Amino acids are organic compounds containing amine (-NH2) and carboxyl
(-COOH) functional groups, along with a side chain (R group) specific
to each amino acid. The key elements of an amino acid are
carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), although other
elements are found in the side chains of certain amino acids. About
500 naturally occurring amino acids are known (though only 20 appear
in the genetic code) and can be classified in many ways. They can
be classified according to the core structural functional groups'
locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-)
amino acids; other categories relate to polarity, pH level, and side
chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or
sulfur, etc.). In the form of proteins, amino acid residues form the
second-largest component (water is the largest) of human muscles and
other tissues. Beyond their role as residues in proteins, amino
acids participate in a number of processes such as neurotransmitter
transport and biosynthesis.
In biochemistry, amino acids having both the amine and the carboxylic
acid groups attached to the first (alpha-) carbon atom have particular
importance. They are known as 2-, alpha-, or α-amino acids (generic
formula H2NCHRCOOH in most cases, 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" isomers),
although a few
D-amino acids ("right-handed") occur in bacterial
envelopes, as a neuromodulator (D-serine), and in some
Twenty of the proteinogenic amino acids are encoded directly by
triplet codons in the genetic code and are known as "standard" amino
acids. The other two ("non-standard" or "non-canonical") are
selenocysteine (present in many prokaryotes as well as most
eukaryotes, but not coded directly by DNA), and pyrrolysine (found
only in some archea and one bacterium).
Pyrrolysine and selenocysteine
are encoded via variant codons; for example, selenocysteine is encoded
by stop codon and SECIS element. 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.
Many important proteinogenic and non-proteinogenic amino acids have
biological functions. For example, in the human brain, glutamate
(standard glutamic acid) and gamma-amino-butyric acid ("GABA",
non-standard gamma-amino acid) are, respectively, the main excitatory
and inhibitory neurotransmitters. Hydroxyproline, a major
component of the connective tissue collagen, is synthesised from
Glycine is a biosynthetic precursor to porphyrins used in red
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
Essential amino acids may also
differ between species.
Because of their biological significance, amino acids are important in
nutrition and are commonly used in nutritional supplements,
fertilizers, and food technology. Industrial uses include the
production of drugs, biodegradable plastics, and chiral catalysts.
2 General structure
2.2 Side chains
2.4 Isoelectric point
3 Occurrence and functions in biochemistry
Proteinogenic amino acids
3.2 Non-proteinogenic amino acids
D-amino acid natural abundance
3.4 Non-standard amino acids
3.5 In human nutrition
3.6 Non-protein functions
4 Uses in industry
4.1 Expanded genetic code
4.3 Chemical building blocks
4.4 Biodegradable plastics
5.1 Chemical synthesis
Peptide bond formation
6 Physicochemical properties of amino acids
6.1 Table of standard amino acid abbreviations and properties
7 See also
8 References and notes
9 Further reading
10 External links
The first few amino acids were discovered in the early 19th
century. In 1806, French chemists
Louis-Nicolas Vauquelin and
Pierre Jean Robiquet
Pierre Jean Robiquet isolated a compound in asparagus that was
subsequently named asparagine, the first amino acid to be
Cystine was discovered in 1810, although its
monomer, cysteine, remained undiscovered until 1884. Glycine
and leucine were discovered in 1820. 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
The unity of the chemical category was recognized by Wurtz in 1865,
but he gave no particular name to it. Usage of the term "amino
acid" in the English language is from 1898, while the German term,
Aminosäure, was used earlier. Proteins were found to yield amino
acids after enzymatic digestion or acid hydrolysis. In 1902, Emil
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".
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)
In the structure shown at the top of the page, R represents a side
chain specific to each amino acid. The carbon atom next to the
carboxyl group (which is therefore numbered 2 in the carbon chain
starting from that functional group) is called the α–carbon. Amino
acids containing an amino group bonded directly to the alpha carbon
are referred to as alpha amino acids. These include amino acids
such as proline which contain secondary amines, which used to be often
referred to as "imino acids".
