Protein

A protein (from the Greek protas meaning "of primary importance") is a complex, high-molecular-mass, 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.

Different proteins perform a wide variety of biological functions. Some proteins are enzymes, which catalyze chemical reactions. Other proteins play structural or mechanical roles, such as those that form the struts and joints of the cytoskeleton, which is like a system of scaffolding within a cell. Still more functions filled by proteins include immune response and the storage and transport of various ligands.

Proteins are a class of bio-macromolecules, alongside polysaccharides, lipids, and nucleic acids, that make up the primary constituents of biological organisms. Proteins are essentially polymers made up of a specific sequence of amino acids. The details of this sequence are stored in the code of a gene. Through the processes of transcription and translation, a cell reads the genetic information and uses it to construct the protein. In many cases, the resulting protein is then chemically altered (post-translational modification), before becoming functional. It is very common for proteins to work together to achieve a particular function, and often physically associate with one another to form a complex.

In nutrition, proteins are broken down through digestion back into free amino acids for the organism, including those the organism may not be able to synthesize itself.

Proteins are among the most actively-studied molecules in biochemistry, and were discovered by Jons Jakob Berzelius in 1838.

Properties of protein

Components and synthesis

Proteins are polymers built from 20 different L-alpha-amino acids. Proteins are assembled from amino acids using information present in genes. Genes are transcribed into RNA, RNA is then subject to post-transcriptional modification and control, resulting in a mature mRNA that undergoes translation into a protein. mRNA is translated by ribosomes that match the three-base codons of the mRNA to the three-base anti-codons of the appropriate tRNA. The enzyme aminoacyl tRNA synthetase catalyzes the addition of the correct amino acid to their tRNAs.

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.

Structure

Proteins 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. Thus, proteins are their own polymers, with amino acids being the monomers. 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 and are formed by hydrogen bonding. Secondary structures are 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; primarily formed by hydrophobic interactions, but hydrogen bonds, ionic interactions, and disulfide bonds are usually involved too.
- Quaternary structure: the shape or structure that results from the union of more than one protein molecule, usually called protein 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 structures are usually referred to as "conformations," and transitions between them are called conformational changes.

The process by which the higher structures are formed is called protein folding and is a consequence of the primary structure. The mechanism of protein folding is not entirely understood. 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 one.

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.

Diversity

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) however protein masses are generally measured in kiloDaltons (kDa). 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 (like insulin), 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. 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 some of the structure of animals: examples include tubulin, actin, collagen and keratin, all of which are important components of skin, hair, 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.

Role of protein

Functions

Proteins are involved in practically every function performed by a cell, including regulation of cellular functions such as signal transduction and metabolism. Life, chemically speaking, is nothing but the function of proteins, although the information to make a unique protein resides, passively, in the DNA. The protein involved in functions control almost all the molecular processes of the body. Proteins are the actors, that do everything that happens within us. Although proteins do almost everything in an organism, several particularly important functional classes may be recognized:

- enzymes, that catalyze all of the reactions of metabolism;
- structural proteins, such as tubulin, or collagen;
- regulatory proteins, such as transcription factors or cyclins that regulate the cell cycle;
- signalling molecules or their receptors such as some hormones and their receptors;
- defensive proteins, which can include everything from antibodies of the immune system, to toxins (e.g., dendrotoxins of snakes), to proteins that include unusual amino acids like canavanine.

Nutrition

In nutrition, proteins are broken down through digestion, which begins in the stomach. There proteins are broken down into proteases and polypeptides to provide amino acids for the organism, including those the organism may not be able to synthesize itself. Pepsinogen is converted into the enzyme pepsin when it comes into contact with hydrochloric acid. Pepsin is the only proteolytic enzyme that digests collagen, the major protein of connective tissue. Most protein digestion takes place in the duodenum with the overall contribution from the stomach being small. Almost all protein is absorbed when it reaches the jejunum with only 1% of ingested protein left in the feces. Some amino acids remain in the epithelial cells and are used for synthesis of new proteins, including some intestinal proteins, constantly being digested, recycled and absorbed from the small intestine.

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