Editing Metabolism (section)

== Key biochemicals ==
{{further|Biomolecule|Cell (biology)|Biochemistry}}
[[File:Trimyristin-3D-vdW.png|right|thumb|upright=1.15|Structure of a [[triacylglycerol]] lipid]]
Most of the structures that make up animals, plants and microbes are made from four basic classes of [[molecule]]s: [[amino acid]]s, [[carbohydrate]]s, [[nucleic acid]] and [[lipid]]s (often called [[fat]]s). As these molecules are vital for life, metabolic reactions either focus on making these molecules during the construction of cells and tissues, or on breaking them down and using them to obtain energy, by their digestion. These biochemicals can be joined to make [[polymer]]s such as [[DNA]] and [[protein]]s, essential [[macromolecules]] of life.<ref>{{cite journal| vauthors = Cooper GM |date=2000|title=The Molecular Composition of Cells|url=https://www.ncbi.nlm.nih.gov/books/NBK9879/|journal=The Cell: A Molecular Approach | edition = 2nd |language=en|access-date=25 June 2020|archive-date=27 August 2020|archive-url=https://web.archive.org/web/20200827120320/https://www.ncbi.nlm.nih.gov/books/NBK9879/|url-status=live}}</ref>
{| class="wikitable" style="margin-left: auto; margin-right: auto;"
!Type of molecule
!Name of [[monomer]] forms
!Name of [[polymer]] forms
!Examples of polymer forms
|- style="text-align:center;" 
||[[Amino acid]]s
||Amino acids
||[[Protein]]s (made of polypeptides)
||[[Fibrous protein]]s and [[globular protein]]s
|- style="text-align:center;" 
||[[Carbohydrate]]s
||[[Monosaccharide]]s
||[[Polysaccharide]]s
||[[Starch]], [[glycogen]] and [[cellulose]]
|- style="text-align:center;" 
||[[Nucleic acid]]s
||[[Nucleotide]]s
||[[Polynucleotide]]s
||[[DNA]] and [[RNA]]
|}

===Amino acids and proteins===
{{Main|Protein}}

Proteins are made of [[amino acid]]s arranged in a linear chain joined by [[peptide bond]]s. Many proteins are [[enzyme]]s that [[catalysis|catalyze]] the chemical reactions in metabolism. Other proteins have structural or mechanical functions, such as those that form the [[cytoskeleton]], a system of [[scaffolding]] that maintains the cell shape.<ref>{{cite journal | vauthors = Michie KA, Löwe J | title = Dynamic filaments of the bacterial cytoskeleton | journal = [[Annual Review of Biochemistry]] | volume = 75 | pages = 467–92 | year = 2006 | pmid = 16756499 | doi = 10.1146/annurev.biochem.75.103004.142452 | s2cid = 4550126 }}</ref> Proteins are also important in [[cell signaling]], [[antibody|immune responses]], [[cell adhesion]], [[active transport]] across membranes, and the [[cell cycle]].<ref name="Nelson-2005">{{cite book | vauthors = Nelson DL, Cox MM | title = Lehninger Principles of Biochemistry | publisher = W. H. Freeman and company | year = 2005 | location = New York | page = [https://archive.org/details/lehningerprincip00lehn_0/page/841 841] | isbn = 978-0-7167-4339-2 | url-access = registration | url = https://archive.org/details/lehningerprincip00lehn_0/page/841 }}</ref> Amino acids also contribute to cellular energy metabolism by providing a carbon source for entry into the citric acid cycle ([[tricarboxylic acid cycle]]),<ref>{{cite journal | vauthors = Kelleher JK, Bryan BM, Mallet RT, Holleran AL, Murphy AN, Fiskum G | title = Analysis of tricarboxylic acid-cycle metabolism of hepatoma cells by comparison of 14CO2 ratios | journal = The Biochemical Journal | volume = 246 | issue = 3 | pages = 633–9 | date = September 1987 | pmid = 3120698 | pmc = 1148327 | doi = 10.1042/bj2460633 }}</ref> especially when a primary source of energy, such as [[glucose]], is scarce, or when cells undergo metabolic stress.<ref>{{cite journal | vauthors = Hothersall JS, Ahmed A | title = Metabolic fate of the increased yeast amino Acid uptake subsequent to catabolite derepression | journal = Journal of Amino Acids | volume = 2013 | pages = 461901 | year = 2013 | pmid = 23431419 | pmc = 3575661 | doi = 10.1155/2013/461901 | doi-access = free }}</ref>