The alpha amino acids are the most common form found in nature, but
only when occurring in the L-isomer. The alpha carbon is a chiral
carbon atom, with the exception of glycine which has two
indistinguishable hydrogen atoms on the alpha carbon. Therefore,
all alpha amino acids but glycine can exist in either of two
enantiomers, called L or D amino acids, which are mirror images of
each other (see also Chirality). While L-amino acids represent all of
the amino acids found in proteins during translation in the ribosome,
D-amino acids are found in some proteins produced by enzyme
posttranslational modifications after translation and translocation to
the endoplasmic reticulum, as in exotic sea-dwelling organisms such as
cone snails. They are also abundant components of the
peptidoglycan cell walls of bacteria, and D-serine may act as a
neurotransmitter in the brain.
D-amino acids are used in racemic
crystallography to create centrosymmetric crystals, which (depending
on the protein) may allow for easier and more robust protein structure
determination. The L and D convention for amino acid configuration
refers not to the optical activity of the amino acid itself but rather
to the optical activity of the isomer of glyceraldehyde from which
that amino acid can, in theory, be synthesized (D-glyceraldehyde is
dextrorotatory; L-glyceraldehyde is levorotatory). In alternative
fashion, the (S) and (R) designators are used to indicate the absolute
stereochemistry. Almost all of the amino acids in proteins are (S) at
the α carbon, with cysteine being (R) and glycine non-chiral.
Cysteine has its side chain in the same geometric position as the
other amino acids, but the R/S terminology is reversed because of the
higher atomic number of sulfur compared to the carboxyl oxygen gives
the side chain a higher priority, whereas the atoms in most other side
chains give them lower priority.
Lysine with carbon atoms labeled by position
In amino acids that have a carbon chain attached to the α–carbon
(such as lysine, shown to the right) the carbons are labeled in order
as α, β, γ, δ, and so on. In some amino acids, the amine group
is attached to the β or γ-carbon, and these are therefore referred
to as beta or gamma amino acids.
Amino acids are usually classified by the properties of their side
chain into four groups. The side chain can make an amino acid a weak
acid or a weak base, and a hydrophile if the side chain is polar or a
hydrophobe if it is nonpolar. The chemical structures of the 22
standard amino acids, along with their chemical properties, are
described more fully in the article on these proteinogenic amino
The phrase "branched-chain amino acids" or BCAA refers to the amino
acids having aliphatic side chains that are non-linear; these are
leucine, isoleucine, and valine.
Proline is the only proteinogenic
amino acid whose side-group links to the α-amino group and, thus, is
also the only proteinogenic amino acid containing a secondary amine at
this position. In chemical terms, proline is, therefore, an imino
acid, since it lacks a primary amino group, although it is still
classed as an amino acid in the current biochemical nomenclature,
and may also be called an "N-alkylated alpha-amino acid".
An amino acid in its (1) un-ionized and (2) zwitterionic forms
The α-carboxylic acid group of amino acids is a weak acid, meaning
that it releases a hydron (such as a proton) at moderate pH values. In
other words, carboxylic acid groups (−CO2H) can be deprotonated to
become negative carboxylates (−CO2− ). The negatively charged
carboxylate ion predominates at pH values greater than the pKa of the
carboxylic acid group (mean for the 20 common amino acids is about
2.2, see the table of amino acid structures above). In a complementary
fashion, the α-amine of amino acids is a weak base, meaning that it
accepts a proton at moderate pH values. In other words, α-amino
groups (NH2−) can be protonated to become positive α-ammonium
groups (+NH3−). The positively charged α-ammonium group
predominates at pH values less than the pKa of the α-ammonium group
(mean for the 20 common α-amino acids is about 9.4).
Because all amino acids contain amine and carboxylic acid functional
groups, they share amphiprotic properties. Below pH 2.2, the
predominant form will have a neutral carboxylic acid group and a
positive α-ammonium ion (net charge +1), and above pH 9.4, a negative
carboxylate and neutral α-amino group (net charge −1). But at pH
between 2.2 and 9.4, an amino acid usually contains both a negative
carboxylate and a positive α-ammonium group, as shown in structure
(2) on the right, so has net zero charge. This molecular state is
known as a zwitterion, from the German Zwitter meaning hermaphrodite
or hybrid. The fully neutral form (structure (1) on the left) is a
very minor species in aqueous solution throughout the pH range (less
than 1 part in 107).
