Amino acid

From Wikipedia, the free encyclopedia

The generic structure of an alpha amino acid in its un-ionized form

The 21 proteinogenic α-amino acids found in eukaryotes, grouped according to their side-chains' pK_a values and charges carried at physiological pH 7.4

Amino acids (/əˈmiːnoʊ/, /əˈmaɪnoʊ/, or /ˈæmɪnoʊ/) are biologically important organic compounds composed of amine (-NH₂) and carboxylic acid (-COOH) functional groups, along with a side-chain specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen, though other elements are found in the side-chains of certain amino acids. About 500 amino acids are known^[1] and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side-chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acids comprise the second-largest component (water is the largest) of human muscles, cells and other tissues.^[2] Outside proteins, amino acids perform critical roles in processes such as neurotransmitter transport and biosynthesis.

In biochemistry, amino acids having both the amine and the carboxylic acid groups attached to the first (alpha-) carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids (generic formula H₂NCHRCOOH in most cases^[3] where R is an organic substituent known as a "side-chain");^[4] often the term "amino acid" is used to refer specifically to these. They include the 23 proteinogenic ("protein-building") amino acids,^[5][6][7] which combine into peptide chains ("polypeptides") to form the building-blocks of a vast array of proteins.^[8] These are all L-stereoisomers ("left-handed" isomers), although a few D-amino acids ("right-handed") occur in bacterial envelopes and some antibiotics.^[9] 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 three ("non-standard" or "non-canonical") are selenocysteine (present in many noneukaryotes as well as most eukaryotes, but not coded directly by DNA), pyrrolysine (found only in some archea and one bacterium) and N-formylmethionine (which is often the initial amino acid of proteins in bacteria, mitochondria, and chloroplasts). Pyrrolysine and selenocysteine are encoded via variant codons; for example, selenocysteine is encoded by stop codon and SECIS element.^[10][11][12] 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.^[13][14][15]

Many important proteinogenic and non-proteinogenic amino acids also play critical non-protein roles within the body. For example, in the human brain, glutamate (standard glutamic acid) and gamma-amino-butyric acid ("GABA", non-standard gamma-amino acid) are, respectively, the main excitatory and inhibitory neurotransmitters;^[16] hydroxyproline (a major component of the connective tissue collagen) is synthesised from proline; the standard amino acid glycine is used to synthesise porphyrins used in red blood cells; and the non-standard carnitine is used in lipid transport.

Nine proteinogenic amino acids are called "essential" for humans because they cannot be created from other compounds by the human body and, so, must be taken in as food. Others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also differ between species.^[17]

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, and chiral catalysts.

§History

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, the first amino acid to be discovered.^[18][19] Cystine was discovered in 1810,^[20] although its monomer, cysteine, remained undiscovered until 1884.^[19][21] Glycine and leucine were discovered in 1820.^[22] Usage of the term amino acid in the English language is from 1898.^[23] Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis. In 1902, Emil Fischer and Franz Hofmeister proposed that proteins are the result of the formation of bonds between the amino group of one amino acid with the carboxyl group of another, in a linear structure that Fischer termed "peptide".^[24]

§General structure

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 carboxyl group (which is therefore numbered 2 in the carbon chain starting from that functional group) is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as alpha amino acids.^[25] These includes amino acids such as proline which contain secondary amines, which formerly were often referred to as "imino acids".^[26][27][28]

§Isomerism

The two enantiomers of alanine, D-alanine and L-alanine

The alpha amino acids are the most common form found in nature, but only when occurring in the L-isomer. The alpha carbon is a chiral carbon atom, with the exception of glycine which has two indistinguishable hydrogen atoms on the alpha carbon.^[29] Therefore, all alpha amino acids but glycine can exist in either of two enantiomers, called L or D amino acids, which are mirror images of each other (see also Chirality). While L-amino acids represent all of the amino acids found in proteins during translation in the ribosome, D-amino acids are found in some proteins produced by enzyme posttranslational modifications after translation and translocation to the endoplasmic reticulum, as in exotic sea-dwelling organisms such as cone snails.^[30] They are also abundant components of the peptidoglycan cell walls of bacteria,^[31] and D-serine may act as a neurotransmitter in the brain.^[32] D-amino acids are used in racemic crystallography to create centrosymmetric crystals, which (depending on the protein) may allow for easier and more robust protein structure determination.^[33] The L and D convention for amino acid configuration refers not to the optical activity of the amino acid itself but rather to the optical activity of the isomer of glyceraldehyde from which that amino acid can, in theory, be synthesized (D-glyceraldehyde is dextrorotatory; L-glyceraldehyde is levorotatory). In alternative fashion, the (S) and (R) designators are used to indicate the absolute stereochemistry. Almost all of the amino acids in proteins are (S) at the α carbon, with cysteine being (R) and glycine non-chiral.^[34] Cysteine is unusual since it has a sulfur atom at the second position in its side-chain, which has a larger atomic mass than the groups attached to the first carbon, which is attached to the α-carbon in the other standard amino acids, thus the (R) instead of (S).

§Side chains

Lysine with the carbon atoms in the side-chain labeled

In amino acids that have a carbon chain attached to the α–carbon (such as lysine, shown to the right) the carbons are labeled in order as α, β, γ, δ, and so on.^[35] In some amino acids, the amine group is attached to the β or γ-carbon, and these are therefore referred to as beta or gamma amino acids.

Amino acids are usually classified by the properties of their side-chain into four groups. The side-chain can make an amino acid a weak acid or a weak base, and a hydrophile if the side-chain is polar or a hydrophobe if it is nonpolar.^[29] The chemical structures of the 22 standard amino acids, along with their chemical properties, are described more fully in the article on these proteinogenic amino acids.

