Amino acid

Short description: Organic compounds containing amine and carboxylic groups

Structure of a typical L-alpha-amino acid in the "neutral" form

Amino acids[lower-alpha 1] are organic compounds that contain both amino and carboxylic acid functional groups.[2]: 71 Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins.[3] Only these 22 appear in the genetic code of life.[4][5]

Amino acids can be classified according to the locations of the core structural functional groups (alpha- (α-), beta- (β-), gamma- (γ-) amino acids, etc.);[2]: 77 other categories relate to polarity, ionization, and side-chain group type (aliphatic, acyclic, aromatic, polar, etc.).[2]: 71–76 In the form of proteins, amino-acid residues form the second-largest component (water being the largest) of human muscles and other tissues.[6] Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis. It is thought that they played a key role in enabling life on Earth and its emergence.[7]

Amino acids are formally named by the IUPAC-IUBMB Joint Commission on Biochemical Nomenclature in terms of the fictitious "neutral" structure shown in the illustration. For example, the systematic name of alanine is 2-aminopropanoic acid, based on the formula CH
3–CH(NH
2)–COOH. The Commission justified this approach as follows:[8]

> The systematic names and formulas given refer to hypothetical forms in which amino groups are unprotonated and carboxyl groups are undissociated. This convention is useful to avoid various nomenclatural problems but should not be taken to imply that these structures represent an appreciable fraction of the amino-acid molecules.

## Contents

* 1 History
* 2 Structure
* 2.1 α-amino acids
* 2.2 β- and γ-amino acids
* 2.3 Chirality
* 2.4 Side chains
* 2.4.1 Polar charged
* 2.4.2 Polar uncharged
* 2.4.3 Hydrophobic
* 2.4.4 Classification outliers
* 3 Physicochemical properties
* 3.1 Acid-base behavior
* 3.1.1 Zwitterions
* 3.1.2 Isoelectric point
* 3.2 Abbreviation and property tables
* 4 Biological roles and occurrence
* 4.1 Proteinogenic
* 4.2 Standard and nonstandard forms
* 4.3 Non-proteinogenic
* 4.4 Physiological roles beyond proteins
* 4.4.1 Standard
* 4.4.2 Nonstandard
* 4.5 In mammalian nutrition
* 4.5.1 Conditional requirements
* 5 Industrial uses
* 5.1 Animal feed
* 5.2 Food
* 5.3 Chemical building blocks
* 6 Potential uses
* 6.1 Fertilizer
* 6.2 Biodegradable plastics
* 7 Synthesis
* 7.1 Chemical synthesis
* 7.2 Biosynthesis
* 7.3 Primordial synthesis
* 8 Reactions
* 8.1 Peptide bond formation
* 8.2 Catabolism
* 8.3 Complexation
* 9 Chemical analysis
* 10 See also
* 11 Notes
* 12 References
* 13 Further reading
* 14 External links

## History

The first few amino acids were discovered in the early 1800s.[9][10] In 1806, French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound from asparagus that was subsequently named asparagine, the first amino acid to be discovered.[11][12] Cystine was discovered in 1810,[13] although its monomer, cysteine, remained undiscovered until 1884.[14][12][lower-alpha 2] Glycine and leucine were discovered in 1820.[15] The last of the 20 common amino acids to be discovered was threonine in 1935 by William Cumming Rose, who also determined the essential amino acids and established the minimum daily requirements of all amino acids for optimal growth.[16][17]

The unity of the chemical category was recognized by Wurtz in 1865, but he gave no particular name to it.[18] The first use of the term "amino acid" in the English language dates from 1898,[19] while the German term, Aminosäure, was used earlier.[20] Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis. In 1902, Emil Fischer and Franz Hofmeister independently proposed that proteins are formed from many amino acids, whereby bonds are formed between the amino group of one amino acid with the carboxyl group of another, resulting in a linear structure that Fischer termed "peptide".[21]

## Structure

### α-amino acids

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)

2-, alpha-, or α-amino acids[22] have the generic formula H
2NCHRCOOH in most cases,[lower-alpha 3] where R is an organic substituent known as a "side chain".[23]

Of the many hundreds of described amino acids, 22 are proteinogenic ("protein-building").[24][25][26] It is these 22 compounds that combine to give a vast array of peptides and proteins assembled by ribosomes.[27] Non-proteinogenic amino acids may arise through nonribosomal peptide synthesis.[28] Modified amino acids, by contrast, typically result from post-translational modification.[29]

### β- and γ-amino acids

Amino acids with the structure NH+
3–CXY–CXY–CO−
2, such as β-alanine, a component of carnosine and a few other peptides, are β-amino acids. Ones with the structure NH+
3–CXY–CXY–CXY–CO−
2 are γ-amino acids, and so on, where X and Y are two substituents (one of which is normally H).[8]

### Chirality

The carbon atom next to the carboxyl group is called the α–carbon. In proteinogenic amino acids, it bears the amine and the R group or side chain specific to each amino acid, as well as a hydrogen atom. With the exception of glycine, for which the side chain is also a hydrogen atom, the α–carbon is stereogenic. All chiral proteogenic amino acids have the L configuration. They are "left-handed" enantiomers, which refers to the stereoisomers of the alpha carbon.[2]: 80–83

A few D-amino acids ("right-handed") have been found in nature, e.g., in bacterial envelopes, as a neuromodulator (D-serine), and in some antibiotics.[30][31] Rarely, D-amino acid residues are found in proteins, and are converted from the L-amino acid as a post-translational modification.[32][lower-alpha 4]

### Side chains

#### Polar charged

Five amino acids possess a charge at neutral pH. Often these side chains appear at the surfaces on proteins to enable their solubility in water, and side chains with opposite charges form important electrostatic contacts called salt bridges that maintain structures within a single protein or between interfacing proteins.[35] Many proteins bind metal into their structures specifically, and these interactions are commonly mediated by charged side chains such as aspartate, glutamate and histidine. Under certain conditions, each ion-forming group can be charged, forming double salts.[36]

The two negatively charged amino acids at neutral pH are aspartate (Asp, D) and glutamate (Glu, E). The anionic carboxylate groups behave as Brønsted bases in most circumstances.[35] Enzymes in very low pH environments, like the aspartic protease pepsin in mammalian stomachs, may have catalytic aspartate or glutamate residues that act as Brønsted acids.[37][38]

File:Histidine lysine arginine sidechains.svgFunctional groups found in histidine (top), lysine (middle) and arginine (bottom) in their charged (protonated) and uncharged forms

There are three amino acids with side chains that are cations at neutral pH: arginine (Arg, R), lysine (Lys, K) and histidine (His, H). Arginine has a charged guanidino group and lysine a charged alkyl amino group, and are fully protonated at pH 7. Histidine's imidazole group has a pKa of 6.0, and is only around 10% protonated at neutral pH. Because histidine is easily found in its basic and conjugate acid forms it often participates in catalytic proton transfers in enzyme reactions.[35]

#### Polar uncharged

The polar, uncharged amino acids serine (Ser, S), threonine (Thr, T), asparagine (Asn, N) and glutamine (Gln, Q) readily form hydrogen bonds with water and other amino acids.[35] They do not ionize in normal conditions, a prominent exception being the catalytic serine in serine proteases. This is an example of severe perturbation, and is not characteristic of serine residues in general. Threonine has two chiral centers, not only the L (2S) chiral center at the α-carbon shared by all amino acids apart from achiral glycine, but also (3R) at the β-carbon. The full stereochemical specification is (2S,3R)-L-threonine.[39]

Because of the presence of phenolic hydroxyl group with a pKa = ~10, tyrosine is best classified as a neutral polar amino acid,[2]: 74 but with amphipathic character that makes it less polar than classical small polar amino acid residues.[40]

#### Hydrophobic

Nonpolar amino acid interactions are the primary driving force behind the processes that fold proteins into their functional three dimensional structures.[35] None of these amino acids' side chains ionize easily, and therefore do not have pKas.[41]

#### Classification outliers

Several side chains are not described well by the charged, polar and hydrophobic categories. Glycine (Gly, G) could be considered a polar amino acid since its small size means that its solubility is largely determined by the amino and carboxylate groups. However, the lack of any side chain provides glycine with a unique flexibility among amino acids with large ramifications to protein folding.[35] Cysteine (Cys, C) can also form hydrogen bonds readily, which would place it in the polar amino acid category, though it can often be found in protein structures forming covalent bonds, called disulphide bonds, with other cysteines. These bonds influence the folding and stability of proteins, and are essential in the formation of antibodies. Proline (Pro, P) has an alkyl side chain and could be considered hydrophobic, but because the side chain joins back onto the alpha amino group it becomes particularly inflexible when incorporated into proteins. Similar to glycine this influences protein structure in a way unique among amino acids. Selenocysteine (Sec, U) is a rare amino acid not directly encoded by DNA, but is incorporated into proteins via the ribosome. Selenocysteine has a lower redox potential compared to the similar cysteine, and participates in several unique enzymatic reactions.[42] Pyrrolysine (Pyl, O) is another amino acid not encoded in DNA, but synthesized into protein by ribosomes.[43] It is found in archaeal species where it participates in the catalytic activity of several methyltransferases.[44]

## 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.[31] 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.[45] There are various hydrophobicity scales of amino acid residues.[46]

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.[47]

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.[45][48][49]

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),[50] or glycoproteins (that are hydrophilic)[51] 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.[52]

### Acid-base behavior

#### Zwitterions

Main article: Physics:Zwitterion

Ionization and Brønsted character of N-terminal amino, C-terminal carboxylate, and side chains of amino acid residues

The common natural forms of amino acids have a zwitterionic structure, with –NH+
3 (–NH+
2– in the case of proline) and –CO−
2 functional groups attached to the same C atom, and are thus α-amino acids, and are the only ones found in proteins during translation in the ribosome. In aqueous solution at pH close to neutrality, amino acids are energetically favored in their zwitterionic form, with a deprotonated CO−
2 group and a protonated NH+
3 group, because the high dielectric constant of water and its hydrogen-bonding network effectively stabilize separated charges. Thus, the overall structure is NH+
3–CHR–CO−
2, and the so-called "neutral forms" –NH
2–CHR–CO
2H are not present to any measurable degree at physiological pH.[53] A zwitterion has a net charge of zero, but because it contains both positively and negatively charged sites, it is misleading to describe it as “uncharged.”[54]

