Amino acids

Most of the approximately 500 known amino acids were discovered after 1953, for example, during the search for new antibiotics among microorganisms, fungi, seeds, plants, fruits, and animal fluids. About 240 of them are found in nature in free form, and the rest only as intermediate elements of metabolism. ^[one]

Discovery of amino acids in proteins

Essential Amino Acids Bold

In physical properties, amino acids differ sharply from the corresponding acids and bases. All of them are crystalline substances, better soluble in water than in organic solvents, have fairly high melting points; many of them have a sweet taste. These properties clearly indicate the salt-like nature of these compounds. Features of the physical and chemical properties of amino acids are due to their structure - the presence of two functional groups that are opposite in properties: acidic and basic .

All amino acids are amphoteric compounds; they can exhibit both acidic properties due to the presence of a carboxyl group in their molecules — C O O H , and the main properties due to the amino group — N H ₂ . Amino acids interact with acids and alkalis :

N H ₂ - C H ₂ - C O O H + H Cl → H Cl • N H ₂ - C H ₂ - C O O H ( Hydrogen chloride glycine )

N H ₂ - C H ₂ - C O O H + Na O H → H ₂ O + N H ₂ - C H ₂ - C O O Na ( glycine sodium)

Due to this, solutions of amino acids in water possess the properties of buffer solutions , that is, they are in the state of internal salts.

N H ₂ - C H ₂ C O O H   N ⁺ H ₃ - C H ₂ C O O ^-

Amino acids can usually enter into all reactions characteristic of carboxylic acids and amines .

Esterification :

N H ₂ - C H ₂ - C O O H + C H ₃ O H → H ₂ O + N H ₂ - C H ₂ - C O O C H ₃ (glycine methyl ester)

An important feature of amino acids is their ability to polycondensate , leading to the formation of polyamides , including peptides , proteins , nylon , nylon .

Peptide formation reaction:

H O O C - C H ₂ - N H - H + H O O C - C H ₂ - N H ₂ → H O O C - C H ₂ - N H - C O - C H ₂ - N H ₂ + H ₂ O

The isoelectric point of an amino acid is the pH value at which the maximum proportion of amino acid molecules has zero charge. At this pH, the amino acid is the least mobile in the electric field, and this property can be used to separate amino acids, as well as proteins and peptides .

A zwitterion is an amino acid molecule in which the amino group is represented as -NH ₃ ⁺ and the carboxy group is represented as -COO ^- . Such a molecule has a significant dipole moment at zero total charge. It is from these molecules that the crystals of most amino acids are built.

Some amino acids have several amino groups and carboxyl groups. For these amino acids, it is difficult to talk about any particular zwitterion .

Most amino acids can be obtained during the hydrolysis of proteins or as a result of chemical reactions:

C H ₃ C O O H + Cl ₂ + (catalyst) → C H ₂ Cl C O O H + H Cl ; C H ₂ Cl C O O H + 2 N H ₃ → N H ₂ - C H ₂ C O O H + N H ₄ Cl

All α-amino acids that are part of living organisms, except glycine , contain an asymmetric carbon atom ( threonine and isoleucine contain two asymmetric atoms) and have optical activity. Almost all naturally-occurring α-amino acids have an L-configuration, and only L-amino acids are included in the protein synthesized on ribosomes .

Asparagine residues in metabolically inactive structural proteins undergo slow spontaneous non-enzymatic racemization: in dentin and tooth enamel proteins, L-aspartate transforms into D-form at a rate of ~ 0.1% per year ^[4] , which can be used to determine the age of mammals. Racemization of aspartate is also noted in aging collagen ; It is assumed that such racemization is specific for aspartic acid and proceeds due to the formation of a succinimide ring during intramolecular acylation of the nitrogen atom of the peptide bond with the free carboxyl group of aspartic acid ^[5] .

With the development of trace amino acid analysis, D-amino acids were first found in the cell walls of certain bacteria ( 1966 ), and then in the tissues of higher organisms. ^[6] Thus, D-aspartate and D-methionine are presumably neurotransmitters in mammals ^[7] .