The phrase "branched-chain amino acids" or BCAA refers to the amino acids having aliphatic side-chains that are non-linear; these are leucine, isoleucine, and valine. Proline is the only proteinogenic amino acid whose side-group links to the α-amino group and, thus, is also the only proteinogenic amino acid containing a secondary amine at this position.^[29] In chemical terms, proline is, therefore, an imino acid, since it lacks a primary amino group,^[36] although it is still classed as an amino acid in the current biochemical nomenclature,^[37] and may also be called an "N-alkylated alpha-amino acid".^[38]

§Zwitterions

An amino acid in its (1) un-ionized and (2) zwitterionic forms

The α-carboxylic acid group of amino acids is a weak acid, meaning that it releases a hydron (such as a proton) at moderate pH values. In other words, carboxylic acid groups (−CO₂H) can be deprotonated to become negative carboxylates (−CO₂⁻ ). The negatively charged carboxylate ion predominates at pH values greater than the pKa of the carboxylic acid group (mean for the 20 common amino acids is about 2.2, see the table of amino acid structures above). In a complementary fashion, the α-amine of amino acids is a weak base, meaning that it accepts a hydron at moderate pH values. In other words, α-amino groups (NH₂−) can be protonated to become positive α-ammonium groups (⁺NH₃−). The positively charged α-ammonium group predominates at pH values less than the pKa of the α-ammonium group (mean for the 20 common α-amino acids is about 9.4).

Because all amino acids contain amine and carboxylic acid functional groups, they share amphiprotic properties.^[29] Below pH 2.2, the predominant form will have a neutral carboxylic acid group and a positive α-ammonium ion (net charge +1), and above pH 9.4, a negative carboxylate and neutral α-amino group (net charge −1). But at pH between 2.2 and 9.4, an amino acid usually contains both a negative carboxylate and a positive α-ammonium group, as shown in structure (2) on the right, so has net zero charge. This molecular state is known as a zwitterion, from the German Zwitter meaning hermaphrodite or hybrid.^[39] The fully neutral form (structure (1) on the right) is a very minor species in aqueous solution throughout the pH range (less than 1 part in 10⁷). Amino acids exist as zwitterions also in the solid phase, and crystallize with salt-like properties unlike typical organic acids or amines.

§Isoelectric point

The variation in titration curves when the amino acids are grouped by category can be seen here. With the exception of tyrosine, using titration to differentiate between hydrophobic amino acids is problematic.

Composite of Titration Curves Grouped by Side Chain Category using applet http://cti.itc.virginia.edu/~cmg/Demo/compareAA/compareAAApplet.html

At pH values between the two pKa values, the zwitterion predominates, but coexists in dynamic equilibrium with small amounts of net negative and net positive ions. At the exact midpoint between the two pKa values, the trace amount of net negative and trace of net positive ions exactly balance, so that average net charge of all forms present is zero.^[40] This pH is known as the isoelectric point pI, so pI = ½(pKa₁ + pKa₂). The individual amino acids all have slightly different pKa values, so have different isoelectric points. For amino acids with charged side-chains, the pKa of the side-chain is involved. Thus for Asp, Glu with negative side-chains, pI = ½(pKa₁ + pKa_R), where pKa_R is the side-chain pKa. Cysteine also has potentially negative side-chain with pKa_R = 8.14, so pI should be calculated as for Asp and Glu, even though the side-chain is not significantly charged at neutral pH. For His, Lys, and Arg with positive side-chains, pI = ½(pKa_R + pKa₂). Amino acids have zero mobility in electrophoresis at their isoelectric point, although this behaviour is more usually exploited for peptides and proteins than single amino acids. Zwitterions have minimum solubility at their isoelectric point and some amino acids (in particular, with non-polar side-chains) can be isolated by precipitation from water by adjusting the pH to the required isoelectric point.

§Occurrence and functions in biochemistry

A polypeptide is an unbranched chain of amino acids.

§Proteinogenic amino acids

The amino acid selenocysteine

Amino acids are the structural units (monomers) that make up proteins. They join together to form short polymer chains called peptides or longer chains called either polypeptides or proteins. These polymers are linear and unbranched, with each amino acid within the chain attached to two neighboring amino acids. The process of making proteins is called translation and involves the step-by-step addition of amino acids to a growing protein chain by a ribozyme that is called a ribosome.^[41] The order in which the amino acids are added is read through the genetic code from an mRNA template, which is a RNA copy of one of the organism's genes.

Twenty-three amino acids are naturally incorporated into polypeptides and are called proteinogenic or natural amino acids.^[29] Of these, 21 are encoded by the universal genetic code. The remaining 2, selenocysteine and pyrrolysine, are incorporated into proteins by unique synthetic mechanisms. Selenocysteine is incorporated when the mRNA being translated includes a SECIS element, which causes the UGA codon to encode selenocysteine instead of a stop codon.^[42] Pyrrolysine is used by some methanogenic archaea in enzymes that they use to produce methane. It is coded for with the codon UAG, which is normally a stop codon in other organisms.^[43] This UAG codon is followed by a PYLIS downstream sequence.^[44]

§Non-proteinogenic amino acids

β-alanine and its α-alanine isomer

Aside from the 23 proteinogenic amino acids, there are many other amino acids that are called non-proteinogenic. Those either are not found in proteins (for example carnitine, GABA) or are not produced directly and in isolation by standard cellular machinery (for example, hydroxyproline and selenomethionine).

