Metabolism is the set of
chemical reactionA chemical reaction is a process that leads to the transformation of one set of chemical substances to another. They are studied by chemists under a field of science called chemistry. Chemical reactions can be either spontaneous, requiring no input of energy, or non-spontaneous, often coming about...
s that occur in living
organismIn biology, an organism is any living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homeostasis as a stable whole...
s to maintain
lifeLife is a characteristic that distinguishes objects that have self-sustaining biological processes from those that do not—either because such functions have ceased , or else because they lack such functions and are classified as "inanimate."In biology, the science of living organisms, "life"...
. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories.
CatabolismCatabolism is the set of metabolic pathways that break down molecules into smaller units and release energy. In catabolism, large molecules such as polysaccharides, lipids, nucleic acids and proteins are broken down into smaller units such as monosaccharides, fatty acids, nucleotides and amino...
breaks down organic matter, for example to harvest energy in
cellular respirationCellular respiration is one of the key ways a cell gains useful energy. It is the set of the metabolic reactions and processes that take place in organisms' cells to convert biochemical energy from nutrients into adenosine triphosphate , and then release waste products...
.
AnabolismAnabolism is the set of metabolic pathways that construct molecules from smaller units. These reactions require energy. One way of categorizing metabolic processes, whether at the cellular, organ or organism level is as 'anabolic' or as 'catabolic', which is the opposite...
, uses energy to construct components of cells such as
proteinProteins are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer chain are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues...
s and
nucleic acidA nucleic acid is a macromolecule composed of chains of monomeric nucleotides. In biochemistry these molecules carry genetic information or form structures within cells. The most common nucleic acids are deoxyribonucleic acid and ribonucleic acid . Nucleic acids are universal in living things, as...
s.
The chemical reactions of metabolism are organized into
metabolic pathway-Cellular respiration:Several distinct but linked metabolic pathways are used by cells to transfer the energy released by breakdown of fuel molecules to ATP...
s, in which one chemical is transformed through a series of steps into another chemical, by a sequence of
enzymeEnzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, called the products. Almost all processes in a biological cell need enzymes to occur at...
s. Enzymes are crucial to metabolism because they allow organisms to drive desirable but
thermodynamicallyBiological thermodynamics is a phrase that is sometimes used to refer to bioenergetics, the study of energy transformation in the biological sciences...
unfavorable reactions by
couplingIn physics, two systems are coupled if they are interacting with each other. Of special interest is the coupling of two vibratory systems by means of springs or magnetic fields, etc...
them to favorable ones, and because they act as
catalystsCatalysis is the process in which the rate of a chemical reaction is either increased or decreased by means of a chemical substance known as a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. The catalyst may participate...
to allow these reactions to proceed quickly and efficiently. Enzymes also allow the
regulationControl theory is an interdisciplinary branch of engineering and mathematics, that deals with the behavior of dynamical systems. The desired output of a system is called the reference...
of metabolic pathways in response to changes in the
cell'sThe cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of an organism that is classified as living, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos...
environment or
signalsCell signaling is part of a complex system of communication that governs basic cellular activities and coordinates cell actions. The ability of cells to perceive and correctly respond to their microenvironment is the basis of development, tissue repair, and immunity as well as normal tissue...
from other cells.
The metabolism of an organism determines which substances it will find
nutritiousNutrition is the provision, to cells and organisms, of the materials necessary to support life. Many common health problems can be prevented or alleviated with a healthy diet....
and which it will find
poisonIn the context of biology, poisons are substances that can cause disturbances to organisms, usually by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by an organism...
ous. For example, some
prokaryoteThe prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. They differ from the eukaryotes, which have a cell nucleus. Most are unicellular, but a few prokaryotes such as myxobacteria have multicellular stages in their life cycles...
s use
hydrogen sulfideHydrogen sulfide is the chemical compound with the formula H
2S. This colorless, toxic and flammable gas is partially responsible for the foul odor of rotten eggs and flatulence....
as a nutrient, yet this gas is poisonous to
animalAnimals are a major group of mostly multicellular, eukaryotic organisms of the kingdom Animalia or Metazoa. Their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later on in their life. Most animals are motile, meaning they can move spontaneously...
s. The speed of metabolism, the
metabolic rateBasal metabolic rate , and the closely related resting metabolic rate , is the amount of energy expended while at rest in a [neutrally temperate environment, in the post-absorptive state...
, 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
carboxylic acidCarboxylic acids are organic acids characterized by the presence of a carboxyl group, which has the formula -COH, usually written -COOH or -CO2H. Carboxylic acids are Brønsted-Lowry acids — they are proton donors. Salts and anions of carboxylic acids are called...
s that are best known as the intermediates in the
citric acid cycleThe citric acid cycle — also known as the tricarboxylic acid cycle , the Krebs cycle, or more rarely, the Szent-Györgyi-Krebs cycle — is a series of enzyme-catalysed chemical reactions, which is of central importance in all living cells that use oxygen as part of cellular respiration...
are present in all organisms, being found in species as diverse as the
unicellularA microorganism or microbe is an organism that is microscopic...
bacteriaThe bacteria are a large group of unicellular microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
Escherichia coliEscherichia coli , is a Gram negative bacterium that is commonly found in the lower intestine of warm-blooded organisms . Most E...
and huge
multicellularMulticellular organisms are organisms consisting of more than one cell, and having differentiated cells that perform specialized functions in the organism...
organisms like
elephantElephants are large land mammals in two genera of the family Elephantidae: Elephas and Loxodonta. Three species of elephant are living today: the African Bush Elephant, the African Forest Elephant and the Asian Elephant...
s. These striking similarities in metabolism are probably due to the high efficiency of these pathways, and their early appearance in
evolutionary historyThe evolutionary history of life on Earth traces the processes by which living and fossil organisms evolved. It stretches back over , possibly as far as , and evolution continues, even in humans. All present-day organisms use the same large set of complex chemical reactions, which indicates that...
.
Key biochemicals
Most of the structures that make up animals, plants and microbes are made from three basic classes of
moleculeA molecule is defined as an electrically neutral group of at least two atoms in a definite arrangement held together by very strong chemical bonds. Molecules are distinguished from polyatomic ions in this strict sense...
:
amino acidAmino acids are molecules containing an amine group, a carboxylic acid group and one of the twenty R-groups. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H
2NCHRCOOH, where R is an organic substituent...
s,
carbohydrateCarbohydrates
[Means "hydrates of carbon"] or saccharides
[The word comes from the Greek σάκχαρον, sákcharon, meaning "sugar").] are the most abundant of the four major classes of biomolecules...
s and
lipidLipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins , monoglycerides, diglycerides, phospholipids, and others...
s (often called
fatFats consist of a wide group of compounds that are generally soluble in organic solvents and largely insoluble in water. Chemically, fats are generally triesters of glycerol and fatty acids. Fats may be either solid or liquid at normal room temperature, depending on their structure and composition...
s). 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
polymerA polymer is a large molecule composed of repeating structural units typically connected by covalent chemical bonds. While polymer in popular usage suggests plastic, the term actually refers to a large class of natural and synthetic materials with a variety of properties.Due to the extraordinary...
s such as
DNADeoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information...
and proteins. These macromolecules are essential parts of all living organisms. Some of the most common biological polymers are listed in the table below.
| Type of molecule |
Name of monomer A monomer is a small molecule that may become chemically bonded to other monomers to form a polymer...
forms |
Name of polymer A polymer is a large molecule composed of repeating structural units typically connected by covalent chemical bonds. While polymer in popular usage suggests plastic, the term actually refers to a large class of natural and synthetic materials with a variety of properties.Due to the extraordinary...
forms |
Examples of polymer forms |
Amino acidAmino acids are molecules containing an amine group, a carboxylic acid group and one of the twenty R-groups. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H 2NCHRCOOH, where R is an organic substituent...
s |
Amino acids |
Protein Proteins are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer chain are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues...
s (also called polypeptides) |
Fibrous protein Scleroproteins are one of the two main classes of protein Quaternary structure .They are also called fibrous proteins.-Characteristics:...
s and globular proteinGlobular proteins, or spheroproteins are one of the three main protein classes, comprising "globe"-like proteins that are more or less soluble in aqueous solutions...
s |
CarbohydrateCarbohydrates [Means "hydrates of carbon"] or saccharides [The word comes from the Greek σάκχαρον, sákcharon, meaning "sugar").] are the most abundant of the four major classes of biomolecules...
s |
MonosaccharideMonosaccharides are the most basic unit of carbohydrates. They are the simplest form of sugar and are usually colorless, water-soluble, crystalline solids. Some monosaccharides have a sweet taste. Examples of monosaccharides include glucose , fructose , galactose, xylose and ribose...
s |
Polysaccharide Polysaccharides are polymeric carbohydrate structures, formed of repeating units joined together by glycosidic bonds. These structures are often linear, but may contain various degrees of branching. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit...
s |
StarchStarch or amylum is a polysaccharide carbohydrate consisting of a large number of glucose units joined together by glycosidic bonds.Starch is produced by all green plants as an energy store and is a major food source for humans....
, glycogenGlycogen is the molecule that functions as the secondary long-term energy storage in animal cells. It is made primarily by the liver and the muscles, but can also be made by glycogenesis within the brain and stomach...
and celluloseCellulose is an organic compound with the formula , a polysaccharide consisting of a linear chain of several hundred to over ten thousand β linked D-glucose units....
|
| Nucleic acid A nucleic acid is a macromolecule composed of chains of monomeric nucleotides. In biochemistry these molecules carry genetic information or form structures within cells. The most common nucleic acids are deoxyribonucleic acid and ribonucleic acid . Nucleic acids are universal in living things, as...
s |
NucleotideNucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides play central roles in metabolism...
s |
Polynucleotide A polynucleotide molecule is an organic polymer molecule composed of nucleotide monomers covalently bonded in a chain. DNA and RNA are examples of polynucleotides with distinct biological function...
s |
DNADeoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information...
and RNARibonucleic acid is a biologically important type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate...
|
Amino acids and proteins
ProteinProteins are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer chain are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues...
s are made of
amino acidAmino acids are molecules containing an amine group, a carboxylic acid group and one of the twenty R-groups. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H
2NCHRCOOH, where R is an organic substituent...
s arranged in a linear chain and joined together by
peptide bondA peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amine group of the other molecule, thereby releasing a molecule of water . This is a dehydration synthesis reaction, and usually occursbetween amino acids...
s. Many proteins are the
enzymeEnzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, called the products. Almost all processes in a biological cell need enzymes to occur at...
s that
catalyzeCatalysis is the process in which the rate of a chemical reaction is either increased or decreased by means of a chemical substance known as a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. The catalyst may participate...
the chemical reactions in metabolism. Other proteins have structural or mechanical functions, such as the proteins that form the
cytoskeletonThe cytoskeleton is a cellular "scaffolding" or "skeleton" contained within the cytoplasm. The cytoskeleton is present in all cells; it was once thought this structure was unique to eukaryotes, but recent research has identified the prokaryotic cytoskeleton...
, a system of
scaffoldingScaffolding is a temporary frame used to support people and material in the construction or repair of buildings and other large structures. It is usually a modular system of metal pipes , although it can be made out of other materials...
that maintains the cell shape. Proteins are also important in
cell signalingCell signaling is part of a complex system of communication that governs basic cellular activities and coordinates cell actions. The ability of cells to perceive and correctly respond to their microenvironment is the basis of development, tissue repair, and immunity as well as normal tissue...
,
immune responsesAntibodies are gamma globulin proteins that are found in blood or other bodily fluids of vertebrates, and are used by the immune system to identify and neutralize foreign objects, such as bacteria and viruses...
,
cell adhesionCellular adhesion is the binding of a cell to a surface, extracellular matrix or another cell using cell adhesion molecules such as selectins, integrins, and cadherins.- Process :...
,
active transportActive transport is the mediated process of moving particles across a biological membrane against a concentration gradient. If the process uses chemical energy, such as from adenosine triphosphate , it is termed primary active transport. Secondary active transport involves the use of an...
across membranes, and the
cell cycleThe cell cycle, or cell-division cycle, is the series of events that take place in a cell leading to its division and duplication . In cells without a nucleus , the cell cycle occurs via a process termed binary fission...
.
Lipids
LipidLipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins , monoglycerides, diglycerides, phospholipids, and others...
s are the most diverse group of biochemicals. Their main structural uses are as part of
biological membraneA biological membrane or biomembrane is an enclosing or separating amphipathic layer that acts as a barrier within or around a cell. It is almost invariably a lipid bilayer, composed of a double layer of lipid molecules and proteins that may constitute close to 50% of membrane...
s such as the
cell membraneThe cell membrane is the biological membrane separating the interior of a cell from the outside environment....
