Metabolism (from Greek: μεταβολή metabolē, "change") is the
set of life-sustaining chemical transformations within the cells of
organisms. The three main purposes of metabolism are the conversion of
food/fuel to energy to run cellular processes, the conversion of
food/fuel to building blocks for proteins, lipids, nucleic acids, and
some carbohydrates, and the elimination of nitrogenous wastes. These
enzyme-catalyzed reactions allow organisms to grow and reproduce,
maintain their structures, and respond to their environments. The word
metabolism can also refer to the sum of all chemical reactions that
occur in living organisms, including digestion and the transport of
substances into and between different cells, in which case the set of
reactions within the cells is called intermediary metabolism or
Metabolism is usually divided into two categories: catabolism, the
breaking down of organic matter for example, the breaking down of
glucose to pyruvate, by cellular respiration, and anabolism, the
building up of components of cells such as proteins and nucleic acids.
Usually, breaking down releases energy and building up consumes
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.
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
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.
1 Key biochemicals
1.1 Amino acids and proteins
1.6 Minerals and cofactors
Energy from organic compounds
3.1 Oxidative phosphorylation
Energy from inorganic compounds
Energy from light
4.2 Carbohydrates and glycans
4.3 Fatty acids, isoprenoids and steroids
Nucleotide synthesis and salvage
5 Xenobiotics and redox metabolism
6 Thermodynamics of living organisms
Regulation and control
9 Investigation and manipulation
11 See also
13 Further reading
14 External links
Further information: Biomolecule, Cell (biology), and Biochemistry
Structure of a triacylglycerol lipid
This is a diagram depicting a large set of human metabolic pathways.
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
Proteins (made of polypeptides)
Fibrous proteins and globular proteins
Starch, glycogen and cellulose
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 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.
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.
be linked together to form polysaccharides in almost limitless
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
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
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
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
Nicotinamide adenine dinucleotide
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
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
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
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 is the set of metabolic processes that break down large
molecules. These include breaking down and oxidizing food molecules.
The purpose of the catabolic reactions is to provide the energy and
components needed by anabolic reactions which build molecules. The
exact nature of these catabolic reactions differ from organism to
organism, and organisms can be classified based on their sources of
energy and carbon (their primary nutritional groups), as shown in the
table below. Organic molecules are used as a source of energy by
organotrophs, while lithotrophs use inorganic substrates, and
phototrophs capture sunlight as chemical energy. However, all these
different forms of metabolism depend on redox reactions that involve
the transfer of electrons from reduced donor molecules such as organic
molecules, water, ammonia, hydrogen sulfide or ferrous ions to
acceptor molecules such as oxygen, nitrate or sulfate. In animals,
these reactions involve complex organic molecules that are broken down
to simpler molecules, such as carbon dioxide and water. In
photosynthetic organisms, such as plants and cyanobacteria, these
electron-transfer reactions do not release energy but are used as a
way of storing energy absorbed from sunlight.
Classification of organisms based on their metabolism
The most common set of catabolic reactions in animals can be separated
into three main stages. In the first stage, large organic molecules,
such as proteins, polysaccharides or lipids, are digested into their
smaller components outside cells. Next, these smaller molecules are
taken up by cells and converted to smaller molecules, usually acetyl
coenzyme A (acetyl-CoA), which releases some energy. Finally, the
acetyl group on the CoA is oxidised to water and carbon dioxide in the
citric acid cycle and electron transport chain, releasing the energy
that is stored by reducing the coenzyme nicotinamide adenine
dinucleotide (NAD+) into NADH.
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, including the stomach and pancreas,
and salivary glands. The amino acids or sugars released by these
extracellular enzymes are then pumped into cells by active transport
A simplified outline of the catabolism of proteins, carbohydrates and
Energy from organic compounds
Further information: Cellular respiration, Fermentation
Fat catabolism, and Protein
Carbohydrate catabolism is the breakdown of carbohydrates into smaller
units. Carbohydrates are usually taken into cells once they have been
digested into monosaccharides. Once inside, the major route of
breakdown is glycolysis, where sugars such as glucose and fructose are
converted into pyruvate and some ATP is generated.
Pyruvate is an
intermediate in several metabolic pathways, but the majority is
converted to acetyl-CoA through aerobic (with oxygen) glycolysis and
fed into the citric acid cycle. Although some more ATP is generated in
the citric acid cycle, the most important product is NADH, which is
made from NAD+ as the acetyl-CoA is oxidized. This oxidation releases
carbon dioxide as a waste product. In anaerobic conditions, glycolysis
produces lactate, through the enzyme lactate dehydrogenase
re-oxidizing NADH to NAD+ for re-use in glycolysis. An alternative
route for glucose breakdown is the pentose phosphate pathway, which
reduces the coenzyme
NADPH and produces pentose sugars such as ribose,
the sugar component of nucleic acids.
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).
Further information: Oxidative phosphorylation, Chemiosmosis, and
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
Microbial metabolism and
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, and 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
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.
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 according to the number of constructed molecules in
their cells. Autotrophs such as plants can construct the complex
organic molecules in cells such as polysaccharides and proteins from
simple molecules like carbon dioxide and water. Heterotrophs, on the
other hand, require a source of more complex substances, such as
monosaccharides and amino acids, to produce these complex molecules.
Organisms can be further classified by ultimate source of their
energy: photoautotrophs and photoheterotrophs obtain energy from
light, whereas chemoautotrophs and chemoheterotrophs obtain energy
from inorganic oxidation reactions.
Further information: Photosynthesis,
Carbon fixation, and
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
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,
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.
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
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
Fatty acid synthesis and
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.
then be converted into other steroids such as cholesterol and
Protein biosynthesis and
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
through an ester bond. This aminoacyl-t
RNA precursor is produced in an
ATP-dependent reaction carried out by an aminoacyl tRNA
synthetase. This aminoacyl-t
RNA 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
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
Drug metabolism, Alcohol
metabolism, and Antioxidant
All organisms are constantly exposed to compounds that they cannot use
as foods and would be harmful if they accumulated in cells, as they
have no metabolic function. These potentially damaging compounds are
called 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
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
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
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
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
Insulin causes glycogen synthesis by activating protein
phosphatases and producing a decrease in the phosphorylation of these
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 common ancestor.
This universal ancestral cell was prokaryotic and probably a
methanogen that had extensive amino acid, nucleotide, carbohydrate and
lipid metabolism. The retention of these ancient pathways
during later evolution may be the result of these reactions having
been an optimal solution to their particular metabolic problems, with
pathways such as glycolysis and the citric acid cycle producing their
end products highly efficiently and in a minimal number of
steps. 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
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
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
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
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
History of biochemistry
History of biochemistry and History of molecular
The term metabolism is derived from the Greek
Μεταβολισμός – "Metabolismos" for "change", or
Aristotle's metabolism as an open flow model
The Parts of Animals
The Parts of Animals sets out enough details of his views
on metabolism for an open flow model to be made. He believed that at
each stage of the process, materials from food were transformed, with
heat being released as the classical element of fire, and residual
materials being excreted as urine, bile, or faeces.
