, an amino group, and an "R" group. The "R" group is what makes each amino acid different. When Amino acids combine, they form a special bond called a peptide bond, and become a polypeptide, or a protein.

Nucleic acids are very important in biochemistry, as they are what make up DNA, something all cellular organism use to store their genetic information. The most common nucleic acids are deoxyribonucleic acid and ribonucleic acid. Their monomers are called nucleotides. The most common nucleotides are called adenine, cytosine, guanine, thymine, and uracil. Adenine binds with thymine and uracil, thymine only binds with adenine, and cytosine and guanine can only bind with each other.

The function of carbohydrates includes energy storage and providing structure. Sugars are carbohydrates, but not all carbohydrates are sugars. There are more carbohydrates on Earth than any other known type of biomolecule; they are used to store energy and genetic information, as well as play important roles in cell to cell interactions and communications.

The simplest type of carbohydrate is a monosaccharide, which among other properties contains carbon, hydrogen, and oxygen, mostly in a ratio of 1:2:1 (generalized formula CnH2nOn, where n is at least 3). Glucose, one of the most important carbohydrates, is an example of a monosaccharide. So is fructose, the sugar that gives fruits their sweet taste. Some carbohydrates (especially after condensation to oligo- and polysaccharides) contain less carbon relative to H and O, which still are present in 2:1 (H:O) ratio. Monosaccharides can be grouped into aldoses (having an aldehyde group at the end of the chain, e. g. glucose) and ketoses (having a keto group in their chain; e. g. fructose). Both aldoses and ketoses occur in an equilibrium between the open-chain forms and (starting with chain lengths of C4) cyclic forms. These are generated by bond formation between one of the hydroxyl groups of the sugar chain with the carbon of the aldehyde or keto group to form a hemiacetal bond. This leads to saturated five-membered (in furanoses) or six-membered (in pyranoses) heterocyclic rings containing one O as heteroatom.

Two monosaccharides can be joined together using dehydration synthesis, in which a hydrogen atom is removed from the end of one molecule and a hydroxyl group (—OH) is removed from the other; the remaining residues are then attached at the sites from which the atoms were removed. The H—OH or H2O is then released as a molecule of water, hence the term dehydration. The new molecule, consisting of two monosaccharides, is called a disaccharide and is conjoined together by a glycosidic or ether bond. The reverse reaction can also occur, using a molecule of water to split up a disaccharide and break the glycosidic bond; this is termed hydrolysis. The most well-known disaccharide is sucrose, ordinary sugar (in scientific contexts, called table sugar or cane sugar to differentiate it from other sugars). Sucrose consists of a glucose molecule and a fructose molecule joined together. Another important disaccharide is lactose, consisting of a glucose molecule and a galactose molecule. As most humans age, the production of lactase, the enzyme that hydrolyzes lactose back into glucose and galactose, typically decreases. This results in lactase deficiency, also called lactose intolerance.

Sugar polymers are characterised by having reducing or non-reducing ends. A reducing end of a carbohydrate is a carbon atom which can be in equilibrium with the open-chain aldehyde or keto form. If the joining of monomers takes place at such a carbon atom, the free hydroxy group of the pyranose or furanose form is exchanged with an OH-side chain of another sugar, yielding a full acetal. This prevents opening of the chain to the aldehyde or keto form and renders the modified residue non-reducing. Lactose contains a reducing end at its glucose moiety, whereas the galactose moiety form a full acetal with the C4-OH group of glucose. Saccharose does not have a reducing end because of full acetal formation between the aldehyde carbon of glucose (C1) and the keto carbon of fructose (C2).

When a few (around three to six) monosaccharides are joined together, it is called an oligosaccharide (oligo- meaning "few"). These molecules tend to be used as markers and signals, as well as having some other uses. Many monosaccharides joined together make a polysaccharide. They can be joined together in one long linear chain, or they may be branched. Two of the most common polysaccharides are cellulose and glycogen, both consisting of repeating glucose monomers.

Glucose is the major energy source in most life forms. For instance, polysaccharides are broken down into their monomers (glycogen phosphorylase removes glucose residues from glycogen). Disaccharides like lactose or sucrose are cleaved into their two component monosaccharides.

Glucose is mainly metabolized by a very important and ancient ten-step pathway called glycolysis, the net result of which is to break down one molecule of glucose into two molecules of pyruvate; this also produces a net two molecules of ATP, the energy currency of cells, along with two reducing equivalents in the form of converting NAD+ to NADH. This does not require oxygen; if no oxygen is available (or the cell cannot use oxygen), the NAD is restored by converting the pyruvate to lactate (lactic acid) (e. g. in humans) or to ethanol plus carbon dioxide (e. g. in yeast). Other monosaccharides like galactose and fructose can be converted into intermediates of the glycolytic pathway.

In aerobic cells with sufficient oxygen, like most human cells, the pyruvate is further metabolized. It is irreversibly converted to acetyl-CoA, giving off one carbon atom as the waste product carbon dioxide, generating another reducing equivalent as NADH. The two molecules acetyl-CoA (from one molecule of glucose) then enter the citric acid cycle, producing two more molecules of ATP, six more NADH molecules and two reduced (ubi)quinones (via FADH2 as enzyme-bound cofactor), and releasing the remaining carbon atoms as carbon dioxide. The produced NADH and quinol molecules then feed into the enzyme complexes of the respiratory chain, an electron transport system transferring the electrons ultimately to oxygen and conserving the released energy in the form of a proton gradient over a membrane (inner mitochondrial membrane in eukaryotes). Thereby, oxygen is reduced to water and the original electron acceptors NAD+ and quinone are regenerated. This is why humans breathe in oxygen and breathe out carbon dioxide. The energy released from transferring the electrons from high-energy states in NADH and quinol is conserved first as proton gradient and converted to ATP via ATP synthase. This generates an additional 28 molecules of ATP (24 from the 8 NADH + 4 from the 2 quinols), totaling to 32 molecules of ATP conserved per degraded glucose (two from glycolysis + two from the citrate cycle). It is clear that using oxygen to completely oxidize glucose provides an organism with far more energy than any oxygen-independent metabolic feature, and this is thought to be the reason why complex life appeared only after Earth's atmosphere accumulated large amounts of oxygen.