, or as a source of energy. Lipids are usually defined as
hydrophobicIn chemistry, hydrophobicity is the physical property of a molecule that is repelled from a mass of water....
or
amphipathicAmphiphile is a term describing a chemical compound possessing both hydrophilic and lipophilic properties. Such a compound is called amphiphilic or amphipathic. This forms the basis for a number of areas of research in chemistry and biochemistry, notably that of lipid polymorphism...
biological molecules that will dissolve in organic solvents such as
benzeneBenzene, or benzol, is an organic chemical compound with the molecular formula C6H6. It is sometimes abbreviated Ph–H. Benzene is a colorless and highly flammable liquid with a sweet smell and a relatively high melting point...
or
chloroformChloroform is the organic compound with formula CHCl
3. This colourless, sweet-smelling, dense liquid is a trihalomethane. It is also considered somewhat hazardous...
. The
fatFats consist of a wide group of compounds that are generally soluble in organic solvents and largely insoluble in water. Chemically, fats are generally triesters of glycerol and fatty acids. Fats may be either solid or liquid at normal room temperature, depending on their structure and composition...
s are a large group of compounds that contain
fatty acidIn chemistry, especially biochemistry, a fatty acid is a carboxylic acid often with a long unbranched aliphatic tail , which is either saturated or unsaturated...
s and
glycerolGlycerol is an organic compound, also commonly called glycerin or glycerine. It is a colorless, odorless, viscous liquid that is widely used in pharmaceutical formulations. Glycerol has three hydrophilic hydroxyl groups that are responsible for its solubility in water and its hygroscopic nature. ...
; a glycerol molecule attached to three fatty acid
esterEsters are chemical compounds derived by reacting an oxoacid with a hydroxyl compound such as an alcohol or phenol. Esters are usually derived from an inorganic acid or organic acid in which at least one -OH group is replaced by an -O-alkyl group, and most commonly from carboxylic acids and...
s is a
triacylglycerideis a glyceride in which the glycerol is esterified with three fatty acids. It is the main constituent of vegetable oil and animal fats.- Chemical structure :...
. Several variations on this basic structure exist, including alternate backbones such as
sphingosineSphingosine is an 18-carbon amino alcohol with an unsaturated hydrocarbon chain, which forms a primary part of sphingolipids, a class of cell membrane lipids that include sphingomyelin, an important phospholipid.-Functions:...
in the
sphingolipidSphingolipids are a class of lipids derived from the aliphatic amino alcohol sphingosine. These compounds play important roles in signal transmission and cell recognition...
s, and
hydrophilicHydrophile, from the Greek "water" and φιλια "friendship," refers to a physical property of a molecule that can transiently bond with water through hydrogen bonding. This is thermodynamically favorable, and makes these molecules soluble not only in water, but also in other polar solvents...
groups such as
phosphateA phosphate, an inorganic chemical, is a salt of phosphoric acid. In organic chemistry, a phosphate, or organophosphate, is an ester of phosphoric acid. Organic phosphates are important in biochemistry and biogeochemistry or ecology. Inorganic phosphates are mined to obtain phosphorus for use in...
in
phospholipidPhospholipids are a class of lipids and are a major component of all cell membranes as they can form lipid bilayers. Most phospholipids contain a diglyceride, a phosphate group, and a simple organic molecule such as choline; one exception to this rule is sphingomyelin, which is derived from...
s.
SteroidA steroid is a terpenoid lipid characterized by its sterane core and additional functional groups. The core is a carbon structure of four fused rings: three cyclohexane rings and one cyclopentane ring. The steroids vary by the functional groups attached to these rings and the oxidation state of the...
s such as
cholesterolCholesterol is a lipidic, waxy steroid found in the cell membranes and transported in the blood plasma of all animals. It is an essential component of mammalian cell membranes, where it is required to establish proper membrane permeability and fluidity...
are another major class of lipids that are made in cells.
Carbohydrates
CarbohydrateCarbohydrates
[Means "hydrates of carbon"] or saccharides
[The word comes from the Greek σάκχαρον, sákcharon, meaning "sugar").] are the most abundant of the four major classes of biomolecules...
s are straight-chain
aldehydeAn aldehyde is an organic compound containing a terminal carbonyl group. This functional group, which consists of a carbon atom bonded to a hydrogen atom and double-bonded to an oxygen atom , is called the aldehyde group...
s or
ketoneIn organic chemistry, a ketone is a type of compound that features a carbonyl group bonded to two other carbon atoms, i.e., R3CCO-CR3 where R can be a variety of atoms and groups of atoms...
s with many
hydroxylIn chemistry, hydroxyl is composed of molecules consisting of an oxygen atom and a hydrogen atom connected by a covalent bond . The neutral form is a hydroxyl radical. The hydroxyl anion is called hydroxide; it is a diatomic ion with a charge of negative one...
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
energyIn physics, energy is a scalar physical quantity that describes the amount of work that can be performed by a force, an attribute of objects and systems that is subject to a conservation law...
(
starchStarch or amylum is a polysaccharide carbohydrate consisting of a large number of glucose units joined together by glycosidic bonds.Starch is produced by all green plants as an energy store and is a major food source for humans....
,
glycogenGlycogen is the molecule that functions as the secondary long-term energy storage in animal cells. It is made primarily by the liver and the muscles, but can also be made by glycogenesis within the brain and stomach...
) and structural components (
celluloseCellulose is an organic compound with the formula , a polysaccharide consisting of a linear chain of several hundred to over ten thousand β linked D-glucose units....
in plants,
chitinChitin n is a long-chain polymer of a N-acetylglucosamine, a derivative of glucose, and is found in many places throughout the natural world. It is the main component of the cell walls of fungi, the exoskeletons of arthropods, such as crustaceans Chitin...
in animals). The basic carbohydrate units are called
monosaccharideMonosaccharides are the most basic unit of carbohydrates. They are the simplest form of sugar and are usually colorless, water-soluble, crystalline solids. Some monosaccharides have a sweet taste. Examples of monosaccharides include glucose , fructose , galactose, xylose and ribose...
s and include
galactoseGalactose is a type of sugar which is less sweet than glucose. It is considered a nutritive sweetener because it has food energy. Its name comes from the Ancient Greek word for milk, γάλακτος ....
,
fructoseFructose is a simple monosaccharide found in many foods. It is a white solid that dissolves readily in water. Honey, tree fruits, berries, melons, and some root vegetables, contain significant amounts of the fructose derivative sucrose...
, and most importantly
glucoseGlucose , a monosaccharide also known as - grape sugar, blood sugar, or corn sugar, is a very important carbohydrate in biology. The living cell uses it as a source of energy and metabolic intermediate...
. Monosaccharides can be linked together to form
polysaccharidePolysaccharides are polymeric carbohydrate structures, formed of repeating units joined together by glycosidic bonds. These structures are often linear, but may contain various degrees of branching. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit...
s in almost limitless ways.
Nucleotides
The polymers
DNADeoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information...
and
RNARibonucleic acid is a biologically important type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate...
are long chains of
nucleotideNucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides play central roles in metabolism...
s. These molecules are critical for the storage and use of genetic information, through the processes of
transcriptionTranscription, or RNA synthesis, is the process of creating an equivalent RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA in the presence of the correct enzymes...
and
protein biosynthesisProtein synthesis is the process in which cells build proteins. The term is sometimes used to refer only to protein translation but more often it refers to a multi-step process, beginning with amino acid synthesis and transcription of nuclear DNA into messenger RNA which is then used as input to...
. This information is protected by
DNA repairDNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as UV light and Radiation can cause DNA damage, resulting in as many as 1...
mechanisms and propagated through
DNA replicationDNA replication, the basis for biological inheritance, is a fundamental process occurring in all living organisms to copy their DNA. This process is "semiconservative" in that each strand of the original double-stranded DNA molecule serves as template for the reproduction of the complementary strand...
. A few
virusA virus is an infectious agent too small to be seen directly with a light microscope. They are not made of cells and can only replicate inside the cells of another organism . Viruses infect all types of organisms, from animals and plants to bacteria and archaea...
es have an RNA genome, for example
HIVHuman immunodeficiency virus is a lentivirus that causes acquired immunodeficiency syndrome , a condition in humans in which the immune system begins to fail, leading to life-threatening opportunistic infections. Infection with HIV occurs by the transfer of blood, semen, vaginal fluid,...
, which uses reverse transcription to create a DNA template from its viral RNA genome. RNA in
ribozymeA ribozyme is an RNA molecule that catalyzes a chemical reaction...
s such as
spliceosomeA spliceosome is a complex of specialized RNA and protein subunits that removes introns from a transcribed pre-mRNA segment. This process is generally referred to as splicing.-Composition:...
s and
ribosomeRibosomes are complexes of RNA and protein that are found in all cells. The ribosome is part of the mechanism that translates the DNA sequence into the protein sequence. Ribosomes from bacteria, archaea and eukaryotes , have significantly different structure and RNA...
s is similar to enzymes as it can catalyze chemical reactions. Individual
nucleosideNucleosides are glycosylamines consisting of a nucleobase bound to a ribose or deoxyribose sugar. Examples of these include cytidine, uridine, adenosine, guanosine, thymidine and inosine....
s are made by attaching a
nucleobaseNucleobases are the parts of DNA and RNA that may be involved in pairing . The main ones are cytosine, guanine, adenine , thymine and uracil , abbreviated as C, G, A, T, and U, respectively. They are usually simply called bases in genetics...
to a
riboseRibose, primarily occurring as
D-ribose, is an organic compound that occurs widely in nature. It is an aldopentose, that is a monosaccharide containing five carbon atoms that, in its acyclic form, has an aldehyde functional group at one end. This species predominantly exists in the...
sugar. These bases are heterocyclic rings containing nitrogen, classified as purines or pyrimidines. Nucleotides also act as coenzymes in metabolic group transfer reactions.
Coenzymes
Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of
functional groupIn organic chemistry, functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. The same functional group will undergo the same or similar chemical reaction regardless of the size of the molecule it is a part...
s. 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
substrateIn biochemistry, a substrate is a molecule upon which an enzyme acts. Enzymes catalyze chemical reactions involving the substrate. In the case of a single substrate, the substrate binds with the enzyme active site, and an enzyme-substrate complex is formed. The substrate is transformed into one or...
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.
One central coenzyme is
adenosine triphosphateAdenosine-5'-triphosphate is a multifunctional nucleotide that plays an important role in cell biology as a coenzyme, that is, the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...
(ATP), the universal energy currency of cells. This
nucleotideNucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides play central roles in metabolism...
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
phosphorylationPhosphorylation is the addition of a phosphate group to a protein or other organic molecule. Phosphorylation turns many protein enzymes on and off, causing or preventing the mechanisms of diseases such as cancer and diabetes....
reactions.
A
vitaminA vitamin is an organic compound required as a nutrient in tiny amounts by an organism. The term 'vitamin' first became popular in the early 1800's as a contraction of the words 'vital' and 'mineral', though the actual meaning of the word has developed somewhat since that time...
is an organic compound needed in small quantities that cannot be made in the cells. In human
nutritionNutrition is the provision, to cells and organisms, of the materials necessary to support life. Many common health problems can be prevented or alleviated with a healthy diet....
, 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 dinucleotideNicotinamide adenine dinucleotide, abbreviated NAD
+, is a coenzyme found in all living cells. The compound is a dinucleotide, since it consists of two nucleotides joined through their phosphate groups, with one nucleotide containing an adenine base and the other containing...
(NADH), a derivative of vitamin B
3 (
niacinNiacin, also known as vitamin B
3 or nicotinic acid, is a water-soluble vitamin. It is an organic compound with the molecular formula C
6H
5NO
2. It is a derivative of pyridine, with a carboxyl group at the 3-position...
), is an important coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of
dehydrogenaseA dehydrogenase is an enzyme that oxidizes a substrate by transferring one or more hydrides to an acceptor, usually NAD+/NADP+ or a flavin coenzyme such as FAD or FMN.-Examples:...
s remove electrons from their substrates and
reduceRedox describes all chemical reactions in which atoms have their oxidation number changed....
NAD
+ into NADH. This reduced form of the coenzyme is then a substrate for any of the
reductaseA reductase is an enzyme that lowers the activation energy for a reduction reaction. -Examples:* 5-alpha reductase* Dihydrofolate reductase* HMG-CoA reductase* Methemoglobin reductase* Ribonucleotide reductase* Thioredoxin reductase...
s 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.
Minerals and cofactors
Inorganic elements play critical roles in metabolism; some are abundant (e.g.
sodiumSodium is a metallic element with a symbol Na and atomic number 11. It is a soft, silvery-white, highly reactive metal and is a member of the alkali metals within "group 1"...
and
potassiumPotassium is the chemical element with the symbol K , atomic number 19, and atomic mass 39.0983. Potassium was first isolated from potash...
) while others function at minute concentrations. About 99% of mammals' mass are the elements
carbonCarbon is the chemical element with symbol C and atomic number 6. As a member of group 14 on the periodic table, it is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds...
,
nitrogenNitrogen is a chemical element that has the symbol N and atomic number 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless and mostly inert diatomic gas at standard conditions, constituting 78% by volume of Earth's atmosphere.Many industrially important...
,
calciumCalcium is the chemical element with the symbol Ca and atomic number 20. It has an atomic mass of 40.078 amu. Calcium is a soft grey alkaline earth metal, and is the fifth most abundant element by mass in the Earth's crust...