Ibn al-Nafis described metabolism in his 1260 AD work titled
Al-Risalah al-Kamiliyyah fil Siera al-Nabawiyyah (The Treatise of
Kamil on the Prophet's Biography) which included the following phrase
"Both the body and its parts are in a continuous state of dissolution
and nourishment, so they are inevitably undergoing permanent
change." 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
Santorio Santorio in his steelyard balance, from Ars de statica
medicina, first published 1614
In these early studies, the mechanisms of these metabolic processes
had not been identified and a 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
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.
Underwater diving portal
Basal metabolic rate
Inborn error of metabolism
Iron-sulfur world theory, a "metabolism first" theory of the origin of
Primary nutritional groups
Thermic effect of food
^ a b Friedrich C (1998). "Physiology and genetics of sulfur-oxidizing
bacteria". Adv Microb Physiol. Advances in Microbial Physiology. 39:
ISBN 978-0-12-027739-1. PMID 9328649.
^ Pace NR (January 2001). "The universal nature of biochemistry".
Proc. Natl. Acad. Sci. U.S.A. 98 (3): 805–8.
PMC 33372 . PMID 11158550.
^ a b Smith E, Morowitz H (2004). "Universality in intermediary
metabolism". Proc Natl Acad Sci USA. 101 (36): 13168–73.
PMC 516543 . PMID 15340153.
^ a b 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.
doi:10.1006/bulm.2000.0197. PMID 11146883.
^ a b 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.
doi:10.1007/BF02338838. PMID 8703096.
^ Michie K, Löwe J (2006). "Dynamic filaments of the bacterial
cytoskeleton". Annu Rev Biochem. 75: 467–92.
^ a b c d e Nelson, David L.; Michael M. Cox (2005). Lehninger
Principles of Biochemistry. New York: W. H. Freeman and company.
p. 841. ISBN 0-7167-4339-6.
^ Kelleher J, Bryan 3rd, B, Mallet R, Holleran A, Murphy A, and Fiskum
G (1987). "Analysis of tricarboxylic acid-cycle metabolism of hepatoma
cells by comparison of 14CO2 ratios". Biochem J. 246 (3): 633–639.
doi:10.1042/bj2460633. PMC 1148327 .
PMID 3120698. CS1 maint: Uses authors parameter (link)
^ Hothersall, J & Ahmed, A (2013). "Metabolic fate of the
increased yeast amino acid uptake subsequent to catabolite
derepression". J Amino Acids. 2013: e461901. doi:10.1155/2013/461901.
PMC 3575661 . PMID 23431419.
^ Fahy E, Subramaniam S, Brown H, Glass C, Merrill A, Murphy R, Raetz
C, Russell D, Seyama Y, Shaw W, Shimizu T, Spener F, van Meer G,
VanNieuwenhze M, White S, Witztum J, Dennis E (2005). "A comprehensive
classification system for lipids". J
Lipid Res. 46 (5): 839–61.
doi:10.1194/jlr.E400004-JLR200. PMID 15722563.
^ "Nomenclature of Lipids". IUPAC-IUB Commission on Biochemical
Nomenclature (CBN). Retrieved 2007-03-08.
^ Hegardt F (1999). "Mitochondrial 3-hydroxy-3-methylglutaryl-CoA
synthase: a control enzyme in ketogenesis". Biochem J. 338 (Pt 3):
569–82. doi:10.1042/0264-6021:3380569. PMC 1220089 .
^ Raman R, Raguram S, Venkataraman G, Paulson J, Sasisekharan R
(2005). "Glycomics: an integrated systems approach to
structure-function relationships of glycans". Nat Methods. 2 (11):
817–24. doi:10.1038/nmeth807. PMID 16278650.
^ Sierra S, Kupfer B, Kaiser R (2005). "Basics of the virology of
HIV-1 and its replication". J Clin Virol. 34 (4): 233–44.
doi:10.1016/j.jcv.2005.09.004. PMID 16198625.
^ a b Wimmer M, Rose I (1978). "Mechanisms of enzyme-catalyzed group
transfer reactions". Annu Rev Biochem. 47: 1031–78.
doi:10.1146/annurev.bi.47.070178.005123. PMID 354490.
^ 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.
doi:10.1111/j.1432-1033.1979.tb12934.x. PMID 378655.
^ a b c d Dimroth P, von Ballmoos C, Meier T (March 2006). "Catalytic
and mechanical cycles in F-ATP synthases: Fourth in the Cycles Review
Series". EMBO Rep. 7 (3): 276–82. doi:10.1038/sj.embor.7400646.
PMC 1456893 . PMID 16607397.
^ Coulston, Ann; Kerner, John; Hattner, JoAnn; Srivastava, Ashini
Nutrition Principles and Clinical Nutrition". Stanford School
Nutrition Courses. SUMMIT.
^ 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. doi:10.1042/BJ20061638.
PMC 1798440 . PMID 17295611.
^ a b Heymsfield S, Waki M, Kehayias J, Lichtman S, Dilmanian F, Kamen
Y, Wang J, Pierson R (1991). "Chemical and elemental analysis of
humans in vivo using improved body composition models". Am J Physiol.
261 (2 Pt 1): E190–8. PMID 1872381.
^ Sychrová H (2004). "
Yeast as a model organism to study transport
and homeostasis of alkali metal cations" (PDF). Physiol Res. 53 Suppl
1: S91–8. PMID 15119939.
^ Levitan I (1988). "Modulation of ion channels in neurons and other
cells". Annu Rev Neurosci. 11: 119–36.
doi:10.1146/annurev.ne.11.030188.001003. PMID 2452594.
^ Dulhunty A (2006). "Excitation-contraction coupling from the 1950s
into the new millennium". Clin Exp Pharmacol Physiol. 33 (9):
^ Mahan D, Shields R (1998). "Macro- and micromineral composition of
pigs from birth to 145 kilograms of body weight" (PDF). J Anim Sci. 76
(2): 506–12. PMID 9498359.
^ Husted S, Mikkelsen B, Jensen J, Nielsen N (2004). "Elemental
fingerprint analysis of barley (Hordeum vulgare) using inductively
coupled plasma mass spectrometry, isotope-ratio mass spectrometry, and
multivariate statistics". Anal Bioanal Chem. 378 (1): 171–82.
doi:10.1007/s00216-003-2219-0. PMID 14551660.
