metabolism

代謝 　 　

WordNet

1. the organic processes (in a cell or organism) that are necessary for life (同)metabolic_process
2. breakdown in living organisms of more complex substances into simpler ones together with release of energy (同)katabolism, dissimilation, destructive metabolism
3. produce by metabolism (同)metabolise

PrepTutorEJDIC

1. 新陳代謝,物質交代
2. (動植物の)異化作用

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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2015/07/14 14:55:38」(JST)

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エネルギー代謝の中心的中間体である補酵素、アデノシン三リン酸の空間充填モデル。

代謝（たいしゃ、metabolism）とは、生命の維持のために有機体が行う、外界から取り入れた無機物や有機化合物を素材として行う一連の合成や化学反応のことであり、新陳代謝の略称である。これらの経路によって有機体はその成長と生殖を可能にし、その体系を維持している。代謝は大きく異化 (catabolism) と同化 (anabolism) の2つに区分される。異化は高分子など有機物質を分解し低分子化することによってエネルギーを得る過程であり、例えば細胞呼吸がある。同化はこの逆で、エネルギーを使って有機物質を合成する過程であり、例えばタンパク質・核酸・多糖・脂質の合成がある。

代謝の化学反応は代謝経路によって体系づけられ、1つの化学物質は他の化学物質から酵素によって変換される。酵素は触媒として、熱力学的に不利な反応を有利に進めるため極めて重要な存在である。また、酵素は、細胞の環境もしくは他の細胞からの信号（シグナル伝達）の変化に反応することにより代謝経路の調節も行う。

有機体の代謝はその物質の栄養価の高さがどれだけか、また、毒性の高さがどれだけかを決定する。例えば、いくつかの原核生物は硫化水素を使って栄養を得ているが、この気体は動物にとっては毒であることが知られている。また、代謝速度はその有機体がどれだけの食物を必要としているかに影響を与える。

目的

代謝の目的は、以下の4つが挙げられる。

1. エネルギーを獲得する
2. 摂取した栄養素を、生体を構成するための前駆体へ転換する
3. 前駆体から生体の成分を合成する
4. 細胞が使う生理活性物質を合成または分解する

物質とエネルギーの代謝

代謝と言う用語は、主に物質代謝をさして使用される場合が多いが、物質代謝そのものはエネルギーの代謝によって起きている。またエネルギー代謝も物質の交代によって起きているので、相互に共役していると考える。したがって、物質代謝およびエネルギー代謝を包括して指す言葉として本記事の『代謝』の正確な定義となる。

物質およびエネルギー代謝などの簡単な定義および位置づけは以下の通りである。

• 物質代謝：物質の変換
  • 異化：外部基質の分解反応
  • 同化：生体高分子の合成反応
• エネルギー代謝：生体活動に関わるエネルギーの出入りや変換および利用
  • 化学エネルギー：化学エネルギーが基本となり以下のエネルギー、あるいは物質代謝に利用される
    • 力学エネルギー：筋肉、鞭毛、繊毛、細胞分裂など
    • 電気エネルギー：発電器官、神経伝達
    • 光エネルギー：発光

なお、代謝反応のほとんど全ては各々の反応を担当する酵素あるいはタンパク質による。代謝マップにてその基質および生産物のみが描かれているが、その反応自体は酵素が担当している。代謝系において特定の物質ないしエネルギーの偏りが出来ないように基質、酵素化学、発現レベルにおける調節が見られ、その調節機構は非常に多様で厳密である。

物質代謝

物質代謝とは、細胞内における物質の変換を意味する。別名、物質交代など。上記にもあるようにエネルギー代謝との関連により両者を分けて考えるのは困難だが、物質の変換に注目してみた場合の『代謝』が物質代謝である。物質代謝は異化および同化に分けられる。

異化と同化反応は関連している。例えば異化反応である解糖系の逆行は糖新生経路（糖の合成）であり、酸化的クエン酸回路（異化）の逆行である還元的クエン酸回路では炭酸固定（同化）が行われる。また、カルビン - ベンソン回路（同化）は解糖系の一種であるペントースリン酸経路（異化）が還元的に働いたものである。

しかしながら、この両者は反応の方向性とATPあるいは還元型ピリジンヌクレオチド (NADH or NADPH) が生成されるか否かに注目すると容易に区別がつく（ATPおよび還元型ピリジンヌクレオチドの生成を行うのが異化、異化により生成したエネルギーを用いて生体高分子の合成を行うのが同化）。

異化

タンパク質(Proteins)、炭水化物（polysaccharides）、脂質（fats）の異化の概略。

異化（異化作用）とは外部から取り入れた高分子量の有機物あるいは無機物を水やアンモニアなどの単純な低分子まで分解し、その過程でエネルギーを得てATPを合成する代謝である。現生する生物は地球上に存在するほとんどの有機化合物を代謝できると言われているが、異化代謝系が各々に存在しているわけではなく、代表的なATP生成機構に最終的には集約されていく。それらの機構とは発酵、呼吸、光合成の3つである。光合成はカルビン - ベンソン回路が含まれる場合は同化反応となりうるが、光化学反応においては、NADPHおよびATPが生産されるために異化反応に分類される。またATP合成を主たる目的とした循環的光リン酸化はより異化反応的側面が強い。

発酵

発酵は、基質レベルのリン酸化によるATP生成を行うが、電子伝達系を通らずエネルギー効率としてはきわめて低い。しかしながら機構の単純さや酸素が要らないなどの理由から多くの微生物にてよく見られる。なお無酸素運動における筋肉でも解糖系が乳酸発酵へと転じている（筋肉痛）。

電子供与体および電子受容体はともに有機物であり、電子供与体となる還元物質には通常、糖が使用される。しかしながら微生物はある種の有機酸（酢酸、乳酸など）、アミノ酸、ヌクレオチドなどを基質に発酵する能力を有する。

