HOME

TheInfoList




Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of
life Life is a characteristic that distinguishes physical entities A bubble of exhaled gas in water In common usage and classical mechanics, a physical object or physical body (or simply an object or body) is a collection of matter within a ...

life
-sustaining
chemical reactions A chemical reaction is a process that leads to the chemical transformation of one set of chemical substances to another. Classically, chemical A chemical substance is a form of matter having constant chemical composition and characteristic ...

chemical reactions
in
organisms In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological me ...

organisms
. The three main purposes of metabolism are: the conversion of the energy in food to
energy In , energy is the that must be to a or to perform on the body, or to it. Energy is a ; the law of states that energy can be in form, but not created or destroyed. The unit of measurement in the (SI) of energy is the , which is the ...

energy
available to run cellular processes; the conversion of food to building blocks for
protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No ...

protein
s,
lipid In and , a lipid is a macro that is soluble in solvents. are typically s used to dissolve other naturally occurring hydrocarbon lipid s that do not (or do not easily) dissolve in water, including s, es, s, fat-soluble s (such as vitamins A, ...
s,
nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all Organism, known forms of life. They are composed of nucleotides, which are the monomers made of three components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. ...

nucleic acid
s, and some
carbohydrate is a disaccharide A disaccharide (also called a double sugar or ''biose'') is the sugar formed when two monosaccharides are joined by glycosidic linkage. Like monosaccharides, disaccharides are simple sugars soluble in water. Three common ex ...
s; and the elimination of
metabolic waste Metabolic wastes or excrements are Chemical substance, substances left over from metabolism, metabolic processes (such as cellular respiration) which cannot be used by the organism (they are surplus or toxicity, toxic), and must therefore be excre ...
s. These
enzyme Enzymes () are protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins diff ...

enzyme
-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including
digestion Digestion is the breakdown of large insoluble food Food is any substance consumed to provide nutritional Nutrition is the biochemical Biochemistry or biological chemistry, is the study of chemical processes within and relating to liv ...
and the transportation of substances into and between different cells, in which case the above described set of reactions within the cells is called intermediary (or intermediate) metabolism. Metabolic reactions may be categorized as ''
catabolic Catabolism () is the set of metabolic pathways that breaks down molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an ...
'' – the ''breaking down'' of compounds (for example, of glucose to pyruvate by
cellular respiration upright=2.5, Typical eukaryotic cell Cellular respiration is a set of metabolic Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life Life is a characteristic that distinguishes physical entities ...

cellular respiration
); or ''
anabolic Anabolism () is the set of metabolic pathway In biochemistry Biochemistry or biological chemistry, is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be d ...
'' – the ''building up'' (
synthesis Synthesis or synthesize may also refer to: Science Chemistry and biochemistry *Chemical synthesis, the execution of chemical reactions to form a more complex molecule from chemical precursors **Organic synthesis, the chemical synthesis of or ...

synthesis
) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy. The chemical reactions of metabolism are organized into
metabolic pathway In biochemistry, a metabolic pathway is a linked series of chemical reaction A chemical reaction is a process that leads to the IUPAC nomenclature for organic transformations, chemical transformation of one set of chemical substances to another. ...
s, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific
enzyme Enzymes () are protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins diff ...

enzyme
. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require
energy In , energy is the that must be to a or to perform on the body, or to it. Energy is a ; the law of states that energy can be in form, but not created or destroyed. The unit of measurement in the (SI) of energy is the , which is the ...

energy
and will not occur by themselves, by
coupling A coupling is a device used to connect two shafts together at their ends for the purpose of transmitting power. The primary purpose of couplings is to join two pieces of rotating equipment while permitting some degree of misalignment or end move ...
them to
spontaneous reactions
spontaneous reactions
that release energy. Enzymes act as
catalysts that utilizes a low-temperature oxidation catalyst to convert carbon monoxide to less toxic carbon dioxide Carbon dioxide (chemical formula ) is a colorless gas with a density about 53% higher than that of dry air. Carbon dioxide molecules ...

catalysts
– they allow a reaction to proceed more rapidly – and they also allow the
regulation Regulation is the management of complex systems A complex system is a system composed of many components which may interaction, interact with each other. Examples of complex systems are Earth's global climate, organisms, the human brain, infras ...

regulation
of the rate of a metabolic reaction, for example in response to changes in the cell's environment or to signals from other cells. The metabolic system of a particular organism determines which substances it will find
nutritious Nutrition is the biochemical and physiological process by which an organism uses food to support its life. It includes ingestion, Absorption (biology), absorption, Assimilation (biology), assimilation, biosynthesis, catabolism and excretion. The ...
and which
poison In biology, poisons are Chemical substance, substances that can cause death, injury or harm to organs, Tissue (biology), tissues, Cell (biology), cells, and DNA usually by chemical reactions or other activity (chemistry), activity on the molecul ...

poison
ous. For example, some
prokaryote A prokaryote () is a single-celled organism A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contig ...
s use
hydrogen sulfide Hydrogen sulfide is a chemical compound A chemical compound is a chemical substance A chemical substance is a form of matter In classical physics and general chemistry, matter is any substance that has mass and takes up space by havi ...

hydrogen sulfide
as a nutrient, yet this gas is poisonous to animals. The basal metabolic rate of an organism is the measure of the amount of energy consumed by all of these chemical reactions. A striking feature of metabolism is the similarity of the basic metabolic pathways among vastly different species. For example, the set of
carboxylic acid A carboxylic acid is an organic acid An organic acid is an organic compound with acidic properties. The most common organic acids are the carboxylic acids, whose acidity is associated with their carboxyl group –COOH. Sulfonic acid ...
s that are best known as the intermediates in the
citric acid cycle The citric acid cycle (CAC) – also known as the TCA cycle (tricarboxylic acid cycle) or the Krebs cycle – is a series of chemical reaction A chemical reaction is a process that leads to the IUPAC nomenclature for organic transfor ...

citric acid cycle
are present in all known organisms, being found in species as diverse as the
unicellular A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Or ...
bacterium ''
Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative Gram-negative bacteria are bacteria that do not retain the crystal violet st ...

Escherichia coli
'' and huge
multicellular organism A multicellular organism is an organism In biology, an organism () is any organic, life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biol ...
s like
elephant Elephants are the largest existing land animals. Three living species In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, ...

elephant
s. These similarities in metabolic pathways are likely due to their early appearance in
evolutionary history The history of life on Earth traces the processes by which living and fossil organisms evolved, from the earliest emergence of life to the present. Earth formed about 4.5 billion years ago (abbreviated as ''Ga'', for ''Year#SI prefix multiplier ...
, and their retention is likely due to their
efficacy Efficacy is the ability to perform a task to a satisfactory or expected degree. The word comes from the same roots as ''effectiveness Effectiveness is the capability of producing a desired result or the ability to produce desired output. When ...

efficacy
. In various diseases, such as
type II diabetes Type 2 diabetes (T2D), formerly known as adult-onset diabetes, is a form of diabetes Diabetes mellitus (DM), commonly known as diabetes, is a group of metabolic disorders characterized by a high blood sugar level over a prolonged period of ...
,
metabolic syndrome Metabolic syndrome is a clustering of at least three of the following five medical conditions: abdominal obesity Abdominal obesity, also known as central obesity and truncal obesity, is a condition when excessive abdominal fat around the stomach ...
, and
cancer Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body. These contrast with benign tumor A benign tumor is a mass of cells Cell most often refers to: * Cell (biolo ...

cancer
, normal metabolism is disrupted. The metabolism of cancer cells is also different from the metabolism of normal cells, and these differences can be used to find targets for therapeutic intervention in cancer.


