Editing Biomolecule

{{Short description|Molecule produced by a living organism}}

{{Biochemistry sidebar}}

[[Image:Myoglobin.png|thumb|200px|A representation of the structure of [[myoglobin]], showing [[alpha helix|alpha helices]], represented by ribbons. This protein was the first to have its structure solved by [[X-ray crystallography]] by [[Max Perutz]] and [[John Kendrew]] in 1958, for which they received a [[Nobel Prize in Chemistry]]]]
 
A '''biomolecule''' or '''biological molecule''' is loosely defined as a [[molecule]] produced by a living [[organism]] and essential to one or more typically [[biological process]]es.<ref>Bunge, M. (1979). ''Treatise on Basic Philosophy'', vol. 4. Ontology II: A World of Systems, p. 61-2. [https://books.google.com/books?id=4hpNzUzH1E4C&lpg=PP1&hl=pt-BR&pg=PA61 link].</ref> Biomolecules include large [[macromolecule]]s such as [[protein]]s, [[carbohydrate]]s, [[lipid]]s, and [[nucleic acid]]s, as well as [[small molecule]]s such as vitamins and hormones. A general name for this class of material is ''biological materials''. Biomolecules are an important element of living organisms. They are often [[endogeny (biology)|endogenous]],<ref>{{cite book |author1=Voon, C. H. |author2=Sam, S. T. |title=Nanobiosensors for Biomolecular Targeting |date=2019 |publisher=Elsevier |isbn=978-0-12-813900-4 |language=en |chapter=2.1 Biosensors}}</ref> i.e. produced within the organism,<ref>[https://medical-dictionary.thefreedictionary.com/endogeny endogeny]. (2011) ''Segen's Medical Dictionary''. [http://www.thefreedictionary.com The Free Dictionary by Farlex.] Farlex, Inc. Accessed June 27, 2019.</ref> but organisms usually also need [[exogeny|exogenous]] biomolecules, for example certain [[nutrient]]s, to survive.

Biomolecules and their [[organic reaction|reactions]] are studied in [[biology]] and its subfields of [[biochemistry]] and [[molecular biology]]. Most biomolecules are [[organic compound]]s, and just four [[chemical element|elements]]—[[oxygen]], [[carbon]], [[hydrogen]], and [[nitrogen]]—make up 96% of the [[human body]]'s mass. But many other elements, such as the various [[biometal (biology)|biometals]],  are also present in small amounts.

The uniformity of both specific types of molecules (the biomolecules) and of certain [[metabolic pathway]]s are invariant features among the wide diversity of life forms; thus these biomolecules and metabolic pathways are referred to as "biochemical universals"<ref>{{cite book |last1=Green |first1=D. E. |last2=Goldberger |first2=R. |title=Molecular Insights into the Living Process |publisher=Academic Press |location=New York |year=1967 |url=https://books.google.com/books?id=xi6FAAAAIAAJ |via=[[Google Books]] }}</ref> or "theory of material unity of the living beings", a unifying concept in biology, along with [[cell theory]] and [[evolution theory]].<ref>{{cite book |last=Gayon |first=J. |chapter=La philosophie et la biologie |title=Encyclopédie philosophique universelle |volume=IV, Le Discours philosophique |editor-first=J. F. |editor-last=Mattéi |publisher=Presses Universitaires de France |year=1998 |pages=2152–2171 |isbn=9782130448631 |url=https://books.google.com/books?id=CWcKAQAAMAAJ |via=Google Books }}</ref>

==Types of biomolecules==
A diverse range of biomolecules exist, including:

* [[Small molecule]]s:
** [[Lipid]]s, [[fatty acid]]s, [[glycolipid]]s, [[sterol]]s, [[monosaccharide]]s 
** [[Vitamin]]s
** [[Hormone]]s, [[neurotransmitter]]s 
** [[Metabolite]]s
* [[Monomer]]s, [[oligomer]]s and [[polymer]]s:

{| class="wikitable"
|-
! Biomonomers !! Bio-oligo !! [[Biopolymer]]s !! [[Polymerization]] process !! [[Covalent bond]] name between monomers 
|-
| [[Amino acid]]s || [[Oligopeptide]]s || [[Polypeptide]]s, proteins ([[hemoglobin]]...) || [[Polycondensation]] || [[Peptide bond]]
|-
| [[Monosaccharide]]s || [[Oligosaccharide]]s|| [[Polysaccharide]]s ([[cellulose]]...) || Polycondensation || [[Glycosidic bond]]
|-
| [[Isoprene]] || [[Terpene]]s || Polyterpenes: cis-1,4-polyisoprene [[natural rubber]] and trans-1,4-polyisoprene [[gutta-percha]] || [[Polyaddition]] ||
|}

==Nucleosides and nucleotides==
{{Main|Nucleosides|Nucleotides}}

'''Nucleosides'''  are molecules formed by attaching a [[nucleobase]] to a [[ribose]] or [[deoxyribose]] ring. Examples of these include [[cytidine]] (C), [[uridine]] (U), [[adenosine]] (A), [[guanosine]] (G), and [[thymidine]] (T).

Nucleosides can be [[phosphorylation|phosphorylated]] by specific [[kinase]]s in the cell, producing [[nucleotide]]s. 
Both [[DNA]] and [[RNA]] are [[polymer]]s, consisting of long, linear molecules assembled by [[polymerase]] enzymes from repeating structural units, or monomers, of mononucleotides. DNA uses the deoxynucleotides C, G, A, and T, while RNA uses the ribonucleotides (which have an extra hydroxyl(OH) group on the pentose ring) C, G, A, and U. Modified bases are fairly common (such as with methyl groups on the base ring), as found in [[ribosome|ribosomal]] RNA or [[transfer RNA]]s or for discriminating the new from old strands of DNA after replication.<ref name=slabaugh>{{cite book |author1=Slabaugh, Michael R. |author2=Seager, Spencer L.  |name-list-style=amp|title=Organic and Biochemistry for Today |publisher=[[Brooks Cole]] |location=Pacific Grove |year=2007 |isbn=978-0-495-11280-8 |edition=6th}}</ref>

Each nucleotide is made of an acyclic [[nitrogenous base]], a [[pentose]] and one to three [[phosphate|phosphate groups]]. They contain carbon, nitrogen, oxygen, hydrogen and phosphorus. They serve as sources of chemical energy ([[adenosine triphosphate]] and [[guanosine triphosphate]]), participate in [[cell (biology)|cellular]] signaling ([[cyclic guanosine monophosphate]] and [[cyclic adenosine monophosphate]]), and are incorporated into important cofactors of enzymatic reactions ([[coenzyme A]], [[flavin adenine dinucleotide]], [[flavin mononucleotide]], and [[nicotinamide adenine dinucleotide phosphate]]).<ref name=Alberts>{{cite book |vauthors=Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Wlater P |title=Molecular biology of the cell |publisher=[[Garland Science]] |location=New York |year=2002 |pages=120–1 |isbn=0-8153-3218-1 |edition=4th |url=https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.TOC&depth=2}}</ref>

===DNA and RNA structure===
{{Main|DNA|Nucleic acid structure}}

DNA structure is dominated by the well-known [[double helix]] formed by Watson-Crick [[base-pair]]ing of C with G and A with T. This is known as [[B-DNA|B-form]] DNA, and is overwhelmingly the most favorable and common state of DNA; its highly specific and stable base-pairing is the basis of reliable genetic information storage. DNA can sometimes occur as single strands (often needing to be stabilized by single-strand binding proteins) or as [[A-DNA|A-form]] or [[Z-DNA|Z-form]] helices, and occasionally in more complex 3D structures such as the crossover at [[Holliday junction]]s during DNA replication.<ref name=Alberts/>