In vertebrates, vigorously contracting skeletal muscles (during weightlifting or sprinting, for example) do not receive enough oxygen to meet the energy demand, and so they shift to anaerobic metabolism, converting glucose to lactate. The liver regenerates the glucose, using a process called gluconeogenesis. This process is not quite the opposite of glycolysis, and actually requires three times the amount of energy gained from glycolysis (six molecules of ATP are used, compared to the two gained in glycolysis). Analogous to the above reactions, the glucose produced can then undergo glycolysis in tissues that need energy, be stored as glycogen (or starch in plants), or be converted to other monosaccharides or joined into di- or oligosaccharides. The combined pathways of glycolysis during exercise, lactate's crossing via the bloodstream to the liver, subsequent gluconeogenesis and release of glucose into the bloodstream is called the Cori cycle.

Like carbohydrates, some proteins perform largely structural roles. For instance, movements of the proteins actin and myosin ultimately are responsible for the contraction of skeletal muscle. One property many proteins have is that they specifically bind to a certain molecule or class of molecules—they may be extremely selective in what they bind. Antibodies are an example of proteins that attach to one specific type of molecule. In fact, the enzyme-linked immunosorbent assay (ELISA), which uses antibodies, is currently one of the most sensitive tests modern medicine uses to detect various biomolecules. Probably the most important proteins, however, are the enzymes. These molecules recognize specific reactant molecules called substrates; they then catalyze the reaction between them. By lowering the activation energy, the enzyme speeds up that reaction by a rate of 1011 or more: a reaction that would normally take over 3,000 years to complete spontaneously might take less than a second with an enzyme. The enzyme itself is not used up in the process, and is free to catalyze the same reaction with a new set of substrates. Using various modifiers, the activity of the enzyme can be regulated, enabling control of the biochemistry of the cell as a whole.

In essence, proteins are chains of amino acids. An amino acid consists of a carbon atom bound to four groups. One is an amino group, —NH2, and one is a carboxylic acid group, —COOH (although these exist as —NH3+ and —COO− under physiologic conditions). The third is a simple hydrogen atom. The fourth is commonly denoted "—R" and is different for each amino acid. There are twenty standard amino acids. Some of these have functions by themselves or in a modified form; for instance, glutamate functions as an important neurotransmitter.

Amino acids can be joined together via a peptide bond. In this dehydration synthesis, a water molecule is removed and the peptide bond connects the nitrogen of one amino acid's amino group to the carbon of the other's carboxylic acid group. The resulting molecule is called a dipeptide, and short stretches of amino acids (usually, fewer than around thirty) are called peptides or polypeptides. Longer stretches merit the title proteins. As an example, the important blood serum protein albumin contains 585 amino acid residues.

The structure of proteins is traditionally described in a hierarchy of four levels. The primary structure of a protein simply consists of its linear sequence of amino acids; for instance, "alanine-glycine-tryptophan-serine-glutamate-asparagine-glycine-lysine-…". Secondary structure is concerned with local morphology. Some combinations of amino acids will tend to curl up in a coil called an α-helix or into a sheet called a β-sheet; some α-helixes can be seen in the hemoglobin schematic above. Tertiary structure is the entire three-dimensional shape of the protein. This shape is determined by the sequence of amino acids. In fact, a single change can change the entire structure. The alpha chain of hemoglobin contains 146 amino acid residues; substitution of the glutamate residue at position 6 with a valine residue changes the behavior of hemoglobin so much that it results in sickle-cell disease. Finally quaternary structure is concerned with the structure of a protein with multiple peptide subunits, like hemoglobin with its four subunits. Not all proteins have more than one subunit.

Ingested proteins are usually broken up into single amino acids or dipeptides in the small intestine, and then absorbed. They can then be joined together to make new proteins. Intermediate products of glycolysis, the citric acid cycle, and the pentose phosphate pathway can be used to make all twenty amino acids, and most bacteria and plants possess all the necessary enzymes to synthesize them. Humans and other mammals, however, can only synthesize half of them. They cannot synthesize isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. These are the essential amino acids, since it is essential to ingest them. Mammals do possess the enzymes to synthesize alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine, the nonessential amino acids. While they can synthesize arginine and histidine, they cannot produce it in sufficient amounts for young, growing animals, and so these are often considered essential amino acids.

If the amino group is removed from an amino acid, it leaves behind a carbon skeleton called an α-keto acid. Enzymes called transaminases can easily transfer the amino group from one amino acid (making it an α-keto acid) to another α-keto acid (making it an amino acid). This is important in the biosynthesis of amino acids, as for many of the pathways, intermediates from other biochemical pathways are converted to the α-keto acid skeleton, and then an amino group is added, often via transamination. The amino acids may then be linked together to make a protein.

