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{{short description|The set of life-sustaining chemical transformations within the cells of organisms }}

{{redirect|Cell metabolism|the journal|Cell Metabolism}}

{{about||the architectural movement|Metabolism (architecture)}}

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{{Use dmy dates|date=August 2018}}

{{Biochemistry sidebar}}

[[File:Metabolism.png|thumb|Simplified view of the cellular metabolism]]

Simplified view of the cellular metabolism

细胞新陈代谢的简化观点

[[File:ATP-3D-vdW.png|thumb|right|Structure of [[adenosine triphosphate]] (ATP), a central intermediate in energy metabolism]]

Structure of [[adenosine triphosphate (ATP), a central intermediate in energy metabolism]]

三磷酸腺苷的结构[[能量代谢中的中枢中间体，三磷酸腺苷]]

'''Metabolism''' ({{IPAc-en|m|ə|ˈ|t|æ|b|ə|l|ɪ|z|ə|m}}, from {{lang-el|μεταβολή}} ''metabolē'', "change") is the set of [[life]]-sustaining [[chemical reactions]] in [[organisms]]. The three main purposes of metabolism are: the conversion of food to [[energy]] to run cellular processes; the conversion of food/fuel to building blocks for [[protein]]s, [[lipid]]s, [[nucleic acid]]s, and some [[carbohydrate]]s; and the elimination of [[Metabolic waste|metabolic wastes]]. These [[enzyme]]-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. (The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including [[digestion]] and the transport of substances into and between different cells, in which case the above described set of reactions within the cells is called intermediary metabolism or intermediate metabolism).

Metabolism (, from metabolē, "change") is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes; the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of metabolic wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. (The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including digestion and the transport of substances into and between different cells, in which case the above described set of reactions within the cells is called intermediary metabolism or intermediate metabolism).

新陈代谢(，来自 metabol，“变化”)是生物体内维持生命的化学反应。新陈代谢的三个主要目的是: 将食物转化为能量以进行细胞处理; 将食物/燃料转化为蛋白质、脂类、核酸和某些碳水化合物的组成部分; 以及消除新陈代谢废物。这些酶催化的反应使生物体能够生长和繁殖，维持它们的结构，并对它们的环境作出反应。(新陈代谢一词也可指生物体内发生的所有化学反应的总和，包括消化和物质在不同细胞之间的运输，在这种情况下，上述细胞内的一系列反应称为中间代谢或中间代谢)。

Metabolic reactions may be categorized as ''[[catabolic]]'' – the ''breaking down'' of compounds (for example, the breaking down of glucose to pyruvate by [[cellular respiration]]); or ''[[anabolic]]'' – the ''building up'' ([[biosynthesis|synthesis]]) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy.

Metabolic reactions may be categorized as catabolic – the breaking down of compounds (for example, the breaking down of glucose to pyruvate by cellular respiration); or anabolic – the building up (synthesis) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy.

代谢反应可分为分解代谢-分解化合物(例如，葡萄糖被唿吸作用分解为丙酮酸) ; 或合成-合成(合成)化合物(例如蛋白质、碳水化合物、脂类和核酸)。通常，分解代谢释放能量，合成代谢消耗能量。

The chemical reactions of metabolism are organized into [[metabolic pathway]]s, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific [[enzyme]]. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require [[energy]] that will not occur by themselves, by [[Coupling (physics)|coupling]] them to [[spontaneous process|spontaneous reactions]] that release energy. Enzymes act as [[Catalysis|catalysts]] – they allow a reaction to proceed more rapidly – and they also allow the [[Metabolic pathway#Regulation|regulation]] of the rate of a metabolic reaction, for example in response to changes in the [[cell (biology)|cell's]] environment or to [[cell signaling|signals]] from other cells.

The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific enzyme. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts – they allow a reaction to proceed more rapidly – and they also allow the regulation of the rate of a metabolic reaction, for example in response to changes in the cell's environment or to signals from other cells.

新陈代谢的化学反应被组织成新陈代谢途径，其中一种化学物质通过一系列步骤转化成另一种化学物质，每一步都由一种特定的酶促进。酶对于新陈代谢是至关重要的，因为它们通过将生物体与释放能量的自发反应耦合起来，使生物体能够驱动需要能量的理想反应，而这些反应本身不会发生。酶起催化剂的作用——它们使反应进行得更快——它们还可以调节代谢反应的速度，例如对细胞环境的变化或其他细胞发出的信号作出反应。

The metabolic system of a particular organism determines which substances it will find [[nutrition|nutritious]] and which [[poison]]ous. For example, some [[prokaryote]]s use [[hydrogen sulfide]] as a nutrient, yet this gas is poisonous to animals.<ref name="Physiology1">{{cite book |author=Friedrich C |title=Physiology and genetics of sulfur-oxidizing bacteria |journal=Adv Microb Physiol |volume=39 |issue= |pages=235–89 |year=1998 |pmid=9328649 |doi=10.1016/S0065-2911(08)60018-1 |series=Advances in Microbial Physiology |isbn=978-0-12-027739-1}}</ref> The [[basal metabolic rate]] of an organism is the measure of the amount of energy consumed by all of these chemical reactions.

The metabolic system of a particular organism determines which substances it will find nutritious and which poisonous. For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals. The basal metabolic rate of an organism is the measure of the amount of energy consumed by all of these chemical reactions.

特定生物体的新陈代谢系统决定了哪些物质有营养，哪些有毒。例如，一些原核生物利用硫化氢作为营养物质，然而这种气体对动物是有毒的。生物体的基础代谢率是对所有这些化学反应所消耗的能量的度量。

A striking feature of metabolism is the similarity of the basic metabolic pathways among vastly different species.<ref>{{cite journal | vauthors = Pace NR | title = The universal nature of biochemistry | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 98 | issue = 3 | pages = 805–8 | date = January 2001 | pmid = 11158550 | pmc = 33372 | doi = 10.1073/pnas.98.3.805 | bibcode = 2001PNAS...98..805P }}</ref> For example, the set of [[carboxylic acid]]s that are best known as the intermediates in the [[citric acid cycle]] are present in all known organisms, being found in species as diverse as the [[Unicellular organism|unicellular]] bacterium ''[[Escherichia coli]]'' and huge [[multicellular organism]]s like [[elephant]]s.<ref name=SmithE>{{cite journal | vauthors = Smith E, Morowitz HJ | title = Universality in intermediary metabolism | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 101 | issue = 36 | pages = 13168–73 | date = September 2004 | pmid = 15340153 | pmc = 516543 | doi = 10.1073/pnas.0404922101 | bibcode = 2004PNAS..10113168S }}</ref> These similarities in metabolic pathways are likely due to their early appearance in [[evolutionary history of life|evolutionary history]], and their retention because of their [[efficacy]].<ref name=Ebenhoh>{{cite journal | vauthors = Ebenhöh O, Heinrich R | title = Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems | journal = Bulletin of Mathematical Biology | volume = 63 | issue = 1 | pages = 21–55 | date = January 2001 | pmid = 11146883 | doi = 10.1006/bulm.2000.0197 | s2cid = 44260374 }}</ref><ref name=Cascante>{{cite journal | vauthors = Meléndez-Hevia E, Waddell TG, Cascante M | title = The puzzle of the Krebs citric acid cycle: assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution | journal = Journal of Molecular Evolution | volume = 43 | issue = 3 | pages = 293–303 | date = September 1996 | pmid = 8703096 | doi = 10.1007/BF02338838 | s2cid = 19107073 | bibcode = 1996JMolE..43..293M }}</ref> The metabolism of cancer cells is also different from the metabolism of normal cells and these differences can be used to find targets for therapeutic intervention in cancer.<ref name="Vander_Heiden_2017">{{cite journal | vauthors = Vander Heiden MG, DeBerardinis RJ | title = Understanding the Intersections between Metabolism and Cancer Biology | journal = Cell | volume = 168 | issue = 4 | pages = 657–669 | date = February 2017 | pmid = 28187287 | pmc = 5329766 | doi = 10.1016/j.cell.2016.12.039 }}</ref>

A striking feature of metabolism is the similarity of the basic metabolic pathways among vastly different species. For example, the set of carboxylic acids that are best known as the intermediates in the citric acid cycle are present in all known organisms, being found in species as diverse as the unicellular bacterium Escherichia coli and huge multicellular organisms like elephants. These similarities in metabolic pathways are likely due to their early appearance in evolutionary history, and their retention because of their efficacy. The metabolism of cancer cells is also different from the metabolism of normal cells and these differences can be used to find targets for therapeutic intervention in cancer.

新陈代谢的一个显著特征是，不同物种之间的基本新陈代谢途径具有相似性。例如，最为人所知的三羧酸循环中的中间产物羧酸存在于所有已知的生物体中，在单细胞细菌大肠桿菌和大象等巨大的多细胞生物体中都可以找到。这些代谢途径的相似性很可能是由于它们在进化史上的早期出现，以及它们的保持是由于它们的功效。肿瘤细胞的代谢也不同于正常细胞的代谢，这些差异可以用来寻找肿瘤治疗的靶点。

== Key biochemicals ==

{{further|Biomolecule|Cell (biology)|Biochemistry}}

[[File:Trimyristin-3D-vdW.png|right|thumb|upright=1.15|Structure of a [[triacylglycerol]] lipid]]

Structure of a [[triacylglycerol lipid]]

[三酰甘油脂]的结构

[[File:Human Metabolism - Pathways.jpg|thumb|This is a diagram depicting a large set of human metabolic pathways.]]

This is a diagram depicting a large set of human metabolic pathways.

这是一张描绘了一系列人体新陈代谢途径的图表。

Most of the structures that make up animals, plants and microbes are made from four basic classes of [[molecule]]: [[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 by breaking them down and using them as a source of energy, by their digestion. These biochemicals can be joined together to make [[polymer]]s such as [[DNA]] and [[protein]]s, essential [[macromolecules]] of life.<ref>{{cite journal|last=Cooper|first=Geoffrey M.| name-list-style = vanc |date=2000|title=The Molecular Composition of Cells|url=https://www.ncbi.nlm.nih.gov/books/NBK9879/|journal=The Cell: A Molecular Approach. 2nd Edition|language=en}}</ref>

Most of the structures that make up animals, plants and microbes are made from four basic classes of molecule: amino acids, carbohydrates , nucleic acid and lipids (often called fats). As these molecules are vital for life, metabolic reactions either focus on making these molecules during the construction of cells and tissues, or by breaking them down and using them as a source of energy, by their digestion. These biochemicals can be joined together to make polymers such as DNA and proteins, essential macromolecules of life.

构成动物、植物和微生物的大多数结构由四种基本分子组成: 氨基酸、碳水化合物、核酸和脂类(通常称为脂肪)。由于这些分子对生命至关重要，新陈代谢反应要么专注于在构建细胞和组织的过程中制造这些分子，要么通过消化将它们分解并用作能量来源。这些生物化学物质可以结合在一起形成聚合物，如 DNA 和蛋白质，这些都是生命必不可少的大分子。

{| class="wikitable" style="margin-left: auto; margin-right: auto;"

{| class="wikitable" style="margin-left: auto; margin-right: auto;"

{ | class = “ wikitable” style = “ margin-left: auto; margin-right: auto; ”

!Type of molecule

!Type of molecule

! 分子类型

!Name of [[monomer]] forms

!Name of monomer forms

! 单体形式的名称

!Name of [[polymer]] forms

!Name of polymer forms

! 聚合物形式的名称

!Examples of polymer forms

!Examples of polymer forms

! 聚合物形态的例子

|- style="text-align:center;"

|- style="text-align:center;"

|-style = “ text-align: center; ”

||[[Amino acid]]s

||Amino acids

氨基酸

||Amino acids

||Amino acids

氨基酸

||[[Protein]]s (made of polypeptides)

||Proteins (made of polypeptides)

蛋白质(由多肽组成)

||[[Fibrous protein]]s and [[globular protein]]s

||Fibrous proteins and globular proteins

纤维蛋白质和球状蛋白质

|- style="text-align:center;"

|- style="text-align:center;"

|-style = “ text-align: center; ”

||[[Carbohydrate]]s

||Carbohydrates

碳水化合物

||[[Monosaccharide]]s

||Monosaccharides

单糖

||[[Polysaccharide]]s

||Polysaccharides

多糖

||[[Starch]], [[glycogen]] and [[cellulose]]

||Starch, glycogen and cellulose

淀粉，糖原和纤维素

|- style="text-align:center;"

|- style="text-align:center;"

|-style = “ text-align: center; ”

||[[Nucleic acid]]s

||Nucleic acids

核酸

||[[Nucleotide]]s

||Nucleotides

核苷酸

||[[Polynucleotide]]s

||Polynucleotides

多核苷酸

||[[DNA]] and [[RNA]]

||DNA and RNA

DNA 和 RNA

|}

|}

|}

===Amino acids and proteins===

[[Protein]]s are made of [[amino acid]]s arranged in a linear chain joined together 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 | issue = | 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>{{cite book | last1 = Nelson | first1 = David L. | first2 = Michael M. | last2 = Cox | name-list-style = vanc | 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 }}</ref>

Proteins are made of amino acids arranged in a linear chain joined together by peptide bonds. Many proteins are enzymes that 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. Proteins are also important in cell signaling, immune responses, cell adhesion, active transport across membranes, and the cell cycle. Amino acids also contribute to cellular energy metabolism by providing a carbon source for entry into the citric acid cycle (tricarboxylic acid cycle), especially when a primary source of energy, such as glucose, is scarce, or when cells undergo metabolic stress.

蛋白质是由氨基酸组成的，氨基酸排列成一条由肽键连接起来的线性链。许多蛋白质是在新陈代谢中催化化学反应的酶。其他蛋白质具有结构或机械功能，例如那些形成细胞骨架的蛋白质，这是一个维持细胞形状的支架系统。蛋白质在细胞信号传导、免疫反应、细胞粘附、主动跨膜转运和细胞周期中也很重要。氨基酸还通过提供碳源进入细胞三羧酸循环，促进细胞的能量代谢，尤其是在葡萄糖等主要能量来源匮乏或细胞受到代谢压力的时候。

===Lipids===

[[Lipid]]s are the most diverse group of biochemicals. Their main structural uses are as part of [[biological membrane]]s both internal and external, such as the [[cell membrane]], or as a source of energy.<ref name=Nelson/> Lipids are usually defined as [[hydrophobe|hydrophobic]] or [[amphiphiles|amphipathic]] biological molecules but will dissolve in [[organic solvent]]s such as [[ethanol|alcohol]], [[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 acid [[ester]]s 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=www.qmul.ac.uk}}</ref> Several variations on this basic structure exist, including backbones such as [[sphingosine]] in the [[sphingomyelin]], and [[hydrophile|hydrophilic]] groups such as [[phosphate]] as 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>

Lipids are the most diverse group of biochemicals. Their main structural uses are as part of biological membranes both internal and external, such as the cell membrane, or as a source of energy. The fats are a large group of compounds that contain fatty acids and glycerol; a glycerol molecule attached to three fatty acid esters is called a triacylglyceride. Several variations on this basic structure exist, including backbones such as sphingosine in the sphingomyelin, and hydrophilic groups such as phosphate as in phospholipids. Steroids such as sterol are another major class of lipids.

脂类是最多样化的生物化学物质。它们的主要结构用途是作为生物膜的内部和外部的一部分，如细胞膜，或作为能源。脂肪是一大类含有脂肪酸和甘油的化合物，一个甘油分子连接到三个脂肪酸酯称为三酰甘油酯。这种基本结构存在一些变异，包括主骨(如鞘氨醇)和亲水基(如磷脂中的磷酸盐)。类固醇，如甾醇是另一类主要的脂类。

===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.]]

[[Glucose can exist in both a straight-chain and ring form.]]

[葡萄糖可以以直链和环的形式存在。]

[[Carbohydrate]]s 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/> 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>

Carbohydrates are aldehydes or ketones, 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).

碳水化合物是醛或酮，上面有许多羟基，它们可以以直链或环的形式存在。碳水化合物是最丰富的生物分子，具有多种功能，如储存和运输能量(淀粉、糖原)和结构成分(植物中的纤维素、动物中的甲壳素)。

===Nucleotides===

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/> 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>{{cite journal | vauthors = Wimmer MJ, Rose IA | title = Mechanisms of enzyme-catalyzed group transfer reactions | journal = Annual Review of Biochemistry | volume = 47 | issue = | pages = 1031–78 | year = 1978 | pmid = 354490 | doi = 10.1146/annurev.bi.47.070178.005123 }}</ref>

The two nucleic acids, DNA and RNA, are polymers of nucleotides. 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 and protein biosynthesis. RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can catalyze chemical reactions. Individual nucleosides are made by attaching a nucleobase to a ribose sugar. These bases are heterocyclic rings containing nitrogen, classified as purines or pyrimidines. Nucleotides also act as coenzymes in metabolic-group-transfer reactions.

这两种核酸，DNA 和 RNA，是核苷酸的聚合物。每个核苷酸都是由一个磷酸组成，磷酸连接到一个核糖或脱氧核糖糖基上，再连接到一个含氮硷基上。核酸对于基因信息的存储和使用至关重要，并且通过转录和蛋白质生物合成来解释。核酶如剪接体和核糖体中的 RNA 与酶类似，因为它能催化化学反应。单个核苷是通过将核苷酸酶连接到核糖上而形成的。这些碱基是含氮的杂环，分类为嘌呤或嘧啶。核苷酸在代谢-基团转移反应中也作为辅酶。

===Coenzymes===

[[File:Acetyl-CoA-2D.svg|thumb|right|upright=1.35|Structure of the [[coenzyme]] [[acetyl-CoA]].The transferable [[acetyl|acetyl group]] is bonded to the sulfur atom at the extreme left.]]

Structure of the [[coenzyme acetyl-CoA.The transferable acetyl group is bonded to the sulfur atom at the extreme left.]]

[[辅酶乙酰辅酶 a。可转移的乙酰基与最左边的硫原子结合。]]的结构

{{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 }}</ref> This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions.<ref name=Wimmer/> 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>{{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>

Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups of atoms and their bonds within molecules. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions.

新陈代谢涉及大量的化学反应，但大多数属于几种基本类型的反应，涉及原子的官能团及其在分子中的键的转移。这种常见的化学反应允许细胞使用一小组代谢中间物在不同反应之间携带化学基团。

One central coenzyme is [[adenosine triphosphate]] (ATP), the universal 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/> 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>

One central coenzyme is adenosine triphosphate (ATP), the universal 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.

其中一个中心辅酶是三磷酸腺苷，是细胞的通用能量货币。这种核苷酸用于在不同的化学反应之间传递化学能。细胞中只有少量的三磷酸腺苷，但是随着细胞不断再生，人体每天可以使用大约自身重量的三磷酸腺苷。

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|last1=Berg|first1=Jeremy M.|last2=Tymoczko|first2=John L.|last3=Stryer|first3=Lubert | name-list-style = vanc |date=2002|title=Vitamins Are Often Precursors to Coenzymes|url=https://www.ncbi.nlm.nih.gov/books/NBK22549/|journal=Biochemistry. 5th Edition|language=en}}</ref> [[Nicotinamide adenine dinucleotide]] (NAD+), a derivative of vitamin B3 ([[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+ into NADH. This reduced form of the coenzyme is then a substrate for any of the [[reductase]]s in the cell that need to reduce 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+/NADH form is more important in catabolic reactions, while NADP+/NADPH is used in anabolic reactions.<ref>{{cite book|last=Fatih|first=Yildiz | name-list-style = vanc |title=Advances in food biochemistry|publisher=CRC Press|year=2009|isbn=978-1-4200-0769-5|location=Boca Raton|pages=228|oclc=607553259}}</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. Nicotinamide adenine dinucleotide (NAD+), a derivative of vitamin B3 (niacin), is an important coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of dehydrogenases remove electrons from their substrates and reduce NAD+ into NADH. This reduced form of the coenzyme is then a substrate for any of the reductases in the cell that need to reduce their substrates. Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The NAD+/NADH form is more important in catabolic reactions, while NADP+/NADPH is used in anabolic reactions.

