Proteins and enzymes are fundamental molecules that drive the essential processes of life. Proteins serve as structural components, transporters, regulators, and defenders, while enzymes, a specialized subset of proteins, act as biological catalysts that speed up chemical reactions. Without them, life's biochemical reactions would be too slow to sustain cellular functions. Their intricate structures and diverse roles make them essential for maintaining cellular integrity, signaling, metabolism, and immune responses.

In this article, Creative Enzymes provides an in-depth overview of proteins and enzymes, highlighting their functions and interrelationships. We offer a wide range of high-quality enzyme and protein products for various applications. Explore our product list to find the right solutions for your research and industrial needs.

Proteins: The Versatile Macromolecules

Definition and Basic Structure

Proteins are essential biological macromolecules composed of long chains of amino acids linked together by peptide bonds. Each amino acid, the building block of proteins, consists of a central carbon atom bonded to an amino group (NH₂), a carboxyl group (COOH), and a unique side chain (R group) that determines its chemical properties. The sequence and arrangement of these amino acids define a protein's structure and, ultimately, its function. Proteins are involved in virtually every biological process, from catalyzing chemical reactions to providing structural support and facilitating communication within and between cells.

Figure 1. Chemical structure of the peptide bond (bottom) and the three-dimensional structure of a peptide bond between an alanine and an adjacent amino acid (top/inset). The bond itself is made of the CH-ON elements.

Levels of Protein Structure

• Primary Structure: The primary structure of a protein refers to the linear sequence of amino acids in a polypeptide chain. This sequence is determined by the genetic code stored in DNA, which is transcribed into messenger RNA (mRNA) and then translated into a polypeptide. The specific order of the amino acids in the primary structure is critical because even a single change can alter the function or stability of the protein.
• Secondary Structure: Secondary structure describes the local folding patterns within a polypeptide chain that are stabilized by hydrogen bonds between the backbone atoms. The most common secondary structures are alpha helices and beta sheets. α-helices are coiled structures, while β-sheets consist of multiple parallel or antiparallel strands of polypeptide. These structural elements impart rigidity and stability to the protein.
• Tertiary Structure: The tertiary structure refers to the overall three-dimensional shape of a single polypeptide chain. It is formed by the folding of secondary structural elements into a compact, functional unit. This folding is driven by various interactions, including hydrophobic interactions (where non-polar amino acids cluster together), disulfide bonds (covalent bonds between cysteine residues), and ionic interactions between charged amino acids. The tertiary structure is essential for the biological activity of the protein.
• Quaternary Structure: Some proteins consist of several polypeptide subunits that are assembled into a functional protein complex. This assembly, known as a quaternary structure, is seen in proteins such as hemoglobin, which is composed of four subunits. The quaternary structure allows for cooperative interactions and enhanced functionality, such as the oxygen-binding capacity of hemoglobin.

Figure 2. Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure, in this case hemoglobin containing heme units.

Types of Proteins

• Structural Proteins: Structural proteins provide mechanical support and strength to cells and tissues. Examples include collagen, which is a major component of connective tissue and the most abundant protein in the human body, and keratin, which forms the structural framework of hair, nails, and skin. These proteins are characterized by their fibrous and insoluble nature.
• Transport Proteins: Transport proteins facilitate the movement of molecules within cells and throughout the body. For example, hemoglobin transports oxygen from the lungs to the tissues and carbon dioxide back to the lungs. Ion channels and transporters are another class of transport proteins that regulate the movement of ions across cell membranes to maintain cellular homeostasis.
• Regulatory Proteins: Regulatory proteins control various cellular functions and processes. Hormones, such as insulin, regulate metabolism and blood glucose levels. Receptor proteins, such as growth factor receptors, are embedded in cell membranes and transmit signals from the extracellular environment to the interior of the cell, initiating specific cellular responses.
• Storage Proteins: Storage proteins are specialized for storing essential molecules. Ferritin, for example, stores iron in a soluble and non-toxic form, making it available for use when needed. Other storage proteins include casein in milk and ovalbumin in egg whites, which provide essential nutrients during early development.
• Defensive Proteins: These proteins protect organisms from pathogens and harmful substances. Antibodies, produced by the immune system, recognize and neutralize foreign invaders such as bacteria and viruses. Other defense proteins include lysozyme, which breaks down bacterial cell walls, and complement proteins, which enhance the immune response.

Figure 3. Different types of proteins.