基質レベルのリン酸化によるATP生成の式は以下の通りである。

• グルコース + ADP + P_i + NAD⁺　→　ピルビン酸 + ATP + NADH

しかしながら、生じた還元型ピリジンヌクレオチド (NADH) は生物にとっては有害なピルビン酸の異化反応に使用される（以下乳酸発酵の例）。

• ピルビン酸 + NADH　→　乳酸 + NAD⁺

微生物の行う発酵の電子受容体（産物）としては、乳酸、エタノールをはじめブタノール、酪酸、イソプロパノール、酢酸、プロピオン酸、ギ酸、アセトンなどがある。

詳しくは発酵を参照。

呼吸

呼吸は基質レベルのリン酸化過程（解糖系、クエン酸回路）および電子伝達系を通り、ATPの生成を行う。上記の代謝系は電子供与体として有機物を用いる多くの従属栄養生物に見られるATP合成系であるが、最終電子受容体に使用できるのはほとんどが数種の無機物である。また、無機物を電子供与体とする化学合成独立栄養生物の行う呼吸も含まれる。そのような無機物には水素、一酸化炭素、アンモニア、亜硝酸塩、一価鉄、硫化水素などがある。

最終電子受容体として酸素を用いる呼吸を『好気呼吸』それ以外の無機物を用いるものを『嫌気呼吸』という。化学合成独立栄養の場合は、多くは酸素を最終電子受容体として用いるが、嫌気呼吸の電子伝達系を併せ持つものも存在する。なお、嫌気呼吸の電子受容体には硝酸塩、硫酸塩、亜硝酸塩、二価鉄等の無機物や、トリメチルアミンオキサイド (TMAO) やジメチルスルフォキシド (DMSO) といった有機物を用いるものもある。

基質レベルのリン酸化は解糖系およびクエン酸回路で発生する。またそのとき生じた還元型ピリジンヌクレオチドは電子伝達系を通って、ATP生成に使用される。基質レベルのリン酸化ではわずかグルコース1分子辺り4分子のATPしか生成し得ないが、電子伝達系においては平均して34分子のATPが生産可能である（ただし計算によっては34分子以上生産されているかもしれない）。

最終産物は酸素を用いた場合は水、硝酸塩は窒素など（あるいは一酸化窒素、一酸化二窒素など）、硫酸塩の場合は硫化水素などである。

詳しくは呼吸、解糖系、クエン酸回路、電子伝達系、嫌気呼吸を参照。

光化学反応

代表的な光化学反応である光合成で最も一般的なものは、植物細胞に含まれる葉緑体によって行われるものである

光化学反応は光エネルギーによる電子の励起およびそれに伴う電子伝達によってATP生成が行われる。光合成反応は植物および一部の細菌（光合成細菌；シアノバクテリア、紅色硫黄細菌など）のみが有している。電子供与体には酸素発生型光合成の場合H₂Oが使用される。また酸素非発生型光合成の場合は、硫化水素、水素をはじめ幾つかの有機化合物（プロパノールなど）を電子供与体として利用する。

酸素発生型光合成の場合、水2分子あたり4分子のATPおよび2分子のNADPHが生産される。うち3分子のATPおよび2分子のNADPHを用いて炭酸同化を行う。また電子がピリジンヌクレオチド（あるいはフェレドキシン）に伝達された後に再び電子伝達系に戻る光化学反応を循環的光リン酸化というが、こちらは電子が光合成電子伝達系を回転するために、光励起を受ける限りATP生成が行われる。明条件かつ有機物の少ない環境ではこのような異化反応が見られる。循環的光リン酸化の収支は以下の通りである。

• 光化学系I　→　光励起P700（光化学反応中心）
• 光励起P700（光化学反応中心）　→　初発電子受容体A₀
• 初発電子受容体A₀　→　フェレドキシン
• フェレドキシン　→　プラストキノン
• プラストキノン　→　シトクロムb₆/f複合体
• シトクロムb₆/f複合体　→　光化学系I（上に戻る）

なお、光合成反応は好気的な反応と思われがちだが、必ずしもそうではない。酸素を発生するために好気条件のように見えるが、酸素非発生型光合成を行う光合成細菌のほとんどが極度の嫌気性である（シアノバクテリアは除く）。酸素発生型光合成の起源は光合成細菌の光化学系を起源とするので、光化学反応は『明条件かつ嫌気的な』代謝系である。

詳しくは光合成、光化学反応を参照。

同化

同化（同化作用）とは、外部から取り込んだ物質を生合成する事を指す。ATPや還元型ピリジンヌクレオチドなどの異化反応によって得られたエネルギーを用い、酵素反応を利用し、単純な前駆体を経て核酸、タンパク質、多糖、脂質など複雑な生体高分子さらには増殖を行う過程である。

同化反応は異化のように代謝系に注目するよりも、低分子無機物の取り込み、無機物から低分子有機物の構築、ならびに生体高分子の構築という順に、生体分子の構築過程に注目すると理解しやすい。

なお、無機態の炭素、窒素、硫黄の取り込みを可能にするのは独立栄養生物のみであり、従属栄養生物は生体高分子（有機物）の異化から生合成系へ流れていく。したがって、この点でも異化と同化は関連していることがわかる。

無機態炭素、窒素、硫黄の取り込み

無機態の炭素は主に二酸化炭素として固定される。炭酸固定経路は光合成のカルビン - ベンソン回路や還元的クエン酸回路、メタン生成経路などによる。カルビン回路は光化学反応によって生じたATPおよびNADPH、還元的クエン酸回路はピルビン酸：フェレドキシン酸化還元酵素による、通常のクエン酸回路の逆行、メタン生成経路はATP合成と炭酸固定が同時に行われる。炭酸固定によって生じた生産物は通常は糖としてあるいは異化の中間代謝物として、高次の生合成に組み込まれる。詳しくは当該記事へ。

