Amino acid

From Wikipedia, the free encyclopedia

Amino acids are organic compounds containing amine (-NH2) and carboxyl (-COOH) functional groups,
along with a side chain (R group) specific to each amino acid.[1][2][3] The key elements of an amino acid
are carbon, hydrogen, oxygen, and nitrogen, although other elements are found in the side chains of certain
amino acids. About 500 amino acids are known (though only 20 appear in the genetic code) and can be
classified in many ways.[4] 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 acid residues form the second-largest component (water is the largest)
The structure of an alpha amino
of human muscles and other tissues.[5] Beyond their role as residues in proteins, amino acids participate in acid in its un-ionized form
a number of 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,[6] where R is
an organic substituent known as a "side chain");[7] often the term
"amino acid" is used to refer specifically to these. They include the 22
proteinogenic ("protein-building") amino acids,[8][9][10] which
combine into peptide chains ("polypeptides") to form the building-
blocks of a vast array of proteins.[11] These are all L-stereoisomers
("left-handed" isomers), although a few D-amino acids ("right-
handed") occur in bacterial envelopes, as a neuromodulator (D-
serine), and in some antibiotics.[12]

Twenty of the proteinogenic amino acids are encoded directly by
triplet codons in the genetic code and are known as "standard" amino
acids. The other two ("non-standard" or "non-canonical") are
selenocysteine (present in many prokaryotes as well as most
eukaryotes, but not coded directly by DNA), and pyrrolysine (found
only in some archea and one bacterium). Pyrrolysine and
selenocysteine are encoded via variant codons; for example,
selenocysteine is encoded by stop codon and SECIS
element.[13][14][15] N-formylmethionine (which is often the initial
amino acid of proteins in bacteria, mitochondria, and chloroplasts) is
generally considered as a form of methionine rather than as a separate
proteinogenic amino acid. Codon–tRNA combinations not found in
nature can also be used to "expand" the genetic code and form novel
proteins known as alloproteins incorporating non-proteinogenic
amino acids.[16][17][18] The 21 proteinogenic α-amino acids found in eukaryotes, grouped according
to their side chains' pKa values and charges carried at physiological pH 7.4
Many important proteinogenic and non-proteinogenic amino acids
have biological functions. 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.[19] Hydroxyproline, a major component of the connective tissue collagen, is synthesised from
proline. Glycine is a biosynthetic precursor to porphyrins used in red blood cells. Carnitine is used in lipid transport.

Nine proteinogenic amino acids are called "essential" for humans because they cannot be produced 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.[20]

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.

Contents
1 History
2 General structure
2.1 Isomerism
2.2 Side chains
2.3 Zwitterions
2.4 Isoelectric point