Amino acids exist as zwitterions also in the
solid phase, and crystallize with salt-like properties unlike typical
organic acids or amines.
Composite of titration curves of twenty proteinogenic amino acids
grouped by side chain category
The variation in titration curves when the amino acids can be grouped
by category.[clarification needed] With the exception of tyrosine,
using titration to distinguish among hydrophobic amino acids is
At pH values between the two pKa values, the zwitterion predominates,
but coexists in dynamic equilibrium with small amounts of net negative
and net positive ions. At the exact midpoint between the two pKa
values, the trace amount of net negative and trace of net positive
ions exactly balance, so that average net charge of all forms present
is zero. This pH is known as the isoelectric point pI, so pI =
½(pKa1 + pKa2). The individual amino acids all have slightly
different pKa values, so have different isoelectric points. For amino
acids with charged side chains, the pKa of the side chain is involved.
Thus for Asp, Glu with negative side chains, pI = ½(pKa1 + pKaR),
where pKaR is the side chain pKa.
Cysteine also has potentially
negative side chain with pKaR = 8.14, so pI should be calculated as
for Asp and Glu, even though the side chain is not significantly
charged at neutral pH. For His, Lys, and Arg with positive side
chains, pI = ½(pKaR + pKa2).
Amino acids have zero mobility in
electrophoresis at their isoelectric point, although this behaviour is
more usually exploited for peptides and proteins than single amino
acids. Zwitterions have minimum solubility at their isoelectric point
and some amino acids (in particular, with non-polar side chains) can
be isolated by precipitation from water by adjusting the pH to the
required isoelectric point.
Occurrence and functions in biochemistry
A polypeptide is an unbranched chain of amino acids
β-alanine and its α-alanine isomer
The amino acid selenocysteine
Proteinogenic amino acids
Proteinogenic amino acids
Protein primary structure and Posttranslational modification
Amino acids are the structural units (monomers) that make up proteins.
They join together to form short polymer chains called peptides or
longer chains called either polypeptides or proteins. These polymers
are linear and unbranched, with each amino acid within the chain
attached to two neighboring amino acids. The process of making
proteins 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
RNA template, which is a
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
RNA 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.
Non-proteinogenic amino acids
Main article: 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
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
Some non-proteinogenic amino acids are not found in proteins. Examples
2-aminoisobutyric acid and the neurotransmitter
Non-proteinogenic amino acids
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 coenzyme A.
D-amino acid natural abundance
D-isomers are uncommon in live organisms. For instance, gramicidin is
a polypeptide made up from mixture of D- and L-amino acids. Other
D-amino acid are tyrocidine and valinomycin.
These compounds disrupt bacterial cell walls, particularly in
Gram-positive bacteria. Only 837
D-amino acids were found in
Swiss-Prot database (187 million amino acids analysed).
Non-standard amino acids
The 20 amino acids that are encoded directly by the codons of the
universal genetic code are called standard or canonical amino acids. 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
non-standard or non-canonical. Most of the non-standard 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 non-standard 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
one bacterium). The incorporation of these non-standard amino acids is
rare. For example, 25 human proteins include selenocysteine (Sec) in
their primary structure, and the structurally characterized
enzymes (selenoenzymes) employ Sec as the catalytic moiety in their
Pyrrolysine and selenocysteine are encoded via
variant codons. For example, selenocysteine is encoded by stop codon
and SECIS element.
In human nutrition
Share of amino acid in different 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: Essential amino acids
Protein (nutrient) and
Amino acid synthesis
When taken up into the human body from the diet, the 20 standard amino
acids either are used to synthesize proteins and other biomolecules or
are oxidized to urea and carbon dioxide as a source of energy. The
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
Glucogenic amino acids
Glucogenic amino acids can also be converted into
glucose, through gluconeogenesis. 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. In addition, cysteine,
taurine, tyrosine, and arginine are considered semiessential
amino-acids in children (though taurine is not technically an amino
acid), because the metabolic pathways that synthesize these amino
acids are not fully developed. The amounts required also
depend on the age and health of the individual, so it is hard to make
general statements about the dietary requirement for some amino acids.
