Proteinogenic Amino Acid

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 isotopes at their natural abundances. Note that forming a peptide bond results in elimination of a molecule of water, so the mass of an amino acid unit within a protein chain is reduced by 18.01524 Da.

General chemical properties

Amino Acid Short Abbrev. Avg. Mass (Da) pI pK1

(α-COOH)

pK2
(α-+NH3)
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 168.053 5.47
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

[edit] Side chain properties

Amino Acid Short Abbrev. Side chain Hydro-
phobic
pKa Polar pH Small Tiny Aromatic
or Aliphatic
van der Waals
volume
Alanine A Ala -CH3 X X X 67
Cysteine C Cys -CH2SH 8.18 acidic X X 86
Aspartic acid D Asp -CH2COOH 3.90 X acidic X 91
Glutamic acid E Glu -CH2CH2COOH 4.07 X acidic 109
Phenylalanine F Phe -CH2C6H5 X Aromatic 135
Glycine G Gly -H X X X 48
Histidine H His -CH2C3H3N2 6.04 X weak basic Aromatic 118
Isoleucine I Ile -CH(CH3)CH2CH3 X Aliphatic 124
Lysine K Lys -(CH2)4NH2 10.54 X basic 135
Leucine L Leu -CH2CH(CH3)2 X Aliphatic 124
Methionine M Met -CH2CH2SCH3 X 124
Asparagine N Asn -CH2CONH2 X X 96
Pyrrolysine O Pyl -(CH2)4NHCOC4H5NCH3 X
Proline P Pro -CH2CH2CH2 X X 90
Glutamine Q Gln -CH2CH2CONH2 X 114
Arginine R Arg -(CH2)3NH-C(NH)NH2 12.48 X strongly basic 148
Serine S Ser -CH2OH X X X 73
Threonine T Thr -CH(OH)CH3 X weak acidic X 93
Selenocysteine U Sec -CH2SeH 5.73 X X
Valine V Val -CH(CH3)2 X X Aliphatic 105
Tryptophan W Trp -CH2C8H6N Aromatic 163
Tyrosine Y Tyr -CH2-C6H4OH 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.

[edit] Gene expression and biochemistry

Alaninea> Cysteinea> Aspartic acida> Glutamic acida> Phenylalaninea> Glycinea> Histidinea> Isoleucinea> Lysinea> Leucinea> Methioninea> Asparaginea> Pyrrolysinea> Prolinea> Glutaminea> Argininea> Serinea> Threoninea> Selenocysteinea> Valinea> Tryptophana> Tyrosinea>
Amino Acid Short Abbrev. Codon(s) Occurrence

in human proteins
(%)

Essentiala> in humans
A Ala GCU, GCC, GCA, GCG 7.8
C Cys UGU, UGC 1.9 Conditionally
D Asp GAU, GAC 5.3
E Glu GAA, GAG 6.3 Conditionally
F Phe UUU, UUC 3.9 Yes
G Gly GGU, GGC, GGA, GGG 7.2 Conditionally
H His CAU, CAC 2.3 Yes
I Ile AUU, AUC, AUA 5.3 Yes
K Lys AAA, AAG 5.9 Yes
L Leu UUA, UUG, CUU, CUC, CUA, CUG 9.1 Yes
M Met AUG 2.3 Yes
N Asn AAU, AAC 4.3
O Pyl U*a>
P Pro CCU, CCC, CCA, CCG 5.2
Q Gln CAA, CAG 4.2
R Arg CGU, CGC, CGA, CGG, AGA, AGG 5.1 Conditionally
S Ser UCU, UCC, UCA, UCG, AGU, AGC 6.8
T Thr ACU, ACC, ACA, ACG 5.9 Yes
U Sec U**a>
V Val GUU, GUC, GUA, GUG 6.6 Yes
W Trp UGG 1.4 Yes
Y Tyr UAU, UAC 3.2 Conditionally
Stop cod Term UAA, UAG,††

* UAG is normaamber stop codonodon, but encodes pyrrolysiPYLIS elementment is present.
** UGA is normally the opal (or umber) stop codon, but encodes selenocysteiSECIS elementment is present.