[37] D- amino acids are used in racemic crystallography to create centrosymmetric crystals. which used to be often referred to as "imino acids". cysteine.3 D-amino acid natural abundance 3. In 1806.4 Catabolism 6 Physicochemical properties of amino acids 6.1 Table of standard amino acid abbreviations and properties 7 See also 8 References and notes 9 Further reading 10 External links History The first few amino acids were discovered in the early 19th century.[29] General structure In the structure shown at the top of the page. remained undiscovered until 1884. which are mirror images of each other (see also Chirality). as in The two enantiomers of alanine.[28] Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis.1 Chemical synthesis 5. In alternative fashion. be synthesized (D- glyceraldehyde is dextrorotatory.[30] These include amino acids such as proline which contain secondary amines. which (depending on the protein) may allow for easier and more robust protein structure determination. the first amino acid to be discovered. While L-amino acids represent all of the amino acids found in proteins during translation in the ribosome. D- exotic sea-dwelling organisms such as cone snails. the (S) and (R) designators are used to indicate the absolute stereochemistry.[38] 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. D-amino acids are found in some proteins produced by enzyme posttranslational modifications after translation and translocation to the endoplasmic reticulum.[39] Cysteine has its side chain in the same geometric position as the other amino acids.[36] and D-serine may act as a neurotransmitter in the brain. Side chains . called L or D amino acids.2 Non-proteinogenic amino acids 3. with cysteine being (R) and glycine non-chiral. In 1902. whereas the atoms in most other side chains give them lower priority. who also determined the essential amino acids and established the minimum daily requirements of all amino acids for optimal growth.1 Proteinogenic amino acids 3. in theory. but the R/S terminology is reversed because of the higher atomic number of sulfur compared to the carboxyl oxygen gives the side chain a higher priority. in a linear structure that Fischer termed "peptide".[21][22] Cystine was discovered in 1810.[35] They are also abundant components of the alanine and L-alanine peptidoglycan cell walls of bacteria.4 Non-standard amino acids 3. Almost all of the amino acids in proteins are (S) at the α carbon.[26][27] Usage of the term amino acid in the English language is from 1898.6 Non-protein functions 4 Uses in industry 4.1 Expanded genetic code 4. all alpha amino acids but glycine can exist in either of two enantiomers.2 Nullomers 4. but only when occurring in the L- isomer.5 In human nutrition 3. French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that was subsequently named asparagine.[25] The last of the 20 common amino acids to be discovered was threonine in 1935 by William Cumming Rose.[23] although its monomer.4 Biodegradable plastics 5 Reactions 5. 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. The alpha carbon is a chiral carbon atom. 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. L-glyceraldehyde is levorotatory).3 Biosynthesis 5. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as alpha amino acids.[22][24] Glycine and leucine were discovered in 1820. with the exception of glycine which has two indistinguishable hydrogen atoms on the alpha carbon.[34] Therefore.3 Chemical building blocks 4.2 Peptide bond formation 5. 3 Occurrence and functions in biochemistry 3.[31][32][33] Isomerism The alpha amino acids are the most common form found in nature.

pI = ½(pKaR + pKa2). proline is. Proline is the only proteinogenic amino acid whose side-group links to the α-amino group and.[34] In chemical terms.[41] although it is still classed as an amino acid in the current biochemical nomenclature. with non-polar side chains) can be isolated chain category. and valine.14. For His. meaning that it accepts a proton at moderate pH values. even though the side chain is not significantly charged at neutral pH.[42] and may also be called an "N-alkylated alpha-amino acid".[34] Below pH 2. so that average net charge of all forms present is zero. therefore. α-amino An amino acid in its (1) un-ionized groups (NH2−) can be protonated to become positive α-ammonium groups (+NH3−).[34] The chemical structures of the 22 standard amino acids. Amino acids have zero mobility in electrophoresis at their isoelectric point. With the exception of tyrosine. Zwitterions have minimum solubility at their isoelectric point and some amino Composite of titration curves of twenty proteinogenic amino acids grouped by side acids (in particular. along with their chemical properties.2. In other words. where pKaR is the side chain pKa. and crystallize with salt-like properties unlike typical organic acids or amines. The side chain can make an amino acid a weak acid or a weak base. This molecular state is known as a zwitterion. Cysteine also has potentially negative side chain with pKaR = 8. The positively and (2) zwitterionic forms 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. so pI should be calculated as for Asp and Glu. 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 2.4. using titration to distinguish between hydrophobic amino acids is problematic. the pKa of the side chain is involved. The phrase "branched-chain amino acids" or BCAA refers to the amino acids having aliphatic side chains that are non-linear. and a hydrophile if the side chain is polar or a hydrophobe if it is nonpolar. are described more fully in the article on these proteinogenic amino acids. In other words. Isoelectric point The variation in titration curves when the amino acids are grouped by category can be seen here. a negative carboxylate and neutral α-amino group (net charge −1). an amino acid usually contains both a negative carboxylate and a positive α-ammonium group. carboxylic acid groups (−CO2H) can be deprotonated to become negative carboxylates (−CO2− ). the α-amine of amino acids is a weak base. since it lacks a primary amino group. the amine group is attached to the β or γ-carbon. these are leucine. Amino acids exist as zwitterions also in the solid phase. Because all amino acids contain amine and carboxylic acid functional groups. see the table of amino acid structures above). shown to the right) the carbons are labeled in order as α. Lys.[43] Zwitterions The α-carboxylic acid group of amino acids is a weak acid.4. At the exact midpoint between the two pKa values. In a complementary fashion. the trace amount of net negative and trace of net positive ions exactly balance. . At pH values between the two pKa values. and so on.2 and 9. is also the only proteinogenic amino Lysine with carbon atoms labeled acid containing a secondary amine at this position. from the German Zwitter meaning hermaphrodite or hybrid. isoleucine. although this behaviour is more usually exploited for peptides and proteins than single amino acids. an imino acid. Glu with negative side chains. thus. as shown in structure (2) on the right. and above pH 9.[40] In some amino acids. β. so have different isoelectric points.4). and Arg with positive side chains. so pI = ½(pKa1 + pKa2). Amino acids are usually classified by the properties of their side chain into four groups. so has net zero charge.[44] The fully neutral form (structure (1) on the left) is a very minor species in aqueous solution throughout the pH range (less than 1 part in 107).In amino acids that have a carbon chain attached to the α–carbon (such as lysine. they share amphiprotic properties. For amino acids with charged side chains. Thus for Asp. γ. pI = ½(pKa1 + pKaR).2. by precipitation from water by adjusting the pH to the required isoelectric point. but coexists in dynamic equilibrium with small amounts of net negative and net positive ions. the predominant form will have a neutral carboxylic acid group and a positive α-ammonium ion (net charge +1).[45] This pH is known as the isoelectric point pI. and these are therefore referred to as beta or gamma amino acids. meaning that it releases a hydron (such as a proton) at moderate pH values. But at pH between 2. The individual amino acids all have slightly different pKa values. δ. the zwitterion predominates.

