MODULE 3 - AMINO ACIDS AND PEPTIDES (Dynamic Biomolecules)
Amino acids
- are the building blocks of proteins
It is an amino acid which has an amino group (-NH2) and a carboxylic acid (-COOH) that are attached
to a central alpha carbon (Cα), hence the name. In the non-ionized form the –NH2 and –COOH have
no charges, but remember the acidic –COOH can donate a proton (H+) while the basic –NH2 group
can accept a proton.
- An amino acid can therefore exist in the zwitterionic form wherein the acidic and basic
functional groups are ionized (as –COO- and –NH3+ respectively) but the net charge of the
molecule is still zero.
The amino and carboxylic acid moieties are common to all amino acids. What gives variety to their
structure is the variable group (R), also known as the side chain, which determines the identity and
properties of an amino acid. There are a total of 20 standard amino acids which can be broken down
into several clusters based on their polarity and net charge as illustrated in Figure 2. Non-polar
amino acids have neutral hydrophobic side chain and include the aliphatic amino acids glycine (G),
alanine (A), valine (V), leucine (L), and isoelucine (I); the cyclic and secondary amine or imino acid
proline (P); the aromatic amino acids phenylalanine (F) and tryptophan (W); and the sulfur amino
acids cysteine (C) and methionine (M). Meanwhile, polar amino acids have neutral hydrophilic side
chain particularly the alcohol amino acids serine (S) and threonine (T); the phenolic amino acid
tyrosine; and the amide amino acids asparagine (N) and glutamine (Q). Positively-charged amino
acids have polar and basic amino side chain which forms a positively-charged ammonium group and
includes lysine (K), histidine (H), and arginine (R). Lastly, negatively-charged amino acids have polar
and acidic carboxylic acid side chain which forms a negatively-charged carboxylate group and
includes aspartic acid (D) and glutamic acid (E).
Moreover, amino acids are also classified based on their nutritional requirements; essential,
conditionally essential and nonessential amino acid. By definition essential amino acid are those that
cannot be synthesized by the body and therefore must be obtained from the diet. The conditionally
essential amino acids are those that are considered essential under certain circumstances of
conditions. The table below shows the amino acid based on their nutritional classification.
Structutr and Propeties of Peptides
Amino acids can link with each other to form peptides and eventually protein. The general reaction
involved in the formation of the peptide bond is shown below which involves the condensation of
the carboxyl group of one amino acid to the amino group of another amino acid. The peptide bond is
actually an amide bond.
In a peptide, the leftmost amino acid has the free amino group, hence, is called the N-terminal end
or terminus. Meanwhile the rightmost amino acid has the free carboxyl group,hence is called the C-
terminal end or terminus. In naming a peptide, the name of all amino acids are changed to -yl except
for the C-terminal amino acid and the number prefix term such as di-, tri-, tetra-, penta-, etc. is
written to indicate dthe number of amino acids in the peptide. For example, the peptide formed by
methionine, leucine, and aspartic acid is illustrated in the figure below.