Amino acid? |
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In chemistry, an amino acid is any molecule that contains both amino and carboxylic acid functional groups. In biochemistry, this shorter and more general term is frequently used to refer to alpha amino acids: those amino acids in which the amino and carboxylate functionalities are attached to the same carbon.
Amino acid residue is what is left of an amino acid once a water molecule has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond .
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Overview
Amino acids are the basic structural building units of proteins. They form short polymer chains called peptides or polypeptides which in turn form structures called proteins.
Twenty amino acids are encoded by the standard genetic code and are called proteinogenic or standard amino acids. Rarer, more complicated ones are produced by the body and are called nonstandard. Proline is the only proteinogenic amino acid whose side group is cyclic and links to the a-amino group, forming a secondary amino group. Formerly, proline was misleadingly called an imino acid. Other amino acids contained in proteins are usually formed by post-translational modification, that is modification after translation (protein synthesis). These modifications are often essential for the function of the protein. At least two amino acids other than the standard 20 are sometimes incorporated into proteins during translation:
- Selenocysteine is incorporated into some proteins at a UGA codon, which is normally a stop codon.
- Pyrrolysine is used by some methanogens in enzymes that they use to produce methane. It is coded for similarity to selenocysteine but with the codon UAG instead.
Although only 20 amino acids are genetically coded, over 100 have been found in nature. Some of these have been detected in meteorites, especially in a type known as carbonaceous chondrites. Microorganisms and plants often produce very uncommon amino acids, which can be found in peptidic antibiotics (e.g. nisin or alamethicin). Lanthionine is a sulfide-bridged alanine dimer which is found together with unsaturated amino acids in lantibiotics (antibiotic peptides of microbial origin). 1-Aminocyclopropane-1-carboxylic acid (ACC) is a small disubstituted cyclic amino acid and a key intermediate in the production of the plant hormone ethylene.
In addition to protein synthesis, amino acids have other biologically important roles. Glycine, and glutamate, are used both as neurotransmitters and as standard amino acids in proteins. Many amino acids are used to synthesize other molecules, such as tryptophan which is a precursor of the neurotransmitter serotonin, and glycine which is one of the reactants in the synthesis of porphyrins such as heme. Numerous non-standard amino acids are also biologically important: GABA (another neurotransmitter), carnitine (used in lipid transport within a cell), ornithine, citrulline, homocysteine, hydroxyproline, hydroxylysine, and sarcosine.
Some of the 20 standard amino acids are called essential amino acids, because they cannot be synthesized by the body from other compounds through chemical reactions, but instead must be taken in with food. In humans, the essential amino acids are lysine, leucine, isoleucine, methionine, phenylalanine, threonine, tryptophan, valine, and (in children) histidine and arginine.
General structure
The general structure of proteinogenic alpha amino acids is:
COOH | H-C-R | NH2
Where "R" represents a side chain specific to each amino acid. Amino acids are usually classified by properties of the side chain into four groups: acidic, basic, hydrophilic (polar), and hydrophobic (nonpolar).
Isomerism
Except for glycine, where R = H, amino acids occur in two possible optical isomers, called D and L. The L amino acids represent the vast majority of amino acids found in proteins. D amino acids are found in some proteins produced by exotic sea-dwelling organisms, such as cone snails. They are also abundant components of the cell walls of bacteria.
Reactions
Proteins are created by polymerization of amino acids by peptide bonds in a process called translation.
1. Amino acid; 2, zwitterion structure; 3, two amino acids forming a peptide bond. (See also bond.)
List of standard amino acids
Structures
Structures and symbols of the 20 amino acids present in genetic code.