In contrast, in low-dielectric hydrophobic environments such as organic solvents or cell membrane interiors, charge separation is poorly stabilized and proton transfer tends to yield a neutral form, while in the gas phase, where there is essentially no dielectric screening or solvation, spectroscopic and computational studies show that the lowest-energy structures of most amino acids are also neutral unless specific intramolecular interactions or stepwise hydration provide sufficient stabilization of the zwitterion.[55]

In strongly acidic conditions (pH below 3), the carboxylate group becomes protonated and the structure becomes an ammonio carboxylic acid, NH+
3–CHR–CO
2H.[41] This is relevant for enzymes like pepsin that are active in acidic environments such as the mammalian stomach and lysosomes, but does not significantly apply to intracellular enzymes.[56] In highly basic conditions (pH greater than 10, not normally seen in physiological conditions), the ammonio group is deprotonated to give NH
2–CHR–CO−
2.[41]

Although various definitions of acids and bases are used in chemistry, the only one that is useful for chemistry in aqueous solution is that of Brønsted:[57][58] an acid is a species that can donate a proton to another species, and a base is one that can accept a proton. This criterion is used to label the groups in the above illustration. The carboxylate side chains of aspartate and glutamate residues are the principal Brønsted bases in proteins. Likewise, lysine, tyrosine and cysteine will typically act as a Brønsted acid. Histidine under these conditions can act both as a Brønsted acid and a base.[59]

#### Isoelectric point

Composite of titration curves of twenty proteinogenic amino acids grouped by side chain category

For amino acids with uncharged side-chains the zwitterion predominates at pH values between the two pKa values, but coexists in equilibrium with small amounts of net negative and net positive ions. At the midpoint between the two pKa values, the trace amount of net negative and trace of net positive ions balance, so that average net charge of all forms present is zero.[60] This pH is known as the isoelectric point pI, so pI = ⁠1/2⁠(pKa1 \+ pKa2).

For amino acids with charged side chains, the pKa of the side chain is involved. Thus for aspartate or glutamate with negative side chains, the terminal amino group is essentially entirely in the charged form –NH+
3, but this positive charge needs to be balanced by the state with just one C-terminal carboxylate group is negatively charged. This occurs halfway between the two carboxylate pKa values: pI = ⁠1/2⁠(pKa1 \+ pKa(R)), where pKa(R) is the side chain pKa.[58]

Similar considerations apply to other amino acids with ionizable side-chains, including not only glutamate (similar to aspartate), but also cysteine, histidine, lysine, tyrosine and arginine with positive side chains.[58]

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.[61] Zwitterionic amino acids exhibit minimal solubility at their isoelectric point, and in some cases can be isolated from aqueous solution by adjusting the pH to the appropriate isoelectric value.[62]

### Abbreviation and property tables

"Amino acid code" redirects here. For base-pair encoding of amino acids, see Genetic code § Codons.

Main article: Chemistry:Proteinogenic amino acid

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".[8]

The one-letter notation was chosen by IUPAC-IUB based on the following rules:[63]

* Initial letters are used where there is no ambiguity: C cysteine, H histidine, I isoleucine, M methionine, S serine, V valine,[63]
* Where arbitrary assignment is needed, the structurally simpler amino acids are given precedence: A Alanine, G glycine, L leucine, P proline, T threonine,[63]
* F PHenylalanine and R aRginine are assigned by being phonetically suggestive,[63]
* W tryptophan is assigned based on the double ring being visually suggestive to the bulky letter W,[63]
* K lysine and Y tyrosine are assigned as alphabetically nearest to their initials L and T (note that U was avoided for its similarity with V, while X was reserved for undetermined or atypical amino acids); for tyrosine the mnemonic tYrosine was also proposed,[64]
* D aspartate was assigned arbitrarily, with the proposed mnemonic asparDic acid;[65] E glutamate was assigned in alphabetical sequence being larger by merely one methylene –CH2– group,[64]
* N asparagine was assigned arbitrarily, with the proposed mnemonic asparagiNe;[65] Q glutamine was assigned in alphabetical sequence of those still available (note again that O was avoided due to similarity with D), with the proposed mnemonic Qlutamine.[65]

Amino acid  | 3- and 1-letter symbols  | Side chain  | Hydropathy
index[66] | Molar absorptivity[67] | Molecular mass | Abundance in proteins (%)[68] | Standard genetic coding,
IUPAC notation

|
|
|
|
|
|
|

3  | 1  | Class  | Chemical polarity[69] | Net charge
at pH 7.4[69] | 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[lower-alpha 5]
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  | Cationic  | 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[lower-alpha 6]
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:[70]

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 summarize 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.[71][72]

Ambiguous amino acids  | 3-letter  | 1-letter  | Amino acids included  | Codons included

|
|
|
|

Any / unknown  | Xaa [73] | 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[lower-alpha 7]
Hydrophobic |  | Φ  | V, I, L, F, W, Y, M  | NTN, TAY, TGG
Aromatic  |  | Ω  | F, W, Y, H  | YWY, TTY, TGG[lower-alpha 8]
Aliphatic (non-aromatic)  |  | Ψ  | V, I, L, M  | VTN, TTR[lower-alpha 9]
Small  |  | π  | P, G, A, S  | BCN, RGY, GGR
Hydrophilic |  | ζ  | S, T, H, N, Q, E, D, K, R  | VAN, WCN, CGN, AGY[lower-alpha 10]
Positively-charged  |  | \+  | K, R, H  | ARR, CRY, CGR
Negatively-charged  |  | −  | D, E  | GAN

Unk[74] is sometimes used instead of Xaa,[73] but is less standard.[75]

Ter or * (from termination) is used in notation for mutations in proteins when a stop codon occurs. It corresponds to no amino acid at all.[76]

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).[77]

## Biological roles and occurrence

A polypeptide is an unbranched chain of amino acids.

β-Alanine and its α-alanine isomer

The amino acid selenocysteine

### Proteinogenic

Main article: Proteinogenic amino acid

See also: Protein primary structure and Posttranslational modification

Amino acids are the precursors to proteins.[27] 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 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.[78] The order in which the amino acids are added is read through the genetic code from an mRNA template, which is an RNA derived from one of the organism's genes.[79]

There are 22 amino acids that get naturally incorporated into polypeptides; these are called proteinogenic amino acids or natural amino acids.[31] 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.[80] 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.[81]

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.[82][83][84]

### Standard and nonstandard forms

The 20 amino acids that are encoded directly by the codons of the universal genetic code are called standard or canonical amino acids.[85][86] 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 plastids (including chloroplasts).[87] Other amino acids are called nonstandard or non-canonical.[88] 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.[89]

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).[90][91] The incorporation of these nonstandard amino acids is rare. For example, 25 human proteins include selenocysteine in their primary structure,[92] and the structurally characterized enzymes (selenoenzymes) employ selenocysteine as the catalytic moiety in their active sites.[93] Pyrrolysine and selenocysteine are encoded via variant codons. For example, selenocysteine is encoded by stop codon and SECIS element.[94][95][96]

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.[97][98][99]

### Non-proteinogenic

Main article: Chemistry:Non-proteinogenic amino acids

Aside from the 22 proteinogenic amino acids, many non-proteinogenic amino acids are known.[100][101] These either are not found in proteins (for example carnitine, GABA, ornithine) or are not produced directly and in isolation by standard cellular machinery. For example, hydroxyproline is synthesized from proline,[102] and selenomethionine is produced by metabolic modification of methionine.[103]

Non-proteinogenic amino acids that are found in proteins are formed by post-translational modification. 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.[104] Examples:

* the carboxylation of glutamate allows for better binding of calcium cations,[105]
* Hydroxyproline, generated by hydroxylation of proline, is a major component of the connective tissue collagen.[106]
* Hypusine in the translation initiation factor EIF5A, contains a modification of lysine.[107]

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).[108] 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.[109]

### Physiological roles beyond proteins

{{Annotated image 4 | caption = {{{caption|In humans, catecholamines and phenethylaminergic trace amines are derived from the amino acid {{nowrap|L-phenylalanine}}.}}} | header_background = #F0F8FF | header = Biosynthetic pathways for catecholamines and trace amines in the human brain<ref name="Trace amine template 1">Broadley KJ (March 2010). "The vascular effects of trace amines and amphetamines". Pharmacol. Ther. 125 (3): 363–375. doi:10.1016/j.pharmthera.2009.11.005. PMID 19948186. </ref>[110][111] | alt = Graphic of catecholamine and trace amine biosynthesis | image = Catecholamine and trace amine biosynthesis.png | image-width = 580 | image-left = 5 | image-top = 0 | align = right | width = 590 | height = 585 | annot-font-size = 14 | annot-text-align = center | annotations =

L-Phenylalanine

L-Tyrosine

L-DOPA

{{annotation|50|565|{{if pagename|Adrenaline=Adrenaline|Epinephrine=Epinephrine|Catecholamine=Epinephrine|other=Epinephrine}}}}

{{annotation|245|60|{{if pagename|Phenethylamine=Phenethylamine|Trace amine=Phenethylamine|Neurobiological effects of physical exercise={{highlight|Phenethylamine}}|other=Phenethylamine}}}}

p-Tyramine

Dopamine

{{annotation|245|565|{{if pagename|Norepinephrine=Norepinephrine|Adrenaline=Noradrenaline|Catecholamine=Norepinephrine|other=Norepinephrine}}}}

N-Methylphenethylamine

N-Methyltyramine

{{annotation|440|295|p-Octopamine}}}}

Synephrine

3-Methoxytyramine

AADC

AADC

AADC

primary
pathway

PNMT

PNMT

PNMT

PNMT

AAAH

AAAH

brain
CYP2D6

minor
pathway

COMT

DBH

DBH

Many proteinogenic and non-proteinogenic amino acids have biological functions beyond being precursors to proteins and peptides. In humans, amino acids also have important roles in diverse biosynthetic pathways. Defenses against herbivores in plants sometimes employ amino acids.[112] Examples:

#### Standard

* Tryptophan is a precursor of the neurotransmitter serotonin.[113][114]
* Tyrosine (and its precursor phenylalanine) are precursors of the catecholamine neurotransmitters dopamine, epinephrine and norepinephrine and various trace amines.[115][116]
* Phenylalanine is a precursor of phenethylamine and tyrosine in humans.[117] In plants, it is a precursor of various phenylpropanoids, which are important in plant metabolism.[118]
* Glycine is a precursor of porphyrins such as heme.[119]
* Arginine is a precursor of nitric oxide.[120]
* Ornithine and S-adenosylmethionine are precursors of polyamines.[121]
* Aspartate, glycine, and glutamine are precursors of nucleotides.[122]

#### Nonstandard

* Carnitine is an essential cofactor for mitochondrial transport of long‑chain fatty acids (a major lipid class) into the matrix for β‑oxidation.[123][124]
* gamma-aminobutyric acid is a neurotransmitter.[125]
* 5-HTP (5-hydroxytryptophan) is used for experimental treatment of depression.[126]
* L-DOPA (L-dihydroxyphenylalanine) for Parkinson's treatment,[127]
* Eflornithine inhibits ornithine decarboxylase and used in the treatment of sleeping sickness.[128]
* Canavanine, an analogue of arginine found in many legumes is an antifeedant, protecting the plant from predators.[129]
* Mimosine found in some legumes, is another possible antifeedant.[130] This compound is an analogue of tyrosine and can poison animals that graze on these plants.[131]

However, not all of the functions of other abundant nonstandard amino acids are known.[132]

### In mammalian nutrition

Share of amino acid in various human diets and the resulting mix of amino acids in human blood serum. Glutamate and glutamine are the most frequent in food at over 10%, while alanine, glutamine, and glycine are the most common in blood.