^ Finney L, O'Halloran T (2003). "
Transition metal speciation in the
cell: insights from the chemistry of metal ion receptors". Science.
300 (5621): 931–6. Bibcode:2003Sci...300..931F.
doi:10.1126/science.1085049. PMID 12738850.
^ Cousins R, Liuzzi J, Lichten L (2006). "Mammalian zinc transport,
trafficking, and signals". J Biol Chem. 281 (34): 24085–9.
doi:10.1074/jbc.R600011200. PMID 16793761.
^ Dunn L, Rahmanto Y, Richardson D (2007). "
Iron uptake and metabolism
in the new millennium". Trends Cell Biol. 17 (2): 93–100.
doi:10.1016/j.tcb.2006.12.003. PMID 17194590.
^ Nealson K, Conrad P (1999). "Life: past, present and future". Philos
Trans R Soc Lond B Biol Sci. 354 (1392): 1923–39.
doi:10.1098/rstb.1999.0532. PMC 1692713 .
^ a b Nelson N, Ben-Shem A (2004). "The complex architecture of
oxygenic photosynthesis". Nat Rev Mol Cell Biol. 5 (12): 971–82.
doi:10.1038/nrm1525. PMID 15573135.
^ Häse C, Finkelstein R (December 1993). "Bacterial extracellular
zinc-containing metalloproteases". Microbiol Rev. 57 (4): 823–37.
PMC 372940 . PMID 8302217.
^ Gupta R, Gupta N, Rathi P (2004). "Bacterial lipases: an overview of
production, purification and biochemical properties". Appl Microbiol
Biotechnol. 64 (6): 763–81. doi:10.1007/s00253-004-1568-8.
^ Hoyle T (1997). "The digestive system: linking theory and practice".
Br J Nurs. 6 (22): 1285–91. PMID 9470654.
^ Souba W, Pacitti A (1992). "How amino acids get into cells:
mechanisms, models, menus, and mediators". JPEN J Parenter Enteral
Nutr. 16 (6): 569–78. doi:10.1177/0148607192016006569.
^ Barrett M, Walmsley A, Gould G (1999). "Structure and function of
facilitative sugar transporters". Curr Opin Cell Biol. 11 (4):
^ Bell G, Burant C, Takeda J, Gould G (1993). "Structure and function
of mammalian facilitative sugar transporters". J Biol Chem. 268 (26):
19161–4. PMID 8366068.
^ a b Bouché C, Serdy S, Kahn C, Goldfine A (2004). "The cellular
fate of glucose and its relevance in type 2 diabetes". Endocr Rev. 25
(5): 807–30. doi:10.1210/er.2003-0026. PMID 15466941.
^ Wipperman, Matthew, F.; Thomas, Suzanne, T.; Sampson, Nicole, S.
(2014). "Pathogen roid rage:
Cholesterol utilization by Mycobacterium
tuberculosis". Crit. Rev. Biochem. Mol. Biol. 49 (4): 269–93.
doi:10.3109/10409238.2014.895700. PMC 4255906 .
^ Sakami W, Harrington H (1963). "
Amino acid metabolism". Annu Rev
Biochem. 32: 355–98. doi:10.1146/annurev.bi.32.070163.002035.
^ Brosnan J (2000). "Glutamate, at the interface between amino acid
and carbohydrate metabolism". J Nutr. 130 (4S Suppl): 988S–90S.
^ Young V, Ajami A (2001). "Glutamine: the emperor or his clothes?". J
Nutr. 131 (9 Suppl): 2449S–59S; discussion 2486S–7S.
^ Hosler J, Ferguson-Miller S, Mills D (2006). "
Proton Transfer Through the Respiratory Complexes". Annu Rev Biochem.
75: 165–87. doi:10.1146/annurev.biochem.75.062003.101730.
PMC 2659341 . PMID 16756489.
^ Schultz B, Chan S (2001). "Structures and proton-pumping strategies
of mitochondrial respiratory enzymes". Annu Rev Biophys Biomol Struct.
30: 23–65. doi:10.1146/annurev.biophys.30.1.23.
^ Capaldi R, Aggeler R (2002). "Mechanism of the F(1)F(0)-type ATP
synthase, a biological rotary motor". Trends Biochem Sci. 27 (3):
154–60. doi:10.1016/S0968-0004(01)02051-5. PMID 11893513.
^ Friedrich B, Schwartz E (1993). "
Molecular biology of hydrogen
utilization in aerobic chemolithotrophs". Annu Rev Microbiol. 47:
^ Weber K, Achenbach L, Coates J (2006). "Microorganisms pumping iron:
anaerobic microbial iron oxidation and reduction". Nat Rev Microbiol.
4 (10): 752–64. doi:10.1038/nrmicro1490. PMID 16980937.
^ Jetten M, Strous M, van de Pas-Schoonen K, Schalk J, van Dongen U,
van de Graaf A, Logemann S, Muyzer G, van Loosdrecht M, Kuenen J
(1998). "The anaerobic oxidation of ammonium". FEMS Microbiol Rev. 22
(5): 421–37. doi:10.1111/j.1574-6976.1998.tb00379.x.
^ Simon J (2002). "
Enzymology and bioenergetics of respiratory nitrite
ammonification". FEMS Microbiol Rev. 26 (3): 285–309.
doi:10.1111/j.1574-6976.2002.tb00616.x. PMID 12165429.
^ Conrad R (1996). "Soil microorganisms as controllers of atmospheric
trace gases (H2, CO, CH4, OCS, N2O, and NO)". Microbiol Rev. 60 (4):
609–40. PMC 239458 . PMID 8987358.
^ Barea J, Pozo M, Azcón R, Azcón-Aguilar C (2005). "Microbial
co-operation in the rhizosphere". J Exp Bot. 56 (417): 1761–78.
doi:10.1093/jxb/eri197. PMID 15911555.
^ van der Meer M, Schouten S, Bateson M, Nübel U, Wieland A, Kühl M,
de Leeuw J, Sinninghe Damsté J, Ward D (July 2005). "Diel Variations
Metabolism by Green Nonsulfur-Like
Bacteria in Alkaline
Siliceous Hot Spring Microbial Mats from Yellowstone National Park".
Appl Environ Microbiol. 71 (7): 3978–86.
doi:10.1128/AEM.71.7.3978-3986.2005. PMC 1168979 .
^ Tichi M, Tabita F (2001). "Interactive Control of Rhodobacter
capsulatus Redox-Balancing Systems during Phototrophic Metabolism". J
Bacteriol. 183 (21): 6344–54. doi:10.1128/JB.183.21.6344-6354.2001.