,
sodiumSodium is a metallic element with a symbol Na and atomic number 11. It is a soft, silvery-white, highly reactive metal and is a member of the alkali metals within "group 1"...
,
chlorineChlorine Chlorine Chlorine ( , from the Greek word 'χλωρóς' (khlôros, meaning 'pale green'), is the chemical element with atomic number 17 and symbol Cl. It is a halogen, found in the periodic table in group 17 (formerly VII, VIIa, or VIIb). As the chloride ion, which is part of common salt and...
,
potassiumPotassium is the chemical element with the symbol K , atomic number 19, and atomic mass 39.0983. Potassium was first isolated from potash...
,
hydrogenHydrogen is the chemical element with atomic number 1. It is represented by the symbol H. At standard temperature and pressure, hydrogen is a colorless, odorless, nonmetallic, tasteless, highly flammable diatomic gas with the molecular formula H
2...
,
phosphorusPhosphorus is the chemical element that has the symbol P and atomic number 15. A multivalent nonmetal of the nitrogen group, phosphorus is commonly found in inorganic phosphate rocks. Elemental phosphorus exists in two major forms - white phosphorus and red phosphorus...
,
oxygenOxygen Oxygen Oxygen (acid, literally "sharp", from the taste of acids) and -γενής (-genēs) (producer, literally begetter) is the element with atomic number 8 and represented by the symbol O...
and
sulfurSulfur or sulphur is the chemical element that has the atomic number 16. It is denoted with the symbol S. It is an abundant, multivalent non-metal. Sulfur, in its native form, is a yellow crystalline solid. In nature, it can be found as the pure element and as sulfide and sulfate minerals...
. The
organic compoundAn organic compound is any member of a large class of chemical compounds whose molecules contain carbon. For historical reasons discussed below, a few types of compounds such as carbonates, simple oxides of carbon and cyanides, as well as the allotropes of carbon, are considered inorganic...
s (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
ionAn ion is an atom or molecule where the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge...
ic
electrolyteIn chemistry, an electrolyte is any substance containing free ions that behaves as an electrically conductive medium, usually when in a solution...
s. The most important ions are
sodiumSodium is a metallic element with a symbol Na and atomic number 11. It is a soft, silvery-white, highly reactive metal and is a member of the alkali metals within "group 1"...
,
potassiumPotassium is the chemical element with the symbol K , atomic number 19, and atomic mass 39.0983. Potassium was first isolated from potash...
,
calciumCalcium is the chemical element with the symbol Ca and atomic number 20. It has an atomic mass of 40.078 amu. Calcium is a soft grey alkaline earth metal, and is the fifth most abundant element by mass in the Earth's crust...
,
magnesiumMagnesium is a chemical element with the symbol Mg, atomic number 12 and common oxidation number +2. It is an alkaline earth metal and the eighth most abundant element in the earth's crust by mass, although ninth in the Universe as a whole...
,
chlorideThe chloride ion is formed when the element chlorine picks up one electron to form an anion Cl
−...
,
phosphateA phosphate, an inorganic chemical, is a salt of phosphoric acid. In organic chemistry, a phosphate, or organophosphate, is an ester of phosphoric acid. Organic phosphates are important in biochemistry and biogeochemistry or ecology. Inorganic phosphates are mined to obtain phosphorus for use in...
, and the organic ion
bicarbonateIn inorganic chemistry, bicarbonate is an intermediate form in the deprotonation of carbonic acid...
. The maintenance of precise gradients across
cell membraneThe cell membrane is the biological membrane separating the interior of a cell from the outside environment....
s maintains
osmotic pressureOsmotic pressure is the pressure that must be applied to a solution to prevent the inward flow of water across a semipermeable membrane.Jacobus Henricus van 't Hoff first proposed a formula for calculating the osmotic pressure, but this was later improved upon by Harmon Northrop Morse.A related...
and
pHpH is a measure of the acidity or basicity of a solution. It is defined as the cologarithm of the activity of dissolved hydrogen ions . Hydrogen ion activity coefficients cannot be measured experimentally, so they are based on theoretical calculations...
. Ions are also critical for
nerveA nerve is an enclosed, cable-like bundle of peripheral axons . A nerve provides a common pathway for the electrochemical nerve impulses that are transmitted along each of the axons. Nerves are found only in the peripheral nervous system...
s and
muscleMuscle is the contractile tissue of the body and is derived from the mesodermal layer of embryonic germ cells. Muscle cells contain contractile filaments that move past each other and change the size of the cell. They are classified as skeletal, cardiac, or smooth muscles. Their function is to...
s, as
action potentialAn action potential is a transient alteration of the transmembrane voltage across an excitable membrane generated by the activity of voltage-gated ion channels embedded in the membrane. Action potentials play multiple roles in several types of excitable cells such as neurons, myocytes, and...
s in these tissues are produced by the exchange of electrolytes between the
extracellular fluidExtracellular fluid usually denotes all body fluid outside of cells. The remainder is called intracellular fluid.In some animals, including mammals, the extracellular fluid can be divided into two major subcompartments, interstitial fluid and blood plasma...
and the
cytosolThe cytosol or intracellular fluid is the liquid found inside cells. In eukaryotes this liquid is separated by cell membranes from the contents of the organelles suspended in the cytosol, such as the mitochondrial matrix inside the mitochondrion...
. Electrolytes enter and leave cells through proteins in the cell membrane called ion channels. For example,
muscle contractionMuscle fiber generates tension through the action of actin and myosin cross-bridge cycling. While under tension, the muscle may lengthen, shorten or remain the same...
depends upon the movement of calcium, sodium and potassium through ion channels in the cell membrane and
T-tubuleA T-tubule is a deep invagination of the sarcolemma, which is the plasma membrane, only found in skeletal and cardiac muscle cells...
s.
The
transition metalThe term transition metal has two possible meanings:*In the past it referred to any element in the d-block of the periodic table, which includes groups 3 to 12 on the periodic table...
s are usually present as
trace elementIn analytical chemistry, a trace element is an element in a sample that has an average concentration of less than 100 parts per million measured in atomic count, or less than 100 micrograms per gram....
s in organisms, with
zincZinc , also known as spelter, is a metallic chemical element; it has the symbol Zn and atomic number 30. It is the first element in group 12 of the periodic table. Zinc is, in some respects, chemically similar to magnesium, because its ion is of similar size and its only common oxidation state is +2...
and
ironIron is a metallic chemical element with the symbol Fe and atomic number 26. Iron is a group 8 and period 4 element and is therefore classified as a transition metal. Iron and iron alloys are by far the most common metals and the most common ferromagnetic materials in everyday use...
being most abundant. These metals are used in some proteins as
cofactorsA cofactor is a non-protein chemical compound that is bound to a protein and is required for the protein's biological activity. These proteins are commonly enzymes and cofactors can be considered "helper molecules/ions" that assist in biochemical transformations...
and are essential for the activity of enzymes such as
catalaseCatalase is a common enzyme found in nearly all living organisms which are exposed to oxygen, where it functions to catalyze the decomposition of hydrogen peroxide to water and oxygen...
and oxygen-carrier proteins such as
hemoglobinHemoglobin is the iron-containing oxygen-transport metalloprotein in the red blood cells of vertebrates, and the tissues of some invertebrates....
. 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
ferritinFerritin is a globular protein complex consisting of 24 protein subunits and is the primary intracellular iron-storage protein in both prokaryotes and eukaryotes, keeping iron in a soluble and non-toxic form...
or
metallothioneinMetallothionein is a family of cysteine-rich, low molecular weight proteins. MTs have the capacity to bind both physiological and xenobiotic heavy metals through the thiol group of its cysteine residues, which represents nearly the 30% of its amino acidic residues.MT was...
when not being used.
Catabolism
Catabolism is the set of metabolic processes that break down large molecules. These include breaking down and oxidising food molecules. The purpose of the catabolic reactions is to provide the energy and components needed by anabolic reactions. The exact nature of these catabolic reactions differ from organism to organism and organisms can be classified based on their sources of energy and carbon (their
primary nutritional groupsPrimary nutritional groups are groups of organisms, divided according to the sources of energy and carbon, needed for living, growth and reproduction...
), as shown in the table below. Organic molecules being used as a source of energy in
organotrophAn organotroph is an organism that obtains hydrogen or electrons from organic substrates . Antonym: Lithotroph...
s, while
lithotrophA lithotroph is an organism that uses an inorganic substrate to obtain reducing equivalents for use in biosynthesis or energy conservation via aerobic or anaerobic respiration. Known lithotrophs are exclusively microbes or plants; No known macrofauna possesses the ability to utilize inorganic...
s use inorganic substrates and
phototrophPhotoautotrophs or Phototroph are organisms that carry out photosynthesis to acquire energy. Energy from sunlight, carbon dioxide and water are converted into organic materials to be used in cellular functions such as biosynthesis and respiration...
s capture
sunlightSunlight, in the broad sense, is the total spectrum of the electromagnetic radiation given off by the Sun. On Earth, sunlight is filtered through the atmosphere, and the solar radiation is obvious as daylight when the Sun is above the horizon. Near the poles in summer, the days are longer and the...
as chemical energy. However, all these different forms of metabolism depend on
redoxRedox describes all chemical reactions in which atoms have their oxidation number changed....
reactions that involve the transfer of electrons from reduced donor molecules such as organic molecules,
waterWater is an ubiquitous chemical substance that is composed of hydrogen and oxygen and is essential for all known forms of life.In typical usage, water refers only to its liquid form or state, but the substance also has a solid state, ice, and a gaseous state, water vapor or steam. Water covers 71%...
,
ammoniaAmmonia is a compound of nitrogen and hydrogen with the formula NH
3. It is normally encountered as a gas with a characteristic pungent odor. Ammonia contributes significantly to the nutritional needs of terrestrial organisms by serving as a precursor to foodstuffs and fertilizers...
,
hydrogen sulfideHydrogen sulfide is the chemical compound with the formula H
2S. This colorless, toxic and flammable gas is partially responsible for the foul odor of rotten eggs and flatulence....
or
ferrous ionsFerrous, in chemical science, indicates a bivalent iron compound , as opposed to ferric, which indicates a trivalent iron compound ....
to acceptor molecules such as
oxygenOxygen Oxygen Oxygen (acid, literally "sharp", from the taste of acids) and -γενής (-genēs) (producer, literally begetter) is the element with atomic number 8 and represented by the symbol O...
,
nitrateIn inorganic chemistry, a nitrate is a salt of nitric acid with an ion composed of one nitrogen and three oxygen atoms . In organic chemistry the esters of nitric acid and various alcohols are called nitrates.-Chemical properties:...
or
sulfateIn inorganic chemistry, a sulfate is a salt of sulfuric acid.-Chemical properties:...
. In animals these reactions involve complex organic molecules being broken down to simpler molecules, such as
carbon dioxideCarbon dioxide is a chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom. It is a gas at standard temperature and pressure and exists in Earth's atmosphere in this state...
and water. In
photosyntheticPhotosynthesis is a process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight. Photosynthesis occurs in plants, algae, and many species of Bacteria, but not in Archaea...
organisms such as plants and
cyanobacteriaCyanobacteria, also known as blue-green algae, blue-green bacteria or Cyanophyta, is a phylum of bacteria that obtain their energy through photosynthesis. The name "cyanobacteria" comes from the color of the bacteria = blue)...
, these electron-transfer reactions do not release energy, but are used as a way of storing energy absorbed from sunlight.
-
-
- Classification of organisms based on their metabolism
| energy source |
sunlight |
photo- |
|
-troph |
| preformed molecules |
chemo- |
| electron donor |
organic compound An organic compound is any member of a large class of chemical compounds whose molecules contain carbon. For historical reasons discussed below, a few types of compounds such as carbonates, simple oxides of carbon and cyanides, as well as the allotropes of carbon, are considered inorganic...
|
|
organo- |
|
| inorganic compound Traditionally, inorganic compounds are considered to be of a mineral, not biological, origin. Complementarily, most organic compounds are traditionally viewed as being of biological origin...
|
litho- |
| carbon source |
organic compound An organic compound is any member of a large class of chemical compounds whose molecules contain carbon. For historical reasons discussed below, a few types of compounds such as carbonates, simple oxides of carbon and cyanides, as well as the allotropes of carbon, are considered inorganic...
|
|
hetero- |
| inorganic compound Traditionally, inorganic compounds are considered to be of a mineral, not biological, origin. Complementarily, most organic compounds are traditionally viewed as being of biological origin...
|
auto- |
The most common set of catabolic reactions in animals can be separated into three main stages. In the first, large organic molecules such as
proteinProteins are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer chain are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues...
s,
polysaccharidePolysaccharides are polymeric carbohydrate structures, formed of repeating units joined together by glycosidic bonds. These structures are often linear, but may contain various degrees of branching. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit...
s or
lipidLipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins , monoglycerides, diglycerides, phospholipids, and others...
s are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to yet smaller molecules, usually
acetyl coenzyme AAcetyl-CoA is an important molecule in metabolism, used in many biochemical reactions. Its main use is to convey the carbon atoms within the acetyl group to the citric acid cycle to be oxidized for energy production. In chemical structure, acetyl-CoA is the thioester between coenzyme A and acetic...