†stop codonodon is not an amino acid, but is included for completeness.
†† UAG and UGA do not always act as stop codons (see above).
‡essential amino acidacid 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.

editedit] Mass spectrometrymass spectrometryetry of peptides and proteins, it is useful to know the masses of the residues. The mass of the peptide or protein is the sum of the residue masses plus the waterater.[3]pan>

AlanineanineCysteineteineAspartic acid acidGlutamic acid acidPhenylalanineanineGlycineycineHistidineidineIsoleucineucineLysineysineLeucineucineMethionineonineAsparagineaginePyrrolysineysineProlineolineGlutamineamineArginineinineSerineerineThreonineonineSelenocysteineteineValinealineTryptophanophanTyrosineosine
Amino Acid Short Abbrev. Formula M§e"Dat">Da) AvDat">Da)
A Ala C3H5NO 71.03711 71.0788
C Cys C3H5NOS 103.00919 103.1388
D Asp C4H5NO3 115.02694 115.0886
E Glu C5H7NO3 129.04259 129.1155
F Phe C9H9NO 147.06841 147.1766
G Gly C2H3NO 57.02146 57.0519
H His C6H7N3O 137.05891 137.1411
I Ile C6H11NO 113.08406 113.1594
K Lys C6H12N2O 128.09496 128.1741
L Leu C6H11NO 113.08406 113.1594
M Met C5H9NOS 131.04049 131.1986
N Asn C4H6N2O2 114.04293 114.1039
O Pyl C12H21N3O3 255.15829 255.3172
P Pro C5H7NO 97.05276 97.1167
Q Gln C5H8N2O2 128.05858 128.1307
R Arg C6H12N4O 156.10111 156.1875
S Ser C3H5NO2 87.03203 87.0782
T Thr C4H7NO2 101.04768 101.1051
U Sec C3H5NOSe 150.95364 150.0388
V Val C5H9NO 99.06841 99.1326
W Trp C11H10N2O 186.07931 186.2132
Y Tyr C9H9NO2 163.06333 163.1760

Monoisotopic mass mass

edit>edit] Stoichiometry and metabolic cost in cell

Following table lists the abundance of amino acids in E.coli cell and the metabolic cost (ATP) for synthesis the amino acids. Negative numbers indicate the metabolic processes are energy favorable and do not cost net ATP of the cell.[4]span> Note that the abundance of amino acids include amino acids in free-form and in polymerization form (proteins).

AlanineanineCysteineteineAspartic acid acidGlutamic acid acidPhenylalanineanineGlycineycineHistidineidineIsoleucineucineLysineysineLeucineucineMethionineonineAsparagineagineProlineolineGlutamineamineArginineinineSerineerineThreonineonineTryptophanophanTyrosineosineValinealine
Amino acid Abundance
(# of molecules (×108)E. coli coli cell)
ATP cost in synthesis
under aerobic

condition

ATP cost in synthesis
under anaerobic
condition
2.9 -1 1
0.52 11 15
1.4 0 2
1.5 -7 -1
1.1 -6 2
3.5 -2 2
0.54 1 7
1.7 7 11
2.0 5 9
2.6 -9 1
0.88 21 23
1.4 3 5
1.3 -2 4
1.5 -6 0
1.7 5 13
1.2 -2 2
1.5 6 8
0.33 -7 7
0.79 -8 2
2.4 -2 2

