Protein Structures and Functions: From Amino Acids to Enzymes
Proteins: Structures and Functions
Proteins are organic biomolecules formed by carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), often containing sulfur (S), iron (Fe), zinc (Zn), and copper (Cu). They account for 50% of the dry matter of a living being. Their molecular weight is quite high despite being composed of core building blocks (monomers) of low molecular mass. The monomer of proteins is called an alpha-amino acid. Proteins have a variety of functions to perform, and they are found all over the cell and therefore the whole organism.
Peptide Bond
The link between two alpha amino acids (aa) is called a peptide bond. This link is established between the hydroxyl group of the first amino acid and the amino group of the following amino acid.
Primary Structure
The primary structure is the linear sequence or order in which amino acids are arranged in a protein. This sequence is genetically determined for each protein, so it will present a specific number of amino acids in a specific order. In this structure, peptide bonds are crucial for the formation of other structures. When a protein is denatured, it loses all structures except the primary one, so if the conditions return to normal, the structure is renatured.
Secondary Structure
The secondary structure of proteins is the folding that the polypeptide chain adopts through the formation of hydrogen bonds between atoms that form the peptide bond, i.e., a type of non-covalent bond.
Alpha Helix
Amino acids in an alpha helix are arranged in a right-handed helical structure, with about 3.6 amino acids per turn. Each amino acid corresponds to a 100° turn in the helix, and the alpha carbons of two adjacent amino acids are separated by 1.5 Å. The helix is tightly packed, so there is almost no free space within it. All amino acid side chains are arranged toward the outside of the helix. The amino group of amino acid (n) can establish a hydrogen bond with the carbonyl group of amino acid (n+4). Thus, each amino acid (n) of the helix forms two hydrogen bonds with the peptide bond of amino acid (n+4) and (n-4), resulting in a total of 7 hydrogen bonds per turn. This greatly stabilizes the helix. This is one of the organizational levels of the protein.
Beta Sheet
The beta sheet is formed by positioning two parallel chains of amino acids within the same protein, in which the amino groups of one chain form hydrogen bonds with the carbonyl groups of the opposite chain. It is a very stable structure that can result from the rupture of hydrogen bonds during the formation of an alpha helix. The side chains of this structure are positioned above and below the plane of the sheet. These substituents should not be too large, or they will create steric hindrance, which would affect the structure of the sheet.
Tertiary Structure
The tertiary structure refers to the way in which the polypeptide chain folds in space, i.e., how a certain protein, either globular or fibrous, is arranged. It is the arrangement of domains in space. The tertiary structure is formed in such a way that nonpolar amino acids are located inwards and polar amino acids outwards in aqueous media. This leads to stabilization through hydrophobic interactions, van der Waals forces, disulfide bonds (covalent bonds between properly oriented cysteine amino acids), and ionic interactions.
Quaternary Structure
The quaternary structure is derived from a combination of several peptide chains that associate to form an entity, a multimer, which has properties different from those of its monomer components. These subunits associate with each other through noncovalent interactions, such as hydrogen bonding, hydrophobic interactions, or salt bridges. In the case of a protein composed of two monomers, a dimer, this may be a homodimer if the constituent monomers are the same, or a heterodimer if they are not. Hemoglobin is a tetrameric protein that is usually used as an example of a protein with a quaternary structure.
Protein Denaturation
Denaturation of a protein refers to the breaking of bonds that maintained its quaternary, tertiary, and secondary structures, keeping only the primary structure. In these cases, the proteins are transformed into linear and thin filaments that interlock to form fibrous and insoluble compounds in water. Agents that can denature a protein include excessive heat, substances that alter the pH, impaired concentration, high salinity, and molecular agitation. The most visible impact of this phenomenon is that the proteins become less soluble or insoluble and lose their biological activity. Most proteins denature when heated between 50 and 60°C; others also denature when cooled below 10 to 15°C. Denaturation can be reversible (renaturation), but in many cases, it is irreversible.
Enzymes: Biological Catalysts
Enzymes are molecules of protein origin that catalyze chemical reactions, where thermodynamically possible (though they cannot make the process more thermodynamically favorable). In these reactions, enzymes act on molecules called substrates, which are converted into different molecules called products. Almost all processes in the cell need enzymes to occur at significant rates. Reactions mediated by enzymes are called enzyme reactions. Because enzymes are extremely selective for their substrates and speed up only a few reactions from among many possibilities, the set of enzymes made in a cell determines the metabolism that occurs in each cell. In turn, this synthesis depends on the regulation of gene expression. Like all catalysts, enzymes work by lowering the activation energy (ΔG‡) for a reaction, so that it substantially accelerates the reaction rate. Enzymes do not alter the energy balance of the reactions involved, nor do they change the equilibrium of the reaction, but they can speed up the process even millions of times. A reaction that occurs under the control of an enzyme, or a catalyst in general, reaches equilibrium much faster than the corresponding uncatalyzed reaction.