(acetyl-CoA), which releases some energy. Finally, the acetyl group on the CoA is oxidised to water and carbon dioxide in the
citric acid cycleThe citric acid cycle — also known as the tricarboxylic acid cycle , the Krebs cycle, or more rarely, the Szent-Györgyi-Krebs cycle — is a series of enzyme-catalysed chemical reactions, which is of central importance in all living cells that use oxygen as part of cellular respiration...
and
electron transport chainAn electron transport chain couples a chemical reaction between an electron donor and an electron acceptor to the transfer of H+ ions across a membrane, through a set of mediating biochemical reactions...
, releasing the energy that is stored by reducing the coenzyme
nicotinamide adenine dinucleotideNicotinamide adenine dinucleotide, abbreviated NAD
+, is a coenzyme found in all living cells. The compound is a dinucleotide, since it consists of two nucleotides joined through their phosphate groups, with one nucleotide containing an adenine base and the other containing...
(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
proteaseA protease breaks down proteins. A protease is any enzyme that conducts proteolysis, that is, begins protein catabolism by hydrolysis of the peptide bonds that link amino acids together in the polypeptide chain forming the protein...
s that digest proteins into amino acids, as well as
glycoside hydrolaseGlycoside hydrolases catalyze the hydrolysis of the glycosidic linkage to generate two smaller sugars. They are extremely common enzymes with roles in nature including degradation of biomass such as cellulose and hemicellulose, in anti-bacterial defense strategies , in pathogenesis mechanisms and...
s 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 transportActive transport is the mediated process of moving particles across a biological membrane against a concentration gradient. If the process uses chemical energy, such as from adenosine triphosphate , it is termed primary active transport. Secondary active transport involves the use of an...
proteins.
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
monosaccharideMonosaccharides are the most basic unit of carbohydrates. They are the simplest form of sugar and are usually colorless, water-soluble, crystalline solids. Some monosaccharides have a sweet taste. Examples of monosaccharides include glucose , fructose , galactose, xylose and ribose...
s. Once inside, the major route of breakdown is
glycolysisGlycolysis is the metabolic pathway that converts glucose, C
6H
12O
6, into pyruvate, C
3H
6O
3-...
, where sugars such as
glucoseGlucose , a monosaccharide also known as - grape sugar, blood sugar, or corn sugar, is a very important carbohydrate in biology. The living cell uses it as a source of energy and metabolic intermediate...
and
fructoseFructose is a simple monosaccharide found in many foods. It is a white solid that dissolves readily in water. Honey, tree fruits, berries, melons, and some root vegetables, contain significant amounts of the fructose derivative sucrose...
are converted into
pyruvatePyruvic acid is an organic acid. It is also a ketone, as well as being the simplest alpha-keto acid. The carboxylate ion of pyruvic acid, CH
3COCOO
-, is known as pyruvate, and is a key intersection in several metabolic pathways...
and some ATP is generated. Pyruvate is an intermediate in several metabolic pathways, but the majority is converted to
acetyl-CoAAcetyl-CoA is an important molecule in metabolism, used in many biochemical reactions. Its main use is to convey the carbon atoms within the acetyl group to the citric acid cycle to be oxidized for energy production. In chemical structure, acetyl-CoA is the thioester between coenzyme A and acetic...
and fed into the
citric acid cycleThe citric acid cycle — also known as the tricarboxylic acid cycle , the Krebs cycle, or more rarely, the Szent-Györgyi-Krebs cycle — is a series of enzyme-catalysed chemical reactions, which is of central importance in all living cells that use oxygen as part of cellular respiration...
. 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 dioxideCarbon dioxide is a chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom. It is a gas at standard temperature and pressure and exists in Earth's atmosphere in this state...
as a waste product. In anaerobic conditions, glycolysis produces
lactateLactic acid , also known as milk acid, is a chemical compound that plays a role in several biochemical processes. It was first isolated in 1780 by a Swedish chemist, Carl Wilhelm Scheele, and is a carboxylic acid with a chemical formula of C
3H
6O
3...
, through the enzyme
lactate dehydrogenaseLactate dehydrogenase is an enzyme present in a wide variety of organisms, including plants and animals.Lactate dehydrogenases exist in four distinct enzyme classes. Two of them are cytochrome c-dependent enzymes with each acting on either D-lactate or L-lactate...
re-oxidizing NADH to NAD+ for re-use in glycolysis. An alternative route for glucose breakdown is the
pentose phosphate pathwayThe pentose phosphate pathway is a process that generates NADPH and pentoses sugars. There are two distinct phases in the pathway. The first is the oxidative phase, in which NADPH is generated, and the second is the non-oxidative synthesis of 5-carbon sugars...
, which reduces the coenzyme NADPH and produces
pentoseA pentose is a monosaccharide with five carbon atoms.They either have an aldehyde functional group in position 1 , or a ketone functional group in position 2 ....
sugars such as
riboseRibose, primarily occurring as
D-ribose, is an organic compound that occurs widely in nature. It is an aldopentose, that is a monosaccharide containing five carbon atoms that, in its acyclic form, has an aldehyde functional group at one end. This species predominantly exists in the...
, the sugar component of
nucleic acidA nucleic acid is a macromolecule composed of chains of monomeric nucleotides. In biochemistry these molecules carry genetic information or form structures within cells. The most common nucleic acids are deoxyribonucleic acid and ribonucleic acid . Nucleic acids are universal in living things, as...
s.
Fats are catabolised by
hydrolysisHydrolysis is a chemical reaction during which one or more water molecules are split into hydrogen and hydroxide ions, which may go on to participate in further reactions. It is the type of reaction that is used to break down certain polymers, especially those made by step-growth polymerization...
to free fatty acids and glycerol. The glycerol enters glycolysis and the fatty acids are broken down by
beta oxidationBeta oxidation is the process by which fatty acids, in the form of Acyl-CoA molecules, are broken down in mitochondria and/or in peroxisomes to generate Acetyl-CoA, the entry molecule for the Krebs cycle.-Activation of fatty acids:...
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 acidAmino acids are molecules containing an amine group, a carboxylic acid group and one of the twenty R-groups. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H
2NCHRCOOH, where R is an organic substituent...
s are either used to synthesize proteins and other biomolecules, or oxidized to
ureaUrea or carbamide is an organic compound with the chemical formula
2CO. The molecule has two amine residues joined by a carbonyl functional group....
and carbon dioxide as a source of energy. The oxidation pathway starts with the removal of the amino group by a
transaminaseIn biochemistry, a transaminase or an aminotransferase is an enzyme that catalyzes a type of reaction between an amino acid and an α-keto acid. Specifically, this reaction involves removing the amino group from the amino acid, leaving behind an α-keto acid, and transferring it to...
. The amino group is fed into the
urea cycleThe urea cycle is a cycle of biochemical reactions occurring in many animals that produces urea
2CO from ammonia . This cycle was the first metabolic cycle discovered...
, leaving a deaminated carbon skeleton in the form of a
keto acidKeto acids are organic acids containing a ketone functional group and a carboxylic acid group.Common types of keto acids include:*Alpha-keto acid, or 2-oxo acids, such as pyruvic acid have the keto group adjacent to the carboxylic acid...
. Several of these keto acids are intermediates in the citric acid cycle, for example the deamination of glutamate forms α-
ketoglutarateα-Ketoglutaric acid is one of two ketone derivatives of glutaric acid. Its anion, α-ketoglutarate is an important biological compound...
. The
glucogenic amino acidA glucogenic amino acid is an amino acid that can be converted into glucose through gluconeogenesis. This is in contrast to the ketogenic amino acids, which are converted into ketone bodies....
s can also be converted into glucose, through
gluconeogenesisGluconeogenesis is a metabolic pathway that results in the generation of glucose from non-carbohydrate carbon substrates such as lactate, glycerol, and glucogenic amino acids....
(discussed below).
Oxidative phosphorylation
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 is used to make ATP. This is done in
eukaryoteA eukaryote is an organism whose cells contain complex structures enclosed within membranes. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear envelope, within which the genetic material is carried...
s by a series of proteins in the membranes of mitochondria called the
electron transport chainAn electron transport chain couples a chemical reaction between an electron donor and an electron acceptor to the transfer of H+ ions across a membrane, through a set of mediating biochemical reactions...
. In
prokaryoteThe prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. They differ from the eukaryotes, which have a cell nucleus. Most are unicellular, but a few prokaryotes such as myxobacteria have multicellular stages in their life cycles...
s, these proteins are found in the cell's
inner membraneBacteria, despite their simplicity, contain a well developed cell structure which is responsible for many of their unique biological properties. Many structural features are unique to bacteria and are not found among archaea or eukaryotes...
. These proteins use the energy released from passing electrons from
reducedA reducing agent is the element or compound in a redox reaction that reduces another species. In doing so, it becomes oxidized, and is therefore the electron donor in the redox...
molecules like NADH onto
oxygenOxygen Oxygen Oxygen (acid, literally "sharp", from the taste of acids) and -γενής (-genēs) (producer, literally begetter) is the element with atomic number 8 and represented by the symbol O...
to pump
protonThe proton is a subatomic particle with an electric charge of +1 elementary charge. It is found in the nucleus of each atom but is also stable by itself and has a second identity as the hydrogen ion, H
+...
s across a membrane.
Pumping protons out of the mitochondria creates a proton
concentration differenceMolecular diffusion, often called simply diffusion, is a net transport of molecules from a region of higher concentration to one of lower concentration by random molecular motion. The result of diffusion is a gradual mixing of material...
across the membrane and generates an
electrochemical gradientAn electrochemical gradient is a spatial variation of both electrical potential and chemical concentration across a membrane. Both components are often due to ion gradients, particularly proton gradients, and the result can be a type of potential energy available for work in a cell...
. This force drives protons back into the mitochondrion through the base of an enzyme called
ATP synthaseAn ATP synthase is a general term for an enzyme that can synthesize adenosine triphosphate from adenosine diphosphate and inorganic phosphate by using some form of energy...
. The flow of protons makes the stalk subunit rotate, causing the
active siteThe active site of an enzyme contains the catalytic and binding sites. The structure and chemical properties of the active site allow the recognition and binding of the substrate....
of the synthase domain to change shape and phosphorylate
adenosine diphosphateAdenosine diphosphate, abbreviated ADP, is a nucleotide. It is an ester of pyrophosphoric acid with the nucleoside adenosine. ADP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase adenine....
- turning it into ATP.
Energy from inorganic compounds
Chemolithotrophy is a type of metabolism found in
prokaryoteThe prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. They differ from the eukaryotes, which have a cell nucleus. Most are unicellular, but a few prokaryotes such as myxobacteria have multicellular stages in their life cycles...
s where energy is obtained from the oxidation of inorganic compounds. These organisms can use
hydrogenHydrogen is the chemical element with atomic number 1. It is represented by the symbol H. At standard temperature and pressure, hydrogen is a colorless, odorless, nonmetallic, tasteless, highly flammable diatomic gas with the molecular formula H
2...
, reduced
sulfurSulfur or sulphur is the chemical element that has the atomic number 16. It is denoted with the symbol S. It is an abundant, multivalent non-metal. Sulfur, in its native form, is a yellow crystalline solid. In nature, it can be found as the pure element and as sulfide and sulfate minerals...
compounds (such as
sulfideA sulfide is a chemical compound containing sulfur in its lowest oxidation number of −2.- Properties :...
,
hydrogen sulfideHydrogen sulfide is the chemical compound with the formula H
2S. This colorless, toxic and flammable gas is partially responsible for the foul odor of rotten eggs and flatulence....
and
thiosulfateThiosulfate , sometimes spelled Thiosulphate, is an oxyanion of sulfur produced by the reaction of sulfite ions with elemental sulfur in boiling water. Thiosulfate occurs naturally in hot springs and geysers, and is produced by certain biochemical processes...
),
ferrous iron (FeII)Iron oxide, also known as ferrous oxide, iron oxide/oxidized iron or more commonly rusted iron, is one of the iron oxides. It is a black-colored powder with the chemical formula . It consists of the chemical element iron in the oxidation state of 2 bonded to oxygen. Its mineral form is known as...
or
ammoniaAmmonia is a compound of nitrogen and hydrogen with the formula NH
3. It is normally encountered as a gas with a characteristic pungent odor. Ammonia contributes significantly to the nutritional needs of terrestrial organisms by serving as a precursor to foodstuffs and fertilizers...
as sources of reducing power and they gain energy from the oxidation of these compounds with electron acceptors such as
oxygenOxygen Oxygen Oxygen (acid, literally "sharp", from the taste of acids) and -γενής (-genēs) (producer, literally begetter) is the element with atomic number 8 and represented by the symbol O...
or
nitriteThe nitrite ion is NO2−. The anion is bent, being isoelectronic with ozone. More generally, a nitrite compound is either a salt or an ester of nitrous acid.-Examples:* nitrous acid, HNO2...
