• Description
• Functions

Description

A protein (in Greek πρωτεϊνη = first element) is a complex, high molecular weight organic compound that consists of amino acids joined by peptide bonds. Proteins are essential to the structure and function of all living cells and viruses. Many proteins are enzymes or subunits of enzymes. Other proteins play structural or mechanical roles, such as those that form the struts and joints of the cytoskeleton. Still more functions filled by proteins include immune response and the storage and transport of various ligands. In nutrition, proteins serve as the source of amino acids for organisms that do not synthesize those amino acids natively.

Proteins are one of the classes of bio-macromolecules, alongside polysaccharides, lipids, and nucleic acids, that make up the primary constituents of living things. They are amongst the most actively studied molecules in biochemistry and were discovered by Jöns Jakob Berzelius, in 1838.

Most natural proteins are encoded by DNA. DNA is transcribed to yield RNA, which serves as a template for translation ribosomes<.

Structure

Proteins are amino acid chains that fold into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its native state , which is determined by its sequence of amino acids. Biochemists refer to four distinct aspects of a protein's structure:

• Primary structure: the amino acid sequence
• Secondary structure: highly patterned sub-structures—alpha helix and beta sheet—or segments of chain that assume no stable shape. Secondary structures are locally defined, meaning that there can be many different secondary motifs present in one single protein molecule.
• Tertiary structure: the overall shape of a single protein molecule; the spatial relationship of the secondary structural motifs to one another
• Quaternary structure: the shape or structure that results from the union of more than one protein molecule, usually called subunit proteins subunits in this context, which function as part of the larger assembly or protein complex.

In addition to these levels of structure, proteins may shift between several similar structures in performing their biological function. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as "conformations," and transitions between them are called conformational changes.

The primary structure is held together by covalent peptide bonds, which are made during the process of translation. The secondary structures are held together by hydrogen bonds. The tertiary structure is held together primarily by hydrophobic interactions but hydrogen bonds, ionic interactions, and disulfide bonds are usually involved too.

The process by which the higher structures form is called protein folding and is a consequence of the primary structure. Although any unique polypeptide may have more than one stable folded conformation, each conformation has its own biological activity and only one conformation is considered to be the active, or native conformation.

The two ends of the amino acid chain are referred to as the carboxy terminus (C-terminus) and the amino terminus (N-terminus) based on the nature of the free group on each extremity.

Functions

Proteins are involved in practically every function performed by a cell, including regulation of cellular functions such as signal transduction and metabolism. For example, protein catabolism requires only a few enzymes termed proteases. Mechanisms of protein regulation Various molecules and ions are able to bind to specific sites on proteins. These sites are called binding sites. They exhibit chemical specificity. The particle that binds is called a ligand. The strength of ligand-protein binding is a property of the binding site known as affinity. Since proteins are involved in practically every function performed by a cell, the mechanisms for controlling these functions therefore depend on controlling protein activity. Regulation can involve a protein's shape or concentration. Some forms of regulation include:

• Allosteric modulation: When the binding of a ligand at one site on a protein affects the binding of ligand at another site.
• Covalent modulation: When the covalent modification of a protein affects the binding of a ligand or some other aspect of the protein's function.

Proteins are sensitive to their environment. They may only be active in their native state, over a small pH range, and under solution conditions with a minimum quantity of electrolytes. A protein in its native state is often described as folded. A protein that is not in its native state is said to be denatured. Denatured proteins generally have no well-defined secondary structure. Many proteins denature and will not remain in solution in distilled water.

One of the more striking discoveries of the 20th century was that the native and denatured states in many proteins were interconvertible, that by careful control of solution conditions (by for example, dialyzing away a denaturing chemical), a denatured protein could be converted to native form. The issue of how proteins arrive at their native state is an important area of biochemical study, called the study of protein folding.

Through genetic engineering, researchers can alter the sequence and hence the structure, "targeting", susceptibility to regulation and other properties of a protein. The genetic sequences of different proteins may be spliced together to create "chimeric" proteins that possess properties of both. This form of tinkering represents one of the chief tools of cell and molecular biologists to change and to probe the workings of cells. Another area of protein research attempts to engineer proteins with entirely new properties or functions, a field known as protein engineering.

Protein and nutrition In carnivores protein is one of the largest component of the diet. The metabolism of proteins by the body releases ammonia, an extremely toxic substance. It is then converted in the liver into urea, a much less toxic chemical, which is excreted in urine. Some animals convert it into uric acid instead.

Protein nutrition in humans

In terms of human nutritional needs, proteins differ in their ability to provide all eight of the amino acids (threonine, valine, tryptophan, isoleucine, leucine, lysine, phenylalanine, and methionine) that humans cannot produce themselves. While all natural foods contain all of these amino acids, some contain less of one or more of them (called limiting amino acids), which means that if this kind of protein was the only kind eaten over one or several days the body may not fully utilize all of it. Formerly, this effect was expressed in the form of the so-called biological value (BV), which has since found to be flawed and has been superseded by the PDCAAS. This measure may still be considered incomplete, since human diets, except in times of famine, almost never contain only one kind of protein - however, calculating the PDCAAS of a diet solely based on the PDCAAS of the individual constituents is impossible. This is because one food may provide an abundance of an amino acid that the other is missing, which means that in this case the PDCAAS of the diet is higher than that of any one of the constituents. To arrive at the final result, all individual amino acids would have to be taken into account, though, so the PDCAAS of each constituent is largely useless.