Dietary exposure to the non-standard amino acid BMAA has been linked
to human neurodegenerative diseases, including ALS.
Diagram of the molecular signaling cascades that are involved in
myofibrillar muscle protein synthesis and mitochondrial biogenesis in
response to physical exercise and specific amino acids or their
derivatives (primarily L-leucine and HMB). Many amino acids
derived from food protein promote the activation of mTORC1 and
increase protein synthesis by signaling through Rag GTPases.
Abbreviations and representations:
• PLD: phospholipase D
• PA: phosphatidic acid
• mTOR: mechanistic target of rapamycin
• AMP: adenosine monophosphate
• ATP: adenosine triphosphate
• AMPK: AMP-activated protein kinase
• PGC‐1α: peroxisome proliferator-activated receptor gamma
• S6K1: p70S6 kinase
• 4EBP1: eukaryotic translation initiation factor 4E-binding
• eIF4E: eukaryotic translation initiation factor 4E
• RPS6: ribosomal protein S6
• eEF2: eukaryotic elongation factor 2
• RE: resistance exercise; EE: endurance exercise
• Myo: myofibrillar; Mito: mitochondrial
• AA: amino acids
• HMB: β-hydroxy β-methylbutyric acid
• ↑ represents activation
• Τ represents inhibition
Resistance training stimulates muscle protein synthesis (MPS) for a
period of up to 48 hours following exercise (shown by lighter
dotted line). Ingestion of a protein-rich meal at any point during
this period will augment the exercise-induced increase in muscle
protein synthesis (shown by solid lines).
Biosynthetic pathways for catecholamines and trace amines in the human
Catecholamines and trace amines are synthesized from phenylalanine and
tyrosine in humans.
Amino acid neurotransmitter
In humans, non-protein amino acids also have important roles as
metabolic intermediates, such as in the biosynthesis of the
neurotransmitter gamma-amino-butyric acid (GABA). Many amino acids are
used to synthesize other molecules, for example:
Tryptophan is a precursor of the neurotransmitter serotonin.
Tyrosine (and its precursor phenylalanine) are precursors of the
catecholamine neurotransmitters dopamine, epinephrine and
norepinephrine and various trace amines.
Phenylalanine is a precursor of phenethylamine and tyrosine in humans.
In plants, it is a precursor of various phenylpropanoids, which are
important in plant metabolism.
Glycine is a precursor of porphyrins such as heme.
Arginine is a precursor of nitric oxide.
Ornithine and S-adenosylmethionine are precursors of polyamines.
Aspartate, glycine, and glutamine are precursors of nucleotides.
However, not all of the functions of other abundant non-standard amino
acids are known.
Some non-standard amino acids are used as defenses against herbivores
in plants. For example, canavanine is an analogue of arginine that
is found in many legumes, and in particularly large amounts in
Canavalia gladiata (sword bean). This amino acid protects the
plants from predators such as insects and can cause illness in people
if some types of legumes are eaten without processing. The
non-protein amino acid mimosine is found in other species of legume,
in particular Leucaena leucocephala. This compound is an analogue
of tyrosine and can poison animals that graze on these plants.
Uses in industry
Amino acids are used for a variety of applications in industry, but
their main use is as additives to animal feed. This is necessary,
since many of the bulk components of these feeds, such as soybeans,
either have low levels or lack some of the essential amino acids:
lysine, methionine, threonine, and tryptophan are most important in
the production of these feeds. In this industry, amino acids are
also used to chelate metal cations in order to improve the absorption
of minerals from supplements, which may be required to improve the
health or production of these animals.