Only 837 D-amino acids were found in Swiss-Prot database (187 million amino acids analysed). with each amino acid within the chain attached to two neighboring amino acids. generated by hydroxylation of proline. The two non-standard proteinogenic amino acids are selenocysteine (present in many non-eukaryotes as well as most eukaryotes. Other amino acids are called non-standard or non-canonical.[52] Such modifications can also determine the localization of the protein. of amino acids. Non-proteinogenic amino acids that are found in proteins are formed by post-translational modification.[55] D-amino acid natural abundance D-isomers are uncommon in live organisms. For example. are incorporated into proteins by unique synthetic mechanisms. a component of coenzyme A. mitochondria and chloroplasts.[58] and the structurally characterized enzymes (selenoenzymes) employ Sec as the catalytic moiety in their active sites. which is used in plants and microorganisms in the synthesis of pantothenic acid (vitamin B5). hydroxyproline and selenomethionine).[59] Pyrrolysine and selenocysteine are encoded via variant codons. Most of the non-standard amino acids are also non-proteinogenic (i.. which is a RNA A polypeptide is an unbranched chain copy of one of the organism's genes. Those either are not found in proteins (for example carnitine.[56] Other compounds containing D-amino acid are tyrocidine and valinomycin. which is normally a stop codon in other organisms. e. through modification of a lysine residue. They join together to form short polymer chains called peptides or longer chains called either polypeptides or proteins.[34] Of these. selenocysteine and pyrrolysine.[47] Pyrrolysine is used by some methanogenic archaea in enzymes that they use to produce methane. For example.[53] Some non-proteinogenic amino acids are not found in proteins. These polymers are linear and unbranched. 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. the carboxylation of glutamate allows for better The amino acid selenocysteine binding of calcium cations.e. For instance. These modifications are often essential for the function or regulation of a protein.[13][14][15] In human nutrition .[51] Another example is the formation of hypusine in the translation initiation factor EIF5A. A modified form of methionine (N-formylmethionine) is often incorporated in place of methionine as the initial amino acid of proteins in bacteria. Non-proteinogenic amino acids often occur as β-alanine and its α-alanine isomer intermediates in the metabolic pathways for standard amino acids – for example. GABA. Levothyroxine) or are not produced directly and in isolation by standard cellular machinery (for example. the addition of long hydrophobic groups can cause a protein to bind to a phospholipid membrane.[54] A rare exception to the dominance of α-amino acids in biology is the β-amino acid beta alanine (3-aminopropanoic acid).[57] 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. but two of them are proteinogenic.[46] The order in which the amino acids are added is read through the genetic code from an mRNA template. 25 human proteins include selenocysteine (Sec) in their primary structure. ornithine and citrulline occur in the urea cycle. gramicidin is a polypeptide made up from mixture of D. The incorporation of these non-standard amino acids is rare. Twenty-two amino acids are naturally incorporated into polypeptides and are called proteinogenic or natural amino acids. For example. These compounds disrupt bacterial cell walls.and L-amino acids.[48] This UAG codon is followed by a PYLIS downstream sequence. selenocysteine is encoded by stop codon and SECIS element. part of amino acid catabolism (see below). which is modification after translation during protein synthesis.Occurrence and functions in biochemistry Proteinogenic amino acids Amino acids are the structural units (monomers) that make up proteins. as they can be incorporated translationally into proteins by exploiting information not encoded in the universal genetic code. they cannot be incorporated into proteins during translation). which causes the UGA codon to encode selenocysteine instead of a stop codon. Selenocysteine is incorporated when the mRNA being translated includes a SECIS element. Examples include 2-aminoisobutyric acid and the neurotransmitter gamma-aminobutyric acid. 20 are encoded by the universal genetic code. many non-proteinogenic amino acids are known. but not coded directly by DNA) and pyrrolysine (found only in some archaea and one bacterium).[49] Non-proteinogenic amino acids Aside from the 22 proteinogenic amino acids. The remaining 2.[50] and collagen contains hydroxyproline.g. It is coded for with the codon UAG. particularly in Gram- positive bacteria.

