Metabolism



  Metabolism is the set of chemical reactions that occur in living organisms in order to maintain life. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories. nucleic acids.

The chemical reactions of metabolism are organized into signals from other cells.

The metabolism of an organism determines which substances it will find nutritious and which it will find poisonous. For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals.[1] The speed of metabolism, the metabolic rate, also influences how much food an organism will require.

A striking feature of metabolism is the similarity of the basic metabolic pathways between even vastly different species. For example, the set of unicellular bacteria Escherichia coli and huge multicellular organisms like elephants.[2] These striking similarities in metabolism are most likely the result of the high efficiency of these pathways, and of their early appearance in evolutionary history.[3][4]

Key biochemicals

Further information: biochemistry

  Most of the structures that make up animals, plants and microbes are made from three basic classes of macromolecules are essential parts of all living organisms. Some of the most common biological polymers are listed in the table below.

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 cellulose
Nucleic acids Nucleotides Polynucleotides RNA

Amino acids and proteins

immune responses, cell adhesion, active transport across membranes and the cell cycle.[6]

Lipids

cholesterol are another major class of lipids that are made in cells.[9]

Carbohydrates

  polysaccharides in almost limitless ways.[10]

Nucleotides

The polymers pyrimidines. Nucleotides also act as coenzymes in metabolic group transfer reactions.[12]

Coenzymes

 

Further information: Coenzyme

Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of substrate for a set of enzymes that produce it, and a set of enzymes that consume it. These coenzymes are therefore continuously being made, consumed and then recycled.[14]

One central coenzyme is phosphorylation reactions.

A 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.[16] 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.

 

Minerals and cofactors

Further information: Physiology, iron metabolism

Inorganic elements play critical roles in metabolism; some are abundant (e.g. organic compounds (proteins, lipids and carbohydrates) contain the majority of the carbon and nitrogen and most of the oxygen and hydrogen is present as water.[17]

The abundant inorganic elements act as action potentials in these tissues are produced by the exchange of electrolytes between the extracellular fluid and the cytosol.[19] 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.[20]

The metallothionein when not being used.[24][25]

Catabolism

Further information: Catabolism

Catabolism is the set of metabolic processes that break down large molecules. These include breaking down and oxidising 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, with organic molecules being used as a source of energy in cyanobacteria, these electron-transfer reactions do not release energy, but are used as a way of storing energy absorbed from sunlight.[6]

The most common set of catabolic reactions in animals can be separated into three main stages. In the first, large organic molecules such as 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 need to 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 glycoside hydrolases that digest polysaccharides into monosaccharides.

Microbes simply secrete digestive enzymes into their surroundings,[27][28] while animals only secrete these enzymes from specialized cells in their guts.[29] The amino acids or sugars released by these extracellular enzymes are then pumped into cells by specific active transport proteins.[30][31]  

Energy from organic compounds

Further information: protein catabolism

Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. Carbohydrates are usually taken into cells once they have been digested into nucleic acids.

Fats are catabolised 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.

gluconeogenesis (discussed below).[36]

Energy transformations

Oxidative phosphorylation

 

Further information: mitochondrion

In oxidative phosphorylation, the electrons removed from food molecules in pathways such as the citric acid cycle are transferred to oxygen and the energy released used to make ATP. This is done in eukaryotes by a series of proteins in the membranes of mitochondria called the protons across a membrane.[38]

Pumping protons out of the mitochondria creates a proton 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.[14]

Energy from inorganic compounds

Further information: 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 nitrification and denitrification and are critical for soil fertility.[45][46]

Energy from light

Further information: Phototroph, 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.[47][48]

The capture of solar energy is a process that is similar in principle to oxidative phosphorylation, as it involves energy being stored as a proton concentration gradient and this proton motive force then driving ATP synthesis.[14] The electrons needed to drive this electron transport chain come from light-gathering proteins called photosynthetic pigment present, with most photosynthetic bacteria only having one type of reaction center, while plants and cyanobacteria have two.[49]

In plants, Calvin cycle which is discussed below, or recycled for further ATP generation.[51]

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. Firstly, the production of precursors such as 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: carbon fixation and chemosynthesis

 

Photosynthesis is the synthesis of carbohydrates from sunlight, 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.[53]

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,[54] or the carboxylation of acetyl-CoA.[55][56] Prokaryotic chemoautotrophs also fix CO2 through the Calvin – Benson cycle, but use energy from inorganic compounds to drive the reaction.[57]

Carbohydrates and glycans

Further information: glycosylation

In carbohydrate anabolism, simple organic acids can be converted into 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.[58][59]

Although fat is a common way of storing energy, in vertebrates such as humans the oxaloacetate, where it can be used for the production of glucose.[62][60]

Polysaccharides and oligosaccharyltransferases.[64][65]

Fatty acids, isoprenoids and steroids

Further information: steroid metabolism

  Fatty acids are made by plastids and bacteria separate type II enzymes perform each step in the pathway.[67][68]

cholesterol and ergosterol.[74][73]

Proteins

Further information: 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 synthesize only the ten nonessential amino acids.[6] Thus, the transaminated to form an amino acid.[75]

Amino acids are made into proteins by being joined together in a chain by ribosome, which joins the amino acid onto the elongating protein chain, using the sequence information in a messenger RNA.[77]