维生素是一种细胞不能合成的少量有机化合物。在人类营养中，大多数维生素在修饰后起辅酶的作用，例如，所有水溶性维生素在细胞中被磷酸化或与核苷酸结合。烟酰胺腺嘌呤二核苷酸(NAD + )是维生素 b 3 (烟酸)的衍生物，是一种重要的辅酶，作为氢受体。数百种不同类型的脱氢酶清除底物上的电子，并将 NAD + 减少为 NADH。这种还原形式的辅酶然后是一个底物的任何还原酶在细胞中，需要减少他们的底物。烟酰胺腺嘌呤二核苷酸以 NADH 和 NADPH 这两种相关的形式存在于细胞中。NAD + /NADH 形式在分解代谢反应中起重要作用，而 NADP + /NADPH 形式在分解代谢反应中起重要作用。

[[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}}.]]

The structure of iron-containing [[hemoglobin. The protein subunits are in red and blue, and the iron-containing heme groups in green. From .]]

含铁[血红蛋白]的结构。蛋白质亚基为红色和蓝色，含铁血红素基团为绿色。[]

===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">{{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>

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 compounds (proteins, lipids and carbohydrates) contain the majority of the carbon and nitrogen; most of the oxygen and hydrogen is present as water.

无机元素在新陈代谢中起着关键作用; 有些元素含量丰富(例如:。钠和钾) ，而其他的在微小的浓度下起作用。人体重量的99% 由碳、氮、钙、钠、氯、钾、氢、磷、氧和硫等元素组成。有机化合物(蛋白质、脂类和碳水化合物)包含大部分的碳和氮; 大部分的氧和氢以水的形式存在。

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 |date=| 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 }}</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 |last1=Lodish |first1=Harvey |last2=Berk |first2=Arnold |last3=Zipursky |first3=S. Lawrence |last4=Matsudaira |first4=Paul |last5=Baltimore |first5=David |last6=Darnell |first6=James | name-list-style = vanc |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}}</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>

The abundant inorganic elements act as electrolytes. The most important ions are sodium, potassium, calcium, magnesium, chloride, phosphate and the organic ion bicarbonate. The maintenance of precise ion gradients across cell membranes maintains osmotic pressure and pH. Ions are also critical for nerve and muscle function, as action potentials in these tissues are produced by the exchange of electrolytes between the extracellular fluid and the cell's fluid, the cytosol. Electrolytes enter and leave cells through proteins in the cell membrane called ion channels. For example, muscle contraction depends upon the movement of calcium, sodium and potassium through ion channels in the cell membrane and T-tubules.

丰富的无机元素充当电解质。最重要的离子是钠、钾、钙、镁、氯化物、磷酸盐和有机离子重碳酸盐。维持细胞膜上精确的离子梯度可以维持渗透压和 ph 值。离子对于神经和肌肉功能也是至关重要的，因为这些组织中的动作电位是由细胞外液和细胞液细胞溶胶之间的电解质交换产生的。电解质通过细胞膜上称为离子通道的蛋白质进出细胞。例如，肌肉收缩依赖于钙、钠和钾通过细胞膜和 t 管的离子通道的运动。

[[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> These metals are used in some proteins as [[Cofactor (biochemistry)|cofactors]] and are essential for the activity of enzymes such as [[catalase]] and oxygen-carrier proteins such as [[hemoglobin]]<ref>{{cite book|last=Craig Will|first=Leonard Ashley | name-list-style = vanc |title=Manufacturing Engineering & Technology|publisher=Scientific e-Resources|year=2019|isbn=9781839472428|location=Waltham Abbey|pages=190–196}}</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 | url = https://www.jbc.org/content/281/34/24085 | 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>

Transition metals are usually present as trace elements in organisms, with zinc and iron being most abundant of those. These metals are used in some proteins as cofactors and are essential for the activity of enzymes such as catalase and oxygen-carrier proteins such as hemoglobin 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.

过渡金属通常以微量元素的形式存在于生物体内，其中锌和铁最为丰富。这些金属元素在某些蛋白质中作为辅助因子，对于过氧化氢酶和氧载体蛋白质的活性至关重要，如血红蛋白金属辅助因子与蛋白质中的特定位点紧密结合，虽然酶辅助因子在催化过程中可以被修饰，但是它们总是在催化反应结束时恢复到原来的状态。金属微量营养素通过特定的转运体进入生物体内，并在不使用时与铁蛋白或金属硫蛋白等储存蛋白结合。

==Catabolism==

[[Catabolism]] is the set of metabolic processes that break down large molecules. These include breaking down and oxidizing food molecules. The purpose of the catabolic reactions is to provide the energy and components needed by anabolic reactions which build molecules.<ref name="Alberts 2002">{{cite book |last1=Alberts|first1=Bruce|last2=Johnson|first2=Alexander|last3=Lewis|first3=Julian|last4=Raff|first4=Martin|last5=Roberts|first5=Keith|last6=Walter|first6=Peter| name-list-style = vanc |date=2002|chapter =How Cells Obtain Energy from Food|url=https://www.ncbi.nlm.nih.gov/books/NBK26882/|title =Molecular Biology of the Cell | edition = 4th |language=en|via=NCBI}}</ref> The exact nature of these catabolic reactions differ from organism to organism, and organisms can be classified based on their sources of energy and carbon (their [[primary nutritional groups]]), as shown in the table below. Organic molecules are used as a source of energy by [[organotroph]]s, while [[lithotroph]]s use inorganic substrates, and [[phototroph]]s capture sunlight as [[Potential energy#Chemical potential energy|chemical energy]].<ref>{{cite journal|last=Raven|first=Ja| name-list-style = vanc |date=2009-09-03|title=Contributions of anoxygenic and oxygenic phototrophy and chemolithotrophy to carbon and oxygen fluxes in aquatic environments|url=http://www.int-res.com/abstracts/ame/v56/n2-3/p177-192/|journal=Aquatic Microbial Ecology|language=en|volume=56|pages=177–192|doi=10.3354/ame01315|issn=0948-3055|doi-access=free}}</ref> However, all these different forms of metabolism depend on [[redox]] reactions that involve the transfer of electrons from reduced donor molecules such as [[organic molecule]]s, water, [[ammonia]], [[hydrogen sulfide]] or [[Ferrous|ferrous ions]] to acceptor molecules such as [[oxygen]], [[nitrate]] or [[sulfate]]. In animals, these reactions involve complex [[organic molecule]]s that are broken down to simpler molecules, such as [[carbon dioxide]] and water. In [[photosynthesis|photosynthetic]] organisms, such as plants and [[cyanobacteria]], these electron-transfer reactions do not release energy but are used as a way of storing energy absorbed from sunlight.<ref name=Nelson2004>{{cite journal | vauthors = Nelson N, Ben-Shem A | title = The complex architecture of oxygenic photosynthesis | journal = Nature Reviews. Molecular Cell Biology | volume = 5 | issue = 12 | pages = 971–82 | date = December 2004 | pmid = 15573135 | doi = 10.1038/nrm1525 | s2cid = 5686066 }}</ref>

Catabolism is the set of metabolic processes that break down large molecules. These include breaking down and oxidizing food molecules. The purpose of the catabolic reactions is to provide the energy and components needed by anabolic reactions which build molecules. The exact nature of these catabolic reactions differ from organism to organism, and organisms can be classified based on their sources of energy and carbon (their primary nutritional groups), as shown in the table below. Organic molecules are used as a source of energy by organotrophs, while lithotrophs use inorganic substrates, and phototrophs capture sunlight as chemical energy. However, all these different forms of metabolism depend on redox reactions that involve the transfer of electrons from reduced donor molecules such as organic molecules, water, ammonia, hydrogen sulfide or ferrous ions to acceptor molecules such as oxygen, nitrate or sulfate. In animals, these reactions involve complex organic molecules that are broken down to simpler molecules, such as carbon dioxide and water. In photosynthetic organisms, such as plants and cyanobacteria, these electron-transfer reactions do not release energy but are used as a way of storing energy absorbed from sunlight.

分解代谢是一系列分解大分子的新陈代谢过程。其中包括分解和氧化食物分子。分解代谢反应的目的是为生成分子的分解代谢反应提供所需的能量和成分。这些分解代谢反应的确切性质因生物体而异，生物体可根据其能量来源和碳(其主要营养组)加以分类，如下表所示。有机养生物利用有机分子作为能量来源，而岩养生物利用无机基质，光养生物利用阳光作为化学能。然而，所有这些不同形式的新陈代谢依赖于氧化还原反应，包括电子从还原供体分子，如有机分子，水，氨，硫化氢或亚铁离子转移到受体分子，如氧，硝酸盐或硫酸盐。在动物中，这些反应包括复杂的有机分子，它们被分解成更简单的分子，如二氧化碳和水。在诸如植物和蓝藻这样的光合生物体中，这些电子转移反应不释放能量，而是用来储存从阳光中吸收的能量。

{| class="wikitable float-right" style="text-align:center; width:50%;"

{| class="wikitable float-right" style="text-align:center; width:50%;"

{ | class = “ wikitable float-right” style = “ text-align: center; width: 50% ; ”

|+Classification of organisms based on their metabolism <ref>{{cite book| vauthors = Madigan MT, Martinko JM |title=Brock Mikrobiologie|date=2006|publisher=Pearson Studium|isbn=3-8273-7187-2|edition=11., überarb. Aufl|location=München|pages=604, 621|oclc=162303067}}</ref>

|+Classification of organisms based on their metabolism

| + 根据其新陈代谢对生物进行分类

|-

|-

|-

| rowspan="2" style="background:#ff0;"|Energy source || style="background:#ff0;"| sunlight || style="background:#ff0;"| photo- || rowspan=2 colspan=2 |   || rowspan="6" style="background:#7fc31c;"| -troph

| rowspan="2" style="background:#ff0;"|Energy source || style="background:#ff0;"| sunlight || style="background:#ff0;"| photo- || rowspan=2 colspan=2 |   || rowspan="6" style="background:#7fc31c;"| -troph

2 style = “ background: # ff0; ” | Energy source | style = “ background: # ff0; ”

|- style="background:#ff0;"

|- style="background:#ff0;"

|-style = “ background: # ff0; ”

|| Preformed molecules || style="background:#ff0;"| chemo-

|| Preformed molecules || style="background:#ff0;"| chemo-

预制分子 | | | | style = ”背景: # ff0; ” | 化疗-

|-

|-

|-

| rowspan="2" style="background:#ffb300;"| Electron donor || style="background:#ffb300;"| [[organic compound]] || rowspan=2 |   || style="background:#ffb300;"| organo- || rowspan=2 |  

| rowspan="2" style="background:#ffb300;"| Electron donor || style="background:#ffb300;"| organic compound || rowspan=2 |   || style="background:#ffb300;"| organo- || rowspan=2 |  

有机化合物 | rowspan = 2 | | | style = ”背景: # ffb300; ” | organic compound = 2 | | | style = ”背景: # ffb300; ” | organo-| rowspan = 2 |

|- style="background:#ffb300;"

|- style="background:#ffb300;"

|-style = ”背景: # ffb300; ”

|| [[inorganic compound]] || style="background:#ffb300;"| litho-

|| inorganic compound || style="background:#ffb300;"| litho-

背景无机化合物: # ffb300

|-

|-

|-

| rowspan="2" style="background:#fb805f;"| Carbon source || style="background:#fb805f;"| [[organic compound]] || rowspan=2 colspan=2 |   || style="background:#fb805f;"| hetero-

| rowspan="2" style="background:#fb805f;"| Carbon source || style="background:#fb805f;"| organic compound || rowspan=2 colspan=2 |   || style="background:#fb805f;"| hetero-

2 | | rowspan = 2 | | | style = “ background: # fb805f; ” | Carbon source | style = “ background: # fb805f; ” | organic compound | rowspan = 2 colspan = 2 | | | | style = “ background: # fb805f; ” | hetero-

|- style="background:#fb805f;"

|- style="background:#fb805f;"

|-style = “ background: # fb805f; ”

|| [[inorganic compound]] || style="background:#fb805f;"| auto-

|| inorganic compound || style="background:#fb805f;"| auto-

无机化合物风格背景: fb805f

|}

|}

|}

The most common set of catabolic reactions in animals can be separated into three main stages. In the first stage, large organic molecules, such as [[protein]]s, [[polysaccharide]]s or [[lipid]]s, are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to smaller molecules, usually [[acetyl-CoA|acetyl coenzyme A]] (acetyl-CoA), which releases some energy. Finally, the acetyl group on the CoA is oxidised to water and carbon dioxide in the [[citric acid cycle]] and [[electron transport chain]], releasing the energy that is stored by reducing the coenzyme [[nicotinamide adenine dinucleotide]] (NAD+) into NADH.<ref name="Alberts 2002"/>

The most common set of catabolic reactions in animals can be separated into three main stages. In the first stage, large organic molecules, such as proteins, polysaccharides or lipids, are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to smaller molecules, usually acetyl coenzyme A (acetyl-CoA), which releases some energy. Finally, the acetyl group on the CoA is oxidised to water and carbon dioxide in the citric acid cycle and electron transport chain, releasing the energy that is stored by reducing the coenzyme nicotinamide adenine dinucleotide (NAD+) into NADH.

动物中最常见的分解代谢反应可以分为三个主要阶段。在第一阶段，大的有机分子，如蛋白质，多糖或脂类，被消化成细胞外的更小的组成部分。接下来，这些较小的分子被细胞吸收，转化成较小的分子，通常是乙酰辅酶A (乙酰辅酶 a) ，释放出一些能量。最后，辅酶 a 上的乙酰基被氧化成三羧酸循环和电子传递链中的水和二氧化碳，通过还原辅酶烟酰胺腺嘌呤二核苷酸(NAD + )而释放出能量。

===Digestion===

Microbes simply secrete digestive enzymes into their surroundings, while animals only secrete these enzymes from specialized cells in their guts, including the stomach and pancreas, and salivary glands. The amino acids or sugars released by these extracellular enzymes are then pumped into cells by active transport proteins.

微生物只是简单地将消化酶分泌到周围环境中，而动物只是从它们肠道中的特定细胞分泌这些酶，包括胃、胰腺和唾液腺。这些细胞外酶释放的氨基酸或糖通过活性转运蛋白被泵入细胞内。

{{further|Digestion|Gastrointestinal tract}}

A simplified outline of the catabolism of [[proteins, carbohydrates and fats]]

[蛋白质，碳水化合物和脂肪]分解代谢的简化轮廓

Macromolecules cannot be directly processed by cells. Macromolecules must be broken into smaller units before they can be used in cell metabolism. Different classes of enzymes were being used to digest these polymers. These [[digestive enzyme]]s include [[protease]]s that digest proteins into amino acids, as well as [[glycoside hydrolase]]s that digest polysaccharides into simple sugars known as [[monosaccharides]]<ref>{{cite book|last=Demirel, Yaşar|title=Energy : production, conversion, storage, conservation, and coupling|publisher=Springer|year=2016|isbn=978-3-319-29650-0|edition=Second|location=Lincoln|pages=431|oclc=945435943}}</ref>

Microbes simply secrete digestive enzymes into their surroundings,<ref>{{cite journal | vauthors = Häse CC, Finkelstein RA | title = Bacterial extracellular zinc-containing metalloproteases | journal = Microbiological Reviews | volume = 57 | issue = 4 | pages = 823–37 | date = December 1993 | pmid = 8302217 | pmc = 372940 | doi = 10.1128/MMBR.57.4.823-837.1993 }}</ref><ref>{{cite journal | vauthors = Gupta R, Gupta N, Rathi P | title = Bacterial lipases: an overview of production, purification and biochemical properties | journal = Applied Microbiology and Biotechnology | volume = 64 | issue = 6 | pages = 763–81 | date = June 2004 | pmid = 14966663 | doi = 10.1007/s00253-004-1568-8 | s2cid = 206934353 }}</ref> while animals only secrete these enzymes from specialized cells in their [[Gastrointestinal tract|guts]], including the [[stomach]] and [[pancreas]], and [[salivary gland]]s.<ref>{{cite journal | vauthors = Hoyle T | title = The digestive system: linking theory and practice | journal = British Journal of Nursing | volume = 6 | issue = 22 | pages = 1285–91 | year = 1997 | pmid = 9470654 | doi = 10.12968/bjon.1997.6.22.1285 }}</ref> The amino acids or sugars released by these extracellular enzymes are then pumped into cells by [[active transport]] proteins.<ref>{{cite journal | vauthors = Souba WW, Pacitti AJ | title = How amino acids get into cells: mechanisms, models, menus, and mediators | journal = JPEN. Journal of Parenteral and Enteral Nutrition | volume = 16 | issue = 6 | pages = 569–78 | year = 1992 | pmid = 1494216 | doi = 10.1177/0148607192016006569 }}</ref><ref>{{cite journal | vauthors = Barrett MP, Walmsley AR, Gould GW | title = Structure and function of facilitative sugar transporters | journal = Current Opinion in Cell Biology | volume = 11 | issue = 4 | pages = 496–502 | date = August 1999 | pmid = 10449337 | doi = 10.1016/S0955-0674(99)80072-6 }}</ref>

[[File:Catabolism schematic.svg|thumb|left|upright=1.35|A simplified outline of the catabolism of [[protein]]s, [[carbohydrate]]s and [[fat]]s]]

Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. Carbohydrates are usually taken into cells once they have been digested into monosaccharides. Once inside, the major route of breakdown is glycolysis, where sugars such as glucose and fructose are converted into pyruvate and some ATP is generated. Pyruvate is an intermediate in several metabolic pathways, but the majority is converted to acetyl-CoA through aerobic (with oxygen) glycolysis and fed into the citric acid cycle. Although some more ATP is generated in the citric acid cycle, the most important product is NADH, which is made from NAD+ as the acetyl-CoA is oxidized. This oxidation releases carbon dioxide as a waste product. In anaerobic conditions, glycolysis produces lactate, through the enzyme lactate dehydrogenase re-oxidizing NADH to NAD+ for re-use in glycolysis. An alternative route for glucose breakdown is the pentose phosphate pathway, which reduces the coenzyme NADPH and produces pentose sugars such as ribose, the sugar component of nucleic acids.

碳水化合物分解代谢是将碳水化合物分解成更小的单位。碳水化合物一旦被消化成单糖，通常就被带入细胞。一旦进入细胞内，糖酵解是主要的分解途径，葡萄糖和果糖等糖类被转化为丙酮酸，产生一些 ATP。丙酮酸是几种代谢途径中的中间体，但大多数通过有氧糖酵解转化为乙酰辅酶 a 并进入三羧酸循环。虽然三羧酸循环中有更多的 ATP 产生，但最重要的产物是 NADH，它是由 NAD + 氧化乙酰辅酶 a 而产生的。这种氧化作为废物释放出二氧化碳。在厌氧条件下，糖酵解通过乳酸脱氢酶还原 NADH 生成 NAD + ，再用于糖酵解，从而产生乳酸。葡萄糖分解的另一种途径是磷酸戊糖途径，它降低辅酶 NADPH 并产生戊糖，如核糖，核酸的糖组成部分。

===Energy from organic compounds===

{{further|Cellular respiration|Fermentation (biochemistry)|Carbohydrate catabolism|Fat catabolism|Protein catabolism}}

Fats are catabolised by hydrolysis to free fatty acids and glycerol. The glycerol enters glycolysis and the fatty acids are broken down by beta oxidation to release acetyl-CoA, which then is fed into the citric acid cycle. Fatty acids release more energy upon oxidation than carbohydrates because carbohydrates contain more oxygen in their structures. Steroids are also broken down by some bacteria in a process similar to beta oxidation, and this breakdown process involves the release of significant amounts of acetyl-CoA, propionyl-CoA, and pyruvate, which can all be used by the cell for energy. M. tuberculosis can also grow on the lipid cholesterol as a sole source of carbon, and genes involved in the cholesterol use pathway(s) have been validated as important during various stages of the infection lifecycle of M. tuberculosis.