taurine. and arginine are considered semiessential amino-acids in children (though taurine is not technically an Share of amino acid in different human diets and the resulting mix of amino acids in amino acid). for example: Tryptophan is a precursor of the neurotransmitter serotonin.[68][69] Diagram of the molecular signaling cascades that are involved in Resistance training stimulates muscle protein synthesis (MPS) for a myofibrillar muscle protein synthesis and mitochondrial biogenesis in period of up to 48 hours following exercise (shown by dotted response to physical exercise and specific amino acids or their line).[70][71] Abbreviations and representations: • PLD: phospholipase D • PA: phosphatidic acid • mTOR: mechanistic target of rapamycin • AMP: adenosine monophosphate • ATP: adenosine triphosphate • AMPK: AMP-activated protein kinase • PGC‐1α: peroxisome proliferator-activated receptor gamma coactivator-1α • S6K1: p70S6 kinase • 4EBP1: eukaryotic translation initiation factor 4E-binding protein 1 • eIF4E: eukaryotic translation initiation factor 4E • RPS6: ribosomal protein S6 • eEF2: eukaryotic elongation factor 2 • RE: resistance exercise. Lys.[62] Of the 20 standard amino acids.[61] Glucogenic amino acids can also be converted into glucose. so they must be obtained from food. so it is hard to make general statements about the dietary requirement for some amino acids. including ALS. and glycine are the most common in blood. through gluconeogenesis.[60] The oxidation pathway starts with the removal of the amino group by a transaminase. glutamine. Phe. tyrosine.[76] . Thr. Met. amounts required also depend on the age and health of the individual.[63][64][65] In addition.When taken up into the human body from the diet. Ile. Mito: mitochondrial • AA: amino acids • HMB: β-hydroxy β-methylbutyric acid • ↑ represents activation • Τ represents inhibition Non-protein functions In humans. Dietary exposure to the non-standard amino acid BMAA has been linked to human neurodegenerative diseases. EE: endurance exercise • Myo: myofibrillar. cysteine. non-protein amino acids also have important roles as metabolic intermediates. the 20 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. the amino group is then fed into the urea cycle.[66][67] The 10%. while alanine. Glutamate and glutamine are the most frequent in food at over these amino acids are not fully developed.[72] increase protein synthesis by signaling through Rag GTPases. because the metabolic pathways that synthesize human blood serum. nine (His. Many amino acids are used to synthesize other molecules. Trp and Val) are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth.[72] Ingestion of a protein-rich meal at any point during this derivatives (primarily L-leucine and HMB). such as in the biosynthesis of the neurotransmitter gamma-amino-butyric acid (GABA). Leu.[70] Many amino acids period will augment the exercise-induced increase in muscle protein derived from food protein promote the activation of mTORC1 and synthesis (shown by solid lines). The other product of transamidation is a keto acid that enters the citric acid cycle.