Main article: Chemistry:Essential amino acid

Animals ingest amino acids in the form of protein. The protein is broken down into its constituent amino acids in the process of digestion. The amino acids are then used to synthesize new proteins and other nitrogenous biomolecules, or they are further catabolized through oxidation to provide a source of energy.[133] 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.[134] Glucogenic amino acids can also be converted into glucose, through gluconeogenesis.[135]

Of the 20 standard amino acids, nine (His, Ile, Leu, Lys, Met, Phe, Thr, 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, so they must be obtained from food.[136][137][138]

#### Conditional requirements

In addition, cysteine, tyrosine, and arginine are considered semiessential amino acids, and taurine a semi-essential aminosulfonic acid in children. Some amino acids are conditionally essential for certain ages or medical conditions. Essential amino acids may also vary from species to species.[lower-alpha 11] The metabolic pathways that synthesize these monomers are not fully developed.[139][140]

## Industrial uses

### Animal feed

Amino acids are sometimes added to animal feed because some of the components of these feeds, such as soybeans, have low levels of some of the essential amino acids, especially of lysine, methionine, threonine, and tryptophan.[141] Likewise amino acids are used to chelate metal cations in order to improve the absorption of minerals from feed supplements.[142]

### Food

The food industry is a major consumer of amino acids, especially glutamic acid, which is used as a flavor enhancer,[143] and aspartame (aspartylphenylalanine 1-methyl ester), which is used as an artificial sweetener.[144] Amino acids are sometimes added to food by manufacturers to alleviate symptoms of mineral deficiencies, such as anemia, by improving mineral absorption and reducing negative side effects from inorganic mineral supplementation.[145]

### Chemical building blocks

Amino acids are low-cost feedstocks used in chiral pool synthesis as enantiomerically pure building blocks.[146][147]

Amino acids are used in the synthesis of some cosmetics.[141]

## Potential uses

### Fertilizer

The chelating ability of amino acids is sometimes used in fertilizers 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 to improve the overall health of the plants.[148]

### Biodegradable plastics

Amino acids have been considered as components of biodegradable polymers, which have applications as environmentally friendly packaging and in medicine in drug delivery and the construction of prosthetic implants.[149] An interesting example of such materials is polyaspartate, a water-soluble biodegradable polymer that may have applications in disposable diapers and agriculture.[150] Due to its solubility and ability to chelate metal ions, polyaspartate is also being used as a biodegradable antiscaling agent and a corrosion inhibitor.[151][152]

## Synthesis

Main article: Biology:Amino acid synthesis

### Chemical synthesis

The commercial production of amino acids usually relies on mutant bacteria that overproduce individual amino acids using glucose as a carbon source. Some amino acids are produced by enzymatic conversions of synthetic intermediates. 2-Aminothiazoline-4-carboxylic acid is an intermediate in one industrial synthesis of L-cysteine for example. Aspartic acid is produced by the addition of ammonia to fumarate using a lyase.[145]

### Biosynthesis

In plants, nitrogen is first assimilated into organic compounds in the form of glutamate, formed from alpha-ketoglutarate and ammonia in the mitochondrion. For other amino acids, plants use transaminases to move the amino group from glutamate to another alpha-keto acid. For example, aspartate aminotransferase converts glutamate and oxaloacetate to alpha-ketoglutarate and aspartate.[153] Other organisms use transaminases for amino acid synthesis, too.[154][155]

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-adenosylmethionine,[156] while hydroxyproline is made by a post translational modification of proline.[157]

Microorganisms and plants 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.[158] However, in plants, 1-aminocyclopropane-1-carboxylic acid is a small disubstituted cyclic amino acid that is an intermediate in the production of the plant hormone ethylene.[159]

### Primordial synthesis

The formation of amino acids and peptides is assumed to have preceded and perhaps induced the emergence of life on earth. Amino acids can form from simple precursors under various conditions.[160] Surface-based chemical metabolism of amino acids and very small compounds may have led to the build-up of amino acids, coenzymes and phosphate-based small carbon molecules.[161][160][162] Amino acids and similar building blocks could have been elaborated into proto-peptides, with peptides being considered key players in the origin of life.[163]

The Strecker amino acid synthesis

In the famous Urey-Miller experiment, the passage of an electric arc through a mixture of methane, hydrogen, and ammonia produces a large number of amino acids. Since then, scientists have discovered a range of ways and components by which the potentially prebiotic formation and chemical evolution of peptides may have occurred, such as condensing agents, the design of self-replicating peptides and a number of non-enzymatic mechanisms by which amino acids could have emerged and elaborated into peptides.[163] Several hypotheses invoke the Strecker synthesis whereby hydrogen cyanide, simple aldehydes, ammonia, and water produce amino acids.[160]

According to a review, amino acids, and even peptides, "turn up fairly regularly in the various experimental broths that have been allowed to be cooked from simple chemicals. This is because nucleotides are far more difficult to synthesize chemically than amino acids." For a chronological order, it suggests that there must have been a 'protein world' or at least a 'polypeptide world', possibly later followed by the 'RNA world' and the 'DNA world'.[164] Codon–amino acids mappings may be the biological information system at the primordial origin of life on Earth.[165] While amino acids and consequently simple peptides must have formed under different experimentally probed geochemical scenarios, the transition from an abiotic world to the first life forms is to a large extent still unresolved.[166]

## Reactions

Amino acids undergo the reactions expected of the constituent functional groups.[167][168]

### Peptide bond formation

See also: Biology:Peptide synthesis and Peptide bond

The condensation of two amino acids to form a dipeptide. The two amino acid residues are linked 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.[169] 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.[170] As a result of this mechanism, all proteins made by ribosomes are synthesized starting at their N-terminus and moving toward their C-terminus.[171]

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.[172] In the first step, gamma-glutamylcysteine synthetase condenses cysteine and glutamate 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.[173]

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.[174] Libraries of peptides are used in drug discovery through high-throughput screening.[175]

The combination of functional groups allow amino acids to be effective polydentate ligands for metal–amino acid chelates.[176] The side chains of amino acids can also undergo posttranslational chemical reactions.[177][178][179]

### Catabolism

Catabolism of proteinogenic amino acids. Amino acids can be classified according to the properties of their main degradation products:[180]
* 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.

Degradation of an amino acid often begins with transamination, in which its amino group is transferred to α-ketoglutarate, forming glutamate. This process involves transaminases, often the same enzymes used in amino acid synthesis. In many vertebrates, the amino group is subsequently released as ammonia and converted to urea via the urea cycle for excretion. However, amino acid degradation can result in uric acid or ammonia instead, depending on the organism. For example, serine dehydratase converts serine directly to pyruvate and ammonia.[122] After removal of one or more amino groups, the remaining carbon skeleton of an amino acid can serve as a precursor for synthesizing other amino acids, be further metabolized for energy after conversion into intermediates of glycolysis (typically via gluconeogenesis) or of the citric acid cycle, or be used for fatty acid synthesis and storage as triacylglycerol.[181][182]

### Complexation

Amino acids are bidentate ligands, forming transition metal amino acid complexes.[183]

## Chemical analysis

The total nitrogen content of organic matter is mainly formed by the amino groups in proteins. The total Kjeldahl nitrogen (TKN) is a measure of nitrogen widely used in the analysis of (waste) water, soil, food, feed and organic matter in general. As the name suggests, the Kjeldahl method is applied. More sensitive methods are available.[184][185]

## See also

* Amino acid dating
* Beta-peptide
* Degron
* Erepsin
* Homochirality
* Hyperaminoacidemia
* Leucines
* Miller–Urey experiment
* Nucleic acid sequence
* RNA codon table

## Notes

1. ↑ 'Amino' pronunciations:[1]

* /əˈmiː.nəʊ/ (Audio file "Amino uk ver1.ogg" not found) uh-MEE-noh
* /əˈmʌɪ.nəʊ/ (Audio file "Amino UK eng ver2.ogg" not found) uh-MIGH-noh

2. ↑ The late discovery is explained by the fact that cysteine becomes oxidized to cystine in air.
3. ↑ Proline and other cyclic amino acids are an exception to this general formula. Cyclization of the α-amino acid creates the corresponding secondary amine. These are occasionally referred to as imino acids.
4. ↑ 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). An alternative convention is to use the (S) and (R) designators to specify the absolute configuration.[33] Almost all of the amino acids in proteins are (S) at the α carbon, with cysteine being (R) and glycine non-chiral.[34] Cysteine has its side chain in the same geometric location as the other amino acids, but the R/S terminology is reversed because sulfur has higher atomic number compared to the carboxyl oxygen which gives the side chain a higher priority by the Cahn-Ingold-Prelog sequence rules.
5. ↑ Codons can also be expressed by: CGN, AGR.
6. ↑ Codons can also be expressed by: CUN, UUR.
7. ↑ Codons can also be expressed by: CTN, ATH, TTR; MTY, YTR, ATA; MTY, HTA, YTG.
8. ↑ Codons can also be expressed by: TWY, CAY, TGG.
9. ↑ Codons can also be expressed by: NTR, VTY.
10. ↑ Codons can also be expressed by: VAN, WCN, MGY, CGP.
11. ↑ For example, ruminants such as cows obtain a number of amino acids via microbes in the first two stomach chambers.