. These microbial processes are important in global
biogeochemical cycleIn ecology and Earth science, a biogeochemical cycle or nutrient cycle is a pathway by which a chemical element or molecule moves through both biotic and abiotic compartments of Earth...
s such as
acetogenesisAcetogenesis is a process through which acetate is produced by anaerobic bacteria from a variety of energy and carbon sources...
,
nitrificationNitrification is the biological oxidation of ammonia with oxygen into nitrite followed by the oxidation of these nitrites into nitrates. Degradation of ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an important step in the nitrogen cycle in soil...
and
denitrificationDenitrification is a microbially facilitated process of dissimilatory nitrate reduction that may ultimately produce molecular nitrogen through a series of intermediate gaseous nitrogen oxide products. This respiratory process reduces oxidized forms of nitrogen in response to the oxidation of an...
and are critical for soil fertility.
Energy from light
The energy in sunlight is captured by plants,
cyanobacteriaCyanobacteria, also known as blue-green algae, blue-green bacteria or Cyanophyta, is a phylum of bacteria that obtain their energy through photosynthesis. The name "cyanobacteria" comes from the color of the bacteria = blue)...
,
purple bacteriaPurple bacteria or purple photosynthetic bacteria are proteobacteria that are phototrophic, that is capable of producing energy through photosynthesis. They are pigmented with bacteriochlorophyll a or b, together with various carotenoids...
,
green sulfur bacteriaThe green sulfur bacteria are a family of the blue tiregs in the animalia phylum family of obligately anaerobic photoautotrophic bacteria. Most closely related to the distant Bacteroidetes, they are accordingly assigned their own phylum....
and some
protistProtists , are a diverse group of eukaryotic microorganisms. Historically, protists were treated as the kingdom Protista but this group is no longer recognized in modern taxonomy...
s. This process is often coupled to the conversion of carbon dioxide into organic compounds, as part of photosynthesis, which is discussed below. The energy capture and carbon fixation systems can however operate separately in prokaryotes, as purple bacteria and green sulfur bacteria can use sunlight as a source of energy, while switching between carbon fixation and the fermentation of organic compounds.
In many organisms the capture of solar energy is similar in principle to oxidative phosphorylation, as it involves 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 centreA photosynthetic reaction center is a complex of three types of protein that is the site where molecular excitations originating from sunlight are transformed into a series of electron-transfer reactions. The reaction center proteins bind functional co-factors, chromophores or pigments such as...
s or
rhodopsinRhodopsin, also known as visual purple, is a pigment of the retina that is responsible for both the formation of the photoreceptor cells and the first events in the perception of light. Rhodopsins belong to the G-protein coupled receptor family and are extremely sensitive to light, enabling vision...
s. Reaction centers are classed into two types depending on the type of
photosynthetic pigmentA photosynthetic pigment is a pigment that is present in chloroplasts or photosynthetic bacteria and captures the light energy necessary for photosynthesis.- Plants :...
present, with most photosynthetic bacteria only having one type, while plants and cyanobacteria have two.
In plants, algae, and cyanobateria,
photosystem IIPhotosystems are protein complexes involved in photosynthesis. They are found in the thylakoid membranes of plants, algae and cyanobacteria , or in the cytoplasmic membrane of photosynthetic bacteria...
uses light energy to remove electrons from water, releasing oxygen as a waste product. The electrons then flow to the
cytochrome b6f complexThe cytochrome b6f complex of chloroplasts and cyanobacteria transfers electrons between the two reaction center complexes of oxygenic photosynthetic membranes, photosystem I and photosystem II, and participates in formation of the transmembrane electrochemical proton gradient by also...
, which uses their energy to pump protons across the
thylakoidA thylakoid is a membrane-bound compartment inside chloroplasts and cyanobacteria. They are the site of the light-dependent reactions of photosynthesis. The word "thylakoid" is derived from the Greek thylakos, meaning "sac". Thylakoids consists of a thylakoid membrane surrounding a thylakoid lumen...
membrane in the
chloroplastChloroplasts are organelles found in plant cells and other eukaryotic organisms that conduct photosynthesis. Chloroplasts capture light energy to conserve free energy in the form of ATP and reduce NADP to NADPH through a complex set of processes called photosynthesis.The word chloroplast is...
. These protons move back through the membrane as they drive the ATP synthase, as before. The electrons then flow through
photosystem IPhotosystems are protein complexes involved in photosynthesis. They are found in the thylakoid membranes of plants, algae and cyanobacteria , or in the cytoplasmic membrane of photosynthetic bacteria...
and can then either be used to reduce the coenzyme NADP
+, for use in the
Calvin cycleThe Calvin cycle or Calvin-Benson-Bassham cycle is a series of biochemical reactions that take place in the stroma of chloroplasts in photosynthetic organisms. It was discovered by Melvin Calvin, James Bassham and Andrew Benson at the University of California, Berkeley by using the radioactive...
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 acidAmino acids are molecules containing an amine group, a carboxylic acid group and one of the twenty R-groups. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H
2NCHRCOOH, where R is an organic substituent...
s,
monosaccharideMonosaccharides are the most basic unit of carbohydrates. They are the simplest form of sugar and are usually colorless, water-soluble, crystalline solids. Some monosaccharides have a sweet taste. Examples of monosaccharides include glucose , fructose , galactose, xylose and ribose...
s,
isoprenoidsThe terpenoids , sometimes called isoprenoids, are a large and diverse class of naturally-occurring organic chemicals similar to terpenes, derived from five-carbon isoprene units assembled and modified in thousands of ways. Most are multicyclic structures that differ from one another not only in...
and
nucleotideNucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides play central roles in metabolism...
s, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as
proteinProteins are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer chain are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues...
s,
polysaccharidePolysaccharides are polymeric carbohydrate structures, formed of repeating units joined together by glycosidic bonds. These structures are often linear, but may contain various degrees of branching. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit...
s,
lipidLipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins , monoglycerides, diglycerides, phospholipids, and others...
s and
nucleic acidA nucleic acid is a macromolecule composed of chains of monomeric nucleotides. In biochemistry these molecules carry genetic information or form structures within cells. The most common nucleic acids are deoxyribonucleic acid and ribonucleic acid . Nucleic acids are universal in living things, as...
s.
Organisms differ in how many of the molecules in their cells they can construct for themselves.
AutotrophAn autotroph is an organism that produces complex organic compounds from simple inorganic molecules using energy from light or inorganic chemical reactions....
s such as plants can construct the complex organic molecules in cells such as polysaccharides and proteins from simple molecules like
carbon dioxideCarbon dioxide is a chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom. It is a gas at standard temperature and pressure and exists in Earth's atmosphere in this state...
and water.
HeterotrophA Heterotroph is an organism that uses organic carbon for growth. This contrasts with autotrophs, such as plants, which are able to directly use sources of energy, such as light to produce organic substrates from inorganic carbon dioxide.- Ecology :Heterotrophs are known as consumers in food...
s, 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 carbohydrates from sunlight and
carbon dioxideCarbon dioxide is a chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom. It is a gas at standard temperature and pressure and exists in Earth's atmosphere in this state...
(CO
2). 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 centreA photosynthetic reaction center is a complex of three types of protein that is the site where molecular excitations originating from sunlight are transformed into a series of electron-transfer reactions. The reaction center proteins bind functional co-factors, chromophores or pigments such as...
s, as described above, to convert CO
2 into
glycerate 3-phosphate3-Phosphoglyceric acid , or glycerate 3-phosphate , is a biochemically significant 3-carbon molecule that is a metabolic intermediate in both glycolysis and the Calvin cycle. This chemical is often termed PGA when referring to the Calvin cycle. 3-Phosphoglycerate is the resultant of the split of 6...
, which can then be converted into glucose. This carbon-fixation reaction is carried out by the enzyme
RuBisCORibulose-1,5-bisphosphate carboxylase oxygenase, most commonly known by the shorter name RuBisCO, is an enzyme that is used in the Calvin cycle to catalyze the first major step of carbon fixation, a process by which the atoms of atmospheric carbon dioxide are made available to organisms in the...
as part of the
Calvin – Benson cycleThe Calvin cycle or Calvin-Benson-Bassham cycle is a series of biochemical reactions that take place in the stroma of chloroplasts in photosynthetic organisms. It was discovered by Melvin Calvin, James Bassham and Andrew Benson at the University of California, Berkeley by using the radioactive...
. Three types of photosynthesis occur in plants,
C3 carbon fixation carbon fixation is a metabolic pathway for carbon fixation in photosynthesis. This process converts carbon dioxide and ribulose bisphosphate into 3-phosphoglycerate through the following reaction:...
,
C4 carbon fixationC
4 carbon fixation is one of three biochemical mechanisms, along with C
3 and CAM photosynthesis, functioning in land plants to "fix" carbon dioxide for sugar production through photosynthesis...
and
CAM photosynthesisCrassulacean acid metabolism, also known as CAM photosynthesis, is an elaborate carbon fixation pathway in some plants. These plants fix carbon dioxide during the night, storing it as the four carbon acid malate. The is released during the day, where it is concentrated around the enzyme...
. These differ by the route that carbon dioxide takes to the Calvin cycle, with C3 plants fixing CO
2 directly, while C4 and CAM photosynthesis incorporate the CO
2 into other compounds first, as adaptations to deal with intense sunlight and dry conditions.
In photosynthetic
prokaryoteThe prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. They differ from the eukaryotes, which have a cell nucleus. Most are unicellular, but a few prokaryotes such as myxobacteria have multicellular stages in their life cycles...
s the mechanisms of carbon fixation are more diverse. Here, carbon dioxide can be fixed by the Calvin – Benson cycle, a
reversed citric acidThe reverse Krebs cycle...
cycle, or the carboxylation of acetyl-CoA. Prokaryotic
chemoautotrophsChemotrophs are organisms that obtain energy by the oxidation of electron donating molecules in their environments. These molecules can be organic or inorganic . The chemotroph designation is in contrast to phototrophs which utilize solar energy...
also fix CO
2 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
monosaccharideMonosaccharides are the most basic unit of carbohydrates. They are the simplest form of sugar and are usually colorless, water-soluble, crystalline solids. Some monosaccharides have a sweet taste. Examples of monosaccharides include glucose , fructose , galactose, xylose and ribose...
s such as
glucoseGlucose , a monosaccharide also known as - grape sugar, blood sugar, or corn sugar, is a very important carbohydrate in biology. The living cell uses it as a source of energy and metabolic intermediate...
and then used to assemble
polysaccharidePolysaccharides are polymeric carbohydrate structures, formed of repeating units joined together by glycosidic bonds. These structures are often linear, but may contain various degrees of branching. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit...
s such as
starchStarch or amylum is a polysaccharide carbohydrate consisting of a large number of glucose units joined together by glycosidic bonds.Starch is produced by all green plants as an energy store and is a major food source for humans....
. The generation of
glucoseGlucose , a monosaccharide also known as - grape sugar, blood sugar, or corn sugar, is a very important carbohydrate in biology. The living cell uses it as a source of energy and metabolic intermediate...
from compounds like pyruvate,
lactateLactic acid , also known as milk acid, is a chemical compound that plays a role in several biochemical processes. It was first isolated in 1780 by a Swedish chemist, Carl Wilhelm Scheele, and is a carboxylic acid with a chemical formula of C
3H
6O
3...
,
glycerolGlycerol is an organic compound, also commonly called glycerin or glycerine. It is a colorless, odorless, viscous liquid that is widely used in pharmaceutical formulations. Glycerol has three hydrophilic hydroxyl groups that are responsible for its solubility in water and its hygroscopic nature. ...
,
glycerate 3-phosphate3-Phosphoglyceric acid , or glycerate 3-phosphate , is a biochemically significant 3-carbon molecule that is a metabolic intermediate in both glycolysis and the Calvin cycle. This chemical is often termed PGA when referring to the Calvin cycle. 3-Phosphoglycerate is the resultant of the split of 6...
and amino acids is called
gluconeogenesisGluconeogenesis is a metabolic pathway that results in the generation of glucose from non-carbohydrate carbon substrates such as lactate, glycerol, and glucogenic amino acids....
. Gluconeogenesis converts pyruvate to
glucose-6-phosphateGlucose 6-phosphate is glucose sugar phosphorylated on carbon 6. This compound is very common in cells as the vast majority of glucose entering a cell will become phosphorylated in this way....
through a series of intermediates, many of which are shared with
glycolysisGlycolysis is the metabolic pathway that converts glucose, C
6H
12O
6, into pyruvate, C
3H
6O
3-...
. However, this pathway is not simply
glycolysisGlycolysis is the metabolic pathway that converts glucose, C
6H
12O
6, into pyruvate, C
3H
6O
3-...
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 cycleA futile cycle, also known as a substrate cycle, occurs when two metabolic pathways run simultaneously in opposite directions and have no overall effect other than to dissipate energy in the form of heat...
.