水圏以外にも豊富に存在する窒素源としては大気中の窒素ガスが挙げられる。窒素ガスは窒素固定という代謝系のみでアンモニアまで還元される。窒素固定は根粒菌などでは呼吸による、シアノバクテリアでは光化学系Iの循環的光リン酸化によるATP生成にて窒素固定が行われる。窒素固定反応は以下の通りである。

• N₂ + 6Fd^red + 12ATP + 6H⁺　→　2NH₃ + 12ADP + 12P_i
• 2H⁺ + 2Fd^red + 4ATP　→　H₂ + 4ADP + 4P_i

硝酸塩は有機物窒素と比べて酸化的であり、同化的硝酸還元と言う過程にてアンモニアまで還元される。

• NO₃^- + NAD(P)H + H⁺　→　NO₂^- + NAD(P)⁺ + H₂O
• NO₂^- + 6Fd^red　→　NH₃ + 2H₂O

最終産物のアンモニアは下記の系によりアミノ酸に取り込まれる。 また、アンモニアに含まれる窒素の酸化レベルは有機物窒素と同一であり、還元型ピリジンヌクレオチドなどは必要としない。アンモニア同化反応は以下の3つがある。

• ケトグルタル酸（クエン酸回路中間体） + NH₃　→　グルタミン酸
• グルタミン酸 + NH₃　→　グルタミン
• アスパラギン酸 + NH₃　→　アスパラギン

硫黄は同化的硫酸還元によってタンパク質にチオールあるいはスルホ基として取り込まれる。硫酸塩はタンパク質中の硫黄と比べて還元的であり、アデノシンと結合することにより活性型の硫黄（ホスホアデノシンホスホ硫酸；PAPS）の状態でタンパク質と硫黄が結合する。

• SO₄^- + ATP　→　APS + PP_i
• APS + ATP　→　PAPS + ADP
• PAPS + Protein-SH基　→　Protein-S-SO₃^-（このProteinの末端は含硫黄アミノ酸であるシステイン）
• Protein-S-SO₃^- + 6Fd^red　→　S₂^-（有機物として利用され得る硫黄） + S-S結合を有するタンパク質
• Protein S-S bond + NADPH　→　Protein-SH + NADP⁺

S₂^-はその後、システイン、ホモシステインを経てメチオニンに取り込まれる。ただし、硫黄代謝は更に多様であると考えられており、異化型硫酸還元や硫黄酸化などでは、更に複雑な中間体が生じている可能性が示唆されている。

ヌクレオチド、アミノ酸、炭水化物および脂肪酸の生合成

上記の反応により細胞内取り込まれた炭素、窒素、硫黄は豊富に存在している水と化合し、生体高分子の単量体であるヌクレオチド、アミノ酸、糖などの有機物を生合成する。これらの生体高分子のモノマーには前駆体として中央代謝系（解糖系、クエン酸回路）の中間代謝物が用いられることが多い。

核酸 (DNA、RNA) のモノマーであるヌクレオチドはプリン、ピリミジン塩基に五炭糖であるリボースあるいはデオキシリボースの5'位にリン酸が結合している構造をとっている。プリン（アデニン、グアニン）ピリミジン（ウラシル、シトシン）ヌクレオチドはそれぞれ異なる経路にて合成される。まずピリミジンヌクレオチドの合成系は以下のとおりである。

1. カルバモイルリン酸 + アスパラギン酸　→　オロチン酸
2. リボース5リン酸 + ATP　→　ホスホリボシル1ピロリン酸
3. オロチン酸 + ホスホリボシル1ピロリン酸　→　オロチジン5'リン酸 (OMP)
4. オロチジン5'リン酸　→　ウリジン5'リン酸 (UMP) + CO₂
5. ウリジン5'リン酸(UMP) + ATP　→　ウリジン三リン酸 (UTP)
6. ウリジン三リン酸 + グルタミン　→　シチジン三リン酸 (CTP)

リボース5リン酸はペントースリン酸経路より生じている。またアスパラギン酸は後述するアミノ酸合成系より生じている。カルバモイルリン酸はアミノ酸とリン酸を基質としてカルバモイルリン酸合成酵素により合成される。プリン合成系については以下のとおりである。

1. リボース5リン酸 + ATP　→　ホスホリボシル1ピロリン酸
2. ホスホリボシル1ピロリン酸 + アスパラギンあるいはグルタミン酸由来のアミノ基　→　ホスホリボシルアミン
3. ホスホリボシルアミン + グリシン + ATP　→　グリシナマイドヌクレオチド
4. グリシナマイドヌクレオチド + グルタミン由来アミノ基 + ATP + ホルミルTHFA由来のアルデヒド基　→　5アミノイミダゾールリボヌクレオチド
5. 5アミノイミダゾールリボヌクレオチド + ATP + CO₂ + アスパラギン酸由来のアミノ基　→　5アミノイミダゾール4サクシノカルボキサミドリボヌクレオチド
6. 5アミノイミダゾール4サクシノカルボキサミドリボヌクレオチド + ホルミルTHFA由来のアルデヒド基　→　イノシン5'リン酸 (IMP)
7. イノシン5'リン酸 + アスパラギン酸 + ATP　→　アデノシン三リン酸 (ATP)
8. イノシン5'リン酸 + グルタミン + ATP　→　グアノシン三リン酸 (GTP)

上記の過程で合成されたリボヌクレオチド (RNA) はリボース部位が還元を受けることによってデオキシリボースとなり、デオキシリボヌクレオチド (DNA) が合成される。また、DNAにおいてアデニンと相補的塩基対を構成するチミンはピリミジン塩基でありながらはウラシル、シトシンとは異なる経路にて合成される。チミン合成系には葉酸およびコバミド（ビタミンB12の補酵素形）を要求することがわかっている。また、上記の新生経路（de novo経路）のみならず、使用済みの核酸を再利用するサルベージ経路も存在する。