A similar process is used to break down proteins. It is first hydrolyzed into its component amino acids. Free ammonia (NH3), existing as the ammonium ion (NH4+) in blood, is toxic to life forms. A suitable method for excreting it must therefore exist. Different strategies have evolved in different animals, depending on the animals' needs. Unicellular organisms, of course, simply release the ammonia into the environment. Similarly, bony fish can release the ammonia into the water where it is quickly diluted. In general, mammals convert the ammonia into urea, via the urea cycle.

The term lipid comprises a diverse range of molecules and to some extent is a catchall for relatively water-insoluble or nonpolar compounds of biological origin, including waxes, fatty acids, fatty-acid derived phospholipids, sphingolipids, glycolipids and terpenoids (eg. retinoids and steroids). Some lipids are linear aliphatic molecules, while others have ring structures. Some are aromatic, while others are not. Some are flexible, while others are rigid.

Most lipids have some polar character in addition to being largely nonpolar. Generally, the bulk of their structure is nonpolar or hydrophobic ("water-fearing"), meaning that it does not interact well with polar solvents like water. Another part of their structure is polar or hydrophilic ("water-loving") and will tend to associate with polar solvents like water. This makes them amphiphilic molecules (having both hydrophobic and hydrophilic portions). In the case of cholesterol, the polar group is a mere -OH (hydroxyl or alcohol). In the case of phospholipids, the polar groups are considerably larger and more polar, as described below.

Lipids are an integral part of our daily diet. Most oils and milk products that we use for cooking and eating like butter, cheese, ghee etc, are comprised of fats. Vegetable oils are rich in various polyunsaturated fatty acids (PUFA). Lipid-containing foods undergo digestion within the body and are broken into fatty acids and glycerol, which are the final degradation products of fats and lipids.

A nucleic acid is a complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that convey genetic information. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are found in all living cells and viruses. Aside from the genetic material of the cell, nucleic acids often play a role as second messengers, as well as forming the base molecule for adenosine triphosphate, the primary energy-carrier molecule found in all living organisms.

Nucleic acid, so called because of its prevalence in cellular nuclei, is the generic name of the family of biopolymers. The monomers are called nucleotides, and each consists of three components: a nitrogenous heterocyclic base (either a purine or a pyrimidine), a pentose sugar, and a phosphate group. Different nucleic acid types differ in the specific sugar found in their chain (e.g. DNA or deoxyribonucleic acid contains 2-deoxyriboses). Also, the nitrogenous bases possible in the two nucleic acids are different: adenine, cytosine, and guanine occur in both RNA and DNA, while thymine occurs only in DNA and uracil occurs in RNA.

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Max Planck Institute of Biochemistry

MPIBioChem Logo.png

The Max Planck Institute of Biochemistry is a research institute of the Max Planck Society located in Martinsried, a suburb of Munich. The Institute, founded 1912 as a Kaiser Wilhelm Institute, was relocated from Berlin in 1945 to Tübingen and moved once more in 1956 to Munich. During this time from 1933 on Adolf Butenandt was director of the institute.

The institute in Munich was founded 1973 by the merger of three former independent institutes, the Max Planck Institute of Biochemistry, , the Max Planck Institute of Protein and Leather Research, founded 1954 in Regensburg, and the Max Planck Institute of Cell Chemistry, founded 1956 in Munich.

The International Max Planck Research School (IMPRS) for Molecular and Cellular Life Sciences is a PhD program covering various aspects of life science ranging from biochemistry to molecular medicine. The school is run in cooperation with the Max Planck Institute of Neurobiology, the Max Planck Institute of Psychiatry, Ludwig Maximilians University of Munich and the Technical University of Munich.

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History of biochemistry

Eduard Buchner

The history of biochemistry spans approximately 400 years. Although the term “biochemistry” seems to have been first used in 1882, it is generally accepted that the word "biochemistry" was first proposed in 1903 by Carl Neuberg, a German chemist.

Originally, it was generally believed that life was not subject to the laws of science the way non-life was. It was thought that only living beings could produce the molecules of life (from other, previously existing biomolecules). Then, in 1828, Friedrich Wöhler published a paper about the synthesis of urea, proving that organic compounds can be created artificially.

As early as the late 18th century and early 19th century, the digestion of meat by stomach secretions and the conversion of starch to sugars by plant extracts and saliva were known. However, the mechanism by which this occurred had not been identified.

In 1878 German physiologist Wilhelm Kühne (1837–1900) coined the term enzyme, which comes from Greek ενζυμον "in leaven", to describe this process. The word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment used to refer to chemical activity produced by living organisms.

In 1897 Eduard Buchner began to study the ability of yeast extracts to ferment sugar despite the absence of living yeast cells. In a series of experiments at the University of Berlin, he found that the sugar was fermented even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose "zymase". In 1907 he received the Nobel Prize in Chemistry "for his biochemical research and his discovery of cell-free fermentation". Following Buchner's example; enzymes are usually named according to the reaction they carry out. Typically the suffix -ase is added to the name of the substrate (e.g., lactase is the enzyme that cleaves lactose) or the type of reaction (e.g., DNA polymerase forms DNA polymers).

Having shown that enzymes could function outside a living cell, the next step was to determine their biochemical nature. Many early workers noted that enzymatic activity was associated with proteins, but several scientists (such as Nobel laureate Richard Willstätter) argued that proteins were merely carriers for the true enzymes and that proteins per se were incapable of catalysis. However, in 1926, James B. Sumner showed that the enzyme urease was a pure protein and crystallized it; Sumner did likewise for the enzyme catalase in 1937. The conclusion that pure proteins can be enzymes was definitively proved by Northrop and Stanley, who worked on the digestive enzymes pepsin (1930), trypsin and chymotrypsin. These three scientists were awarded the 1946 Nobel Prize in Chemistry.

This discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This was first done for lysozyme, an enzyme found in tears, saliva and egg whites that digests the coating of some bacteria; the structure was solved by a group led by David Chilton Phillips and published in 1965. This high-resolution structure of lysozyme marked the beginning of the field of structural biology and the effort to understand how enzymes work at an atomic level of detail.

The term metabolism is derived from the Greek Μεταβολισμός – Metabolismos for "change", or "overthrow". The history of the scientific study of metabolism spans 400 years. The first controlled experiments in human metabolism were published by Santorio Santorio in 1614 in his book Ars de statica medecina. This book describes how he weighed himself before and after eating, sleeping, working, sex, fasting, drinking, and excreting. He found that most of the food he took in was lost through what he called "insensible perspiration".

Since then, biochemistry has advanced, especially since the mid-20th century, with the development of new techniques such as chromatography, X-ray diffraction, NMR spectroscopy, radioisotopic labelling, electron microscopy and molecular dynamics simulations. These techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle (citric acid cycle). One of the most prolific of these modern biochemists was Hans Krebs who made huge contributions to the study of metabolism. He discovered the urea cycle and later, working with Hans Kornberg, the citric acid cycle and the glyoxylate cycle.

Today, the findings of biochemistry are used in many areas, from genetics to molecular biology and from agriculture to medicine.

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Alternative biochemistry

A hypothetical silicon-based life-form

Alternative biochemistry is the speculative biochemistry of alien life forms that differ radically from those known on Earth. It includes biochemistries that use elements other than carbon to construct primary cellular structures and/or use solvents besides water. Theories about extraterrestrial life based on alternative biochemistries are common in science fiction.

Perhaps the least unusual "alternative" biochemistry would be one with differing chirality of its biomolecules. In known Earth-based life, amino acids are almost universally of the L form and sugars are of the D form. Molecules of opposite chirality have identical chemical properties to their mirrored forms, so life that used D amino acids and/or L sugars may be possible.

Scientists have speculated about the pros and cons of using atoms other than carbon to form the molecular structures necessary for life, but no one has proposed a theory employing such atoms to form all the molecular machinery necessary for life. Since humans are carbon-based beings and have never encountered any life that has evolved outside the earth’s environment, excluding the possibility of all other elements may be considered carbon chauvinism.

The most commonly proposed basis for an alternative biochemical system is the silicon atom, since silicon has many chemical properties similar to carbon and is in the same periodic table group, the carbon group.

But silicon has a number of handicaps as a carbon alternative. Because silicon atoms are much bigger, having a larger mass and atomic radius, they have difficulty forming double or triple covalent bonds, which are important for a biochemical system. Silanes, which are chemical compounds of hydrogen and silicon that are analogous to the alkane hydrocarbons, are highly reactive with water, and long-chain silanes spontaneously decompose. Molecules incorporating polymers of alternating silicon and oxygen atoms instead of direct bonds between silicon, known collectively as silicones, are much more stable. It has been suggested that silicone-based chemicals would be more stable than equivalent hydrocarbons in a sulfuric-acid-rich environment, as is found in some extraterrestrial locations. In general, however, complex long-chain silicone molecules are still more unstable than their carbon counterparts.

Another obstacle is that silicon dioxide (a common ingredient of many sands), the analog of carbon dioxide, is a non-soluble solid at the temperature range where water is liquid, making it difficult for silicon to be introduced into water-based biochemical systems even if the necessary range of biochemical molecules could be constructed out of it. The added problem with silicon dioxide is that it would be the product of aerobic respiration. If a silicon-based life form were to respire using oxygen, as life on Earth does, it would possibly produce silicon dioxide as a by product of this, assuming that the only difference between the two types of life is the presence of silicon in place of carbon.

Finally, of the varieties of molecules identified in the interstellar medium as of 1998, 84 are based on carbon and 8 are based on silicon. Moreover, of those 8 compounds, four also include carbon within them. The cosmic abundance of carbon to silicon is roughly 10 to 1. This may suggest a greater variety of complex carbon compounds throughout the cosmos, providing less of a foundation upon which to build silicon-based biologies, at least under the conditions prevalent on the surface of planets.

Earth, as well as other terrestrial planets, is exceptionally silicon-rich and carbon-poor. However, terrestrial life is carbon-based. The fact that carbon, though rare, has proven to be much more successful as a life base than the much more abundant silicon may be evidence that silicon is poorly suited for biochemistry on Earth-like planets.

Even so, silica is used by some existing Earth life, such as the silicate skeletal structure of diatoms. See biogenic silica. This suggests that extraterrestrial life-forms may have silicon based structure-molecules and carbon based proteins for metabolic purposes, therefore enabling the ability to feed on a rather common resource on a terrestrial planet like Earth for building up the silicone based part of their body.

It is also possible that silicon compounds may be biologically useful under temperatures or pressures very different from the surface of a terrestrial planet, either in conjunction with or in a role less directly analogous to carbon.

A. G. Cairns-Smith has proposed that the first living organisms to exist were clay minerals - which were probably based on silicon.

Nitrogen and phosphorus also offer possibilities as the basis for biochemical molecules. Like carbon, phosphorus can form long chain molecules on its own, which would potentially allow it to form complex macromolecules if it were not so reactive. However, in combination with nitrogen, it can form much more stable covalent bonds and create a wide range of molecules, including rings.