Non-proteinogenic amino acids that are found in proteins are formed by post-translational modification, which is modification after translation during protein synthesis. These modifications are often essential for the function or regulation of a protein; for example, the carboxylation of glutamate allows for better binding of calcium cations,^[45] and the hydroxylation of proline is critical for maintaining connective tissues.^[46] Another example is the formation of hypusine in the translation initiation factor EIF5A, through modification of a lysine residue.^[47] Such modifications can also determine the localization of the protein, e.g., the addition of long hydrophobic groups can cause a protein to bind to a phospholipid membrane.^[48]

Some non-proteinogenic amino acids are not found in proteins. Examples include lanthionine, 2-aminoisobutyric acid, dehydroalanine, and the neurotransmitter gamma-aminobutyric acid. Non-proteinogenic amino acids often occur as intermediates in the metabolic pathways for standard amino acids – for example, ornithine and citrulline occur in the urea cycle, part of amino acid catabolism (see below).^[49] A rare exception to the dominance of α-amino acids in biology is the β-amino acid beta alanine (3-aminopropanoic acid), which is used in plants and microorganisms in the synthesis of pantothenic acid (vitamin B₅), a component of coenzyme A.^[50]

§Non-standard amino acids

The 20 amino acids that are encoded directly by the codons of the universal genetic code are called standard or canonical amino acids. The others are called non-standard or non-canonical. Most of the non-standard amino acids are also non-proteinogenic (i.e. they cannot be used to build proteins), but three of them are proteinogenic, as they can be used to build proteins by exploiting information not encoded in the universal genetic code.

The three non-standard proteinogenic amino acids are selenocysteine (present in many noneukaryotes as well as most eukaryotes, but not coded directly by DNA), pyrrolysine (found only in some archea and one bacterium), and N-formylmethionine (which is often the initial amino acid of proteins in bacteria, mitochondria, and chloroplasts). For example, 25 human proteins include selenocysteine (Sec) in their primary structure,^[51] and the structurally characterized enzymes (selenoenzymes) employ Sec as the catalytic moiety in their active sites.^[52] Pyrrolysine and selenocysteine are encoded via variant codons. For example, selenocysteine is encoded by stop codon and SECIS element.^[10][11][12]

§In human nutrition

When taken up into the human body from the diet, the 22 standard amino acids either are used to synthesize proteins and other biomolecules or are oxidized to urea and carbon dioxide as a source of energy.^[53] The oxidation pathway starts with the removal of the amino group by a transaminase; the amino group is then fed into the urea cycle. The other product of transamidation is a keto acid that enters the citric acid cycle.^[54] Glucogenic amino acids can also be converted into glucose, through gluconeogenesis.^[55]
Pyrrolysine trait is restricted to several microbes, and only one organism has both Pyl and Sec. Of the 22 standard amino acids, 9 are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth, so they must be obtained from food.^[56] In addition, cysteine, taurine, tyrosine, and arginine are considered semiessential amino-acids in children (though taurine is not technically an amino acid), because the metabolic pathways that synthesize these amino acids are not fully developed.^[57][58] The amounts required also depend on the age and health of the individual, so it is hard to make general statements about the dietary requirement for some amino acids.

Essential	Nonessential
Histidine	Alanine
Isoleucine	Arginine*
Leucine	Asparagine
Lysine	Aspartic acid
Methionine	Cysteine*
Phenylalanine	Glutamic acid
Threonine	Glutamine*
Tryptophan	Glycine
Valine	Pyrrolysine*
	Proline*
	Selenocysteine*
	Serine*
	Tyrosine*

(*) Essential only in certain cases.^[59][60]

§Classification

Although there are many ways to classify amino acids, these molecules can be assorted into six main groups, on the basis of their structure and the general chemical characteristics of their R groups.

Class	Name of the amino acids
Aliphatic	Glycine, Alanine, Valine, Leucine, Isoleucine
Hydroxyl or Sulfur/Selenium-containing	Serine, Cysteine, Selenocysteine, Threonine, Methionine
Cyclic	Proline
Aromatic	Phenylalanine, Tyrosine, Tryptophan
Basic	Histidine, Lysine, Arginine
Acidic and their Amide	Aspartate, Glutamate, Asparagine, Glutamine

§Non-protein functions

In humans, non-protein amino acids also have important roles as metabolic intermediates, such as in the biosynthesis of the neurotransmitter gamma-amino-butyric acid (GABA). Many amino acids are used to synthesize other molecules, for example:

• Tryptophan is a precursor of the neurotransmitter serotonin.^[61]
• Tyrosine (and its precursor phenylalanine) are precursors of the catecholamine neurotransmitters dopamine, epinephrine and norepinephrine.
• Glycine is a precursor of porphyrins such as heme.^[62]
• Arginine is a precursor of nitric oxide.^[63]
• Ornithine and S-adenosylmethionine are precursors of polyamines.^[64]
• Aspartate, glycine, and glutamine are precursors of nucleotides.^[65]
• Phenylalanine is a precursor of various phenylpropanoids, which are important in plant metabolism.

However, not all of the functions of other abundant non-standard amino acids are known.

Some non-standard amino acids are used as defenses against herbivores in plants.^[66] For example, canavanine is an analogue of arginine that is found in many legumes,^[67] and in particularly large amounts in Canavalia gladiata (sword bean).^[68] This amino acid protects the plants from predators such as insects and can cause illness in people if some types of legumes are eaten without processing.^[69] The non-protein amino acid mimosine is found in other species of legume, in particular Leucaena leucocephala.^[70] This compound is an analogue of tyrosine and can poison animals that graze on these plants.