タンパク質を構成する20種のアミノ酸については各アミノ酸の炭素骨格から生合成経路が決定される。アミノ酸は炭素骨格によって以下の『族』に分類することが可能である。

• グルタミン酸族：グルタミン酸、グルタミン、アルギニン、プロリン
• アスパラギン酸族：アスパラギン酸、アスパラギン、リシン、メチオニン、スレオニン、イソロイシン
• 芳香族：トリプトファン、フェニルアラニン、チロシン
• セリン族：セリン、グリシン、システイン
• ピルビン酸族：アラニン、バリン、ロイシン

なお、それぞれの族の前駆体および由来する代謝系は以下のとおりである。

• グルタミン酸族：ケトグルタル酸（クエン酸回路）
• アスパラギン酸族：オキサロ酢酸（クエン酸回路）
• 芳香族：ホスホエノールピルビン酸（解糖系：EM経路、ED経路） + エリトロース4リン酸（ペントースリン酸経路）
• セリン族：3ホスホグリセリン酸（解糖系：EM経路、ED経路）
• ピルビン酸族：ピルビン酸（解糖系：EM経路、ED経路）

なお、上記の例は中央代謝系を基準にしたものであり、中央代謝系以外に回路を所持している、例えば植物などでは芳香族はシキミ酸経路、セリン族はカルビン - ベンソン回路由来のグリセリン酸リン酸より生合成を行う。なお、ヒスチジンのみが上記の族に属さずペントースリン酸経路由来のリボース5リン酸より合成される。

すべての前駆体は中央代謝系に由来するものであり、理論上、糖さえ摂取すればすべてのアミノ酸を合成できるはずだが、マウス、ヒトにおいては必須アミノ酸といわれる一群のアミノ酸を経口摂取する必要がある。それらは芳香族、アスパラギン酸族およびピルビン酸族のアミノ酸である。

糖については、解糖系の逆行である糖新生系にて合成される。また、ペントースリン酸経路においては多種多様な糖が合成される。また還元的ペントースリン酸経路と呼称されるカルビン - ベンソン回路においても同様である。

脂肪酸はアセチルCoAを基質として脂肪酸合成経路にて合成される。アセチルCoAは解糖系に由来するものであるが必要な還元力にはNADPHが使用される。NADPHはペントースリン酸経路より供給され、後述するが異化経路と同化経路の密接なかかわりをここにも見ることができる。

生体高分子の生合成

上記の過程にて合成された核酸、タンパク質、多糖の各モノマーはポリマーとなって生体高分子となる。各単量体の名称および結合の名称は以下のとおりである。

• 核酸：ヌクレオチドのホスホジエステル結合ポリマー
• タンパク質：アミノ酸のペプチド結合ポリマー
• 多糖：単糖のグリコシド結合ポリマー

ただし、各モノマーが重合するよりもポリマーが加水分解を受ける方が自由エネルギー的に低く、したがって各モノマーは活性化されなければならない。各モノマーの活性化された形状とは以下のとおりである。

• ヌクレオチド：ヌクレオシド三リン酸
• アミノ酸：アミノアシルtRNA
• 糖：糖-ヌクレオシド二リン酸

核酸にはゲノムDNA、プラスミド、ミトコンドリアDNA、葉緑体DNAあるいはrRNA、tRNA、mRNAといったいくつかの種類が存在している。遺伝情報を保存したDNAが合成される際は複製という過程にて、生合成が行われる。また、遺伝情報を発現する際に用いられるRNAはすべてが転写によって生合成される。転写された各RNAの共同的な働きにより遺伝情報は翻訳され、タンパク質の生合成が行われる。各過程の詳細な説明は、該当記事参照。

多糖の合成については不明な部分が多いが、糖新生系あるいはカルビン - ベンソン回路にてデンプンが合成される。またもっとも現存量の多い有機物であるセルロースはドリコールというアルコールおよびタンパク質が多糖キャリアーとなって生合成が行われる。

異化と同化の関連、代謝マップのつながり

上記、代謝を異化と同化に分けて説明を行ったが、これまでの文中にもあるように異化と同化は関連している。それらの関連については、異化によって得られたエネルギーを同化に使用すると言う点のほかに、何らかの有機物が不足した際に代謝系の連結によって不足した物質をある程度補えるという点がある。

生物を構成する物質を大まかに分類すると糖（核酸など）、アミノ酸（タンパク質）、脂肪酸（生体膜）となる。いずれの物質も生物にとって必要欠くべからざるものであり、一部の例外（寄生を行う生物など）を除いてはこれらの物質に関する代謝系（異化、同化のいずれも）を有している。それぞれの物質に対応する代謝系は以下の通りである。

• 糖・・・同化：糖新生系（解糖系の逆行）、異化：解糖系。
• アミノ酸・・・同化：解糖系とクエン酸回路を中心としたアミノ酸合成系、異化：解糖系とクエン酸回路を中心とした分解経路。詳細はアミノ酸の代謝分解
• 脂肪酸・・・同化：脂肪酸生合成系、異化：β酸化経路。

これらのうち、解糖系はほとんどの生物が持っている基本的なエネルギー獲得経路であり、クエン酸回路も真核生物ではミトコンドリア、原生生物では膜系で行われる。脂肪酸生合成系の出発物質およびβ酸化の最終産物は解糖系の最終産物であるアセチルCoAである。また、各アミノ酸の分解における中間代謝物質は、以下の通りである。

• 中間代謝物を解糖系に含むもの
  • ピルビン酸：アラニン、システイン、グリシン、セリン、スレオニン
  • アセチルCoA：ロイシン、イソロイシン、トリプトファン
  • アセトアセチルCoA：フェニルアラニン、チロシン、リシン、ロイシン、トリプトファン
• 中間代謝物をクエン酸回路に含むもの
  • オキサロ酢酸：アスパラギン酸、アスパラギン
  • フマル酸：チロシン、フェニルアラニン
  • スクシニルCoA：イソロイシン、バリン、メチオニン
  • 2-オキソグルタル酸（正確にはグルタミン酸）：アルギニン、ヒスチジン、グルタミン、プロリン

