Proteins are amino acid chains that fold into unique 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 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:single protein ; the spatial relationship of thecondary 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 evels of structure, proteins may shift between several siilar structures in performing their biological function. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as 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 but hydrogen bonds, ionic interactions, and disulfide bonds are usually involved too.process by which thestructures form is called protein folding and is a consequence of the primary structure. The mechanism of protein folding is not understood. Alhough 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 and the amino terminus based on the nature of the free group on each extremity.

Proteins are involved in practically every function performed by a cell, including regulation of cellular functions such as signal transduction and metabolism. For example, catabolism requires enzymes termed proteases and other enzymes such as glycosidases.
Mechanisms of protein regulations 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 everyperformed by a cell, the mechanisms for controlling these functions therefore depend on controlling protein activity. Regulation can involve a protein's shape concentration. Some forms 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 generally large molecules, 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 rarely, "oligopeptides". The dividing line is undefined, though "polypeptide" usually refers to an amino acid chain lacking tertiary structure which may be more likely to act as a hormone , rather than as an enzyme which depends on its defined tertiary structure for functionality.Proteins are generally classified as soluble, filamentous or membrane-associated Nearly all the biological catalysts known as enzymes are soluble proteins with a recent notable execption being the discovery of ribozymes, RNA molecules with the catalytic properties of enzymes Antibodies, the basis of the adaptive immune system, are another example of soluble proteins. Membrane-associated proteins include 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. Filamentous proteins make up the cytoskeleton of cells and much of the structure of animals: examples include tubulin, actin, collagen and keratin, all of which are important components of skin, , and cartilage. Another special class of proteins consists of motor proteins such as myosin, kinesin, and dynein. These proteins are "molecular motors," generating physical force which can move organelles, cells, and entire muscles.

Working with proteins
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 electrolytes. A protein in its native state is often described as folded. A proteinis 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 conditionsdialyzing away a denaturing chemica, 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 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 change and to probe the workings of cells. Another area of protein research attempts to engineer proteins entirely new properties or functions, a field known as protein engineering.Protein-protein interactions can be screened for using two-hybrid screening.

Protein and nutrition
Protein is an important macronutrient to the human diet, supplying the body's needs for nitrogen and amino acids. The exact amount of dietary protein needed to satisfy these requirements may vary widely depending on age, sex, level of physical activity, and medical condition. However, the figure of .75g per kilogram of body weight for a sedentary male is widely given as a daily requirement. Proteins are found in most food but are particularly concentrated in legumes, nuts, meat, and dairy . As it is used, much protein is converted by protein catabolism to ammonia which, due to its toxicity, must be converted to either urea or uric acid (in some animals) to be excreted in Protein is the major component of muscles, tendons, enzymes, skin, hair, eyes, and a tremendous variety of other organs and processes.

The quality of protein intake is important because different proteins supply essential amino acids in different proportions. Given an adequate intake of nitrogen, the human body can manufacture 10 of the 18 amino acids from glucose. The remaining 8 amino acids (threonine, valine, tryptophan, isoleucine, leucine, lysine, phenylalanine, and methionine) be manufactured by the body and must be acquired through dietary sources. Thus, they are termed essential amino acids. Proteins possessing equal proportions of all essential amino acids in relatively abundant quantities are often termed "complete". Despite this suggestive label, good nutrition need not depend on upon so-called "complete" proteins because non-complete proteins in complementary combinations can readily complete spectrum of essential amino acids. The present method of rating the completeness of protein is known as the PDCAAS (Protein Digestibility Corrected Amino Acid Score).

Protein deficiency can lead to symptoms such as fatigue, insulin resistance, hair loss, loss of hair pigment that should be black becomes reddish), loss of muscle mass proteins repair muscle tissue, low body temperature, and hormonal irregularities. Severe protein deficiency, encountered only in times of famine, is fatal.Excess protein can cause problems as well, such as causing the immune system to overreact, liver dysfunction from increased toxic residues, bone loss due to increased acidity in the blood and foundering in horses. The assumption high protein diets are bad for bones came from the fact that calium excretion is increased when dietary protein intake is increased. However, it has recently been shown that uptake of calcium by the intestine is also increased and as long as calcium intake is maintained, high protein intake may have benefits for bone in older women [1].

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 casein, the protein in milk; gluten, the protein in wheat and other grains; the particular proteins found in peanuts; or those in shellfish or other seafoods. It is extremely unusual for the same person to adversely react to more than two different types of proteins.

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