§Uses in industry

Amino acids are used for a variety of applications in industry, but their main use is as additives to animal feed. This is necessary, since many of the bulk components of these feeds, such as soybeans, either have low levels or lack some of the essential amino acids: Lysine, methionine, threonine, and tryptophan are most important in the production of these feeds.^[71] In this industry, amino acids are also used to chelate metal cations in order to improve the absorption of minerals from supplements, which may be required to improve the health or production of these animals.^[72]

The food industry is also a major consumer of amino acids, in particular, glutamic acid, which is used as a flavor enhancer,^[73] and Aspartame (aspartyl-phenylalanine-1-methyl ester) as a low-calorie artificial sweetener.^[74] Similar technology to that used for animal nutrition is employed in the human nutrition industry to alleviate symptoms of mineral deficiencies, such as anemia, by improving mineral absorption and reducing negative side effects from inorganic mineral supplementation.^[75]

The chelating ability of amino acids has been used in fertilizers for agriculture to facilitate the delivery of minerals to plants in order to correct mineral deficiencies, such as iron chlorosis. These fertilizers are also used to prevent deficiencies from occurring and improving the overall health of the plants.^[76] The remaining production of amino acids is used in the synthesis of drugs and cosmetics.^[71]

Amino acid derivative	Pharmaceutical application
5-HTP (5-hydroxytryptophan)	Experimental treatment for depression.[77]
L-DOPA (L-dihydroxyphenylalanine)	Treatment for Parkinson's.[78]
Eflornithine	Drug that inhibits ornithine decarboxylase and is used in the treatment of sleeping sickness.[79]

§Expanded genetic code

Since 2001, 40 non-natural amino acids have been added into protein by creating a unique codon (recoding) and a corresponding transfer-RNA:aminoacyl – tRNA-synthetase pair to encode it with diverse physicochemical and biological properties in order to be used as a tool to exploring protein structure and function or to create novel or enhanced proteins.^[13][14]

§Nullomers

Nullomers are codons that in theory code for an amino acid, however in nature there is a selective bias against using this codon in favor of another, for example bacteria prefer to use CGA instead of AGA to code for arginine.^[80] This creates some sequences that do not appear in the genome. This characteristic can be taken advantage of and used to create new selective cancer-fighting drugs^[81] and to prevent cross-contamination of DNA samples from crime-scene investigations.^[82]

§Chemical building blocks

Amino acids are important as low-cost feedstocks. These compounds are used in chiral pool synthesis as enantiomerically pure building-blocks.^[83]
Amino acids have been investigated as precursors chiral catalysts, e.g., for asymmetric hydrogenation reactions, although no commercial applications exist.^[84]

§Biodegradable plastics

Amino acids are under development as components of a range of biodegradable polymers. These materials have applications as environmentally friendly packaging and in medicine in drug delivery and the construction of prosthetic implants. These polymers include polypeptides, polyamides, polyesters, polysulfides, and polyurethanes with amino acids either forming part of their main chains or bonded as side-chains. These modifications alter the physical properties and reactivities of the polymers.^[85] An interesting example of such materials is polyaspartate, a water-soluble biodegradable polymer that may have applications in disposable diapers and agriculture.^[86] Due to its solubility and ability to chelate metal ions, polyaspartate is also being used as a biodegradeable anti-scaling agent and a corrosion inhibitor.^[87][88] In addition, the aromatic amino acid tyrosine is being developed as a possible replacement for toxic phenols such as bisphenol A in the manufacture of polycarbonates.^[89]

§Reactions

As amino acids have both a primary amine group and a primary carboxyl group, these chemicals can undergo most of the reactions associated with these functional groups. These include nucleophilic addition, amide bond formation, and imine formation for the amine group, and esterification, amide bond formation, and decarboxylation for the carboxylic acid group.^[90] The combination of these functional groups allow amino acids to be effective polydentate ligands for metal-amino acid chelates.^[91] The multiple side-chains of amino acids can also undergo chemical reactions.^[92] The types of these reactions are determined by the groups on these side-chains and are, therefore, different between the various types of amino acid.

The Strecker amino acid synthesis

§Chemical synthesis

Several methods exist to synthesize amino acids. One of the oldest methods begins with the bromination at the α-carbon of a carboxylic acid. Nucleophilic substitution with ammonia then converts the alkyl bromide to the amino acid.^[93] In alternative fashion, the Strecker amino acid synthesis involves the treatment of an aldehyde with potassium cyanide and ammonia, this produces an α-amino nitrile as an intermediate. Hydrolysis of the nitrile in acid then yields a α-amino acid.^[94] Using ammonia or ammonium salts in this reaction gives unsubstituted amino acids, whereas substituting primary and secondary amines will yield substituted amino acids.^[95] Likewise, using ketones, instead of aldehydes, gives α,α-disubstituted amino acids.^[96] The classical synthesis gives racemic mixtures of α-amino acids as products, but several alternative procedures using asymmetric auxiliaries^[97] or asymmetric catalysts^[98][99] have been developed.^[100]
At the current time, the most-adopted method is an automated synthesis on a solid support (e.g., polystyrene beads), using protecting groups (e.g., Fmoc and t-Boc) and activating groups (e.g., DCC and DIC).

§Peptide bond formation

The condensation of two amino acids to form a dipeptide through a peptide bond

As both the amine and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage. This polymerization of amino acids is what creates proteins. This condensation reaction yields the newly formed peptide bond and a molecule of water. In cells, this reaction does not occur directly; instead, the amino acid is first activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase.^[101] This aminoacyl-tRNA is then a substrate for the ribosome, which catalyzes the attack of the amino group of the elongating protein chain on the ester bond.^[102] As a result of this mechanism, all proteins made by ribosomes are synthesized starting at their N-terminus and moving toward their C-terminus.

