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Proteins (originally meaning first thing when discovered in 1838 by Berzelius) are one of the primary constituents of living things and viruses, and as such as one of the chief classes of molecules studied in biochemistry. As enzymes, proteins are often considered the "machines of the cell." They are an important component of human nutrition.

Proteins can be used for energy, but they must first be converted to common metabolic intermediates. This 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.

Proteins differ from chiefly from carbohydrates in that they contain much nitrogen and a little bit of sulfur, besides carbon, oxygen and hydrogen.

Proteins are biopolymers consisting of one or more strings of amino acid residues joined head-to-tail via peptide bonds. Each string folds into a 3-dimensional structures. There are four levels of protein structure:

Primary structure: the linear amino acid sequence forming the polypeptide
Secondary structure: structures stabilized by hydrogen bonds between the C=O and N-H groups of different peptide bonds.
Tertiary structure: structures stabilized by interactions between the amino acid side chains on a single polypeptide
Quaternary structure: the association of multiple polypeptide subunits to form a functional protein.

The primary structure is held together by covalent bonds, which are made during the process of translation. 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.

If a region of a protein has any secondary structure, it is either an alpha helix or beta sheet. The string is folded further into larger 3-dimensional structures that are held together by hydrogen bonds, hydrophobic interactions, and/or disulfide bonds.

Proteins are generally large molecules, sometimes having molecular masses of up to 3,000,000 (the muscle protein titin[?] has a single amino acid chain 27,000 subunits long). Such long chains of amino acids are almost universally referred to as proteins, but shorter strings of amino acids are referred to as "polypeptides," "peptides" or very rarely "oligopeptides". The dividing line is somewhat undefined, although a polypeptide may be less likely to have tertiary structure and may be more likely to act as a hormone (like insulin) rather than as an enzyme or structural element.

Proteins are generally classified as soluble, filamentous or membrane-associated (see integral membrane protein). Nearly all the biological catalysts known as enzymes are proteins. (Certain RNA sequences were shown in the late 20th century to have catalytic properties as well.) Membrane-associated exchangers[?] and ion channels, which move their substrates from place to place but do not change them; receptors, which do not modify their substrates but may simply shift shape upon binding them; and antibodies, which appear to do nothing more than bind, all are proteins as well. Finally, the filamentous material that makes up the cytoskeleton of cells and much of the structure of animals is also protein: collagen and keratin are components of skin, hair, and cartilage; and muscles are composed largely of proteins.

Proteins can be picky about the environment in which they are found. They may only exist in their active, or native state[?], in a small range of pH values and under solution conditions with a minimum quantity of electrolytes, as many proteins will not remain in solution in distilled water. A protein that loses its native state is said to be denatured. Denatured proteins generally have no secondary structure other than random coil. A protein in its native state is often described as folded.

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 protein engineering.

Protein deficiency is often discussed in relation to nutrition especially as it relates to starvation and malnourishment in Third World Countries. It may be an overlooked health factor even in developed countries such as the United States, where diets may rely heavily on carbohydrates, may lack essential amino acids, and there is societal pressure to be thin. Protein deficiency can lead to sympotoms such as fatigue, insulin resistance, hair loss, loss of hair pigment (hair that should be black becomes reddish), loss of muscle mass (proteins repair muscle tissue, low body temperature, and hormonal irregularities. Severe protein deficiency is fatal.

Excess protein can cause problems as well, such as foundering (foot problems) in horses.

Proteins can often figure in allergies and allergic reactions to certain foods. This is because the structure of each form of protein is slightly different, and some may trigger a response from the immune system while others are perfectly safe. Many people are allergic to the particular proteins found in peanuts, or those in shellfish or other seafoods, for example, but it is extremely unusual for the same person to react to all three.