Module 10: Proteins

Primary structure: Amino acids link together to form a linear polypeptide.

The primary structure of a protein is the linear sequence of its amino acids. An amino acid
monomer (Figure 1) includes a central carbon atom, called the alpha (α) carbon. The alpha
carbon bonds to

1. a hydrogen atom,
2. an amino group (–NH3+),
3. a carboxyl group (–COO-) and
4. a side chain or R-group.

Secondary structure: Hydrogen bonds between atoms in the polypeptide backbone create
a folded or coiled shape.
Segments of the polypeptide chain can form coiled or folded patterns called the secondary
structure. Hydrogen bonds between repeating atoms in the peptide backbone produce these
secondary structures, which contribute to the overall shape of the protein. Different patterns are
formed by different hydrogen bond formations. Different segments of a polypeptide chain can
form different secondary structures, although not all regions of a polypeptide contain secondary
structure.

Consider two primary types of secondary structure in detail. Looping coils called α-helices
develop from the hydrogen bonds that form between the oxygen of a carbonyl group and the
amino group hydrogen of the amino acid four residues later in the chain. Folded patterns called
β-pleated sheets form when two or more strands of a polypeptide are parallel (in the same or
opposite directions), and hydrogen bonds form between adjacent carbonyl oxygen and amino
hydrogen atoms. Hydrogen bonds that form between strands in slightly different planes produce
a pleated pattern. The hydrogen bonds also serve to hold the parallel strands together in a sheet-
like structure

Tertiary structure: Interactions between side chains create a three-dimensional shape.

Tertiary structure is the main, three-dimensional shape of a polypeptide chain. This shape
results from, and is held together by, bonds and interactions between R-groups and atoms of the
peptide backbone and between different R-groups themselves. These bonds and interactions are
highly dependent on the chemical properties of the R-groups and include

• Hydrophobic interactions — clustering of nonpolar side chains, which are

hydrophobic, with each other and toward the core of the protein in a manner that minimizes
contact with water molecules in the surrounding fluid.
• Hydrogen bonding — polar R-groups can form hydrogen bonds with other polar R-
groups, carbonyl and amino groups in the peptide backbone, and water molecules in the
surrounding fluid.
• Disulfide bridges — the sulfur-containing R-group of cysteine can bind covalently
with the R-group of an adjacent cysteine, forming what is known as a disulphide bridge between
the two cysteine residues.
• Ionic bonding — an ionic bridge can form between adjacent positively and negatively
charged R-groups.
 • van der Waals forces — when non polar amino acids are close together, these weak
electrostatic forces can add stability to the structure.

Quaternary structure: Associations of polypeptides form a functional protein.

Many proteins contain multiple polypeptide units assembled into a functional macromolecule,
which may include multiple copies of the same polypeptide unit, different polypeptide units, or
both. These proteins have a quaternary structure resulting from the aggregation of separate
identical or different polypeptides, known as subunits.

Hemoglobin is an oxygen-transport protein found in the red blood cells of most vertebrates. It is
a quaternary structure of four separate polypeptides and is therefore sometimes called a
tetramer. Click on the interactive diagram in Figure 6 to investigate the levels of structure in
hemoglobin.

Collagen is one of the most ubiquitous proteins in the bodies of vertebrates. Collagen is made up
of three separate polypeptides, each with a left-handed helical secondary structure.