===Lipids===
{{Main|Biolipid}}
Lipids are the most diverse group of biochemicals. Their main structural uses are as part of internal and external [[biological membrane]]s, such as the [[cell membrane]].<ref name="Nelson-2005"/> Their [[chemical energy]] can also be used. Lipids contain a long, non-polar [[Aliphatic compound|hydrocarbon chain]] with a small polar region containing oxygen. Lipids are usually defined as [[hydrophobe|hydrophobic]] or [[amphiphiles|amphipathic]] biological molecules but will dissolve in [[organic solvent]]s such as [[ethanol]], [[benzene]] or [[chloroform]].<ref>{{cite journal | vauthors = Fahy E, Subramaniam S, Brown HA, Glass CK, Merrill AH, Murphy RC, Raetz CR, Russell DW, Seyama Y, Shaw W, Shimizu T, Spener F, van Meer G, VanNieuwenhze MS, White SH, Witztum JL, Dennis EA | display-authors = 6 | title = A comprehensive classification system for lipids | journal = Journal of Lipid Research | volume = 46 | issue = 5 | pages = 839–61 | date = May 2005 | pmid = 15722563 | doi = 10.1194/jlr.E400004-JLR200 | doi-access = free }}</ref> The [[fat]]s are a large group of compounds that contain [[fatty acid]]s and [[glycerol]]; a glycerol molecule attached to three fatty acids by [[ester]] linkages is called a [[triglyceride|triacylglyceride]].<ref>{{cite web|title=Lipid nomenclature Lip-1 & Lip-2|url=https://www.qmul.ac.uk/sbcs/iupac/lipid/lip1n2.html#p11|access-date=2020-06-06|website=qmul.ac.uk|archive-date=6 June 2020|archive-url=https://web.archive.org/web/20200606140055/https://www.qmul.ac.uk/sbcs/iupac/lipid/lip1n2.html#p11|url-status=live}}</ref> Several variations of the basic structure exist, including backbones such as [[sphingosine]] in [[sphingomyelin]], and [[hydrophile|hydrophilic]] groups such as [[phosphate]] in [[phospholipid]]s. [[Steroid]]s such as [[sterol]] are another major class of lipids.<ref>{{cite book|edition=8|title=Biochemistry|location=New York|isbn=978-1-4641-2610-9|oclc=913469736 | vauthors = Berg JM, Tymoczko JL, Gatto Jr GJ, Stryer L |date=8 April 2015|publisher=W. H. Freeman|pages=362}}</ref>

===Carbohydrates===
[[File:Glucose Fisher to Haworth.gif|thumb|upright=1.15|right|alt=The straight chain form consists of four C H O H groups linked in a row, capped at the ends by an aldehyde group C O H and a methanol group C H 2 O H.  To form the ring, the aldehyde group combines with the O H group of the next-to-last carbon at the other end, just before the methanol group.|[[Glucose]] can exist in both a straight-chain and ring form.]]{{Main|Carbohydrate}}
Carbohydrates are [[aldehyde]]s or [[ketone]]s, with many [[hydroxyl]] groups attached, that can exist as straight chains or rings. Carbohydrates are the most abundant biological molecules, and fill numerous roles, such as the storage and transport of [[energy]] ([[starch]], [[glycogen]]) and structural components ([[cellulose]] in plants, [[chitin]] in animals).<ref name="Nelson-2005" /> The basic carbohydrate units are called [[monosaccharide]]s and include [[galactose]], [[fructose]], and most importantly [[glucose]]. Monosaccharides can be linked together to form [[polysaccharide]]s in almost limitless ways.<ref>{{cite journal | vauthors = Raman R, Raguram S, Venkataraman G, Paulson JC, Sasisekharan R | title = Glycomics: an integrated systems approach to structure-function relationships of glycans | journal = Nature Methods | volume = 2 | issue = 11 | pages = 817–24 | date = November 2005 | pmid = 16278650 | doi = 10.1038/nmeth807 | s2cid = 4644919 }}</ref>

