Protein

In chemistry, proteins (or protides) are biological macromolecules consisting of chains of amino acids linked to each other by a peptide bond (i.e., a bond between the amino group of one amino acid and the carboxyl group of the other amino acid, created through a condensation reaction with loss of a molecule of water). Proteins perform a wide range of functions within living organisms, including catalysis of metabolic reactions, synthesis function as DNA replication, response to stimuli, and transport of molecules from one place to another. Proteins differ from each other primarily in their amino acid sequence, which is dictated by the nucleotide sequence conserved in genes and usually results in protein folding and a specific three-dimensional structure that determines its activity.

In analogy to other biological macromolecules such as polysaccharides and nucleic acids, proteins are an essential part of living organisms and participate in virtually every process that takes place within cells. Many belong to the category of enzymes, whose function is to catalyze biochemical reactions vital to the metabolism of organisms. Proteins also have structural or mechanical functions, such as actin and myosin in muscles and the proteins that make up the cytoskeleton, which form a structure that allows the cell to maintain its shape. Others are critical for the transmission of inter- and intracellular signals, in the immune response, for cell adhesion, and for the cell cycle. Proteins are also necessary elements in the nutrition of animals, since they cannot synthesize all the amino acids they need and must obtain the essential ones through food. Through the process of digestion, animals break down ingested proteins into individual amino acids, which are then used in metabolism.

Once synthesized in the body, proteins exist only for a certain period of time and then are degraded and recycled through cellular mechanisms for the process of protein turnover. The duration of a protein is measured in terms of half-life and can vary widely. Some may exist for only a few minutes, others up to a few years, however the average duration in mammalian cells is between 1 and 2 days. Abnormal and misfolded proteins can cause instability if they are not degraded more rapidly.

Proteins can be purified from other cellular components using a variety of techniques such as ultracentrifugation, precipitation, electrophoresis, and chromatography; the advent of genetic engineering has made possible a number of methods to facilitate such purification. Methods commonly used to study protein structure and function include immunohistochemistry, site-specific mutagenesis, X-ray crystallography, and nuclear magnetic resonance. Proteins are differentiated primarily by the sequence of amino acids that compose them, which in turn depends on the nucleotide sequence of the genes within the cell that express their synthesis.

A linear chain of amino acid residues is called a “polypeptide” (i.e., a chain of multiple amino acids linked by peptide bonds). A protein generally consists of one or more long polypeptides possibly coordinated to nonpeptide groups, called prosthetic groups or cofactors. Short polypeptides, containing less than about 20-30 amino acids, are rarely considered proteins and are commonly called peptides or sometimes oligopeptides. The sequence of amino acids in a protein is defined by the sequence present in a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; however, in some organisms the code may include selenocysteine (SEC), and in some archaea, pyrrolysine and finally a 23rd amino acid, N-formylmethionine, a derivative of methionine, which initiates protein synthesis in some bacteria.

Shortly after or even during protein synthesis, the residues of a protein are often chemically modified through post-translational modification, which if present alters the physical and chemical properties, folding, stability, activity, and ultimately the function of the protein. Proteins can also work together to achieve a particular function and often associate in stable multiprotein complexes.

Proteins that contain the same type and number of amino acids may differ in the order in which they are located in the structure of the molecule. This aspect is very important because a small variation in the sequence of amino acids of a protein (i.e. in the order in which the various types of amino acids follow each other) can lead to variations in the three-dimensional structure of the macromolecule that can make the protein non-functional. A well-known example is the case of the beta chain of human hemoglobin, which in its normal sequence carries a stretch formed by: valine-histidine-leucine-threonine-proline-glutamic acid-lysine.

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of proteins, each with a unique function. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.

TypeExamplesFunctions
Digestive EnzymesAmylase, lipase, pepsin, trypsinHelp in food by catabolizing nutrients into monomeric units
TransportHemoglobin, albuminCarry substances in the blood or lymph throughout the body
StructuralActin, tubulin, keratinConstruct different structures, like the cytoskeleton
HormonesInsulin, thyroxineCoordinate different body systems’ activity
DefenseImmunoglobulinsProtect the body from foreign pathogens
ContractileActin, myosinEffect muscle contraction
StorageLegume storage proteins, egg white (albumin)Provide nourishment in early embryo development and the seedling

Proteins have different shapes and molecular weights. Some proteins are globular in shape; whereas, others are fibrous in nature. For example, hemoglobin is a globular protein, but collagen, located in our skin, is a fibrous protein. Protein shape is critical to its function, and many different types of chemical bonds maintain this shape. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the protein’s shape, leading to loss of function, or denaturation. Different arrangements of the same types of amino acids comprise all proteins.

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