## References

1. ↑ "Amino". https://www.oed.com/dictionary/amino_n?tl=true&tab=factsheet.
2. ↑ 2.0 2.1 2.2 2.3 2.4 Biochemistry: the molecular basis of cell structure and function (2nd ed.). New York: Worth Publishers. 1975. ISBN 0-87901-047-9.
3. ↑ "Norine: update of the nonribosomal peptide resource". Nucleic Acids Research 48 (D1): D465–D469. January 2020. doi:10.1093/nar/gkz1000. PMID 31691799.
4. ↑ "Newsletter 2009". Biochemical Nomenclature Committee of IUPAC and NC-IUBMB. 2009. Pyrrolysine. http://www.chem.qmul.ac.uk/iubmb/newsletter/2009.html#item35.
5. ↑ "Selenocysteine, pyrrolysine, and the unique energy metabolism of methanogenic archaea". Archaea 2010: 1–14. August 2010. doi:10.1155/2010/453642. PMID 20847933.
6. ↑ "Chapter 8. Body composition, the functions of food, metabolism and energy". Human nutrition in the developing world. Food and Nutrition Series – No. 29. Rome: Food and Agriculture Organization of the United Nations. 1997. http://www.fao.org/docrep/W0073E/w0073e04.htm#P1625_217364. Retrieved 9 September 2012.
7. ↑ The Emergence of Life: From Chemical Origins to Synthetic Biology. Cambridge University Press. 13 July 2006. p. 13. ISBN 978-1-139-45564-0. https://books.google.com/books?id=1Oxfq5VTcDkC. Retrieved 5 August 2024. "Of course if on Earth there had only been diketopiperazines and not amino acids; or if sugars did not have the size they have; or if lipids were three times shorter, then we would not have life."
8. ↑ 8.0 8.1 8.2 "Nomenclature and Symbolism for Amino Acids and Peptides". IUPAC-IUB Joint Commission on Biochemical Nomenclature. 1983. http://www.chem.qmul.ac.uk/iupac/AminoAcid/AA1n2.html.
9. ↑ "The history of the discovery of the amino acids". Chem. Rev. 9 (2): 169–318. 1931. doi:10.1021/cr60033a001.
10. ↑ "Die Entdeckung der proteinogenen Aminosäuren von 1805 in Paris bis 1935 in Illinois" (in de). Berlin. May 2015. https://www.arginium.de/wp-content/uploads/2015/12/Entdeckung-der-Aminosäuren.pdf.
11. ↑ "The discovery of a new plant principle in Asparagus sativus". Annales de Chimie 57: 88–93. 1806.
12. ↑ 12.0 12.1 Advances in Protein Chemistry. New York: Academic Press. 1972. pp. 99, 103. ISBN 978-0-12-034226-6. https://archive.org/details/advancesinprotei26anfi/page/99.
13. ↑ "On cystic oxide, a new species of urinary calculus". Philosophical Transactions of the Royal Society 100 (145): 223–230. 1810. doi:10.1098/rstl.1810.0015. PMID 30493165.
14. ↑ "Über cystin und cystein". Z Physiol Chem 8 (4): 299–305. 1884. http://vlp.mpiwg-berlin.mpg.de/library/data/lit16533. Retrieved 28 March 2011.
15. ↑ "Sur la conversion des matières animales en nouvelles substances par le moyen de l'acide sulfurique". Annales de Chimie et de Physique. 2nd Series 13: 113–125. 1820.
16. ↑ "The discovery of the amino acid threonine: the work of William C. Rose [classical article]". The Journal of Biological Chemistry 277 (37): E25. September 2002. doi:10.1016/S0021-9258(20)74369-3. PMID 12218068.
17. ↑ "Feeding Experiments with Mixtures of Highly Purified Amino Acids. VIII. Isolation and Identification of a New Essential Amino Acid". Journal of Biological Chemistry 112: 283–302. 1935. doi:10.1016/S0021-9258(18)74986-7.
18. ↑ Menten, P. Dictionnaire de chimie: Une approche étymologique et historique. De Boeck, Bruxelles. link .
19. ↑ "amino-". Online Etymology Dictionary. https://www.etymonline.com/word/amino-.
20. ↑ "Ueber die Einwirkung von Phenyl-i-cyanat auf organische Aminosäuren". Berichte der Deutschen Chemischen Gesellschaft 27: 974–979. 1894. doi:10.1002/cber.189402701205. https://zenodo.org/record/1425732.
21. ↑ "Chapter 5- Emil Fischer and Franz Hofmeister". Contrasts in Scientific Style: Research Groups in the Chemical and Biochemical Sciences. 191. American Philosophical Society. 1990. pp. 163–165. ISBN 978-0-87169-191-0. https://books.google.com/books?id=tRlC9NyNNN8C&pg=PA163.
22. ↑ "Alpha amino acid". Merriam-Webster Medical. http://www.merriam-webster.com/medical/alpha-amino acid. .
23. ↑ "An introduction to amino acids". August 2007. http://www.chemguide.co.uk/organicprops/aminoacids/background.html.
24. ↑ "Amino acids". Peptides from A to Z: A Concise Encyclopedia. Germany: Wiley-VCH. 2008. p. 20. ISBN 978-3-527-62117-0. https://books.google.com/books?id=doe9NwgJTAsC&pg=PA20. Retrieved 5 January 2016.
25. ↑ Unnatural Amino Acids: Methods and Protocols. Methods in Molecular Biology. 794. Humana Press. 2012. p. v. doi:10.1007/978-1-61779-331-8. ISBN 978-1-61779-331-8. OCLC 756512314.
26. ↑ "Biosynthesis and charging of pyrrolysine, the 22nd genetically encoded amino acid". Angewandte Chemie 50 (41): 9540–9541. October 2011. doi:10.1002/anie.201103769. PMID 21796749. Bibcode: 2011ACIE...50.9540H.
27. ↑ 27.0 27.1 "Chapter 1: Proteins are the Body's Worker Molecules". National Institute of General Medical Sciences. 27 October 2011. https://publications.nigms.nih.gov/structlife/chapter1.html.
28. ↑ "Chapter 5: Peptide Natural Products II: Nonribosomal Peptides". Natural product biosynthesis: chemical logic and enzymatic machinery (2nd ed.). London: Royal Society of Chemistry. 2023. pp. 150–191. doi:10.1039/BK9781839165641-00150. ISBN 978-1-83916-801-7.
29. ↑ "Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications". Medcomm 4 (3). June 2023. doi:10.1002/mco2.261. PMID 37143582.
30. ↑ Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology (2nd ed.). Oxford: Wiley-Blackwell. 2012. p. 5. ISBN 978-0-470-14684-2.
31. ↑ 31.0 31.1 31.2 "Chapter 1". Proteins: structures and molecular properties. San Francisco: W. H. Freeman. 1993. ISBN 978-0-7167-7030-5. https://archive.org/details/proteinsstructur0000crei.
32. ↑ "An overview on D-amino acids". Amino Acids 49 (9): 1521–1533. September 2017. doi:10.1007/s00726-017-2459-5. PMID 28681245.
33. ↑ "Specification of Molecular Chirality". Angewandte Chemie International Edition 5 (4): 385–415. 1966. doi:10.1002/anie.196603851.
34. ↑ "Gas chromatographic determination of Amino Acid Enantiomers in tobacco and bottled wines". University of Giessen. 2006. http://geb.uni-giessen.de/geb/volltexte/2006/3038/index.html.
35. ↑ 35.0 35.1 35.2 35.3 35.4 35.5 Biochemistry (4th ed.). Belmont, CA: Brooks/Cole, Cengage Learning. 2010. pp. 74,134–176,430–442. ISBN 978-0-495-10935-8. OCLC 297392560.
36. ↑ "What kind of interactions we may get moving from zwitter to "dritter" ions: C–O⋯Re(O4) and Re–O⋯Re(O4) anion⋯anion interactions make structural difference between L-histidinium perrhenate and pertechnetate" (in en). CrystEngComm 26: 61–69. 2023-12-01. doi:10.1039/D3CE01164J. ISSN 1466-8033.4)+and+Re–O⋯Re(O4)+anion⋯anion+interactions+make+structural+difference+between+L-histidinium+perrhenate+and+pertechnetate&rft.jtitle=CrystEngComm&rft.date=2023-12-01&rft.volume=26&rft.pages=61–69&rft_id=info:doi/10.1039/D3CE01164J&rft.issn=1466-8033&rfr_id=info:sid/en.wikibooks.org:Chemistry:Amino_acid">
37. ↑ "4.3: Mechanisms of Catalysis". Biochemistry Free For All. Biology LibreTexts, LibreTexts. 21 March 2024. https://bio.libretexts.org/Bookshelves/Biochemistry/Book:_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/04:_Catalysis/4.03:_Mechanisms_of_Catalysis.
38. ↑ "Structure and mechanism of the pepsin-like family of aspartic peptidases". Chemical Reviews 102 (12): 4431–4458. December 2002. doi:10.1021/cr010167q. PMID 12475196. Bibcode: 2002ChRv..102.4431D.
39. ↑ "Stereochemistry at Tetrahedral Centers: Diastereomers". Organic chemistry (10th ed.). Houston, Texas: OpenStax. 2023. ISBN 978-1-951693-98-5. https://openstax.org/books/organic-chemistry/pages/5-6-diastereomers.
40. ↑ "The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins". ACS Chemical Biology 4 (5): 325–334. May 2009. doi:10.1021/cb800314v. PMID 19298050.
41. ↑ 41.0 41.1 41.2 "Amino Acid Properties: Polarity and Ionization". BIOC 2580: Introduction to Biochemistry.. Pressbooks. 2021. https://ecampusontario.pressbooks.pub/bioc2580/chapter/bioc2580-lecture-2-amino-acid-properties-polarity-and-ionization/.
42. ↑ "From selenium to selenoproteins: synthesis, identity, and their role in human health". Antioxidants & Redox Signaling 9 (7): 775–806. July 2007. doi:10.1089/ars.2007.1528. PMID 17508906.
43. ↑ "A new UAG-encoded residue in the structure of a methanogen methyltransferase". Science 296 (5572): 1462–1466. May 2002. doi:10.1126/science.1069556. PMID 12029132. Bibcode: 2002Sci...296.1462H.
44. ↑ "Functional context, biosynthesis, and genetic encoding of pyrrolysine". Current Opinion in Microbiology 14 (3): 342–349. June 2011. doi:10.1016/j.mib.2011.04.001. PMID 21550296.
45. ↑ 45.0 45.1 "Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved". Nucleic Acids Research 47 (19): 9998–10009. November 2019. doi:10.1093/nar/gkz730. PMID 31504783.
46. ↑ "The change in Gibbs free energy for hydrophobic association: Derivation and evaluation by means of inverse temperature transitions". Chemical Physics Letters 399 (1–3): 177–183. 2004. doi:10.1016/S0009-2614(04)01565-9. Bibcode: 2004CPL...399..177U.