brain minor not all of the functions of other p-Octopamine AAAH CYP2D6 pathway abundant non-standard amino acids are known. methionine.[88] and aspartame (aspartyl-phenylalanine-1-methyl ester) as a low-calorie artificial sweetener. such as anemia.[81] For pathway example.[77] PNMT Arginine is a precursor of nitric oxide. by improving mineral absorption and reducing negative side effects from inorganic mineral supplementation.[83] This amino acid protects the plants from predators such as insects and can cause illness in people if some PNMT types of legumes are eaten without processing. but their main use is as additives to animal feed.[92] L-DOPA (L-dihydroxyphenylalanine) for Parkinson's treatment. Catecholamines and trace amines are synthesized from phenylalanine and tyrosine in humans.[80] However. This is necessary. it is a precursor of various phenylpropanoids.[91] The remaining production of amino acids is used in the synthesis of drugs and cosmetics.[82] Synephrine and in particularly large amounts in Canavalia DBH COMT gladiata (sword bean). in particular Leucaena leucocephala.[86] Similarly. such as iron chlorosis. which is used as a flavor enhancer. which are important in plant metabolism. Tyrosine (and its precursor phenylalanine) are precursors of the Biosynthetic pathways for catecholamines and trace amines in the human catecholamine neurotransmitters brain[73][74][75] dopamine.[87] The food industry is also a major consumer of amino acids. Uses in industry Amino acids are used for a variety of applications in industry. 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.[84] The non-protein amino acid Epinephrine Norepinephrine 3-Methoxytyramine mimosine is found in other species of legume. epinephrine and norepinephrine and various trace AADC PNMT amines.[90] 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. some amino acids derivatives are used in pharmaceutical industry. In plants.[16][17] Nullomers . amino acids are also used to chelate metal cations in order to improve the absorption of minerals from supplements. glutamic acid. such as soybeans. in particular. AAAH Glycine is a precursor of porphyrins N-Methyltyramine such as heme. either have low levels or lack some of the essential amino acids: lysine. They include 5-HTP (5-hydroxytryptophan) used for experimental treatment of depression. and tryptophan are most important in the production of these feeds.[89] Similar technology to that used for animal nutrition is employed in the human nutrition industry to alleviate symptoms of mineral deficiencies.[94] Expanded genetic code Since 2001.[79] L-Tyrosine p-Tyramine DBH Aspartate. canavanine is an analogue of L-DOPA Dopamine arginine that is found in many legumes. glycine.[78] AADC Ornithine and S-adenosylmethionine are precursors of polyamines. These fertilizers are also used to prevent deficiencies from occurring and improving the overall health of the plants. since many of the bulk components of these feeds. Phenylalanine is a precursor of L-Phenylalanine Phenethylamine N-Methylphenethylamine phenethylamine and tyrosine in humans. and glutamine are precursors of nucleotides. which may be required to improve the health or production of these animals.[85] This compound is an analogue of tyrosine and can poison animals that graze on these plants.[93] and eflornithine drug that inhibits ornithine decarboxylase and used in the treatment of sleeping sickness.[86] In this industry. threonine. PNMT Some non-standard amino acids are used as AADC primary defenses against herbivores in plants.

