Molecular Biology

How Proteins are Broken down into Amino Acids

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In humans and most other animals, dietary proteins cannot be absorbed in an intact form. They must be broken down into amino acids by enzymes secreted in pancreatic juice as well as those within the enterocytes lining the small intestine. The enzymes that accomplish this task are collectively referred to as peptidases or proteases. This article will focus on the enzymatic breakdown of proteins, as opposed to proteolysis performed by inorganic chemical methods.

Before discussing proteases themselves, it is important to understand a bit about protein architecture as well as the chemical structure of the peptide bond. Biochemists describe proteins in terms of a four tiered structural hierarchy. A protein's primary structure consists of its amino acid sequence from the initial N-terminus to the C-terminus along with any disulfide bonds present between cysteine residues. Although a protein's amino acid sequence is the fundamental determinant of its three dimensional structure, scientists are often unable to predict a protein's 3D conformation on the basis of primary structure alone. Sophisticated methods such as NMR and X-ray crystallography remain essentlal in determining the detailed structure of large proteins. 

Secondary protein structure consists of defined, localized shapes, namely alpha helices, beta pleated sheets, beta strands, and hairpin turns. In some proteins, these elements form supersecondary structures called motifs, each with distinct functions. For example, the EF hand motif of calmodulin binds calcium ions whereas the helix-loop-helix motif in many transcription factors recognizes DNA. Motifs are themselves organized into higher order structures called domains, which may contain the catalytically active site of an enzyme or the binding region of a globular protein.

Tertiary structure refers to the overall three dimensional shape of a protein. It is often difficult to draw a sharp line between domains and tertiary structure, as some proteins consist of little more than a single domain. In other proteins, amino acids from distant parts of the primary sequence are folded together to form the active site. At any rate, this is the highest level of architecture in monomeric (single subunit) proteins. In contrast, proteins consisting of multiple subunits, such as hemoglobin, are said to exhibit quaternary structure.

In spite of the almost endless variety of proteins in nature, their common denominator is a backbone formed by peptide bonds. Organic chemists describe the peptide bond as an amide, which is a planar unit consisting of a carbonyl group (C=O) whose carbon atom is bonded to the nitrogen atom of an NH group (also known as a secondary amine). Under acidic or alkaline conditions, an amide can be split by hydrolysis, which literally means destruction by water. Hydrolysis of a peptide bond yields a carboxyl group (COO-) at one end and an NH2 group at the other end. Successive hydrolysis reactions can cleave even the largest proteins into individual amino acids.

Biochemists have identified four major families of proteases, all capable of hydrolyzing peptide bonds: serine proteases, zinc proteases, thiol proteases, and acid proteases.

Serine proteases - As the name suggests, these enzymes contain a serine residue at their active sites, along with histidine and aspartate, forming a so called catalytic triad. The most well studied members of this family include the digestive enzymes trypsin, chymotrypsin, and elastase; the clotting factors responsible for blood coagulation; and the immunological complement cascade. Serine proteases are selective as to which peptide bonds they cleave. Chymotrypsin, for instance, hydrolyzes the C-terminal ends of the amino acids phenylalanine, tyrosine, tryptophan, and methionine. Digestive enzymes and clotting factors must be stored as inactive precursors called zymogens, or else they would destroy the intestinal lining or cause blood to clot inappropriately. These enzymes, as well as the complement cascade, are also held in check by various inhibitory proteins including alpha-1 antitrypsin, antithrombin III, and C1 INH, respectively.  

Zinc proteases contain a zinc ion as a cofactor in their active sites. As with serine proteases, they tend to hydrolyze amino acids with aromatic or bulky side chains. Important zinc proteases in humans include carboxypeptidase A, collagenase, and matrix metalloproteases.

Thiol proteases  contain a cysteine residue in their active sites. One example is papain, an enzyme found in papaya juice.

Acid proteases require a low pH to become activated. In humans, they include the digestive enzyme pepsin, secreted by gastric chief cells; as well as several lysosomal enzymes.

More about this author: Dr. Bryan Katz

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