Amino acids

Amino Acid Structure

Amino NH2 Group, Carboxyl COO- group, H, R (side chain)

Peptide bond = bond b/w Amino group of one AA and carboxyl group of second AA

Glycine

Gly/G
literally just an H
Neither strongly polar nor nonpolar

Alanine

Ala/A
Just a methyl group (CH3)
Non polar

Valine

Val/V
HC—(CH3)2
Non polar

Leucine

Leu/L
Nonpolar
CH2—CH—(CH3)2

Isoleucine

Ile/I
Nonpolar
CH3—*CH—CH2—CH3
*marks the beta carbon attached to the alpha carbon

Serine

Ser/S
CH2—OH
Neither strongly polar nor nonpolar

Threonine

Thr/T
OH—*C—CH3
*marks the C attached to the alpha C
Neither strongly polar nor nonpolar

Aspartate/aspartic acid

Asp/D
*CH2—COO^-
Polar
Acidic (can be - charged, typically charged at pH7)

Asparagine

Asn/N
*CH2—CON
Polar

Glutamate/Glutamic Acid

Glu/E
*CH2—CH—COO^-
Polar
Acidic (can be - charged, typically charged at pH7)

Glutamine

Gln/Q
*CH2—CH2—CONH2
Polar

Lysine

Lys/K
*CH2—CH2—CH2—CH2—NH3+
Polar
Basic (can be + charged, typically charged at pH7)
Can be a chemical modification on proteins

Arginine

Arg/R
*CH2—CH2—CH2—NH—CNH₂⁺NH₂
Note: The NH₂⁺ is doubly bonded to the C, which is why it is positive charged
Polar
Basic (can be + charged, typically at pH7)

Histidine

His/H
Aromatic ring structure
*CH=CH—NH⁺=CH—NH—reattached to the beta C to form a ring
Polar
Basic (can be + charged, typically at pH7)
Often at enzyme active site accepting/donating H+
This ring structure can interconvert! Resonance!!

Tryptophan

Trp/W
Aromatic ring structure → 2 rings!!
Nonpolar

Phenylalanine

Phe/F
Alanine but with a phenyl attached! *CH2—Ph
Aromatic ring!!
Nonpolar

Tyrosine

Tyr/Y
*CH2—Ph—OH
Aromatic Ring!!
Neither strongly polar nor nonpolar

Proline

Pro/P
Special ring structure → it is relinked to the backbone N (amino group)
*CH2—CH2—CH2—NH2⁺ (the amino group on the alpha C)
Neither strongly polar nor nonpolar
restricted fit inside protein due to ring structure
Cannot be an H-bond donor if peptide bonded because it will not have an N—H

Cysteine

Cys/C
*CH2—SH
Nonpolar at pH<8
Can make disulfide bonds with itself

Methionine

Met/M
*CH2—CH2—S—CH3
Nonpolar

Aliphatic amino acids

hydrocarbons

Glycine, alanine, valine, leucine, isoleucine

Aromatic amino acids

Phenylalanine, tyrosine, tryptophan (and histidine)

Sulfur containing amino acids

Cysteine and methionine

Aliphatic-OH amino acids

containing OH, often in enzyme active site
Can be chemically modified (like with a phosphate) to change the enzyme

Serine and threonine

Acidic vs amid amino acids

Aspartate and glutamate are acidic and contain a -COOH group
Acidic AA will be at enzyme active site to donate/accept H+ and strongly interact with H2O and ions
Typically charged near pH7

Asparagine and glutamine will have the same structure as there similarly named counterpart, but with an amid (-CONH2) instead of COOH

Basic amino acids

Histidine, arginine, lysine
Typically charged near pH7