What are Amino acids?

jpt mascot with peptideAmino acids (aa) are the fundamental building blocks of proteins, essential for the structure, function, and regulation of biological systems. All amino acids contain an amino group (-NH2) and a carboxyl group (-COOH). In alpha-amino acids (α-amino acids), the two functional groups are bound to a central carbon atom known as the alpha carbon. At the alpha carbon is also a hydrogen atom and a variable side chain, often referred to as the R-group, which gives each amino acid its unique chemical properties.

1. The 22 Proteinogenic Amino Acids

Hundreds of amino acids exist in nature, but only 22 are proteinogenic amino acids encoded by the genetic code (20 standard aa plus selenocysteine and pyrrolysine), each with distinct chemical and physical characteristics. 

These amino acids are alpha amino acids and classified based on the properties of their R-groups:

Nonpolar, hydrophobic amino acids 

Nonpolar amino acids have R-groups that are mostly composed of hydrocarbons and are hydrophobic. Examples include glycine (Gly), alanine (Ala), valine (Val), leucine (Leu), isoleucine (Ile), proline (Pro), methionine (Met), and phenylalanine (Phe).

Polar, uncharged amino acids 

Polar amino acids have R-groups that contain polar functional groups but do not ionize under physiological conditions. Examples include serine (Ser), threonine (Thr), cysteine (Cys), asparagine (Asn), and glutamine (Gln).

Positively charged (basic) amino acids 

Basic amino acids have R-groups that contain positively charged functional groups, which can form ionic bonds with negatively charged groups. Examples include lysine (Lys), arginine (Arg), and histidine (His). Often charged side chains appear at the protein surface to enable solubility in water. Neighboring side chains with positive and negative charges can form electrostatic contacts called salt bridges that maintain structures within a single protein or between interfacing proteins.

Negatively charged (acidic) amino acids 

 Acidic amino acids have R-groups that contain negatively charged functional groups, which can form ionic bonds with positively charged groups. Examples include aspartic acid (Asp) and glutamic acid (Glu). Some proteins use charged side chains to bind metals that are important for the proteins function.

Amino Acid Chart

Amino Acid Chart

Download Amino Acid Chart as PDF:  Download

Amino Acid Table

3-letter code
1-letter code
Molecular formula
Molecular weight
pKa α-COOH
pKa α-NH3+
pKa side chain
Isoelectric point (pI)
Alanine Ala A C3H7N1O2 89,09 2,35 9,87 6,01 non-polar, uncharged GCU,GCC,GCA,GCG
Arginine Arg R C6H14N4O2 174,2 1,82 8,99 12,48 10,76 basic CGU,CGC,CGA, CGG,AGA,AGG
Asparagine Asn N C4H8N2O3 132,12 2,14 8,72 5,41 polar, uncharged AAU, AAC
Aspartaic acid Asp D C4H7N1O4 133,1 1,99 9,90 3,65 2,85 acidic GAU, GAC
Cysteine Cys C C3H7N1O2S1 121,16 1,92 10,70 8,18 5,05 polar, uncharged UGU, UGC
Glutamic Acid Glu E C5H9N1O4 147,13 2,10 9,47 4,25 3,15 acidic GAA, GAG
Glutamine Gln Q C5H10N2O3 146,15 2,17 9,13 5,65 polar, uncharged CAA, CAG
Glycine Gly G C2H5N1O2 75,07 2,35 9,78 6,06 polar, uncharged GGU, GGC, GGA, GGG
Histidine His H C6H9N3O2 155,16 1,80 9,33 6,0 7,60 basic CAU, CAC
Isoleucine Ile I C6H13N1O2 131,17 2,32 9,76 6,05 non-polar, uncharged AUU, AUC, AUA
Leucine Leu L C6H13N1O2 131,17 2,33 9,74 6,01 non-polar, uncharged UUA, UUG, CUU, CUC, CUA, CUG
Lysine Lys K C6H14N2O2 146,19 2,16 9,06 10,53 9,60 basic AAA, AAG
Methionine Met M C5H11N1O2S1 149,21 2,13 9,28 5,74 non-polar, uncharged AUG
Phenylalanine Phe F C9H11N1O2 165,19 2,20 9,31 5,49 non-polar, uncharged UUU, UUC
Proline Pro P C5H9N1O2 115,13 1,95 10,64 6,30 non-polar, uncharged CCU, CCC, CCA, CCG
Pyrrolysine Pyl O C12H21N3O3 255,31 na na na na basic UAG
Selenocysteine Sec U C3H7N1O2Se1 168,05 1,91 10,00 5,43 5,47 polar UGA
Serine Ser S C3H7N1O3 105,09 2,21 9,15 5,68 polar, uncharged UCU, UCC, UCA, UCG, AGU, AGC
Threonine Thr T C4H9N1O3 119,12 2,09 9,10 5,60 polar, uncharged ACU, ACC, ACA, ACG
Tryptophan Trp W C11H12N2O2 204,23 2,46 9,41 5,89 non-polar, uncharged UGG
Tyrosine Tyr Y C9H11N1O3 181,19 2,20 9,21 10,07 5,64 polar, uncharged UAU, UAC
Valine Val V C5H11N1O2 117,15 2,39 9,74 6,00 non-polar, uncharged GUU, GUC, GUA, GUG

Download Amino Acid Table as PDF:  Download

2. Non-Proteinogenic Amino Acids

Unusual or non-proteinogenic amino acids (aa) are distinct from the 22 proteinogenic amino acids that are naturally encoded in the genome for protein biosynthesis. More than 140 non-proteinogenic amino acids naturally occur in proteins. They play significant biological roles as intermediates in biosynthesis, in post-translational modification of proteins, as components of bacterial cell walls, and as neurotransmitters or toxins. 