===Nucleotides===
{{Main|Nucleotide}}
The two nucleic acids, DNA and [[RNA]], are polymers of [[nucleotide]]s. Each nucleotide is composed of a phosphate attached to a [[ribose]] or [[deoxyribose]] sugar group which is attached to a [[nitrogenous base]]. Nucleic acids are critical for the storage and use of genetic information, and its interpretation through the processes of [[transcription (genetics)|transcription]] and [[protein biosynthesis]].<ref name="Nelson-2005"/> This information is protected by [[DNA repair]] mechanisms and propagated through [[DNA replication]]. Many [[virus]]es have an [[RNA virus|RNA genome]], such as [[HIV]], which uses [[reverse transcription]] to create a DNA template from its viral RNA genome.<ref>{{cite journal | vauthors = Sierra S, Kupfer B, Kaiser R | title = Basics of the virology of HIV-1 and its replication | journal = Journal of Clinical Virology | volume = 34 | issue = 4 | pages = 233–44 | date = December 2005 | pmid = 16198625 | doi = 10.1016/j.jcv.2005.09.004 }}</ref> RNA in [[ribozyme]]s such as [[spliceosome]]s and [[ribosome]]s is similar to enzymes as it can catalyze chemical reactions. Individual [[nucleoside]]s are made by attaching a [[nucleobase]] to a [[ribose]] sugar. These bases are [[heterocyclic]] rings containing nitrogen, classified as [[purine]]s or [[pyrimidine]]s. Nucleotides also act as coenzymes in metabolic-group-transfer reactions.<ref name="Wimmer-1978">{{cite journal | vauthors = Wimmer MJ, Rose IA | title = Mechanisms of enzyme-catalyzed group transfer reactions | journal = [[Annual Review of Biochemistry]] | volume = 47 | pages = 1031–78 | year = 1978 | pmid = 354490 | doi = 10.1146/annurev.bi.47.070178.005123 }}</ref>

===Coenzymes===
[[File:Adenosintriphosphat protoniert.svg|thumb|class=skin-invert|alt=Skeletal formula of adenosine triphosphate|Structure of [[adenosine triphosphate]] (ATP), a central intermediate in energy metabolism]]
{{main|Coenzyme}}
Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of [[functional group]]s of atoms and their bonds within molecules.<ref>{{cite journal | vauthors = Mitchell P | title = The Ninth Sir Hans Krebs Lecture. Compartmentation and communication in living systems. Ligand conduction: a general catalytic principle in chemical, osmotic and chemiosmotic reaction systems | journal = European Journal of Biochemistry | volume = 95 | issue = 1 | pages = 1–20 | date = March 1979 | pmid = 378655 | doi = 10.1111/j.1432-1033.1979.tb12934.x | doi-access = free }}</ref> This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions.<ref name="Wimmer-1978"/> These group-transfer intermediates are called [[coenzyme]]s. Each class of group-transfer reactions is carried out by a particular coenzyme, which is the [[Substrate (biochemistry)|substrate]] for a set of enzymes that produce it, and a set of enzymes that consume it. These coenzymes are therefore continuously made, consumed and then recycled.<ref name="Dimroth-2006">{{cite journal | vauthors = Dimroth P, von Ballmoos C, Meier T | title = Catalytic and mechanical cycles in F-ATP synthases. Fourth in the Cycles Review Series | journal = EMBO Reports | volume = 7 | issue = 3 | pages = 276–82 | date = March 2006 | pmid = 16607397 | pmc = 1456893 | doi = 10.1038/sj.embor.7400646 }}</ref>