Earth's atmosphere is approximately 78% nitrogen, but this would probably not be of much use to a phosphorus-nitrogen (P-N) life-form since molecular nitrogen (N2) is nearly inert and energetically expensive to "fix" due to its triple bond. (On the other hand, certain Earth plants such as legumes can fix nitrogen using symbiotic anaerobic bacteria contained in their root nodules.) A nitrogen dioxide (NO2) or ammonia (NH3) atmosphere would be more useful. Nitrogen also forms a number of oxides, such as nitrogen monoxide, dinitrogen oxide, and dinitrogen tetroxide, and all would be present in a nitrogen-dioxide-rich atmosphere.

Debate continues, as several aspects of a phosphorus-nitrogen cycle biology would be energy deficient. Also, nitrogen and phosphorus are unlikely to occur in the ratios and quantity required in the real universe. Carbon, being preferentially formed during nuclear fusion, is more abundant and is more likely to end up in a preferred location. Moreover, if an ammoniated atmosphere would be possible and stable at first view, it is doubtful that an atmosphere rich in nitrogen dioxide could exist. Since the nitrogen oxides are all endoenergétques compared with molecular nitrogen and oxygen; and they are very oxidizing, and would decompose by stellar radiation and by catalysis on rocks of surface when they are produced.

Physicists have noted that, while photosynthesis on Earth generally involves green plants, a variety of other colored plants could also support photosynthesis, essential for most life on Earth, and that other colors might be preferred in places that receive a different mix of solar radiation than that received on Earth. These studies indicate that no photosynthetic plants would be blue-colored, because blue light provides some of the highest photosynthetic yields in the light spectrum (therefore it is important for blue light to be absorbed rather than reflected). The physicists base their conclusions not on chemistry, but on the physical quality of different frequencies of light produced by known types of stars.

One terrestrial example of energy conversion based on something other than ordinary light involves fungi that convert high energy (compared to visible light) gamma rays into useful energy using the pigment melanin. In most organisms, melanin, a black pigment, instead protects the organisms against ultraviolet and solar radiation. Ordinarily fungi derived their energy from decomposing other biomass, rather than by converting radiation into energy for itself.

The gasses present in the atmosphere on Earth have varied greatly over its history. Traditional plant photosynthesis has terraformed the atmosphere by sequestering carbon from carbon dioxide, increasing the proportion of molecular oxygen, and by participating in the nitrogen cycle. Modern oxygen breathing animals would have been biochemically impossible until earlier photosynthetic life transformed Earth's atmosphere, giving rise to the Cambrian explosion. Precambrian life had to have biochemistries that did not require oxygen.

Changes in the gas mixture in the atmosphere, even in an atmosphere made up predominantly of the same molecules of Earth's atmosphere, impacts the biochemistry and morphology of life. For example, periods of high oxygen concentrations determined from ice core samples have been associated with fauna of a larger scale in the fossil record, while periods associated with of low oxygen concentrations have been associated with fauna of a smaller scale in the fossil record.

Also, while it is customary to think of plants, which are on one side of the oxygen and nitrogen cycles as being sessile, and animals which are on the other as being motile, this is not a biological imperative. There are animals which are sessile for all or most of their lives (such as corals), and there are plants (such as tumbleweeds and venus fly traps) that exhibit more mobility than is customarily associated with plants. On a slowly rotating planet, for example, it might be adaptive for photosynthesis to be performed by "plants" that can move to remain in the light, while non-photosynthetic "animals," much like Earth's fungi, might have a lesser need to move from place to place on their own. This would be a sort of mirror image of Earth's ecology.

Many Earth plants and animals also undergo major biochemical changes during their life cycles as a response to changing environmental conditions, for example, by having a spore or hibernation state that can be sustained for years or even millennia between more active life stages. Thus, it would be biochemically possible to sustain life in environments that are only periodically consistent with life as we know it.

Similarly, frogs in cold climates can survive for extended periods of time with most of their body water in a frozen state, while desert frogs in Australia can become inactive and dehydrate in dry periods, losing up to 75% of their fluids, yet return to life by rapidly rehydrating in wet periods. Either type of frog would appear biochemically inactive (i.e. not living) in dormant periods to anything other than the most acute means of sensing this activity.

In addition to carbon compounds, all currently known terrestrial life also requires water as a solvent. It is sometimes assumed that water is the only suitable chemical to fill this role. Some of the properties of water that are important for life processes include a large temperature range over which it is liquid, a high heat capacity useful for temperature regulation, a large heat of vaporization, and the ability to dissolve a wide variety of compounds. There are other chemicals with similar properties that have sometimes been proposed as alternatives. Additionally, water is the only compound listed here that is less dense as a solid (ice) than as a liquid. This is why bodies of water freeze over but do not freeze solid (from the bottom up). If ice was denser than liquid water (as is true for nearly all other compounds) then large bodies of liquid would slowly freeze solid, which would not be conducive to the formation of life.

Ammonia is perhaps the most commonly proposed alternative. Numerous chemical reactions are possible in an ammonia solution, and liquid ammonia has some chemical similarities with water. Ammonia can dissolve most organic molecules at least as well as water does, and in addition it is capable of dissolving many elemental metals. Given this set of chemical properties it has been theorized that ammonia-based life forms might be possible.