Although fat is a common way of storing energy, in
vertebrateVertebrates are members of the subphylum Vertebrata, chordates with backbones or spinal columns. About 58,000 species of vertebrates have been described. Vertebrata is the largest subphylum of chordates, and contains many familiar groups of large land animals. Vertebrates comprise cyclostomes, bony...
s such as
humanHumans are bipedal primates belonging to the species Homo sapiens in Hominidae, the great ape family. They are the only surviving member of the genus Homo. Humans have a highly developed brain, capable of abstract reasoning, language, introspection, and problem solving...
s the
fatty acidIn chemistry, especially biochemistry, a fatty acid is a carboxylic acid often with a long unbranched aliphatic tail , which is either saturated or unsaturated...
s in these stores cannot be converted to glucose through
gluconeogenesisGluconeogenesis is a metabolic pathway that results in the generation of glucose from non-carbohydrate carbon substrates such as lactate, glycerol, and glucogenic amino acids....
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 bodiesKetone bodies are three water-soluble compounds that are produced as by-products when fatty acids are broken down for energy in the liver and kidney. They are used as a source of energy in the heart and brain. In the brain, they are a vital source of energy during fasting...
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 cycleThe glyoxylate cycle is an anabolic metabolic pathway occurring in plants, and several microorganisms, such as E. coli and yeast. It has long been thought to be absent in most animals, such as vertebrates and insects, although it has been suggested that it might operate in some circumstances...
, which bypasses the
decarboxylationDecarboxylation is any chemical reaction in which a carboxyl group is split off from a compound as carbon dioxide .- Common examples :Common biosynthetic decarboxylations of amino acids to amines are:* tryptophan to tryptamine...
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
glycansThe term glycan refers to a polysaccharide or oligosaccharide. Glycan may also be used to refer to the carbohydrate portion of a glycoconjugate, such as a glycoprotein, glycolipid, or a proteoglycan. Glycans usually consist solely of O-glycosidic linkages of monosaccharides...
are made by the sequential addition of monosaccharides by
glycosyltransferaseGlycosyltransferases are enzymes that act as a catalyst for the transfer of a monosaccharide unit from an activated nucleotide sugar to an Glycosyl acceptor molecule, usually an alcohol....
from a reactive sugar-phosphate donor such as
uridine diphosphate glucoseUridine diphosphate glucose is a nucleotide sugar. It is involved in glycosyltransferase reactions in metabolism.-Functions:...
(UDP-glucose) to an acceptor
hydroxylIn chemistry, hydroxyl is composed of molecules consisting of an oxygen atom and a hydrogen atom connected by a covalent bond . The neutral form is a hydroxyl radical. The hydroxyl anion is called hydroxide; it is a diatomic ion with a charge of negative one...
group on the growing polysaccharide. As any of the
hydroxylIn chemistry, hydroxyl is composed of molecules consisting of an oxygen atom and a hydrogen atom connected by a covalent bond . The neutral form is a hydroxyl radical. The hydroxyl anion is called hydroxide; it is a diatomic ion with a charge of negative one...
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
oligosaccharyltransferaseOligosaccharyltransferase or OST is a membrane protein complex that transfers a 14-sugar oligosaccharide from dolichol to nascent protein. It is a type of glycosyltransferase...
s.
Fatty acids, isoprenoids and steroids
Fatty acids are made by
fatty acid synthaseFatty acid synthase is enzymatic system composed of 272 kDa multifunctional polypeptide, in which substrates are handed from one functional domain to the next.-Metabolic function:...
s 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 actyl group, reduce it to an alcohol,
dehydrateIn chemistry, a dehydration reaction is usually defined as a chemical reaction that involves the loss of water from the reacting molecule. Dehydration reactions are a subset of elimination reactions...
it to an
alkeneIn organic chemistry, an alkene, olefin, or olefine is an unsaturated chemical compound containing at least one carbon-to-carbon double bond...
group and then reduce it again to an
alkaneAlkanes, also known as paraffins, are chemical compounds that consist only of the elements carbon and hydrogen , wherein these atoms are linked together exclusively by single bonds without any cyclic structure...
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
plastidPlastids are major organelles found in the cells of plants and algae. Plastids are the site of manufacture and storage of important chemical compounds used by the cell...
s and bacteria separate type II enzymes perform each step in the pathway.
TerpeneTerpenes are a large and varied class of hydrocarbons, produced primarily by a wide variety of plants, particularly conifers, though also by some insects such as termites or swallowtail butterflies, which emit terpenes from their osmeterium....
s and
isoprenoidsThe terpenoids , sometimes called isoprenoids, are a large and diverse class of naturally-occurring organic chemicals similar to terpenes, derived from five-carbon isoprene units assembled and modified in thousands of ways. Most are multicyclic structures that differ from one another not only in...
are a large class of lipids that include the
carotenoidCarotenoids are organic pigments that are naturally occurring in the chloroplasts and chromoplasts of plants and some other photosynthetic organisms like algae, some types of fungus and some bacteria....
s and form the largest class of plant
natural productA natural product is a chemical compound or substance produced by a living organism - found in nature that usually has a pharmacological or biological activity for use in pharmaceutical drug discovery and drug design...
s. These compounds are made by the assembly and modification of
isopreneIsoprene or 2-methyl-1,3-butadiene is a common organic compound with the formula CH2=CCH=CH2. It is present under standard conditions as a colorless liquid...
units donated from the reactive precursors
isopentenyl pyrophosphateIsopentenyl pyrophosphate is an intermediate in the classical, HMG-CoA reductase pathway used by organisms in the biosynthesis of terpenes and terpenoids. IPP is formed from acetyl-CoA via mevalonic acid...
and
dimethylallyl pyrophosphateDimethylallyl pyrophosphate is an intermediate product of both mevalonic acid pathway and DOXP/MEP pathway. It is an isomer of isopentenyl pyrophosphate and exists in virtually all life forms....
. 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 pathwayThe non-mevalonate pathway or 2-C-methyl-D-erythritol 4-phosphate/1-deoxy-D-xylulose 5-phosphate pathway of isoprenoid biosynthesis is an alternative metabolic pathway leading to the formation of isopentenyl pyrophosphate and dimethylallyl pyrophosphate that has been elucidated only...
uses pyruvate and
glyceraldehyde 3-phosphateGlyceraldehyde 3-phosphate, also known as triose phosphate or 3-phosphoglyceraldehyde and abbreviated as G3P, GADP, GAP, TP, GALP or PGAL, is a chemical compound that occurs as an intermediate in several central metabolic pathways of all organisms...
as substrates. One important reaction that uses these activated isoprene donors is steroid biosynthesis. Here, the isoprene units are joined together to make
squaleneSqualene is a natural organic compound originally obtained for commercial purposes primarily from shark liver oil, though botanic sources are used as well, including amaranth seed, rice bran, wheat germ, and olives. All higher organisms produce squalene, including humans. It is a hydrocarbon and a...
and then folded up and formed into a set of rings to make
lanosterolLanosterol is a tetracyclic triterpenoid, which is the compound from which all steroids are derived.-Role in creation of steroids:Elaboration of lanosterol under enzyme catalysis leads to the core structure of steroids. 14-Demethylation of lanosterol by CYP51 eventually yields...
. Lanosterol can then be converted into other steroids such as
cholesterolCholesterol is a lipidic, waxy steroid found in the cell membranes and transported in the blood plasma of all animals. It is an essential component of mammalian cell membranes, where it is required to establish proper membrane permeability and fluidity...
and
ergosterolErgosterol , a sterol, is a biological precursor to vitamin D
2. It is turned into viosterol by ultraviolet light, and is then converted into ergocalciferol, which is a form of vitamin D....
.
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 acidAn essential amino acid or indispensable amino acid is an amino acid that cannot be synthesized de novo by the organism , and therefore must be supplied in the diet.-Essentiality vs...
s 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
glutamineGlutamine is one of the 20 amino acids encoded by the standard genetic code. Its side chain is an amide formed by replacing the side-chain hydroxyl of glutamic acid with an amine functional group. It can therefore be considered the amide of glutamic acid. Its codons are CAA and CAG. Glutamine is...
. Amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then
transaminatedIn biochemistry, a transaminase or an aminotransferase is an enzyme that catalyzes a type of reaction between an amino acid and an α-keto acid. Specifically, this reaction involves removing the amino group from the amino acid, leaving behind an α-keto acid, and transferring it to...
to form an amino acid.
Amino acids are made into proteins by being joined together in a chain by
peptide bondA peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amine group of the other molecule, thereby releasing a molecule of water . This is a dehydration synthesis reaction, and usually occursbetween amino acids...
s. Each different protein has a unique sequence of amino acid residues: this is its
primary structureIn biochemistry, the primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms...
. 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 RNATransfer RNA is a small RNA molecule that transfers a specific active amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has a 3' terminal site for amino acid attachment. This covalent linkage is catalyzed by an aminoacyl tRNA synthetase...
molecule through an
esterEsters are chemical compounds derived by reacting an oxoacid with a hydroxyl compound such as an alcohol or phenol. Esters are usually derived from an inorganic acid or organic acid in which at least one -OH group is replaced by an -O-alkyl group, and most commonly from carboxylic acids and...
bond. This aminoacyl-tRNA precursor is produced in an
ATPAdenosine-5'-triphosphate is a multifunctional nucleotide that plays an important role in cell biology as a coenzyme, that is, the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...
-dependent reaction carried out by an
aminoacyl tRNA synthetaseAn aminoacyl tRNA synthetase is an enzyme that catalyzes the esterification of a specific amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA.-Mechanism:...
. This aminoacyl-tRNA is then a substrate for the
ribosomeRibosomes are complexes of RNA and protein that are found in all cells. The ribosome is part of the mechanism that translates the DNA sequence into the protein sequence. Ribosomes from bacteria, archaea and eukaryotes , have significantly different structure and RNA...
, which joins the amino acid onto the elongating protein chain, using the sequence information in a
messenger RNAMessenger ribonucleic acid is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcribed from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes. Here, the nucleic acid polymer is translated into a polymer of amino...
.
Nucleotide synthesis and salvage
Nucleotides are made from amino acids, carbon dioxide and
formic acidFormic acid is the simplest carboxylic acid. Its formula is HCOOH or CH2O2. It is an important intermediate in chemical synthesis and occurs naturally, most notably in the venom of bee and ant stings.In nature, it is found in the stings and bites of many insects of the order...
in pathways that require large amounts of metabolic energy. Consequently, most organisms have efficient systems to salvage preformed nucleotides.
PurineA purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring. Purines, including substituted purines and their tautomers, are the most widely distributed kind of nitrogen-containing heterocycle in nature....
s are synthesized as
nucleosideNucleosides are glycosylamines consisting of a nucleobase bound to a ribose or deoxyribose sugar. Examples of these include cytidine, uridine, adenosine, guanosine, thymidine and inosine....
s (bases attached to
riboseRibose, primarily occurring as
D-ribose, is an organic compound that occurs widely in nature. It is an aldopentose, that is a monosaccharide containing five carbon atoms that, in its acyclic form, has an aldehyde functional group at one end. This species predominantly exists in the...
). Both
adenineAdenine is a nucleobase with a variety of roles in biochemistry including cellular respiration, in the form of both the energy-rich adenosine triphosphate and the cofactors nicotinamide adenine dinucleotide and flavin adenine dinucleotide , and protein synthesis, as a chemical component of DNA...
and
guanineGuanine is one of the five main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, thymine, and uracil. In DNA, guanine is paired with cytosine. With the formula C
5H
5N
5O, guanine is a derivative of purine, consisting of a fused...
are made from the precursor nucleoside
inosineInosine is a nucleoside that is formed when hypoxanthine is attached to a ribose ring via a β-N
9-glycosidic bond....
monophosphate, which is synthesized using atoms from the amino acids
glycineGlycine is an organic compound with the formula NH2CH2COOH. With only a hydrogen atom as its side chain, glycine is the smallest of the 20 amino acids commonly found in proteins....
,
glutamineGlutamine is one of the 20 amino acids encoded by the standard genetic code. Its side chain is an amide formed by replacing the side-chain hydroxyl of glutamic acid with an amine functional group. It can therefore be considered the amide of glutamic acid. Its codons are CAA and CAG. Glutamine is...
, and
aspartic acidAspartic acid is an α-amino acid with the chemical formula HO2CCHCH2CO2H. The carboxylate anion of aspartic acid is known as aspartate...
, as well as
formateFormate or methanoate is the ion CHOO− or HCOO− . It is the simplest carboxylate anion.A formate is a salt or ester of formic acid.See also formic acid....
transferred from the coenzyme
tetrahydrofolateFolic acid and folate , as well as pteroyl-L-glutamic acid and pteroyl-L-glutamate, are forms of the water-soluble vitamin B
9...
.
PyrimidinePyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring...
s, on the other hand, are synthesized from the base
orotateOrotic acid is a heterocyclic compound and an acid; it is also known as pyrimidinecarboxylic acid. It was once believed to be part of the vitamin B complex and was called vitamin B
13, but it is now known that it is not a vitamin but is instead manufactured in the body by intestinal...