脂肪通过水解分解为游离脂肪酸和甘油。甘油进入糖酵解，脂肪酸被 β 氧化分解，释放出乙酰辅酶 a，然后进入三羧酸循环。脂肪酸在氧化时比碳水化合物释放更多的能量，因为碳水化合物的结构中含有更多的氧。一些细菌在类似于 β 氧化的过程中也会分解甾体，这个分解过程包括大量的乙酰辅酶 a、丙酰辅酶 a 和丙酮酸的释放，这些都可以被细胞用来提供能量。结核分枝杆菌也可以在作为碳的唯一来源的脂质胆固醇上生长，而且胆固醇使用途径中的基因已被证实在结核分枝杆菌感染生命周期的各个阶段都是重要的。

Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. Carbohydrates are usually taken into cells once they have been digested into [[monosaccharide]]s.<ref>{{cite journal | vauthors = Bell GI, Burant CF, Takeda J, Gould GW | title = Structure and function of mammalian facilitative sugar transporters | journal = The Journal of Biological Chemistry | volume = 268 | issue = 26 | pages = 19161–4 | date = September 1993 | pmid = 8366068 }}</ref> Once inside, the major route of breakdown is [[glycolysis]], where sugars such as [[glucose]] and [[fructose]] are converted into [[pyruvic acid|pyruvate]] and some ATP is generated.<ref name=Bouche>{{cite journal | vauthors = Bouché C, Serdy S, Kahn CR, Goldfine AB | title = The cellular fate of glucose and its relevance in type 2 diabetes | journal = Endocrine Reviews | volume = 25 | issue = 5 | pages = 807–30 | date = October 2004 | pmid = 15466941 | doi = 10.1210/er.2003-0026 | df = dmy-all | doi-access = free }}</ref> Pyruvate is an intermediate in several metabolic pathways, but the majority is converted to [[acetyl-CoA]] through aerobic (with oxygen) glycolysis and fed into the [[citric acid cycle]]. Although some more ATP is generated in the citric acid cycle, the most important product is NADH, which is made from NAD+ as the acetyl-CoA is oxidized. This oxidation releases [[carbon dioxide]] as a waste product. In anaerobic conditions, glycolysis produces [[lactic acid|lactate]], through the enzyme [[lactate dehydrogenase]] re-oxidizing NADH to NAD+ for re-use in glycolysis.<ref>{{cite journal | vauthors = Alfarouk KO, Verduzco D, Rauch C, Muddathir AK, Adil HH, Elhassan GO, Ibrahim ME, David Polo Orozco J, Cardone RA, Reshkin SJ, Harguindey S | display-authors = 6 | title = Glycolysis, tumor metabolism, cancer growth and dissemination. A new pH-based etiopathogenic perspective and therapeutic approach to an old cancer question | journal = Oncoscience | volume = 1 | issue = 12 | pages = 777–802 | date = 18 December 2014 | pmid = 25621294 | pmc = 4303887 | doi = 10.18632/oncoscience.109 | doi-access = free }}</ref> An alternative route for glucose breakdown is the [[pentose phosphate pathway]], which reduces the coenzyme [[NADPH]] and produces [[pentose]] sugars such as [[ribose]], the sugar component of [[nucleic acid]]s.

Amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and carbon dioxide as a source of energy. The oxidation pathway starts with the removal of the amino group by a transaminase. The amino group is fed into the urea cycle, leaving a deaminated carbon skeleton in the form of a keto acid. Several of these keto acids are intermediates in the citric acid cycle, for example the deamination of glutamate forms α-ketoglutarate. The glucogenic amino acids can also be converted into glucose, through gluconeogenesis (discussed below).

氨基酸可以用来合成蛋白质和其他生物分子，也可以被氧化成尿素和二氧化碳作为能量来源。氧化途径从转氨酶去除氨基开始。氨基进入尿素循环，留下酮酸形式的脱氨基碳骨架。其中一些酮酸是三羧酸循环的中间产物，例如谷氨酸的脱氨反应形成 α- 酮戊二酸。葡萄糖原氨基酸也可以通过葡萄糖异生转化为葡萄糖(下面讨论)。

Fats are catabolised by [[hydrolysis]] to free fatty acids and glycerol. The glycerol enters glycolysis and the fatty acids are broken down by [[beta oxidation]] to release acetyl-CoA, which then is fed into the citric acid cycle. Fatty acids release more energy upon oxidation than carbohydrates because carbohydrates contain more oxygen in their structures. Steroids are also broken down by some bacteria in a process similar to beta oxidation, and this breakdown process involves the release of significant amounts of acetyl-CoA, propionyl-CoA, and pyruvate, which can all be used by the cell for energy. ''M. tuberculosis'' can also grow on the lipid [[cholesterol]] as a sole source of carbon, and genes involved in the cholesterol use pathway(s) have been validated as important during various stages of the infection lifecycle of ''M. tuberculosis''.<ref>{{cite journal | vauthors = Wipperman MF, Sampson NS, Thomas ST | title = Pathogen roid rage: cholesterol utilization by Mycobacterium tuberculosis | journal = Critical Reviews in Biochemistry and Molecular Biology | volume = 49 | issue = 4 | pages = 269–93 | date = 2014 | pmid = 24611808 | pmc = 4255906 | doi = 10.3109/10409238.2014.895700 }}</ref>

[[Amino acid]]s are either used to synthesize proteins and other biomolecules, or oxidized to [[urea]] and carbon dioxide as a source of energy.<ref>{{cite journal | vauthors = Sakami W, Harrington H | title = Amino Acid Metabolism | journal = Annual Review of Biochemistry | volume = 32 | issue = | pages = 355–98 | year = 1963 | pmid = 14144484 | doi = 10.1146/annurev.bi.32.070163.002035 }}</ref> The oxidation pathway starts with the removal of the amino group by a [[transaminase]]. The amino group is fed into the [[urea cycle]], leaving a deaminated carbon skeleton in the form of a [[keto acid]]. Several of these keto acids are intermediates in the citric acid cycle, for example the deamination of [[glutamate]] forms α-[[alpha-Ketoglutaric acid|ketoglutarate]].<ref>{{cite journal | vauthors = Brosnan JT | title = Glutamate, at the interface between amino acid and carbohydrate metabolism | journal = The Journal of Nutrition | volume = 130 | issue = 4S Suppl | pages = 988S–90S | date = April 2000 | pmid = 10736367 | doi = 10.1093/jn/130.4.988S | doi-access = free }}</ref> The [[glucogenic amino acid]]s can also be converted into glucose, through [[gluconeogenesis]] (discussed below).<ref>{{cite journal | vauthors = Young VR, Ajami AM | title = Glutamine: the emperor or his clothes? | journal = The Journal of Nutrition | volume = 131 | issue = 9 Suppl | pages = 2449S–59S; discussion 2486S–7S | date = September 2001 | pmid = 11533293 | doi = 10.1093/jn/131.9.2449S | doi-access = free }}</ref>

==Energy transformations==

In oxidative phosphorylation, the electrons removed from organic molecules in areas such as the protagon acid cycle are transferred to oxygen and the energy released is used to make ATP. This is done in eukaryotes by a series of proteins in the membranes of mitochondria called the electron transport chain. In prokaryotes, these proteins are found in the cell's inner membrane. These proteins use the energy released from passing electrons from reduced molecules like NADH onto oxygen to pump protons across a membrane.

在21氧化磷酸化，从有机分子中分离出来的电子被转移到氧气中，释放出来的能量被用来制造 ATP。这在真核生物中是通过一系列蛋白质在线粒体膜上完成的，这些蛋白质被称为电子传递链。在原核生物中，这些蛋白质存在于细胞的内膜中。这些蛋白质利用像 NADH 这样的还原分子通过电子释放到氧气上的能量，让质子穿过膜。

===Oxidative phosphorylation===

Mechanism of [[ATP synthase. ATP is shown in red, ADP and phosphate in pink and the rotating stalk subunit in black.]]

[ ATP 合成酶]的作用机制。ATP 显示为红色，ADP 和磷酸显示为粉红色，转柄亚基显示为黑色

{{further|Oxidative phosphorylation|Chemiosmosis|Mitochondrion}}

Pumping protons out of the mitochondria creates a proton concentration difference across the membrane and generates an electrochemical gradient. This force drives protons back into the mitochondrion through the base of an enzyme called ATP synthase. The flow of protons makes the stalk subunit rotate, causing the active site of the synthase domain to change shape and phosphorylate adenosine diphosphate – turning it into ATP. reduced sulfur compounds (such as sulfide, hydrogen sulfide and thiosulfate), or ammonia as sources of reducing power and they gain energy from the oxidation of these compounds with electron acceptors such as oxygen or nitrite. These microbial processes are important in global biogeochemical cycles such as acetogenesis, nitrification and denitrification and are critical for soil fertility.

将质子泵出线粒体会产生跨膜质子浓度的差异，并产生电化梯度。这种力量驱使质子通过一种叫做 ATP 合酶的酶的底部回到线粒体。质子流使茎亚单位旋转，导致合成酶结构域的活性位点改变形状并磷酸化二磷酸腺苷-将其转化为 ATP。还原硫化物(如硫化物、硫化氢和硫代硫酸盐)或氨作为还原能源，它们通过这些化合物与电子受体如氧或亚硝酸盐的氧化而获得能量。这些微生物过程在全球生物地球化学循环中具有重要作用，如醋酸生成、硝化和反硝化作用，对土壤肥力至关重要。

In oxidative phosphorylation, the electrons removed from organic molecules in areas such as the protagon acid cycle are transferred to oxygen and the energy released is used to make ATP. This is done in [[eukaryote]]s by a series of proteins in the membranes of mitochondria called the [[electron transport chain]]. In [[prokaryote]]s, these proteins are found in the cell's [[bacterial cell structure|inner membrane]].<ref>{{cite journal | vauthors = Hosler JP, Ferguson-Miller S, Mills DA | title = Energy transduction: proton transfer through the respiratory complexes | journal = Annual Review of Biochemistry | volume = 75 | issue = | pages = 165–87 | year = 2006 | pmid = 16756489 | pmc = 2659341 | doi = 10.1146/annurev.biochem.75.062003.101730 }}</ref> These proteins use the energy released from passing electrons from [[reducing agent|reduced]] molecules like NADH onto [[oxygen]] to pump [[proton]]s across a membrane.<ref>{{cite journal | vauthors = Schultz BE, Chan SI | title = Structures and proton-pumping strategies of mitochondrial respiratory enzymes | journal = Annual Review of Biophysics and Biomolecular Structure | volume = 30 | issue = | pages = 23–65 | year = 2001 | pmid = 11340051 | doi = 10.1146/annurev.biophys.30.1.23 | url = https://authors.library.caltech.edu/1623/1/SCHarbbs01.pdf }}</ref>

[[File:ATPsyn.gif|thumb|right|Mechanism of [[ATP synthase]]. ATP is shown in red, ADP and phosphate in pink and the rotating stalk subunit in black.]]

Pumping protons out of the mitochondria creates a proton [[diffusion|concentration difference]] across the membrane and generates an [[electrochemical gradient]].<ref>{{cite journal | vauthors = Capaldi RA, Aggeler R | title = Mechanism of the F(1)F(0)-type ATP synthase, a biological rotary motor | journal = Trends in Biochemical Sciences | volume = 27 | issue = 3 | pages = 154–60 | date = March 2002 | pmid = 11893513 | doi = 10.1016/S0968-0004(01)02051-5 }}</ref> This force drives protons back into the mitochondrion through the base of an enzyme called [[ATP synthase]]. The flow of protons makes the stalk subunit rotate, causing the [[active site]] of the synthase domain to change shape and phosphorylate [[adenosine diphosphate]] – turning it into ATP.<ref name=Dimroth/>

The energy in sunlight is captured by plants, cyanobacteria, purple bacteria, green sulfur bacteria and some protists. This process is often coupled to the conversion of carbon dioxide into organic compounds, as part of photosynthesis, which is discussed below. The energy capture and carbon fixation systems can however operate separately in prokaryotes, as purple bacteria and green sulfur bacteria can use sunlight as a source of energy, while switching between carbon fixation and the fermentation of organic compounds.

阳光中的能量被植物、蓝藻、紫色细菌、绿菌门和一些原生生物吸收。作为光合作用的一部分，这个过程通常与二氧化碳转化为有机化合物相联系，下面将对此进行讨论。然而，原核生物中的能量捕获和固碳系统可以分开工作，因为紫细菌和绿菌门可以利用阳光作为能量来源，同时在固碳和发酵有机化合物之间切换。

===Energy from inorganic compounds===

{{further|Microbial metabolism|Nitrogen cycle}}

In many organisms, the capture of solar energy is similar in principle to oxidative phosphorylation, as it involves the storage of energy as a proton concentration gradient. This proton motive force then drives ATP synthesis The electrons needed to drive this electron transport chain come from light-gathering proteins called photosynthetic reaction centres. Reaction centers are classed into two types depending on the nature of photosynthetic pigment present, with most photosynthetic bacteria only having one type, while plants and cyanobacteria have two.

在许多生物体中，太阳能的获取原则上类似于氧化磷酸化，因为它包括以质子浓度梯度的形式储存能量。这种质子动力驱动 ATP 的合成驱动这种电子传递链所需的电子来自于聚光蛋白质，这种蛋白质叫做光合反应中心。根据存在的光合色素的性质，反应中心分为两种类型，大多数光合细菌只有一种类型，而植物和蓝藻有两种类型。

[[Chemolithotroph]]y is a type of metabolism found in [[prokaryote]]s where energy is obtained from the oxidation of [[inorganic compound]]s. These organisms can use [[hydrogen]],<ref>{{cite journal | vauthors = Friedrich B, Schwartz E | title = Molecular biology of hydrogen utilization in aerobic chemolithotrophs | journal = Annual Review of Microbiology | volume = 47 | issue = | pages = 351–83 | year = 1993 | pmid = 8257102 | doi = 10.1146/annurev.mi.47.100193.002031 }}</ref> reduced [[sulfur]] compounds (such as [[sulfide]], [[hydrogen sulfide]] and [[thiosulfate]]),<ref name=Physiology1/> [[Iron(II) oxide|ferrous iron (FeII)]]<ref>{{cite journal | vauthors = Weber KA, Achenbach LA, Coates JD | title = Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction | journal = Nature Reviews. Microbiology | volume = 4 | issue = 10 | pages = 752–64 | date = October 2006 | pmid = 16980937 | doi = 10.1038/nrmicro1490 | url = https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1203&context=bioscifacpub | s2cid = 8528196 }}</ref> or [[ammonia]]<ref>{{cite journal | vauthors = Jetten MS, Strous M, van de Pas-Schoonen KT, Schalk J, van Dongen UG, van de Graaf AA, Logemann S, Muyzer G, van Loosdrecht MC, Kuenen JG | display-authors = 6 | title = The anaerobic oxidation of ammonium | journal = FEMS Microbiology Reviews | volume = 22 | issue = 5 | pages = 421–37 | date = December 1998 | pmid = 9990725 | doi = 10.1111/j.1574-6976.1998.tb00379.x | doi-access = free }}</ref> as sources of reducing power and they gain energy from the oxidation of these compounds with electron acceptors such as [[oxygen]] or [[nitrite]].<ref>{{cite journal | vauthors = Simon J | title = Enzymology and bioenergetics of respiratory nitrite ammonification | journal = FEMS Microbiology Reviews | volume = 26 | issue = 3 | pages = 285–309 | date = August 2002 | pmid = 12165429 | doi = 10.1111/j.1574-6976.2002.tb00616.x | doi-access = free }}</ref> These microbial processes are important in global [[biogeochemical cycle]]s such as [[acetogenesis]], [[nitrification]] and [[denitrification]] and are critical for [[fertility (soil)|soil fertility]].<ref>{{cite journal | vauthors = Conrad R | title = Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO) | journal = Microbiological Reviews | volume = 60 | issue = 4 | pages = 609–40 | date = December 1996 | pmid = 8987358 | pmc = 239458 | doi = 10.1128/MMBR.60.4.609-640.1996 }}</ref><ref>{{cite journal | vauthors = Barea JM, Pozo MJ, Azcón R, Azcón-Aguilar C | title = Microbial co-operation in the rhizosphere | journal = Journal of Experimental Botany | volume = 56 | issue = 417 | pages = 1761–78 | date = July 2005 | pmid = 15911555 | doi = 10.1093/jxb/eri197 | doi-access = free }}</ref>

In plants, algae, and cyanobacteria, photosystem II uses light energy to remove electrons from water, releasing oxygen as a waste product. The electrons then flow to the cytochrome b6f complex, which uses their energy to pump protons across the thylakoid membrane in the chloroplast.fThese cooenzyme can be used in the Calvin cycle, which is discussed below, or recycled for further ATP generation.

在植物、藻类和蓝细菌中，光系统 II 利用光能将电子从水中移走，作为废物释放氧气。然后电子流向细胞色素b6f蛋白复合体，利用它们的能量穿过叶绿体中的类囊体膜，泵出质子。这些库酶可以用于卡尔文循环，下面将讨论这个循环，或者循环用于生成更多的 ATP。

===Energy from light===

{{further|Phototroph|Photophosphorylation|Chloroplast}}

The energy in sunlight is captured by [[plant]]s, [[cyanobacteria]], [[purple bacteria]], [[green sulfur bacteria]] and some [[protist]]s. This process is often coupled to the conversion of carbon dioxide into organic compounds, as part of photosynthesis, which is discussed below. The energy capture and carbon fixation systems can however operate separately in prokaryotes, as purple bacteria and green sulfur bacteria can use sunlight as a source of energy, while switching between carbon fixation and the fermentation of organic compounds.<ref>{{cite journal | vauthors = van der Meer MT, Schouten S, Bateson MM, Nübel U, Wieland A, Kühl M, de Leeuw JW, Sinninghe Damsté JS, Ward DM | display-authors = 6 | title = Diel variations in carbon metabolism by green nonsulfur-like bacteria in alkaline siliceous hot spring microbial mats from Yellowstone National Park | journal = Applied and Environmental Microbiology | volume = 71 | issue = 7 | pages = 3978–86 | date = July 2005 | pmid = 16000812 | pmc = 1168979 | doi = 10.1128/AEM.71.7.3978-3986.2005 }}</ref><ref>{{cite journal | vauthors = Tichi MA, Tabita FR | title = Interactive control of Rhodobacter capsulatus redox-balancing systems during phototrophic metabolism | journal = Journal of Bacteriology | volume = 183 | issue = 21 | pages = 6344–54 | date = November 2001 | pmid = 11591679 | pmc = 100130 | doi = 10.1128/JB.183.21.6344-6354.2001 }}</ref>

Anabolism is the set of constructive metabolic processes where the energy released by catabolism is used to synthesize complex molecules. In general, the complex molecules that make up cellular structures are constructed step-by-step from small and simple precursors. Anabolism involves three basic stages. First, the production of precursors such as amino acids, monosaccharides, isoprenoids and nucleotides, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as proteins, polysaccharides, lipids and nucleic acids.

