Metabolism is the set of chemical reactions that occur in living organisms in order to maintain life. A chemical reaction is a process that always results in the interconversion of Chemical substances The substance or substances initially involved in a chemical reaction are called Life is a state that distinguishes Organisms from non-living objects such as non-life and dead organisms being manifested by growth through Metabolism These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories. Catabolism breaks down large molecules, for example to harvest energy in cellular respiration. For the related metabolic process see Anabolism. Catabolism is the set of Metabolic pathways which break down molecules into Cellular respiration is the set of the metabolic reactions and processes that take place in Organisms cells to convert biochemical energy from Anabolism, on the other hand, uses energy to construct components of cells such as proteins and nucleic acids. Anabolism is the set of Metabolic pathways that construct molecules from smaller units Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl A nucleic acid is a Macromolecule composed of chains of monomeric Nucleotides In Biochemistry these Molecules carry Genetic information
The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed into another by a sequence of enzymes. In Biochemistry, a metabolic pathway is a series of chemical reactions occurring within a cell. Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins Enzymes are crucial to metabolism because they allow organisms to drive desirable but thermodynamically unfavorable reactions by coupling them to favorable ones. Biological thermodynamics is a phrase that is sometimes used to refer to Bioenergetics, the study of Energy transformation in the Biological sciences Biological In Physics, two systems are coupled if they are interacting with each other Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or signals from other cells. Control theory is an interdisciplinary branch of Engineering and Mathematics, that deals with the behavior of Dynamical systems The desired output The cell is the 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 Cell signaling is part of a Complex system of Communication that governs basic cellular activities and coordinates cell actions
The metabolism of an organism determines which substances it will find nutritious and which it will find poisonous. Nutrition (also called nourishment or aliment) is the provision to cells and Organisms of the materials necessary (in the form of food to support In the context of Biology, poisons are substances that can cause damage, Illness, or Death to Organisms usually by For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals. The prokaryotes (proʊˈkærioʊts singular prokaryote /proʊˈkæriət/ are a group of Organisms that lack a Cell nucleus (= karyon or any other Hydrogen sulfide (or hydrogen sulphide) is the Chemical compound with the formula H 2 S. [1] The speed of metabolism, the metabolic rate, also influences how much food an organism will require.
A striking feature of metabolism is the similarity of the basic metabolic pathways between even vastly different species. For example, the set of carboxylic acids that are best known as the intermediates in the citric acid cycle are present in all organisms, being found in species as diverse as the unicellular bacteria Escherichia coli and huge multicellular organisms like elephants. Carboxylic acids are Organic acids characterized by the presence of a Carboxyl group, which has the formula -C(=OOH usually written -COOH or -CO2H The citric acid cycle, also known as the tricarboxylic acid cycle ( TCA cycle) or the Krebs cycle, (or rarely the Szent-Györgyi–Krebs cycle A microorganism (also spelled micro organism or micro-organism and also called a microbe) is an Organism that is Microscopic (usually The Bacteria ( singular: bacterium) are a large group of unicellular Microorganisms Typically a few Micrometres in length bacteria have Multicellular organisms are Organisms consisting of more than one cell, and having Differentiated cells that perform specialized functions Elephants ( family: Elephantidae) are large land Mammals of the order Proboscidea. [2] These striking similarities in metabolism are most likely the result of the high efficiency of these pathways, and of their early appearance in evolutionary history. [3][4]
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Key biochemicals
- Further information: Biomolecule, cell (biology) and biochemistry
Most of the structures that make up animals, plants and microbes are made from three basic classes of molecule: amino acids, carbohydrates and lipids (often called fats). In Chemistry, a molecule is defined as a sufficiently stable electrically neutral group of at least two Atoms in a definite arrangement held together by In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this Carbohydrates (from ' Hydrates of Carbon ' or saccharides ( Greek σάκχαρον meaning " Sugar " are the most Lipids are broadly defined as any fat- Soluble ( lipophilic) naturally-occurring Molecule, such as fats oils waxes cholesterol sterols fat-soluble Fats consist of a wide group of compounds that are generally soluble in organic solvents and largely insoluble in water As these molecules are vital for life, metabolism focuses on making these molecules, in the construction of cells and tissues, or breaking them down and using them as a source of energy, in the digestion and use of food. Many important biochemicals can be joined together to make polymers such as DNA and proteins. A polymer is a large Molecule ( Macromolecule) composed of repeating Structural units typically connected by Covalent Chemical bonds Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl These macromolecules are essential parts of all living organisms. The term macromolecule by definition implies "large Molecule " Some of the most common biological polymers are listed in the table below.
| Type of molecule | Name of monomer forms | Name of polymer forms | Examples of polymer forms |
|---|---|---|---|
| Amino acids | Amino acids | Proteins (also called polypeptides) | Fibrous proteins and globular proteins |
| Carbohydrates | Monosaccharides | Polysaccharides | Starch, glycogen and cellulose |
| Nucleic acids | Nucleotides | Polynucleotides | DNA and RNA |
Amino acids and proteins
Proteins are made of amino acids arranged in a linear chain and joined together by peptide bonds. A monomer (from Greek mono "one" and meros "part" is a small Molecule that may become chemically bonded to other A polymer is a large Molecule ( Macromolecule) composed of repeating Structural units typically connected by Covalent Chemical bonds In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl Fibrous proteins, also called scleroproteins, are one of the two main classes of protein Quaternary structure (the other being Globular proteins. Globular proteins, or spheroproteins are one of the two main Protein classes comprising "globe" -like proteins that are more or less soluble in Carbohydrates (from ' Hydrates of Carbon ' or saccharides ( Greek σάκχαρον meaning " Sugar " are the most Monosaccharides (from Greek monos: single sacchar: sugar are the most basic unit of Carbohydrates They consist of one sugar and Polysaccharides are relatively complex Carbohydrates They are Polymers made up of many Monosaccharides joined together by Glycosidic bonds Starch, CAS # 9005-25-8 Chemical formula (C6H10O5n is a Polysaccharide Glycogen is a Polysaccharide of Glucose (Glc which functions as the secondary short term energy storage in Animal cells Cellulose is an Organic compound with the formula, a Polysaccharide consisting of a linear chain of several hundred to over ten thousand β(1→4 A nucleic acid is a Macromolecule composed of chains of monomeric Nucleotides In Biochemistry these Molecules carry Genetic information Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group A polynucleotide molecule is an organic Polymer molecule composed of Nucleotide Monomers covalently bonded in a chain Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this A peptide bond is a Chemical bond formed between two Molecules when the Carboxyl group of one molecule reacts with the Many proteins are the enzymes that catalyze the chemical reactions in metabolism. Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins Catalysis is the process in which the rate of a Chemical reaction is increased by means of a Chemical substance known as a catalyst Other proteins have structural or mechanical functions, such as the proteins that form the cytoskeleton, a system of scaffolding that maintains the cell shape. cytoskeleton (also CSK is a cellular " Scaffolding " or " Skeleton " contained within the Cytoplasm. Scaffolding is a temporary framework used to support people and material in the construction or repair of buildings and other large structures [5] Proteins are also important in cell signaling, immune responses, cell adhesion, active transport across membranes and the cell cycle. Cell signaling is part of a Complex system of Communication that governs basic cellular activities and coordinates cell actions Antibodies (also known as immunoglobulins, abbreviated Ig) are Gamma globulin Proteins that are found in Blood or other Bodily Cellular adhesion is the binding of a cell to another cell or to a Surface or matrix. Active transport is the mediated process of moving particles across Biological membrane against the concentration gradient The cell cycle, or cell-division cycle, is the series of events that take place in a eukaryotic cell leading to its replication [6]
Lipids
Lipids are the most diverse group of biochemicals. Lipids are broadly defined as any fat- Soluble ( lipophilic) naturally-occurring Molecule, such as fats oils waxes cholesterol sterols fat-soluble Their main structural uses are as part of biological membranes such as the cell membrane, or as a source of energy. MembraneA biological membrane or biomembrane is an enclosing or separating Amphipathic layer that acts as a barrier within or around a cell. The cell membrane (also called the plasma membrane, plasmalemma, or "phospholipid bilayer" is a Selectively permeable Lipid bilayer [6] Lipids are usually defined as hydrophobic or amphipathic biological molecules that will dissolve in organic solvents such as benzene or chloroform. In Chemistry, hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear phobos) refers to the physical property of Amphiphile (from the Greek αμφις amphis both and φιλíα Philia: love friendship is a term describing a Chemical compound possessing both A solvent is a liquid or gas that dissolves a solid liquid or gaseous Solute, resulting in a Solution. Benzene, or benzol, is an organic Chemical compound and a known Carcinogen with the molecular formula C 6 H 6 Chloroform, also known as trichloromethane and methyl trichloride, is a Chemical compound with formula C[[Hydrogen H]] Cl [7] The fats are a large group of compounds that contain fatty acids and glycerol; a glycerol molecule attached to three fatty acid esters is a triacylglyceride. Fats consist of a wide group of compounds that are generally soluble in organic solvents and largely insoluble in water In Chemistry, especially Biochemistry, a fatty acid is a Carboxylic acid often with a long unbranched Aliphatic tail ( chain) which Esters are a class of Chemical compounds and Functional groups Esters consist of an inorganic or organic Acid in which at least (more properly known as, TAG or triacylglyceride) is Glyceride in which the Glycerol is Esterified with three Fatty acids It is the [8] Several variations on this basic structure exist, including alternate backbones such as sphingosine in the sphingolipids, and hydrophilic groups such as phosphate in phospholipids. Sphingosine (2-amino-4-octadecene-13-diol is an 18-carbon Amino alcohol with an unsaturated hydrocarbon chain which forms a primary part of Sphingolipids a class Sphingolipids are a class of Lipids derived from the Aliphatic amino alcohol Sphingosine. Hydrophile, from the Greek (hydros "water" and φιλια (philia "friendship" refers to a physical property of a Molecule A phosphate, an Inorganic chemical, is a salt of Phosphoric acid. Phospholipids are a class of Lipids and are a major component of all Biological membranes All phospholipids contain a Diglyceride, a Phosphate Steroids such as cholesterol are another major class of lipids that are made in cells. A steroid is a Terpenoid Lipid characterized by a Carbon skeleton with four fused rings generally arranged in a 6-6-6-5 fashion Cholesterol is a Lipid found in the Cell membranes and transported in the Blood plasma of all Animals It is an essential component of mammalian [9]