PMC 100130 . PMID 11591679.
^ Allen J, Williams J (1998). "Photosynthetic reaction centers". FEBS
Lett. 438 (1–2): 5–9. doi:10.1016/S0014-5793(98)01245-9.
^ Munekage Y, Hashimoto M, Miyake C, Tomizawa K, Endo T, Tasaka M,
Shikanai T (2004). "Cyclic electron flow around photosystem I is
essential for photosynthesis". Nature. 429 (6991): 579–82.
^ Miziorko H, Lorimer G (1983). "Ribulose-1,5-bisphosphate
carboxylase-oxygenase". Annu Rev Biochem. 52: 507–35.
doi:10.1146/annurev.bi.52.070183.002451. PMID 6351728.
^ Dodd A, Borland A, Haslam R, Griffiths H, Maxwell K (2002).
"Crassulacean acid metabolism: plastic, fantastic". J Exp Bot. 53
(369): 569–80. doi:10.1093/jexbot/53.369.569.
^ Hügler M, Wirsen C, Fuchs G, Taylor C, Sievert S (May 2005).
"Evidence for Autotrophic CO2 Fixation via the Reductive Tricarboxylic
Acid Cycle by Members of the ɛ Subdivision of Proteobacteria". J
Bacteriol. 187 (9): 3020–7. doi:10.1128/JB.187.9.3020-3027.2005.
PMC 1082812 . PMID 15838028.
^ Strauss G, Fuchs G (1993). "
Enzymes of a novel autotrophic CO2
fixation pathway in the phototrophic bacterium Chloroflexus
aurantiacus, the 3-hydroxypropionate cycle". Eur J Biochem. 215 (3):
^ Wood H (1991). "
Life with CO or CO2 and H2 as a source of carbon and
energy". FASEB J. 5 (2): 156–63. PMID 1900793.
^ Shively J, van Keulen G, Meijer W (1998). "Something from almost
nothing: carbon dioxide fixation in chemoautotrophs". Annu Rev
Microbiol. 52: 191–230. doi:10.1146/annurev.micro.52.1.191.
^ Boiteux A, Hess B (1981). "Design of glycolysis". Philos Trans R Soc
Lond B Biol Sci. 293 (1063): 5–22. Bibcode:1981RSPTB.293....5B.
doi:10.1098/rstb.1981.0056. PMID 6115423.
^ Pilkis S, el-Maghrabi M, Claus T (1990). "Fructose-2,6-bisphosphate
in control of hepatic gluconeogenesis. From metabolites to molecular
genetics". Diabetes Care. 13 (6): 582–99.
doi:10.2337/diacare.13.6.582. PMID 2162755.
^ a b Ensign S (2006). "Revisiting the glyoxylate cycle: alternate
pathways for microbial acetate assimilation". Mol Microbiol. 61 (2):
^ Finn P, Dice J (2006). "Proteolytic and lipolytic responses to
starvation". Nutrition. 22 (7–8): 830–44.
doi:10.1016/j.nut.2006.04.008. PMID 16815497.
^ a b Kornberg H, Krebs H (1957). "Synthesis of cell constituents from
C2-units by a modified tricarboxylic acid cycle". Nature. 179 (4568):
988–91. Bibcode:1957Natur.179..988K. doi:10.1038/179988a0.
^ Rademacher T, Parekh R, Dwek R (1988). "Glycobiology". Annu Rev
Biochem. 57: 785–838. doi:10.1146/annurev.bi.57.070188.004033.
^ Opdenakker G, Rudd P, Ponting C, Dwek R (1993). "Concepts and
principles of glycobiology". FASEB J. 7 (14): 1330–7.
^ McConville M, Menon A (2000). "Recent developments in the cell
biology and biochemistry of glycosylphosphatidylinositol lipids
(review)". Mol Membr Biol. 17 (1): 1–16.
doi:10.1080/096876800294443. PMID 10824734.
^ Chirala S, Wakil S (2004). "Structure and function of animal fatty
acid synthase". Lipids. 39 (11): 1045–53.
doi:10.1007/s11745-004-1329-9. PMID 15726818.
^ White S, Zheng J, Zhang Y (2005). "The structural biology of type II
fatty acid biosynthesis". Annu Rev Biochem. 74: 791–831.
^ Ohlrogge J, Jaworski J (1997). "
Regulation of fatty acid synthesis".
Plant Mol Biol. 48: 109–136.
doi:10.1146/annurev.arplant.48.1.109. PMID 15012259.
^ Dubey V, Bhalla R, Luthra R (2003). "An overview of the
non-mevalonate pathway for terpenoid biosynthesis in plants" (PDF). J
Biosci. 28 (5): 637–46. doi:10.1007/BF02703339. PMID 14517367.
Archived from the original (PDF) on 2007-04-15.
^ a b Kuzuyama T, Seto H (2003). "Diversity of the biosynthesis of the
isoprene units". Nat Prod Rep. 20 (2): 171–83. doi:10.1039/b109860h.
^ Grochowski L, Xu H, White R (May 2006). "Methanocaldococcus
jannaschii Uses a Modified Mevalonate Pathway for Biosynthesis of
Isopentenyl Diphosphate". J Bacteriol. 188 (9): 3192–8.
doi:10.1128/JB.188.9.3192-3198.2006. PMC 1447442 .
^ Lichtenthaler H (1999). "The 1-Ddeoxy-D-xylulose-5-phosphate pathway
of isoprenoid biosynthesis in plants". Annu Rev
Plant Physiol Plant
Mol Biol. 50: 47–65. doi:10.1146/annurev.arplant.50.1.47.
^ a b Schroepfer G (1981). "Sterol biosynthesis". Annu Rev Biochem.
50: 585–621. doi:10.1146/annurev.bi.50.070181.003101.
^ Lees N, Skaggs B, Kirsch D, Bard M (1995). "Cloning of the late
genes in the ergosterol biosynthetic pathway of Saccharomyces
cerevisiae—a review". Lipids. 30 (3): 221–6.
doi:10.1007/BF02537824. PMID 7791529.
^ Himmelreich R, Hilbert H, Plagens H, Pirkl E, Li BC, Herrmann R
(November 1996). "Complete sequence analysis of the genome of the
bacterium Mycoplasma pneumoniae". Nucleic Acids Res. 24 (22):
4420–49. doi:10.1093/nar/24.22.4420. PMC 146264 .
^ Guyton, Arthur C.; John E. Hall (2006). Textbook of Medical
Physiology. Philadelphia: Elsevier. pp. 855–6.
^ Ibba M, Söll D (2001). "The renaissance of aminoacyl-tRNA
synthesis". EMBO Rep. 2 (5): 382–7. doi:10.1093/embo-reports/kve095.