なお、上述したアミノ酸生合成経路と若干異なる点については、代謝の調節に関わっている（後述）。

中央代謝系を中心としたそれぞれの物質の異化と同化が行われる点について、例えば糖が不足した際にはアミノ酸および脂肪酸を摂取していれば生合成が可能である。脂肪酸の場合も同様で糖、アミノ酸から生合成できる。唯一アミノ酸は窒素および生体成分における硫黄の供給源となるので、ある程度摂取しなければならないが無機態の窒素および硫黄を利用可能な代謝系が存在することは上述の通りである。

代謝の調節

生命の恒常性に際しては異化と同化両方の代謝系の調和が成立しなければならない。代謝系のほとんど全ての反応は酵素によるものであるが、したがって個々の反応の調節がなされなければならない。全ての酵素反応を調節するには、非常に複雑で膨大なシステムの存在をイメージするが、生物はその過程をシンプルかつ最小のエネルギーで行えるよう優れたシステムを構築している。

主たる酵素反応の調節には、以下の 4 つがあげられる。

1. 形質膜を用いた酵素の局所化
2. 生体成分の異化および同化を異なる経路で行うこと
3. 熱力学的な反応の調節（基質の濃度差やpHの変化）
4. 酵素活性および酵素の発現量による調節

1. の酵素の局所化については、原核生物の場合は形質膜構造は原則として1つであり、細胞内、細胞外のほか膜内といった区別しかなされない。したがって、原核生物の代謝調節における 1. の依存度は真核生物ほどではない。一方真核生物は、ミトコンドリア、小胞体、リソソームといった多くの形質膜構造からなるオルガネラを有しており、個々の器官において特有の代謝系を有している。例えばミトコンドリアはクエン酸回路および電子伝達系のほかβ酸化系を有している。

2. の異化と同化を別経路に分ける点については上述の異化と代謝のつながりにも筆記している。例えば解糖系と糖新生系は多くの酵素に関しては同一であるが、一部不可逆反応を交えることにより、結果として別経路となっている。また、そのような不可逆反応を行う酵素は酵素活性そのものの調節を受けるアロステリック酵素である場合が多い（後述）。

3. の熱力学的な反応の調節については、基質の濃度差の変化に伴うケースが多い。例えば A→B→C という反応が存在し、細胞のフェーズとして C が必要であるとすると A あるいは B を何らかの形で外部から摂取し、細胞内の A あるいは B の濃度を高めることで C の生合成を助ける。その結果、最終的に C が使用されなくなり C の濃度が細胞内で増加したとすると B→C の反応は濃度差の解消により化学平衡に達する。B と C 間の反応が可逆であり B の濃度が減少すると今度は C から B へと反応が起きる。

4. の酵素活性そのものの調節や酵素の発現量による調節は特に後者は原核生物にて、非常によく研究が進んでいる。酵素活性の調節はアロステリック効果をはじめとした最終産物阻害を中心に、複雑なカスケード系あるいは酵素そのものの化学修飾（一例としてプロテインキナーゼを参照）などがある。酵素の発現量による調節はジャコブとモノーのオペロン説を中心に遺伝子発現と生体成分の協同的なモデルがある（一例としてラクトースオペロンを参照）。

エネルギー代謝

エネルギー代謝とは物質代謝に対して生命現象をエネルギーという観点から見た、より熱力学的要素の強い代謝の視点である。具体的には、エネルギー獲得系は光・食物・ある種の細菌では無機物などを元に、ミトコンドリア内膜や葉緑体などの生体膜で H⁺ 輸送反応を介して生体のエネルギー通貨である ATP を合成する反応（ATP 合成系）である。エネルギー利用系は、筋肉を動かすミオシン等の収縮性タンパク質やイオン輸送を行うATPアーゼは ATP を加水分解する。分子合成は酵素リガーゼが ATP を消費して行う。

また、この ATP の化学エネルギーをさかのぼると異化によって生じることから独立栄養生物による有機物生産が大元であり、それらの生産は太陽光の還元力（特殊な環境においては地球科学的起源の水素、硫化水素と置き換えても良い）が出発点であることがわかる。太陽光の（あるいは地球に残存した）還元力は生体的な代謝のエネルギーのみならず、石油や天然ガスといった人間活動に使用しているエネルギーをも供給している。

二次代謝

詳細は「二次代謝」および「二次代謝産物」を参照

上述の糖、アミノ酸、脂肪酸に関連した異化同化の両反応およびそれらに関するエネルギー代謝を中央代謝あるいは一次代謝という。対して、それらの中央代謝系から外れた生命維持における役割の不明な物質を生産する特定の生物に限定的な代謝のことを二次代謝という。

二次代謝産物としては、以下のような物質があげられる。

アルカロイド

植物が主として生産する窒素を含有する塩基性物質の総称。少量で顕著な生理活性を示し、種類も非常に多い。

テルペノイド

メバロン酸経路から生産されるイソプレンの重合した物質。有名なテルペンとしてはコレステロールなどがある。

フェノール類

植物の木質成分の大半を占めるリグニンなどはフェノール類の重合体である。えてして反応性に乏しく、資化されにくい。

配糖体

主として植物の生産する糖のヒドロキシ基が何らかの化合物で置換された物質の総称。アントシアニンなどの色素のほか強心配糖体といった薬理作用を示すものも存在する。

抗生物質

アオカビなど真菌や放線菌の生産する原核生物特異的に作用する生理活性物質。

特殊アミノ酸

植物が主として生産する、タンパク質に含まれない特殊なアミノ酸。植物自体への生理活性は現在のところ不明であるが、植物の生育とともに生産量や種類などが変化する。別名非タンパク質性アミノ酸。

これらにあげたのは一部であり、生物界には未分類の微量生体成分が非常に多数存在すると言われている。二次代謝産物の多くは顕著な生理活性を示すものが多く、毒物や薬物として分類されるものも多い。

薬物代謝（異物代謝）

生物は薬、毒物などの生体外物質（ゼノバイオティクスXenobiotics、異物ともいう）にさらされており、これらを分解あるいは排出するための代謝も行う。詳しくは薬物代謝の項を参照。

脚注

参考文献

• 『生化学辞典第2版』 東京化学同人、1995年、第2版第6刷。ISBN 4-8079-0340-3。

関連項目

• 代謝経路
• 代謝マップ
• 呼吸
• 光合成
• 生体高分子
• 恒常性
• 生理的熱量
• 新陳代謝
• 薬物代謝
• 基礎代謝
• メタボロミクス

外部リンク

• 代謝マップ Interactive Map of the Major Metabolic Pathways (英語)

wiki en

[Wiki en表示]

"Cell metabolism" redirects here. For the journal, see Cell Metabolism.