However, ammonia does have some problems as a basis for life. The hydrogen bonds between ammonia molecules are weaker than those in water, causing ammonia's heat of vaporization to be half that of water, its surface tension to be three times smaller, and reducing its ability to concentrate non-polar molecules through a hydrophobic effect. For these reasons, science questions how well ammonia could hold prebiotic molecules together in order to allow the emergence of a self-reproducing system. Ammonia is also combustible and oxidizable and could not exist sustainably in a biosphere that oxidizes it. It would, however, be stable in a reducing environment.

A biosphere based on ammonia would likely exist at temperatures or air pressures that are extremely unusual for terrestrial life. Terrestrial life usually exists within the melting point and boiling point of water at normal pressure, between 0 °C (273 K) and 100 °C (373 K); at normal pressure ammonia's melting and boiling points are between −78 °C (195 K) and −33 °C (240 K). Such extremely cold temperatures create problems, as they slow biochemical reactions tremendously and may cause biochemical precipitation out of solution due to high melting points. Ammonia could be a liquid at normal temperatures, but at much higher pressures; for example, at 60 atm, ammonia melts at −77 °C (196 K) and boils at 98 °C (371 K).

Ammonia and ammonia-water mixtures remain liquid at temperatures far below the freezing point of pure water, so such biochemistries might be well suited to planets and moons orbiting outside the water-based habitability zone. Such conditions could exist, for example, under the surface of Saturn's largest moon Titan.

Hydrogen fluoride, like water, is a polar molecule, and due to its polarity it can dissolve many ionic compounds. Its melting point is -84 °C and its boiling point is 19.54 °C (at atmospheric pressure); the difference between the two is little more than 100 °C. HF also makes hydrogen bonds with its neighbor molecules as do water and ammonia. All of these things would make HF a candidate to host life on other planets.

Not much research has been done on liquid HF in regards to its ability to dissolve and react with non-polar molecules. It is possible that the biota in an HF ocean could use the fluorine as an electron acceptor to photosynthesize energy.

HF is very dangerous to the systems of molecules that earth-life is made of, but the paraffins are stable with it.

But presence of great amounts of free HF in a planetary scale, like water on Earth, is doubtful, even next to impossible: certainly water would be present in it, forming a solution of fluorhydric acid that would change all its properties. The hypothetical planet would also surely contain silicates that would react with HF to form inert compounds as silicon fluorides, as soon as HF would be present; thus preventing its concentration in great quantities in an hypothetical planetary environment.

Cosmic abundance of fluorine is quite low, and bonds in inert compounds rapidly in interstellar nebulae, just after been out of dying stars, because it's the most reactive element.

Other solvents sometimes proposed include formamide, methanol, hydrogen sulfide and hydrogen chloride. The latter two suffer from a relatively low cosmic abundance of sulfur and chlorine, and their high reactivity which tend to be bound up in solid minerals. And the two firsts couldn't be thought to be found in vast quantities in a planetary scale, only could be part of an internal physiology of organisms.

A mixture of hydrocarbons, such as the methane/ethane lakes detected on Titan by the Cassini spacecraft, could act as a solvent over a wide range of temperatures but would lack polarity. Isaac Asimov, the biochemist and science fiction writer, suggested that poly-lipids could form a substitute for proteins in a non-polar solvent such as methane or liquid hydrogen.

A proposal has been made that life on Mars may actually exist and be using a mixture of water and hydrogen peroxide as its solvent. A 61.2 percent (by weight) mix of water and hydrogen peroxide has a freezing point of -56.5 degrees Celsius, and also tends to super-cool rather than crystallizing. It is also hygroscopic, an advantage in a water-scarce environment.

In 2007 V. N. Tsytovich and colleagues discovered the possibility of life-like behaviors being exhibited by dust particles suspended in a plasma, similar to conditions in interstellar space. Computer models showed that when the dust became charged the particles could self-organize into microscopic helical structures capable of replicating themselves, interacting with other neighboring structures, and evolving into more stable forms. Similar forms of life were speculated on in Fred Hoyle's classic novel The Black Cloud.

In the realm of science fiction there have occasionally been forms of life proposed that, while often highly speculative and unsupported by rigorous theoretical examination, are nevertheless interesting and in some cases even somewhat plausible.

An example of silicon based life forms takes place in the novel Sentenced to Prism by Alan Dean Foster in which the protagonist Evan Orgell finds himself trapped on a planet whose entire ecosystem is mostly silicon-based.

Perhaps the most extreme example in science fiction is James White's Sector General: a series of novels and short stories about multienvironment hospital for the strangest life-forms imaginable, some of them breathing methane, chlorine, water and sometimes also oxygen. Some of the species metabolise directly hard radiation and their environment doesn't differ much from the atmosphere of a star, while others live in near absolute zero temperatures. All of the life forms are classified according to their metabolism, internal and external features, and more extreme abilities (telepathy, empathy, hive mind, etc) with four letter codes. Humans from Earth share the DBDG specification with small furry beings called Nidians.

One of the major sentient species in Terry Pratchett's Discworld universe are the "earth"-based (ranging from Detritus to Diamond) Trolls.

Pratchett has also written the science fiction novel The Dark Side of the Sun which features a range of extraordinary life-forms, including a telepathic body of water, creatures called "Sundogs", which are capable of interstellar travel from birth, and a sentient planet: effectively a giant silicon-based computer.

Fred Hoyle's classic novel The Black Cloud features a life form consisting of a vast cloud of interstellar dust, the individual particles of which interact via electromagnetic signalling analogous to how the individual cells of multicellular terrestrial life interact. Outside of science-fiction, life in interstellar dust has been proposed as part of the panspermia hypothesis. The low temperatures and densities of interstellar clouds would seem to imply that life processes would operate much more slowly there than on Earth. Inorganic dust-based life has been speculated upon based on recent computer simulations.

