An introduction
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Contents
Articles
Cells and water
Biochemistry Cells Water 1 1 10 21 43 44 44 47 55 79 79 93 108 118 124 141 141 148 148 163 163 174 175 179 186 186 193
Enzyme mechanisms
Enzyme catalysis
Enzyme kinetics
Enzyme kinetics
Carbohydrate structure
Carbohydrate Polysaccharide
200 201 201 221 221 234 237 241 245 245 253 253 269 269 283 283 290 292 299 301 305 305 310 313 318 322 322 326 335 349
Carbohydrate metabolism
Glycolysis Gluconeogenesis Glycogen Pentose phosphate pathway
Oxidative phosphorylation
Oxidative phosphorylation
Photosynthesis
Photosynthesis
Lipid metabolism
Fatty acid synthesis Lipogenesis Acetyl-CoA carboxylase Fatty acid degradation Beta oxidation
Nitrogen metabolism
Nitrogen fixation Amino acid synthesis Nucleotide Urea cycle
Integration of metabolism
Hormone Signal transduction Diabetes mellitus
Informational Macromolecules
350 350 358 370 374 374 380 385 385 389 393 395
References
Article Sources and Contributors Image Sources, Licenses and Contributors 409 420
Article Licenses
License 427
History
It once was generally believed that life and its materials had some essential property or substance distinct from any found in non-living matter, and it was thought that only living beings could produce the molecules of life. Then, in 1828, Friedrich Whler published a paper on the synthesis of urea, proving that organic compounds can be created artificially.[2] [3] The dawn of biochemistry may have been the discovery of the first enzyme, diastase (today called amylase), in 1833 by Anselme Payen. Eduard Buchner contributed the first demonstration of a complex biochemical process outside of a cell in 1896: alcoholic fermentation in cell extracts of yeast. Although the term biochemistry seems to have been first used in 1882, it is generally accepted that the formal coinage of biochemistry occurred in 1903 by Carl Neuberg, a German chemist. Previous to this time, this area would have been referred to as physiological chemistry. Since then, biochemistry has advanced, especially since the mid-20th century, with the development of new techniques such as chromatography, X-ray diffraction, dual polarisation interferometry, NMR spectroscopy, radioisotopic labeling, electron microscopy, and molecular dynamics simulations. These techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle (citric acid cycle). Another significant historic event in biochemistry is the discovery of the gene and its role in the transfer of information in the cell. This part of biochemistry is often called molecular biology. In the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, and Maurice Wilkins were instrumental in solving DNA structure and suggesting its relationship with genetic transfer of information. In 1958, George Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that one gene produces one enzyme. In 1988, Colin Pitchfork was the first person
Biochemistry convicted of murder with DNA evidence, which led to growth of forensic science. More recently, Andrew Z. Fire and Craig C. Mello received the 2006 Nobel Prize for discovering the role of RNA interference (RNAi), in the silencing of gene expression.
Biomolecules
The four main classes of molecules in biochemistry are carbohydrates, lipids, proteins, and nucleic acids. Many biological molecules are polymers: in this terminology, monomers are relatively small micromolecules that are linked together to create large macromolecules, which are known as polymers. When monomers are linked together to synthesize a biological polymer, they undergo a process called dehydration synthesis.
Carbohydrates
Carbohydrates are made from monomers called monosaccharides. Some of these monosaccharides include glucose (C6H12O6), fructose (C6H12O6), and deoxyribose (C5H10O4). When two monosaccharides undergo dehydration synthesis, water is produced, as two hydrogen atoms and one oxygen atom are lost from the two monosaccharides' hydroxyl group.
Lipids
Lipids are usually made from one molecule of glycerol combined with other molecules. In triglycerides, the main group of bulk lipids, there is one molecule of glycerol and three fatty acids. Fatty acids are considered the monomer in that case, and may be saturated (no double bonds in the carbon chain) or unsaturated (one or more double bonds in the carbon chain). Lipids, especially phospholipids, are also used in various pharmaceutical products, either as co-solubilisers (e.g., in parenteral infusions) or else as drug carrier components (e.g., in a liposome or transfersome).
A triglyceride with a glycerol molecule on the left and three fatty acids coming off it.
Biochemistry
Proteins
Proteins are very large molecules macro-biopolymers made from monomers called amino acids. There are 20 standard amino acids, each containing a carboxyl group, an amino group, and a side-chain (known as an "R" group). The "R" group is what makes each amino acid different, and the properties of the side-chains greatly influence the overall three-dimensional conformation of a protein. When amino acids combine, they form a special bond called a peptide bond through dehydration synthesis, and become a polypeptide, or protein. In order to determine whether two proteins are related, or in other words to decide whether they are homologous or not, scientists use sequence-comparison methods. Methods like Sequence Alignments and Structural Alignments are powerful tools that help scientists identify homologies between related molecules.
The general structure of an -amino acid, with the amino group on the left and the carboxyl group on the right.
The relevance of finding homologies among proteins goes beyond forming an evolutionary pattern of protein families. By finding how similar two protein sequences are, we acquire knowledge about their structure and therefore their function.
Nucleic acids
Nucleic acids are the molecules that make up DNA, an extremely important substance that all cellular organisms use to store their genetic information. The most common nucleic acids are deoxyribonucleic acid and ribonucleic acid. Their monomers are called nucleotides. The most common nucleotides are adenine, cytosine, guanine, thymine, and uracil. Adenine binds with thymine and uracil; Thymine binds only with adenine; and cytosine and guanine can bind only with each other.
Carbohydrates
The function of carbohydrates includes energy storage and providing structure. Sugars are carbohydrates, but not all carbohydrates are sugars. There are more carbohydrates on Earth than any other known type of biomolecule; they are used to store energy and genetic information, as well as play important roles in cell to cell interactions and communications.
The structure of deoxyribonucleic acid (DNA), the picture shows the monomers being put together.
Monosaccharides
The simplest type of carbohydrate is a monosaccharide, which among other properties contains carbon, hydrogen, and oxygen, mostly in a ratio of 1:2:1 (generalized formula CnH2nOn, where n is at least 3). Glucose, one of the most important carbohydrates, is an example of a monosaccharide. So is fructose, the sugar commonly associated with the sweet taste of fruits.[5] [a] Some carbohydrates (especially after
Glucose
Biochemistry condensation to oligo- and polysaccharides) contain less carbon relative to H and O, which still are present in 2:1 (H:O) ratio. Monosaccharides can be grouped into aldoses (having an aldehyde group at the end of the chain, e.g. glucose) and ketoses (having a keto group in their chain; e.g. fructose). Both aldoses and ketoses occur in an equilibrium (starting with chain lengths of C4) cyclic forms. These are generated by bond formation between one of the hydroxyl groups of the sugar chain with the carbon of the aldehyde or keto group to form a hemiacetal bond. This leads to saturated five-membered (in furanoses) or six-membered (in pyranoses) heterocyclic rings containing one O as heteroatom.
Disaccharides
Two monosaccharides can be joined together using dehydration synthesis, in which a hydrogen atom is removed from the end of one molecule and a hydroxyl group (OH) is removed from the other; the remaining residues are then attached at the sites from which the atoms were removed. The HOH or H2O is then released as a molecule of water, hence the term dehydration. The new molecule, consisting of Sucrose: ordinary table sugar and probably the two monosaccharides, is called a disaccharide and is conjoined most familiar carbohydrate. together by a glycosidic or ether bond. The reverse reaction can also occur, using a molecule of water to split up a disaccharide and break the glycosidic bond; this is termed hydrolysis. The most well-known disaccharide is sucrose, ordinary sugar (in scientific contexts, called table sugar or cane sugar to differentiate it from other sugars). Sucrose consists of a glucose molecule and a fructose molecule joined together. Another important disaccharide is lactose, consisting of a glucose molecule and a galactose molecule. As most humans age, the production of lactase, the enzyme that hydrolyzes lactose back into glucose and galactose, typically decreases. This results in lactase deficiency, also called lactose intolerance. Sugar polymers are characterised by having reducing or non-reducing ends. A reducing end of a carbohydrate is a carbon atom that can be in equilibrium with the open-chain aldehyde or keto form. If the joining of monomers takes place at such a carbon atom, the free hydroxy group of the pyranose or furanose form is exchanged with an OH-side-chain of another sugar, yielding a full acetal. This prevents opening of the chain to the aldehyde or keto form and renders the modified residue non-reducing. Lactose contains a reducing end at its glucose moiety, whereas the galactose moiety form a full acetal with the C4-OH group of glucose. Saccharose does not have a reducing end because of full acetal formation between the aldehyde carbon of glucose (C1) and the keto carbon of fructose (C2).
Cellulose is made by plants and is an important structural component of their cell walls. Humans can neither manufacture nor digest it. Glycogen, on the other hand, is an animal carbohydrate; humans and other animals use it as a form of energy storage.
Biochemistry
Biochemistry
Proteins
Like carbohydrates, some proteins perform largely structural roles. For instance, movements of the proteins actin and myosin ultimately are responsible for the contraction of skeletal muscle. One property many proteins have is that they specifically bind to a certain molecule or class of moleculesthey may be extremely selective in what they bind. Antibodies are an example of proteins that attach to one specific type of molecule. In fact, the enzyme-linked immunosorbent assay (ELISA), which uses antibodies, is currently one of the most sensitive tests modern medicine uses to detect various biomolecules. Probably the most important proteins, however, are the enzymes. These molecules recognize specific reactant A schematic of hemoglobin. The red and molecules called substrates; they then catalyze the reaction between them. By blue ribbons represent the protein globin; lowering the activation energy, the enzyme speeds up that reaction by a rate the green structures are the heme groups. of 1011 or more: a reaction that would normally take over 3,000 years to complete spontaneously might take less than a second with an enzyme. The enzyme itself is not used up in the process, and is free to catalyze the same reaction with a new set of substrates. Using various modifiers, the activity of the enzyme can be regulated, enabling control of the biochemistry of the cell as a whole. In essence, proteins are chains of amino acids. An amino acid consists of a carbon atom bound to four groups. One is an amino group, NH2, and one is a carboxylic acid group, COOH (although these exist as NH3+ and COO under physiologic conditions). The third is a simple hydrogen atom. The fourth is commonly denoted "R" and is different for each amino acid. There are twenty standard amino acids. Some of these have functions by themselves or in a modified form; for instance, glutamate functions as an important neurotransmitter. Amino acids can be joined together via a peptide bond. In this dehydration synthesis, a water molecule is removed and the peptide bond connects the nitrogen of one amino acid's amino group to the carbon of the other's Generic amino acids (1) in neutral form, (2) as they exist physiologically, and (3) joined carboxylic acid group. The resulting together as a dipeptide. molecule is called a dipeptide, and short stretches of amino acids (usually, fewer than thirty) are called peptides or polypeptides. Longer stretches merit the title proteins. As an example, the important blood serum protein albumin contains 585 amino acid residues. The structure of proteins is traditionally described in a hierarchy of four levels. The primary structure of a protein simply consists of its linear sequence of amino acids; for instance, "alanine-glycine-tryptophan-serine-glutamate-asparagine-glycine-lysine-". Secondary structure is concerned with local morphology (morphology being the study of structure). Some combinations of amino acids will tend to curl up in a coil called an -helix or into a sheet called a -sheet; some -helixes can be seen in the hemoglobin schematic above. Tertiary structure is the entire three-dimensional shape of the protein. This shape is determined by the sequence of amino acids. In fact, a single change can change the entire structure. The alpha chain of hemoglobin contains 146 amino acid residues; substitution of the glutamate residue at position 6 with a valine residue changes the behavior of hemoglobin so much that it results in sickle-cell disease. Finally, quaternary structure is concerned with the structure of a protein with multiple peptide subunits, like hemoglobin with its four subunits. Not all proteins have more than one subunit.
Biochemistry Ingested proteins are usually broken up into single amino acids or dipeptides in the small intestine, and then absorbed. They can then be joined together to make new proteins. Intermediate products of glycolysis, the citric acid cycle, and the pentose phosphate pathway can be used to make all twenty amino acids, and most bacteria and plants possess all the necessary enzymes to synthesize them. Humans and other mammals, however, can synthesize only half of them. They cannot synthesize isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. These are the essential amino acids, since it is essential to ingest them. Mammals do possess the enzymes to synthesize alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine, the nonessential amino acids. While they can synthesize arginine and histidine, they cannot produce it in sufficient amounts for young, growing animals, and so these are often considered essential amino acids. If the amino group is removed from an amino acid, it leaves behind a carbon skeleton called an -keto acid. Enzymes called transaminases can easily transfer the amino group from one amino acid (making it an -keto acid) to another -keto acid (making it an amino acid). This is important in the biosynthesis of amino acids, as for many of the pathways, intermediates from other biochemical pathways are converted to the -keto acid skeleton, and then an amino group is added, often via transamination. The amino acids may then be linked together to make a protein. A similar process is used to break down proteins. It is first hydrolyzed into its component amino acids. Free ammonia (NH3), existing as the ammonium ion (NH4+) in blood, is toxic to life forms. A suitable method for excreting it must therefore exist. Different strategies have evolved in different animals, depending on the animals' needs. Unicellular organisms, of course, simply release the ammonia into the environment. Likewise, bony fish can release the ammonia into the water where it is quickly diluted. In general, mammals convert the ammonia into urea, via the urea cycle.
Lipids
The term lipid comprises a diverse range of molecules and to some extent is a catchall for relatively water-insoluble or nonpolar compounds of biological origin, including waxes, fatty acids, fatty-acid derived phospholipids, sphingolipids, glycolipids, and terpenoids (e.g., retinoids and steroids). Some lipids are linear aliphatic molecules, while others have ring structures. Some are aromatic, while others are not. Some are flexible, while others are rigid. Most lipids have some polar character in addition to being largely nonpolar. In general, the bulk of their structure is nonpolar or hydrophobic ("water-fearing"), meaning that it does not interact well with polar solvents like water. Another part of their structure is polar or hydrophilic ("water-loving") and will tend to associate with polar solvents like water. This makes them amphiphilic molecules (having both hydrophobic and hydrophilic portions). In the case of cholesterol, the polar group is a mere -OH (hydroxyl or alcohol). In the case of phospholipids, the polar groups are considerably larger and more polar, as described below. Lipids are an integral part of our daily diet. Most oils and milk products that we use for cooking and eating like butter, cheese, ghee etc., are composed of fats. Vegetable oils are rich in various polyunsaturated fatty acids (PUFA). Lipid-containing foods undergo digestion within the body and are broken into fatty acids and glycerol, which are the final degradation products of fats and lipids.
Nucleic acids
A nucleic acid is a complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that convey genetic information. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are found in all living cells and viruses. Aside from the genetic material of the cell, nucleic acids often play a role as second messengers, as well as forming the base molecule for adenosine triphosphate, the primary energy-carrier molecule found in all living organisms. Nucleic acid, so called because of its prevalence in cellular nuclei, is the generic name of the family of biopolymers. The monomers are called nucleotides, and each consists of three components: a nitrogenous heterocyclic base (either
Biochemistry a purine or a pyrimidine), a pentose sugar, and a phosphate group. Different nucleic acid types differ in the specific sugar found in their chain (e.g., DNA or deoxyribonucleic acid contains 2-deoxyriboses). Also, the nitrogenous bases possible in the two nucleic acids are different: adenine, cytosine, and guanine occur in both RNA and DNA, while thymine occurs only in DNA and uracil occurs in RNA.
Genetics is the study of the effect of genetic differences on organisms. Often this can be inferred by the absence of a normal component (e.g., one gene). The study of "mutants" organisms with a changed gene that leads to the organism being different with respect to the so-called "wild type" or normal phenotype. Genetic interactions (epistasis) can often confound simple interpretations of such "knock-out" or "knock-in" studies. Molecular biology is the study of molecular underpinnings of the process of replication, transcription and translation of the genetic material. The central dogma of molecular biology where genetic material is transcribed into RNA and then translated into protein, despite being an oversimplified picture of molecular biology, still provides a good starting point for understanding the field. This picture, however, is undergoing revision in light of emerging novel roles for RNA. Chemical Biology seeks to develop new tools based on small molecules that allow minimal perturbation of biological systems while providing detailed information about their function. Further, chemical biology employs biological systems to create non-natural hybrids between biomolecules and synthetic devices (for example emptied viral capsids that can deliver gene therapy or drug molecules).
Biochemistry
Notes
a. It should be noted that fructose is not the only sugar found in fruits. Glucose and sucrose are also found in varying quantities in various fruits, and indeed sometimes exceed the fructose present. For example, 32% of the edible portion of date is glucose, compared with 23.70% fructose and 8.20% sucrose. However, peaches contain more sucrose (6.66%) than they do fructose (0.93%) or glucose (1.47%).[6]
References
[1] Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life (http:/ / www. phschool. com/ el_marketing. html). Boston, Massachusetts: Pearson Prentice Hall. ISBN0-13-250882-6. . [2] Whler, F. (1828). "Ueber knstliche Bildung des Harnstoffs". Ann. Phys. Chem. 12: 253256. [3] Kauffman, G. B. and Chooljian, S.H. (2001). "Friedrich Whler (18001882), on the Bicentennial of His Birth". The Chemical Educator 6 (2): 121133. doi:10.1007/s00897010444a. [4] Ultratrace minerals. Authors: Nielsen, Forrest H. USDA, ARS Source: Modern nutrition in health and disease / editors, Maurice E. Shils ... et al.. Baltimore : Williams & Wilkins, c1999., p. 283-303. Issue Date: 1999 URI: (http:/ / hdl. handle. net/ 10113/ 46493) [5] Whiting, G.C (1970). "Sugars". In A.C. Hulme. The Biochemistry of Fruits and their Products. Volume 1. London & New York: Academic Press. pp.1=31 [6] Whiting, G.C. (1970), p.5
Further reading
Hunter, Graeme K. (2000). Vital Forces: The Discovery of the Molecular Basis of Life. San Diego: Academic Press. ISBN0-12-361810-X. OCLC162129355 191848148 44187710.
External links
The Virtual Library of Biochemistry and Cell Biology (http://www.biochemweb.org/) Biochemistry, 5th ed. (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=stryer. TOC&depth=2) Full text of Berg, Tymoczko, and Stryer, courtesy of NCBI. Biochemistry, 2nd ed. (http://www.web.virginia.edu/Heidi/home.htm) Full text of Garrett and Grisham. Biochemistry Animation (http://www.1lec.com/Biochemistry/) (Narrated Flash animations.) SystemsX.ch - The Swiss Initiative in Systems Biology (http://www.systemsX.ch/) Biochemistry Online Resources (http://www.icademic.org/97445/Biochemistry/) Lists of Biochemistry departments, websites, journals, books and reviews, employment opportunities and events. biochemical families: prot nucl carb (glpr, alco, glys) lipd (fata/i, phld, strd, gllp, eico) amac/i ncbs/i ttpy/i
Cells
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Cells
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life.[1] Organisms can be classified as unicellular (consisting of a single cell; including most bacteria) or multicellular (including plants and animals). Humans contain about 100 trillion cells; a typical cell size is 10m and a typical cell mass is 1nanogram. The human cell extrema are: largest - anterior horn in the spinal cord (135 vs. 120 for the ovum), longest - pseudounipolar cells which reach from extremities, including the toes to the lower brain stem, and smallest - granule cells in the cerebellum, at 4.[2] The largest known cells are unfertilised ostrich egg cells, which weigh 3.3 pounds.[3] [4]
The cell was discovered by Robert Hooke in 1665. In 1835, before the final cell theory was developed, Jan Evangelista Purkyn observed small "granules" while looking at the plant tissue through a microscope. The cell Cells in culture, stained for keratin (red) and theory, first developed in 1839 by DNA (green) Matthias Jakob Schleiden and Theodor Schwann, states that all organisms are composed of one or more cells, that all cells come from preexisting cells, that vital functions of an organism occur within cells, and that all cells contain the hereditary information necessary for regulating cell functions and for transmitting information to the next generation of cells.[5] The word cell comes from the Latin cellula, meaning "a small room". The
Cells
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descriptive term for the smallest living biological structure was coined by Robert Hooke in a book he published in 1665 when he compared the cork cells he saw through his microscope to the small rooms monks lived in.[6]
Drawing of the structure of cork as it appeared under the microscope to Robert Hooke from Micrographia, which is the origin of the word "cell" being used to describe the smallest unit of a living organism
Anatomy
There are two types of cells: eukaryotic and prokaryotic. Prokaryotic cells are usually independent, while eukaryotic cells are often found in multicellular organisms.
nucleoid region; no real nucleus real nucleus with double membrane circular (usually) coupled in cytoplasm linear molecules (chromosomes) with histone proteins RNA-synthesis inside the nucleus protein synthesis in cytoplasm 60S+40S
Ribosomes
50S+30S
Cells
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very few structures flagella made of flagellin none none usually single cells highly structured by endomembranes and a cytoskeleton flagella and cilia containing microtubules; lamellipodia and filopodia containing actin one to several thousand (though some lack mitochondria) in algae and plants single cells, colonies, higher multicellular organisms with specialized cells
Prokaryotic cells
The prokaryote cell is simpler, and therefore smaller, than a eukaryote cell, lacking a nucleus and most of the other organelles of eukaryotes. There are two kinds of prokaryotes: bacteria and archaea; these share a similar structure. Nuclear material of prokaryotic cell consist of a single chromosome that is in direct contact with cytoplasm. Here, the undefined nuclear region in the cytoplasm is called nucleoid. A prokaryotic cell architectural regions: has three
On the outside, flagella and pili project from the cell's surface. These are structures (not present in all prokaryotes) made of proteins that facilitate movement and communication between cells;
Enclosing the cell is the cell envelope generally consisting of a cell wall covering a plasma membrane though some bacteria also have a further covering layer called a capsule. The envelope gives rigidity to the cell and separates the interior of the cell from its environment, serving as a protective filter. Though most prokaryotes have a cell wall, there are exceptions such as Mycoplasma (bacteria) and Thermoplasma (archaea). The cell wall consists of peptidoglycan in bacteria, and acts as an additional barrier against exterior forces. It also prevents the cell from expanding and finally bursting (cytolysis) from osmotic pressure against a hypotonic environment. Some eukaryote cells (plant cells and fungi cells) also have a cell wall; Inside the cell is the cytoplasmic region that contains the cell genome (DNA) and ribosomes and various sorts of inclusions. A prokaryotic chromosome is usually a circular molecule (an exception is that of the bacterium Borrelia burgdorferi, which causes Lyme disease). Though not forming a nucleus, the DNA is condensed in a nucleoid. Prokaryotes can carry extrachromosomal DNA elements called plasmids, which are usually circular. Plasmids enable additional functions, such as antibiotic resistance.
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Eukaryotic cells
Plants, animals, fungi, slime moulds, protozoa, & algae are all Eukaryotic. These cells are about 15 times wider than a typical prokaryote and can be as much as 1000 times greater in volume. The major difference between prokaryotes and eukaryotes is that eukaryotic cells contain membrane-bound compartments in which specific metabolic activities take place. Most important among these is a cell nucleus, a membrane-delineated compartment that houses the eukaryotic cell's DNA. This nucleus gives the eukaryote its name, which means "true nucleus." Other differences include: The plasma membrane resembles that of prokaryotes in function, with minor differences in the setup. Cell walls may or may not be present. The eukaryotic DNA is organized in one or more linear molecules, called chromosomes, which are associated with histone proteins. All chromosomal DNA is stored in the cell nucleus, separated from the cytoplasm by a membrane. Some eukaryotic organelles such as mitochondria also contain some DNA. Many eukaryotic cells are ciliated with primary cilia. Primary cilia play important roles in chemosensation, mechanosensation, and thermosensation. Cilia may thus be "viewed as sensory cellular antennae that coordinate a large number of cellular signaling pathways, sometimes coupling the signaling to ciliary motility or alternatively to cell division and differentiation."[7] Eukaryotes can move using motile cilia or flagella. The flagella are more complex than those of prokaryotes.
Cells
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Subcellular components
All cells, whether prokaryotic or eukaryotic, have a membrane that envelops the cell, separates its interior from its environment, regulates what moves in and out (selectively permeable), and maintains the electric potential of the cell. Inside the membrane, a salty cytoplasm takes up most of the cell volume. All cells possess DNA, the hereditary material of genes, and RNA, containing the information necessary to build various proteins such as enzymes, the cell's primary machinery. There are also other kinds of biomolecules in cells. This article lists these primary components of the cell, then briefly describe their function.
Membrane
The cytoplasm of a cell is surrounded by a cell membrane or plasma membrane. The plasma membrane in plants and prokaryotes is usually covered by a cell wall. This membrane serves to separate and protect a cell from its surrounding environment and is made mostly from a double layer of lipids (hydrophobic fat-like molecules) and hydrophilic phosphorus molecules. Hence, the layer is called a phospholipid bilayer. It may also be called a fluid mosaic membrane. Embedded within this membrane is a variety of protein molecules that act as channels and pumps that move different molecules into and out of the cell. The membrane is said to be 'semi-permeable', in that it can either let a substance (molecule or ion) pass through freely, pass through to a limited extent or not pass through at all. Cell surface membranes also contain receptor proteins that allow cells to detect external signaling molecules such as hormones.
Cytoskeleton
The cytoskeleton acts to organize and maintain the cell's shape; anchors organelles in place; helps during endocytosis, the uptake of external materials by a cell, and cytokinesis, the separation of daughter cells after cell division; and moves parts of the cell in processes of growth and mobility. The eukaryotic cytoskeleton is composed of microfilaments, intermediate filaments and microtubules. There is a great number of proteins associated with them, each controlling a cell's structure by directing, bundling, and aligning filaments. The prokaryotic cytoskeleton is less well-studied but is involved in the maintenance of cell shape, polarity and cytokinesis.[8]
Genetic material
Bovine Pulmonary Artery Endothelial cell: nuclei stained blue, mitochondria stained red, and F-actin, an important component in microfilaments, stained green. Cell imaged on a fluorescent microscope.
Two different kinds of genetic material exist: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Most organisms use DNA for their long-term information storage, but some viruses (e.g., retroviruses) have RNA as their genetic material. The biological information contained in an organism is encoded in its DNA or RNA sequence. RNA is also used for information transport (e.g., mRNA) and enzymatic functions (e.g., ribosomal RNA) in organisms that use DNA for the genetic code itself. Transfer RNA (tRNA) molecules are used to add amino acids during protein translation. Prokaryotic genetic material is organized in a simple circular DNA molecule (the bacterial chromosome) in the nucleoid region of the cytoplasm. Eukaryotic genetic material is divided into different, linear molecules called chromosomes inside a discrete nucleus, usually with additional genetic material in some organelles like mitochondria and chloroplasts (see endosymbiotic theory).
Cells A human cell has genetic material contained in the cell nucleus (the nuclear genome) and in the mitochondria (the mitochondrial genome). In humans the nuclear genome is divided into 23 pairs of linear DNA molecules called chromosomes. The mitochondrial genome is a circular DNA molecule distinct from the nuclear DNA. Although the mitochondrial DNA is very small compared to nuclear chromosomes, it codes for 13 proteins involved in mitochondrial energy production and specific tRNAs. Foreign genetic material (most commonly DNA) can also be artificially introduced into the cell by a process called transfection. This can be transient, if the DNA is not inserted into the cell's genome, or stable, if it is. Certain viruses also insert their genetic material into the genome.
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Organelles
The human body contains many different organs, such as the heart, lung, and kidney, with each organ performing a different function. Cells also have a set of "little organs," called organelles, that are adapted and/or specialized for carrying out one or more vital functions. Both eukaryotic and prokaryotic cells have organelles but organelles in eukaryotes are generally more complex and may be membrane bound. There are several types of organelles in a cell. Some (such as the nucleus and golgi apparatus) are typically solitary, while others (such as mitochondria, peroxisomes and lysosomes) can be numerous (hundreds to thousands). The cytosol is the gelatinous fluid that fills the cell and surrounds the organelles.
Cell nucleus eukaryotes only - a cell's information center The cell nucleus is the most conspicuous organelle found in a eukaryotic cell. It houses the cell's chromosomes, and is the place where almost all DNA replication and RNA synthesis (transcription) occur. The nucleus is spherical and separated from the cytoplasm by a double membrane called the nuclear envelope. The nuclear envelope isolates and protects a cell's DNA from various molecules that could accidentally damage its structure or interfere with its processing. During processing, DNA is transcribed, or copied into a special RNA, called messenger RNA (mRNA). This mRNA is then transported out of the nucleus, where it is translated into a specific protein molecule. The nucleolus is a specialized region within the nucleus where ribosome subunits are assembled. In prokaryotes, DNA processing takes place in the cytoplasm.
Diagram of a cell nucleus Mitochondria and Chloroplasts eukaryotes only - the power generators Mitochondria are self-replicating organelles that occur in various numbers, shapes, and sizes in the cytoplasm of all eukaryotic cells. Mitochondria play a critical role in generating energy in the eukaryotic cell. Mitochondria generate the cell's energy by oxidative phosphorylation, using oxygen to release energy stored in cellular nutrients (typically pertaining to glucose) to generate ATP. Mitochondria multiply by splitting in two. Respiration occurs in the cell mitochondria. Endoplasmic reticulum eukaryotes only The endoplasmic reticulum (ER) is the transport network for molecules targeted for certain modifications and specific destinations, as compared to molecules that float freely in the cytoplasm. The ER has two forms: the rough ER, which has ribosomes on its surface and secretes proteins into the cytoplasm, and the smooth ER, which lacks them. Smooth ER plays a role in calcium sequestration and release.
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Golgi apparatus eukaryotes only The primary function of the Golgi apparatus is to process and package the macromolecules such as proteins and lipids that are synthesized by the cell.
Ribosomes The ribosome is a large complex of RNA and protein molecules. They each consist of two subunits, and act as an assembly line where RNA from the nucleus is used to synthesise proteins from amino acids. Ribosomes can be found either floating freely or bound to a membrane (the rough endoplasmatic reticulum in [9] eukaryotes, or the cell membrane in prokaryotes). Lysosomes and Peroxisomes eukaryotes only Lysosomes contain digestive enzymes (acid hydrolases). They digest excess or worn-out organelles, food particles, and engulfed viruses or bacteria. Peroxisomes have enzymes that rid the cell of toxic peroxides. The cell could not house these destructive enzymes if they were not contained in a membrane-bound system. Centrosome the cytoskeleton organiser The centrosome produces the microtubules of a cell a key component of the cytoskeleton. It directs the transport through the ER and the Golgi apparatus. Centrosomes are composed of two centrioles, which separate during cell division and help in the formation of the mitotic spindle. A single centrosome is present in the animal cells. They are also found in some fungi and algae cells. Vacuoles Vacuoles store food and waste. Some vacuoles store extra water. They are often described as liquid filled space and are surrounded by a membrane. Some cells, most notably Amoeba, have contractile vacuoles, which can pump water out of the cell if there is too much water. The vacuoles of eukaryotic cells are usually larger in those of plants than animals.
Flagella
Flagella are the organelles of cellular mobility. They arise from cytoplasm and extrude through the cell wall. They are long and thick thread-like appendages, protein in nature. Are most commonly found in bacteria cells but are found in animal cells as well.
Cells
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Fimbriae (pili)
They are short and thin hair like filaments, formed of protein called pilin (antigenic). Fimbriae are responsible for attachment of bacteria to specific receptors of human cell (adherence). There are special types of pili called (sex pili) involved in conjunction.
Functions
Growth and metabolism
Between successive cell divisions, cells grow through the functioning of cellular metabolism. Cell metabolism is the process by which individual cells process nutrient molecules. Metabolism has two distinct divisions: catabolism, in which the cell breaks down complex molecules to produce energy and reducing power, and anabolism, in which the cell uses energy and reducing power to construct complex molecules and perform other biological functions. Complex sugars consumed by the organism can be broken down into a less chemically complex sugar molecule called glucose. Once inside the cell, glucose is broken down to make adenosine triphosphate (ATP), a form of energy, through two different pathways. The first pathway, glycolysis, requires no oxygen and is referred to as anaerobic metabolism. Each reaction is designed to produce some hydrogen ions that can then be used to make energy packets (ATP). In prokaryotes, glycolysis is the only method used for converting energy. The second pathway, called the Krebs cycle, or citric acid cycle, occurs inside the mitochondria and can generate enough ATP to run all the cell functions.
Cells
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Creation
Cell division involves a single cell (called a mother cell) dividing into two daughter cells. This leads to growth in multicellular organisms (the growth of tissue) and to procreation (vegetative reproduction) in unicellular organisms. Prokaryotic cells divide by binary fission. Eukaryotic cells usually undergo a process of nuclear division, called mitosis, followed by division of the cell, called cytokinesis. A diploid cell may also undergo meiosis to produce haploid cells, usually four. Haploid cells serve as gametes in multicellular organisms, fusing to form new diploid cells. DNA replication, or the process of duplicating a cell's genome, is required every time a cell divides. Replication, like all cellular activities, requires specialized proteins for carrying out the job.
Protein synthesis
Cells are capable of synthesizing new proteins, which are essential for the modulation and maintenance of cellular activities. This process involves the formation of new protein molecules from amino acid building blocks based on information encoded in DNA/RNA. Protein synthesis generally consists of two major steps: transcription and translation. Transcription is the process where genetic information in DNA is used to produce a complementary RNA strand. This RNA strand is then processed to give messenger RNA (mRNA), which is free to migrate through the cell. mRNA molecules bind to protein-RNA complexes called ribosomes located in the cytosol, where they are translated into polypeptide sequences. The ribosome mediates the formation of a polypeptide sequence based on the mRNA sequence. The mRNA sequence directly relates to the polypeptide sequence by binding to transfer RNA (tRNA) adapter molecules in binding pockets within the ribosome. The new polypeptide then folds into a functional three-dimensional protein molecule.
Movement or motility
Cells can move during many processes: such as wound healing, the immune response and cancer metastasis. For wound healing to occur, white blood cells and cells that ingest bacteria move to the wound site to kill the microorganisms that cause infection. At the same time fibroblasts (connective tissue cells) move there to remodel damaged structures. In the case of tumor development, cells from a primary tumor move away and spread to other parts of the body. Cell motility involves many receptors, crosslinking, bundling, binding, adhesion, motor and other proteins.[10] The process is divided into three steps protrusion of the leading edge of the cell, adhesion of the leading edge and de-adhesion at the cell body and rear, and cytoskeletal contraction to pull the cell forward. Each step is driven by physical forces generated by unique segments of the cytoskeleton.[11] [12]
An overview of protein synthesis.Within the nucleus of the cell (light blue), genes (DNA, dark blue) are transcribed into RNA. This RNA is then subject to post-transcriptional modification and control, resulting in a mature mRNA (red) that is then transported out of the nucleus and into the cytoplasm (peach), where it undergoes translation into a protein. mRNA is translated by ribosomes (purple) that match the three-base codons of the mRNA to the three-base anti-codons of the appropriate tRNA. Newly synthesized proteins (black) are often further modified, such as by binding to an effector molecule (orange), to become fully active.
Cells
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Evolution
The origin of cells has to do with the origin of life, which began the history of life on Earth.
History
16321723: Antonie van Leeuwenhoek teaches himself to grind lenses, builds a microscope and draws protozoa, such as Vorticella from rain water, and bacteria from his own mouth. 1665: Robert Hooke discovers cells in cork, then in living plant tissue using an early microscope.[6] 1839: Theodor Schwann and Matthias Jakob Schleiden elucidate the principle that plants and animals are made of cells, concluding that cells are a common unit of structure and development, and thus founding the cell theory. The belief that life forms can occur spontaneously (generatio spontanea) is contradicted by Louis Pasteur (18221895) (although Francesco Redi had performed an experiment in 1668 that suggested the same conclusion). 1855: Rudolf Virchow states that cells always emerge from cell divisions (omnis cellula ex cellula). 1931: Ernst Ruska builds first transmission electron microscope (TEM) at the University of Berlin. By 1935, he has built an EM with twice the resolution of a light microscope, revealing previously unresolvable organelles.
Cells 1953: Watson and Crick made their first announcement on the double-helix structure for DNA on February 28. 1981: Lynn Margulis published Symbiosis in Cell Evolution detailing the endosymbiotic theory.
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References
[1] Cell Movements and the Shaping of the Vertebrate Body (http:/ / www. ncbi. nlm. nih. gov/ entrez/ query. fcgi?cmd=Search& db=books& doptcmdl=GenBookHL& term=Cell+ Movements+ and+ the+ Shaping+ of+ the+ Vertebrate+ Body+ AND+ mboc4[book]+ AND+ 374635[uid]& rid=mboc4. section. 3919) in Chapter 21 of Molecular Biology of the Cell (http:/ / www. ncbi. nlm. nih. gov/ entrez/ query. fcgi?cmd=Search& db=books& doptcmdl=GenBookHL& term=cell+ biology+ AND+ mboc4[book]+ AND+ 373693[uid]& rid=mboc4) fourth edition, edited by Bruce Alberts (2002) published by Garland Science. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos. It is also common to describe small molecules such as amino acids as " molecular building blocks (http:/ / www. ncbi. nlm. nih. gov/ entrez/ query. fcgi?cmd=Search& db=books& doptcmdl=GenBookHL& term="all+ cells"+ AND+ mboc4[book]+ AND+ 372023[uid]& rid=mboc4. section. 4#23)". [2] Integrative Biology 131 - Lecture 03: Skeletal System (https:/ / www. youtube. com/ watch?v=EvrWHa1PLUQ) on YouTube first 12 minutes of the lecture covers cells (by Marian Diamond). [3] Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life (http:/ / www. phschool. com/ el_marketing. html). Boston, Massachusetts: Pearson Prentice Hall. ISBN0-13-250882-6. . [4] Mitzi Perdue. "Facts about Birds and Eggs" (http:/ / www. eggscape. com/ birds. htm). . Retrieved 2010-04-15. [5] Maton, Anthea; Hopkins, Jean Johnson, Susan LaHart, David Quon Warner, Maryanna Wright, Jill D (1997). Cells Building Blocks of Life. New Jersey: Prentice Hall. ISBN0-13-423476-6. [6] "... I could exceedingly plainly perceive it to be all perforated and porous, much like a Honey-comb, but that the pores of it were not regular [..] these pores, or cells, [..] were indeed the first microscopical pores I ever saw, and perhaps, that were ever seen, for I had not met with any Writer or Person, that had made any mention of them before this. . ." Hooke describing his observations on a thin slice of cork. Robert Hooke (http:/ / www. ucmp. berkeley. edu/ history/ hooke. html) [7] Satir, P; Christensen, ST; Sren T. Christensen (2008-03-26). "Structure and function of mammalian cilia" (http:/ / www. springerlink. com/ content/ x5051hq648t3152q/ ). Histochemistry and Cell Biology (Springer Berlin / Heidelberg) 129 (6): 687693. doi:10.1007/s00418-008-0416-9. PMC2386530. PMID18365235. 1432-119X. . Retrieved 2009-09-12. [8] Michie K, Lwe J (2006). "Dynamic filaments of the bacterial cytoskeleton". Annu Rev Biochem 75: 46792. doi:10.1146/annurev.biochem.75.103004.142452. PMID16756499. [9] Mntret JF, Schaletzky J, Clemons WM, et al., CW; Akey (December 2007). "Ribosome binding of a single copy of the SecY complex: implications for protein translocation". Mol. Cell 28 (6): 108392. doi:10.1016/j.molcel.2007.10.034. PMID18158904. [10] Revathi Ananthakrishnan1 *, Allen Ehrlicher2 . "The Forces Behind Cell Movement" (http:/ / www. biolsci. org/ v03p0303. htm). Biolsci.org. . Retrieved 2009-04-17. [11] Alberts B, Johnson A, Lewis J. et al. Molecular Biology of the Cell, 4e. Garland Science. 2002 [12] Ananthakrishnan R, Ehrlicher A. The Forces Behind Cell Movement. Int J Biol Sci 2007; 3:303317. http:/ / www. biolsci. org/ v03p0303. htm [13] Orgel LE (1998). "The origin of life--a review of facts and speculations". Trends Biochem Sci 23 (12): 4915. doi:10.1016/S0968-0004(98)01300-0. PMID9868373. [14] Griffiths G (December 2007). "Cell evolution and the problem of membrane topology". Nature reviews. Molecular cell biology 8 (12): 101824. doi:10.1038/nrm2287. PMID17971839. [15] Sterrer W (2002). "On the origin of sex as vaccination". Journal of Theoretical Biology 216: 387396. doi:10.1006/jtbi.2002.3008. PMID12151256.
This article incorporates public domain material from the NCBI document "Science Primer" (http://www. ncbi.nlm.nih.gov/About/primer/index.html).
External links
Inside the Cell (http://publications.nigms.nih.gov/insidethecell/) Virtual Cell's Educational Animations (http://vcell.ndsu.nodak.edu/animations/) The Inner Life of A Cell (http://www.studiodaily.com/main/searchlist/6850.html), a flash video showing what happens inside of a cell. Daniel Reda of Singularity University narrates (beginning at 22:24) (http://www. youtube.com/watch?v=It83JKAxejM) The Virtual Cell (http://www.ibiblio.org/virtualcell/tour/cell/cell.htm) Cells Alive! (http://www.cellsalive.com/) Journal of Cell Biology (http://www.jcb.org/)
Cells The Biology Project > Cell Biology (http://www.biology.arizona.edu/cell_bio/cell_bio.html) Centre of the Cell online (http://www.centreofthecell.org/) The Image & Video Library of The American Society for Cell Biology (http://cellimages.ascb.org/), a collection of peer-reviewed still images, video clips and digital books that illustrate the structure, function and biology of the cell. HighMag Blog (http://highmagblog.blogspot.com/), still images of cells from recent research articles. New Microscope Produces Dazzling 3D Movies of Live Cells (http://www.hhmi.org/news/betzig20110304. html), March 4, 2011 - Howard Hughes Medical Institute. WormWeb.org: Interactive Visualization of the C. elegans Cell lineage (http://wormweb.org/celllineage) Visualize the entire cell lineage tree of the nematode C. elegans
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Textbooks
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Molecular Biology of the Cell (http://www. ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.TOC&depth=2) (4th ed.). Garland. ISBN0815332181. Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipurksy SL, Darnell J (2004). Molecular Cell Biology (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.TOC) (5th ed.). WH Freeman: New York, NY. ISBN978-0716743668. Cooper GM (2000). The cell: a molecular approach (http://www.ncbi.nlm.nih.gov/books/bv. fcgi?rid=cooper.TOC&depth=2) (2nd ed.). Washington, D.C: ASM Press. ISBN0-87893-102-3.
Water
Water is a chemical substance with the chemical formula H2O. A water molecule contains one oxygen and two hydrogen atoms connected by covalent bonds. Water is a liquid at ambient conditions, but it often co-exists on Earth with its solid state, ice, and gaseous state (water vapor or steam). Water also exists in a liquid crystal state near hydrophilic surfaces.[1] [2] Under nomenclature used to name chemical compounds, Dihydrogen monoxide is the scientific name for water, though it is almost never used.[3]
Water in three states: liquid, solid (ice), and (invisible) water vapor in the air. Clouds are accumulations of water droplets, condensed from vapor-saturated air.
Water covers 70.9% of the Earth's surface,[4] and is vital for all known forms of life.[5] On Earth, 96.5% of the planet's water is found mostly in oceans; 1.7% in groundwater; 1.7% in glaciers and the ice caps of Antarctica and Greenland; a small fraction in other large water bodies, and 0.001% in the air as vapor, clouds (formed of solid and liquid water particles suspended in air), and precipitation.[6] [7] Only 2.5% of the Earth's water is freshwater, and 98.8% of that water is in ice and groundwater. Less than 0.3% of all freshwater is in rivers, lakes, and the atmosphere, and an even smaller amount of the Earth's freshwater (0.003%) is contained within biological bodies and manufactured products.[6] Water on Earth moves continually through the hydrological cycle of evaporation and transpiration (evapotranspiration), condensation, precipitation, and runoff, usually reaching the sea. Evaporation and transpiration contribute to the precipitation over land.
Water Safe drinking water is essential to humans and other lifeforms. Access to safe drinking water has improved over the last decades in almost every part of the world, but approximately one billion people still lack access to safe water and over 2.5 billion lack access to adequate sanitation.[8] There is a clear correlation between access to safe water and GDP per capita.[9] However, some observers have estimated that by 2025 more than half of the world population will be facing water-based vulnerability.[10] A recent report (November 2009) suggests that by 2030, in some developing regions of the world, water demand will exceed supply by 50%.[11] Water plays an important role in the world economy, as it functions as a solvent for a wide variety of chemical substances and facilitates industrial cooling and transportation. Approximately 70% of the fresh water used by humans goes to agriculture.[12]
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Since the water molecule is not linear and the oxygen atom has a higher electronegativity than hydrogen atoms, it carries a slight negative charge, whereas the hydrogen atoms are slightly positive. As a result, water is a polar molecule with an electrical dipole moment. Water also can form an unusually large number of intermolecular hydrogen bonds (four) for a molecule of its size. These factors lead to strong attractive forces between molecules of water, giving rise to water's high surface tension[15] and capillary forces. The capillary action refers to the tendency of water to move up a narrow tube against the force of gravity. This property is relied upon by all vascular plants, such as trees.[16]
Impact from a water drop causes an upward "rebound" jet surrounded by circular capillary waves.
Water Water is a good solvent and is often referred to as the universal solvent. Substances that dissolve in water, e.g., salts, sugars, acids, alkalis, and some gases especially oxygen, carbon dioxide (carbonation) are known as hydrophilic (water-loving) substances, while those that do not mix well with water (e.g., fats and oils), are known as hydrophobic (water-fearing) substances. All the major components in cells (proteins, DNA and polysaccharides) are also dissolved in water. Pure water has a low electrical conductivity, but this increases significantly with the dissolution of a small amount of ionic material such as sodium chloride. The boiling point of water (and all other liquids) is dependent on the barometric pressure. For example, on the top of Mt. Everest water boils at 68 C (154F), compared to 100 C (212F) at sea level. Conversely, water deep in the ocean near geothermal vents can reach temperatures of hundreds of degrees and remain liquid. At 4181.3 J/(kgK), water has the second highest specific heat capacity of any known substance (after ammonia), as well as a high heat of vaporization (40.65 kJmol1), both of which are a result of the extensive hydrogen bonding between its molecules. These two unusual properties allow water to moderate Earth's climate by buffering large fluctuations in temperature. The maximum density of water occurs at 3.98 C (39.16F).[17] It has the anomalous property of becoming less dense, not more, when it is cooled down to its solid form, ice. It expands to occupy 9% greater volume in this solid state, which accounts for the fact of ice floating on liquid water, as in icebergs. Its density is 1,000kg/m3 liquid (4C), weighs 62.4lb/ft.3 (917kg/m3, solid). It weighs 8.3454lb/gal. (US, liquid).[18]
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Water Water is miscible with many liquids, such as ethanol, in all proportions, forming a single homogeneous liquid. On the other hand, water and most oils are immiscible, usually forming layers according to increasing density from the top. As a gas, water vapor is completely miscible with air. Water forms an azeotrope with many other solvents. Water can be split by electrolysis into hydrogen and oxygen. As an oxide of hydrogen, water is formed when hydrogen or hydrogen-containing compounds burn or react with oxygen or oxygen-containing compounds. Water is not a fuel, it is an end-product of the combustion of hydrogen. The energy required to split water into hydrogen and oxygen by electrolysis or any other means is greater than the energy that can be collected when the hydrogen and oxygen recombine.[19]
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Elements which are more electropositive than hydrogen such as lithium, sodium, calcium, potassium and caesium displace hydrogen from water, forming hydroxides. Being a flammable gas, the hydrogen given off is dangerous and the reaction of water with the more electropositive of these elements may be violently explosive.
Distribution in nature
In the universe
Much of the universe's water is produced as a byproduct of star formation. When stars are born, their birth is accompanied by a strong outward wind of gas and dust. When this outflow of material eventually impacts the surrounding gas, the shock waves that are created compress and heat the gas. The water observed is quickly produced in this warm dense gas.[20] On 22 July 2011, a report described the discovery of a gigantic cloud of water vapor, containing "140 trillion times more water than all of Earth's oceans combined," around a quasar located 12 billion light years from Earth. According to the researchers, the "discovery shows that water has been prevalent in the universe for nearly its entire existence."[21] [22] Water has been detected in interstellar clouds within our galaxy, the Milky Way. Water probably exists in abundance in other galaxies, too, because its components, hydrogen and oxygen, are among the most abundant elements in the universe. Interstellar clouds eventually condense into solar nebulae and solar systems such as ours. Water vapor is present in Atmosphere of Mercury: 3.4%, and large amounts of water in Mercury's exosphere[23] Atmosphere of Venus: 0.002% Earth's atmosphere: ~0.40% over full atmosphere, typically 14% at surface Atmosphere of Mars: 0.03% Atmosphere of Jupiter: 0.0004%
Water Atmosphere of Saturn in ices only Enceladus (moon of Saturn): 91% exoplanets known as HD 189733 b[24] and HD 209458 b.[25] Liquid water is present on Earth: 71% of surface Europa: 100km deep subsurface ocean Strong evidence suggests that liquid water is present just under the surface of Saturn's moon Enceladus. Water ice is present on Earth mainly as ice sheets polar ice caps on Mars Moon Titan Europa Saturn's rings[26] Enceladus Pluto and Charon[26]
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Comets and comet source populations (Kuiper belt and Oort cloud objects). Water ice may be present on Ceres and Tethys. Water and other volatiles probably comprise much of the internal structures of Uranus and Neptune and the water in the deeper layers may be in the form of ionic water in which the molecules break down into a soup of hydrogen and oxygen ions, and deeper down as superionic water in which the oxygen crystallises but the hydrogen ions float around freely within the oxygen lattice.[13] Some of the Moon's minerals contain water molecules. For instance, in 2008 a laboratory device which ejects and identifies particles found small amounts of the compound in the inside of volcanic rock brought from Moon to Earth by the Apollo 15 crew in 1971.[27] NASA reported the detection of water molecules by NASA's Moon Mineralogy Mapper aboard the Indian Space Research Organization's Chandrayaan-1 spacecraft in September 2009.[28]
Water
26
On Earth
Hydrology is the study of the movement, distribution, and quality of water throughout the Earth. The study of the distribution of water is hydrography. The study of the distribution and movement of groundwater is hydrogeology, of glaciers is glaciology, of inland waters is limnology and distribution of oceans is oceanography. Ecological processes with hydrology are in focus of ecohydrology. The collective mass of water found on, under, and over the surface of a planet is called the hydrosphere. Earth's approximate water volume (the total water supply of the world) is 1,338,000,000km3 (321,000,000mi3).[6] Liquid water is found in bodies of water, such as an ocean, sea, lake, river, stream, canal, pond, or puddle. The majority of water on Earth is sea water. Water is also present in the atmosphere in solid, liquid, and vapor states. It also exists as groundwater in aquifers. Water is important in many geological oceans contain 96.5% of the Earth's water. The processes. Groundwater is present in Antarctic ice sheet, which contains 61% of all fresh water on Earth, is visible at the bottom. most rocks, and the pressure of this Condensed atmospheric water can be seen as groundwater affects patterns of clouds, contributing to the Earth's albedo. faulting. Water in the mantle is responsible for the melt that produces volcanoes at subduction zones. On the surface of the Earth, water is important in both chemical and physical weathering processes. Water and, to a lesser but still significant extent, ice, are also responsible for a large amount of sediment transport that occurs on the surface of the earth. Deposition of transported sediment forms many types of sedimentary rocks, which make up the geologic record of Earth history.
Water covers 71% of the Earth's surface; the
Water
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Water cycle
The water cycle (known scientifically as the hydrologic cycle) refers to the continuous exchange of water within the hydrosphere, between the atmosphere, soil water, surface water, groundwater, and plants. Water moves perpetually through each of these regions in the water cycle consisting of following transfer processes: evaporation from oceans and other water bodies into the air and transpiration from land plants and animals into air. precipitation, from water vapor condensing from the air and falling to earth or ocean. runoff from the land usually reaching the sea. Most water vapor over the oceans returns to the oceans, but winds carry water vapor over land at the same rate as runoff into the sea, about 47Tt per year. Over land, evaporation and transpiration contribute another 72Tt per year. Precipitation, at a rate of 119 Tt per year over land, has several forms: most commonly rain, snow, and hail, with some contribution from fog and dew.[33] Condensed water in the air may also refract sunlight to produce rainbows. Water runoff often collects over watersheds flowing into rivers. A mathematical model used to simulate river or stream flow and calculate water quality parameters is hydrological transport model. Some of water is diverted to irrigation for agriculture. Rivers and seas offer opportunity for travel and commerce. Through erosion, runoff shapes the environment creating river valleys and deltas which provide rich soil and level ground for the establishment of population centers. A flood occurs when an area of land, usually low-lying, is covered with water. It is when a river overflows its banks or flood from the sea. A drought is an extended period of months or years when a region notes a deficiency in its water supply. This occurs when a region receives consistently below average precipitation.
Water cycle
The Bay of Fundy at high tide (left) and low tide (right)
Water Some runoff water is trapped for periods of time, for example in lakes. At high altitude, during winter, and in the far north and south, snow collects in ice caps, snow pack and glaciers. Water also infiltrates the ground and goes into aquifers. This groundwater later flows back to the surface in springs, or more spectacularly in hot springs and geysers. Groundwater is also extracted artificially in wells. This water storage is important, since clean, fresh water is essential to human and other land-based life. In many parts of the world, it is in short supply.
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Sea water
Sea water contains about 3.5% salt on average, plus smaller amounts of other substances. The physical properties of sea water differ from fresh water in some important respects. It freezes at a lower temperature (about 1.9 C) and its density increases with decreasing temperature to the freezing point, instead of reaching maximum density at a temperature above freezing. The salinity of water in major seas varies from about 0.7% in the Baltic Sea to 4.0% in the Red Sea.
