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 nonpolar side chains) can be isolated by precipitation from water by adjusting the ph to the required isoelectric point. physicochemical properties the 20 canonical amino acids can be classified according to their properties. important factors are charge, hydrophilicity or hydrophobicity, size, and functional groups. these properties influence 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. (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 in the lipid bilayer. some peripheral membrane proteins have a patch of hydrophobic amino acids on their surface that sticks to the membrane. in a similar fashion, proteins that have to bind to positively charged molecules have surfaces rich in negatively charged amino acids such as glutamate and aspartate, while proteins binding to negatively charged molecules have surfaces rich in positively charged amino acids like lysine and arginine. for example, lysine and arginine are present in large amounts in the low-complexity regions of nucleic-acid binding proteins. there are various hydrophobicity scales of amino acid residues. some amino acids have special properties. cysteine can form covalent disulfide bonds to other cysteine residues. proline forms a cycle to the polypeptide backbone, and glycine is more flexible than other amino acids. glycine and proline are strongly present within low complexity regions of both eukaryotic and prokaryotic proteins, whereas the opposite is the case with cysteine, phenylalanine, tryptophan, methionine, valine, leucine, isoleucine, which are highly reactive, or complex, or hydrophobic. many proteins undergo a range of posttranslational modifications, whereby additional chemical groups are attached to the amino acid residue side chains sometimes producing lipoproteins (that are hydrophobic), or glycoproteins (that are hydrophilic) allowing the protein to attach temporarily to a membrane. for example, a signaling protein can attach and then detach from a cell membrane, because it contains cysteine residues that can have the fatty acid palmitic acid added to them and subsequently removed. table of standard amino acid abbreviations and properties although one-letter symbols are included in the table, iupac–iubmb recommend that "use of the one-letter symbols should be restricted to the comparison of long sequences". amino acid 3- and 1-letter symbols side chain hydropathy index molar absorptivity molecular mass abundance inproteins (%) standard genetic coding,iupac notation 3 1 class polarity net chargeat ph 7.4 wavelength,λmax (nm) coefficient ε(mm−1·cm−1) alanine ala a aliphatic nonpolar neutral 1.8 89.094 8.76 gcn arginine arg r fixed cation basic polar positive −4.5 174.203 5.78 mgr, cgy asparagine asn n amide polar neutral −3.5 132.119 3.93 aay aspartate asp d anion brønsted base negative −3.5 133.104 5.49 gay cysteine cys c thiol brønsted acid neutral 2.5 250 0.3 121.154 1.38 ugy glutamine gln q amide polar neutral −3.5 146.146 3.9 car glutamate glu e anion brønsted base negative −3.5 147.131 6.32 gar glycine gly g aliphatic nonpolar neutral −0.4 75.067 7.03 ggn histidine his h aromatic cation brønsted acid and base positive, 10%neutral, 90% −3.2 211 5.9 155.156 2.26 cay isoleucine ile i aliphatic nonpolar neutral 4.5 131.175 5.49 auh leucine leu l aliphatic nonpolar neutral 3.8 131.175 9.68 yur, cuy lysine lys k cation brønsted acid positive −3.9 146.189 5.19 aar methionine met m thioether nonpolar neutral 1.9 149.208 2.32 aug phenylalanine phe f aromatic nonpolar neutral 2.8 257, 206, 188 0.2, 9.3, 60.0 165.192 3.87 uuy proline pro p cyclic nonpolar neutral −1.6 115.132 5.02 ccn serine ser s hydroxylic polar neutral −0.8 105.093 7.14 ucn, agy threonine thr t hydroxylic polar neutral −0.7 119.119 5.53 acn tryptophan trp w aromatic nonpolar neutral −0.9 280, 219 5.6, 47.0 204.228 1.25 ugg tyrosine tyr y aromatic brønsted acid neutral −1.3 274, 222, 193 1.4, 8.0, 48.0 181.191 2.91 uay valine val v aliphatic nonpolar neutral 4.2 117.148 6.73 gun 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 molecular mass selenocysteine sec u 168.064 pyrrolysine pyl o 255.313 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. they are also used to summarise conserved protein sequence motifs. the use of single letters to indicate sets of similar residues is similar to the use of abbreviation codes for degenerate bases. ambiguous amino acids 3-letter 1-letter amino acids included codons included any / unknown xaa x all nnn asparagine or aspartate asx b d, n ray glutamine or glutamate glx z e, q sar leucine or isoleucine xle j i, l ytr, ath, cty hydrophobic φ v, i, l, f, w, y, m ntn, tay, tgg aromatic ω f, w, y, h ywy, tty, tgg aliphatic (non-aromatic) ψ v, i, l, m vtn, ttr small π p, g, a, s bcn, rgy, ggr hydrophilic ζ s, t, h, n, q, e, d, k, r van, wcn, cgn, agy positively-charged + k, r, h arr, cry, cgr negatively-charged − d, e gan unk is sometimes used instead of xaa, but