, which is formed from glutamine and aspartate.
Xenobiotics and redox metabolism
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
xenobioticA xenobiotic is a chemical which is found in an organism but which is not normally produced or expected to be present in it. It can also cover substances which are present in much higher concentrations than are usual...
s. Xenobiotics such as
synthetic drugsA drug, broadly speaking, is any substance that, when absorbed into the body of a living organism, alters normal bodily function. There is no single, precise definition, as there are different meanings in drug control law, government regulations, medicine, and colloquial usage.In pharmacology, a...
,
natural poisonsIn the context of biology, poisons are substances that can cause disturbances to organisms, usually by chemical reaction or other activity on the molecular scale, when a sufficient quantity is absorbed by an organism...
and
antibioticIn common usage, an antibiotic is a substance or compound that kills or inhibits the growth of bacteria...
s are detoxified by a set of xenobiotic-metabolizing enzymes. In humans, these include cytochrome P450 oxidases,
UDP-glucuronosyltransferasesUridine 5'-diphospho-glucuronosyltransferase is a glycosyltransferase that catalyzes the glucuronidation reaction.Alternative names:*glucuronyltransferase-Function:...
, and
glutathione S-transferases]Enzymes of the glutathione S-transferase family are composed of many cytosolic, mitochondrial, and microsomal proteins. GSTs are present in eukaryotes and Gram-negative bacteria, where they catalyze a variety of reactions and accept endogenous and xenobiotic substrates.GSTs can constitute up to...
. 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
ecologyEcology is the interdisciplinary scientific study of the interactions between organisms and the interactions of these organisms with their environment....
, these reactions are particularly important in microbial
biodegradationBiodegradation is the material breakdown of chemicals by a physiological environment. The term is often used in relation to ecology, waste management and environmental remediation . Organic material can be degraded aerobically with oxygen, or anaerobically, without oxygen...
of pollutants and the
bioremediationBioremediation can be defined as any process that uses microorganisms, fungi, green plants or their enzymes to return the natural environment altered by contaminants to its original condition. Bioremediation may be employed to attack specific soil contaminants, such as degradation of chlorinated...
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 pollutantPersistent organic pollutants are organic compounds that are resistant to environmental degradation through chemical, biological, and photolytic processes...
s such as
organochlorideAn organochloride, organochlorine, chlorocarbon, chlorinated hydrocarbon, or chlorinated solvent is an organic compound containing at least one covalently bonded chlorine atom. Their wide structural variety and divergent chemical properties lead to a broad range of applications...
compounds.
A related problem for
aerobic organismAn aerobic organism or aerobe is an organism that can survive and grow in an oxygenated environment. -Types:*Obligate aerobes require oxygen for aerobic cellular respiration...
s is
oxidative stressOxidative stress is caused by an imbalance between the production of reactive oxygen and a biological system's ability to readily detoxify the reactive intermediates or easily repair the resulting damage. All forms of life maintain a reducing environment within their cells...
. Here, processes including
oxidative phosphorylationOxidative phosphorylation is a metabolic pathway that uses energy released by the oxidation of nutrients to produce adenosine triphosphate . Although the many forms of life on earth use a range of different nutrients, almost all carry out oxidative phosphorylation to produce ATP, the molecule that...
and the formation of
disulfide bondIn chemistry, a disulfide bond is a covalent bond, usually derived by the coupling of two thiol groups. The linkage is also called an SS-bond or disulfide bridge. The overall connectivity is therefore C-S-S-C. The terminology is widely used in biochemistry...
s during
protein foldingProtein folding is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil....
produce
reactive oxygen speciesReactive oxygen species are free radicals that contain the oxygen atom. They are very small molecules that include oxygen ions and peroxides and can be either inorganic or organic. They are highly reactive due to the presence of unpaired valence shell electrons.ROS form as a natural byproduct of...
such as
hydrogen peroxideHydrogen peroxide is a very pale blue liquid, slightly more viscous than water, that appears colorless in dilute solution. It is a weak acid, has strong oxidizing properties, and is a powerful bleaching agent. It is used as a disinfectant, antiseptic, oxidizer, and in rocketry as a propellant...
. These damaging oxidants are removed by
antioxidantAn antioxidant is a molecule capable of slowing or preventing the oxidation of other molecules. Oxidation is a chemical reaction that transfers electrons from a substance to an oxidizing agent. Oxidation reactions can produce free radicals, which start chain reactions that damage cells...
metabolites such as
glutathioneGlutathione is a tripeptide. It contains an unusual peptide linkage between the amine group of cysteine and the carboxyl group of the glutamate side chain. Glutathione, an antioxidant, helps protect cells from reactive oxygen species such as free radicals and peroxides...
and enzymes such as
catalaseCatalase is a common enzyme found in nearly all living organisms which are exposed to oxygen, where it functions to catalyze the decomposition of hydrogen peroxide to water and oxygen...
s and
peroxidasePeroxidases are a large family of enzymes that typically catalyze a reaction of the form:For many of these enzymes the optimal substrate is hydrogen peroxide, but others are more active with organic hydroperoxides such as lipid peroxides...
s.
Thermodynamics of living organisms
Living organisms must obey the
laws of thermodynamicsThe laws of thermodynamics, in principle, describe the specifics for the transport of heat and work in thermodynamic processes. Since their inception, however, these laws have become some of the most important in all of physics and other types of science associated with thermodynamics.It is wise to...
, which describe the transfer of
heatIn physics and thermodynamics, heat is the process of energy transfer from one body or system due to thermal contact, which in turn is defined as an energy transfer to a body in any other way than due to work performed on the body....
and
workIn thermodynamics, work performed by a system is the quantity of energy transferred by the system to another due to changes in the external parameters of the system. If these changes happen in a reversible way, then the performed work does not lead to a change of the entropy. It is a...
. The
second law of thermodynamicsThe second law of thermodynamics is an expression of the universal principle of entropy, stating that the entropy of an isolated system which is not in equilibrium will tend to increase over time, approaching a maximum value at equilibrium, and that the entropy change dS of a system undergoing any...
states that in any
closed systemA closed system is a system in the "state of being isolated from its surrounding environment." The term often refers to an idealized system in which closure is perfect. In reality no system can be completely closed; there are only varying degrees of closure....
, the amount of
entropyEntropy is a concept of information maintaining great importance in physics, chemistry, and information theory...
(disorder) will tend to increase. Although living organisms' amazing complexity appears to contradict this law, life is possible as all organisms are open systems that exchange matter and energy with their surroundings. Thus living systems are not in
equilibriumIn thermodynamics, a thermodynamic system is said to be in thermodynamic equilibrium when it is in thermal equilibrium, mechanical equilibrium, radiative equilibrium, and chemical equilibrium. Classical thermodynamics deals with dynamic equilibrium states...
, but instead are
dissipative systemA dissipative system is a thermodynamically open system which is operating far from thermodynamic equilibrium in an environment with which it exchanges energy and matter.- Overview :...
s 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 processA spontaneous process is the time-evolution of a system in which it releases free energy and moves to a lower, more thermodynamically stable, energy state...
es of catabolism to the non-spontaneous processes of anabolism. In
thermodynamicNon-equilibrium thermodynamics is a branch of thermodynamics concerned with systems that are not in thermodynamic equilibrium. Most systems found in nature are not in thermodynamic equilibrium because they are not isolated from their environment and are therefore continuously sharing matter and...
terms, metabolism maintains order by creating disorder.
Regulation and control
As the environments of most organisms are constantly changing, the reactions of metabolism must be finely
regulatedControl theory is an interdisciplinary branch of engineering and mathematics, that deals with the behavior of dynamical systems. The desired output of a system is called the reference...
to maintain a constant set of conditions within cells, a condition called
homeostasisHomeostasis is the property of a system, either open or closed, that regulates its internal environment and tends to maintain a stable, constant condition...
. 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
fluxIn the various subfields of physics, there exist two common usages of the term flux, both with rigorous mathematical frameworks.* In the study of transport phenomena , flux is defined as the amount that flows through a unit area per unit time...
through the pathway). For example, an enzyme may show large changes in activity (
i.e. it is highly regulated) but if these changes have little effect on the flux of a metabolic pathway, then this enzyme is not involved in the control of the pathway.
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
fluxIn the various subfields of physics, there exist two common usages of the term flux, both with rigorous mathematical frameworks.* In the study of transport phenomena , flux is defined as the amount that flows through a unit area per unit time...
through the pathway to compensate. This type of regulation often involves
allosteric regulationIn biochemistry, allosteric regulation is the regulation of an enzyme or other protein by binding an effector molecule at the protein's allosteric site . Effectors that enhance the protein's activity are referred to as allosteric activators, whereas those that decrease the protein's activity are...
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
hormoneA hormone is a chemical released by one or more cells that affects cells in other parts of the organism. Only a small amount of hormone is required to alter cell metabolism. It is essentially a chemical messenger that transports a signal from one cell to another. All multicellular organisms...
s and
growth factorA growth factor is a naturally occurring substance capable of stimulating cellular growth, proliferation and cellular differentiation. Usually it is a protein or a steroid hormone. Growth factors are important for regulating a variety of cellular processes....
s and are detected by specific
receptorsIn biochemistry, a receptor is a protein molecule, embedded in either the plasma membrane or cytoplasm of a cell, to which a mobile signaling molecule may attach...
on the cell surface. These signals are then transmitted inside the cell by
second messenger systemIn cell physiology, a secondary messenger system is a method of cellular signaling whereby a diffusable signaling molecule is rapidly produced/secreted, which can then go on to activate effector proteins within the cell to exert a cellular response...
s that often involved the
phosphorylationPhosphorylation is the addition of a phosphate group to a protein or other organic molecule. Phosphorylation turns many protein enzymes on and off, causing or preventing the mechanisms of diseases such as cancer and diabetes....
of proteins.
A very well understood example of extrinsic control is the regulation of glucose metabolism by the hormone
insulinInsulin is a hormone that has extensive effects on metabolism and other body functions, such as vascular compliance. Insulin causes cells in the liver, muscle, and fat tissue to take up glucose from the blood, storing it as glycogen in the liver and muscle, and stopping use of fat as an energy...
. Insulin is produced in response to rises in
blood glucose levelsBlood sugar concentration, or glucose level, refers to the amount of glucose present in the blood of a human or animal. Normally, in mammals the blood glucose level is maintained at a reference range between about 3.6 and 5.8 mM...
. Binding of the hormone to
insulin receptorIn molecular biology, the insulin receptor is a transmembrane receptor that is activated by insulin. It belongs to the large class of tyrosine kinase receptors....
s on cells then activates a cascade of
protein kinaseA protein kinase is a kinase enzyme that modifies other proteins by chemically adding phosphate groups to them . Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins...
s that cause the cells to take up glucose and convert it into storage molecules such as fatty acids and
glycogenGlycogen is the molecule that functions as the secondary long-term energy storage in animal cells. It is made primarily by the liver and the muscles, but can also be made by glycogenesis within the brain and stomach...
. The metabolism of glycogen is controlled by activity of
phosphorylasePhosphorylase is a family of allosteric enzymes that catalyze the production of glucose-1-phosphate from a polyglucose such as glycogen, starch or maltodextrin. Phosphorylase is also a common name used for glycogen phosphorylase in honor of Earl W. Sutherland Jr. who in the late 1930's discovered...
, the enzyme that breaks down glycogen, and
glycogen synthaseGlycogen synthase is a glycosyltransferase enzyme that catalyses the reaction of UDP-glucose and n to yield UDP and n+1.In other words, this enzyme...
, the enzyme that makes it. These enzymes are regulated in a reciprocal fashion, with phosphorylation inhibiting glycogen synthase, but activating phosphorylase. Insulin causes glycogen synthesis by activating
protein phosphatasesA phosphatase is an enzyme that removes a phosphate group from its substrate by hydrolysing phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxyl group . This action is directly opposite to that of phosphorylases and kinases, which attach phosphate groups to their...
and producing a decrease in the phosphorylation of these enzymes.
Evolution
The central pathways of metabolism described above, such as glycolysis and the citric acid cycle, are present in all
three domainsThe three-domain system is a biological classification introduced by Carl Woese in 1990 that divides cellular life forms into archaea, bacteria, and eukaryote domains. In particular, it emphasizes the separation of prokaryotes into two groups, originally called Eubacteria and Archaebacteria...
of living things and were present in the
last universal ancestorThe last universal ancestor is the most recent organism from which all organisms now living on Earth descend. Thus it is the most recent common ancestor of all current life on Earth...
. This universal ancestral cell was
prokaryoticThe prokaryotes are a group of organisms that lack a cell nucleus , or any other membrane-bound organelles. They differ from the eukaryotes, which have a cell nucleus. Most are unicellular, but a few prokaryotes such as myxobacteria have multicellular stages in their life cycles...
and probably a
methanogenMethanogens are microorganisms that produce methane as a metabolic byproduct in anoxic conditions. They were once classified as archaebacteria but archaebacteria have now been reclasified as archaea a group quite distinct from bacteria...
that had extensive amino acid, nucleotide, carbohydrate and lipid metabolism. The retention of these ancient pathways during later
evolutionIn biology, evolution is change in the genetic material of a population of organisms from one generation to the next. Though changes produced in any one generation are normally small, differences accumulate with each generation and can, over time, cause substantial changes in the population, a...
may be the result of these reactions being an optimal solution to their particular metabolic problems, with pathways such as glycolysis and the citric acid cycle producing their end products highly efficiently and in a minimal number of steps.