Nucleotide synthesis and salvage

Further information: Nucleotide salvage, purine metabolism

Nucleotides are made from amino acids, carbon dioxide and Pyrimidines, on the other hand, are synthesized from the base orotate, which is formed from glutamine and aspartate.[80]

Xenobiotics and redox metabolism

Further information: 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 organochloride compounds.[86]

A related problem for peroxidases.[89][90]

Thermodynamics of living organisms

Further information: Biological thermodynamics

Living organisms must obey the thermodynamic terms, metabolism maintains order by creating disorder.[92]

Regulation and control

Further information: 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.[93][94] Metabolic regulation also allows organisms to respond to signals and interact actively with their environments.[95] 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).[96] 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.[97]  

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.[96] This type of regulation often involves phosphorylation of proteins.[100]

A very well understood example of extrinsic control is the regulation of glucose metabolism by the hormone protein phosphatases and producing a decrease in the phosphorylation of these enzymes.[103]

Evolution

Further information: Molecular evolution and phylogenetics

  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 methanogen that had extensive amino acid, nucleotide, carbohydrate and lipid metabolism.[105][106] The retention of these ancient pathways during later evolution may be the result of these reactions being 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.[3][4] The first pathways of enzyme-based metabolism may have been parts of RNA world.[107]

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.[108] 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 being created from pre-existing steps in the pathway.[109] 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) [110] These recruitment processes result in an evolutionary enzymatic mosaic. [111] 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.[112]

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.[113] Similar reduced metabolic capabilities are seen in endosymbiotic organisms.[114]

Investigation and manipulation

Further information: metabolomics and metabolic network modelling

 

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.[115] The enzymes that catalyze these chemical reactions can then be 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.[116]

An idea of the complexity of the DNA microarray studies.[119]

A major technological application of this information is metabolic engineering. Here, organisms such as shikimic acid.[120] These genetic modifications usually aim to reduce the amount of energy used to produce the product, increase yields and reduce the production of wastes.[121]

History

Further information: history of molecular biology

  The term metabolism is derived from the Greek Μεταβολισμός – "Metabolismos" for "change", or "overthrow".[122] 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 concept of metabolism dates back to Ibn al-Nafis (1213-1288), who stated that "the body and its parts are in a continuous state of dissolution and nourishment, so they are inevitably undergoing permanent change."[123] The first controlled experiments in human metabolism were published by Santorio Santorio in 1614 in his book Ars de statica medecina.[124] He described how he weighed himself before and after eating, sleeping, 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 urea,[127] 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 molecular dynamics simulations. These techniques have allowed the discovery and detailed analysis of the many molecules and metabolic pathways in cells.

See also

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Topic:Biochemistry

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Further reading

Introductory

  • Rose, S. and Mileusnic, R., The Chemistry of Life. (Penguin Press Science, 1999), ISBN 0-14027-273-9
  • Schneider, E. D. and Sagan, D., Into the Cool: Energy Flow, Thermodynamics, and Life. (University Of Chicago Press, 2005), ISBN 0-22673-936-8
  • Lane, N., Oxygen: The Molecule that Made the World. (Oxford University Press, USA, 2004), ISBN 0-19860-783-0

Advanced

  • Price, N. and Stevens, L., Fundamentals of Enzymology: Cell and Molecular Biology of Catalytic Proteins. (Oxford University Press, 1999), ISBN 0-19850-229-X
  • Berg, J. Tymoczko, J. and Stryer, L., Biochemistry. (W. H. Freeman and Company, 2002), ISBN 0-71674-955-6
  • Cox, M. and Nelson, D. L., Lehninger Principles of Biochemistry. (Palgrave Macmillan, 2004), ISBN 0-71674-339-6
  • Brock, T. D. Madigan, M. T. Martinko, J. and Parker J., Brock's Biology of Microorganisms. (Benjamin Cummings, 2002), ISBN 0-13066-271-2
  • 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 0-19855-598-9
  • Nicholls, D. G. and Ferguson, S. J., Bioenergetics. (Academic Press Inc., 2002), ISBN 0-12518-121-3

External links

External links
General information
  • Interactive Flow Chart of the Major Metabolic Pathways
  • 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.
  • Article on metabolism at The Encyclopœdia Britannica Concentrates on human metabolism (Free access).
Glossaries and dictionaries
  • Glossary of biochemical terms
  • Glossary of biochemical terms
  • On-line biology dictionary
Human metabolism
  • Topics in Medical Biochemistry Guide to human metabolic pathways. School level.
  • THE Medical Biochemistry Page Comprehensive resource on human metabolism.
Databases
  • The BioCyc Collection of Pathway/Genome Databases
  • Flow Chart of Metabolic Pathways at ExPASy
  • The KEGG PATHWAY Database
  • IUBMB-Nicholson Metabolic Pathways Chart
  • Reactome - a knowledgebase of biological processes
Metabolic pathways
  • Guide to Glycolysis School level.
  • The Nitrogen cycle and Nitrogen fixation at the Internet Archive Wayback Machine
  • Downloadable guide to photosynthesis School level.
  • What is Photosynthesis? Collection of photosynthesis articles and resources.


v • d • e
Metabolism
Anabolism

Aerobic)

Iron metabolism
 
This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Metabolism". A list of authors is available in Wikipedia.