protein

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protein,

any of the group of highly complex organic compounds found in all living cells and comprising the most abundant class of all biological molecules. Protein comprises approximately 50% of cellular dry weight. Hundreds of protein molecules have been isolated in pure, homogeneous form; many have been crystallized. All contain carbon, hydrogen, and oxygen, and nearly all contain sulfur as well. Some proteins also incorporate phosphorous, iron, zinc, and copper. Proteins are large molecules with high molecular weights (from about 10,000 for small ones [of 50–100 amino acids] to more than 1,000,000 for certain forms); they are composed of varying amounts of the same 20 amino acidsamino acid
, any one of a class of simple organic compounds containing carbon, hydrogen, oxygen, nitrogen, and in certain cases sulfur. These compounds are the building blocks of proteins.
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, which in the intact protein are united through covalent chemical linkages called peptidepeptide,
organic compound composed of amino acids linked together chemically by peptide bonds. The peptide bond always involves a single covalent link between the α-carboxyl (oxygen-bearing carbon) of one amino acid and the amino nitrogen of a second amino acid.
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 bonds. The amino acids, linked together, form linear unbranched polymeric structures called polypeptide chains; such chains may contain hundreds of amino-acid residues; these are arranged in specific order for a given species of protein.

Types of Proteins

A protein molecule that consists of but a single polypeptide chain is said to be monomeric; proteins made up of more than one polypeptide chain, as many of the large ones are, are called oligomeric. Based upon chemical composition, proteins are divided into two major classes: simple proteins, which are composed of only amino acids, and conjugated proteins, which are composed of amino acids and additional organic and inorganic groupings, certain of which are called prosthetic groupsprosthetic group,
non-amino acid portions of certain protein molecules. The key part of the prosthetic group may be either organic (such as a vitamin) or inorganic (such as a metal) and is usually required for biological activity, especially when the prosthetic group is
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. Conjugated proteins include glycoproteinsglycoprotein
, organic compound composed of both a protein and a carbohydrate joined together in covalent chemical linkage. These structures occur in many life forms; they are prevalent and important in mammalian tissues.
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, which contain carbohydrates; lipoproteinslipoprotein
, any organic compound that is composed of both protein and the various fatty substances classed as lipids, including fatty acids and steroids such as cholesterol.
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, which contain lipids; and nucleoproteins, which contain nucleic acidsnucleic acid,
any of a group of organic substances found in the chromosomes of living cells and viruses that play a central role in the storage and replication of hereditary information and in the expression of this information through protein synthesis.
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.

Classified by biological function, proteins include the enzymesenzyme,
biological catalyst. The term enzyme comes from zymosis, the Greek word for fermentation, a process accomplished by yeast cells and long known to the brewing industry, which occupied the attention of many 19th-century chemists.
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, which are responsible for catalyzing the thousands of chemical reactions of the living cell; keratinkeratin
, any one of a class of fibrous protein molecules that serve as structural units for various living tissues. The keratins are the major protein components of hair, wool, nails, horn, hoofs, and the quills of feathers.
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, elastin, and collagencollagen
, any of a group of proteins found in skin, ligaments, tendons, bone and cartilage, and other connective tissue. Cells called fibroblasts form the various fibers in connective tissue in the body.
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, which are important types of structural, or support, proteins; hemoglobinhemoglobin
, respiratory protein found in the red blood cells (erythrocytes) of all vertebrates and some invertebrates. A hemoglobin molecule is composed of a protein group, known as globin, and four heme groups, each associated with an iron atom.
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 and other gas transport proteins; ovalbumin, caseincasein
, well-defined group of proteins found in milk, constituting about 80% of the proteins in cow's milk, but only 40% in human milk. Casein is a remarkably efficient nutrient, supplying not only essential amino acids, but also some carbohydrates and the inorganic elements
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, and other nutrient molecules; antibodiesantibody,
protein produced by the immune system (see immunity) in response to the presence in the body of antigens: foreign proteins or polysaccharides such as bacteria, bacterial toxins, viruses, or other cells or proteins.
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, which are molecules of the immune system (see immunityimmunity,
ability of an organism to resist disease by identifying and destroying foreign substances or organisms. Although all animals have some immune capabilities, little is known about nonmammalian immunity.
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); protein hormoneshormone,
secretory substance carried from one gland or organ of the body via the bloodstream to more or less specific tissues, where it exerts some influence upon the metabolism of the target tissue.
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, which regulate metabolismmetabolism,
sum of all biochemical processes involved in life. Two subcategories of metabolism are anabolism, the building up of complex organic molecules from simpler precursors, and catabolism, the breakdown of complex substances into simpler molecules, often accompanied by
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; and proteins that perform mechanical work, such as actinactin,
a protein abundantly present in many cells, especially muscle cells, that significantly contributes to the cell's structure and motility. Actin can very quickly assemble into long polymer rods called microfilaments.
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 and myosinmyosin
, one of the two major protein constituents responsible for contraction of muscle. In muscle cells myosin is arranged in long filaments called thick filaments that lie parallel to the microfilaments of actin.
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, the contractile muscle proteins.