Tides
Tides are the cyclic rising and falling of local sea levels caused by the tidal forces of the Moon and the Sun acting on the oceans. Tides cause changes in the depth of the marine and estuarine water bodies and produce oscillating currents known as tidal streams. The changing tide produced at a given location is the result of the changing positions of the Moon and Sun relative to the Earth coupled with the effects of Earth rotation and the local bathymetry. The strip of seashore that is submerged at high tide and exposed at low tide, the intertidal zone, is an important ecological product of ocean tides.
Effects on life
From a biological standpoint, water has many distinct properties that are critical for the proliferation of life that set it apart from other substances. It carries out this role by allowing organic compounds to react in ways that ultimately allow replication. All known forms of life depend on water. Water is vital both as a solvent in which many of the body's solutes dissolve and as an essential part of many metabolic processes within the body. Metabolism is the sum total of anabolism and catabolism. In anabolism, water is removed from molecules (through energy requiring enzymatic chemical reactions) in order to An oasis is an isolated water source with grow larger molecules (e.g. starches, triglycerides and proteins for vegetation in a desert storage of fuels and information). In catabolism, water is used to break bonds in order to generate smaller molecules (e.g. glucose, fatty acids and amino acids to be used for fuels for energy use or other purposes). Without water, these particular metabolic processes could not exist. Water is fundamental to photosynthesis and respiration. Photosynthetic cells use the sun's energy to split off water's hydrogen from oxygen. Hydrogen is combined with CO2 (absorbed from air or water) to form glucose and release oxygen. All living cells use such fuels and oxidize the hydrogen and carbon to capture the sun's energy and reform water and CO2 in the process (cellular respiration).
Water
29
Water is also central to acid-base neutrality and enzyme function. An acid, a hydrogen ion (H+, that is, a proton) donor, can be neutralized by a base, a proton acceptor such as hydroxide ion (OH) to form water. Water is considered to be neutral, with a pH (the negative log of the hydrogen ion concentration) of 7. Acids have pH values less than 7 while bases have values greater than 7.
Overview of photosynthesis and respiration. Water (at right), together with carbon dioxide (CO2), form oxygen and organic compounds (at left), which can be respired to water and (CO2).
Water
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Water fountain
Water In the USA, non-potable forms of wastewater generated by humans may be referred to as greywater, which is treatable and thus easily able to be made potable again, and blackwater, which generally contains sewage and other forms of waste which require further treatment in order to be made reusable. Greywater composes 5080% of residential wastewater generated by a household's sanitation equipment (sinks, showers and kitchen runoff, but not toilets, which generate blackwater.) These terms may have different meanings in other countries and cultures. This natural resource is becoming scarcer in certain places, and its availability is a major social and economic concern. Currently, about a billion people around the world routinely drink unhealthy water. Most countries accepted the goal of halving by 2015 the number of people worldwide who do not have access to safe water and sanitation during the 2003 G8 Evian summit.[34] Even if this difficult goal is met, it will still leave more than an estimated half a billion people without access to safe drinking water and over a billion without access to adequate sanitation. Poor water quality and bad sanitation are deadly; some five million deaths a year are caused by polluted drinking water. The World Health Organization estimates that safe water could prevent 1.4 million child deaths from diarrhea each year.[35] Water, however, is not a finite resource, but rather re-circulated as potable water in precipitation in quantities many degrees of magnitude higher than human consumption. Therefore, it is the relatively small quantity of water in reserve in the earth (about 1% of our drinking water supply, which is replenished in aquifers around every 1 to 10 years), that is a non-renewable resource, and it is, rather, the distribution of potable and irrigation water which is scarce, rather than the actual amount of it that exists on the earth. Water-poor countries use importation of goods as the primary method of importing water (to leave enough for local human consumption), since the manufacturing process uses around 10 to 100 times products' masses in water. In the developing world, 90% of all wastewater still goes untreated into local rivers and streams.[36] Some 50 countries, with roughly a third of the worlds population, also suffer from medium or high water stress, and 17 of these extract more water annually than is recharged through their natural water cycles.[37] The strain not only affects surface freshwater bodies like rivers and lakes, but it also degrades groundwater resources.
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Human uses
Further information: Water supply Agriculture The most important use of water in agriculture is for irrigation, which is a key component to produce enough food. Irrigation takes up to 90% of water withdrawn in some developing countries[38] and significant proportions in more economically developed countries (United States, 30% of freshwater usage is for irrigation).[39] It takes around 3,000 litres of water, converted from liquid to vapour, to produce enough food to satisfy one person's daily dietary need. This is a considerable amount, when compared to that required for drinking, which is between two and five litres. To produce food for the 6.5 billion or so Irrigation of field crops people who inhabit the planet today requires the water that would fill a canal ten metres deep, 100 metres wide and 7.1 million kilometres long that's enough to circle the globe 180 times. Fifty years ago, the common perception was that water was an infinite resource. At this time, there were fewer than half the current number of people on the planet. People were not as wealthy as today, consumed fewer calories and ate less meat, so less water was needed to produce their food. They required a third of the volume of water we presently take from rivers. Today, the competition for the fixed amount of water resources is much more intense, giving rise to the concept of peak water.[40] This is because there are now nearly seven billion people on the planet, their consumption of water-thirsty meat and vegetables is rising, and there is increasing competition for water from industry, urbanisation and biofuel crops. In future, even more water will be needed to produce food because the
Water Earth's population is forecast to rise to 9 billion by 2050.[41] An additional 2.5 or 3 billion people, choosing to eat fewer cereals and more meat and vegetables could add an additional five million kilometres to the virtual canal mentioned above. An assessment of water management in agriculture was conducted in 2007 by the International Water Management Institute in Sri Lanka to see if the world had sufficient water to provide food for its growing population.[42] It assessed the current availability of water for agriculture on a global scale and mapped out locations suffering from water scarcity. It found that a fifth of the world's people, more than 1.2 billion, live in areas of physical water scarcity, where there is not enough water to meet all demands. A further 1.6 billion people live in areas experiencing economic water scarcity, where the lack of investment in water or insufficient human capacity make it impossible for authorities to satisfy the demand for water. The report found that it would be possible to produce the food required in future, but that continuation of today's food production and environmental trends would lead to crises in many parts of the world. To avoid a global water crisis, farmers will have to strive to increase productivity to meet growing demands for food, while industry and cities find ways to use water more efficiently.[43] As a scientific standard On 7 April 1795, the gram was defined in France to be equal to "the absolute weight of a volume of pure water equal to a cube of one hundredth of a meter, and to the temperature of the melting ice."[44] For practical purposes though, a metallic reference standard was required, one thousand times more massive, the kilogram. Work was therefore commissioned to determine precisely the mass of one liter of water. In spite of the fact that the decreed definition of the gram specified water at 0C a highly reproducible temperature the scientists chose to redefine the standard and to perform their measurements at the temperature of highest water density, which was measured at the time as 4 C (39F).[45] The Kelvin temperature scale of the SI system is based on the triple point of water, defined as exactly 273.16K or 0.01C. The scale is an absolute temperature scale with the same increment as the Celsius temperature scale, which was originally defined according the boiling point (set to 100C) and melting point (set to 0C) of water. Natural water consists mainly of the isotopes hydrogen-1 and oxygen-16, but there is also small quantity of heavier isotopes such as hydrogen-2 (deuterium). The amount of deuterium oxides or heavy water is very small, but it still affects the properties of water. Water from rivers and lakes tends to contain less deuterium than seawater. Therefore, standard water is defined in the Vienna Standard Mean Ocean Water specification. For drinking The human body contains from 55% to 78% water, depending on body size.[46] To function properly, the body requires between one and seven liters of water per day to avoid dehydration; the precise amount depends on the level of activity, temperature, humidity, and other factors. Most of this is ingested through foods or beverages other than drinking straight water. It is not clear how much water intake is needed by healthy people, though most advocates agree that approximately 2 liters (6 to 7 glasses) of water daily is the minimum to maintain proper hydration.[47] Medical literature favors a lower consumption, typically A young girl drinking bottled water 1 liter of water for an average male, excluding extra requirements due to fluid loss from exercise or warm weather.[48] For those who have healthy kidneys, it is rather difficult to drink too much water, but (especially in warm humid weather and while exercising) it is
32
Water
33
dangerous to drink too little. People can drink far more water than necessary while exercising, however, putting them at risk of water intoxication (hyperhydration), which can be fatal.[49] [50] The popular claim that "a person should consume eight glasses of water per day" seems to have no real basis in science.[51] Similar misconceptions concerning the effect of water on weight loss and constipation have also been dispelled.[52]
An original recommendation for water intake in 1945 by the Food and Nutrition Board of the United States National Research Council read: "An ordinary standard for diverse persons is 1 milliliter for each calorie of food. Most of this quantity is contained in prepared foods."[53] The latest dietary reference intake report by the United States National Research Council in general recommended (including food sources): 3.7 liters for men and 2.7 liters of water total for women.[54] Specifically, pregnant and breastfeeding women need additional fluids to stay hydrated. The Institute of Medicine (U.S.) recommends that, on average, men consume 3.0 liters and women 2.2 liters; pregnant women should increase intake to 2.4 liters (10 cups) and breastfeeding women should get 3 liters (12 cups), since an especially large amount Hazard symbol for non-potable water of fluid is lost during nursing.[55] Also noted is that normally, about 20% of water intake comes from food, while the rest comes from drinking water and beverages (caffeinated included). Water is excreted from the body in multiple forms; through urine and feces, through sweating, and by exhalation of water vapor in the breath. With physical exertion and heat exposure, water loss will increase and daily fluid needs may increase as well. Humans require water with few impurities. Common impurities include metal salts and oxides, including copper, iron, calcium and lead,[56] and/or harmful bacteria, such as Vibrio. Some solutes are acceptable and even desirable for taste enhancement and to provide needed electrolytes.[57] The single largest (by volume) freshwater resource suitable for drinking is Lake Baikal in Siberia.[58] Washing The propensity of water to form solutions and emulsions is useful in various washing processes. Many industrial processes rely on reactions using chemicals dissolved in water, suspension of solids in water slurries or using water to dissolve and extract substances. Washing is also an important component of several aspects of personal body hygiene. Transportation The use of water for transportation of materials through rivers and canals as well as the international shipping lanes is an important part of the world economy.
Water Chemical uses Water is widely used in chemical reactions as a solvent or reactant and less commonly as a solute or catalyst. In inorganic reactions, water is a common solvent, dissolving many ionic compounds. In organic reactions, it is not usually used as a reaction solvent, because it does not dissolve the reactants well and is amphoteric (acidic and basic) and nucleophilic. Nevertheless, these properties are sometimes desirable. Also, acceleration of Diels-Alder reactions by water has been observed. Supercritical water has recently been a topic of research. Oxygen-saturated supercritical water combusts organic pollutants efficiently. Heat exchange Water and steam are used as heat transfer fluids in diverse heat exchange systems, due to its availability and high heat capacity, both as a coolant and for heating. Cool water may even be naturally available from a lake or the sea. Condensing steam is a particularly efficient heating fluid because of the large heat of vaporization. A disadvantage is that water and steam are somewhat corrosive. In almost all electric power stations, water is the coolant, which vaporizes and drives steam turbines to drive generators. In the U.S., cooling power plants is the largest use of water.[39] In the nuclear power industry, water can also be used as a neutron moderator. In most nuclear reactors, water is both a coolant and a moderator. This provides something of a passive safety measure, as removing the water from the reactor also slows the nuclear reaction down however other methods are favored for stopping a reaction and it is preferred to keep the nuclear core covered with water so as to ensure adequate cooling. Fire extinction Water has a high heat of vaporization and is relatively inert, which makes it a good fire extinguishing fluid. The evaporation of water carries heat away from the fire. It is dangerous to use water on fires involving oils and organic solvents, because many organic materials float on water and the water tends to spread the burning liquid. Use of water in fire fighting should also take into account the hazards of a steam explosion, which may occur when water is used on very hot fires in confined spaces, and of a hydrogen explosion, when substances which react with water, such as certain metals or hot carbon such as coal, charcoal, coke graphite, decompose the water, producing water gas.
34
The power of such explosions was seen in the Chernobyl disaster, although the water involved did not come from fire-fighting at that time but the reactor's own water cooling system. A steam explosion occurred when the extreme overheating of the core caused water to flash into steam. A hydrogen explosion may have occurred as a result of reaction between steam and hot zirconium.
Water Recreation Humans use water for many recreational purposes, as well as for exercising and for sports. Some of these include swimming, waterskiing, boating, surfing and diving. In addition, some sports, like ice hockey and ice skating, are played on ice. Lakesides, beaches and waterparks are popular places for people to go to relax and enjoy recreation. Many find the sound and appearance of flowing water to be calming, and fountains and other water features are popular decorations. Some keep fish and other life in aquariums or ponds for show, fun, and companionship. Humans also use water for snow sports i.e. skiing, sledding, snowmobiling or snowboarding, which requires the water to be frozen.
35
Grand Anse Beach, St. George's, Grenada, West Indies, often reported as one of the top 10 beaches in the world.
Water industry The water industry provides drinking water and wastewater services (including sewage treatment) to households and industry. Water supply facilities include water wells cisterns for rainwater harvesting, water supply network, water purification facilities, water tanks, water towers, water pipes including old aqueducts. Atmospheric water generators are in development. Drinking water is often collected at springs, extracted from artificial borings (wells) in the ground, or pumped from lakes and rivers. Building more wells in adequate places is thus a possible way to produce more water, assuming the aquifers can supply an adequate flow. Other water sources include rainwater collection. Water may require purification for human consumption. This may involve removal of undissolved substances, dissolved substances and harmful microbes. Popular methods are filtering with sand which only removes undissolved material, while chlorination and boiling kill harmful microbes. Distillation does all three functions. More advanced techniques exist, such as reverse osmosis. Desalination of abundant seawater is a more expensive solution used in coastal arid climates. The distribution of drinking water is done through municipal water systems, tanker delivery or as bottled water. Governments in many countries have programs to distribute water to the needy at no charge. Reducing usage by using drinking (potable) water only for human consumption is another option. In some cities such as Hong Kong, sea water is extensively used for flushing toilets citywide in order to conserve fresh water resources. Polluting water may be the biggest single misuse of water; to the extent that a pollutant limits other uses of the water, it becomes a waste of the resource, regardless of benefits to the polluter. Like other types of
A water-carrier in India, 1882. In many places where running water is not available, water has to be transported by people.
Water
36 pollution, this does not enter standard accounting of market costs, being conceived as externalities for which the market cannot account. Thus other people pay the price of water pollution, while the private firms' profits are not redistributed to the local population victim of this pollution. Pharmaceuticals consumed by humans often end up in the waterways and can have detrimental effects on aquatic life if they bioaccumulate and if they are not biodegradable.
Water purification facility
Wastewater facilities are storm sewers and wastewater treatment plants. Another way to remove pollution from surface runoff water is bioswale.
Industrial applications Water is used in power generation. Hydroelectricity is electricity obtained from hydropower. Hydroelectric power comes from water driving a water turbine connected to a generator. Hydroelectricity is a low-cost, non-polluting, renewable energy source. The energy is supplied by the motion of water. Typically a dam is constructed on a river, creating an artificial lake behind it. Water flowing out of the lake is forced through turbines that turn generators.
Three Gorges Dam is the largest hydro-electric power station. Pressurized water is used in water blasting and water jet cutters. Also, very high pressure water guns are used for precise cutting. It works very well, is relatively safe, and is not harmful to the environment. It is also used in the cooling of machinery to prevent overheating, or prevent saw blades from overheating. Water is also used in many industrial processes and machines, such as the steam turbine and heat exchanger, in addition to its use as a chemical solvent. Discharge of untreated water from industrial uses is pollution. Pollution includes discharged solutes (chemical pollution) and discharged coolant water (thermal pollution). Industry requires pure water for many applications and utilizes a variety of purification techniques both in water supply and discharge.
Water Food processing Water plays many critical roles within the field of food science. It is important for a food scientist to understand the roles that water plays within food processing to ensure the success of their products. Solutes such as salts and sugars found in water affect the physical properties of water. The boiling and freezing points of water are affected by solutes, as well as air pressure, which is in turn affected by altitude. Water boils at lower temperatures with the lower air pressure which occurs at higher elevations. One mole of sucrose (sugar) per kilogram of water raises the boiling point of water by 0.51 C, and one Water can be used to cook foods such as noodles. mole of salt per kg raises the boiling point by 1.02 C; similarly, increasing the number of dissolved particles lowers water's freezing [59] point. Solutes in water also affect water activity which affects many chemical reactions and the growth of microbes in food.[60] Water activity can be described as a ratio of the vapor pressure of water in a solution to the vapor pressure of pure water.[59] Solutes in water lower water activity. This is important to know because most bacterial growth ceases at low levels of water activity.[60] Not only does microbial growth affect the safety of food but also the preservation and shelf life of food. Water hardness is also a critical factor in food processing. It can dramatically affect the quality of a product as well as playing a role in sanitation. Water hardness is classified based on the amounts of removable calcium carbonate salt it contains per gallon. Water hardness is measured in grains; 0.064 g calcium carbonate is equivalent to one grain of hardness.[59] Water is classified as soft if it contains 1 to 4 grains, medium if it contains 5 to 10 grains and hard if it contains 11 to 20 grains. [59] The hardness of water may be altered or treated by using a chemical ion exchange system. The hardness of water also affects its pH balance which plays a critical role in food processing. For example, hard water prevents successful production of clear beverages. Water hardness also affects sanitation; with increasing hardness, there is a loss of effectiveness for its use as a sanitizer.[59] Boiling, steaming, and simmering are popular cooking methods that often require immersing food in water or its gaseous state, steam. Water is also used for dishwashing.
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Water
38
An estimate of the share of people in developing countries with access to potable water 19702000
A 2006 United Nations report stated that "there is enough water for everyone", but that access to it is hampered by mismanagement and corruption.[63] In addition, global initiatives to improve the efficiency of aid delivery, such as the Paris Declaration on Aid Effectiveness, have not been taken up by water sector donors as effectively as they have in education and health, potentially leaving multiple donors working on overlapping projects and recipient governments without empowerment to act.[64] The authors of the 2007 Comprehensive Assessment of Water Management in Agriculture cited poor governance as one reason for some forms of water scarcity. Water governance is the set of formal and informal processes through which decisions related to water management are made. Good water governance is primarily about knowing what processes work best in a particular physical and socioeconomic context. Mistakes have sometimes been made by trying to apply 'blueprints' that work in the developed world to developing world locations and contexts. The Mekong river is one example; a review by the International Water Management Institute of policies in six countries that rely on the Mekong river for water found that thorough and transparent cost-benefit analyses and environmental impact assessments were rarely undertaken. They also discovered that Cambodia's draft water law was much more complex than it needed to be.[65] The UN World Water Development Report (WWDR, 2003) from the World Water Assessment Program indicates that, in the next 20 years, the quantity of water available to everyone is predicted to decrease by 30%. 40% of the world's inhabitants currently have insufficient fresh water for minimal hygiene. More than 2.2 million people died in 2000 from waterborne diseases (related to the consumption of contaminated water) or drought. In 2004, the UK charity WaterAid reported that a child dies every 15 seconds from easily preventable water-related diseases; often this means lack of sewage disposal; see toilet. Organizations concerned with water protection include International Water Association (IWA), WaterAid, Water 1st, American Water Resources Association [66]. The International Water Management Institute undertakes projects with the aim of using effective water management to reduce poverty. Water related conventions are United Nations Convention to Combat Desertification (UNCCD), International Convention for the Prevention of Pollution from Ships, United Nations Convention on the Law of the Sea and Ramsar Convention. World Day for Water takes place on 22 March and World Ocean Day on 8 June.
39
In culture
Religion
Water is considered a purifier in most religions. Major faiths that incorporate ritual washing (ablution) include Christianity, Islam, Hinduism, Rastafari movement, Shinto, Taoism, Judaism, and Wicca. Immersion (or aspersion or affusion) of a person in water is a central sacrament of Christianity (where it is called baptism); it is also a part of the practice of other religions, including Judaism (mikvah) and Sikhism (Amrit Sanskar). In addition, a ritual bath in pure water is performed for the dead in many religions including Judaism and Islam. In Islam, the five daily prayers can be done in most cases (see Tayammum) after completing washing certain parts of the body using clean water (wudu). In Shinto, water is used in almost all rituals to cleanse a person or an area (e.g., in the ritual of misogi). Water is mentioned numerous times in the Bible, for example: "The earth was formed out of water and by water" (NIV). In the Qur'an it is stated that "Living things are made of water" and it is often used to describe paradise.
Philosophy
The Ancient Greek philosopher Empedocles held that water is one of the four classical elements along with fire, earth and air, and was regarded as the ylem, or basic substance of the universe. Water was considered cold and moist. In the theory of the four bodily humors, water was associated with phlegm. The classical element of Water was also one of the five elements in traditional Chinese philosophy, along with earth, fire, wood, and metal. Water is also taken as a role model in some parts of traditional and popular Asian philosophy. James Legge's 1891 translation of the Dao De Jing states "The highest excellence is like (that of) water. The excellence of water appears in its benefiting all things, and in its occupying, without striving (to the contrary), the low place which all men dislike. Hence (its way) is near to (that of) the Tao" and "There is nothing in the world more soft and weak than water, and yet for attacking things that are firm and strong there is nothing that can take precedence of itfor there is nothing (so effectual) for which it can be changed."[67]
Literature
Water is used in literature as a symbol of purification. Examples include the critical importance of a river in As I Lay Dying by William Faulkner and the drowning of Ophelia in Hamlet. Sherlock Holmes held that "From a drop of water, a logician could infer the possibility of an Atlantic or a Niagara without having seen or heard of one or the other."[68]
References
[1] Henniker, J. C. (1949). "The Depth of the Surface Zone of a Liquid". Reviews of Modern Physics (Reviews of Modern Physics) 21 (2): 322341. doi:10.1103/RevModPhys.21.322. [2] Pollack, Gerald. "Water Science" (http:/ / faculty. washington. edu/ ghp/ researcthemes/ water-science). University of Washington, Pollack Laboratory. . Retrieved 2011-02-05. "Water has three phases gas, liquid, and solid; but recent findings from our laboratory imply the presence of a surprisingly extensive fourth phase that occurs at interfaces." [3] Bramer, Scott. "Chemical Nomenclature" (http:/ / science. widener. edu/ svb/ pset/ nomen_b. html). Widener University, Department of Chemistry. . Retrieved 20 September 2011. [4] "CIA- The world fact book" (https:/ / www. cia. gov/ library/ publications/ the-world-factbook/ geos/ xx. html#Geo). Central Intelligence Agency. . Retrieved 2008-12-20. [5] "United Nations" (http:/ / www. un. org/ waterforlifedecade/ background. html). Un.org. 2005-03-22. . Retrieved 2010-07-25. [6] Gleick, P.H., ed (1993). Water in Crisis: A Guide to the World's Freshwater Resources. Oxford University Press. p.13, Table 2.1 "Water reserves on the earth". [7] Water Vapor in the Climate System (http:/ / www. agu. org/ sci_soc/ mockler. html), Special Report, [AGU], December 1995 (linked 4/2007). Vital Water (http:/ / www. unep. org/ dewa/ assessments/ ecosystems/ water/ vitalwater/ ) UNEP.
Water
[8] "MDG Report 2008" (http:/ / mdgs. un. org/ unsd/ mdg/ Resources/ Static/ Products/ Progress2008/ MDG_Report_2008_En. pdf#page=44). . Retrieved 2010-07-25. [9] "Public Services" (http:/ / www. gapminder. org/ videos/ gapcasts/ gapcast-9-public-services/ ), Gapminder video [10] Kulshreshtha, S.N (1998). "A Global Outlook for Water Resources to the Year 2025". Water Resources Management 12 (3): 167184. doi:10.1023/A:1007957229865. [11] "Charting Our Water Future: Economic frameworks to inform decision-making" (http:/ / www. mckinsey. com/ App_Media/ Reports/ Water/ Charting_Our_Water_Future_Full_Report_001. pdf) (PDF). . Retrieved 2010-07-25. [12] Baroni, L.; Cenci, L.; Tettamanti, M.; Berati, M. (2007). "Evaluating the environmental impact of various dietary patterns combined with different food production systems". European Journal of Clinical Nutrition 61 (2): 279286. doi:10.1038/sj.ejcn.1602522. PMID17035955. [13] Weird water lurking inside giant planets (http:/ / www. newscientist. com/ article/ mg20727764. 500-weird-water-lurking-inside-giant-planets. html), New Scientist,01 September 2010, Magazine issue 2776. [14] Braun, Charles L.; Sergei N. Smirnov (1993). "Why is water blue?" (http:/ / www. dartmouth. edu/ ~etrnsfer/ water. htm). J. Chem. Educ. 70 (8): 612. doi:10.1021/ed070p612. . [15] Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life (http:/ / www. phschool. com/ el_marketing. html). Boston, Massachusetts: Pearson Prentice Hall. ISBN0-13-250882-6. . [16] Capillary Action Liquid, Water, Force, and Surface JRank Articles (http:/ / science. jrank. org/ pages/ 1182/ Capillary-Action. html). Science.jrank.org. Retrieved on 2011-11-03. [17] Kotz, J. C., Treichel, P., & Weaver, G. C. (2005). Chemistry & Chemical Reactivity. Thomson Brooks/Cole. ISBN053439597X. [18] Online Conversion Density (http:/ / www. kidsnewsroom. org/ elmer/ infocentral/ conversions/ density. htm), Kidsnewsroom.org/elmer/infocentral/conversions [19] Ball, Philip (14 September 2007). "Burning water and other myths" (http:/ / www. nature. com/ news/ 2007/ 070910/ full/ 070910-13. html). Nature News. . Retrieved 2007-09-14. [20] Melnick, Gary, Harvard-Smithsonian Center for Astrophysics and Neufeld, David, Johns Hopkins University quoted in: "Discover of Water Vapor Near Orion Nebula Suggests Possible Origin of H20 in Solar System (sic)" (http:/ / www. news. harvard. edu/ gazette/ 1998/ 04. 23/ DiscoverofWater. html). The Harvard University Gazette. April 23, 1998. . "Space Cloud Holds Enough Water to Fill Earth's Oceans 1 Million Times" (http:/ / www. jhu. edu/ news_info/ news/ home98/ apr98/ clouds. html). Headlines@Hopkins, JHU. April 9, 1998. . "Water, Water Everywhere: Radio telescope finds water is common in universe" (http:/ / news. harvard. edu/ gazette/ 1999/ 02. 25/ telescope. html). The Harvard University Gazette. February 25, 1999. .(linked 4/2007) [21] Clavin, Whitney; Buis, Alan (22 July 2011). "Astronomers Find Largest, Most Distant Reservoir of Water" (http:/ / www. nasa. gov/ topics/ universe/ features/ universe20110722. html). NASA. . Retrieved 2011-07-25. [22] Staff (22 July 2011). "Astronomers Find Largest, Oldest Mass of Water in Universe" (http:/ / www. space. com/ 12400-universe-biggest-oldest-cloud-water. html). Space.com. . Retrieved 2011-07-23. [23] "MESSENGER Scientists 'Astonished' to Find Water in Mercury's Thin Atmosphere" (http:/ / www. planetary. org/ news/ 2008/ 0703_MESSENGER_Scientists_Astonished_to. html). Planetary Society. 2008-07-03. . Retrieved 2008-07-05. [24] Water Found on Distant Planet (http:/ / www. time. com/ time/ health/ article/ 0,8599,1642811,00. html) July 12, 2007 By Laura Blue, Time [25] Water Found in Extrasolar Planet's Atmosphere (http:/ / www. space. com/ scienceastronomy/ 070410_water_exoplanet. html) Space.com [26] Sparrow, Giles (2006). The Solar System. Thunder Bay Press. ISBN1592235794. [27] Versteckt in Glasperlen: Auf dem Mond gibt es Wasser Wissenschaft [[Der Spiegel (http:/ / www. spiegel. de/ wissenschaft/ weltall/ 0,1518,564911,00. html)] Nachrichten] [28] Water Molecules Found on the Moon (http:/ / science. nasa. gov/ headlines/ y2009/ 24sep_moonwater. htm), NASA, September 24, 2009 [29] Ehlers, E.; Krafft, T, ed (2001). "J. C. I. Dooge. "Integrated Management of Water Resources"". Understanding the Earth System: compartments, processes, and interactions. Springer. p.116. [30] "Habitable Zone" (http:/ / www. daviddarling. info/ encyclopedia/ H/ habzone. html). The Encyclopedia of Astrobiology, Astronomy and Spaceflight. . [31] Shiga, David (6 May 2007). "Strange alien world made of "hot ice"" (http:/ / space. newscientist. com/ article/ dn11864-strange-alien-world-made-of-hot-ice-and-steam. html). New Scientist. . Retrieved 2010-03-28. [32] Aguilar, David A. (16 December 2009). "Astronomers Find Super-Earth Using Amateur, Off-the-Shelf Technology" (http:/ / www. cfa. harvard. edu/ news/ 2009/ pr200924. html). Harvard-Smithsonian Center for Astrophysics. . Retrieved 2010-03-28. [33] Gleick, P.H., ed (1993). Water in Crisis: A Guide to the World's Freshwater Resources. Oxford University Press. p.15, Table 2.3. [34] "G8 "Action plan" decided upon at the 2003 Evian summit" (http:/ / www. g8. fr/ evian/ english/ navigation/ 2003_g8_summit/ summit_documents/ water_-_a_g8_action_plan. html). G8.fr. 2003-06-02. . Retrieved 2010-07-25. [35] "World Health Organization. Safe Water and Global Health" (http:/ / www. who. int/ features/ qa/ 70/ en/ ). Who.int. 2008-06-25. . Retrieved 2010-07-25. [36] UNEP International Environment (2002). Environmentally Sound Technology for Wastewater and Stormwater Management: An International Source Book. IWA Publishing. ISBN1843390086. OCLC49204666. [37] Ravindranath, Nijavalli H.; Jayant A. Sathaye (2002). Climate Change and Developing Countries. Springer. ISBN1402001045. OCLC231965991. [38] "WBCSD Water Facts & Trends" (http:/ / www. wbcsd. org/ includes/ getTarget. asp?type=d& id=MTYyNTA). . Retrieved 2010-07-25. [39] Water Use in the United States (http:/ / nationalatlas. gov/ articles/ water/ a_wateruse. html), National Atlas.gov
40
Water
[40] Gleick, P.H. (2010). "Peak Water" (http:/ / www. pacinst. org/ press_center/ press_releases/ peak_water_pnas. pdf). Proceedings National Academy of Science (National Academy of Science) 107 (125): 1115511162. . Retrieved 2011-10-11. [41] United Nations Press Release POP/952, 13 March 2007. World population will increase by 2.5 billion by 2050 (http:/ / www. un. org/ News/ Press/ docs/ 2007/ pop952. doc. htm) [42] Molden, D. (Ed). Water for food, Water for life: A Comprehensive Assessment of Water Management in Agriculture. Earthscan/IWMI, 2007. [43] Chartres, C. and Varma, S. Out of water. From Abundance to Scarcity and How to Solve the Worlds Water Problems FT Press (USA), 2010 [44] Dcret relatif aux poids et aux mesures. 18 germinal an 3 (7 avril 1795) (http:/ / smdsi. quartier-rural. org/ histoire/ 18germ_3. htm). Decree relating to the weights and measurements (in French). quartier-rural.org [45] here L'Histoire Du Mtre, La Dtermination De L'Unit De Poids (http:/ / histoire. du. metre. free. fr/ fr/ index. htm). histoire.du.metre.free.fr [46] Re: What percentage of the human body is composed of water? (http:/ / www. madsci. org/ posts/ archives/ 2000-05/ 958588306. An. r. html) Jeffrey Utz, M.D., The MadSci Network [47] "Healthy Water Living" (http:/ / www. bbc. co. uk/ health/ healthy_living/ nutrition/ drinks_water. shtml). BBC. . Retrieved 2007-02-01. [48] Rhoades RA, Tanner GA (2003). Medical Physiology (2nd ed.). Baltimore: Lippincott Williams & Wilkins. ISBN0781719364. OCLC50554808. [49] Noakes TD, Goodwin N, Rayner BL, et al. (1985). "Water intoxication: a possible complication during endurance exercise" (http:/ / journals. lww. com/ acsm-msse/ Abstract/ 1985/ 06000/ Water_intoxication__a_possible_complication_during. 12. aspx). Med Sci Sports Exerc 17 (3): 370375. PMID4021781. . [50] Noakes TD, Goodwin N, Rayner BL, Branken T, Taylor RK (2005). "Water intoxication: a possible complication during endurance exercise, 1985". Wilderness Environ Med 16 (4): 2217. PMID16366205. [51] "Drink at least eight glasses of water a day." Really? Is there scientific evidence for "8 8"? (http:/ / ajpregu. physiology. org/ cgi/ content/ full/ 283/ 5/ R993) by Heinz Valdin, Department of Physiology, Dartmouth Medical School, Lebanon, New Hampshire [52] Drinking Water How Much? (http:/ / www. factsmart. org/ h2o/ h2o. htm), Factsmart.org web site and references within [53] Food and Nutrition Board, National Academy of Sciences. Recommended Dietary Allowances.. National Research Council, Reprint and Circular Series, No. 122. 1945. pp.318. [54] Dietary Reference Intakes: Water, Potassium, Sodium, Chloride, and Sulfate (http:/ / www. iom. edu/ report. asp?id=18495), Food and Nutrition Board [55] "Water: How much should you drink every day?" (http:/ / www. mayoclinic. com/ health/ water/ NU00283). Mayoclinic.com. . Retrieved 2010-07-25. [56] "Conquering Chemistry" 4th Ed. Published 2008 [57] Maton, Anthea; Jean Hopkins, Charles William McLaughlin, Susan Johnson, Maryanna Quon Warner, David LaHart, Jill D. Wright (1993). Human Biology and Health. Englewood Cliffs, New Jersey, USA: Prentice Hall. ISBN0-13-981176-1. OCLC32308337. [58] Unesco (2006). Water: a shared responsibility (http:/ / books. google. com/ ?id=1cV8tziHZ5sC& pg=PA125). Berghahn Books. p.125. ISBN1845451775. . [59] Vaclavik, Vickie A. and Christian, Elizabeth W (2007). Essentials of Food Science (http:/ / books. google. com/ ?id=iCCsvwZrguUC& printsec=frontcover). Springer. ISBN0387699392. . [60] DeMan, John M (1999). Principles of Food Chemistry (http:/ / books. google. com/ ?id=kDYJ7a1HbD0C& pg=PA434). Springer. ISBN083421234X. . [61] The Millennium Development Goals Report (http:/ / mdgs. un. org/ unsd/ mdg/ Resources/ Static/ Products/ Progress2008/ MDG_Report_2008_En. pdf#page=44), United Nations, 2008 [62] Lomborg, Bjrn (2001). The Skeptical Environmentalist (http:/ / www. lomborg. com/ dyn/ files/ basic_items/ 69-file/ skeptenvironChap1. pdf). Cambridge University Press. p.22. ISBN0521010683. . [63] UNESCO, (2006), Water, a shared responsibility. The United Nations World Water Development Report 2 (http:/ / unesdoc. unesco. org/ images/ 0014/ 001444/ 144409E. pdf). [64] Welle, Katharina; Evans, Barbara; Tucker, Josephine and Nicol, Alan (2008) Is water lagging behind on Aid Effectiveness? (http:/ / www. odi. org. uk/ resources/ download/ 1894. pdf) [65] Water governance (http:/ / www. iwmi. cgiar. org/ Publications/ Water_Issue_Briefs/ index. aspx), Water Issue Brief, Issue 5, 2010, IWMI [66] http:/ / www. awra. org/ [67] "Internet Sacred Text Archive Home" (http:/ / www. sacred-texts. com/ tao/ taote. htm). Sacred-texts.com. . Retrieved 2010-07-25. [68] Arthur Conan Doyle, A Study in Scarlet, Chapter 2, "The Science of Deduction"
41
Water
42
Further reading
Jones, OA., JN Lester and N Voulvoulis, Pharmaceuticals: a threat to drinking water? TRENDS in Biotechnology 23(4): 163, 2005 Franks, F (Ed), Water, A comprehensive treatise, Plenum Press, New York, 19721982 Water in Crisis (http:/ / www. oup. com/ us/ catalog/ general/ subject/ EarthSciences/ Oceanography/ ?view=usa& ci=9780195076288) Gleick,PH., (editor), The World's Water: The Biennial Report on Freshwater Resources. Island Press, Washington, D.C. (published every two years, beginning in 1998.) The World's Water, Island Press (http://www. worldwater.org) Postel,S., Last Oasis: Facing Water Scarcity. W.W. Norton and Company, New York. 1992 Reisner,M., Cadillac Desert: The American West and Its Disappearing Water. Penguin Books, New York. 1986. Debenedetti,PG., and HE Stanley, "Supercooled and Glassy Water", Physics Today 56 (6), p.4046 (2003). Downloadable PDF (1.9 MB) (http://polymer.bu.edu/hes/articles/ds03.pdf) Journal of Contemporary Water Resources and Education (http://ucowr.org/updates/index.html) United Nations World Water Development Report. Produced every three years. UN World Water Development Report (http://www.unesco.org/water/wwap/wwdr/)
External links
OECD Water statistics (http://stats.oecd.org/wbos/Index.aspx?DataSetCode=ENV_WAT) The World's Water Data Page (http://www.worldwater.org) FAO Comprehensive Water Database, AQUASTAT (http://www.fao.org/nr/water/aquastat/main/index.stm) The Water Conflict Chronology: Water Conflict Database (http://worldwater.org/conflict.html) US Geological Survey Water for Schools information (http://ga.water.usgs.gov/edu/) Portal to The World Bank's strategy, work and associated publications on water resources (http://water. worldbank.org/water/)
43
Structural Biochemistry
44
Nucleic acids
Nucleic acid
Nucleic acids are biological molecules essential for life, and include DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information. Nucleic acids were first discovered by Friedrich Miescher in 1871.[1] Experimental studies of nucleic acids constitute a major part of modern biological and medical research, and form a foundation for genome and forensic science, as well as the biotechnology and pharmaceutical industries.[2] [3] [4]
Nucleic acid of nucleic acid molecules are referred to as 5'-end and 3'-end. The nucleobases are joined to the sugars via an N-glycosidic linkage involving a nucleobase ring nitrogen (N-1 for pyrimidines and N-9 for purines) and the 1' carbon of the pentose sugar ring. Non-standard nucleosides are also found in both RNA and DNA and usually arise from modification of the standard nucleosides within the DNA molecule or the primary (initial) RNA transcript. Transfer RNA (tRNA) molecules contain a particularly large number of modified nucleosides.[12]
45
Topology
Double-stranded nucleic acids are made up of complementary sequences, in which extensive Watson-Crick base pairing results in the a highly repeated and quite uniform double-helical three-dimensional structure.[13] In contrast, single-stranded RNA and DNA molecules are not constrained to a regular double helix, and can adopt highly complex three-dimensional structures that are based on short stretches of intramolecular base-paired sequences that include both Watson-Crick and noncanonical base pairs, as well as a wide range of complex tertiary interactions.[14] Nucleic acid molecules are usually unbranched, and may occur as linear and circular molecules. For example, bacterial chromosomes, plasmids, mitochondrial DNA and chloroplast DNA are usually circular double-stranded DNA molecules, while chromosomes of the eukaryotic nucleus are usually linear double-stranded DNA molecules.[7] Most RNA molecules are linear, single-stranded molecules, but both circular and branched molecules can result from RNA splicing reactions.[5]
Ribonucleic acid
Ribonucleic acid (RNA) functions in converting genetic information from genes into the amino acid sequences of proteins. The three universal types of RNA include transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA). Messenger RNA acts to carry genetic sequence information between DNA and ribosomes, directing protein synthesis. Ribosomal RNA is a major component of the ribosome, and catalyzes peptide bond formation. Transfer RNA serves as the carrier molecule for amino acids to be used in protein synthesis, and is responsible for decoding the mRNA. In addition, many other classes of RNA are now known.
Nucleic acid
46
References
[1] Dahm, R (Jan 2008). "Discovering DNA: Friedrich Miescher and the early years of nucleic acid research". Human genetics 122 (6): 56581. doi:10.1007/s00439-007-0433-0. ISSN0340-6717. PMID17901982. [2] International Human Genome Sequencing Consortium (2001). "Initial sequencing and analysis of the human genome." (http:/ / www. nature. com/ nature/ journal/ v409/ n6822/ pdf/ 409860a0. pdf) (PDF). Nature 409 (6822): 860921. doi:10.1038/35057062. PMID11237011. . [3] Venter, JC, et al. (2001). "The sequence of the human genome." (http:/ / www. sciencemag. org/ cgi/ reprint/ 291/ 5507/ 1304. pdf) (PDF). Science 291 (5507): 13041351. doi:10.1126/science.1058040. PMID11181995. . [4] Budowle B, van Daal A (April 2009). "Extracting evidence from forensic DNA analyses: future molecular biology directions". BioTechniques 46 (5): 33940, 34250. doi:10.2144/000113136. PMID19480629. [5] Alberts, Bruce (2008). Molecular biology of the cell. New York: Garland Science. ISBN0-8153-4105-9. [6] Elson D (1965). "Metabolism of nucleic acids (macromolecular DNA and RNA)". Annu. Rev. Biochem. 34: 44986. doi:10.1146/annurev.bi.34.070165.002313. PMID14321176. [7] Brock, Thomas D.; Madigan, Michael T. (2009). Brock biology of microorganisms. Pearson / Benjamin Cummings. ISBN0-321-53615-0. [8] Mullis, Kary B. The Polymerase Chain Reaction (Nobel Lecture). 1993. (retrieved December 1, 2010) http:/ / nobelprize. org/ nobel_prizes/ chemistry/ laureates/ 1993/ mullis-lecture. html [9] Verma S, Eckstein F (1998). "Modified oligonucleotides: synthesis and strategy for users". Annu. Rev. Biochem. 67: 99134. doi:10.1146/annurev.biochem.67.1.99. PMID9759484. [10] Stryer, Lubert; Berg, Jeremy Mark; Tymoczko, John L. (2007). Biochemistry. San Francisco: W.H. Freeman. ISBN0-7167-6766-X. [11] Gregory SG, Barlow KF, McLay KE, et al. (May 2006). "The DNA sequence and biological annotation of human chromosome 1". Nature 441 (7091): 31521. doi:10.1038/nature04727. PMID16710414. [12] Rich A, RajBhandary UL (1976). "Transfer RNA: molecular structure, sequence, and properties". Annu. Rev. Biochem. 45: 80560. doi:10.1146/annurev.bi.45.070176.004105. PMID60910. [13] Watson JD, Crick FH (April 1953). "Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid". Nature 171 (4356): 7378. Bibcode1953Natur.171..737W. doi:10.1038/171737a0. PMID13054692. [14] Ferr-D'Amar AR, Doudna JA (1999). "RNA folds: insights from recent crystal structures". Annu Rev Biophys Biomol Struct 28: 5773. doi:10.1146/annurev.biophys.28.1.57. PMID10410795. [15] Gilbert, Walter G. 1980. DNA Sequencing and Gene Structure (Nobel Lecture) http:/ / nobelprize. org/ nobel_prizes/ chemistry/ laureates/ 1980/ gilbert-lecture. html [16] Sanger, Frederick. 1980. Determination of Nucleotide Sequences in DNA (Nobel Lecture) http:/ / nobelprize. org/ nobel_prizes/ chemistry/ laureates/ 1980/ sanger-lecture. html
Further reading
Wolfram Saenger, Principles of Nucleic Acid Structure, 1984, Springer-Verlag New York Inc. Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter Molecular Biology of the Cell, 2007, ISBN 978-0-8153-4105-5. Fourth edition is available online through the NCBI Bookshelf: link (http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=mboc4) Jeremy M Berg, John L Tymoczko, and Lubert Stryer, Biochemistry 5th edition, 2002, W H Freeman. Available online through the NCBI Bookshelf: link (http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=stryer)
Nucleic acid
47
External links
Interview with Aaron Klug, Nobel Laureate for structural elucidation of biologically important nucleic-acid protein complexes (http://www.vega.org.uk/video/programme/122) provided by the Vega Science Trust. Nucleic Acids Research (Journal) (http://nar.oxfordjournals.org/)
RNA
Ribonucleic acid (English pronunciation: /rab.njukle.k sd/), or RNA, is one of the three major macromolecules (along with DNA and proteins) that are essential for all known forms of life. Like DNA, RNA is made up of a long chain of components called nucleotides. Each nucleotide consists of a nucleobase (sometimes called a nitrogenous base), a ribose sugar, and a phosphate group. The sequence of nucleotides allows RNA to encode genetic information. All cellular organisms use messenger RNA (mRNA) to carry the genetic information that directs the synthesis of proteins. In addition, some viruses use RNA instead of DNA as their genetic material; perhaps a reflection of the suggested key role of RNA in the evolutionary history of life on Earth.[1] [2] Like proteins, some RNA molecules play an active role in cells by catalyzing biological reactions, controlling gene expression, or sensing and communicating responses to cellular signals. One of these active processes is protein synthesis, a universal function whereby mRNA molecules direct the assembly of proteins on ribosomes. This process uses transfer RNA (tRNA) molecules to deliver amino acids to the ribosome, where ribosomal RNA (rRNA) links amino acids together to form proteins. In 2011, it was demonstrated that the methylation of mRNA has a critical role in human energy homeostasis. This opens up the field of RNA epigenetics.[3]
The chemical structure of RNA is very similar to that of DNA, with two differences: (a) RNA contains the sugar ribose, while DNA contains the slightly different sugar deoxyribose (a type of ribose that lacks one oxygen atom), and (b) RNA has the nucleobase uracil while DNA contains thymine. Uracil and thymine have similar base-pairing properties. Unlike DNA, most RNA molecules are single-stranded. Single-stranded RNA molecules adopt very complex three-dimensional structures, since they are not restricted to the repetitive double-helical form of double-stranded DNA. RNA is made within living cells by RNA polymerases, enzymes that act to copy a DNA or RNA template into a new RNA strand through processes known as transcription or RNA replication, respectively.
A hairpin loop from a pre-mRNA. Highlighted are the nucleobases (green) and the ribose-phosphate backbone (blue).
RNA
48
Structure
Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, in general, adenine (A), cytosine (C), guanine (G), or uracil (U). Adenine and guanine are purines, cytosine, and uracil are pyrimidines. A phosphate group is attached to the 3' position of one ribose and the 5' position of the next. The phosphate groups have a negative charge each at physiological pH, making RNA a charged molecule (polyanion). The bases may form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil.[7] However, other interactions are possible, such as a group of adenine bases binding to each other in a bulge,[8] or the GNRA tetraloop that has a guanineadenine base-pair.[7]
RNA
49 An important structural feature of RNA that distinguishes it from DNA is the presence of a hydroxyl group at the 2' position of the ribose sugar. The presence of this functional group causes the helix to adopt the A-form geometry rather than the B-form most commonly observed in DNA.[9] This results in a very deep and narrow major groove and a shallow and wide minor groove.[10] A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule (that is, not involved in formation of a double helix), it can chemically attack the adjacent phosphodiester bond to cleave the backbone.[11]
Chemical structure of RNA
RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil),[12] but these bases and attached sugars can be modified in numerous ways as the RNAs mature. Pseudouridine (), in which the linkage between uracil and ribose is changed from a CN bond to a CC bond, and ribothymidine (T) are found in various places (the most notable ones being in the TC loop of tRNA).[13] Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine (I). Inosine plays a key role in the wobble hypothesis of the genetic code.[14]
There are nearly 100 other naturally occurring modified nucleosides,[15] of which pseudouridine and nucleosides with 2'-O-methylribose are the most common.[16] The specific roles of many of these modifications in RNA are not fully understood. However, it is notable that, in ribosomal RNA, many of the post-transcriptional modifications occur in highly functional regions, such as the peptidyl transferase center and the subunit interface, implying that they are important for normal function.[17] The functional form of single stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements that are hydrogen bonds within the molecule. This leads to several recognizable "domains" of secondary structure like hairpin loops, bulges, and internal loops.[18] Since RNA is charged, metal ions such as Mg2+ are needed to stabilise many secondary and tertiary structures.[19]
Synthesis
Synthesis of RNA is usually catalyzed by an enzymeRNA polymeraseusing DNA as a template, a process known as transcription. Initiation of transcription begins with the binding of the enzyme to a promoter sequence in the DNA (usually found "upstream" of a gene). The DNA double helix is unwound by the helicase activity of the enzyme. The enzyme then progresses along the template strand in the 3 to 5 direction, synthesizing a complementary RNA molecule with elongation occurring in the 5 to 3 direction. The DNA sequence also dictates where termination of RNA synthesis will occur.[20] RNAs are often modified by enzymes after transcription. For example, a poly(A) tail and a 5' cap are added to eukaryotic pre-mRNA and introns are removed by the spliceosome. There are also a number of RNA-dependent RNA polymerases that use RNA as their template for synthesis of a new strand of RNA. For instance, a number of RNA viruses (such as poliovirus) use this type of enzyme to replicate their genetic material.[21] Also, RNA-dependent RNA polymerase is part of the RNA interference pathway in many
RNA organisms.[22]
50
Types of RNA
Overview
Messenger RNA (mRNA) is the RNA that carries information from DNA to the ribosome, the sites of protein synthesis (translation) in the cell. The coding sequence of the mRNA determines the amino acid sequence in the protein that is produced.[23] Many RNAs do not code for protein however (about 97% of the transcriptional output is non-protein-coding in eukaryotes [24] [25] [26] [27] ). These so-called non-coding RNAs ("ncRNA") can be encoded by their own genes (RNA genes), but can also derive from mRNA introns.[28] The most prominent examples of non-coding RNAs are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation.[4] There are also non-coding RNAs involved in gene regulation, RNA processing and other roles. Certain RNAs are able to catalyse chemical reactions such as cutting and ligating other RNA molecules,[29] and the catalysis of peptide bond formation in the ribosome;[6] these are known as ribozymes.
In translation
Messenger RNA (mRNA) carries information about a protein sequence Structure of a hammerhead ribozyme, a ribozyme to the ribosomes, the protein synthesis factories in the cell. It is coded that cuts RNA so that every three nucleotides (a codon) correspond to one amino acid. In eukaryotic cells, once precursor mRNA (pre-mRNA) has been transcribed from DNA, it is processed to mature mRNA. This removes its intronsnon-coding sections of the pre-mRNA. The mRNA is then exported from the nucleus to the cytoplasm, where it is bound to ribosomes and translated into its corresponding protein form with the help of tRNA. In prokaryotic cells, which do not have nucleus and cytoplasm compartments, mRNA can bind to ribosomes while it is being transcribed from DNA. After a certain amount of time the message degrades into its component nucleotides with the assistance of ribonucleases.[23] Transfer RNA (tRNA) is a small RNA chain of about 80 nucleotides that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has sites for amino acid attachment and an anticodon region for codon recognition that binds to a specific sequence on the messenger RNA chain through hydrogen bonding.[28] Ribosomal RNA (rRNA) is the catalytic component of the ribosomes. Eukaryotic ribosomes contain four different rRNA molecules: 18S, 5.8S, 28S and 5S rRNA. Three of the rRNA molecules are synthesized in the nucleolus, and one is synthesized elsewhere. In the cytoplasm, ribosomal RNA and protein combine to form a nucleoprotein called a ribosome. The ribosome binds mRNA and carries out protein synthesis. Several ribosomes may be attached to a single mRNA at any time.[23] Nearly all the RNA found in a typical eukaryotic cell is rRNA. Transfer-messenger RNA (tmRNA) is found in many bacteria and plastids. It tags proteins encoded by mRNAs that lack stop codons for degradation and prevents the ribosome from stalling.[30]
RNA
51
Regulatory RNAs
Several types of RNA can downregulate gene expression by being complementary to a part of an mRNA or a gene's DNA. MicroRNAs (miRNA; 21-22nt) are found in eukaryotes and act through RNA interference (RNAi), where an effector complex of miRNA and enzymes can cleave complementary mRNA, block the mRNA from being translated, or accelerate its degradation.[31] [32] While small interfering RNAs (siRNA; 20-25nt) are often produced by breakdown of viral RNA, there are also endogenous sources of siRNAs.[33] [34] siRNAs act through RNA interference in a fashion similar to miRNAs. Some miRNAs and siRNAs can cause genes they target to be methylated, thereby decreasing or increasing transcription of those genes.[35] [36] [37] Animals have Piwi-interacting RNAs (piRNA; 29-30nt) which are active in germline cells and are thought to be a defense against transposons and play a role in gametogenesis.[38] [39] Many prokaryotes have CRISPR RNAs, a regulatory system similar to RNA interference.[40] Antisense RNAs are widespread; most downregulate a gene, but a few are activators of transcription.[41] One way antisense RNA can act is by binding to an mRNA, forming double-stranded RNA that is enzymatically degraded.[42] There are many long noncoding RNAs that regulate genes in eukaryotes,[43] one such RNA is Xist, which coats one X chromosome in female mammals and inactivates it.[44] An mRNA may contain regulatory elements itself, such as riboswitches, in the 5' untranslated region or 3' untranslated region; these cis-regulatory elements regulate the activity of that mRNA.[45] The untranslated regions can also contain elements that regulate other genes.[46]
In RNA processing
Many RNAs are involved in modifying other RNAs. Introns are spliced out of pre-mRNA by spliceosomes, which contain several small nuclear RNAs (snRNA),[4] or the introns can be ribozymes that are spliced by themselves.[47] RNA can also be altered by having its nucleotides modified to other nucleotides than A, C, G and U. In eukaryotes, modifications of RNA nucleotides are generally directed by small nucleolar RNAs (snoRNA; 60-300nt),[28] found in the Uridine to pseudouridine is a common RNA modification. nucleolus and cajal bodies. snoRNAs associate with enzymes and guide them to a spot on an RNA by basepairing to that RNA. These enzymes then perform the nucleotide modification. rRNAs and tRNAs are extensively modified, but snRNAs and mRNAs can also be the target of base modification.[48] [49] RNA can also be methylated.[50] [51]
RNA genomes
Like DNA, RNA can carry genetic information. RNA viruses have genomes composed of RNA which encodes a number of proteins. The viral genome is replicated by some of those proteins, while other proteins protect the genome as the virus particle moves to a new host cell. Viroids are another group of pathogens, but they consist only of RNA, do not encode any protein and are replicated by a host plant cell's polymerase.[52]
In reverse transcription
Reverse transcribing viruses replicate their genomes by reverse transcribing DNA copies from their RNA; these DNA copies are then transcribed to new RNA. Retrotransposons also spread by copying DNA and RNA from one another,[53] and telomerase contains an RNA that is used as template for building the ends of eukaryotic chromosomes.[54]
RNA
52
Double-stranded RNA
Double-stranded RNA (dsRNA) is RNA with two complementary strands, similar to the DNA found in all cells. dsRNA forms the genetic material of some viruses (double-stranded RNA viruses). Double-stranded RNA such as viral RNA or siRNA can trigger RNA interference in eukaryotes, as well as interferon response in vertebrates.[55] [56]
[57]
References
[1] Yarus, Michael (2011). Getting Past the RNA World: The Initial Darwinian Ancestor. Cold Spring Harb Perspect Biol April 2011;3:a003590 First published online April 21, 2010 doi:10.1101/cshperspect.a003590. http:/ / cshperspectives. cshlp. org/ content/ 3/ 4/ a003590. full [2] Cech TR. (2011). The RNA Worlds in Context. Source: Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado 80309-0215. Cold Spring Harb Perspect Biol. 2011 Feb 16. pii: cshperspect.a006742v1. doi: 10.1101/cshperspect.a006742. [Epub ahead of print] http:/ / cshperspectives. cshlp. org/ content/ early/ 2011/ 02/ 14/ cshperspect. a006742. full. pdf+ html [3] http:/ / www. physorg. com/ news/ 2011-10-links-common-rna-modification-obesity. html [4] Berg JM, Tymoczko JL, Stryer L (2002). Biochemistry (5th ed.). WH Freeman and Company. pp.11819, 781808. ISBN0-7167-4684-0. OCLC179705944 48055706 59502128. [5] Higgs PG (2000). "RNA secondary structure: physical and computational aspects". Quarterly Reviews of Biophysics 33: 199253. doi:10.1017/S0033583500003620. PMID11191843.