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 one letter symbol for an undetermined amino acid is X. The three letter symbol Asx or one letter symbol B means the amino acid is either asparagine or aspartic acid, while Glx or Z means either glutamic acid or glutamine.
| Abbrev. | Full Name | Side chain type | Mass | pI | pK1 (α-COOH) |
pK2 (α-+NH3) |
pKr (R) | Remarks | |
|---|---|---|---|---|---|---|---|---|---|
| A | Ala | Alanine | hydrophobic | 89.09 | 6.11 | 2.35 | 9.87 | Very abundant, very versatile. More stiff than glycine, but small enough to pose only small steric limits for the protein conformation. It behaves fairly neutral, can be located in both hydrophilic regions on the protein outside and the hydrophobic areas inside. | |
| C | Cys | Cysteine | hydrophobic (Nagano, 1999) | 121.16 | 5.05 | 1.92 | 10.70 | 8.37 | Under oxidizing conditions, two cysteines can join together by a disulfide bond to form the amino acid cystine. When cysteines are part of a protein, insulin for example, this enforces tertiary structure and makes the protein more resistant to unfolding and denaturation; cysteine bridges are therefore common in proteins that have to function in harsh environments - digestive enzymes (eg. pepsin and chymotrypsin) or structural proteins (eg. keratin), and proteins too small to hold their shape on their own, eg. insulin. The sulfur atom binds readily to heavy metal ions. |
| D | Asp | Aspartic acid | acidic | 133.10 | 2.85 | 1.99 | 9.90 | 3.90 | Behaves similar to glutamic acid. Carries hydrophilic acidic group with strong negative charge. Usually is located on the outer surface of the protein, making it water soluble. Binds to positively charged molecules and ions, often used in enzymes to fix the metal ion. When located inside of the protein, aspartate and glutamate are usually paired with arginine and lysine. |
| E | Glu | Glutamic acid | acidic | 147.13 | 3.15 | 2.10 | 9.47 | 4.07 | Behaves similar to aspartic acid. Has longer, slightly more flexible side chain. |
| F | Phe | Phenylalanine | hydrophobic | 165.19 | 5.49 | 2.20 | 9.31 | Essential for humans. Phenylalanine, tyrosine, and tryptophan contain large rigid aromatic group on the side chain. These are the biggest aminoacids. Like isoleucine, leucine and valine, these are hydrophobic and tend to orient towards the interior of the folded protein molecule. | |
| G | Gly | Glycine | hydrophilic | 75.07 | 6.06 | 2.35 | 9.78 | Because of the two hydrogen atoms at the α carbon, glycine is not optically active. It is the tiniest amino acid, rotates easily, adds flexibility to the protein chain. It is able to fit into the tightest spaces, eg. the triple helix of collagen. As too much flexibility is usually not desired, as a structural component it is less common than alanine. | |
| H | His | Histidine | basic | 155.16 | 7.60 | 1.80 | 9.33 | 6.04 | In even slightly acidic conditions protonation of the nitrogen occurs, changing the properties of histidine and the polypeptide as a whole. It is used by many proteins as a regulatory mechanism, changing the conformation and behavior of the polypeptide in acidic regions such as the late endosome or lysosome, enforcing conformation change in enzymes. However only a few histidines are needed for this, so it is comparatively scarce. |
| I | Ile | Isoleucine | hydrophobic | 131.17 | 6.05 | 2.32 | 9.76 | Essential for humans. Isoleucine, leucine and valine have large aliphatic hydrophobic side chains. Their molecules are rigid, and their mutual hydrophobic interactions are important for the correct folding of proteins, as these chains tend to be located inside of the protein molecule. | |