合成代谢是一套建设性的新陈代谢过程，其中分解代谢所释放的能量被用来合成复杂的分子。一般来说，组成细胞结构的复杂分子是由小而简单的前体逐步构成的。合成代谢包括三个基本阶段。首先，前体物质如氨基酸、单糖、异戊二烯和核苷酸的生成，其次，它们利用 ATP 的能量活化成反应形式，第三，这些前体物质组装成复杂的分子，如蛋白质、多糖、脂类和核酸。

In many organisms, the capture of solar energy is similar in principle to oxidative phosphorylation, as it involves the storage of energy as a proton concentration gradient. This proton motive force then drives ATP synthesis<ref>{{cite book |last1=Alberts|first1=Bruce|last2=Johnson|first2=Alexander|last3=Lewis|first3=Julian|last4=Raff|first4=Martin|last5=Roberts|first5=Keith|last6=Walter|first6=Peter | name-list-style = vanc |date=2002|chapter =Energy Conversion: Mitochondria and Chloroplasts|url=https://www.ncbi.nlm.nih.gov/books/NBK21063/|title =Molecular Biology of the Cell. 4th edition|language=en}}</ref> The electrons needed to drive this electron transport chain come from light-gathering proteins called [[photosynthetic reaction centre]]s. Reaction centers are classed into two types depending on the nature of [[photosynthetic pigment]] present, with most photosynthetic bacteria only having one type, while plants and cyanobacteria have two.<ref>{{cite journal | vauthors = Allen JP, Williams JC | title = Photosynthetic reaction centers | journal = FEBS Letters | volume = 438 | issue = 1–2 | pages = 5–9 | date = October 1998 | pmid = 9821949 | doi = 10.1016/S0014-5793(98)01245-9 | s2cid = 21596537 }}</ref>

Anabolism in organisms can be different according to the source of constructed molecules in their cells. Autotrophs such as plants can construct the complex organic molecules in cells such as polysaccharides and proteins from simple molecules like carbon dioxide and water. Heterotrophs, on the other hand, require a source of more complex substances, such as monosaccharides and amino acids, to produce these complex molecules. Organisms can be further classified by ultimate source of their energy: photoautotrophs and photoheterotrophs obtain energy from light, whereas chemoautotrophs and chemoheterotrophs obtain energy from inorganic oxidation reactions. Three types of photosynthesis occur in plants, C3 carbon fixation, C4 carbon fixation and CAM photosynthesis. These differ by the route that carbon dioxide takes to the Calvin cycle, with C3 plants fixing CO2 directly, while C4 and CAM photosynthesis incorporate the CO2 into other compounds first, as adaptations to deal with intense sunlight and dry conditions.

生物体的合成代谢可以根据其细胞中构建分子的来源而有所不同。像植物这样的自养生物可以从二氧化碳和水这样的简单分子中构建复杂的细胞有机分子，如多糖和蛋白质。另一方面，异养菌需要更复杂的物质来源，如单糖和氨基酸，来产生这些复杂的分子。生物可以根据其能量的最终来源进一步分类: 光自养生物和光异养生物从光中获得能量，而化能自养生物和化能异养生物从无机氧化反应中获得能量。植物有3种类型的光合作用，c 3固碳作用，C4类二氧化碳固定和 CAM 光合作用。二氧化碳进入卡尔文循环的途径不同，C3植物直接固定 CO 2 ，而 C4和 CAM 首先将 CO 2 合并到其他化合物中，以适应强烈的阳光和干燥条件。

In plants, algae, and cyanobacteria, [[photosystem|photosystem II]] uses light energy to remove electrons from water, releasing oxygen as a waste product. The electrons then flow to the [[cytochrome b6f complex]], which uses their energy to pump protons across the [[thylakoid]] membrane in the [[chloroplast]].<ref name=Nelson2004/> These protons move back through the membrane as they drive the ATP synthase, as before. The electrons then flow through [[photosystem|photosystem I]] and can then either be used to reduce the coenzyme NADP+.<ref>{{cite journal | vauthors = Munekage Y, Hashimoto M, Miyake C, Tomizawa K, Endo T, Tasaka M, Shikanai T | title = Cyclic electron flow around photosystem I is essential for photosynthesis | journal = Nature | volume = 429 | issue = 6991 | pages = 579–82 | date = June 2004 | pmid = 15175756 | doi = 10.1038/nature02598 | bibcode = 2004Natur.429..579M | s2cid = 4421776 }}</ref>fThese cooenzyme can be used in the [[Calvin cycle]], which is discussed below, or recycled for further ATP generation.

In photosynthetic prokaryotes the mechanisms of carbon fixation are more diverse. Here, carbon dioxide can be fixed by the Calvin – Benson cycle, a reversed citric acid cycle, or the carboxylation of acetyl-CoA. Prokaryotic chemoautotrophs also fix CO2 through the Calvin–Benson cycle, but use energy from inorganic compounds to drive the reaction.

在光合作用的原核生物中，碳固定的机制更加多样。在这里，二氧化碳可以通过卡尔文-本森循环、反向三羧酸循环或乙酰辅酶 a 的羧化作用得到固定。原核化能自养生物也通过卡尔文-本森循环固定 CO 2 ，但利用无机化合物的能量来驱动反应。

==Anabolism==

{{further|Anabolism}}

'''Anabolism''' is the set of constructive metabolic processes where the energy released by catabolism is used to synthesize complex molecules. In general, the complex molecules that make up cellular structures are constructed step-by-step from small and simple precursors. Anabolism involves three basic stages. First, the production of precursors such as [[amino acid]]s, [[monosaccharide]]s, [[Terpenoid|isoprenoids]] and [[nucleotide]]s, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as [[protein]]s, [[polysaccharide]]s, [[lipid]]s and [[nucleic acid]]s.<ref name=":0">{{cite web|last=Mandal|first=Ananya| name-list-style = vanc |date=2009-11-26|title=What is Anabolism?|url=https://www.news-medical.net/life-sciences/What-is-Anabolism.aspx|access-date=2020-07-04|website=News-Medical.net|language=en}}</ref>

In carbohydrate anabolism, simple organic acids can be converted into monosaccharides such as glucose and then used to assemble polysaccharides such as starch. The generation of glucose from compounds like pyruvate, lactate, glycerol, glycerate 3-phosphate and amino acids is called gluconeogenesis. Gluconeogenesis converts pyruvate to glucose-6-phosphate through a series of intermediates, many of which are shared with glycolysis.

在碳水化合物的合成代谢过程中，简单的有机酸可以转化为单糖如葡萄糖，然后用来聚集多糖如淀粉。从丙酮酸、乳酸、甘油、3- 磷酸甘油和氨基酸等化合物产生葡萄糖称为糖异生。葡萄糖异生通过一系列中间体将丙酮酸转化为葡萄糖-6-磷酸，其中许多中间体与糖酵解共享。

Anabolism in organisms can be different according to the source of constructed molecules in their cells. [[Autotroph]]s such as plants can construct the complex organic molecules in cells such as polysaccharides and proteins from simple molecules like [[carbon dioxide]] and water. [[Heterotroph]]s, on the other hand, require a source of more complex substances, such as monosaccharides and amino acids, to produce these complex molecules. Organisms can be further classified by ultimate source of their energy: photoautotrophs and photoheterotrophs obtain energy from light, whereas chemoautotrophs and chemoheterotrophs obtain energy from inorganic oxidation reactions.<ref name=":0" />

Although fat is a common way of storing energy, in vertebrates such as humans the fatty acids in these stores cannot be converted to glucose through gluconeogenesis as these organisms cannot convert acetyl-CoA into pyruvate; plants do, but animals do not, have the necessary enzymatic machinery. As a result, after long-term starvation, vertebrates need to produce ketone bodies from fatty acids to replace glucose in tissues such as the brain that cannot metabolize fatty acids. In other organisms such as plants and bacteria, this metabolic problem is solved using the glyoxylate cycle, which bypasses the decarboxylation step in the citric acid cycle and allows the transformation of acetyl-CoA to oxaloacetate, where it can be used for the production of glucose. Other than fat, glucose is stored in most tissues, as an energy resource available within the tissue through glycogenesis which was usually being used to maintained glucose level in blood.

虽然脂肪是储存能量的一种常见方式，但在脊椎动物如人类中，这些储存的脂肪酸不能通过糖异生作用转化为葡萄糖，因为这些生物不能将乙酰辅酶 a 转化为丙酮酸; 植物有，但动物没有。因此，在长期饥饿之后，脊椎动物需要从脂肪酸中产生酮体来代替大脑中不能代谢脂肪酸的葡萄糖。在其他生物体中，如植物和细菌，这种新陈代谢问题可以通过乙醛酸循环来解决，它绕过了三羧酸循环中的脱羧步骤，允许乙酰辅酶 a 转化为草酰乙酸，在那里它可以用来生产葡萄糖。除了脂肪，葡萄糖储存在大多数组织中，作为一种能量资源，通过糖生成在组织中可用于维持血液中的葡萄糖水平。

===Carbon fixation===

Polysaccharides and glycans are made by the sequential addition of monosaccharides by glycosyltransferase from a reactive sugar-phosphate donor such as uridine diphosphate glucose (UDP-Glc) to an acceptor hydroxyl group on the growing polysaccharide. As any of the hydroxyl groups on the ring of the substrate can be acceptors, the polysaccharides produced can have straight or branched structures. The polysaccharides produced can have structural or metabolic functions themselves, or be transferred to lipids and proteins by enzymes called oligosaccharyltransferases.

多糖和聚糖是由糖基转移酶从活性糖-磷酸盐供体如尿苷二磷酸葡萄糖(UDP-Glc)顺序加入到生长中的多糖的受体羟基上形成的单糖。由于底物环上的任何羟基都可以作为受体，所以产生的多糖可以具有直的或分枝的结构。产生的多糖本身具有结构或代谢功能，或通过被称为寡糖转移酶的酶转移到脂质和蛋白质中。

{{further|Photosynthesis|Carbon fixation|Chemosynthesis}}

[[File:Plagiomnium affine laminazellen.jpeg|thumb|Plant cells (bounded by purple walls) filled with chloroplasts (green), which are the site of photosynthesis]]

Photosynthesis is the synthesis of carbohydrates from sunlight and [[carbon dioxide]] (CO2). In plants, cyanobacteria and algae, oxygenic photosynthesis splits water, with oxygen produced as a waste product. This process uses the ATP and NADPH produced by the [[photosynthetic reaction centre]]s, as described above, to convert CO2 into [[glycerate 3-phosphate]], which can then be converted into glucose. This carbon-fixation reaction is carried out by the enzyme [[RuBisCO]] as part of the [[Calvin cycle|Calvin – Benson cycle]].<ref>{{cite journal | vauthors = Miziorko HM, Lorimer GH | title = Ribulose-1,5-bisphosphate carboxylase-oxygenase | journal = Annual Review of Biochemistry | volume = 52 | issue = | pages = 507–35 | year = 1983 | pmid = 6351728 | doi = 10.1146/annurev.bi.52.070183.002451 }}</ref> Three types of photosynthesis occur in plants, [[C3 carbon fixation]], [[C4 carbon fixation]] and [[Crassulacean acid metabolism|CAM photosynthesis]]. These differ by the route that carbon dioxide takes to the Calvin cycle, with C3 plants fixing CO2 directly, while C4 and CAM photosynthesis incorporate the CO2 into other compounds first, as adaptations to deal with intense sunlight and dry conditions.<ref>{{cite journal | vauthors = Dodd AN, Borland AM, Haslam RP, Griffiths H, Maxwell K | title = Crassulacean acid metabolism: plastic, fantastic | journal = Journal of Experimental Botany | volume = 53 | issue = 369 | pages = 569–80 | date = April 2002 | pmid = 11886877 | doi = 10.1093/jexbot/53.369.569 | doi-access = free }}</ref>

Simplified version of the [[steroid synthesis pathway with the intermediates isopentenyl pyrophosphate (IPP), dimethylallyl pyrophosphate (DMAPP), geranyl pyrophosphate (GPP) and squalene shown. Some intermediates are omitted for clarity.]]

简化的[[含中间体焦磷酸异戊烷(IPP) ，焦磷酸二甲基烯丙酯(DMAPP) ，焦磷酸香叶基(GPP)和角鲨烯的甾体合成途径]。为了清晰起见，省略了一些中间步骤。]

Fatty acids are made by fatty acid synthases that polymerize and then reduce acetyl-CoA units. The acyl chains in the fatty acids are extended by a cycle of reactions that add the acyl group, reduce it to an alcohol, dehydrate it to an alkene group and then reduce it again to an alkane group. The enzymes of fatty acid biosynthesis are divided into two groups: in animals and fungi, all these fatty acid synthase reactions are carried out by a single multifunctional type I protein, while in plant plastids and bacteria separate type II enzymes perform each step in the pathway.

脂肪酸是由脂肪酸合酶聚合，然后减少乙酰辅酶 a 单位。脂肪酸中的酰基链通过一系列反应得到延伸，这些反应加上酰基基团，将其还原成醇，将其还原成烯烃基团，然后再还原成烷烃基团。脂肪酸生物合成的酶分为两组: 在动物和真菌中，所有这些脂肪酸合酶反应都是由一个单一的多功能 i 型蛋白进行的，而在植物质体和细菌中，分离的 II 型酶在这个途径中执行每一步。

In photosynthetic [[prokaryote]]s the mechanisms of carbon fixation are more diverse. Here, carbon dioxide can be fixed by the Calvin – Benson cycle, a [[Reverse Krebs cycle|reversed citric acid]] cycle,<ref>{{cite journal | vauthors = Hügler M, Wirsen CO, Fuchs G, Taylor CD, Sievert SM | title = Evidence for autotrophic CO2 fixation via the reductive tricarboxylic acid cycle by members of the epsilon subdivision of proteobacteria | journal = Journal of Bacteriology | volume = 187 | issue = 9 | pages = 3020–7 | date = May 2005 | pmid = 15838028 | pmc = 1082812 | doi = 10.1128/JB.187.9.3020-3027.2005 }}</ref> or the carboxylation of acetyl-CoA.<ref>{{cite journal | vauthors = Strauss G, Fuchs G | title = Enzymes of a novel autotrophic CO2 fixation pathway in the phototrophic bacterium Chloroflexus aurantiacus, the 3-hydroxypropionate cycle | journal = European Journal of Biochemistry | volume = 215 | issue = 3 | pages = 633–43 | date = August 1993 | pmid = 8354269 | doi = 10.1111/j.1432-1033.1993.tb18074.x }}</ref><ref>{{cite journal | vauthors = Wood HG | title = Life with CO or CO2 and H2 as a source of carbon and energy | journal = FASEB Journal | volume = 5 | issue = 2 | pages = 156–63 | date = February 1991 | pmid = 1900793 | doi = 10.1096/fasebj.5.2.1900793 | s2cid = 45967404 }}</ref> Prokaryotic [[Chemotroph|chemoautotrophs]] also fix CO2 through the Calvin–Benson cycle, but use energy from inorganic compounds to drive the reaction.<ref>{{cite journal | vauthors = Shively JM, van Keulen G, Meijer WG | title = Something from almost nothing: carbon dioxide fixation in chemoautotrophs | journal = Annual Review of Microbiology | volume = 52 | issue = | pages = 191–230 | year = 1998 | pmid = 9891798 | doi = 10.1146/annurev.micro.52.1.191 }}</ref>

Terpenes and isoprenoids are a large class of lipids that include the carotenoids and form the largest class of plant natural products. These compounds are made by the assembly and modification of isoprene units donated from the reactive precursors isopentenyl pyrophosphate and dimethylallyl pyrophosphate. These precursors can be made in different ways. In animals and archaea, the mevalonate pathway produces these compounds from acetyl-CoA, while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates. One important reaction that uses these activated isoprene donors is sterol biosynthesis. Here, the isoprene units are joined together to make squalene and then folded up and formed into a set of rings to make lanosterol. Lanosterol can then be converted into other sterol such as cholesterol and ergosterol.

萜烯和类异戊二烯是类脂的一大类，包括类胡萝卜素和形成最大类的植物天然产品。这些化合物是通过组装和改性异戊二烯单元而得到的，异戊二烯单元来自反应前体焦磷酸异戊烷和焦磷酸二甲基烯丙酯。这些前体可以用不同的方法制造。在动物和古生菌中，甲羟戊酸途径从乙酰辅酶 a 中产生这些化合物，而在植物和细菌中，非甲羟戊酸途径使用丙酮酸和甘油醛3-磷酸作为底物。使用这些活性异戊二烯供体的一个重要反应是甾醇生物合成。在这里，异戊二烯单元连接在一起生成角鲨烯，然后折叠起来形成一系列环状物，生成羊毛甾醇。羊毛甾醇可以转化为其他甾醇，如胆固醇和麦角甾醇。

===Carbohydrates and glycans===

{{further|Gluconeogenesis|Glyoxylate cycle|Glycogenesis|Glycosylation}}

In carbohydrate anabolism, simple organic acids can be converted into [[monosaccharide]]s such as [[glucose]] and then used to assemble [[polysaccharide]]s such as [[starch]]. The generation of [[glucose]] from compounds like [[pyruvate]], [[lactic acid|lactate]], [[glycerol]], [[glycerate 3-phosphate]] and [[amino acid]]s is called [[gluconeogenesis]]. Gluconeogenesis converts pyruvate to [[glucose-6-phosphate]] through a series of intermediates, many of which are shared with [[glycolysis]].<ref name=Bouche/> However, this pathway is not simply [[glycolysis]] run in reverse, as several steps are catalyzed by non-glycolytic enzymes. This is important as it allows the formation and breakdown of glucose to be regulated separately, and prevents both pathways from running simultaneously in a [[futile cycle]].<ref>{{cite journal | vauthors = Boiteux A, Hess B | title = Design of glycolysis | journal = Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume = 293 | issue = 1063 | pages = 5–22 | date = June 1981 | pmid = 6115423 | doi = 10.1098/rstb.1981.0056 | doi-access = free | bibcode = 1981RSPTB.293....5B }}</ref><ref>{{cite journal | vauthors = Pilkis SJ, el-Maghrabi MR, Claus TH | title = Fructose-2,6-bisphosphate in control of hepatic gluconeogenesis. From metabolites to molecular genetics | journal = Diabetes Care | volume = 13 | issue = 6 | pages = 582–99 | date = June 1990 | pmid = 2162755 | doi = 10.2337/diacare.13.6.582 | s2cid = 44741368 }}</ref>

Organisms vary in their ability to synthesize the 20 common amino acids. Most bacteria and plants can synthesize all twenty, but mammals can only synthesize eleven nonessential amino acids, so nine essential amino acids must be obtained from food. All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen is provided by glutamate and glutamine. Nonessensial amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then transaminated to form an amino acid.