The first pathways of enzyme-based metabolism may have been parts of
purineA purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring. Purines, including substituted purines and their tautomers, are the most widely distributed kind of nitrogen-containing heterocycle in nature....
nucleotide metabolism, with previous metabolic pathways being part of the ancient
RNA worldThe RNA world hypothesis proposes that a world filled with life based on ribonucleic acid predates the current world of life based on deoxyribonucleic acid . RNA, which can both store information like DNA and act as an enzyme, may have supported cellular or pre-cellular life...
.
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 being 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 databaseThe Molecular Ancestry Network database is a bioinformatics database that maps evolutionary relationships of protein architectures directly onto biological networks. It was originally developed by Hee Shin Kim, Jay E...
) 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
hostIn biology, a host is an organism that harbors a parasite , or a mutual or commensal symbiont, typically providing nourishment and shelter. In botany, a host plant is one that supplies food resources and substrate for certain insects or other fauna...
. Similar reduced metabolic capabilities are seen in
endosymbioticAn endosymbiont is any organism that lives within the body or cells of another organism, i.e. forming an endosymbiosis...
organisms.
Investigation and manipulation
Classically, metabolism is studied by a
reductionistReductionism can either mean an approach to understand the nature of complex things by reducing them to the interactions of their parts, or to simpler or more fundamental things or a philosophical position that a complex system is nothing but the sum of its parts, and that an account of it can be...
approach that focuses on a single metabolic pathway. Particularly valuable is the use of
radioactive tracerA radioactive tracer, also called a radioactive label, is a substance containing a radioisotope. Tracers can be used to measure the speed of chemical processes and to track the movement of a substance through a natural system such as a cell or a tissue...
s 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
purifiedProtein purification is a series of processes intended to isolate a single type of protein from a complex mixture. Protein purification is vital for the characterisation of the function, structure and interactions of the protein of interest. The starting material is usually a biological tissue or...
and their
kineticsEnzyme kinetics is the study of the chemical reactions that are catalysed by enzymes. In enzyme kinetics the reaction rate is measured and the effects of varying the conditions of the reaction investigated...
and responses to
inhibitorsEnzyme inhibitors are molecules that bind to enzymes and decrease their activity. Since blocking an enzyme's activity can kill a pathogen or correct a metabolic imbalance, many drugs are enzyme inhibitors. They are also used as herbicides and pesticides...
investigated. A parallel approach is to identify the small molecules in a cell or tissue; the complete set of these molecules is called the
metabolomeMetabolome refers to the complete set of small-molecule metabolites to be found within a biological sample, such as a single organism...
. 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 networkA metabolic network is the complete set of metabolic and physical processes that determine the physiological and biochemical properties of a cell...
s 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
holisticHolism is the idea that all the properties of a given system cannot be determined or explained by its component parts alone...
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 expressionGene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as rRNA genes or tRNA genes, the product is a functional RNA...
from
proteomicProteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
and
DNA microarrayA DNA microarray is a multiplex technology used in molecular biology and in medicine. It consists of an arrayed series of thousands of microscopic spots of DNA oligonucleotides, called features, each containing picomoles of a specific DNA sequence...
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 being used in
network analysisNetwork analysis can refer to:* Analysis of general networks: see network theory.* Electrical network analysis see Network analysis .* Social network analysis....
, to classify human diseases into groups that share common proteins or metabolites.
A major technological application of this information is
metabolic engineeringMetabolic engineering is the practice of optimizing genetic and regulatory processes within cells to increase the cells' production of a certain substance. Metabolic engineers commonly work to reduce cellular energy use and to reduce waste production...
. Here, organisms such as
yeastYeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with about 1,500 species currently described; they dominate fungal diversity in the oceans. Most reproduce asexually by budding, although a few do so by binary fission...
,
plantPlants are living organisms belonging to the kingdom Plantae. They include familiar organisms such as trees, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The scientific study of plants, known as botany, has identified about 350,000 extant species of plants, defined as seed plants,...
s or
bacteriaThe bacteria are a large group of unicellular microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
are genetically modified to make them more useful in
biotechnologyBiotechnology is technology based on biology, agriculture, food science, and medicine. Modern use of the term usually refers to genetic engineering as well as cell- and tissue culture technologies...
and aid the production of
drugA drug, broadly speaking, is any substance that, when absorbed into the body of a living organism, alters normal bodily function. There is no single, precise definition, as there are different meanings in drug control law, government regulations, medicine, and colloquial usage.In pharmacology, a...
s such as
antibioticIn common usage, an antibiotic is a substance or compound that kills or inhibits the growth of bacteria...
s or industrial chemicals such as
1,3-propanediol1,3-Propanediol is the organic compound with the formula CH22. This three-carbon diol is a colorless viscous liquid that is miscible with water.- Products :...
and
shikimic acidShikimic acid, more commonly known as its anionic form shikimate, is an important biochemical intermediate in plants and microorganisms. Its name comes from the Japanese flower shikimi , from which it was first isolated....
. These genetic modifications usually aim to reduce the amount of energy used to produce the product, increase yields and reduce the production of wastes.
History
The term
metabolism is derived from the
GreekGreek , an independent branch of the Indo-European family of languages, is the language of the Greeks. Native to the southern Balkans, it has the longest documented history of any Indo-European language, spanning 34 centuries of written records. In its ancient form, it is the language of classical...
Μεταβολισμός – "Metabolismos" for "change", or "overthrow". The history of the scientific study of metabolism spans several centuries and has moved from examining whole animals in early studies, to examining individual metabolic reactions in modern biochemistry. The concept of metabolism dates back to Ibn al-Nafis (1213-1288), who stated that "the body and its parts are in a continuous state of dissolution and
nourishmentNutrition is the provision, to cells and organisms, of the materials necessary to support life. Many common health problems can be prevented or alleviated with a healthy diet....
, so they are inevitably undergoing permanent change." The first controlled
experimentIn scientific research, an experiment is a method of investigating causal relationships among variables, or to test a hypothesis. An experiment is a cornerstone of the empirical approach to acquiring data about the world and is used in both natural sciences and social sciences...
s in human metabolism were published by Santorio Santorio in 1614 in his book
Ars de statica medecina. He described how he weighed himself before and after eating, sleep, working, sex, fasting, drinking, and excreting. He found that most of the food he took in was lost through what he called "insensible perspiration".
In these early studies, the mechanisms of these metabolic processes had not been identified and a
vital forceVitalism, as defined by the Merriam-Webster dictionary, is#a doctrine that the functions of a living organism are due to a vital principle distinct from biochemical reactions...
was thought to animate living tissue. In the 19th century, when studying the
fermentationFermentation in food processing typically is the conversion of carbohydrates to alcohols and carbon dioxide or organic acids using yeasts, bacteria, or a combination thereof, under anaerobic conditions. A more restricted definition of fermentation is the chemical conversion of sugars into ethanol...
of sugar to
alcoholIn chemistry, an alcohol is any organic compound in which a hydroxyl group is bound to a carbon atom of an alkyl or substituted alkyl group. An important group of acohols is formed by the simple acyclic alcohols, the general formula for which is C
nH
2n+1OH...
by
yeastYeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with about 1,500 species currently described; they dominate fungal diversity in the oceans. Most reproduce asexually by budding, although a few do so by binary fission...
,
Louis PasteurLouis Pasteur was a French chemist and microbiologist born in Dole. He is best known for his remarkable breakthroughs in the causes and preventions of disease. His discoveries reduced mortality from puerperal fever, and he created the first vaccine for rabies. His experiments supported the germ...
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 the chemical synthesis of
ureaUrea or carbamide is an organic compound with the chemical formula
2CO. The molecule has two amine residues joined by a carbonyl functional group....
, 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
enzymeEnzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, called the products. Almost all processes in a biological cell need enzymes to occur at...
s at the beginning of the 20th century by
Eduard BuchnerEduard Buchner was a German chemist and zymologist, the winner of the 1907 Nobel Prize in Chemistry for his work on fermentation.-Early years:...
that separated the study of the chemical reactions of metabolism from the biological study of cells, and marked the beginnings of
biochemistryBiochemistry is the study of the chemical processes in living organisms. It deals with the structure and function of cellular components such as proteins, carbohydrates, lipids, nucleic acids and other biomolecules....
. The mass of biochemical knowledge grew rapidly throughout the early 20th century. One of the most prolific of these modern biochemists was
Hans KrebsSir Hans Adolf Krebs was a German born British physician and biochemist. Krebs is best known for his identification of two important metabolic cycles: the urea cycle and the citric acid cycle...
who made huge contributions to the study of metabolism. He discovered the urea cycle and later, working with
Hans KornbergProfessor Sir Hans Leo Kornberg, FRS is a British biochemist.-Early Life, Education and Career:Kornberg was born in 1928 in Germany of Jewish parents. In 1939 he left Nazi Germany , and moved to the care of an uncle in Yorkshire...
, the citric acid cycle and the glyoxylate cycle. Modern biochemical research has been greatly aided by the development of new techniques such as
chromatographyChromatography is the collective term for a set of laboratory techniques for the separation of mixtures....
, X-ray diffraction,
NMR spectroscopyProtein nuclear magnetic resonance spectroscopy is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins. The field was pioneered by, among others, Kurt Wüthrich, who shared the Nobel Prize in Chemistry in 2002...
, radioisotopic labelling,
electron microscopyAn electron microscope is a type of microscope, a scientific instrument which is used to magnify things on a fine scale. That uses a particle beam of electrons to illuminate a specimen and create a highly-magnified image...
and
molecular dynamicsMolecular dynamics is a form of computer simulation in which atoms and molecules are allowed to interact for a period of time by approximations of known physics,...
simulations. These techniques have allowed the discovery and detailed analysis of the many molecules and metabolic pathways in cells.
See also
- Anthropogenic metabolism
Anthropogenic metabolism is a term used in material flow analysis, substance flow analysis and waste management. It covers not only the physiological metabolism but also includes the thousands of goods and substances necessary to sustain modern life. Anthropogenic stands for man-made...
- Basal metabolic rate
Basal metabolic rate , and the closely related resting metabolic rate , is the amount of energy expended while at rest in a [neutrally temperate environment, in the post-absorptive state...
- Calorimetry
Calorimetry is the science of measuring the heat of chemical...
- Inborn error of metabolism
Inborn errors of metabolism comprise a large class of genetic diseases involving disorders of metabolism. The majority are due to defects of single genes that code for enzymes that facilitate conversion of various substances into others...
- Iron-sulfur world theory
The iron-sulfur world theory is a set of proposals for the origin of life and the early evolution of life advanced by Günter Wächtershäuser, a Munich chemist and patent lawyer, involving forms of iron and sulfur...
, a "metabolism first" theory of the origin of life.
- Respirometry
Respirometry is a general term that encompass a number of techniques for obtaining estimates of the rates of metabolism of vertebrates, invertebrates, plants, tissues, cells, or microorganisms via an indirect measure of heat production ....
- Thermic effect of food
Thermic effect of food , or TEF in shorthand, is the increment in energy expenditure above resting metabolic rate due to the cost of processing food for storage and use.1 It is one of the components of metabolism along with the resting metabolic rate, and the exercise component...
- Water metabolism
- Sulphur metabolism
- Antimetabolite
An antimetabolite is a chemical that inhibits the use of a metabolite, which is another chemical that is part of normal metabolism. Such substances are often similar in structure to the metabolite that they interfere with, such as the antifolates that interfere with the use of folic acid...
Further reading
Introductory and ,
The Chemistry of Life. (Penguin Press Science, 1999), ISBN 0-14027-273-9 and ,
Into the Cool: Energy Flow, Thermodynamics, and Life. (University Of Chicago Press, 2005), ISBN 0-22673-936-8,
Oxygen: The Molecule that Made the World. (Oxford University Press, USA, 2004), ISBN 0-19860-783-0
Advanced and ,
Fundamentals of Enzymology: Cell and Molecular Biology of Catalytic Proteins. (Oxford University Press, 1999), ISBN 0-19850-229-X and ,
Biochemistry. (W. H. Freeman and Company, 2002), ISBN 0-71674-955-6 and ,
Lehninger Principles of Biochemistry. (Palgrave Macmillan, 2004), ISBN 0-71674-339-6 and ,
Brock's Biology of Microorganisms. (Benjamin Cummings, 2002), ISBN 0-13066-271-2 and ,
The Biological Chemistry of the Elements: The Inorganic Chemistry of Life. (Clarendon Press, 1991), ISBN 0-19855-598-9 and ,
Bioenergetics. (Academic Press Inc., 2002), ISBN 0-12518-121-3
External links