Similarly, Arthur C. Clarke's "Crusade" revolves around a planetwide life-form based on silicon and superfluid helium located in deep intergalactic space, processing its thoughts very slowly by human standards, that sends probes to look for similar life in nearby galaxies. It concludes that it needs to make planets more habitable for similar life-forms, and sends out other probes to foment supernovae in order to do so. Clarke implies that this is what accounts for most supernovae having occurred in the same region of space and warns that the effort will eventually reach Earth.

Robert L. Forward's Camelot 30K describes an ecosystem existing on the surface of Kuiper belt objects that is based on a fluorocarbon chemistry with OF2 as the principal solvent instead of H2O. The organisms in this ecology keep themselves warm by secreting a pellet of uranium-235 inside themselves and then moderating its nuclear fission using a boron-rich carapace around it. Kuiper belt objects are known to be rich in organic compounds such as tholins, so some form of life existing on their surfaces is not entirely implausible–though perhaps not going so far as to develop natural internal nuclear reactors, as have Forward's. Fluorine is also of low cosmic abundance, so its use in this manner is unlikely.

In Forward's Rocheworld series, a relatively Earth-like biochemistry is proposed that uses a mixture of water and ammonia as its solvent. In Dragon's Egg and Starquake, Forward proposes life on the surface of a neutron star utilizing "nuclear chemistry" in the degenerate matter crust. Since such life utilised strong nuclear forces instead of electromagnetic interactions, it was posited that life might function millions of times faster than typical on Earth.

Gregory Benford and David Brin's Heart of the Comet features a comet with a conventional carbon-and-water-based ecosystem that becomes active near the perihelion when the Sun warms it. Brin's own novel Sundiver is an example of science fiction proposing a form of life existing within the plasma atmosphere of a star using complex self-sustaining magnetic fields. Similar sorts of plasmoid life have sometimes been proposed to exist in other places, such as planetary ionospheres or interstellar space, but usually only by fringe theorists (see ball lightning for some additional discussion). Gregory Benford had a form of plasma-based life exist in the accretion disk of a primordial black hole in his novel Eater.

The suggestion that life could even occur within the plasma of a star has been picked up by other science fiction writers, as in David Brin's Uplift Saga. Any place in which reactions occur–even an incredible environment as a star–presents a possible medium for some chain of events that could produce a system able to replicate itself.

The Outsiders in Larry Niven's Known Space universe are cryogenic creatures based on liquid helium. They derive thermoelectric energy from a temperature gradient by basking half their body in sunlight, keeping the other half in shadow and exposed to interstellar vacuum.

Stephen Baxter has imagined perhaps some of the most unusual exotic life-forms in his Xeelee series of novels and stories, including supersymmetric photino-based life that congregate in the gravity wells of stars, and the Qax, who thrive in any form of convection cells, from swamp gas to the atmospheres of gas giants.

In his novel Diaspora, Greg Egan posits the existence of entire virtual universes implemented on Turing Machines encoded by Wang Tiles in gargantuan polysaccharide 'carpets.' The sentient ocean that covers much of the surface of Solaris in Stanislaw Lem's eponymous novel also seems, from much of the fictional research quoted and discussed in the book, to based on some element other than carbon.

In her novel Brain Plague, Joan Slonczewski describes a species of intelligent microrganisms with arsenic based chemistries that live symbiotically with human hosts.

Sergeant Schlock is one of the lead characters in the webcomic Schlock Mercenary. His species, Carbosilicate Amorphs, evolved from self-repairing distributed data storage devices, and as such, redundantly distribute their 'brain' throughout their body. They are highly resistant to Hard Vacuum, explosive decompression, projectile weapons, chemical-based explosives, and dismemberment. Their only specialty organ is their eyes, which they harvest as fruit from the Ghanj-Rho eye-tree on their home planet. While the Amorphs have the ability to move fast, quietly, and sprout appendages at will, they excel at 'closer-than-melee-range combat, primarily "meme-toxins" against other Amorphs.

A more farcical example comes from the Hitchhiker's Guide to the Galaxy, where the Hooloovoo are a hyperintelligent shade of the colour blue.

Alien warriors recruited by the god Klael in David Eddings' "Tamuli" trilogy are noted by their human opponents to breathe marsh-gas (methane). Within Eddings' universe, this limits their capacity for exertion in an oxygen atmosphere, and also determines the tactics used to fight them and eventually to destroy them in their encampments.

A well-known example of a non–carbon-based life-form in science fiction is the Horta in the original Star Trek episode "Devil in the Dark". A highly intelligent silicon-based creature made almost entirely of pure rock, it tunnels through rock as easily as humans move through air. The entire species dies out every 50,000 years save for one who tends all the eggs, which take the form of silicon nodules scattered throughout the caverns and tunnels of its home planet, Janus VI. The inadvertent destruction of many of these eggs by a human mining colony led the mother Horta to respond by murdering the colonists and sabotaging their equipment; it was only through a Vulcan mind meld that the race's benevolence and intelligence were discovered and peaceful relations established.

Star Trek would later offer other corporeal life-forms with an alternative biochemistry. The Tholians of "The Tholian Web" are depicted and described, in that episode and later in the Star Trek: Enterprise episode "In a Mirror, Darkly" as being primarily of mineral-based composition and thriving only in superheated conditions. Another episode from TOS's third season, "The Savage Curtain," depicted another rock creature called an Excalbian, which is believed in fanon to also have been silicon-based.

