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Proteinogenic amino acids are
amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha ...
s that are incorporated biosynthetically into
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
s during
translation Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. The English language draws a terminological distinction (which does not exist in every language) between ''transla ...
. The word "proteinogenic" means "protein creating". Throughout known
life Life is a quality that distinguishes matter that has biological processes, such as signaling and self-sustaining processes, from that which does not, and is defined by the capacity for growth, reaction to stimuli, metabolism, energy ...
, there are 22 genetically encoded (proteinogenic) amino acids, 20 in the standard
genetic code The genetic code is the set of rules used by living cells to translate information encoded within genetic material ( DNA or RNA sequences of nucleotide triplets, or codons) into proteins. Translation is accomplished by the ribosome, which links ...
and an additional 2 (
selenocysteine Selenocysteine (symbol Sec or U, in older publications also as Se-Cys) is the 21st proteinogenic amino acid. Selenoproteins contain selenocysteine residues. Selenocysteine is an analogue of the more common cysteine with selenium in place of the ...
and
pyrrolysine Pyrrolysine (symbol Pyl or O; encoded by the 'amber' stop codon UAG) is an α-amino acid that is used in the biosynthesis of proteins in some methanogenic archaea and bacteria; it is not present in humans. It contains an α-amino group (which ...
) that can be incorporated by special translation mechanisms. In contrast,
non-proteinogenic amino acids In biochemistry, non-coded or non-proteinogenic amino acids are distinct from the 22 proteinogenic amino acids (21 in eukaryotesplus formylmethionine in eukaryotes with prokaryote organelles like mitochondria) which are naturally encoded in the ge ...
are amino acids that are either not incorporated into proteins (like GABA, L-DOPA, or
triiodothyronine Triiodothyronine, also known as T3, is a thyroid hormone. It affects almost every physiological process in the body, including growth and development, metabolism, body temperature, and heart rate. Production of T3 and its prohormone thyrox ...
), misincorporated in place of a genetically encoded amino acid, or not produced directly and in isolation by standard cellular machinery (like
hydroxyproline (2''S'',4''R'')-4-Hydroxyproline, or L-hydroxyproline ( C5 H9 O3 N), is an amino acid, abbreviated as Hyp or O, ''e.g.'', in Protein Data Bank. Structure and discovery In 1902, Hermann Emil Fischer isolated hydroxyproline from hydrolyzed gelatin ...
). The latter often results from
post-translational modification Post-translational modification (PTM) is the covalent and generally enzymatic modification of proteins following protein biosynthesis. This process occurs in the endoplasmic reticulum and the golgi apparatus. Proteins are synthesized by ribo ...
of proteins. Some non-proteinogenic amino acids are incorporated into nonribosomal peptides which are synthesized by non-ribosomal peptide synthetases. Both
eukaryote Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacter ...
s and
prokaryote A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Con ...
s can incorporate
selenocysteine Selenocysteine (symbol Sec or U, in older publications also as Se-Cys) is the 21st proteinogenic amino acid. Selenoproteins contain selenocysteine residues. Selenocysteine is an analogue of the more common cysteine with selenium in place of the ...
into their proteins via a nucleotide sequence known as a
SECIS element In biology, the SECIS element (SECIS: ''selenocysteine insertion sequence'') is an RNA element around 60 nucleotides in length that adopts a stem-loop structure. This structural motif (pattern of nucleotides) directs the cell to translate UGA ...
, which directs the cell to translate a nearby UGA
codon The genetic code is the set of rules used by living cells to translate information encoded within genetic material ( DNA or RNA sequences of nucleotide triplets, or codons) into proteins. Translation is accomplished by the ribosome, which links ...
as
selenocysteine Selenocysteine (symbol Sec or U, in older publications also as Se-Cys) is the 21st proteinogenic amino acid. Selenoproteins contain selenocysteine residues. Selenocysteine is an analogue of the more common cysteine with selenium in place of the ...
(UGA is normally a
stop codon In molecular biology (specifically protein biosynthesis), a stop codon (or termination codon) is a codon (nucleotide triplet within messenger RNA) that signals the termination of the translation process of the current protein. Most codons in mess ...
). In some methanogenic prokaryotes, the UAG codon (normally a stop codon) can also be translated to
pyrrolysine Pyrrolysine (symbol Pyl or O; encoded by the 'amber' stop codon UAG) is an α-amino acid that is used in the biosynthesis of proteins in some methanogenic archaea and bacteria; it is not present in humans. It contains an α-amino group (which ...