Carbohydrates
Carbohydrates are straight-chain aldehydes or ketones with many hydroxyl groups that can exist as straight chains or rings. Carbohydrates (from ' Hydrates of Carbon ' or saccharides ( Greek σάκχαρον meaning " Sugar " are the most An aldehyde is an organic compound containing a terminal Carbonyl group. A ketone (pronounced as key tone) is either the Functional group characterized by a Carbonyl group (O=C linked to two other Carbon atoms or Hydroxyl in Chemistry stands for a molecule consisting of an Oxygen atom and a Hydrogen atom connected by a Covalent bond. Carbohydrates are the most abundant biological molecules, and fill numerous roles, such as the storage and transport of energy (starch, glycogen) and structural components (cellulose in plants, chitin in animals). In Physics and other Sciences energy (from the Greek grc ἐνέργεια - Energeia, "activity operation" from grc ἐνεργός Starch, CAS # 9005-25-8 Chemical formula (C6H10O5n is a Polysaccharide Glycogen is a Polysaccharide of Glucose (Glc which functions as the secondary short term energy storage in Animal cells Cellulose is an Organic compound with the formula, a Polysaccharide consisting of a linear chain of several hundred to over ten thousand β(1→4 Chitin ( C 8 H 13 O 5 N)n (ˈkaɪtən is a long-chain Polymer of a N-acetylglucosamine [6] The basic carbohydrate units are called monosaccharides and include galactose, fructose, and most importantly glucose. Monosaccharides (from Greek monos: single sacchar: sugar are the most basic unit of Carbohydrates They consist of one sugar and Galactose (Gal (also called brain sugar) is a type of Sugar which is less sweet than Glucose. Fructose (also levulose or laevulose) is a simple reducing Sugar ( Monosaccharide) found in many foods and is one of the three Glucose (Glc a Monosaccharide (or simple Sugar) also known as grape sugar, is an important Carbohydrate in Biology. Monosaccharides can be linked together to form polysaccharides in almost limitless ways. Polysaccharides are relatively complex Carbohydrates They are Polymers made up of many Monosaccharides joined together by Glycosidic bonds [10]
Nucleotides
The polymers DNA and RNA are long chains of nucleotides. Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group These molecules are critical for the storage and use of genetic information, through the processes of transcription and protein biosynthesis. Transcription is the synthesis of RNA under the direction of DNA Protein biosynthesis (synthesis is the process in which cells build Proteins The term is sometimes used to refer only to protein translation but more [6] This information is protected by DNA repair mechanisms and propagated through DNA replication. DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its Genome. DNA replication is the process of copying a double-stranded DNA molecule to form two double-stranded molecules A few viruses have an RNA genome, for example HIV, which uses reverse transcription to create a DNA template from its viral RNA genome. A virus (from the Latin virus meaning Toxin or Poison) is a sub-microscopic infectious agent that is unable Human immunodeficiency virus ( HIV) is a Lentivirus (a member of the Retrovirus family that can lead to acquired immunodeficiency syndrome Reverse transcription is the process of making a double stranded DNA (deoxyribonucleic acid molecule from a single stranded RNA (ribonucleic acid template [11] RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can catalyze chemical reactions. A ribozyme (from ribo nucleic acid en' zyme', also called RNA Enzyme or catalytic RNA is an RNA Molecule that catalyzes A spliceosome is a complex of specialized RNA and Protein subunits that removes Introns from a transcribed pre- mRNA ( HnRNA Ribosomes ( from ribo nucleic acid and "Greek soma ( meaning body") are complexes of RNA and Protein that Individual nucleosides are made by attaching a nucleobase to a ribose sugar. See also Adenosine triphosphate (ATP Structure The "skeleton" of adenine Ribose (ɹˈaɪbəʊs ɹˈaɪbəɹʊs primarily seen as D-ribose, is an Aldopentose — a Monosaccharide containing five Carbon These bases are heterocyclic rings containing nitrogen, classified as purines or pyrimidines. Purine ( 1) is a heterocyclic Aromatic Organic compound, consisting of a Pyrimidine ring fused to an Imidazole ring Pyrimidine is a Heterocyclic Aromatic Organic compound similar to Benzene and Pyridine, containing two Nitrogen Atoms Nucleotides also act as coenzymes in metabolic group transfer reactions. [12]
Coenzymes
- Further information: Coenzyme
Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups. Coenzymes are small organic non- Protein Molecules that carry chemical groups between Enzymes Coenzymes are sometimes referred to as cosubstrates In Organic chemistry, functional groups are specific groups of Atoms within Molecules that are responsible for the characteristic Chemical reactions [13] This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. [12] These group-transfer intermediates are called coenzymes. Coenzymes are small organic non- Protein Molecules that carry chemical groups between Enzymes Coenzymes are sometimes referred to as cosubstrates Each class of group-transfer reaction is carried out by a particular coenzyme, which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it. These coenzymes are therefore continuously being made, consumed and then recycled. [14]
One central coenzyme is adenosine triphosphate (ATP), the universal energy currency of cells. Adenosine-5'-triphosphate ( ATP) is a multifunctional Nucleotide that is most important as a " molecular currency" of intracellular Energy This nucleotide is used to transfer chemical energy between different chemical reactions. Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group 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. [14] ATP acts as a bridge between catabolism and anabolism, with catabolic reactions generating ATP and anabolic reactions consuming it. It also serves as a carrier of phosphate groups in phosphorylation reactions. Phosphorylation is the addition of a Phosphate (PO4 group to a Protein molecule or a small molecule
A vitamin is an organic compound needed in small quantities that cannot be made in the cells. A vitamin is an Organic compound required as a Nutrient in tiny amounts by an Organism. 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. Nutrition (also called nourishment or aliment) is the provision to cells and Organisms of the materials necessary (in the form of food to support [15] Nicotinamide adenine dinucleotide (NADH), a derivative of vitamin B3 (niacin), is an important coenzyme that acts as a hydrogen acceptor. Nicotinamide adenine dinucleotide, abbreviated NAD+, is a Coenzyme found in all living cells The compound is a dinucleotide since it consists Niacin, also known as vitamin B3, is a water-soluble vitamin which prevents the deficiency disease Pellagra. Hundreds of separate types of dehydrogenases remove electrons from their substrates and reduce NAD+ into NADH. A dehydrogenase is an Enzyme that Oxidizes a substrate by transferring one or more Protons and a pair of electrons to an acceptor usually Redox (shorthand for reduction-oxidation reaction describes all Chemical reactions in which atoms have their Oxidation number ( Oxidation state This reduced form of the coenzyme is then a substrate for any of the reductases in the cell that need to reduce their substrates. A reductase is an Enzyme which lowers the Activation energy for a reduction reaction. [16] Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The NAD+/NADH form is more important in catabolic reactions, while NADP+/NADPH is used in anabolic reactions.
Minerals and cofactors
- Further information: Physiology, bioinorganic chemistry, cofactor and iron metabolism
Inorganic elements play critical roles in metabolism; some are abundant (e. Physiology (from Greek grc φύσις physis, "nature origin" and grc -λογία -logia) is the study of the mechanical physical Bioinorganic chemistry is a specialized field that spans the Chemistry of Metal -containing Molecules within biological systems Human iron metabolism is the set of chemical reactions maintaining Human homeostasis of Iron. g. sodium and potassium) while others function at minute concentrations. Sodium (ˈsoʊdiəm is an element which has the symbol Na( Latin natrium, from Arabic natrun) atomic number 11 atomic mass 22 Potassium (pəˈtæsiəm is a Chemical element. It has the symbol K (kalium from qalīy Atomic number 19 and Atomic mass 39 About 99% of mammals' mass are the elements carbon, nitrogen, calcium, sodium, chlorine, potassium, hydrogen, phosphorus, oxygen and sulfur. Carbon (kɑɹbən is a Chemical element with the symbol C and its Atomic number is 6 Nitrogen (ˈnaɪtɹəʤɪn is a Chemical element that has the symbol N and Atomic number 7 and Atomic weight 14 Calcium (ˈkælsiəm is the Chemical element with the symbol Ca and Atomic number 20 Sodium (ˈsoʊdiəm is an element which has the symbol Na( Latin natrium, from Arabic natrun) atomic number 11 atomic mass 22 Chlorine (ˈklɔriːn from the Greek word 'χλωρóς' ( khlôros, meaning 'pale green' is the Chemical element with Atomic number 17 and Potassium (pəˈtæsiəm is a Chemical element. It has the symbol K (kalium from qalīy Atomic number 19 and Atomic mass 39 Hydrogen (ˈhaɪdrədʒən is the Chemical element with Atomic number 1 Phosphorus, (ˈfɒsfərəs is the Chemical element that has the symbol P and Atomic number 15 Oxygen (from the Greek roots ὀξύς (oxys (acid literally "sharp" from the taste of acids and -γενής (-genēs (producer literally begetteris the Sulfur or sulphur (ˈsʌlfɚ see spelling below) is the Chemical element that has the Atomic number 16 [17] The organic compounds (proteins, lipids and carbohydrates) contain the majority of the carbon and nitrogen and most of the oxygen and hydrogen is present as water. An organic compound is any member of a large class of Chemical compounds whose Molecules contain Carbon. [17]
The abundant inorganic elements act as ionic electrolytes. An ion is an Atom or Molecule which has lost or gained one or more Valence electrons giving it a positive or negative electrical charge An electrolyte is any substance containing free Ions that behaves as an electrically conductive medium The most important ions are sodium, potassium, calcium, magnesium, chloride, phosphate, and the organic ion bicarbonate. Sodium (ˈsoʊdiəm is an element which has the symbol Na( Latin natrium, from Arabic natrun) atomic number 11 atomic mass 22 Potassium (pəˈtæsiəm is a Chemical element. It has the symbol K (kalium from qalīy Atomic number 19 and Atomic mass 39 Calcium (ˈkælsiəm is the Chemical element with the symbol Ca and Atomic number 20 Magnesium (mægˈniːziəm is a Chemical element with the symbol Mg, Atomic number 12 Atomic weight 24 The chloride Ion is formed when the element Chlorine picks up one Electron to form an Anion (negatively-charged ion Cl&minus A phosphate, an Inorganic chemical, is a salt of Phosphoric acid. In Inorganic chemistry, bicarbonate ( IUPAC -recommended nomenclature hydrogencarbonate) is an intermediate form in the Deprotonation The maintenance of precise gradients across cell membranes maintains osmotic pressure and pH. In Cellular biology, an electrochemical gradient is a spatial variation of both Electrical potential and chemical Concentration across a membrane The cell membrane (also called the plasma membrane, plasmalemma, or "phospholipid bilayer" is a Selectively permeable Lipid bilayer Osmotic pressure is the hydrostatic pressure produced by a difference in concentration between solutions on the two sides of a surface such as a semipermeable membrane pH is the measure of the acidity or alkalinity of a Solution. [18] Ions are also critical for nerves and muscles, as action potentials in these tissues are produced by the exchange of electrolytes between the extracellular fluid and the cytosol. A nerve is an enclosed cable-like bundle of peripheral Axons (the long slender projections of Neurons. Muscle (from Latin musculus, diminutive of mus "mouse" is contractile tissue of the body and is derived from the In Neurophysiology, the action potential is a self-regenerating Wave of Electrochemical activity that allows Nerve cells to carry a signal Extracellular fluid (ECF usually denotes all body fluid outside of cells The cytosol or intracellular fluid (or cytoplasmic matrix) is the liquid found inside cells. [19] Electrolytes enter and leave cells through proteins in the cell membrane called ion channels. Ion channels are pore-forming Proteins that help establish and control the small Voltage Gradient across the Plasma membrane of all living For example, muscle contraction depends upon the movement of calcium, sodium and potassium through ion channels in the cell membrane and T-tubules. A muscles contraction (also known as a muscle twitch or simply twitch) occurs when a Muscle fibre generates tension through the action of Actin A T-tubule (or transverse tubule) is a deep Invagination of the Plasma membrane found in skeletal and Cardiac muscle cells [20]