However, not all peptide bonds are formed in this way. In a few cases, peptides are synthesized by specific enzymes. For example, the tripeptide glutathione is an essential part of the defenses of cells against oxidative stress. This peptide is synthesized in two steps from free amino acids.^[103] In the first step, gamma-glutamylcysteine synthetase condenses cysteine and glutamic acid through a peptide bond formed between the side-chain carboxyl of the glutamate (the gamma carbon of this side-chain) and the amino group of the cysteine. This dipeptide is then condensed with glycine by glutathione synthetase to form glutathione.^[104]

In chemistry, peptides are synthesized by a variety of reactions. One of the most-used in solid-phase peptide synthesis uses the aromatic oxime derivatives of amino acids as activated units. These are added in sequence onto the growing peptide chain, which is attached to a solid resin support.^[105] The ability to easily synthesize vast numbers of different peptides by varying the types and order of amino acids (using combinatorial chemistry) has made peptide synthesis particularly important in creating libraries of peptides for use in drug discovery through high-throughput screening.^[106]

§Biosynthesis

In plants, nitrogen is first assimilated into organic compounds in the form of glutamate, formed from alpha-ketoglutarate and ammonia in the mitochondrion. In order to form other amino acids, the plant uses transaminases to move the amino group to another alpha-keto carboxylic acid. For example, aspartate aminotransferase converts glutamate and oxaloacetate to alpha-ketoglutarate and aspartate.^[107] Other organisms use transaminases for amino acid synthesis, too.

Nonstandard amino acids are usually formed through modifications to standard amino acids. For example, homocysteine is formed through the transsulfuration pathway or by the demethylation of methionine via the intermediate metabolite S-adenosyl methionine,^[108] while hydroxyproline is made by a posttranslational modification of proline.^[109]

Microorganisms and plants can synthesize many uncommon amino acids. For example, some microbes make 2-aminoisobutyric acid and lanthionine, which is a sulfide-bridged derivative of alanine. Both of these amino acids are found in peptidic lantibiotics such as alamethicin.^[110] However, in plants, 1-aminocyclopropane-1-carboxylic acid is a small disubstituted cyclic amino acid that is a key intermediate in the production of the plant hormone ethylene.^[111]

§Catabolism

Catabolism of proteinogenic amino acids. Amino acids can be classified according to the properties of their main products as either of the following:^[112]
* Glucogenic, with the products having the ability to form glucose by gluconeogenesis
* Ketogenic, with the products not having the ability to form glucose. These products may still be used for ketogenesis or lipid synthesis.
* Amino acids catabolized into both glucogenic and ketogenic products.

Amino acids must first pass out of organelles and cells into blood circulation via amino acid transporters, since the amine and carboxylic acid groups are typically ionized. Degradation of an amino acid, occurring in the liver and kidneys, often involves deamination by moving its amino group to alpha-ketoglutarate, forming glutamate. This process involves transaminases, often the same as those used in amination during synthesis. In many vertebrates, the amino group is then removed through the urea cycle and is excreted in the form of urea. However, amino acid degradation can produce uric acid or ammonia instead. For example, serine dehydratase converts serine to pyruvate and ammonia.^[113] After removal of one or more amino groups, the remainder of the molecule can sometimes be used to synthesize new amino acids, or it can be used for energy by entering glycolysis or the citric acid cycle, as detailed in image at right.

§Physicochemical properties of amino acids

The 20 amino acids encoded directly by the genetic code can be divided into several groups based on their properties. Important factors are charge, hydrophilicity or hydrophobicity, size, and functional groups.^[29] These properties are important for protein structure and protein–protein interactions. The water-soluble proteins tend to have their hydrophobic residues (Leu, Ile, Val, Phe, and Trp) buried in the middle of the protein, whereas hydrophilic side-chains are exposed to the aqueous solvent. (Note that in biochemistry, a residue refers to a specific monomer within the polymeric chain of a polysaccharide, protein or nucleic acid.) The integral membrane proteins tend to have outer rings of exposed hydrophobic amino acids that anchor them into the lipid bilayer. In the case part-way between these two extremes, some peripheral membrane proteins have a patch of hydrophobic amino acids on their surface that locks onto the membrane. In similar fashion, proteins that have to bind to positively charged molecules have surfaces rich with negatively charged amino acids like glutamate and aspartate, while proteins binding to negatively charged molecules have surfaces rich with positively charged chains like lysine and arginine. There are different hydrophobicity scales of amino acid residues.^[114]

Some amino acids have special properties such as cysteine, that can form covalent disulfide bonds to other cysteine residues, proline that forms a cycle to the polypeptide backbone, and glycine that is more flexible than other amino acids.