Protein Structure

Every protein molecule has a characteristic three-dimensional shape, or conformation. Fibrous proteins, such as collagen and keratin, consist of polypeptide chains arranged in roughly parallel fashion along a single linear axis, thus forming tough, usually water-insoluble, fibers or sheets. Globular proteins, e.g., many of the known enzymes, show a tightly folded structural geometry approximating the shape of an ellipsoid or sphere.

Because the physiological activity of most proteins is closely linked to their three-dimensional architecture, specific terms are used to refer to different aspects of protein structure. The term primary structure denotes the precise linear sequence of amino acids that constitutes the polypeptide chain of the protein molecule. Automated techniques for amino-acid sequencing have made possible the determination of the primary structure of hundreds of proteins.

The physical interaction of sequential amino-acid subunits results in a so-called secondary structure, which often can either be a twisting of the polypeptide chain approximating a linear helix (α-configuration), or a zigzag pattern (β-configuration). Most globular proteins also undergo extensive folding of the chain into a complex three-dimensional geometry designated as tertiary structure. Many globular protein molecules are easily crystallized and have been examined by X-ray diffraction, a technique that allows the visualization of the precise three-dimensional positioning of atoms in relation to each other in a crystal.

The tertiary structure of several protein molecules has been determined from X-ray diffraction analysis. Two or more polypeptide chains that behave in many ways as a single structural and functional entity are said to exhibit quaternary structure. The separate chains are not linked through covalent chemical bonds but by weak forces of association.

The precise three-dimensional structure of a protein molecule is referred to as its native state and appears, in almost all cases, to be required for proper biological function (especially for the enzymes). If the tertiary or quaternary structure of a protein is altered, e.g., by such physical factors as extremes of temperature, changes in pH, or variations in salt concentration, the protein is said to be denatured; it usually exhibits reduction or loss of biological activity.

Protein Synthesis

The cell's ability to synthesize protein is, in essence, the expression of its genetic makeup. Protein synthesis is a sequence of chemical reactions that occur in four distinct stages, i.e., activation of the amino acids that ultimately will be joined together by peptide bonds; initiation of the polypeptide chain at a cell organelle known as the ribosome; elongation of the polypeptide by stepwise addition of single amino acids to the chain; and termination of amino-acid additions and release of the completed protein from the ribosome. The information for the synthesis of specific amino-acid sequences is carried by a nucleic acid molecule called messenger RNA (see nucleic acidnucleic acid,
any of a group of organic substances found in the chromosomes of living cells and viruses that play a central role in the storage and replication of hereditary information and in the expression of this information through protein synthesis.
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). Proteins are needed in the diet mainly for their amino acids, which the body uses to build new proteins (see nutritionnutrition,
study of the materials that nourish an organism and of the manner in which the separate components are used for maintenance, repair, growth, and reproduction. Nutrition is achieved in various ways by different forms of life.
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).