Key biochemicals

Most of the structures that make up animals, plants and microbes are made from four basic classes of
molecule A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically Electricity is the set of physical phenomena associated with the presence and motion I ...

molecule
s:
amino acid Amino acids are organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, c ...

amino acid
s,
carbohydrate is a disaccharide A disaccharide (also called a double sugar or ''biose'') is the sugar formed when two monosaccharides are joined by glycosidic linkage. Like monosaccharides, disaccharides are simple sugars soluble in water. Three common ex ...
s,
nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all Organism, known forms of life. They are composed of nucleotides, which are the monomers made of three components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. ...

nucleic acid
and
lipid In and , a lipid is a macro that is soluble in solvents. are typically s used to dissolve other naturally occurring hydrocarbon lipid s that do not (or do not easily) dissolve in water, including s, es, s, fat-soluble s (such as vitamins A, ...
s (often called
fat In nutrition Nutrition is the biochemical Biochemistry or biological chemistry, is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided ...

fat
s). As these molecules are vital for life, metabolic reactions either focus on making these molecules during the construction of cells and tissues, or on breaking them down and using them to obtain energy, by their digestion. These biochemicals can be joined to make
polymer A polymer (; Greek ''poly- Poly, from the Greek :wikt:πολύς, πολύς meaning "many" or "much", may refer to: Businesses * China Poly Group Corporation, a Chinese business group, and its subsidiaries: ** Poly Property, a Hong Kong inc ...

polymer
s such as
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

DNA
and
protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No ...

protein
s, essential
macromolecules macromolecule A macromolecule is a very large molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neu ...
of life.


Amino acids and proteins

Protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No ...

Protein
s are made of
amino acid Amino acids are organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, c ...

amino acid
s arranged in a linear chain joined by
peptide bond In organic chemistry, a peptide bond is an amide type of Covalent bond, covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another, along a peptide o ...

peptide bond
s. Many proteins are
enzyme Enzymes () are protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins diff ...

enzyme
s that
catalyze that utilizes a low-temperature oxidation catalyst to convert carbon monoxide to less toxic carbon dioxide Carbon dioxide (chemical formula ) is a colorless gas with a density about 53% higher than that of dry air. Carbon dioxide molecules ...

catalyze
the chemical reactions in metabolism. Other proteins have structural or mechanical functions, such as those that form the
cytoskeleton The cytoskeleton is a complex, dynamic network of interlinking s present in the of all , excluding and . It extends from the to the and is composed of similar proteins in the various organisms. In , it is composed of three main components, , ...

cytoskeleton
, a system of
scaffolding Scaffolding, also called scaffold or staging, is a temporary structure used to support a work crew and materials to aid in the construction, maintenance and repair of buildings, bridges and all other man-made structures. Scaffolds are widely us ...

scaffolding
that maintains the cell shape. Proteins are also important in
cell signaling In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanisms ...
,
immune responses
immune responses
,
cell adhesion 300px, Schematic of cell adhesion Cell adhesion is the process by which cells interact and attach to neighbouring cells through specialised molecules of the cell surface. This process can occur either through direct contact between cell surfaces ...
,
active transport In cellular biology Cell biology (also cellular biology or cytology) is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processe ...

active transport
across membranes, and the
cell cycle The cell cycle, or cell-division cycle, is the series of events that take place in a cell Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Closed spaces * Monastic cell, a small room, ...

cell cycle
. Amino acids also contribute to cellular energy metabolism by providing a carbon source for entry into the citric acid cycle (
tricarboxylic acid cycle The citric acid cycle (CAC) – also known as the TCA cycle (tricarboxylic acid cycle) or the Krebs cycle – is a series of chemical reactions used by all aerobic organisms to release stored energy through the redox, oxidation of acety ...
), especially when a primary source of energy, such as
glucose Glucose is a simple with the . Glucose is the most abundant , a subcategory of s. Glucose is mainly made by and most during from water and carbon dioxide, using energy from sunlight, where it is used to make in s, the most abundant carbohydr ...

glucose
, is scarce, or when cells undergo metabolic stress.


Lipids

Lipid In and , a lipid is a macro that is soluble in solvents. are typically s used to dissolve other naturally occurring hydrocarbon lipid s that do not (or do not easily) dissolve in water, including s, es, s, fat-soluble s (such as vitamins A, ...
s are the most diverse group of biochemicals. Their main structural uses are as part of
biological membrane A biological membrane, biomembrane or cell membrane is a selectively permeable membrane Image:Schematic size.jpg, up150px, Schematic of size-based membrane exclusion A membrane is a selective barrier; it allows some things to pass through but s ...
s both internal and external, such as the
cell membrane cell membrane vs. Prokaryotes A prokaryote is a typically unicellular organism that lacks a nuclear membrane-enclosed cell nucleus, nucleus. The word ''prokaryote'' comes from the Greek language, Greek (, 'before') and (, 'nut' or 'kernel').C ...

cell membrane
, or to unlock the
chemical energy Chemical energy is the energy of chemical substance A chemical substance is a form of matter In classical physics and general chemistry, matter is any substance that has mass and takes up space by having volume. All everyday objects th ...
of
oxygen Oxygen is the chemical element Image:Simple Periodic Table Chart-blocks.svg, 400px, Periodic table, The periodic table of the chemical elements In chemistry, an element is a pure substance consisting only of atoms that all have the same ...
.Schmidt-Rohr, K. (2020). "Oxygen Is the High-Energy Molecule Powering Complex Multicellular Life: Fundamental Corrections to Traditional Bioenergetics". ''ACS Omega'' 5: 2221-2233. http://dx.doi.org/10.1021/acsomega.9b03352. Lipids are the polymers of fatty acids that contain a long, non-polar hydrocarbon chain with a small polar region containing oxygen. Lipids are usually defined as
hydrophobic In chemistry Chemistry is the science, scientific study of the properties and behavior of matter. It is a natural science that covers the Chemical element, elements that make up matter to the chemical compound, compounds composed of at ...
or
amphipathic 250px, Cross-section view of the structures that can be formed by phospholipids, biological amphiphiles in aqueous solutions. Unlike this illustration, micelles are usually formed by non-biological, single-chain, amphiphiles, soaps or detergents, ...
biological molecules but will dissolve in
organic solvent A solvent (from the Latin Latin (, or , ) is a classical language belonging to the Italic languages, Italic branch of the Indo-European languages. Latin was originally spoken in the area around Rome, known as Latium. Through the power of the ...
s such as
alcohol In , alcohol is an that carries at least one (−OH) bound to a atom. The term alcohol originally referred to the primary alcohol (ethyl alcohol), which is and is the main alcohol present in s. An important class of alcohols, of which ...

alcohol
,
benzene Benzene is an organic Organic may refer to: * Organic, of or relating to an organism, a living entity * Organic, of or relating to an anatomical organ (anatomy), organ Chemistry * Organic matter, matter that has come from a once-living organi ...

benzene
or
chloroform Chloroform, or trichloromethane, is an organic compound with formula CH Cl3. It is a colorless, strong-smelling, dense liquid that is produced on a large scale as a precursor to PTFE Polytetrafluoroethylene (PTFE) is a synthetic fluoropoly ...