RNA
[6] Nissen P, Hansen J, Ban N, Moore PB, Steitz TA (2000). "The structural basis of ribosome activity in peptide bond synthesis". Science 289 (5481): 92030. doi:10.1126/science.289.5481.920. PMID10937990. [7] Lee JC, Gutell RR (2004). "Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs". J. Mol. Biol. 344 (5): 122549. doi:10.1016/j.jmb.2004.09.072. PMID15561141. [8] Barciszewski J, Frederic B, Clark C (1999). RNA biochemistry and biotechnology. Springer. pp.7387. ISBN0792358627. OCLC52403776. [9] Salazar M, Fedoroff OY, Miller JM, Ribeiro NS, Reid BR (1992). "The DNA strand in DNAoRNA hybrid duplexes is neither B-form nor A-form in solution". Biochemistry 32 (16): 420715. doi:10.1021/bi00067a007. PMID7682844. [10] Hermann T, Patel DJ (2000). "RNA bulges as architectural and recognition motifs". Structure 8 (3): R47R54. doi:10.1016/S0969-2126(00)00110-6. PMID10745015. [11] Mikkola S, Nurmi K, Yousefi-Salakdeh E, Strmberg R, Lnnberg H (1999). "The mechanism of the metal ion promoted cleavage of RNA phosphodiester bonds involves a general acid catalysis by the metal aquo ion on the departure of the leaving group". Perkin transactions 2 (8): 161926. doi:10.1039/a903691a. [12] Jankowski JAZ, Polak JM (1996). Clinical gene analysis and manipulation: Tools, techniques and troubleshooting. Cambridge University Press. pp.14. ISBN0521478960. OCLC33838261. [13] Yu Q, Morrow CD (2001). "Identification of critical elements in the tRNA acceptor stem and TC loop necessary for human immunodeficiency virus type 1 infectivity". J Virol. 75 (10): 49026. doi:10.1128/JVI.75.10.4902-4906.2001. PMID11312362. [14] Elliott MS, Trewyn RW (1983). "Inosine biosynthesis in transfer RNA by an enzymatic insertion of hypoxanthine". J. Biol. Chem. 259 (4): 240710. PMID6365911. [15] Sll D, RajBhandary U (1995). TRNA: Structure, biosynthesis, and function. ASM Press. pp.165. ISBN155581073X. OCLC183036381 30663724. [16] Kiss T (2001). "Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs". The EMBO Journal 20: 361722. doi:10.1093/emboj/20.14.3617. PMC125535. PMID11447102. [17] King TH, Liu B, McCully RR, Fournier MJ (2002). "Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center". Molecular Cell 11 (2): 42535. doi:10.1016/S1097-2765(03)00040-6. PMID12620230. [18] Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (2004). "Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure". Proc. Natl. Acad. Sci. USA 101 (19): 728792. Bibcode2004PNAS..101.7287M. doi:10.1073/pnas.0401799101. PMC409911. PMID15123812. [19] Tan ZJ, Chen SJ (2008). "Salt dependence of nucleic acid hairpin stability". Biophys. J. 95 (2): 73852. doi:10.1529/biophysj.108.131524. PMC2440479. PMID18424500. [20] Nudler E, Gottesman ME (2002). "Transcription termination and anti-termination in E. coli". Genes to Cells 7: 75568. doi:10.1046/j.1365-2443.2002.00563.x. PMID12167155. [21] Jeffrey L Hansen, Alexander M Long, Steve C Schultz (1997). "Structure of the RNA-dependent RNA polymerase of poliovirus". Structure 5 (8): 110922. doi:10.1016/S0969-2126(97)00261-X. PMID9309225. [22] Ahlquist P (2002). "RNA-Dependent RNA Polymerases, Viruses, and RNA Silencing". Science 296 (5571): 127073. doi:10.1126/science.1069132. PMID12016304. [23] Cooper GC, Hausman RE (2004). The Cell: A Molecular Approach (3rd ed.). Sinauer. pp.26176, 297, 33944. ISBN0-87893-214-3. OCLC174924833 52121379 52359301 56050609. [24] Mattick JS, Gagen MJ (1 September 2001). "The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms" (http:/ / mbe. oxfordjournals. org/ cgi/ pmidlookup?view=long& pmid=11504843). Mol. Biol. Evol. 18 (9): 161130. PMID11504843. . [25] Mattick, JS (2001). "Noncoding RNAs: the architects of eukaryotic complexity" (http:/ / emboreports. npgjournals. com/ cgi/ content/ full/ 2/ 11/ 986). EMBO Reports 2 (11): 98691. doi:10.1093/embo-reports/kve230. PMC1084129. PMID11713189. . [26] Mattick JS (October 2003). "Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms" (http:/ / www. imb-jena. de/ jcb/ journal_club/ mattick2003. pdf). BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology 25 (10): 9309. doi:10.1002/bies.10332. PMID14505360. . [27] Mattick JS (October 2004). "The hidden genetic program of complex organisms" (http:/ / www. sciam. com/ article. cfm?articleID=00045BB6-5D49-1150-902F83414B7F4945). Scientific American 291 (4): 607. doi:10.1038/scientificamerican1004-60. PMID15487671. . [28] Wirta W (2006). Mining the transcriptome methods and applications (http:/ / kth. diva-portal. org/ smash/ get/ diva2:10803/ FULLTEXT01). Stockholm: School of Biotechnology, Royal Institute of Technology. ISBN91-7178-436-5. OCLC185406288. . [29] Rossi, JJ (2004). "Ribozyme diagnostics comes of age". Chemistry & Biology 11 (7): 89495. doi:10.1016/j.chembiol.2004.07.002. PMID15271347. [30] Gueneau de Novoa P, Williams KP (2004). "The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts". Nucleic Acids Res. 32 (Database issue): D1048. doi:10.1093/nar/gkh102. PMC308836. PMID14681369. [31] Wu L, Belasco JG (January 2008). "Let me count the ways: mechanisms of gene regulation by miRNAs and siRNAs". Mol. Cell 29 (1): 17. doi:10.1016/j.molcel.2007.12.010. PMID18206964. [32] Matzke MA, Matzke AJM (2004). "Planting the seeds of a new paradigm". PLoS Biology 2 (5): e133. doi:10.1371/journal.pbio.0020133. PMC406394. PMID15138502.
53
RNA
[33] Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, Hilbert J, Bartel DP, Crt P (2004). "Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs". Molecular Cell 16 (1): 6979. doi:10.1016/j.molcel.2004.09.028. PMID15469823. [34] Watanabe T, Totoki Y, Toyoda A, et al. (May 2008). "Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes". Nature 453 (7194): 53943. doi:10.1038/nature06908. PMID18404146. [35] Sontheimer EJ, Carthew RW (July 2005). "Silence from within: endogenous siRNAs and miRNAs". Cell 122 (1): 912. doi:10.1016/j.cell.2005.06.030. PMID16009127. [36] Doran G (2007). "RNAi Is one suffix sufficient?" (http:/ / libpubmedia. co. uk/ RNAiJ-Issues/ Issue-5/ Doran. htm). Journal of RNAi and Gene Silencing 3 (1): 21719. . [37] Pushparaj PN, Aarthi JJ, Kumar SD, Manikandan J (2008). "RNAi and RNAa - The Yin and Yang of RNAome". Bioinformation 2 (6): 2357. PMC2258431. PMID18317570. [38] Horwich MD, Li C Matranga C, Vagin V, Farley G, Wang P, Zamore PD (2007). "The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC". Current Biology 17: 126572. doi:10.1016/j.cub.2007.06.030. PMID17604629. [39] Girard A, Sachidanandam R, Hannon GJ, Carmell MA (2006). "A germline-specific class of small RNAs binds mammalian Piwi proteins". Nature 442 (7099): 199202. doi:10.1038/nature04917. PMID16751776. [40] Horvath P, Barrangou R (2010). "CRISPR/Cas, the Immune System of Bacteria and Archaea" (http:/ / www. sciencemag. org/ cgi/ content/ abstract/ 327/ 5962/ 167). Science 327 (5962): 16770. doi:10.1126/science.1179555. PMID20056882. . [41] Wagner EG, Altuvia S, Romby P (2002). "Antisense RNAs in bacteria and their genetic elements". Adv Genet. 46: 36198. doi:10.1016/S0065-2660(02)46013-0. PMID11931231. [42] Gilbert SF (2003). Developmental Biology (7th ed.). Sinauer. pp.1013. ISBN0878932585. OCLC154656422 154663147 174530692 177000492 177316159 51544170 54743254 59197768 61404850 66754122. [43] Amaral PP, Mattick JS (October 2008). "Noncoding RNA in development". Mammalian genome : official journal of the International Mammalian Genome Society 19 (78): 45492. doi:10.1007/s00335-008-9136-7. PMID18839252. [44] Heard E, Mongelard F, Arnaud D, Chureau C, Vourc'h C, Avner P (1999). "Human XIST yeast artificial chromosome transgenes show partial X inactivation center function in mouse embryonic stem cells". Proc. Natl. Acad. Sci. USA 96 (12): 684146. doi:10.1073/pnas.96.12.6841. PMC22003. PMID10359800. [45] Batey RT (2006). "Structures of regulatory elements in mRNAs". Curr. Opin. Struct. Biol. 16 (3): 299306. doi:10.1016/j.sbi.2006.05.001. PMID16707260. [46] Scotto L, Assoian RK (June 1993). "A GC-rich domain with bifunctional effects on mRNA and protein levels: implications for control of transforming growth factor beta 1 expression" (http:/ / mcb. asm. org/ cgi/ pmidlookup?view=long& pmid=8497272). Mol. Cell. Biol. 13 (6): 358897. PMC359828. PMID8497272. . [47] Steitz TA, Steitz JA (1993). "A general two-metal-ion mechanism for catalytic RNA". Proc. Natl. Acad. Sci. U.S.A. 90 (14): 6498502. doi:10.1073/pnas.90.14.6498. PMC46959. PMID8341661. [48] Xie J, Zhang M, Zhou T, Hua X, Tang L, Wu W (2007). "Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs". Nucleic Acids Res. 35 (Database issue): D1837. doi:10.1093/nar/gkl873. PMC1669756. PMID17099227. [49] Omer AD, Ziesche S, Decatur WA, Fournier MJ, Dennis PP (2003). "RNA-modifying machines in archaea". Molecular Microbiology 48 (3): 61729. doi:10.1046/j.1365-2958.2003.03483.x. PMID12694609. [50] Cavaill J, Nicoloso M, Bachellerie JP (1996). "Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides". Nature 383 (6602): 7325. doi:10.1038/383732a0. PMID8878486. [51] Kiss-Lszl Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T (1996). "Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs". Cell 85 (7): 107788. doi:10.1016/S0092-8674(00)81308-2. PMID8674114. [52] Dars JA, Elena SF, Flores R (2006). "Viroids: an Ariadne's thread into the RNA labyrinth". EMBO Rep. 7 (6): 5938. doi:10.1038/sj.embor.7400706. PMC1479586. PMID16741503. [53] Kalendar R, Vicient CM, Peleg O, Anamthawat-Jonsson K, Bolshoy A, Schulman AH (2004). "Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes". Genetics 166 (3): D339. doi:10.1534/genetics.166.3.1437. PMC1470764. PMID15082561. [54] Podlevsky JD, Bley CJ, Omana RV, Qi X, Chen JJ (2008). "The telomerase database". Nucleic Acids Res. 36 (Database issue): D33943. doi:10.1093/nar/gkm700. PMC2238860. PMID18073191. [55] Blevins T et al. (2006). "Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing". Nucleic Acids Res 34 (21): 623346. doi:10.1093/nar/gkl886. PMC1669714. PMID17090584. [56] Jana S, Chakraborty C, Nandi S, Deb JK (2004). "RNA interference: potential therapeutic targets". Appl. Microbiol. Biotechnol. 65 (6): 64957. doi:10.1007/s00253-004-1732-1. PMID15372214. [57] Schultz U, Kaspers B, Staeheli P (2004). "The interferon system of non-mammalian vertebrates". Dev. Comp. Immunol. 28 (5): 499508. doi:10.1016/j.dci.2003.09.009. PMID15062646. [58] Dahm R (2005). "Friedrich Miescher and the discovery of DNA". Developmental Biology 278 (2): 27488. doi:10.1016/j.ydbio.2004.11.028. PMID15680349. [59] Caspersson T, Schultz J (1939). "Pentose nucleotides in the cytoplasm of growing tissues". Nature 143 (3623): 6023. doi:10.1038/143602c0.
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RNA
[60] Ochoa S (1959). "Enzymatic synthesis of ribonucleic acid" (http:/ / nobelprize. org/ nobel_prizes/ medicine/ laureates/ 1959/ ochoa-lecture. pdf). Nobel Lecture. . [61] Holley RW et al. (1965). "Structure of a ribonucleic acid". Science 147 (3664): 146265. doi:10.1126/science.147.3664.1462. PMID14263761. [62] Siebert S (2006). "Common sequence structure properties and stable regions in RNA secondary structures" (http:/ / deposit. ddb. de/ cgi-bin/ dokserv?idn=982323891& dok_var=d1& dok_ext=pdf& filename=982323891. pdf). Dissertation, Albert-Ludwigs-Universitt, Freiburg im Breisgau. pp. 1. . [63] Szathmry E (1999). "The origin of the genetic code: amino acids as cofactors in an RNA world". Trends Genet. 15 (6): 2239. doi:10.1016/S0168-9525(99)01730-8. PMID10354582. [64] Fiers W et al. (1976). "Complete nucleotide-sequence of bacteriophage MS2-RNA: primary and secondary structure of replicase gene". Nature 260 (5551): 5007. Bibcode1976Natur.260..500F. doi:10.1038/260500a0. PMID1264203. [65] Napoli C, Lemieux C, Jorgensen R (1990). "Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans". Plant Cell 2 (4): 27989. doi:10.1105/tpc.2.4.279. PMC159885. PMID12354959. [66] Dafny-Yelin M, Chung SM, Frankman EL, Tzfira T (December 2007). "pSAT RNA interference vectors: a modular series for multiple gene down-regulation in plants". Plant Physiol. 145 (4): 127281. doi:10.1104/pp.107.106062. PMC2151715. PMID17766396. [67] Ruvkun G (2001). "Glimpses of a tiny RNA world". Science 294 (5543): 79799. doi:10.1126/science.1066315. PMID11679654. [68] Fichou Y, Frec C (2006). "The potential of oligonucleotides for therapeutic applications". Trends in Biotechnology 24 (12): 56370. doi:10.1016/j.tibtech.2006.10.003. PMID17045686.
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External links
RNA World website (http://www.imb-jena.de/RNA.html) Link collection (structures, sequences, tools, journals) Nucleic Acid Database (http://ndbserver.rutgers.edu/atlas/xray/) Images of DNA, RNA and complexes. EteRNA (http://eterna.cmu.edu/content/EteRNA) a game forming RNA by pairing bases.
DNA
Deoxyribonucleic acid (English pronunciation: /diksirab.njukle.k sd/( listen); DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms (with the exception of RNA viruses). The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Along with RNA and proteins, DNA is one of the three major macromolecules that are essential for all known forms of life. DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester
The structure of the DNA double helix. The atoms in the structure are colour coded by element and the detailed structure of two base pairs is shown in the bottom right.
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bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called nucleobases (informally, bases). It is the sequence of these four nucleobases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA in a process called transcription. Within cells DNA is organized into long structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, providing each cell its own complete set of chromosomes. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts.[1] In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.
The structure of part of a DNA double helix
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Properties
DNA is a long polymer made from repeating units called nucleotides.[2] [3] [4] As first discovered by James D. Watson and Francis Crick, the structure of DNA of all species comprises two helical chains each coiled round the same axis, and each with a pitch of 34ngstrms (3.4nanometres) and a radius of 10ngstrms (1.0nanometres).[5] According to another study, when measured in a particular solution, the DNA chain measured 22 to 26ngstrms wide (2.2 to 2.6nanometres), and one nucleotide unit measured 3.3 (0.33nm) long.[6] Although each individual repeating unit is very small, DNA polymers can be very large molecules containing millions of nucleotides. For instance, the largest human chromosome, chromosome number 1, is approximately 220 million base pairs long.[7] In living organisms DNA does not usually Chemical structure of DNA. Hydrogen bonds shown as dotted lines. exist as a single molecule, but instead as a pair of molecules that are held tightly together.[5] [8] These two long strands entwine like vines, in the shape of a double helix. The nucleotide repeats contain both the segment of the backbone of the molecule, which holds the chain together, and a nucleobase, which interacts with the other DNA strand in the helix. A nucleobase linked to a sugar is called a nucleoside and a base linked to a sugar and one or more phosphate groups is called a nucleotide. Polymers comprising multiple linked nucleotides (as in DNA) are called a polynucleotide.[9] The backbone of the DNA strand is made from alternating phosphate and sugar residues.[10] The sugar in DNA is 2-deoxyribose, which is a pentose (five-carbon) sugar. The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings. These asymmetric bonds mean a strand of DNA has a direction. In a double helix the direction of the nucleotides in one strand is opposite to their direction in the other strand: the strands are antiparallel. The asymmetric ends of DNA strands are called the 5 (five prime) and 3 (three prime) ends, with the 5' end having a terminal phosphate group and the 3' end a terminal hydroxyl group. One major difference between DNA and RNA is the sugar, with the 2-deoxyribose in DNA being replaced by the alternative pentose sugar ribose in RNA.[8]
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The DNA double helix is stabilized primarily by two forces: hydrogen bonds between nucleotides and base-stacking interactions among the aromatic nucleobases.[12] In the aqueous environment of the cell, the conjugated bonds of nucleotide bases align perpendicular to the axis of the DNA molecule, minimizing their interaction with the solvation shell and therefore, the Gibbs free energy. The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T). These four bases are attached to the sugar/phosphate to form the complete nucleotide, as shown for adenosine monophosphate. The nucleobases are classified into two types: the purines, A and G, being fused five- and six-membered heterocyclic compounds, and the pyrimidines, the six-membered rings C and T.[8] A fifth pyrimidine nucleobase, uracil (U), usually takes the place of thymine in RNA and differs from thymine by lacking a methyl group on its ring. Uracil is not usually found in DNA, occurring only as a breakdown product of cytosine. In addition to RNA and DNA a large number of artificial nucleic acid analogues have also been created to study the proprieties of nucleic acids, or for use in biotechnology.[13]
A section of DNA. The bases lie horizontally between the two [11] spiraling strands. Animated version at File:DNA orbit animated.gif.
Grooves
Twin helical strands form the DNA backbone. Another double helix may be found by tracing the spaces, or grooves, between the strands. These voids are adjacent to the base pairs and may provide a binding site. As the strands are not directly opposite each other, the grooves are unequally sized. One groove, the major groove, is 22 wide and the other, the minor groove, is 12 wide.[14] The narrowness of the minor groove means that the edges of the bases are more accessible in the Major and minor grooves of DNA. Minor groove major groove. As a result, proteins like transcription factors that can is a binding site for the dye Hoechst 33258. bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.[15] This situation varies in unusual conformations of DNA within the cell (see below), but the major and minor grooves are always named to reflect the differences in size that would be seen if the DNA is twisted back into the ordinary B form.
Base pairing
Further information: Base pair In a DNA double helix, each type of nucleobase on one strand normally interacts with just one type of nucleobase on the other strand. This is called complementary base pairing. Here, purines form hydrogen bonds to pyrimidines, with A bonding only to T, and C bonding only to G. This arrangement of two nucleotides binding together across the double helix is called a base pair. As hydrogen bonds are not covalent, they can be broken and rejoined relatively easily. The two strands of DNA in a double helix can therefore be pulled apart like a zipper, either by a mechanical force or high temperature.[16] As a result of this complementarity, all the information in the double-stranded sequence of a DNA helix is duplicated on each strand, which is vital in DNA replication. Indeed, this reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms.[3]
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Top, a GC base pair with three hydrogen bonds. Bottom, an AT base pair with two hydrogen bonds. Non-covalent hydrogen bonds between the pairs are shown as dashed lines. The two types of base pairs form different numbers of hydrogen bonds, AT forming two hydrogen bonds, and GC forming three hydrogen bonds (see figures, left). DNA with high GC-content is more stable than DNA with low GC-content. Although it is often stated that this is due to the added stability of an additional hydrogen bond, this is incorrect. DNA with high GC-content is more stable due to intra-strand base stacking interactions. As noted above, most DNA molecules are actually two polymer strands, bound together in a helical fashion by noncovalent bonds; this double stranded structure (dsDNA) is maintained largely by the intrastrand base stacking interactions, which are strongest for G,C stacks. The two strands can come apart a process known as melting to form two ss DNA molecules. Melting occurs when conditions favor ssDNA; such conditions are high temperature, low salt and high pH (low pH also melts DNA, but since DNA is unstable due to acid depurination, low pH is rarely used). The stability of the dsDNA form depends not only on the GC-content (% G,C basepairs) but also on sequence (since stacking is sequence specific) and also length (longer molecules are more stable). The stability can be measured in various ways; a common way is the "melting temperature", which is the temperature at which 50% of the ds molecules are converted to ss molecules; melting temperature is dependent on ionic strength and the concentration of DNA. As a result, it is both the percentage of GC base pairs and the overall length of a DNA double helix that determine the strength of the association between the two strands of DNA. Long DNA helices with a high GC-content have stronger-interacting strands, while short helices with high AT content have weaker-interacting strands.[17] In biology, parts of the DNA double helix that need to separate easily, such as the TATAAT Pribnow box in some promoters, tend to have a high AT content, making the strands easier to pull apart.[18] In the laboratory, the strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds, their melting temperature (also called Tm value). When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two entirely independent molecules. These single-stranded DNA molecules (ssDNA) have no single common shape, but some conformations are more stable than others.[19]
DNA other strand. In bacteria, this overlap may be involved in the regulation of gene transcription,[24] while in viruses, overlapping genes increase the amount of information that can be encoded within the small viral genome.[25]
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Supercoiling
Further information: DNA supercoil DNA can be twisted like a rope in a process called DNA supercoiling. With DNA in its "relaxed" state, a strand usually circles the axis of the double helix once every 10.4 base pairs, but if the DNA is twisted the strands become more tightly or more loosely wound.[26] If the DNA is twisted in the direction of the helix, this is positive supercoiling, and the bases are held more tightly together. If they are twisted in the opposite direction, this is negative supercoiling, and the bases come apart more easily. In nature, most DNA has slight negative supercoiling that is introduced by enzymes called topoisomerases.[27] These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as transcription and DNA replication.[28]
The first published reports of A-DNA X-ray diffraction patterns and also B-DNA used analyses based on Patterson transforms that provided only a limited amount of structural information for oriented fibers of DNA.[30] [31] An alternate analysis was then proposed by Wilkins et al., in 1953, for the in vivo B-DNA X-ray diffraction/scattering patterns of highly hydrated DNA fibers in terms of squares of Bessel functions.[32] In the same journal, James D. Watson and Francis Crick presented their molecular modeling analysis of the DNA X-ray diffraction patterns to suggest that the structure was a double-helix.[5] Although the `B-DNA form' is most common under the conditions found in cells,[33] it is not a well-defined conformation but a family of related DNA conformations[34] that occur at the high hydration levels present in living cells. Their corresponding X-ray diffraction and scattering patterns are characteristic of molecular paracrystals with a significant degree of disorder.[35] [36] Compared to B-DNA, the A-DNA form is a wider right-handed spiral, with a shallow, wide minor groove and a narrower, deeper major groove. The A form occurs under non-physiological conditions in partially dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands, as well as in enzyme-DNA complexes.[37] [38] Segments of DNA where the bases have been chemically modified by methylation may undergo a larger change in conformation and adopt the Z form. Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form.[39] These unusual structures can be recognized by specific Z-DNA binding proteins and may be involved in the regulation of transcription.[40]
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Quadruplex structures
Further information: G-quadruplex At the ends of the linear chromosomes are specialized regions of DNA called telomeres. The main function of these regions is to allow the cell to replicate chromosome ends using the enzyme telomerase, as the enzymes that normally replicate DNA cannot copy the extreme 3 ends of chromosomes.[44] These specialized chromosome caps also help protect the DNA ends, and stop the DNA repair systems in the cell from treating them as damage to be corrected.[45] In human cells, telomeres are usually lengths of single-stranded DNA containing several thousand repeats of a simple TTAGGG sequence.[46] These guanine-rich sequences may stabilize chromosome ends by forming structures of stacked sets of four-base units, rather than the usual base pairs found in other DNA molecules. Here, four guanine bases form a flat plate and these flat four-base units then stack on top of each other, to form a stable G-quadruplex structure.[48] These structures are stabilized by hydrogen bonding between the edges of the bases and chelation of a metal ion in the centre of each four-base unit.[49] Other structures can also be formed, with the central set of four bases coming from either a single strand folded around the bases, or several different parallel strands, each contributing one base to the central structure.
In addition to these stacked structures, telomeres also form large loop structures called telomere loops, or T-loops. Here, the single-stranded DNA curls around in a long circle stabilized by telomere-binding proteins.[50] At the very end of the T-loop, the single-stranded telomere DNA is held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical DNA and base pairing to one of the two strands. This triple-stranded structure is called a displacement loop or D-loop.[48]
DNA quadruplex formed by telomere repeats. The looped conformation of the DNA backbone [47] is very different from the typical DNA helix.
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Single branch Multiple branches
Branched DNA
Further information: Branched DNA and DNA nanotechnology In DNA fraying occurs when non-complementary regions exist at the end of an otherwise complementary double-strand of DNA. However, branched DNA can occur if a third strand of DNA is introduced and contains adjoining regions able to hybridize with the frayed regions of the pre-existing double-strand. Although the simplest example of branched DNA involves only three strands of DNA, complexes involving additional strands and multiple branches are also possible.[51] Branched DNA can be used in nanotechnology to construct geometric shapes, see the section on uses in technology below.
Vibration
DNA may carry out low-frequency collective motion as observed by the Raman spectroscopy[52] with a quasi-continuum model.[54] [55]
[53]
and analyzed
Chemical modifications
cytosine
5-methylcytosine
thymine
Structure of cytosine with and without the 5-methyl group. Deamination converts 5-methylcytosine into thymine.
Base modifications
Further information: DNA methylation The expression of genes is influenced by how the DNA is packaged in chromosomes, in a structure called chromatin. Base modifications can be involved in packaging, with regions that have low or no gene expression usually containing high levels of methylation of cytosine bases. For example, cytosine methylation, produces 5-methylcytosine, which is important for X-chromosome inactivation.[56] The average level of methylation varies between organisms the worm Caenorhabditis elegans lacks cytosine methylation, while vertebrates have higher levels, with up to 1% of their DNA containing 5-methylcytosine.[57] Despite the importance of 5-methylcytosine, it can deaminate to leave a thymine base, so methylated cytosines are particularly prone to mutations.[58] Other base modifications include adenine methylation in bacteria, the presence of 5-hydroxymethylcytosine in the brain,[59] and the glycosylation of uracil to produce the "J-base" in kinetoplastids.[60] [61]
DNA
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Damage
Further information: Mutation DNA can be damaged by many sorts of mutagens, which change the DNA sequence. Mutagens include oxidizing agents, alkylating agents and also high-energy electromagnetic radiation such as ultraviolet light and X-rays. The type of DNA damage produced depends on the type of mutagen. For example, UV light can damage DNA by producing thymine dimers, which are cross-links between pyrimidine bases.[63] On the other hand, oxidants such as free radicals or hydrogen peroxide produce multiple forms of damage, including base modifications, particularly of guanosine, and double-strand breaks.[64] A typical human cell contains about 150,000 bases that have suffered oxidative damage.[65] Of these oxidative lesions, the most dangerous are double-strand breaks, as these are difficult to repair and can produce point mutations, insertions and deletions from the DNA sequence, as well as chromosomal translocations.[66] Many mutagens fit into the space between two adjacent base pairs, this A covalent adduct between a metabolically is called intercalation. Most intercalators are aromatic and planar activated form of benzo[a]pyrene, the major molecules; examples include ethidium bromide, acridines, [62] mutagen in tobacco smoke, and DNA daunomycin, and doxorubicin. In order for an intercalator to fit between base pairs, the bases must separate, distorting the DNA strands by unwinding of the double helix. This inhibits both transcription and DNA replication, causing toxicity and mutations.[67] As a result, DNA intercalators may be carcinogens, and in the case of thalidomide, a teratogen.[68] Others such as benzo[a]pyrene diol epoxide and aflatoxin form DNA adducts which induce errors in replication.[69] Nevertheless, due to their ability to inhibit DNA transcription and replication, other similar toxins are also used in chemotherapy to inhibit rapidly growing cancer cells.[70]
Biological functions
DNA usually occurs as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. The set of chromosomes in a cell makes up its genome; the human genome has approximately 3 billion base pairs of DNA arranged into 46 chromosomes.[71] The information carried by DNA is held in the sequence of pieces of DNA called genes. Transmission of genetic information in genes is achieved via complementary base pairing. For example, in transcription, when a cell uses the information in a gene, the DNA sequence is copied into a complementary RNA sequence through the attraction between the DNA and the correct RNA nucleotides. Usually, this RNA copy is then used to make a matching protein sequence in a process called translation, which depends on the same interaction between RNA nucleotides. In alternative fashion, a cell may simply copy its genetic information in a process called DNA replication. The details of these functions are covered in other articles; here we focus on the interactions between DNA and other molecules that mediate the function of the genome.
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biosynthesis A gene is a sequence of DNA that contains genetic information and can influence the phenotype of an organism. Within a gene, the sequence of bases along a DNA strand defines a messenger RNA sequence, which then defines one or more protein sequences. The relationship between the nucleotide sequences of genes and the amino-acid sequences of proteins is determined by the rules of translation, known collectively as the genetic code. The genetic code consists of three-letter 'words' called codons formed from a sequence of three nucleotides (e.g. ACT, CAG, TTT). In transcription, the codons of a gene are copied into messenger RNA by RNA polymerase. This RNA copy is then decoded by a ribosome that reads the RNA sequence by base-pairing the messenger RNA to transfer RNA, which carries amino acids. Since there are 4 bases in 3-letter combinations, there are 64 possible codons ( combinations). These encode the twenty standard amino acids, giving most amino acids more than one possible codon. There are also three 'stop' or 'nonsense' codons signifying the end of the coding region; these are the TAA, TGA and TAG codons.
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Replication
Further information: DNA replication Cell division is essential for an organism to grow, but, when a cell divides, it must replicate the DNA in its genome so that the two daughter cells have the same genetic information as their parent. The double-stranded structure of DNA provides a simple mechanism for DNA DNA replication. The double helix is unwound by a helicase and topoisomerase. Next, replication. Here, the two strands are one DNA polymerase produces the leading strand copy. Another DNA polymerase binds to the lagging strand. This enzyme makes discontinuous segments (called Okazaki separated and then each strand's fragments) before DNA ligase joins them together. complementary DNA sequence is recreated by an enzyme called DNA polymerase. This enzyme makes the complementary strand by finding the correct base through complementary base pairing, and bonding it onto the original strand. As DNA polymerases can only extend a DNA strand in a 5 to 3 direction, different mechanisms are used to copy the antiparallel strands of the double helix.[80] In this way, the base on the old strand dictates which base appears on the new strand, and the cell ends up with a perfect copy of its DNA.
DNA-binding proteins
Further information: DNA-binding protein
Interaction of DNA (shown in orange) with histones (shown in blue). These proteins' basic amino acids bind to the acidic phosphate groups on DNA. Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. Within chromosomes, DNA is held in complexes with structural proteins. These proteins organize the DNA into a compact structure called chromatin. In eukaryotes this structure involves DNA binding to a complex of small basic proteins called histones, while in prokaryotes multiple types of proteins are involved.[81] [82] The histones form a disk-shaped complex called a nucleosome, which contains two complete turns of double-stranded DNA wrapped around its surface. These non-specific interactions are formed through basic residues in the histones making ionic bonds to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence.[83] Chemical modifications of these basic amino acid residues include methylation, phosphorylation and acetylation.[84]
DNA These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription.[85] Other non-specific DNA-binding proteins in chromatin include the high-mobility group proteins, which bind to bent or distorted DNA.[86] These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that make up chromosomes.[87] A distinct group of DNA-binding proteins are the DNA-binding proteins that specifically bind single-stranded DNA. In humans, replication protein A is the best-understood member of this family and is used in processes where the double helix is separated, including DNA replication, recombination and DNA repair.[88] These binding proteins seem to stabilize single-stranded DNA and protect it from forming stem-loops or being degraded by nucleases. In contrast, other proteins have evolved to bind to particular DNA sequences. The most intensively studied of these are the various transcription factors, which are proteins that regulate transcription. Each transcription factor binds to one particular set of DNA sequences and activates or inhibits the transcription of genes that have these sequences close to their promoters. The transcription factors do this in two ways. Firstly, they can bind the RNA polymerase responsible for transcription, either directly or through other mediator proteins; this locates the polymerase at the promoter and allows it to begin transcription.[90] Alternatively, transcription factors can bind enzymes that modify the histones at the promoter; this will change the accessibility of the DNA template to the polymerase.[91] As these DNA targets can occur throughout an organism's genome, changes in The lambda repressor the activity of one type of transcription factor can affect thousands of genes.[92] helix-turn-helix transcription factor Consequently, these proteins are often the targets of the signal transduction [89] bound to its DNA target processes that control responses to environmental changes or cellular differentiation and development. The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to "read" the DNA sequence. Most of these base-interactions are made in the major groove, where the bases are most accessible.[15]
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DNA-modifying enzymes
Nucleases and ligases Nucleases are enzymes that cut DNA strands by catalyzing the hydrolysis of the phosphodiester bonds. Nucleases that hydrolyse nucleotides from the ends of DNA strands are called exonucleases, while endonucleases cut within strands. The most frequently used nucleases in molecular biology are the restriction endonucleases, which The restriction enzyme EcoRV (green) in a [93] cut DNA at specific sequences. For instance, the EcoRV enzyme complex with its substrate DNA shown to the left recognizes the 6-base sequence 5-GAT|ATC-3 and makes a cut at the vertical line. In nature, these enzymes protect bacteria against phage infection by digesting the phage DNA when it enters the bacterial cell, acting as part of the restriction modification system.[94] In technology, these sequence-specific nucleases are used in molecular cloning and DNA fingerprinting. Enzymes called DNA ligases can rejoin cut or broken DNA strands.[95] Ligases are particularly important in lagging strand DNA replication, as they join together the short segments of DNA produced at the replication fork into a complete copy of the DNA template. They are also used in DNA repair and genetic recombination.[95]
DNA Topoisomerases and helicases Topoisomerases are enzymes with both nuclease and ligase activity. These proteins change the amount of supercoiling in DNA. Some of these enzymes work by cutting the DNA helix and allowing one section to rotate, thereby reducing its level of supercoiling; the enzyme then seals the DNA break.[27] Other types of these enzymes are capable of cutting one DNA helix and then passing a second strand of DNA through this break, before rejoining the helix.[96] Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription.[28] Helicases are proteins that are a type of molecular motor. They use the chemical energy in nucleoside triphosphates, predominantly ATP, to break hydrogen bonds between bases and unwind the DNA double helix into single strands.[97] These enzymes are essential for most processes where enzymes need to access the DNA bases. Polymerases Polymerases are enzymes that synthesize polynucleotide chains from nucleoside triphosphates. The sequence of their products are copies of existing polynucleotide chains which are called templates. These enzymes function by adding nucleotides onto the 3 hydroxyl group of the previous nucleotide in a DNA strand. As a consequence, all polymerases work in a 5 to 3 direction.[98] In the active site of these enzymes, the incoming nucleoside triphosphate base-pairs to the template: this allows polymerases to accurately synthesize the complementary strand of their template. Polymerases are classified according to the type of template that they use. In DNA replication, a DNA-dependent DNA polymerase makes a copy of a DNA sequence. Accuracy is vital in this process, so many of these polymerases have a proofreading activity. Here, the polymerase recognizes the occasional mistakes in the synthesis reaction by the lack of base pairing between the mismatched nucleotides. If a mismatch is detected, a 3 to 5 exonuclease activity is activated and the incorrect base removed.[99] In most organisms, DNA polymerases function in a large complex called the replisome that contains multiple accessory subunits, such as the DNA clamp or helicases.[100] RNA-dependent DNA polymerases are a specialized class of polymerases that copy the sequence of an RNA strand into DNA. They include reverse transcriptase, which is a viral enzyme involved in the infection of cells by retroviruses, and telomerase, which is required for the replication of telomeres.[44] [101] Telomerase is an unusual polymerase because it contains its own RNA template as part of its structure.[45] Transcription is carried out by a DNA-dependent RNA polymerase that copies the sequence of a DNA strand into RNA. To begin transcribing a gene, the RNA polymerase binds to a sequence of DNA called a promoter and separates the DNA strands. It then copies the gene sequence into a messenger RNA transcript until it reaches a region of DNA called the terminator, where it halts and detaches from the DNA. As with human DNA-dependent DNA polymerases, RNA polymerase II, the enzyme that transcribes most of the genes in the human genome, operates as part of a large protein complex with multiple regulatory and accessory subunits.[102]
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DNA
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Genetic recombination
Structure of the Holliday junction intermediate in genetic recombination. The four separate DNA strands are coloured red, blue, green and yellow.[103] Further information: Genetic recombination A DNA helix usually does not interact with other segments of DNA, and in human cells the different chromosomes even occupy separate areas in the nucleus called "chromosome territories".[104] This physical separation of different chromosomes is important for the ability of DNA to function as a stable repository for information, as one of the few times chromosomes interact is during chromosomal crossover when they recombine. Chromosomal crossover is when two DNA helices break, swap a section and then rejoin. Recombination allows chromosomes to exchange genetic information and produces new combinations of genes, which increases the efficiency of natural selection and can be important in the rapid evolution of new proteins.[105] Genetic recombination can also be involved in DNA repair, particularly in the cell's response to double-strand breaks.[106] The most common form of chromosomal crossover is homologous recombination, where the two chromosomes involved share very similar sequences. Non-homologous recombination can be damaging to cells, as it can produce chromosomal translocations and genetic abnormalities. The recombination reaction is catalyzed by enzymes known as recombinases, such as RAD51.[107] The first step in recombination is a double-stranded break either caused by an endonuclease or damage to the DNA.[108] A series of steps catalyzed in part by the recombinase then leads to joining of the two helices by at least one Holliday junction, in which a segment of a single strand in each helix is annealed to the complementary strand in the other helix. The Holliday junction is a tetrahedral junction structure that can be moved along the pair of chromosomes, swapping one strand for another. The recombination reaction is then halted by cleavage of the junction and re-ligation of the released DNA.[109]
Recombination involves the breakage and rejoining of two chromosomes (M and F) to produce two re-arranged chromosomes (C1 and C2).
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Evolution
Further information: RNA world hypothesis DNA contains the genetic information that allows all modern living things to function, grow and reproduce. However, it is unclear how long in the 4-billion-year history of life DNA has performed this function, as it has been proposed that the earliest forms of life may have used RNA as their genetic material.[98] [110] RNA may have acted as the central part of early cell metabolism as it can both transmit genetic information and carry out catalysis as part of ribozymes.[111] This ancient RNA world where nucleic acid would have been used for both catalysis and genetics may have influenced the evolution of the current genetic code based on four nucleotide bases. This would occur, since the number of different bases in such an organism is a trade-off between a small number of bases increasing replication accuracy and a large number of bases increasing the catalytic efficiency of ribozymes.[112] However, there is no direct evidence of ancient genetic systems, as recovery of DNA from most fossils is impossible. This is because DNA will survive in the environment for less than one million years and slowly degrades into short fragments in solution.[113] Claims for older DNA have been made, most notably a report of the isolation of a viable bacterium from a salt crystal 250 million years old,[114] but these claims are controversial.[115] [116] On August 8, 2011, a report, based on NASA studies with meteorites found on Earth, was published suggesting building blocks of DNA (adenine, guanine and related organic molecules) may have been formed extraterrestrially in outer space.[117] [118] [119]
Uses in technology
Genetic engineering
Further information: Molecular biology, nucleic acid methods and genetic engineering Methods have been developed to purify DNA from organisms, such as phenol-chloroform extraction, and to manipulate it in the laboratory, such as restriction digests and the polymerase chain reaction. Modern biology and biochemistry make intensive use of these techniques in recombinant DNA technology. Recombinant DNA is a man-made DNA sequence that has been assembled from other DNA sequences. They can be transformed into organisms in the form of plasmids or in the appropriate format, by using a viral vector.[120] The genetically modified organisms produced can be used to produce products such as recombinant proteins, used in medical research,[121] or be grown in agriculture.[122] [123]
Forensics
Further information: DNA profiling Forensic scientists can use DNA in blood, semen, skin, saliva or hair found at a crime scene to identify a matching DNA of an individual, such as a perpetrator. This process is formally termed DNA profiling, but may also be called "genetic fingerprinting". In DNA profiling, the lengths of variable sections of repetitive DNA, such as short tandem repeats and minisatellites, are compared between people. This method is usually an extremely reliable technique for identifying a matching DNA.[124] However, identification can be complicated if the scene is contaminated with DNA from several people.[125] DNA profiling was developed in 1984 by British geneticist Sir Alec Jeffreys,[126] and first used in forensic science to convict Colin Pitchfork in the 1988 Enderby murders case.[127] The development of forensic science,and the ability to now obtain genetic matching on minute samples of blood, skin, saliva or hair has led to a re-examination of a number of cases. Evidence can now be uncovered that was not scientifically possible at the time of the original examination. Combined with the removal of the double jeopardy law, this allows cases to be reopened where previous trials have failed to produce sufficient evidence to convince a jury. People charged with serious crimes may be required to provide a sample of DNA for matching purposes. The most obvious defence to DNA matches obtained forensically is to claim that cross-contamination of evidence has
DNA taken place. This has resulted in meticulous strict handling procedures with new cases of serious crime. DNA profiling is also be used to identify victims of mass casualty incidents.[128] As well as positively identifying bodies or body parts in serious accidents, DNA profiling is being successfully used to identify individual victims in mass war graves - matching to family members.
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Bioinformatics
Further information: Bioinformatics Bioinformatics involves the manipulation, searching, and data mining of biological data, and this includes DNA sequence data. The development of techniques to store and search DNA sequences have led to widely applied advances in computer science, especially string searching algorithms, machine learning and database theory.[129] String searching or matching algorithms, which find an occurrence of a sequence of letters inside a larger sequence of letters, were developed to search for specific sequences of nucleotides.[130] The DNA sequenced may be aligned with other DNA sequences to identify homologous sequences and locate the specific mutations that make them distinct. These techniques, especially multiple sequence alignment, are used in studying phylogenetic relationships and protein function.[131] Data sets representing entire genomes' worth of DNA sequences, such as those produced by the Human Genome Project, are difficult to use without the annotations that identify the locations of genes and regulatory elements on each chromosome. Regions of DNA sequence that have the characteristic patterns associated with protein- or RNA-coding genes can be identified by gene finding algorithms, which allow researchers to predict the presence of particular gene products and their possible functions in an organism even before they have been isolated experimentally.[132] Entire genomes may also be compared which can shed light on the evolutionary history of particular organism and permit the examination of complex evolutionary events.
DNA nanotechnology
Further information: nanotechnology DNA
DNA nanotechnology uses the unique molecular recognition properties of DNA and other nucleic acids to create self-assembling branched DNA complexes with useful properties.[133] DNA is thus used as a structural material rather than as a carrier of biological information. This has led to the creation of two-dimensional The DNA structure at left (schematic shown) will self-assemble into the structure periodic lattices (both tile-based as visualized by atomic force microscopy at right. DNA nanotechnology is the field that well as using the "DNA origami" seeks to design nanoscale structures using the molecular recognition properties of DNA method) as well as three-dimensional molecules. Image from Strong, 2004 (doi:10.1371/journal.pbio.0020073). structures in the shapes of polyhedra.[134] Nanomechanical devices and algorithmic self-assembly have also been demonstrated,[135] and these DNA structures have been used to template the arrangement of other molecules such as gold nanoparticles and streptavidin proteins.[136]
DNA Because DNA collects mutations over time, which are then inherited, it contains historical information, and, by comparing DNA sequences, geneticists can infer the evolutionary history of organisms, their phylogeny.[137] This field of phylogenetics is a powerful tool in evolutionary biology. If DNA sequences within a species are compared, population geneticists can learn the history of particular populations. This can be used in studies ranging from ecological genetics to anthropology; For example, DNA evidence is being used to try to identify the Ten Lost Tribes of Israel.[138] [139] DNA has also been used to look at modern family relationships, such as establishing family relationships between the descendants of Sally Hemings and Thomas Jefferson. This usage is closely related to the use of DNA in criminal investigations detailed above. Indeed, some criminal investigations have been solved when DNA from crime scenes has matched relatives of the guilty individual.[140]
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James D. Watson and Francis Crick (right), co-originators of the double-helix model, with Maclyn McCarty (left).
In 1927 Nikolai Koltsov proposed that inherited traits would be inherited via a "giant hereditary molecule" which would be made up of "two mirror strands that would replicate in a semi-conservative fashion using each strand as a template".[145] In 1928, Frederick Griffith discovered that traits of the "smooth" form of the Pneumococcus could be transferred to the "rough" form of the same bacteria by mixing killed "smooth" bacteria with the live "rough" form.[146] This system provided the first clear suggestion that DNA carries genetic informationthe AveryMacLeodMcCarty experimentwhen Oswald Avery, along with coworkers Colin MacLeod and Maclyn McCarty, identified DNA as the transforming principle in 1943.[147] DNA's role in heredity was confirmed in 1952, when Alfred Hershey and Martha Chase in the HersheyChase experiment showed that DNA is the genetic material of the T2 phage.[148] In 1953, James D. Watson and Francis Crick suggested what is now accepted as the first correct double-helix model of DNA structure in the journal Nature.[5] Their double-helix, molecular model of DNA was then based on a single X-ray diffraction image (labeled as "Photo 51")[149] taken by Rosalind Franklin and Raymond Gosling in May 1952, as well as the information that the DNA bases are paired also obtained through private communications from Erwin Chargaff in the previous years. Chargaff's rules played a very important role in establishing double-helix configurations for B-DNA as well as A-DNA. Experimental evidence supporting the Watson and Crick model were published in a series of five articles in the same issue of Nature.[150] Of these, Franklin and Gosling's paper was the first publication of their own X-ray diffraction data and original analysis method that partially supported the Watson and Crick model;[31] [151] this issue also contained an article on DNA structure by Maurice Wilkins and two of his colleagues, whose analysis and in vivo B-DNA X-ray patterns also supported the presence in vivo of the double-helical DNA configurations as proposed by
DNA Crick and Watson for their double-helix molecular model of DNA in the previous two pages of Nature.[32] In 1962, after Franklin's death, Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine.[152] However, Nobel rules of the time allowed only living recipients, but a vigorous debate continues on who should receive credit for the discovery.[153] In an influential presentation in 1957, Crick laid out the central dogma of molecular biology, which foretold the relationship between DNA, RNA, and proteins, and articulated the "adaptor hypothesis".[154] Final confirmation of the replication mechanism that was implied by the double-helical structure followed in 1958 through the MeselsonStahl experiment.[155] Further work by Crick and coworkers showed that the genetic code was based on non-overlapping triplets of bases, called codons, allowing Har Gobind Khorana, Robert W. Holley and Marshall Warren Nirenberg to decipher the genetic code.[156] These findings represent the birth of molecular biology.
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References
[1] Russell, Peter (2001). iGenetics. New York: Benjamin Cummings. ISBN0-8053-4553-1. [2] Saenger, Wolfram (1984). Principles of Nucleic Acid Structure. New York: Springer-Verlag. ISBN0-387-90762-9. [3] Alberts, Bruce; Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts and Peter Walters (2002). Molecular Biology of the Cell; Fourth Edition (http:/ / www. ncbi. nlm. nih. gov/ books/ bv. fcgi?call=bv. View. . ShowTOC& rid=mboc4. TOC& depth=2). New York and London: Garland Science. ISBN0-8153-3218-1. OCLC145080076 48122761 57023651 69932405. . [4] Butler, John M. (2001). Forensic DNA Typing. Elsevier. ISBN978-0-12-147951-0. OCLC223032110 45406517. pp. 1415. [5] Watson J.D. and Crick F.H.C. (1953). "A Structure for Deoxyribose Nucleic Acid" (http:/ / www. nature. com/ nature/ dna50/ watsoncrick. pdf) (PDF). Nature 171 (4356): 737738. Bibcode1953Natur.171..737W. doi:10.1038/171737a0. PMID13054692. . [6] Mandelkern M, Elias J, Eden D, Crothers D (1981). "The dimensions of DNA in solution". J Mol Biol 152 (1): 15361. doi:10.1016/0022-2836(81)90099-1. PMID7338906. [7] Gregory S; Barlow, KF; McLay, KE; Kaul, R; Swarbreck, D; Dunham, A; Scott, CE; Howe, KL et al. (2006). "The DNA sequence and biological annotation of human chromosome 1". Nature 441 (7091): 31521. Bibcode2006Natur.441..315G. doi:10.1038/nature04727. PMID16710414. [8] Berg J., Tymoczko J. and Stryer L. (2002) Biochemistry. W. H. Freeman and Company ISBN 0-7167-4955-6 [9] Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents (http:/ / www. chem. qmul. ac. uk/ iupac/ misc/ naabb. html) IUPAC-IUB Commission on Biochemical Nomenclature (CBN). Retrieved 03 January 2006. [10] Ghosh A, Bansal M (2003). "A glossary of DNA structures from A to Z". Acta Crystallogr D 59 (4): 6206. doi:10.1107/S0907444903003251. PMID12657780. [11] Created from PDB 1D65 (http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1D65) [12] Yakovchuk P, Protozanova E, Frank-Kamenetskii MD (2006). "Base-stacking and base-pairing contributions into thermal stability of the DNA double helix". Nucleic Acids Res. 34 (2): 56474. doi:10.1093/nar/gkj454. PMC1360284. PMID16449200. [13] Verma S, Eckstein F (1998). "Modified oligonucleotides: synthesis and strategy for users". Annu. Rev. Biochem. 67: 99134. doi:10.1146/annurev.biochem.67.1.99. PMID9759484. [14] Wing R, Drew H, Takano T, Broka C, Tanaka S, Itakura K, Dickerson R (1980). "Crystal structure analysis of a complete turn of B-DNA". Nature 287 (5784): 7558. Bibcode1980Natur.287..755W. doi:10.1038/287755a0. PMID7432492. [15] Pabo C, Sauer R (1984). "Protein-DNA recognition". Annu Rev Biochem 53: 293321. doi:10.1146/annurev.bi.53.070184.001453. PMID6236744. [16] Clausen-Schaumann H, Rief M, Tolksdorf C, Gaub H (2000). "Mechanical stability of single DNA molecules". Biophys J 78 (4): 19972007. Bibcode2000BpJ....78.1997C. doi:10.1016/S0006-3495(00)76747-6. PMC1300792. PMID10733978. [17] Chalikian T, Vlker J, Plum G, Breslauer K (1999). "A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volumetric techniques". Proc Natl Acad Sci USA 96 (14): 78538. Bibcode1999PNAS...96.7853C. doi:10.1073/pnas.96.14.7853. PMC22151. PMID10393911. [18] deHaseth P, Helmann J (1995). "Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA". Mol Microbiol 16 (5): 81724. doi:10.1111/j.1365-2958.1995.tb02309.x. PMID7476180. [19] Isaksson J, Acharya S, Barman J, Cheruku P, Chattopadhyaya J (2004). "Single-stranded adenine-rich DNA and RNA retain structural characteristics of their respective double-stranded conformations and show directional differences in stacking pattern". Biochemistry 43 (51): 159966010. doi:10.1021/bi048221v. PMID15609994. [20] Designation of the two strands of DNA (http:/ / www. chem. qmul. ac. uk/ iubmb/ newsletter/ misc/ DNA. html) JCBN/NC-IUB Newsletter 1989, Accessed 07 May 2008 [21] Httenhofer A, Schattner P, Polacek N (2005). "Non-coding RNAs: hope or hype?". Trends Genet 21 (5): 28997. doi:10.1016/j.tig.2005.03.007. PMID15851066. [22] Munroe S (2004). "Diversity of antisense regulation in eukaryotes: multiple mechanisms, emerging patterns". J Cell Biochem 93 (4): 66471. doi:10.1002/jcb.20252. PMID15389973.
