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adenosine triphosphate, a central intermediate in energy metabolism.
Metabolism is the complete set of chemical reactions that occur in living cell (biology). These processes are the basis of
life, allowing cells to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories.
Catabolism yields energy, an example being the breakdown of food in cellular respiration. Anabolism, on the other hand, uses this energy to construct components of cells such as
proteins and
nucleic acids.
The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed into another by a sequence of enzymes. Enzymes are crucial to metabolism because they allow cells to drive desirable but biological thermodynamics unfavorable reactions by Coupling (physics) them to favorable ones. Enzymes also allow the Control theory of metabolic pathways in response to changes in the cell's environment or
cell signaling from other cells.
The metabolism of an organism determines which substances it will find nutrition and which it will find 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, 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 chemical intermediates in the
citric acid cycle are found universally, among living cells as diverse as the microorganism bacteria
Escherichia coli and huge
multicellular organism organisms like
elephants. This shared metabolic structure is most likely the result of the high efficiency of these pathways, and of their early appearance in evolutionary history.
Key biochemicals
lipid.Most of the structures that make up animals, plants and microbes are made from three basic classes of molecule:
amino acids, carbohydrates and lipids (often called fats). As these molecules are vital for life, metabolism focuses on making these molecules, in the construction of cells and tissues, or breaking them down and using them as a source of energy, in the digestion and use of food. Many important biochemicals can be joined together to make polymers such as
DNA and
proteins. These macromolecules are essential parts of all living organisms. Some of the most common biological polymers are listed in the table below.{] forms!Name of polymer forms!Examples of polymer forms]s|align="center" |Amino acids|align="center" |
Proteins (also called polypeptides)]s and globular proteins]s|align="center" |Monosaccharides]s|align="center" |Starch,
glycogen and
celluloses|align="center" |[Nucleotides]s|align="center" |DNA and RNA|}
Amino acids and proteins
Proteins are made of
amino acids arranged in a linear chain and joined together by
peptide bonds. Many proteins are the enzymes that catalysis the chemical reactions in metabolism. Other proteins have structural or mechanical functions, such as the proteins in the
cytoskeleton that form a system of scaffolding to maintain cell shape. Proteins are also important in cell signaling,
antibodys,
cell adhesion, active transport across membranes and the cell cycle.
Lipids
Lipids are the most diverse group of biochemicals. Their main structural uses are as part of biological membranes such as the cell membrane, or as a source of energy. Lipids are usually defined as
hydrophobe or
amphiphiles biological molecules that 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 a
triglyceride. Several variations on this basic structure exist, including alternate backbones such as
sphingosine in the sphingolipids, and
hydrophile groups such as phosphate in
phospholipids. Steroids such as cholesterol are another major class of lipids that are made in cells.
Carbohydrates
can exist in both a straight-chain and ring form.
Carbohydrates are straight-chain
aldehydes or ketones with many
hydroxyl groups that can exist as straight chains or rings. Carbohydrates are the most abundant biological molecules, and fill numerous roles, such as the storage and transport of
energy (
starch,
glycogen) and structural components (cellulose in plants, chitin in animals). The basic carbohydrate units are called monosaccharides and include
galactose,
fructose, and most importantly
glucose. Monosaccharides can be linked together to form
polysaccharides in almost limitless ways.
Nucleotides
The polymers DNA and RNA are long chains of nucleotides. These molecules are critical for the storage and use of genetic information, through the processes of transcription (genetics) and
protein biosynthesis. This information is protected by
DNA repair mechanisms and propagated through
DNA replication. A few
viruses have an RNA genome, for example
HIV, which uses
reverse transcription to create a DNA template from its viral RNA genome. RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can catalyze chemical reactions. Individual
nucleosides are made by attaching a
nucleobase to a ribose sugar. These bases are
heterocyclic rings containing nitrogen, classified as purines or pyrimidines. Nucleotides also act as coenzymes in metabolic group transfer reactions.
