Chapter 27: Amino Acids, Peptides and Proteins

The generic structure of an α-amino acid

• The 20 naturally occurring α-amino acids used by cells to synthesise proteins can be generally represented by the generic formula shown above.
• The means the main difference between the various amino acids lies in the structure of the "R" group.
• These 20 α-amino acids can be sub-classified according to how the properties of other functional groups in the "R" group influence the system.
• non-polar side chains (e.g. alkyl groups)
• polar (e.g. amides, alcohols)
• acidic (e.g. carboxylic acids, phenols)
• basic (e.g. amines)

Amino acids with non-polar side chains. The hydrophobic side chains are chemically unreactive and tend to aggregate rather than be exposed to the aqueous environment, so they tend to found on the interior of proteins.  Hydrophobic means "water hating" - remember "oil and water don't mix" and "like dissolves like" - this is because non-polar hydrocarbons do not interact with polar water molecules in an energetically favourable way - they would rather interact with another non-polar hydrocarbon molecule : this it the hydrophobic effect - the aggregation of non-polar systems in an aqueous environment.
(see also "micelles")
 

Amino acid	Abbreviations	Structural Formula	3D-representation
Glycine	Gly (G)
Alanine	Ala (A)
Valine	Val (V)
Leucine	Leu (L)
Isoleucine	Ile (I)
Methionine	Met (M)
Proline	Pro (P)
Phenylalanine	Phe (F)
Tryptophan	Trp (W)

Amino acids with polar side chains.  These are side chains can be involved in hydrogen bonding interactions. Cysteine is important because of its ability to form disulfide bonds.

Amino acid	Abbreviations	Structural Formula	3D-representation
Asparagine	Asn (N)
Glutamine	Gln (Q)
Serine	Ser (S)
Threonine	Thr (T)
Tyrosine	Tyr (Y)
Cysteine	Cys (C)

Amino acids with acidic side chains. These carboxylate group will be -ve at physiological pH.   Often involved at the active sites of enzymes, in hydrogen bonding interactions and in acid/base type reactivity.
 

Amino acid	Abbreviations	Structural Formula	3D-representation
Aspartic acid	Asp (D)
Glutamic acid	Glu (E)

Amino acids with basic side chains.  Often involved at the active sites of enzymes, in hydrogen bonding interactions and in acid/base type reactivity (e.g. histidine)

Amino acid	Abbreviations	Structural Formula	3D-representation
Lysine	Lys (K)
Arginine	Arg (R)
Histidine	His (H)

© Dr. Ian Hunt, Department of Chemistry