Amino acids have important roles in living organisms: they are the subunits (building blocks) of peptides and proteins.
There are 23 naturally occuring amino acids present in all organisms. Their structure is shown below: the NH3+ is an amine (amino); the COOH forms COO- at ph7 (acid); and the R represents the functional group, which is different in each amino acid.
The functional group is also called the side chain because amino acids are linked to one another in such a way that the R groups just hang off the side of the peptide chain.
The final folded structure of a protein is determined by its amino acid sequence, aided by molecular chaperones and stabilized primarily by noncovalent interactions.
This native conformation is crucial to its function. Proteins translated by the ribosome contain all L amino acids, though some proteins are later modified to include D amino acids (see Fischer Projection nomenclature).
Sequences of amino acids (aka peptide sequences are named according to their amino acids, which are assumed to all be L unless indicated otherwise.
Free Amino Acid Structure
Approximate pKa of α-carboxyl of free amino acid: 2
Approximate pKa of α-amino of free amino acid: 9.5
Amino Acid Peptide Bond (aka Amine Linkage)
Approximate pKa of C-terminal carboxyl of peptide: 3
Approximate pKa of N-terminal amino of peptide: 8
Aliphatic (Non-Polar) Amino Acids
Glycine, Gly, G
GGU GGC GGA GGG
Alanine, Ala, A
GCU GCC GCA GCG
Valine, Val, V
GUU GUC GUA GUG
Leucine, Leu, L
UUA UUG CUU CUC CUA CUG
Isoleucine, Ile, I
AUU AUC AUA
Proline, Pro, P
CCU CCC CCA CCG
Aromatic Amino Acids
The aromatic amino acids are rather nonpolar and thereby exhibit hydropathy (they are hydrophobic).
Phenylalanine is the least polar. Tyrosine's hydroxyl and tryptophan's indole ring increase their polarity, but they are still hydrophobic. Tyrosine and tryptophan, and to a much lesser extent phenylalanine, are able to absorb ultraviolet light at a wavelength of 280nm.
Thus, proteins have this same property; researchers exploit this when characterizing proteins.
Phenylalanine, Phe, F
Tyrosine, Tyr, Y
UAU UAC. Approximate pKa of tyrosine hydroxyl: 10.5. Tyrosine's hydroxyl can form hydrogen bonds, and is an important functional group for some enzymes.
Tryptophan, Trp, W
Polar Non-Charged (Hydroxilic) Amino Acids
Serine, Ser, S
UCU UCC UCA UCG AGU AGC. Approximate pKa of serine hydroxyl: 13.
Threonine, Thr, T
ACU ACC ACA ACG. Approximate pKa of threonine hydroxyl: 13.
Polar Non-Charged (Sulfurous) Amino Acids
Cysteine, Cys, C
UGU UGC. Approximate pKa of cysteine sulfhydryl: 8.5. C and S have very close electronegativities so C-S bonds are not really polar. Thus, cysteine does not really behave like a polar molecule.
Methionine, Met, M
Polar Non-Charged Amidic Amino Acids
Asparagine, Asn, N
Glutamine, Gln, Q
Positively Charged (Basic) Amino Acids
Lysine, Lys, K
AAA AAG. Approximate pKa of lysine amino: 10.5.
Arginine, Arg, R
CGU CGC CGA CGG AGA AGG. Approximate pKa of arginine guanidino: 12.5
Histidine, His, H
CAU CAC. Approximate pKa of histidine imidazole: 6.
Negatively Charged (Acidic) Amino Acids
Aspartate, Asp, D
GAU GAC. Approximate pKa of aspartate carboxyl: 4.
Glutamate, Glu, E
GAA GAG. Approximate pKa of glutamate carboxyl: 4.