Amino acid

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

free unlinked 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)

amino acid peptide bond amine linkage structure

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

amino acid glycine structure

GGU GGC GGA GGG

Alanine, Ala, A

amino acid alanine structure

GCU GCC GCA GCG

Valine, Val, V

amino acid valine structure

GUU GUC GUA GUG

Leucine, Leu, L

amino acid leucine structure

UUA UUG CUU CUC CUA CUG

Isoleucine, Ile, I

amino acid isoleucine structure

AUU AUC AUA

Proline, Pro, P

amino acid proline structure

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

amino acid phenylalanine structure

UUU UUC

Tyrosine, Tyr, Y

amino acid tyrosine structure

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

amino acid tryptophan tryptofane structure

UGG

Polar Non-Charged (Hydroxilic) Amino Acids

Serine, Ser, S

amino acid serine structure

UCU UCC UCA UCG AGU AGC. Approximate pKa of serine hydroxyl: 13.

Threonine, Thr, T

amino acid threonine structure

ACU ACC ACA ACG. Approximate pKa of threonine hydroxyl: 13.

Polar Non-Charged (Sulfurous) Amino Acids

Cysteine, Cys, C

amino acid cysteine structure

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

amino acid methionine structure

AUG

Polar Non-Charged Amidic Amino Acids

Asparagine, Asn, N

amino acid asparagine structure

AAU AAC

Glutamine, Gln, Q

amino acid glutamine structure

CAA CAG

Positively Charged (Basic) Amino Acids

Lysine, Lys, K

amino acid lysine structure

AAA AAG. Approximate pKa of lysine amino: 10.5.

Arginine, Arg, R

amino acid arginine structure

CGU CGC CGA CGG AGA AGG. Approximate pKa of arginine guanidino: 12.5

Histidine, His, H

amino acid histidine structure

CAU CAC. Approximate pKa of histidine imidazole: 6.

Negatively Charged (Acidic) Amino Acids

Aspartate, Asp, D

amino acid aspartate structure

GAU GAC. Approximate pKa of aspartate carboxyl: 4.

Glutamate, Glu, E

amino acid glutamate structure

GAA GAG. Approximate pKa of glutamate carboxyl: 4.

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