Enzymes: The Biological Catalysts

Enzymes are specialized proteins that act as biological catalysts, greatly accelerating the rate of biochemical reactions in living organisms. Each enzyme is highly specific, typically binding to a particular substrate or group of substrates, providing precise control over metabolic processes. They work by lowering the activation energy required for a reaction to proceed, thereby facilitating the conversion of substrates to products without being consumed in the process. Enzymes are essential for nearly all cellular functions, including energy production, digestion, DNA replication and protein synthesis. Their activity is regulated by a variety of mechanisms, including allosteric modulation, feedback inhibition, and post-translational modifications, which allow cells to fine-tune metabolic pathways in response to environmental changes or internal needs.

Enzymes operate optimally within specific temperature and pH ranges, and their efficiency can be affected by the presence of cofactors or inhibitors. In addition to their critical role in sustaining life, enzymes are widely used in industrial applications such as food processing, pharmaceuticals and biofuels due to their specificity, efficiency and environmental friendliness.

The Relationship Between Proteins and Enzymes

Most enzymes are composed of proteins and serve as biological catalysts that speed up chemical reactions in living organisms. However, a unique subset of RNA molecules known as ribozymes also exhibit enzymatic activity, facilitating specific biochemical transformations without the need for protein components. But not all proteins are enzymes, many proteins play structural, regulatory, or transport roles within cells, contributing to various biological processes beyond catalysis.

Some Proteins Function as Enzyme Regulators

Not all proteins work as direct catalysts for chemical reactions—some proteins regulate enzyme activity by acting as inhibitors or activators. These regulatory proteins play a critical role in controlling metabolic pathways and ensuring that enzymes function appropriately in response to the needs of the cell.

• Allosteric proteins are an important class of regulatory proteins. These proteins can bind to enzymes at specific locations, known as allosteric sites, that are distinct from the enzyme's active site. Binding to an allosteric site induces a conformational change in the enzyme that can either enhance or inhibit its activity. This mechanism is critical for the regulation of enzymes that control important biochemical pathways. For example, the enzyme phosphofructokinase, which plays a central role in glycolysis, is allosterically regulated by ATP levels. When ATP levels are high, ATP binds to an allosteric site and inhibits the enzyme, slowing glycolysis. Conversely, when ATP levels drop, the inhibition is released and glycolysis is activated to produce more ATP.

Figure 4. Functions of allosteric protein. (Basu et al. 2020)

• Enzyme inhibitors can be natural or synthetic molecules that bind to enzymes, either irreversibly or reversibly, and prevent them from functioning. Competitive inhibitors bind to the active site of the enzyme, blocking substrate binding, while non-competitive inhibitors bind elsewhere on the enzyme, causing a change in the shape of the enzyme that affects its activity. A natural example of a competitive inhibitor is the drug methotrexate, which inhibits the enzyme dihydrofolate reductase in cancer cells, preventing their growth. In contrast, enzyme activators bind to enzymes and increase their catalytic activity, ensuring that the enzyme works efficiently when needed.
• Post-translational modifications of enzymes, such as phosphorylation, methylation, or acetylation, also act as regulatory mechanisms. These chemical modifications can either activate or inhibit enzymes, providing a fine-tuned control system for cellular processes. For example, the phosphorylation of enzymes like glycogen phosphorylase regulates its ability to break down glycogen into glucose, a key process in maintaining blood sugar levels.

Ribozymes

Ribozymes, or catalytic RNA molecules, are a unique class of enzymes composed entirely of RNA rather than protein. They are capable of catalyzing specific biochemical reactions, such as RNA splicing, peptide bond formation and self-cleavage, without the need for protein-based enzymatic activity. The discovery of ribozymes challenged the long-held belief that only proteins could function as biological catalysts. Notable examples include the self-splicing group I and group II introns and the peptidyl transferase center of the ribosome, an RNA-based enzyme responsible for protein synthesis. Ribozymes play essential roles in various cellular processes and have significant implications for evolutionary biology, supporting the "RNA world" hypothesis, which suggests that early life may have relied on RNA for both genetic information storage and catalysis.

Figure 5. 3D structure of a hammerhead ribozyme.

In summary, proteins and enzymes are the molecular engines of life, shaping every biological function, from structural support to catalysis. Their versatility underlies their critical role in health, medicine, and biotechnology.

Creative Enzymes uses its expertise in enzyme production to provide customers with enzymes for use in life science research and various industries. In addition to enzyme products, we offer coenzymes, zymogens, enzyme protectants & stabilizers, and a wide range of product categories. Contact us today to explore our product offerings or to discuss your requirements with our experts.