PMC 1083889 . PMID 11375928. Archived from the original on
^ Lengyel P, Söll D (1969). "Mechanism of protein biosynthesis".
Bacteriol Rev. 33 (2): 264–301. PMC 378322 .
^ a b Rudolph F (1994). "The biochemistry and physiology of
nucleotides". J Nutr. 124 (1 Suppl): 124S–127S.
PMID 8283301. Zrenner R, Stitt M, Sonnewald U, Boldt R
Pyrimidine and purine biosynthesis and degradation in
plants". Annu Rev
Plant Biol. 57: 805–36.
^ Stasolla C, Katahira R, Thorpe T, Ashihara H (2003). "
pyrimidine nucleotide metabolism in higher plants". J
160 (11): 1271–95. doi:10.1078/0176-1617-01169.
^ Davies O, Mendes P, Smallbone K, Malys N (2012). "Characterisation
of multiple substrate-specific (d)ITP/(d)XTPase and modelling of
deaminated purine nucleotide metabolism". BMB Reports. 45 (4):
259–64. doi:10.5483/BMBRep.2012.45.4.259. PMID 22531138.
^ Smith J (1995). "
Enzymes of nucleotide synthesis". Curr Opin Struct
Biol. 5 (6): 752–7. doi:10.1016/0959-440X(95)80007-7.
^ Testa B, Krämer S (2006). "The biochemistry of drug metabolism—an
introduction: part 1. Principles and overview". Chem Biodivers. 3
(10): 1053–101. doi:10.1002/cbdv.200690111.
^ Danielson P (2002). "The cytochrome P450 superfamily: biochemistry,
evolution and drug metabolism in humans". Curr
Drug Metab. 3 (6):
561–97. doi:10.2174/1389200023337054. PMID 12369887.
^ King C, Rios G, Green M, Tephly T (2000).
Drug Metab. 1 (2): 143–61.
doi:10.2174/1389200003339171. PMID 11465080.
^ Sheehan D, Meade G, Foley V, Dowd C (November 2001). "Structure,
function and evolution of glutathione transferases: implications for
classification of non-mammalian members of an ancient enzyme
superfamily". Biochem J. 360 (Pt 1): 1–16.
doi:10.1042/0264-6021:3600001. PMC 1222196 .
^ Galvão T, Mohn W, de Lorenzo V (2005). "Exploring the microbial
biodegradation and biotransformation gene pool". Trends Biotechnol. 23
(10): 497–506. doi:10.1016/j.tibtech.2005.08.002.
^ Janssen D, Dinkla I, Poelarends G, Terpstra P (2005). "Bacterial
degradation of xenobiotic compounds: evolution and distribution of
novel enzyme activities". Environ Microbiol. 7 (12): 1868–82.
doi:10.1111/j.1462-2920.2005.00966.x. PMID 16309386.
^ Davies K (1995). "Oxidative stress: the paradox of aerobic life".
Biochem Soc Symp. 61: 1–31. doi:10.1042/bss0610001.
^ Tu B, Weissman J (2004). "Oxidative protein folding in eukaryotes:
mechanisms and consequences". J Cell Biol. 164 (3): 341–6.
doi:10.1083/jcb.200311055. PMC 2172237 .
^ Sies H (1997). "Oxidative stress: oxidants and antioxidants" (PDF).
Exp Physiol. 82 (2): 291–5. doi:10.1113/expphysiol.1997.sp004024.
^ Vertuani S, Angusti A, Manfredini S (2004). "The antioxidants and
pro-antioxidants network: an overview". Curr Pharm Des. 10 (14):
1677–94. doi:10.2174/1381612043384655. PMID 15134565.
^ 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. doi:10.1016/S0005-2728(99)00065-1.
^ Demirel Y, Sandler S (2002). "Thermodynamics and bioenergetics".
Biophys Chem. 97 (2–3): 87–111. doi:10.1016/S0301-4622(02)00069-8.
^ Albert R (2005). "Scale-free networks in cell biology". J Cell Sci.
118 (Pt 21): 4947–57. doi:10.1242/jcs.02714.
^ Brand M (1997). "
Regulation analysis of energy metabolism". J Exp
Biol. 200 (Pt 2): 193–202. PMID 9050227.
^ Soyer O, Salathé M, Bonhoeffer S (2006). "Signal transduction
networks: topology, response and biochemical processes". J Theor Biol.
238 (2): 416–25. doi:10.1016/j.jtbi.2005.05.030.
^ a b Salter M, Knowles R, Pogson C (1994). "Metabolic control".
Essays Biochem. 28: 1–12. PMID 7925313.
^ Westerhoff H, Groen A, Wanders R (1984). "Modern theories of
metabolic control and their applications (review)". Biosci Rep. 4 (1):
1–22. doi:10.1007/BF01120819. PMID 6365197.
^ Fell D, Thomas S (1995). "Physiological control of metabolic flux:
the requirement for multisite modulation". Biochem J. 311 (Pt 1):
35–9. PMC 1136115 . PMID 7575476.
^ Hendrickson W (2005). "Transduction of biochemical signals across
cell membranes". Q Rev Biophys. 38 (4): 321–30.
doi:10.1017/S0033583506004136. PMID 16600054.
^ Cohen P (2000). "The regulation of protein function by multisite
phosphorylation—a 25 year update". Trends Biochem Sci. 25 (12):
^ Lienhard G, Slot J, James D, Mueckler M (1992). "How cells absorb
glucose". Sci Am. 266 (1): 86–91.
doi:10.1038/scientificamerican0192-86. PMID 1734513.
^ Roach P (2002). "
Glycogen and its metabolism". Curr Mol Med. 2 (2):
101–20. doi:10.2174/1566524024605761. PMID 11949930.
^ Newgard C, Brady M, O'Doherty R, Saltiel A (2000). "Organizing
glucose disposal: emerging roles of the glycogen targeting subunits of
protein phosphatase-1" (PDF). Diabetes. 49 (12): 1967–77.
doi:10.2337/diabetes.49.12.1967. PMID 11117996.
^ Romano A, Conway T (1996). "
Evolution of carbohydrate metabolic
pathways". Res Microbiol. 147 (6–7): 448–55.
doi:10.1016/0923-2508(96)83998-2. PMID 9084754.
^ Koch A (1998). "How did bacteria come to be?". Adv Microb Physiol.
Advances in Microbial Physiology. 40: 353–99.
doi:10.1016/S0065-2911(08)60135-6. ISBN 978-0-12-027740-7.
^ Ouzounis C, Kyrpides N (1996). "The emergence of major cellular
processes in evolution". FEBS Lett. 390 (2): 119–23.
doi:10.1016/0014-5793(96)00631-X. PMID 8706840.
