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[[Image:TCA.svg|thumb|right|300px|Overview of the [[citric acid cycle]]]]
[[Image:TCA.svg|thumb|right|300px|Overview of the [[citric acid cycle]]]]

===Extracellular digestion===
In animals, macromolecules such as proteins and polysaccharides are digested into their component amino acids or sugars in the gut, before absorption into the body.<ref>{{cite journal |author=Hoyle T |title=The digestive system: linking theory and practice |journal=Br J Nurs |volume=6 |issue=22 |pages=1285-91 |year= |pmid=9470654}}</ref><ref>{{cite journal |author=Carey M, Small D, Bliss C |title=Lipid digestion and absorption |journal=Annu Rev Physiol |volume=45 |issue= |pages=651-77 |year= |pmid=6342528}}</ref> In microbes, digestive enzymes such as [[protease]]es and [[lipase]]s are secreted and their digestion products taken up as nutrients.<ref>{{cite journal |author=Häse C, Finkelstein R |title=Bacterial extracellular zinc-containing metalloproteases |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8302217 |journal=Microbiol Rev |volume=57 |issue=4 |pages=823-37 |year=1993 |pmid=8302217}}</ref><ref>{{cite journal |author=Gupta R, Gupta N, Rathi P |title=Bacterial lipases: an overview of production, purification and biochemical properties |journal=Appl Microbiol Biotechnol |volume=64 |issue=6 |pages=763-81 |year=2004 |pmid=14966663}}</ref>


===Carbohydrate catabolism===
===Carbohydrate catabolism===

Revision as of 06:21, 7 March 2007

A few of the metabolic pathways in a cell. metabolites are shown as dots and enzyme reactions as lines.

Metabolism is the complete set of chemical reactions that occur in living cells. These metabolic processes are the basis of life, as they allow cells to maintain their structures, respond to their environments, grow and reproduce. Metabolism has two distinct divisions: catabolism, in which a cell breaks down complex molecules to yield energy and anabolism, in which a cell uses this energy to construct complex molecules and perform its functions.

In cells, chemical reactions are organised into metabolic pathways, where one chemical is transformed to another by a sequence of enzymes. Enzymes are crucial to metabolism because they allow cells to drive unfavourable reactions by coupling them to favourable ones. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or signals from other cells.

A striking feature of metabolism is how little the basic metabolic pathways differ between even vastly different species. For example, the series of chemical steps in a pathway such as the citric acid cycle are universal between living cells as diverse as the unicellular bacteria Escherichia coli and multicellular elephants.[1] This shared metabolic structure is most likely the result of both the high efficiency of these pathways, and their early appearance in evolutionary history.[2][3]

Thermodynamics of living organisms

Living organisms obey the laws of thermodynamics. The second law of thermodynamics states that in any closed system, the amount of entropy (chaos) will tend to increase. 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.[4] 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 chaos.[5]

Coenzymes as central intermediates

Space-filling model of the coenzyme nicotinamide adenine dinucleotide.

Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of group transfer reactions.[6] This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions.[7] These group-transfer intermediates are called coenzymes. Each class of group-transfer reaction 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. An example of this are the dehydrogenases that use nicotinamide adenine dinucleotide (NADH) as a cofactor. Here, hundreds of separate types of enzymes remove electrons from their substrates and reduce NADH and this reduced coenzyme is then a substrate for any of the reductases in the cell that need to reduce their substrates.[8]

Catabolism

Catabolism involves processes that release energy, the purpose of these catabolic reactions is to provide the energy and components needed by anabolic reactions. Usually these reactions involves complex organic molecules being broken down to simpler molecules, such as carbon dioxide and water. 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, which releases some energy. Finally, the acetyl group on the coenzyme A is oxidized to water and carbon dioxide, which generates a great deal of energy.

The exact nature of these catabolic reactions differ from organism to organism, with organic molecules being used as a source of energy in organotrophs, while lithotrophs use inorganic substrates and phototrophs obtain chemical energy from capturing visible light. 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 sulphate.[9]

File:TCA.svg
Overview of the citric acid cycle

Extracellular digestion

In animals, macromolecules such as proteins and polysaccharides are digested into their component amino acids or sugars in the gut, before absorption into the body.[10][11] In microbes, digestive enzymes such as proteasees and lipases are secreted and their digestion products taken up as nutrients.[12][13]

Carbohydrate catabolism

Main article: Carbohydrate catabolism

Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. The general formula for carbohydrates, like that of their monomer counterparts, is CX(H2YOY). Carbohydrates literally undergo combustion to retrieve the large amounts of energy in their bonds. Read more about mitochondria to find out more about the reaction and how its energy is secured in ATP.