Later on, in Star Trek: The Next Generation, the Crystalline Entity appeared in two episodes, "Datalore" and "Silicon Avatar". This was an enormous spacefaring crystal lattice that had taken thousands of lives in its quest for energy. It may have been unaware of this, however, but it was destroyed before communications could be established at a level sufficient to ascertain it.

In the Star Wars movie The Empire Strikes Back, two life-forms were encountered by the characters that were non-carbon based entities. Although details of their physiology were not mentioned on screen, the Space slug, (a giant worm-like creature that lived on asteroids in the freezing vacuum of space), and the Mynock, (pesky bat-like vermin that would attach themselves to spaceship hulls and chew through power conduits to feed off the raw energy), are said to be silicon-based organisms in expanded universe sources. Also from The Empire Strikes Back, the bounty hunter Zuckuss is a member of the Gand race, an ammonia-based life-form. However, it is worth noting that the Gand are divided into two subspecies, only one of which breathes at all, the other drawing all their required sustenance from food intake and producing speech by means of essentially modulated flatulence.

Appearing only in the expanded universe is the Spice Spider of Kessel, a creature made of glitterstim spice and silicon that spun crystalline webs harvested by miners as glitterstim spice, an illegal psychoactive narcotic. The spider used the webs to catch bogeys, tiny energy creatures that it consumed for energy.

In the movie Alien the science officer Ash notes that the facehugger creature replaces its cells with polarised silicon in order to give it "prolonged resistance to adverse environmental conditions". Both stages of the alien cycle also have a highly corrosive blood, normally understood to be some kind of acid, which would be inconsistent with any known terrestrial biochemistry.

In the movie The Monolith Monsters, a silicon meteor reproduces itself, draining silicates from everything it touches. It needs water to start its cycle and contains molecular structures typical of many kinds of rocks, mixed together. A geologist says that its structure is nearly impossible. The meteor is killed by salt water, which can stop the cycle.

In "Firewalker", a second-season episode of The X-Files, a silicon-based plant that infects humans parasitically through its spores is discovered living deep in a volcano.

Also from The X-Files, the first-season episode 'Ice' deal with an ammonia-based vermiform parasite.

A key plot point in the comedy Evolution involves nitrogen-based life forms, and using selenium-based shampoo to poison them (with the bonus of a product placement for Head & Shoulders).

In the Stargate SG-1 fourth season episode "Scorched Earth", a Human society known as the Enkarans are threatened on their new homeworld by an alien ship that is terraforming the planet to be suitable for the sulfur-based Gadmeer species.

In Ben 10, both the Omnitrix alien Diamondhead and the alien Bounty hunter Tetrax are members of the Petrosapien species, which are a form of silicon-based life.

In Dragon Ball Z, shortly before the destruction of Planet Namek, Frieza tells Goku that he does not need to breathe. This would allow him to survive the destruction of the planet and suggest that he is not a carbon-based life-form.

Indiana Jones and the Kingdom of the Crystal Skull (2008) introduces thirteen "extra dimensional beings" with crystal skeletons, who founded a city that became the basis of the El Dorado myth. Though their flesh has died and rotted away, their minds still live on within their skeletons, which communicate telepathically.

In the Command & Conquer real-time strategy games, both the gameplay and storyline revolve heavily around the introduction to Earth of an extraterrestrial mutagen called Tiberium via meteor, which displays strikingly lifelike behaviours such as self-replication, evolution, and homeostasis, without necessarily undergoing anything like common carbon-based metabolic cycles, and which appears to be colonising the Earth, converting it into an environment unsuited to carbon-based biology. Earth creatures (such as animals, plants and even humans) exposed to Tiberium can either be killed because of the radiation or be transformed into Tiberium-based life-forms, to whom Tiberium radiation is curative rather than toxic. It is later revealed that Tiberium was introduced to earth by the Scrin, an extremely advanced race of Tiberium-based aliens bent on mining the planet after the Tiberium deposits have reached maturity.

In the Halo video game series, a race of Covenant aliens named "Grunts" by humans require a breathing apparatus while fighting the humans in an Earth-like atmosphere. According to the novelizations of the video game, the Grunts' apparatus allows them to breathe the methane they need to survive.

In the Master of Orion series of space strategy games, there exists an extraterrestrial race called Silicoids, whose appearance (and presumably composition) is similar to crystalline mineral structures. The game posits that this grants them immunity to the effects of hostile environments and pollution, at the expense of impeding their reproductive rate and their ability to interact with other intelligent species.

In the Metroid Prime Series, Phazon is a highly radioactive, self regenerating mineral with organic properties that is generated by the sentient planet Phaaze.

In Metroid Prime Hunters, Spire is a rock-like, silicon based alien. He is the last Diamont (presumably a play on the word diamond, which is composed of carbon).

In the Star Control series, the Chenjesu, are intelligent, peaceful silicon-based life-forms that were the backbone of the Alliance of Free Stars. Also, there are the Slylandro who are gas beings resideng in the upper atmosphere of a gas giant.

In the game of Xenosaga, artificial life forms known as Realians have been created using silicon-based chemistry. They resemble humans in every aspect, except they are considered to be lower than humans on the social ladder.

In "Mass Effect" the alien turians and quarians , are both dextro-amino acid-based organisms, as opposed to humans, a deoxyribonucleic acid life-form. There are also the volus, an amonia based species that must wear pressure suits to survive in environments suited to the other races.

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Source : Wikipedia