The mechanism of action of many widely used antibiotics, such as streptomycinstreptomycin
, antibiotic produced by soil bacteria of the genus Streptomyces and active against both gram-positive and gram-negative bacteria (see Gram's stain), including species resistant to other antibiotics, e.g.
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, chloramphenicolchloramphenicol
, antibiotic effective against a wide range of gram-negative and gram-positive bacteria (see Gram's stain). It was originally isolated from a species of Streptomyces bacteria.
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, and tetracyclinetetracycline
, any of a group of antibiotics produced by bacteria of the genus Streptomyces. They are effective against a wide range of Gram positive and Gram negative bacteria, interfering with protein synthesis in these microorganisms (see Gram's stain).
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, can be understood in terms of their ability to interfere with some stage of protein synthesis in bacteria.

Protein

A biological macromolecule made up of various α-amino acids that are joined by peptide bonds. A peptide bond is an amide bond formed by the reaction of an α-amino group (—NH2) of one amino acid with the carboxyl group (—COOH) of another, as shown below. Proteins generally contain from 50 to 1000 amino acid residues per polypeptide chain. See Peptide

Occurrence

Proteins are of importance in all biological systems, playing a wide variety of structural and functional roles. They form the primary organic basis of structures such as hair, tendons, muscle, skin, and cartilage. All of the enzymes, the catalysts in biochemical transformations, are protein in nature. Many hormones, such as insulin and growth hormone, are proteins. The substances responsible for oxygen and electron transport (hemoglobin and the cytochromes, respectively) are conjugated proteins that contain a metalloporphyrin as the prosthetic group. Chromosomes are highly complex nucleoproteins, that is, proteins conjugated with nucleic acid. Viruses are also nucleoprotein in nature. Of the more than 200 amino acids that have been discovered either in the free state or in small peptides, only 20 amino acids are present in mammalian

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proteins. Thus, proteins play a fundamental role in the processes of life. See Amino acids

Specificity

The linear arrangement of the amino acid residues in a protein is termed its sequence (primary structure). The sequence in which the different amino acids are linked in any given protein is highly specific and characteristic for that particular protein.

This specificity of sequence is one of the most remarkable aspects of protein chemistry. The number of possible permutations of sequence in even so small a protein as insulin, of molecular weight 5732 and with 51 amino acid residues, is astronomic: 1051 permutations. Yet it has been established that the pancreatic cell of a given species has only one of these possible sequences. The elucidation of the mechanism conferring such a high degree of specificity on the biosynthetic reactions by which proteins are built up from free amino acids has been one of the key problems of modern biochemistry. See Molecular biology

Proteins are not stretched polymers; rather, the polypeptide backbone of the molecule can fold in several ways by means of hydrogen bonds between the carbonyl oxygen and the amide nitrogen. The folding of each protein is determined by its particular sequence of amino acids. The long polypeptide chains of proteins, particularly those of the fibrous proteins, are held together in a rather well-defined configuration. The backbone is coiled in a regular fashion, forming an extended helix. As a result of this coiling, peptide bonds separated from one another by several amino acid residues are brought into close spatial approximation. The stability of the helical configuration can be attributed to hydrogen bonds between these peptide bonds.

In addition to hydrogen bonds, there are electrostatic interactions, such as those between COO- and NH3+ groups of the side chains, and van der Waals forces, that is, hydrophobic interactions, which help to determine the configuration of the polypeptide chain. The term secondary structure is used to refer to all those structural features of the polypeptide chain determined by noncovalent bonding interactions.

In addition to the α-helical sections of proteins, there are segments that contain β-structures in which there are hydrogen bonds between two polypeptide chains that run in parallel or antiparallel fashion.