Coenzymes
acetyl-CoA.The transferable acetyl is bonded to the sulphur atom at the extreme left.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. 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 reaction is carried out by a particular coenzyme, which is the substrate (biochemistry) 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.
The most 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, with catabolic reactions generating ATP and anabolic reactions consuming 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 the cells. In human nutrition, most vitamins function as coenzymes after modification; for example, all water-soluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells.
Nicotinamide adenine dinucleotide (NADH), 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 redox NAD+ into NADH. This reduced form of the coenzyme is then a substrate for any of the reductases in the cell that need to reduce their substrates. Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The NAD+/NADH form is more important in catabolic reactions, while NADP+/NADPH is used in anabolic reactions.
. The protein subunits are in red and blue, and the iron-containing heme groups in green. From .
Minerals and cofactors
Inorganic elements play critical roles in metabolism; some are abundant (e.g. sodium and
potassium) while others function at minute concentrations. About 99% of mammals' mass are the elements
carbon,
nitrogen,
calcium, sodium, chlorine,
potassium,
hydrogen,
oxygen and
sulfur. The 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.
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
nerves and
muscles, as action potentials in these tissues are produced by the exchange of electrolytes between the
extracellular fluid and 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.
The
transition metals are usually present as trace elements in organisms, with
zinc and
iron being most abundant. 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. These
cofactors are bound tightly to a specific protein; although enzyme cofactors can be modified during catalysis, cofactors always return to their original state after catalysis has taken place. The metal micronutrients are taken up into organisms by specific transporters and bound to storage proteins such as ferritin or
metallothionein when not being used.
Catabolism
Catabolism is the set of metabolic processes that release energy. These include breaking down and oxidising food molecules as well as reactions that trap the energy in sunlight. The purpose of these 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
organotrophs, while
lithotrophs use inorganic substrates and
phototrophs capture
sunlight as
potential energy#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 to acceptor molecules such as
oxygen, nitrate or sulphate. In animals these reactions involve complex
organic molecules being broken down to simpler molecules, such as
carbon dioxide and water. In
photosynthesis 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.
The most common set of catabolic reactions in animals can be separated into three main stages. In the first, large organic molecules such as
proteins, polysaccharides or lipids are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to yet smaller molecules, usually coenzyme A (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
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
proteases that digest proteins into amino acids, as well as
glycoside hydrolases that digest polysaccharides into monosaccharides.
Microbes simply secrete digestive enzymes into their surroundings, while animals only secrete these enzymes from specialized cells in their guts. The amino acids or sugars released by these extracellular enzymes are then pumped into cells by specific
active transport proteins.s,
carbohydrates and
fats.
Energy from organic compounds
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
pyruvic acid and some ATP is generated. Pyruvate is an intermediate in several metabolic pathways, but the majority is converted to acetyl-CoA and fed into the
citric acid cycle. Although some more ATP is generated in the citric acid cycle, the most important product is NADH, which is made from NAD+ as the acetyl-CoA is oxidized. This oxidation releases carbon dioxide as a waste product. In anaerobic conditions, glycolysis produces
lactate, through the enzyme
lactate dehydrogenase re-oxidizing NADH to NAD+ for re-use in glycolysis. An alternative route for glucose breakdown is the
pentose phosphate pathway, which reduces the coenzyme
NADPH and produces
pentose sugars such as
ribose, the sugar component of nucleic acids.
Fats are catabolised by hydrolysis to free fatty acids and glycerol. The glycerol enters glycolysis and the fatty acids are broken down by
beta oxidation to release acetyl-CoA, which then is fed into the citric acid cycle. Fatty acids release more energy upon oxidation than carbohydrates because carbohydrates contain more oxygen in their structures.
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-Ketoglutaric acid. The
glucogenic amino acids can also be converted into glucose, through
gluconeogenesis (discussed below).
Oxidative phosphorylation
, the proton channel and rotating stalk are shown in blue and the synthase subunits in red.
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
electron transport chain. In prokaryotes, these proteins are found in the cell's
bacterial cell structure. These proteins use the energy released from passing electrons from reducing agent molecules like NADH onto
oxygen to pump
protons across a membrane.