47. ↑ "Correction: Uncovering protein structure". Essays in Biochemistry 65 (2): 407. July 2021. doi:10.1042/EBC-2019-0042C_COR. PMID 34269795.
48. ↑ "A census of protein repeats". Journal of Molecular Biology 293 (1): 151–160. October 1999. doi:10.1006/jmbi.1999.3136. PMID 10512723. Bibcode: 1999JMBio.293..151M.
49. ↑ "Low-complexity sequences and single amino acid repeats: not just "junk" peptide sequences". Genome 53 (10): 753–762. October 2010. doi:10.1139/G10-063. PMID 20962881.
50. ↑ "Fatty acylation and prenylation of proteins: what's hot in fat". Current Opinion in Cell Biology 17 (2): 190–196. April 2005. doi:10.1016/j.ceb.2005.02.003. PMID 15780596.
51. ↑ "Deciphering the glycocode: the complexity and analytical challenge of glycomics". Current Opinion in Chemical Biology 11 (3): 300–305. June 2007. doi:10.1016/j.cbpa.2007.05.002. PMID 17500024.
52. ↑ "Palmitoylation of intracellular signaling proteins: regulation and function". Annual Review of Biochemistry 73 (1): 559–587. 2004. doi:10.1146/annurev.biochem.73.011303.073954. PMID 15189153. Bibcode: 2004ARBio..73..559S.
53. ↑ Multiple equilibria in proteins. New York: Academic Press. 1969. pp. 176–21. ISBN 978-0-12-665450-9.
54. ↑ "Zwitterionic Biomaterials". Chemical Reviews 122 (23): 17073–17154. December 2022. doi:10.1021/acs.chemrev.2c00344. PMID 36201481. Bibcode: 2022ChRv..12217073L.
55. ↑ "Gas phase hydration of amino acids and dipeptides: effects on the relative stability of zwitterion vs. canonical conformers.". RSC Advances 4 (31): 16352–16361. 2014. doi:10.1039/C4RA01217H. Bibcode: 2014RSCAd...416352K.
56. ↑ "3.7: The Effect of pH on Enzyme Kinetics". Chem 107B: Physical Chemistry for Life Scientists. Chemistry LibreTexts. 2023. https://chem.libretexts.org/Courses/University_of_California_Davis/Chem_107B:_Physical_Chemistry_for_Life_Scientists/Chapters/3:_Enzyme_Kinetics/3.7:_The_Effect_of_pH_on_Enzyme_Kinetics. Retrieved 7 December 2025.
57. ↑ "Einige Bemerkungen über den Begriff der Säuren und Basen". Recueil des Travaux Chimiques des Pays-Bas 42 (8): 718–728. 1923. doi:10.1002/recl.19230420815.
58. ↑ 58.0 58.1 58.2 Organic chemistry: structure and function (5th ed.). New York: W.H. Freeman. 2007. pp. 58–66. ISBN 978-0-7167-9949-8. OCLC 61448218.
59. ↑ "Understanding the functional roles of amino acid residues in enzyme catalysis". Journal of Molecular Biology 390 (3): 560–577. July 2009. doi:10.1016/j.jmb.2009.05.015. PMID 19447117.
60. ↑ Food Chemistry 3rd Ed. CRC Press. 1996-06-19. pp. 327–328. ISBN 978-0-8247-9691-4.
61. ↑ "Isoelectric Point Separations of Peptides and Proteins". Proteomes 5 (1). January 2017. doi:10.3390/proteomes5010004. PMID 28248255.
62. ↑ "Zwitterions". The Encyclopedia of Biochemistry. Reinhold Publishing / Van Nostrand Reinhold. 1967. p. 358. https://archive.org/details/TheEncyclopediaOfBiochemistry/page/n189/mode/2up. "Zwitterions have minimal solubility at their isolectric point and amino acids are often isolated by precipitation from water after adjusting the pH to their isolectric point."
63. ↑ 63.0 63.1 63.2 63.3 63.4 "IUPAC-IUB Commission on Biochemical Nomenclature A One-Letter Notation for Amino Acid Sequences" (in en). Journal of Biological Chemistry 243 (13): 3557–3559. 10 July 1968. doi:10.1016/S0021-9258(19)34176-6.
64. ↑ 64.0 64.1 "Amino acid names and parlor games: from trivial names to a one-letter code, amino acid names have strained students' memories. Is a more rational nomenclature possible?" (in en). Biochemical Education 26 (2): 116–118. April 1998. doi:10.1016/S0307-4412(97)00167-2.
65. ↑ 65.0 65.1 65.2 "Letters to the editor" (in en). Biochemical Education 16 (1): 49. January 1988. doi:10.1016/0307-4412(88)90026-X.
66. ↑ "A simple method for displaying the hydropathic character of a protein". Journal of Molecular Biology 157 (1): 105–132. May 1982. doi:10.1016/0022-2836(82)90515-0. PMID 7108955.
67. ↑ Physical Biochemistry (2nd ed.). W. H. Freeman and Company. 1983. ISBN 978-0-7167-1315-9.
68. ↑ "Proteome-pI: proteome isoelectric point database". Nucleic Acids Research 45 (D1): D1112–D1116. January 2017. doi:10.1093/nar/gkw978. PMID 27789699.
69. ↑ 69.0 69.1 The cell: a molecular approach. Washington, D.C.: ASM Press. 2004. p. 51. ISBN 978-0-87893-214-6.
70. ↑ "Distinct genetic code expansion strategies for selenocysteine and pyrrolysine are reflected in different aminoacyl-tRNA formation systems". FEBS Letters 584 (2): 342–349. January 2010. doi:10.1016/j.febslet.2009.11.005. PMID 19903474. Bibcode: 2010FEBSL.584..342Y.
71. ↑ "Normalization of nomenclature for peptide motifs as ligands of modular protein domains". FEBS Letters 513 (1): 141–144. February 2002. doi:10.1111/j.1432-1033.1968.tb00350.x. PMID 11911894.
72. ↑ "A one-letter notation for amino acid sequences". Pure and Applied Chemistry 31 (4): 641–645. 1972. doi:10.1351/pac197231040639. PMID 5080161.
73. ↑ 73.0 73.1 Standard ST.26: Recommended Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings Using XML (Extensible Markup Language) (PDF) (Version 2.0 ed.). Geneva, Switzerland: World Intellectual Property Organization. 2025. p. 3.26.vi.22. https://www.wipo.int/documents/d/standards/docs-en-03-26-01.pdf. Retrieved 23 December 2025.
74. ↑ "UNK Ligand Summary". Chemical Component Dictionary. RCSB Protein Data Bank. https://www.rcsb.org/ligand/UNK.
75. ↑ "Amino acids, Peptides, and Proteins". The Chemistry of Food (Second ed.). Chichester, West Sussex: Wiley-Blackwell/John Wiley & Sons Ltd. 2020. p. 6. ISBN 978-1-119-53764-9. https://books.google.com/books?id=Il_wDwAAQBAJ. "Table 2.1: In addition to the specific amino acid codes, three-letter code, and one letter-code, placeholders are used tor ambiguous amino acids, e.g. Asx and B for aspartic acid or asparagine, Glx for glutamic acid and glutamine, Xle and J for leucine and isoleucine, and Xaa (Unk) and X for unspecified (unknown) amino acid."
76. ↑ "Sequence Variant Nomenclature, Protein Recommendations". Human Genome Variation Society (HGVS). http://varnomen.hgvs.org/recommendations/protein/variant/substitution/.
77. ↑ "Photo-leucine and photo-methionine allow identification of protein-protein interactions in living cells". Nature Methods 2 (4): 261–267. April 2005. doi:10.1038/nmeth752. PMID 15782218.
78. ↑ "How ribosomes make peptide bonds". Trends in Biochemical Sciences 32 (1): 20–26. January 2007. doi:10.1016/j.tibs.2006.11.007. PMID 17157507.
79. ↑ "From RNA to Protein.". Molecular Biology of the Cell (4th ed.). New York: Garland Science. 2002. ISBN 978-0-8153-3218-3. https://www.ncbi.nlm.nih.gov/books/NBK26829/.
80. ↑ "Mechanism and regulation of selenoprotein synthesis". Annual Review of Nutrition 23 (1): 17–40. 2003. doi:10.1146/annurev.nutr.23.011702.073318. PMID 12524431. Bibcode: 2003ARNut..23...17D.
81. ↑ "The direct genetic encoding of pyrrolysine". Current Opinion in Microbiology 8 (6): 706–712. December 2005. doi:10.1016/j.mib.2005.10.009. PMID 16256420.
82. ↑ "A co-evolution theory of the genetic code". Proceedings of the National Academy of Sciences of the United States of America 72 (5): 1909–1912. May 1975. doi:10.1073/pnas.72.5.1909. PMID 1057181. Bibcode: 1975PNAS...72.1909T.
83. ↑ "Consensus temporal order of amino acids and evolution of the triplet code". Gene 261 (1): 139–151. December 2000. doi:10.1016/S0378-1119(00)00476-5. PMID 11164045.
84. ↑ "A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code". Astrobiology 9 (5): 483–490. June 2009. doi:10.1089/ast.2008.0280. PMID 19566427. Bibcode: 2009AsBio...9..483H.
85. ↑ "Is there a twenty third amino acid in the genetic code?". Trends in Genetics 22 (7): 357–60. July 2006. doi:10.1016/j.tig.2006.05.002. PMID 16713651.
86. ↑ "Frozen, but no accident - why the 20 standard amino acids were selected". The FEBS Journal 284 (9): 1296–1305. May 2017. doi:10.1111/febs.13982. PMID 27926995.
87. ↑ "Bioactive Compounds as Modulators of N-Formyl Peptide Signaling in Chronic Diseases". Molecules (Basel, Switzerland) 30 (14): 2981. July 2025. doi:10.3390/molecules30142981. PMID 40733247.
88. ↑ "Future prospects for noncanonical amino acids in biological therapeutics". Current Opinion in Biotechnology 60: 168–178. December 2019. doi:10.1016/j.copbio.2019.02.020. PMID 30974337.
89. ↑ "How selenium has altered our understanding of the genetic code". Molecular and Cellular Biology 22 (11): 3565–76. June 2002. doi:10.1128/MCB.22.11.3565-3576.2002. PMID 11997494. Bibcode: 2002MolCB..22.3565H.
90. ↑ "[Expanding genetic code: amino acids 21 and 22--selenocysteine and pyrrolysine]" (in Russian). Genetika 46 (8): 1013–1032. August 2010. PMID 20873198.
91. ↑ "High content of proteins containing 21st and 22nd amino acids, selenocysteine and pyrrolysine, in a symbiotic deltaproteobacterium of gutless worm Olavius algarvensis". Nucleic Acids Research 35 (15): 4952–4963. 2007. doi:10.1093/nar/gkm514. PMID 17626042.