For the architectural movement, see Metabolism (architecture).

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

Metabolism (from Greek: μεταβολή metabolē, "change") is the set of life-sustaining chemical transformations within the cells of living organisms. 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 all chemical reactions that occur in living organisms, including digestion and the transport of substances into and between different cells, in which case the set of reactions within the cells is called intermediary metabolism or intermediate metabolism.

Metabolism is usually divided into two categories. Catabolism, that breaks down organic matter and harvests energy by way of cellular respiration, and anabolism that uses energy to construct components of cells such as proteins and nucleic acids.

The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, by a sequence of enzymes. 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 that allow the reactions to proceed more rapidly. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or to signals from other cells.

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 speed of metabolism, the metabolic rate, influences how much food an organism will require, and also affects how it is able to obtain that food.

A striking feature of metabolism is the similarity of the basic metabolic pathways and components between even 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 striking similarities in metabolic pathways are likely due to their early appearance in evolutionary history, and their retention because of their efficacy.

Key biochemicals

Further information: Biomolecule, cell (biology) and biochemistry

Structure of a triacylglycerol lipid

Most of the structures that make up animals, plants and microbes are made from three basic classes of molecule: amino acids, carbohydrates 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.

Type of molecule	Name of monomer forms	Name of polymer forms	Examples of polymer forms
Amino acids	Amino acids	Proteins (also called polypeptides)	Fibrous proteins and globular proteins
Carbohydrates	Monosaccharides	Polysaccharides	Starch, glycogen and cellulose
Nucleic acids	Nucleotides	Polynucleotides	DNA and RNA

Amino acids and proteins

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.

Lipids

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. Lipids are usually defined as hydrophobic or amphipathic biological molecules but will dissolve in organic solvents such as benzene or chloroform. 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 alternate backbones such as sphingosine in the sphingolipids, and hydrophilic groups such as phosphate as in phospholipids. Steroids such as cholesterol are another major class of lipids.

Carbohydrates

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

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). The basic carbohydrate units are called monosaccharides and include galactose, fructose, and most importantly glucose. Monosaccharides can be linked together to form polysaccharides in almost limitless ways.

Nucleotides

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. This information is protected by DNA repair mechanisms and propagated through DNA replication. Many viruses have an RNA genome, such as HIV, which uses reverse transcription to create a DNA template from its viral RNA genome. 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.

Coenzymes

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

Main article: 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 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. These group-transfer intermediates are called coenzymes. Each class of group-transfer reactions is carried out by a particular coenzyme, which is the 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.

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. 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.

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.

Structure of hemoglobin. The protein subunits are in red and blue, and the iron-containing heme groups in green. From PDB: 1GZX .

Minerals and cofactors

Further information: Metal Ions in Life Sciences, Metal metabolism, and 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 mammal's mass 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.

The abundant inorganic elements act as ionic 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.

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.

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. 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.

Classification of organisms based on their metabolism

Energy source	sunlight	photo-			-troph
	Preformed molecules	chemo-
Electron donor	organic compound		organo-
	inorganic compound		litho-
Carbon source	organic compound			hetero-
	inorganic compound			auto-

The most common set of catabolic reactions in animals can be separated into three main stages. In the first, 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 yet 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.

Digestion

Further information: Digestion and gastrointestinal tract

Macromolecules such as starch, cellulose or proteins cannot be rapidly taken up by cells and must be broken into their smaller units before they can be used in cell metabolism. Several common classes of enzymes digest these polymers. These digestive enzymes include proteases that digest proteins into amino acids, as well as glycoside hydrolases that digest polysaccharides into simple sugars known as monosaccharides.

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

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

Energy from organic compounds

Further information: Cellular respiration, fermentation, carbohydrate catabolism, fat catabolism and protein catabolism

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 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.

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.

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).

Energy transformations

Oxidative phosphorylation

Further information: Oxidative phosphorylation, chemiosmosis and mitochondrion

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.

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 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.

Energy from inorganic compounds

Further information: Microbial metabolism and nitrogen cycle

Chemolithotrophy is a type of metabolism found in prokaryotes where energy is obtained from the oxidation of inorganic compounds. These organisms can use hydrogen, reduced sulfur compounds (such as sulfide, hydrogen sulfide and thiosulfate), ferrous iron (FeII) 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.

Energy from light

Further information: Phototroph, photophosphorylation, chloroplast

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.

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 or rhodopsins. Reaction centers are classed into two types depending on the type of photosynthetic pigment present, with most photosynthetic bacteria only having one type, while plants and cyanobacteria have two.

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. These protons move back through the membrane as they drive the ATP synthase, as before. The electrons then flow through photosystem I and can then either be used to reduce the coenzyme NADP⁺, for use in the Calvin cycle, which is discussed below, or recycled for further ATP generation.

Anabolism

Further information: 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 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.

Organisms differ in how many of the molecules in their cells they can construct for themselves. 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.

Carbon fixation

Further information: Photosynthesis, carbon fixation and chemosynthesis

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 centres, 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 – Benson cycle. 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.

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.

Carbohydrates and glycans

Further information: Gluconeogenesis, glyoxylate cycle, glycogenesis and glycosylation

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. 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.