[[Image:Twort groupI intron RNAribbon stereo.jpg|thumb|right|Stereo 3D image of a group I intron ribozyme (PDB file 1Y0Q); gray lines show base pairs; ribbon arrows show double-helix regions, blue to red from 5' to 3'{{definition|date=September 2020}} end; white ribbon is an RNA product.]] 
RNA, in contrast, forms large and complex 3D tertiary structures reminiscent of proteins, as well as the loose single strands with locally folded regions that constitute [[messenger RNA]] molecules. Those RNA structures contain many stretches of A-form double helix, connected into definite 3D arrangements by single-stranded loops, bulges, and junctions.<ref>{{cite book |author=Saenger W |year=1984 |title=Principles of Nucleic Acid Structure |publisher=[[Springer-Verlag]] |isbn=0387907629}}</ref> Examples are tRNA, ribosomes, [[ribozyme]]s, and [[riboswitch]]es. These complex structures are facilitated by the fact that RNA backbone has less local flexibility than DNA but a large set of distinct conformations, apparently because of both positive and negative interactions of the extra OH on the ribose.<ref>{{cite journal |vauthors=Richardson JS, Schneider B, Murray LW, Kapral GJ, Immormino RM, Headd JJ, Richardson DC, Ham D, Hershkovits E, Williams LD, Keating KS, Pyle AM, Micallef D, Westbrook J, Berman HM |year=2008 |title=RNA Backbone: Consensus all-angle conformers and modular string nomenclature |journal=RNA |volume=14 |issue=3 |pages=465–481 |pmc=2248255 |doi=10.1261/rna.657708 |pmid=18192612}}</ref> Structured RNA molecules can do highly specific binding of other molecules and can themselves be recognized specifically; in addition, they can perform enzymatic catalysis (when they are known as "[[ribozyme]]s", as initially discovered by Tom Cech and colleagues).<ref>{{cite journal |vauthors=Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR |year=1982 |title=Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena |journal=Cell |volume=31 |issue=1 |pages=147–157 |doi=10.1016/0092-8674(82)90414-7 |pmid=6297745|s2cid=14787080 }}</ref>

==Saccharides==
[[Monosaccharide|'''Monosaccharides''']] are the simplest form of [[carbohydrate]]s with only one simple sugar. They essentially contain an [[aldehyde]] or [[ketone]] group in their structure.<ref name="Peng09">{{Cite journal |last=Moran |first=Timothy H. |date=June 2009 |title=Fructose and Satiety |journal=The Journal of Nutrition |language=en |volume=139 |issue=6 |pages=1253S–1256S |doi=10.3945/jn.108.097956 |pmc=6459054 |pmid=19403706}}</ref> The presence of an aldehyde group in a monosaccharide is indicated by the prefix ''aldo-''. Similarly, a ketone group is denoted by the prefix ''keto-''.<ref name=slabaugh/> Examples of monosaccharides are the [[hexose]]s,  [[glucose]], [[fructose]], [[Triose]]s, [[Tetrose]]s, [[Heptose]]s, [[galactose]], [[pentose]]s, ribose, and deoxyribose. Consumed fructose and [[glucose]] have different rates of gastric emptying, are differentially absorbed and have different metabolic fates, providing multiple opportunities for two different saccharides to differentially affect food intake.<ref name=Peng09/> Most saccharides eventually provide fuel for cellular respiration.

'''[[Disaccharide]]s''' are formed when two monosaccharides, or two single simple sugars, form a bond with removal of water. They can be hydrolyzed to yield their saccharin building blocks by boiling with dilute acid or reacting them with appropriate enzymes.<ref name=slabaugh/> Examples of disaccharides include [[sucrose]], [[maltose]], and [[lactose]].