DNA
[23] Makalowska I, Lin C, Makalowski W (2005). "Overlapping genes in vertebrate genomes". Comput Biol Chem 29 (1): 112. doi:10.1016/j.compbiolchem.2004.12.006. PMID15680581. [24] Johnson Z, Chisholm S (2004). "Properties of overlapping genes are conserved across microbial genomes". Genome Res 14 (11): 226872. doi:10.1101/gr.2433104. PMC525685. PMID15520290. [25] Lamb R, Horvath C (1991). "Diversity of coding strategies in influenza viruses". Trends Genet 7 (8): 2616. PMID1771674. [26] Benham C, Mielke S (2005). "DNA mechanics". Annu Rev Biomed Eng 7: 2153. doi:10.1146/annurev.bioeng.6.062403.132016. PMID16004565. [27] Champoux J (2001). "DNA topoisomerases: structure, function, and mechanism". Annu Rev Biochem 70: 369413. doi:10.1146/annurev.biochem.70.1.369. PMID11395412. [28] Wang J (2002). "Cellular roles of DNA topoisomerases: a molecular perspective". Nat Rev Mol Cell Biol 3 (6): 43040. doi:10.1038/nrm831. PMID12042765. [29] Basu H, Feuerstein B, Zarling D, Shafer R, Marton L (1988). "Recognition of Z-RNA and Z-DNA determinants by polyamines in solution: experimental and theoretical studies". J Biomol Struct Dyn 6 (2): 299309. PMID2482766. [30] Franklin RE, Gosling RG (6 March 1953). "The Structure of Sodium Thymonucleate Fibres I. The Influence of Water Content" (http:/ / hekto. med. unc. edu:8080/ CARTER/ carter_WWW/ Bioch_134/ PDF_files/ Franklin_Gossling. pdf). Acta Crystallogr 6 (89): 6737. doi:10.1107/S0365110X53001939. . Franklin RE, Gosling RG (1953). "The structure of sodium thymonucleate fibres. II. The cylindrically symmetrical Patterson function". Acta Crystallogr 6 (89): 67885. doi:10.1107/S0365110X53001940. [31] Franklin, Rosalind and Gosling, Raymond (1953). "Molecular Configuration in Sodium Thymonucleate. Franklin R. and Gosling R.G" (http:/ / www. nature. com/ nature/ dna50/ franklingosling. pdf) (PDF). Nature 171 (4356): 7401. Bibcode1953Natur.171..740F. doi:10.1038/171740a0. PMID13054694. . [32] Wilkins M.H.F., A.R. Stokes A.R. & Wilson, H.R. (1953). "Molecular Structure of Deoxypentose Nucleic Acids" (http:/ / www. nature. com/ nature/ dna50/ wilkins. pdf) (PDF). Nature 171 (4356): 738740. Bibcode1953Natur.171..738W. doi:10.1038/171738a0. PMID13054693. . [33] Leslie AG, Arnott S, Chandrasekaran R, Ratliff RL (1980). "Polymorphism of DNA double helices". J. Mol. Biol. 143 (1): 4972. doi:10.1016/0022-2836(80)90124-2. PMID7441761. [34] Baianu, I.C. (1980). "Structural Order and Partial Disorder in Biological systems". Bull. Math. Biol. 42 (4): 137141. http:/ / cogprints. org/ 3822/ [35] Hosemann R., Bagchi R.N., Direct analysis of diffraction by matter, North-Holland Publs., Amsterdam New York, 1962. [36] Baianu, I.C. (1978). "X-ray scattering by partially disordered membrane systems". Acta Crystallogr A 34 (5): 751753. Bibcode1978AcCrA..34..751B. doi:10.1107/S0567739478001540. [37] Wahl M, Sundaralingam M (1997). "Crystal structures of A-DNA duplexes". Biopolymers 44 (1): 4563. doi:10.1002/(SICI)1097-0282(1997)44:1<45::AID-BIP4>3.0.CO;2-#. PMID9097733. [38] Lu XJ, Shakked Z, Olson WK (2000). "A-form conformational motifs in ligand-bound DNA structures". J. Mol. Biol. 300 (4): 81940. doi:10.1006/jmbi.2000.3690. PMID10891271. [39] Rothenburg S, Koch-Nolte F, Haag F (2001). "DNA methylation and Z-DNA formation as mediators of quantitative differences in the expression of alleles". Immunol Rev 184: 28698. doi:10.1034/j.1600-065x.2001.1840125.x. PMID12086319. [40] Oh D, Kim Y, Rich A (2002). "Z-DNA-binding proteins can act as potent effectors of gene expression in vivo". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 1666671. Bibcode2002PNAS...9916666O. doi:10.1073/pnas.262672699. PMC139201. PMID12486233. [41] "Arsenic-loving bacteria may help in hunt for alien life" (http:/ / www. bbc. co. uk/ news/ science-environment-11886943). BBC News. December 2, 2010. . Retrieved 2010-12-02. [42] Bortman, Henry (2010-12-02). "Arsenic-Eating Bacteria Opens New Possibilities for Alien Life" (http:/ / www. space. com/ scienceastronomy/ arsenic-bacteria-alien-life-101202. html). Space.Com web site (http:/ / www. space. com/ ) (Space.com). . Retrieved 2010-12-02. [43] "Arsenic-eating microbe may redefine chemistry of life" (http:/ / www. nature. com/ news/ 2010/ 101202/ full/ news. 2010. 645. html). Nature News. 2 December 2010. . Retrieved 2010-12-02. [44] Greider C, Blackburn E (1985). "Identification of a specific telomere terminal transferase activity in Tetrahymena extracts". Cell 43 (2 Pt 1): 40513. doi:10.1016/0092-8674(85)90170-9. PMID3907856. [45] Nugent C, Lundblad V (1998). "The telomerase reverse transcriptase: components and regulation". Genes Dev 12 (8): 107385. doi:10.1101/gad.12.8.1073. PMID9553037. [46] Wright W, Tesmer V, Huffman K, Levene S, Shay J (1997). "Normal human chromosomes have long G-rich telomeric overhangs at one end". Genes Dev 11 (21): 28019. doi:10.1101/gad.11.21.2801. PMC316649. PMID9353250. [47] Created from NDB UD0017 (http:/ / ndbserver. rutgers. edu/ atlas/ xray/ structures/ U/ ud0017/ ud0017. html) [48] Burge S, Parkinson G, Hazel P, Todd A, Neidle S (2006). "Quadruplex DNA: sequence, topology and structure". Nucleic Acids Res 34 (19): 540215. doi:10.1093/nar/gkl655. PMC1636468. PMID17012276. [49] Parkinson G, Lee M, Neidle S (2002). "Crystal structure of parallel quadruplexes from human telomeric DNA". Nature 417 (6891): 87680. doi:10.1038/nature755. PMID12050675. [50] Griffith J, Comeau L, Rosenfield S, Stansel R, Bianchi A, Moss H, de Lange T (1999). "Mammalian telomeres end in a large duplex loop". Cell 97 (4): 50314. doi:10.1016/S0092-8674(00)80760-6. PMID10338214.
73
DNA
[51] Seeman NC (2005). "DNA enables nanoscale control of the structure of matter". Q. Rev. Biophys. 38 (4): 36371. doi:10.1017/S0033583505004087. PMID16515737. [52] Painter PC, Mosher LE, Rhoads C (1982). "Low-frequency modes in the Raman spectra of proteins". Biopolymers 21 (7): 146972. doi:10.1002/bip.360210715. PMID7115900. [53] Urabe H, Tominaga Y, Kubota K (1983). "Experimental evidence of collective vibrations in DNA double helix (Raman spectroscopy)". Journal of Chemical Physics 78 (10): 59375939. Bibcode1983JChPh..78.5937U. doi:10.1063/1.444600. [54] Chou KC (1984). "Low-frequency vibrations of DNA molecules". Biochem. J. 221 (1): 2731. PMC1143999. PMID6466317. [55] Chou KC, Maggiora GM, Mao B (1989). "Quasi-continuum models of twist-like and accordion-like low-frequency motions in DNA". Biophys. J. 56 (2): 295305. Bibcode1989BpJ....56..295C. doi:10.1016/S0006-3495(89)82676-1. PMC1280479. PMID2775828. [56] Klose R, Bird A (2006). "Genomic DNA methylation: the mark and its mediators". Trends Biochem Sci 31 (2): 8997. doi:10.1016/j.tibs.2005.12.008. PMID16403636. [57] Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev 16 (1): 621. doi:10.1101/gad.947102. PMID11782440. [58] Walsh C, Xu G (2006). "Cytosine methylation and DNA repair". Curr Top Microbiol Immunol. Current Topics in Microbiology and Immunology 301: 283315. doi:10.1007/3-540-31390-7_11. ISBN3-540-29114-8. PMID16570853. [59] Kriaucionis S, Heintz N (2009). "The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain". Science 324 (5929): 92930. Bibcode2009Sci...324..929K. doi:10.1126/science.1169786. PMID19372393. [60] Ratel D, Ravanat J, Berger F, Wion D (2006). "N6-methyladenine: the other methylated base of DNA". Bioessays 28 (3): 30915. doi:10.1002/bies.20342. PMC2754416. PMID16479578. [61] Gommers-Ampt J, Van Leeuwen F, de Beer A, Vliegenthart J, Dizdaroglu M, Kowalak J, Crain P, Borst P (1993). "beta-D-glucosyl-hydroxymethyluracil: a novel modified base present in the DNA of the parasitic protozoan T. brucei". Cell 75 (6): 112936. doi:10.1016/0092-8674(93)90322-H. PMID8261512. [62] Created from PDB 1JDG (http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1JDG) [63] Douki T, Reynaud-Angelin A, Cadet J, Sage E (2003). "Bipyrimidine photoproducts rather than oxidative lesions are the main type of DNA damage involved in the genotoxic effect of solar UVA radiation". Biochemistry 42 (30): 92216. doi:10.1021/bi034593c. PMID12885257. [64] Cadet J, Delatour T, Douki T, Gasparutto D, Pouget J, Ravanat J, Sauvaigo S (1999). "Hydroxyl radicals and DNA base damage". Mutat Res 424 (12): 921. doi:10.1016/S0027-5107(99)00004-4. PMID10064846. [65] Beckman KB, Ames BN (1997). "Oxidative decay of DNA". J. Biol. Chem. 272 (32): 196336. doi:10.1074/jbc.272.32.19633. PMID9289489. [66] Valerie K, Povirk L (2003). "Regulation and mechanisms of mammalian double-strand break repair". Oncogene 22 (37): 5792812. doi:10.1038/sj.onc.1206679. PMID12947387. [67] Ferguson L, Denny W (1991). "The genetic toxicology of acridines". Mutat Res 258 (2): 12360. PMID1881402. [68] Stephens T, Bunde C, Fillmore B (2000). "Mechanism of action in thalidomide teratogenesis". Biochem Pharmacol 59 (12): 148999. doi:10.1016/S0006-2952(99)00388-3. PMID10799645. [69] Jeffrey A (1985). "DNA modification by chemical carcinogens". Pharmacol Ther 28 (2): 23772. doi:10.1016/0163-7258(85)90013-0. PMID3936066. [70] Braa M, Cacho M, Gradillas A, de Pascual-Teresa B, Ramos A (2001). "Intercalators as anticancer drugs". Curr Pharm Des 7 (17): 174580. doi:10.2174/1381612013397113. PMID11562309. [71] Venter J; Adams, MD; Myers, EW; Li, PW; Mural, RJ; Sutton, GG; Smith, HO; Yandell, M et al. (2001). "The sequence of the human genome". Science 291 (5507): 130451. Bibcode2001Sci...291.1304V. doi:10.1126/science.1058040. PMID11181995. [72] Thanbichler M, Wang S, Shapiro L (2005). "The bacterial nucleoid: a highly organized and dynamic structure". J Cell Biochem 96 (3): 50621. doi:10.1002/jcb.20519. PMID15988757. [73] Wolfsberg T, McEntyre J, Schuler G (2001). "Guide to the draft human genome". Nature 409 (6822): 8246. doi:10.1038/35057000. PMID11236998. [74] Gregory T (2005). "The C-value enigma in plants and animals: a review of parallels and an appeal for partnership". Ann Bot (Lond) 95 (1): 13346. doi:10.1093/aob/mci009. PMID15596463. [75] The ENCODE Project Consortium (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature 447 (7146): 799816. Bibcode2007Natur.447..799B. doi:10.1038/nature05874. PMC2212820. PMID17571346. [76] Created from PDB 1MSW (http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1MSW) [77] Pidoux A, Allshire R (2005). "The role of heterochromatin in centromere function". Philos Trans R Soc Lond B Biol Sci 360 (1455): 56979. doi:10.1098/rstb.2004.1611. PMC1569473. PMID15905142. [78] Harrison P, Hegyi H, Balasubramanian S, Luscombe N, Bertone P, Echols N, Johnson T, Gerstein M (2002). "Molecular Fossils in the Human Genome: Identification and Analysis of the Pseudogenes in Chromosomes 21 and 22". Genome Res 12 (2): 27280. doi:10.1101/gr.207102. PMC155275. PMID11827946. [79] Harrison P, Gerstein M (2002). "Studying genomes through the aeons: protein families, pseudogenes and proteome evolution". J Mol Biol 318 (5): 115574. doi:10.1016/S0022-2836(02)00109-2. PMID12083509. [80] Alb M (2001). "Replicative DNA polymerases". Genome Biol 2 (1): REVIEWS3002. doi:10.1186/gb-2001-2-1-reviews3002. PMC150442. PMID11178285. [81] Sandman K, Pereira S, Reeve J (1998). "Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome". Cell Mol Life Sci 54 (12): 135064. doi:10.1007/s000180050259. PMID9893710.
74
DNA
[82] Dame RT (2005). "The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin". Mol. Microbiol. 56 (4): 85870. doi:10.1111/j.1365-2958.2005.04598.x. PMID15853876. [83] Luger K, Mder A, Richmond R, Sargent D, Richmond T (1997). "Crystal structure of the nucleosome core particle at 2.8 A resolution". Nature 389 (6648): 25160. Bibcode1997Natur.389..251L. doi:10.1038/38444. PMID9305837. [84] Jenuwein T, Allis C (2001). "Translating the histone code". Science 293 (5532): 107480. doi:10.1126/science.1063127. PMID11498575. [85] Ito T (2003). "Nucleosome assembly and remodelling". Curr Top Microbiol Immunol. Current Topics in Microbiology and Immunology 274: 122. doi:10.1007/978-3-642-55747-7_1. ISBN978-3-540-44208-0. PMID12596902. [86] Thomas J (2001). "HMG1 and 2: architectural DNA-binding proteins". Biochem Soc Trans 29 (Pt 4): 395401. doi:10.1042/BST0290395. PMID11497996. [87] Grosschedl R, Giese K, Pagel J (1994). "HMG domain proteins: architectural elements in the assembly of nucleoprotein structures". Trends Genet 10 (3): 94100. doi:10.1016/0168-9525(94)90232-1. PMID8178371. [88] Iftode C, Daniely Y, Borowiec J (1999). "Replication protein A (RPA): the eukaryotic SSB". Crit Rev Biochem Mol Biol 34 (3): 14180. doi:10.1080/10409239991209255. PMID10473346. [89] Created from PDB 1LMB (http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1LMB) [90] Myers L, Kornberg R (2000). "Mediator of transcriptional regulation". Annu Rev Biochem 69: 72949. doi:10.1146/annurev.biochem.69.1.729. PMID10966474. [91] Spiegelman B, Heinrich R (2004). "Biological control through regulated transcriptional coactivators". Cell 119 (2): 15767. doi:10.1016/j.cell.2004.09.037. PMID15479634. [92] Li Z, Van Calcar S, Qu C, Cavenee W, Zhang M, Ren B (2003). "A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells". Proc Natl Acad Sci USA 100 (14): 81649. Bibcode2003PNAS..100.8164L. doi:10.1073/pnas.1332764100. PMC166200. PMID12808131. [93] Created from PDB 1RVA (http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1RVA) [94] Bickle T, Krger D (1993). "Biology of DNA restriction". Microbiol Rev 57 (2): 43450. PMC372918. PMID8336674. [95] Doherty A, Suh S (2000). "Structural and mechanistic conservation in DNA ligases". Nucleic Acids Res 28 (21): 40518. doi:10.1093/nar/28.21.4051. PMC113121. PMID11058099. [96] Schoeffler A, Berger J (2005). "Recent advances in understanding structure-function relationships in the type II topoisomerase mechanism". Biochem Soc Trans 33 (Pt 6): 146570. doi:10.1042/BST20051465. PMID16246147. [97] Tuteja N, Tuteja R (2004). "Unraveling DNA helicases. Motif, structure, mechanism and function". Eur J Biochem 271 (10): 184963. doi:10.1111/j.1432-1033.2004.04094.x. PMID15128295. [98] Joyce C, Steitz T (1995). "Polymerase structures and function: variations on a theme?". J Bacteriol 177 (22): 63219. PMC177480. PMID7592405. [99] Hubscher U, Maga G, Spadari S (2002). "Eukaryotic DNA polymerases". Annu Rev Biochem 71: 13363. doi:10.1146/annurev.biochem.71.090501.150041. PMID12045093. [100] Johnson A, O'Donnell M (2005). "Cellular DNA replicases: components and dynamics at the replication fork". Annu Rev Biochem 74: 283315. doi:10.1146/annurev.biochem.73.011303.073859. PMID15952889. [101] Tarrago-Litvak L, Androla M, Nevinsky G, Sarih-Cottin L, Litvak S (1 May 1994). "The reverse transcriptase of HIV-1: from enzymology to therapeutic intervention". FASEB J 8 (8): 497503. PMID7514143. [102] Martinez E (2002). "Multi-protein complexes in eukaryotic gene transcription". Plant Mol Biol 50 (6): 92547. doi:10.1023/A:1021258713850. PMID12516863. [103] Created from PDB 1M6G (http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1M6G) [104] Cremer T, Cremer C (2001). "Chromosome territories, nuclear architecture and gene regulation in mammalian cells". Nat Rev Genet 2 (4): 292301. doi:10.1038/35066075. PMID11283701. [105] Pl C, Papp B, Lercher M (2006). "An integrated view of protein evolution". Nat Rev Genet 7 (5): 33748. doi:10.1038/nrg1838. PMID16619049. [106] O'Driscoll M, Jeggo P (2006). "The role of double-strand break repair insights from human genetics". Nat Rev Genet 7 (1): 4554. doi:10.1038/nrg1746. PMID16369571. [107] Visp S, Defais M (1997). "Mammalian Rad51 protein: a RecA homologue with pleiotropic functions". Biochimie 79 (910): 58792. doi:10.1016/S0300-9084(97)82007-X. PMID9466696. [108] Neale MJ, Keeney S (2006). "Clarifying the mechanics of DNA strand exchange in meiotic recombination". Nature 442 (7099): 1538. Bibcode2006Natur.442..153N. doi:10.1038/nature04885. PMID16838012. [109] Dickman M, Ingleston S, Sedelnikova S, Rafferty J, Lloyd R, Grasby J, Hornby D (2002). "The RuvABC resolvasome". Eur J Biochem 269 (22): 5492501. doi:10.1046/j.1432-1033.2002.03250.x. PMID12423347. [110] Orgel L (2004). "Prebiotic chemistry and the origin of the RNA world". Crit Rev Biochem Mol Biol 39 (2): 99123. doi:10.1080/10409230490460765. PMID15217990. [111] Davenport R (2001). "Ribozymes. Making copies in the RNA world". Science 292 (5520): 1278. doi:10.1126/science.292.5520.1278a. PMID11360970. [112] Szathmry E (1992). "What is the optimum size for the genetic alphabet?". Proc Natl Acad Sci USA 89 (7): 26148. Bibcode1992PNAS...89.2614S. doi:10.1073/pnas.89.7.2614. PMC48712. PMID1372984.
75
DNA
[113] Lindahl T (1993). "Instability and decay of the primary structure of DNA". Nature 362 (6422): 70915. Bibcode1993Natur.362..709L. doi:10.1038/362709a0. PMID8469282. [114] Vreeland R, Rosenzweig W, Powers D (2000). "Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal". Nature 407 (6806): 897900. doi:10.1038/35038060. PMID11057666. [115] Hebsgaard M, Phillips M, Willerslev E (2005). "Geologically ancient DNA: fact or artefact?". Trends Microbiol 13 (5): 21220. doi:10.1016/j.tim.2005.03.010. PMID15866038. [116] Nickle D, Learn G, Rain M, Mullins J, Mittler J (2002). "Curiously modern DNA for a "250 million-year-old" bacterium". J Mol Evol 54 (1): 1347. doi:10.1007/s00239-001-0025-x. PMID11734907. [117] Callahan, M.P.; Smith, K.E.; Cleaves, H.J.; Ruzica, J.; Stern, J.C.; Glavin, D.P.; House, C.H.; Dworkin, J.P. (11 August 2011). "Carbonaceous meteorites contain a wide range of extraterrestrial nucleobases" (http:/ / www. pnas. org/ content/ early/ 2011/ 08/ 10/ 1106493108). PNAS. doi:10.1073/pnas.1106493108. . Retrieved 2011-08-15. [118] Steigerwald, John (08 August 2011). "NASA Researchers: DNA Building Blocks Can Be Made in Space" (http:/ / www. nasa. gov/ topics/ solarsystem/ features/ dna-meteorites. html). NASA. . Retrieved 2011-08-10. [119] ScienceDaily Staff (09 August 2011). "DNA Building Blocks Can Be Made in Space, NASA Evidence Suggests" (http:/ / www. sciencedaily. com/ releases/ 2011/ 08/ 110808220659. htm). ScienceDaily. . Retrieved 2011-08-09. [120] Goff SP, Berg P (1976). "Construction of hybrid viruses containing SV40 and lambda phage DNA segments and their propagation in cultured monkey cells". Cell 9 (4 PT 2): 695705. doi:10.1016/0092-8674(76)90133-1. PMID189942. [121] Houdebine L (2007). "Transgenic animal models in biomedical research". Methods Mol Biol 360: 163202. doi:10.1385/1-59745-165-7:163. ISBN1-59745-165-7. PMID17172731. [122] Daniell H, Dhingra A (2002). "Multigene engineering: dawn of an exciting new era in biotechnology". Curr Opin Biotechnol 13 (2): 13641. doi:10.1016/S0958-1669(02)00297-5. PMID11950565. [123] Job D (2002). "Plant biotechnology in agriculture". Biochimie 84 (11): 110510. doi:10.1016/S0300-9084(02)00013-5. PMID12595138. [124] Collins A, Morton N (1994). "Likelihood ratios for DNA identification". Proc Natl Acad Sci USA 91 (13): 600711. Bibcode1994PNAS...91.6007C. doi:10.1073/pnas.91.13.6007. PMC44126. PMID8016106. [125] Weir B, Triggs C, Starling L, Stowell L, Walsh K, Buckleton J (1997). "Interpreting DNA mixtures". J Forensic Sci 42 (2): 21322. PMID9068179. [126] Jeffreys A, Wilson V, Thein S (1985). "Individual-specific 'fingerprints' of human DNA". Nature 316 (6023): 769. Bibcode1985Natur.316...76J. doi:10.1038/316076a0. PMID2989708. [127] Colin Pitchfork first murder conviction on DNA evidence also clears the prime suspect (http:/ / web. archive. org/ web/ 20061214004903/ http:/ / www. forensic. gov. uk/ forensic_t/ inside/ news/ list_casefiles. php?case=1) Forensic Science Service Accessed 23 December 2006 [128] "DNA Identification in Mass Fatality Incidents" (http:/ / massfatality. dna. gov/ Introduction/ ). National Institute of Justice. September 2006. . [129] Baldi, Pierre; Brunak, Soren (2001). Bioinformatics: The Machine Learning Approach. MIT Press. ISBN978-0-262-02506-5. OCLC45951728. [130] Gusfield, Dan. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, 15 January 1997. ISBN 978-0-521-58519-4. [131] Sjlander K (2004). "Phylogenomic inference of protein molecular function: advances and challenges". Bioinformatics 20 (2): 1709. doi:10.1093/bioinformatics/bth021. PMID14734307. [132] Mount DM (2004). Bioinformatics: Sequence and Genome Analysis (2 ed.). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. ISBN0-87969-712-1. OCLC55106399. [133] Rothemund PW (2006). "Folding DNA to create nanoscale shapes and patterns". Nature 440 (7082): 297302. Bibcode2006Natur.440..297R. doi:10.1038/nature04586. PMID16541064. [134] Andersen ES, Dong M, Nielsen MM (2009). "Self-assembly of a nanoscale DNA box with a controllable lid". Nature 459 (7243): 736. Bibcode2009Natur.459...73A. doi:10.1038/nature07971. PMID19424153. [135] Ishitsuka Y, Ha T (2009). "DNA nanotechnology: a nanomachine goes live". Nat Nanotechnol 4 (5): 2812. Bibcode2009NatNa...4..281I. doi:10.1038/nnano.2009.101. PMID19421208. [136] Aldaye FA, Palmer AL, Sleiman HF (2008). "Assembling materials with DNA as the guide". Science 321 (5897): 17959. Bibcode2008Sci...321.1795A. doi:10.1126/science.1154533. PMID18818351. [137] Wray G; Martindale, Mark Q. (2002). "Dating branches on the Tree of Life using DNA". Genome Biol 3 (1): REVIEWS0001. doi:10.1046/j.1525-142X.1999.99010.x. PMC150454. PMID11806830. [138] Lost Tribes of Israel, NOVA, PBS airdate: 22 February 2000. Transcript available from PBS.org (http:/ / www. pbs. org/ wgbh/ nova/ transcripts/ 2706israel. html). Retrieved 4 March 2006. [139] Kleiman, Yaakov. "The Cohanim/DNA Connection: The fascinating story of how DNA studies confirm an ancient biblical tradition". (http:/ / www. aish. com/ societywork/ sciencenature/ the_cohanim_-_dna_connection. asp) aish.com (January 13, 2000). Retrieved 4 March 2006. [140] Bhattacharya, Shaoni. "Killer convicted thanks to relative's DNA". (http:/ / www. newscientist. com/ article. ns?id=dn4908) newscientist.com (20 April 2004). Retrieved 22 December 06.
76
DNA
[141] Dahm R (2008). "Discovering DNA: Friedrich Miescher and the early years of nucleic acid research". Hum. Genet. 122 (6): 56581. doi:10.1007/s00439-007-0433-0. PMID17901982. [142] Jones, Mary Ellen (September 1953). "Albrecht Kossel, A Biographical Sketch". Yale Journal of Biology and Medicine (National Center for Biotechnology Information) 26 (1): 8097. PMC2599350. PMID13103145. [143] Levene P, (1 December 1919). "The structure of yeast nucleic acid". J Biol Chem 40 (2): 41524. [144] Astbury W, (1947). "Nucleic acid". Symp. SOC. Exp. Biol. 1 (66). [145] Valery N. Soyfer (2001). "The consequences of political dictatorship for Russian science". Nature Reviews Genetics 2 (9): 723729. doi:10.1038/35088598. PMID11533721. [146] Lorenz MG, Wackernagel W (1994). "Bacterial gene transfer by natural genetic transformation in the environment". Microbiol. Rev. 58 (3): 563602. PMC372978. PMID7968924. [147] Avery O, MacLeod C, McCarty M (1944). "STUDIES ON THE CHEMICAL NATURE OF THE SUBSTANCE INDUCING TRANSFORMATION OF PNEUMOCOCCAL TYPES : INDUCTION OF TRANSFORMATION BY A DESOXYRIBONUCLEIC ACID FRACTION ISOLATED FROM PNEUMOCOCCUS TYPE III". J Exp Med 79 (2): 137158. doi:10.1084/jem.79.2.137. PMC2135445. PMID19871359. [148] Hershey A, Chase M (1952). "INDEPENDENT FUNCTIONS OF VIRAL PROTEIN AND NUCLEIC ACID IN GROWTH OF BACTERIOPHAGE". J Gen Physiol 36 (1): 3956. doi:10.1085/jgp.36.1.39. PMC2147348. PMID12981234. [149] The B-DNA X-ray pattern on the right of this linked image (http:/ / osulibrary. oregonstate. edu/ specialcollections/ coll/ pauling/ dna/ pictures/ sci9. 001. 5. html) was obtained by Rosalind Franklin and Raymond Gosling in May 1952 at high hydration levels of DNA and it has been labeled as "Photo 51" [150] Nature Archives Double Helix of DNA: 50 Years (http:/ / www. nature. com/ nature/ dna50/ archive. html) [151] "Original X-ray diffraction image" (http:/ / osulibrary. oregonstate. edu/ specialcollections/ coll/ pauling/ dna/ pictures/ franklin-typeBphoto. html). Osulibrary.oregonstate.edu. . Retrieved 2011-02-06. [152] The Nobel Prize in Physiology or Medicine 1962 (http:/ / nobelprize. org/ nobel_prizes/ medicine/ laureates/ 1962/ ) Nobelprize .org Accessed 22 December 06 [153] Brenda Maddox (23 January 2003). "The double helix and the 'wronged heroine'" (http:/ / www. biomath. nyu. edu/ index/ course/ hw_articles/ nature4. pdf) (PDF). Nature 421 (6921): 407408. doi:10.1038/nature01399. PMID12540909. . [154] Crick, F.H.C. On degenerate templates and the adaptor hypothesis (PDF). (http:/ / genome. wellcome. ac. uk/ assets/ wtx030893. pdf) genome.wellcome.ac.uk (Lecture, 1955). Retrieved 22 December 2006. [155] Meselson M, Stahl F (1958). "THE REPLICATION OF DNA IN ESCHERICHIA COLI". Proc Natl Acad Sci USA 44 (7): 67182. Bibcode1958PNAS...44..671M. doi:10.1073/pnas.44.7.671. PMC528642. PMID16590258. [156] The Nobel Prize in Physiology or Medicine 1968 (http:/ / nobelprize. org/ nobel_prizes/ medicine/ laureates/ 1968/ ) Nobelprize.org Accessed 22 December 06
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Further reading
Berry, Andrew; Watson, James D. (2003). DNA: the secret of life. New York: Alfred A. Knopf. ISBN0-375-41546-7. Calladine, Chris R.; Drew, Horace R.; Luisi, Ben F. and Travers, Andrew A. (2003). Understanding DNA: the molecule & how it works. Amsterdam: Elsevier Academic Press. ISBN0-12-155089-3. Dennis, Carina; Julie Clayton (2003). 50 years of DNA. Basingstoke: Palgrave Macmillan. ISBN1-4039-1479-6. Judson, Horace F. 1979. The Eighth Day of Creation: Makers of the Revolution in Biology. Touchstone Books, ISBN 0-671-22540-5. 2nd edition: Cold Spring Harbor Laboratory Press, 1996 paperback: ISBN 0-87969-478-5. Olby, Robert C. (1994). The path to the double helix: the discovery of DNA. New York: Dover Publications. ISBN0-486-68117-3., first published in October 1974 by MacMillan, with foreword by Francis Crick;the definitive DNA textbook,revised in 1994 with a 9 page postscript Micklas, David. 2003. DNA Science: A First Course. Cold Spring Harbor Press: ISBN 978-0879696368 Ridley, Matt (2006). Francis Crick: discoverer of the genetic code. Ashland, OH: Eminent Lives, Atlas Books. ISBN0-06-082333-X. Olby, Robert C. (2009). Francis Crick: A Biography. Plainview, N.Y: Cold Spring Harbor Laboratory Press. ISBN0-87969-798-9. Rosenfeld, Israel. 2010. DNA: A Graphic Guide to the Molecule that Shook the World. Columbia University Press: ISBN 978-0231142717 Schultz, Mark and Zander Cannon. 2009. The Stuff of Life: A Graphic Guide to Genetics and DNA. Hill and Wang: ISBN 0809089475
DNA Stent, Gunther Siegmund; Watson, James D. (1980). The double helix: a personal account of the discovery of the structure of DNA. New York: Norton. ISBN0-393-95075-1. Watson, James D. 2004. DNA: The Secret of Life. Random House: ISBN 978-0099451846 Wilkins, Maurice (2003). The third man of the double helix the autobiography of Maurice Wilkins. Cambridge, Eng: University Press. ISBN0-19-860665-6.
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External links
DNA (http://www.dmoz.org/Science/Biology/Biochemistry_and_Molecular_Biology/Biomolecules/ Nucleic_Acids/DNA//) at the Open Directory Project DNA binding site prediction on protein (http://pipe.scs.fsu.edu/displar.html) DNA coiling to form chromosomes (http://biostudio.com/c_ education mac.htm) DNA the Double Helix Game (http://nobelprize.org/educational_games/medicine/dna_double_helix/) From the official Nobel Prize web site DNA under electron microscope (http://www.fidelitysystems.com/Unlinked_DNA.html) Dolan DNA Learning Center (http://www.dnalc.org/) Double Helix: 50 years of DNA (http://www.nature.com/nature/dna50/archive.html), Nature Proteopedia DNA (http://www.proteopedia.org/wiki/index.php/DNA) Double Helix 19532003 (http://www.ncbe.reading.ac.uk/DNA50/) National Centre for Biotechnology Education Francis Crick and James Watson talking on the BBC in 1962, 1972, and 1974 (http://www.bbc.co.uk/bbcfour/ audiointerviews/profilepages/crickwatson1.shtml) Genetic Education Modules for Teachers (http://www.genome.gov/10506718)DNA from the Beginning Study Guide Guide to DNA cloning (http://www.blackwellpublishing.com/trun/artwork/Animations/cloningexp/ cloningexp.html) Olby R (2003). "Quiet debut for the double helix" (http://chem-faculty.ucsd.edu/joseph/CHEM13/DNA1. pdf). Nature 421 (6921): 4025. doi:10.1038/nature01397. PMID12540907. DNA from the Beginning (http://www.dnaftb.org/dnaftb/) Another DNA Learning Center site on DNA, genes, and heredity from Mendel to the human genome project. DNA Lab, demonstrates how to extract DNA from wheat using readily available equipment and supplies. (http:// ca.youtube.com/watch?v=iyb7fwduuGM) PDB Molecule of the Month pdb23_1 (http://www.rcsb.org/pdb/static.do?p=education_discussion/ molecule_of_the_month/pdb23_1.html) Rosalind Franklin's contributions to the study of DNA (http://mason.gmu.edu/~emoody/rfranklin.html) The Register of Francis Crick Personal Papers 1938 2007 (http://orpheus.ucsd.edu/speccoll/testing/html/ mss0660a.html#abstract) at Mandeville Special Collections Library, University of California, San Diego U.S. National DNA Day (http://www.genome.gov/10506367)watch videos and participate in real-time chat with top scientists Clue to chemistry of heredity found (http://www.nytimes.com/packages/pdf/science/dna-article.pdf) The New York Times June 1953. First American newspaper coverage of the discovery of the DNA structure An Introduction to DNA and Chromosomes (http://hopes.stanford.edu/basics/dna/b0.html) from HOPES: Huntington's Disease Outreach Project for Education at Stanford
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One of the most distinguishing features of polypeptides is their ability to fold into a globular state. The extent to which proteins fold into a defined structure varies widely. Some proteins fold into a highly rigid structure with small fluctuations and are therefore considered to be single structure. Other proteins undergo large rearrangements from one conformation to another. This conformational change is often associated with a signaling event. Thus, the structure of a protein serves as a medium through which to regulate either the function of a protein or activity of an enzyme. Not all proteins require a folding process in order to function, as some function in an unfolded state. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. Many proteins are enzymes that catalyze biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. Proteins are also necessary in animals' diets, since animals cannot synthesize all the amino acids they need and must obtain essential amino acids from food. Through the process of digestion, animals break down ingested protein into free amino acids that are then used in metabolism. Proteins were first described by the Dutch chemist Gerardus Johannes Mulder and named by the Swedish chemist Jns Jacob Berzelius in 1838. Early nutritional scientists such as the German Carl von Voit believed that protein was the most important nutrient for maintaining the structure of the body, because it was generally believed that "flesh makes flesh."[1] The central role of proteins as enzymes in living organisms was however not fully appreciated until 1926, when James B. Sumner showed that the enzyme urease was in fact a protein.[2] The first protein to be sequenced was insulin, by Frederick Sanger, who won the Nobel Prize for this achievement in 1958. The first protein
A representation of the 3D structure of the protein myoglobin showing colored alpha helices. This protein was the first to have its structure solved by X-ray crystallography. Towards the right-center among the coils, a prosthetic group called a heme group is shown colored largely in green.
Protein structures to be solved were hemoglobin and myoglobin, by Max Perutz and Sir John Cowdery Kendrew, respectively, in 1958.[3] [4] The three-dimensional structures of both proteins were first determined by X-ray diffraction analysis; Perutz and Kendrew shared the 1962 Nobel Prize in Chemistry for these discoveries. Proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugation, precipitation, electrophoresis, and chromatography; the advent of genetic engineering has made possible a number of methods to facilitate purification. Methods commonly used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, nuclear magnetic resonance and mass spectrometry. Distributed computing is a relatively new tool researchers are using to examine the infamously complex interactions that govern protein folding; the statistical analysis techniques employed to calculate a protein's probable tertiary structure from its amino acid sequence (primary structure) are well-suited for the distributed computing environment, which has made this otherwise prohibitively expensive and time consuming problem significantly more manageable.
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Biochemistry
Most proteins consist of linear polymers built from series of up to 20 different L--amino acids. All proteinogenic amino acids possess common structural features, including an -carbon to which an amino group, a carboxyl group, and a variable side chain are bonded. Only proline differs from this basic structure as it contains an unusual ring to the N-end amine group, which forces the CONH amide moiety into a fixed conformation.[5] The side chains of the standard amino acids, detailed in the list of standard amino acids, have a great variety of chemical structures and properties; it is the combined effect of all of the amino acid side chains in a protein that ultimately determines its Chemical structure of the peptide bond (bottom) and the three-dimensional structure and its chemical reactivity.[6] The three-dimensional structure of a peptide bond between an alanine and an adjacent amino acid (top/inset) amino acids in a polypeptide chain are linked by peptide bonds. Once linked in the protein chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen, and oxygen atoms are known as the main chain or protein backbone.[7] The peptide bond has two resonance forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar. The other two dihedral angles in the Resonance structures of the peptide bond that links individual amino peptide bond determine the local shape assumed by the acids to form a protein polymer protein backbone.[8] The end of the protein with a free carboxyl group is known as the C-terminus or carboxy terminus, whereas the end with a free amino group is known as the N-terminus or amino terminus. The words protein, polypeptide, and peptide are a little ambiguous and can overlap in meaning. Protein is generally used to refer to the complete biological molecule in a stable conformation, whereas peptide is generally reserved for a short amino acid oligomers often lacking a stable three-dimensional structure. However, the boundary between the two is not well defined and usually lies near 2030 residues.[9] Polypeptide can refer to any single linear chain of amino acids, usually regardless of length, but often implies an absence of a defined conformation.
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Synthesis
Proteins are assembled from amino acids using information encoded in genes. Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein. The genetic code is a set of three-nucleotide sets called codons and each three-nucleotide combination designates an amino acid, for example AUG (adenine-uracil-guanine) is the code for methionine. Because DNA contains four nucleotides, the total number of possible codons is 64; hence, there is some redundancy in the genetic code, with some amino acids specified by more than one codon.[10] Genes A ribosome produces a protein using mRNA as template. encoded in DNA are first transcribed into pre-messenger RNA (mRNA) by proteins such as RNA polymerase. Most organisms then process the pre-mRNA (also known as a primary transcript) using various forms of Post-transcriptional modification to form the mature mRNA, which is then used as a template for protein synthesis by the ribosome. In prokaryotes the mRNA may either be used as soon as it is produced, or be bound by a ribosome after having moved away from the nucleoid. In contrast, eukaryotes make mRNA in the cell nucleus The DNA sequence of a gene encodes the amino acid sequence of a protein. and then translocate it across the nuclear membrane into the cytoplasm, where protein synthesis then takes place. The rate of protein synthesis is higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per second.[11] The process of synthesizing a protein from an mRNA template is known as translation. The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer RNA molecule, which carries the amino acid corresponding to the codon it recognizes. The enzyme aminoacyl tRNA synthetase "charges" the tRNA molecules with the correct amino acids. The growing polypeptide is often termed the nascent chain. Proteins are always biosynthesized from N-terminus to C-terminus.[10] The size of a synthesized protein can be measured by the number of amino acids it contains and by its total molecular mass, which is normally reported in units of daltons (synonymous with atomic mass units), or the derivative unit kilodalton (kDa). Yeast proteins are on average 466 amino acids long and 53 kDa in mass.[9] The largest known proteins are the titins, a component of the muscle sarcomere, with a molecular mass of almost 3,000 kDa and a total length of almost 27,000 amino acids.[12]
Chemical synthesis
Short proteins can also be synthesized chemically by a family of methods known as peptide synthesis, which rely on organic synthesis techniques such as chemical ligation to produce peptides in high yield.[13] Chemical synthesis allows for the introduction of non-natural amino acids into polypeptide chains, such as attachment of fluorescent probes to amino acid side chains.[14] These methods are useful in laboratory biochemistry and cell biology, though generally not for commercial applications. Chemical synthesis is inefficient for polypeptides longer than about 300 amino acids, and the synthesized proteins may not readily assume their native tertiary structure. Most chemical synthesis methods proceed from C-terminus to N-terminus, opposite the biological reaction.[15]
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Structure
Further information: Protein structure prediction Mostproteins fold into unique 3-dimensional structures. The shape into which a protein naturally folds is known as its native conformation.[16] Although many proteins can fold unassisted, simply through the chemical properties of their amino acids, others require the aid of molecular chaperones to fold into their native states.[17] Biochemists often refer to four distinct aspects of a protein's structure:[18] Primary structure: the amino acid sequence. Secondary structure: regularly repeating local structures stabilized by hydrogen bonds. The most common examples are the alpha helix, beta sheet and turns. Because secondary structures are local, many regions of different secondary structure can be present in the same protein molecule.
Tertiary structure: the overall shape of a single protein molecule; the spatial relationship of the secondary structures to one another. Tertiary structure is generally stabilized by nonlocal interactions, most commonly the formation of a hydrophobic core, but also through salt bridges, hydrogen bonds, disulfide bonds, and even posttranslational modifications. The term "tertiary structure" is often used as synonymous with the term fold. The tertiary structure is what controls the basic function of the protein. Quaternary structure: the structure formed by several protein molecules (polypeptide chains), usually called protein subunits in this context, which function as a single protein complex.
Three possible representations of the three-dimensional structure of the protein triose phosphate isomerase. Left: all-atom representation colored by atom type. Middle: Simplified representation illustrating the backbone conformation, colored by secondary structure. Right: Solvent-accessible surface representation colored by residue type (acidic residues red, basic residues blue, polar residues green, nonpolar residues white)
Proteins are not entirely rigid molecules. In addition to these levels of structure, proteins may shift between several related structures while they perform their functions. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as "conformations", and transitions between them are called conformational changes. Such changes are often induced by the binding of a substrate molecule to an enzyme's active site, or the physical region of the protein that participates in chemical catalysis. In solution proteins also undergo variation in structure through thermal vibration and the collision with other molecules.[19]
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Proteins can be informally divided into three main classes, which correlate with typical tertiary structures: globular proteins, fibrous proteins, and membrane proteins. Almost all globular proteins are soluble and many are enzymes. Fibrous proteins are often Molecular surface of several proteins showing their comparative sizes. From left to structural, such as collagen, the major right are: immunoglobulin G (IgG, an antibody), hemoglobin, insulin (a hormone), component of connective tissue, or keratin, adenylate kinase (an enzyme), and glutamine synthetase (an enzyme). the protein component of hair and nails. Membrane proteins often serve as receptors or provide channels for polar or charged molecules to pass through the cell membrane.[20] A special case of intramolecular hydrogen bonds within proteins, poorly shielded from water attack and hence promoting their own dehydration, are called dehydrons.[21]
Structure determination
Discovering the tertiary structure of a protein, or the quaternary structure of its complexes, can provide important clues about how the protein performs its function. Common experimental methods of structure determination include X-ray crystallography and NMR spectroscopy, both of which can produce information at atomic resolution. However, NMR experiments are able to provide information from which a subset of distances between pairs of atoms can be estimated, and the final possible conformations for a protein are determined by solving a distance geometry problem. Dual polarisation interferometry is a quantitative analytical method for measuring the overall protein conformation and conformational changes due to interactions or other stimulus. Circular dichroism is another laboratory technique for determining internal beta sheet/ helical composition of proteins. Cryoelectron microscopy is used to produce lower-resolution structural information about very large protein complexes, including assembled viruses;[22] a variant known as electron crystallography can also produce high-resolution information in some cases, especially for two-dimensional crystals of membrane proteins.[23] Solved structures are usually deposited in the Protein Data Bank (PDB), a freely available resource from which structural data about thousands of proteins can be obtained in the form of Cartesian coordinates for each atom in the protein.[24] Many more gene sequences are known than protein structures. Further, the set of solved structures is biased toward proteins that can be easily subjected to the conditions required in X-ray crystallography, one of the major structure determination methods. In particular, globular proteins are comparatively easy to crystallize in preparation for X-ray crystallography. Membrane proteins, by contrast, are difficult to crystallize and are underrepresented in the PDB.[25] Structural genomics initiatives have attempted to remedy these deficiencies by systematically solving representative structures of major fold classes. Protein structure prediction methods attempt to provide a means of generating a plausible structure for proteins whose structures have not been experimentally determined.
Cellular functions
Proteins are the chief actors within the cell, said to be carrying out the duties specified by the information encoded in genes.[9] With the exception of certain types of RNA, most other biological molecules are relatively inert elements upon which proteins act. Proteins make up half the dry weight of an Escherichia coli cell, whereas other macromolecules such as DNA and RNA make up only 3% and 20%, respectively.[26] The set of proteins expressed in a particular cell or cell type is known as its proteome.
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The chief characteristic of proteins that also allows their diverse set of functions is their ability to bind other molecules specifically and tightly. The region of the protein responsible for binding another molecule is known as the binding site and is often a depression or "pocket" on the molecular surface. This binding ability is mediated by the tertiary structure of the protein, which defines the binding site pocket, and by the chemical properties of the surrounding amino acids' side chains. Protein binding can be extraordinarily tight and specific; for example, the ribonuclease inhibitor protein binds to human The enzyme hexokinase is shown as a angiogenin with a sub-femtomolar dissociation constant (<1015 M) conventional ball-and-stick molecular model. To scale in the top right-hand corner are two of its but does not bind at all to its amphibian homolog onconase (>1 M). substrates, ATP and glucose. Extremely minor chemical changes such as the addition of a single methyl group to a binding partner can sometimes suffice to nearly eliminate binding; for example, the aminoacyl tRNA synthetase specific to the amino acid valine discriminates against the very similar side chain of the amino acid isoleucine.[27] Proteins can bind to other proteins as well as to small-molecule substrates. When proteins bind specifically to other copies of the same molecule, they can oligomerize to form fibrils; this process occurs often in structural proteins that consist of globular monomers that self-associate to form rigid fibers. Proteinprotein interactions also regulate enzymatic activity, control progression through the cell cycle, and allow the assembly of large protein complexes that carry out many closely related reactions with a common biological function. Proteins can also bind to, or even be integrated into, cell membranes. The ability of binding partners to induce conformational changes in proteins allows the construction of enormously complex signaling networks.[28] Importantly, as interactions between proteins are reversible, and depend heavily on the availability of different groups of partner proteins to form aggregates that are capable to carry out discrete sets of function, study of the interactions between specific proteins is a key to understand important aspects of cellular function, and ultimately the properties that distinguish particular cell types.[29] [30]
Enzymes
The best-known role of proteins in the cell is as enzymes, which catalyze chemical reactions. Enzymes are usually highly specific and accelerate only one or a few chemical reactions. Enzymes carry out most of the reactions involved in metabolism, as well as manipulating DNA in processes such as DNA replication, DNA repair, and transcription. Some enzymes act on other proteins to add or remove chemical groups in a process known as posttranslational modification. About 4,000 reactions are known to be catalyzed by enzymes.[31] The rate acceleration conferred by enzymatic catalysis is often enormousas much as 1017-fold increase in rate over the uncatalyzed reaction in the case of orotate decarboxylase (78 million years without the enzyme, 18 milliseconds with the enzyme).[32] The molecules bound and acted upon by enzymes are called substrates. Although enzymes can consist of hundreds of amino acids, it is usually only a small fraction of the residues that come in contact with the substrate, and an even smaller fractionthree to four residues on averagethat are directly involved in catalysis.[33] The region of the enzyme that binds the substrate and contains the catalytic residues is known as the active site.
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Many ligand transport proteins bind particular small biomolecules and transport them to other locations in the body of a multicellular organism. These proteins must have a high binding affinity when their ligand is present in high concentrations, but must also release the ligand when it is present at low concentrations in the target tissues. The canonical example of a ligand-binding protein is haemoglobin, which transports oxygen from the lungs to other organs and tissues in all vertebrates and has close homologs in every biological kingdom.[36] Lectins are sugar-binding proteins which are highly specific for their sugar moieties. Lectins typically play a role in biological recognition phenomena involving cells and proteins.[37] Receptors and hormones are highly specific binding proteins. Transmembrane proteins can also serve as ligand transport proteins that alter the permeability of the cell membrane to small molecules and ions. The membrane alone has a hydrophobic core through which polar or charged molecules cannot diffuse. Membrane proteins contain internal channels that allow such molecules to enter and exit the cell. Many ion channel proteins are specialized to select for only a particular ion; for example, potassium and sodium channels often discriminate for only one of the two ions.[38]
Ribbon diagram of a mouse antibody against cholera that binds a carbohydrate antigen
Structural proteins
Structural proteins confer stiffness and rigidity to otherwise-fluid biological components. Most structural proteins are fibrous proteins; for example, actin and tubulin are globular and soluble as monomers, but polymerize to form long, stiff fibers that make up the cytoskeleton, which allows the cell to maintain its shape and size. Collagen and elastin are critical components of connective tissue such as cartilage, and keratin is found in hard or filamentous structures such as hair, nails, feathers, hooves, and some animal shells.[39] Other proteins that serve structural functions are motor proteins such as myosin, kinesin, and dynein, which are capable of generating mechanical forces. These proteins are crucial for cellular motility of single celled organisms and the sperm of many multicellular organisms which reproduce sexually. They also generate the forces exerted by contracting muscles.[40]
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Methods of study
As some of the most commonly studied biological molecules, the activities and structures of proteins are examined both in vitro and in vivo. In vitro studies of purified proteins in controlled environments are useful for learning how a protein carries out its function: for example, enzyme kinetics studies explore the chemical mechanism of an enzyme's catalytic activity and its relative affinity for various possible substrate molecules. By contrast, in vivo experiments on proteins' activities within cells or even within whole organisms can provide complementary information about where a protein functions and how it is regulated.
