Protein Structure Levels & Enzyme Function

Proteins

Proteins are polymers of amino acids, also known as polypeptides. They are essential biomolecules, as nearly all life depends on them.

Protein Structural Levels

Proteins can have thousands of amino acids, and therefore, their thousands of atoms can adopt a wide variety of positions. Importantly, a protein consists of thousands of amino acids linked one after another through peptide bonds, forming long linear chains. However, the final spatial structure of a protein is not a linear chain; it adopts a specific three-dimensional form in space, which is essential for its function.

Primary Structure

Consists of the amino acid sequence of a protein. It is the most basic and arguably the most important level of structural organization.

Secondary Structure

Defines the regular and repetitive arrangement of amino acids in localized regions of the polypeptide chain. The two most important and abundant secondary structures in proteins are the alpha helix and beta conformation.

Tertiary Structure

Describes the overall three-dimensional spatial relationships between all the amino acids in the polypeptide chain, providing a complete 3D image of the molecule. This level analyzes the positions in space of amino acids that are not consecutive in the primary sequence.

Quaternary Structure

Occurs when a protein is composed of several polypeptide chains, each called a monomer or subunit. This level describes the arrangement and spatial relationship of these subunits within the overall protein complex.

Protein Classification

From a chemical point of view, proteins are distinguished into two main groups: simple proteins, which are composed solely of amino acids, and conjugated proteins, which, in addition to amino acids, contain other types of molecules called a prosthetic group. The peptide fraction of a conjugated protein is named the apoprotein.

Enzymes

To speed up metabolic processes, cells utilize specific biological catalysts called enzymes. Enzymes function under the cellular environmental conditions of temperature, pH, and pressure, compatible with metabolic needs.

Enzyme Catalysis Characteristics

• Enzymes have high catalytic efficiency.
• Like any catalyst, enzymes recover their initial state after each catalytic cycle.
• They are specific catalysts. Their catalytic activity can be regulated by cellular mechanisms, acting according to the needs of the organism.

The catalytic properties of enzymes are due to the existence of an active center, where the substrate binds during the catalytic cycle. This is a well-defined region of the enzyme protein capable of binding to the substrate, forming a substrate-enzyme complex, and catalyzing its transformation. The active center is therefore responsible for the specificity and catalytic activity of the enzyme. The properties of an enzyme's active center are closely related to its shape or structure and, consequently, to the type and arrangement of the side chains of the amino acids present in that region.

Enzyme Classification & Nomenclature

The name of an enzyme should ideally identify the type of reaction it catalyzes and its preferred physiological substrate. However, this ideal classification often results in names that are too long and cumbersome. Therefore, in practice, two types of nomenclature are used, both retaining the suffix '-ase'. The recommended nomenclature is intended to be informative and easy to use. The systematic nomenclature is less convenient for everyday use but is more specific and rigorous.