Many proteins undergo a range of posttranslational modifications, when additional chemical groups are attached to the amino acids in proteins. Some modifications can produce hydrophobic lipoproteins,^[115] or hydrophilic glycoproteins.^[116] These type of modification allow the reversible targeting of a protein to a membrane. For example, the addition and removal of the fatty acid palmitic acid to cysteine residues in some signaling proteins causes the proteins to attach and then detach from cell membranes.^[117]

§Table of standard amino acid abbreviations and properties

Amino Acid	3-Letter[118]	1-Letter[118]	Side-chain polarity[118]	Side-chain charge (pH 7.4)[118]	Hydropathy index[119]	Absorbance λmax(nm)[120]	ε at λmax (mM−1 cm−1)[120]	MW(Weight)[121]
Alanine	Ala	A	nonpolar	neutral	1.8			89
Arginine	Arg	R	Basic polar	positive	−4.5			174
Asparagine	Asn	N	polar	neutral	−3.5			132
Aspartic acid	Asp	D	acidic polar	negative	−3.5			133
Cysteine	Cys	C	nonpolar	neutral	2.5	250	0.3	121
Glutamic acid	Glu	E	acidic polar	negative	−3.5			147
Glutamine	Gln	Q	polar	neutral	−3.5			146
Glycine	Gly	G	nonpolar	neutral	−0.4			75
Histidine	His	H	Basic polar	positive(10%) neutral(90%)	−3.2	211	5.9	155
Isoleucine	Ile	I	nonpolar	neutral	4.5			131
Leucine	Leu	L	nonpolar	neutral	3.8			131
Lysine	Lys	K	Basic polar	positive	−3.9			146
Methionine	Met	M	nonpolar	neutral	1.9			149
Phenylalanine	Phe	F	nonpolar	neutral	2.8	257, 206, 188	0.2, 9.3, 60.0	165
Proline	Pro	P	nonpolar	neutral	−1.6			115
Serine	Ser	S	polar	neutral	−0.8			105
Threonine	Thr	T	polar	neutral	−0.7			119
Tryptophan	Trp	W	nonpolar	neutral	−0.9	280, 219	5.6, 47.0	204
Tyrosine	Tyr	Y	polar	neutral	−1.3	274, 222, 193	1.4, 8.0, 48.0	181
Valine	Val	V	nonpolar	neutral	4.2			117

Two additional amino acids are in some species coded for by codons that are usually interpreted as stop codons:

21st and 22nd amino acids	3-Letter	1-Letter
Selenocysteine	Sec	U
Pyrrolysine	Pyl	O

In addition to the specific amino acid codes, placeholders are used in cases where chemical or crystallographic analysis of a peptide or protein cannot conclusively determine the identity of a residue.

Ambiguous Amino Acids	3-Letter	1-Letter
Asparagine or aspartic acid	Asx	B
Glutamine or glutamic acid	Glx	Z
Leucine or Isoleucine	Xle	J
Unspecified or unknown amino acid	Xaa	X

Unk is sometimes used instead of Xaa, but is less standard.

In addition, many non-standard amino acids have a specific code. For example, several peptide drugs, such as Bortezomib and MG132, are artificially synthesized and retain their protecting groups, which have specific codes. Bortezomib is Pyz-Phe-boroLeu, and MG132 is Z-Leu-Leu-Leu-al. To aid in the analysis of protein structure, photo-reactive amino acid analogs are available. These include photoleucine (pLeu) and photomethionine (pMet).^[122]

Humidity

From Wikipedia, the free encyclopedia

Tropical forests often have high humidity.

Humidity is the amount of water vapor in the air. Water vapor is the gaseous state of water and is invisible.^[1] Humidity indicates the likelihood of precipitation, dew, or fog. Higher humidity reduces the effectiveness of sweating in cooling the body by reducing the rate of evaporation of moisture from the skin. This effect is calculated in a heat index table or humidex, used during summer weather.

There are three main measurements of humidity: absolute, relative and specific. Absolute humidity is the water content of air.^[2] Relative humidity, expressed as a percent, measures the current absolute humidity relative to the maximum for that temperature. Specific humidity is a ratio of the water vapor content of the mixture to the total air content on a mass basis.

§Types

Paranal is one of the driest places on earth.^[3]

§Absolute humidity

Absolute humidity is the total amount of water vapor present in a given volume of air. It does not take temperature into consideration. Absolute humidity in the atmosphere ranges from near zero to roughly 30 grams per cubic meter when the air is saturated at 30 °C.^[4]

Absolute humidity is the mass of the water vapor (), divided by the volume of the air and water vapor mixture (), which can be expressed as:

The absolute humidity changes as air temperature or pressure changes. This makes it unsuitable for chemical engineering calculations, e.g. for clothes dryers, where temperature can vary considerably. As a result, absolute humidity in chemical engineering may refer to mass of water vapor per unit mass of dry air, also known as the mass mixing ratio (see "specific humidity" below), which is better suited for heat and mass balance calculations. Mass of water per unit volume as in the equation above is also defined as volumetric humidity. Because of the potential confusion, British Standard BS 1339 (revised 2002) suggests avoiding the term "absolute humidity". Units should always be carefully checked. Many humidity charts are given in g/kg or kg/kg, but any mass units may be used.

The field concerned with the study of physical and thermodynamic properties of gas–vapor mixtures is named psychrometrics.

§Relative humidity

The relative humidity of an air-water mixture is defined as the ratio of the partial pressure of water vapor (H₂O) in the mixture to the saturated vapor pressure of water at a given temperature. Thus the relative humidity of air is a function of both water content and temperature.
Relative humidity is normally expressed as a percentage and is calculated by using the following equation:^[5]

Relative humidity is an important metric used in weather forecasts and reports, as it is an indicator of the likelihood of precipitation, dew, or fog. In hot summer weather, a rise in relative humidity increases the apparent temperature to humans (and other animals) by hindering the evaporation of perspiration from the skin. For example, according to the Heat Index, a relative humidity of 75% at 80.0 °F (26.7 °C) would feel like 83.6 °F ±1.3 °F (28.7 °C ±0.7 °C) at ~44% relative humidity.^[6][7]

§Specific humidity

Specific humidity (or moisture content) is the ratio of water vapor mass () to the air parcel's total (i.e., including dry) mass () and is sometimes referred to as the humidity ratio.^[8] Specific humidity is approximately equal to the "mixing ratio", which is defined as the ratio of the mass of water vapor in an air parcel to the mass of dry air for the same parcel.^[8]

Specific Humidity is defined as:

Specific humidity can be expressed in other ways including:

or:

Using this definition of specific humidity, the relative humidity can be expressed as

However, specific humidity is also defined as the ratio of water vapor to the total mass of the system (dry air plus water vapor).^[9] For example, the ASHRAE 2009 Handbook, Ch1,1.2, (9a) defines specific humidity as "the ratio of the mass of water vapor to total mass of the moist air sample".

