Post-translational modification in the context of "Proteinogenic amino acid"

Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA). Sophisticated programs of gene expression are widely observed in biology, for example to trigger developmental pathways, respond to environmental stimuli, or adapt to new food sources. Virtually any step of gene expression can be modulated, from transcriptional initiation, to RNA processing, and to the post-translational modification of a protein. Often, one gene regulator controls another, and so on, in a gene regulatory network.

Gene regulation is essential for viruses, prokaryotes and eukaryotes as it increases the versatility and adaptability of an organism by allowing the cell to express protein when needed. Although as early as 1951, Barbara McClintock showed interaction between two genetic loci, Activator (Ac) and Dissociator (Ds), in the color formation of maize seeds, the first discovery of a gene regulation system is widely considered to be the identification in 1961 of the lac operon, discovered by François Jacob and Jacques Monod, in which some enzymes involved in lactose metabolism are expressed by E. coli only in the presence of lactose and absence of glucose.

Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity.

A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; but in certain organisms the genetic code can include selenocysteine and—in certain archaea—pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Some proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can work together to achieve a particular function, and they often associate to form stable protein complexes.

In general, flux in biology relates to movement of a substance between compartments. There are several cases where the concept of flux is important.

• The movement of molecules across a membrane: in this case, flux is defined by the rate of diffusion or transport of a substance across a permeable membrane. Except in the case of active transport, net flux is directly proportional to the concentration difference across the membrane, the surface area of the membrane, and the membrane permeability constant.
• In ecology, flux is often considered at the ecosystem level – for instance, accurate determination of carbon fluxes using techniques like eddy covariance (at a regional and global level) is essential for modeling the causes and consequences of global warming.
• Metabolic flux refers to the rate of flow of metabolites through a biochemical network, along a linear metabolic pathway, or through a single enzyme. A calculation may also be made of carbon flux or flux of other elemental components of biomolecules (e.g. nitrogen). The general unit of flux is chemical mass /time (e.g., micromole/minute; mg/kg/minute). Flux rates are dependent on a number of factors, including: enzyme concentration; the concentration of precursor, product, and intermediate metabolites; post-translational modification of enzymes; and the presence of metabolic activators or repressors. Metabolic flux in biologic systems can refer to biosynthesis rates of polymers or other macromolecules, such as proteins, lipids, polynucleotides, or complex carbohydrates, as well as the flow of intermediary metabolites through pathways. Metabolic control analysis and flux balance analysis provide frameworks for understanding metabolic fluxes and their constraints.

Vitamin K is a family of structurally similar, fat-soluble vitamers found in foods and marketed as dietary supplements. The human body requires vitamin K for post-synthesis modification of certain proteins that are required for blood coagulation ("K" from Danish koagulation, for "coagulation") and for controlling binding of calcium in bones and other tissues. The complete synthesis involves final modification of these so-called "Gla proteins" by the enzyme gamma-glutamyl carboxylase that uses vitamin K as a cofactor.

Vitamin K is used in the liver as the intermediate VKH₂ to deprotonate a glutamate residue and then is reprocessed into vitamin K through a vitamin K oxide intermediate. The presence of uncarboxylated proteins indicates a vitamin K deficiency. Carboxylation allows them to bind (chelate) calcium ions, which they cannot do otherwise. Without vitamin K, blood coagulation is seriously impaired, and uncontrolled bleeding occurs. Research suggests that deficiency of vitamin K may also weaken bones, potentially contributing to osteoporosis, and may promote calcification of arteries and other soft tissues.

Glycosylation is the reaction in which a carbohydrate (or 'glycan'), i.e. a glycosyl donor, is attached to a hydroxyl or other functional group of another molecule (a glycosyl acceptor) in order to form a glycoconjugate. In biology (but not always in chemistry), glycosylation usually refers to an enzyme-catalysed reaction, whereas glycation (also 'non-enzymatic glycation' and 'non-enzymatic glycosylation') may refer to a non-enzymatic reaction.

Glycosylation is a form of co-translational and post-translational modification. Glycans serve a variety of structural and functional roles in membrane and secreted proteins. The majority of proteins synthesized in the rough endoplasmic reticulum undergo glycosylation. Glycosylation is also present in the cytoplasm and nucleus as the O-GlcNAc modification. Aglycosylation is a feature of engineered antibodies to bypass glycosylation. Five classes of glycans are produced: