Bughao, Maria Angelika A.

BSN-1B

The Secondary Structure of Protein

 The chain of covalently linked of amino acid, folds or align into regularly repeating patterns that
resemble designs in a tapestry. These repeating patterns define as the Secondary structure of the
protein. The secondary structure is the result of hydrogen bonding between the amide hydrogens
and carbonyl oxygens of the peptide bonds. Many hydrogens bonds are needed to maintain the
secondary structure and there by the overall structure of the protein. Different regions of the
protein chain may have different types of secondary structure. Some regions of a protein chain
may have a random or non-regular structure.
 In all secondary structures the hydrogen bonding is between backbone –C=O and H-N- groups, a
characteristic that distinguishes between secondary and tertiary structures. In the latter, as we
shall see, the hydrogen bonding can take place between R groups on the side chains
 The two most common secondary structures encountered in proteins are the α-helix and the β-
pleated sheet, which were proposed by Linus Pauling and Robert Corey in the 1940s. In contrast,
those protein conformations that do not exhibit a repeated pattern are called “random coils”.

The Two Most Common Types of Secondary Structure:

1. α-helix

The most common type of Secondary structure is a coiled, helical conformation known as the α-
helix or alpha α-helix.

Important Features:

 Every amide hydrogen and carbonyl oxygen associated with the peptide backbone is involved in a
hydrogen bond when the chain coils into an α-helix. These hydrogen bonds lock the α-helix into
place.
 Every Carbonyl oxygen is hydrogen- bonded to an amide hydrogen four amino acids away in the
chain.
 The hydrogen bonds of the α-helix are parallel to the long axis of the helix.
 The shape of the helix is maintained by numerous Intramolecular hydrogen bonds that exist
between the backbone –C=O and H-N- groups.
  These hydrogen bonds are in just the right position to cause the molecules (or a portion of it) to
maintain a helical shape. Each –H-N points upward and each –C=O points downward. All the
amino acid side chains point outward from the helix.
 Keratin, a fibrous protein of hair, fingernails, horns, and wool, is one protein that does have a
predominantly α-helix structures.

To N- Terminal

To C- Terminal

2. β-pleated sheet

 The pleated folds of drapery and is known as the β-pleated sheet. All of the carbonyl oxygens and
amide hydrogens in a β-pleated sheet are involved in hydrogen bonds and the polypeptide chain is
nearly completely extended. The polypeptide chains in a β-pleated sheet can have z orientations.
 If the N-Termini are head to head, the structure is known as a parallel β-pleated sheet. And if the
N-Terminus of one chain is aligned with the C- Terminus of second chain (head to tail), the
structure is known as an antiparallel β-pleated sheet.
 β-pleated sheet can also occur intramolecularly when the polypeptide chain makes a U-turn
forming a hairpin structure, and the pleated sheet is antiparallel.
 Formed when 2 or more polypeptides line up side by side.
  Individual polypeptide- beta strand.
 Each beta strand is fully 3 extended.
 Silk is made of fibroin, another fibrous protein, which exists mainly in the β-pleated sheet form.
Silkworm silk and especially spider silk exhibit a combination of strength and toughness that is
unmatched by high-performance synthetic fibers. In its primary structure, silk contains sections
that consist of only alanine (25%) and glycine (42%). The formation of β-pleated sheet, largely
by the alanine sections, allows microcrystals to orient themselves along the fiber axis, which
account for the materials superior tensile strength.

Another Repeating Pattern Classified as a Secondary Structure is the…

Extended Helix

 It is quite different from the α-helix. Collagen is the structural protein of connective tissues (bone,
cartilage, tendon, blood vessels, skin), where it provides strength and elasticity.
 The most abundant protein in humans, it makes up about 30% by weight of all the body’s protein.
 Each strand of collagen consist of repetitive units that can be symbolized as Gly-x-y; that is every
third amino acid in the chain is glycine. Of course, has the shortest side chain (-H) of all amino
acids. About one third of the X amino acid is proline, and the Y is often hydroxyproline.
Other Information about Secondary Structure of Protein:

 Few protein have predominantly α-helix or β-pleated sheet structures. Most proteins, especially
globular ones, have only certain portions of their molecules in these conformations. The rest of
the molecule consist of random coil. Many globular proteins contains all three kinds of secondary
structures in different parts of their molecules; α-helix, β-pleated sheet, and random coil. Shows a
schematic representation of such structure.

References:

Bettelheim F., et al. (2007). Bettelheim’s Introduction to General, Organic, and Biochemistry 8 th edition.
Quezon City. C&E Publishing, Inc.

Bettelheim F., et al. (2016). Biochemistry. Quezon City. C&E Publishing, Inc.

Denniston K., et al. (2014).General, Organic, and Biochemistry. New York. Mc Graw-hill Companies.