The food industry is also a major consumer of amino acids, in
particular, glutamic acid, which is used as a flavor enhancer, and
aspartame (aspartyl-phenylalanine-1-methyl ester) as a low-calorie
artificial sweetener. Similar technology to that used for animal
nutrition is employed in the human nutrition industry to alleviate
symptoms of mineral deficiencies, such as anemia, by improving mineral
absorption and reducing negative side effects from inorganic mineral
The chelating ability of amino acids has been used in fertilizers for
agriculture to facilitate the delivery of minerals to plants in order
to correct mineral deficiencies, such as iron chlorosis. These
fertilizers are also used to prevent deficiencies from occurring and
improving the overall health of the plants. The remaining
production of amino acids is used in the synthesis of drugs and
Similarly, some amino acids derivatives are used in pharmaceutical
industry. They include
5-HTP (5-hydroxytryptophan) used for
experimental treatment of depression, L-DOPA
Parkinson's treatment, and
eflornithine drug that inhibits ornithine decarboxylase and used in
the treatment of sleeping sickness.
Expanded genetic code
Main article: Expanded genetic code
Since 2001, 40 non-natural amino acids have been added into protein by
creating a unique codon (recoding) and a corresponding
transfer-RNA:aminoacyl – tRNA-synthetase pair to encode it with
diverse physicochemical and biological properties in order to be used
as a tool to exploring protein structure and function or to create
novel or enhanced proteins.
Main article: Nullomers
Nullomers are codons that in theory code for an amino acid, however in
nature there is a selective bias against using this codon in favor of
another, for example bacteria prefer to use CGA instead of AGA to code
for arginine. This creates some sequences that do not appear in
the genome. This characteristic can be taken advantage of and used to
create new selective cancer-fighting drugs and to prevent
DNA samples from crime-scene
Chemical building blocks
Further information: Asymmetric synthesis
Amino acids are important as low-cost feedstocks. These compounds are
used in chiral pool synthesis as enantiomerically pure
Amino acids have been investigated as precursors chiral catalysts,
e.g., for asymmetric hydrogenation reactions, although no commercial
Biodegradable plastic and Biopolymer
Amino acids are under development as components of a range of
biodegradable polymers. These materials have applications as
environmentally friendly packaging and in medicine in drug delivery
and the construction of prosthetic implants. These polymers include
polypeptides, polyamides, polyesters, polysulfides, and polyurethanes
with amino acids either forming part of their main chains or bonded as
side chains. These modifications alter the physical properties and
reactivities of the polymers. An interesting example of such
materials is polyaspartate, a water-soluble biodegradable polymer that
may have applications in disposable diapers and agriculture. Due
to its solubility and ability to chelate metal ions, polyaspartate is
also being used as a biodegradeable anti-scaling agent and a corrosion
inhibitor. In addition, the aromatic amino acid tyrosine is
being developed as a possible replacement for toxic phenols such as
bisphenol A in the manufacture of polycarbonates.
As amino acids have both a primary amine group and a primary carboxyl
group, these chemicals can undergo most of the reactions associated
with these functional groups. These include nucleophilic addition,
amide bond formation, and imine formation for the amine group, and
esterification, amide bond formation, and decarboxylation for the
carboxylic acid group. The combination of these functional groups
allow amino acids to be effective polydentate ligands for metal-amino
acid chelates. The multiple side chains of amino acids can also
undergo chemical reactions. The types of these reactions are
determined by the groups on these side chains and are, therefore,
different between the various types of amino acid.
The Strecker amino acid synthesis
See also: Category:Chemical synthesis of amino acids
Several methods exist to synthesize amino acids. One of the oldest
methods begins with the bromination at the α-carbon of a carboxylic
Nucleophilic substitution with ammonia then converts the alkyl
bromide to the amino acid. In alternative fashion, the Strecker
amino acid synthesis involves the treatment of an aldehyde with
potassium cyanide and ammonia, this produces an α-amino nitrile as an
Hydrolysis of the nitrile in acid then yields a α-amino
acid. Using ammonia or ammonium salts in this reaction gives
unsubstituted amino acids, whereas substituting primary and secondary
amines will yield substituted amino acids. Likewise, using
ketones, instead of aldehydes, gives α,α-disubstituted amino
acids. The classical synthesis gives racemic mixtures of α-amino
acids as products, but several alternative procedures using asymmetric
auxiliaries or asymmetric catalysts have been
At the current time, the most-adopted method is an automated synthesis
on a solid support (e.g., polystyrene beads), using protecting groups
(e.g., Fmoc and t-Boc) and activating groups (e.g., DCC and DIC).