. In eukaryotes, there are only 21 proteinogenic amino acids, the 20 of the standard genetic code, plus
selenocysteine Selenocysteine (symbol Sec or U, in older publications also as Se-Cys) is the 21st proteinogenic amino acid. Selenoproteins contain selenocysteine residues. Selenocysteine is an analogue of the more common cysteine with selenium in place of the ...
. Humans can synthesize 12 of these from each other or from other molecules of intermediary metabolism. The other nine must be consumed (usually as their protein derivatives), and so they are called
essential amino acid An essential amino acid, or indispensable amino acid, is an amino acid that cannot be synthesized from scratch by the organism fast enough to supply its demand, and must therefore come from the diet. Of the 21 amino acids common to all life form ...
s. The essential amino acids are
histidine Histidine (symbol His or H) is an essential amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated –NH3+ form under biological conditions), a carboxylic acid group (which is in the ...
,
isoleucine Isoleucine (symbol Ile or I) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH form under biological conditions), an α-carboxylic acid group (which is in the depr ...
,
leucine Leucine (symbol Leu or L) is an essential amino acid that is used in the biosynthesis of proteins. Leucine is an α-amino acid, meaning it contains an α- amino group (which is in the protonated −NH3+ form under biological conditions), an α- ...
,
lysine Lysine (symbol Lys or K) is an α-amino acid that is a precursor to many proteins. It contains an α-amino group (which is in the protonated form under biological conditions), an α-carboxylic acid group (which is in the deprotonated − ...
,
methionine Methionine (symbol Met or M) () is an essential amino acid in humans. As the precursor of other amino acids such as cysteine and taurine, versatile compounds such as SAM-e, and the important antioxidant glutathione, methionine plays a critical ...
,
phenylalanine Phenylalanine (symbol Phe or F) is an essential α-amino acid with the formula . It can be viewed as a benzyl group substituted for the methyl group of alanine, or a phenyl group in place of a terminal hydrogen of alanine. This essential amin ...
,
threonine Threonine (symbol Thr or T) is an amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated −NH form under biological conditions), a carboxyl group (which is in the deprotonated −COO� ...
,
tryptophan Tryptophan (symbol Trp or W) is an α-amino acid that is used in the biosynthesis of proteins. Tryptophan contains an α-amino group, an α-carboxylic acid group, and a side chain indole, making it a polar molecule with a non-polar aromatic ...
, and
valine Valine (symbol Val or V) is an α-amino acid that is used in the biosynthesis of proteins. It contains an α- amino group (which is in the protonated −NH3+ form under biological conditions), an α- carboxylic acid group (which is in the deprotona ...
(i.e. H, I, L, K, M, F, T, W, V). The proteinogenic amino acids have been found to be related to the set of
amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha ...
s that can be recognized by
ribozyme Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozymes demons ...
autoaminoacylation systems. Thus, non-proteinogenic amino acids would have been excluded by the contingent evolutionary success of nucleotide-based life forms. Other reasons have been offered to explain why certain specific non-proteinogenic amino acids are not generally incorporated into proteins; for example,
ornithine Ornithine is a non-proteinogenic amino acid that plays a role in the urea cycle. Ornithine is abnormally accumulated in the body in ornithine transcarbamylase deficiency. The radical is ornithyl. Role in urea cycle L-Ornithine is one of the produ ...
and homoserine cyclize against the peptide backbone and fragment the protein with relatively short
half-lives Half-life (symbol ) is the time required for a quantity (of substance) to reduce to half of its initial value. The term is commonly used in nuclear physics to describe how quickly unstable atoms undergo radioactive decay or how long stable ato ...
, while others are toxic because they can be mistakenly incorporated into proteins, such as the arginine analog
canavanine L-(+)-(''S'')-Canavanine is a non-proteinogenic amino acid found in certain leguminous plants. It is structurally related to the proteinogenic α-amino acid L-arginine Arginine is the amino acid with the formula (H2N)(HN)CN(H)(CH2)3CH(NH2)CO2H ...
. The
evolution Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
ary selection of certain proteinogenic amino acids from the
primordial soup Primordial soup, also known as, primordial goo, primordial ooze, prebiotic soup and prebiotic broth, is the hypothetical set of conditions present on the Earth around 3.7 to 4.0 billion years ago. It is an aspect of the heterotrophic theory (also k ...
has been suggested to be because of their better incorporation into a polypeptide chain as opposed to non-proteinogenic amino acids.