The transition metals are usually present as trace elements in organisms, with zinc and iron being most abundant. In Chemistry, the term transition metal (sometimes also called a transition element) has two possible meanings It commonly refers to any element in In Analytical chemistry, a trace element is an element in a sample that has an average Concentration of less than 100 Parts per million atoms Zinc (ˈzɪŋk from Zink is a Metallic Chemical element with the symbol Zn and Atomic number 30 Iron (ˈаɪɚn is a Chemical element with the symbol Fe (ferrum and Atomic number 26 [21][22] These metals are used in some proteins as cofactors and are essential for the activity of enzymes such as catalase and oxygen-carrier proteins such as hemoglobin. Catalase is a common Enzyme found in nearly all living organisms where it functions to catalyze the decomposition of Hydrogen peroxide to Hemoglobin ( also spelled haemoglobin and abbreviated Hb or Hgb) is the Iron -containing Oxygen -transport Metalloprotein [23] These cofactors are bound tightly to a specific protein; although enzyme cofactors can be modified during catalysis, cofactors always return to their original state after catalysis has taken place. The metal micronutrients are taken up into organisms by specific transporters and bound to storage proteins such as ferritin or metallothionein when not being used. Ferritin is a Globular protein complex consisting of 24 protein subunits and is the main intracellular iron storage protein in both Prokaryotes Metallothionein (MT is a family of Cysteine -rich low molecular weight (MW ranging from 3500 to 14000 Da) Proteins MTs have the capacity to [24][25]
Catabolism
- Further information: Catabolism
Catabolism is the set of metabolic processes that break down large molecules. For the related metabolic process see Anabolism. Catabolism is the set of Metabolic pathways which break down molecules into These include breaking down and oxidising food molecules. The purpose of the catabolic reactions is to provide the energy and components needed by anabolic reactions. The exact nature of these catabolic reactions differ from organism to organism, with organic molecules being used as a source of energy in organotrophs, while lithotrophs use inorganic substrates and phototrophs capture sunlight as chemical energy. An organotroph is an organism that obtains hydrogen or electrons from organic substrates A lithotroph is an Organism that uses an Inorganic substrate (usually of mineral origin to obtain reducing equivalents for use in biosynthesis (e Photoautotrophs or Phototroph ( Gk: photo = light auto = self troph = nourishment are Organisms (commonly plants that carry out Photosynthesis Sunlight, in the broad sense is the total spectrum of the Electromagnetic radiation given off by the Sun. Potential energy can be thought of as Energy stored within a physical system However, all these different forms of metabolism depend on redox reactions that involve the transfer of electrons from reduced donor molecules such as organic molecules, water, ammonia, hydrogen sulfide or ferrous ions to acceptor molecules such as oxygen, nitrate or sulfate. Redox (shorthand for reduction-oxidation reaction describes all Chemical reactions in which atoms have their Oxidation number ( Oxidation state An organic compound is any member of a large class of Chemical compounds whose Molecules contain Carbon. Water is a common Chemical substance that is essential for the survival of all known forms of Life. Ammonia is a compound with the formula N[[hydrogen H3]] It is normally encountered as a Gas with a characteristic pungent Odor Hydrogen sulfide (or hydrogen sulphide) is the Chemical compound with the formula H 2 S. Ferrous, in the chemical science realm indicates a bivalent iron compound (+2 oxidation state (as opposed to Ferric, which indicates a trivalent iron compound (+3 oxidation Oxygen (from the Greek roots ὀξύς (oxys (acid literally "sharp" from the taste of acids and -γενής (-genēs (producer literally begetteris the In Inorganic chemistry, a nitrate is a salt of Nitric acid with an Ion composed of one Nitrogen and three Oxygen atoms [26] In animals these reactions involve complex organic molecules being broken down to simpler molecules, such as carbon dioxide and water. An organic compound is any member of a large class of Chemical compounds whose Molecules contain Carbon. Carbon dioxide ( Chemical formula:) is a Chemical compound composed of two Oxygen Atoms covalently bonded to a single In photosynthetic organisms such as plants and cyanobacteria, these electron-transfer reactions do not release energy, but are used as a way of storing energy absorbed from sunlight. Photosynthesis is a Metabolic pathway that converts Light Energy into Chemical energy. Cyanobacteria, also known as blue-green algae, blue-green bacteria or Cyanophyta, is a phylum of Bacteria that obtain their energy [6]
The most common set of catabolic reactions in animals can be separated into three main stages. In the first, large organic molecules such as proteins, polysaccharides or lipids are digested into their smaller components outside cells. Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl Polysaccharides are relatively complex Carbohydrates They are Polymers made up of many Monosaccharides joined together by Glycosidic bonds Lipids are broadly defined as any fat- Soluble ( lipophilic) naturally-occurring Molecule, such as fats oils waxes cholesterol sterols fat-soluble Next, these smaller molecules are taken up by cells and converted to yet smaller molecules, usually acetyl coenzyme A (CoA), which releases some energy. Coenzyme A ( CoA, CoASH, or HSCoA) is a Coenzyme, notable for its role in the synthesis and oxidation of Fatty acids Finally, the acetyl group on the CoA is oxidised to water and carbon dioxide in the citric acid cycle and electron transport chain, releasing the energy that is stored by reducing the coenzyme nicotinamide adenine dinucleotide (NAD+) into NADH. The citric acid cycle, also known as the tricarboxylic acid cycle ( TCA cycle) or the Krebs cycle, (or rarely the Szent-Györgyi–Krebs cycle An electron transport chain couples a chemical reaction between an electron donor (such as NADH) and an electron acceptor (such as O2) to the transfer Nicotinamide adenine dinucleotide, abbreviated NAD+, is a Coenzyme found in all living cells The compound is a dinucleotide since it consists
Digestion
- Further information: Digestion and gastrointestinal tract
Macromolecules such as starch, cellulose or proteins cannot be rapidly taken up by cells and need to be broken into their smaller units before they can be used in cell metabolism. Digestion is the breaking down of chemicals in the body into a form that can be absorbed Several common classes of enzymes digest these polymers. These digestive enzymes include proteases that digest proteins into amino acids, as well as glycoside hydrolases that digest polysaccharides into monosaccharides. A protease is any Enzyme that conducts Proteolysis, that is begins protein Catabolism by Hydrolysis of the Peptide bonds that link Glycoside hydrolases (also called glycosidases) catalyze the Hydrolysis of the Glycosidic linkage to generate two smaller Sugars They
Microbes simply secrete digestive enzymes into their surroundings,[27][28] while animals only secrete these enzymes from specialized cells in their guts. [29] The amino acids or sugars released by these extracellular enzymes are then pumped into cells by specific active transport proteins. Active transport is the mediated process of moving particles across Biological membrane against the concentration gradient [30][31]
Energy from organic compounds
- Further information: Cellular respiration, fermentation, carbohydrate catabolism, fat catabolism and protein catabolism
Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. Cellular respiration is the set of the metabolic reactions and processes that take place in Organisms cells to convert biochemical energy from Fermentation is the process of deriving energy from the oxidation of organic compounds such as carbohydrates using an endogenous electron acceptor which is Carbohydrate catabolism is the breakdown of carbohydrates into smaller units Fatty acids are an important source of Energy for many organisms Protein catabolism is the breakdown of Proteins into Amino acids and simple derivative compounds for transport into the cell through the Plasma membrane Carbohydrates are usually taken into cells once they have been digested into monosaccharides. Monosaccharides (from Greek monos: single sacchar: sugar are the most basic unit of Carbohydrates They consist of one sugar and [32] Once inside, the major route of breakdown is glycolysis, where sugars such as glucose and fructose are converted into pyruvate and some ATP is generated. See also Gluconeogenesis, which carries out a process wherein glucose is synthesized rather than catabolized Glucose (Glc a Monosaccharide (or simple Sugar) also known as grape sugar, is an important Carbohydrate in Biology. Fructose (also levulose or laevulose) is a simple reducing Sugar ( Monosaccharide) found in many foods and is one of the three Pyruvic acid (CH3COCO2H is an alpha-keto acid. The Carboxylate Anion of pyruvic acid is known as pyruvate. [33] Pyruvate is an intermediate in several metabolic pathways, but the majority is converted to acetyl-CoA and fed into the citric acid cycle. Acetyl-CoA is an important molecule in metabolism used in many biochemical reactions The citric acid cycle, also known as the tricarboxylic acid cycle ( TCA cycle) or the Krebs cycle, (or rarely the Szent-Györgyi–Krebs 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. Carbon dioxide ( Chemical formula:) is a Chemical compound composed of two Oxygen Atoms covalently bonded to a single In anaerobic conditions, glycolysis produces lactate, through the enzyme lactate dehydrogenase re-oxidizing NADH to NAD+ for re-use in glycolysis. Lactic acid ( IUPAC Systematic name: 2-hydroxypropanoic acid) also known as milk acid, is a Chemical compound that plays a role Lactate dehydrogenase ( LDH) is an Enzyme ( present in a wide variety of organisms including plants and animals An alternative route for glucose breakdown is the pentose phosphate pathway, which reduces the coenzyme NADPH and produces pentose sugars such as ribose, the sugar component of nucleic acids. The pentose phosphate pathway (also called Phosphogluconate Pathway or HexoseMonophosphate Shunt shunt is a process that serves to generate NADPH and the synthesis of pentose Nicotinamide adenine dinucleotide phosphate ( NADP+, in older notation triphosphopyridine nucleotide TPN) is used in anabolic reactions such as Lipid A pentose is a Monosaccharide with five Carbon Atoms They either have an Aldehyde Functional group in position 1 ( aldopentoses Ribose (ɹˈaɪbəʊs ɹˈaɪbəɹʊs primarily seen as D-ribose, is an Aldopentose — a Monosaccharide containing five Carbon A nucleic acid is a Macromolecule composed of chains of monomeric Nucleotides In Biochemistry these Molecules carry Genetic information
Fats are catabolised by hydrolysis to free fatty acids and glycerol. Hydrolysis 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 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. Beta 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 Fatty acids release more energy upon oxidation than carbohydrates because carbohydrates contain more oxygen in their structures.
Amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and carbon dioxide as a source of energy. In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this Urea is an Organic compound with the Chemical formula ( N[[hydrogen H]]22 C[[oxygen O]] [34] The oxidation pathway starts with the removal of the amino group by a transaminase. In Biochemistry, a transaminase or an aminotransferase is an Enzyme that Catalyzes a type of reaction between an Amino acid and an The amino group is fed into the urea cycle, leaving a deaminated carbon skeleton in the form of a keto acid. The urea cycle (also known as the ornithine cycle) is a cycle of biochemical reactions occurring in many animals that produces Urea ( N[[hydrogen Keto acids are organic Acids containing a Ketone Functional group and a Carboxylic acid group Several of these keto acids are intermediates in the citric acid cycle, for example the deamination of glutamate forms α-ketoglutarate. Glutamic acid (abbreviated as Glu or E) is one of the 20 Alpha Amino acids It is not among the human Essential amino acids Its Alpha-ketoglutaric acid is one of two Ketone derivatives of Glutaric acid. [35] The glucogenic amino acids can also be converted into glucose, through gluconeogenesis (discussed below). A glucogenic amino acid is an Amino acid that can be converted into Glucose through Gluconeogenesis. Gluconeogenesis (abreviated GNG) is a Metabolic pathway that results in the generation of Glucose from non- Carbohydrate carbon substrates such [36]
Energy transformations
Oxidative phosphorylation
- Further information: Oxidative phosphorylation, chemiosmosis and mitochondrion
In oxidative phosphorylation, the electrons removed from food molecules in pathways such as the citric acid cycle are transferred to oxygen and the energy released used to make ATP. Oxidative phosphorylation is a Metabolic pathway that uses energy released by the oxidation of Nutrients to produce Adenosine triphosphate (ATP Chemiosmosis is the diffusion of Ions across a selectively-permeable membrane In Cell biology, a mitochondrion (plural mitochondria) is a membrane-enclosed Organelle found in most eukaryotic cells. This is done in eukaryotes by a series of proteins in the membranes of mitochondria called the electron transport chain. Animals Plants fungi, and Protists are eukaryotes (juːˈkærɪɒt or -oʊt Organisms whose cells are organized into complex An electron transport chain couples a chemical reaction between an electron donor (such as NADH) and an electron acceptor (such as O2) to the transfer In prokaryotes, these proteins are found in the cell's inner membrane. The prokaryotes (proʊˈkærioʊts singular prokaryote /proʊˈkæriət/ are a group of Organisms that lack a Cell nucleus (= karyon or any other Bacteria, despite their apparent simplicity contain a well developed cell structure which is responsible for many of their unique biological properties [37] These proteins use the energy released from passing electrons from reduced molecules like NADH onto oxygen to pump protons across a membrane. A reducing agent (also called a reductant or reducer) is the element or a compound in a Redox (reduction-oxidation reaction (see Electrochemistry Oxygen (from the Greek roots ὀξύς (oxys (acid literally "sharp" from the taste of acids and -γενής (-genēs (producer literally begetteris the The proton ( Greek πρῶτον / proton "first" is a Subatomic particle with an Electric charge of one positive [38]
Pumping protons out of the mitochondria creates a proton concentration difference across the membrane and generates an electrochemical gradient. Diffusion is the net movement of particles (typically molecules from an area of high concentration to an area of low concentration by uncoordinated random movement In Cellular biology, an electrochemical gradient is a spatial variation of both Electrical potential and chemical Concentration across a membrane [39] This force drives protons back into the mitochondrion through the base of an enzyme called ATP synthase. An ATP synthase ( is a general term for an Enzyme that can synthesize Adenosine triphosphate (ATP from Adenosine diphosphate (ADP and inorganic 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. The active site of an Enzyme contains the catalytic and Binding sites. Adenosine diphosphate, abbreviated ADP, is a Nucleotide. It is an Ester of Pyrophosphoric acid with the Nucleoside Adenosine [14]
Energy from inorganic compounds
- Further information: Microbial metabolism and nitrogen cycle
Chemolithotrophy is a type of metabolism found in prokaryotes where energy is obtained from the oxidation of inorganic compounds. Microbial metabolism is the means by which a Microbe obtains the energy and nutrients (e The nitrogen cycle is the Biogeochemical cycle that describes the transformations of Nitrogen and nitrogen-containing compounds in nature A lithotroph is an Organism that uses an Inorganic substrate (usually of mineral origin to obtain reducing equivalents for use in biosynthesis (e The prokaryotes (proʊˈkærioʊts singular prokaryote /proʊˈkæriət/ are a group of Organisms that lack a Cell nucleus (= karyon or any other Traditionally inorganic compounds are considered to be of mineral not biological origin These organisms can use hydrogen,[40] reduced sulfur compounds (such as sulfide, hydrogen sulfide and thiosulfate),[41] ferrous iron (FeII)[42] or ammonia[43] as sources of reducing power and they gain energy from the oxidation of these compounds with electron acceptors such as oxygen or nitrite. Hydrogen (ˈhaɪdrədʒən is the Chemical element with Atomic number 1 Sulfur or sulphur (ˈsʌlfɚ see spelling below) is the Chemical element that has the Atomic number 16 The term sulfide ( sulphide in British English) refers to several types of Chemical compounds containing Sulfur in its lowest Oxidation Hydrogen sulfide (or hydrogen sulphide) is the Chemical compound with the formula H 2 S. Thiosulfate (S2O32&minus is an Oxyanion of Sulfur produced by the reaction of Sulfite ions with elemental sulfur Iron(II oxide, also known as ferrous oxide, iron oxide/oxidized iron or more commonly rusted Ammonia is a compound with the formula N[[hydrogen H3]] It is normally encountered as a Gas with a characteristic pungent Odor Oxygen (from the Greek roots ὀξύς (oxys (acid literally "sharp" from the taste of acids and -γενής (-genēs (producer literally begetteris the The nitrite Ion is NO2− The anion is bent being Isoelectronic with O3. [44] These microbial processes are important in global biogeochemical cycles such as acetogenesis, nitrification and denitrification and are critical for soil fertility. In Ecology and Earth science, a biogeochemical cycle is a circuit or pathway by which a Chemical element or Molecule moves through both biotic Acetogenesis is a process through which Acetate is produced by Anaerobic bacteria from a variety of energy (for example Hydrogen) and carbon (for example Nitrification is the biological oxidation of Ammonia with oxygen into Nitrite followed by the oxidation of these nitrites into Nitrates Degradation Denitrification is a microbially facilitated process of dissimilatory nitrate reduction that may ultimately produce molecular Nitrogen (N2 through a series of intermediate Soil fertility is the characteristic of soil that supports abundant plant life [45][46]
Energy from light
- Further information: Phototroph, photophosphorylation, chloroplast
The energy in sunlight is captured by plants, cyanobacteria, purple bacteria, green sulfur bacteria and some protists. Photoautotrophs or Phototroph ( Gk: photo = light auto = self troph = nourishment are Organisms (commonly plants that carry out Photosynthesis The production of ATP using the energy of sunlight is called photophosphorylation. Chloroplasts are Organelles found in Plant cells and eukaryotic Algae that conduct Photosynthesis. Plants are living Organisms belonging to the kingdom Plantae. Cyanobacteria, also known as blue-green algae, blue-green bacteria or Cyanophyta, is a phylum of Bacteria that obtain their energy Purple bacteria or purple photosynthetic bacteria are Proteobacteria that are Phototrophic i The green sulfur bacteria are a family of obligately anaerobic Photoautotrophic bacteria. Protists (ˈproʊtɨst are a diverse group of eukaryotic Microorganisms Historically protists were treated as the kingdom Protista but this This process is often coupled to the conversion of carbon dioxide into organic compounds, as part of photosynthesis, which is discussed below. The energy capture and carbon fixation systems can however operate separately in prokaryotes, as purple bacteria and green sulfur bacteria can use sunlight as a source of energy, while switching between carbon fixation and the fermentation of organic compounds. [47][48]
The capture of solar energy is a process that is similar in principle to oxidative phosphorylation, as it involves energy being stored as a proton concentration gradient and this proton motive force then driving ATP synthesis. [14] The electrons needed to drive this electron transport chain come from light-gathering proteins called photosynthetic reaction centres. A 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 These structures are classed into two types depending on the type of photosynthetic pigment present, with most photosynthetic bacteria only having one type of reaction center, while plants and cyanobacteria have two. A photosynthetic pigment ( accessory pigment; chloroplast pigment; antenna pigment) is a Pigment that is present in Chloroplasts or [49]
In plants, photosystem II uses light energy to remove electrons from water, releasing oxygen as a waste product. Photosystems (ancient Greek: phos = light and systema = assembly are Protein complexes involved in Photosynthesis. The electrons then flow to the cytochrome b6f complex, which uses their energy to pump protons across the thylakoid membrane in the chloroplast. The cytochrome b 6 f complex (plastoquinol&mdashplastocyanin reductase) of Chloroplasts and Cyanobacteria transfers electrons between the A Thylakoid is a membrane-bound compartment inside Chloroplasts and cyanobacteria. Chloroplasts are Organelles found in Plant cells and eukaryotic Algae that conduct Photosynthesis. [50] These protons move back through the membrane as they drive the ATP synthase, as before. The electrons then flow through photosystem I and can then either be used to reduce the coenzyme NADP+, for use in the Calvin cycle which is discussed below, or recycled for further ATP generation. Photosystems (ancient Greek: phos = light and systema = assembly are Protein complexes involved in Photosynthesis. The Calvin cycle (or Calvin-Benson-Bassham cycle or carbon fixation is a series of biochemical reactions that takes place in the Stroma of Chloroplasts [51]
Anabolism
- Further information: Anabolism
Anabolism is the set of constructive metabolic processes where the energy released by catabolism is used to synthesize complex molecules. Anabolism is the set of Metabolic pathways that construct molecules from smaller units In general, the complex molecules that make up cellular structures are constructed step-by-step from small and simple precursors. Anabolism involves three basic stages. Firstly, the production of precursors such as amino acids, monosaccharides, isoprenoids and nucleotides, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as proteins, polysaccharides, lipids and nucleic acids. In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this Monosaccharides (from Greek monos: single sacchar: sugar are the most basic unit of Carbohydrates They consist of one sugar and The terpenoids, sometimes referred to as isoprenoids, are a large and diverse class of naturally-occurring organic chemicals similar to Terpenes derived Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl Polysaccharides are relatively complex Carbohydrates They are Polymers made up of many Monosaccharides joined together by Glycosidic bonds Lipids are broadly defined as any fat- Soluble ( lipophilic) naturally-occurring Molecule, such as fats oils waxes cholesterol sterols fat-soluble A nucleic acid is a Macromolecule composed of chains of monomeric Nucleotides In Biochemistry these Molecules carry Genetic information
Organisms differ in how many of the molecules in their cells they can construct for themselves. Autotrophs such as plants can construct the complex organic molecules in cells such as polysaccharides and proteins from simple molecules like carbon dioxide and water. An autotroph (from the Greek autos = self and trophe = nutrition is an Organism that produces complex Organic compounds from simple Carbon dioxide ( Chemical formula:) is a Chemical compound composed of two Oxygen Atoms covalently bonded to a single Heterotrophs, on the other hand, require a source of more complex substances, such as monosaccharides and amino acids, to produce these complex molecules. A heterotrophs, or chemoorganotrophy ( Greek heterone = (another and trophe = nutrition is an Organism that requires Organisms can be further classified by ultimate source of their energy: photoautotrophs and photoheterotrophs obtain energy from light, whereas chemoautotrophs and chemoheterotrophs obtain energy from inorganic oxidation reactions.