Protein purification
In order to perform in vitro analysis, a protein must be purified away from other cellular components. This process usually begins with cell lysis, in which a cell's membrane is disrupted and its internal contents released into a solution known as a crude lysate. The resulting mixture can be purified using ultracentrifugation, which fractionates the various cellular components into fractions containing soluble proteins; membrane lipids and proteins; cellular organelles, and nucleic acids. Precipitation by a method known as salting out can concentrate the proteins from this lysate. Various types of chromatography are then used to isolate the protein or proteins of interest based on properties such as molecular weight, net charge and binding affinity.[41] The level of purification can be monitored using various types of gel electrophoresis if the desired protein's molecular weight and isoelectric point are known, by spectroscopy if the protein has distinguishable spectroscopic features, or by enzyme assays if the protein has enzymatic activity. Additionally, proteins can be isolated according their charge using electrofocusing.[42] For natural proteins, a series of purification steps may be necessary to obtain protein sufficiently pure for laboratory applications. To simplify this process, genetic engineering is often used to add chemical features to proteins that make them easier to purify without affecting their structure or activity. Here, a "tag" consisting of a specific amino acid sequence, often a series of histidine residues (a "His-tag"), is attached to one terminus of the protein. As a result, when the lysate is passed over a chromatography column containing nickel, the histidine residues ligate the nickel and attach to the column while the untagged components of the lysate pass unimpeded. A number of different tags have been developed to help researchers purify specific proteins from complex mixtures.[43]
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Cellular localization
The study of proteins in vivo is often concerned with the synthesis and localization of the protein within the cell. Although many intracellular proteins are synthesized in the cytoplasm and membrane-bound or secreted proteins in the endoplasmic reticulum, the specifics of how proteins are targeted to specific organelles or cellular structures is often unclear. A useful technique for assessing cellular localization uses genetic engineering to express in a cell a fusion protein or chimera consisting of the natural protein of interest linked to a "reporter" such as green fluorescent protein (GFP).[44] The fused protein's position within the cell can be cleanly and efficiently visualized using microscopy,[45] as shown in the figure opposite. Other methods for elucidating the cellular location of proteins requires the use of known compartmental markers for regions such as the ER, the Golgi, lysosomes/vacuoles, mitochondria, chloroplasts, plasma membrane, etc. With the use of fluorescently tagged versions Proteins in different cellular compartments and structures tagged with green of these markers or of antibodies to known fluorescent protein (here, white) markers, it becomes much simpler to identify the localization of a protein of interest. For example, indirect immunofluorescence will allow for fluorescence colocalization and demonstration of location. Fluorescent dyes are used to label cellular compartments for a similar purpose.[46] Other possibilities exist, as well. For example, immunohistochemistry usually utilizes an antibody to one or more proteins of interest that are conjugated to enzymes yielding either luminescent or chromogenic signals that can be compared between samples, allowing for localization information. Another applicable technique is cofractionation in sucrose (or other material) gradients using isopycnic centrifugation.[47] While this technique does not prove colocalization of a compartment of known density and the protein of interest, it does increase the likelihood, and is more amenable to large-scale studies. Finally, the gold-standard method of cellular localization is immunoelectron microscopy. This technique also uses an antibody to the protein of interest, along with classical electron microscopy techniques. The sample is prepared for normal electron microscopic examination, and then treated with an antibody to the protein of interest that is conjugated to an extremely electro-dense material, usually gold. This allows for the localization of both ultrastructural details as well as the protein of interest.[48] Through another genetic engineering application known as site-directed mutagenesis, researchers can alter the protein sequence and hence its structure, cellular localization, and susceptibility to regulation. This technique even allows the incorporation of unnatural amino acids into proteins, using modified tRNAs,[49] and may allow the rational design of new proteins with novel properties.[50]
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Nutrition
Further information: Protein (nutrient) Most microorganisms and plants can biosynthesize all 20 standard amino acids, while animals (including humans) must obtain some of the amino acids from the diet.[26] The amino acids that an organism cannot synthesize on its own are referred to as essential amino acids. Key enzymes that synthesize certain amino acids are not present in animals such as aspartokinase, which catalyzes the first step in the synthesis of lysine, methionine, and threonine from aspartate. If amino acids are present in the environment, microorganisms can conserve energy by taking up the amino acids from their surroundings and downregulating their biosynthetic pathways.
Protein In animals, amino acids are obtained through the consumption of foods containing protein. Ingested proteins are then broken down into amino acids through digestion, which typically involves denaturation of the protein through exposure to acid and hydrolysis by enzymes called proteases. Some ingested amino acids are used for protein biosynthesis, while others are converted to glucose through gluconeogenesis, or fed into the citric acid cycle. This use of protein as a fuel is particularly important under starvation conditions as it allows the body's own proteins to be used to support life, particularly those found in muscle.[66] Amino acids are also an important dietary source of nitrogen.
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Footnotes
[1] Bischoff TLW, Voit, C (1860) (in German). Die Gesetze der Ernaehrung des Pflanzenfressers durch neue Untersuchungen festgestellt. Leipzig, Heidelberg. [2] Sumner JB (1926). "The isolation and crystallization of the enzyme urease. Preliminary paper" (http:/ / www. jbc. org/ content/ 69/ 2/ 435. full. pdf+ html) (PDF). Journal of Biological Chemistry 69 (2): 43541. . [3] Muirhead H, Perutz M (1963). "Structure of hemoglobin. A three-dimensional fourier synthesis of reduced human hemoglobin at 5.5 resolution". Nature 199 (4894): 63338. doi:10.1038/199633a0. PMID14074546. [4] Kendrew J, Bodo G, Dintzis H, Parrish R, Wyckoff H, Phillips D (1958). "A three-dimensional model of the myoglobin molecule obtained by X-ray analysis". Nature 181 (4610): 66266. Bibcode1958Natur.181..662K. doi:10.1038/181662a0. PMID13517261. [5] Nelson DL, Cox MM (2005). Lehninger's Principles of Biochemistry (4th ed.). New York, New York: W. H. Freeman and Company. [6] Gutteridge A, Thornton JM (2005). "Understanding nature's catalytic toolkit". Trends in Biochemical Sciences 30 (11): 62229. doi:10.1016/j.tibs.2005.09.006. PMID16214343. [7] Murray et al., p. 19. [8] Murray et al., p. 31. [9] Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipurksy SL, Darnell J (2004). Molecular Cell Biology (5th ed.). New York, New York: WH Freeman and Company. [10] van Holde and Mathews, pp. 100242. [11] Dobson CM (2000). "The nature and significance of protein folding". In Pain RH (ed.). Mechanisms of Protein Folding. Oxford, Oxfordshire: Oxford University Press. pp.128. ISBN0-19-963789-X. [12] Fulton A, Isaacs W (1991). "Titin, a huge, elastic sarcomeric protein with a probable role in morphogenesis". Bioessays 13 (4): 15761. doi:10.1002/bies.950130403. PMID1859393. [13] Bruckdorfer T, Marder O, Albericio F (2004). "From production of peptides in milligram amounts for research to multi-tons quantities for drugs of the future". Current Pharmaceutical Biotechnology 5 (1): 2943. doi:10.2174/1389201043489620. PMID14965208. [14] Schwarzer D, Cole P (2005). "Protein semisynthesis and expressed protein ligation: chasing a protein's tail". Current Opinions in Chemical Biology 9 (6): 56169. doi:10.1016/j.cbpa.2005.09.018. PMID16226484. [15] Kent SB (2009). "Total chemical synthesis of proteins". Chemical Society Reviews 38 (2): 33851. doi:10.1039/b700141j. PMID19169452. [16] Murray et al., p. 36. [17] Murray et al., p. 37. [18] Murray et al., pp. 3034. [19] van Holde and Mathews, pp. 36875. [20] van Holde and Mathews, pp. 16585. [21] Fernndez A, Scott R (2003). "Dehydron: a structurally encoded signal for protein interaction" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S0006-3495(03)74619-0). Biophysical Journal 85 (3): 191428. Bibcode2003BpJ....85.1914F. doi:10.1016/S0006-3495(03)74619-0. PMC1303363. PMID12944304. . [22] Branden and Tooze, pp. 34041. [23] Gonen T, Cheng Y, Sliz P, Hiroaki Y, Fujiyoshi Y, Harrison SC, Walz T (2005). "Lipid-protein interactions in double-layered two-dimensional AQP0 crystals". Nature 438 (7068): 63338. doi:10.1038/nature04321. PMC1350984. PMID16319884. [24] Standley DM, Kinjo AR, Kinoshita K, Nakamura H (2008). "Protein structure databases with new web services for structural biology and biomedical research" (http:/ / bib. oxfordjournals. org/ cgi/ pmidlookup?view=long& pmid=18430752). Briefings in Bioinformatics 9 (4): 27685. doi:10.1093/bib/bbn015. PMID18430752. . [25] Walian P, Cross TA, Jap BK (2004). "Structural genomics of membrane proteins" (http:/ / genomebiology. com/ 2004/ 5/ 4/ 215). Genome Biology 5 (4): 215. doi:10.1186/gb-2004-5-4-215. PMC395774. PMID15059248. . [26] Voet D, Voet JG. (2004). Biochemistry Vol 1 3rd ed. Wiley: Hoboken, NJ. [27] Sankaranarayanan R, Moras D (2001). "The fidelity of the translation of the genetic code". Acta Biochimica Polonica 48 (2): 32335. PMID11732604. [28] van Holde and Mathews, pp. 83049. [29] Copland JA, Sheffield-Moore M, Koldzic-Zivanovic N, Gentry S, Lamprou G, Tzortzatou-Stathopoulou F, Zoumpourlis V, Urban RJ, Vlahopoulos SA (2009). "Sex steroid receptors in skeletal differentiation and epithelial neoplasia: is tissue-specific intervention possible?". BioEssays: news and reviews in molecular, cellular and developmental biology 31 (6): 62941. doi:10.1002/bies.200800138. PMID19382224. [30] Samarin S, Nusrat A (2009). "Regulation of epithelial apical junctional complex by Rho family GTPases". Frontiers in bioscience: a journal and virtual library 14: 112942. PMID19273120. [31] Bairoch A (2000). "The ENZYME database in 2000" (http:/ / www. expasy. org/ NAR/ enz00. pdf). Nucleic Acids Research 28 (1): 304305. doi:10.1093/nar/28.1.304. PMC102465. PMID10592255. . [32] Radzicka A, Wolfenden R (1995). "A proficient enzyme". Science 6 (267): 9093. doi:10.1126/science.7809611. PMID7809611. [33] EBI External Services (2010-01-20). "The Catalytic Site Atlas at The European Bioinformatics Institute" (http:/ / www. ebi. ac. uk/ thornton-srv/ databases/ CSA/ ). Ebi.ac.uk. . Retrieved 2011-01-16. [34] Branden and Tooze, pp. 25181.
Protein
[35] van Holde and Mathews, pp. 24750. [36] van Holde and Mathews, pp. 22029. [37] Rdiger H, Siebert HC, Sols D, Jimnez-Barbero J, Romero A, von der Lieth CW, Diaz-Mario T, Gabius HJ (2000). "Medicinal chemistry based on the sugar code: fundamentals of lectinology and experimental strategies with lectins as targets". Current Medicinal Chemistry 7 (4): 389416. PMID10702616. [38] Branden and Tooze, pp. 23234. [39] van Holde and Mathews, pp. 17881. [40] van Holde and Mathews, pp. 25864; 272. [41] Murray et al., pp. 2124. [42] Hey J, Posch A, Cohen A, Liu N, Harbers A (2008). "Fractionation of complex protein mixtures by liquid-phase isoelectric focusing". Methods in Molecular Biology 424: 22539. doi:10.1007/978-1-60327-064-9_19. PMID18369866. [43] Terpe K (2003). "Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems". Applied Microbiology and Biotechnology 60 (5): 52333. doi:10.1007/s00253-002-1158-6. PMID12536251. [44] Stepanenko OV, Verkhusha VV, Kuznetsova IM, Uversky VN, Turoverov KK (2008). "Fluorescent proteins as biomarkers and biosensors: throwing color lights on molecular and cellular processes". Current Protein & Peptide Science 9 (4): 33869. doi:10.2174/138920308785132668. PMC2904242. PMID18691124. [45] Yuste R (2005). "Fluorescence microscopy today". Nature Methods 2 (12): 902904. doi:10.1038/nmeth1205-902. PMID16299474. [46] Margolin W (2000). "Green fluorescent protein as a reporter for macromolecular localization in bacterial cells" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S1046-2023(99)90906-4). Methods (San Diego, Calif.) 20 (1): 6272. doi:10.1006/meth.1999.0906. PMID10610805. . [47] Walker JH, Wilson K (2000). Principles and Techniques of Practical Biochemistry. Cambridge, UK: Cambridge University Press. pp.28789. ISBN0-521-65873-X. [48] Mayhew TM, Lucocq JM (2008). "Developments in cell biology for quantitative immunoelectron microscopy based on thin sections: a review". Histochemistry and Cell Biology 130 (2): 299313. doi:10.1007/s00418-008-0451-6. PMC2491712. PMID18553098. [49] Hohsaka T, Sisido M (2002). "Incorporation of non-natural amino acids into proteins". Current Opinion in Chemical Biology 6 (6): 80915. doi:10.1016/S1367-5931(02)00376-9. PMID12470735. [50] Cedrone F, Mnez A, Qumneur E (2000). "Tailoring new enzyme functions by rational redesign". Current Opinion in Structural Biology 10 (4): 40510. doi:10.1016/S0959-440X(00)00106-8. PMID10981626. [51] Grg A, Weiss W, Dunn MJ (2004). "Current two-dimensional electrophoresis technology for proteomics". Proteomics 4 (12): 366585. doi:10.1002/pmic.200401031. PMID15543535. [52] Conrotto P, Souchelnytskyi S (2008). "Proteomic approaches in biological and medical sciences: principles and applications" (http:/ / www. exp-oncology. com. ua/ en/ archives/ 36/ 699. html). Experimental Oncology 30 (3): 17180. PMID18806738. . [53] Joos T, Bachmann J (2009). "Protein microarrays: potentials and limitations" (http:/ / www. bioscience. org/ 2009/ v14/ af/ 3534/ fulltext. htm). Frontiers in Bioscience 14 (14): 437685. doi:10.2741/3534. PMID19273356. . [54] Koegl M, Uetz P (2007). "Improving yeast two-hybrid screening systems" (http:/ / bfgp. oxfordjournals. org/ cgi/ pmidlookup?view=long& pmid=18218650). Briefings in Functional Genomics & Proteomics 6 (4): 30212. doi:10.1093/bfgp/elm035. PMID18218650. . [55] Plewczyski D, Ginalski K (2009). "The interactome: predicting the proteinprotein interactions in cells". Cellular & Molecular Biology Letters 14 (1): 122. doi:10.2478/s11658-008-0024-7. PMID18839074. [56] Zhang C, Kim SH (2003). "Overview of structural genomics: from structure to function". Current Opinion in Chemical Biology 7 (1): 2832. doi:10.1016/S1367-5931(02)00015-7. PMID12547423. [57] Zhang Y (2008). "Progress and challenges in protein structure prediction". Current Opinions in Structural Biology 18 (3): 34248. doi:10.1016/j.sbi.2008.02.004. PMC2680823. PMID18436442. [58] Xiang Z (2006). "Advances in homology protein structure modeling". Current Protein and Peptide Science 7 (3): 21727. doi:10.2174/138920306777452312. PMC1839925. PMID16787261. [59] Zhang Y, Skolnick J (2005). "The protein structure prediction problem could be solved using the current PDB library" (http:/ / www. pnas. org/ cgi/ pmidlookup?view=long& pmid=15653774). Proceedings of the National Academy of Sciences U.S.A. 102 (4): 102934. doi:10.1073/pnas.0407152101. PMC545829. PMID15653774. . [60] Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D (2003). "Design of a novel globular protein fold with atomic-level accuracy" (http:/ / www. sciencemag. org/ cgi/ pmidlookup?view=long& pmid=14631033). Science 302 (5649): 136468. Bibcode2003Sci...302.1364K. doi:10.1126/science.1089427. PMID14631033. . [61] Ritchie DW (2008). "Recent progress and future directions in proteinprotein docking". Current Protein and Peptide Science 9 (1): 115. doi:10.2174/138920308783565741. PMID18336319. [62] Scheraga HA, Khalili M, Liwo A (2007). "Protein-folding dynamics: overview of molecular simulation techniques". Annual Review of Physical Chemistry 58: 5783. doi:10.1146/annurev.physchem.58.032806.104614. PMID17034338. [63] Zagrovic B, Snow CD, Shirts MR, Pande VS (2002). "Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing". Journal of Molecular Biology 323 (5): 92737. doi:10.1016/S0022-2836(02)00997-X. PMID12417204. [64] Herges T, Wenzel W (2005). "In silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom force field". Physical Review Letters 94 (1): 018101. Bibcode2005PhRvL..94a8101H. doi:10.1103/PhysRevLett.94.018101. PMID15698135. [65] Hoffmann M, Wanko M, Strodel P, Knig PH, Frauenheim T, Schulten K, Thiel W, Tajkhorshid E, Elstner M (2006). "Color tuning in rhodopsins: the mechanism for the spectral shift between bacteriorhodopsin and sensory rhodopsin II". Journal of the American Chemical
91
Protein
Society 128 (33): 1080818. doi:10.1021/ja062082i. PMID16910676. [66] Brosnan J (June 2003). "Interorgan amino acid transport and its regulation" (http:/ / jn. nutrition. org/ cgi/ content/ full/ 133/ 6/ 2068S). Journal of Nutrition 133 (6 Suppl 1): 2068S72S. PMID12771367. . [67] Perrett D (2007). "From 'protein' to the beginnings of clinical proteomics". Proteomics Clinical Applications 1 (8): 72038. doi:10.1002/prca.200700525. PMID21136729. [68] New Oxford Dictionary of English [69] Reynolds JA, Tanford C (2003). Nature's Robots: A History of Proteins (Oxford Paperbacks). New York, New York: Oxford University Press. p.15. ISBN0-19-860694-X. [70] Pauling L, Corey RB, Branson HR (1951). "The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain" (http:/ / www. pnas. org/ site/ misc/ Protein8. pdf) (PDF). Proceedings of the National Academy of Sciences U.S.A. 37 (5): 23540. Bibcode1951PNAS...37..235P. doi:10.1073/pnas.37.5.235. PMC1063348. PMID14834145. . [71] Kauzmann W (1956). "Structural factors in protein denaturation". Journal of Cellular Physiology. Supplement 47 (Suppl 1): 11331. doi:10.1002/jcp.1030470410. PMID13332017. [72] Kauzmann W (1959). "Some factors in the interpretation of protein denaturation". Advances in Protein Chemistry 14: 163. doi:10.1016/S0065-3233(08)60608-7. PMID14404936. [73] Kalman SM, Linderstrom-Lang K, Ottesen M, Richards FM (1955). "Degradation of ribonuclease by subtilisin". Biochimica et Biophysica Acta 16 (2): 29799. doi:10.1016/0006-3002(55)90224-9. PMID14363272. [74] Sanger F (1949). "The terminal peptides of insulin". Biochemical Journal 45 (5): 56374. PMC1275055. PMID15396627. [75] "RCSB Protein Data Bank" (http:/ / www. rcsb. org/ pdb/ home/ home. do). . Retrieved 2009-04-14. [76] Zhou ZH (2008). "Towards atomic resolution structural determination by single-particle cryo-electron microscopy". Current Opinion in Structural Biology 18 (2): 21828. doi:10.1016/j.sbi.2008.03.004. PMC2714865. PMID18403197. [77] Keskin O, Tuncbag N, Gursoy A (2008). "Characterization and prediction of protein interfaces to infer protein-protein interaction networks". Current Pharmaceutical Biotechnology 9 (2): 6776. doi:10.2174/138920108783955191. PMID18393863.
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References
Branden C, Tooze J (1999). Introduction to Protein Structure. New York: Garland Pub. ISBN0-8153-2305-0. Murray RF, Harper HW, Granner DK, Mayes PA, Rodwell VW (2006). Harper's Illustrated Biochemistry. New York: Lange Medical Books/McGraw-Hill. ISBN0-07-146197-3. Van Holde KE, Mathews CK (1996). Biochemistry. Menlo Park, California: Benjamin/Cummings Pub. Co., Inc. ISBN0-8053-3931-0.
External links
Databases and projects
Comparative Toxicogenomics Database (http://ctd.mdibl.org/) curates proteinchemical interactions, as well as gene/proteindisease relationships and chemical-disease relationships. Bioinformatic Harvester (http://harvester.fzk.de) A Meta search engine (29 databases) for gene and protein information. The Protein Databank (http://www.rcsb.org) (see also PDB Molecule of the Month (http://www.rcsb.org/ pdb/static.do?p=education_discussion/molecule_of_the_month/index.html), presenting short accounts on selected proteins from the PDB) Proteopedia Life in 3D (http://www.proteopedia.org): rotatable, zoomable 3D model with wiki annotations for every known protein molecular structure. UniProt the Universal Protein Resource (http://www.expasy.uniprot.org) neXtProt Exploring the universe of human proteins (http://www.nextprot.org): human-centric protein knowledge resource The Protein Naming Utility (http://www.jcvi.org/pn-utility) Human Protein Atlas (http://www.proteinatlas.org) NCBI Entrez Protein database (http://www.ncbi.nlm.nih.gov/sites/entrez?db=protein) NCBI Protein Structure database (http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure) Human Protein Reference Database (http://www.hprd.org/)
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Amino acid
Amino acids (pronounced/mino ..., mano ..., mno .../) are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen. They are particularly important in biochemistry, where the term usually refers to alpha-amino acids. An alpha-amino acid has the generic formula H2NCHRCOOH, where R is an organic substituent;[1] the amino group is attached to the carbon atom immediately adjacent to the carboxylate group The generic structure of an alpha amino acid in its (the carbon). Other types of amino acid exist when the amino unionized form group is attached to a different carbon atom; for example, in gamma-amino acids (such as gamma-amino-butyric acid) the carbon atom to which the amino group attaches is separated from the carboxylate group by two other carbon atoms. The various alpha-amino acids differ in which side-chain (R-group) is attached to their alpha carbon, and can vary in size from just one hydrogen atom in glycine to a large heterocyclic group in tryptophan. Amino acids are critical to life, and have many functions in metabolism. One particularly important function is to serve as the building blocks of proteins, which are linear chains of amino acids. Amino acids can be linked together in varying sequences to form a vast variety of proteins.[2] Twenty-two amino acids
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are naturally incorporated into polypeptides and are called proteinogenic or standard amino acids. Of these, 20 are encoded by the universal genetic code. Nine standard amino acids are called "essential" for humans because they cannot be created from other compounds by the human body, and so must be taken in as food. Due to their central role in biochemistry, amino acids are important in nutrition and are commonly used in nutrition supplements, fertilizers, food technology and industry. In industry, applications include the production of biodegradable plastics, drugs, and chiral catalysts.
The 21 amino acids found in eukaryotes, grouped according to their side-chains' pKas and charge at physiological pH 7.4
History
The first few amino acids were discovered in the early 19th century. In 1806, the French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that proved to be asparagine, the first amino acid to be discovered.[3] [4] Another amino acid that was discovered in the early 19th century was cystine, in 1810,[5] although its monomer, cysteine, was discovered much later, in 1884.[4] [6] Glycine and leucine were also discovered around this time, in 1820.[7] Usage of the term amino acid in the English language is from 1898.[8]
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General structure
Further information: Proteinogenic amino acid In the structure shown at the top of the page, R represents a side-chain specific to each amino acid. The carbon atom next to the carboxyl group is called the carbon and amino acids with a side-chain bonded to this carbon are referred to as alpha amino acids. These are the most common form found in nature. In the alpha amino acids, the carbon is a chiral carbon atom, with the exception of glycine.[9] In amino acids that have a carbon chain attached to the carbon (such as lysine, shown to the right) the carbons are labeled in order as , , , , and so on.[10] In some amino acids, the amine group is attached to the or -carbon, and these are therefore referred to as beta or gamma amino acids. Amino acids are usually classified by the properties of their side-chain into four groups. The side-chain can make an amino acid a weak acid or a weak base, and a hydrophile if the side-chain is polar or a hydrophobe if it is nonpolar.[9] The chemical structures of the 22 standard amino acids, along with their chemical properties, are described more fully in the article on these proteinogenic amino acids.
The phrase "branched-chain amino acids" or BCAA refers to the amino acids having aliphatic side-chains that are non-linear; these are leucine, isoleucine, and valine. Proline is the only proteinogenic amino acid whose side-group links to the -amino group and, thus, is also the only proteinogenic amino acid containing a secondary amine at this position.[9] In chemical terms, proline is, therefore, an imino acid, since it lacks a primary amino group,[11] although it is still classed as an amino acid in the current biochemical nomenclature,[12] and may also be called an "N-alkylated alpha-amino acid".[13]
Isomerism
Of the standard -amino acids, all but glycine can exist in either of two optical isomers, called L or D amino acids, which are mirror images of each other (see also Chirality). While L-amino acids represent all of the amino acids found in proteins during translation in the ribosome, D-amino acids are found in some proteins produced by enzyme posttranslational modifications after translation and translocation to the endoplasmic reticulum, as in exotic sea-dwelling organisms such as The two optical isomers of alanine, D-Alanine cone snails.[14] They are also abundant components of the and L-Alanine peptidoglycan cell walls of bacteria,[15] and D-serine may act as a neurotransmitter in the brain.[16] The L and D convention for amino acid configuration refers not to the optical activity of the amino acid itself, but rather to the optical activity of the isomer of glyceraldehyde from which that amino acid can, in theory, be synthesized (D-glyceraldehyde is dextrorotary; L-glyceraldehyde is levorotary). In alternative fashion, the (S) and (R) designators are used to indicate the absolute stereochemistry. Almost all of the amino acids in proteins are (S) at the carbon, with cysteine being (R) and glycine non-chiral.[17] Cysteine is unusual since it has a sulfur atom at the second position in its side-chain, which has a larger atomic mass than the groups attached to the first carbon, which is attached to the -carbon in the other standard amino acids, thus the (R) instead of (S).
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Zwitterions
The amine and carboxylic acid functional groups found in amino acids allow them to have amphiprotic properties.[9] Carboxylic acid groups (-CO2H) can be deprotonated to become negative carboxylates (-CO2- ), and -amino groups (NH2-) can be protonated to become positive + -ammonium groups ( NH3-). At pH An amino acid in its (1) unionized and (2) zwitterionic forms values greater than the pKa of the carboxylic acid group (mean for the 20 common amino acids is about 2.2, see the table of amino acid structures above), the negative carboxylate ion predominates. At pH values lower than the pKa of the -ammonium group (mean for the 20 common -amino acids is about 9.4), the nitrogen is predominantly protonated as a positively charged -ammonium group. Thus, at pH between 2.2 and 9.4, the predominant form adopted by -amino acids contains a negative carboxylate and a positive -ammonium group, as shown in structure (2) on the right, so has net zero charge. This molecular state is known as a zwitterion, from the German Zwitter meaning hermaphrodite or hybrid.[18] Below pH 2.2, the predominant form will have a neutral carboxylic acid group and a positive -ammonium ion (net charge +1), and above pH 9.4, a negative carboxylate and neutral -amino group (net charge -1). The fully neutral form (structure (1) on the right) is a very minor species in aqueous solution throughout the pH range (less than 1 part in 107). Amino acids also exist as zwitterions in the solid phase, and crystallize with salt-like properties unlike typical organic acids or amines.
Isoelectric point
At pH values between the two pKa values, the zwitterion predominates, but coexists in dynamic equilibrium with small amounts of net negative and net positive ions. At the exact midpoint between the two pKa values, the trace amount of net negative and trace of net positive ions exactly balance, so that average net charge of all forms present is zero.[19] This pH is known as the isoelectric point pI, so pI = (pKa1 + pKa2). The individual amino acids all have slightly different pKa values, so have different isoelectric points. For amino acids with charged side-chains, the pKa of the side-chain is involved. Thus for Asp, Glu with negative side-chains, pI = (pKa1 + pKaR), where pKaR is the side-chain pKa. Cysteine also has potentially negative side-chain with pKaR = 8.14, so pI should be calculated as for Asp and Glu, even though the side-chain is not significantly charged at neutral pH. For His, Lys, and Arg with positive side-chains, pI = (pKaR + pKa2). Amino acids have zero mobility in electrophoresis at their isoelectric point, although this behaviour is more usually exploited for peptides and proteins than single amino acids. Zwitterions have minimum solubility at their isolectric point and some amino acids (in particular, with non-polar side-chains) can be isolated by precipitation from water by adjusting the pH to the required isoelectric point.
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Some nonstandard amino acids are not found in proteins. Examples include lanthionine, 2-aminoisobutyric acid, dehydroalanine, and the neurotransmitter gamma-aminobutyric acid. Nonstandard amino acids often occur as intermediates in the metabolic pathways for standard amino acids for example, ornithine and citrulline occur in the urea cycle, part of amino acid catabolism (see below).[28] A -alanine and its -alanine isomer rare exception to the dominance of -amino acids in biology is the -amino acid beta alanine (3-aminopropanoic acid), which is used in plants and microorganisms in the synthesis of pantothenic acid (vitamin B5), a component of coenzyme A.[29]
In human nutrition
Further information: Protein in nutrition and Amino acid synthesis When taken up into the human body from the diet, the 22 standard amino acids either are used to synthesize proteins and other biomolecules or are oxidized to urea and carbon dioxide as a source of energy.[30] The oxidation pathway starts with the removal of the amino group by a transaminase, the amino group is then fed into the urea cycle. The other product of transamidation is a keto acid that enters the citric acid cycle.[31] Glucogenic amino acids can also be converted into glucose, through gluconeogenesis.[32] Pyrrolysine trait is restricted to several microbes, and only one organism has both Pyl and Sec. Of the 22 standard amino acids, 9 are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth, so they must be obtained from food.[33] In addition, cysteine, taurine, tyrosine, histidine, and arginine are semiessential amino-acids in children, because the metabolic pathways that synthesize these amino acids are not fully developed.[34] [35] The amounts required also depend on the age and health of the individual, so it is hard to make general statements about the dietary requirement for some amino acids.
Essential Histidine Isoleucine Leucine Lysine Methionine Nonessential Alanine Arginine* Asparagine Aspartic acid Cysteine*
Phenylalanine Glutamic acid Threonine Tryptophan Valine Glutamine* Glycine Ornithine* Proline* Selenocysteine* Serine* Taurine* Tyrosine*
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Non-protein functions
Further information: Amino acid neurotransmitter In humans, non-protein amino acids also have important roles as metabolic intermediates, such as in the biosynthesis of the neurotransmitter gamma-aminobutyric acid. Many amino acids are used to synthesize other molecules, for example: Tryptophan is a precursor of the neurotransmitter serotonin.[38] Tyrosine is a precursor of the neurotransmitter dopamine. Glycine is a precursor of porphyrins such as heme.[39] Arginine is a precursor of nitric oxide.[40] Ornithine and S-adenosylmethionine are precursors of polyamines.[41] Aspartate, glycine, and glutamine are precursors of nucleotides.[42] Phenylalanine is a precursor of various phenylpropanoids, which are important in plant metabolism.
However, not all of the functions of other abundant non-standard amino acids are known. For example, taurine is a major amino acid in muscle and brain tissues, but, although many functions have been proposed, its precise role in the body has not been determined.[43] Some non-standard amino acids are used as defenses against herbivores in plants.[44] For example canavanine is an analogue of arginine that is found in many legumes,[45] and in particularly large amounts in Canavalia gladiata (sword bean).[46] This amino acid protects the plants from predators such as insects and can cause illness in people if some types of legumes are eaten without processing.[47] The non-protein amino acid mimosine is found in other species of legume, particularly Leucaena leucocephala.[48] This compound is an analogue of tyrosine and can poison animals that graze on these plants.
Uses in technology
Amino acids are used for a variety of applications in industry, but their main use is as additives to animal feed. This is necessary, since many of the bulk components of these feeds, such as soybeans, either have low levels or lack some of the essential amino acids: Lysine, methionine, threonine, and tryptophan are most important in the production of these feeds.[49] In this industry, amino acids are also used to chelate metal cations in order to improve the absorption of minerals from supplements, which may be required to improve the health or production of these animals.[50] The food industry is also a major consumer of amino acids, in particular, glutamic acid, which is used as a flavor enhancer,[51] and Aspartame (aspartyl-phenylalanine-1-methyl ester) as a low-calorie artificial sweetener.[52] Similar technology to that used for animal nutrition is employed in the human nutrition industry to alleviate symptoms of mineral deficiencies, such as anemia, by improving mineral absorption and reducing negative side effects from inorganic mineral supplementation. [53] The chelating ability of amino acids has been used in fertilizers for agriculture to facilitate the delivery of minerals to plants in order to correct mineral deficiencies, such as iron chlorosis. These fertilizers are also used to prevent deficiencies from occurring and improving the overall health of the plants.[54] The remaining production of amino acids is used in the synthesis of drugs and cosmetics.[49]
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Pharmaceutical application Experimental treatment for depression. Treatment for Parkinsonism. [56] [57] [55]
Drug that inhibits ornithine decarboxylase and is used in the treatment of sleeping sickness.
Biodegradable plastics
Further information: Biodegradable plastics and Biopolymers Amino acids are under development as components of a range of biodegradable polymers. These materials have applications as environmentally friendly packaging and in medicine in drug delivery and the construction of prosthetic implants. These polymers include polypeptides, polyamides, polyesters, polysulfides, and polyurethanes with amino acids either forming part of their main chains or bonded as side-chains. These modifications alter the physical properties and reactivities of the polymers.[62] An interesting example of such materials is polyaspartate, a water-soluble biodegradable polymer that may have applications in disposable diapers and agriculture.[63] Due to its solubility and ability to chelate metal ions, polyaspartate is also being used as a biodegradeable anti-scaling agent and a corrosion inhibitor.[64] [65] In addition, the aromatic amino acid tyrosine is being developed as a possible replacement for toxic phenols such as bisphenol A in the manufacture of polycarbonates.[66]
Reactions
As amino acids have both a primary amine group and a primary carboxyl group, these chemicals can undergo most of the reactions associated with these functional groups. These include nucleophilic addition, amide bond formation and imine formation for the amine group and esterification, amide bond formation and decarboxylation for the carboxylic acid group.[67] The combination of these functional groups allow amino acids to be effective polydentate ligands for metal-amino acid chelates.[68] The multiple side-chains of amino acids can also undergo chemical reactions.[69] The types of these reactions are determined by the groups on these side-chains and are, therefore, different between the various types of amino acid.
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Chemical synthesis
Several methods exist to synthesize amino acids. One of the oldest methods begins with the bromination at the -carbon of a carboxylic acid. The Strecker amino acid synthesis Nucleophilic substitution with ammonia then converts the alkyl bromide to the amino acid.[70] In alternative fashion, the Strecker amino acid synthesis involves the treatment of an aldehyde with potassium cyanide and ammonia, this produces an -amino nitrile as an intermediate. Hydrolysis of the nitrile in acid then yields a -amino acid.[71] Using ammonia or ammonium salts in this reaction gives unsubstituted amino acids, while substituting primary and secondary amines will yield substituted amino acids.[72] Likewise, using ketones, instead of aldehydes, gives ,-disubstituted amino [73] acids. The classical synthesis gives racemic mixtures of -amino acids as products, but several alternative procedures using asymmetric auxiliaries [74] or asymmetric catalysts [75] [76] have been developed.[77] At the current time, the most-adopted method is an automated synthesis on a solid support (e.g., polystyrene beads), using protecting groups (e.g., Fmoc and t-Boc) and activating groups (e.g., DCC and DIC).
Amino acid In chemistry, peptides are synthesized by a variety of reactions. One of the most-used in solid-phase peptide synthesis uses the aromatic oxime derivatives of amino acids as activated units. These are added in sequence onto the growing peptide chain, which is attached to a solid resin support.[82] The ability to easily synthesize vast numbers of different peptides by varying the types and order of amino acids (using combinatorial chemistry) has made peptide synthesis particularly important in creating libraries of peptides for use in drug discovery through high-throughput screening.[83]
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Biosynthesis
In plants, nitrogen is first assimilated into organic compounds in the form of glutamate, formed from alpha-ketoglutarate and ammonia in the mitochondrion. In order to form other amino acids, the plant uses transaminases to move the amino group to another alpha-keto carboxylic acid. For example, aspartate aminotransferase converts glutamate and oxaloacetate to alpha-ketoglutarate and aspartate.[84] Other organisms use transaminases for amino acid synthesis, too. Nonstandard amino acids are usually formed through modifications to standard amino acids. For example, homocysteine is formed through the transsulfuration pathway or by the demethylation of methionine via the intermediate metabolite S-adenosyl methionine,[43] while hydroxyproline is made by a posttranslational modification of proline.[85] Microorganisms and plants can synthesize many uncommon amino acids. For example, some microbes make 2-aminoisobutyric acid and lanthionine, which is a sulfide-bridged derivative of alanine. Both of these amino acids are found in peptidic lantibiotics such as alamethicin.[86] While in plants, 1-aminocyclopropane-1-carboxylic acid is a small disubstituted cyclic amino acid that is a key intermediate in the production of the plant hormone ethylene.[87]
Catabolism
Degradation of an amino acid often involves deamination by moving its amino group to alpha-ketoglutarate, forming glutamate. This process involves transaminases, often the same as those used in amination during synthesis. In many vertebrates, the amino group is then removed through the urea cycle and is excreted in the form of urea. However, amino acid degradation can produce uric acid or ammonia instead. For example, serine dehydratase converts serine to pyruvate and ammonia.[89]
Catabolism of proteinogenic amino acids. Amino acids can be classified according [88] to the properties of their main products as either of the following: Glucogenic, with the products having the ability to form glucose by gluconeogenesisKetogenic, with the products not having the ability to form glucose. These products may still be used for ketogenesis or lipid synthesis.Amino acids catabolized into both glucogenic and ketogenic products.
The 20 amino acids encoded directly by the genetic code can be divided into several groups based on their properties. Important factors are charge, hydrophilicity or hydrophobicity, size, and functional groups.[9] These properties are important for protein structure and proteinprotein interactions. The water-soluble proteins tend to have their hydrophobic residues (Leu, Ile, Val, Phe, and Trp) buried in the middle of the protein, whereas hydrophilic side-chains are exposed to the aqueous solvent. The integral membrane proteins tend to have outer rings of exposed hydrophobic amino acids that anchor them into the lipid bilayer. In the case part-way between
Amino acid these two extremes, some peripheral membrane proteins have a patch of hydrophobic amino acids on their surface that locks onto the membrane. In similar fashion, proteins that have to bind to positively-charged molecules have surfaces rich with negatively charged amino acids like glutamate and aspartate, while proteins binding to negatively-charged molecules have surfaces rich with positively charged chains like lysine and arginine. There are different hydrophobicity scales of amino acid residues.[90] Some amino acids have special properties such as cysteine, that can form covalent disulfide bonds to other cysteine residues, proline that forms a cycle to the polypeptide backbone, and glycine that is more flexible than other amino acids. Many proteins undergo a range of posttranslational modifications, when additional chemical groups are attached to the amino acids in proteins. Some modifications can produce hydrophobic lipoproteins,[91] or hydrophilic glycoproteins.[92] These type of modification allow the reversible targeting of a protein to a membrane. For example, the addition and removal of the fatty acid palmitic acid to cysteine residues in some signaling proteins causes the proteins to attach and then detach from cell membranes.[93]
103
Alanine Arginine Asparagine Aspartic acid Cysteine Glutamic acid Glutamine Glycine Histidine
A R N D C E Q G H
Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine
Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
I L K M F P S T W Y V
nonpolar nonpolar polar nonpolar nonpolar nonpolar polar polar nonpolar polar nonpolar
4.5 3.8 3.9 1.9 2.8 1.6 0.8 0.7 0.9 1.3 4.2 280, 219 274, 222, 193 5.6, 47.0 1.4, 8.0, 48.0 257, 206, 188 0.2, 9.3, 60.0
In addition, there are two additional amino acids that are incorporated by overriding stop codons:
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1-Letter U O
In addition to the specific amino acid codes, placeholders are used in cases where chemical or crystallographic analysis of a peptide or protein cannot conclusively determine the identity of a residue.
Ambiguous Amino Acids Asparagine or aspartic acid Glutamine or glutamic acid Leucine or Isoleucine Unspecified or unknown amino acid 3-Letter Asx Glx Xle Xaa 1-Letter B Z J X
Unk is sometimes used instead of Xaa, but is less standard. In addition, many non-standard amino acids have a specific code. For example, several peptide drugs, such as Bortezomib and MG132, are artificially synthesized and retain their protecting groups, which have specific codes. Bortezomib is Pyz-Phe-boroLeu, and MG132 is Z-Leu-Leu-Leu-al. To aid in the analysis of protein structure, photocrosslinking amino acid analogues are available. These include photoleucine (pLeu) and photomethionine (pMet).[97]
Amino acid
[17] Hatem, Salama Mohamed Ali (2006). "Gas chromatographic determination of Amino Acid Enantiomers in tobacco and bottled wines" (http:/ / geb. uni-giessen. de/ geb/ volltexte/ 2006/ 3038/ index. html). University of Giessen. . Retrieved 2008-11-17. [18] Simmons, William J.; Gerhard Meisenberg (2006). Principles of medical biochemistry. Mosby Elsevier. p.19. ISBN0-323-02942-6. [19] Fennema OR. Food Chemistry 3rd Ed. CRC Press. pp.3278. ISBN0-8247-9691-8. [20] Rodnina MV, Beringer M, Wintermeyer W (January 2007). "How ribosomes make peptide bonds". Trends in Biochemical Sciences 32 (1): 206. doi:10.1016/j.tibs.2006.11.007. PMID17157507. [21] Driscoll DM, Copeland PR (2003). "Mechanism and regulation of selenoprotein synthesis". Annual Review of Nutrition 23 (1): 1740. doi:10.1146/annurev.nutr.23.011702.073318. PMID12524431. [22] Krzycki JA (December 2005). "The direct genetic encoding of pyrrolysine". Current Opinion in Microbiology 8 (6): 70612. doi:10.1016/j.mib.2005.10.009. PMID16256420. [23] Thobald-Dietrich A, Gieg R, Rudinger-Thirion J (2005). "Evidence for the existence in mRNAs of a hairpin element responsible for ribosome dependent pyrrolysine insertion into proteins". Biochimie 87 (910): 8137. doi:10.1016/j.biochi.2005.03.006. PMID16164991. [24] Vermeer C (March 1990). "Gamma-carboxyglutamate-containing proteins and the vitamin K-dependent carboxylase". The Biochemical Journal 266 (3): 62536. PMC1131186. PMID2183788. [25] Bhattacharjee A, Bansal M (March 2005). "Collagen structure: the Madras triple helix and the current scenario". IUBMB Life 57 (3): 16172. doi:10.1080/15216540500090710. PMID16036578. [26] Park MH (February 2006). "The post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5A (eIF5A)". Journal of Biochemistry 139 (2): 1619. doi:10.1093/jb/mvj034. PMC2494880. PMID16452303. [27] Blenis J, Resh MD (December 1993). "Subcellular localization specified by protein acylation and phosphorylation". Current Opinion in Cell Biology 5 (6): 9849. doi:10.1016/0955-0674(93)90081-Z. PMID8129952. [28] Curis E, Nicolis I, Moinard C, et al. (November 2005). "Almost all about citrulline in mammals". Amino Acids 29 (3): 177205. doi:10.1007/s00726-005-0235-4. PMID16082501. [29] Coxon KM, Chakauya E, Ottenhof HH, et al. (August 2005). "Pantothenate biosynthesis in higher plants". Biochemical Society Transactions 33 (Pt 4): 7436. doi:10.1042/BST0330743. PMID16042590. [30] Sakami W, Harrington H (1963). "Amino acid metabolism". Annual Review of Biochemistry 32 (1): 35598. doi:10.1146/annurev.bi.32.070163.002035. PMID14144484. [31] Brosnan JT (April 2000). "Glutamate, at the interface between amino acid and carbohydrate metabolism" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=10736367). The Journal of Nutrition 130 (4S Suppl): 988S90S. PMID10736367. . [32] Young VR, Ajami AM (September 2001). "Glutamine: the emperor or his clothes?" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=11533293). The Journal of Nutrition 131 (9 Suppl): 2449S59S; discussion 2486S7S. PMID11533293. . [33] Young VR (August 1994). "Adult amino acid requirements: the case for a major revision in current recommendations" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=8064412). The Journal of Nutrition 124 (8 Suppl): 1517S1523S. PMID8064412. . [34] Imura K, Okada A (January 1998). "Amino acid metabolism in pediatric patients". Nutrition 14 (1): 1438. doi:10.1016/S0899-9007(97)00230-X. PMID9437700. [35] Loureno R, Camilo ME (2002). "Taurine: a conditionally essential amino acid in humans? An overview in health and disease". Nutricin Hospitalaria 17 (6): 26270. PMID12514918. [36] Frst P, Stehle P (June 2004). "What are the essential elements needed for the determination of amino acid requirements in humans?" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=15173430). The Journal of Nutrition 134 (6 Suppl): 1558S1565S. PMID15173430. . [37] Reeds PJ (July 2000). "Dispensable and indispensable amino acids for humans" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=10867060). The Journal of Nutrition 130 (7): 1835S40S. PMID10867060. . [38] Savelieva KV, Zhao S, Pogorelov VM, et al. (2008). Bartolomucci, Alessandro. ed. "Genetic disruption of both tryptophan hydroxylase genes dramatically reduces serotonin and affects behavior in models sensitive to antidepressants". PloS ONE 3 (10): e3301. Bibcode2008PLoSO...3.3301S. doi:10.1371/journal.pone.0003301. PMC2565062. PMID18923670. [39] Shemin D, Rittenberg D (1 December 1946). "The biological utilization of glycine for the synthesis of the protoporphyrin of hemoglobin" (http:/ / www. jbc. org/ cgi/ reprint/ 166/ 2/ 621). Journal of Biological Chemistry 166 (2): 6215. PMID20276176. . [40] Tejero J, Biswas A, Wang ZQ, et al. (November 2008). "Stabilization and characterization of a heme-oxy reaction intermediate in inducible nitric-oxide synthase". The Journal of Biological Chemistry 283 (48): 33498507. doi:10.1074/jbc.M806122200. PMC2586280. PMID18815130. [41] Rodrguez-Caso C, Montaez R, Cascante M, Snchez-Jimnez F, Medina MA (August 2006). "Mathematical modeling of polyamine metabolism in mammals". The Journal of Biological Chemistry 281 (31): 21799812. doi:10.1074/jbc.M602756200. PMID16709566. [42] Stryer, Lubert; Berg, Jeremy Mark; Tymoczko, John L. (2002). Biochemistry. San Francisco: W.H. Freeman. pp.6938. ISBN0-7167-4684-0. [43] Brosnan JT, Brosnan ME (June 2006). "The sulfur-containing amino acids: an overview" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=16702333). The Journal of Nutrition 136 (6 Suppl): 1636S1640S. PMID16702333. . [44] Hylin, John W. (1969). "Toxic peptides and amino acids in foods and feeds". Journal of Agricultural and Food Chemistry 17 (3): 4926. doi:10.1021/jf60163a003. [45] Turner, B. L.; Harborne, J. B. (1967). "Distribution of canavanine in the plant kingdom". Phytochemistry 6 (6): 86366. doi:10.1016/S0031-9422(00)86033-1.
105
Amino acid
[46] Ekanayake S, Skog K, Asp NG (May 2007). "Canavanine content in sword beans (Canavalia gladiata): analysis and effect of processing". Food and Chemical Toxicology 45 (5): 797803. doi:10.1016/j.fct.2006.10.030. PMID17187914. [47] Rosenthal GA (2001). "L-Canavanine: a higher plant insecticidal allelochemical". Amino Acids 21 (3): 31930. doi:10.1007/s007260170017. PMID11764412. [48] Hammond AC (May 1995). "Leucaena toxicosis and its control in ruminants" (http:/ / jas. fass. org/ cgi/ pmidlookup?view=long& pmid=7665380). Journal of Animal Science 73 (5): 148792. PMID7665380. . [49] Leuchtenberger W, Huthmacher K, Drauz K (November 2005). "Biotechnological production of amino acids and derivatives: current status and prospects". Applied Microbiology and Biotechnology 69 (1): 18. doi:10.1007/s00253-005-0155-y. PMID16195792. [50] Ashmead, H. DeWayne (1993). The Role of Amino Acid Chelates in Animal Nutrition. Westwood: Noyes Publications. [51] Garattini S (April 2000). "Glutamic acid, twenty years later" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=10736350). The Journal of Nutrition 130 (4S Suppl): 901S9S. PMID10736350. . [52] Stegink LD (July 1987). "The aspartame story: a model for the clinical testing of a food additive" (http:/ / www. ajcn. org/ cgi/ pmidlookup?view=long& pmid=3300262). The American Journal of Clinical Nutrition 46 (1 Suppl): 20415. PMID3300262. . [53] Albion Laboratories, Inc.. "Albion Ferrochel Website" (http:/ / www. albionferrochel. com). . Retrieved Cited: July 12, 2011. [54] Ashmead, H. DeWayne (1986). Foliar Feeding of Plants with Amino Acid Chelates. Park Ridge: Noyes Publications. [55] Turner EH, Loftis JM, Blackwell AD (March 2006). "Serotonin a la carte: supplementation with the serotonin precursor 5-hydroxytryptophan". Pharmacology & Therapeutics 109 (3): 32538. doi:10.1016/j.pharmthera.2005.06.004. PMID16023217. [56] Kostrzewa RM, Nowak P, Kostrzewa JP, Kostrzewa RA, Brus R (March 2005). "Peculiarities of L: -DOPA treatment of Parkinson's disease". Amino Acids 28 (2): 15764. doi:10.1007/s00726-005-0162-4. PMID15750845. [57] Heby O, Persson L, Rentala M (August 2007). "Targeting the polyamine biosynthetic enzymes: a promising approach to therapy of African sleeping sickness, Chagas' disease, and leishmaniasis". Amino Acids 33 (2): 35966. doi:10.1007/s00726-007-0537-9. PMID17610127. [58] Xie J, Schultz PG (December 2005). "Adding amino acids to the genetic repertoire". Curr Opin Chem Biol 9 (6): 54854. doi:10.1016/j.cbpa.2005.10.011. PMID16260173. [59] Wang Q, Parrish AR, Wang L (March 2009). "Expanding the genetic code for biological studies". Chem. Biol. 16 (3): 32336. doi:10.1016/j.chembiol.2009.03.001. PMC2696486. PMID19318213. [60] Hanessian, S. (1993). "Reflections on the total synthesis of natural products: Art, craft, logic, and the chiron approach". Pure and Applied Chemistry 65 (6): 1189204. doi:10.1351/pac199365061189. [61] Blaser, Hans Ulrich (1992). "The chiral pool as a source of enantioselective catalysts and auxiliaries". Chemical Reviews 92 (5): 93552. doi:10.1021/cr00013a009. [62] Sanda, Fumio; Endo, Takeshi (1999). "Feature Article Syntheses and functions of polymers based on amino acids". Macromolecular Chemistry and Physics 200 (12): 265161. doi:10.1002/(SICI)1521-3935(19991201)200:12<2651::AID-MACP2651>3.0.CO;2-P. [63] Gross, R. A.; Kalra, B. (2002). "Biodegradable Polymers for the Environment" (http:/ / www. sciencemag. org/ cgi/ content/ abstract/ 297/ 5582/ 803). Science 297 (5582): 803807. Bibcode2002Sci...297..803G. doi:10.1126/science.297.5582.803. PMID12161646. . [64] Low, K. C.; Wheeler, A. P.; Koskan, L. P. (1996). Commercial poly(aspartic acid) and Its Uses. Advances in Chemistry Series. 248. Washington, D.C.: American Chemical Society. [65] Thombre, S.M.; Sarwade, B.D. (2005). "Synthesis and Biodegradability of Polyaspartic Acid: A Critical Review" (http:/ / www. informaworld. com/ index/ 718581646. pdf). Journal of Macromolecular Science, Part A 42 (9): 12991315. doi:10.1080/10601320500189604. . [66] Bourke, S. L.; Kohn, J. (2003). "Polymers derived from the amino acid l-tyrosine: polycarbonates, polyarylates and copolymers with poly(ethylene glycol)" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S0169409X03000383). Advanced Drug Delivery Reviews 55 (4): 447466. doi:10.1016/S0169-409X(03)00038-3. PMID12706045. . [67] Elmore, Donald Trevor; Barrett, G. C. (1998). Amino acids and peptides. Cambridge, UK: Cambridge University Press. pp.4860. ISBN0-521-46827-2. [68] Konar, Sanjit; et al. (2010). "Structural determination and characterization of copper and zinc bis-glycinates with X-ray crystallography and mass spectrometry". Journal of Coordination Chemistry 63 (19). [69] Gutteridge A, Thornton JM (November 2005). "Understanding nature's catalytic toolkit". Trends in Biochemical Sciences 30 (11): 6229. doi:10.1016/j.tibs.2005.09.006. PMID16214343. [70] McMurry, John (1996). Organic chemistry. Pacific Grove, CA, USA: Brooks/Cole. p.1064. ISBN0-534-23832-7. [71] Strecker, Adolph (1850). "Ueber die knstliche Bildung der Milchsure und einen neuen, dem Glycocoll homologen Krper". Justus Liebigs Annalen der Chemie 75 (1): 2745. doi:10.1002/jlac.18500750103. [72] Strecker, Adolph (1854). "Ueber einen neuen aus Aldehyd - Ammoniak und Blausure entstehenden Krper". Justus Liebigs Annalen der Chemie 91 (3): 34951. doi:10.1002/jlac.18540910309. [73] Masumoto S, Usuda H, Suzuki M, Kanai M, Shibasaki M (May 2003). "Catalytic enantioselective Strecker reaction of ketoimines". Journal of the American Chemical Society 125 (19): 56345. doi:10.1021/ja034980. PMID12733893. [74] Davis, F. A.; Reddy, Rajarathnam E.; Portonovo, Padma S. (1994). "Asymmetric strecker synthesis using enantiopure sulfinimines: A convenient synthesis of -amino acids". Tetrahedron Letters 35 (50): 9351. doi:10.1016/S0040-4039(00)78540-6. [75] Ishitani, Haruro; Komiyama, Susumu; Hasegawa, Yoshiki; Kobayashi, Sh (2000). "Catalytic Asymmetric Strecker Synthesis. Preparation of Enantiomerically Pure -Amino Acid Derivatives from Aldimines and Tributyltin Cyanide or Achiral Aldehydes, Amines, and Hydrogen Cyanide Using a Chiral Zirconium Catalyst". Journal of the American Chemical Society 122 (5): 7626. doi:10.1021/ja9935207.