There are different groups of natural non-proteinogenic amino acids:

Non-alpha amino acids

The amino group is located not at α carbon but second or third carbon. Examples are β-alanine and GABA (γ-aminobutyric acid).

D-amino acids

D-amino acids are of opposite chirality than the standard L-amino acids, which is the case D-alanine and D-glutamate contained in bacterial peptidoglycan.

Amino acids with no hydrogen at α carbon 

These occur in fungal aminoisobutyric acid or in dehydroamino acids whereas all proteinogenic amino acids have at least one hydrogen at the α-arbon.

Amino acids with two stereocenters

Two stereocenters will emerge when two amino acids crosslink for example if two cysteine residues form a disulfide bond to form cysteine.

Amino acid variants

Straight side chain variants occur on homoalanine, norvaline and norleucine. Variations of serine, and cysteine are homoserine, homocysteine, selenocysteine, selenohomocysteine, selenomethionine.

Post-translational modified amino acids (PTMs)

Some non-proteinogenic amino acids are nevertheless found in proteins because they are post-translationally modified variants of proteinogenic amino acids. Examples are hydroxyproline, phosphorylated aa and hypusine. 

These non-proteinogenic amino acids can be incorporated into peptides during custom peptide synthesis for all kinds of applications. In addition to the commercially available amino acids, we are able to synthesize a wide range of amino acids that are not commercially available. Please inquire about your specific requirements.

3. Unnatural Amino Acids

Besides the naturally occurring amino acids (both proteinogenic and non-proteinogenic) thousands more can be chemically synthesized. They have proven to be powerful tools in peptide synthesis, offering researchers unprecedented control over peptide structure and function. These unnatural amino acids (UAAs) are often modifications of their native analogues with a versatility of unique chemical properties, which can introduce novel functionalities and structural motifs into peptides.

Unnatural amino acids are incorporated into custom peptides for various purposes, such as increasing activity, selectivity, or plasma stability of peptides, for example to be used as inhibitors in drug discovery projects. They are also useful for investigating the structure and dynamics of proteins, to study protein interactions, or to modulate the activity of proteins in living cells. In materials science, peptides containing unnatural amino acids are used to design functional biomaterials with tailored mechanical, electrical, or optical properties. 

Unnatural amino acids can be classified into several categories based on their structural features, including non-natural side chains, modified backbone structures, and non-proteinogenic amino acids derived from natural sources or synthesized de novo. Commonly used unnatural amino acids include 

  • D-amino acids
  • homo amino acids
  • N-methyl amino acids
  • alpha-methyl amino acids
  • beta (homo) amino acids
  • gamma amino acids
  • helix/turn stabilizing motifs
  • backbone modifications (such as peptoids). 

peptide synthesis, unnatural amino acids are typically introduced using solid-phase peptide synthesis (SPPS), where they are incorporated into the growing peptide chain alongside natural amino acids. This process allows for precise control over the sequence and composition of the resulting peptide, enabling the creation of peptides with tailored properties for various applications. 

In addition to the readily available amino acids, we can also synthesize a wide range of non-commercial amino acids for the synthesis of modified peptides. Please request a quote for your specific peptide sequence! Our peptide library service allows the incorporation of up to 200 unnatural amino acids per synthesis run, enabling the rapid generation of large combinatorial peptide libraries.

4. Chirality in Amino Acids

JPT mascot chiralityIn proteinogenic amino acids, the α–carbon is bound to the carboxyl and amino groups as well as the R group or side chain specific to each amino acid and an hydrogen atom. With these four different groups at the α–carbon all α-amino acids are chiral except glycine (which has a second hydrogen as side chain), which means that there are two versions of a molecule that cannot by any rotation or translation be made to cover its mirror image (like our two hands). Amino acids can exist in the L and the D confirmation but all chiral proteogenic amino acids have the L configuration. However, some D-amino acids exist in nature, e.g. in bacteria, as a neuromodulator (D-serine), and in some antibiotics.

5. Amino acids in proteins

The amino acid sequence of a protein determines its three-dimensional structure and its function. Many proteins are subject to post-translational modifications, such as phosphorylation, acetylation, and glycosylation, which may change their structure and functions. Amino acids are not only the building blocks of proteins, but some are also precursors for neurotransmitters (e.g., serotonin, dopamine), signaling molecules (e.g., nitric oxide), and metabolic intermediates (e.g., α-ketoglutarate, oxaloacetate).

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