Structure and Nomenclature of Peptides and Proteins
Peptides
A peptide consists of short chain of amino acids linked by a peptide (amide) bonds formed between the carboxyl group of one amino acid and the amino group of another with the removal of water molecule.
The number of amino-acid molecules present in a peptide is indicated by a prefix: a dipeptide contains two amino acids; a tripeptide containing three amino acids; tetrapeptide containing four amino acids ; an octapeptide, eight ; a polypeptide, many.
Polypeptides are formed by long peptide chains containing large numbers of peptide bonds. Polymers of up to 100 amino acids are termed polypeptides and those with more than 100 are generally termed proteins.
The amino acid component retaining a free amine group is drawn at the left end (the N-terminus) of the peptide chain, and the amino acid retaining a free carboxylic acid is drawn on the right (the C-terminus). As expected, the free amine and carboxylic acid functions on a peptide chain form a zwitter ionic structure at their isoelectric pH.
Peptides v/s Proteins
Peptides and proteins have similarities in form and function.
Functionally, both play vital roles in a wide array of biological functions. They serve as the body’s building blocks.
For peptides and proteins, size refers to the number of amino acids it contains. Here’s how they differ:
- Peptides – 2-10 amino acids
- Polypeptides (a subcategory of peptides) – 10-50 amino acids
- Proteins – 51 and more amino acids
Essentially, one or more polypeptides make up proteins. So, a protein is a large peptide.
Depending on the amino acid sequence and interactions with their environment, proteins fold into a three-dimensional structure, which allows them to interact with other proteins and molecules and perform their function.
Levels of Proteins
Primary structure
The primary structure of a protein refers to the sequence of amino acids in the polypeptide chain. The primary structure is held together by peptide bonds that are made during the process of protein biosynthesis.
The exact sequence of the proteins is very important as it determines the final fold and therefore the function of the protein.
Secondary structure
These polypeptide chains usually fold due to the interaction between the amine and carboxyl group of the peptide link.They are found to exist in two different types of structures α – helix and β – pleated sheet structures.
These secondary structures are defined by patterns of hydrogen bonds between the main-chain peptide groups. Both the α-helix and the β-sheet represent a way of saturating all the hydrogen bond donors and acceptors in the peptide backbone.
In an α helix, the carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid.This pattern of bonding pulls the polypeptide chain into a helical structure that resembles a curled ribbon.
In a β pleated sheet, two or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds.
The strands of a β pleated sheet may be parallel, pointing in the same direction (meaning that their N- and C-termini match up), or antiparallel, pointing in opposite directions (meaning that the N-terminus of one strand is positioned next to the C-terminus of the other).
Tertiary structure
This structure arises from further folding of the secondary structure of the protein.H-bonds, electrostatic forces, disulphide linkages, and Vander Waals forces stabilize this structure.The tertiary structure of proteins represents overall folding of the polypeptide chains, further folding of the secondary structure.It gives rise to two major molecular shapes called fibrous and globular.The main forces which stabilize the secondary and tertiary structures of proteins are hydrogen bonds, disulphide linkages, van der Waals and electrostatic forces of attraction.
There’s one special type of covalent bond that can contribute to tertiary structure: the disulfide bond. Disulfide bonds, covalent linkages between the sulfur-containing side chains of cysteines, are much stronger than the other types of bonds that contribute to tertiary structure. They act like molecular "safety pins," keeping parts of the polypeptide firmly attached to one another.
Quartenary structure
Quaternary structure is the three-dimensional structure consisting of the aggregation of two or more individual polypeptide chains (subunits) that operate as a single functional unit.
The resulting multimer is stabilized by the same non-covalent interactions and disulfide bonds as in tertiary structure.Complexes of two or more polypeptides (i.e. multiple subunits) are called multimers.
Proteins are frequently described as consisting of several structural units. These units include domains, motifs, and folds. Despite the fact that there are about 100,000 different proteins expressed in eukaryotic systems, there are many fewer different domains, structural motifs and folds.
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