Secondary and Tertiary Structures of Protein

Overview:
A protein molecule is very big compared to most of the other organic molecules. It is
composed of small units called amino acids organised in long chains and similar proteins
have similar structure. There are 20 different kinds of natural amino acids. There are 4 levels
to structures of proteins, namely-
• Primary Structure
• Secondary Structure
• Tertiary Structure
• Quaternary Structure
Here we will be talking only about the Secondary and Tertiary structures.

Secondary Structure:
The localized organization of parts of the polypeptide chain refers to the secondary
structure. It can assume a number of different spatial arrangements and single polypeptide
may exhibit all types of secondary structure. Without any stabilizing interactions, a
polypeptide assumes a random-coil structure. However, when stabilizing hydrogen bonds
form between certain parts of the chain, the backbone folds periodically into one of two
geometric arrangements:

 α-helix is a spiral right-handed coiled strand. The side-chain substituents of the

amino acid groups in an α-helix extend to the outside. Hydrogen bonds form
between the oxygen of each C=O bond in the strand and the hydrogen of each N-H
group four amino acids below it in the helix. The hydrogen bonds make this structure
especially stable. The side-chain substituents of the amino acids fit in beside the N-H
groups.
  β sheet, a planar structure composed of alignments of two or more β strands, which
are relatively short, fully extended segments of the backbone. The hydrogen bonding
in a ß-sheet is between strands (inter-strand) rather than within strands (intra-
strand). The sheet conformation consists of pairs of strands lying side-by-side. The
carbonyl oxygens in one strand bonds with the amino hydrogens of the adjacent
strand. The two strands can be either parallel or anti-parallel depending on whether
the strand directions (N-terminus to C-terminus) are the same or opposite. The anti-
parallel ß-sheet is more stable due to the more well-aligned hydrogen bonds.

Tertiary Structure:
Tertiary structure refers to the complete 3-dimensional structure of the whole protein or
sum of all the secondary structure units. It is a unique and defining feature of proteins. If a
protein loses its three-dimensional shape, it is usually no longer functional. The protein
molecule will achieve an orientation to attain lowest energy state or maximum stability. This
structure of proteins is defined by various chemical interactions like hydrophobic
interactions, ionic bonding, hydrogen bonding and disulphide linkages.
disulphide bridges are formed by oxidation of the sulfhydryl groups on cysteine
and they are an important aspect of the stabilization of tertiary structure, they allow
different parts of the protein chain to be held together. Additionally, hydrogen bonds may
form between different side-chain groups. As with disulphide bridges, these hydrogen bonds
can bring together two parts of a chain that are some distance away in terms of sequence.
Salt bridges, ionic interactions between positively and negatively charged sites on amino
acid side chains, also help to stabilize the tertiary structure of a protein. These are the
important non covalent interactions which help stabilize the tertiary structure of proteins.

Submitted by- Girish

Roll no.- UG/2020/012