chloroform
. The
fat In nutrition Nutrition is the biochemical Biochemistry or biological chemistry, is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided ...

fat
s are a large group of compounds that contain
fatty acid In chemistry Chemistry is the study of the properties and behavior of . It is a that covers the that make up matter to the composed of s, s and s: their composition, structure, properties, behavior and the changes they undergo during ...
s and
glycerol Glycerol (; also called glycerine in British English and glycerin in American English) is a simple polyol compound. It is a colorless, odorless, viscous liquid that is sweet-tasting and non-toxic. The glycerol backbone is found in lipids known ...
; a glycerol molecule attached to three fatty acids by
ester An ester is a derived from an (organic or inorganic) in which at least one –OH group is replaced by an –O– () group, as in the substitution reaction of a and an . s are s of ; they are important in biology, being one of the main classe ...

ester
linkages is called a
triacylglyceride 300px, Example of an unsaturated fat triglyceride (C55H98O6). Left part: glycerol; right part, from top to bottom: palmitic acid, oleic acid">palmitic_acid.html" ;"title="glycerol; right part, from top to bottom: palmitic acid">glycerol; right par ...

triacylglyceride
. Several variations on this basic structure exist, including backbones such as
sphingosine Sphingosine (2-amino-4-trans-octadecene-1,3-diol) 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 phospholipi ...

sphingosine
in
sphingomyelin Sphingomyelin (SPH, ˌsfɪŋɡoˈmaɪəlɪn) is a type of sphingolipid Sphingolipids are a class of lipids containing a backbone of sphingoid bases, a set of aliphatic amino alcohols that includes sphingosine. They were discovered in brain extrac ...

sphingomyelin
, and
hydrophilic A hydrophile is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral group of two or more atoms ...

hydrophilic
groups such as
phosphate In chemistry Chemistry is the study of the properties and behavior of . It is a that covers the that make up matter to the composed of s, s and s: their composition, structure, properties, behavior and the changes they undergo durin ...

phosphate
as in
phospholipid Phospholipids, also known as phosphatides, are a class of lipid In and , a lipid is a macro that is soluble in solvents. are typically s used to dissolve other naturally occurring hydrocarbon lipid s that do not (or do not easily) disso ...

phospholipid
s.
Steroid A steroid is a biologically active organic compound In , organic compounds are generally any s that contain - . Due to carbon's ability to (form chains with other carbon s), millions of organic compounds are known. The study of the prope ...

Steroid
s such as
sterol Sterol is an organic compound In , organic compounds are generally any s that contain - . Due to carbon's ability to (form chains with other carbon s), millions of organic compounds are known. The study of the properties, reactions, and synth ...

sterol
are another major class of lipids.


Carbohydrates

Carbohydrate is a disaccharide A disaccharide (also called a double sugar or ''biose'') is the sugar formed when two monosaccharides are joined by glycosidic linkage. Like monosaccharides, disaccharides are simple sugars soluble in water. Three common ex ...
s are
aldehyde Chemically, an aldehyde is a compound containing a functional group In organic chemistry, a functional group is a substituent or moiety (chemistry), moiety in a molecule that causes the molecule's characteristic chemical reactions. The same fu ...

aldehyde
s or
ketone In chemistry, a ketone is a functional group with the structure R2C=O, where R can be a variety of carbon-containing substituents. Ketones contain a carbonyl group (a carbon-oxygen double bond). The simplest ketone is acetone (R = R' = methyl) ...
s, with many
hydroxyl A hydroxy or hydroxyl group is a functional group with the chemical formula -OH and composed of one oxygen Oxygen is the chemical element Image:Simple Periodic Table Chart-blocks.svg, 400px, Periodic table, The periodic table of the ...

hydroxyl
groups attached, that can exist as straight chains or rings. Carbohydrates are the most abundant biological molecules, and fill numerous roles, such as the storage and transport of
energy In , energy is the that must be to a or to perform on the body, or to it. Energy is a ; the law of states that energy can be in form, but not created or destroyed. The unit of measurement in the (SI) of energy is the , which is the ...

energy
(
starch Starch or amylum is a consisting of numerous units joined by s. This is produced by most green s for energy storage. Worldwide, it is the most common carbohydrate in human diets, and is contained in large amounts in s like , es, (corn), , ...
,
glycogen Glycogen is a multibranched of that serves as a form of energy storage in s, , and bacteria. The polysaccharide structure represents the main storage form of glucose in the body. Glycogen functions as one of two forms of energy reserves, g ...

glycogen
) and structural components (
cellulose Cellulose is an organic compound with the chemical formula, formula , a polysaccharide consisting of a linear chain of several hundred to many thousands of glycosidic bond, β(1→4) linked glucose, D-glucose units. Cellulose is an important stru ...

cellulose
in plants,
chitin units that repeat to form long chains in β-(1→4)-linkage. of the chitin molecule. Chitin ( carbon, C8H13O5N)n ( ) is a long-chain polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical su ...

chitin
in animals). The basic carbohydrate units are called
monosaccharide Monosaccharides (from Greek#REDIRECT Greek Greek may refer to: Greece Anything of, from, or related to Greece Greece ( el, Ελλάδα, , ), officially the Hellenic Republic, is a country located in Southeast Europe. Its population is ap ...
s and include
galactose Galactose (, '' galacto-'' + ''-ose The suffix In linguistics Linguistics is the science, scientific study of language. It encompasses the analysis of every aspect of language, as well as the methods for studying and modeling them. ...
,
fructose Fructose, or fruit sugar, is a ketonic simple sugar Monosaccharides (from Greek language, Greek ''wikt:μόνος, monos'': single, ''sacchar'': sugar), also called simple sugars, are the simplest form of sugar and the most basic units (monomers ...

fructose
, and most importantly
glucose Glucose is a simple with the . Glucose is the most abundant , a subcategory of s. Glucose is mainly made by and most during from water and carbon dioxide, using energy from sunlight, where it is used to make in s, the most abundant carbohydr ...

glucose
. Monosaccharides can be linked together to form
polysaccharide Polysaccharides (), or polycarbohydrates, are the most abundant found in . They are long chain carbohydrates composed of units bound together by . This carbohydrate can react with water () using as catalyst, which produces constituent sugars ...
s in almost limitless ways.


Nucleotides

The two nucleic acids, DNA and
RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large molecules, or macromolecules, composed of many Repe ...

RNA
, are polymers of
nucleotide Nucleotides are organic molecules , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, ...

nucleotide
s. Each nucleotide is composed of a phosphate attached to a
ribose Ribose is a simple sugar and carbohydrate with molecular formula C5H10O5 and the linear-form composition H−(C=O)−(CHOH)4−H. The naturally-occurring form, , is a component of the ribonucleotides from which RNA is built, and so this compoun ...

ribose
or
deoxyribose Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide Monosaccharides (from Greek '' monos'': single, ''sacchar'': sugar), also called simple sugars, are the simplest form of sugar Sugar is the generic name for Sweetness, sweet ...

deoxyribose
sugar group which is attached to a
nitrogenous base Nucleobases, also known as ''nitrogenous bases'' or often simply ''bases'', are nitrogen-containing biological compounds that form nucleosides Nucleosides are glycosylamines that can be thought of as nucleotide Nucleotides are organic mo ...
. Nucleic acids are critical for the storage and use of genetic information, and its interpretation through the processes of transcription and
protein biosynthesis Protein biosynthesis (or protein synthesis) is a core biological process, occurring inside cells Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Closed spaces * Monastic cell, a small ro ...
. This information is protected by
DNA repair DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome In the fields of molecular biology and genetics Genetics is a branch of biology concerned with th ...