Peptide bond formation
Peptide synthesis and
The condensation of two amino acids to form a dipeptide through a
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-t
RNA is produced in an ATP-dependent
reaction carried out by an aminoacyl t
RNA synthetase. This
RNA is then a substrate for the ribosome, which catalyzes
the attack of the amino group of the elongating protein chain on the
ester bond. As a result of this mechanism, all proteins made by
ribosomes are synthesized starting at their N-terminus and moving
toward their C-terminus.
However, not all peptide bonds are formed in this way. In a few cases,
peptides are synthesized by specific enzymes. For example, the
tripeptide glutathione is an essential part of the defenses of cells
against oxidative stress. This peptide is synthesized in two steps
from free amino acids. In the first step, gamma-glutamylcysteine
synthetase condenses cysteine and glutamic acid through a peptide bond
formed between the side chain carboxyl of the glutamate (the gamma
carbon of this side chain) and the amino group of the cysteine. This
dipeptide is then condensed with glycine by glutathione synthetase to
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. The ability to easily synthesize vast
numbers of different peptides by varying the types and order of amino
acids (using combinatorial chemistry) has made peptide synthesis
particularly important in creating libraries of peptides for use in
drug discovery through high-throughput screening.
Amino acid synthesis
In plants, nitrogen is first assimilated into organic compounds in the
form of glutamate, formed from alpha-ketoglutarate and ammonia in the
mitochondrion. In order to form other amino acids, the plant uses
transaminases to move the amino group to another alpha-keto carboxylic
acid. For example, aspartate aminotransferase converts glutamate and
oxaloacetate to alpha-ketoglutarate and aspartate. Other
organisms use transaminases for amino acid synthesis, too.
Nonstandard amino acids are usually formed through modifications to
standard amino acids. For example, homocysteine is formed through the
transsulfuration pathway or by the demethylation of methionine via the
intermediate metabolite S-adenosyl methionine, while
hydroxyproline is made by a posttranslational modification of
Microorganisms and plants can synthesize many uncommon amino acids.
For example, some microbes make
2-aminoisobutyric acid and
lanthionine, which is a sulfide-bridged derivative of alanine. Both of
these amino acids are found in peptidic lantibiotics such as
alamethicin. However, in plants, 1-aminocyclopropane-1-carboxylic
acid is a small disubstituted cyclic amino acid that is a key
intermediate in the production of the plant hormone ethylene.
Catabolism of proteinogenic amino acids.
Amino acids can be classified
according to the properties of their main products as either of the
* Glucogenic, with the products having the ability to form glucose by
* Ketogenic, with the products not having the ability to form glucose.
These products may still be used for ketogenesis or lipid synthesis.
Amino acids catabolized into both glucogenic and ketogenic products.
Amino acids must first pass out of organelles and cells into blood
circulation via amino acid transporters, since the amine and
carboxylic acid groups are typically ionized. Degradation of an amino
acid, occurring in the liver and kidneys, often involves deamination
by moving its amino group to alpha-ketoglutarate, forming glutamate.
This process involves transaminases, often the same as those used in
amination during synthesis. In many vertebrates, the amino group is
then removed through the urea cycle and is excreted in the form of
urea. However, amino acid degradation can produce uric acid or ammonia
instead. For example, serine dehydratase converts serine to pyruvate
and ammonia. After removal of one or more amino groups, the
remainder of the molecule can sometimes be used to synthesize new
amino acids, or it can be used for energy by entering glycolysis or
the citric acid cycle, as detailed in image at right.
Physicochemical properties of amino acids
The 20 amino acids encoded directly by the genetic code can be divided
into several groups based on their properties. Important factors are
charge, hydrophilicity or hydrophobicity, size, and functional
groups. These properties are important for protein structure and
protein–protein interactions. The water-soluble proteins tend to
have their hydrophobic residues (Leu, Ile, Val, Phe, and Trp) buried
in the middle of the protein, whereas hydrophilic side chains are
exposed to the aqueous solvent. (Note that in biochemistry, a residue
refers to a specific monomer within the polymeric chain of a
polysaccharide, protein or nucleic acid.) The integral membrane
proteins tend to have outer rings of exposed hydrophobic amino acids
that anchor them into the lipid bilayer. In the case part-way between
these two extremes, some peripheral membrane proteins have a patch of
hydrophobic amino acids on their surface that locks onto the membrane.