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.

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-glucose) 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.

Fatty acids, isoprenoids and steroids

Further information: Fatty acid synthesis, steroid metabolism

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 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.

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 steroid 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 steroids such as cholesterol and ergosterol.

Proteins

Further information: 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 acids must be obtained from food. Some simple parasites, such as the bacteria Mycoplasma pneumoniae, lack all amino acid synthesis and take their amino acids directly from their hosts. 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. Amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then transaminated to form an amino acid.

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.

Nucleotide synthesis and salvage

Further information: Nucleotide salvage, pyrimidine biosynthesis, and purine 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.

Xenobiotics and redox metabolism

Further information: Xenobiotic metabolism, drug metabolism, Alcohol metabolism and antioxidants

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.

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.

Thermodynamics of living organisms

Further information: Biological thermodynamics

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.

Regulation and control

Further information: Metabolic pathway, metabolic control analysis, hormone, regulatory enzymes, and cell signaling

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.

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. This type of regulation often involves allosteric regulation of the activities of multiple enzymes in the pathway. 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 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.

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.

Evolution

Further information: Molecular evolution and phylogenetics

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.

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 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. Mutation changes that affect non-coding DNA segments may merely affect the metabolic efficiency of the individual for whom the mutation occurs. 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.

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.

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.

Investigation and manipulation

Further information: Protein methods, proteomics, metabolomics and metabolic network modelling

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.

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.

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 45,000 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.

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.

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.

History

Further information: History of biochemistry and history of molecular biology

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

The term metabolism is derived from the Greek Μεταβολισμός – "Metabolismos" for "change", or "overthrow". The first documented references of metabolism were made by Ibn al-Nafis 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.". 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".

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.

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.

See also

• Anthropogenic metabolism
• Antimetabolite
• Basal metabolic rate
• Calorimetry
• Isothermal microcalorimetry
• Inborn error of metabolism
• Iron-sulfur world theory, a "metabolism first" theory of the origin of life.
• Primary nutritional groups
• Respirometry
• Stream metabolism
• Sulfur metabolism
• Thermic effect of food
• Water metabolism

References

Further reading

Library resources about Metabolism

Online books Resources in your library Resources in other libraries

Introductory

• Rose, S. and Mileusnic, R., The Chemistry of Life. (Penguin Press Science, 1999), ISBN 0-14-027273-9
• Schneider, E. D. and Sagan, D., Into the Cool: Energy Flow, Thermodynamics, and Life. (University Of Chicago Press, 2005), ISBN 0-226-73936-8
• Lane, N., Oxygen: The Molecule that Made the World. (Oxford University Press, USA, 2004), ISBN 0-19-860783-0

Advanced

• Price, N. and Stevens, L., Fundamentals of Enzymology: Cell and Molecular Biology of Catalytic Proteins. (Oxford University Press, 1999), ISBN 0-19-850229-X
• Berg, J. Tymoczko, J. and Stryer, L., Biochemistry. (W. H. Freeman and Company, 2002), ISBN 0-7167-4955-6
• Cox, M. and Nelson, D. L., Lehninger Principles of Biochemistry. (Palgrave Macmillan, 2004), ISBN 0-7167-4339-6
• Brock, T. D. Madigan, M. T. Martinko, J. and Parker J., Brock's Biology of Microorganisms. (Benjamin Cummings, 2002), ISBN 0-13-066271-2
• Da Silva, J.J.R.F. and Williams, R. J. P., The Biological Chemistry of the Elements: The Inorganic Chemistry of Life. (Clarendon Press, 1991), ISBN 0-19-855598-9
• Nicholls, D. G. and Ferguson, S. J., Bioenergetics. (Academic Press Inc., 2002), ISBN 0-12-518121-3

External links

External links

General information

• Metabolism, Cellular Respiration and Photosynthesis The Virtual Library of Biochemistry and Cell Biology at biochemweb.org
• The Biochemistry of Metabolism
• Advanced Animal Metabolism Calculators/ Interactive Learning Tools
• Microbial metabolism Simple overview. School level.
• Metabolic Pathways of Biochemistry Graphical representations of major metabolic pathways.
• Chemistry for biologists Introduction to the chemistry of metabolism. School level.
• Sparknotes SAT biochemistry Overview of biochemistry. School level.
• MIT Biology Hypertextbook Undergraduate-level guide to molecular biology.

Human metabolism

• Topics in Medical Biochemistry Guide to human metabolic pathways. School level.
• http://themedicalbiochemistrypage.org/ THE Medical Biochemistry Page] Comprehensive resource on human metabolism.

Databases

• Flow Chart of Metabolic Pathways at ExPASy
• IUBMB-Nicholson Metabolic Pathways Chart
• SuperCYP: Database for Drug-Cytochrome-Metabolism

Metabolic pathways

• Interactive Flow Chart of the Major Metabolic Pathways
• Metabolism reference Pathway
• Guide to Glycolysis School level.
• The Nitrogen cycle and Nitrogen fixation at the Wayback Machine
• Downloadable guide to photosynthesis School level.
• What is Photosynthesis? Collection of photosynthesis articles and resources.

UpToDate Contents

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• 1. 筋肉におけるエネルギー代謝 energy metabolism in muscle
• 2. 運動生理学 exercise physiology
• 3. 先天性代謝異常：分類 inborn errors of metabolism classification
• 4. 成人における抗癌剤の投与 dosing of anticancer agents in adults
• 5. 先天性代謝異常：代謝性救急疾患 inborn errors of metabolism metabolic emergencies

English Journal

• Efficient production and secretion of pyruvate from Halomonas sp. KM-1 under aerobic conditions.