DNA repair
mechanisms and propagated through
DNA replication In , DNA replication is the of producing two identical replicas of DNA from one original molecule. DNA replication occurs in all acting as the most essential part for . This is essential for cell division during growth and repair of damaged tis ...

DNA replication
. Many
virus A virus is a submicroscopic infectious agent In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecu ...

virus
es have an
RNA genome Ribonucleic acid (RNA) is a polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large molecules, or macromolecules, composed of many Rep ...
, such as
HIV The human immunodeficiency viruses (HIV) are two species of '' Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause AIDS, acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the ...

HIV
, which uses
reverse transcription A reverse transcriptase (RT) is an enzyme Enzymes () are proteins that act as biological catalysts (biocatalysts). Catalysts accelerate chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrate ...

reverse transcription
to create a DNA template from its viral RNA genome. RNA in
ribozyme Ribozymes (ribonucleic acid enzymes) are RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes. The 1982 discovery of ribozymes demonst ...

ribozyme
s such as
spliceosome A spliceosome is a large ribonucleoprotein (RNP) complex found primarily within the nucleus ''Nucleus'' (plural nuclei) is a Latin word for the seed inside a fruit. It most often refers to: *Atomic nucleus, the very dense central region of an atom ...
s and ribosomes is similar to enzymes as it can catalyze chemical reactions. Individual nucleosides are made by attaching a nucleobase to a
ribose Ribose is a simple sugar and carbohydrate with molecular formula C5H10O5 and the linear-form composition H−(C=O)−(CHOH)4−H. The naturally-occurring form, , is a component of the ribonucleotides from which RNA is built, and so this compoun ...

ribose
sugar. These bases are heterocyclic rings containing nitrogen, classified as purines or pyrimidines. Nucleotides also act as coenzymes in metabolic-group-transfer reactions.


Coenzymes

Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups of atoms and their bonds within molecules. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These group-transfer intermediates are called coenzymes. Each class of group-transfer reactions is carried out by a particular coenzyme, which is the substrate (biochemistry), substrate for a set of enzymes that produce it, and a set of enzymes that consume it. These coenzymes are therefore continuously made, consumed and then recycled. One central coenzyme is adenosine triphosphate (ATP), the universal energy currency of cells. This nucleotide is used to transfer chemical energy between different chemical reactions. There is only a small amount of ATP in cells, but as it is continuously regenerated, the human body can use about its own weight in ATP per day. ATP acts as a bridge between catabolism and anabolism. Catabolism breaks down molecules, and anabolism puts them together. Catabolic reactions generate ATP, and anabolic reactions consume it. It also serves as a carrier of phosphate groups in phosphorylation reactions. A vitamin is an organic compound needed in small quantities that cannot be made in cells. In human nutrition, most vitamins function as coenzymes after modification; for example, all water-soluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells. Nicotinamide adenine dinucleotide (NAD+), a derivative of vitamin B3 (niacin), is an important coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of dehydrogenases remove electrons from their substrates and redox, reduce NAD+ into NADH. This reduced form of the coenzyme is then a substrate for any of the reductases in the cell that need to transfer hydrogen atoms to 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.


Mineral and cofactors

Inorganic elements play critical roles in metabolism; some are abundant (e.g. sodium and potassium) while others function at minute concentrations. About 99% of a human's body weight is made up of the elements carbon, nitrogen, calcium, sodium, chlorine, potassium, hydrogen, phosphorus, oxygen and sulfur. Organic compounds (proteins, lipids and carbohydrates) contain the majority of the carbon and nitrogen; most of the oxygen and hydrogen is present as water. The abundant inorganic elements act as electrolytes. The most important ions are sodium, potassium, calcium, magnesium, chloride,
phosphate In chemistry Chemistry is the study of the properties and behavior of . It is a that covers the that make up matter to the composed of s, s and s: their composition, structure, properties, behavior and the changes they undergo durin ...

phosphate
and the organic ion bicarbonate. The maintenance of precise ion gradients across
cell membrane cell membrane vs. Prokaryotes A prokaryote is a typically unicellular organism that lacks a nuclear membrane-enclosed cell nucleus, nucleus. The word ''prokaryote'' comes from the Greek language, Greek (, 'before') and (, 'nut' or 'kernel').C ...

cell membrane
s maintains osmotic pressure and pH. Ions are also critical for nerve and muscle function, as action potentials in these tissues are produced by the exchange of electrolytes between the extracellular fluid and the cell's fluid, the cytosol. Electrolytes enter and leave cells through proteins in the cell membrane called ion channels. For example, muscle contraction depends upon the movement of calcium, sodium and potassium through ion channels in the cell membrane and T-tubules. Transition metals are usually present as trace elements in organisms, with zinc and iron being most abundant of those. Metal cofactors are bound tightly to specific sites in proteins; although enzyme cofactors can be modified during catalysis, they always return to their original state by the end of the reaction catalyzed. Metal micronutrients are taken up into organisms by specific transporters and bind to storage proteins such as ferritin or metallothionein when not in use.


Catabolism

Catabolism is the set of metabolic processes that break down large molecules. These include breaking down and oxidizing food molecules. The purpose of the catabolic reactions is to provide the energy and components needed by anabolic reactions which build molecules. The exact nature of these catabolic reactions differ from organism to organism, and organisms can be classified based on their sources of energy, hydrogen, and carbon (their primary nutritional groups), as shown in the table below. Organic molecules are used as a source of hydrogen atoms or electrons by organotrophs, while lithotrophs use inorganic substrates. Whereas phototrophs convert sunlight to Potential energy#Chemical potential energy, chemical energy, chemotrophs depend on redox reactions that involve the transfer of electrons from reduced donor molecules such as organic molecules, hydrogen,
hydrogen sulfide Hydrogen sulfide is a chemical compound A chemical compound is a chemical substance A chemical substance is a form of matter In classical physics and general chemistry, matter is any substance that has mass and takes up space by havi ...

hydrogen sulfide
or Ferrous, ferrous ions to energy-rich acceptor molecules such as oxygen, nitrate or sulfate. In animals, these reactions involve complex organic molecules that are broken down to simpler molecules, such as carbon dioxide and water. photosynthesis, Photosynthetic organisms, such as plants and cyanobacteria, use similar electron-transfer reactions to store energy absorbed from sunlight. The most common set of catabolic reactions in animals can be separated into three main stages. In the first stage, large organic molecules, such as
protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No ...

protein
s,
polysaccharide Polysaccharides (), or polycarbohydrates, are the most abundant found in . They are long chain carbohydrates composed of units bound together by . This carbohydrate can react with water () using as catalyst, which produces constituent sugars ...
s or
lipid In and , a lipid is a macro that is soluble in solvents. are typically s used to dissolve other naturally occurring hydrocarbon lipid s that do not (or do not easily) dissolve in water, including s, es, s, fat-soluble s (such as vitamins A, ...
s, are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to smaller molecules, usually acetyl-CoA, acetyl coenzyme A (acetyl-CoA), which releases some energy. Finally, the acetyl group on the CoA is oxidized to water and carbon dioxide in the
citric acid cycle The citric acid cycle (CAC) – also known as the TCA cycle (tricarboxylic acid cycle) or the Krebs cycle – is a series of chemical reaction A chemical reaction is a process that leads to the IUPAC nomenclature for organic transfor ...

citric acid cycle
and electron transport chain, releasing the energy of O2 while reducing the coenzyme nicotinamide adenine dinucleotide (NAD+) into NADH.


