Editing Biomolecule (section)

==Amino acids==
[[Amino acids]] contain both [[amino]] and [[carboxylic acid]] [[functional group]]s. (In [[biochemistry]], the term amino acid is used when referring to those amino acids in which the amino and carboxylate functionalities are attached to the same carbon, plus [[proline]] which is not actually an amino acid).

Modified amino acids are sometimes observed in proteins; this is usually the result of enzymatic modification after [[translation (biology)|translation]] ([[protein synthesis]]). For example, phosphorylation of serine by [[kinases]] and dephosphorylation by [[phosphatases]] is an important control mechanism in the [[cell cycle]]. Only two amino acids other than the standard twenty are known to be incorporated into proteins during translation, in certain organisms:

* [[Selenocysteine]] is incorporated into some proteins at a UGA [[codon]], which is normally a stop codon.
* [[Pyrrolysine]] is incorporated into some proteins at a UAG codon. For instance, in some [[methanogen]]s in enzymes that are used to produce [[methane]].

Besides those used in [[protein synthesis]], other biologically important amino acids include [[carnitine]] (used in lipid transport within a cell), [[ornithine]], [[GABA]] and [[taurine]].

===Protein structure===
{{Main|Protein structure|Protein primary structure|Protein secondary structure|Protein tertiary structure|Protein quaternary structure}}
The particular series of amino acids that form a protein is known as that protein's [[primary structure]]. This sequence is determined by the genetic makeup of the individual. It specifies the order of side-chain groups along the linear polypeptide "backbone".

Proteins have two types of well-classified, frequently occurring elements of local structure defined by a particular pattern of [[hydrogen bond]]s along the backbone: [[alpha helix]] and [[beta sheet]]. Their number and arrangement is called the [[secondary structure]] of the protein. Alpha helices are regular spirals stabilized by hydrogen bonds between the backbone CO group ([[carbonyl]]) of one amino acid residue and the backbone NH group ([[amide]]) of the i+4 residue. The spiral has about 3.6 amino acids per turn, and the amino acid side chains stick out from the cylinder of the helix. Beta pleated sheets are formed by backbone hydrogen bonds between individual beta strands each of which is in an "extended", or fully stretched-out, conformation. The strands may lie parallel or antiparallel to each other, and the side-chain direction alternates above and below the sheet. Hemoglobin contains only helices, natural silk is formed of beta pleated sheets, and many enzymes have a pattern of alternating helices and beta-strands. The secondary-structure elements are connected by "loop" or "coil" regions of non-repetitive conformation, which are sometimes quite mobile or disordered but usually adopt a well-defined, stable arrangement.<ref>{{cite journal | last = Richardson | first = JS | author-link = Jane S. Richardson | year = 1981 | title = The Anatomy and Taxonomy of Proteins | journal = Advances in Protein Chemistry | volume = 34 | pages = 167&ndash;339 | url = http://kinemage.biochem.duke.edu/teaching/Anatax/ | doi = 10.1016/S0065-3233(08)60520-3 | pmid = 7020376 | access-date = 2012-06-24 | archive-date = 2019-03-16 | archive-url = https://web.archive.org/web/20190316165752/http://kinemage.biochem.duke.edu/teaching/anatax/ | url-status = dead | url-access = subscription }}</ref>

The overall, compact, [[dimension|3D]] structure of a protein is termed its [[tertiary structure]] or its "fold". It is formed as result of various attractive forces like [[hydrogen bonding]], [[disulfide bridges]], [[hydrophobic interactions]], [[hydrophilic]] interactions, [[van der Waals force]] etc.

When two or more [[polypeptide]] chains (either of identical or of different sequence) cluster to form a protein, [[quaternary structure]] of protein is formed. Quaternary structure is an attribute of [[polymer]]ic (same-sequence chains) or [[heteromeric]] (different-sequence chains) proteins like [[hemoglobin]], which consists of two "alpha" and two "beta" polypeptide chains.

====Apoenzymes====
An [[apoenzyme]] (or, generally, an apoprotein) is the protein without any small-molecule cofactors, substrates, or inhibitors bound. It is often important as an inactive storage, transport, or secretory form of a protein. This is required, for instance, to protect the secretory cell from the activity of that protein.
Apoenzymes become active enzymes on addition of a [[cofactor (biochemistry)|cofactor]]. Cofactors can be either inorganic (e.g., metal ions and [[iron-sulfur clusters]]) or organic compounds, (e.g., [Flavin group|flavin] and [[heme]]). Organic cofactors can be either [[prosthetic groups]], which are tightly bound to an enzyme, or [[coenzymes]], which are released from the enzyme's active site during the reaction.

====Isoenzymes====
[[Isoenzymes]], or isozymes, are multiple forms of an enzyme, with slightly different [[protein sequence]] and closely similar but usually not identical functions. They are either products of different [[genes]], or else different products of [[alternative splicing]]. They may either be produced in different organs or cell types to perform the same function, or several isoenzymes may be produced in the same cell type under differential regulation to suit the needs of changing development or environment. LDH ([[lactate dehydrogenase]]) has multiple isozymes, while [[fetal hemoglobin]] is an example of a developmentally regulated isoform of a non-enzymatic protein. The relative levels of isoenzymes in blood can be used to diagnose problems in the organ of secretion .