Amino Acids

amino acids can be hydrophobic, hydrophilic, or charged (3 groups)

Hydrophobic groups (nonpolar):

• glycine(gly, G), Alanine (Ala, A), Valine (Val,V), Leucine (Leu,L), Isoleucine (Ile,I), Methionine (Met, M), Phenylalanine (Phe, F), Tryptophan (Trp, W), Proline(Pro,P)

  • Proline: side chain is connected to the main chain

Hydrophilic (polar)

• Serine(Ser, S), Threonine (Thr, T), Cysteine(Cys, C), Tyrosine(Tyr, Y), Asparagine(Asn, N), Glutamine(Gln, Q)

Charged

• acidic negatively charged (very polar) (negative oxygen at the end)

  • aspartic acid (asp, D), Glutamic acid(Glu, E)

• basic positively charged (amino groups at the end)

  • Lysine(lys,K), Arginine(Arg, R), Histidine(His, H)

Glycine is most flexible amino acid because it has smallest side chain and can move rotate and bend easier

Aliphatic side chains: alanine, valine, isoleucine, leucine

Hydroxyl containing side chains: serine, threonine

negatively charged acidic residues: aspartate, glutamate

basic side chains: lysine, arginine (NOT HISTIDINE bc at pH 7, 90% not charged)

amid-containing residues: asparagine, glutamine

proline: cyclic ring imposes constraints on N-Ca bond

Histidine: partially charged around pH7

aromatic residues: phenylalanine, tyrosine, tryptophan

Sulphur containing residues: cysteine and methionine

cysteine may get close to another cysteine and form a covalent bond (only amino acid whose side chain can form covalent bond ie. disulfide bond) which makes it more durable

• acts as antibody

  • antibodies always have heavy chain with 2 disulfide bonds and is very sturdy and light chain connected by disulfide bond

    • heavy chain is in all antibodies
      ALL AMINO ACIDS

Alanine(A, Ala): nonpolar, small sidechain, unreactive

Arginine (R, Arg): positively charged, ionic interactions with negatively charges, contains acid

Asparagine(N, Asn): polar, uncharged, can form hydrogen bonds, small, frequently abundant, hydrophilic

Aspartate(D, Asp): negatively charged, interacts with positively charged groups

Cysteine(C, Cys): contains SH group (sulfur), very reactive, polar, can form polar bond with other cysteine, hydrophilic

Glutamine(Q, Gln): polar, uncharged, hydrogen bond, hydrophilic, contains acid

Glutamate(E, Glu): negatively charged, commonly replaces aspartate (acid)

Glycine(G, Gly): uncharged, smallest, very replaceable, hydrophobic, nonpolar

Histidine(H, His): contains C3N2H4 ring, positively charged (partially), basic, pH around 7

Isoleucine(I, Ile): hydrophobic, non polar, unreactive, aliphatic, commonly replaces valine

Leucine(L, Leu): hydrophobic, nonpolar, aliphatic

Lysine(K, Lys): positively charged, ionic interactions, basic

Methionine(M, Met): contains Sulfur, unreactive, nonpolar, hydrophobic

Phenylalanine(F, Phe): hydrophobic, aromatic, unreactive, nonpolar

Proline(P, Pro): cyclic ring, hydrophobic, nonpolar

Serine(S, Ser), polar, uncharged, contains -OH hydroxyl group, hydrogen bonds, hydrophilic, commonly replaces alanine and threonine

Threonine(T, Thr): polar, uncharged, contains -OH hydroxyl group, hydrogen bonds. hydrophilic

Tryptophan(W, Trp): large, hydrophobic, aromatic, reactive w/ nitrogen, nonpolar

Tyrosine(Y, Tyr): aromatic, contains -OH hydroxyl group, ionizes at pH 0, hydrophilic

Valine(V, Val): hydrophobic, aliphatic, nonpolar, hydrophobic

Polar side chains: will have electronegative elements such as O, S, N

Acidic: negatively charged O

Basic: positively charge N