Digestion

Macromolecules cannot be directly processed by cells. Macromolecules must be broken into smaller units before they can be used in cell metabolism. Different classes of enzymes were being used to digest these polymers. These digestive enzymes include proteases that digest proteins into amino acids, as well as glycoside hydrolases that digest polysaccharides into simple sugars known as monosaccharides. Microbes simply secrete digestive enzymes into their surroundings, while animals only secrete these enzymes from specialized cells in their Gastrointestinal tract, guts, including the stomach and pancreas, and in salivary glands. The amino acids or sugars released by these extracellular enzymes are then pumped into cells by
active transport In cellular biology Cell biology (also cellular biology or cytology) is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processe ...

active transport
proteins.


Energy from organic compounds

Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. Carbohydrates are usually taken into cells after they have been digested into
monosaccharide Monosaccharides (from Greek#REDIRECT Greek Greek may refer to: Greece Anything of, from, or related to Greece Greece ( el, Ελλάδα, , ), officially the Hellenic Republic, is a country located in Southeast Europe. Its population is ap ...
s. Once inside, the major route of breakdown is glycolysis, where sugars such as
glucose Glucose is a simple with the . Glucose is the most abundant , a subcategory of s. Glucose is mainly made by and most during from water and carbon dioxide, using energy from sunlight, where it is used to make in s, the most abundant carbohydr ...

glucose
and
fructose Fructose, or fruit sugar, is a ketonic simple sugar Monosaccharides (from Greek language, Greek ''wikt:μόνος, monos'': single, ''sacchar'': sugar), also called simple sugars, are the simplest form of sugar and the most basic units (monomers ...

fructose
are converted into pyruvic acid, pyruvate and some ATP is generated. Pyruvate is an intermediate in several metabolic pathways, but the majority is converted to acetyl-CoA through aerobic (with oxygen) glycolysis and fed into the
citric acid cycle The citric acid cycle (CAC) – also known as the TCA cycle (tricarboxylic acid cycle) or the Krebs cycle – is a series of chemical reaction A chemical reaction is a process that leads to the IUPAC nomenclature for organic transfor ...

citric acid cycle
. Although some more ATP is generated in the citric acid cycle, the most important product is NADH, which is made from NAD+ as the acetyl-CoA is oxidized. This oxidation releases carbon dioxide as a waste product. In anaerobic conditions, glycolysis produces lactic acid, lactate, through the enzyme lactate dehydrogenase re-oxidizing NADH to NAD+ for re-use in glycolysis. An alternative route for glucose breakdown is the pentose phosphate pathway, which reduces the coenzyme NADPH and produces pentose sugars such as
ribose Ribose is a simple sugar and carbohydrate with molecular formula C5H10O5 and the linear-form composition H−(C=O)−(CHOH)4−H. The naturally-occurring form, , is a component of the ribonucleotides from which RNA is built, and so this compoun ...

ribose
, the sugar component of
nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all Organism, known forms of life. They are composed of nucleotides, which are the monomers made of three components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. ...

nucleic acid
s. Fats are catabolized by hydrolysis to free fatty acids and glycerol. The glycerol enters glycolysis and the fatty acids are broken down by beta oxidation to release acetyl-CoA, which then is fed into the citric acid cycle. Fatty acids release more energy upon oxidation than carbohydrates because carbohydrates contain more oxygen in their structures.Schmidt-Rohr, K. (2015). "Why Combustions Are Always Exothermic, Yielding About 418 kJ per Mole of O2", ''J. Chem. Educ.'' 92: 2094-2099. http://dx.doi.org/10.1021/acs.jchemed.5b00333. Steroids are also broken down by some bacteria in a process similar to beta oxidation, and this breakdown process involves the release of significant amounts of acetyl-CoA, propionyl-CoA, and pyruvate, which can all be used by the cell for energy. ''M. tuberculosis'' can also grow on the lipid cholesterol as a sole source of carbon, and genes involved in the cholesterol-use pathway(s) have been validated as important during various stages of the infection lifecycle of ''M. tuberculosis''. Amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and carbon dioxide to produce energy. The oxidation pathway starts with the removal of the amino group by a transaminase. The amino group is fed into the urea cycle, leaving a deaminated carbon skeleton in the form of a keto acid. Several of these keto acids are intermediates in the citric acid cycle, for example α-alpha-Ketoglutaric acid, ketoglutarate formed by deamination of glutamate. The glucogenic amino acids can also be converted into glucose, through gluconeogenesis (discussed below).


Energy transformations


Oxidative phosphorylation

In oxidative phosphorylation, the electrons removed from organic molecules in areas such as the citric acid cycle are transferred to oxygen and the energy released is used to make ATP. This is done in eukaryotes by a series of proteins in the membranes of mitochondria called the electron transport chain. In
prokaryote A prokaryote () is a single-celled organism A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contig ...
s, these proteins are found in the cell's bacterial cell structure, inner membrane. These proteins use the energy released by oxygen as it receives electrons from reducing agent, reduced molecules like NADH to pump protons across a membrane. Pumping protons out of the mitochondria creates a proton diffusion, concentration difference across the membrane and generates an electrochemical gradient. This force drives protons back into the mitochondrion through the base of an enzyme called ATP synthase. The flow of protons makes the stalk subunit rotate, causing the active site of the synthase domain to change shape and phosphorylate adenosine diphosphate – turning it into ATP.


Energy from inorganic compounds

Chemolithotrophy is a type of metabolism found in
prokaryote A prokaryote () is a single-celled organism A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contig ...
s where energy is obtained from the oxidation of inorganic compounds. These organisms can use hydrogen, reduced sulfur compounds (such as sulfide,
hydrogen sulfide Hydrogen sulfide is a chemical compound A chemical compound is a chemical substance A chemical substance is a form of matter In classical physics and general chemistry, matter is any substance that has mass and takes up space by havi ...

hydrogen sulfide
and thiosulfate), Iron(II) oxide, ferrous iron (Fe(II)) or ammonia as sources of reducing power and they gain energy from the oxidation of these compounds with high-energy electron acceptors such as oxygen or nitrate. These microbial processes are important in global biogeochemical cycles such as acetogenesis, nitrification and denitrification and are critical for fertility (soil), soil fertility.