92. ↑ "Characterization of mammalian selenoproteomes". Science 300 (5624): 1439–1443. May 2003. doi:10.1126/science.1083516. PMID 12775843. Bibcode: 2003Sci...300.1439K.
93. ↑ "The thioredoxin system--from science to clinic". Medicinal Research Reviews 24 (1): 40–89. January 2004. doi:10.1002/med.10051. PMID 14595672.
94. ↑ Tjong H (2008). Modeling Electrostatic Contributions to Protein Folding and Binding (PhD thesis). Florida State University. pp. 1 footnote. Archived from the original on 28 January 2020. Retrieved 28 January 2020.
95. ↑ "Whole Gene Synthesis: A Gene-O-Matic Future". Frontiers in Drug Design & Discovery. 1. Bentham Science Publishers. 2005. pp. 299. doi:10.2174/1574088054583318. ISBN 978-1-60805-199-1. https://books.google.com/books?id=VoJw6fIISSkC&pg=PA299. Retrieved 5 January 2016.
96. ↑ "The Genetic Codes". National Center for Biotechnology Information (NCBI). 7 April 2008. https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c.
97. ↑ "Adding amino acids to the genetic repertoire". Current Opinion in Chemical Biology 9 (6): 548–554. December 2005. doi:10.1016/j.cbpa.2005.10.011. PMID 16260173.
98. ↑ "Expanding the genetic code for biological studies". Chemistry & Biology 16 (3): 323–336. March 2009. doi:10.1016/j.chembiol.2009.03.001. PMID 19318213.
99. ↑ Emergent computation: emphasizing bioinformatics. New York: AIP Press/Springer Science+Business Media. 2005. pp. 105–106. ISBN 978-0-387-22046-8. https://archive.org/details/emergentcomputat00simo_754.
100. ↑ "Introduction: Non-proteinogenic amino acids". Amino Acids and Peptides. Cambridge New York: Cambridge University Press. 1998. ISBN 978-0-521-46292-1. https://assets.cambridge.org/97805214/68275/sample/9780521468275web.pdf.
101. ↑ "Non-protein amino acids: a review of the biosynthesis and taxonomic significance.". Natural Product Communications 3 (1): 91–110. June 2008. doi:10.1177/1934578X0800300. https://journals.sagepub.com/doi/pdf/10.1177/1934578X0800300117.
102. ↑ "Catabolism of Hydroxyproline in Vertebrates: Physiology, Evolution, Genetic Diseases and New siRNA Approach for Treatment". International Journal of Molecular Sciences 23 (2): 1005. January 2022. doi:10.3390/ijms23021005. PMID 35055190.
103. ↑ "Selenomethionine: a review of its nutritional significance, metabolism and toxicity". The Journal of Nutrition 130 (7): 1653–6. July 2000. doi:10.1093/jn/130.7.1653. PMID 10867031.
104. ↑ "Subcellular localization specified by protein acylation and phosphorylation". Current Opinion in Cell Biology 5 (6): 984–989. December 1993. doi:10.1016/0955-0674(93)90081-Z. PMID 8129952.
105. ↑ "Gamma-carboxyglutamate-containing proteins and the vitamin K-dependent carboxylase". The Biochemical Journal 266 (3): 625–636. March 1990. doi:10.1042/bj2660625. PMID 2183788.
106. ↑ "Collagen structure: the Madras triple helix and the current scenario". IUBMB Life 57 (3): 161–172. March 2005. doi:10.1080/15216540500090710. PMID 16036578.
107. ↑ "The post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5A (eIF5A)". Journal of Biochemistry 139 (2): 161–169. February 2006. doi:10.1093/jb/mvj034. PMID 16452303.
108. ↑ "Almost all about citrulline in mammals". Amino Acids 29 (3): 177–205. November 2005. doi:10.1007/s00726-005-0235-4. PMID 16082501.
109. ↑ "Pantothenate biosynthesis in higher plants". Biochemical Society Transactions 33 (Pt 4): 743–746. August 2005. doi:10.1042/BST0330743. PMID 16042590.
110. ↑ "A renaissance in trace amines inspired by a novel GPCR family". Trends Pharmacol. Sci. 26 (5): 274–281. May 2005. doi:10.1016/j.tips.2005.03.007. PMID 15860375.
111. ↑ "The endogenous substrates of brain CYP2D". Eur. J. Pharmacol. 724: 211–218. February 2014. doi:10.1016/j.ejphar.2013.12.025. PMID 24374199.
112. ↑ "Toxic peptides and amino acids in foods and feeds". Journal of Agricultural and Food Chemistry 17 (3): 492–496. 1969. doi:10.1021/jf60163a003. Bibcode: 1969JAFC...17..492H.
113. ↑ "Genetic disruption of both tryptophan hydroxylase genes dramatically reduces serotonin and affects behavior in models sensitive to antidepressants". PLOS ONE 3 (10). 2008. doi:10.1371/journal.pone.0003301. PMID 18923670. Bibcode: 2008PLoSO...3.3301S.
114. ↑ "Tryptophan Metabolic Pathways and Brain Serotonergic Activity: A Comparative Review". Frontiers in Endocrinology 10. 2019. doi:10.3389/fendo.2019.00158. PMID 31024440.
115. ↑ "Tyrosine, phenylalanine, and catecholamine synthesis and function in the brain". The Journal of Nutrition 137 (6 Suppl 1): 1539S–1547S; discussion 1548S. June 2007. doi:10.1093/jn/137.6.1539S. PMID 17513421.
116. ↑ "Biosynthesis of Catecholamines.". Basic Neurochemistry: Molecular, Cellular and Medical Aspects. (6th ed.). Philadelphia: Lippincott-Raven. 1999. https://www.ncbi.nlm.nih.gov/books/NBK27988/.
117. ↑ "An overview of phenylalanine and tyrosine kinetics in humans". The Journal of Nutrition 137 (6 Suppl 1): 1549S–1555S; discussion 1573S–1575S. June 2007. doi:10.1093/jn/137.6.1549S. PMID 17513423.
118. ↑ "Structure-function relationships in plant phenylpropanoid biosynthesis". Current Opinion in Plant Biology 8 (3): 249–53. June 2005. doi:10.1016/j.pbi.2005.03.013. PMID 15860421. Bibcode: 2005COPB....8..249N.
119. ↑ "The biological utilization of glycine for the synthesis of the protoporphyrin of hemoglobin". The Journal of Biological Chemistry 166 (2): 621–625. December 1946. doi:10.1016/S0021-9258(17)35200-6. PMID 20276176.
120. ↑ "Stabilization and characterization of a heme-oxy reaction intermediate in inducible nitric-oxide synthase". The Journal of Biological Chemistry 283 (48): 33498–33507. November 2008. doi:10.1074/jbc.M806122200. PMID 18815130.
121. ↑ "Mathematical modeling of polyamine metabolism in mammals". The Journal of Biological Chemistry 281 (31): 21799–21812. August 2006. doi:10.1074/jbc.M602756200. PMID 16709566. Bibcode: 2006JBiCh.28121799R.
122. ↑ 122.0 122.1 Biochemistry (5th ed.). New York: W.H. Freeman. 2002. pp. 693–698. ISBN 978-0-7167-4684-3. https://archive.org/details/biochemistry200100jere.
123. ↑ "Carnitine transport and fatty acid oxidation". Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1863 (10): 2422–35. October 2016. doi:10.1016/j.bbamcr.2016.01.023. PMID 26828774.
124. ↑ "CCarnitine Homeostasis, Mitochondrial Function, and Cardiovascular Disease". Drug Discovery Today: Disease Mechanisms 6 (1–4): e31–e39. 2009. doi:10.1016/j.ddmec.2009.02.001. PMID 20648231.
125. ↑ "GABA and glutamate in the human brain". The Neuroscientist 8 (6): 562–573. December 2002. doi:10.1177/1073858402238515. PMID 12467378.
126. ↑ "Serotonin a la carte: supplementation with the serotonin precursor 5-hydroxytryptophan". Pharmacology & Therapeutics 109 (3): 325–338. March 2006. doi:10.1016/j.pharmthera.2005.06.004. PMID 16023217. https://escholarship.org/uc/item/58h866d5.
127. ↑ "Peculiarities of L: -DOPA treatment of Parkinson's disease". Amino Acids 28 (2): 157–164. March 2005. doi:10.1007/s00726-005-0162-4. PMID 15750845.
128. ↑ "Targeting the polyamine biosynthetic enzymes: a promising approach to therapy of African sleeping sickness, Chagas' disease, and leishmaniasis". Amino Acids 33 (2): 359–366. August 2007. doi:10.1007/s00726-007-0537-9. PMID 17610127.
129. ↑ "L-Canavanine: a higher plant insecticidal allelochemical". Amino Acids 21 (3): 319–330. 2001. doi:10.1007/s007260170017. PMID 11764412.
130. ↑ "Leucaena toxicosis and its control in ruminants". Journal of Animal Science 73 (5): 1487–1492. May 1995. doi:10.2527/1995.7351487x. PMID 7665380. Bibcode: 1995JAniS..73.1487H.
131. ↑ "A review on the nutritive value and toxic aspects of Leucaena leucocephala.". Tropical Animal Health and Production 4 (2): 113–126. 1979. https://cipav.org.co/TAP/TAP/TAP42/4_2_1.pdf.
132. ↑ "Nonproteinogenic amino acid building blocks for nonribosomal peptide and hybrid polyketide scaffolds". Angewandte Chemie (International ed. In English) 52 (28): 7098–124. July 2013. doi:10.1002/anie.201208344. PMID 23729217. Bibcode: 2013ACIE...52.7098W.
133. ↑ "Amino Acid Metabolism". Annual Review of Biochemistry 32 (1): 355–398. 1963. doi:10.1146/annurev.bi.32.070163.002035. PMID 14144484. Bibcode: 1963ARBio..32..355S.
134. ↑ "Glutamate, at the interface between amino acid and carbohydrate metabolism". The Journal of Nutrition 130 (4S Suppl): 988S–990S. April 2000. doi:10.1093/jn/130.4.988S. PMID 10736367.
135. ↑ "Glutamine: the emperor or his clothes?". The Journal of Nutrition 131 (9 Suppl): 2449S–2459S, 2486S–2487S. September 2001. doi:10.1093/jn/131.9.2449S. PMID 11533293.
136. ↑ "Adult amino acid requirements: the case for a major revision in current recommendations". The Journal of Nutrition 124 (8 Suppl): 1517S–1523S. August 1994. doi:10.1093/jn/124.suppl_8.1517S. PMID 8064412.
137. ↑ "What are the essential elements needed for the determination of amino acid requirements in humans?". The Journal of Nutrition 134 (6 Suppl): 1558S–1565S. June 2004. doi:10.1093/jn/134.6.1558S. PMID 15173430.
