Proteinogenic amino acid 427499 224377445 2008-07-08T16:14:41Z Kumorifox 3295299 /* Gene expression and biochemistry */ {{Unreferenced|date=September 2007}} '''Proteinogenic''' [[amino acid]]s, also known as standard, normal, or primary amino acids, are those 20 amino acids that are found in [[protein]]s and that are coded for in the standard [[genetic code]]. Proteinogenic literally means ''protein building''. Proteinogenic amino acids are assembled into a [[polypeptide]] (the subunit of a protein) through a process known as [[Translation (biology)|translation]] (the second stage of protein biosynthesis, part of the overall process of [[biosemiotic|gene expression]]). '''Non-proteinogenic''' amino acids are either not found in proteins (like [[carnitine]], [[GABA]], or [[L-DOPA]]), or not coded for in the standard [[genetic code]] (like [[hydroxyproline]] and [[selenomethionine]]). The latter often result from [[posttranslational modification]] of proteins. Some non-proteinogenic amino acids, such as [[ornithine]] and [[homoserine]] have clear reasons why organisms have not [[evolution|evolved]] to incorporate them into proteins; both of these amino acids will cyclize against the peptide backbone and fragment the protein with relatively short half-lives. Some non-proteinogenic amino acids are toxic because they can be mistakenly incorporated into proteins, one example is the [[arginine]] analog [[canavanine]]. == Structures == Structures and symbols of the 20 amino acids which are directly encoded for protein synthesis by the standard genetic code <gallery> image:L-alanine-skeletal.png|[[Alanine|<small>L</small>-Alanine]]<br>(Ala&nbsp;/&nbsp;A) image:L-arginine-skeletal-(tall).png|[[Arginine|<small>L</small>-Arginine]]<br>(Arg&nbsp;/&nbsp;R) image:L-asparagine-skeletal.png|[[Asparagine|<small>L</small>-Asparagine]]<br>(Asn&nbsp;/&nbsp;N) image:L-aspartic-acid-skeletal.png|[[Aspartic acid|<small>L</small>-Aspartic acid]]<br>(Asp&nbsp;/&nbsp;D) image:L-cysteine-skeletal.png|[[Cysteine|<small>L</small>-Cysteine]]<br>(Cys&nbsp;/&nbsp;C) image:L-glutamic-acid-skeletal.png|[[Glutamic acid|<small>L</small>-Glutamic acid]]<br>(Glu&nbsp;/&nbsp;E) image:L-glutamine-skeletal.png|[[Glutamine|<small>L</small>-Glutamine]]<br>(Gln&nbsp;/&nbsp;Q) image:Glycine-skeletal.png|[[Glycine]]<br>(Gly&nbsp;/&nbsp;G) image:L-histidine-skeletal.png|[[Histidine|<small>L</small>-Histidine]]<br>(His&nbsp;/&nbsp;H) image:L-isoleucine-skeletal.png|[[Isoleucine|<small>L</small>-Isoleucine]]<br>(Ile&nbsp;/&nbsp;I) image:L-leucine-skeletal.png|[[Leucine|<small>L</small>-Leucine]]<br>(Leu&nbsp;/&nbsp;L) image:L-lysine-skeletal.png|[[Lysine|<small>L</small>-Lysine]]<br>(Lys&nbsp;/&nbsp;K) image:L-methionine-skeletal.png|[[Methionine|<small>L</small>-Methionine]]<br>(Met&nbsp;/&nbsp;M) image:L-phenylalanine-skeletal.png|[[Phenylalanine|<small>L</small>-Phenylalanine]]<br>(Phe&nbsp;/&nbsp;F) image:L-proline-skeletal.png|[[Proline|<small>L</small>-Proline]]<br>(Pro&nbsp;/&nbsp;P) image:L-serine-skeletal.png|[[Serine|<small>L</small>-Serine]]<br>(Ser&nbsp;/&nbsp;S) image:L-threonine-skeletal.png|[[Threonine|<small>L</small>-Threonine]]<br>(Thr&nbsp;/&nbsp;T) image:L-tryptophan-skeletal.png|[[Tryptophan|<small>L</small>-Tryptophan]]<br>(Trp&nbsp;/&nbsp;W) image:L-tyrosine-skeletal.png|[[Tyrosine|<small>L</small>-Tyrosine]]<br>(Tyr&nbsp;/&nbsp;Y) image:L-valine-skeletal.png|[[Valine|<small>L</small>-Valine]]<br>(Val&nbsp;/&nbsp;V) </gallery> == 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]]s at their [[natural abundance]]s. Note that forming a [[peptide bond]] results in elimination of a molecule of [[water (molecule)|water]], so the mass of an amino acid unit within a protein chain is reduced by 18.01524 Da. 