^ Caetano-Anolles G, Kim HS, Mittenthal JE (2007). "The origin of
modern metabolic networks inferred from phylogenomic analysis of
protein architecture". Proc Natl Acad Sci USA. 104 (22): 9358–63.
PMC 1890499 . PMID 17517598.
^ Schmidt S, Sunyaev S, Bork P, Dandekar T (2003). "Metabolites: a
helping hand for pathway evolution?". Trends Biochem Sci. 28 (6):
336–41. doi:10.1016/S0968-0004(03)00114-2. PMID 12826406.
^ Light S, Kraulis P (2004). "Network analysis of metabolic enzyme
evolution in Escherichia coli". BMC Bioinformatics. 5: 15.
doi:10.1186/1471-2105-5-15. PMC 394313 .
PMID 15113413. Alves R, Chaleil R, Sternberg M (2002).
Evolution of enzymes in metabolism: a network perspective". J Mol
Biol. 320 (4): 751–70. doi:10.1016/S0022-2836(02)00546-6.
^ Kim HS, Mittenthal JE, Caetano-Anolles G (2006). "MANET: tracing
evolution of protein architecture in metabolic networks". BMC
Bioinformatics. 7: 351. doi:10.1186/1471-2105-7-351.
PMC 1559654 . PMID 16854231.
^ Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C
(2001). "Small-molecule metabolsim: an enzyme mosaic". Trends
Biotechnol. 19 (12): 482–6. doi:10.1016/S0167-7799(01)01813-3.
^ Spirin V, Gelfand M, Mironov A, Mirny L (June 2006). "A metabolic
network in the evolutionary context: Multiscale structure and
modularity". Proc Natl Acad Sci USA. 103 (23): 8774–9.
PMC 1482654 . PMID 16731630.
^ Lawrence J (2005). "Common themes in the genome strategies of
pathogens". Curr Opin Genet Dev. 15 (6): 584–8.
doi:10.1016/j.gde.2005.09.007. PMID 16188434. Wernegreen J
(2005). "For better or worse: genomic consequences of intracellular
mutualism and parasitism". Curr Opin Genet Dev. 15 (6): 572–83.
doi:10.1016/j.gde.2005.09.013. PMID 16230003.
^ Pál C, Papp B, Lercher M, Csermely P, Oliver S, Hurst L (2006).
"Chance and necessity in the evolution of minimal metabolic networks".
Nature. 440 (7084): 667–70. Bibcode:2006Natur.440..667P.
doi:10.1038/nature04568. PMID 16572170.
^ Rennie M (1999). "An introduction to the use of tracers in nutrition
and metabolism". Proc Nutr Soc. 58 (4): 935–44.
doi:10.1017/S002966519900124X. PMID 10817161.
^ Phair R (1997). "Development of kinetic models in the nonlinear
world of molecular cell biology". Metabolism. 46 (12): 1489–95.
doi:10.1016/S0026-0495(97)90154-2. PMID 9439549.
^ Sterck L, Rombauts S, Vandepoele K, Rouzé P, Van de Peer Y (2007).
"How many genes are there in plants (... and why are they
there)?". Curr Opin
Plant Biol. 10 (2): 199–203.
doi:10.1016/j.pbi.2007.01.004. PMID 17289424.
^ Borodina I, Nielsen J (2005). "From genomes to in silico cells via
metabolic networks". Curr Opin Biotechnol. 16 (3): 350–5.
doi:10.1016/j.copbio.2005.04.008. PMID 15961036.
^ Gianchandani E, Brautigan D, Papin J (2006). "Systems analyses
characterize integrated functions of biochemical networks". Trends
Biochem Sci. 31 (5): 284–91. doi:10.1016/j.tibs.2006.03.007.
^ Duarte NC, Becker SA, Jamshidi N, et al. (February 2007). "Global
reconstruction of the human metabolic network based on genomic and
bibliomic data". Proc. Natl. Acad. Sci. U.S.A. 104 (6): 1777–82.
PMC 1794290 . PMID 17267599.
^ Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabási AL (May
2007). "The human disease network". Proc. Natl. Acad. Sci. U.S.A. 104
(21): 8685–90. Bibcode:2007PNAS..104.8685G.
doi:10.1073/pnas.0701361104. PMC 1885563 .
^ Lee DS, Park J, Kay KA, Christakis NA, Oltvai ZN, Barabási AL (July
2008). "The implications of human metabolic network topology for
disease comorbidity". Proc. Natl. Acad. Sci. U.S.A. 105 (29):
9880–9885. Bibcode:2008PNAS..105.9880L. doi:10.1073/pnas.0802208105.
PMC 2481357 . PMID 18599447.
^ Csete M, Doyle J (2004). "Bow ties, metabolism and disease". Trends
Biotechnol. 22 (9): 446–50. doi:10.1016/j.tibtech.2004.07.007.
^ Ma HW, Zeng AP (2003). "The connectivity structure, giant strong
component and centrality of metabolic networks". Bioinformatics. 19
(11): 1423–30. CiteSeerX 10.1.1.605.8964 .
doi:10.1093/bioinformatics/btg177. PMID 12874056.
^ Zhao J, Yu H, Luo JH, Cao ZW, Li YX (2006). "Hierarchical modularity
of nested bow-ties in metabolic networks". BMC Bioinformatics. 7: 386.
doi:10.1186/1471-2105-7-386. PMC 1560398 .
^ Thykaer J, Nielsen J (2003). "
Metabolic engineering of beta-lactam
production". Metab Eng. 5 (1): 56–69.
doi:10.1016/S1096-7176(03)00003-X. PMID 12749845.
González-Pajuelo M, Meynial-Salles I, Mendes F, Andrade J,
Vasconcelos I, Soucaille P (2005). "
Metabolic engineering of
Clostridium acetobutylicum for the industrial production of
1,3-propanediol from glycerol". Metab Eng. 7 (5–6): 329–36.
doi:10.1016/j.ymben.2005.06.001. PMID 16095939. Krämer M,
Bongaerts J, Bovenberg R, Kremer S, Müller U, Orf S, Wubbolts M,
Raeven L (2003). "
Metabolic engineering for microbial production of
shikimic acid". Metab Eng. 5 (4): 277–83.
doi:10.1016/j.ymben.2003.09.001. PMID 14642355.
^ Koffas M, Roberge C, Lee K, Stephanopoulos G (1999). "Metabolic
engineering". Annu Rev Biomed Eng. 1: 535–57.
doi:10.1146/annurev.bioeng.1.1.535. PMID 11701499.
^ "Metabolism". The Online Etymology Dictionary. Retrieved
^ Leroi, Armand Marie (2014). The Lagoon: How
Science. Bloomsbury. pp. 400–401.