Carbon fixation
- Further information: Photosynthesis, carbon fixation and chemosynthesis
Photosynthesis is the synthesis of carbohydrates from sunlight, carbon dioxide (CO2) and water, with oxygen produced as a waste product. Carbon dioxide ( Chemical formula:) is a Chemical compound composed of two Oxygen Atoms covalently bonded to a single 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. A 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 This carbon-fixation reaction is carried out by the enzyme RuBisCO as part of the Calvin – Benson cycle. Ribulose-15-bisphosphate carboxylase/oxygenase, most commonly known by the shorter name RuBisCO, is an Enzyme ( that is used in the Calvin cycle The Calvin cycle (or Calvin-Benson-Bassham cycle or carbon fixation is a series of biochemical reactions that takes place in the Stroma of Chloroplasts [52] Three types of photosynthesis occur in plants, C3 carbon fixation, C4 carbon fixation and CAM photosynthesis. carbon fixation is a Metabolic pathway for Carbon fixation in Photosynthesis. C4 carbon fixation is one of three biochemical mechanisms along with C3 and CAM photosynthesis, functioning in land Plants to Crassulacean acid metabolism, also known as CAM photosynthesis, is an elaborate Carbon fixation pathway in some Plants These plants fix carbon dioxide These differ by the route that carbon dioxide takes to the Calvin cycle, with C3 plants fixing CO2 directly, while C4 and CAM photosynthesis incorporate the CO2 into other compounds first, as adaptations to deal with intense sunlight and dry conditions. [53]
In photosynthetic prokaryotes the mechanisms of carbon fixation are more diverse. The prokaryotes (proʊˈkærioʊts singular prokaryote /proʊˈkæriət/ are a group of Organisms that lack a Cell nucleus (= karyon or any other Here, carbon dioxide can be fixed by the Calvin – Benson cycle, a reversed citric acid cycle,[54] or the carboxylation of acetyl-CoA. The reverse Krebs cycle (also known as the reverse tricarboxylic acid cycle, the reverse TCA cycle, or the reverse citric acid cycle) is a sequence of [55][56] Prokaryotic chemoautotrophs also fix CO2 through the Calvin – Benson cycle, but use energy from inorganic compounds to drive the reaction. Chemotrophs are organisms that obtain Energy by the Oxidation of Electron donating Molecules in their environments [57]
Carbohydrates and glycans
- Further information: Gluconeogenesis, glyoxylate cycle, glycogenesis and glycosylation
In carbohydrate anabolism, simple organic acids can be converted into monosaccharides such as glucose and then used to assemble polysaccharides such as starch. Gluconeogenesis (abreviated GNG) is a Metabolic pathway that results in the generation of Glucose from non- Carbohydrate carbon substrates such The glyoxylate cycle is a Metabolic pathway occurring in Plants certain Vertebrates and several Microorganisms such as E Glycogenesis is the process of Glycogen synthesis in which Glucose molecules are added to chains of glycogen Glycosylation is the enzymatic process that links Saccharides to produce glycans, either free or attached to Proteins and Lipids This enzymatic Monosaccharides (from Greek monos: single sacchar: sugar are the most basic unit of Carbohydrates They consist of one sugar and Glucose (Glc a Monosaccharide (or simple Sugar) also known as grape sugar, is an important Carbohydrate in Biology. Polysaccharides are relatively complex Carbohydrates They are Polymers made up of many Monosaccharides joined together by Glycosidic bonds Starch, CAS # 9005-25-8 Chemical formula (C6H10O5n is a Polysaccharide The generation of glucose from compounds like pyruvate, lactate, glycerol, glycerate 3-phosphate and amino acids is called gluconeogenesis. Glucose (Glc a Monosaccharide (or simple Sugar) also known as grape sugar, is an important Carbohydrate in Biology. Pyruvic acid (CH3COCO2H is an alpha-keto acid. The Carboxylate Anion of pyruvic acid is known as pyruvate. Lactic acid ( IUPAC Systematic name: 2-hydroxypropanoic acid) also known as milk acid, is a Chemical compound that plays a role In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this Gluconeogenesis (abreviated GNG) is a Metabolic pathway that results in the generation of Glucose from non- Carbohydrate carbon substrates such Gluconeogenesis converts pyruvate to glucose-6-phosphate through a series of intermediates, many of which are shared with glycolysis. Glucose 6-phosphate (also known as Robison ester) is Glucose sugar Phosphorylated on carbon 6 See also Gluconeogenesis, which carries out a process wherein glucose is synthesized rather than catabolized [33] However, this pathway is not simply glycolysis run in reverse, as several steps are catalyzed by non-glycolytic enzymes. See also Gluconeogenesis, which carries out a process wherein glucose is synthesized rather than catabolized 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. A Futile cycle is when two Metabolic pathways run simultaneously in opposite directions and have no overall effect other than wasting energy [58][59]
Although fat is a common way of storing energy, in vertebrates such as humans the fatty acids in these stores cannot be converted to glucose through gluconeogenesis as these organisms cannot convert acetyl-CoA into pyruvate; plants do, but animals do not, have the necessary enzymatic machinery. Vertebrates are members of the Subphylum Vertebrata, Chordates with backbones or spinal columns The grouping sometimes includes Human beings, humans or man (Origin 1590–1600 L homō man OL hemō the earthly one (see Humus In Chemistry, especially Biochemistry, a fatty acid is a Carboxylic acid often with a long unbranched Aliphatic tail ( chain) which Gluconeogenesis (abreviated GNG) is a Metabolic pathway that results in the generation of Glucose from non- Carbohydrate carbon substrates such Pyruvic acid (CH3COCO2H is an alpha-keto acid. The Carboxylate Anion of pyruvic acid is known as pyruvate. [60] As a result, after long-term starvation, vertebrates need to produce ketone bodies from fatty acids to replace glucose in tissues such as the brain that cannot metabolize fatty acids. Ketone bodies are three water-soluble compounds that are produced as by-products when Fatty acids are broken down for energy in the Liver and [61] 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. The glyoxylate cycle is a Metabolic pathway occurring in Plants certain Vertebrates and several Microorganisms such as E Decarboxylation is any Chemical reaction in which a Carboxyl group (-COOH is split off from a compound as Carbon dioxide (CO2 Oxaloacetic acid is an Organic compound with the chemical formula HO2CC(OCH2CO2H [62][60]
Polysaccharides and glycans are made by the sequential addition of monosaccharides by glycosyltransferase from a reactive sugar-phosphate donor such as uridine diphosphate glucose (UDP-glucose) to an acceptor hydroxyl group on the growing polysaccharide. The term glycan refers to a Polysaccharide or Oligosaccharide. Glycosyltransferases are Enzymes ( EC 24) that act as a Catalyst for the transfer of a Monosaccharide unit from an activated sugar Phosphate Uridine diphosphate glucose ( uracil-diphosphate glucose, UDP-glucose) is a Nucleotide sugar. Hydroxyl in Chemistry stands for a molecule consisting of an Oxygen atom and a Hydrogen atom connected by a Covalent bond. As any of the hydroxyl groups on the ring of the substrate can be acceptors, the polysaccharides produced can have straight or branched structures. Hydroxyl in Chemistry stands for a molecule consisting of an Oxygen atom and a Hydrogen atom connected by a Covalent bond. [63] The polysaccharides produced can have structural or metabolic functions themselves, or be transferred to lipids and proteins by enzymes called oligosaccharyltransferases. Oligosaccharyltransferase or OST ( is a Membrane protein complex that transfers a 14- Sugar Oligosaccharide from Dolichol [64][65]
Fatty acids, isoprenoids and steroids
- Further information: Fatty acid synthesis, steroid metabolism
Fatty acids are made by fatty acid synthases that polymerize and then reduce acetyl-CoA units. Fatty acid synthase (FAS is Enzymatic system composed of 272 kDa multifunctional Polypeptide, in which Substrates are handed from one functional domain The acyl chains in the fatty acids are extended by a cycle of reactions that add the actyl group, reduce it to an alcohol, dehydrate it to an alkene group and then reduce it again to an alkane group. In Chemistry, a dehydration reaction is usually defined as a chemical reaction that involves the loss of water from the reacting molecule In Organic chemistry, an alkene, olefin, or olefine is an unsaturated Chemical compound containing at least one Carbon Alkanes, also known as Paraffins are Chemical compounds that consist only of the elements Carbon (C and Hydrogen (H (i 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,[66] while in plant plastids and bacteria separate type II enzymes perform each step in the pathway. Plastids are major Organelles found in plants and algae Plastids often contain pigments used in photosynthesis and the types of pigments present can change [67][68]
Terpenes and isoprenoids are a large class of lipids that include the carotenoids and form the largest class of plant natural products. Terpenes are a large and varied class of Hydrocarbons, produced primarily by a wide variety of plants particularly Conifers though also by some insects such The terpenoids, sometimes referred to as isoprenoids, are a large and diverse class of naturally-occurring organic chemicals similar to Terpenes derived Carotenoids are organic Pigments that are naturally occurring in Chromoplasts of plants and some other photosynthetic Organisms A 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 [69] These compounds are made by the assembly and modification of isoprene units donated from the reactive precursors isopentenyl pyrophosphate and dimethylallyl pyrophosphate. Isoprene is a common synonym for the chemical compound 2-methylbuta-13-diene Isopentenyl pyrophosphate (IPP is an intermediate in the classical HMG-CoA reductase pathway used by organisms in the biosynthesis of Terpenes and Terpenoids Dimethylallyl pyrophosphate (or -diphosphate (DMAPP is an intermediate product of both Mevalonic acid (MVA pathway and DOXP/ MEP pathway [70] These precursors can be made in different ways. In animals and archaea, the mevalonate pathway produces these compounds from acetyl-CoA,[71] while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates. The mevalonate pathway or HMG-CoA reductase pathway or mevalonate-dependent (MAD route, is an important cellular Metabolic pathway present The non-mevalonate pathway or 2- C -methyl-D-erythritol 4-phosphate/1-deoxy-D-xylulose 5-phosphate pathway ( MEP/DOXP pathway) of isoprenoid biosynthesis is an alternative Glyceraldehyde 3-phosphate, also known as triose phosphate or 3-phosphoglyceraldehyde and abbreviated as G3P, GADP, GAP or PGAL [72][70] One important reaction that uses these activated isoprene donors is steroid biosynthesis. Steroid metabolism is the complete set of Chemical reactions in organisms that produce modify and consume Steroids These Metabolic pathways include Here, the isoprene units are joined together to make squalene and then folded up and formed into a set of rings to make lanosterol. Squalene is a natural Organic compound originally obtained for commercial purposes primarily from Shark liver oil, though there are botanic sources as well including Lanosterol is a tetracyclic triterpenoid, which is the compound from which all Steroids are derived [73] Lanosterol can then be converted into other steroids such as cholesterol and ergosterol. Cholesterol is a Lipid found in the Cell membranes and transported in the Blood plasma of all Animals It is an essential component of mammalian Ergosterol (ergosta-5722-trien-3β-ol a Sterol, is a biological precursor (a Provitamin) to Vitamin D2. [74][73]
Proteins
- Further information: Protein biosynthesis, amino acid synthesis
Organisms vary in their ability to synthesize the 20 common amino acids. Protein biosynthesis (synthesis is the process in which cells build Proteins The term is sometimes used to refer only to protein translation but more For the non-biological synthesis of amino acids see Strecker amino acid synthesis Amino acid synthesis is the set of Biochemical processes ( Metabolic Most bacteria and plants can synthesize all twenty, but mammals can synthesize only the ten nonessential amino acids. [6] Thus, the essential amino acids must be obtained from food. An essential amino acid or indispensable amino acid is an Amino acid that cannot be synthesized de novo by the organism (usually referring to 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. Glutamic acid (abbreviated as Glu or E) is one of the 20 Alpha Amino acids It is not among the human Essential amino acids Its Glutamine (abbreviated as Gln or Q; the abbreviation Glx or Z represents either glutamate or Glutamic acid) is one of the 20 Amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then transaminated to form an amino acid. In Biochemistry, a transaminase or an aminotransferase is an Enzyme that Catalyzes a type of reaction between an Amino acid and an [75]