The tertiary structure (third level of folding) of a protein comes about through various interactions between different parts of the molecule. Disulfide bridges formed between cysteine residues at different locations in the molecule can stabilize parts of a three-dimensional structure by introducing a primary valence bond as a cross-link. Hydrogen bonds between different segments of the protein, hydrophobic bonds between nonpolar side chains of amino acids such a phenylalanine and leucine, and salt bridges such as those between positively charged lysyl side chains and negatively charged aspartyl side chains all contribute to the individual tertiary structure of a protein.

Finally, for those proteins that contain more than one polypeptide chain per molecule, there is usually a high degree of interaction between each subunit, for example, between the α- and β-polypeptide chains of hemoglobin. This feature of the protein structure is termed its quarternary structure.

Properties

The properties of proteins are determined in part by their amino acid composition. As macromolecules that contain many side chains that can be protonated and unprotonated depending upon the pH of the medium, proteins are excellent buffers. The fact that the pH of blood varies only very slightly in spite of the numerous metabolic processes in which it participates is due to the very large buffering capacity of the blood proteins.

Biosynthesis

The processes by which proteins are synthesized biologically have become one of the central themes of molecular biology. The sequence of amino acid residues in a protein is controlled by the sequence of the DNA as expressed in messenger RNA at ribosomes. See Deoxyribonucleic acid (DNA), Ribonucleic acid (RNA), Ribosomes

Degradation

As with many other macromolecular components of the organism, most body proteins are in a dynamic state of synthesis and degradation (proteolysis). During proteolysis, the peptide bond that links the amino acids to each other is hydrolyzed, and free amino acids are released. The process is carried out by a diverse group of enzymes called proteases. During proteolysis, the energy invested in generation of the proteins is released. See Enzyme

Distinct proteolytic mechanisms serve different physiological requirements. Proteins can be divided into extracellular and intracellular, and the two groups are degraded by two distinct mechanisms. Extracellular proteins such as the plasma immunoglobulins and albumin are degraded in a process known as receptor-mediated endocytosis. Ubiquitin-mediated proteolysis of a variety of cellular proteins plays an important role in many basic cellular processes such as the regulation of cell cycle and division, differentiation, and development; DNA repair; regulation of the immune and inflammatory responses; and biogenesis of organelles.

Molecular chaperones

Molecular chaperones are specialized cellular proteins that bind nonnative forms of other proteins and assist them to reach a functional conformation. The role of chaperone proteins under conditions of stress, such as heat shock, is to protect proteins by binding to misfolded conformations when they are just starting to form, preventing aggregation; then, following return of normal conditions, they allow refolding to occur. Chaperones also play essential roles in folding under normal conditions, providing kinetic assistance to the folding process, and thus improving the overall rate and extent of productive folding.

Protein engineering

The amino acid sequences, sizes, and three-dimensional conformations of protein molecules can be manipulated by protein engineering, in which the basic techniques of genetic engineering are used to alter the genes that encode proteins. These manipulations are used to generate proteins with novel activities or properties for specific applications, to discover structure-function relationships, and to generate biologically active minimalist proteins (containing only those sequences necessary for biological activity) that are smaller than their naturally occurring counterparts.

Many subtle variations in a particular protein can be generated by making amino acid replacements at specific positions in the polypeptide sequence. For example, at any specific position an amino acid can be replaced by another to generate a mutant protein that may have different characteristics by virtue of the single replaced amino acid. Amino acids can also be deleted from a protein sequence, either individually or in groups. These proteins are referred to as deletion mutants. Deletion mutants may or may not be missing one or more functions or properties of the full, naturally occurring protein. Moreover, part or all of a protein sequence can be joined or fused to that of another protein. The resulting protein is called a hybrid or fusion protein, which generally has characteristics that combine those of each of the joined partners.

protein

[′prō‚tēn]
(biochemistry)
Any of a class of high-molecular-weight polymer compounds composed of a variety of α-amino acids joined by peptide linkages.

protein

any of a large group of nitrogenous compounds of high molecular weight that are essential constituents of all living organisms. They consist of one or more chains of amino acids linked by peptide bonds and are folded into a specific three-dimensional shape maintained by further chemical bonding