is less standard. ter or * (from termination) is used in notation for mutations in proteins when a stop codon occurs. it correspond to no amino acid at all. in addition, many nonstandard 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). occurrence and functions in biochemistry a polypeptide is an unbranched chain of amino acidsβ-alanine and its α-alanine isomerthe amino acid selenocysteine amino acids which have the amine group attached to the (alpha-) carbon atom next to the carboxyl group have primary importance in living organisms since they participate in protein synthesis. they are known as 2-, alpha-, or α-amino acids (generic formula h2nchrcooh in most cases, where r is an organic substituent known as a "side chain"); often the term "amino acid" is used to refer specifically to these. they include the 22 proteinogenic ("protein-building") amino acids, which combine into peptide chains ("polypeptides") to form the building blocks of a vast array of proteins. these are all l-stereoisomers ("left-handed" enantiomers), although a few d-amino acids ("right-handed") occur in bacterial envelopes, as a neuromodulator (d-serine), and in some antibiotics. many proteinogenic and non-proteinogenic amino acids have biological functions. for example, in the human brain, glutamate (standard glutamic acid) and gamma-aminobutyric acid ("gaba", nonstandard gamma-amino acid) are, respectively, the main excitatory and inhibitory neurotransmitters. 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 vary from species to species. because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, feed, and food technology. industrial uses include the production of drugs, biodegradable plastics, and chiral catalysts. proteinogenic amino acids amino acids are the precursors to proteins. they join by condensation reactions to form short polymer chains called peptides or longer chains called either polypeptides or proteins. these chains are linear and unbranched, with each amino acid residue within the chain attached to two neighboring amino acids. in nature, the process of making proteins encoded by dna/rna genetic material 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 order in which the amino acids are added is read through the genetic code from an mrna template, which is an rna copy of one of the organism's genes. twenty-two amino acids are naturally incorporated into polypeptides and are called proteinogenic or natural amino acids. of these, 20 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. 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. this uag codon is followed by a pylis downstream sequence. several independent evolutionary studies have suggested that gly, ala, asp, val, ser, pro, glu, leu, thr may belong to a group of amino acids that constituted the early genetic code, whereas cys, met, tyr, trp, his, phe may belong to a group of amino acids that constituted later additions of the genetic code. standard vs nonstandard 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. a modified form of methionine (n-formylmethionine) is often incorporated in place of methionine as the initial amino acid of proteins in bacteria, mitochondria and chloroplasts. other amino acids are called nonstandard or non-canonical. most of the nonstandard amino acids are also non-proteinogenic (i.e. they cannot be incorporated into proteins during translation), but two of them are proteinogenic, as they can be incorporated translationally into proteins by exploiting information not encoded in the universal genetic code. the two nonstandard proteinogenic amino acids are selenocysteine (present in many non-eukaryotes as well as most eukaryotes, but not coded directly by dna) and pyrrolysine (found only in some archaea and at least one bacterium). the incorporation of these nonstandard amino acids is rare. for example, 25 human proteins include selenocysteine in their primary structure, and the structurally characterized enzymes (selenoenzymes) employ selenocysteine as the catalytic moiety in their active sites. pyrrolysine and selenocysteine are encoded via variant codons. for example, selenocysteine is encoded by stop codon and secis element. 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. non-proteinogenic amino acids aside from the 22 proteinogenic amino acids, many non-proteinogenic amino acids are known. those either are not found in proteins (for example carnitine, gaba, levothyroxine) 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, and collagen contains hydroxyproline, generated by hydroxylation of proline. another example is the formation of hypusine in the translation initiation factor eif5a, through modification of a lysine residue. 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. some non-proteinogenic amino acids are not found in proteins. examples include 2-aminoisobutyric acid 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). 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