Pumping protons out of the mitochondria creates a proton
diffusion across the membrane and generates a
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
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),
Iron(II) oxide 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
fertility (soil).
Energy from light
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.
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. The electrons needed to drive this electron transport chain come from light-gathering proteins called
photosynthetic reaction centres. These structures are classed into two types depending on the type of photosynthetic pigment present, with most photosynthetic bacteria only having one type of reaction center, while plants and cyanobacteria have two.
In plants,
photosystem 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 and can then either be used to reduce the coenzyme NADP+, for use in the Calvin cycle which is discussed below, or recycled for further ATP generation.
Anabolism
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 amino acids, monosaccharides,
Terpenoid and
nucleotides, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as
proteins, polysaccharides, lipids and
nucleic acids.
Organisms differ in how many of the molecules in their cells they can construct for themselves. Autotrophs such as plants can construct the complex organic molecules in cells such as polysaccharides and proteins from simple molecules like carbon dioxide and water.
Heterotrophs, on the other hand, require a source of more complex substances, such as monosaccharides and amino acids, to produce these complex molecules. Organisms can be further classified by ultimate source of their energy: photoautotrophs and photoheterotrophs obtain energy from light, whereas chemoautotrophs and chemoheterotrophs obtain energy from inorganic oxidation reactions.
Carbon fixation
Photosynthesis is the synthesis of glucose from sunlight,
carbon dioxide (CO2) and 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 cycle. Three types of photosynthesis occur in plants, C3 carbon fixation, C4 carbon fixation and Crassulacean acid metabolism. 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 Reverse Krebs cycle cycle, or the carboxylation of acetyl-CoA. Prokaryotic
Chemotroph also fix CO2 through the Calvin – Benson cycle, but use energy from inorganic compounds to drive the reaction.
Carbohydrates and glycans
In carbohydrate anabolism, simple organic acids can be converted into monosaccharides such as
glucose and then used to assemble
polysaccharides such as
starch. The generation of
glucose from compounds like
pyruvate, lactate,
glycerol, glycerate 3-phosphate and
amino acids is called
gluconeogenesis. Gluconeogenesis converts pyruvate to
glucose-6-phosphate through a series of intermediates, many of which are shared with glycolysis. However, this pathway is not simply
glycolysis run in reverse, as several steps are catalyzed by non-glycolytic enzymes. This is important as it allows the formation and breakdown of glucose to be regulated separately and prevents both pathways from running simultaneously in a
futile cycle.
Although fat is a common way of storing energy, in
vertebrates such as
humans the fatty acids in these stores cannot be converted to glucose through
gluconeogenesis as these organisms cannot convert acetyl-CoA into pyruvate. 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
(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 reduce acetyl-CoA units. The acyl chains in the fatty acids are extended by a cycle of reactions that add the actyl group, reduce it to the alcohol, dehydration reaction 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
terpenoid are a large class of lipids that include the carotenoids and form the largest class of plant
natural products. These compounds are made by the assembly and modification of
isoprene units donated from the reactive precursors
isopentenyl pyrophosphate and dimethylallyl pyrophosphate. These precursors can be made in different ways. In animals and archaea, the
mevalonate pathway produces these compounds from acetyl-CoA, while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates. One important reaction that uses these activated isoprene donors is
steroid biosynthesis. Here, the isoprene units are joined together to make squalene and then folded up and formed into a set of rings to make
lanosterol. Lanosterol can then be converted into other steroids such as
cholesterol and
ergosterol.
Proteins
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. Thus, the
essential amino acids must be obtained from food. All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen is provided by
glutamate and glutamine. Amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then
Transaminase to form an amino acid.
Amino acids are made into proteins by being joined together in a chain by peptide bonds. Each different protein has a unique sequence of amino acid residues: this is its
primary structure. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a
transfer RNA molecule through an
ester bond. This aminoacyl-tRNA precursor is produced in an
Adenosine triphosphate-dependent reaction carried out by an
aminoacyl tRNA synthetase.
adenosine triphosphate, a central intermediate in energy metabolism.