生物体合成20种常见氨基酸的能力各不相同。大多数细菌和植物都能合成这二十种氨基酸，但是哺乳动物只能合成十一种非必需氨基酸，所以必须从食物中获得9种必需氨基酸。所有的氨基酸都是由糖酵解、三羧酸循环或磷酸戊糖途径的中间体合成的。氮由谷氨酸和谷氨酰胺提供。非氨基酸合成依赖于合适的 α- 酮酸的形成，然后转氨基酸形成氨基酸。

Although fat is a common way of storing energy, in [[vertebrate]]s such as humans the [[fatty acid]]s in these stores cannot be converted to glucose through [[gluconeogenesis]] as these organisms cannot convert acetyl-CoA into [[pyruvate]]; plants do, but animals do not, have the necessary enzymatic machinery.<ref name=Ensign>{{cite journal | vauthors = Ensign SA | title = Revisiting the glyoxylate cycle: alternate pathways for microbial acetate assimilation | journal = Molecular Microbiology | volume = 61 | issue = 2 | pages = 274–6 | date = July 2006 | pmid = 16856935 | doi = 10.1111/j.1365-2958.2006.05247.x | s2cid = 39986630 }}</ref> As a result, after long-term starvation, vertebrates need to produce [[Ketone body|ketone bodies]] from fatty acids to replace glucose in tissues such as the brain that cannot metabolize fatty acids.<ref>{{cite journal | vauthors = Finn PF, Dice JF | title = Proteolytic and lipolytic responses to starvation | journal = Nutrition | volume = 22 | issue = 7–8 | pages = 830–44 | year = 2006 | pmid = 16815497 | doi = 10.1016/j.nut.2006.04.008 }}</ref> In other organisms such as plants and bacteria, this metabolic problem is solved using the [[glyoxylate cycle]], which bypasses the [[decarboxylation]] step in the citric acid cycle and allows the transformation of acetyl-CoA to [[oxaloacetate]], where it can be used for the production of glucose.<ref name=Ensign/><ref name=Kornberg>{{cite journal | vauthors = Kornberg HL, Krebs HA | title = Synthesis of cell constituents from C2-units by a modified tricarboxylic acid cycle | journal = Nature | volume = 179 | issue = 4568 | pages = 988–91 | date = May 1957 | pmid = 13430766 | doi = 10.1038/179988a0 | s2cid = 40858130 | bibcode = 1957Natur.179..988K }}</ref> Other than fat, glucose is stored in most tissues, as an energy resource available within the tissue through glycogenesis which was usually being used to maintained glucose level in blood.<ref>{{cite journal|last1=Evans|first1=Rhys D.|last2=Heather|first2=Lisa C. | name-list-style = vanc |date=June 2016|title=Metabolic pathways and abnormalities|journal=Surgery (Oxford)|volume=34|issue=6|pages=266–272|doi=10.1016/j.mpsur.2016.03.010|issn=0263-9319|url=https://ora.ox.ac.uk/objects/uuid:84c0a8e7-38e9-4de2-ba19-9f129a07987a}}</ref>

Amino acids are made into proteins by being joined together in a chain of peptide bonds. Each different protein has a unique sequence of amino acid residues: this is its primary structure. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA precursor is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase. This aminoacyl-tRNA is then a substrate for the ribosome, which joins the amino acid onto the elongating protein chain, using the sequence information in a messenger RNA.

氨基酸通过肽链连接在一起形成蛋白质。每个不同的蛋白质都有一个独特的氨基酸残基序列: 这是它的一级结构。正如字母表中的字母可以组合成几乎无穷无尽的单词一样，氨基酸可以以不同的顺序连接成各种各样的蛋白质。蛋白质是由氨基酸组成的，氨基酸通过酯键附着在转移 RNA 分子上而被激活。这个氨基酰基 trna 前体是由氨酰-tRNA合成酶通过依赖 atp 的反应生成的。这个氨基酰基 trna 是核糖体的底物，核糖体利用信使 RNA 中的序列信息将氨基酸连接到伸长的蛋白质链上。

Polysaccharides and [[glycan]]s are made by the sequential addition of monosaccharides by [[glycosyltransferase]] from a reactive sugar-phosphate donor such as [[uridine diphosphate glucose]] (UDP-Glc) to an acceptor [[hydroxyl]] group on the growing polysaccharide. As any of the [[hydroxyl]] groups on the ring of the substrate can be acceptors, the polysaccharides produced can have straight or branched structures.<ref>{{cite book |last1=Freeze|first1=Hudson H. | name-list-style = vanc | chapter =Glycosylation Precursors|date=2015|url=http://www.ncbi.nlm.nih.gov/books/NBK453043/| title = Essentials of Glycobiology|editor-last=Varki|editor-first=Ajit|edition=3rd|place=Cold Spring Harbor (NY)|publisher=Cold Spring Harbor Laboratory Press|pmid=28876856|access-date=2020-07-08|last2=Hart|first2=Gerald W.|last3=Schnaar|first3=Ronald L.|doi=10.1101/glycobiology.3e.005 |doi-broken-date=1 November 2020 |editor2-last=Cummings|editor2-first=Richard D.|editor3-last=Esko|editor3-first=Jeffrey D.|editor4-last=Stanley|editor4-first=Pamela }}</ref> The polysaccharides produced can have structural or metabolic functions themselves, or be transferred to lipids and proteins by enzymes called [[oligosaccharyltransferase]]s.<ref>{{cite journal | vauthors = Opdenakker G, Rudd PM, Ponting CP, Dwek RA | title = Concepts and principles of glycobiology | journal = FASEB Journal | volume = 7 | issue = 14 | pages = 1330–7 | date = November 1993 | pmid = 8224606 | doi = 10.1096/fasebj.7.14.8224606 | s2cid = 10388991 }}</ref><ref>{{cite journal | vauthors = McConville MJ, Menon AK | title = Recent developments in the cell biology and biochemistry of glycosylphosphatidylinositol lipids (review) | journal = Molecular Membrane Biology | volume = 17 | issue = 1 | pages = 1–16 | year = 2000 | pmid = 10824734 | doi = 10.1080/096876800294443 | doi-access = free }}</ref>

===Fatty acids, isoprenoids and sterol===

{{further|Fatty acid synthesis|Steroid metabolism}}

Nucleotides are made from amino acids, carbon dioxide and formic acid in pathways that require large amounts of metabolic energy. Consequently, most organisms have efficient systems to salvage preformed nucleotides. Purines are synthesized as nucleosides (bases attached to ribose). Both adenine and guanine are made from the precursor nucleoside inosine monophosphate, which is synthesized using atoms from the amino acids glycine, glutamine, and aspartic acid, as well as formate transferred from the coenzyme tetrahydrofolate. Pyrimidines, on the other hand, are synthesized from the base orotate, which is formed from glutamine and aspartate.

核苷酸是由氨基酸，二氧化碳和甲酸在途径，需要大量的代谢能量。因此，大多数生物体都有有效的系统来回收预先形成的核苷酸。嘌呤被合成为核苷(核糖上的碱基)。腺嘌呤和鸟嘌呤都是由前体核苷苷单磷酸合成的，单磷酸是由甘氨酸、谷氨酰胺和天冬氨酸的氨基酸原子，以及从辅酶四氢叶酸转移来的甲酸盐合成的。另一方面，嘧啶是由由谷氨酰胺和天冬氨酸形成的碱性橙酸盐合成的。

[[File:Sterol synthesis.svg|thumb|right|upright=1.6|Simplified version of the [[steroid synthesis]] pathway with the intermediates [[isopentenyl pyrophosphate]] (IPP), [[dimethylallyl pyrophosphate]] (DMAPP), [[geranyl pyrophosphate]] (GPP) and [[squalene]] shown. Some intermediates are omitted for clarity.]]

Fatty acids are made by [[fatty acid synthase]]s that polymerize and then reduce acetyl-CoA units. The acyl chains in the fatty acids are extended by a cycle of reactions that add the acyl group, reduce it to an alcohol, [[dehydration reaction|dehydrate]] it to an [[alkene]] group and then reduce it again to an [[alkane]] group. The enzymes of fatty acid biosynthesis are divided into two groups: in animals and fungi, all these fatty acid synthase reactions are carried out by a single multifunctional type I protein,<ref>{{cite journal | vauthors = Chirala SS, Wakil SJ | title = Structure and function of animal fatty acid synthase | journal = Lipids | volume = 39 | issue = 11 | pages = 1045–53 | date = November 2004 | pmid = 15726818 | doi = 10.1007/s11745-004-1329-9 | s2cid = 4043407 }}</ref> while in plant [[plastid]]s and bacteria separate type II enzymes perform each step in the pathway.<ref>{{cite journal | vauthors = White SW, Zheng J, Zhang YM | title = The structural biology of type II fatty acid biosynthesis | journal = Annual Review of Biochemistry | volume = 74 | issue = | pages = 791–831 | year = 2005 | pmid = 15952903 | doi = 10.1146/annurev.biochem.74.082803.133524 }}</ref><ref>{{cite journal | vauthors = Ohlrogge JB, Jaworski JG | title = Regulation of Fatty Acid Synthesis | journal = Annual Review of Plant Physiology and Plant Molecular Biology | volume = 48 | issue = | pages = 109–136 | date = June 1997 | pmid = 15012259 | doi = 10.1146/annurev.arplant.48.1.109 | s2cid = 46348092 }}</ref>

[[Terpene]]s and [[terpenoid|isoprenoids]] are a large class of lipids that include the [[carotenoid]]s and form the largest class of plant [[natural product]]s.<ref>{{cite journal | vauthors = Dubey VS, Bhalla R, Luthra R | title = An overview of the non-mevalonate pathway for terpenoid biosynthesis in plants | journal = Journal of Biosciences | volume = 28 | issue = 5 | pages = 637–46 | date = September 2003 | pmid = 14517367 | doi = 10.1007/BF02703339 | url = http://www.ias.ac.in/jbiosci/sep2003/637.pdf | url-status = dead | s2cid = 27523830 | archive-url = https://web.archive.org/web/20070415213325/http://www.ias.ac.in/jbiosci/sep2003/637.pdf | df = | archive-date = 15 April 2007 }}</ref> These compounds are made by the assembly and modification of [[isoprene]] units donated from the reactive precursors [[isopentenyl pyrophosphate]] and [[dimethylallyl pyrophosphate]].<ref name=Kuzuyama>{{cite journal | vauthors = Kuzuyama T, Seto H | title = Diversity of the biosynthesis of the isoprene units | journal = Natural Product Reports | volume = 20 | issue = 2 | pages = 171–83 | date = April 2003 | pmid = 12735695 | doi = 10.1039/b109860h }}</ref> These precursors can be made in different ways. In animals and archaea, the [[mevalonate pathway]] produces these compounds from acetyl-CoA,<ref>{{cite journal | vauthors = Grochowski LL, Xu H, White RH | title = Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate | journal = Journal of Bacteriology | volume = 188 | issue = 9 | pages = 3192–8 | date = May 2006 | pmid = 16621811 | pmc = 1447442 | doi = 10.1128/JB.188.9.3192-3198.2006 }}</ref> while in plants and bacteria the [[non-mevalonate pathway]] uses pyruvate and [[glyceraldehyde 3-phosphate]] as substrates.<ref name=Kuzuyama/><ref>{{cite journal | vauthors = Lichtenthaler HK | title = The 1-Deoxy-D-Xylulose-5-Phosphate Pathway of Isoprenoid Biosynthesis in Plants | journal = Annual Review of Plant Physiology and Plant Molecular Biology | volume = 50 | issue = | pages = 47–65 | date = June 1999 | pmid = 15012203 | doi = 10.1146/annurev.arplant.50.1.47 }}</ref> One important reaction that uses these activated isoprene donors is [[steroid biosynthesis|sterol biosynthesis]]. Here, the isoprene units are joined together to make [[squalene]] and then folded up and formed into a set of rings to make [[lanosterol]].<ref name=Schroepfer>{{cite journal | vauthors = Schroepfer GJ | title = Sterol biosynthesis | journal = Annual Review of Biochemistry | volume = 50 | issue = | pages = 585–621 | year = 1981 | pmid = 7023367 | doi = 10.1146/annurev.bi.50.070181.003101 }}</ref> Lanosterol can then be converted into other sterol such as [[cholesterol]] and [[ergosterol]].<ref name=Schroepfer/><ref>{{cite journal | vauthors = Lees ND, Skaggs B, Kirsch DR, Bard M | title = Cloning of the late genes in the ergosterol biosynthetic pathway of Saccharomyces cerevisiae--a review | journal = Lipids | volume = 30 | issue = 3 | pages = 221–6 | date = March 1995 | pmid = 7791529 | doi = 10.1007/BF02537824 | s2cid = 4019443 }}</ref>

All organisms are constantly exposed to compounds that they cannot use as foods and would be harmful if they accumulated in cells, as they have no metabolic function. These potentially damaging compounds are called xenobiotics. Xenobiotics such as synthetic drugs, natural poisons and antibiotics are detoxified by a set of xenobiotic-metabolizing enzymes. In humans, these include cytochrome P450 oxidases, UDP-glucuronosyltransferases, and glutathione S-transferases. This system of enzymes acts in three stages to firstly oxidize the xenobiotic (phase I) and then conjugate water-soluble groups onto the molecule (phase II). The modified water-soluble xenobiotic can then be pumped out of cells and in multicellular organisms may be further metabolized before being excreted (phase III). In ecology, these reactions are particularly important in microbial biodegradation of pollutants and the bioremediation of contaminated land and oil spills. Many of these microbial reactions are shared with multicellular organisms, but due to the incredible diversity of types of microbes these organisms are able to deal with a far wider range of xenobiotics than multicellular organisms, and can degrade even persistent organic pollutants such as organochloride compounds.

所有的生物都不断地暴露在它们不能用作食物的化合物中，如果它们在细胞中积累起来就会有害，因为它们没有新陈代谢功能。这些具有潜在破坏性的化合物被称为异生物质。合成药物、天然毒物和抗生素等异生物是通过一系列异生物代谢酶来解毒的。在人类中，这些包括细胞色素 P450氧化酶、葡萄糖醛酸转移酶和谷胱甘肽 s- 转移酶。这个酶系统分为三个阶段，首先氧化异生物(第一阶段) ，然后将水溶性基团共轭到分子上(第二阶段)。经过修饰的水溶性异生物随后可以从细胞中泵出，在多细胞生物中，可以在排出之前进一步代谢(第三期)。在生态学中，这些反应在污染物的微生物降解以及污染土地和石油溢漏的生物修复中特别重要。许多这样的微生物反应是多细胞生物共有的，但是由于难以置信的微生物种类多样性，这些微生物能够处理比多细胞生物更广泛的异生物，甚至能够降解有机氯化合物等持久性有机污染物。

===Proteins===

A related problem for aerobic organisms is oxidative stress. Here, processes including oxidative phosphorylation and the formation of disulfide bonds during protein folding produce reactive oxygen species such as hydrogen peroxide. These damaging oxidants are removed by antioxidant metabolites such as glutathione and enzymes such as catalases and peroxidases.

对于需氧生物来说，一个相关的问题是氧化应激。在这里，包括氧化磷酸化和蛋白质折叠过程中二硫键形成的过程产生了活性氧类，如过氧化氢。这些破坏性的氧化剂被抗氧化代谢物，如谷胱甘肽和酶，如过氧化氢酶和过氧化物酶去除。

{{further|Protein biosynthesis|Amino acid synthesis}}

Organisms vary in their ability to synthesize the 20 common amino acids. Most bacteria and plants can synthesize all twenty, but mammals can only synthesize eleven nonessential amino acids, so nine [[essential amino acid]]s must be obtained from food.<ref name=Nelson/> Some simple [[parasite]]s, such as the bacteria ''[[Mycoplasma pneumoniae]]'', lack all amino acid synthesis and take their amino acids directly from their hosts.<ref>{{cite journal | vauthors = Himmelreich R, Hilbert H, Plagens H, Pirkl E, Li BC, Herrmann R | title = Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae | journal = Nucleic Acids Research | volume = 24 | issue = 22 | pages = 4420–49 | date = November 1996 | pmid = 8948633 | pmc = 146264 | doi = 10.1093/nar/24.22.4420 }}</ref> All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen is provided by [[glutamate]] and [[glutamine]]. Nonessensial amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then [[Transaminase|transaminated]] to form an amino acid.<ref>{{cite book |last1 = Guyton |first1 = Arthur C. | first2 = John E. | last2 = Hall | name-list-style = vanc |title=Textbook of Medical Physiology |url=https://archive.org/details/textbookmedicalp00acgu |url-access=limited |publisher=Elsevier |year=2006 |location=Philadelphia |pages=[https://archive.org/details/textbookmedicalp00acgu/page/n889 855]–6 |isbn=978-0-7216-0240-0}}</ref>

Living organisms must obey the laws of thermodynamics, which describe the transfer of heat and work. The second law of thermodynamics states that in any closed system, the amount of entropy (disorder) cannot decrease. Although living organisms' amazing complexity appears to contradict this law, life is possible as all organisms are open systems that exchange matter and energy with their surroundings. Thus living systems are not in equilibrium, but instead are dissipative systems that maintain their state of high complexity by causing a larger increase in the entropy of their environments. The metabolism of a cell achieves this by coupling the spontaneous processes of catabolism to the non-spontaneous processes of anabolism. In thermodynamic terms, metabolism maintains order by creating disorder.

活的有机体必须服从热力学定律，它描述了热和功的传递。热力学第二定律指出，在任何封闭系统中，熵(无序)的数量不能减少。虽然生物体惊人的复杂性似乎与这一定律相矛盾，但生命是可能的，因为所有生物体都是开放的系统，与周围环境交换物质和能量。因此，生命系统不是处于平衡状态，而是耗散系统，它们通过引起环境熵的增加来维持其高度复杂的状态。细胞的新陈代谢是通过将自发的分解代谢过程与非自发的合成代谢过程耦合起来来实现这一点的。在热力学术语中，新陈代谢通过创造无序来维持秩序。

Amino acids are made into proteins by being joined together in a chain of [[peptide bond]]s. Each different protein has a unique sequence of amino acid residues: this is its [[primary structure]]. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a [[transfer RNA]] molecule through an [[ester]] bond. This [[aminoacyl-tRNA]] precursor is produced in an [[Adenosine triphosphate|ATP]]-dependent reaction carried out by an [[aminoacyl tRNA synthetase]].<ref>{{cite journal | vauthors = Ibba M, Söll D | title = The renaissance of aminoacyl-tRNA synthesis | journal = EMBO Reports | volume = 2 | issue = 5 | pages = 382–7 | date = May 2001 | pmid = 11375928 | pmc = 1083889 | doi = 10.1093/embo-reports/kve095 | url = http://www.molcells.org/home/journal/include/downloadPdf.asp?articleuid={A158E3B4-2423-4806-9A30-4B93CDA76DA0} | url-status = dead | archive-url = https://web.archive.org/web/20110501181419/http://www.molcells.org/home/journal/include/downloadPdf.asp?articleuid=%7BA158E3B4-2423-4806-9A30-4B93CDA76DA0%7D | df = | archive-date = 1 May 2011 }}</ref> This aminoacyl-tRNA is then a substrate for the [[ribosome]], which joins the amino acid onto the elongating protein chain, using the sequence information in a [[messenger RNA]].<ref>{{cite journal | vauthors = Lengyel P, Söll D | title = Mechanism of protein biosynthesis | journal = Bacteriological Reviews | volume = 33 | issue = 2 | pages = 264–301 | date = June 1969 | pmid = 4896351 | pmc = 378322 | doi = 10.1128/MMBR.33.2.264-301.1969 }}</ref>

===Nucleotide synthesis and salvage===

{{further|Nucleotide salvage|Pyrimidine biosynthesis|Purine#Metabolism}}

As the environments of most organisms are constantly changing, the reactions of metabolism must be finely regulated to maintain a constant set of conditions within cells, a condition called homeostasis. Metabolic regulation also allows organisms to respond to signals and interact actively with their environments. Two closely linked concepts are important for understanding how metabolic pathways are controlled. Firstly, the regulation of an enzyme in a pathway is how its activity is increased and decreased in response to signals. Secondly, the control exerted by this enzyme is the effect that these changes in its activity have on the overall rate of the pathway (the flux through the pathway). For example, an enzyme may show large changes in activity (i.e. it is highly regulated) but if these changes have little effect on the flux of a metabolic pathway, then this enzyme is not involved in the control of the pathway.