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[76] Huang, Jinkun; Corey, E. J. (2004). "A New Chiral Catalyst for the Enantioselective Strecker Synthesis of -Amino Acids". Orgic Letters 62 (6): 50279. doi:10.1021/ol047698w. PMID15606127. [77] Duthaler, Rudolf O. (1994). "Recent developments in the stereoselective synthesis of -aminoacids". Tetrahedron 50 (6): 15391650. doi:10.1016/S0040-4020(01)80840-1. [78] Ibba M, Sll D (May 2001). "The renaissance of aminoacyl-tRNA synthesis" (http:/ / www. nature. com/ embor/ journal/ v2/ n5/ full/ embor420. html). EMBO Reports 2 (5): 3827. doi:10.1093/embo-reports/kve095 (inactive 2010-02-18). PMC1083889. PMID11375928. . [79] Lengyel P, Sll D (June 1969). "Mechanism of protein biosynthesis" (http:/ / mmbr. asm. org/ cgi/ pmidlookup?view=long& pmid=4896351). Bacteriological Reviews 33 (2): 264301. PMC378322. PMID4896351. . [80] Wu G, Fang YZ, Yang S, Lupton JR, Turner ND (March 2004). "Glutathione metabolism and its implications for health" (http:/ / jn. nutrition. org/ cgi/ pmidlookup?view=long& pmid=14988435). The Journal of Nutrition 134 (3): 48992. PMID14988435. . [81] Meister A (November 1988). "Glutathione metabolism and its selective modification" (http:/ / www. jbc. org/ cgi/ pmidlookup?view=long& pmid=3053703). The Journal of Biological Chemistry 263 (33): 172058. PMID3053703. . [82] Carpino, Louis A. (1992). "1-Hydroxy-7-azabenzotriazole. An efficient peptide coupling additive". Journal of the American Chemical Society 115 (10): 43978. doi:10.1021/ja00063a082. [83] Marasco D, Perretta G, Sabatella M, Ruvo M (October 2008). "Past and future perspectives of synthetic peptide libraries". Current Protein & Peptide Science 9 (5): 44767. doi:10.2174/138920308785915209. PMID18855697. [84] Jones, Russell Celyn; Buchanan, Bob B.; Gruissem, Wilhelm (2000). Biochemistry & molecular biology of plants. Rockville, Md: American Society of Plant Physiologists. pp.3712. ISBN0-943088-39-9. [85] Kivirikko KI, Pihlajaniemi T (1998). "Collagen hydroxylases and the protein disulfide isomerase subunit of prolyl 4-hydroxylases". Advances in Enzymology and Related Areas of Molecular Biology 72: 32598. PMID9559057. [86] Whitmore L, Wallace BA (May 2004). "Analysis of peptaibol sequence composition: implications for in vivo synthesis and channel formation". European Biophysics Journal 33 (3): 2337. doi:10.1007/s00249-003-0348-1. PMID14534753. [87] Alexander L, Grierson D (October 2002). "Ethylene biosynthesis and action in tomato: a model for climacteric fruit ripening". Journal of Experimental Botany 53 (377): 203955. doi:10.1093/jxb/erf072. PMID12324528. [88] Chapter 20 (Amino Acid Degradation and Synthesis) in: Denise R., PhD. Ferrier. Lippincott's Illustrated Reviews: Biochemistry (Lippincott's Illustrated Reviews). Hagerstwon, MD: Lippincott Williams & Wilkins. ISBN0-7817-2265-9. [89] Stryer, Lubert; Berg, Jeremy Mark; Tymoczko, John L. (2002). Biochemistry. San Francisco: W.H. Freeman. pp.63949. ISBN0-7167-4684-0. [90] Urry, Dan W. (2004). "The change in Gibbs free energy for hydrophobic association: Derivation and evaluation by means of inverse temperature transitions". Chemical Physics Letters 399 (13): 17783. doi:10.1016/S0009-2614(04)01565-9. [91] Magee T, Seabra MC (April 2005). "Fatty acylation and prenylation of proteins: what's hot in fat". Current Opinion in Cell Biology 17 (2): 1906. doi:10.1016/j.ceb.2005.02.003. PMID15780596. [92] Pilobello KT, Mahal LK (June 2007). "Deciphering the glycocode: the complexity and analytical challenge of glycomics". Current Opinion in Chemical Biology 11 (3): 3005. doi:10.1016/j.cbpa.2007.05.002. PMID17500024. [93] Smotrys JE, Linder ME (2004). "Palmitoylation of intracellular signaling proteins: regulation and function". Annual Review of Biochemistry 73 (1): 55987. doi:10.1146/annurev.biochem.73.011303.073954. PMID15189153. [94] Hausman, Robert E.; Cooper, Geoffrey M. (2004). The cell: a molecular approach. Washington, D.C: ASM Press. p.51. ISBN0-87893-214-3. [95] Kyte J, Doolittle RF (May 1982). "A simple method for displaying the hydropathic character of a protein". Journal of Molecular Biology 157 (1): 10532. doi:10.1016/0022-2836(82)90515-0. PMID7108955. [96] Freifelder, D. (1983). Physical Biochemistry (2nd ed.). W. H. Freeman and Company. ISBN0-7167-1315-2. [97] Suchanek M, Radzikowska A, Thiele C (April 2005). "Photo-leucine and photo-methionine allow identification of protein-protein interactions in living cells". Nature Methods 2 (4): 2617. doi:10.1038/nmeth752. PMID15782218.
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Further reading
Doolittle, R.F. (1989) Redundancies in protein sequences. In Predictions of Protein Structure and the Principles of Protein Conformation (Fasman, G.D. ed) Plenum Press, New York, pp.599623 David L. Nelson and Michael M. Cox, Lehninger Principles of Biochemistry, 3rd edition, 2000, Worth Publishers, ISBN 1-57259-153-6 Meierhenrich, U.J.: Amino acids and the asymmetry of life, Springer-Verlag, Berlin, New York, 2008. ISBN 978-3-540-76885-2 Morelli, Robert J. "Studies of amino acid absorption from the small intestine." San Francisco: Morelli, 1952.
Amino acid
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External links
Amino acids overview (http://www.peptideguide.com/amino-acids/index.html) physical-chemistry properties, 3D structures, etc. List of Standard Amino Acids (http://www.unc.edu/~bzafer/aminoacids/) The Detailed PDF List of Standard Amino Acids (including 3D depictions) Nomenclature and Symbolism for Amino Acids and Peptides (http://www.chem.qmul.ac.uk/iupac/ AminoAcid/) IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) Molecular Expressions: The Amino Acid Collection (http://micro.magnet.fsu.edu/aminoacids/index.html) Has detailed information and microscopy photographs of each amino acid. Amino acid properties (http://www.russell.embl.de/aas/) Properties of the amino acids (a tool aimed mostly at molecular geneticists trying to understand the meaning of mutations) Synthesis of Amino Acids and Derivatives (http://www.organic-chemistry.org/synthesis/C1C/nitrogen/ alpha-amino-acids2.shtm) Learn the 20 proteinogenic amino acids online (http://www.mathiasbader.de/studium/biology/index. php?lng=en) The origin of the single-letter code for the amino acids (http://www.biology.arizona.edu/biochemistry/ problem_sets/aa/Dayhoff.html) Amino acid solutions pH, titration and isoelectric point calculation free spreadsheet (http://www2.iq.usp.br/ docente/gutz/Curtipot_.html) Interactive Amino Map Web Application at DNA.UTAH.EDU (http://www.dna.utah.edu/utensils/amino. php)
109
Structures
The following illustrates the structures and abbreviations of the 21 amino acids that are directly encoded for protein synthesis by the genetic code of eukaryotes. The structures given below are standard chemical structures, not the typical zwitterion forms that exist in aqueous solutions.
Grouped table of 21 amino acids' structures, nomenclature, and their side groups' pKa's.
L-Alanine (Ala/A)
L-Arginine (Arg/R)
L-Asparagine (Asn/N)
L-Cysteine (Cys/C)
L-Glutamine (Gln/Q)
Glycine (Gly/G)
110
L-Histidine (His/H)
L-Isoleucine (Ile/I)
L-Leucine (Leu/L)
L-Lysine (Lys/K)
L-Methionine (Met/M)
L-Phenylalanine (Phe/F)
L-Proline (Pro/P)
L-Serine (Ser/S)
L-Threonine (Thr/T)
L-Tryptophan (Trp/W)
L-Tyrosine (Tyr/Y)
L-Valine (Val/V)
IUPAC/IUBMB now also recommends standard abbreviations for the following two amino acids:
L-Selenocysteine (Sec/U)
L-Pyrrolysine (Pyl/O)
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Non-specific abbreviations
Sometimes the specific identity of an amino acid cannot be determined unambiguously. Certain protein sequencing techniques do not distinguish among certain pairs. Thus, the following codes are used: Asx (B) is "asparagine or aspartic acid" Glx (Z) is "glutamic acid or glutamine" Xle (J) is "leucine or isoleucine" In addition, the symbol X is used to indicate an amino acid that is completely unidentified.
Chemical properties
Following is a table listing the one-letter symbols, the three-letter symbols, and the chemical properties of the side-chains of the standard amino acids. The masses listed are based on weighted averages of the elemental isotopes at their natural abundances. Note that forming a peptide bond results in elimination of a molecule of water, so the mass of an amino acid unit within a protein chain is reduced by 18.01524 Da. General chemical properties
Amino Acid Short Abbrev. Avg. Mass (Da) pI pK1 pK2 (-COOH) (-+NH ) 3 2.35 1.92 1.99 2.10 2.20 2.35 1.80 2.32 2.16 2.33 2.13 2.14 9.87 10.70 9.90 9.47 9.31 9.78 9.33 9.76 9.06 9.74 9.28 8.72
Alanine Cysteine Aspartic acid Glutamic acid Phenylalanine Glycine Histidine Isoleucine Lysine Leucine Methionine Asparagine Pyrrolysine Proline Glutamine Arginine Serine Threonine Selenocysteine Valine Tryptophan Tyrosine
A C D E F G H I K L M N O P Q R S T U V W Y
Ala Cys Asp Glu Phe Gly His Ile Lys Leu Met Asn Pyl Pro Gln Arg Ser Thr Sec Val Trp Tyr
89.09404 121.15404 133.10384 147.13074 165.19184 75.06714 155.15634 131.17464 146.18934 131.17464 149.20784 132.11904
6.01 5.05 2.85 3.15 5.49 6.06 7.60 6.05 9.60 6.01 5.74 5.41
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Alanine Cysteine
A C
Ala Cys Asp Glu Phe Gly His Ile Lys Leu Met Asn Pyl Pro Gln Arg
-CH3 -CH2SH -CH2COOH -CH2CH2COOH -CH2C6H5 -H -CH2-C3H3N2 -CH(CH3)CH2CH3 -(CH2)4NH2 -CH2CH(CH3)2 -CH2CH2SCH3 -CH2CONH2
X X X X X X X -
X X X -
X X X X X
X X -
Aspartic acid D Glutamic acid E Phenylalanine F Glycine Histidine Isoleucine Lysine Leucine Methionine Asparagine Pyrrolysine Proline Glutamine Arginine G H I K L M N O P Q R
10.54 X X
-CH2CH2CH2-CH2CH2CONH2
X -
X -
90 114 148
12.48 X
Serine Threonine
S T
5.73 -
X X -
X X X X -
X -
73 93
10.46 X
Note: The pKa values of amino acids are typically slightly different when the amino acid is inside a protein. Protein pKa calculations are sometimes used to calculate the change in the pKa value of an amino acid in this situation.
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Amino Acid
Short
Abbrev.
Codon(s)
Occurrence in human proteins (%) 7.8 1.9 5.3 6.3 3.9 7.2 2.3 5.3 5.9
Essential in humans
Alanine Cysteine
A C
Ala Cys Asp Glu Phe Gly His Ile Lys Leu Met Asn Pyl Pro Gln Arg Ser Thr Sec Val Trp Tyr Term
GCU, GCC, GCA, GCG UGU, UGC GAU, GAC GAA, GAG UUU, UUC GGU, GGC, GGA, GGG CAU, CAC AUU, AUC, AUA AAA, AAG
Aspartic acid D Glutamic acid E Phenylalanine F Glycine Histidine Isoleucine Lysine Leucine Methionine Asparagine Pyrrolysine Proline Glutamine Arginine Serine Threonine G H I K L M N O P Q R S T
UUA, UUG, CUU, CUC, CUA, CUG 9.1 AUG AAU, AAC UAG* CCU, CCC, CCA, CCG CAA, CAG 5.2 4.2 2.3 4.3
Conditionally Yes -
CGU, CGC, CGA, CGG, AGA, AGG 5.1 UCU, UCC, UCA, UCG, AGU, AGC 6.8 ACU, ACC, ACA, ACG UGA** GUU, GUC, GUA, GUG UGG UAU, UAC UAA, UAG, UGA 6.6 1.4 3.2 5.9
* UAG is normally the amber stop codon, but encodes pyrrolysine if a PYLIS element is present. ** UGA is normally the opal (or umber) stop codon, but encodes selenocysteine if a SECIS element is present. The stop codon is not an amino acid, but is included for completeness. An essential amino acid cannot be synthesized in humans and must, therefore, be supplied in the diet. Conditionally essential amino acids are not normally required in the diet, but must be supplied exogenously to specific populations that do not synthesize it in adequate amounts.
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Mass spectrometry
In mass spectrometry of peptides and proteins, it is useful to know the masses of the residues. The mass of the peptide or protein is the sum of the residue masses plus the mass of water.[2]
Amino Acid Alanine Cysteine Aspartic acid Glutamic acid Phenylalanine Glycine Histidine Isoleucine Lysine Leucine Methionine Asparagine Pyrrolysine Proline Glutamine Arginine Serine Threonine Selenocysteine Valine Tryptophan Tyrosine Short A C D E F G H I K L M N O P Q R S T U V W Y Abbrev. Ala Cys Asp Glu Phe Gly His Ile Lys Leu Met Asn Pyl Pro Gln Arg Ser Thr Sec Val Trp Tyr Formula C3H5NO C3H5NOS C4H5NO3 C5H7NO3 C9H9NO C2H3NO C6H7N3O C6H11NO C6H12N2O C6H11NO C5H9NOS C4H6N2O2 C12H21N3O3 C5H7NO C5H8N2O2 C6H12N4O C3H5NO2 C4H7NO2 C3H5NOSe C5H9NO C11H10N2O C9H9NO2 Mon. Mass (Da) Avg. Mass (Da) 71.03711 103.00919 115.02694 129.04259 147.06841 57.02146 137.05891 113.08406 128.09496 113.08406 131.04049 114.04293 255.15829 97.05276 128.05858 156.10111 87.03203 101.04768 150.95364 99.06841 186.07931 163.06333 71.0788 103.1388 115.0886 129.1155 147.1766 57.0519 137.1411 113.1594 128.1741 113.1594 131.1986 114.1039 255.3172 97.1167 128.1307 156.1875 87.0782 101.1051 150.0388 99.1326 186.2132 163.1760
Monoisotopic mass
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Amino acid
Abundance (# of molecules (108) per E. coli cell) 2.9 0.52 1.4 1.5 1.1 3.5 0.54 1.7 2.0 2.6 0.88 1.4 1.3 1.5 1.7 1.2 1.5 0.33 0.79 2.4
Alanine Cysteine Aspartic acid Glutamic acid Phenylalanine Glycine Histidine Isoleucine Lysine Leucine Methionine Asparagine Proline Glutamine Arginine Serine Threonine Tryptophan Tyrosine Valine
Remarks
Amino Acid Abbrev. Remarks
Alanine
Ala Very abundant, very versatile. More stiff than glycine, but small enough to pose only small steric limits for the protein conformation. It behaves fairly neutrally, and can be located in both hydrophilic regions on the protein outside and the hydrophobic areas inside. Asx A placeholder when either amino acid may occupy a position.
Cys The sulfur atom bonds readily to heavy metal ions. Under oxidizing conditions, two cysteines can join together in a disulfide bond to form the amino acid cystine. When cystines are part of a protein, insulin for example, the tertiary structure is stabilized, which makes the protein more resistant to denaturation; therefore, disulfide bonds are common in proteins that have to function in harsh environments including digestive enzymes (e.g., pepsin and chymotrypsin) and structural proteins (e.g., keratin). Disulfides are also found in peptides too small to hold a stable shape on their own (eg. insulin). Asp Behaves similarly to glutamic acid. Carries a hydrophilic acidic group with strong negative charge. Usually is located on the outer surface of the protein, making it water-soluble. Binds to positively-charged molecules and ions, often used in enzymes to fix the metal ion. When located inside of the protein, aspartate and glutamate are usually paired with arginine and lysine.
Aspartic acid
116
E F
Glu Behaves similar to aspartic acid. Has longer, slightly more flexible side chain. Phe Essential for humans. Phenylalanine, tyrosine, and tryptophan contain large rigid aromatic group on the side-chain. These are the biggest amino acids. Like isoleucine, leucine and valine, these are hydrophobic and tend to orient towards the interior of the folded protein molecule. Phenylalanine can be converted into Tyrosine. Gly Because of the two hydrogen atoms at the carbon, glycine is not optically active. It is the smallest amino acid, rotates easily, adds flexibility to the protein chain. It is able to fit into the tightest spaces, e.g., the triple helix of collagen. As too much flexibility is usually not desired, as a structural component it is less common than alanine. His In even slightly acidic conditions protonation of the nitrogen occurs, changing the properties of histidine and the polypeptide as a whole. It is used by many proteins as a regulatory mechanism, changing the conformation and behavior of the polypeptide in acidic regions such as the late endosome or lysosome, enforcing conformation change in enzymes. However only a few histidines are needed for this, so it is comparatively scarce. Ile Essential for humans. Isoleucine, leucine and valine have large aliphatic hydrophobic side chains. Their molecules are rigid, and their mutual hydrophobic interactions are important for the correct folding of proteins, as these chains tend to be located inside of the protein molecule.
Glycine
Histidine
Isoleucine
Lys Essential for humans. Behaves similarly to arginine. Contains a long flexible side-chain with a positively-charged end. The flexibility of the chain makes lysine and arginine suitable for binding to molecules with many negative charges on their surfaces. E.g., DNA-binding proteins have their active regions rich with arginine and lysine. The strong charge makes these two amino acids prone to be located on the outer hydrophilic surfaces of the proteins; when they are found inside, they are usually paired with a corresponding negatively-charged amino acid, e.g., aspartate or glutamate. Leu Essential for humans. Behaves similar to isoleucine and valine. See isoleucine. Met Essential for humans. Always the first amino acid to be incorporated into a protein; sometimes removed after translation. Like cysteine, contains sulfur, but with a methyl group instead of hydrogen. This methyl group can be activated, and is used in many reactions where a new carbon atom is being added to another molecule. Asn Similar to aspartic acid. Asn contains an amide group where Asp has a carboxyl. Pyl Similar to lysine, with a pyrroline ring attached.
Leucine Methionine
L M
N O P
Pro Contains an unusual ring to the N-end amine group, which forces the CO-NH amide sequence into a fixed conformation. Can disrupt protein folding structures like helix or sheet, forcing the desired kink in the protein chain. Common in collagen, where it often undergoes a posttranslational modification to hydroxyproline. Gln Similar to glutamic acid. Gln contains an amide group where Glu has a carboxyl. Used in proteins and as a storage for ammonia. The most abundant Amino Acid in the body. Arg Functionally similar to lysine. Ser Serine and threonine have a short group ended with a hydroxyl group. Its hydrogen is easy to remove, so serine and threonine often act as hydrogen donors in enzymes. Both are very hydrophilic, therefore the outer regions of soluble proteins tend to be rich with them.
Glutamine
Arginine Serine
R S
T U V W
Thr Essential for humans. Behaves similarly to serine. Sec Selenated form of cysteine, which replaces sulfur. Val Essential for humans. Behaves similarly to isoleucine and leucine. See isoleucine. Trp Essential for humans. Behaves similarly to phenylalanine and tyrosine (see phenylalanine). Precursor of serotonin. Naturally fluorescent. Xaa Placeholder when the amino acid is unknown or unimportant. Tyr Behaves similarly to phenylalanine (precursor to Tyrosine) and tryptophan (see phenylalanine). Precursor of melanin, epinephrine, and thyroid hormones. Naturally fluorescent, although fluorescence is usually quenched by energy transfer to tryptophans. Glx A placeholder when either amino acid may occupy a position.
Unknown Tyrosine
X Y
117
Catabolism
[4] Amino acids can be classified according to the properties of their main products as either of the following: Glucogenic, with the products having the ability to form glucose by gluconeogenesisKetogenic, with the products not having the ability to form glucose. These products may still be used for ketogenesis or lipid synthesis.Amino acids catabolized into both glucogenic and ketogenic products.
References
[1] Ambrogelly A, Palioura S, Sll D (Jan 2007). "Natural expansion of the genetic code" (http:/ / www. nature. com/ nchembio/ journal/ v3/ n1/ abs/ nchembio847. html). Nat Chem Biol 3 (1): 2935. doi:10.1038/nchembio847. PMID17173027. . [2] "The amino acid masses" (http:/ / education. expasy. org/ student_projects/ isotopident/ htdocs/ aa-list. html). ExPASy. . Retrieved 2009-01-06. [3] Physical Biology of the Cell (Garland Science) p. 178 [4] Chapter 20 (Amino Acid Degradation and Synthesis) in: Denise R., PhD. Ferrier. Lippincott's Illustrated Reviews: Biochemistry (Lippincott's Illustrated Reviews). Hagerstwon, MD: Lippincott Williams & Wilkins. ISBN0-7817-2265-9.
Nelson, David L.; Cox, Michael M. (2000). Lehninger Principles of Biochemistry (3rd ed.). Worth Publishers. ISBN1-57259-153-6. Kyte, J.; Doolittle, R. F. (1982). "A simple method for displaying the hydropathic character of a protein". J. Mol. Biol. 157 (1): 105132. doi:10.1016/0022-2836(82)90515-0. PMID7108955. Meierhenrich, Uwe J. (2008). Amino acids and the asymmetry of life (1st ed.). Springer. ISBN978-3-540-76885-2.
Myoglobin
118
Myoglobin
Myoglobin
[1]
PDB 1m6c [2], 1m6m [3], 1mdn [4], 1mnh [5], 1mni [6], 1mnj [7], 1mnk [8], 1mno [9], 1mwc [10], 1mwd [11], 1myg [12], 1myh [13] [14] [15] [16] [17] [18] [19] , 1myi , 1myj , 1pmb , 1yca , 1ycb , 2mm1 Identifiers Symbols External IDs MB
[20]
; MGC13548; PVALB
[21]
MGI: 96922
[22]
HomoloGene: 3916
[23]
GeneCards: MB Gene
[24]
Molecular function oxygen transporter activity [25] [26] iron ion binding [27] oxygen binding [28] heme binding [29] metal ion binding Biological process response to hypoxia [31] transport [32] oxygen transport [33] enucleate erythrocyte differentiation
[34] [30]
Sources: Amigo
/ QuickGO
[35]
[36]
Myoglobin
[37] [39] [38] [40]
119
4151
17189
ENSG00000198125 P02144
[41] [43]
ENSMUSG00000018893 Q3UVB1
[42] [44]
NM_005368 NP_005359
NM_013593 NP_038621
[45]
[46]
PubMed search
Myoglobin is an iron- and oxygen-binding protein found in the muscle tissue of vertebrates in general and in almost all mammals. It is related to hemoglobin, which is the iron- and oxygen-binding protein in blood, specifically in the red blood cells. The only time myoglobin is found in the bloodstream is when it is released following muscle injury. It is an abnormal finding, and can be diagnostically relevant when found in blood. [51] Myoglobin (abbreviated Mb) is a single-chain globular protein of 153[52] or 154[53] amino acids, containing a heme (iron-containing porphyrin) prosthetic group in the center around which the remaining apoprotein folds. It has eight alpha helices and a hydrophobic core. It has a molecular weight of 17,699 daltons (with heme), and is the primary oxygen-carrying pigment of muscle tissues.[53] Unlike the blood-borne hemoglobin, to which it is structurally related,[54] this protein does not exhibit cooperative binding of oxygen, since positive cooperativity is a property of multimeric/oligomeric proteins only. Instead, the binding of oxygen by myoglobin is unaffected by the oxygen pressure in the surrounding tissue. Myoglobin is often cited as having an "instant binding tenacity" to oxygen given its hyperbolic oxygen dissociation curve. High concentrations of myoglobin in muscle cells allow organisms to hold their breaths longer. Diving mammals such as whales and seals have muscles with particularly high myoglobin abundance.[51] Myoglobin was the first protein to have its three-dimensional structure revealed.[55] In 1958, John Kendrew and associates successfully determined the structure of myoglobin by high-resolution X-ray crystallography.[56] For this discovery, John Kendrew shared the 1962 Nobel Prize in chemistry with Max Perutz.[57] Despite being one of the most studied proteins in biology, its true physiological function is not yet conclusively established: mice genetically engineered to lack myoglobin are viable, but showed a 30% reduction in cardiac systolic output. They adapted to this deficiency through hypoxic genetic mechanisms and increased vasodilation.[58] In humans myoglobin is encoded by the MB gene.[59]
Myoglobin
120
Meat color
Myoglobin forms pigments responsible for making meat red. The color that meat takes is partly determined by the oxidation states of the iron atom in myoglobin and the oxygen species attached to it. When meat is in its raw state, the iron atom is in the +2 oxidation state, and is bound to a dioxygen molecule (O2). Meat cooked well done is brown because the iron atom is now in the +3 oxidation state, having lost an electron, and is now coordinated by a water molecule. Under some conditions, meat can also remain pink all through cooking, despite being heated to high temperatures. If meat has been exposed to nitrites, it will remain pink because the iron atom is bound to NO, nitric oxide (true of, e.g., corned beef or cured hams). Grilled meats can also take on a pink An X-ray diffraction image for the protein myoglobin "smoke ring" that comes from the iron binding to a molecule of carbon monoxide to give metmyoglobin.[60] Raw meat packed in a carbon monoxide atmosphere also shows this same pink "smoke ring" due to the same coordination chemistry. Notably, the surface of this raw meat also displays the pink color, which is usually associated in consumers' minds with fresh meat. This artificially-induced pink color can persist in the meat for a very long time, reportedly up to one year.[61] Hormel and Cargill are both reported to use this meat-packing process, and meat treated this way has been in the consumer market since 2003.[62] Myoglobin is found in Type I muscle, Type II A and Type II B, but most texts consider myoglobin not to be found in smooth muscle.
Role in disease
Myoglobin is released from damaged muscle tissue (rhabdomyolysis), which has very high concentrations of myoglobin. The released myoglobin is filtered by the kidneys but is toxic to the renal tubular epithelium and so may cause acute renal failure.[63] It is not the myoglobin itself that is toxic (it is a protoxin) but the ferrihemate portion that is dissociated from myoglobin in acidic environments (e.g., acidic urine, lysozymes). Myoglobin is a sensitive marker for muscle injury, making it a potential marker for heart attack in patients with chest pain.[64] However, elevated myoglobin has low specificity for acute myocardial infarction (AMI) and thus CK-MB, cTnT, ECG, and clinical signs should be taken into account to make the diagnosis.
Myoglobin
121
References
[1] PDB 1MBO (http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1MBO); Takano T (March 1977). "Structure of myoglobin refined at 2.0 resolution. II. Structure of deoxymyoglobin from sperm whale". J. Mol. Biol. 110 (3): 56984. doi:10.1016/S0022-2836(77)80112-5. PMID845960. [2] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1m6c [3] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1m6m [4] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1mdn [5] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1mnh [6] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1mni [7] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1mnj [8] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1mnk [9] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1mno [10] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1mwc [11] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1mwd [12] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1myg [13] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1myh [14] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1myi [15] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1myj [16] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1pmb [17] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1yca [18] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=1ycb [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] http:/ / www. rcsb. org/ pdb/ cgi/ explore. cgi?pdbId=2mm1 http:/ / www. genenames. org/ data/ hgnc_data. php?hgnc_id=6915 http:/ / omim. org/ entry/ 160000 http:/ / www. informatics. jax. org/ searches/ accession_report. cgi?id=MGI:96922 http:/ / www. ncbi. nlm. nih. gov/ entrez/ query. fcgi?cmd=Retrieve& db=homologene& dopt=HomoloGene& list_uids=3916 http:/ / www. genecards. org/ cgi-bin/ carddisp. pl?id_type=entrezgene& id=4151 http:/ / amigo. geneontology. org/ cgi-bin/ amigo/ go. cgi?view=details& search_constraint=terms& depth=0& query=GO:0005344 http:/ / amigo. geneontology. org/ cgi-bin/ amigo/ go. cgi?view=details& search_constraint=terms& depth=0& query=GO:0005506 http:/ / amigo. geneontology. org/ cgi-bin/ amigo/ go. cgi?view=details& search_constraint=terms& depth=0& query=GO:0019825 http:/ / amigo. geneontology. org/ cgi-bin/ amigo/ go. cgi?view=details& search_constraint=terms& depth=0& query=GO:0020037 http:/ / amigo. geneontology. org/ cgi-bin/ amigo/ go. cgi?view=details& search_constraint=terms& depth=0& query=GO:0046872 http:/ / amigo. geneontology. org/ cgi-bin/ amigo/ go. cgi?view=details& search_constraint=terms& depth=0& query=GO:0001666 http:/ / amigo. geneontology. org/ cgi-bin/ amigo/ go. cgi?view=details& search_constraint=terms& depth=0& query=GO:0006810 http:/ / amigo. geneontology. org/ cgi-bin/ amigo/ go. cgi?view=details& search_constraint=terms& depth=0& query=GO:0015671 http:/ / amigo. geneontology. org/ cgi-bin/ amigo/ go. cgi?view=details& search_constraint=terms& depth=0& query=GO:0043353 http:/ / amigo. geneontology. org/ cgi-bin/ amigo/ gp-assoc. cgi?gp=UniProtKB:P02144 http:/ / www. ebi. ac. uk/ QuickGO/ GProtein?ac=P02144 http:/ / biogps. org/ gene/ 4151/ http:/ / www. ncbi. nlm. nih. gov/ entrez/ query. fcgi?db=gene& cmd=retrieve& dopt=default& list_uids=4151& rn=1 http:/ / www. ncbi. nlm. nih. gov/ entrez/ query. fcgi?db=gene& cmd=retrieve& dopt=default& list_uids=17189& rn=1 http:/ / www. ensembl. org/ Homo_sapiens/ geneview?gene=ENSG00000198125;db=core http:/ / www. ensembl. org/ Mus_musculus/ geneview?gene=ENSMUSG00000018893;db=core http:/ / www. uniprot. org/ uniprot/ P02144 http:/ / www. uniprot. org/ uniprot/ Q3UVB1 http:/ / www. ncbi. nlm. nih. gov/ entrez/ viewer. fcgi?val=NM_005368 http:/ / www. ncbi. nlm. nih. gov/ entrez/ viewer. fcgi?val=NM_013593 http:/ / www. ncbi. nlm. nih. gov/ entrez/ viewer. fcgi?val=NP_005359 http:/ / www. ncbi. nlm. nih. gov/ entrez/ viewer. fcgi?val=NP_038621 http:/ / genome. ucsc. edu/ cgi-bin/ hgTracks?org=Human& db=hg18& position=chr22:34332757-34349347 http:/ / genome. ucsc. edu/ cgi-bin/ hgTracks?org=Mouse& db=mm8& position=chr15:76842742-76877925 http:/ / www. ncbi. nlm. nih. gov/ sites/ entrez?db=gene& cmd=Link& LinkName=gene_pubmed& from_uid=4151 http:/ / www. ncbi. nlm. nih. gov/ sites/ entrez?db=gene& cmd=Link& LinkName=gene_pubmed& from_uid=17189 Nelson, D. L.; Cox, M. M. (2000). Lehninger Principles of Biochemistry (3rd ed.). New York: Worth Publishers. p.206. ISBN071676203X.
[52] Hendgen-Cotta, U.; Kelm, M.; Rassaf, T. (2009). "A highlight of myoglobin diversity: the nitrite reductase activity during myocardial ischemia-reperfusion". Nitric oxide : biology and chemistry / official journal of the Nitric Oxide Society 22 (2): 7582. doi:10.1016/j.niox.2009.10.003. PMID19836457.
Myoglobin
[53] George A. Ordway and Daniel J. Garry (2004). "Myoglobin: an essential hemoprotein in striated muscle". Journal of Experimental Biology 207 (Pt 20): 34416. doi:10.1242/jeb.01172. PMID15339940. [54] Harvey Lodish, Arnold Berk, Lawrence S. Zipursky, Paul Matsudaira, David Baltimore and James Darnell (2000). "Evolutionary tree showing the globin protein family members myoglobin and hemoglobin" (http:/ / www. ncbi. nlm. nih. gov/ entrez/ query. fcgi?cmd=Search& db=books& doptcmdl=GenBookHL& term=myoglobin+ AND+ mcb[book]+ AND+ 105134[uid]& rid=mcb. figgrp. 540). Molecular Cell Biology (4th ed.). W. H. Freeman. ISBN0-7167-3136-3. . [55] (U.S.) National Science Foundation: Protein Data Bank Chronology (Jan. 21, 2004) (http:/ / www. nsf. gov/ news/ news_summ. jsp?cntn_id=100689). Retrieved 3.17.2010 [56] JC Kendrew, G Bodo, HM Dintzis, RG Parrish, H Wyckoff, and DC Phillips (1958). "A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis". Nature 181 (4610): 6626. Bibcode1958Natur.181..662K. doi:10.1038/181662a0. PMID13517261. [57] The Nobel Prize in Chemistry 1962 (http:/ / nobelprize. org/ chemistry/ laureates/ 1962/ index. html) [58] Mammen PP, Kanatous SB, Yuhanna IS, Shaul PW, Garry MG, Balaban RS, Garry DJ (2003). "Hypoxia-induced left ventricular dysfunction in myoglobin-deficient mice". American Journal of Physiology. Heart and Circulatory Physiology 285 (5): H213241. doi:10.1152/ajpheart.00147.2003. PMID12881221. [59] Akaboshi E (1985). "Cloning of the human myoglobin gene". Gene 33 (3): 2419. doi:10.1016/0378-1119(85)90231-8. PMID2989088. [60] McGee, H (2004). On Food and Cooking: The Science and Lore of the Kitchen. New York: Scribner. p.148. ISBN0-684-80001-2. [61] Minneapolis Star Tribune, Nov. 14, 2007 http:/ / www. startribune. com/ 10223/ story/ 1548852. html [62] Minneapolis Star Tribune, October 31, 2007 http:/ / www. startribune. com/ 535/ story/ 1518775. html [63] Toshio Naka, Daryl Jones, Ian Baldwin, Nigel Fealy, Samantha Bates, Hermann Goehl, Stanislao Morgera, Hans H. Neumayer and Rinaldo Bellomo (2005). "Myoglobin clearance by super high-flux hemofiltration in a case of severe rhabdomyolysis: a case report". Critical Care 9 (2): R905. doi:10.1186/cc3034. PMC1175920. PMID15774055. [64] M. Weber, M. Rau, K. Madlener, A. Elsaesser, D. Bankovic, V. Mitrovic and C. Hamm (2005). "Diagnostic utility of new immunoassays for the cardiac markers cTnI, myoglobin and CK-MB mass". Clinical Biochemistry 38 (11): 102730. doi:10.1016/j.clinbiochem.2005.07.011. PMID16125162. [65] J. P. Collman, J. I. Brauman, T. R. Halbert, and K. S. Suslick (1976). "Nature of Oxygen and Carbon Monoxide Binding to Metalloporphyrins and Heme Proteins" (http:/ / www. pnas. org/ cgi/ content/ abstract/ 73/ 10/ 3333). Proceedings of the National Academy of Sciences of the United States of America 73 (10): 33337. doi:10.1073/pnas.73.10.3333. PMC431107. PMID1068445. .
122
Further reading
J. P. Collman, R. Boulatov, C. J. Sunderland and L. Fu (2004). "Functional Analogues of Cytochrome c Oxidase, Myoglobin, and Hemoglobin". Chem. Rev. 104 (2): 561588. doi:10.1021/cr0206059. PMID14871135. Reeder, BJ; Svistunenko DA, Cooper CE, Wilson MT (December 2004). "The radical and redox chemistry of myoglobin and hemoglobin: from in vitro studies to human pathology". Antioxid Redox Signal 6 (6): 95466. doi:10.1089/ars.2004.6.954. PMID15548893. Schlieper, G; Kim JH, Molojavyi A, Jacoby C, Laussmann T, Flogel U, Godecke A, Schrader J (April 2004). "Adaptation of the myoglobin knockout mouse to hypoxic stress". Am J Physiol Regul Integr Comp Physiol 286 (4): R78692. doi:10.1152/ajpregu.00043.2003. PMID14656764. Takano, T (1977). "Structure of myoglobin refined at 2-0 A resolution. II. Structure of deoxymyoglobin from sperm whale". J. Mol. Biol. 110 (3): 569584. doi:10.1016/S0022-2836(77)80112-5. PMID845960. Roy, A; Sen S, Chakraborti AS (February 2004). "In vitro nonenzymatic glycation enhances the role of myoglobin as a source of oxidative stress". Free Radic Res. 38 (2): 13946. doi:10.1080/10715160310001638038. PMID15104207. Stewart, JM; Blakely JA, Karpowicz PA, Kalanxhi E, Thatcher BJ, Martin BM (March 2004). "Unusually weak oxygen binding, physical properties, partial sequence, autoxidation rate and a potential phosphorylation site of beluga whale (Delphinapterus leucas) myoglobin". Comp Biochem Physiol B Biochem Mol Biol 137 (3): 40112. doi:10.1016/j.cbpc.2004.01.007. PMID15050527. Wu, G; Wainwright LM, Poole RK (2003). "Microbial globins". Adv Microb Physiol 47: 255310. doi:10.1016/S0065-2911(03)47005-7. PMID14560666.
Myoglobin
123
External links
The Myoglobin Protein (http://macromoleculeinsights.com/myoglobin.php) Protein Database featured molecule (http://pdbdev.sdsc.edu:48346/pdb/molecules/mb1.html) Online 'Mendelian Inheritance in Man' (OMIM) 160000 (http://omim.org/entry/160000) human genetics Which Cut Is Older? (It's a Trick Question) (http://www.nytimes.com/2006/02/21/national/21meat.html) New York Times, February 21, 2006 article regarding meat industry use of carbon monoxide to keep meat looking red. Stores React to Meat Reports (http://www.nytimes.com/2006/03/01/dining/01meat.html) New York Times, March 1, 2006 article on the use of carbon monoxide to make meat appear fresh.
Hemoglobin
124
Hemoglobin
Hemoglobin, human, adult
(heterotetramer, ()2)
Structure of human hemoglobin. The protein's and subunits are in red and blue, and the iron-containing heme groups in green. From PDB 1GZX
Gene
Chromosomal Locus Chr. 16 p13.3 Chr. 16 p13.3 Chr. 11 p15.5 [3] [3] [4]
Hemoglobin (English pronunciation: /himlobn/; also rendered as haemoglobin and abbreviated Hb or Hgb) is the iron-containing oxygen-transport metalloprotein in the red blood cells of all vertebrates,[5] with the exception of the fish family Channichthyidae,[6] as well as the tissues of some invertebrates. Hemoglobin in the blood carries oxygen from the respiratory organs (lungs or gills) to the rest of the body (i.e.,the tissues) where it releases the oxygen to burn nutrients to provide energy to power the functions of the organism, and collects the resultant carbon dioxide to bring it back to the respiratory organs to be dispensed from the organism. In mammals, the protein makes up about 97% of the red blood cells' dry content, and around 35% of the total content (including water). Hemoglobin has an oxygen binding capacity of 1.34 ml O2 per gram of hemoglobin,[7] which increases the total blood oxygen capacity seventy-fold compared to dissolved oxygen in blood. The mammalian hemoglobin molecule can bind (carry) up to four oxygen molecules.[8] Hemoglobin is involved in the transport of other gases: it carries some of the body's respiratory carbon dioxide (about 10% of the total) as carbaminohemoglobin, in which CO2 is bound to the globin protein. The molecule also carries the important regulatory molecule nitric oxide bound to a globin protein thiol group, releasing it at the same time as oxygen.[9] Hemoglobin is also found outside red blood cells and their progenitor lines. Other cells that contain hemoglobin include the A9 dopaminergic neurons in the substantia nigra, macrophages, alveolar cells, and mesangial cells in the kidney. In these tissues, hemoglobin has a non-oxygen-carrying function as an antioxidant and a regulator of iron
Hemoglobin metabolism.[10] Hemoglobin and hemoglobin-like molecules are also found in many invertebrates, fungi, and plants. In these organisms, hemoglobins may carry oxygen, or they may act to transport and regulate other things such as carbon dioxide, nitric oxide, hydrogen sulfide and sulfide. A variant of the molecule, called leghemoglobin, is used to scavenge oxygen, to keep it from poisoning anaerobic systems, such as nitrogen-fixing nodules of leguminous plants.
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Research history
The oxygen-carrying protein hemoglobin was discovered by Hnefeld in 1840.[11] In 1851,[12] Otto Funke published a series of articles in which he described growing hemoglobin crystals by successively diluting red blood cells with a solvent such as pure water, alcohol or ether, followed by slow evaporation of the solvent from the resulting protein solution.[13] Hemoglobin's reversible oxygenation was described a few years later by Felix Hoppe-Seyler.[14] In 1959 Max Perutz determined the molecular structure of hemoglobin by X-ray crystallography.[15] resulted in his sharing with John Kendrew the 1962 Nobel Prize in Chemistry.
[16]
This work
The role of hemoglobin in the blood was elucidated by physiologist Claude Bernard. The name hemoglobin is derived from the words heme and globin, reflecting the fact that each subunit of hemoglobin is a globular protein with an embedded heme group. Each heme group contains one iron atom, that can bind one oxygen molecule through ion-induced dipole forces. The most common type of hemoglobin in mammals contains four such subunits.
Genetics
Hemoglobin consists mostly of protein (the "globin" chains) subunits, and these proteins, in turn, are folded chains of a large number of different amino acids called polypeptides. The amino acid sequence of any polypeptide created by a cell, is in turn determined by the stretches of DNA called genes. In all proteins, it is the amino acid sequence, which determines the protein's chemical properties and function. There is more than one hemoglobin gene. The amino acid sequences of the globin proteins in hemoglobins usually differ between species. These differences grow with evolutionary distance between species. For example, the most common hemoglobin sequences in humans and chimpanzees are nearly identical, differing by only one amino acid in both the alpha and the beta globin protein chains. These differences grow larger between less closely related species. Even within a species, different variants of hemoglobin always exist, although one sequence is usually a "most common" one in each species. Mutations in the genes for the hemoglobin protein in a species result in hemoglobin variants.[17] [18] Many of these mutant forms of hemoglobin cause no disease. Some of these mutant forms of hemoglobin, however, cause a group of hereditary diseases termed the hemoglobinopathies. The best known hemoglobinopathy is sickle-cell disease, which was the first human disease whose mechanism was understood at the molecular level. A (mostly) separate set of diseases called thalassemias involves underproduction of normal and sometimes abnormal hemoglobins, through problems and mutations in globin gene regulation. All these diseases produce anemia.[19] Variations in hemoglobin amino acid sequences, as with other proteins, may be adaptive. For example, recent studies have suggested genetic variants in deer mice that help explain how deer mice that live in the mountains are able to survive in the thin air that accompanies high altitudes. A researcher from the University of Nebraska-Lincoln found mutations in four different genes that can account for differences between deer mice that live in lowland prairies versus the mountains. After examining wild mice captured from both highlands and lowlands, it was found that: the genes of the two breeds are virtually identicalexcept for those that govern the oxygen-carrying capacity of their hemoglobin. The genetic difference enables highland mice to make more efficient use of their oxygen, since less is available at higher altitudes, such as those in the mountains.[20] Mammoth hemoglobin featured mutations that allowed for oxygen delivery at lower temperatures, thus enabling mammoths to migrate to higher latitudes during the
Hemoglobin Pleistocene.[21]
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Synthesis
Hemoglobin (Hb) is synthesized in a complex series of steps. The heme part is synthesized in a series of steps in the mitochondria and the cytosol of immature red blood cells, while the globin protein parts are synthesized by ribosomes in the cytosol.[22] Production of Hb continues in the cell throughout its early development from the proerythroblast to the reticulocyte in the bone marrow. At this point, the nucleus is lost in mammalian red blood cells, but not in birds and many other species. Even after the loss of the nucleus in mammals, residual ribosomal RNA allows further synthesis of Hb until the reticulocyte loses its RNA soon after entering the vasculature (this hemoglobin-synthetic RNA in fact gives the reticulocyte its reticulated appearance and name).
Structure
Hemoglobin has a quaternary structure characteristic of many multi-subunit globular proteins.[23] Most of the amino acids in hemoglobin form alpha helices, connected by short non-helical segments. Hydrogen bonds stabilize the helical sections inside this protein, causing attractions within the molecule, folding each polypeptide chain into a specific shape.[24] Hemoglobin's quaternary structure comes from its four subunits in roughly a tetrahedral arrangement.[23] In most vertebrates, the hemoglobin molecule is an assembly of four globular protein subunits. Each subunit is composed of a protein chain tightly associated with a non-protein heme group. Each protein chain arranges into a set of alpha-helix structural segments connected together in a globin fold arrangement, so called because this Heme b group arrangement is the same folding motif used in other heme/globin proteins such as myoglobin.[25] [26] This folding pattern contains a pocket that strongly binds the heme group. A heme group consists of an iron (Fe) ion (charged atom) held in a heterocyclic ring, known as a porphyrin. This porphyrin ring consists of four pyrrole molecules cyclically linked together (by methene bridges) with the iron ion bound in the center.[27] The iron ion, which is the site of oxygen binding, coordinates with the four nitrogens in the center of the ring, which all lie in one plane. The iron is bound strongly (covalently) to the globular protein via the imidazole ring of the F8 histidine residue (also known as the proximal histidine) below the porphyrin ring. A sixth position can reversibly bind oxygen by a coordinate covalent bond,[28] completing the octahedral group of six ligands. Oxygen binds in an "end-on bent" geometry where one oxygen atom binds Fe and the other protrudes at an angle. When oxygen is not bound, a very weakly bonded water molecule fills the site, forming a distorted octahedron. Even though carbon dioxide is carried by hemoglobin, it does not compete with oxygen for the iron-binding positions, but is actually bound to the protein chains of the structure. The iron ion may be either in the Fe2+ or in the Fe3+ state, but ferrihemoglobin (methemoglobin) (Fe3+) cannot bind oxygen.[29] In binding, oxygen temporarily and reversibly oxidizes (Fe2+) to (Fe3+) while oxygen temporally turns into superoxide, thus iron must exist in the +2 oxidation state to bind oxygen. If superoxide ion associated to Fe3+ is protonated the hemoglobin iron will remain oxidized and incapable to bind oxygen. In such cases, the enzyme methemoglobin reductase will be able to eventually reactivate methemoglobin by reducing the iron center. In adult humans, the most common hemoglobin type is a tetramer (which contains 4 subunit proteins) called hemoglobin A, consisting of two and two subunits non-covalently bound, each made of 141 and 146 amino acid
Hemoglobin residues, respectively. This is denoted as 22. The subunits are structurally similar and about the same size. Each subunit has a molecular weight of about 17,000daltons, for a total molecular weight of the tetramer of about 64,000daltons (64,458 g/mol).[30] Thus, 1 g/dL = 0.1551mmol/L. Hemoglobin A is the most intensively studied of the hemoglobin molecules. In human infants, the hemoglobin molecule is made up of 2 chains and 2 gamma chains. The gamma chains are gradually replaced by chains as the infant grows.[31] The four polypeptide chains are bound to each other by salt bridges, hydrogen bonds, and the hydrophobic effect.
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Oxygen saturation
In general, hemoglobin can be saturated with oxygen molecules (oxyhemoglobin), or desaturated with oxygen molecules (deoxyhemoglobin).[32] Oxyhemoglobin Oxyhemoglobin is formed during physiological respiration when oxygen binds to the heme component of the protein hemoglobin in red blood cells. This process occurs in the pulmonary capillaries adjacent to the alveoli of the lungs. The oxygen then travels through the blood stream to be dropped off at cells where it is utilized in glycolysis and in the production of ATP by the process of oxidative phosphorylation. It does not, however, help to counteract a decrease in blood pH. Ventilation, or breathing, may reverse this condition by removal of carbon dioxide, thus causing a shift up in pH.[33] Hemoglobin exists in two forms, a taut form (T) and a relaxed form (R). Various factors such as low pH, high CO2 and high 2,3 BPG at the level of the tissues favor the taut form, which has low oxygen affinity and releases oxygen in the tissues. Conversely, a high pH, low CO2, or low 2,3 BPG favors the relaxed form which can better bind oxygen. Deoxygenated hemoglobin Deoxygenated hemoglobin is the form of hemoglobin without the bound oxygen. The absorption spectra of oxyhemoglobin and deoxyhemoglobin differ. The oxyhemoglobin has significantly lower absorption of the 660nm wavelength than deoxyhemoglobin, while at 940nm its absorption is slightly higher. This difference is used for measurement of the amount of oxygen in patient's blood by an instrument called pulse oximeter. This difference also accounts for the presentation of cyanosis, the blue to purplish color that tissues develop during hypoxia.
Hemoglobin 1. Low-spin Fe2+ binds to singlet oxygen. Both low-spin iron and singlet oxygen are diamagnetic. However, the singlet form of oxygen is the higher-energy form of the molecule. 2. Low-spin Fe3+ binds to .O2- (the superoxide ion) and the two unpaired electrons couple antiferromagnetically, giving diamagnetic properties. 3. Low-spin Fe4+ binds to peroxide, O22-. Both are diamagnetic. Direct experimental data: X-ray photoelectron spectroscopy suggests iron has an oxidation state of approximately 3.2 infrared stretching frequencies of the O-O bond suggests a bond length fitting with superoxide (a bond order of about 1.6, with superoxide being 1.5). X-ray Absorption Near Edge Structures at the iron K-edge. The energy shift of 5 eV between Deoxyhemoglobin and Oxyhemoglobin, as for all the Methemoglobin species, strongly suggests an actual local charge closer to Fe3+ than Fe2+.[34] [35] [36] Thus, the nearest formal oxidation state of iron in Hb-O2 is the +3 state, with oxygen in the -1 state (as superoxide .O2-). The diamagnetism in this configuration arises from the single unpaired electron on superoxide aligning antiferromagnetically from the single unpaired electron on iron, to give no net spin to the entire configuration, in accordance with diamagnetic oxyhemoglobin from experiment.[37] [38] The second choice of the three logical possibilities above for diamagnetic oxyhemoglobin being found correct by experiment, is not surprising: singlet oxygen (possibility #1) and large separations of charge (possibility #3) are both unfavorably high-energy states. Iron's shift to a higher oxidation state in Hb-O2 decreases the atom's size, and allows it into the plane of the porphyrin ring, pulling on the coordinated histidine residue and initiating the allosteric changes seen in the globulins. Early postulates by bio-inorganic chemists claimed that possibility #1 (above) was correct and that iron should exist in oxidation state II. This seemed particularly likely since the iron oxidation state III as methemoglobin, when not accompanied by superoxide .O2- to "hold" the oxidation electron, was known to render hemoglobin incapable of binding normal triplet O2 as it occurs in the air. It was thus assumed that iron remained as Fe(II) when oxygen gas was bound in the lungs. The iron chemistry in this previous classical model was elegant, but the required presence of the required diamagnetic high-energy singlet oxygen was never explained. It was classically argued that the binding of an oxygen molecule placed high-spin iron(II) in an octahedral field of strong-field ligands; this change in field would increase the crystal field splitting energy, causing iron's electrons to pair into the low-spin configuration, which would be diamagnetic in Fe(II). This forced low-spin pairing is indeed thought to happen in iron when oxygen binds, but is not enough to explain iron's change in size. Extraction of an additional electron from iron by oxygen is required to explain both iron's smaller size and observed increased oxidation state, and oxygen's weaker bond. It should be noted that the assignment of a whole-number oxidation state is a formalism, as the covalent bonds are not required to have perfect bond orders involving whole electron-transfer. Thus, all three models for paramagnetic Hb-O2 may contribute to some small degree (by resonance) to the actual electronic configuration of Hb-O2. However, the model of iron in Hb-O2 being Fe(III) is more correct than the classical idea that it remains Fe(II).
128
Hemoglobin
129
Cooperative
When oxygen binds to the iron complex, it causes the iron atom to move back toward the center of the plane of the porphyrin ring (see moving diagram). At the same time, the imidazole side-chain of the histidine residue interacting at the other pole of the iron is pulled toward the porphyrin ring. This interaction forces the plane of the ring sideways toward the outside of the tetramer, and also induces a strain in the protein helix containing the histidine as it moves nearer to the iron atom. This strain is transmitted to the remaining three monomers in the tetramer, where it induces a similar conformational change in the other heme sites such that binding of oxygen to these sites becomes easier. In the tetrameric form of normal adult hemoglobin, the binding of oxygen is, thus, a cooperative process. The binding affinity of hemoglobin for oxygen is increased by the oxygen saturation of the molecule, with the first oxygens bound influencing the shape of the binding sites for the next oxygens, in a way favorable for binding. This positive cooperative binding is achieved through steric conformational changes of the hemoglobin protein complex as discussed above; i.e., when one subunit protein in hemoglobin becomes oxygenated, a conformational or structural change in the whole complex is initiated, causing the other subunits to gain an increased affinity for oxygen. As a consequence, the oxygen binding curve of hemoglobin is sigmoidal, or S-shaped, as opposed to the normal hyperbolic curve associated with noncooperative binding.