138. ↑ "Dispensable and indispensable amino acids for humans". The Journal of Nutrition 130 (7): 1835S–1840S. July 2000. doi:10.1093/jn/130.7.1835S. PMID 10867060.
139. ↑ "Amino acid metabolism in pediatric patients". Nutrition 14 (1): 143–148. January 1998. doi:10.1016/S0899-9007(97)00230-X. PMID 9437700.
140. ↑ "Taurine: a conditionally essential amino acid in humans? An overview in health and disease". Nutricion Hospitalaria 17 (6): 262–270. 2002. PMID 12514918.
141. ↑ 141.0 141.1 "Biotechnological production of amino acids and derivatives: current status and prospects". Applied Microbiology and Biotechnology 69 (1): 1–8. November 2005. doi:10.1007/s00253-005-0155-y. PMID 16195792.
142. ↑ The Role of Amino Acid Chelates in Animal Nutrition. Westwood: Noyes Publications. 1993.
143. ↑ "Glutamic acid, twenty years later". The Journal of Nutrition 130 (4S Suppl): 901S–909S. April 2000. doi:10.1093/jn/130.4.901S. PMID 10736350.
144. ↑ "The aspartame story: a model for the clinical testing of a food additive". The American Journal of Clinical Nutrition 46 (1 Suppl): 204–215. July 1987. doi:10.1093/ajcn/46.1.204. PMID 3300262.
145. ↑ 145.0 145.1 "Ullmann's Encyclopedia of Industrial Chemistry". Ullmann's Encyclopedia of Industrial Chemistry. Weinheim: Wiley-VCH. 2007. doi:10.1002/14356007.a02_057.pub2.
146. ↑ "Reflections on the total synthesis of natural products: Art, craft, logic, and the chiron approach". Pure and Applied Chemistry 65 (6): 1189–1204. 1993. doi:10.1351/pac199365061189.
147. ↑ "The chiral pool as a source of enantioselective catalysts and auxiliaries". Chemical Reviews 92 (5): 935–952. 1992. doi:10.1021/cr00013a009.
148. ↑ Foliar Feeding of Plants with Amino Acid Chelates. Park Ridge: Noyes Publications. 1986.
149. ↑ "Syntheses and functions of polymers based on amino acids". Macromolecular Chemistry and Physics 200 (12): 2651–2661. 1999. doi:10.1002/(SICI)1521-3935(19991201)200:12<2651::AID-MACP2651>3.0.CO;2-P.
150. ↑ "Biodegradable polymers for the environment". Science 297 (5582): 803–807. August 2002. doi:10.1126/science.297.5582.803. PMID 12161646. Bibcode: 2002Sci...297..803G. https://zenodo.org/record/1231185. Retrieved 12 June 2019.
151. ↑ Commercial poly(aspartic acid) and Its Uses. Advances in Chemistry Series. 248. Washington, D.C.: American Chemical Society. 1996.
152. ↑ "Synthesis and Biodegradability of Polyaspartic Acid: A Critical Review". Journal of Macromolecular Science, Part A 42 (9): 1299–1315. 2005. doi:10.1080/10601320500189604.
153. ↑ Biochemistry & molecular biology of plants. Rockville, Md: American Society of Plant Physiologists. 2000. pp. 371–372. ISBN 978-0-943088-39-6. https://archive.org/details/biochemistrymole00buch/page/371.
154. ↑ "Evolutionary origin and functional diversification of aminotransferases". The Journal of Biological Chemistry 298 (8). August 2022. doi:10.1016/j.jbc.2022.102122. PMID 35697072.
155. ↑ "Multisubstrate specificity shaped the complex evolution of the aminotransferase family across the tree of life". Proceedings of the National Academy of Sciences of the United States of America 121 (26). June 2024. doi:10.1073/pnas.2405524121. PMID 38885378. Bibcode: 2024PNAS..12105524K.
156. ↑ "The sulfur-containing amino acids: an overview". The Journal of Nutrition 136 (6 Suppl): 1636S–1640S. June 2006. doi:10.1093/jn/136.6.1636S. PMID 16702333.
157. ↑ "Collagen Hydroxylases and the Protein Disulfide Isomerase Subunit of Prolyl 4-Hydroxylases". Advances in Enzymology and Related Areas of Molecular Biology. Advances in Enzymology – and Related Areas of Molecular Biology. 72. 1998. pp. 325–398. doi:10.1002/9780470123188.ch9. ISBN 978-0-470-12318-8.
158. ↑ "Analysis of peptaibol sequence composition: implications for in vivo synthesis and channel formation". European Biophysics Journal 33 (3): 233–237. May 2004. doi:10.1007/s00249-003-0348-1. PMID 14534753.
159. ↑ "Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening". Journal of Experimental Botany 53 (377): 2039–2055. October 2002. doi:10.1093/jxb/erf072. PMID 12324528.
160. ↑ 160.0 160.1 160.2 "Origins of building blocks of life: A review". Geoscience Frontiers 9 (4): 1117–1153. 2018. doi:10.1016/j.gsf.2017.07.007. Bibcode: 2018GeoFr...9.1117K.
161. ↑ "From chemical metabolism to life: the origin of the genetic coding process". Beilstein Journal of Organic Chemistry 13 (1): 1119–1135. 12 June 2017. doi:10.3762/bjoc.13.111. PMID 28684991.
162. ↑ "Origins of Life: Emergence of Amino Acids". Wiley Encyclopedia of Chemical Biology. December 2007. pp. 1–7. doi:10.1002/9780470048672.wecb423. ISBN 978-0-471-75477-0.
163. ↑ 163.0 163.1 "Prebiotic Peptides: Molecular Hubs in the Origin of Life". Chemical Reviews 120 (11): 4707–4765. June 2020. doi:10.1021/acs.chemrev.9b00664. PMID 32101414. Bibcode: 2020ChRv..120.4707F.
164. ↑ "Protein three-dimensional structures at the origin of life". Interface Focus 9 (6). December 2019. doi:10.1098/rsfs.2019.0057. PMID 31641431.
165. ↑ "The Coevolution of Biomolecules and Prebiotic Information Systems in the Origin of Life: A Visualization Model for Assembling the First Gene". Life 12 (6): 834. June 2022. doi:10.3390/life12060834. PMID 35743865. Bibcode: 2022Life...12..834C.
166. ↑ "The coenzyme/protein pair and the molecular evolution of life". Natural Product Reports 38 (5): 993–1010. May 2021. doi:10.1039/D0NP00037J. PMID 33206101.
167. ↑ Amino acids and peptides. Cambridge, UK: Cambridge University Press. 1998. pp. 48–60. ISBN 978-0-521-46827-5. https://archive.org/details/aminoacidspeptid00barr_040.
168. ↑ "Understanding nature's catalytic toolkit". Trends in Biochemical Sciences 30 (11): 622–629. November 2005. doi:10.1016/j.tibs.2005.09.006. PMID 16214343.
169. ↑ "The renaissance of aminoacyl-tRNA synthesis". EMBO Reports 2 (5): 382–387. May 2001. doi:10.1093/embo-reports/kve095. PMID 11375928.
170. ↑ "Mechanism of protein biosynthesis". Bacteriological Reviews 33 (2): 264–301. June 1969. doi:10.1128/MMBR.33.2.264-301.1969. PMID 4896351.
171. ↑ "26.2: Protein Synthesis". Fundamentals of Biochemistry. Vol. III – Information Pathways. Biology LibreTexts. 2025. https://bio.libretexts.org/Bookshelves/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03:_Unit_III-_Information_Pathway/26:_Protein_Metabolism/26.02:_Protein_Synthesis. Retrieved 2025-12-09.
172. ↑ "Glutathione metabolism and its implications for health". The Journal of Nutrition 134 (3): 489–492. March 2004. doi:10.1093/jn/134.3.489. PMID 14988435.
173. ↑ "Glutathione metabolism and its selective modification". The Journal of Biological Chemistry 263 (33): 17205–17208. November 1988. doi:10.1016/S0021-9258(19)77815-6. PMID 3053703.
174. ↑ "1-Hydroxy-7-azabenzotriazole. An efficient peptide coupling additive". Journal of the American Chemical Society 115 (10): 4397–4398. 1992. doi:10.1021/ja00063a082.
175. ↑ "Past and future perspectives of synthetic peptide libraries". Current Protein & Peptide Science 9 (5): 447–467. October 2008. doi:10.2174/138920308785915209. PMID 18855697.
176. ↑ "Structural determination and characterization of copper and zinc bis-glycinates with X-ray crystallography and mass spectrometry". Journal of Coordination Chemistry 63 (19): 3335–3347. 2010. doi:10.1080/00958972.2010.514336.
177. ↑ "Chemical and functional aspects of posttranslational modification of proteins". Acta Naturae 1 (3): 29–51. October 2009. doi:10.32607/20758251-2009-1-3-29-51. PMID 22649613.
178. ↑ "Discovering the landscape of protein modifications". Molecular Cell 81 (9): 1868–1878. May 2021. doi:10.1016/j.molcel.2021.03.015. PMID 33798408.
179. ↑ "Post-translational modifications in the Protein Data Bank". Acta Crystallographica, Section D 80 (Pt 9): 647–660. September 2024. doi:10.1107/S2059798324007794. PMID 39207896. Bibcode: 2024AcCrD..80..647S.
180. ↑ Biochemical, Physiological, & Molecular Aspects of Human Nutrition (2nd ed.). Saunders Elsevier. 2006.
181. ↑ "Chapter 14: Amino Acid Metabolism". Basicmedical Key. BasicMedicalKey.com. 2017. https://basicmedicalkey.com/amino-acid-metabolism-2/. Retrieved 23 December 2025.
182. ↑ "Amino Acid Metabolism". Cold Spring Harbor Perspectives in Biology 13 (4). April 2021. doi:10.1101/cshperspect.a040584. PMID 33795250.
183. ↑ "The Use of Carbon Monoxide and Imines as Peptide Derivative Synthons: A Facile Palladium-Catalyzed Synthesis of α-Amino Acid Derived Imidazolines". Angewandte Chemie 40 (17): 3228–3230. September 2001. doi:10.1002/(SICI)1521-3773(19980703)37:12<1634::AID-ANIE1634>3.0.CO;2-C. PMID 29712039.
184. ↑ "A review of methods for sensing the nitrogen status in plants: advantages, disadvantages and recent advances". Sensors 13 (8): 10823–10843. August 2013. doi:10.3390/s130810823. PMID 23959242. Bibcode: 2013Senso..1310823M.
185. ↑ "Determination of soil organic carbon and nitrogen at thefield level using near-infrared spectroscopy". Canadian Journal of Soil Science 82 (4): 413–422. 2002. doi:10.4141/S01-054. Bibcode: 2002CaJSS..82..413M.