Amino acids are made into proteins by being joined together in a chain by peptide bonds. A peptide bond is a Chemical bond formed between two Molecules when the Carboxyl group of one molecule reacts with the Each different protein has a unique sequence of amino acid residues: this is its primary structure. In Biochemistry, the primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a transfer RNA molecule through an ester bond. Transfer RNA (abbreviated tRNA) is a small RNA (usually about 74-95 nucleotides that transfers a specific Amino acid to a growing polypeptide chain at Esters are a class of Chemical compounds and Functional groups Esters consist of an inorganic or organic Acid in which at least This aminoacyl-tRNA precursor is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase. Adenosine-5'-triphosphate ( ATP) is a multifunctional Nucleotide that is most important as a " molecular currency" of intracellular Energy An aminoacyl tRNA synthetase ( aaRS) is an Enzyme that catalyzes the Esterification of a specific Amino acid or its precursor to one of all its compatible [76] 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. Ribosomes ( from ribo nucleic acid and "Greek soma ( meaning body") are complexes of RNA and Protein that Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product [77]
Nucleotide synthesis and salvage
- Further information: Nucleotide salvage, pyrimidine biosynthesis, and purine metabolism
Nucleotides are made from amino acids, carbon dioxide and formic acid in pathways that require large amounts of metabolic energy. A salvage pathway is a pathway in which Nucleotides ( Purine and Pyrimidine) are synthesized from intermediates in the degradative pathway for Pyrimidine biosynthesis occurs both in the body and through organic synthesis Purine ( 1) is a heterocyclic Aromatic Organic compound, consisting of a Pyrimidine ring fused to an Imidazole ring Formic acid (systematically called methanoic acid) is the simplest Carboxylic acid. [78] Consequently, most organisms have efficient systems to salvage preformed nucleotides. [78][79] Purines are synthesized as nucleosides (bases attached to ribose). Purine ( 1) is a heterocyclic Aromatic Organic compound, consisting of a Pyrimidine ring fused to an Imidazole ring See also Adenosine triphosphate (ATP Ribose (ɹˈaɪbəʊs ɹˈaɪbəɹʊs primarily seen as D-ribose, is an Aldopentose — a Monosaccharide containing five Carbon Both adenine and guanine are made from the precursor nucleoside inosine monophosphate, which is synthesized using atoms from the amino acids glycine, glutamine, and aspartic acid, as well as formate transferred from the coenzyme tetrahydrofolate. Adenine is a Purine with a variety of roles in Biochemistry including Cellular respiration, in the form of both the energy-rich Adenosine Guanine is one of the five main Nucleobases found in the Nucleic acids DNA and RNA, the others being Adenine, Cytosine, Inosine is a Nucleoside that is formed when Hypoxanthine is attached to a Ribose ring (also known as a Ribofuranose) via a β-N9- Glycine (abbreviated as Gly or G) is the Organic compound with the formula NH2CH2COOH Glutamine (abbreviated as Gln or Q; the abbreviation Glx or Z represents either glutamate or Glutamic acid) is one of the 20 Aspartic acid (abbreviated as Asp or D; Asx or B represent either aspartic acid or Asparagine) is an α- Amino acid Formate or methanoate is the ion CHOO&minus ( Formic acid minus one Hydrogen ion) Coenzymes are small organic non- Protein Molecules that carry chemical groups between Enzymes Coenzymes are sometimes referred to as cosubstrates Folic acid (also known as Vitamin M and Folacin) and Folate (the Anionic form are forms of the water-soluble Vitamin B9 Pyrimidines, on the other hand, are synthesized from the base orotate, which is formed from glutamine and aspartate. Pyrimidine is a Heterocyclic Aromatic Organic compound similar to Benzene and Pyridine, containing two Nitrogen Atoms Orotic acid is a Heterocyclic compound and an Acid; it is also known as pyrimidinecarboxylic acid. [80]
Xenobiotics and redox metabolism
- Further information: Xenobiotic metabolism, drug metabolism and antioxidants
All organisms are constantly exposed to compounds that they cannot use as foods and would be harmful if they accumulated in cells, as they have no metabolic function. Xenobiotic metabolism is the set of Metabolic pathways that modify the chemical structure of Xenobiotics which are compounds foreign to an organism's normal biochemistry Drug metabolism is the Metabolism of drugs, their Biochemical modification or degradation usually through specialized enzymatic systems An antioxidant is a Molecule capable of slowing or preventing the oxidation of other molecules These potentially damaging compounds are called xenobiotics. A xenobiotic is a Chemical which is found in an Organism but which is not normally produced or expected to be present in it [81] Xenobiotics such as synthetic drugs, natural poisons and antibiotics are detoxified by a set of xenobiotic-metabolizing enzymes. A drug, broadly speaking is any chemical substance that when absorbed into the body In the context of Biology, poisons are substances that can cause damage, Illness, or Death to Organisms usually by In modern usage an antibiotic is a Chemotherapeutic agent with activity against Microorganisms such as Bacteria, fungi or Protozoa In humans, these include cytochrome P450 oxidases,[82] UDP-glucuronosyltransferasess,[83] and glutathione S-transferases. Cytochrome P450 (abbreviated CYP, P450, infrequently CYP450) is a very large and diverse superfamily of Hemoproteins found in all Domains Uridine 5'-diphospho-glucuronosyltransferase ( UDP -glucuronosyltransferase UGT is a Glycosyltransferase ( that catalyzes the Glucuronidation The glutathione S -transferase (GST family of Enzymes comprises a long list of Cytosolic, Mitochondrial, and Microsomal [84] 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. Ecology (from Greek grc οἶκος oikos, "house(hold" and grc -λογία -logia) is the scientific study of Biodegradation is the process by which organic substances are broken down by the enzymes produced by living organisms Bioremediation can be defined as any process that uses Microorganisms Fungi, green plants or their Enzymes to return the natural environment altered [85] 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. Persistent organic pollutants ( POP s are organic compounds that are resistant to environmental degradation through chemical, biological, and photolytic Applications The simplest form of organochlorides are chlorinated Hydrocarbons These consist of simple Hydrocarbons in which one or more hydrogen atoms have [86]
A related problem for aerobic organisms is oxidative stress. An aerobic organism or aerobe is an Organism that has an Oxygen based Metabolism. Oxidative 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 [87] Here, processes including oxidative phosphorylation and the formation of disulfide bonds during protein folding produce reactive oxygen species such as hydrogen peroxide. Oxidative phosphorylation is a Metabolic pathway that uses energy released by the oxidation of Nutrients to produce Adenosine triphosphate (ATP In Chemistry, a disulfide bond is a single Covalent bond derived from the coupling of Thiol groups Protein folding is the physical process by which a Polypeptide folds into its characteristic and functional three-dimensional structure. Reactive oxygen species (ROS are ions or very small molecules that include Oxygen Ions free radicals, and Peroxides both inorganic and Hydrogen peroxide (H2O2 is a very pale blue liquid which appears colorless in a dilute solution slightly more Viscous than water [88] These damaging oxidants are removed by antioxidant metabolites such as glutathione and enzymes such as catalases and peroxidases. An antioxidant is a Molecule capable of slowing or preventing the oxidation of other molecules Glutathione ( GSH) is a Tripeptide. It contains an unusual Peptide linkage between the amine group of Cysteine and the Carboxyl Catalase is a common Enzyme found in nearly all living organisms where it functions to catalyze the decomposition of Hydrogen peroxide to Peroxidases ( EC number 1111x are a large family of Enzymes A majority of peroxidase protein sequences can be found in the PeroxiBase database [89][90]
Thermodynamics of living organisms
- Further information: Biological thermodynamics
Living organisms must obey the laws of thermodynamics, which describe the transfer of heat and work. Biological thermodynamics is a phrase that is sometimes used to refer to Bioenergetics, the study of Energy transformation in the Biological sciences Biological The laws of thermodynamics, in principle describe the specifics for the transport of Heat and work in Thermodynamic processes. In Physics, heat, symbolized by Q, is Energy transferred from one body or system to another due to a difference in Temperature In Thermodynamics, work is the quantity of Energy transferred from one system to another without an accompanying transfer of Entropy. The second law of thermodynamics states that in any closed system, the amount of entropy (disorder) will tend to increase. The second law of Thermodynamics is an expression of the universal law of increasing Entropy, stating that the entropy of an Isolated system which A Closed system is a System in the state of being isolated from the environment In Thermodynamics (a branch of Physics) entropy, symbolized by S, is a measure of the unavailability of a system ’s Energy 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. An open system is a state of a System, in which a system continuously interacts with its environment Thus living systems are not in equilibrium, but instead are dissipative systems that maintain their state of high complexity by causing a larger increase in the entropy of their environments. In Thermodynamics, a thermodynamic system is said to be in thermodynamic equilibrium when it is in thermal equilibrium Mechanical equilibrium, and Another meaning of "dissipative system" is one that dissipates heat see heat dissipation. [91] The metabolism of a cell achieves this by coupling the spontaneous processes of catabolism to the non-spontaneous processes of anabolism. A spontaneous process is the time-evolution of a system in which it releases free energy (most often as heat and moves to a lower more thermodynamically stable energy state In thermodynamic terms, metabolism maintains order by creating disorder. Non-equilibrium thermodynamics is a branch of Thermodynamics concerned with studying Time -dependent Thermodynamic systems irreversible transformations [92]
Regulation and control
- Further information: Metabolic pathway, metabolic control analysis, hormone, regulatory enzymes, and cell signaling
As the environments of most organisms are constantly changing, the reactions of metabolism must be finely regulated to maintain a constant set of conditions within cells, a condition called homeostasis. In Biochemistry, a metabolic pathway is a series of chemical reactions occurring within a cell. Metabolic control analysis (MCA is a mathematical framework for describing metabolic, signaling and genetic pathways. Hormones (from Greek ὁρμή - "impetus" are chemicals released by cells that affect cells in other parts of the body A regulatory enzyme is an Enzyme in a Biochemical pathway which through its responses to the presence of certain other Biomolecules, regulates Cell signaling is part of a Complex system of Communication that governs basic cellular activities and coordinates cell actions Control theory is an interdisciplinary branch of Engineering and Mathematics, that deals with the behavior of Dynamical systems The desired output Homeostasis (from Greek: ὅμος hómos, "equal" and ιστημι istēmi, "to stand" lit [93][94] Metabolic regulation also allows organisms to respond to signals and interact actively with their environments. [95] Two closely-linked concepts are important for understanding how metabolic pathways are controlled. Firstly, the regulation of an enzyme in a pathway is how its activity is increased and decreased in response to signals. Secondly, the control exerted by this enzyme is the effect that these changes in its activity have on the overall rate of the pathway (the flux through the pathway). In the various subfields of Physics, there exist two common usages of the term flux, both with rigorous mathematical frameworks [96] For example, an enzyme may show large changes in activity (i. e. it is highly regulated) but if these changes have little effect on the flux of a metabolic pathway, then this enzyme is not involved in the control of the pathway. [97]