A schematic visual model of oxygen-binding process, showing all four monomers and hemes, and protein chains only as diagramatic coils, to facilitate visualization into the molecule. Oxygen is not shown in this model, but, for each of the iron atoms, it binds to the iron (red sphere) in the flat heme. For example, in the upper left of the four hemes shown, oxygen binds at the left of the iron atom shown in the upper left of diagram. This causes the iron atom to move backward into the heme which holds it (the iron moves upward as it binds oxygen, in this illustration), tugging the histidine residue (modeled as a red pentagon on the right of the iron) closer, as it does. This, in turn, pulls on the protein chain holding the histidine.
The dynamic mechanism of the cooperativity in hemoglobin and its relation with the low-frequency resonance has been discussed.[40]
Competitive
Hemoglobin's oxygen-binding capacity is decreased in the presence of carbon monoxide because both gases compete for the same binding sites on hemoglobin, carbon monoxide binding preferentially in place of oxygen. The binding of oxygen is affected by molecules such as carbon monoxide (CO) (for example, from tobacco smoking, car exhaust, and incomplete combustion in furnaces). CO competes with oxygen at the heme binding site. Hemoglobin binding affinity for CO is 250 times greater than its affinity for oxygen,[41] meaning that small amounts of CO dramatically reduce hemoglobin's ability to transport oxygen. Since Carbon Monoxide is a colorless, odorless and tasteless gas, and poses a potentially fatal threat detectors have become commercially available to warn of dangerous levels in residences. When hemoglobin combines with CO, it forms a very bright red compound called carboxyhemoglobin, which may cause the skin of CO poisoning victims to appear pink in death, instead of white or blue. When inspired air contains CO levels as low as 0.02%, headache and nausea occur; if the CO concentration is increased to 0.1%, unconsciousness will follow. In heavy smokers, up to 20% of the oxygen-active sites can be blocked by CO. In similar fashion, hemoglobin also has competitive binding affinity for cyanide (CN-), sulfur monoxide (SO), nitric oxide (NO), and sulfide(S2-), including hydrogen sulfide (H2S). All of these bind to iron in heme without changing its oxidation state, but they nevertheless inhibit oxygen-binding, causing grave toxicity.
Hemoglobin The iron atom in the heme group must initially be in the ferrous (Fe2+) oxidation state to support oxygen and other gases' binding and transport (it temporarily switches to ferric during the time oxygen is bound, as explained above). Initial oxidation to the ferric (Fe3+) state without oxygen converts hemoglobin into "hemiglobin" or methemoglobin (pronounced "MET-hemoglobin"), which cannot bind oxygen. Hemoglobin in normal red blood cells is protected by a reduction system to keep this from happening. Nitric oxide is capable of converting a small fraction of hemoglobin to methemoglobin in red blood cells. The latter reaction is a remnant activity of the more ancient nitric oxide dioxygenase function of globins.
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Allosteric
Further information: Oxygen-hemoglobin dissociation curve Carbon dioxide occupies a different binding site on the hemoglobin. Carbon dioxide is more readily dissolved in deoxygenated blood, facilitating its removal from the body after the oxygen has been released to tissues undergoing metabolism. This increased affinity for carbon dioxide by the venous blood is known as the Haldane effect. Through the enzyme carbonic anhydrase, carbon dioxide reacts with water to give carbonic acid, which decomposes into bicarbonate and protons: CO2 + H2O H2CO3 HCO3- + H+ Hence blood with high carbon dioxide levels is also lower in pH (more acidic). Hemoglobin can bind protons and carbon dioxide, which causes a conformational change in the protein and facilitates the release of oxygen. Protons bind at various places on the protein, while carbon dioxide binds at the -amino group.[42] Carbon dioxide binds to hemoglobin and forms carbaminohemoglobin.[43] This decrease in hemoglobin's affinity for oxygen by the binding of carbon dioxide and acid is known as the Bohr effect (shifts the O2-saturation curve to the right). Conversely, when the carbon dioxide levels in the blood decrease (i.e., in the lung capillaries), carbon dioxide and protons are released from hemoglobin, increasing the oxygen The sigmoidal shape of hemoglobin's oxygen-dissociation curve results affinity of the protein. A reduction in the total from cooperative binding of oxygen to hemoglobin. binding capacity of hemoglobin to oxygen (i.e. shifting the curve down, not just to the right) due to reduced pH is called the root effect. This is seen in bony fish. It is necessary for hemoglobin to release the oxygen that it binds; if not, there is no point in binding it. The sigmoidal curve of hemoglobin makes it efficient in binding (taking up O2 in lungs), and efficient in unloading (unloading O2 in tissues).[44] In people acclimated to high altitudes, the concentration of 2,3-Bisphosphoglycerate (2,3-BPG) in the blood is increased, which allows these individuals to deliver a larger amount of oxygen to tissues under conditions of lower oxygen tension. This phenomenon, where molecule Y affects the binding of molecule X to a transport molecule Z, is called a heterotropic allosteric effect. A variant hemoglobin, called fetal hemoglobin (HbF, 22), is found in the developing fetus, and binds oxygen with greater affinity than adult hemoglobin. This means that the oxygen binding curve for fetal hemoglobin is left-shifted (i.e., a higher percentage of hemoglobin has oxygen bound to it at lower oxygen tension), in comparison to that of adult hemoglobin. As a result, fetal blood in the placenta is able to take oxygen from maternal blood.
Hemoglobin Hemoglobin also carries nitric oxide in the globin part of the molecule. This improves oxygen delivery in the periphery and contributes to the control of respiration. NO binds reversibly to a specific cysteine residue in globin; the binding depends on the state (R or T) of the hemoglobin. The resulting S-nitrosylated hemoglobin influences various NO-related activities such as the control of vascular resistance, blood pressure and respiration. NO is not released in the cytoplasm of erythrocytes but transported by an anion exchanger called AE1 out of them.[45] A study was performed to examine the influence of the form of hemoglobin (Hb) on the partitioning of inhaled volatile organic compounds (VOCs) into [human and animal] blood. Benzene was the prototypic VOC used in the investigations for this research due to the similar properties it shares with many other VOCs. To be specific, this study analyses the influence of the water solubility of Hb on the partitioning coefficient (PC) of a VOC as compared to the influence of the species or form of Hb. The different forms of blood used include: human hemoglobin (HbA), rat Hb, and sickle-cell hemoglobin (HbS). Rat Hb contains little water and is in a quasi-crystalline form, found inside the red blood cells (RBC), meaning they are more hydrophobic than human Hb, which are water-soluble. Sickle-cell hemoglobin (HbS) is water-soluble, however it can become water-insoluble, forming hydrophobic polymers, when deoxygenated. The findings state that the benzene PC for rat Hb was much higher than human that for Hb; however, the tests that measured the PCs of the oxygenated and deoxygenated forms of HbA and HbS did not differ, indicating that the affinity of benzene was not affected by the water solubility of Hb.[46]
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Types in humans
Hemoglobin variants are a part of the normal embryonic and fetal development, but may also be pathologic mutant forms of hemoglobin in a population, caused by variations in genetics. Some well-known hemoglobin variants such as sickle-cell anemia are responsible for diseases, and are considered hemoglobinopathies. Other variants cause no detectable pathology, and are thus considered non-pathological variants.[47] [48] In the embryo: Gower 1 (22) Gower 2 (22) (PDB 1A9W [49]) Hemoglobin Portland (22) In the fetus: Hemoglobin F (22) (PDB 1FDH [50]) In adults: Hemoglobin A (22) (PDB 1BZ0 [51]) - The most common with a normal amount over 95% Hemoglobin A2 (22) - chain synthesis begins late in the third trimester and in adults, it has a normal range of 1.5-3.5% Hemoglobin F (22) - In adults Hemoglobin F is restricted to a limited population of red cells called F-cells. However, the level of Hb F can be elevated in persons with sickle-cell disease and beta-thalassemia.
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Variant forms that cause disease: Hemoglobin H (4) - A variant form of hemoglobin, formed by a tetramer of chains, which may be present in variants of thalassemia. Hemoglobin Barts (4) - A variant form of hemoglobin, formed by a tetramer of chains, which may be present in variants of thalassemia. Hemoglobin S (2S2) - A variant form of hemoglobin found in people with sickle cell disease. There is a variation in the -chain gene, causing a change in the properties of hemoglobin, which results in sickling of red blood cells.
Hemoglobin C (2C2) - Another variant due to a variation in the -chain gene. This variant causes a mild chronic hemolytic anemia.
Gene expression of hemoglobin before and after birth. Also identifies the types of cells and organs in which the gene expression (data on Wood W.G., (1976). Br. Med. Bull. 32, 282.)
Hemoglobin E (2E2) - Another variant due to a variation in the -chain gene. This variant causes a mild chronic hemolytic anemia. Hemoglobin AS - A heterozygous form causing Sickle cell trait with one adult gene and one sickle cell disease gene Hemoglobin SC disease - Another heterozygous form with one sickle gene and another encoding Hemoglobin C.
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Role in disease
Hemoglobin deficiency can be caused either by decreased amount of hemoglobin molecules, as in anemia, or by decreased ability of each molecule to bind oxygen at the same partial pressure of oxygen. Hemoglobinopathies (genetic defects resulting in abnormal structure of the hemoglobin molecule)[53] may cause both. In any case, hemoglobin deficiency decreases blood oxygen-carrying capacity. Hemoglobin deficiency is, in general, strictly distinguished from hypoxemia, defined as decreased partial pressure of oxygen in blood,[54] [55] [56] [57] although both are causes of hypoxia (insufficient oxygen supply to tissues). Other common causes of low hemoglobin include loss of blood, nutritional deficiency, bone marrow problems, chemotherapy, kidney failure, or abnormal hemoglobin (such as that of sickle-cell disease). High hemoglobin levels may be caused by exposure to high altitudes, smoking, dehydration, or tumors.[31] The ability of each hemoglobin molecule to carry oxygen is normally modified by altered blood pH or CO2, causing an altered oxygenhemoglobin dissociation curve. However, it can also be pathologically altered in, e.g., carbon monoxide poisoning.
Decrease of hemoglobin, with or without an absolute decrease of red blood cells, leads to symptoms of anemia. Anemia has many different causes, although iron deficiency and its resultant iron deficiency anemia are the most common causes in the Western world. As absence of iron decreases heme synthesis, red blood cells in iron deficiency anemia are hypochromic (lacking the red hemoglobin pigment) and microcytic (smaller than normal). Other anemias are rarer. In hemolysis (accelerated breakdown of red blood cells), associated jaundice is caused by the hemoglobin metabolite bilirubin, and the circulating hemoglobin can cause renal failure. Some mutations in the globin chain are associated with the hemoglobinopathies, such as sickle-cell disease and thalassemia. Other mutations, as discussed at the beginning of the article, are benign and are referred to merely as hemoglobin variants. There is a group of genetic disorders, known as the porphyrias that are characterized by errors in metabolic pathways of heme synthesis. King George III of the United Kingdom was probably the most famous porphyria sufferer. To a small extent, hemoglobin A slowly combines with glucose at the terminal valine (an alpha aminoacid) of each chain. The resulting molecule is often referred to as Hb A1c. As the concentration of glucose in the blood increases, the percentage of Hb A that turns into Hb A1c increases. In diabetics whose glucose usually runs high, the percent Hb A1c also runs high. Because of the slow rate of Hb A combination with glucose, the Hb A1c percentage is representative of glucose level in the blood averaged over a longer time (the half-life of red blood cells, which is typically 5055 days). Glycosylated hemoglobin is the form of hemoglobin to which glucose is bound. The binding of glucose to amino acids in the hemoglobin takes place spontaneously (without the help of an enzyme) in many proteins, and is not known to serve a useful purpose. However, the binding to hemoglobin does serve as a record for average blood glucose levels over the lifetime of red cells, which is approximately 120 days. The levels of glycosylated hemoglobin are therefore measured in order to monitor the long-term control of the chronic disease of type 2 diabetes mellitus (T2DM). Poor control of T2DM results in high levels of glycosylated hemoglobin in the red blood cells. The normal
In sickle cell hemoglobin (HbS) glutamic acid in position 6 (in beta chain) is mutated to valine. This change allows the deoxygenated form of the hemoglobin to stick to itself.
Hemoglobin reference range is approximately 45.9 %. Though difficult to obtain, values less than 7 % are recommended for people with T2DM. Levels greater than 9 % are associated with poor control of the glycosylated hemoglobin, and levels greater than 12 % are associated with very poor control. Diabetics who keep their glycosylated hemoglobin levels close to 7 % have a much better chance of avoiding the complications that may accompany diabetes (than those whose levels are 8 % or higher).[58] Elevated levels of hemoglobin are associated with increased numbers or sizes of red blood cells, called polycythemia. This elevation may be caused by congenital heart disease, cor pulmonale, pulmonary fibrosis, too much erythropoietin, or polycythemia vera.[59] Elevation in levels of hemoglobin were found in one study of the yogic practice of Yoga Nidra (yogic sleep) for half an hour daily.[60] A recent study done in Pondicherry, India, shows its importance in coronary artery disease.[61]
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Diagnostic uses
Hemoglobin concentration measurement is among the most commonly performed blood tests, usually as part of a complete blood count. For example it is typically tested before or after blood donation. Results are reported in g/L, g/dL or mol/L. 1 g/dL equals about 0.6206 mmol/L.[62] Normal levels are: Men: 13.8 to 18.0 g/dL (138 to 182 g/L, or 8.56 to 11.3mmol/L) Women: 12.1 to 15.1 g/dL (121 to 151 g/L, or 7.51 to 9.37mmol/L) Children: 11 to 16 g/dL (111 to 160 g/L, or 6.83 to 9.93mmol/L) Pregnant women: 11 to 12 g/dL (110 to 120 g/L, or 6.83 to 7.45mmol/L) [63] [64]
Normal values of hemoglobin in the 1st and 3rd trimesters of pregnant women must be at least 11 g/dL and at least 10.5 g/dL during the 2nd trimester.[65] Dehydration or hyperhydration can greatly influence measured hemoglobin levels. Albumin can indicate hydration status. If the concentration is below normal, this is called anemia. Anemias are classified by the size of red blood cells, the cells that contain hemoglobin in vertebrates. The anemia is called "microcytic" if red cells are small, "macrocytic" if they are large, and "normocytic" otherwise. Hematocrit, the proportion of blood volume occupied by red blood cells, is typically about three times the hemoglobin level. For example, if the hemoglobin is measured at 17, that compares with a hematocrit of 51.[66] Laboratory hemoglobin test methods require a blood sample (arterial, venous, or capillary) and analysis on hematology analyzer and CO-oximeter. Additionally, a new noninvasive hemoglobin (SpHb) test method called Pulse CO-Oximetry is also available with comparable accuracy to invasive methods.[67] Long-term control of blood sugar concentration can be measured by the concentration of Hb A1c. Measuring it directly would require many samples because blood sugar levels vary widely through the day. Hb A1c is the product of the irreversible reaction of hemoglobin A with glucose. A higher glucose concentration results in more Hb A1c. Because the reaction is slow, the Hb A1c proportion represents glucose level in blood averaged over the half-life of red blood cells, is typically 5055 days. An Hb A1c proportion of 6.0% or less show good long-term glucose control, while values above 7.0% are elevated. This test is especially useful for diabetics.[68] The functional magnetic resonance imaging (fMRI) machine uses the signal from deoxyhemoglobin, which is sensitive to magnetic fields since it is paramagnetic.
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One of the most striking occurrences and uses of hemoglobin in red hemoglobin-containing plumes organisms is in the giant tube worm (Riftia pachyptila, also called Vestimentifera), which can reach 2.4 meters length and populates ocean volcanic vents. Instead of a digestive tract, these worms contain a population of bacteria constituting half the organism's weight. The bacteria react with H2S from the vent and O2 from the water to produce energy to make food from H2O and CO2. The worms end with a deep red fan-like structure ("plume"), which extends into the water and absorbs H2S and O2 for the bacteria, and CO2 for use as synthetic raw material similar to photosynthetic plants. The structures are bright-red due to their containing several extraordinarily complex hemoglobins that have up to 144 globin chains, each including associated heme structures. These hemoglobins are remarkable for being able to carry oxygen in the presence of sulfide, and even to carry sulfide, without being completely "poisoned" or inhibited by it as hemoglobins in most other species are.[70] [71]
Hemoglobin Some marine invertebrates and a few species of annelid use this iron-containing non-heme protein to carry oxygen in their blood. Appears pink/violet when oxygenated, clear when not. Chlorocruorin Found in many annelids, it is very similar to erythrocruorin, but the heme group is significantly different in structure. Appears green when deoxygenated and red when oxygenated. Vanabins Also known as vanadium chromagens, they are found in the blood of sea squirts. There were once hypothesized to use the rare metal vanadium as an oxygen binding prosthetic group. However, although they do contain vanadium by preference, they apparently bind little oxygen, and thus have some other function, which has not been elucidated (sea squirts also contain some hemoglobin). They may act as toxins. Erythrocruorin Found in many annelids, including earthworms, it is a giant free-floating blood protein containing many dozenspossibly hundredsof iron- and heme-bearing protein subunits bound together into a single protein complex with a molecular mass greater than 3.5 million daltons. Pinnaglobin Only seen in the mollusc Pinna squamosa. Brown manganese-based porphyrin protein. Leghemoglobin In leguminous plants, such as alfalfa or soybeans, the nitrogen fixing bacteria in the roots are protected from oxygen by this iron heme containing oxygen-binding protein. The specific enzyme protected is nitrogenase, which is unable to reduce nitrogen gas in the presence of free oxygen. Coboglobin A synthetic cobalt-based porphyrin. Coboprotein would appear colorless when oxygenated, but yellow when in veins.
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Artist Julian Voss-Andreae created a sculpture called "Heart of Steel (Hemoglobin)" in 2005, based on the protein's backbone. The sculpture was made from glass and weathering steel. The intentional rusting of the initially shiny work of art mirrors hemoglobin's fundamental chemical reaction of oxygen binding to iron.[76] [77] Rock band Placebo recorded a song Heart of Steel (Hemoglobin) (2005) by Julian Voss-Andreae. The images show the 5' called "Haemoglobin" with the lyrics (1.60m) tall sculpture right after installation, after 10 days, and after several months of exposure to the elements. "Haemoglobin is the key to a healthy heartbeat". French rap artist MC Solaar also had a successful single titled "La Concubine de L'Hemoglobin" in 1994.
References
[1] http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1GZX [2] [3] [4] [5] http:/ / www. proteopedia. org/ wiki/ index. php/ Hemoglobin http:/ / www. ncbi. nlm. nih. gov/ Omim/ getmap. cgi?chromosome=16p13. 3 http:/ / www. ncbi. nlm. nih. gov/ Omim/ getmap. cgi?chromosome=11p15. 5 Maton, Anthea; Jean Hopkins, Charles William McLaughlin, Susan Johnson, Maryanna Quon Warner, David LaHart, Jill D. Wright (1993). Human Biology and Health. Englewood Cliffs, New Jersey, USA: Prentice Hall. ISBN0-13-981176-1. [6] Sidell, Bruce; Kristin O'Brien (2006). "When bad things happen to good fish: the loss of hemoglobin and myglobin expression in Antarctic icefishes". The Journal of Experimental Biology 209 (Pt 10): 17911802. doi:10.1242/jeb.02091. PMID16651546. [7] Dominguez de Villota ED, Ruiz Carmona MT, Rubio JJ, de Andrs S (December 1981). "Equality of the in vivo and in vitro oxygen-binding capacity of haemoglobin in patients with severe respiratory disease". Br J Anaesth 53 (12): 13258. doi:10.1093/bja/53.12.1325. ISSN0007-0912. PMID7317251. [8] Costanzo, Linda S. (2007). Physiology. Hagerstwon, MD: Lippincott Williams & Wilkins. ISBN0-7817-7311-3. [9] Respiratory Function of Hemoglobin. Connie C.W. Hsia, M.D. N Engl J Med 1998; 338:239-248 January 22, 1998 [10] Biagioli M, Pinto M, Cesselli D, Zaninello M, Lazarevic D, Roncaglia P, Simone R, Vlachouli C, Plessy C, Bertin N, Beltrami A, Kobayashi K, Gallo V, Santoro C, Ferrer I, Rivella S, Beltrami CA, Carninci P, Raviola E, Gustincich S. (2009). Unexpected expression of {alpha}- and {beta}-globin in mesencephalic dopaminergic neurons and glial cells. (http:/ / www. pubmedcentral. nih. gov/ picrender. fcgi?artid=2732704& blobtype=pdf) Proc Natl Acad Sci U S A. 106:1545415459. PMID 19717439 doi:10.1073/pnas.0813216106 [11] Hnefeld F.L. (1840). Die Chemismus in der thierischen Organization. Leipzig. [12] Funke O (1851). "ber das milzvenenblut". Z Rat Med 1: 172218.
Hemoglobin
[13] "A NASA Recipe For Protein Crystallography" (http:/ / www. okcareertech. org/ cimc/ special/ nochild/ downloads/ science/ Protein. Crystallography. pdf) (PDF). Educational Brief. National Aeronautics and Space Administration. . Retrieved 2008-10-12. [14] Hoppe-Seyler F (1866). "ber die oxydation in lebendem blute". Med-chem Untersuch Lab 1: 133140. [15] Perutz, M.F.; Rossmann, M.G.; Cullis, A.F.; Muirhead, H.; Will, G.; North, A.C.T. (1960). "Structure of H". Nature 185 (4711): 416422. doi:10.1038/185416a0. PMID18990801. [16] Perutz MF (November 1960). "Structure of haemoglobin". Brookhaven symposia in biology 13: 16583. ISSN0068-2799. PMID13734651. [17] A Syllabus of Human Hemoglobin Variants (1996) (http:/ / globin. cse. psu. edu/ html/ huisman/ variants/ ) [18] Hemoglobin Variants (http:/ / www. labtestsonline. org/ understanding/ analytes/ hemoglobin_var/ glance-3. html) [19] Uthman, MD, Ed. "Hemoglobinopathies and Thalassemias" (http:/ / web2. airmail. net/ uthman/ hemoglobinopathy/ hemoglobinopathy. html). . Retrieved 2007-12-26. [20] Reed, Leslie. "Adaptation found in mouse genes." Omaha World-Herald 11 Aug. 2009: EBSCO. Web. 30 Oct. 2009. [21] "Mammoths had anti-freeze blood" (http:/ / news. bbc. co. uk/ 2/ hi/ science/ nature/ 8657464. stm). BBC. 2010-05-02. . Retrieved 2010-05-02. [22] "Hemoglobin Synthesis" (http:/ / sickle. bwh. harvard. edu/ hbsynthesis. html). April 14, 2002. . Retrieved 2007-12-26. [23] van Kessel et al. "2.4 Proteins - Natural Polyamides." Chemistry 12. Toronto: Nelson, 2003. 122. Print. [24] "Hemoglobin Tutorial." University of Massachusetts Amherst. N.p., n.d. Web. 23 Oct. 2009. <http://www.umass.edu/molvis/tutorials/hemoglobin/index.htm>. [25] Steinberg 2001, p.95 [26] Hardison 1996, p.1 [27] "Hemoglobin." School of Chemistry - Bristol University - UK. N.p., n.d. Web. 12 Oct. 2009. <http://www.chm.bris.ac.uk/motm/hemoglobin/hemoglobjm.htm>. [28] WikiPremed > Coordination Chemistry (http:/ / wikipremed. com/ interdisciplinary_course. php?code=0213000100000000) Retrieved on July 2, 2009 [29] Linberg R, Conover CD, Shum KL, Shorr RG (Mar 1998). "Hemoglobin based oxygen carriers: how much methemoglobin is too much?". Artif Cells Blood Substit Immobil Biotechnol 26 (2): 13348. doi:10.3109/10731199809119772. ISSN1073-1199. PMID9564432. [30] Van Beekvelt MC, Colier WN, Wevers RA, Van Engelen BG (Feb 2001). "Performance of near-infrared spectroscopy in measuring local O2 consumption and blood flow in skeletal muscle" (http:/ / jap. physiology. org/ cgi/ pmidlookup?view=long& pmid=11160049). J Appl Physiol 90 (2): 511519. ISSN8750-7587. PMID11160049. . [31] "Hemoglobin." MedicineNet. N.p., n.d. Web. 12 Oct. 2009. <www.medicinenet.com/hemoglobin/article.htm>. [32] "Hemoglobin Home." Biology @ Davidson. N.p., n.d. Web. 12 Oct. 2009. <http://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2005/Heiner/hemoglobin.html>. [33] Baillie/Simpson. "Online model of the hemoglobin binding and the effects of hyperventilation" (http:/ / www. altitude. org/ hemoglobin_saturation. php). . Retrieved 2006-08-10. [34] Pin S, Alpert B, Michalowicz A. (Oct 1982). "Oxygen bonding in human hemoglobin and its isolated subunits: A XANES study". FEBS Lett. 147 (1): 10610. doi:10.1016/0014-5793(82)81021-1. PMID7140986. [35] S Pin, P Valat, R Cortes, A Michalowicz, and B Alpert (December 1985). "Ligand binding processes in hemoglobin. Chemical reactivity of iron studied by XANES spectroscopy". Biophys J. 48(6): 99710. [36] A. Bianconi, A. Congiu-Castellanoa, M. Dell'Aricciaa, A. Giovannellia, E. Burattinib and P. J. Durhamc (August 1985). "Increase of the Fe effective charge in hemoproteins during oxygenation process". Biochemical and Biophysical Research Communications 30 (1): 98102. doi:10.1016/0006-291X(85)91775-9. PMID4038310. [37] Childs PE (2001). "Haemoglobin - a molecular lung: 2" (http:/ / www. ul. ie/ ~childsp/ CinA/ Issue65/ TOC28_Haemoglobin. htm). Chemistry in Action (65). ISSN0332-2637. . [38] Chen H, Ikeda-Saito M, Shaik S (11 2008). "Nature of the Fe-O2 bonding in oxy-myoglobin: effect of the protein" (http:/ / pubs. acs. org/ doi/ abs/ 10. 1021/ ja805434m). Journal of the American Chemical Society 130 (44): 1477814790. doi:10.1021/ja805434m. PMID18847206. . [39] Jensen, Frank B (4/9/2009). "The dual roles of red blood cells in tissue oxygen delivery: oxygen carriers and regulators of local blood flow". Journal of Experimental Biology (The Company of Biologists) 212 (Pt 21): 33873393. doi:10.1242/jeb.023697. PMID19837879. [40] Chou KC (June 1989). "Low-frequency resonance and cooperativity of hemoglobin". Trends Biochem. Sci. 14 (6): 2123. doi:10.1016/0968-0004(89)90026-1. PMID2763333. [41] Guyton A C: Medical Physiology 12ed. 2010, page 502 [42] Nelson, D. L.; Cox, M. M. (2000). Lehninger Principles of Biochemistry, 3rd ed. New York, NY: Worth Publishers. p 217 [43] Guyton, Arthur C.; John E. Hall (2006). Textbook of Medical Physiology (11 ed.). Philadelphia: Elsevier Saunders. p.511. ISBN0721602401. [44] "YouTube - Lecture - 12 Myoglobin and Hemoglobin." YouTube - Broadcast Yourself.. N.p., n.d. Web. 30 Oct. 2009. <http://www.youtube.com/watch?v=6AfRX6oh9-E>. [45] Rang, H.P.; Dale M.M., Ritter J.M., Moore P.K. (2003). Pharmacology, Fifth Edition. Elsevier. ISBN0443072027. [46] Wiester et al. "Partitioning of Benzene in Blood: Influence of Hemoglobin Type in Humans and Animals." Environmental Health Perspectives 110.3 (2002): p255-261. EBSCO. Web. 1 Nov. 2009.
138
Hemoglobin
[47] "Hemoglobin Variants" (http:/ / www. labtestsonline. org/ understanding/ analytes/ hemoglobin_var/ glance-3. html). Lab Tests Online. American Association for Clinical Chemistry. 2007-11-10. . Retrieved 2008-10-12. [48] Huisman THJ (1996). "A Syllabus of Human Hemoglobin Variants" (http:/ / globin. cse. psu. edu/ html/ huisman/ variants/ ). Globin Gene Server. Pennsylvania State University. . Retrieved 2008-10-12. [49] http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1A9W [50] http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1FDH [51] http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1BZ0 [52] Kikuchi, G.; Yoshida, T.; Noguchi, M. (2005). "Heme oxygenase and heme degradation". Biochemical and Biophysical Research Communications 338 (1): 558567. doi:10.1016/j.bbrc.2005.08.020. PMID16115609. [53] " hemoglobinopathy (http:/ / web. archive. org/ web/ 20090616022448/ http:/ / www. mercksource. com/ pp/ us/ cns/ cns_hl_dorlands_split. jsp?pg=/ ppdocs/ us/ common/ dorlands/ dorland/ four/ 000048231. htm)" at Dorland's Medical Dictionary [54] britannica.com --> blood disease (http:/ / www. britannica. com/ EBchecked/ topic/ 280141/ hypoxemia), stating hypoxemia (reduced oxygen tension in the blood). Retrieved on May 25, 2009 [55] Biology-Online.org --> Dictionary H Hypoxemia (http:/ / www. biology-online. org/ dictionary/ Hypoxemia) last modified 00:05, 29 December 2008 [56] Page 430 -> Pathophysiology of acute respiratory failure (http:/ / books. google. dk/ books?id=3H3AIEtvc8YC& pg=PA430& lpg=PA430& dq=hypoxemia+ definition+ "partial+ pressure"& source=bl& ots=p3N6uD-dVb& sig=UvR-_OjG_K-1y4yId6PIBw7owXg& hl=en& ei=QUAaSqL0OofU-QbNw-XLDg& sa=X& oi=book_result& ct=result& resnum=6) in Trauma By William C. Wilson, Christopher M. Grande, David B. Hoyt Edition: illustrated Published by CRC Press, 2007 ISBN 0-8247-2920-X, 9780824729202 1384 pages [57] Hazards of hypoxemia: How to protect your patient from low oxygen levels (http:/ / findarticles. com/ p/ articles/ mi_qa3689/ is_199605/ ai_n8735092/ ) In Nursing , May 1996 by McGaffigan, Patricia A [58] "Definition of Glycosylated Hemoglobin." Medicine Net. N.p., n.d. Web. 12 Oct. 2009. <www.medterms.com/script/main/art.asp?articlekey=16295>. [59] Hemoglobin (http:/ / www. nlm. nih. gov/ medlineplus/ ency/ article/ 003645. htm#What abnormal results mean) at Medline Plus [60] Kumar, Dr. Kamakhya; The Healing Sleep, Yoga, Mind Body Spirit; Yoga Magazine, 26 York Street London, Vol. 50 page 42-44. [61] Padmanaban P, Toora BD. Hemoglobin: Emerging marker in stable coronary artery disease. Chron Young Sci [serial online] 2011 [cited 2011 Jul 24];2:109-10. Available from: http:/ / www. cysonline. org/ text. asp?2011/ 2/ 2/ 109/ 82971. [62] http:/ / www. unc. edu/ ~rowlett/ units/ scales/ clinical_data. html [63] Hemoglobin Level Test (http:/ / ibdcrohns. about. com/ od/ diagnostictesting/ p/ testhemo. htm) [64] Although other sources can have slightly differing values, such as http:/ / www. gpnotebook. co. uk/ simplepage. cfm?ID=1026883654 [65] Murray S.S. & McKinney E.S.(2006). Foundations of Maternal-Newborn Nursing.(4th ed., p 919).Philadelphia: Saunders Elsevier [66] "Hematocrit (HCT) or Packed Cell Volume (PCV)" (http:/ / www. doctorslounge. com/ hematology/ labs/ hematocrit. htm). DoctorsLounge.com. . Retrieved 2007-12-26. [67] Frasca D., Dahyot-Fizelier C., Catherine K., Levrat Q., Debaene B., Mimoz O. Crit Care Med. 2011 Oct;39(10):2277-82. [68] This Hb A1c level is only useful in individuals who have red blood cells (RBCs) with normal survivals (i.e., normal half-life). In individuals with abnormal RBCs, whether due to abnormal hemoglobin molecules (such as Hemoglobin S in Sickle Cell Anemia) or RBC membrane defects - or other problems, the RBC half-life is frequently shortened. In these individuals, an alternative test called "fructosamine level" can be used. It measures the degree of glycation (glucose binding) to albumin, the most common blood protein, and reflects average blood glucose levels over the previous 18-21 days, which is the half-life of albumin molecules in the circulation. [69] Weber RE, Vinogradov SN (Apr 2001). "Nonvertebrate hemoglobins: functions and molecular adaptations" (http:/ / physrev. physiology. org/ cgi/ pmidlookup?view=long& pmid=11274340). Physiol. Rev. 81 (2): 569628. ISSN0031-9333. PMID11274340. . [70] Zal F, Lallier FH, Green BN, Vinogradov SN, Toulmond A (Apr 1996). "The multi-hemoglobin system of the hydrothermal vent tube worm Riftia pachyptila. II. Complete polypeptide chain composition investigated by maximum entropy analysis of mass spectra" (http:/ / www. jbc. org/ cgi/ pmidlookup?view=long& pmid=8621529). J. Biol. Chem. 271 (15): 887581. doi:10.1074/jbc.271.15.8875. ISSN0021-9258. PMID8621529. . [71] Minic Z, Herv G (Aug 2004). "Biochemical and enzymological aspects of the symbiosis between the deep-sea tubeworm Riftia pachyptila and its bacterial endosymbiont". Eur. J. Biochem. 271 (15): 3093102. doi:10.1111/j.1432-1033.2004.04248.x. ISSN0014-2956. PMID15265029. [72] Liu L, Zeng M, Stamler JS (June 1999). "Hemoglobin induction in mouse macrophages". Proceedings of the National Academy of Sciences of the United States of America 96 (12): 66437. doi:10.1073/pnas.96.12.6643. PMC21968. PMID10359765. [73] Newton DA, Rao KM, Dluhy RA, Baatz JE (March 2006). "Hemoglobin Is Expressed by Alveolar Epithelial Cells" (http:/ / www. jbc. org/ cgi/ reprint/ 281/ 9/ 5668). Journal of Biological Chemistry 281 (9): 566876. doi:10.1074/jbc.M509314200. PMID16407281. . [74] Nishi H, Inagi R, Kato H, et al. (August 2008). "Hemoglobin Is Expressed by Mesangial Cells and Reduces Oxidant Stress" (http:/ / www. pubmedcentral. nih. gov/ articlerender. fcgi?tool=pubmed& pubmedid=18448584). Journal of the American Society of Nephrology 19 (8): 15008. doi:10.1681/ASN.2007101085. PMC2488266. PMID18448584. . [75] Boh, Larry (2001). Pharmacy Practice Manual: A Guide to the Clinical Experience. Lippincott Williams & Wilkins. ISBN0781725410. [76] Holden, Constance (30 September 2005). "Blood and Steel" (http:/ / www. sciencemag. org/ cgi/ reprint/ 309/ 5744/ 2160d. pdf) (pdf). Science 309 (5744): 2160. doi:10.1126/science.309.5744.2160d. . [77] Moran L, Horton RA, Scrimgeour G, Perry M (2011). Principles of Biochemistry. Boston, MA: Pearson. pp.127. ISBN0-321-70733-8.
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Hemoglobin
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Further reading
Campbell, MK (1999). Biochemistry (Third Edition). Harcourt. ISBN0-03-024426-9 Eshaghian, S; Horwich, TB; Fonarow, GC (January 2006). "An unexpected inverse relationship between HbA1c levels and mortality in patients with diabetes and advanced systolic heart failure". Am Heart J 151 (1): 91. doi:10.1016/j.ahj.2005.10.008. PMID16368297. Ganong, WF (2003). Review of Medical Physiology (Twenty-First Edition). Lange. ISBN0-07-140236-5. Hager, T (1995). Force of Nature: The Life of Linus Pauling. Simon and Schuster. ISBN0-684-80909-5. Hardison, RC (June 11, 1996). "A brief history of hemoglobins: plant, animal, protist, and bacteria" (http:/ / www. pubmedcentral. gov/ articlerender. fcgi?tool=pubmed& pubmedid=8650150). Proc Natl Acad Sci USA 93 (12): 56759. doi:10.1073/pnas.93.12.5675. PMC39118. PMID8650150. PMID 8650150. Kneipp, J; Balakrishnan, G; Chen, R, Shen TJ, Sahu SC, Ho NT, Giovannelli JL, Simplaceanu V, Ho C, Spiro TG (November 22, 2005). "Dynamics of allostery in hemoglobin: roles of the penultimate tyrosine H bonds". J Mol Biol. PMID 16368110. Steinberg, MH (2001). Disorders of Hemoglobin: Genetics, Pathophysiology, and Clinical Management (http:/ / books. google. com/ books?vid=ISBN0521632668). Cambridge University Press. ISBN0-521-63266-8.
External links
Interactive hemoglobin saturation curves (http://www.altitude.org/hemoglobin_saturation.php) Interactive models of hemoglobin (http://www.ufp.pt/~pedros/anim/2frame-hben.htm) (Requires MDL Chime (http://www.mdl.com/products/framework/chime/)) Hemoglobin. . (http://medzeit.ru/analizy/krov/ norma-gemoglobina-v-krovi.html) National Anemia Action Council (http://www.anemia.org/) - anemia.org New hemoglobin type causes mock diagnosis with pulse oxymeters (http://www.life-of-science.net/medicine/ news/new-hemoglobin-type-discovered-causing-mock-diagnosis-of-cardiac-insufficiency.html)
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Enzyme mechanisms
Enzyme catalysis
Enzyme catalysis is the catalysis of chemical reactions by specialized proteins known as enzymes. Catalysis of biochemical reactions in the cell is vital due to the very low reaction rates of the uncatalysed reactions. The mechanism of enzyme catalysis is similar in principle to other types of chemical catalysis. By providing an alternative reaction route and by stabilizing intermediates the enzyme reduces the energy required to reach the highest energy transition state of the reaction. The reduction of activation energy (Ea) increases the number of reactant molecules with enough energy to reach the activation energy and form the product.
Induced fit
The favored model for the enzyme-substrate interaction is the induced fit model.[1] This model proposes that the initial interaction between enzyme and substrate is relatively weak, but that these weak interactions rapidly induce conformational changes in the enzyme that strengthen binding.
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142
It is important to clarify, however, that the induced fit concept cannot be used to rationalize catalysis. That is, the chemical catalysis is defined as the reduction of Ea (when the system is already in the ES) relative to Ea in the uncatalyzed reaction in water (without the enzyme). The induced fit only suggests that the barrier is lower in the closed form of the enzyme but does not tell us what the reason for the barrier reduction is. Induced fit may be beneficial to the fidelity of molecular recognition in the presence of competition and noise via the conformational proofreading mechanism .[2]
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143
For example: Substrate, bound substrate, and transition state conformations of lysozyme.
The substrate, on binding, is distorted from the typical 'chair' hexose ring into the 'sofa' conformation, which is similar in shape to the transition state.
The effective concentration of acetate in the intramolecular reaction can be estimated as k2/k1 = 2 x 105 Molar.
However, the situation might be more complex, since modern computational studies have established that traditional examples of proximity effects cannot be related directly to enzyme entropic effects.[6] [7] [8] Also, the original entropic proposal[9] has been found to largely overestimate the contribution of orientation entropy to catalysis.[10]
Enzyme catalysis
144
The pKa is can be modified significantly by the environment, to the extent that residues which are basic in solution may act as proton donors, and vice versa.
For example: Serine protease catalytic mechanism
The initial step of the serine protease catalytic mechanism involves the histidine of the active site accepting a proton from the serine residue. This prepares the serine as a nucleophile to attack the amide bond of the substrate. This mechanism includes donation of a proton from serine (a base, pKa 14) to histidine (an acid, pKa 6), made possible due to the local environment of the bases.
It is important to clarify that the modification of the pKas is a pure part of the electrostatic mechanism.[4] Furthermore, the catalytic effect of the above example is mainly associated with the reduction of the pKa of the oxy anion and the increase in the pKa of the histidine, while the proton transfer from the serine to the histidine is not catalyzed significantly, since it is not the rate determining barrier.[11]
Enzyme catalysis
145
Electrostatic catalysis
Stabilization of charged transition states can also be by residues in the active site forming ionic bonds (or partial ionic charge interactions) with the intermediate. These bonds can either come from acidic or basic side chains found on amino acids such as lysine, arginine, aspartic acid or glutamic acid or come from metal cofactors such as zinc. Metal ions are particularly effective and can reduce the pKa of water enough to make it an effective nucleophile. Systematic computer simulation studies established that electrostatic effects give, by far, the largest contribution to catalysis.[4] In particular, it has been found that enzyme provides an environment which is more polar than water, and that the ionic transition states are stabilized by fixed dipoles. This is very different from transition state stabilization in water, where the water molecules must pay with "reorganization energy".[12] in order to stabilize ionic and charged states. Thus, the catalysis is associated with the fact that the enzyme polar groups are preorganized
[13]
The tetrahedral intermediate is stabilised by a partial ionic bond between the Zn2+ ion and the negative charge on the oxygen.
Covalent catalysis
Covalent catalysis involves the substrate forming a transient covalent bond with residues in the active site or with a cofactor. This adds an additional covalent intermediate to the reaction, and helps to reduce the energy of later transition states of the reaction. The covalent bond must, at a later stage in the reaction, be broken to regenerate the enzyme. This mechanism is found in enzymes such as proteases like chymotrypsin and trypsin, where an acyl-enzyme intermediate is formed. Schiff base formation using the free amine from a lysine residue is another mechanism, as seen in the enzyme aldolase during glycolysis. Some enzymes utilize non-amino acid cofactors such as pyridoxal phosphate (PLP) or thiamine pyrophosphate (TPP) to form covalent intermediates with reactant molecules.[14] [15] Such covalent intermediates function to reduce the energy of later transition states, similar to how covalent intermediates formed with active site amino acid residues allow stabilization, but the capabilities of cofactors allow enzymes to carryout reactions that amino acid side residues alone could not. Enzymes utilizing such cofactors include the PLP-dependent enzyme aspartate transaminase and the TPP-dependent enzyme pyruvate dehydrogenase.[16] [17] It is important to clarify that covalent catalysis does correspond in most cases to simply the use of a specific mechanism rather than to true catalysis.[4] For example, the energetics of the covalent bond to the serine molecule in chymotrypsin should be compared to the well-understood covalent bond to the nucleophile in the uncatalyzed solution reaction. A true proposal of a covalent catalysis (where the barrier is lower than the corresponding barrier in
Enzyme catalysis solution) would require, for example, a partial covalent bond to the transition state by an enzyme group (e.g., a very strong hydrogen bond), and such effects do not contribute significantly to catalysis.
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Quantum tunneling
These traditional "over the barrier" mechanisms have been challenged in some cases by models and observations of "through the barrier" mechanisms (quantum tunneling). Some enzymes operate with kinetics which are faster than what would be predicted by the classical G. In "through the barrier" models, a proton or an electron can tunnel through activation barriers.[18] [19] Quantum tunneling for protons has been observed in tryptamine oxidation by aromatic amine dehydrogenase.[20] Interestingly, quantum tunneling does not appear to provide a major catalytic advantage, since the tunneling contributions are similar in the catalyzed and the uncatalyzed reactions in solution.[19] [21] [22] [23] However, the tunneling contribution (typically enhancing rate constants by a factor of ~1000[20] compared to the rate of reaction for the classical 'over the barrier' route) is likely crucial to the viability of biological organisms. This emphasizes the general importance of tunneling reactions in biology. In 1971-1972 the first quantum-mechanical model of enzyme catalysis was formulated.[24] [25]
Trypsin
Trypsin (EC 3.4.21.4 residues.
[27]
) is a serine protease that cleaves protein substrates at lysine and arginine amino acid
Aldolase
Aldolase (EC 4.1.2.13 [28]) catalyses the breakdown of fructose 1,6-bisphosphate (F-1,6-BP) into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP).
References
[1] Koshland DE (February 1958). "Application of a Theory of Enzyme Specificity to Protein Synthesis". Proc. Natl. Acad. Sci. U.S.A. 44 (2): 98104. doi:10.1073/pnas.44.2.98. PMC335371. PMID16590179. [2] Savir Y & Tlusty T (2007). Scalas, Enrico. ed. "Conformational Proofreading: The Impact of Conformational Changes on the Specificity of Molecular Recognition" (http:/ / www. weizmann. ac. il/ complex/ tlusty/ papers/ PLoSONE2007. pdf). PLoS ONE 2 (5): e468. doi:10.1371/journal.pone.0000468. PMC1868595. PMID17520027. . [3] Jencks W.P. "Catalysis in Chemistry and Enzymology" 1987, Dover, New York [4] Warshel, A.; Sharma, P.K.; Kato, M.; Xiang, Y.; Liu, H.; Olsson, M.H.M. (2006). "Electrostatic Basis of Enzyme Catalysis". Chem. Rev. 106 (8): 32103235. doi:10.1021/cr0503106. PMID16895325. [5] Warshel, A.; Levitt, M. (1976). "Theoretical Studies of Enzymatic Reactions: Dielectric Electrostatic and Steric Stabilization of the Carbonium Ion in the Reaction of Lysozyme". J. Mol. Biol. 103 (2): 22749. doi:10.1016/0022-2836(76)90311-9. PMID985660. [6] Stanton, R.V.; Perakyla, M.; Bakowies, D.; Kollman, P.A. (1998). "Combined ab initio and Free Energy Calculations To Study Reactions in Enzymes and Solution: Amide Hydrolysis in Trypsin and Aqueous Solution". J. Am. Chem. Soc 120 (14): 34483457. doi:10.1021/ja972723x. [7] Kuhn, B.; Kollman, P.A. (2000). "QM-FE and Molecular Dynamics Calculations on Catechol O-Methyltransferase: Free Energy of Activation in the Enzyme and in Aqueous Solution and Regioselectivity of the Enzyme-Catalyzed Reaction". J. Am. Chem. Soc 122 (11): 25862596. doi:10.1021/ja992218v.
Enzyme catalysis
[8] Bruice, T.C.; Lightstone, F.C. (1999). "Ground State and Transition State Contributions to the Rates of Intramolecular and Enzymatic Reactions". Acc. Chem. Res. 32 (2): 127136. doi:10.1021/ar960131y. [9] Page, M.I.; Jencks, W.P.. "Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and the Chelate Effect". Proc. Natl. Acad. Sci. USA 1971 (68): 16781683. doi:10.1073/pnas.68.8.1678. PMC389269. PMID5288752. [10] Warshel, A.; Parson, W.W. (2001). "Dynamics of Biochemical and Biophysical Reactions: Insight from Computer Simulations". Quart. Rev. Biophys 34: 563679. [11] Warshel, A.; Naray-Szabo, G.; Sussman, F.; Hwang, J.-K. (1989). "How do Serine Proteases Really Work?". Biochemistry 1989 (28): 362937. doi:10.1021/bi00435a001. PMID2665806. [12] Marcus R. A. "On the Theory of Electron-Transfer Reactions. VI. Unified Treatment for Homogeneous and Electrode Reactions" J. Chem. Phys. 1965 43:679-701 [13] Warshel A. "Energetics of Enzyme Catalysis", Proc. Natl. Acad. Sci. USA, 1978 75: 5250 [14] Toney, M. D. "Reaction specificity in pyridoxal enzymes." Archives of biochemistry and biophysics (2005) 433: 279-287 [15] Micronutrient Information Center, Oregon State University (http:/ / lpi. oregonstate. edu/ infocenter/ vitamins/ thiamin/ ) [16] Voet, Donald; Judith Voet (2004). Biochemistry. John Wiley & Sons Inc. pp.986989. ISBN0-471-25090-2. [17] Voet, Donald; Judith Voet (2004). Biochemistry. John Wiley & Sons Inc. pp.604606. ISBN0-471-25090-2. [18] Garcia-Viloca, M; Gao, J; Karplus, M; Truhlar, DG (2004). "How enzymes work: analysis by modern rate theory and computer simulations". Science 303 (5655): 18695. doi:10.1126/science.1088172. PMID14716003. [19] Olsson, MH; Siegbahn, PE; Warshel, A (2004). "Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase". Journal of the American Chemical Society 126 (9): 28208. doi:10.1021/ja037233l. PMID14995199. [20] Masgrau, L; Roujeinikova, A; Johannissen, LO; Hothi, P; Basran, J; Ranaghan, KE; Mulholland, AJ; Sutcliffe, MJ et al. (2006). "Atomic description of an enzyme reaction dominated by proton tunneling". Science 312 (5771): 23741. doi:10.1126/science.1126002. PMID16614214. [21] Hwang, J.-K.; Warshel, A.. "How important are quantum mechanical nuclear motions in enzyme catalysis". J. Am. Chem. Soc 1996 (118): 1174511751. [22] Ball, P. (2004). "Enzymes: By chance, or by design?". Nature 431 (7007): 396. Bibcode2004Natur.431..396B. doi:10.1038/431396a. [23] Olsson, M.H.M.; Parson, W.W.; Warshel, A.. "Dynamical Contributions to Enzyme Catalysis: Critical Tests of A Popular Hypothesis". Chem. Rev. 2006 (105): 17371756. [24] Volkenshtein M.V., Dogonadze R.R., Madumarov A.K., Urushadze Z.D., Kharkats Yu.I. Theory of Enzyme Catalysis.- Molekuliarnaya Biologia, Moscow, 6, 1972, 431-439 [25] Volkenshtein M.V., Dogonadze R.R., Madumarov A.K., Urushadze Z.D., Kharkats Yu.I. Electronic and Conformational Interactions in Enzyme Catalysis. In: E.L. Andronikashvili (Ed.), Konformatsionnie Izmenenia Biopolimerov v Rastvorakh, Publishing House "Nauka", Moscow, 1973, 153-157 [26] http:/ / enzyme. expasy. org/ EC/ 5. 3. 1. 1 [27] http:/ / enzyme. expasy. org/ EC/ 3. 4. 21. 4 [28] http:/ / enzyme. expasy. org/ EC/ 4. 1. 2. 13
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Further reading
Alan Fersht, Structure and Mechanism in Protein Science : A Guide to Enzyme Catalysis and Protein Folding. W. H. Freeman, 1998. ISBN 0-7167-3268-8 Dedicated issue of Philosophical Transactions B on Quantum catalysis in enzymes freely available. (http:// publishing.royalsociety.org/quantum-catalysis)
148
Enzyme kinetics
Enzyme kinetics
Enzyme kinetics is the study of the chemical reactions that are catalysed by enzymes. In enzyme kinetics, the reaction rate is measured and the effects of varying the conditions of the reaction investigated. Studying an enzyme's kinetics in this way can reveal the catalytic mechanism of this enzyme, its role in metabolism, how its activity is controlled, and how a drug or an agonist might inhibit the enzyme. Enzymes are usually protein molecules that manipulate other molecules the enzymes' substrates. These target molecules bind to an enzyme's active site and are transformed into products through a series of steps known as the enzymatic mechanism. These mechanisms can be divided into single-substrate and multiple-substrate mechanisms. Kinetic studies on enzymes that only bind one substrate, such as triosephosphate isomerase, aim to measure the affinity with which the enzyme binds this substrate and the turnover rate. When enzymes bind multiple substrates, such as (right) and NADPH (left), bound in the active site. The protein is shown as a dihydrofolate reductase (shown right), enzyme ribbon diagram, with alpha helices in red, beta sheets in yellow and loops in [1] blue. Generated from 7DFR . kinetics can also show the sequence in which these substrates bind and the sequence in which products are released. An example of enzymes that bind a single substrate and release multiple products are proteases, which cleave one protein substrate into two polypeptide products. Others join two substrates together, such as DNA polymerase linking a nucleotide to DNA. Although these mechanisms are often a complex series of steps, there is typically one rate-determining step that determines the overall kinetics. This rate-determining step may be a chemical reaction or a conformational change of the enzyme or substrates, such as those involved in the release of product(s) from the enzyme. Knowledge of the enzyme's structure is helpful in interpreting kinetic data. For example, the structure can suggest how substrates and products bind during catalysis; what changes occur during the reaction; and even the role of particular amino acid residues in the mechanism. Some enzymes change shape significantly during the mechanism; in such cases, it is helpful to determine the enzyme structure with and without bound substrate analogues that do not undergo the enzymatic reaction.
Dihydrofolate reductase from E. coli with its two substrates, dihydrofolate
Enzyme kinetics Not all biological catalysts are protein enzymes; RNA-based catalysts such as ribozymes and ribosomes are essential to many cellular functions, such as RNA splicing and translation. The main difference between ribozymes and enzymes is that RNA catalysts are composed of nucleotides, whereas enzymes are composed of amino acids. Ribozymes also perform a more limited set of reactions, although their reaction mechanisms and kinetics can be analysed and classified by the same methods.
149
General principles
The reaction catalysed by an enzyme uses exactly the same reactants and produces exactly the same products as the uncatalysed reaction. Like other catalysts, enzymes do not alter the position of equilibrium between substrates and products.[2] However, unlike uncatalysed chemical reactions, enzyme-catalysed reactions display saturation kinetics. For a given enzyme concentration and for relatively low substrate concentrations, the reaction rate As larger amounts of substrate are added to a reaction, the available enzyme increases linearly with substrate binding sites become filled to the limit of . Beyond this limit the enzyme is concentration; the enzyme molecules are saturated with substrate and the reaction rate ceases to increase. largely free to catalyse the reaction, and increasing substrate concentration means an increasing rate at which the enzyme and substrate molecules encounter one another. However, at relatively high substrate concentrations, the reaction rate asymptotically approaches the theoretical maximum; the enzyme active sites are almost all occupied and the reaction rate is determined by the intrinsic turnover rate of the enzyme. The substrate concentration midway between these two limiting cases is denoted by KM. The two most important kinetic properties of an enzyme are how quickly the enzyme becomes saturated with a particular substrate, and the maximum rate it can achieve. Knowing these properties suggests what an enzyme might do in the cell and can show how the enzyme will respond to changes in these conditions.