These modifications alter the physical properties and reactivities of the polymers. all proteins made by ribosomes are synthesized starting at their N-terminus and moving toward their C-terminus. One of the oldest methods begins with the bromination at the α-carbon of a carboxylic acid.g. These materials have applications as environmentally friendly packaging and in medicine in drug delivery and the construction of prosthetic implants.[106] The multiple side chains of amino acids can also undergo chemical reactions. polyamides. e. Chemical synthesis Several methods exist to synthesize amino acids.[115] At the current time. In a few cases.. therefore.[97] Chemical building blocks Amino acids are important as low-cost feedstocks.[108] In alternative fashion. for asymmetric hydrogenation reactions. polyesters.Nullomers are codons that in theory code for an amino acid. polystyrene beads). using protecting groups (e. This condensation reaction yields the newly formed peptide bond and a molecule of water.[101] 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. and esterification. gives α. These compounds are used in chiral pool synthesis as enantiomerically pure building- blocks. These polymers include polypeptides.[100] An interesting example of such materials is polyaspartate. instead. these chemicals can undergo most of the reactions associated with these functional groups.. amide bond formation. In cells. DCC and DIC). However.[109] Using ammonia or ammonium salts in this reaction gives unsubstituted amino acids. but several alternative procedures using asymmetric auxiliaries[112] or asymmetric catalysts[113][114] have been developed. instead of aldehydes.[105] The combination of these functional groups allow amino acids to be effective polydentate ligands for metal-amino acid chelates. Hydrolysis of the nitrile in acid then yields a α-amino acid. the tripeptide glutathione is an essential part of the defenses of cells against oxidative stress. whereas substituting primary and secondary amines will yield substituted amino acids.[119] .[110] Likewise.[107] The types of these reactions are determined by the groups on these side chains and are. the aromatic amino acid tyrosine is being developed as a possible replacement for toxic phenols such as bisphenol A in the manufacture of polycarbonates. This peptide is synthesized in two steps from free amino acids.α- disubstituted amino acids. amide bond formation.g. This aminoacyl-tRNA is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase.[118] In the first step. for example bacteria prefer to use CGA instead of AGA to code for arginine. one amino acid molecule can react with another and become joined through an amide linkage. and decarboxylation for the carboxylic acid group.[111] The classical synthesis gives racemic mixtures of α-amino acids as products. using ketones. not all peptide bonds are formed in this way. This polymerization of amino acids is what creates proteins.[104] Reactions As amino acids have both a primary amine group and a primary carboxyl group. These include nucleophilic addition. different between the various types of amino acid. the amino acid is first activated by attachment to a transfer RNA molecule through an ester bond. which catalyzes the attack of the amino group of the elongating protein chain on the ester bond.[116] This aminoacyl-tRNA is then a substrate for the ribosome. and imine formation for the amine group. the most-adopted method is an automated synthesis on a solid support (e. although no commercial applications exist.g. 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.g.[99] Biodegradable plastics Amino acids are under development as components of a range of biodegradable polymers. and polyurethanes with amino acids either forming part of their main chains or bonded as side chains.[102][103] In addition. polysulfides. Fmoc and t-Boc) and activating groups (e.[98] Amino acids have been investigated as precursors chiral catalysts.. the Strecker amino acid synthesis involves the treatment of an aldehyde with potassium cyanide and ammonia. Nucleophilic substitution with ammonia then converts the alkyl bromide to The Strecker amino acid synthesis the amino acid. This characteristic can be taken advantage of and used to create new selective cancer-fighting drugs[96] and to prevent cross- contamination of DNA samples from crime-scene investigations.[95] This creates some sequences that do not appear in the genome.. however in nature there is a selective bias against using this codon in favor of another. For example. This dipeptide is then condensed with glycine by glutathione synthetase to form glutathione. this reaction does not occur directly. a water-soluble biodegradable polymer that may have applications in disposable diapers and agriculture.[117] As a result of this mechanism. this produces an α-amino nitrile as an intermediate. peptides are synthesized by specific enzymes. Peptide bond formation As both the amine and carboxylic acid groups of amino acids can react to form amide bonds.