Energy from light

The energy in sunlight is captured by plants, cyanobacteria, purple bacteria, green sulfur bacteria and some protists. This process is often coupled to the conversion of carbon dioxide into organic compounds, as part of photosynthesis, which is discussed below. The energy capture and carbon fixation systems can, however, operate separately in prokaryotes, as purple bacteria and green sulfur bacteria can use sunlight as a source of energy, while switching between carbon fixation and the fermentation of organic compounds. In many organisms, the capture of solar energy is similar in principle to oxidative phosphorylation, as it involves the storage of energy as a proton concentration gradient. This proton motive force then drives ATP synthesis The electrons needed to drive this electron transport chain come from light-gathering proteins called photosynthetic reaction centres. Reaction centers are classified into two types depending on the nature of photosynthetic pigment present, with most photosynthetic bacteria only having one type, while plants and cyanobacteria have two. In plants, algae, and cyanobacteria, photosystem, photosystem II uses light energy to remove electrons from water, releasing oxygen as a waste product. The electrons then flow to the cytochrome b6f complex, which uses their energy to pump protons across the thylakoid membrane in the chloroplast. These protons move back through the membrane as they drive the ATP synthase, as before. The electrons then flow through photosystem, photosystem I and can then be used to reduce the coenzyme NADP+. This cooenzyme can enter the Calvin cycle, which is discussed below, or be 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 smaller and simpler precursors. Anabolism involves three basic stages. First, the production of precursors such as
amino acid Amino acids are organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, c ...

amino acid
s,
monosaccharide Monosaccharides (from Greek#REDIRECT Greek Greek may refer to: Greece Anything of, from, or related to Greece Greece ( el, Ελλάδα, , ), officially the Hellenic Republic, is a country located in Southeast Europe. Its population is ap ...
s, Terpenoid, isoprenoids and
nucleotide Nucleotides are organic molecules , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, ...

nucleotide
s, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as
protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No ...

protein
s,
polysaccharide Polysaccharides (), or polycarbohydrates, are the most abundant found in . They are long chain carbohydrates composed of units bound together by . This carbohydrate can react with water () using as catalyst, which produces constituent sugars ...
s,
lipid In and , a lipid is a macro that is soluble in solvents. are typically s used to dissolve other naturally occurring hydrocarbon lipid s that do not (or do not easily) dissolve in water, including s, es, s, fat-soluble s (such as vitamins A, ...
s and
nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all Organism, known forms of life. They are composed of nucleotides, which are the monomers made of three components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. ...

nucleic acid
s. Anabolism in organisms can be different according to the source of constructed molecules in their cells. Autotrophs such as plants can construct the complex organic molecules in their cells such as polysaccharides and proteins from simple molecules like carbon dioxide and water. Heterotrophs, on the other hand, require a source of more complex substances, such as monosaccharides and amino acids, to produce these complex molecules. Organisms can be further classified by ultimate source of their energy: photoautotrophs and photoheterotrophs obtain energy from light, whereas chemoautotrophs and chemoheterotrophs obtain energy from oxidation reactions.


Carbon fixation

Photosynthesis is the synthesis of carbohydrates from sunlight and carbon dioxide (CO2). In plants, cyanobacteria and algae, oxygenic photosynthesis splits water, with oxygen produced as a waste product. This process uses the ATP and NADPH produced by the photosynthetic reaction centres, as described above, to convert CO2 into glycerate 3-phosphate, which can then be converted into glucose. This carbon-fixation reaction is carried out by the enzyme RuBisCO as part of the Calvin cycle, Calvin – Benson cycle. Three types of photosynthesis occur in plants, C3 carbon fixation, C4 carbon fixation and Crassulacean acid metabolism, CAM photosynthesis. These differ by the route that carbon dioxide takes to the Calvin cycle, with C3 plants fixing CO2 directly, while C4 and CAM photosynthesis incorporate the CO2 into other compounds first, as adaptations to deal with intense sunlight and dry conditions. In photosynthetic
prokaryote A prokaryote () is a single-celled organism A unicellular organism, also known as a single-celled organism, is an organism In biology, an organism (from Ancient Greek, Greek: ὀργανισμός, ''organismos'') is any individual contig ...
s the mechanisms of carbon fixation are more diverse. Here, carbon dioxide can be fixed by the Calvin – Benson cycle, a Reverse Krebs cycle, reversed citric acid cycle, or the carboxylation of acetyl-CoA. Prokaryotic Chemotroph, chemoautotrophs also fix CO2 through the Calvin–Benson cycle, but use energy from inorganic compounds to drive the reaction.


Carbohydrates and glycans

In carbohydrate anabolism, simple organic acids can be converted into
monosaccharide Monosaccharides (from Greek#REDIRECT Greek Greek may refer to: Greece Anything of, from, or related to Greece Greece ( el, Ελλάδα, , ), officially the Hellenic Republic, is a country located in Southeast Europe. Its population is ap ...
s such as
glucose Glucose is a simple with the . Glucose is the most abundant , a subcategory of s. Glucose is mainly made by and most during from water and carbon dioxide, using energy from sunlight, where it is used to make in s, the most abundant carbohydr ...

glucose
and then used to assemble
polysaccharide Polysaccharides (), or polycarbohydrates, are the most abundant found in . They are long chain carbohydrates composed of units bound together by . This carbohydrate can react with water () using as catalyst, which produces constituent sugars ...
s such as
starch Starch or amylum is a consisting of numerous units joined by s. This is produced by most green s for energy storage. Worldwide, it is the most common carbohydrate in human diets, and is contained in large amounts in s like , es, (corn), , ...
. The generation of
glucose Glucose is a simple with the . Glucose is the most abundant , a subcategory of s. Glucose is mainly made by and most during from water and carbon dioxide, using energy from sunlight, where it is used to make in s, the most abundant carbohydr ...

glucose
from compounds like pyruvate, lactic acid, lactate,
glycerol Glycerol (; also called glycerine in British English and glycerin in American English) is a simple polyol compound. It is a colorless, odorless, viscous liquid that is sweet-tasting and non-toxic. The glycerol backbone is found in lipids known ...
, glycerate 3-phosphate and
amino acid Amino acids are organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, c ...

amino acid
s is called gluconeogenesis. Gluconeogenesis converts pyruvate to glucose-6-phosphate through a series of intermediates, many of which are shared with glycolysis. However, this pathway is not simply glycolysis run in reverse, as several steps are catalyzed by non-glycolytic enzymes. This is important as it allows the formation and breakdown of glucose to be regulated separately, and prevents both pathways from running simultaneously in a futile cycle. Although fat is a common way of storing energy, in vertebrates such as humans the
fatty acid In chemistry Chemistry is the study of the properties and behavior of . It is a that covers the that make up matter to the composed of s, s and s: their composition, structure, properties, behavior and the changes they undergo during ...
s in these stores cannot be converted to glucose through gluconeogenesis as these organisms cannot convert acetyl-CoA into pyruvate; plants do, but animals do not, have the necessary enzymatic machinery. As a result, after long-term starvation, vertebrates need to produce Ketone body, ketone bodies from fatty acids to replace glucose in tissues such as the brain that cannot metabolize fatty acids. In other organisms such as plants and bacteria, this metabolic problem is solved using the glyoxylate cycle, which bypasses the decarboxylation step in the citric acid cycle and allows the transformation of acetyl-CoA to oxaloacetate, where it can be used for the production of glucose. Other than fat, glucose is stored in most tissues, as an energy resource available within the tissue through glycogenesis which was usually being used to maintained glucose level in blood. Polysaccharides and glycans are made by the sequential addition of monosaccharides by glycosyltransferase from a reactive sugar-phosphate donor such as uridine diphosphate glucose (UDP-Glc) to an acceptor
hydroxyl A hydroxy or hydroxyl group is a functional group with the chemical formula -OH and composed of one oxygen Oxygen is the chemical element Image:Simple Periodic Table Chart-blocks.svg, 400px, Periodic table, The periodic table of the ...

hydroxyl
group on the growing polysaccharide. As any of the
hydroxyl A hydroxy or hydroxyl group is a functional group with the chemical formula -OH and composed of one oxygen Oxygen is the chemical element Image:Simple Periodic Table Chart-blocks.svg, 400px, Periodic table, The periodic table of the ...

hydroxyl
groups on the ring of the substrate can be acceptors, the polysaccharides produced can have straight or branched structures. The polysaccharides produced can have structural or metabolic functions themselves, or be transferred to lipids and proteins by enzymes called oligosaccharyltransferases.


