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Nomenclatue of Amino acids

Common amino acids

There are 20 common amino acids. They are composed of C, H, O, N and S atoms. They are structurally and chemically different, and also differ in size and volume. Some are branched structures, some are linear, some have ring structures. One of the 20 common amino acids is actually an imino acid. A typical grouping of their chemical nature is as follows:

  • Nonpolar (hydrocarbons and one sulfur-containing amino acid). Dispersion forces and hydrophobic effects predominate in their interactions. They cannot H-bond with water and these side chains have a characteristic hydrophobic effect in water.
  • Polar uncharged. Contain functional groups that can H-bond with water and other amino acids. Include C, H, O, N and S atoms.
  • Acidic. Contain a carboxylic acid functional group with a negative charge at neutral pH. Can H-bond with water, can form ionic interactions, and can also serve as nucleophiles or participate in acid-base chemistry.
  • Basic. Nitrogen containing bases (e.g. guanidino, imidazole or amino groups) with a net positive charge at neutral pH. Can serve as proton donors in chemical reactions, and form ionic interactions.

The amino acids have a name, as well as a three letter or single letter mnemonic code:

Type

Name

R-group Structure

Nonpolar

Leucine

Leu, L

leu.jpg

 

Isoleucine

Ile, I

Ile.jpg

 

Valine

Val, V

val.jpg

 

Alanine

Ala, A

ala.jpg

 

Methionine

Met, M

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Phenylalanine

Phe, F

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Tryptophan

Trp, W

trp.jpg

 

Proline

Pro, P

pro.jpg

 

Glycine

Gly, G

(note: sometimes included in polar group)

gly.jpg

Polar, uncharged

Serine

Ser, S

ser.jpg

 

Asparagine

Asn, N

asn.jpg

 

Glutamine

Gln, Q

 

Threonine

Thr, T

thr.jpg

 

Cysteine

Cys, C

cys.jpg

 

Tyrosine

Tyr, Y

tyr.jpg

Acidic

Aspartic acid

Asp, D

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Glutamic acid

Glu, E

glu.jpg

Basic

Lysine

Lys, K

lys.jpg

 

Arginine

Arg, R

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Histidine

His, H

his.jpg

Uncommon amino acids

In addition to the 20 common amino acids, there are several uncommon ones found:

  • Hydroxylysine and hydroxyproline. These are found in the protein collagen. Collagen is a fibrous protein made up of three polypeptides that form a stable assembly, but only if the proline and lysine residues are hydroxylated. (requires vitamin C for reduction of these amino acids to hydroxy form)
  • Thyroxine, an iodinated derivative of tyrosine, found in thyroglobulin (produced by thyroid gland; requires iodine in diet)
  • g-carboxyglutamic acid (i.e. glutamic acid with two carboxyl groups) found in certain blood clotting enzymes (requires vitamin K for production)
  • N-methyl arginine and n-acetyl lysine. Found in some DNA binding proteins known as histones

Amino acid derivatives not found in proteins

Some amino acids are made that are not intended for incorporation into proteins, rather they have important functionalities on their own

  • Serotonin (derivative of tryptophan) and g-amino butyric acid (a derivative of glutamic acid) are both neurotransmitters
  • Histamine (derivative of histidine) involved in allergic response
  • Adrenaline (derivative of tyrosine) a hormone
  • Various antibiotics are amino acid derivatives (penicillin)