## Further reading

* "Protein Composition and Structure". Biochemistry. New York: W. H. Freeman and company. 2012. pp. 28–31. ISBN 978-1-4292-2936-4. https://archive.org/details/biochemistryseve00berg/page/n61.
* "Redundancies in protein sequences". Predictions of Protein Structure and the Principles of Protein Conformation. New York: Plenum Press. 1989. pp. 599–623. ISBN 978-0-306-43131-9.
* Lehninger Principles of Biochemistry (3rd ed.). Worth Publishers. 2000. ISBN 978-1-57259-153-0. https://archive.org/details/lehningerprincip01lehn.
* Amino acids and the asymmetry of life. Berlin: Springer Verlag. 2008. ISBN 978-3-540-76885-2. http://rogov.zwz.ru/Macroevolution/amino.pdf.

## External links

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Encoded (proteinogenic) amino acids

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* e

Chemical bonds

Intramolecular
(strong)|

| Covalent|

* Electron deficiency
* 3c–2e
* 4c–2e
* Hypervalence
* 3c–4e
* Agostic
* Bent
* Coordinate (dipolar)
* Pi backbond
* Charge-shift
* Hapticity
* Conjugation
* Hyperconjugation
* Aromaticity
* homo
* bicyclo

|

Metallic|

* Metal aromaticity

Ionic|

Intermolecular
(weak)|

| van der Waals
forces|

* London dispersion

|

Hydrogen|

* Low-barrier
* Resonance-assisted
* Symmetric
* Dihydrogen bonds
* C–H···O interaction

Noncovalent
other|

* Mechanical
* Halogen
* Chalcogen
* Metallophilic
* Intercalation
* Stacking
* Cation–pi
* Anion–pi
* Salt bridge

Bond cleavage|

* Heterolysis
* Homolysis

Electron counting rules|

* Octet rule
* 18-electron rule
* Aromaticity
* Hückel's rule
* Baird's rule
* Möbius
* spherical
* Polyhedral skeletal electron pair theory

* v
* t
* e

Protein primary structure and posttranslational modifications

General|

* Peptide bond
* Protein biosynthesis
* Proteolysis
* Racemization
* N-O acyl shift

N terminus|

* Acetylation
* Carbamylation
* Formylation
* Glycation
* Methylation
* Myristoylation (Gly)

C terminus|

* Amidation
* Glycosyl phosphatidylinositol (GPI)
* O-methylation
* Detyrosination

Single specific AAs|

| Serine/Threonine|

* Phosphorylation
* Dephosphorylation
* Glycosylation
* ADP-ribosylation
* Methylidene-imidazolone (MIO) formation

|

Tyrosine|

* Phosphorylation
* Dephosphorylation
* ADP-ribosylation
* Sulfation
* Porphyrin ring linkage
* Adenylylation
* Flavin linkage
* Topaquinone (TPQ) formation
* Detyrosination

Cysteine|

* Palmitoylation
* Prenylation

Aspartate|

* Succinimide formation
* ADP-ribosylation

Glutamate|

* Carboxylation
* ADP-ribosylation
* Methylation
* Polyglutamylation
* Polyglycylation

Asparagine|

* Deamidation
* Glycosylation

Glutamine|

* Transglutamination

Lysine|

* Methylation
* Acetylation
* Acylation
* Adenylylation
* Hydroxylation
* Ubiquitination
* Sumoylation
* ADP-ribosylation
* Deamination
* Oxidative deamination to aldehyde
* O-glycosylation
* Imine formation
* Glycation
* Carbamylation
* Succinylation

Arginine|

* Citrullination
* Methylation
* ADP-ribosylation

Proline|

* Hydroxylation

Histidine|

* Diphthamide formation
* Adenylylation

Tryptophan|

* C-mannosylation

Crosslinks between two AAs|

| Cysteine-Cysteine|

* Disulfide bond
* ADP-ribosylation

|

Methionine-Hydroxylysine|

* Sulfilimine bond

Lysine-Tyrosylquinone|

* Lysine tyrosylquinone (LTQ) formation

Tryptophan-Tryptophylquinone|

* Tryptophan tryptophylquinone (TTQ) formation

Three consecutive AAs
(chromophore formation)|

| Serine–Tyrosine–Glycine|

* p-Hydroxybenzylidene-imidazolinone formation

|

Histidine–Tyrosine–Glycine|

* 4-(p-hydroxybenzylidene)-5-imidazolinone formation

Crosslinks between four AAs|

| Allysine-Allysine-Allysine-Lysine|

* Desmosine

|

* v
* t
* e

Metabolism: Protein metabolism, synthesis and catabolism enzymes

Essential amino acids are in Capitals

K→acetyl-CoA|

| LYSINE→|

* Saccharopine dehydrogenase
* Glutaryl-CoA dehydrogenase

|

LEUCINE→|

* 3-Hydroxybutyryl-CoA dehydrogenase
* Branched-chain amino acid aminotransferase
* Branched-chain alpha-keto acid dehydrogenase complex
* Enoyl-CoA hydratase
* HMG-CoA lyase
* HMG-CoA reductase
* Isovaleryl coenzyme A dehydrogenase
* α-Ketoisocaproate dioxygenase
* Leucine 2,3-aminomutase
* Methylcrotonyl-CoA carboxylase
* Methylglutaconyl-CoA hydratase

(See Template:Leucine metabolism in humans – this diagram does not include the pathway for β-leucine synthesis via leucine 2,3-aminomutase)

TRYPTOPHAN→|

* Indoleamine 2,3-dioxygenase/Tryptophan 2,3-dioxygenase
* Arylformamidase
* Kynureninase
* 3-hydroxyanthranilate oxidase
* Aminocarboxymuconate-semialdehyde decarboxylase
* Aminomuconate-semialdehyde dehydrogenase

PHENYLALANINE→tyrosine→|

* (see below)

| G→pyruvate
→citrate|

| glycine→serine→|

* Serine hydroxymethyltransferase
* Serine dehydratase

* glycine→creatine: Guanidinoacetate N-methyltransferase
* Creatine kinase

|

alanine→|

* Alanine transaminase

cysteine→|

* D-cysteine desulfhydrase

threonine→|

* L-threonine dehydrogenase

G→glutamate→
α-ketoglutarate|

| HISTIDINE→|

* Histidine ammonia-lyase
* Urocanate hydratase
* Formiminotransferase cyclodeaminase

|

proline→|

* Proline oxidase
* Pyrroline-5-carboxylate reductase
* 1-Pyrroline-5-carboxylate dehydrogenase/ALDH4A1
* PYCR1

arginine→|

* Ornithine aminotransferase
* Ornithine decarboxylase
* Agmatinase

→alpha-ketoglutarate→TCA|

* Glutamate dehydrogenase

Other|

* cysteine+glutamate→glutathione: Gamma-glutamylcysteine synthetase
* Glutathione synthetase
* Gamma-glutamyl transpeptidase

* glutamate→glutamine: Glutamine synthetase
* Glutaminase

G→propionyl-CoA→
succinyl-CoA|

| VALINE→|

* Branched-chain amino acid aminotransferase
* Branched-chain alpha-keto acid dehydrogenase complex
* Enoyl-CoA hydratase
* 3-hydroxyisobutyryl-CoA hydrolase
* 3-hydroxyisobutyrate dehydrogenase
* Methylmalonate semialdehyde dehydrogenase

|

ISOLEUCINE→|

* Branched-chain amino acid aminotransferase
* Branched-chain alpha-keto acid dehydrogenase complex
* 3-hydroxy-2-methylbutyryl-CoA dehydrogenase

METHIONINE→|

* generation of homocysteine: Methionine adenosyltransferase
* Adenosylhomocysteinase

* regeneration of methionine: Methionine synthase/Homocysteine methyltransferase
* Betaine-homocysteine methyltransferase

* conversion to cysteine: Cystathionine beta synthase
* Cystathionine gamma-lyase

THREONINE→|

* Threonine aldolase

→succinyl-CoA→TCA|

* Propionyl-CoA carboxylase
* Methylmalonyl CoA epimerase
* Methylmalonyl-CoA mutase

G→fumarate|

| PHENYLALANINE→tyrosine→|

* Phenylalanine hydroxylase
* Tyrosine aminotransferase
* 4-Hydroxyphenylpyruvate dioxygenase
* Homogentisate 1,2-dioxygenase
* Fumarylacetoacetate hydrolase

* tyrosine→melanin: Tyrosinase

|

G→oxaloacetate|

| asparagine→aspartate→|

* Asparaginase/Asparagine synthetase
* Aspartate transaminase

|

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