Some modifications can produce hydrophobic lipoproteins. Both of these amino acids are found in peptidic lantibiotics such as alamethicin.[131] Table of standard amino acid ab breviations and properties . peptides are synthesized by a variety of reactions. protein or nucleic acid. some microbes make 2-aminoisobutyric acid and lanthionine. proteins that have to bind to positively charged molecules have surfaces rich with negatively charged amino acids like glutamate and aspartate. One of the most-used in solid-phase peptide synthesis uses the aromatic oxime derivatives of amino acids as activated units. while proteins binding to negatively charged molecules have surfaces rich with positively charged chains like lysine and arginine. hydrophilic side chains are exposed to the aqueous solvent. formed from alpha-ketoglutarate and ammonia in the mitochondrion. Ile. In order to form other amino acids. which is attached to a solid resin support.[123] while hydroxyproline is made by a posttranslational modification of proline. or it can be used for energy by entering glycolysis or the citric acid cycle. and Trp) buried in the middle of the protein.[126] Catabolism Amino acids must first pass out of organelles and cells into blood circulation via amino acid transporters. aspartate aminotransferase converts glutamate and oxaloacetate to alpha-ketoglutarate and aspartate. forming glutamate. the remainder of the molecule can sometimes be used to synthesize new amino acids.[128] Some amino acids have special properties such as cysteine. and glycine that is more flexible than other amino acids. and functional groups. the plant uses transaminases to move the amino group to another alpha-keto carboxylic acid. which is a sulfide-bridged derivative of alanine. For example. hydrophilicity or hydrophobicity. peptide bond Nonstandard amino acids are usually formed through modifications to standard amino acids. with the products having the ability to based on their properties. However.[120] 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. when additional chemical groups are attached to the amino acids in proteins. The water-soluble proteins tend to have their hydrophobic to form glucose. that can form covalent disulfide bonds to other cysteine residues. Amino Physicochemical properties of amino acids acids can be classified according to the properties of their main products as either of the following:[127] The 20 amino acids encoded directly by the genetic code can be divided into several groups * Glucogenic.[125] However.[34] These properties are important for protein structure and * Ketogenic. In many vertebrates. amino acid degradation can produce uric acid or ammonia instead. In similar fashion.) The integral membrane proteins tend to have outer rings of exposed hydrophobic amino acids that anchor them into the lipid bilayer. often involves deamination by moving its amino group to alpha-ketoglutarate.[122] Other organisms use The condensation of two amino acids to form a dipeptide through a transaminases for amino acid synthesis. 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.[121] Biosynthesis In plants. occurring in the liver and kidneys.[124] Microorganisms and plants can synthesize many uncommon amino acids. nitrogen is first assimilated into organic compounds in the form of glutamate.[130] These type of modification allow the reversible targeting of a protein to a membrane. Phe. too. Val. 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.[129] or hydrophilic glycoproteins. For example. This process involves transaminases. since the amine and carboxylic acid groups are typically ionized. a * Amino acids catabolized into both glucogenic and residue refers to a specific monomer within the polymeric chain of a polysaccharide. For example. form glucose by gluconeogenesis size. the amino group is then removed through the urea cycle and is excreted in the form of urea. These products may still be used residues (Leu. Many proteins undergo a range of posttranslational modifications. some peripheral membrane proteins have a patch of hydrophobic amino acids on their surface that locks onto the membrane. whereas for ketogenesis or lipid synthesis. Degradation of an amino acid. For example. as detailed in image at right. with the products not having the ability protein–protein interactions. Important factors are charge. often the same as those used in amination during synthesis. In the case part- way between these two extremes. For example.[80] After removal of one or more amino groups. serine dehydratase converts serine to pyruvate and ammonia.In chemistry. in plants. (Note that in biochemistry. ketogenic products. These are added in sequence onto the growing peptide chain. homocysteine is formed through the transsulfuration pathway or by the demethylation of methionine via the intermediate metabolite S-adenosyl methionine. proline that forms a cycle to the polypeptide backbone. There are different hydrophobicity scales of amino acid residues. Catabolism of proteinogenic amino acids.

