Proteins (meaning "first thing"; discovered by Berzelius, in 1838) are one of the primary constituents of living things; as such, these are one of the primary biochemical molecule classes. Proteins are polymers composed of amino acid residues. Some (but not all proteins) act as enzymes themselves or form subunits in multi-protein enzyme complexes; they are "cellular machines" that function as catalysts to chemical reactions which would otherwise be irrelevent on the biological timescale. (In addition to proteins, certain RNAs – known as ribozymes – can act catalytically in biological reactions.) Other proteins are used non-enzymatically in a variety of purposes, such as forming structural components of cells. For example, muscle is composed of protein fibers, but these fibers have nothing to do with enzymatic reactions.
Nutrition
Proteins can be used as an energy source, 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.
Nutritionally, proteins come in two forms: complete proteins contain all eight of the essential amino acids while an incomplete protein is missing at least one. The human body requires 14 other amino acids, which it can synthesize from the essential amino acids. When protein is listed on a nutrition label it only refers to the amount of complete proteins in the food, though the food may be very strong in a subset of the essential amino acids. Animal-derived foods contain all of those amino acids, while plants are typically stronger in some acids than others. Complete proteins can be made in an all vegan diet by eating a sufficient variety of foods and by getting enough calories. It was once thought that in order to get the complete proteins vegans needed to do protein combining by getting all amino acids in the same meal (the most common example is eating beans with rice) but nutritionists now know that the benefits of protein combining can be achieved over the longer period of the day. Ovo-lacto vegetarians usually do not have this problem, since egg's white and cow's milk contain all essential amino acids. Peanuts, soy milk, nuts, seeds, green peas, Legumes, the alga spirulina and some grains are some of the richest sources of plant protein.
Proteins differ from carbohydrates chiefly in that they contain much nitrogen and a little bit of sulfur, besides carbon, oxygen and hydrogen.
Biochemistry
A protein molecule is an unbranched biopolymer composed of many amino acids linked together in a chain. The chain folds into a 3-dimensional structure known as the native state, which is determined by its sequence of amino acids. There are four levels of protein structure:
The primary structure is held together by covalent peptide 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 secondary structure, it is generally an alpha helix or beta sheet. The random regions are called random coils. The string is folded further into larger 3-dimensional structures that are held together by hydrogen bonds, hydrophobic interactions, ionic 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 symptoms 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.
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