由于大多数有机体的环境是不断变化的，新陈代谢的反应必须精细地调节，以维持细胞内一套恒定的条件，这种条件称为内环境平衡。代谢调节也使生物体对信号作出反应，并与环境积极互动。两个紧密相连的概念对于理解代谢途径是如何被控制的非常重要。首先，调节一个途径中的酶是如何增加和减少其活性响应信号。其次，这种酶的控制作用是其活性的这些变化对整个通路的速率(通过通路的通量)的影响。例如，一种酶的活性可能会发生很大的变化(例如:。但是如果这些变化对代谢途径的通量影响不大，那么这种酶就不参与控制这条通路。

Nucleotides are made from amino acids, carbon dioxide and [[formic acid]] in pathways that require large amounts of metabolic energy.<ref name=Rudolph>{{cite journal | vauthors = Rudolph FB | title = The biochemistry and physiology of nucleotides | journal = The Journal of Nutrition | volume = 124 | issue = 1 Suppl | pages = 124S–127S | date = January 1994 | pmid = 8283301 | doi = 10.1093/jn/124.suppl_1.124S }} {{cite journal | vauthors = Zrenner R, Stitt M, Sonnewald U, Boldt R | title = Pyrimidine and purine biosynthesis and degradation in plants | journal = Annual Review of Plant Biology | volume = 57 | issue = | pages = 805–36 | year = 2006 | pmid = 16669783 | doi = 10.1146/annurev.arplant.57.032905.105421 }}</ref> Consequently, most organisms have efficient systems to salvage preformed nucleotides.<ref name=Rudolph/><ref>{{cite journal | vauthors = Stasolla C, Katahira R, Thorpe TA, Ashihara H | title = Purine and pyrimidine nucleotide metabolism in higher plants | journal = Journal of Plant Physiology | volume = 160 | issue = 11 | pages = 1271–95 | date = November 2003 | pmid = 14658380 | doi = 10.1078/0176-1617-01169 }}</ref> [[Purine]]s are synthesized as [[nucleoside]]s (bases attached to [[ribose]]).<ref name="pmid 22531138">{{cite journal | vauthors = Davies O, Mendes P, Smallbone K, Malys N | title = Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism | journal = BMB Reports | volume = 45 | issue = 4 | pages = 259–64 | date = April 2012 | pmid = 22531138 | doi = 10.5483/BMBRep.2012.45.4.259 | url = http://wrap.warwick.ac.uk/49510/1/WRAP_Malys_%5B45-4%5D1204261917_%28259-264%29BMB_11-169.pdf }}</ref> Both [[adenine]] and [[guanine]] are made from the precursor nucleoside [[inosine]] monophosphate, which is synthesized using atoms from the amino acids [[glycine]], [[glutamine]], and [[aspartic acid]], as well as [[formate]] transferred from the [[coenzyme]] [[folic acid|tetrahydrofolate]]. [[Pyrimidine]]s, on the other hand, are synthesized from the base [[Pyrimidinecarboxylic acid|orotate]], which is formed from glutamine and aspartate.<ref>{{cite journal | vauthors = Smith JL | title = Enzymes of nucleotide synthesis | journal = Current Opinion in Structural Biology | volume = 5 | issue = 6 | pages = 752–7 | date = December 1995 | pmid = 8749362 | doi = 10.1016/0959-440X(95)80007-7 }}</ref>

Effect of insulin on glucose uptake and metabolism. Insulin binds to its receptor (1), which in turn starts many protein activation cascades (2). These include: translocation of Glut-4 transporter to the [[plasma membrane and influx of glucose (3), glycogen synthesis (4), glycolysis (5) and fatty acid synthesis (6).]]

胰岛素对葡萄糖摄取和代谢的影响。胰岛素与其受体(1)结合，从而启动许多蛋白质激活级联(2)。这些包括: 转运葡萄糖 -4到[质膜和葡萄糖内流(3) ，糖原合成(4) ，糖酵解(5)和脂肪酸合成(6)]。]

==Xenobiotics and redox metabolism==

There are multiple levels of metabolic regulation. In intrinsic regulation, the metabolic pathway self-regulates to respond to changes in the levels of substrates or products; for example, a decrease in the amount of product can increase the flux through the pathway to compensate. Extrinsic control involves a cell in a multicellular organism changing its metabolism in response to signals from other cells. These signals are usually in the form of water soluble messengers such as hormones and growth factors and are detected by specific receptors on the cell surface. These signals are then transmitted inside the cell by second messenger systems that often involved the phosphorylation of proteins.

代谢调节有多个层次。在内在调节中，代谢途径通过自我调节来响应底物或产品水平的变化; 例如，产品数量的减少可以通过通路增加通量来补偿。外部控制包括多细胞生物中的一个细胞响应其他细胞的信号改变其新陈代谢。这些信号通常以水溶性信使的形式存在，如激素和生长因子，并被细胞表面的特定受体检测到。然后，这些信号通过第二信使系统在细胞内传递，这些信使系统通常涉及蛋白质的磷酸化。

{{further|Xenobiotic metabolism|Drug metabolism|Alcohol metabolism|Antioxidant}}

All organisms are constantly exposed to compounds that they cannot use as foods and would be harmful if they accumulated in cells, as they have no metabolic function. These potentially damaging compounds are called [[xenobiotic]]s.<ref>{{cite journal | vauthors = Testa B, Krämer SD | title = The biochemistry of drug metabolism--an introduction: part 1. Principles and overview | journal = Chemistry & Biodiversity | volume = 3 | issue = 10 | pages = 1053–101 | date = October 2006 | pmid = 17193224 | doi = 10.1002/cbdv.200690111 | s2cid = 28872968 }}</ref> Xenobiotics such as [[drug|synthetic drugs]], [[poison|natural poisons]] and [[antibiotic]]s are detoxified by a set of xenobiotic-metabolizing enzymes. In humans, these include [[cytochrome P450|cytochrome P450 oxidases]],<ref>{{cite journal | vauthors = Danielson PB | title = The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans | journal = Current Drug Metabolism | volume = 3 | issue = 6 | pages = 561–97 | date = December 2002 | pmid = 12369887 | doi = 10.2174/1389200023337054 }}</ref> [[Glucuronosyltransferase|UDP-glucuronosyltransferases]],<ref>{{cite journal | vauthors = King CD, Rios GR, Green MD, Tephly TR | title = UDP-glucuronosyltransferases | journal = Current Drug Metabolism | volume = 1 | issue = 2 | pages = 143–61 | date = September 2000 | pmid = 11465080 | doi = 10.2174/1389200003339171 }}</ref> and [[glutathione S-transferase|glutathione ''S''-transferases]].<ref>{{cite journal | vauthors = Sheehan D, Meade G, Foley VM, Dowd CA | title = Structure, function and evolution of glutathione transferases: implications for classification of non-mammalian members of an ancient enzyme superfamily | journal = The Biochemical Journal | volume = 360 | issue = Pt 1 | pages = 1–16 | date = November 2001 | pmid = 11695986 | pmc = 1222196 | doi = 10.1042/0264-6021:3600001 }}</ref> This system of enzymes acts in three stages to firstly oxidize the xenobiotic (phase I) and then conjugate water-soluble groups onto the molecule (phase II). The modified water-soluble xenobiotic can then be pumped out of cells and in multicellular organisms may be further metabolized before being excreted (phase III). In [[ecology]], these reactions are particularly important in microbial [[biodegradation]] of pollutants and the [[bioremediation]] of contaminated land and oil spills.<ref>{{cite journal | vauthors = Galvão TC, Mohn WW, de Lorenzo V | title = Exploring the microbial biodegradation and biotransformation gene pool | journal = Trends in Biotechnology | volume = 23 | issue = 10 | pages = 497–506 | date = October 2005 | pmid = 16125262 | doi = 10.1016/j.tibtech.2005.08.002 }}</ref> Many of these microbial reactions are shared with multicellular organisms, but due to the incredible diversity of types of microbes these organisms are able to deal with a far wider range of xenobiotics than multicellular organisms, and can degrade even [[persistent organic pollutant]]s such as [[organochloride]] compounds.<ref>{{cite journal | vauthors = Janssen DB, Dinkla IJ, Poelarends GJ, Terpstra P | title = Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities | journal = Environmental Microbiology | volume = 7 | issue = 12 | pages = 1868–82 | date = December 2005 | pmid = 16309386 | doi = 10.1111/j.1462-2920.2005.00966.x | url = https://pure.rug.nl/ws/files/3623678/2005EnvironMicrobiolJanssen.pdf }}</ref>

A very well understood example of extrinsic control is the regulation of glucose metabolism by the hormone insulin. Insulin is produced in response to rises in blood glucose levels. Binding of the hormone to insulin receptors on cells then activates a cascade of protein kinases that cause the cells to take up glucose and convert it into storage molecules such as fatty acids and glycogen. The metabolism of glycogen is controlled by activity of phosphorylase, the enzyme that breaks down glycogen, and glycogen synthase, the enzyme that makes it. These enzymes are regulated in a reciprocal fashion, with phosphorylation inhibiting glycogen synthase, but activating phosphorylase. Insulin causes glycogen synthesis by activating protein phosphatases and producing a decrease in the phosphorylation of these enzymes.

外在控制的一个很好理解的例子是通过激素胰岛素调节葡萄糖代谢。胰岛素的产生是对血糖水平上升的反应。这种激素与细胞上的胰岛素受体结合，然后激活一系列蛋白激酶，使细胞吸收葡萄糖并将其转化为储存分子，如脂肪酸和糖原。糖原的新陈代谢受到分解糖原的磷酸化酶和制造糖原的糖原合成酶的活性控制。这些酶是调节在一个相互的方式，磷酸化抑制糖原合成酶，但激活磷酸化酶。胰岛素通过激活蛋白磷酸酶导致糖原合成，并减少这些酶的磷酸化。

A related problem for [[aerobic organism]]s is [[oxidative stress]].<ref name=Davies>{{cite journal | vauthors = Davies KJ | title = Oxidative stress: the paradox of aerobic life | journal = Biochemical Society Symposium | volume = 61 | issue = | pages = 1–31 | year = 1995 | pmid = 8660387 | doi = 10.1042/bss0610001 }}</ref> Here, processes including [[oxidative phosphorylation]] and the formation of [[disulfide bond]]s during [[protein folding]] produce [[reactive oxygen species]] such as [[hydrogen peroxide]].<ref>{{cite journal | vauthors = Tu BP, Weissman JS | title = Oxidative protein folding in eukaryotes: mechanisms and consequences | journal = The Journal of Cell Biology | volume = 164 | issue = 3 | pages = 341–6 | date = February 2004 | pmid = 14757749 | pmc = 2172237 | doi = 10.1083/jcb.200311055 }}</ref> These damaging oxidants are removed by [[antioxidant]] metabolites such as [[glutathione]] and enzymes such as [[catalase]]s and [[peroxidase]]s.<ref name=Sies>{{cite journal | vauthors = Sies H | title = Oxidative stress: oxidants and antioxidants | journal = Experimental Physiology | volume = 82 | issue = 2 | pages = 291–5 | date = March 1997 | pmid = 9129943 | doi = 10.1113/expphysiol.1997.sp004024 | s2cid = 20240552 | url = http://ep.physoc.org/cgi/reprint/82/2/291.pdf | access-date = 9 March 2007 | url-status = dead | archive-url = https://web.archive.org/web/20090325001126/http://ep.physoc.org/cgi/reprint/82/2/291.pdf | archive-date = 25 March 2009 }}</ref><ref name=Vertuani>{{cite journal | vauthors = Vertuani S, Angusti A, Manfredini S | title = The antioxidants and pro-antioxidants network: an overview | journal = Current Pharmaceutical Design | volume = 10 | issue = 14 | pages = 1677–94 | year = 2004 | pmid = 15134565 | doi = 10.2174/1381612043384655 | s2cid = 43713549 }}</ref>

==Thermodynamics of living organisms==

Evolutionary tree showing the common ancestry of organisms from all three domains of life. Bacteria are colored blue, eukaryotes red, and archaea green. Relative positions of some of the phyla included are shown around the tree.]]

进化树显示了来自所有三个生命领域的生物体的共同祖先。细菌呈蓝色，真核生物呈红色，古菌呈绿色。一些门的相对位置被包括在树的周围。]

{{further|Biological thermodynamics}}

The central pathways of metabolism described above, such as glycolysis and the citric acid cycle, are present in all three domains of living things and were present in the last universal common ancestor. This universal ancestral cell was prokaryotic and probably a methanogen that had extensive amino acid, nucleotide, carbohydrate and lipid metabolism. The retention of these ancient pathways during later evolution may be the result of these reactions having been an optimal solution to their particular metabolic problems, with pathways such as glycolysis and the citric acid cycle producing their end products highly efficiently and in a minimal number of steps.

上面描述的代谢中枢途径，如糖酵解和三羧酸循环，存在于生物体的所有3个领域，并存在于最后一个普遍共同祖先。这个普遍的原始细胞是原核的，可能是含有大量氨基酸、核苷酸、碳水化合物和脂质代谢的产甲烷菌。在后期进化过程中保留这些古老的途径可能是这些反应的结果，这些反应是它们特定代谢问题的最佳解决方案，通过糖酵解和三羧酸循环等途径高效且以最少的步骤生产它们的最终产物。

Living organisms must obey the [[laws of thermodynamics]], which describe the transfer of heat and [[work (thermodynamics)|work]]. The [[second law of thermodynamics]] states that in any [[closed system]], the amount of [[entropy]] (disorder) cannot decrease. Although living organisms' amazing complexity appears to contradict this law, life is possible as all organisms are [[open system (systems theory)|open systems]] that exchange matter and energy with their surroundings. Thus living systems are not in [[Thermodynamic equilibrium|equilibrium]], but instead are [[dissipative system]]s that maintain their state of high complexity by causing a larger increase in the entropy of their environments.<ref>{{cite journal | vauthors = von Stockar U, Liu J | title = Does microbial life always feed on negative entropy? Thermodynamic analysis of microbial growth | journal = Biochimica et Biophysica Acta (BBA) - Bioenergetics | volume = 1412 | issue = 3 | pages = 191–211 | date = August 1999 | pmid = 10482783 | doi = 10.1016/S0005-2728(99)00065-1 }}</ref> The metabolism of a cell achieves this by coupling the [[spontaneous process]]es of catabolism to the non-spontaneous processes of anabolism. In [[non-equilibrium thermodynamics|thermodynamic]] terms, metabolism maintains order by creating disorder.<ref>{{cite journal | vauthors = Demirel Y, Sandler SI | title = Thermodynamics and bioenergetics | journal = Biophysical Chemistry | volume = 97 | issue = 2–3 | pages = 87–111 | date = June 2002 | pmid = 12050002 | doi = 10.1016/S0301-4622(02)00069-8 | url = https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1006&context=chemengthermalmech }}</ref>

Many models have been proposed to describe the mechanisms by which novel metabolic pathways evolve. These include the sequential addition of novel enzymes to a short ancestral pathway, the duplication and then divergence of entire pathways as well as the recruitment of pre-existing enzymes and their assembly into a novel reaction pathway. The relative importance of these mechanisms is unclear, but genomic studies have shown that enzymes in a pathway are likely to have a shared ancestry, suggesting that many pathways have evolved in a step-by-step fashion with novel functions created from pre-existing steps in the pathway. An alternative model comes from studies that trace the evolution of proteins' structures in metabolic networks, this has suggested that enzymes are pervasively recruited, borrowing enzymes to perform similar functions in different metabolic pathways (evident in the MANET database) These recruitment processes result in an evolutionary enzymatic mosaic. A third possibility is that some parts of metabolism might exist as "modules" that can be reused in different pathways and perform similar functions on different molecules.

许多模型被提出来描述新的代谢途径进化的机制。其中包括将新的酶连续添加到一个短的祖先途径，整个途径的复制和分化，以及将原有的酶补充并将其组装成一个新的反应途径。这些机制的相对重要性尚不清楚，但基因组学研究表明，一条途径中的酶可能有共同的祖先，这表明许多途径是一步一步地进化的，具有从该途径中已存在的步骤中创造出的新功能。一个替代模型来自于跟踪代谢网络中蛋白质结构进化的研究，这表明酶在不同的代谢途径中普遍被征用，借用酶来执行相似的功能(在 MANET 数据库中显而易见)这些征用过程导致了进化的酶马赛克。第三种可能性是，新陈代谢的某些部分可能作为“模块”存在，可以在不同的途径中重复使用，并对不同的分子执行类似的功能。

==Regulation and control==

{{further|Metabolic pathway|Metabolic control analysis|Hormone|Regulatory enzymes|Cell signaling}}

As well as the evolution of new metabolic pathways, evolution can also cause the loss of metabolic functions. For example, in some parasites metabolic processes that are not essential for survival are lost and preformed amino acids, nucleotides and carbohydrates may instead be scavenged from the host. Similar reduced metabolic capabilities are seen in endosymbiotic organisms.

除了新代谢途径的进化，进化也会导致代谢功能的丧失。例如，在一些寄生虫中，非生存所必需的新陈代谢过程会丢失，而预先形成的氨基酸、核苷酸和碳水化合物可能会从寄主身上清除掉。在内共生生物体中也可以看到类似的代谢能力下降。

As the environments of most organisms are constantly changing, the reactions of metabolism must be finely [[Control theory|regulated]] to maintain a constant set of conditions within cells, a condition called [[homeostasis]].<ref>{{cite journal | vauthors = Albert R | title = Scale-free networks in cell biology | journal = Journal of Cell Science | volume = 118 | issue = Pt 21 | pages = 4947–57 | date = November 2005 | pmid = 16254242 | doi = 10.1242/jcs.02714 | arxiv = q-bio/0510054 | s2cid = 3001195 | bibcode = 2005q.bio....10054A }}</ref><ref>{{cite journal | vauthors = Brand MD | title = Regulation analysis of energy metabolism | journal = The Journal of Experimental Biology | volume = 200 | issue = Pt 2 | pages = 193–202 | date = January 1997 | pmid = 9050227 | url = http://jeb.biologists.org/cgi/reprint/200/2/193 }}</ref> Metabolic regulation also allows organisms to respond to signals and interact actively with their environments.<ref>{{cite journal | vauthors = Soyer OS, Salathé M, Bonhoeffer S | title = Signal transduction networks: topology, response and biochemical processes | journal = Journal of Theoretical Biology | volume = 238 | issue = 2 | pages = 416–25 | date = January 2006 | pmid = 16045939 | doi = 10.1016/j.jtbi.2005.05.030 }}</ref> Two closely linked concepts are important for understanding how metabolic pathways are controlled. Firstly, the ''regulation'' of an enzyme in a pathway is how its activity is increased and decreased in response to signals. Secondly, the ''control'' exerted by this enzyme is the effect that these changes in its activity have on the overall rate of the pathway (the [[flux]] through the pathway).<ref name=Salter>{{cite journal | vauthors = Salter M, Knowles RG, Pogson CI | title = Metabolic control | journal = Essays in Biochemistry | volume = 28 | issue = | pages = 1–12 | year = 1994 | pmid = 7925313 }}</ref> For example, an enzyme may show large changes in activity (''i.e.'' it is highly regulated) but if these changes have little effect on the flux of a metabolic pathway, then this enzyme is not involved in the control of the pathway.<ref>{{cite journal | vauthors = Westerhoff HV, Groen AK, Wanders RJ | title = Modern theories of metabolic control and their applications (review) | journal = Bioscience Reports | volume = 4 | issue = 1 | pages = 1–22 | date = January 1984 | pmid = 6365197 | doi = 10.1007/BF01120819 | s2cid = 27791605 }}</ref>

[[File:Insulin glucose metabolism ZP.svg|thumb|right|upright=1.35|'''Effect of insulin on glucose uptake and metabolism.''' Insulin binds to its receptor (1), which in turn starts many protein activation cascades (2). These include: translocation of Glut-4 transporter to the [[plasma membrane]] and influx of glucose (3), [[glycogen]] synthesis (4), [[glycolysis]] (5) and [[fatty acid]] synthesis (6).]]