One central coenzyme is [[adenosine triphosphate]] (ATP), the energy currency of cells. This [[nucleotide]] is used to transfer chemical energy between different chemical reactions. There is only a small amount of ATP in cells, but as it is continuously regenerated, the human body can use about its own weight in ATP per day.<ref name="Dimroth-2006"/> ATP acts as a bridge between [[catabolism]] and [[anabolism]]. Catabolism breaks down molecules, and anabolism puts them together. Catabolic reactions generate ATP, and anabolic reactions consume it. It also serves as a carrier of phosphate groups in [[phosphorylation]] reactions.<ref>{{cite journal | vauthors = Bonora M, Patergnani S, Rimessi A, De Marchi E, Suski JM, Bononi A, Giorgi C, Marchi S, Missiroli S, Poletti F, Wieckowski MR, Pinton P | display-authors = 6 | title = ATP synthesis and storage | journal = Purinergic Signalling | volume = 8 | issue = 3 | pages = 343–57 | date = September 2012 | pmid = 22528680 | pmc = 3360099 | doi = 10.1007/s11302-012-9305-8 }}</ref>

A [[vitamin]] is an organic compound needed in small quantities that cannot be made in cells. In [[human nutrition]], most vitamins function as coenzymes after modification; for example, all water-soluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells.<ref>{{cite journal| vauthors = Berg JM, Tymoczko JL, Stryer L |date=2002|title=Vitamins Are Often Precursors to Coenzymes|url=https://www.ncbi.nlm.nih.gov/books/NBK22549/|journal=Biochemistry. 5th Edition|language=en|access-date=9 June 2020|archive-date=15 December 2020|archive-url=https://web.archive.org/web/20201215232601/https://www.ncbi.nlm.nih.gov/books/NBK22549/|url-status=live}}</ref> [[Nicotinamide adenine dinucleotide]] (NAD<sup>+</sup>), a derivative of vitamin B<sub>3</sub> ([[Niacin (nutrient)|niacin]]), is an important coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of [[dehydrogenase]]s remove electrons from their substrates and [[redox|reduce]] NAD<sup>+</sup> into NADH. This reduced form of the coenzyme is then a substrate for any of the [[reductase]]s in the cell that need to transfer hydrogen atoms to their substrates.<ref>{{cite journal | vauthors = Pollak N, Dölle C, Ziegler M | title = The power to reduce: pyridine nucleotides--small molecules with a multitude of functions | journal = The Biochemical Journal | volume = 402 | issue = 2 | pages = 205–18 | date = March 2007 | pmid = 17295611 | pmc = 1798440 | doi = 10.1042/BJ20061638 }}</ref> Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The NAD<sup>+</sup>/NADH form is more important in catabolic reactions, while NADP<sup>+</sup>/NADPH is used in anabolic reactions.<ref>{{cite book| vauthors = Fatih Y |title=Advances in food biochemistry|publisher=CRC Press|year=2009|isbn=978-1-4200-0769-5|location=Boca Raton|pages=228|oclc=607553259}}</ref>

[[File:1GZX Haemoglobin.png|thumb|upright=1.35|right|The structure of iron-containing [[hemoglobin]]. The protein subunits are in red and blue, and the iron-containing [[heme]] groups in green. From {{PDB|1GZX}}.]]

===Mineral and cofactors===
{{further||Bioinorganic chemistry}}
Inorganic elements play critical roles in metabolism; some are abundant (e.g. [[sodium]] and [[potassium]]) while others function at minute concentrations. About 99% of a human's body weight is made up of the elements [[carbon]], [[nitrogen]], [[calcium]], [[sodium]], [[chlorine]], [[potassium]], [[hydrogen]], [[phosphorus]], [[oxygen]] and [[sulfur]]. [[Organic compound]]s (proteins, lipids and carbohydrates) contain the majority of the carbon and nitrogen; most of the oxygen and hydrogen is present as water.<ref name="Heymsfield-1991">{{cite journal | vauthors = Heymsfield SB, Waki M, Kehayias J, Lichtman S, Dilmanian FA, Kamen Y, Wang J, Pierson RN | display-authors = 6 | title = Chemical and elemental analysis of humans in vivo using improved body composition models | journal = The American Journal of Physiology | volume = 261 | issue = 2 Pt 1 | pages = E190-8 | date = August 1991 | pmid = 1872381 | doi = 10.1152/ajpendo.1991.261.2.E190 }}</ref>