^ Dr. Abu Shadi Al-Roubi (1982), "Ibn Al-Nafis as a philosopher",
Symposium on Ibn al-Nafis, Second International Conference on Islamic
Medicine: Islamic Medical Organization, Kuwait (cf.
Ibn al-Nafis As a
Philosopher, Encyclopedia of Islamic World )
^ Eknoyan G (1999). "Santorio Sanctorius (1561–1636) –
founding father of metabolic balance studies". Am J Nephrol. 19 (2):
226–33. doi:10.1159/000013455. PMID 10213823.
^ Williams, H. S. (1904) A History of Science: in Five Volumes. Volume
IV: Modern Development of the Chemical and Biological Sciences Harper
and Brothers (New York) Retrieved on 2007-03-26
^ Dubos J. (1951). "Louis Pasteur: Free Lance of Science, Gollancz.
Quoted in Manchester K. L. (1995)
Louis Pasteur (1822–1895)—chance
and the prepared mind". Trends Biotechnol. 13 (12): 511–515.
doi:10.1016/S0167-7799(00)89014-9. PMID 8595136.
^ Kinne-Saffran E, Kinne R (1999). "
Vitalism and synthesis of urea.
From Friedrich Wöhler to Hans A. Krebs". Am J Nephrol. 19 (2):
290–4. doi:10.1159/000013463. PMID 10213830.
^ Eduard Buchner's 1907 Nobel lecture at http://nobelprize.org
^ Kornberg H (2000). "Krebs and his trinity of cycles". Nat Rev Mol
Cell Biol. 1 (3): 225–8. doi:10.1038/35043073.
^ Krebs HA, Henseleit K (1932). "Untersuchungen über die
Harnstoffbildung im tierkorper". Z. Physiol. Chem. 210: 33–66.
Krebs H, Johnson W (April 1937). "
Metabolism of ketonic acids in
animal tissues". Biochem J. 31 (4): 645–60. doi:10.1042/bj0310645.
PMC 1266984 . PMID 16746382.
Library resources about
Resources in your library
Resources in other libraries
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:
Thermodynamics, and Life. (University Of Chicago Press, 2005),
Lane, N., Oxygen: The
Molecule that Made the World. (Oxford University
Press, USA, 2004), ISBN 0-19-860783-0
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),
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
Wikiversity has learning resources about Topic:Biochemistry
Wikibooks has more on the topic of: Metabolism
Look up metabolism in Wiktionary, the free dictionary.
Biochemistry of Metabolism
Sparknotes SAT biochemistry Overview of biochemistry. School level.
MIT Biology Hypertextbook Undergraduate-level guide to molecular
Topics in Medical
Biochemistry Guide to human metabolic pathways.
http://themedicalbiochemistrypage.org/ THE Medical
Comprehensive resource on human metabolism.
Flow Chart of Metabolic Pathways at ExPASy
IUBMB-Nicholson Metabolic Pathways Chart
SuperCYP: Database for Drug-Cytochrome-Metabolism
Metabolism reference Pathway
Nitrogen cycle and
Nitrogen fixation at the Wayback Machine
Articles related to Metabolism
Direct / C4 / CAM
Sugars & Glycans
& Sialic Acids
Acids & Histidine
& Carotenoids (
& Carotenoids (
& Thyroid Hormones
Major metabolic pathways in metro-style map. Click any text (name of
pathway or metabolites) to link to the corresponding article.
Single lines: pathways common to most lifeforms. Double lines:
pathways not in humans (occurs in e.g. plants, fungi, prokaryotes).
Orange nodes: carbohydrate metabolism. Violet nodes: photosynthesis.
Red nodes: cellular respiration. Pink nodes: cell signaling. Blue
nodes: amino acid metabolism. Grey nodes: vitamin and cofactor
metabolism. Brown nodes: nucleotide and protein metabolism. Green
nodes: lipid metabolism.
Metabolism, catabolism, anabolism
Primary nutritional groups
Pyruvate decarboxylation →
Citric acid cycle
Citric acid cycle →
Oxidative phosphorylation (electron transport chain + ATP synthase)
Electron acceptors are other than oxygen
Glycolysis ⇄ Gluconeogenesis
Glycogenolysis ⇄ Glycogenesis
Pentose phosphate pathway
Fatty acid metabolism
Fatty acid degradation (Beta oxidation)
Fatty acid synthesis
Reverse cholesterol transport
Amino acid synthesis
Metabolism: carbohydrate metabolism: glycolysis/gluconeogenesis
Hexokinase (HK1, HK2, HK3, Glucokinase)→/
Phosphofructokinase 1 (Liver, Muscle, Platelet)→/Fructose
Fructose-bisphosphate aldolase (Aldolase A, B, C)
Glyceraldehyde 3-phosphate dehydrogenase
Pyruvate kinase (PKLR, PKM2)
from lactate (Cori cycle):
from alanine (
Fructose 6-P,2-kinase:fructose 2,6-bisphosphatase
PFKFB1, PFKFB2, PFKFB3, PFKFB4
Metabolism: carbohydrate metabolism
fructose and galactose enzymes
Fructose / Fructolysis
Galactose / Galactolysis
Galactose-1-phosphate uridylyltransferase/UDP-glucose 4-epimerase
Mannose phosphate isomerase
Metabolism: carbohydrate metabolism
Metabolism: carbohydrate metabolism · glycoprotein enzymes
Metabolism, lipid metabolism, glycolipid enzymes
Sphingomyelin phosphodiesterase 1
Palmitoyl protein thioesterase
Tripeptidyl peptidase I
Serine C-palmitoyltransferase (SPTLC1)
Ceramide glucosyltransferase (UGCG)
Metabolism: lipid metabolism - eicosanoid metabolism enzymes
5-Lipoxygenase activating protein/Arachidonate 5-lipoxygenase
LTA4 hydrolase (B4 synthesis)
Metabolism: lipid metabolism / fatty acid metabolism, triglyceride and
fatty acid enzymes
ATP citrate lyase
Fatty acid synthesis/
Fatty acid synthase
Β-Ketoacyl ACP reductase
3-Hydroxyacyl ACP dehydrase
Enoyl ACP reductase
Fatty acid desaturases
Carnitine palmitoyltransferase I
Carnitine palmitoyltransferase II
Acyl CoA dehydrogenase
Acyl CoA dehydrogenase (ACADL
Enoyl CoA isomerase
2,4 Dienoyl-CoA reductase
Coenzyme A dehydrogenase
Metabolism: amino acid metabolism - urea cycle enzymes
Carbamoyl phosphate synthetase I
Enzymes involved in neurotransmission
histidine → histamine
Aromatic L-amino acid decarboxylase
Aromatic L-amino acid decarboxylase
Nitric oxide synthase (NOS1, NOS2, NOS3)
Cholinesterase (Acetylcholinesterase, Butyrylcholinesterase)
Enzymes involved in the metabolism of heme and porphyrin
Aminolevulinic acid synthase
Uroporphyrinogen III synthase
Uroporphyrinogen III decarboxylase
Coproporphyrinogen III oxidase