There are multiple levels of metabolic regulation. In intrinsic regulation, the metabolic pathway self-regulates to respond to changes in the levels of substrates or products; for example, a decrease in the amount of product can increase the [[flux]] through the pathway to compensate.<ref name=Salter/> This type of regulation often involves [[allosteric regulation]] of the activities of multiple enzymes in the pathway.<ref>{{cite journal | vauthors = Fell DA, Thomas S | title = Physiological control of metabolic flux: the requirement for multisite modulation | journal = The Biochemical Journal | volume = 311 ( Pt 1) | issue = Pt 1 | pages = 35–9 | date = October 1995 | pmid = 7575476 | pmc = 1136115 | doi = 10.1042/bj3110035 }}</ref> Extrinsic control involves a cell in a multicellular organism changing its metabolism in response to signals from other cells. These signals are usually in the form of water soluble messengers such as [[hormone]]s and [[growth factor]]s and are detected by specific [[receptor (biochemistry)|receptors]] on the cell surface.<ref>{{cite journal | vauthors = Hendrickson WA | title = Transduction of biochemical signals across cell membranes | journal = Quarterly Reviews of Biophysics | volume = 38 | issue = 4 | pages = 321–30 | date = November 2005 | pmid = 16600054 | doi = 10.1017/S0033583506004136 }}</ref> These signals are then transmitted inside the cell by [[second messenger system]]s that often involved the [[phosphorylation]] of proteins.<ref>{{cite journal | vauthors = Cohen P | title = The regulation of protein function by multisite phosphorylation--a 25 year update | journal = Trends in Biochemical Sciences | volume = 25 | issue = 12 | pages = 596–601 | date = December 2000 | pmid = 11116185 | doi = 10.1016/S0968-0004(00)01712-6 }}</ref>

[[Metabolic network of the Arabidopsis thaliana citric acid cycle. Enzymes and metabolites are shown as red squares and the interactions between them as black lines.]]

[代谢网络拟南芥三羧酸循环。酶和代谢物显示为红色方块，它们之间的相互作用显示为黑线。]

A very well understood example of extrinsic control is the regulation of glucose metabolism by the hormone [[insulin]].<ref>{{cite journal | vauthors = Lienhard GE, Slot JW, James DE, Mueckler MM | title = How cells absorb glucose | journal = Scientific American | volume = 266 | issue = 1 | pages = 86–91 | date = January 1992 | pmid = 1734513 | doi = 10.1038/scientificamerican0192-86 | bibcode = 1992SciAm.266a..86L }}</ref> Insulin is produced in response to rises in [[blood sugar|blood glucose levels]]. Binding of the hormone to [[insulin receptor]]s on cells then activates a cascade of [[protein kinase]]s that cause the cells to take up glucose and convert it into storage molecules such as fatty acids and [[glycogen]].<ref>{{cite journal | vauthors = Roach PJ | title = Glycogen and its metabolism | journal = Current Molecular Medicine | volume = 2 | issue = 2 | pages = 101–20 | date = March 2002 | pmid = 11949930 | doi = 10.2174/1566524024605761 }}</ref> The metabolism of glycogen is controlled by activity of [[phosphorylase]], the enzyme that breaks down glycogen, and [[glycogen synthase]], the enzyme that makes it. These enzymes are regulated in a reciprocal fashion, with phosphorylation inhibiting glycogen synthase, but activating phosphorylase. Insulin causes glycogen synthesis by activating [[phosphatase|protein phosphatases]] and producing a decrease in the phosphorylation of these enzymes.<ref>{{cite journal | vauthors = Newgard CB, Brady MJ, O'Doherty RM, Saltiel AR | title = Organizing glucose disposal: emerging roles of the glycogen targeting subunits of protein phosphatase-1 | journal = Diabetes | volume = 49 | issue = 12 | pages = 1967–77 | date = December 2000 | pmid = 11117996 | doi = 10.2337/diabetes.49.12.1967 | url = http://diabetes.diabetesjournals.org/cgi/reprint/49/12/1967.pdf }}</ref>

Classically, metabolism is studied by a reductionist approach that focuses on a single metabolic pathway. Particularly valuable is the use of radioactive tracers at the whole-organism, tissue and cellular levels, which define the paths from precursors to final products by identifying radioactively labelled intermediates and products. The enzymes that catalyze these chemical reactions can then be purified and their kinetics and responses to inhibitors investigated. A parallel approach is to identify the small molecules in a cell or tissue; the complete set of these molecules is called the metabolome. Overall, these studies give a good view of the structure and function of simple metabolic pathways, but are inadequate when applied to more complex systems such as the metabolism of a complete cell.

传统上，新陈代谢的研究是通过一个简化的方法，集中在一个单一的代谢途径。特别有价值的是在整个生物体、组织和细胞层面使用放射性示踪剂，通过确定放射性标记的中间体和产品，确定从前体到最终产品的路径。然后可以提纯催化这些化学反应的酶，并研究它们的动力学和对抑制剂的反应。一种类似的方法是鉴定细胞或组织中的小分子，这些小分子的完整组合被称为代谢组。总的来说，这些研究对简单代谢途径的结构和功能提供了一个很好的观点，但是当应用于更复杂的系统时，例如一个完整的细胞的代谢时，这些研究是不充分的。

==Evolution==

An idea of the complexity of the metabolic networks in cells that contain thousands of different enzymes is given by the figure showing the interactions between just 43 proteins and 40 metabolites to the right: the sequences of genomes provide lists containing anything up to 26.500 genes. However, it is now possible to use this genomic data to reconstruct complete networks of biochemical reactions and produce more holistic mathematical models that may explain and predict their behavior. These models are especially powerful when used to integrate the pathway and metabolite data obtained through classical methods with data on gene expression from proteomic and DNA microarray studies. Using these techniques, a model of human metabolism has now been produced, which will guide future drug discovery and biochemical research. These models are now used in network analysis, to classify human diseases into groups that share common proteins or metabolites.

右边的图显示了43种蛋白质和40种代谢物之间的相互作用: 基因组序列提供了包含26.500个基因的列表。然而，现在有可能利用这些基因组数据来重建完整的生化反应网络，并产生更全面的数学模型来解释和预测它们的行为。这些模型在整合通过经典方法获得的代谢途径和代谢产物数据与蛋白质组学和 DNA 微阵列研究的基因表达数据时尤其强大。利用这些技术，一个人类代谢的模型现在已经产生，这将指导未来的药物发现和生化研究。这些模型现在被用于网络分析，将人类疾病分为共享共同蛋白质或代谢物的组。

{{further|Molecular evolution|Phylogenetics}}

[[File:Tree of life int.svg|thumb|right|upright=1.8|[[Phylogenetic tree|Evolutionary tree]] showing the common ancestry of organisms from all three [[Domain (biology)|domains]] of life. [[Bacteria]] are colored blue, [[eukaryote]]s red, and [[archaea]] green. Relative positions of some of the [[phylum|phyla]] included are shown around the tree.]]

Bacterial metabolic networks are a striking example of bow-tie organization, an architecture able to input a wide range of nutrients and produce a large variety of products and complex macromolecules using a relatively few intermediate common currencies.

细菌代谢网络是蝴蝶结结构的一个突出例子，这种结构能够输入各种营养素，并使用相对较少的中间通用货币生产大量各种各样的产品和复杂的大分子。

The central pathways of metabolism described above, such as glycolysis and the citric acid cycle, are present in all [[Three-domain system|three domains]] of living things and were present in the [[last universal common ancestor]].<ref name=SmithE/><ref>{{cite journal | vauthors = Romano AH, Conway T | title = Evolution of carbohydrate metabolic pathways | journal = Research in Microbiology | volume = 147 | issue = 6–7 | pages = 448–55 | year = 1996 | pmid = 9084754 | doi = 10.1016/0923-2508(96)83998-2 }}</ref> This universal ancestral cell was [[prokaryote|prokaryotic]] and probably a [[methanogen]] that had extensive amino acid, nucleotide, carbohydrate and lipid metabolism.<ref>{{cite book |author=Koch A |title=How did bacteria come to be? |journal=Adv Microb Physiol |volume=40 |pages=353–99 |year=1998 |pmid=9889982 |doi=10.1016/S0065-2911(08)60135-6 |series=Advances in Microbial Physiology |isbn=978-0-12-027740-7}}</ref><ref>{{cite journal | vauthors = Ouzounis C, Kyrpides N | title = The emergence of major cellular processes in evolution | journal = FEBS Letters | volume = 390 | issue = 2 | pages = 119–23 | date = July 1996 | pmid = 8706840 | doi = 10.1016/0014-5793(96)00631-X | s2cid = 39128865 }}</ref> The retention of these ancient pathways during later [[evolution]] may be the result of these reactions having been an optimal solution to their particular metabolic problems, with pathways such as glycolysis and the citric acid cycle producing their end products highly efficiently and in a minimal number of steps.<ref name=Ebenhoh/><ref name=Cascante/> The first pathways of enzyme-based metabolism may have been parts of [[purine]] nucleotide metabolism, while previous metabolic pathways were a part of the ancient [[RNA world hypothesis|RNA world]].<ref>{{cite journal | vauthors = Caetano-Anollés G, Kim HS, Mittenthal JE | title = The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 22 | pages = 9358–63 | date = May 2007 | pmid = 17517598 | pmc = 1890499 | doi = 10.1073/pnas.0701214104 | bibcode = 2007PNAS..104.9358C }}</ref>

A major technological application of this information is metabolic engineering. Here, organisms such as yeast, plants or bacteria are genetically modified to make them more useful in biotechnology and aid the production of drugs such as antibiotics or industrial chemicals such as 1,3-propanediol and shikimic acid. These genetic modifications usually aim to reduce the amount of energy used to produce the product, increase yields and reduce the production of wastes.

这些信息的一个主要技术应用是代谢工程学。在这里，酵母、植物或细菌等生物体都经过基因改造，使它们在生物技术方面更有用处，并有助于生产抗生素等药物或工业化学品，例如1,3- 丙二醇和莽草酸。这些基因改造通常旨在减少用于生产产品的能量，增加产量和减少废物的产生。

Many models have been proposed to describe the mechanisms by which novel metabolic pathways evolve. These include the sequential addition of novel enzymes to a short ancestral pathway, the duplication and then divergence of entire pathways as well as the recruitment of pre-existing enzymes and their assembly into a novel reaction pathway.<ref>{{cite journal | vauthors = Schmidt S, Sunyaev S, Bork P, Dandekar T | title = Metabolites: a helping hand for pathway evolution? | journal = Trends in Biochemical Sciences | volume = 28 | issue = 6 | pages = 336–41 | date = June 2003 | pmid = 12826406 | doi = 10.1016/S0968-0004(03)00114-2 }}</ref> The relative importance of these mechanisms is unclear, but genomic studies have shown that enzymes in a pathway are likely to have a shared ancestry, suggesting that many pathways have evolved in a step-by-step fashion with novel functions created from pre-existing steps in the pathway.<ref>{{cite journal | vauthors = Light S, Kraulis P | title = Network analysis of metabolic enzyme evolution in Escherichia coli | journal = BMC Bioinformatics | volume = 5 | pages = 15 | date = February 2004 | pmid = 15113413 | pmc = 394313 | doi = 10.1186/1471-2105-5-15 }} {{cite journal | vauthors = Alves R, Chaleil RA, Sternberg MJ | title = Evolution of enzymes in metabolism: a network perspective | journal = Journal of Molecular Biology | volume = 320 | issue = 4 | pages = 751–70 | date = July 2002 | pmid = 12095253 | doi = 10.1016/S0022-2836(02)00546-6 }}</ref> An alternative model comes from studies that trace the evolution of proteins' structures in metabolic networks, this has suggested that enzymes are pervasively recruited, borrowing enzymes to perform similar functions in different metabolic pathways (evident in the [[MANET database]])<ref>{{cite journal | vauthors = Kim HS, Mittenthal JE, Caetano-Anollés G | title = MANET: tracing evolution of protein architecture in metabolic networks | journal = BMC Bioinformatics | volume = 7 | pages = 351 | date = July 2006 | pmid = 16854231 | pmc = 1559654 | doi = 10.1186/1471-2105-7-351 }}</ref> These recruitment processes result in an evolutionary enzymatic mosaic.<ref>{{cite journal | vauthors = Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C | title = Small-molecule metabolism: an enzyme mosaic | journal = Trends in Biotechnology | volume = 19 | issue = 12 | pages = 482–6 | date = December 2001 | pmid = 11711174 | doi = 10.1016/S0167-7799(01)01813-3 }}</ref> A third possibility is that some parts of metabolism might exist as "modules" that can be reused in different pathways and perform similar functions on different molecules.<ref>{{cite journal | vauthors = Spirin V, Gelfand MS, Mironov AA, Mirny LA | title = A metabolic network in the evolutionary context: multiscale structure and modularity | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 23 | pages = 8774–9 | date = June 2006 | pmid = 16731630 | pmc = 1482654 | doi = 10.1073/pnas.0510258103 | bibcode = 2006PNAS..103.8774S }}</ref>

As well as the evolution of new metabolic pathways, evolution can also cause the loss of metabolic functions. For example, in some [[parasite]]s metabolic processes that are not essential for survival are lost and preformed amino acids, nucleotides and carbohydrates may instead be scavenged from the [[host (biology)|host]].<ref>{{cite journal | vauthors = Lawrence JG | title = Common themes in the genome strategies of pathogens | journal = Current Opinion in Genetics & Development | volume = 15 | issue = 6 | pages = 584–8 | date = December 2005 | pmid = 16188434 | doi = 10.1016/j.gde.2005.09.007 }} {{cite journal | vauthors = Wernegreen JJ | title = For better or worse: genomic consequences of intracellular mutualism and parasitism | journal = Current Opinion in Genetics & Development | volume = 15 | issue = 6 | pages = 572–83 | date = December 2005 | pmid = 16230003 | doi = 10.1016/j.gde.2005.09.013 }}</ref> Similar reduced metabolic capabilities are seen in [[endosymbiont|endosymbiotic]] organisms.<ref>{{cite journal | vauthors = Pál C, Papp B, Lercher MJ, Csermely P, Oliver SG, Hurst LD | title = Chance and necessity in the evolution of minimal metabolic networks | journal = Nature | volume = 440 | issue = 7084 | pages = 667–70 | date = March 2006 | pmid = 16572170 | doi = 10.1038/nature04568 | s2cid = 4424895 | bibcode = 2006Natur.440..667P }}</ref>

==Investigation and manipulation==

The term metabolism is derived from French "métabolisme" or Ancient Greek μεταβολή – "Metabole" for "a change" which derived from μεταβάλλ –"Metaballein" means "To change"

新陈代谢一词源于法语“ métabolisme”或古希腊语 μταβoλλ something-“ Metaballein” ，意为“改变”

{{further|Protein methods|Proteomics|Metabolomics|Metabolic network modelling}}

[[File:A thaliana metabolic network.png|thumb|upright=1.35|right|[[Metabolic network]] of the ''[[Arabidopsis thaliana]]'' [[citric acid cycle]]. [[Enzyme]]s and [[metabolite]]s are shown as red squares and the interactions between them as black lines.]]

Aristotle's metabolism as an open flow model]]

亚里士多德的新陈代谢作为一个开放流动模型]]

Classically, metabolism is studied by a [[reductionism|reductionist]] approach that focuses on a single metabolic pathway. Particularly valuable is the use of [[radioactive tracer]]s at the whole-organism, tissue and cellular levels, which define the paths from precursors to final products by identifying radioactively labelled intermediates and products.<ref>{{cite journal | vauthors = Rennie MJ | title = An introduction to the use of tracers in nutrition and metabolism | journal = The Proceedings of the Nutrition Society | volume = 58 | issue = 4 | pages = 935–44 | date = November 1999 | pmid = 10817161 | doi = 10.1017/S002966519900124X | doi-access = free }}</ref> The enzymes that catalyze these chemical reactions can then be [[protein purification|purified]] and their [[enzyme kinetics|kinetics]] and responses to [[enzyme inhibitor|inhibitors]] investigated. A parallel approach is to identify the small molecules in a cell or tissue; the complete set of these molecules is called the [[metabolome]]. Overall, these studies give a good view of the structure and function of simple metabolic pathways, but are inadequate when applied to more complex systems such as the metabolism of a complete cell.<ref>{{cite journal | vauthors = Phair RD | title = Development of kinetic models in the nonlinear world of molecular cell biology | journal = Metabolism | volume = 46 | issue = 12 | pages = 1489–95 | date = December 1997 | pmid = 9439549 | doi = 10.1016/S0026-0495(97)90154-2 }}</ref>

Aristotle's The Parts of Animals sets out enough details of his views on metabolism for an open flow model to be made. He believed that at each stage of the process, materials from food were transformed, with heat being released as the classical element of fire, and residual materials being excreted as urine, bile, or faeces.

亚里士多德的《动物的各部分》详细阐述了他关于新陈代谢的观点，以便建立一个开放流模型。他认为，在这个过程的每个阶段，来自食物的物质都发生了转化，释放出的热量成为火的典型元素，残余物质以尿液、胆汁或粪便的形式排出体外。

An idea of the complexity of the [[metabolic network]]s in cells that contain thousands of different enzymes is given by the figure showing the interactions between just 43 proteins and 40 metabolites to the right: the sequences of genomes provide lists containing anything up to 26.500 genes.<ref>{{cite journal | vauthors = Sterck L, Rombauts S, Vandepoele K, Rouzé P, Van de Peer Y | title = How many genes are there in plants (... and why are they there)? | journal = Current Opinion in Plant Biology | volume = 10 | issue = 2 | pages = 199–203 | date = April 2007 | pmid = 17289424 | doi = 10.1016/j.pbi.2007.01.004 }}</ref> However, it is now possible to use this genomic data to reconstruct complete networks of biochemical reactions and produce more [[Holism|holistic]] mathematical models that may explain and predict their behavior.<ref>{{cite journal | vauthors = Borodina I, Nielsen J | title = From genomes to in silico cells via metabolic networks | journal = Current Opinion in Biotechnology | volume = 16 | issue = 3 | pages = 350–5 | date = June 2005 | pmid = 15961036 | doi = 10.1016/j.copbio.2005.04.008 }}</ref> These models are especially powerful when used to integrate the pathway and metabolite data obtained through classical methods with data on [[gene expression]] from [[proteomics|proteomic]] and [[DNA microarray]] studies.<ref>{{cite journal | vauthors = Gianchandani EP, Brautigan DL, Papin JA | title = Systems analyses characterize integrated functions of biochemical networks | journal = Trends in Biochemical Sciences | volume = 31 | issue = 5 | pages = 284–91 | date = May 2006 | pmid = 16616498 | doi = 10.1016/j.tibs.2006.03.007 }}</ref> Using these techniques, a model of human metabolism has now been produced, which will guide future drug discovery and biochemical research.<ref>{{cite journal | vauthors = Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BØ | display-authors = 6 | title = Global reconstruction of the human metabolic network based on genomic and bibliomic data | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 6 | pages = 1777–82 | date = February 2007 | pmid = 17267599 | pmc = 1794290 | doi = 10.1073/pnas.0610772104 | bibcode = 2007PNAS..104.1777D }}</ref> These models are now used in [[Network theory|network analysis]], to classify human diseases into groups that share common proteins or metabolites.<ref>{{cite journal | vauthors = Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabási AL | title = The human disease network | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 21 | pages = 8685–90 | date = May 2007 | pmid = 17502601 | pmc = 1885563 | doi = 10.1073/pnas.0701361104 | bibcode = 2007PNAS..104.8685G }}</ref><ref>{{cite journal | vauthors = Lee DS, Park J, Kay KA, Christakis NA, Oltvai ZN, Barabási AL | title = The implications of human metabolic network topology for disease comorbidity | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 29 | pages = 9880–5 | date = July 2008 | pmid = 18599447 | pmc = 2481357 | doi = 10.1073/pnas.0802208105 | url = http://www.pnas.org/lookup/pmid?view=long&pmid=18599447 | bibcode = 2008PNAS..105.9880L }}</ref>

Bacterial metabolic networks are a striking example of [[Bow tie (biology)|bow-tie]]<ref name="pmid15331224">{{cite journal | vauthors = Csete M, Doyle J | title = Bow ties, metabolism and disease | journal = Trends in Biotechnology | volume = 22 | issue = 9 | pages = 446–50 | date = September 2004 | pmid = 15331224 | pmc = | doi = 10.1016/j.tibtech.2004.07.007 }}</ref><ref name="PMID12874056">{{cite journal | vauthors = Ma HW, Zeng AP | title = The connectivity structure, giant strong component and centrality of metabolic networks | journal = Bioinformatics | volume = 19 | issue = 11 | pages = 1423–30 | date = July 2003 | pmid = 12874056 | doi = 10.1093/bioinformatics/btg177 | citeseerx = 10.1.1.605.8964 }}</ref><ref name="PMID16916470">{{cite journal | vauthors = Zhao J, Yu H, Luo JH, Cao ZW, Li YX | title = Hierarchical modularity of nested bow-ties in metabolic networks | journal = BMC Bioinformatics | volume = 7 | pages = 386 | date = August 2006 | pmid = 16916470 | pmc = 1560398 | doi = 10.1186/1471-2105-7-386 | arxiv = q-bio/0605003 | bibcode = 2006q.bio.....5003Z }}</ref> organization, an architecture able to input a wide range of nutrients and produce a large variety of products and complex macromolecules using a relatively few intermediate common currencies.