Metabolism is the complete set of
chemical reactions that occur in living
cell (biology). These processes are the basis of life, allowing cells to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories. Catabolism yields energy, an example being the breakdown of food in cellular respiration.
Anabolism, on the other hand, uses this energy to construct components of cells such as proteins and
nucleic acids.
The chemical reactions of metabolism are organized into
metabolic pathways, in which one chemical is transformed into another by a sequence of
enzymes. Enzymes are crucial to metabolism because they allow cells to drive desirable but biological thermodynamics unfavorable reactions by Coupling (physics) them to favorable ones. Enzymes also allow the Control theory of metabolic pathways in response to changes in the cell's environment or
cell signaling from other cells.
The metabolism of an organism determines which substances it will find
nutrition and which it will find 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, 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 chemical intermediates in the citric acid cycle are found universally, among living cells as diverse as the
microorganism bacteria Escherichia coli and huge multicellular organism organisms like
elephants. This shared metabolic structure is most likely the result of the high efficiency of these pathways, and of their early appearance in evolutionary history.
Key biochemicals
lipid.Most of the structures that make up animals, plants and microbes are made from three basic classes of molecule: amino acids, carbohydrates and
lipids (often called
fats). As these molecules are vital for life, metabolism focuses on making these molecules, in the construction of cells and tissues, or breaking them down and using them as a source of energy, in the digestion and use of food. Many important biochemicals can be joined together to make polymers such as
DNA and
proteins. These
macromolecules are essential parts of all living organisms. Some of the most common biological polymers are listed in the table below.{] forms!Name of
polymer forms!Examples of polymer forms]s|align="center" |Amino acids|align="center" |
Proteins (also called polypeptides)]s and globular proteins]s|align="center" |
Monosaccharides]s|align="center" |
Starch, glycogen and
celluloses|align="center" |[Nucleotides]s|align="center" |DNA and RNA|}
Amino acids and proteins
Proteins are made of amino acids arranged in a linear chain and joined together by peptide bonds. Many proteins are the enzymes that catalysis the chemical reactions in metabolism. Other proteins have structural or mechanical functions, such as the proteins in the
cytoskeleton that form a system of
scaffolding to maintain cell shape. Proteins are also important in cell signaling,
antibodys,
cell adhesion, active transport across membranes and the cell cycle.
Lipids
Lipids are the most diverse group of biochemicals. Their main structural uses are as part of biological membranes such as the cell membrane, or as a source of energy. Lipids are usually defined as hydrophobe or
amphiphiles biological molecules that 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 a triglyceride. Several variations on this basic structure exist, including alternate backbones such as
sphingosine in the
sphingolipids, and
hydrophile groups such as
phosphate in phospholipids. Steroids such as
cholesterol are another major class of lipids that are made in cells.
Carbohydrates
can exist in both a straight-chain and ring form.
Carbohydrates are straight-chain aldehydes or
ketones with many
hydroxyl groups that can exist as straight chains or rings. Carbohydrates are the most abundant biological molecules, and fill numerous roles, such as the storage and transport of energy (
starch, glycogen) and structural components (cellulose in plants,
chitin in animals). The basic carbohydrate units are called
monosaccharides and include galactose,
fructose, and most importantly
glucose. Monosaccharides can be linked together to form
polysaccharides in almost limitless ways.
Nucleotides
The polymers
DNA and
RNA are long chains of
nucleotides. These molecules are critical for the storage and use of genetic information, through the processes of
transcription (genetics) and protein biosynthesis. This information is protected by DNA repair mechanisms and propagated through DNA replication. A few viruses have an RNA genome, for example HIV, which uses reverse transcription to create a DNA template from its viral RNA genome. RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can catalyze chemical reactions. Individual nucleosides are made by attaching a
nucleobase to a ribose sugar. These bases are
heterocyclic rings containing nitrogen, classified as purines or
pyrimidines. Nucleotides also act as coenzymes in metabolic group transfer reactions.