Structures

The following illustrates the structures and abbreviations of the 21 amino acids that are directly encoded for protein synthesis by the genetic code of eukaryotes. The structures given below are standard chemical structures, not the typical
zwitterion In chemistry, a zwitterion ( ; ), also called an inner salt or dipolar ion, is a molecule that contains an equal number of positively- and negatively-charged functional groups. : With amino acids, for example, in solution a chemical equilibrium wil ...
forms that exist in aqueous solutions. image:L-alanine-skeletal.png, L-Alanine
(Ala / A) image:L-arginine-skeletal-(tall).png, L-Arginine
(Arg / R) image:L-asparagine-skeletal.png, L-Asparagine
(Asn / N) image:L-aspartic-acid-skeletal.png, L-Aspartic acid
(Asp / D) image:L-cysteine-skeletal.png, L-Cysteine
(Cys / C) image:L-glutamic-acid-skeletal.png, L-Glutamic acid
(Glu / E) image:L-glutamine-skeletal.png, L-Glutamine
(Gln / Q) image:Glycine-skeletal.png,
Glycine Glycine (symbol Gly or G; ) is an amino acid that has a single hydrogen atom as its side chain. It is the simplest stable amino acid ( carbamic acid is unstable), with the chemical formula NH2‐ CH2‐ COOH. Glycine is one of the proteinog ...

(Gly / G) image:L-histidine-skeletal.png, L-Histidine
(His / H) image:L-isoleucine-skeletal.svg, L-Isoleucine
(Ile / I) image:L-leucine-skeletal.png, L-Leucine
(Leu / L) image:L-lysine-skeletal.png, L-Lysine
(Lys / K) image:L-methionine-skeletal.png, L-Methionine
(Met / M) image:L-phenylalanine-skeletal.png, L-Phenylalanine
(Phe / F) image:L-proline-skeletal.png, L-Proline
(Pro / P) image:L-serine-skeletal.png, L-Serine
(Ser / S) image:L-threonine-skeletal.png, L-Threonine
(Thr / T) image:L-tryptophan-skeletal.png, L-Tryptophan
(Trp / W) image:L-tyrosine-skeletal.png, L-Tyrosine
(Tyr / Y) image:L-valine-skeletal.png, L-Valine
(Val / V)
IUPAC The International Union of Pure and Applied Chemistry (IUPAC ) is an international federation of National Adhering Organizations working for the advancement of the chemical sciences, especially by developing nomenclature and terminology. It is ...
/ IUBMB now also recommends standard abbreviations for the following two amino acids: image:L-selenocysteine-2D-skeletal.png, L-Selenocysteine
(Sec / U) image:Pyrrolysine.svg, L-Pyrrolysine
(Pyl / O)


Chemical properties

Following is a table listing the one-letter symbols, the three-letter symbols, and the chemical properties of the side chains of the standard amino acids. The masses listed are based on weighted averages of the elemental
isotope Isotopes are two or more types of atoms that have the same atomic number (number of protons in their nuclei) and position in the periodic table (and hence belong to the same chemical element), and that differ in nucleon numbers ( mass num ...
s at their natural abundances. Forming a
peptide bond In organic chemistry, a peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another, along a peptide or protein cha ...
results in elimination of a molecule of
water Water (chemical formula ) is an inorganic, transparent, tasteless, odorless, and nearly colorless chemical substance, which is the main constituent of Earth's hydrosphere and the fluids of all known living organisms (in which it acts as ...
. Therefore, the protein's mass is equal to the mass of amino acids the protein is composed of minus 18.01524 Da per peptide bond.


General chemical properties


Side-chain properties

§: Values for Asp, Cys, Glu, His, Lys & Tyr were determined using the amino acid residue placed centrally in an alanine pentapeptide. The value for Arg is from Pace ''et al.'' (2009). The value for Sec is from Byun & Kang (2011). N.D.: The pKa value of Pyrrolysine has not been reported. Note: The pKa value of an amino-acid residue in a small peptide is typically slightly different when it is inside a protein.
Protein pKa calculations In computational biology, protein p''K''a calculations are used to estimate the p''K''a values of amino acids as they exist within proteins. These calculations complement the p''K''a values reported for amino acids in their free state, and are us ...
are sometimes used to calculate the change in the pKa value of an amino-acid residue in this situation.


Gene expression and biochemistry

* UAG is normally the amber stop codon, but in organisms containing the biological machinery encoded by the pylTSBCD cluster of genes the amino acid pyrrolysine will be incorporated.
** UGA is normally the opal (or umber) stop codon, but encodes selenocysteine if a
SECIS element In biology, the SECIS element (SECIS: ''selenocysteine insertion sequence'') is an RNA element around 60 nucleotides in length that adopts a stem-loop structure. This structural motif (pattern of nucleotides) directs the cell to translate UGA ...
is present.
The
stop codon In molecular biology (specifically protein biosynthesis), a stop codon (or termination codon) is a codon (nucleotide triplet within messenger RNA) that signals the termination of the translation process of the current protein. Most codons in mess ...
is not an amino acid, but is included for completeness.
†† UAG and UGA do not always act as stop codons (see above).
An essential amino acid cannot be synthesized in humans and must, therefore, be supplied in the diet. Conditionally essential amino acids are not normally required in the diet, but must be supplied
exogenously In a variety of contexts, exogeny or exogeneity () is the fact of an action or object originating externally. It contrasts with endogeneity or endogeny, the fact of being influenced within a system. Economics In an economic model, an exogen ...
to specific populations that do not synthesize it in adequate amounts.
& Occurrence of amino acids is based on 135 Archaea, 3775 Bacteria, 614 Eukaryota proteomes and human proteome (21 006 proteins) respectively.