| K | Lys | Lysine | basic | 146.19 | 9.60 | 2.16 | 9.06 | 10.54 | Essential for humans. Behaves similar to arginine. Contains a long flexible chain with positively charged end. The flexibility of the chain makes lysine and arginine suitable for binding to molecules with many negative charges on their surfaces. Eg, DNAinding proteins have their active regions rich with arginine and lysine. The strong charge makes these two aminoacids prone to be located on the outer hydrophilic surfaces of the proteins; when they are found inside, they are usually paired with a corresponding negatively charged aminoacid, eg. aspartate or glutamate. |
| L | Leu | Leucine | hydrophobic | 131.17 | 6.01 | 2.33 | 9.74 | Essential for humans. Behaves similar to isoleucine and valine. See isoleucine. | |
| M | Met | Methionine | hydrophobic | 149.21 | 5.74 | 2.13 | 9.28 | Essential for humans. Always the first amino acid to be incorporated into a protein; sometimes removed after translation. Like cysteine, contains sulfur, but with methyl group instead of hydrogen. This methyl group can be activated, and is used in many reactions where a new carbon atom is being added to another molecule. | |
| N | Asn | Asparagine | hydrophilic | 132.12 | 5.41 | 2.14 | 8.72 | Neutralized version of aspartic acid. | |
| P | Pro | Proline | hydrophobic | 115.13 | 6.30 | 1.95 | 10.64 | Contains an unusual ring to the N-end amine group, which forces the CO-NH amide sequence into a fixed conformation. Can disrupt protein folding structures like α helix or β sheet, forcing the desired kink in the protein chain. Common in collagen, where it undergoes a posttranslational modification to hydroxyproline. Uncommon elsewhere. | |
| Q | Gln | Glutamine | hydrophilic | 146.15 | 5.65 | 2.17 | 9.13 | Neutralized version of glutamic acid. Used in proteins and as a storage for ammonia. | |
| R | Arg | Arginine | basic | 174.20 | 10.76 | 1.82 | 8.99 | 12.48 | Functionally similar to lysine. |
| S | Ser | Serine | hydrophilic | 105.09 | 5.68 | 2.19 | 9.21 | Serine and threonine have a short group ended with a hydroxyl group. Its hydrogen is easy to remove, so serine and threonine often act as hydrogen donors in enzymes. Both are very hydrophylic, therefore the outer regions of soluble proteins tend to be rich with them. | |
| T | Thr | Threonine | hydrophilic | 119.12 | 5.60 | 2.09 | 9.10 | Essential for humans. Behaves similar to serine. | |
| V | Val | Valine | hydrophobic | 117.15 | 6.00 | 2.39 | 9.74 | Essential for humans. Behaves similar to isoleucine and leucine. See isoleucine. | |
| W | Trp | Tryptophan | hydrophobic | 204.23 | 5.89 | 2.46 | 9.41 | Essential for humans. Behaves similar to phenylalanine and tyrosine (see phenylalanine). Precursor of serotonin. | |
| Y | Tyr | Tyrosine | hydrophobic | 181.19 | 5.64 | 2.20 | 9.21 | 10.46 | Behaves similar to phenylalanine and tryptophan (see phenylalanine). Precursor of melanin, epinephrine, and thyroid hormones. |
| Amino acid | Abbrev. | Side chain | Hydro- phobic | Polar | Charged | Small | Tiny | Aromatic or Aliphatic | van der Waals volume | Codon | Occurrence in proteins (%) |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Alanine | Ala, A | -CH3 | X | - | - | X | X | - | 67 | GCU, GCC, GCA, GCG | 7.8 |
| Cysteine | Cys, C | -CH2SH | X | - | - | X | - | - | 86 | UGU, UGC | 1.9 |
| Aspartate | Asp, D | -CH2COOH | - | X | negative | X | - | - | 91 | GAU, GAC | 5.3 |
| Glutamate | Glu, E | -CH2CH2COOH | - | X | negative | - | - | - | 109 | GAA, GAG | 6.3 |
| Phenylalanine | Phe, F | -CH2C6H5 | X | - | - | - | - | Aromatic | 135 | UUU, UUC | 3.9 |
| Glycine | Gly, G | -H | X | - | - | X | X | - | 48 | GGU, GGC, GGA, GGG | 7.2 |
| Histidine | His, H | -CH2-C3H3N2 | - | X | positive | - | - | Aromatic | 118 | CAU, CAC | 2.3 |
| Isoleucine | Ile, I | -CH(CH3)CH2CH3 | X | - | - | - | - | Aliphatic | 124 | AUU, AUC, AUA | 5.3 |
| Lysine | Lys, K | -(CH2)4NH2 | - | X | positive | - | - | - | 135 | AAA, AAG | 5.9 |
| Leucine | Leu, L | -CH2CH(CH3)2 | X | - | - | - | - | Aliphatic | 124 | UUA, UUG, CUU, CUC, CUA, CUG | 9.1 |
| Methionine | Met, M | -CH2CH2SCH3 | X | - | - | - | - | - | 124 | AUG | 2.3 |