The composition of some peptides includes D-amino acids formed during post-translational modification . For example, D-methionine and D-alanine are part of the skin opioid heptapeptides of the South American amphibian phylomedusa ( dermorphin , dermenkefalin and deltorfins ). The presence of D-amino acids determines the high biological activity of these peptides as analgesics .

Peptide antibiotics of bacterial origin are formed in a similar way, acting against gram-positive bacteria - nisin , subtilin and epidermine. ^[8]

More often, D-amino acids are part of peptides and their derivatives, which are formed by non-ribosomal synthesis in the cells of fungi and bacteria. Apparently, in this case, the starting material for the synthesis is also L-amino acids, which are isomerized by one of the subunits of the enzyme complex that performs the synthesis of the peptide .

During protein biosynthesis, 20 α-amino acids encoded by the genetic code are included in the polypeptide chain. In addition to these amino acids, called proteinogenic , or standard , in some proteins there are specific non-standard amino acids that arise from the standard in the process of post-translational modifications. Recently, translationally included selenocysteine (Sec, U) and pyrrolysin (Pyl, O) are sometimes assigned to proteinogenic amino acids. ^{[9] [10]} These are the so-called 21st and 22nd amino acids. ^[eleven]

The question why exactly these 20 amino acids became “chosen” remains unresolved ^[12] . We look at the solution to this issue in ^[13] . It is not clear what these amino acids were preferable to other similar. For example, the α-amino acid homoserine is a key intermediate metabolite of the biosynthesis pathway of threonine , isoleucine and methionine . Obviously, homoserine is a very ancient metabolite , but for threonine , isoleucine and methionine there are aminoacyl-tRNA synthetases , tRNA , but not for homoserine.

The structural formulas of 20 proteinogenic amino acids are usually given in the form of a so-called table of proteinogenic amino acids :

Classification

By radical

• Nonpolar: glycine , alanine , valine , isoleucine , leucine , proline
• Polar uncharged (charges are compensated) at pH = 7: serine , threonine , cysteine , methionine , asparagine , glutamine
• Aromatic: phenylalanine , tryptophan , tyrosine
• Polar charged negatively at pH = 7: aspartate , glutamate
• Polar charged positively at pH = 7: lysine , arginine , histidine ^[16]

By Functional Group

• Aliphatic
  • Monoamine monocarboxylic: glycine , alanine, valine , isoleucine , leucine
  • Oxymonoamino Carboxylic: Serine , Threonine
  • Monoaminodicarboxylic: aspartate , glutamate , due to the second carboxyl group carry a negative charge in solution
  • Monoaminodicarboxylic amides: asparagine , glutamine
  • Diaminomonocarboxylic: lysine , arginine , carry a positive charge in solution
  • Sulfur-containing: cysteine , methionine
• Aromatic : phenylalanine, tyrosine, tryptophan,
• Heterocyclic : tryptophan, histidine, proline
• Imino Acids: Proline

By classes of aminoacyl-tRNA synthetases

• Class I: Valine , Isoleucine , Leucine , Cysteine , Methionine , Glutamate , Glutamine , Arginine , Tyrosine, Tryptophan
• Class II: glycine , alanine, proline , serine , threonine , aspartate , asparagine , histidine , phenylalanine

For the amino acid lysine, there are aminoacyl-tRNA synthetases of both classes.

Pathways of biosynthesis

The pathways of biosynthesis of proteinogenic amino acids are diverse. The same amino acid can be formed in different ways. In addition, completely different paths can have very similar steps. Nevertheless, there are justified attempts to classify amino acids according to their biosynthesis pathways . There is an idea of ​​the following biosynthetic families of amino acids: aspartate , glutamate , serine , pyruvate and pentose . Not always a specific amino acid can be unambiguously attributed to a particular family; corrections are made for specific organisms and given the prevailing path. Amino acids are usually distributed among families as follows:

• Aspartate family: aspartate , asparagine , threonine , isoleucine , methionine , lysine .
• Glutamate family: glutamate , glutamine , arginine , proline .
• Pyruvate family: alanine, valine , leucine .
• Serine family: serine , cysteine , glycine .
• Pentos family: histidine , phenylalanine, tyrosine, tryptophan .