§Measurement

A hygrometer

There are various devices used to measure and regulate humidity. A device used to measure humidity is called a psychrometer or hygrometer. A humidistat is a humidity-triggered switch, often used to control a dehumidifier.

Humidity is also measured on a global scale using remotely placed satellites. These satellites are able to detect the concentration of water in the troposphere at altitudes between 4 and 12 kilometers. Satellites that can measure water vapor have sensors that are sensitive to infrared radiation. Water vapor specifically absorbs and re-radiates radiation in this spectral band. Satellite water vapor imagery plays an important role in monitoring climate conditions (like the formation of thunderstorms) and in the development of future weather forecasts.

§Climate

While humidity itself is a climate variable, it also interacts strongly with other climate variables. The humidity is affected by winds and by rainfall. At the same time, humidity affects the energy budget and thereby influences temperatures in two major ways. First, water vapor in the atmosphere contains "latent" energy. During transpiration or evaporation, this latent heat is removed from surface liquid, cooling the earth's surface. This is the biggest non-radiative cooling effect at the surface. It compensates for roughly 70% of the average net radiative warming at the surface.
Second, water vapor is the most abundant of all greenhouse gases. Water vapor, like a green lens that allows green light to pass through it but absorbs red light, is a "selective absorber". Along with other greenhouse gases, water vapor is transparent to most solar energy, as you can literally see. But it absorbs the infrared energy emitted (radiated) upward by the earth's surface, which is the reason that humid areas experience very little nocturnal cooling but dry desert regions cool considerably at night. This selective absorption causes the greenhouse effect. It raises the surface temperature substantially above its theoretical radiative equilibrium temperature with the sun, and water vapor is the cause of more of this warming than any other greenhouse gas.

Unlike most other greenhouse gases, however, water is not merely below its boiling point in all regions of the Earth, but below its freezing point at many altitudes. As a condensible greenhouse gas, it precipitates, with a much lower scale height and shorter atmospheric lifetime- weeks instead of decades. Without other greenhouse gases, Earth's blackbody temperature, below the freezing point of water, would cause water vapor to be removed from the atmosphere.^[10][11][12] Water vapor is thus a "slave" to the non-condensible greenhouse gases.^[13][14][15]

The most humid cities on earth are generally located closer to the equator, near coastal regions. Cities in South and Southeast Asia are among the most humid. Kuala Lumpur and Singapore have very high humidity all year round because of their proximity to water bodies and the equator and often overcast weather. Some places experience extreme humidity during their rainy seasons combined with warmth giving the feel of a lukewarm sauna, such as Kolkata, Chennai and Cochin in India, and Lahore in Pakistan. Sukkur city located on the Indus River in Pakistan has some of the highest and most uncomfortable dew point in the country frequently exceeding 30 °C (86 °F) in the Monsoon season.^[16] High temperatures couple up with bizarre dew point to create heat index in excess of 65 °C (149 °F). The cities of Manila in the Philippines, Mogadishu in Somalia and Bangkok in Thailand. Darwin, Australia experiences an extremely humid wet season from December to April. Shanghai and Hong Kong in China also have an extreme humid period in their summer months. During the South-west and North-east Monsoon seasons (respectively, late May to September and November to March), expect heavy rains and a relatively high humidity post-rainfall. Outside the monsoon seasons, humidity is high (in comparison to countries North of the Equator), but completely sunny days abound. In cooler places such as Northern Tasmania, Australia, high humidity is experienced all year due to the ocean between mainland Australia and Tasmania. In the summer the hot dry air is absorbed by this ocean and the temperature rarely climbs above 35 °C (95 °F).

In the United States the most humid cities, strictly in terms of relative humidity, are Forks and Olympia, Washington.^[17] This fact may come as a surprise to many, as the climate in this region rarely exhibits the discomfort usually associated with high humidity. This is because high dew points play a more significant role than relative humidity in discomfort, and so the air in these western cities usually does not feel "humid" as a result. In general, dew points are much lower in the Western U.S. than those in the Eastern U.S.

The highest dew points in the US are found in coastal Florida and Texas. When comparing Key West and Houston, two of the most humid cities from those states, coastal Florida seems to have the higher dew points on average. However, Houston lacks the coastal breeze present in Key West, and, as a much larger city, it suffers from the urban heat island effect.^[18] A dew point of 88 °F (31 °C) was recorded in Moorhead Minnesota on July 19, 2011, with a heat index of 133.5, although dew points over 80 °F (27 °C) are rare there.^[19] The US city with the lowest annual humidity is Las Vegas, Nevada, averaging 39% for a high and 21% as a low.^[20]

§Air density and volume

Humidity depends on water vaporization and condensation, which, in turn, mainly depends on temperature. Therefore, when applying more pressure to a gas saturated with water, all components will initially decrease in volume approximately according to the ideal gas law. However, some of the water will condense until returning to almost the same humidity as before, giving the resulting total volume deviating from what the ideal gas law predicted. Conversely, decreasing temperature would also make some water condense, again making the final volume deviate from predicted by the ideal gas law. Therefore, gas volume may alternatively be expressed as the dry volume, excluding the humidity content. This fraction more accurately follows the ideal gas law. On the contrary the saturated volume is the volume a gas mixture would have if humidity was added to it until saturation (or 100% relative humidity).
Humid air is less dense than dry air because a molecule of water (M ≈ 18 u) is less massive than either a molecule of nitrogen (M ≈ 28) or a molecule of oxygen (M ≈ 32). About 78% of the molecules in dry air are nitrogen (N₂). Another 21% of the molecules in dry air are oxygen (O₂). The final 1% of dry air is a mixture of other gases.