Ibn al-Nafis described metabolism in his 1260 AD work titled Al-Risalah al-Kamiliyyah fil Siera al-Nabawiyyah (The Treatise of Kamil on the Prophet's Biography) which included the following phrase "Both the body and its parts are in a continuous state of dissolution and nourishment, so they are inevitably undergoing permanent change."

Ibn al-Nafis 在其公元1260年的著作《 Al-Risalah al-Kamiliyyah fil Siera al-Nabawiyyah 》(《卡米尔关于先知传记的论述》)中描述了新陈代谢，其中包括以下短语: ”身体及其部分处于持续的溶解和营养状态，因此它们不可避免地发生永久性变化

A major technological application of this information is [[metabolic engineering]]. Here, organisms such as [[yeast]], plants or [[bacteria]] are genetically modified to make them more useful in [[biotechnology]] and aid the production of [[drug]]s such as [[antibiotic]]s or industrial chemicals such as [[1,3-Propanediol|1,3-propanediol]] and [[shikimic acid]].<ref>{{cite journal | vauthors = Thykaer J, Nielsen J | title = Metabolic engineering of beta-lactam production | journal = Metabolic Engineering | volume = 5 | issue = 1 | pages = 56–69 | date = January 2003 | pmid = 12749845 | doi = 10.1016/S1096-7176(03)00003-X }}

{{cite journal | vauthors = González-Pajuelo M, Meynial-Salles I, Mendes F, Andrade JC, Vasconcelos I, Soucaille P | title = Metabolic engineering of Clostridium acetobutylicum for the industrial production of 1,3-propanediol from glycerol | journal = Metabolic Engineering | volume = 7 | issue = 5–6 | pages = 329–36 | year = 2005 | pmid = 16095939 | doi = 10.1016/j.ymben.2005.06.001 | hdl-access = free | hdl = 10400.14/3388 }}

The history of the scientific study of metabolism spans several centuries and has moved from examining whole animals in early studies, to examining individual metabolic reactions in modern biochemistry. The first controlled experiments in human metabolism were published by Santorio Santorio in 1614 in his book Ars de statica medicina. He described how he weighed himself before and after eating, sleep, working, sex, fasting, drinking, and excreting. He found that most of the food he took in was lost through what he called "insensible perspiration".

新陈代谢科学研究的历史跨越了几个世纪，已经从早期研究中检测整个动物，到现代生物化学中检测个体的新陈代谢反应。桑托里奥 · 桑托里奥于1614年在他的《医学研究》一书中发表了第一个关于人体代谢的对照实验。他描述了自己在吃饭、睡觉、工作、性生活、禁食、饮酒和排泄前后的称重情况。他发现，他吃进去的大部分食物都是通过他所谓的“不知觉的汗水”而流失的。

{{cite journal | vauthors = Krämer M, Bongaerts J, Bovenberg R, Kremer S, Müller U, Orf S, Wubbolts M, Raeven L | display-authors = 6 | title = Metabolic engineering for microbial production of shikimic acid | journal = Metabolic Engineering | volume = 5 | issue = 4 | pages = 277–83 | date = October 2003 | pmid = 14642355 | doi = 10.1016/j.ymben.2003.09.001 }}</ref> These genetic modifications usually aim to reduce the amount of energy used to produce the product, increase yields and reduce the production of wastes.<ref>{{cite journal | vauthors = Koffas M, Roberge C, Lee K, Stephanopoulos G | title = Metabolic engineering | journal = Annual Review of Biomedical Engineering | volume = 1 | issue = | pages = 535–57 | year = 1999 | pmid = 11701499 | doi = 10.1146/annurev.bioeng.1.1.535 | s2cid = 11814282 }}</ref>

[[Santorio Santorio in his steelyard balance, from Ars de statica medicina, first published 1614]]

[ Santorio Santorio 在他的《秤，来自 Ars de statica medicina，首次发表于1614年]

==History==

{{further|History of biochemistry|History of molecular biology}}

In these early studies, the mechanisms of these metabolic processes had not been identified and a vital force was thought to animate living tissue. In the 19th century, when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur concluded that fermentation was catalyzed by substances within the yeast cells he called "ferments". He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells." This discovery, along with the publication by Friedrich Wöhler in 1828 of a paper on the chemical synthesis of urea, and is notable for being the first organic compound prepared from wholly inorganic precursors. This proved that the organic compounds and chemical reactions found in cells were no different in principle than any other part of chemistry.

在这些早期的研究中，这些新陈代谢过程的机制还没有被确定，并且一种生命的力量被认为可以激活活的组织。在19世纪，当研究酵母将糖发酵成酒精时，路易斯 · 巴斯德得出结论，发酵是由他称之为“发酵”的酵母细胞内的物质催化的。他写道: “酒精发酵是一种与酵母细胞的生命和组织相关的行为，而不是与细胞的死亡或腐败相关。”这一发现，以及弗里德里希·维勒1828年发表的一篇关于尿素化学合成的论文，值得注意的是，它是第一个由全部无机前体制备的有机化合物。这证明了在细胞中发现的有机化合物和化学反应在原理上与化学的其他部分没有什么不同。

The term ''metabolism'' is derived from [[French language|French]] "métabolisme" or [[Ancient Greek]] μεταβολή – "Metabole" for "a change" which derived from μεταβάλλ –"Metaballein" means "To change"<ref>{{Cite web|title=metabolism {{!}} Origin and meaning of metabolism by Online Etymology Dictionary|url=https://www.etymonline.com/word/metabolism|access-date=2020-07-23|website=www.etymonline.com|language=en}}</ref>

It was the discovery of enzymes at the beginning of the 20th century by Eduard Buchner that separated the study of the chemical reactions of metabolism from the biological study of cells, and marked the beginnings of biochemistry. The mass of biochemical knowledge grew rapidly throughout the early 20th century. One of the most prolific of these modern biochemists was Hans Krebs who made huge contributions to the study of metabolism. He discovered the urea cycle and later, working with Hans Kornberg, the citric acid cycle and the glyoxylate cycle. Modern biochemical research has been greatly aided by the development of new techniques such as chromatography, X-ray diffraction, NMR spectroscopy, radioisotopic labelling, electron microscopy and molecular dynamics simulations. These techniques have allowed the discovery and detailed analysis of the many molecules and metabolic pathways in cells.

20世纪初，Eduard Buchner 发现了酶，从而将新陈代谢的化学反应研究与细胞的生物学研究分离开来，标志着生物化学的开始。整个20世纪早期，大量的生物化学知识迅速增长。汉斯 · 克雷布斯是这些现代生物化学家中最多产的一位，他对新陈代谢的研究做出了巨大的贡献。他发现了尿素循环，后来又与 Hans Kornberg、三羧酸循环和乙醛酸循环合作。现代生物化学研究得到了色谱、 x 射线衍射、核磁共振波谱法、放射性同位素标记、电子显微镜和分子动力学模拟等新技术的大力支持。这些技术使人们能够发现和详细分析细胞中的许多分子和代谢途径。

[[File:Aristotle's metabolism.png|thumb|right|upright=1.4|[[Aristotle's biology|Aristotle's metabolism]] as an open flow model]]

===Greek philosophy===

[[Aristotle]]'s ''[[The Parts of Animals]]'' sets out enough details of [[Aristotle's biology|his views on metabolism]] for an open flow model to be made. He believed that at each stage of the process, materials from food were transformed, with heat being released as the [[classical element]] of fire, and residual materials being excreted as urine, bile, or faeces.<ref>{{cite book|author=Leroi, Armand Marie|url=https://archive.org/stream/lagoonhowaristot0000lero?ref=ol#page/402/mode/2up|title=The Lagoon: How Aristotle Invented Science|date=2014|publisher=Bloomsbury|isbn=978-1-4088-3622-4|location=|pages=400–401|authorlink=Armand Marie Leroi}}</ref>

===Islamic medicine===

[[Ibn al-Nafis]] described metabolism in his 1260 AD work titled [[Al-Risalah al-Kamiliyyah fil Siera al-Nabawiyyah]] (The Treatise of Kamil on the Prophet's Biography) which included the following phrase "Both the body and its parts are in a continuous state of dissolution and nourishment, so they are inevitably undergoing permanent change."<ref>{{cite conference | vauthors = Al-Roubi AS | date = 1982 | title = Ibn Al-Nafis as a philosopher | conference = Symposium on Ibn al-Nafis, Second International Conference on Islamic Medicine | publisher = Islamic Medical Organization | location = Kuwait }} (cf. Ibn al-Nafis As a Philosopher, Encyclopedia of Islamic World [1])</ref>

===Application of the scientific method===

The history of the scientific study of metabolism spans several centuries and has moved from examining whole animals in early studies, to examining individual metabolic reactions in modern biochemistry. The first controlled [[experiment]]s in human metabolism were published by [[Santorio Santorio]] in 1614 in his book ''Ars de statica medicina''.<ref>{{cite journal | vauthors = Eknoyan G | title = Santorio Sanctorius (1561-1636) - founding father of metabolic balance studies | journal = American Journal of Nephrology | volume = 19 | issue = 2 | pages = 226–33 | year = 1999 | pmid = 10213823 | doi = 10.1159/000013455 | s2cid = 32900603 }}</ref> He described how he weighed himself before and after eating, [[sleeping|sleep]], working, sex, fasting, drinking, and excreting. He found that most of the food he took in was lost through what he called "[[insensible perspiration]]".

[[File:SantoriosMeal.jpg|thumb|right|upright=0.7|[[Santorio Santorio]] in his steelyard balance, from ''Ars de statica medicina'', first published 1614]]

In these early studies, the mechanisms of these metabolic processes had not been identified and a [[vitalism|vital force]] was thought to animate living tissue.<ref>{{cite book|url=https://archive.org/details/historyofscience04willuoft/page/n7/mode/2up|title=Modern Development of the Chemical and Biological Sciences|vauthors=Williams HA|date=1904|publisher=Harper and Brothers|isbn=|series=A History of Science: in Five Volumes|volume=IV|location=New York|pages=184–185|access-date=26 March 2007}}</ref> In the 19th century, when studying the [[fermentation (food)|fermentation]] of sugar to [[ethanol|alcohol]] by [[yeast]], [[Louis Pasteur]] concluded that fermentation was catalyzed by substances within the yeast cells he called "ferments". He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells."<ref>{{cite journal | vauthors = Manchester KL | title = Louis Pasteur (1822-1895)--chance and the prepared mind | journal = Trends in Biotechnology | volume = 13 | issue = 12 | pages = 511–5 | date = December 1995 | pmid = 8595136 | doi = 10.1016/S0167-7799(00)89014-9 }}</ref> This discovery, along with the publication by [[Friedrich Woehler|Friedrich Wöhler]] in 1828 of a paper on the chemical synthesis of [[urea]],<ref>{{cite journal | vauthors = Kinne-Saffran E, Kinne RK | title = Vitalism and synthesis of urea. From Friedrich Wöhler to Hans A. Krebs | journal = American Journal of Nephrology | volume = 19 | issue = 2 | pages = 290–4 | year = 1999 | pmid = 10213830 | doi = 10.1159/000013463 | s2cid = 71727190 }}</ref> and is notable for being the first organic compound prepared from wholly inorganic precursors. This proved that the organic compounds and chemical reactions found in cells were no different in principle than any other part of chemistry.

It was the discovery of [[enzyme]]s at the beginning of the 20th century by [[Eduard Buchner]] that separated the study of the chemical reactions of metabolism from the biological study of cells, and marked the beginnings of [[biochemistry]].<ref>Eduard Buchner's 1907 [http://nobelprize.org/nobel_prizes/chemistry/laureates/1907/buchner-lecture.html Nobel lecture] at http://nobelprize.org Accessed 20 March 2007</ref> The mass of biochemical knowledge grew rapidly throughout the early 20th century. One of the most prolific of these modern biochemists was [[Hans Adolf Krebs|Hans Krebs]] who made huge contributions to the study of metabolism.<ref>{{cite journal | vauthors = Kornberg H | title = Krebs and his trinity of cycles | journal = Nature Reviews. Molecular Cell Biology | volume = 1 | issue = 3 | pages = 225–8 | date = December 2000 | pmid = 11252898 | doi = 10.1038/35043073 | s2cid = 28092593 }}</ref> He discovered the urea cycle and later, working with [[Hans Kornberg]], the citric acid cycle and the glyoxylate cycle.<ref>{{cite journal |vauthors=Krebs HA, Henseleit K |title=Untersuchungen über die Harnstoffbildung im tierkorper |journal=Z. Physiol. Chem. |volume=210 |issue=1–2 |pages=33–66 |year=1932 |doi=10.1515/bchm2.1932.210.1-2.33}} 

{{cite journal | vauthors = Krebs HA, Johnson WA | title = Metabolism of ketonic acids in animal tissues | journal = The Biochemical Journal | volume = 31 | issue = 4 | pages = 645–60 | date = April 1937 | pmid = 16746382 | pmc = 1266984 | doi = 10.1042/bj0310645 }}</ref><ref name=Kornberg/> Modern biochemical research has been greatly aided by the development of new techniques such as [[chromatography]], [[X-ray diffraction]], [[NMR spectroscopy]], [[radioisotopic labelling]], [[electron microscope|electron microscopy]] and [[molecular dynamics]] simulations. These techniques have allowed the discovery and detailed analysis of the many molecules and metabolic pathways in cells.

== See also ==

{{Portal|Metabolism}}

* {{anli|Anthropogenic metabolism}}

* {{anli|Antimetabolite}}

* {{anli|Basal metabolic rate}}

* {{anli|Calorimetry}}

* {{anli|Isothermal microcalorimetry}}

* {{anli|Inborn errors of metabolism}}

* {{anli|Iron–sulfur world hypothesis}}, a "metabolism first" theory of the [[origin of life]]

{{Library resources box

{图书馆资源框

* {{anli|Metabolic disorder}}

|onlinebooks=yes

是的

* [[Microphysiometry]]

|by=no

不会

* {{anli|Primary nutritional groups}}

|lcheading=Metabolism

| lcheading = 代谢

* {{annotated link|Respirometry}}

|label=Metabolism

| label = Metabolism

* {{anli|Stream metabolism}}

}}

}}

* {{anli|Sulfur metabolism}}

Introductory

开场白

* {{anli|Specific dynamic action|Thermic effect of food}}

* {{anli|Urban metabolism}}

* {{anli|Fluid balance|Water metabolism}}

* {{anli|Overflow metabolism}}

* {{anli|Reactome}}

* {{anli|KEGG}}

Advanced

高级

== References ==

{{Reflist|30em}}

== Further reading ==

{{Library resources box

|onlinebooks=yes

|by=no

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|label=Metabolism

}}

'''Introductory'''

{{refbegin}}

* {{cite book | vauthors = Rose S, Mileusnic R | title = The Chemistry of Life. | publisher = Penguin Press Science | date = 1999 | isbn = 0-14-027273-9 }}

* {{cite book | vauthors = Schneider EC, Sagan D | title = Into the Cool: Energy Flow, Thermodynamics, and Life. | publisher = University of Chicago Press | date = 2005 | isbn = 0-226-73936-8}}

* {{cite book | vauthors = Lane N | title = Oxygen: The Molecule that Made the World. | publisher = Oxford University Press | location= USA | date = 2004 | isbn = 0-19-860783-0 }}

{{refend}}

General information

一般资料

'''Advanced'''

{{refbegin}}

* {{cite book | vauthors = Price N, Stevens L | title = Fundamentals of Enzymology: Cell and Molecular Biology of Catalytic Proteins. | publisher = Oxford University Press | date = 1999 | isbn = 0-19-850229-X }}

* {{cite book | vauthors = Berg J, Tymoczko J, Stryer L | title = Biochemistry | publisher = W. H. Freeman and Company | date = 2002 | isbn = 0-7167-4955-6 }}

* {{cite book | vauthors = Cox M, Nelson DL | title = Lehninger Principles of Biochemistry. | publisher = Palgrave Macmillan | date = 2004 | isbn = 0-7167-4339-6 }}

Human metabolism

人体新陈代谢

* {{cite book | author-link1 = Thomas D. Brock | vauthors = Brock TD, Madigan MR, Martinko J, Parker J | title = Brock's Biology of Microorganisms. | publisher = Benjamin Cummings | date = 2002 | isbn = 0-13-066271-2 }}

* {{cite book | vauthors = Da Silva JJ, Williams RJ | title = The Biological Chemistry of the Elements: The Inorganic Chemistry of Life. | publisher = Clarendon Press | date = 1991 | isbn = 0-19-855598-9 }}

* {{cite book | vauthors = Nicholls DG, Ferguson SJ | title = Bioenergetics | publisher = Academic Press Inc. | date = 2002 | isbn = 0-12-518121-3 }}

* {{cite journal | vauthors = Wood HG | title = Life with CO or CO2 and H2 as a source of carbon and energy | journal = FASEB Journal | volume = 5 | issue = 2 | pages = 156–63 | date = February 1991 | pmid = 1900793 | doi = 10.1096/fasebj.5.2.1900793 | s2cid = 45967404 }}

Databases

数据库

{{refend}}

== External links ==

{{Wikiversity|Topic:Biochemistry}}

{{wikibooks}}

Metabolic pathways

代谢途径

{{Wiktionary}}

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'''General information'''

* {{Britannica|377325|Metabolism (biology)}}

* [https://web.archive.org/web/20050308172226/http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/MB1index.html The Biochemistry of Metabolism]

* [http://www.sparknotes.com/testprep/books/sat2/biology/ Sparknotes SAT biochemistry] Overview of biochemistry. School level.

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'''Human metabolism'''

* [http://library.med.utah.edu/NetBiochem/titles.htm Topics in Medical Biochemistry] Guide to human metabolic pathways. School level.

* [http://themedicalbiochemistrypage.org/ THE Medical Biochemistry Page] Comprehensive resource on human metabolism.

'''Databases'''

* [http://www.expasy.org/cgi-bin/show_thumbnails.pl Flow Chart of Metabolic Pathways] at [[ExPASy]]

* [http://www.iubmb-nicholson.org/pdf/MetabolicPathways_6_17_04_.pdf IUBMB-Nicholson Metabolic Pathways Chart]

* [http://bioinformatics.charite.de/supercyp/ SuperCYP: Database for Drug-Cytochrome-Metabolism]

'''Metabolic pathways'''

* [http://www.genome.ad.jp/kegg/pathway/map/map01100.html Metabolism reference Pathway]

* {{webarchive |url=https://web.archive.org/web/*/helios.bto.ed.ac.uk/bto/microbes/nitrogen.htm |date=* |title=The Nitrogen cycle and Nitrogen fixation }}

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