Phenylalanine, tyrosine, tryptophan are sometimes isolated in the shikimat family .

By the ability of the body to synthesize from its predecessors

• Irreplaceable

  For most animals and humans, essential amino acids are: valine , isoleucine , leucine , threonine , methionine , lysine , phenylalanine , tryptophan .

• Interchangeable

  Replaceable amino acids for most animals and humans are: glycine , alanine , proline , serine , cysteine , aspartate , asparagine , glutamate , glutamine , tyrosine .

The classification of amino acids as interchangeable and irreplaceable is not without drawbacks. For example, tyrosine is an essential amino acid only if phenylalanine is sufficiently supplied. For patients with phenylketonuria, tyrosine becomes an essential amino acid. Arginine is synthesized in the human body and is considered a replaceable amino acid, but in connection with some features of its metabolism under certain physiological conditions of the body, it can be equated with irreplaceable ones. Histidine is also synthesized in the human body, but not always in sufficient quantities, therefore it must be supplied with food.

By the nature of catabolism in animals

Biodegradation of amino acids can go in different ways.

According to the nature of catabolism products in animals, proteinogenic amino acids are divided into three groups:

• Glucogenic - upon decomposition, they produce metabolites that do not increase the level of ketone bodies , which can relatively easily become a substrate for gluconeogenesis : pyruvate , α-ketoglutarate , succinyl-KoA, fumarate , oxaloacetate
• Ketogenic - break down to acetyl-KoA and acetoacetyl-KoA, which increase the level of ketone bodies in the blood of animals and humans and are converted primarily into lipids
• Glucose-ketogenic - metabolites of both types are formed during decay

Amino acids:

• Glucogenic: glycine , alanine, valine , proline , serine , threonine , cysteine , methionine , aspartate , asparagine , glutamate , glutamine , arginine , histidine .
• Ketogenic: leucine , lysine .
• Glucose-ketogenic (mixed): isoleucine , phenylalanine, tyrosine , tryptophan .

Miller Amino Acids

"Miller" amino acids - the generalized name for amino acids obtained under conditions close to the 1953 Stanley L. Miller experiment . The formation of many different amino acids in the form of a racemate has been established, including: glycine , alanine, valine , isoleucine , leucine , proline , serine , threonine , aspartate , glutamate

In medicine, a number of substances capable of performing some biological functions of amino acids are also (although not quite true) called amino acids:

• Taurine

An important feature of amino acids is their ability to polycondensate , leading to the formation of polyamides , including peptides , proteins , nylon , nylon , enanth . ^[19]

Amino acids are part of sports nutrition and animal feed . Amino acids are used in the food industry as flavoring agents , for example, the sodium salt of glutamic acid . ^[twenty]

• Amino Acid Fund
• Triarangucaricalitin
• Codon
• Peptide bond
• Broadcast (biology)
• Essential Amino Acids

• Miller-Urey experiments and discussions:
  • Miller SL Production of amino acids under possible primitive earth conditions. Science, v. 117, May 15, 1953
  • Miller SL and HC Urey. Organic compound synthesis on the primitive earth. Science, v. 130, July 31, 1959
  • Miller Stanley L. and Leslie E. Orgel. The origins of life on the earth. Englewood Cliffs, NJ, Prentice-Hall, 1974.
• General biology. Textbook for grades 9-10 of high school. Ed. Yu. I. Polyansky. Ed. 17th, rev. - M .: Education, 1987 .-- 288s.
• Amino acids, peptides, proteins. Ed. Yu. V. Mitina

• Amino acids // Brockhaus and Efron Encyclopedic Dictionary : in 86 volumes (82 volumes and 4 additional). - SPb. , 1890-1907.
• Amino acids in chemistry
• N. S. Entelis Aminoacyl-tRNA synthetases: two classes of enzymes // Soros Educational Journal, 1998, No. 9, p. 14-21