For any gas, at a given temperature and pressure, the number of molecules present in a particular volume is constant – see ideal gas law. So when water molecules (vapor) are introduced into that volume of dry air, the number of air molecules in the volume must decrease by the same number, if the temperature and pressure remain constant. (The addition of water molecules, or any other molecules, to a gas, without removal of an equal number of other molecules, will necessarily require a change in temperature, pressure, or total volume; that is, a change in at least one of these three parameters. If temperature and pressure remain constant, the volume increases, and the dry air molecules that were displaced will initially move out into the additional volume, after which the mixture will eventually become uniform through diffusion.) Hence the mass per unit volume of the gas—its density—decreases. Isaac Newton discovered this phenomenon and wrote about it in his book Opticks.^[21]

§Effects

§Animals and plants

Humidity is one of the fundamental abiotic factors that defines any habitat, and is a determinant of which animals and plants can thrive in a given environment.^[22]

The human body dissipates heat through perspiration and its evaporation. Heat convection to the surrounding air, and thermal radiation are the primary modes of heat transport from the body. Under conditions of high humidity, the rate of evaporation of sweat from the skin decreases. Also, if the atmosphere is as warm as or warmer than the skin during times of high humidity, blood brought to the body surface cannot dissipate heat by conduction to the air, and a condition called hyperpyrexia results. With so much blood going to the external surface of the body, relatively less goes to the active muscles, the brain, and other internal organs. Physical strength declines, and fatigue occurs sooner than it would otherwise. Alertness and mental capacity also may be affected, resulting in heat stroke or hyperthermia.

§Human comfort

Humans are sensitive to humid air because the human body uses evaporative cooling as the primary mechanism to regulate temperature. Under humid conditions, the rate at which perspiration evaporates on the skin is lower than it would be under arid conditions. Because humans perceive the rate of heat transfer from the body rather than temperature itself, we feel warmer when the relative humidity is high than when it is low.

Some people experience difficulty breathing in high humidity environments. Some cases may possibly be related to respiratory conditions such as asthma, while others may be the product of anxiety. Sufferers will often hyperventilate in response, causing sensations of numbness, faintness, and loss of concentration, among others.^{[citation needed]}

Air conditioning reduces discomfort in the summer not only by reducing temperature, but also by reducing humidity. In winter, heating cold outdoor air can decrease relative humidity levels indoor to below 30%, leading to discomfort such as dry skin and excessive thirst.

§Electronics

Many electronic devices have humidity specifications, for example, 5% to 95%. At the top end of the range, moisture may increase the conductivity of permeable insulators leading to malfunction. Too low humidity may make materials brittle. A particular danger to electronic items, regardless of the stated operating humidity range, is condensation. When an electronic item is moved from a cold place (e.g. garage, car, shed, an air conditioned space in the tropics) to a warm humid place (house, outside tropics), condensation may coat circuit boards and other insulators, leading to short circuit inside the equipment. Such short circuits may cause substantial permanent damage if the equipment is powered on before the condensation has evaporated. A similar condensation effect can often be observed when a person wearing glasses comes in from the cold (i.e. the glasses become foggy).^[23] It is advisable to allow electronic equipment to acclimatise for several hours, after being brought in from the cold, before powering on. Some electronic devices can detect such a change and indicate, when plugged in and usually with a small droplet symbol, that they cannot be used until the risk from condensation has passed. In situations where time is critical, increasing air flow through the device's internals, such as removing the side panel from a PC case and directing a fan to blow into the case, will reduce significantly the time needed to acclimatise to the new environment.

In contrast, a very low humidity level favors the build-up of static electricity, which may result in spontaneous shutdown of computers when discharges occur. Apart from spurious erratic function, electrostatic discharges can cause dielectric breakdown in solid state devices, resulting in irreversible damage. Data centers often monitor relative humidity levels for these reasons.

§Building construction

Common construction methods often produce building enclosures with a poor thermal boundary, an insulation and air barrier system designed to retain indoor environmental conditions while resisting external environmental conditions.^[24] The energy-efficient, heavily-sealed architecture introduced in the 20th century also sealed off the movement of moisture, and this has resulted in a secondary problem of condensation forming in and around walls, which encourages the development of mold and mildew. Additionally, buildings with foundations not properly sealed will allow water to flow through the walls due to capillary action of pores found in masonry products. Solutions for energy-efficient buildings that avoid condensation are a current topic of architecture.

§Industry

High humidity can often have a negative effect on the capacity of chemical plants and refineries that use furnaces as part of the process (e.g. steam reforming, wet sulfuric acid process). The humidity will reduce the oxygen concentration, and the flue gas fans have to pull more air through the system to get the same firing rate (dry air is 20.9% Oxygen, at 100% relative humidity, the air is 20.4% oxygen).^[25]