Mass spectrometry

In
mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a '' mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is u ...
of peptides and proteins, knowledge of the masses of the residues is useful. The mass of the peptide or protein is the sum of the residue masses plus the mass of
water Water (chemical formula ) is an inorganic, transparent, tasteless, odorless, and nearly colorless chemical substance, which is the main constituent of Earth's hydrosphere and the fluids of all known living organisms (in which it acts as ...
(
Monoisotopic mass Monoisotopic mass (Mmi) is one of several types of molecular masses used in mass spectrometry. The theoretical monoisotopic mass of a molecule is computed by taking the sum of the accurate masses (including mass defect) of the most abundant natur ...
= 18.01056 Da; average mass = 18.0153 Da). The residue masses are calculated from the tabulated chemical formulas and atomic weights. In
mass spectrometry Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a '' mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is u ...
, ions may also include one or more
protons A proton is a stable subatomic particle, symbol , H+, or 1H+ with a positive electric charge of +1 ''e'' elementary charge. Its mass is slightly less than that of a neutron and 1,836 times the mass of an electron (the proton–electron m ...
(
Monoisotopic mass Monoisotopic mass (Mmi) is one of several types of molecular masses used in mass spectrometry. The theoretical monoisotopic mass of a molecule is computed by taking the sum of the accurate masses (including mass defect) of the most abundant natur ...
= 1.00728 Da; average mass* = 1.0074 Da). *Protons cannot have an average mass, this confusingly infers to Deuterons as a valid isotope, but they should be a different species (see
Hydron (chemistry) In chemistry, the hydron, informally called proton, is the cationic form of atomic hydrogen, represented with the symbol . The general term "hydron", endorsed by the IUPAC, encompasses cations of hydrogen regardless of their isotopic composition ...
) §
Monoisotopic mass Monoisotopic mass (Mmi) is one of several types of molecular masses used in mass spectrometry. The theoretical monoisotopic mass of a molecule is computed by taking the sum of the accurate masses (including mass defect) of the most abundant natur ...


Stoichiometry and metabolic cost in cell

The table below lists the abundance of amino acids in ''E.coli'' cells and the metabolic cost (ATP) for synthesis of the amino acids. Negative numbers indicate the metabolic processes are energy favorable and do not cost net ATP of the cell. The abundance of amino acids includes amino acids in free form and in polymerization form (proteins).


Remarks


Catabolism

Amino acids can be classified according to the properties of their main products: * Glucogenic, with the products having the ability to form
glucose Glucose is a simple sugar with the molecular formula . Glucose is overall the most abundant monosaccharide, a subcategory of carbohydrates. Glucose is mainly made by plants and most algae during photosynthesis from water and carbon dioxide, u ...
by
gluconeogenesis Gluconeogenesis (GNG) is a metabolic pathway that results in the generation of glucose from certain non- carbohydrate carbon substrates. It is a ubiquitous process, present in plants, animals, fungi, bacteria, and other microorganisms. In verteb ...
* Ketogenic, with the products not having the ability to form glucose: These products may still be used for
ketogenesis Ketogenesis is the biochemical process through which organisms produce ketone bodies by breaking down fatty acids and ketogenic amino acids. The process supplies energy to certain organs, particularly the brain, heart and skeletal muscle, under ...
or lipid synthesis. * Amino acids catabolized into both glucogenic and ketogenic products


See also

*
Glucogenic amino acid A glucogenic amino acid (or glucoplastic amino acid) is an amino acid that can be converted into glucose through gluconeogenesis. This is in contrast to the ketogenic amino acids, which are converted into ketone bodies. The production of glucos ...
*
Ketogenic amino acid A ketogenic amino acid is an amino acid that can be degraded directly into acetyl-CoA, which is the precursor of ketone bodies and myelin, particularly during early childhood, when the developing brain requires high rates of myelin synthesis. Th ...


References


General references

* * * *


External links


The origin of the single-letter code for the amino acids
{{Amino acids Nitrogen cycle Nutrition