In similar fashion, proteins that have to bind to positively charged
molecules have surfaces rich with negatively charged amino acids like
glutamate and aspartate, while proteins binding to negatively charged
molecules have surfaces rich with positively charged chains like
lysine and arginine. There are different hydrophobicity scales of
amino acid residues.
Some amino acids have special properties such as cysteine, that can
form covalent disulfide bonds to other cysteine residues, proline that
forms a cycle to the polypeptide backbone, and glycine that is more
flexible than other amino acids.
Many proteins undergo a range of posttranslational modifications, when
additional chemical groups are attached to the amino acids in
proteins. Some modifications can produce hydrophobic
lipoproteins, or hydrophilic glycoproteins. These type of
modification allow the reversible targeting of a protein to a
membrane. For example, the addition and removal of the fatty acid
palmitic acid to cysteine residues in some signaling proteins causes
the proteins to attach and then detach from cell membranes.
Table of standard amino acid abbreviations and properties
Proteinogenic amino acid
charge (pH 7.4)
λmax (mM−1 cm−1)
in proteins (%)
Coding in the Standard Genetic Code
257, 206, 188
0.2, 9.3, 60.0
274, 222, 193
1.4, 8.0, 48.0
Two additional amino acids are in some species coded for by codons
that are usually interpreted as stop codons:
21st and 22nd amino acids
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
Amino Acids Included
Any / unknown
Asparagine or aspartic acid
Glutamine or glutamic acid
Leucine or Isoleucine
V, I, L, F, W, Y, M
F, W, Y, H
V, I, L, M
P, G, A, S
BCN, RGY, GGR
S, T, H, N, Q, E, D, K, R
K, R, H
ARR, CRY, CGR
Unk is sometimes used instead of Xaa, but is less standard.
In addition, many non-standard amino acids have a specific code. For
example, several peptide drugs, such as
Bortezomib and MG132, are
artificially synthesized and retain their protecting groups, which
have specific codes.
Bortezomib is Pyz-Phe-boroLeu, and
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).
Amino acid dating
Nucleic acid sequence
Proteinogenic amino acid
Table of codons, 3-nucleotide sequences that encode each amino acid
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Media related to
Amino acid at Wikimedia Commons
The encoded amino acid
Branched-chain amino acids (Valine
Positive charge (pKa)
Negative charge (pKa)
Aspartic acid (≈3.9)
Glutamic acid (≈4.1)
Amino acids types: Encoded (proteins)
Protein primary structure and posttranslational modifications
N-O acyl shift
Glycosyl phosphatidylinositol (GPI)
Single specific AAs
Methylidene-imidazolone (MIO) formation
Porphyrin ring linkage
Topaquinone (TPQ) formation
Oxidative deamination to aldehyde
Crosslinks between two AAs
Lysine tyrosylquinone (LTQ) formation
Tryptophan tryptophylquinone (TTQ) formation
Three consecutive AAs
Crosslinks between four AAs
Protein metabolism, synthesis and catabolism enzymes
Essential amino acids
Essential amino acids are in Capitals
Branched-chain amino acid
Branched-chain amino acid aminotransferase
Branched-chain alpha-keto acid dehydrogenase complex
Isovaleryl coenzyme A dehydrogenase
glycine→creatine: Guanidinoacetate N-methyltransferase
cysteine+glutamate→glutathione: Gamma-glutamylcysteine synthetase
Branched-chain amino acid
Branched-chain amino acid aminotransferase
Branched-chain alpha-keto acid dehydrogenase complex
Methylmalonate semialdehyde dehydrogenase
Branched-chain amino acid
Branched-chain amino acid aminotransferase
Branched-chain alpha-keto acid dehydrogenase complex
generation of homocysteine:
regeneration of methionine:
conversion to cysteine: Cystathionine beta synthase
Methylmalonyl CoA epimerase
Molecular and Cellular Biology porta