| Asparagine | Asn, N | -CH2CONH2 | - | X | - | X | - | - | 96 | AAU, AAC | 4.3 |
| Proline | Pro, P | -CH2CH2CH2- | X | - | - | X | - | - | 90 | CCU, CCC, CCA, CCG | 5.2 |
| Glutamine | Gln, Q | -CH2CH2CONH2 | - | X | - | - | - | - | 114 | GGU, GGC, GGA, GGG | 4.2 |
| Arginine | Arg, R | -(CH2)3NH-C(NH)NH2 | - | X | positive | - | - | - | 148 | CGU, CGC, CGA, CGG, AGA, AGG | 5.1 |
| Serine | Ser, S | -CH2OH | - | X | - | X | X | - | 73 | UCU, UCC, UCA, UCG, AGU,AGC | 6.8 |
| Threonine | Thr, T | -CH(OH)CH3 | X | X | - | X | - | - | 93 | ACU, ACC, ACA, ACG | 5.9 |
| Valine | Val, V | -CH(CH3)2 | X | - | - | X | - | Aliphatic | 105 | GUU, GUC, GUA, GUG | 6.6 |
| Tryptophan | Trp, W | -CH2C8H5N | X | - | - | - | - | Aromatic | 163 | UGG | 1.4 |
| Tyrosine | Tyr, Y | -CH2-C6H4OH | X | X | - | - | - | Aromatic | 141 | UAU, UAC | 3.2 |
Hydrophilic and hydrophobic amino acids
Depending on how polar the side chain, aminoacids can be hydrophilic or hydrophobic to various degree. This influences their interaction with other structures, both within the protein itself and within other proteins. The distribution of hydrophilic and hydrophobic aminoacids determines the tertiary structure of the protein, and their physical location on the outside structure of the proteins influences their quaternary structure. For example, soluble proteins have surfaces rich with polar aminoacids like serine and threonine, while integral membrane proteins tend to have outer ring of hydrophobic aminoacids that anchors them to the lipid bilayer, and proteins anchored to the membrane have a hydrophobic end that locks into the membrane. Similarly, proteins that have to bind to positive-charged molecules have surfaces rich with negatively charged aminoacids like glutamate and aspartate, while proteins binding to negative-charged molecules have surfaces rich with positively charged chains like lysine and arginine.
Hydrophilic and hydrophobic interactions of the proteins do not have to rely only on aminoacids themselves. By various posttranslational modifications other chains can be attached to the proteins, forming hydrophobic lipoproteins or hydrophylic glycoproteins.
Nonstandard amino acids
Aside from the twenty standard amino acids, there is a vast number of nonstandard amino acids not used in the body's regular manufacturing of proteins. Examples of nonstandard amino acids include the sulfurontaining taurine and the neurotransmitters GABA and dopamine. Other examples are lanthionine, 1-amino isobutyric acid, dehydroalanine, dehydro-amino-butyric acid,
Nonstandard amino acids are usually formed through modifications to standard amino acids. For example, taurine can be formed by the decarboxylation of cysteine, while dopamine is synthesized from tyrosine and hydroxyproline is made by a posttranslational modification from proline.
Uses of substances derived from amino acids
- Aspartame (aspartyl-phenylalanine-1-methyl ester) is an artificial sweetener.
- 5-HTP (5-hydroxytryptophan) has been used to treat neurological problems associated with PKU (phenylketonuria), as well as depression (as an alternative to L-Tryptophan).
- L-DOPA (L-dihydroxyphenylalanine) is a drug used to treat Parkinsonism.
- Monosodium glutamate is a food additive to enhance flavor.
See also
References
- Doolittle, R.F. (1989) Redundancies in protein sequences. In Predictions of Protein Structure and the Principles of Protein Conformation (Fasman, G.D. ed) Plenum Press, New York, pp. 599-623
- David L. Nelson and Michael M. Cox, Lehninger Principles of Biochemistry, 3rd ion, 2000, Worth Publishers, ISBN 1572591536
- On the hydrophobic nature of cysteine.
External links
- Molecular Expressions: The Amino Acid Collection - Has detailed information and microscopy photographs of each amino acid.
- 22nd amino acid - Press release from Ohio State claiming discovery of a 22nd amino acid.