M Aromatic Ω F. Q.03 basic positive(10%) Histidine His H basic polar −3.38 containing Glutamic acid Glu E acid acidic polar negative −3. H. H Negatively charged − D. R.[136][137] Ambiguous amino acids 3-letter 1-letter Any / unknown Xaa X All Asparagine or aspartic acid Asx B D.192 3. 9.5 174.49 Leucine Leu L aliphatic nonpolar neutral 3.203 5. Tyrosine Tyr Y aromatic polar neutral −1.32 Glutamine Gln Q amide polar neutral −3.2 117. G. They are also used to summarise conserved protein sequence motifs.9 146.067 7.104 5.49 sulfur- Cysteine Cys C nonpolar neutral 2.3 274. 8.5 132. 222.175 5.4. . 193 181.119 5.313 In addition to the specific amino acid codes. E. L Hydrophobic Φ V.76 Arginine Arg R basic basic polar positive −4.25 1.148 6.93 Aspartic acid Asp D acid acidic polar negative −3.208 2. S Hydrophilic ζ S. 206. A. I.132 5. M Small π P.5 147.064 Pyrrolysine Pyl O 255.8 105.119 3.9 149. F. W.0 Proline Pro P cyclic nonpolar neutral −1. ε at Occurrence Side Side chain Absorbance Side chain MW 3.9 Glycine Gly G aliphatic nonpolar neutral −0. The use of single letters to indicate sets of similar residues is similar to the use of abbreviation codes for degenerate bases.5 133. E Unk is sometimes used instead of Xaa. Y. I.78 Asparagine Asn N amide polar neutral −3.8 257. Q Leucine or Isoleucine Xle J I.19 sulfur- Methionine Met M nonpolar neutral 1.131 6.5 131. but is less standard.3 121.91 48.02 hydroxyl- Serine Ser S polar neutral −0.146 3. N. R Positively charged + K.8 131.0 204.26 aromatic neutral(90%) Isoleucine Ile I aliphatic nonpolar neutral 4.8 89. W.87 60. H Aliphatic (non-aromatic) Ψ V.7 119.228 1.2 211 5.189 5.4 75.4)[132] (%)[135] cm−1)[134] Alanine Ala A aliphatic nonpolar neutral 1. L.2.5 146. T.093 7.9 280. 188 165. Phenylalanine Phe F aromatic nonpolar neutral 2. 47. K. chain λmax Amino acid charge (pH Hydropathy in proteins letter[132] letter[132] polarity [132] index[133] λmax(nm)[134] (mM−1 (weight) class 7.154 1.156 2.175 9.3.68 Lysine Lys K basic basic polar positive −3. L.0 Valine Val V aliphatic nonpolar neutral 4.094 8. D.53 containing Tryptophan Trp W aromatic nonpolar neutral −0. Y.0.5 250 0.191 2.14 containing hydroxyl- Threonine Thr T polar neutral −0. 219 5. placeholders are used in cases where chemical or crystallographic analysis of a peptide or protein cannot conclusively determine the identity of a residue. 1.32 containing 0.9 155.6 115.6.73 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 MW (weight) Selenocysteine Sec U 168. N Glutamine or glutamic acid Glx Z E.

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