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1 nm · Molecules

Amino acids

Nonpolar (hydrophobic)

9

  • glycine (zwitterion at pH 7.4)Skeletal structure; 5 heavy atoms; heteroatoms N, O.OO-H3N+

    Glycine

    Gly · G

    side chain –H

    hydrophobic

    pKa 2.34 / 9.60 · pI 5.97

    The only achiral amino acid: its α-carbon carries two hydrogens.

  • L-alanine (zwitterion at pH 7.4)Skeletal structure; 6 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O.OO-H3N+H

    Alanine

    Ala · A

    side chain –CH₃

    hydrophobic

    pKa 2.34 / 9.69 · pI 6.01

    Simplest chiral amino acid; a plain methyl side chain.

  • L-valine (zwitterion at pH 7.4)Skeletal structure; 8 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O.OO-H3N+H

    Valine

    Val · V

    side chain –CH(CH₃)₂

    hydrophobicessential

    pKa 2.32 / 9.62 · pI 5.97

    Branched-chain amino acid (BCAA). Glu→Val at position 6 of β-globin causes sickle cell disease.

  • L-leucine (zwitterion at pH 7.4)Skeletal structure; 9 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O.OO-H3N+H

    Leucine

    Leu · L

    side chain –CH₂CH(CH₃)₂

    hydrophobicessential

    pKa 2.36 / 9.60 · pI 5.98

    BCAA, and one of only two purely ketogenic amino acids.

  • L-isoleucine (zwitterion at pH 7.4)Skeletal structure; 9 heavy atoms; 2 stereocenters shown by wedge or hash; heteroatoms N, O.OO-H3N+HH

    Isoleucine

    Ile · I

    side chain –CH(CH₃)CH₂CH₃

    hydrophobicessential

    pKa 2.36 / 9.68 · pI 6.02

    BCAA with two chiral centers (the α- and β-carbons). Both glucogenic and ketogenic.

  • L-methionine (zwitterion at pH 7.4)Skeletal structure; 9 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O, S.SOO-H3N+H

    Methionine

    Met · M

    side chain –CH₂CH₂SCH₃

    hydrophobicessential

    pKa 2.28 / 9.21 · pI 5.74

    Start codon AUG. Its sulfur is a thioether, so it cannot form disulfide bonds.

  • L-proline (zwitterion at pH 7.4)Skeletal structure; 8 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O.N+H2OO-

    Proline

    Pro · P

    side chain cyclic –CH₂CH₂CH₂– back to N

    hydrophobic

    pKa 1.99 / 10.96 · pI 6.48

    Secondary amine (an imino acid). Its rigid ring kinks α-helices and breaks secondary structure.

  • L-phenylalanine (zwitterion at pH 7.4)Skeletal structure; 12 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O.OO-H3N+H

    Phenylalanine

    Phe · F

    side chain –CH₂–C₆H₅

    hydrophobicessential

    pKa 1.83 / 9.13 · pI 5.48

    Aromatic, purely nonpolar benzyl group. Accumulates in PKU.

  • L-tryptophan (zwitterion at pH 7.4)Skeletal structure; 15 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O.HNOO-H3N+H

    Tryptophan

    Trp · W

    side chain –CH₂–indole

    hydrophobicessential

    pKa 2.38 / 9.39 · pI 5.89

    Bulkiest side chain, an indole ring. Dominates absorbance at 280 nm. Precursor to serotonin and niacin.

Polar, uncharged

6

  • L-serine (zwitterion at pH 7.4)Skeletal structure; 7 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O.OO-H3N+OHH

    Serine

    Ser · S

    side chain –CH₂OH

    polar

    pKa 2.21 / 9.15 · pI 5.68

    Hydroxyl side chain: a phosphorylation site and a catalytic-triad nucleophile.

  • L-threonine (zwitterion at pH 7.4)Skeletal structure; 8 heavy atoms; 2 stereocenters shown by wedge or hash; heteroatoms N, O.OO-H3N+OHHH

    Threonine

    Thr · T

    side chain –CH(OH)CH₃

    polaressential

    pKa 2.11 / 9.62 · pI 5.87

    Hydroxyl and methyl; with isoleucine, one of the two amino acids with two chiral centers.