Coenzymes
acetyl-CoA.The transferable acetyl is bonded to the sulphur atom at the extreme left.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. 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 reaction is carried out by a particular coenzyme, which is the
substrate (biochemistry) 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.
The most 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, with catabolic reactions generating ATP and anabolic reactions consuming 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 the cells. In human nutrition, most vitamins function as coenzymes after modification; for example, all water-soluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells.
Nicotinamide adenine dinucleotide (NADH), 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 redox NAD+ into NADH. This reduced form of the coenzyme is then a substrate for any of the
reductases in the cell that need to reduce their substrates. Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The NAD+/NADH form is more important in catabolic reactions, while NADP+/NADPH is used in anabolic reactions.
. The protein subunits are in red and blue, and the iron-containing heme groups in green. From .
Minerals and cofactors
Inorganic elements play critical roles in metabolism; some are abundant (e.g.
sodium and
potassium) while others function at minute concentrations. About 99% of mammals' mass are the elements carbon, nitrogen, calcium,
sodium, chlorine,
potassium,
hydrogen, oxygen and sulfur. The
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.
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 nerves and muscles, as
action potentials in these tissues are produced by the exchange of electrolytes between the
extracellular fluid and 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.
The
transition metals are usually present as trace elements in organisms, with zinc and iron being most abundant. 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. These cofactors are bound tightly to a specific protein; although enzyme cofactors can be modified during catalysis, cofactors always return to their original state after catalysis has taken place. The metal micronutrients are taken up into organisms by specific transporters and bound to storage proteins such as ferritin or
metallothionein when not being used.
Catabolism
Catabolism is the set of metabolic processes that release energy. These include breaking down and oxidising food molecules as well as reactions that trap the energy in sunlight. The purpose of these 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 organotrophs, while lithotrophs use inorganic substrates and phototrophs capture
sunlight as potential energy#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 to acceptor molecules such as
oxygen,
nitrate or sulphate. In animals these reactions involve complex organic molecules being broken down to simpler molecules, such as carbon dioxide and water. In
photosynthesis 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.
The most common set of catabolic reactions in animals can be separated into three main stages. In the first, large organic molecules such as
proteins,
polysaccharides or lipids are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to yet smaller molecules, usually
coenzyme A (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
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 proteases that digest proteins into amino acids, as well as glycoside hydrolases that digest polysaccharides into monosaccharides.
Microbes simply secrete digestive enzymes into their surroundings, while animals only secrete these enzymes from specialized cells in their
guts. The amino acids or sugars released by these extracellular enzymes are then pumped into cells by specific active transport proteins.s, carbohydrates and
fats.
Energy from organic compounds
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 pyruvic acid and some ATP is generated. Pyruvate is an intermediate in several metabolic pathways, but the majority is converted to acetyl-CoA and fed into the
citric acid cycle. Although some more ATP is generated in the citric acid cycle, the most important product is NADH, which is made from NAD+ as the acetyl-CoA is oxidized. This oxidation releases carbon dioxide as a waste product. In anaerobic conditions, glycolysis produces
lactate, through the enzyme lactate dehydrogenase re-oxidizing NADH to NAD+ for re-use in glycolysis. An alternative route for glucose breakdown is the pentose phosphate pathway, which reduces the coenzyme
NADPH and produces pentose sugars such as
ribose, the sugar component of nucleic acids.
Fats are catabolised by hydrolysis to free fatty acids and glycerol. The glycerol enters glycolysis and the fatty acids are broken down by
beta oxidation to release acetyl-CoA, which then is fed into the citric acid cycle. Fatty acids release more energy upon oxidation than carbohydrates because carbohydrates contain more oxygen in their structures.
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-
Ketoglutaric acid. The
glucogenic amino acids can also be converted into glucose, through gluconeogenesis (discussed below).
Oxidative phosphorylation
, the proton channel and rotating stalk are shown in blue and the synthase subunits in red.
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 electron transport chain. In prokaryotes, these proteins are found in the cell's
bacterial cell structure. These proteins use the energy released from passing electrons from reducing agent molecules like NADH onto
oxygen to pump protons across a membrane.