There are multiple levels of metabolic regulation. In intrinsic regulation, the metabolic pathway self-regulates to respond to changes in the levels of substrates or products; for example, a decrease in the amount of product can increase the flux through the pathway to compensate. In the various subfields of Physics, there exist two common usages of the term flux, both with rigorous mathematical frameworks [96] This type of regulation often involves allosteric regulation of the activities of multiple enzymes in the pathway. In Biochemistry, allosteric regulation is the regulation of an Enzyme or other Protein by binding an effector molecule at the protein's allosteric [98] Extrinsic control involves a cell in a multicellular organism changing its metabolism in response to signals from other cells. These signals are usually in the form of soluble messengers such as hormones and growth factors and are detected by specific receptors on the cell surface. Hormones (from Greek ὁρμή - "impetus" are chemicals released by cells that affect cells in other parts of the body The term growth factor refers to a naturally occurring Protein capable of stimulating cellular growth proliferation and Cellular differentiation. In Biochemistry, a receptor is a Protein molecule embedded in either the Plasma membrane or Cytoplasm of a cell to which a mobile signaling [99] These signals are then transmitted inside the cell by second messenger systems that often involved the phosphorylation of proteins. In Cell physiology, a secondary messenger system (also known as a second messenger system) is a method of cellular signaling whereby a diffusable signaling molecule Phosphorylation is the addition of a Phosphate (PO4 group to a Protein molecule or a small molecule [100]
A very well understood example of extrinsic control is the regulation of glucose metabolism by the hormone insulin. Insulin is a Hormone with intensive effects on both metabolism and several other body systems (eg vascular compliance [101] Insulin is produced in response to rises in blood glucose levels. Blood sugar, used in a physiological context is a misnomer and misleading 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. In Molecular biology, the insulin receptor is a transmembrane receptor that is activated by Insulin. A protein kinase is a Kinase Enzyme that modifies other Proteins by chemically adding Phosphate groups to them ( Phosphorylation) Glycogen is a Polysaccharide of Glucose (Glc which functions as the secondary short term energy storage in Animal cells [102] The metabolism of glycogen is controlled by activity of phosphorylase, the enzyme that breaks down glycogen, and glycogen synthase, the enzyme that makes it. Phosphorylase is a family of allosteric Enzymes that catalyze the production of Glucose-1-phosphate from a polyglucose such as Glycogen Glycogen synthase ( UDP-glucose-glycogen glucosyltransferase') is a Glycosyltransferase Enzyme ( EC number 2 These enzymes are regulated in a reciprocal fashion, with phosphorylation inhibiting glycogen synthase, but activating phosphorylase. Insulin causes glycogen synthesis by activating protein phosphatases and producing a decrease in the phosphorylation of these enzymes. A phosphatase is an Enzyme that removes a Phosphate group from its Substrate by hydrolysing Phosphoric acid mono Esters into [103]
Evolution
- Further information: Molecular evolution and phylogenetics
The central pathways of metabolism described above, such as glycolysis and the citric acid cycle, are present in all three domains of living things and were present in the last universal ancestor. The three-domain system is a Biological classification introduced by Carl Woese in 1990 that divides cellular life forms into Archaea, The last universal ancestor ( LUA) also called the last universal common ancestor ( LUCA) the cenancestor or "number one" [104][2] This universal ancestral cell was prokaryotic and probably a methanogen that had extensive amino acid, nucleotide, carbohydrate and lipid metabolism. The prokaryotes (proʊˈkærioʊts singular prokaryote /proʊˈkæriət/ are a group of Organisms that lack a Cell nucleus (= karyon or any other Methanogens are Archaea that produce Methane as a Metabolic byproduct in Anoxic conditions [105][106] The retention of these ancient pathways during later evolution may be the result of these reactions being an optimal solution to their particular metabolic problems, with pathways such as glycolysis and the citric acid cycle producing their end products highly efficiently and in a minimal number of steps. eVolution is the third Album by eLDee, it was due to be released in 2008 [3][4] The first pathways of enzyme-based metabolism may have been parts of purine nucleotide metabolism, with previous metabolic pathways being part of the ancient RNA world. Purine ( 1) is a heterocyclic Aromatic Organic compound, consisting of a Pyrimidine ring fused to an Imidazole ring The RNA world hypothesis proposes that a world filled with life based on Ribonucleic acid (RNA predated current life based on Deoxyribonucleic acid (DNA [107]
Many models have been proposed to describe the mechanisms by which novel metabolic pathways evolve. These include the sequential addition of novel enzymes to a short ancestral pathway, the duplication and then divergence of entire pathways as well as the recruitment of pre-existing enzymes and their assembly into a novel reaction pathway. [108] The relative importance of these mechanisms is unclear, but genomic studies have shown that enzymes in a pathway are likely to have a shared ancestry, suggesting that many pathways have evolved in a step-by-step fashion with novel functions being created from pre-existing steps in the pathway. [109] An alternative model comes from studies that trace the evolution of proteins' structures in metabolic networks, this has suggested that enzymes are pervasively recruited, borrowing enzymes to perform similar functions in different metabolic pathways (evident in the MANET database)[110] These recruitment processes result in an evolutionary enzymatic mosaic. The Molecular Ancestry Network (MANET database is a Bioinformatics Database that maps evolutionary relationships of protein architectures directly onto biological [111] A third possibility is that some parts of metabolism might exist as "modules" that can be reused in different pathways and perform similar functions on different molecules. [112]
As well as the evolution of new metabolic pathways, evolution can also cause the loss of metabolic functions. For example, in some parasites metabolic processes that are not essential for survival are lost and preformed amino acids, nucleotides and carbohydrates may instead be scavenged from the host. Parasitism is a type of symbiotic relationship between Organisms of different Species. In Biology, a host is an organism that harbors a Virus or Parasite, or a mutual or Commensal Symbiont, typically providing nourishment [113] Similar reduced metabolic capabilities are seen in endosymbiotic organisms. An endosymbiont is any Organism that lives within the body or cells of another organism i [114]
Investigation and manipulation
- Further information: Protein methods, proteomics, metabolomics and metabolic network modelling
Classically, metabolism is studied by a reductionist approach that focuses on a single metabolic pathway. Reductionism can either mean (a an approach to understanding the nature of complex things by reducing them to the interactions of their parts or to simpler or more fundamental things 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. A radioactive tracer, also called a radioactive label, is a substance containing a Radioisotope (which is an isotope that has an unstable nucleus and that stabalizes [115] The enzymes that catalyze these chemical reactions can then be purified and their kinetics and responses to inhibitors investigated. Protein purification is a series of processes intended to isolate a single type of Protein from a complex mixture Enzyme kinetics is the study of the Chemical reactions that are catalysed by Enzymes, with a focus on their Reaction rates The study of Enzyme inhibitors are Molecules that bind to Enzymes and decrease their activity. A parallel approach is to identify the small molecules in a cell or tissue; the complete set of these molecules is called the metabolome. Metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind" - specifically the study of their small-molecule metabolite Overall, these studies give a good view of the structure and function of simple metabolic pathways, but are inadequate when applied to more complex systems such as the metabolism of a complete cell. [116]
An idea of the complexity of the metabolic networks in cells that contain thousands of different enzymes is given by the figure showing the interactions between just 43 proteins and 40 metabolites to the right: the sequences of genomes provide lists containing anything up to 45,000 genes. A metabolic network is the complete set of metabolic and physical processes that determine the physiological and biochemical properties of a cell [117] However, it is now possible to use this genomic data to reconstruct complete networks of biochemical reactions and produce more holistic mathematical models that may explain and predict their behavior. Distinguish from the suffix -holism, which describes addictions [118] These models are especially powerful when used to integrate the pathway and metabolite data obtained through classical methods with data on gene expression from proteomic and DNA microarray studies. Gene expression is the process by which inheritable information from a Gene, such as the DNA sequence, is made into a functional Gene product, such Proteomics is the large-scale study of Proteins particularly their structures and functions. For terminology see glossary below A DNA microarray is a High-throughput technology used in Molecular biology and in [119] Using these techniques, a model of human metabolism has now been produced, which will guide future drug discovery and biochemical research. [120]
A major technological application of this information is metabolic engineering. Metabolic engineering is the practice of optimizing genetic and regulatory processes within cells to increase the cells' production of a certain substance Here, organisms such as yeast, plants or bacteria are genetically-modified to make them more useful in biotechnology and aid the production of drugs such as antibiotics or industrial chemicals such as 1,3-propanediol and shikimic acid. Yeasts are a growth form of eukaryotic Microorganisms classified in the kingdom Fungi, with about 1500 Species currently described Plants are living Organisms belonging to the kingdom Plantae. The Bacteria ( singular: bacterium) are a large group of unicellular Microorganisms Typically a few Micrometres in length bacteria have Biotechnology is Technology based on Biology, especially when used in Agriculture, Food science, and Medicine. A drug, broadly speaking is any chemical substance that when absorbed into the body In modern usage an antibiotic is a Chemotherapeutic agent with activity against Microorganisms such as Bacteria, fungi or Protozoa Shikimic acid, more commonly known as its anionic form shikimate, is an important biochemical Intermediate in plants and microorganisms [121] These genetic modifications usually aim to reduce the amount of energy used to produce the product, increase yields and reduce the production of wastes. [122]
History
- Further information: History of biochemistry and history of molecular biology
The term metabolism is derived from the Greek Μεταβολισμός – "Metabolismos" for "change", or "overthrow". The history of biochemistry spans approximately 400 years Although the term “biochemistry” seems to have been first used in 1882 it is generally accepted that the word "biochemistry" The history of molecular biology begins in the 1930s with the convergence of various previously distinct biological disciplines Biochemistry, Genetics, Microbiology Santorio Santorio ( March 29 1561 Koper &ndash February 22 1636 Venice) also called Santorio Santorii, Greek (el ελληνική γλώσσα or simply el ελληνικά — "Hellenic" is an Indo-European language, spoken today by 15-22 million people mainly [123] The history of the scientific study of metabolism spans several centuries and has moved from examining whole animals in early studies, to examining individual metabolic reactions in modern biochemistry. The concept of metabolism dates back to Ibn al-Nafis (1213-1288), who stated that "the body and its parts are in a continuous state of dissolution and nourishment, so they are inevitably undergoing permanent change. TemplateInfobox Muslim scholars --> Ala al-Din Abu al-Hassan Ali ibn Abi-Hazm al-Qarshi al-Dimashqi ( Nutrition (also called nourishment or aliment) is the provision to cells and Organisms of the materials necessary (in the form of food to support "[124] The first controlled experiments in human metabolism were published by Santorio Santorio in 1614 in his book Ars de statica medecina. In scientific inquiry an experiment ( Latin: Ex- periri, "to try out" is a method of investigating particular types of research questions or Santorio Santorio ( March 29 1561 Koper &ndash February 22 1636 Venice) also called Santorio Santorii, [125] He described how he weighed himself before and after eating, sleeping, working, sex, fasting, drinking, and excreting. He found that most of the food he took in was lost through what he called "insensible perspiration".