Fatty acids, isoprenoids and sterol

Fatty acids are made by fatty acid synthases that polymerize and then reduce acetyl-CoA units. The acyl chains in the fatty acids are extended by a cycle of reactions that add the acyl group, reduce it to an alcohol, dehydration reaction, dehydrate it to an alkene group and then reduce it again to an alkane group. The enzymes of fatty acid biosynthesis are divided into two groups: in animals and fungi, all these fatty acid synthase reactions are carried out by a single multifunctional type I protein, while in plant plastids and bacteria separate type II enzymes perform each step in the pathway. Terpenes and terpenoid, isoprenoids are a large class of lipids that include the carotenoids and form the largest class of plant natural products. These compounds are made by the assembly and modification of isoprene units donated from the reactive precursors isopentenyl pyrophosphate and dimethylallyl pyrophosphate. These precursors can be made in different ways. In animals and archaea, the mevalonate pathway produces these compounds from acetyl-CoA, while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates. One important reaction that uses these activated isoprene donors is steroid biosynthesis, sterol biosynthesis. Here, the isoprene units are joined to make squalene and then folded up and formed into a set of rings to make lanosterol. Lanosterol can then be converted into other sterols such as cholesterol and ergosterol.


Proteins

Organisms vary in their ability to synthesize the 20 common amino acids. Most bacteria and plants can synthesize all twenty, but mammals can only synthesize eleven nonessential amino acids, so nine essential amino acids must be obtained from food. Some simple parasites, such as the bacteria ''Mycoplasma pneumoniae'', lack all amino acid synthesis and take their amino acids directly from their hosts. All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen is provided by glutamate and glutamine. Nonessensial amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then Transaminase, transaminated to form an amino acid. Amino acids are made into proteins by being joined in a chain of
peptide bond In organic chemistry, a peptide bond is an amide type of Covalent bond, covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another, along a peptide o ...

peptide bond
s. Each different protein has a unique sequence of amino acid residues: this is its primary structure. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a transfer RNA molecule through an
ester An ester is a derived from an (organic or inorganic) in which at least one –OH group is replaced by an –O– () group, as in the substitution reaction of a and an . s are s of ; they are important in biology, being one of the main classe ...

ester
bond. This aminoacyl-tRNA precursor is produced in an Adenosine triphosphate, ATP-dependent reaction carried out by an aminoacyl tRNA synthetase. This aminoacyl-tRNA is then a substrate for the ribosome, which joins the amino acid onto the elongating protein chain, using the sequence information in a messenger RNA.


Nucleotide synthesis and salvage

Nucleotides are made from amino acids, carbon dioxide and formic acid in pathways that require large amounts of metabolic energy. Consequently, most organisms have efficient systems to salvage preformed nucleotides. Purines are synthesized as nucleosides (bases attached to
ribose Ribose is a simple sugar and carbohydrate with molecular formula C5H10O5 and the linear-form composition H−(C=O)−(CHOH)4−H. The naturally-occurring form, , is a component of the ribonucleotides from which RNA is built, and so this compoun ...

ribose
). Both adenine and guanine are made from the precursor nucleoside inosine monophosphate, which is synthesized using atoms from the amino acids glycine, glutamine, and aspartic acid, as well as formate transferred from the coenzyme folic acid, tetrahydrofolate. Pyrimidines, on the other hand, are synthesized from the base Pyrimidinecarboxylic acid, orotate, 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 that would be harmful if they accumulated in cells, as they have no metabolic function. These potentially damaging compounds are called xenobiotics. Xenobiotics such as drug, synthetic drugs, poison, natural poisons and antibiotics are detoxified by a set of xenobiotic-metabolizing enzymes. In humans, these include cytochrome P450, cytochrome P450 oxidases, Glucuronosyltransferase, UDP-glucuronosyltransferases, and glutathione S-transferase, glutathione ''S''-transferases. This system of enzymes acts in three stages to firstly oxidize the xenobiotic (phase I) and then conjugate water-soluble groups onto the molecule (phase II). The modified water-soluble xenobiotic can then be pumped out of cells and in multicellular organisms may be further metabolized before being excreted (phase III). In ecology, these reactions are particularly important in microbial biodegradation of pollutants and the bioremediation of contaminated land and oil spills. Many of these microbial reactions are shared with multicellular organisms, but due to the incredible diversity of types of microbes these organisms are able to deal with a far wider range of xenobiotics than multicellular organisms, and can degrade even persistent organic pollutants such as organochloride compounds. A related problem for aerobic organisms is oxidative stress. Here, processes including oxidative phosphorylation and the formation of disulfide bonds during protein folding produce reactive oxygen species such as hydrogen peroxide. These damaging oxidants are removed by antioxidant metabolites such as glutathione and enzymes such as catalases and peroxidases.


Thermodynamics of living organisms

Living organisms must obey the laws of thermodynamics, which describe the transfer of heat and work (thermodynamics), work. The second law of thermodynamics states that in any isolated system, the amount of entropy (disorder) cannot decrease. Although living organisms' amazing complexity appears to contradict this law, life is possible as all organisms are open system (systems theory), open systems that exchange matter and energy with their surroundings. Living systems are not in Thermodynamic equilibrium, equilibrium, but instead are dissipative systems that maintain their state of high complexity by causing a larger increase in the entropy of their environments. The metabolism of a cell achieves this by coupling the spontaneous processes of catabolism to the non-spontaneous processes of anabolism. In non-equilibrium thermodynamics, thermodynamic 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 Control theory, regulated to maintain a constant set of conditions within cells, a condition called homeostasis. Metabolic regulation also allows organisms to respond to signals and interact actively with their environments. Two closely linked concepts are important for understanding how metabolic pathways are controlled. Firstly, the ''regulation'' of an enzyme in a pathway is how its activity is increased and decreased in response to signals. Secondly, the ''control'' exerted by this enzyme is the effect that these changes in its activity have on the overall rate of the pathway (the flux through the pathway). For example, an enzyme may show large changes in activity (''i.e.'' it is highly regulated) but if these changes have little effect on the flux of a metabolic pathway, then this enzyme is not involved in the control of 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 flux through the pathway to compensate. This type of regulation often involves allosteric regulation of the activities of multiple enzymes in the pathway. Extrinsic control involves a cell in a multicellular organism changing its metabolism in response to signals from other cells. These signals are usually in the form of water-soluble messengers such as hormones and growth factors and are detected by specific receptor (biochemistry), receptors on the cell surface. These signals are then transmitted inside the cell by second messenger systems that often involved the phosphorylation of proteins. A very well understood example of extrinsic control is the regulation of glucose metabolism by the hormone insulin. Insulin is produced in response to rises in blood sugar, blood glucose levels. Binding of the hormone to insulin receptors on cells then activates a cascade of protein kinases that cause the cells to take up glucose and convert it into storage molecules such as fatty acids and
glycogen Glycogen is a multibranched of that serves as a form of energy storage in s, , and bacteria. The polysaccharide structure represents the main storage form of glucose in the body. Glycogen functions as one of two forms of energy reserves, g ...