• Kawata Y1, Nishimura T2, Matsushita I2, Tsubota J2.
• AMB Express.AMB Express.2016 Dec;6(1):22. doi: 10.1186/s13568-016-0195-y. Epub 2016 Mar 18.
• The alkaliphilic, halophilic bacterium Halomonas sp. KM-1 can utilize both hexose and pentose sugars for the intracellular storage of bioplastic poly-(R)-3-hydroxybutyric acid (PHB) under aerobic conditions. In this study, we investigated the effects of the sodium nitrate concentration on PHB accumu
• PMID 26989057

• Ratios of central venous-to-arterial carbon dioxide content or tension to arteriovenous oxygen content are better markers of global anaerobic metabolism than lactate in septic shock patients.

• Mallat J1, Lemyze M2, Meddour M3, Pepy F4, Gasan G5, Barrailler S6, Durville E7, Temime J8, Vangrunderbeeck N9, Tronchon L10, Vallet B11, Thevenin D12.
• Annals of intensive care.Ann Intensive Care.2016 Dec;6(1):10. doi: 10.1186/s13613-016-0110-3. Epub 2016 Feb 3.
• BACKGROUND: To evaluate the ability of the central venous-to-arterial CO2 content and tension differences to arteriovenous oxygen content difference ratios (∆ContCO2/∆ContO2 and ∆PCO2/∆ContO2, respectively), blood lactate concentration, and central venous oxygen saturation (ScvO2) to detect
• PMID 26842697

• Nonesterified Fatty Acid-Induced Endoplasmic Reticulum Stress in Cattle Cumulus Oocyte Complexes Alters Cell Metabolism and Developmental Competence.

• Sutton-McDowall ML1, Wu LL2, Purdey M3, Abell AD3, Goldys EM4, MacMillan KL5, Thompson JG6, Robker RL2.
• Biology of reproduction.Biol Reprod.2016 Dec;94(1):23. doi: 10.1095/biolreprod.115.131862. Epub 2015 Dec 9.
• Reduced oocyte quality has been associated with poor fertility of high-performance dairy cows during peak lactation, due to negative energy balance. We examined the role of nonesterified fatty acids (NEFAs), known to accumulate within follicular fluid during under- and overnutrition scenarios, in ca
• PMID 26658709

Japanese Journal

• Diethyl phthalate enhances expression of SIRT1 and DNMT3a during apoptosis in PC12 cells

• Sun Yongkun,Guo Zhikun,Iku Shouhei,Saito Takeshi,Kurasaki Masaaki
• Journal of Applied Toxicology 33(12), 1484-1492, 2013-12-00
• … However, the relationship between DEP and longevity-related factors, sirtuins and epigenetic factors (e.g. DNA methyltransferases) remains unclear, because genome modification caused by chemical toxicity, sirtuins and epigenetic factors have played key roles in abnormal metabolism and development. …
• NAID 120005341790

• Polyunsaturated fatty acid saturation by gut lactic acid bacteria affecting host lipid composition.

• Kishino Shigenobu,Takeuchi Michiki,Park Si-Bum,Hirata Akiko,Kitamura Nahoko,Kunisawa Jun,Kiyono Hiroshi,Iwamoto Ryo,Isobe Yosuke,Arita Makoto,Arai Hiroyuki,Ueda Kazumitsu,Shima Jun,Takahashi Satomi,Yokozeki Kenzo,Shimizu Sakayu,Ogawa Jun
• Proceedings of the National Academy of Sciences of the United States of America, 2013-10-14
• … 2013-10-15.In the representative gut bacterium Lactobacillus plantarum, we identified genes encoding the enzymes involved in a saturation metabolism of polyunsaturated fatty acids and revealed in detail the metabolic pathway that generates hydroxy fatty acids, oxo fatty acids, conjugated fatty acids, and partially saturated trans-fatty acids as intermediates. …
• NAID 120005341879

• Mitochondrial DNA with a Large-Scale Deletion Causes Two Distinct Mitochondrial Disease Phenotypes in Mice

• Katada Shun,Mito Takayuki,Ogasawara Emi,Hayashi Jun-Ichi,Nakada Kazuto,林 純一,中田 和人
• G3: Genes, Genomes, Genetics 3(9), 1545-1552, 2013-09-00
• … Late-stage embryos carrying ≥50% ∆mtDNA showed abnormal hematopoiesis and iron metabolism in livers that were partly similar to PS (PS-like phenotypes), although they did not express sideroblastic anemia that is a typical symptom of PS. More than half of the neonates with PS-like phenotypes died by 1 month after birth, whereas the rest showed a decrease of ∆mtDNA load in the affected tissues, peripheral blood and liver, and they recovered from PS-like phenotypes. …
• NAID 120005342668

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Related Pictures

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★リンクテーブル★

リンク元	「ADME」「catabolism」「metabolic process」「代謝率」「新陳代謝」
拡張検索	「inborn error of metal metabolism」

「ADME」

　　[★]

同

absorption/distribution/metabolism/excretion

関

吸収	Absorption
分布	Distribution
代謝	Metabolism
排泄	Excretion

薬物の投与経路と血中濃度

			血中濃度 ピークまでの時間	血中濃度 ピークの高さ
静脈注射	i.v.	intravenous	++++	++++
筋内注射	i.m.	intramuscular	+++	+++
皮下投与	s.c.	subcutaneous	++	++
経口投与	p.o.	peroral	+	+

「catabolism」

　　[★]

• n.

• (物質代謝における)異化、異化作用 (cf. anabolism)

関

anabolism, catabolic, catabolic reaction, catabolize, catabolized, dissimilation, metabolic process, metabolism, metabonomics

　 　

「metabolic process」

　　[★]

• 代謝過程、代謝経路、代謝プロセス

関

anabolism、catabolism、metabolic network、metabolic pathway、metabolism、metabonomics

「代謝率」

　　[★]

英

metabolic rate MR、metabolism

関

新陳代謝、代謝、代謝速度、物質代謝、代謝量、代謝作用

「新陳代謝」

　　[★]

英

metabolism

関

代謝、物質代謝、代謝率、代謝過程、代謝作用、メタボノミクス

「inborn error of metal metabolism」

　　[★]

• 先天性金属代謝異常