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William of Ockham
Entities should not be multiplied unnecessarily.
Proteins are chains of amino acids. The sequence of amino acids in a chain is known as the primary structure of a protein. The chains fold up to form complex three dimensional shapes. The chains can fold on themselves locally (secondary structure) and wrap around themselves to form a specific three dimensional shape (tertiary structure).
The secondary / tertiary structure of a folded protein is directly related to its function. For example, enzymes are proteins that catalyze reactions. They have binding sites that interact with other molecules. These binding sites are created through the folding of the amino acid chains that gives rise to the three dimensional shape of the enzyme.
Denaturation of proteins involves the disruption and possible destruction of both the secondary and tertiary structures. Since denaturation reactions are not strong enough to break the peptide bonds, the primary structure (sequence of amino acids) remains the same after a denaturation process. Denaturation disrupts the normal sheets in a protein and uncoils it into a random shape.
Denaturation occurs because the bonding interactions responsible for the secondary structure (hydrogen bonds to amides) and tertiary structure are disrupted. In tertiary structure there are four types of bonding interactions between "side chains" including: hydrogen bonding, salt bridges, disulfide bonds, and non-polar hydrophobic interactions. which may be disrupted.
Proteins can be denatured through exposure to heat or chemicals. Denatured proteins lose their three dimensional structure and thus their function.
Digestion of Proteins and Cooking
Protein digestion begins in the stomach, where the acidic environment favors protein denaturation. Denatured proteins are more accessible as substrates for proteolysis than are native proteins. The primary proteolytic enzyme of the stomach is pepsin, a nonspecific protease that is maximally active at pH 2. Thus, pepsin can be active in the highly acidic environment of the stomach, even though other proteins undergo denaturation there.
Heat disrupts hydrogen bonds and non-polar hydrophobic interactions. This occurs because heat increases the kinetic energy and causes the molecules to vibrate so rapidly and violently that the bonds are disrupted.
Foods are cooked to denature the proteins to make it easier for enzymes to digest them. Cooking food denatures some of the proteins in it and makes digestion more efficient. Heating to denature proteins in bacteria and thus destroy the bacteria.