Fat catabolism

Main article: Fat catabolism

Fat catabolism, also known as lipid catabolism, is the process of lipids or phospholipids being broken down by lipases. The opposite of fat catabolism is fat anabolism, involving the storage of energy, and the building of membranes.

Protein catabolism

Main article: Protein catabolism

Protein catabolism is the breakdown of proteins into amino acids and simple derivative compounds, for transport into the cell through the plasma membrane and ultimately for the polymerisation into new proteins via the use of ribonucleic acids (RNA) and ribosomes. Amino acids can also be converted into glucose and used for energy, through gluconeogenesis.

Anabolism

Main article: Anabolism

Anabolism is a constructive metabolic process whereby energy is consumed to synthesize or combine simpler substances, such as monosaccharides, nucleotides or amino acids, into more complex organic compounds, such as polysaccharides, nucleic acids and proteins.

Modelling metabolism

Further information: [[:Metabolic network modelling]]

With the sequencing of complete genomes, it is now possible to reconstruct the network of biochemical reactions in many organisms, from bacteria to human. Several of these networks are available online: Kyoto Encyclopedia of Genes and Genomes (KEGG)[1], EcoCyc [2] and BioCyc [3]. Predicted metabolic networks are powerful tools for studying and modelling metabolism. The study of metabolic networks' topology with graph theory allows predictive toxicology and ADME.

History

Santorio Santorio (1561-1636) in his steelyard balance, from Ars de statica medecina, first published 1614

The first controlled experiments in human metabolism were published by Santorio Santorio in 1614 in his book Ars de statica medecina that made him famous throughout Europe.[14] He describes his long series of experiments in which he weighed himself in a chair suspended from a steelyard balance (see image), before and after eating, sleeping, working, sex, fasting, depriving from drinking, and excreting. He found that by far the greatest part of the food he took in was lost from the body through perspiratio insensibilis (insensible perspiration).

The term metabolism is derived from the Greek Μεταβολισμός – Metabolismos for "change", or "overthrow".[15] The total metabolism is all biochemical processes in an organism, while cell metabolism is all chemical processes in a cell. The dynamic energy budget theory aims to quantify the metabolic rate of individual organisms.

See also

References

  1. ^ Smith E, Morowitz H (2004). "Universality in intermediary metabolism". Proc Natl Acad Sci U S A. 101 (36): 13168–73. PMID 15340153.
  2. ^ Ebenhöh O, Heinrich R (2001). "Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems". Bull Math Biol. 63 (1): 21–55. PMID 11146883.
  3. ^ Meléndez-Hevia E, Waddell T, Cascante M (1996). "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". J Mol Evol. 43 (3): 293–303. PMID 8703096.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ von Stockar U, Liu J (1999). "Does microbial life always feed on negative entropy? Thermodynamic analysis of microbial growth". Biochim Biophys Acta. 1412 (3): 191–211. PMID 10482783.
  5. ^ Demirel Y, Sandler S (2002). "Thermodynamics and bioenergetics". Biophys Chem. 97 (2–3): 87–111. PMID 12050002.
  6. ^ Mitchell P (1979). "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". Eur J Biochem. 95 (1): 1–20. PMID 378655.
  7. ^ Wimmer M, Rose I. "Mechanisms of enzyme-catalyzed group transfer reactions". Annu Rev Biochem. 47: 1031–78. PMID 354490.
  8. ^ Pollak N, Dölle C, Ziegler M (2007). "The power to reduce: pyridine nucleotides--small molecules with a multitude of functions". Biochem J. 402 (2): 205–18. PMID 17295611.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  9. ^ Nealson K, Conrad P (1999). "Life: past, present and future" (PDF). Philos Trans R Soc Lond B Biol Sci. 354 (1392): 1923–39. PMID 10670014.
  10. ^ Hoyle T. "The digestive system: linking theory and practice". Br J Nurs. 6 (22): 1285–91. PMID 9470654.
  11. ^ Carey M, Small D, Bliss C. "Lipid digestion and absorption". Annu Rev Physiol. 45: 651–77. PMID 6342528.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  12. ^ Häse C, Finkelstein R (1993). "Bacterial extracellular zinc-containing metalloproteases". Microbiol Rev. 57 (4): 823–37. PMID 8302217.
  13. ^ Gupta R, Gupta N, Rathi P (2004). "Bacterial lipases: an overview of production, purification and biochemical properties". Appl Microbiol Biotechnol. 64 (6): 763–81. PMID 14966663.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  14. ^ http://www.istrianet.org/istria/illustri/santorio/
  15. ^ http://www.etymonline.com/index.php?term=metabolism

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