edit>edit] Remarks

AlanineanineAsparagineaginaspartic acid acidCysteineteineAspartic acid acidGlutamic acid acidPhenylalanineanineGlycineycineHistidineidineIsoleucineucineLeucineucinisoleucineucineLysineysineLeucineucineMethionineonineAsparagineaginePyrrolysineysineProlineolineGlutamineutamineArgininerginineSerine>SerineThreoninereonineSelenocysteineysteineValine>ValineTryptophanptophanTyrosineyrosineGlutamic acidic aglutamineutamine
Amino Acid Abbrev. Remarks
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, and can be located in both hydrophilic regions on the protein outside and the hydrophobic areas inside.
B Asx A placeholder when either amino acid may occupy a position.
C Cys The sulfur atom bonds reheavy metalmetal ions. Under oxidizing conditions, two cysteines can join togetdisulfide bond bond to form the amcystinestine. When cystines are part of a insulinsulin for examtertiary structurecture is stabilized, which makes the protein more residenaturationation; therefore, disulfide bonds are common in proteins that have to function in harsh environments including digestive enzymepepsinepsinchymotrypsinypsin) and structural proteinkeratinratin). Disulfides are also found in peptides too small to hold a stable shape on their oinsulinsulin).
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.
E Glu Behaves similar to aspartic acid. Has longer, slightly more flexible side chain.
F Phe<Essentialntial for humans. Phenylalanine, tyrosine, and tryptophan contain lararomaticmatic 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. Phenylalanine can be converted into Tyrosine.
G Gly Because of the two hydrogen atoms at the α carbon, glycinoptically activective. 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 collagenlagen. As too much flexibility is usually not desired, as a structural component it is less common than alanine.
H His In even slightly acidic coprotonationation 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 endosomeosomlysosomeosome, enforcing conformation change in enzymes. However only a few histidines are needed for this, so it is comparatively scarce.
I Ile<Essentialntial 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.
J Xle A placeholder when either amino acid may occupy a position
K Lys<Essentialntial 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 surfaceDNA">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.
L Leu<Essentialntial for humans. Behaves similar to isoleucine and valine. See isoleucine.
M Met<Essentialntial for humans. Always the first amino acid to be incorporated into a protein; sometimes removed after translation. Like cysteine, contains sulfur, bumethylethyl 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 Similar to aspartic acid. Asn conamideamide group where Acarboxylboxyl.
O Pyl Silysineysinepyrrolineoline ring attached.
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 structuα helix helβ sheet sheet, forcing the desired kink in the protein chain.collagenollagen, where it often uposttranslational modificationicathydroxyprolineproline. Q Gln Similar to glutamic acid. Gln camide">amide group wherecarboxylarboxyl. Used in proteins and as a sammoniaammonia. The most abundant Amino Acid in the body. R Arg Functionally similar to lysine. S Ser Serine and threonine have a short group enhydroxylydroxyl 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. T ThEssentialsential for humans. Behaves similarly to serine. U SeSelenatedlenated form of cysteine, whicsulfur>sulfur. V VaEssentialsential for humans. Behaves similarly to isoleucine and leucine. See isoleucine. W TrEssentialsential for humans. Behaves similarly to phenylalanine and tyrosine (see phenylalanine). Prserotoninrotonin.fluorescentrescent.
Unknown X Xaa Placeholder when the amino acid is unknown or unimportant. Y Tyr Behaves similarly to phenylalanine (precursor to Tyrosine) and tryptophan (see phenylalanine). Prmelaninmeepinephrineephrinthyroid hormonesormones.fluorescentrescent, although fluorescence is usually quenched by energy transfer to tryptophans. Z Glx A placeholder when either amino acid may occupy a position.

edit9">edit] Catabolism

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Amino acids can be classified according to the properties of their main products as either of the following:[5]

  • Glucogenic, with the products having the abiliglucoseglucgluconeogenesisgenesis
  • Ketogenic, with the products not having the ability to form glucose. These products may still bketogenesisgenelipid synthesisnthesis.
  • Amino acids catabolized into both glucogenic and ketogenic products.
  • Table of α-Amino Acids Found in Proteins

    Amino Acid Symbol Structure* pK1 (COOH) pK2 (NH2) pK R Group

    Amino Acids with Aliphatic R-Groups

    Glycine Gly – G Structure of glycine 2.4 9.8
    Alanine Ala – A Structure of alanine 2.4 9.9
    Valine Val – V Structure of valine 2.2 9.7
    Leucine Leu – L Structure of leucine

    2.3

    9.7
    Isoleucine Ile – I Structure of isoleucine 2.3 9.8
    Non-Aromatic Amino Acids with Hydroxyl R-Groups
    Serine

    Ser – S

    Structure of serine 2.2 9.2 ≈13
    Threonine Thr – T Structure of threonine 2.1 9.1 ≈13
    Amino Acids with Sulfur-Containing R-Groups
    Cysteine Cys – C Structure of cysteine

    1.9

    10.8 8.3
    Methionine Met – M Structure of methionine 2.1 9.3
    Acidic Amino Acids and their Amides
    Aspartic Acid

    Asp – D

    Structure of aspartic acid 2.0 9.9 3.9
    Asparagine Asn – N Structure of asparagine

    2.1

    8.8
    Glutamic Acid Glu – E Structure of glutamic acid 2.1 9.5

    4.1

    Glutamine Gln – Q Structure of glutamine 2.2 9.1
    Basic Amino Acids
    Arginine Arg – R Structure of arginine

    1.8

    9.0 12.5
    Lysine Lys – K Structure of lysine 2.2 9.2

    10.8

    Histidine His – H Structure of histidine 1.8 9.2 6.0

    Amino Acids with Aromatic Rings

    Phenylalanine Phe – F Structure of phenylalanine 2.2 9.2
    Tyrosine Tyr – Y Structure of tyrosine 2.2 9.1

    10.1

    Tryptophan Trp – W Structure of tryptophan

    2.4 9.4

    Imino Acids

    Proline Pro – P Structure of proline 2.0 10.6

    *Backbone
    of the amino acids is red, R-groups are black

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