The abundant inorganic elements act as [[electrolyte]]s. The most important ions are [[sodium]], [[potassium]], [[calcium]], [[magnesium]], [[chloride]], [[phosphate]] and the organic ion [[bicarbonate]]. The maintenance of precise [[ion gradient]]s across [[cell membrane]]s maintains [[osmotic pressure]] and [[pH]].<ref>{{cite book | chapter = Electrolyte Balance | chapter-url = https://opentextbc.ca/anatomyandphysiology/chapter/26-3-electrolyte-balance/ | title = Anatomy and Physiology | publisher = OpenStax | access-date = 23 June 2020 | archive-date = 2 June 2020 | archive-url = https://web.archive.org/web/20200602222138/https://opentextbc.ca/anatomyandphysiology/chapter/26-3-electrolyte-balance/ | url-status = dead }}</ref> Ions are also critical for [[nerve]] and [[muscle]] function, as [[action potential]]s in these tissues are produced by the exchange of electrolytes between the [[extracellular fluid]] and the cell's fluid, the [[cytosol]].<ref>{{cite book | vauthors = Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell J |date=2000 |chapter=The Action Potential and Conduction of Electric Impulses |chapter-url=https://www.ncbi.nlm.nih.gov/books/NBK21668/ |title=Molecular Cell Biology |edition=4th |language=en |via=NCBI |access-date=23 June 2020 |archive-date=30 May 2020 |archive-url=https://web.archive.org/web/20200530112637/https://www.ncbi.nlm.nih.gov/books/NBK21668/ |url-status=live }}</ref> Electrolytes enter and leave cells through proteins in the cell membrane called [[ion channel]]s. For example, [[muscle contraction]] depends upon the movement of calcium, sodium and potassium through ion channels in the cell membrane and [[T-tubule]]s.<ref>{{cite journal | vauthors = Dulhunty AF | title = Excitation-contraction coupling from the 1950s into the new millennium | journal = Clinical and Experimental Pharmacology & Physiology | volume = 33 | issue = 9 | pages = 763–72 | date = September 2006 | pmid = 16922804 | doi = 10.1111/j.1440-1681.2006.04441.x | s2cid = 37462321 }}</ref>

[[Transition metal]]s are usually present as [[trace element]]s in organisms, with [[zinc]] and [[iron]] being most abundant of those.<ref>{{cite book| vauthors = Torres-Romero JC, Alvarez-Sánchez ME, Fernández-Martín K, Alvarez-Sánchez LC, Arana-Argáez V, Ramírez-Camacho M, Lara-Riegos J | chapter=Zinc Efflux in Trichomonas vaginalis: In Silico Identification and Expression Analysis of CDF-Like Genes|date=2018| title =Quantitative Models for Microscopic to Macroscopic Biological Macromolecules and Tissues|pages=149–168| veditors = Olivares-Quiroz L, Resendis-Antonio O |place=Cham|publisher=Springer International Publishing|language=en|doi=10.1007/978-3-319-73975-5_8|isbn=978-3-319-73975-5 }}</ref> Metal cofactors are bound tightly to specific sites in proteins; although enzyme cofactors can be modified during catalysis, they always return to their original state by the end of the reaction catalyzed. Metal micronutrients are taken up into organisms by specific transporters and bind to storage proteins such as [[ferritin]] or [[metallothionein]] when not in use.<ref>{{cite journal | vauthors = Cousins RJ, Liuzzi JP, Lichten LA | title = Mammalian zinc transport, trafficking, and signals | journal = The Journal of Biological Chemistry | volume = 281 | issue = 34 | pages = 24085–9 | date = August 2006 | pmid = 16793761 | doi = 10.1074/jbc.R600011200 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Dunn LL, Suryo Rahmanto Y, Richardson DR | title = Iron uptake and metabolism in the new millennium | journal = Trends in Cell Biology | volume = 17 | issue = 2 | pages = 93–100 | date = February 2007 | pmid = 17194590 | doi = 10.1016/j.tcb.2006.12.003 }}</ref>