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 , hydrogen , oxygen , and nitrogen , although other elements
are found in the side chains of certain amino acids. About 500 amino
acids are known (though only 20 appear in the genetic code ) and can
be classified in many ways. 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
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 antibiotics .
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 ).
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
RNA 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 proline .
Glycine is a biosynthetic precursor to porphyrins used in red blood
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 .
* 1 History
* 2 General structure
* 2.1 Isomerism
* 2.2 Side chains
* 2.3 Zwitterions
* 3 Occurrence and functions in biochemistry
Proteinogenic amino acids
Non-proteinogenic amino acids
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
Expanded genetic code
Expanded genetic code
* 4.3 Chemical building blocks
* 4.4 Biodegradable plastics
* 5 Reactions
* 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 isolated a compound in asparagus that was subsequently named
asparagine , the first amino acid to be discovered.
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 growth.
Usage of the term amino acid in the English language is from 1898.
Proteins were found to yield amino acids after enzymatic digestion or
acid hydrolysis . In 1902, Emil Fischer and
Franz Hofmeister proposed
that proteins are the result of the formation of bonds between the
amino group of one amino acid with the carboxyl group of another, in a
linear structure that Fischer termed "peptide ".
Alpha carbon 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
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 acids
The phrase "branched-chain amino acids " or BCAA refers to the amino
acids having aliphatic side chains that are non-linear; these are
leucine , isoleucine , and valine .
Proline is the only proteinogenic
amino acid whose side-group links to the α-amino group and, thus, is
also the only proteinogenic amino acid containing a secondary amine at
this position. 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. With the exception of tyrosine, using titration to
distinguish among hydrophobic amino acids is problematic.
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 See also:
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 m
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
PYLIS downstream sequence .
NON-PROTEINOGENIC AMINO ACIDS
Non-proteinogenic amino acids
Non-proteinogenic amino acids
Aside from the 22 proteinogenic amino acids , many non-proteinogenic
amino acids are known. Those either are not found in proteins (for
example carnitine , GABA ,
Levothyroxine ) or are not produced
directly and in isolation by standard cellular machinery (for example,
hydroxyproline and selenomethionine ).
Non-proteinogenic amino acids
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.
2-aminoisobutyric acid and the neurotransmitter
gamma-aminobutyric acid .
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
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
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 Further information:
Protein (nutrient) and Amino acid
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 acid cycle . 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
AMP-activated protein kinase
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 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
Amino acid neurotransmitter
Amino acid neurotransmitter
Biosynthetic pathways for catecholamines and trace amines in the
human brain L-
3-Methoxytyramine AADC AADC AADC primary
pathway PNMT PNMT PNMT PNMT AAAH AAAH brain
pathway COMT DBH DBH Catecholamines and trace amines are
synthesized from phenylalanine and tyrosine in humans.
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 cosmetics .
Similarly, some amino acids derivatives are used in pharmaceutical
industry. They include
5-HTP (5-hydroxytryptophan) used for
experimental treatment of depression, L-DOPA
(L-dihydroxyphenylalanine) for Parkinson\'s treatment, and
eflornithine drug that inhibits ornithine decarboxylase and used in
the treatment of sleeping sickness .
EXPANDED GENETIC CODE
Expanded genetic code
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.
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 investigations.
CHEMICAL BUILDING BLOCKS
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
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.
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
acid. 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 developed.
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
Peptide bond The condensation
of two amino acids to form a dipeptide through a peptide bond
As both the amine and carboxylic acid groups of amino acids can react
to form amide bonds, one amino acid molecule can react with another
and become joined through an amide linkage. This polymerization of
amino acids is what creates proteins. This condensation reaction
yields the newly formed peptide bond and a molecule of water. In
cells, this reaction does not occur directly; instead, the amino acid
is first activated by attachment to a transfer
RNA molecule through an
ester bond. This aminoacyl-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
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
S-adenosyl methionine , while hydroxyproline
is made by a posttranslational modification of proline .
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 following:
* 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
* Amino acids catabolized into both glucogenic and ketogenic
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
Proteinogenic amino acid
class Side chain
polarity Side chain
charge (pH 7.4) Hydropathy
λmax(nm) ε at
λmax (mM−1 cm−1) MW
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
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
S, T, H, N, Q, E, D, K, R
K, R, H
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
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).
Amino acid dating
Nucleic acid sequence
Proteinogenic amino acid
Proteinogenic amino acid
* Table of codons , 3-nucleotide sequences that encode each amino
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* Media related to
Amino acid at Wikimedia Commons
The encoded amino acid
* Branched-chain amino acids (
POLAR , UNCHARGED