3.0 AMINO ACIDS, PEPTIDES AND PROTEINS
3.1. Overview
Proteins are the most abundant and functionally diverse molecules in living systems. Virtually
every life process depends on this class of molecules. For example, enzymes and polypeptide
hormones direct and regulate metabolism in the body, whereas contractile proteins in muscle
permit movement. In bone, the protein collagen forms a framework for the deposition of
calcium phosphate crystals, acting like the steel cables in reinforced concrete. In the
bloodstream, proteins, such as haemoglobin and plasma albumin, shuttle molecules essential
to life, whereas immunoglobulins fight infectious bacteria and viruses. In short, proteins
display an incredible diversity of functions, yet all share the common structural feature of being
linear polymers of amino acids. This chapter describes the properties of amino acids and
explores how these simple building blocks are joined to form proteins that have unique three-
dimensional structures, making them capable of performing specific biologic functions.
3.2. Structure of Amino Acids
Although more than 300 different amino acids have been described in nature, only twenty are
commonly found as constituents of mammalian proteins. These 20 are the only amino acids
that are coded for by DNA, the genetic material in the cell. Each amino acid (except for
proline,) has a carboxyl group, an amino group, and a distinctive side chain ("R-group")
bonded to the α-carbon atom. All of the substituents in amino acid are attached (bonded) to a
central α carbon atom. This carbon atom is called α because it is bonded to the carboxyl
(acidic) group. The general formula for the naturally occurring amino acids would be:
• A basic amino group (-NH2)
• An acidic carboxyl group (-COOH)
• A hydrogen atom (-H)
• A distinctive side chain (-R)
At physiologic pH (approximately pH = 7.4), the carboxyl group is dissociated, forming the
negatively charged carboxylate ion (-COO-) and the amino group is protonated (-NH3+). In
, proteins, almost all of these carboxyl and amino groups are combined in peptide linkage and,
in general, are not available for chemical reaction except for hydrogen bond formation. Thus,
it is the nature of the side chains that ultimately dictates the role an amino acid plays in a
protein. It is therefore, useful to classify the amino acids according to the properties of their
side chain; that is, whether they are non-polar (that is, have an even distribution of electrons)
or polar (that is, have an uneven distribution of electrons, such as acids and bases.
3.3. Classification of Amino Acids Based on Structure and Side Chain
Knowledge of the chemical properties of the common amino acids is central to an
understanding of biochemistry. The topic can be simplified by grouping the amino acids into
seven main classes based on the properties of their R groups (Table below), in particular, their
polarity, or tendency to interact with water at biological pH (near pH 7.4). The polarity of the
R groups varies widely, from non-polar and hydrophobic (water-insoluble) to highly polar and
hydrophilic (water-soluble). With the sole exception of glycine, the α-carbon of amino acids is
chiral. The 20 amino acids listed in the table below, classified according to the polarity of their
R-groups.
3.1. Overview
Proteins are the most abundant and functionally diverse molecules in living systems. Virtually
every life process depends on this class of molecules. For example, enzymes and polypeptide
hormones direct and regulate metabolism in the body, whereas contractile proteins in muscle
permit movement. In bone, the protein collagen forms a framework for the deposition of
calcium phosphate crystals, acting like the steel cables in reinforced concrete. In the
bloodstream, proteins, such as haemoglobin and plasma albumin, shuttle molecules essential
to life, whereas immunoglobulins fight infectious bacteria and viruses. In short, proteins
display an incredible diversity of functions, yet all share the common structural feature of being
linear polymers of amino acids. This chapter describes the properties of amino acids and
explores how these simple building blocks are joined to form proteins that have unique three-
dimensional structures, making them capable of performing specific biologic functions.
3.2. Structure of Amino Acids
Although more than 300 different amino acids have been described in nature, only twenty are
commonly found as constituents of mammalian proteins. These 20 are the only amino acids
that are coded for by DNA, the genetic material in the cell. Each amino acid (except for
proline,) has a carboxyl group, an amino group, and a distinctive side chain ("R-group")
bonded to the α-carbon atom. All of the substituents in amino acid are attached (bonded) to a
central α carbon atom. This carbon atom is called α because it is bonded to the carboxyl
(acidic) group. The general formula for the naturally occurring amino acids would be:
• A basic amino group (-NH2)
• An acidic carboxyl group (-COOH)
• A hydrogen atom (-H)
• A distinctive side chain (-R)
At physiologic pH (approximately pH = 7.4), the carboxyl group is dissociated, forming the
negatively charged carboxylate ion (-COO-) and the amino group is protonated (-NH3+). In
, proteins, almost all of these carboxyl and amino groups are combined in peptide linkage and,
in general, are not available for chemical reaction except for hydrogen bond formation. Thus,
it is the nature of the side chains that ultimately dictates the role an amino acid plays in a
protein. It is therefore, useful to classify the amino acids according to the properties of their
side chain; that is, whether they are non-polar (that is, have an even distribution of electrons)
or polar (that is, have an uneven distribution of electrons, such as acids and bases.
3.3. Classification of Amino Acids Based on Structure and Side Chain
Knowledge of the chemical properties of the common amino acids is central to an
understanding of biochemistry. The topic can be simplified by grouping the amino acids into
seven main classes based on the properties of their R groups (Table below), in particular, their
polarity, or tendency to interact with water at biological pH (near pH 7.4). The polarity of the
R groups varies widely, from non-polar and hydrophobic (water-insoluble) to highly polar and
hydrophilic (water-soluble). With the sole exception of glycine, the α-carbon of amino acids is
chiral. The 20 amino acids listed in the table below, classified according to the polarity of their
R-groups.