glycogen
. The metabolism of glycogen is controlled by activity of phosphorylase, the enzyme that breaks down glycogen, and glycogen synthase, the enzyme that makes it. These enzymes are regulated in a reciprocal fashion, with phosphorylation inhibiting glycogen synthase, but activating phosphorylase. Insulin causes glycogen synthesis by activating phosphatase, protein phosphatases 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-domain system, three domains of living things and were present in the last universal common ancestor. This universal ancestral cell was prokaryote, prokaryotic and probably a methanogen that had extensive amino acid, nucleotide, carbohydrate and lipid metabolism. The retention of these ancient pathways during later evolution may be the result of these reactions having been an optimal solution to their particular metabolic problems, with pathways such as glycolysis and the citric acid cycle producing their end products highly efficiently and in a minimal number of steps. The first pathways of enzyme-based metabolism may have been parts of purine nucleotide metabolism, while previous metabolic pathways were a part of the ancient RNA world hypothesis, RNA world. Many models have been proposed to describe the mechanisms by which novel metabolic pathways evolve. These include the sequential addition of novel enzymes to a short ancestral pathway, the duplication and then divergence of entire pathways as well as the recruitment of pre-existing enzymes and their assembly into a novel reaction pathway. The relative importance of these mechanisms is unclear, but genomic studies have shown that enzymes in a pathway are likely to have a shared ancestry, suggesting that many pathways have evolved in a step-by-step fashion with novel functions created from pre-existing steps in the pathway. An alternative model comes from studies that trace the evolution of proteins' structures in metabolic networks, this has suggested that enzymes are pervasively recruited, borrowing enzymes to perform similar functions in different metabolic pathways (evident in the MANET database) These recruitment processes result in an evolutionary enzymatic mosaic. A third possibility is that some parts of metabolism might exist as "modules" that can be reused in different pathways and perform similar functions on different molecules. As well as the evolution of new metabolic pathways, evolution can also cause the loss of metabolic functions. For example, in some parasites metabolic processes that are not essential for survival are lost and preformed amino acids, nucleotides and carbohydrates may instead be scavenged from the host (biology), host. Similar reduced metabolic capabilities are seen in endosymbiont, endosymbiotic organisms.


Investigation and manipulation

Classically, metabolism is studied by a reductionism, reductionist approach that focuses on a single metabolic pathway. Particularly valuable is the use of radioactive tracers at the whole-organism, tissue and cellular levels, which define the paths from precursors to final products by identifying radioactively labelled intermediates and products. The enzymes that catalyze these chemical reactions can then be protein purification, purified and their enzyme kinetics, kinetics and responses to enzyme inhibitor, inhibitors investigated. A parallel approach is to identify the small molecules in a cell or tissue; the complete set of these molecules is called the metabolome. Overall, these studies give a good view of the structure and function of simple metabolic pathways, but are inadequate when applied to more complex systems such as the metabolism of a complete cell. An idea of the complexity of the metabolic networks in cells that contain thousands of different enzymes is given by the figure showing the interactions between just 43 proteins and 40 metabolites to the right: the sequences of genomes provide lists containing anything up to 26.500 genes. However, it is now possible to use this genomic data to reconstruct complete networks of biochemical reactions and produce more Holism, holistic mathematical models that may explain and predict their behavior. These models are especially powerful when used to integrate the pathway and metabolite data obtained through classical methods with data on gene expression from proteomics, proteomic and DNA microarray studies. Using these techniques, a model of human metabolism has now been produced, which will guide future drug discovery and biochemical research. These models are now used in Network theory, network analysis, to classify human diseases into groups that share common proteins or metabolites. Bacterial metabolic networks are a striking example of Bow tie (biology), bow-tie organization, an architecture able to input a wide range of nutrients and produce a large variety of products and complex macromolecules using a relatively few intermediate common currencies. A major technological application of this information is metabolic engineering. Here, organisms such as yeast, plants or bacteria are genetically modified to make them more useful in biotechnology and aid the production of drugs such as antibiotics or industrial chemicals such as 1,3-Propanediol, 1,3-propanediol and shikimic acid. These genetic modifications usually aim to reduce the amount of energy used to produce the product, increase yields and reduce the production of wastes.


History

The term ''metabolism'' is derived from French language, French "métabolisme" or Ancient Greek μεταβολή – "Metabole" for "a change" which derived from μεταβάλλ –"Metaballein" means "To change"


Greek philosophy

Aristotle's ''The Parts of Animals'' sets out enough details of Aristotle's biology, his views on metabolism for an open flow model to be made. He believed that at each stage of the process, materials from food were transformed, with heat being released as the classical element of fire, and residual materials being excreted as urine, bile, or faeces.


Islamic medicine

Ibn al-Nafis described metabolism in his 1260 AD work titled Al-Risalah al-Kamiliyyah fil Siera al-Nabawiyyah (The Treatise of Kamil on the Prophet's Biography) which included the following phrase "Both the body and its parts are in a continuous state of dissolution and nourishment, so they are inevitably undergoing permanent change."


Application of the scientific method

The history of the scientific study of metabolism spans several centuries and has moved from examining whole animals in early studies, to examining individual metabolic reactions in modern biochemistry. The first controlled experiments in human metabolism were published by Santorio Santorio in 1614 in his book ''Ars de statica medicina''. He described how he weighed himself before and after eating, sleeping, 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 vitalism, vital force was thought to animate living tissue. In the 19th century, when studying the fermentation (food), fermentation of sugar to
alcohol In , alcohol is an that carries at least one (−OH) bound to a atom. The term alcohol originally referred to the primary alcohol (ethyl alcohol), which is and is the main alcohol present in s. An important class of alcohols, of which ...

alcohol
by yeast, Louis Pasteur concluded that fermentation was catalyzed by substances within the yeast cells he called "ferments". He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells." This discovery, along with the publication by Friedrich Woehler, Friedrich Wöhler in 1828 of a paper on the chemical synthesis of urea, and is notable for being the first organic compound prepared from wholly inorganic precursors. This proved that the organic compounds and chemical reactions found in cells were no different in principle than any other part of chemistry. It was the discovery of
enzyme Enzymes () are protein Proteins are large s and s that comprise one or more long chains of . Proteins perform a vast array of functions within organisms, including , , , providing and , and from one location to another. Proteins diff ...

enzyme
s at the beginning of the 20th century by Eduard Buchner that separated the study of the chemical reactions of metabolism from the biological study of cells, and marked the beginnings of biochemistry. The mass of biochemical knowledge grew rapidly throughout the early 20th century. One of the most prolific of these modern biochemists was Hans Adolf Krebs, Hans Krebs who made huge contributions to the study of metabolism. He discovered the urea cycle and later, working with Hans Kornberg, the citric acid cycle and the glyoxylate cycle. Modern biochemical research has been greatly aided by the development of new techniques such as chromatography, X-ray diffraction, NMR spectroscopy, radioisotopic labelling, electron microscope , electron microscopy and molecular dynamics simulations. These techniques have allowed the discovery and detailed analysis of the many molecules and metabolic pathways in cells.


See also

* * * * * * , a "metabolism first" theory of the origin of life * * Microphysiometry * * * * * * * * *Oncometabolism * *


References


Further reading

Introductory * * * Advanced * * * * * * *


External links

General information
The Biochemistry of Metabolism

Sparknotes SAT biochemistry
Overview of biochemistry. School level.

Undergraduate-level guide to molecular biology. Human metabolism

Guide to human metabolic pathways. School level.
THE Medical Biochemistry Page
Comprehensive resource on human metabolism. Databases
Flow Chart of Metabolic Pathways
at ExPASy
IUBMB-Nicholson Metabolic Pathways Chart

SuperCYP: Database for Drug-Cytochrome-Metabolism
Metabolic pathways

* {{Authority control, state=collapsed Metabolism, Underwater diving physiology