'''[[Polysaccharide]]s''' are polymerized monosaccharides, or complex carbohydrates. They have multiple simple sugars. Examples are [[starch]], [[cellulose]], and [[glycogen]]. They are generally large and often have a complex branched connectivity. Because of their size, polysaccharides are not water-soluble, but their many hydroxy groups become hydrated individually when exposed to water, and some polysaccharides form thick colloidal dispersions when heated in water.<ref name=slabaugh/> Shorter polysaccharides, with 3 to 10 monomers, are called [[oligosaccharide]]s.<ref>{{cite book
| last =Pigman
| first = W.
|author2=D. Horton
| title = The Carbohydrates |volume=1A
| publisher =[[Academic Press]]
| year = 1972 
| location = San Diego
| page = 3
| isbn =978-0-12-395934-8 }}</ref>
A fluorescent indicator-displacement molecular imprinting sensor was developed for discriminating saccharides. It successfully discriminated three brands of orange juice beverage.<ref>{{cite journal |author1=Jin, Tan |author2=Wang He-Fang |author3=Yan Xiu-Ping  |name-list-style=amp|title=Discrimination of Saccharides with a Fluorescent Molecular Imprinting Sensor Array Based on Phenylboronic Acid Functionalized Mesoporous Silica |journal=Anal. Chem. |volume=81 |issue=13 |pages=5273–80 |year=2009 |pmid=19507843 |doi=10.1021/ac900484x}}</ref> The change in fluorescence intensity of the sensing films resulting is directly related to the saccharide concentration.<ref>{{cite journal |author1=Bo Peng  |author2=Yu Qin  |name-list-style=amp|title=Lipophilic Polymer Membrane Optical Sensor with a Synthetic Receptor for Saccharide Detection |journal=Anal. Chem. |volume=80 |issue=15|pages=6137–41 |year=2008 |pmid=18593197 |doi=10.1021/ac800946p}}</ref>

==Lignin==
[[Lignin]] is a complex polyphenolic macromolecule composed mainly of beta-O4-aryl linkages. After cellulose, lignin is the second most abundant biopolymer and is one of the primary structural components of most plants. It contains subunits derived from [[paracoumaryl alcohol|''p''-coumaryl alcohol]], [[coniferyl alcohol]], and [[sinapyl alcohol]],<ref>{{cite book |editor= K. Freudenberg |editor2=A.C. Nash |year=1968 |title=Constitution and Biosynthesis of Lignin |location=Berlin |publisher=Springer-Verlag}}</ref> and is unusual among biomolecules in that it is [[racemic]]. The lack of optical activity is due to the polymerization of lignin which occurs via [[radical (chemistry)|free radical]] coupling reactions in which there is no preference for either configuration at a [[chirality (chemistry)|chiral center]].

==Lipid==
[[Lipid]]s (oleaginous) are chiefly '''[[fatty acid]] [[ester]]s''', and are the basic building blocks of [[cell membrane|biological membranes]]. Another biological role is energy storage (e.g., [[triglyceride]]s). Most lipids consist of a [[polar molecule|polar]] or [[hydrophilic]] head (typically glycerol) and one to three non polar or [[hydrophobic]] fatty acid tails, and therefore they are [[amphiphilic]]. Fatty acids consist of unbranched chains of carbon atoms that are connected by single bonds alone ('''[[saturated fat|saturated]]''' fatty acids) or by both single and [[double bond]]s ('''[[unsaturated fat|unsaturated]]''' fatty acids). The chains are usually 14–24 carbon groups long, but it is always an even number.

For lipids present in biological membranes, the hydrophilic head is from one of three classes:

* [[Glycolipid]]s, whose heads contain an [[oligosaccharide]] with 1-15 saccharide residues.
* [[Phospholipid]]s, whose heads contain a positively charged group that is linked to the tail by a negatively charged phosphate group.
* [[Sterol]]s, whose heads contain a planar steroid ring, for example, [[cholesterol]].

Other lipids include [[prostaglandins]] and [[leukotrienes]] which are both 20-carbon fatty acyl units synthesized from [[arachidonic acid]].
They are also known as fatty acids

==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 .

==See also==
{{Portal|Biology}}
* [[Biomolecular engineering]]
* [[List of biomolecules]]
* [[Metabolism]]
* [[Multi-state modeling of biomolecules]]

==References==
{{Reflist|30em}}

== External links ==
* [https://web.archive.org/web/20170120182246/http://www.bioexpoonline.com/companies/SBS Society for Biomolecular Sciences] provider of a forum for education and information exchange among professionals within drug discovery and related disciplines.

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