  • L-cysteine (zwitterion at pH 7.4)Skeletal structure; 7 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O, S.OO-H3N+SHH

    Cysteine

    Cys · C

    side chain –CH₂SH

    polar

    pKa 1.96 / 10.28 / R 8.18 · pI 5.07

    A thiol. Two cysteines oxidize to a disulfide bond, forming cystine. The only chiral amino acid with (R) configuration.

  • L-tyrosine (zwitterion at pH 7.4)Skeletal structure; 13 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O.OO-H3N+OHH

    Tyrosine

    Tyr · Y

    side chain –CH₂–C₆H₄–OH

    polar

    pKa 2.20 / 9.11 / R 10.07 · pI 5.66

    Aromatic and polar (a phenol OH). Precursor to thyroid hormone, dopamine and melanin.

  • L-asparagine (zwitterion at pH 7.4)Skeletal structure; 9 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O.OO-H3N+ONH2H

    Asparagine

    Asn · N

    side chain –CH₂CONH₂

    polar

    pKa 2.02 / 8.80 · pI 5.41

    The amide of aspartate: uncharged, not acidic. Site of N-linked glycosylation.

  • L-glutamine (zwitterion at pH 7.4)Skeletal structure; 10 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O.ONH2OO-H3N+H

    Glutamine

    Gln · Q

    side chain –CH₂CH₂CONH₂

    polar

    pKa 2.17 / 9.13 · pI 5.65

    The amide of glutamate. The main carrier of ammonia in blood, to the liver and kidneys.

Acidic (−)

2

  • L-aspartate (net charge −1 at pH 7.4)Skeletal structure; 9 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O.OO-H3N+OO-H

    Aspartic acid

    Asp · D

    side chain –CH₂COO⁻

    acidic

    pKa 1.88 / 9.60 / R 3.65 · pI 2.77

    Negatively charged at pH 7. Donates the second nitrogen of urea in the urea cycle.

  • L-glutamate (net charge −1 at pH 7.4)Skeletal structure; 10 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O.OO-OO-H3N+H

    Glutamic acid

    Glu · E

    side chain –CH₂CH₂COO⁻

    acidic

    pKa 2.19 / 9.67 / R 4.25 · pI 3.22

    Negatively charged at pH 7. Main excitatory neurotransmitter; hub of transamination.

Basic (+)

3

  • L-lysine (net charge +1 at pH 7.4)Skeletal structure; 10 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O.NH3+OO-H3N+H

    Lysine

    Lys · K

    side chain –(CH₂)₄NH₃⁺

    basicessential

    pKa 2.18 / 8.95 / R 10.53 · pI 9.74

    Long, flexible, positively charged amine. Site of histone acetylation. Purely ketogenic.

  • L-arginine (net charge +1 at pH 7.4)Skeletal structure; 12 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O.NH2H2N+NHH3N+OO-H

    Arginine

    Arg · R

    side chain –(CH₂)₃NH–C(=NH₂⁺)NH₂

    basic

    pKa 2.17 / 9.04 / R 12.48 · pI 10.76

    A guanidinium group: the most basic side chain (pKₐ ≈ 12.5), positive at every physiological pH. Conditionally essential: made in the urea cycle, but needed from the diet during growth.

  • L-histidine (zwitterion at pH 7.4)Skeletal structure; 11 heavy atoms; 1 stereocenter shown by wedge or hash; heteroatoms N, O.NHNOO-H3N+H

    Histidine

    His · H

    side chain –CH₂–imidazole

    basicessential

    pKa 1.82 / 9.17 / R 6.00 · pI 7.59

    An imidazole, pKₐ ≈ 6: the only side chain that buffers near physiological pH. Coordinates heme iron.

Bonds and links

  • generic L,L-dipeptide (R1, R2) (zwitterion at pH 7.4)Skeletal structure; 9 heavy atoms; 2 stereocenters shown by wedge or hash; heteroatoms N, O.H3N+R1ONHR2OO-

    Peptide bond

    Formed by dehydration; broken by hydrolysis. Rigid and planar thanks to resonance.

  • L-cystine (zwitterion at pH 7.4)Skeletal structure; 14 heavy atoms; 2 stereocenters shown by wedge or hash; heteroatoms N, O, S.OO-NH3+SSOO-H3N+

    Cystine (disulfide)

    Two cysteines oxidized together. β-mercaptoethanol reduces it back.

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