Biochemistry: Amino Acids

glutamate (Glu) (E)

negatively charged, acidic related to glutamine has 3 carbons in its side chain

aspartate (Asp) (D)

negatively charged, acidic related to asparagine has 2 carbons in its side-chain

hydrophobic amino acids

alanine isoleucine leucine valine phenylalanine all have long alkyl side chain, making them strongly hydrophobic they are more likely to be found on the interior of proteins, away from the aqeuously bathed protein surface

glycine (Gly) (G)

an exception to the chirality of amino acids, as its alpha-carbon is not a stereogenic center due to its side chain being a simple H atom

tyrosine (Tyr) (Y)

aromatic side chain add a hydroxyl group to the benzyl group and you have this this hydroxyl group makes it relatively polar and H-bonding

tryptophan (Trp) (W)

aromatic side chain double-ring system that contains a nitrogen atom

negatively-charged, acidic side chains (2)

aspartic acid (aspartate) glutamic acid (glutamate)

cysteine (Cys) (C)

despite being an L-amino acid, its absolute configuration is R polar, nonaromatic contains a thiol group, which has an S-H bond that is weaker than O-H bonds, making it prone to oxidation contains one carbon in its side chain

hydrophilic amino acids

glutamine arginine asparagine lysine histidine glutamate aspartate they are charged or contain an amide group, making them very hydrophilic and likely to be on the exterior of proteins

nonpolar, nonaromatic side chains (7)

glycine valine (Val) (V) alanine (Ala) A leucine (Leu) (L) isoleucine (Ile) (I) methionine proline

positively charged (basic) side chains

lysine arginine histidine

amino acids

molecules that contain two functional groups: an amino group (-NH2) and a carboxyl group (-COOH) all naturally occurring forms are L isomers, with S absolute configurations (expect cysteine)

methionine (Met) (M)

nonpolar, nonaromatic one of only two amino acids that contains a sulfur atom in its side chain even so, because the sulfur is attached to a methyl group, it is considered relatively nonpolar

proline (Pro) (P)

nonpolar, nonaromatic unique in that is forms a cyclic amino acid the amino nitrogen becomes a part of the side chain, forming a 5-membered ring, placing noticeable constraints on the flexibility of the amino acid (so its not found in some peptide/proteins)

alanine, valine, leucine, isoleucine

nonpolar, nonaromatic have alkyl side chains containing 1, 3 or 4 carbons

serine (Ser) (S)

polar, nonaromatic has a hydroxyl group and one side chain carbon can H-bond

threonine (Thr) (T)

polar, nonaromatic has a hydroxyl group and two side chain carbons can H-bond

glutamine (Gln) (Q)

polar, nonaromatic has an amide side chain, which does not gain or lose protons with changing pH, so it is never a charged side-chain its side-chain has three carbons

aspargine (Asn) (N)

polar, nonaromatic has an amide side chain, which does not gain or lose protons with changing pH, so it is never a charged side-chain its side-chain has two carbons

arginine (Arg) (R)

positively charged has 3 nitrogens in its side-chain, over which the positive charge is delocalized

lysine (Lys) (K)

positively charged has a terminal primary amino group and 4 carbons in its side-chain

histidine (His) (H)

positively charged has an aromatic ring with two nitrogens (an imidazole group) pka of 6, at physiological pH, one N is protonated and the other isn't, until lower pH is met

polar, nonaromatic side chains (5)

serine threonine asparagine glutamine cysteine

R group/side chain

specific to each amino acid, it determines the chemical properties of the amino acid

proteinogenic amino acids

the 20 amino acids encoded by the human genetic code

phenylalanine (Phe) (F)

the smallest aromatic side chain has a benzyl side chain

aromatic side chains (3)

tryptophan phenylalanine tyrosine