Pumping protons out of the mitochondria creates a proton
diffusion across the membrane and generates a
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
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), Iron(II) oxide 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
fertility (soil).
Energy from light
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.
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. The electrons needed to drive this electron transport chain come from light-gathering proteins called photosynthetic reaction centres. These structures are classed into two types depending on the type of photosynthetic pigment present, with most photosynthetic bacteria only having one type of reaction center, while plants and cyanobacteria have two.
In plants,
photosystem 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 and can then either be used to reduce the coenzyme NADP+, for use in the Calvin cycle which is discussed below, or recycled for further ATP generation.
Anabolism
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 amino acids, monosaccharides, Terpenoid and
nucleotides, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as proteins,
polysaccharides,
lipids and nucleic acids.
Organisms differ in how many of the molecules in their cells they can construct for themselves.
Autotrophs such as plants can construct the complex organic molecules in cells such as polysaccharides and proteins from simple molecules like carbon dioxide and water.
Heterotrophs, on the other hand, require a source of more complex substances, such as monosaccharides and amino acids, to produce these complex molecules. Organisms can be further classified by ultimate source of their energy: photoautotrophs and photoheterotrophs obtain energy from light, whereas chemoautotrophs and chemoheterotrophs obtain energy from inorganic oxidation reactions.
Carbon fixation
Photosynthesis is the synthesis of glucose from sunlight, carbon dioxide (CO2) and 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 cycle. Three types of photosynthesis occur in plants,
C3 carbon fixation,
C4 carbon fixation and
Crassulacean acid metabolism. 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
Reverse Krebs cycle cycle, or the carboxylation of acetyl-CoA. Prokaryotic
Chemotroph also fix CO2 through the Calvin – Benson cycle, but use energy from inorganic compounds to drive the reaction.
Carbohydrates and glycans
In carbohydrate anabolism, simple organic acids can be converted into
monosaccharides such as
glucose and then used to assemble polysaccharides such as
starch. The generation of glucose from compounds like pyruvate,
lactate,
glycerol, glycerate 3-phosphate and amino acids is called
gluconeogenesis. Gluconeogenesis converts pyruvate to glucose-6-phosphate through a series of intermediates, many of which are shared with
glycolysis. However, this pathway is not simply
glycolysis run in reverse, as several steps are catalyzed by non-glycolytic enzymes. This is important as it allows the formation and breakdown of glucose to be regulated separately and prevents both pathways from running simultaneously in a futile cycle.
Although fat is a common way of storing energy, in
vertebrates such as humans the fatty acids in these stores cannot be converted to glucose through
gluconeogenesis as these organisms cannot convert acetyl-CoA into
pyruvate. 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
(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 reduce acetyl-CoA units. The acyl chains in the fatty acids are extended by a cycle of reactions that add the actyl group, reduce it to the alcohol, dehydration reaction 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 terpenoid are a large class of lipids that include the carotenoids and form the largest class of plant natural products. These compounds are made by the assembly and modification of
isoprene units donated from the reactive precursors
isopentenyl pyrophosphate and dimethylallyl pyrophosphate. These precursors can be made in different ways. In animals and archaea, the mevalonate pathway produces these compounds from acetyl-CoA, while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates. One important reaction that uses these activated isoprene donors is steroid biosynthesis. Here, the isoprene units are joined together to make
squalene and then folded up and formed into a set of rings to make lanosterol. Lanosterol can then be converted into other steroids such as
cholesterol and ergosterol.
Proteins
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. Thus, the essential amino acids must be obtained from food. All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen is provided by glutamate and
glutamine. Amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then
Transaminase to form an amino acid.
Amino acids are made into proteins by being joined together in a chain by peptide bonds. Each different protein has a unique sequence of amino acid residues: this is its primary structure. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a
transfer RNA molecule through an
ester bond. This aminoacyl-tRNA precursor is produced in an
Adenosine triphosphate-dependent reaction carried out by an aminoacyl tRNA synthetase.
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