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]]; ''Glx'' or ''Z'' means either [[glutamic acid]] or [[glutamine]]; and ''Xle'' or ''J'' means either [[leucine]] or [[isoleucine]]. [[IUPAC]]/[[IUBMB]] now also recommends that ''Sec'' or ''U'' refers to [[selenocysteine]], and ''Pyl'' or ''O'' refers to [[pyrrolysine]]. ===General chemical properties=== {| class="wikitable sortable" style="text-align: center" |- ! Amino Acid ! Short ! Abbrev. ! Avg. Mass ([[Atomic mass unit|Da]]) ! [[Isoelectric point|pI]] ! [[dissociation constant|pK]]<sub>1</sub><br>(α-COOH) ! pK<sub>2</sub><br>(α-<sup>+</sup>NH<sub>3</sub>) |- ! [[Alanine]] | A | Ala | 89.09404 | 6.01 | 2.35 | 9.87 |- ! [[Cysteine]] | C | Cys | 121.15404 | 5.05 | 1.92 | 10.70 |- ! [[Aspartic acid]] | D | Asp | 133.10384 | 2.85 | 1.99 | 9.90 |- ! [[Glutamic acid]] | E | Glu | 147.13074 | 3.15 | 2.10 | 9.47 |- ! [[Phenylalanine]] | F | Phe | 165.19184 | 5.49 | 2.20 | 9.31 |- ! [[Glycine]] | G | Gly | 75.06714 | 6.06 | 2.35 | 9.78 |- ! [[Histidine]] | H | His | 155.15634 | 7.60 | 1.80 | 9.33 |- ! [[Isoleucine]] | I | Ile | 131.17464 | 6.05 | 2.32 | 9.76 |- ! [[Lysine]] | K | Lys | 146.18934 | 9.60 | 2.16 | 9.06 |- ! [[Leucine]] | L | Leu | 131.17464 | 6.01 | 2.33 | 9.74 |- ! [[Methionine]] | M | Met | 149.20784 | 5.74 | 2.13 | 9.28 |- ! [[Asparagine]] | N | Asn | 132.11904 | 5.41 | 2.14 | 8.72 |- ! [[Pyrrolysine]] | O | Pyl | | | | |- ! [[Proline]] | P | Pro | 115.13194 | 6.30 | 1.95 | 10.64 |- ! [[Glutamine]] | Q | Gln | 146.14594 | 5.65 | 2.17 | 9.13 |- ! [[Arginine]] | R | Arg | 174.20274 | 10.76 | 1.82 | 8.99 |- ! [[Serine]] | S | Ser | 105.09344 | 5.68 | 2.19 | 9.21 |- ! [[Threonine]] | T | Thr | 119.12034 | 5.60 | 2.09 | 9.10 |- ! [[Selenocysteine]] | U | Sec | 169.06 | | | |- ! [[Valine]] | V | Val | 117.14784 | 6.00 | 2.39 | 9.74 |- ! [[Tryptophan]] | W | Trp | 204.22844 | 5.89 | 2.46 | 9.41 |- ! [[Tyrosine]] | Y | Tyr | 181.19124 | 5.64 | 2.20 | 9.21 |} ===Side chain properties=== {| class="wikitable sortable" |- align="center" ! Amino Acid ! Short ! Abbrev. ! Side chain ! [[Hydrophobic|Hydro-<br>phobic]] ! [[Acid_dissociation_constant|pKa]] ! [[Chemical polarity|Polar]] ! [[acidity|pH]] ! Small ! Tiny ! [[Aromaticity|Aromatic]]<br>or [[Aliphatic]] ! [[Van der Waals radius|van der Waals<br>volume]] |- ! [[Alanine]] | A | Ala | -CH<sub>3</sub> | X | - | - | - | X | X | - | 67 |- ! [[Cysteine]] | C | Cys | -CH<sub>2</sub>[[Thiol|SH]] | - | 8.18 | - | acidic | X | - | - | 86 |- ! [[Aspartic acid]] | D | Asp | -CH<sub>2</sub>COOH | - | 3.90 | X | acidic | X | - | - | 91 |- ! [[Glutamic acid]] | E | Glu | -CH<sub>2</sub>CH<sub>2</sub>COOH | - | 4.07 | X | acidic | - | - | - | 109 |- ! [[Phenylalanine]] | F | Phe | -CH<sub>2</sub>C<sub>6</sub>H<sub>5</sub> | X | - | - | - | - | - | Aromatic | 135 |- ! [[Glycine]] | G | Gly | -H | - | - | - | - | X | X | - | 48 |- ! [[Histidine]] | H | His | -CH<sub>2</sub>-[[imidazole|C<sub>3</sub>H<sub>3</sub>N<sub>2</sub>]] | - | 6.04 | X | weak basic | - | - | Aromatic | 118 |- ! [[Isoleucine]] | I | Ile | -CH(CH<sub>3</sub>)CH<sub>2</sub>CH<sub>3</sub> | X | - | - | - | - | - | Aliphatic | 124 |- ! [[Lysine]] | K | Lys | -(CH<sub>2</sub>)<sub>4</sub>NH<sub>2</sub> | - | 10.54 | X | basic | - | - | - | 135 |- ! [[Leucine]] | L | Leu | -CH<sub>2</sub>CH(CH<sub>3</sub>)<sub>2</sub> | X | - | - | - | - | - | Aliphatic | 124 |- ! [[Methionine]] | M | Met | -CH<sub>2</sub>CH<sub>2</sub>[[Sulfur|S]]CH<sub>3</sub> | X | - | - | - | - | - | - | 124 |- ! [[Asparagine]] | N | Asn | -CH<sub>2</sub>CONH<sub>2</sub> | - | - | X | - | X | - | - | 96 |- ! [[Pyrrolysine]] | O | Pyl | | | | | | | | | |- ! [[Proline]] | P | Pro | -CH<sub>2</sub>CH<sub>2</sub>CH<sub>2</sub>- | X | - | - | - | X | - | - | 90 |- ! [[Glutamine]] | Q | Gln | -CH<sub>2</sub>CH<sub>2</sub>CONH<sub>2</sub> | - | - | X | - | - | - | - | 114 |- ! [[Arginine]] | R | Arg | -(CH<sub>2</sub>)<sub>3</sub>NH-C(NH)NH<sub>2</sub> | - | 12.48 | X | strongly basic | - | - | - | 148 |- ! [[Serine]] | S | Ser | -CH<sub>2</sub>OH | - | - | X | - | X | X | - | 73 |- ! [[Threonine]] | T | Thr | -CH(OH)CH<sub>3</sub> | - | - | X | weak acidic | X | - | - | 93 |- ! [[Selenocysteine]] | U | Sec | -CH<sub>2</sub>[[Selenol|SeH]] | X | 5.73 | - | - | X | - | - | |- ! [[Valine]] | V | Val | -CH(CH<sub>3</sub>)<sub>2</sub> | X | - | - | - | X | - | Aliphatic | 105 |- ! [[Tryptophan]] | W | Trp | -CH<sub>2</sub>[[indole|C<sub>8</sub>H<sub>6</sub>N]] | X | - | - | - | - | - | Aromatic | 163 |- ! [[Tyrosine]] | Y | Tyr | -CH<sub>2</sub>-C<sub>6</sub>H<sub>4</sub>OH | - | 10.46 | X | - | - | - | Aromatic | 141 |} Note: The pKa values of amino acids are typically slightly different when the amino acid is inside a protein. [[Protein pKa calculations]] are sometimes used to calculate the change in the pKa value of an amino acid in this situation. ===Gene expression and biochemistry=== {| class="wikitable sortable" |- align="center" ! Amino Acid ! Short ! Abbrev. ! [[Codon]](s) ! Occurrence<br>in proteins<br>(%) ! Essential[[#essentialnote|‡]] in humans |- ! [[Alanine]] | A | Ala | GCU, GCC, GCA, GCG | 7.8 | - |- ! [[Cysteine]] | C | Cys | UGU, UGC | 1.9 | Conditionally |- ! [[Aspartic acid]] | D | Asp | GAU, GAC | 5.3 | - |- ! [[Glutamic acid]] | E | Glu | GAA, GAG | 6.3 | Conditionally |- ! [[Phenylalanine]] | F | Phe | UUU, UUC | 3.9 | Yes |- ! [[Glycine]] | G | Gly | GGU, GGC, GGA, GGG | 7.2 | Conditionally |- ! [[Histidine]] | H | His | CAU, CAC | 2.3 | Yes |- ! [[Isoleucine]] | I | Ile | AUU, AUC, AUA | 5.3 | Yes |- ! [[Lysine]] | K | Lys | AAA, AAG | 5.9 | Yes |- ! [[Leucine]] | L | Leu | UUA, UUG, CUU, CUC, CUA, CUG | 9.1 | Yes |- ! [[Methionine]] | M | Met | AUG | 2.3 | Yes |- ! [[Asparagine]] | N | Asn | AAU, AAC | 4.3 | - |- ! [[Pyrrolysine]] | O | Pyl | UAG[[#pyrronote|*]] | | - |- ! [[Proline]] | P | Pro | CCU, CCC, CCA, CCG | 5.2 | - |- ! [[Glutamine]] | Q | Gln | CAA, CAG | 4.2 | - |- ! [[Arginine]] | R | Arg | CGU, CGC, CGA, CGG, AGA, AGG | 5.1 | Conditionally |- ! [[Serine]] | S | Ser | UCU, UCC, UCA, UCG, AGU, AGC | 6.8 | - |- ! [[Threonine]] | T | Thr | ACU, ACC, ACA, ACG | 5.9 | Yes |- ! [[Selenocysteine]] | U | Sec | UGA[[#selenonote|**]] | | - |- ! [[Valine]] | V | Val | GUU, GUC, GUA, GUG | 6.6 | Yes |- ! [[Tryptophan]] | W | Trp | UGG | 1.4 | Yes |- ! [[Tyrosine]] | Y | Tyr | UAU, UAC | 3.2 | Conditionally |- ! Stop codon[[#stopnote|†]] | - | Term | UAA, UAG, UGA | - | - |} <span id="pyrronote">*</span> UAG is normally the amber stop codon, but encodes pyrrolysine if a [[PYLIS element]] is present.<br/> <span id="selenonote">**</span> UGA is normally the opal (or umber) stop codon, but encodes selenocysteine if a [[SECIS element]] is present.<br /> <span id="stopnote">†</span> The [[stop codon]] is not an amino acid, but is included for completeness.<br /> <span id="essentialnote">‡</span> 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 to specific populations that do not synthesize it in adequate amounts. ===Remarks=== {| class="wikitable" |- align="center" ! Amino Acid ! colspan="2" | Abbrev. ! Remarks |- ! [[Alanine]] | A | Ala | Very abundant, very versatile. More stiff than glycine, but small enough to pose only small steric limits for the protein conformation. It behaves fairly neutrally, can be located in both hydrophilic regions on the protein outside and the hydrophobic areas inside. |- ! [[Cysteine]] | C | Cys | The sulfur atom binds readily to [[heavy metals|heavy metal]] ions. Under oxidizing conditions, two cysteines can join together in a [[disulfide bond]] to form the amino acid [[cystine]]. When cystines are part of a protein, [[insulin]] for example, this stabilises [[tertiary structure]] and makes the protein more resistant to [[denaturation (biochemistry)|denaturation]]; disulfide bridges are therefore common in proteins that have to function in harsh environments including digestive enzymes (e.g., [[pepsin]] and [[chymotrypsin]]) and structural proteins (e.g., [[keratin]]). Disulfides are also found in peptides too small to hold a stable shape on their own (eg. [[insulin]]). |- ! [[Aspartic acid]] | D | Asp | Behaves similarly to glutamic acid. Carries a 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. |- ! [[Glutamic acid]] | E | Glu | Behaves similar to aspartic acid. Has longer, slightly more flexible side chain. |- ! [[Phenylalanine]] | F | Phe | [[essential amino acid|Essential]] for humans. Phenylalanine, tyrosine, and tryptophan contain large rigid [[aromaticity|aromatic]] group on the side chain. These are the biggest amino acids. Like isoleucine, leucine and valine, these are hydrophobic and tend to orient towards the interior of the folded protein molecule. |- ! [[Glycine]] | G | Gly | Because of the two hydrogen atoms at the α carbon, glycine is not [[optical isomerism|optically active]]. It is the smallest amino acid, rotates easily, adds flexibility to the protein chain. It is able to fit into the tightest spaces, e.g., the triple helix of [[collagen]]. As too much flexibility is usually not desired, as a structural component it is less common than alanine. |- ! [[Histidine]] | H | His | 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. |- ! [[Isoleucine]] | I | Ile | [[essential amino acid|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. |- ! [[Lysine]] | K | Lys | [[essential amino acid|Essential]] for humans. Behaves similarly to arginine. Contains a long flexible side-chain with a positively-charged end. The flexibility of the chain makes lysine and arginine suitable for binding to molecules with many negative charges on their surfaces. E.g., [[deoxyribonucleic acid|DNA]]-binding proteins have their active regions rich with arginine and lysine. The strong charge makes these two amino acids 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 amino acid, e.g., aspartate or glutamate. |- ! [[Leucine]] | L | Leu | [[essential amino acid|Essential]] for humans. Behaves similar to isoleucine and valine. See isoleucine. |- ! [[Methionine]] | M | Met | [[essential amino acid|Essential]] for humans. Always the first amino acid to be incorporated into a protein; sometimes removed after translation. Like cysteine, contains sulfur, but with a [[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. |- ! [[Asparagine]] | N | Asn | Similar to aspartic acid. Asn contains an [[amide]] group where Asp has a [[carboxyl]]. |- ! [[Proline]] | P | Pro | 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 [[alpha helix|α helix]] or [[beta sheet|β sheet]], forcing the desired kink in the protein chain. Common in [[collagen]], where it often undergoes a [[posttranslational modification]] to [[hydroxyproline]]. Uncommon elsewhere. |- ! [[Glutamine]] | Q | Gln | Similar to glutamic acid. Gln contains an [[amide]] group where Glu has a [[carboxyl]]. Used in proteins and as a storage for [[ammonia]]. |- ! [[Arginine]] | R | Arg | Functionally similar to lysine. |- ! [[Serine]] | S | Ser | 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 hydrophilic, therefore the outer regions of soluble proteins tend to be rich with them. |- ! [[Threonine]] | T | Thr | [[essential amino acid|Essential]] for humans. Behaves similarly to serine. |- ! [[Valine]] | V | Val | [[essential amino acid|Essential]] for humans. Behaves similarly to isoleucine and leucine. See isoleucine. |- ! [[Tryptophan]] | W | Trp | [[essential amino acid|Essential]] for humans. Behaves similarly to phenylalanine and tyrosine (see phenylalanine). Precursor of [[serotonin]]. |- ! [[Tyrosine]] | Y | Tyr | Behaves similarly to phenylalanine and tryptophan (see phenylalanine). Precursor of [[melanin]], [[epinephrine]], and [[thyroid hormone]]s. |} ==References== *{{cite book |last=Nelson |first=David L. |coauthors=Cox, Michael M. |title=Lehninger Principles of Biochemistry |edition=3rd ed |year=2000 |publisher=Worth Publishers |isbn=1-57259-153-6 }} *{{cite journal | last=Kyte | first=J. | coauthors=Doolittle, R. F. | year=1982 | title=A simple method for displaying the hydropathic character of a protein | journal=[[J. Mol. Biol.]] | volume=157 | issue=1 | pages=105–132 | pmid=7108955 | doi=10.1016/0022-2836(82)90515-0 }} ==See also== * [[Glucogenic amino acid]] {{AminoAcids}} [[Category:Proteinogenic amino acids|*]] [[Category:Amino acids| ]] [[Category:Nitrogen metabolism]] [[Category:Nutrition]] [[ar:قائمة الأحماض الأمينية]] [[da:Standardaminosyre]] [[lt:Standartinių aminorūgščių lentelės]] [[ca:Aminoàcid proteïnogènic]] [[el:Πρωτεϊνογενετικά αμινοξέα]] [[zh:蛋白胺基酸]]