In these early studies, the mechanisms of these metabolic processes had not been identified and a vital force was thought to animate living tissue. Vitalism, 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 physicochemical [126] In the 19th century, when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur concluded that fermentation was catalyzed by substances within the yeast cells he called "ferments". Fermentation in Food processing typically refers to the conversion of Sugar to Alcohol using Yeast under Anaerobic conditions In Chemistry, an alcohol is any Organic compound in which a Hydroxyl group ( - O[[hydrogen H]]) is bound to a Carbon Yeasts are a growth form of eukaryotic Microorganisms classified in the kingdom Fungi, with about 1500 Species currently described Louis Pasteur (27 December 1822 – 28 September 1895 a French Chemist and Microbiologist, is best known for remarkable breakthroughs in the causes and 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. "[127] This discovery, along with the publication by Friedrich Wöhler in 1828 of the chemical synthesis of urea,[128] proved that the organic compounds and chemical reactions found in cells were no different in principle than any other part of chemistry. Friedrich Wöhler (31 July 1800 - 23 September 1882 was a German Chemist, best-known for his synthesis of Urea, but also the first to isolate several Urea is an Organic compound with the Chemical formula ( N[[hydrogen H]]22 C[[oxygen O]]
It was the discovery of enzymes 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. Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins Eduard Buchner (May 20 1860 &ndash August 13 1917 was a German chemist and zymologist, the winner of the 1907 Nobel Prize in Chemistry Biochemistry is the study of the chemical processes in living Organisms It deals with the Structure and function of cellular components such as [129] The mass of biochemical knowledge grew rapidly throughout the early 20th century. One of the most prolific of these modern biochemists was Hans Krebs who made huge contributions to the study of metabolism. Hans Adolf Krebs ( August 25, 1900 – November 22, 1981) was a German, later British Medical doctor and [130] He discovered the urea cycle and later, working with Hans Kornberg, the citric acid cycle and the glyoxylate cycle. Professor Sir Hans Leo Kornberg, FRS (born 14 January 1928) is a British Biochemist. [131][62] Modern biochemical research has been greatly aided by the development of new techniques such as chromatography, X-ray diffraction, NMR spectroscopy, radioisotopic labelling, electron microscopy and molecular dynamics simulations. Chromatography (from Greek χρώμα chroma, color and γραφειν"graphein" to write is the collective term for a family of Laboratory X-ray scattering techniques are a family of non-destructive analytical techniques which reveal information about the crystallographic structure chemical composition Protein nuclear magnetic resonance spectroscopy (usually abbreviated protein NMR) is a field of Structural biology in which NMR spectroscopy is used Isotopic labeling is a technique for tracking the passage of a sample of substance through a system An electron microscope is a type of Microscope that uses Electrons to illuminate a specimen and create an enlarged image Molecular dynamics ( MD) is a form of Computer simulation in which atoms and molecules are allowed to interact for a period of time by approximations of These techniques have allowed the discovery and detailed analysis of the many molecules and metabolic pathways in cells.
See also
- Anthropogenic metabolism
- Basal metabolic rate
- Calorimetry
- Inborn error of metabolism
- Individual growth
- Iron-sulfur world theory, a "metabolism first" theory of the origin of life. Anthropogenic metabolism is a term used in Material flow analysis, Substance flow analysis and Waste management. Basal metabolic rate ( BMR) is the amount of energy expended while at rest in a neutrally temperate environment in the post-absorptive state (meaning that the digestive system Calorimetry is the Science of measuring the Heat of Chemical Inborn errors of metabolism comprise a large class of genetic Diseases involving disorders of Metabolism. The iron-sulfur world theory is a hypothesis for the Origin of life advanced by Günter Wächtershäuser, a Munich chemist and patent lawyer involving In the Natural sciences, Abiogenesis, or origin of life, is the study of how Life on Earth emerged from Inanimate Organic
- Respirometry
- Thermic effect of food
- Water metabolism
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Further reading
Introductory
- Rose, S. and Mileusnic, R. , The Chemistry of Life. (Penguin Press Science, 1999), ISBN 0-14027-273-9
- Schneider, E. D. and Sagan, D. , Into the Cool: Energy Flow, Thermodynamics, and Life. (University Of Chicago Press, 2005), ISBN 0-22673-936-8
- Lane, N. , Oxygen: The Molecule that Made the World. (Oxford University Press, USA, 2004), ISBN 0-19860-783-0
Advanced
- Price, N. and Stevens, L. , Fundamentals of Enzymology: Cell and Molecular Biology of Catalytic Proteins. (Oxford University Press, 1999), ISBN 0-19850-229-X
- Berg, J. Tymoczko, J. and Stryer, L. , Biochemistry. (W. H. Freeman and Company, 2002), ISBN 0-71674-955-6
- Cox, M. and Nelson, D. L. , Lehninger Principles of Biochemistry. (Palgrave Macmillan, 2004), ISBN 0-71674-339-6
- Brock, T. D. Madigan, M. T. Martinko, J. and Parker J. , Brock's Biology of Microorganisms. (Benjamin Cummings, 2002), ISBN 0-13066-271-2
- Da Silva, J. J. R. F. and Williams, R. J. P. , The Biological Chemistry of the Elements: The Inorganic Chemistry of Life. (Clarendon Press, 1991), ISBN 0-19855-598-9
- Nicholls, D. G. and Ferguson, S. J. , Bioenergetics. (Academic Press Inc. , 2002), ISBN 0-12518-121-3
External links
- Metabolism, Cellular Respiration and Photosynthesis The Virtual Library of Biochemistry and Cell Biology at biochemweb. org
- The Biochemistry of Metabolism
- Advanced Animal Metabolism Calculators/ Interactive Learning Tools
- Microbial metabolism Simple overview. School level.
- Metabolic Pathways of Biochemistry Graphical representations of major metabolic pathways.
- Chemistry for biologists Introduction to the chemistry of metabolism. School level.
- Sparknotes SAT biochemistry Overview of biochemistry. School level.
- MIT Biology Hypertextbook Undergraduate-level guide to molecular biology.
- Article on metabolism at The Encyclopœdia Britannica Concentrates on human metabolism (Free access).
- Topics in Medical Biochemistry Guide to human metabolic pathways. School level.
- THE Medical Biochemistry Page Comprehensive resource on human metabolism.
- The BioCyc Collection of Pathway/Genome Databases
- Flow Chart of Metabolic Pathways at ExPASy
- The KEGG PATHWAY Database
- IUBMB-Nicholson Metabolic Pathways Chart
- Reactome - a knowledgebase of biological processes
- Interactive Flow Chart of the Major Metabolic Pathways
- Guide to Glycolysis School level. The ExPASy ( E xpert P rotein A nalysis Sy stem is a Proteomics server of the Swiss Institute of Bioinformatics (SIB which
- The Nitrogen cycle and Nitrogen fixation at the Internet Archive Wayback Machine
- Downloadable guide to photosynthesis School level. The Internet Archive ( IA) is a Nonprofit organization dedicated to maintaining an on-line Library and archive of Web and
- What is Photosynthesis? Collection of photosynthesis articles and resources.
Major families of biochemicals
Peptides | Amino acids | Nucleic acids | Carbohydrates | Nucleotide sugars | Lipids | Terpenes | Carotenoids | Tetrapyrroles | Enzyme cofactors | Steroids | Flavonoids | Alkaloids | Polyketides | Glycosides
Biochemistry is the study of the chemical processes in living Organisms It deals with the Structure and function of cellular components such as Peptides (from the Greek πεπτίδια, "small digestibles" are short Polymers formed from the linking in a defined order of α- Amino In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this A nucleic acid is a Macromolecule composed of chains of monomeric Nucleotides In Biochemistry these Molecules carry Genetic information Carbohydrates (from ' Hydrates of Carbon ' or saccharides ( Greek σάκχαρον meaning " Sugar " are the most Nucleotide sugars are Biochemicals that act as donors of Sugar residues in Nucleotide sugars metabolism. Lipids are broadly defined as any fat- Soluble ( lipophilic) naturally-occurring Molecule, such as fats oils waxes cholesterol sterols fat-soluble Terpenes are a large and varied class of Hydrocarbons, produced primarily by a wide variety of plants particularly Conifers though also by some insects such Carotenoids are organic Pigments that are naturally occurring in Chromoplasts of plants and some other photosynthetic Organisms Tetrapyrroles are compounds containing four Pyrrole rings With the exception of Corrin, the four pyrrole rings are interconnected through one-carbon ( Methine A cofactor is a non-protein Chemical compound that is bound (either tightly or loosely to an Enzyme and is required for Catalysis. A steroid is a Terpenoid Lipid characterized by a Carbon skeleton with four fused rings generally arranged in a 6-6-6-5 fashion The term flavonoid (or bioflavonoid refers to a class of Plant Secondary metabolites According to the IUPAC nomenclature they can be classified into This article is about the chemical compounds alkaloids For the Pharmaceutical company in the Republic of Macedonia see Alkaloid (company. Polyketides are Secondary metabolites from bacteria, Fungi, Plants and Animals Polyketides are biosynthesized by the
Dictionary
metabolism
-noun
- (physiology) The complete set of chemical reactions that occur in living cells.
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