GNN | Basics of Protein and Protein Structure

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Protein Backbone

The protein backbone refers to the main structural component of a protein molecule, excluding the side chains of the amino acids. It consists of a repeated sequence of the atoms along the peptide bond, specifically the nitrogen atom (N), the alpha carbon (Cα), and the carbonyl carbon ©. These atoms form the core structure to which the amino acid side chains are attached.

This backbone is responsible for the overall shape and structure of the protein, and it plays a critical role in determining the protein’s three-dimensional conformation through various types of secondary structures like alpha helices and beta sheets. The backbone’s conformation is stabilized by hydrogen bonds and other interactions, which are crucial for the protein’s function.

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Protein

A protein is a large, complex molecule that plays many critical roles in biological organisms. It is made up of one or more long chains of amino acids, which are the building blocks of proteins.

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Amino Acids

Proteins are composed of 20 different amino acids. Each amino acid consists of a central carbon atom (Cα) bonded to an amino group (NH₂), a carboxyl group (COOH), a hydrogen atom, and a distinctive side chain (or R group) that varies between different amino acids.

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Protein Residue

A protein residue refers to an individual amino acid that is part of a larger protein chain, after it has been incorporated into the protein through the process of peptide bond formation. When amino acids join together in a polypeptide chain, they lose water molecules as the peptide bonds form between the amino group of one amino acid and the carboxyl group of another. This leaves behind a “residue” of each amino acid within the chain. Here are the key aspects of a protein residue:

Formation of Protein Residues

Peptide Bonds: As amino acids form peptide bonds during protein synthesis, they lose elements that form water (specifically, two hydrogens and one oxygen atom). What remains in the protein chain after this condensation reaction is considered the residue of the amino acid.
Structure: A residue includes the central carbon (Cα), the amino group, the carboxyl group that’s part of the peptide bond, and the distinctive side chain (R group). The hydrogen atom that originally was part of the amino group is no longer present in the formed peptide bond.

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