Metabolism of vitamins, coenzymes, and cofactors
Fat soluble vitamins
Retinol binding protein
Alpha-tocopherol transfer protein
liver (Sterol 27-hydroxylase or CYP27A1)
25-Hydroxyvitamin D3 1-alpha-hydroxylase
25-Hydroxyvitamin D3 1-alpha-hydroxylase or CYP27B1)
degradation (1,25-Dihydroxyvitamin D3 24-hydroxylase or CYP24A1)
Vitamin K epoxide reductase
Water soluble vitamins
Pantothenic acid (B5)
Folic acid (B9)
GTP cyclohydrolase I
Protein metabolism, synthesis and catabolism enzymes
Essential amino acids are in Capitals
Branched-chain amino acid
Branched-chain amino acid aminotransferase
Branched-chain alpha-keto acid dehydrogenase complex
Isovaleryl coenzyme A dehydrogenase
glycine→creatine: Guanidinoacetate N-methyltransferase
cysteine+glutamate→glutathione: Gamma-glutamylcysteine synthetase
Branched-chain amino acid
Branched-chain amino acid aminotransferase
Branched-chain alpha-keto acid dehydrogenase complex
Methylmalonate semialdehyde dehydrogenase
Branched-chain amino acid
Branched-chain amino acid aminotransferase
Branched-chain alpha-keto acid dehydrogenase complex
generation of homocysteine:
regeneration of methionine:
conversion to cysteine: Cystathionine beta synthase
Methylmalonyl CoA epimerase
Metabolism: amino acid metabolism
AIR synthetase (FGAM cyclase)
Purine nucleoside phosphorylase
Carbamoyl phosphate synthase II
Orotidine 5'-phosphate decarboxylase/Uridine monophosphate synthetase
Metabolism: lipid metabolism – ketones/cholesterol synthesis
Coenzyme A acetyltransferase
HMG-CoA synthase (regulated step)
To Mevalonic acid
Isopentenyl-diphosphate delta isomerase
Cholesterol side-chain cleavage
To sex hormones
Steroid metabolism: sulfatase
Steroidogenic acute regulatory protein
Cholesterol total synthesis
Reverse cholesterol transport
Metabolism: carbohydrate metabolism · pentose phosphate pathway
Metabolism - non-mevalonate pathway enzymes
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
4-hydroxy-3-methylbut-2-enyl diphosphate reductase
Essential fatty acids
"Minerals" (Chemical elements)
Adulterants, food contaminants
Mercury in fish
Monosodium glutamate (MSG)
High-fructose corn syrup
Escherichia coli O104:H4
Escherichia coli O157:H7
Parasitic infections through food
Ethylenediaminetetraacetic acid (EDTA)
Toxins, poisons, environment pollution
Arsenic contamination of groundwater
Benzene in soft drinks
Food contamination incidents
Swill milk scandal
1858 Bradford sweets poisoning
1900 English beer poisoning
Morinaga Milk arsenic poisoning incident
1971 Iraq poison grain disaster
Toxic oil syndrome
1993 Jack in the Box E. coli outbreak
1996 Odwalla E. coli outbreak
2006 North American E. coli outbreaks
ICA meat repackaging controversy
2008 Canada listeriosis outbreak
2008 Chinese milk scandal
2008 Irish pork crisis
2008 United States salmonellosis outbreak
2011 Germany E. coli outbreak
2011 Taiwan food scandal
2011 United States listeriosis outbreak
2013 Bihar school meal poisoning
2013 horse meat scandal
2013 Taiwan food scandal
2014 Taiwan food scandal
2017 Brazil weak meat scandal
2017–18 South African listeriosis outbreak
Food safety incidents in China
Regulation, standards, watchdogs
Acceptable daily intake
Food labeling regulations
Food libel laws
International Food Safety Network
Quality Assurance International
Centre for Food Safety
European Food Safety Authority
Institute for Food Safety and Health
International Food Safety Network
Ministry of Food and
Artificial fat substitutes
Artificial protein substitutes
Acid-hydrolyzed vegetable protein
Artificial sugar substitutes
Hydrogenated starch hydrolysates
Natural food substitutes
International Association for Food Protection
Food and Agriculture Organization
National Agriculture and Food Research Organization
National Food and
Diving medicine, physiology, physics and environment
Atrial septal defect
High-pressure nervous syndrome
Instinctive drowning response
Salt water aspiration syndrome
Swimming-induced pulmonary edema
List of signs and symptoms of diving disorders
Hyperbaric treatment schedules
Fitness to dive
Artificial gills (human)
Cold shock response
Dead space (physiology)
History of decompression research and development
Maximum operating depth
Oxygen window in diving decompression
Physiological response to water immersion
Physiology of decompression
Respiratory exchange ratio
Breathing performance of regulators
Combined gas law
Ideal gas law
List of diving hazards and precautions
Surge (wave action)
Undertow (water waves)
Arthur J. Bachrach
Albert R. Behnke
George F. Bond
Albert A. Bühlmann
John R Clarke
William Paul Fife
John Scott Haldane
Robert William Hamilton Jr.
Leonard Erskine Hill
Brian Andrew Hills
Christian J. Lambertsen
John Rawlins R.N.
Charles Wesley Shilling
Edward D. Thalmann
Aerospace Medical Association
Divers Alert Network
Divers Alert Network (DAN)
Diving Diseases Research Centre
Diving Diseases Research Centre (DDRC)
Diving Medical Advisory Council (DMAC
European Diving Technology Committee
European Diving Technology Committee (EDTC)
European Underwater and Baromedical Society
European Underwater and Baromedical Society (EUBS)
National Board of Diving and Hyperbaric Medical Technology
Naval Submarine Medical Research Laboratory
Royal Australian Navy School of Underwater Medicine
South Pacific Underwater Medicine Society
South Pacific Underwater Medicine Society (SPUMS)
Southern African Underwater and Hyperbaric Medical Association
Southern African Underwater and Hyperbaric Medical Association (SAUHMA
Undersea and Hyperbaric Medical Society
Undersea and Hyperbaric Medical Society (UHMS)
United States Navy Experimental Diving Unit
United States Navy Experimental Diving Unit (NEDU)
Categories: Diving medicine
Underwater diving physiology
Underwater diving physics