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Enzyme assays
Enzyme assays are laboratory procedures that measure the rate of enzyme reactions. Because enzymes are not consumed by the reactions they catalyse, enzyme assays usually follow changes in the concentration of either substrates or products to measure the rate of reaction. There are many methods of measurement. Spectrophotometric assays observe change in the absorbance of light between products and reactants; radiometric assays involve the incorporation or release of radioactivity to measure the amount of product made over time. Spectrophotometric assays are most convenient since they allow the rate of the reaction to be measured continuously. Although radiometric assays Progress curve for an enzyme reaction. The slope in the initial rate period is the initial rate of reaction v. The MichaelisMenten require the removal and counting of samples (i.e., they equation describes how this slope varies with the concentration of are discontinuous assays) they are usually extremely substrate. sensitive and can measure very low levels of enzyme activity.[3] An analogous approach is to use mass spectrometry to monitor the incorporation or release of stable isotopes as substrate is converted into product. The most sensitive enzyme assays use lasers focused through a microscope to observe changes in single enzyme molecules as they catalyse their reactions. These measurements either use changes in the fluorescence of cofactors during an enzyme's reaction mechanism, or of fluorescent dyes added onto specific sites of the protein to report movements that occur during catalysis.[4] These studies are providing a new view of the kinetics and dynamics of single enzymes, as opposed to traditional enzyme kinetics, which observes the average behaviour of populations of millions of enzyme molecules.[5] [6] An example progress curve for an enzyme assay is shown above. The enzyme produces product at an initial rate that is approximately linear for a short period after the start of the reaction. As the reaction proceeds and substrate is consumed, the rate continuously slows (so long as substrate is not still at saturating levels). To measure the initial (and maximal) rate, enzyme assays are typically carried out while the reaction has progressed only a few percent towards total completion. The length of the initial rate period depends on the assay conditions and can range from milliseconds to hours. However, equipment for rapidly mixing liquids allows fast kinetic measurements on initial rates of less than one second.[7] These very rapid assays are essential for measuring pre-steady-state kinetics, which are discussed below. Most enzyme kinetics studies concentrate on this initial, approximately linear part of enzyme reactions. However, it is also possible to measure the complete reaction curve and fit this data to a non-linear rate equation. This way of measuring enzyme reactions is called progress-curve analysis.[8] This approach is useful as an alternative to rapid kinetics when the initial rate is too fast to measure accurately.
Single-substrate reactions
Enzymes with single-substrate mechanisms include isomerases such as triosephosphateisomerase or bisphosphoglycerate mutase, intramolecular lyases such as adenylate cyclase and the hammerhead ribozyme, a RNA lyase.[9] However, some enzymes that only have a single substrate do not fall into this category of mechanisms. Catalase is an example of this, as the enzyme reacts with a first molecule of hydrogen peroxide substrate, becomes oxidised and is then reduced by a second molecule of substrate. Although a single substrate is involved, the existence of a modified enzyme intermediate means that the mechanism of catalase is actually a pingpong mechanism, a type
Enzyme kinetics of mechanism that is discussed in the Multi-substrate reactions section below.
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MichaelisMenten kinetics
As enzyme-catalysed reactions are saturable, their rate of catalysis does not show a linear response to increasing substrate. If the initial rate of the reaction is measured over a range of substrate concentrations (denoted as [S]), the reaction rate (v) increases as [S] increases, as shown on the right. However, as [S] gets higher, the enzyme becomes saturated with substrate and the rate reaches Vmax, the enzyme's maximum rate.
Saturation curve for an enzyme showing the relation between the concentration of substrate and rate.
Single-substrate mechanism for an enzyme reaction. k1, k-1 and k2 are the rate constants for the individual steps.
The MichaelisMenten kinetic model of a single-substrate reaction is shown on the right. There is an initial bimolecular reaction between the enzyme E and substrate S to form the enzymesubstrate complex ES. Although the enzymatic mechanism for the unimolecular reaction can be quite complex, there is typically one rate-determining enzymatic step that allows this reaction to be modelled as a single catalytic step with an apparent unimolecular rate constant kcat. If the reaction path proceeds over one or several intermediates, kcat will be a function of several elementary rate constants, whereas in the simplest case of a single elementary reaction (e.g. no intermediates) it will be identical to the elementary unimolecular rate constant k2. The apparent unimolecular rate constant kcat is also called turnover number and denotes the maximum number of enzymatic reactions catalysed per second. The MichaelisMenten equation[10] describes how the (initial) reaction rate v0 depends on the position of the substrate-binding equilibrium and the rate constant k2. (MichaelisMenten equation) with the constants
Enzyme kinetics
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This MichaelisMenten equation is the basis for most single-substrate enzyme kinetics. Two crucial assumptions underlie this equation (apart from the general assumption about the mechanism only involving no intermediate or product inhibition, and there is no allostericity or cooperativity). The first assumption is the so called quasi-steady-state assumption (or pseudo-steady-state hypothesis), namely that the concentration of the substrate-bound enzyme (and hence also the unbound enzyme) changes much more slowly than those of the product and substrate and thus the change over time of the complex can be set to zero . The second assumption is that the total enzyme concentration does not . A complete derivation can be found here. change over time, thus
The Michaelis constant KM is experimentally defined as the concentration at which the rate of the enzyme reaction is half Vmax, which can be verified by substituting [S] = Km into the MichaelisMenten equation and can also be seen graphically. If the rate-determining enzymatic step is slow compared to substrate dissociation ( ), the Michaelis constant KM is roughly the dissociation constant KD of the ES complex. If is small compared to then the term and also very little ES complex is formed, thus . Therefore, the rate of product formation is
Thus the product formation rate depends on the enzyme concentration as well as on the substrate concentration, the equation resembles a bimolecular reaction with a corresponding pseudo-second order rate constant . This constant is a measure of catalytic efficiency. The most efficient enzymes reach a in the range of 108 1010M1s1. These enzymes are so efficient they effectively catalyse a reaction each time they encounter a substrate molecule and have thus reached an upper theoretical limit for efficiency (diffusion limit); these enzymes have often been termed perfect enzymes.[11]
Direct use of the MichaelisMenten equation for time course kinetic analysis
Further information: Rate equation The observed velocities predicted by the MichaelisMenten equation can be used to directly model the time course disappearance of substrate and the production of product through incorporation of the MichaelisMenten equation into the equation for first order chemical kinetics. This can only be achieved however if one recognises the problem associated with the use of Euler's number in the description of first order chemical kinetics. i.e. e-k is a split constant that introduces a systematic error into calculations and can be rewritten as a single constant which represents the remaining substrate after each time period.[12]
In 1997, Santiago Schnell and Claudio Mendoza derived a closed form solution for the time course kinetics analysis of the Michaelis-Menten mechanism.[13] The solution has the form: where W[] is the Lambert-W function.[14] [15]
Enzyme kinetics
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Naturally, no experimental values can be taken at negative 1/[S]; the lower limiting value 1/[S] = 0 (the y-intercept) corresponds to an infinite substrate concentration, where 1/v=1/Vmax as shown at the right; thus, the x-intercept is an extrapolation of the experimental data taken at positive concentrations. More generally, the LineweaverBurk plot skews the importance of measurements taken at low substrate concentrations and, thus, can yield inaccurate estimates of Vmax and KM.[17] A more accurate linear plotting method is the Eadie-Hofstee plot. In this case, v is plotted against v/[S]. In the third common linear representation, the Hanes-Woolf plot, [S]/v is plotted against [S]. In general, data normalisation can help diminish the amount of experimental work and can increase the reliability of the output, and is suitable for both graphical and numerical analysis.[18]
Enzyme kinetics expression in the synthesis of huge amounts of kinetic and gene expression data into mathematical models of entire organisms. Alternatively, one useful simplification of the metabolic modelling problem is to ignore the underlying enzyme kinetics and only rely on information about the reaction network's stoichiometry, a technique called flux balance analysis.[19] [20]
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where a complex with the enzyme and an intermediate exists and the intermediate is converted into product in a second step. In this case we have a very similar equation[21]
, thus when the last step from EI to E + P is much faster than the and .
previous step, we get again the original equation. Mathematically we have then
Multi-substrate reactions
Multi-substrate reactions follow complex rate equations that describe how the substrates bind and in what sequence. The analysis of these reactions is much simpler if the concentration of substrate A is kept constant and substrate B varied. Under these conditions, the enzyme behaves just like a single-substrate enzyme and a plot of v by [S] gives apparent KM and Vmax constants for substrate B. If a set of these measurements is performed at different fixed concentrations of A, these data can be used to work out what the mechanism of the reaction is. For an enzyme that takes two substrates A and B and turns them into two products P and Q, there are two types of mechanism: ternary complex and pingpong.
Ternary-complex mechanisms
In these enzymes, both substrates bind to the enzyme at the same time to produce an EAB ternary complex. The order of binding can either be random (in a random mechanism) or substrates have to bind in a particular sequence (in an ordered mechanism). When a set of v by [S] curves (fixed A, varying B) from an enzyme with a ternary-complex mechanism are plotted in a LineweaverBurk plot, the set of lines produced will intersect.
Random-order ternary-complex mechanism for an enzyme reaction. The reaction path is shown as a line and enzyme intermediates containing substrates A and B or products P and Q are written below the line.
Enzyme kinetics Enzymes with ternary-complex mechanisms include glutathione S-transferase,[22] dihydrofolate reductase[23] and DNA polymerase.[24] The following links show short animations of the ternary-complex mechanisms of the enzymes dihydrofolate reductase[] and DNA polymerase[].
155
Pingpong mechanisms
As shown on the right, enzymes with a ping-pong mechanism can exist in two states, E and a chemically modified form of the enzyme E*; this modified enzyme Pingpong mechanism for an enzyme reaction. Intermediates contain substrates A is known as an intermediate. In such and B or products P and Q. mechanisms, substrate A binds, changes the enzyme to E* by, for example, transferring a chemical group to the active site, and is then released. Only after the first substrate is released can substrate B bind and react with the modified enzyme, regenerating the unmodified E form. When a set of v by [S] curves (fixed A, varying B) from an enzyme with a pingpong mechanism are plotted in a LineweaverBurk plot, a set of parallel lines will be produced. This is called a secondary plot. Enzymes with pingpong mechanisms include some oxidoreductases such as thioredoxin peroxidase,[25] transferases such as acylneuraminate cytydilyltransferase[26] and serine proteases such as trypsin and chymotrypsin.[27] Serine proteases are a very common and diverse family of enzymes, including digestive enzymes (trypsin, chymotrypsin, and elastase), several enzymes of the blood clotting cascade and many others. In these serine proteases, the E* intermediate is an acyl-enzyme species formed by the attack of an active site serine residue on a peptide bond in a protein substrate. A short animation showing the mechanism of chymotrypsin is linked here.[]
Non-MichaelisMenten kinetics
Some enzymes produce a sigmoid v by [S] plot, which often indicates cooperative binding of substrate to the active site. This means that the binding of one substrate molecule affects the binding of subsequent substrate molecules. This behavior is most common in multimeric enzymes with several interacting active sites.[28] Here, the mechanism of cooperation is similar to that of hemoglobin, with binding of substrate to one active site altering the affinity of the other active sites for substrate molecules. Positive cooperativity occurs when binding of the first substrate molecule increases the affinity of the other active sites for substrate. Negative cooperativity occurs when binding of the first substrate decreases the affinity of
the enzyme for other substrate molecules. Allosteric enzymes include mammalian tyrosyl tRNA-synthetase, which shows negative cooperativity,[29] and bacterial aspartate transcarbamoylase[30] and phosphofructokinase,[31] which show positive cooperativity. Cooperativity is surprisingly common and can help regulate the responses of enzymes to changes in the concentrations of their substrates. Positive cooperativity makes enzymes much more sensitive to [S] and their
Enzyme kinetics activities can show large changes over a narrow range of substrate concentration. Conversely, negative cooperativity makes enzymes insensitive to small changes in [S]. The Hill equation (biochemistry)[32] is often used to describe the degree of cooperativity quantitatively in non-MichaelisMenten kinetics. The derived Hill coefficient n measures how much the binding of substrate to one active site affects the binding of substrate to the other active sites. A Hill coefficient of <1 indicates negative cooperativity and a coefficient of >1 indicates positive cooperativity.
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Pre-steady-state kinetics
In the first moment after an enzyme is mixed with substrate, no product has been formed and no intermediates exist. The study of the next few milliseconds of the reaction is called Pre-steady-state kinetics also referred to as Burst kinetics. Pre-steady-state kinetics is therefore concerned with the formation and consumption of enzymesubstrate intermediates (such as ES or E*) until their steady-state concentrations are reached. This approach was first applied to the hydrolysis reaction catalysed by Pre-steady state progress curve, showing the burst phase of an enzyme reaction. [33] chymotrypsin. Often, the detection of an intermediate is a vital piece of evidence in investigations of what mechanism an enzyme follows. For example, in the pingpong mechanisms that are shown above, rapid kinetic measurements can follow the release of product P and measure the formation of the modified enzyme intermediate E*.[34] In the case of chymotrypsin, this intermediate is formed by an attack on the substrate by the nucleophilic serine in the active site and the formation of the acyl-enzyme intermediate. In the figure to the right, the enzyme produces E* rapidly in the first few seconds of the reaction. The rate then slows as steady state is reached. This rapid burst phase of the reaction measures a single turnover of the enzyme. Consequently, the amount of product released in this burst, shown as the intercept on the y-axis of the graph, also gives the amount of functional enzyme which is present in the assay.[35]
Chemical mechanism
An important goal of measuring enzyme kinetics is to determine the chemical mechanism of an enzyme reaction, i.e., the sequence of chemical steps that transform substrate into product. The kinetic approaches discussed above will show at what rates intermediates are formed and inter-converted, but they cannot identify exactly what these intermediates are. Kinetic measurements taken under various solution conditions or on slightly modified enzymes or substrates often shed light on this chemical mechanism, as they reveal the rate-determining step or intermediates in the reaction. For example, the breaking of a covalent bond to a hydrogen atom is a common rate-determining step. Which of the possible hydrogen transfers is rate determining can be shown by measuring the kinetic effects of substituting each hydrogen by deuterium, its stable isotope. The rate will change when the critical hydrogen is replaced, due to a primary kinetic isotope effect, which occurs because bonds to deuterium are harder to break than bonds to hydrogen.[36] It is also possible to measure similar effects with other isotope substitutions, such as 13C/12C and 18 16 O/ O, but these effects are more subtle.[37]
Enzyme kinetics Isotopes can also be used to reveal the fate of various parts of the substrate molecules in the final products. For example, it is sometimes difficult to discern the origin of an oxygen atom in the final product; since it may have come from water or from part of the substrate. This may be determined by systematically substituting oxygen's stable isotope 18O into the various molecules that participate in the reaction and checking for the isotope in the product.[38] The chemical mechanism can also be elucidated by examining the kinetics and isotope effects under different pH conditions,[39] by altering the metal ions or other bound cofactors,[40] by site-directed mutagenesis of conserved amino acid residues, or by studying the behaviour of the enzyme in the presence of analogues of the substrate(s).[41]
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Reversible inhibitors
Traditionally reversible enzyme inhibitors have been classified as competitive, uncompetitive, or non-competitive, according to their effects on Km and Vmax. These different effects result from the inhibitor binding to the enzyme E, to the enzymesubstrate complex ES, or to both, respectively. The particular type of an inhibitor can be discerned by studying the enzyme kinetics as a function of the inhibitor concentration. The three types of inhibition produce LineweaverBurke and EadieHofstee plots[17] that vary in distinctive ways with inhibitor concentration. For a straightforward qualitative explanation, see[42] Non-linear regression fits of the enzyme kinetics data to rate equations[43] can yield accurate estimates of dissociation constants and yield important information relating to the mechanism of action.
Dividing by [I]+Ki
Enzyme kinetics
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This notation demonstrates that similar to the MichaelisMenten equation,where the rate of reaction depends on the percent of the enzyme population interacting with substrate fraction of the enzyme population bound by substrate
the effect of the inhibitor is a result of the percent of the enzyme population interacting with inhibitor. The only problem with this equation in its present form is that it assumes absolute inhibition of the enzyme with inhibitor binding, when in fact there can be a wide range of affects anywhere from 100% inhibition of substrate turn over to just >0%. To account for this the equation can be easily modified to allow for different degrees of inhibition by including a delta Vmax term.
or
This term can then define the residual enzymatic activity present when the inhibitor is interacting with individual enzymes in the population. However the inclusion of this term has the added value of allowing for the possibility of activation if the secondary Vmax term turns out to be higher than the initial term. To account for the possibly of activation as well the notation can then be rewritten replacing the inhibitor "I" with a modifier term denoted here as "X".
While this terminology results in a simplified way of dealing with kinetic effects relating to the maximum velocity of the MichaelisMenten equation, it highlights potential problems with the term used to describe effects relating to the Km. The Km relating to the affinity of the enzyme for the substrate should in most cases relate to potential changes in the binding site of the enzyme which would directly result from enzyme inhibitor interactions. As such a term similar to the one proposed above to modulate Vmax should be appropriate in most situations.:[44]
Enzyme kinetics
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Irreversible inhibitors
Enzyme inhibitors can also irreversibly inactivate enzymes, usually by covalently modifying active site residues. These reactions, which may be called suicide substrates, follow exponential decay functions and are usually saturable. Below saturation, they follow first order kinetics with respect to inhibitor.
Mechanisms of catalysis
The favoured model for the enzymesubstrate interaction is the induced fit model.[45] This model proposes that the initial interaction between enzyme and substrate is relatively weak, but that these weak interactions rapidly induce conformational changes in the enzyme that strengthen binding. These conformational changes also bring catalytic residues in the active site close to the chemical bonds in the substrate that will be altered in the reaction.[46] Conformational changes can be measured using circular dichroism or dual polarisation interferometry. After binding takes place, one or more mechanisms of The energy variation as a function of reaction coordinate shows the stabilisation of catalysis lower the energy of the reaction's the transition state by an enzyme. transition state by providing an alternative chemical pathway for the reaction. Mechanisms of catalysis include catalysis by bond strain; by proximity and orientation; by active-site proton donors or acceptors; covalent catalysis and quantum tunnelling.[34] [47] Enzyme kinetics cannot prove which modes of catalysis are used by an enzyme. However, some kinetic data can suggest possibilities to be examined by other techniques. For example, a pingpong mechanism with burst-phase pre-steady-state kinetics would suggest covalent catalysis might be important in this enzyme's mechanism. Alternatively, the observation of a strong pH effect on Vmax but not Km might indicate that a residue in the active site needs to be in a particular ionisation state for catalysis to occur.
Footnotes
. Link: Interactive MichaelisMenten kinetics tutorial (Java required) [48] . Link: dihydrofolate reductase mechanism (Gif) [49] . Link: DNA polymerase mechanism (Gif) [50] . Link: Chymotrypsin mechanism (Flash required) [51]
References
[1] http:/ / www. rcsb. org/ pdb/ explore. do?structureId=7DFR [2] Wrighton, Mark S.; Ebbing, Darrell D. (1993). General chemistry (4th ed.). Boston: Houghton Mifflin. ISBN0-395-63696-5. [3] Danson, Michael; Eisenthal, Robert (2002). Enzyme assays: a practical approach. Oxford [Oxfordshire]: Oxford University Press. ISBN0-19-963820-9. [4] Xie XS, Lu HP (June 1999). "Single-molecule enzymology" (http:/ / www. jbc. org/ cgi/ content/ full/ 274/ 23/ 15967). J. Biol. Chem. 274 (23): 1596770. doi:10.1074/jbc.274.23.15967. PMID10347141. .
Enzyme kinetics
[5] Lu H (2004). "Single-molecule spectroscopy studies of conformational change dynamics in enzymatic reactions". Current pharmaceutical biotechnology 5 (3): 2619. doi:10.2174/1389201043376887. PMID15180547. [6] Schnell J, Dyson H, Wright P (2004). "Structure, dynamics, and catalytic function of dihydrofolate reductase". Annual review of biophysics and biomolecular structure 33: 11940. doi:10.1146/annurev.biophys.33.110502.133613. PMID15139807. [7] Gibson QH (1969). "Rapid mixing: Stopped flow". Methods Enzymol. Methods in Enzymology 16: 187228. doi:10.1016/S0076-6879(69)16009-7. ISBN9780121818739. [8] Duggleby RG (1995). "Analysis of enzyme progress curves by non-linear regression". Methods Enzymol. Methods in Enzymology 249: 6190. doi:10.1016/0076-6879(95)49031-0. ISBN9780121821500. PMID7791628. [9] Murray JB, Dunham CM, Scott WG (January 2002). "A pH-dependent conformational change, rather than the chemical step, appears to be rate-limiting in the hammerhead ribozyme cleavage reaction". J. Mol. Biol. 315 (2): 12130. doi:10.1006/jmbi.2001.5145. PMID11779233. [10] Michaelis L. and Menten M.L. Kinetik der Invertinwirkung Biochem. Z. 1913; 49:333369 English translation (http:/ / web. lemoyne. edu/ ~giunta/ menten. html) Accessed 6 April 2007 [11] Stroppolo ME, Falconi M, Caccuri AM, Desideri A (2001). "Superefficient enzymes". Cell. Mol. Life Sci. 58 (10): 145160. doi:10.1007/PL00000788. PMID11693526. [12] Walsh R, Martin E, Darvesh S. A method to describe enzyme-catalyzed reactions by combining steady state and time course enzyme kinetic parameters. Biochim Biophys Acta. 2010 Jan;1800:1-5 [13] Schnell S, Mendoza C. A closed form solution for time-dependent enzyme kinetics. Journal of theoretical Biology, 187 (1997): 207-212 [14] C.T. Goudar, J.R. Sonnad, R.G. Duggleby (1999). Parameter estimation using a direct solution of the integrated Michaelis-Menten equation. Biochimica et Biophysica Acta - Protein Structure and Molecular Enzymology 1429, 377-383. [15] C.T. Goudar, S.K. Harris, M.J. McInerney, J.M Suflita (2004). Progress curve analysis for enzyme and microbial kinetic reactions using explicit solutions based on the Lambert W function. Journal of Microbiological Methods 59, 317-326 [16] Jones ME (1 January 1992). "Analysis of algebraic weighted least-squares estimators for enzyme parameters". Biochem. J. 288 (Pt 2): 5338. PMC1132043. PMID1463456. [17] Tseng SJ, Hsu JP (August 1990). "A comparison of the parameter estimating procedures for the Michaelis-Menten model". J. Theor. Biol. 145 (4): 45764. doi:10.1016/S0022-5193(05)80481-3. PMID2246896. [18] Bravo IG, Busto F, De Arriaga D, et al. (September 2001). "A normalized plot as a novel and time-saving tool in complex enzyme kinetic analysis" (http:/ / www. biochemj. org/ bj/ 358/ 0573/ bj3580573. htm). Biochem. J. 358 (Pt 3): 57383. PMC1222113. PMID11577687. . [19] Almaas E, Kovcs B, Vicsek T, Oltvai ZN, Barabsi AL (February 2004). "Global organization of metabolic fluxes in the bacterium Escherichia coli". Nature 427 (6977): 83943. doi:10.1038/nature02289. PMID14985762. [20] Reed JL, Vo TD, Schilling CH, Palsson BO (2003). "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biol. 4 (9): R54. doi:10.1186/gb-2003-4-9-r54. PMC193654. PMID12952533. [21] for a complete derivation, see here [22] Dirr H, Reinemer P, Huber R (March 1994). "X-ray crystal structures of cytosolic glutathione S-transferases. Implications for protein architecture, substrate recognition and catalytic function". Eur. J. Biochem. 220 (3): 64561. doi:10.1111/j.1432-1033.1994.tb18666.x. PMID8143720. [23] Stone SR, Morrison JF (July 1988). "Dihydrofolate reductase from Escherichia coli: the kinetic mechanism with NADPH and reduced acetylpyridine adenine dinucleotide phosphate as substrates". Biochemistry 27 (15): 54939. doi:10.1021/bi00415a016. PMID3052577. [24] Fisher PA (1994). "Enzymologic mechanism of replicative DNA polymerases in higher eukaryotes". Prog. Nucleic Acid Res. Mol. Biol.. Progress in Nucleic Acid Research and Molecular Biology 47: 37197. doi:10.1016/S0079-6603(08)60257-3. ISBN9780125400473. PMID8016325. [25] Akerman SE, Mller S (August 2003). "2-Cys peroxiredoxin PfTrx-Px1 is involved in the antioxidant defence of Plasmodium falciparum" (http:/ / www. sciencedirect. com/ science?_ob=ArticleURL& _udi=B6T29-49321S6-2& _coverDate=08/ 31/ 2003& _alid=466052639& _rdoc=1& _fmt=& _orig=search& _qd=1& _cdi=4913& _sort=d& view=c& _acct=C000050221& _version=1& _urlVersion=0& _userid=10& md5=965e18a4c2ad0af711ba05d1a46dc855). Mol. Biochem. Parasitol. 130 (2): 7581. doi:10.1016/S0166-6851(03)00161-0. PMID12946843. . [26] Bravo IG, Barrallo S, Ferrero MA, Rodrguez-Aparicio LB, Martnez-Blanco H, Reglero A (September 2001). "Kinetic properties of the acylneuraminate cytidylyltransferase from Pasteurella haemolytica A2" (http:/ / www. biochemj. org/ bj/ 358/ 0585/ bj3580585. htm). Biochem. J. 358 (Pt 3): 58598. PMC1222114. PMID11577688. . [27] Kraut J (1977). "Serine proteases: structure and mechanism of catalysis" (http:/ / arjournals. annualreviews. org/ doi/ abs/ 10. 1146/ annurev. bi. 46. 070177. 001555?url_ver=Z39. 88-2003& rfr_id=ori:rid:crossref. org& rfr_dat=cr_pub=ncbi. nlm. nih. gov). Annu. Rev. Biochem. 46: 33158. doi:10.1146/annurev.bi.46.070177.001555. PMID332063. . [28] Ricard J, Cornish-Bowden A (July 1987). "Co-operative and allosteric enzymes: 20 years on". Eur. J. Biochem. 166 (2): 25572. doi:10.1111/j.1432-1033.1987.tb13510.x. PMID3301336. [29] Ward WH, Fersht AR (July 1988). "Tyrosyl-tRNA synthetase acts as an asymmetric dimer in charging tRNA. A rationale for half-of-the-sites activity". Biochemistry 27 (15): 552530. doi:10.1021/bi00415a021. PMID3179266. [30] Helmstaedt K, Krappmann S, Braus GH (September 2001). "Allosteric Regulation of Catalytic Activity: Escherichia coli Aspartate Transcarbamoylase versus Yeast Chorismate Mutase" (http:/ / mmbr. asm. org/ cgi/ content/ full/ 65/ 3/ 404). Microbiol. Mol. Biol. Rev. 65 (3): 40421, table of contents. doi:10.1128/MMBR.65.3.404-421.2001. PMC99034. PMID11528003. .
160
Enzyme kinetics
[31] Schirmer T, Evans PR (January 1990). "Structural basis of the allosteric behaviour of phosphofructokinase". Nature 343 (6254): 1405. doi:10.1038/343140a0. PMID2136935. [32] Hill, A. V. The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves. J. Physiol. (Lond.), 1910 40, iv-vii. [33] Hartley BS, Kilby BA (February 1954). "The reaction of p-nitrophenyl esters with chymotrypsin and insulin". Biochem. J. 56 (2): 28897. PMC1269615. PMID13140189. [34] Fersht, Alan (1999). Structure and mechanism in protein science: a guide to enzyme catalysis and protein folding. San Francisco: W.H. Freeman. ISBN0-7167-3268-8. [35] Bender ML, Begu-Cantn ML, Blakeley RL, et al. (December 1966). "The determination of the concentration of hydrolytic enzyme solutions: alpha-chymotrypsin, trypsin, papain, elastase, subtilisin, and acetylcholinesterase". J. Am. Chem. Soc. 88 (24): 5890913. doi:10.1021/ja00976a034. PMID5980876. [36] Cleland WW (January 2005). "The use of isotope effects to determine enzyme mechanisms" (http:/ / www. sciencedirect. com/ science?_ob=ArticleURL& _udi=B6WB5-4DD8DXJ-8& _coverDate=01/ 01/ 2005& _alid=466049795& _rdoc=1& _fmt=& _orig=search& _qd=1& _cdi=6701& _sort=d& view=c& _acct=C000050221& _version=1& _urlVersion=0& _userid=10& md5=cf322c4a1c7db6b9f89551a8469a1a2d). Arch. Biochem. Biophys. 433 (1): 212. doi:10.1016/j.abb.2004.08.027. PMID15581561. . [37] Northrop D (1981). "The expression of isotope effects on enzyme-catalyzed reactions". Annu. Rev. Biochem. 50: 10331. doi:10.1146/annurev.bi.50.070181.000535. PMID7023356. [38] Baillie T, Rettenmeier A (1986). "Drug biotransformation: mechanistic studies with stable isotopes". Journal of clinical pharmacology 26 (6): 44851. PMID3734135. [39] Cleland WW (1982). "Use of isotope effects to elucidate enzyme mechanisms". CRC Crit. Rev. Biochem. 13 (4): 385428. doi:10.3109/10409238209108715. PMID6759038. [40] Christianson DW, Cox JD (1999). "Catalysis by metal-activated hydroxide in zinc and manganese metalloenzymes". Annu. Rev. Biochem. 68: 3357. doi:10.1146/annurev.biochem.68.1.33. PMID10872443. [41] Kraut D, Carroll K, Herschlag D (2003). "Challenges in enzyme mechanism and energetics". Annu. Rev. Biochem. 72: 51771. doi:10.1146/annurev.biochem.72.121801.161617. PMID12704087. [42] Waldrop GL (January 2009). "A qualitative approach to enzyme inhibition". Biochemistry and Molecular Biology Education 37 (1): 1115. doi:10.1002/bmb.20243. PMID21567682. [43] Leatherbarrow RJ (December 1990). "Using linear and non-linear regression to fit biochemical data". Trends Biochem. Sci. 15 (12): 4558. doi:10.1016/0968-0004(90)90295-M. PMID2077683. [44] Walsh R, Martin E, Darvesh S. A versatile equation to describe reversible enzyme inhibition and activation kinetics: modeling beta-galactosidase and butyrylcholinesterase. Biochim Biophys Acta. 2007 1770:733-46. [45] Koshland DE (February 1958). "Application of a Theory of Enzyme Specificity to Protein Synthesis". Proc. Natl. Acad. Sci. U.S.A. 44 (2): 98104. doi:10.1073/pnas.44.2.98. PMC335371. PMID16590179. [46] Hammes G (2002). "Multiple conformational changes in enzyme catalysis". Biochemistry 41 (26): 82218. doi:10.1021/bi0260839. PMID12081470. [47] Sutcliffe M, Scrutton N (2002). "A new conceptual framework for enzyme catalysis. Hydrogen tunnelling coupled to enzyme dynamics in flavoprotein and quinoprotein enzymes" (http:/ / content. febsjournal. org/ cgi/ content/ full/ 269/ 13/ 3096). Eur. J. Biochem. 269 (13): 3096102. doi:10.1046/j.1432-1033.2002.03020.x. PMID12084049. . [48] http:/ / cti. itc. virginia. edu/ ~cmg/ Demo/ scriptFrame. html [49] http:/ / chem-faculty. ucsd. edu/ kraut/ dhfr. html [50] http:/ / chem-faculty. ucsd. edu/ kraut/ dNTP. html [51] http:/ / courses. cm. utexas. edu/ jrobertus/ ch339k/ overheads-2/ 06_21_chymotrypsin. html
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Further reading
Introductory Cornish-Bowden, Athel (2004). Fundamentals of enzyme kinetics (3rd ed.). London: Portland Press. ISBN1-85578-158-1. Stevens, Lewis; Price, Nicholas C. (1999). Fundamentals of enzymology: the cell and molecular biology of catalytic proteins. Oxford [Oxfordshire]: Oxford University Press. ISBN0-19-850229-X. Bugg, Tim (2004). Introduction to Enzyme and Coenzyme Chemistry. Cambridge, MA: Blackwell Publishers. ISBN1-4051-1452-5. Advanced Segel, Irwin H. (1993). Enzyme kinetics: behavior and analysis of rapid equilibrium and steady state enzyme systems (New ed.). New York: Wiley. ISBN0-471-30309-7.
Enzyme kinetics Fersht, Alan (1999). Structure and mechanism in protein science: a guide to enzyme catalysis and protein folding. San Francisco: W.H. Freeman. ISBN0-7167-3268-8. Santiago Schnell, Philip K. Maini (2004). "A century of enzyme kinetics: Reliability of the KM and vmax estimates" (http://www.informatics.indiana.edu/schnell/papers/ctb8_169.pdf). Comments on Theoretical Biology 8 (23): 16987. doi:10.1080/08948550302453. Walsh, Christopher (1979). Enzymatic reaction mechanisms. San Francisco: W. H. Freeman. ISBN0-7167-0070-0. Cleland, William Wallace; Cook, Paul (2007). Enzyme kinetics and mechanism. New York: Garland Science. ISBN0-8153-4140-7.
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External links
Animation of an enzyme assay (http://www.kscience.co.uk/animations/model.swf) Shows effects of manipulating assay conditions MACiE (http://www.ebi.ac.uk/thornton-srv/databases/MACiE/) A database of enzyme reaction mechanisms ENZYME (http://us.expasy.org/enzyme/) Expasy enzyme nomenclature database ENZO (http://enzo.cmm.ki.si) Web application for easy construction and quick testing of kinetic models of enzyme catalyzed reactions. ExCatDB (http://mbs.cbrc.jp/EzCatDB/) A database of enzyme catalytic mechanisms BRENDA (http://www.brenda-enzymes.info/) Comprehensive enzyme database, giving substrates, inhibitors and reaction diagrams SABIO-RK (http://sabio.villa-bosch.de/SABIORK/) A database of reaction kinetics Joseph Kraut's Research Group, University of California San Diego (http://chem-faculty.ucsd.edu/kraut/dhfr. html) Animations of several enzyme reaction mechanisms Symbolism and Terminology in Enzyme Kinetics (http://www.chem.qmul.ac.uk/iubmb/kinetics/) A comprehensive explanation of concepts and terminology in enzyme kinetics An introduction to enzyme kinetics (http://orion1.paisley.ac.uk/kinetics/contents.html) An accessible set of on-line tutorials on enzyme kinetics Enzyme kinetics animated tutorial (http://www.wiley.com/college/pratt/0471393878/student/animations/ enzyme_kinetics/index.html) An animated tutorial with audio
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Categories of lipids
Lipid
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Fatty acyls
Fatty acyls, a generic term for describing fatty acids, their conjugates, and derivatives, are a diverse group of molecules synthesized by chain-elongation of an acetyl-CoA primer with malonyl-CoA or methylmalonyl-CoA groups in a process called fatty acid synthesis.[6] [7] They are made of a hydrocarbon chain that terminates with a carboxylic acid group; this arrangement confers the molecule with a polar, hydrophilic end, and a nonpolar, hydrophobic end that is insoluble in water. The fatty acid structure is one of the most fundamental categories of biological lipids, and is commonly used as a building-block of more structurally complex lipids. The carbon chain, typically between four and 24 carbons long,[8] may be saturated or unsaturated, and may be attached to functional groups containing oxygen, halogens, nitrogen, and sulfur. Where a double bond exists, there is the possibility of either a cis or a trans geometric isomerism, which significantly affects the molecule's molecular configuration. Cis-double bonds cause the fatty acid chain to bend, an effect that is more pronounced the more double bonds there are in a chain. This in turn plays an important role in the structure and function of cell membranes.[9] Most naturally occurring fatty acids are of the cis configuration, although the trans form does exist in some natural and partially hydrogenated fats and oils.[10] Examples of biologically important fatty acids are the eicosanoids, derived primarily from arachidonic acid and eicosapentaenoic acid, which include prostaglandins, leukotrienes, and thromboxanes. Other major lipid classes in the fatty acid category are the fatty esters and fatty amides. Fatty esters include important biochemical intermediates such as wax esters, fatty acid thioester coenzyme A derivatives, fatty acid thioester ACP derivatives and fatty acid carnitines. The fatty amides include N-acyl ethanolamines, such as the cannabinoid neurotransmitter anandamide.[11]
Glycerolipids
Glycerolipids are composed mainly of mono-, di-, and tri-substituted glycerols,[12] the most well-known being the fatty acid triesters of glycerol (triacylglycerols), also known as triglycerides. In these compounds, the three hydroxyl groups of glycerol are each esterified, usually by different fatty acids. Because they function as a food store, these lipids comprise the bulk of storage fat in animal tissues. The hydrolysis of the ester bonds of triacylglycerols and the release of glycerol and fatty acids from adipose tissue is called fat mobilization.[13] Additional subclasses of glycerolipids are represented by glycosylglycerols, which are characterized by the presence of one or more sugar residues attached to glycerol via a glycosidic linkage. Examples of structures in this category are the digalactosyldiacylglycerols found in plant membranes[14] and seminolipid from mammalian sperm cells.[15]
Glycerophospholipids
Glycerophospholipids, also referred to as phospholipids, are ubiquitous in nature and are key components of the lipid bilayer of cells, as well as being involved in metabolism and cell signaling. Neural tissue (including the brain) contains relatively high amounts of glycerophospholipids, and alterations in their composition has been implicated in various neurological disorders.[16] Glycerophospholipids may be subdivided into distinct classes, based on the nature of the polar headgroup at the sn-3 position of the glycerol backbone in eukaryotes and eubacteria, or the sn-1 position in the case of archaebacteria.[17] Examples of glycerophospholipids found in biological membranes are phosphatidylcholine (also known as PC, GPCho or lecithin), phosphatidylethanolamine (PE or GPEtn) and phosphatidylserine (PS or GPSer). In addition to serving as a primary component of cellular membranes and binding sites for intra- and intercellular proteins, some glycerophospholipids in eukaryotic cells, such as phosphatidylinositols and phosphatidic acids are either precursors of or, themselves,
Phosphatidylethanolamine
Lipid membrane-derived second messengers.[18] Typically, one or both of these hydroxyl groups are acylated with long-chain fatty acids, but there are also alkyl-linked and 1Z-alkenyl-linked (plasmalogen) glycerophospholipids, as well as dialkylether variants in archaebacteria.[19]
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Sphingolipids
Sphingolipids are a complex family of compounds[20] that share a common structural feature, a sphingoid base backbone that is synthesized de novo from the amino acid serine and a long-chain fatty acyl CoA, then converted into ceramides, phosphosphingolipids, glycosphingolipids and other compounds. The major sphingoid base of mammals is commonly referred to as sphingosine. Ceramides (N-acyl-sphingoid bases) are a major subclass of sphingoid base derivatives with an amide-linked fatty acid. The fatty acids are typically saturated or mono-unsaturated with chain lengths from 16 to 26 carbon atoms.[21] The major phosphosphingolipids of mammals are sphingomyelins (ceramide phosphocholines),[22] whereas insects contain mainly ceramide phosphoethanolamines[23] and fungi have phytoceramide phosphoinositols and mannose-containing headgroups.[24] The Sphingomyelin glycosphingolipids are a diverse family of molecules composed of one or more sugar residues linked via a glycosidic bond to the sphingoid base. Examples of these are the simple and complex glycosphingolipids such as cerebrosides and gangliosides.
Sterol lipids
Sterol lipids, such as cholesterol and its derivatives, are an important component of membrane lipids,[25] along with the glycerophospholipids and sphingomyelins. The steroids, all derived from the same fused four-ring core structure, have different biological roles as hormones and signaling molecules. The eighteen-carbon (C18) steroids include the estrogen family whereas the C19 steroids comprise the androgens such as testosterone and androsterone. The C21 subclass includes the progestogens as well as the glucocorticoids and mineralocorticoids.[26] The secosteroids, comprising various forms of vitamin D, are characterized by cleavage of the B ring of the core structure.[27] Other examples of sterols are the bile acids and their conjugates,[28] which in mammals are oxidized derivatives of cholesterol and are synthesized in the liver. The plant equivalents are the phytosterols, such as -sitosterol, stigmasterol, and brassicasterol; the latter compound is also used as a biomarker for algal growth.[29] The predominant sterol in fungal cell membranes is ergosterol.[30]
Prenol lipids
Prenol lipids are synthesized from the 5 carbon precursors isopentenyl diphosphate and dimethylallyl diphosphate that are produced mainly via the mevalonic acid (MVA) pathway.[31] The simple isoprenoids (linear alcohols, diphosphates, etc.) are formed by the successive addition of C5 units, and are classified according to number of these terpene units. Structures containing greater than 40 carbons are known as polyterpenes. Carotenoids are important simple isoprenoids that function as antioxidants and as precursors of vitamin A.[32] Another biologically important class of molecules is exemplified by the quinones and hydroquinones, which contain an isoprenoid tail attached to a quinonoid core of non-isoprenoid origin.[33] Vitamin E and vitamin K, as well as the ubiquinones, are examples of this class. Prokaryotes synthesize polyprenols (called bactoprenols) in which the terminal isoprenoid unit attached to oxygen remains unsaturated, whereas in animal polyprenols (dolichols) the terminal isoprenoid is reduced.[34]
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Saccharolipids
Saccharolipids describe compounds in which fatty acids are linked directly to a sugar backbone, forming structures that are compatible with membrane bilayers. In the saccharolipids, a monosaccharide substitutes for the glycerol backbone present in glycerolipids and glycerophospholipids. The most familiar saccharolipids are the acylated glucosamine precursors of the LipidA component of the lipopolysaccharides in Gram-negative bacteria. Typical lipidA molecules are disaccharides of glucosamine, which are derivatized with as many as seven fatty-acyl chains. The minimal lipopolysaccharide required for growth in E. coli is Kdo2-Lipid A, a hexa-acylated disaccharide of glucosamine that is glycosylated with two 3-deoxy-D-manno-octulosonic acid (Kdo) residues.[35]
[35] Structure of the saccharolipid Kdo2-Lipid A. Glucosamine residues in blue, Kdo residues in red, acyl chains in black and phosphate groups in green.
Polyketides
Polyketides are synthesized by polymerization of acetyl and propionyl subunits by classic enzymes as well as iterative and multimodular enzymes that share mechanistic features with the fatty acid synthases. They comprise a large number of secondary metabolites and natural products from animal, plant, bacterial, fungal and marine sources, and have great structural diversity.[36] [37] Many polyketides are cyclic molecules whose backbones are often further modified by glycosylation, methylation, hydroxylation, oxidation, and/or other processes. Many commonly used anti-microbial, anti-parasitic, and anti-cancer agents are polyketides or polyketide derivatives, such as erythromycins, tetracyclines, avermectins, and antitumor epothilones.[38]
Biological functions
Membranes
Eukaryotic cells are compartmentalized into membrane-bound organelles that carry out different biological functions. The glycerophospholipids are the main structural component of biological membranes, such as the cellular plasma membrane and the intracellular membranes of organelles; in animal cells the plasma membrane physically separates the intracellular components from the extracellular environment. The glycerophospholipids are amphipathic molecules (containing both hydrophobic and hydrophilic regions) that contain a glycerol core linked to two fatty acid-derived "tails" by ester linkages and to one "head" group by a phosphate ester linkage. While glycerophospholipids are the major component of biological membranes, other non-glyceride lipid components such as sphingomyelin and sterols (mainly cholesterol in animal cell membranes) are also found in biological membranes.[39] In plants and algae, the galactosyldiacylglycerols,[40] and sulfoquinovosyldiacylglycerol,[14] which lack a phosphate group, are important components of membranes of chloroplasts and related organelles and are the most abundant lipids in photosynthetic tissues, including those of higher plants, algae and certain bacteria.
Lipid Bilayers have been found to exhibit high levels of birefringence, which can be used to probe the degree of order (or disruption) within the bilayer using techniques such as dual polarization interferometry A biological membrane is a form of lipid bilayer. The formation of lipid bilayers is an energetically preferred process when the glycerophospholipids described above are in an aqueous environment.[41] In an aqueous system, the polar heads of lipids align towards the polar, aqueous environment, while the hydrophobic tails minimize their contact with water and tend to cluster together, forming a vesicle; depending on the concentration of the lipid, this biophysical interaction may result in the formation of micelles, liposomes, or lipid bilayers. Other aggregations are also observed and form part of the polymorphism of amphiphile (lipid) behavior. Phase behavior is an area of study within biophysics and is the subject of current academic research.[42] [43] Micelles and bilayers form in the polar medium by a process known as the hydrophobic effect.[44] When dissolving a lipophilic or amphiphilic substance in a polar environment, the polar molecules (i.e., water in an aqueous solution) become more Self-organization of phospholipids: a spherical liposome, a micelle, ordered around the dissolved lipophilic substance, since and a lipid bilayer. the polar molecules cannot form hydrogen bonds to the lipophilic areas of the amphiphile. So in an aqueous environment, the water molecules form an ordered "clathrate" cage around the dissolved lipophilic molecule.[45]
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Energy storage
Triacylglycerols, stored in adipose tissue, are a major form of energy storage in animals. The adipocyte, or fat cell, is designed for continuous synthesis and breakdown of triacylglycerols, with breakdown controlled mainly by the activation of hormone-sensitive enzyme lipase.[46] The complete oxidation of fatty acids provides high caloric content, about 9kcal/g, compared with 4kcal/g for the breakdown of carbohydrates and proteins. Migratory birds that must fly long distances without eating use stored energy of triacylglycerols to fuel their flights.[47]
Signaling
In recent years, evidence has emerged showing that lipid signaling is a vital part of the cell signaling.[48] Lipid signaling may occur via activation of G protein-coupled or nuclear receptors, and members of several different lipid categories have been identified as signaling molecules and cellular messengers.[49] These include sphingosine-1-phosphate, a sphingolipid derived from ceramide that is a potent messenger molecule involved in regulating calcium mobilization,[50] cell growth, and apoptosis;[51] diacylglycerol (DAG) and the phosphatidylinositol phosphates (PIPs), involved in calcium-mediated activation of protein kinase C;[52] the prostaglandins, which are one type of fatty-acid derived eicosanoid involved in inflammation and immunity;[53] the steroid hormones such as estrogen, testosterone and cortisol, which modulate a host of functions such as reproduction, metabolism and blood pressure; and the oxysterols such as 25-hydroxy-cholesterol that are liver X receptor agonists.[54]
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Other functions
The "fat-soluble" vitamins (A, D, E and K) which are isoprene-based lipids are essential nutrients stored in the liver and fatty tissues, with a diverse range of functions. Acyl-carnitines are involved in the transport and metabolism of fatty acids in and out of mitochondria, where they undergo beta oxidation.[55] Polyprenols and their phosphorylated derivatives also play important transport roles, in this case the transport of oligosaccharides across membranes. Polyprenol phosphate sugars and polyprenol diphosphate sugars function in extra-cytoplasmic glycosylation reactions, in extracellular polysaccharide biosynthesis (for instance, peptidoglycan polymerization in bacteria), and in eukaryotic protein N-glycosylation.[56] [57] Cardiolipins are a subclass of glycerophospholipids containing four acyl chains and three glycerol groups that are particularly abundant in the inner mitochondrial membrane.[58] [59] [60] They are believed to activate enzymes involved with oxidative phosphorylation.[61] Lipids also form the basis of steroid hormones. [62]
Metabolism
The major dietary lipids for humans and other animals are animal and plant triglycerides, sterols, and membrane phospholipids. The process of lipid metabolism synthesizes and degrades the lipid stores and produces the structural and functional lipids characteristic of individual tissues.
Biosynthesis
In animals, when there is an oversupply of dietary carbohydrate, the excess carbohydrate is converted to triacylglycerol. This involves the synthesis of fatty acids from acetyl-CoA and the esterification of fatty acids in the production of triacylglycerol, a process called lipogenesis.[63] Fatty acids are made by fatty acid synthases that polymerize and then reduce acetyl-CoA units. The acyl chains in the fatty acids are extended by a cycle of reactions that add the acetyl group, reduce it to an alcohol, dehydrate it to an alkene group and then reduce it again to an alkane group. The enzymes of fatty acid biosynthesis are divided into two groups, in animals and fungi all these fatty acid synthase reactions are carried out by a single multifunctional protein,[64] while in plant plastids and bacteria separate enzymes perform each step in the pathway.[65] [66] The fatty acids may be subsequently converted to triacylglycerols that are packaged in lipoproteins and secreted from the liver. The synthesis of unsaturated fatty acids involves a desaturation reaction, whereby a double bond is introduced into the fatty acyl chain. For example, in humans, the desaturation of stearic acid by stearoyl-CoA desaturase-1 produces oleic acid. The doubly unsaturated fatty acid linoleic acid as well as the triply unsaturated -linolenic acid cannot be synthesized in mammalian tissues, and are therefore essential fatty acids and must be obtained from the diet.[67] Triacylglycerol synthesis takes place in the endoplasmic reticulum by metabolic pathways in which acyl groups in fatty acyl-CoAs are transferred to the hydroxyl groups of glycerol-3-phosphate and diacylglycerol.[68] Terpenes and isoprenoids, including the carotenoids, are made by the assembly and modification of isoprene units donated from the reactive precursors isopentenyl pyrophosphate and dimethylallyl pyrophosphate.[69] These precursors can be made in different ways. In animals and archaea, the mevalonate pathway produces these compounds from acetyl-CoA,[70] while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates.[69] [71] One important reaction that uses these activated isoprene donors is steroid biosynthesis. Here, the isoprene units are joined together to make squalene and then folded up and formed into a set of rings to make lanosterol.[72] Lanosterol can then be converted into other steroids such as cholesterol and ergosterol.[72] [73]
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Degradation
Beta oxidation is the metabolic process by which fatty acids are broken down in the mitochondria and/or in peroxisomes to generate acetyl-CoA. For the most part, fatty acids are oxidized by a mechanism that is similar to, but not identical with, a reversal of the process of fatty acid synthesis. That is, two-carbon fragments are removed sequentially from the carboxyl end of the acid after steps of dehydrogenation, hydration, and oxidation to form a beta-keto acid, which is split by thiolysis. The acetyl-CoA is then ultimately converted into ATP, CO2, and H2O using the citric acid cycle and the electron transport chain. Hence the Krebs Cycle can start at acetyl-CoA when fat is being broken down for energy if there is little or no glucose available. The energy yield of the complete oxidation of the fatty acid palmitate is 106 ATP.[74] Unsaturated and odd-chain fatty acids require additional enzymatic steps for degradation.
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References
[1] [2] [3] [4] Stryer et al., p. 328. Maitland, Jr Jones (1998). Organic Chemistry. W W Norton & Co Inc (Np). p.139. ISBN0-393-97378-6. Stryer et al., p. 330. Fahy E, Subramaniam S, Murphy R, Nishijima M, Raetz C, Shimizu T, Spener F, Van Meer G, Wakelam M and Dennis E.A (2009). "Update of the LIPID MAPS comprehensive classification system for lipids". Journal of Lipid Research 50: S9S14. doi:10.1194/jlr.R800095-JLR200. PMID19098281. [5] Michelle A, Hopkins J, McLaughlin CW, Johnson S, Warner MQ, LaHart D, Wright JD (1993). Human Biology and Health. Englewood Cliffs, New Jersey, USA: Prentice Hall. ISBN0-13-981176-1. OCLC32308337. [6] Vance JE, Vance DE (2002). Biochemistry of Lipids, Lipoproteins and Membranes. Amsterdam: Elsevier. ISBN0444511393. OCLC51001207. [7] Brown HA, ed (2007). Lipodomics and Bioactive Lipids: Mass Spectrometry Based Lipid Analysis, Volume 432 (Methods in Enzymology). Boston: Academic Press. ISBN0123738954. OCLC166624879. [8] Hunt SM, Groff JL, Gropper SAS (1995). Advanced Nutrition and Human Metabolism. Belmont, CA: West Pub. Co. p.98. ISBN0-314-04467-1. [9] Devlin, pp. 19395. [10] Hunter JE (November 2006). "Dietary trans fatty acids: review of recent human studies and food industry responses". Lipids 41 (11): 96792. doi:10.1007/s11745-006-5049-y. PMID17263298. [11] Fezza F, De Simone C, Amadio D, Maccarrone M (2008). "Fatty acid amide hydrolase: a gate-keeper of the endocannabinoid system". Subcellular Biochemistry 49: 10132. doi:10.1007/978-1-4020-8831-5_4. PMID18751909. [12] Coleman RA, Lee DP (2004). "Enzymes of triacylglycerol synthesis and their regulation". Progress in Lipid Research 43 (2): 13476. doi:10.1016/S0163-7827(03)00051-1. PMID14654091. [13] van Holde and Mathews, p. 63031. [14] Hlzl G, Drmann P (2007). "Structure and function of glycoglycerolipids in plants and bacteria" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S0163-7827(07)00015-X). Progress in Lipid Research 46 (5): 22543. doi:10.1016/j.plipres.2007.05.001. PMID17599463. . [15] Honke K, Zhang Y, Cheng X, Kotani N, Taniguchi N (2004). "Biological roles of sulfoglycolipids and pathophysiology of their deficiency" (http:/ / www. kluweronline. com/ art. pdf?issn=0282-0080& volume=21& page=59). Glycoconjugates Journal 21 (12): 5962. doi:10.1023/B:GLYC.0000043749.06556.3d. PMID15467400. . [16] Farooqui AA, Horrocks LA, Farooqui T (2000). "Glycerophospholipids in brain: their metabolism, incorporation into membranes, functions, and involvement in neurological disorders" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S0009-3084(00)00128-6). Chemistry and Physics of Lipids 106 (1): 129. doi:10.1016/S0009-3084(00)00128-6. PMID10878232. . Retrieved 2009-04-12. [17] Ivanova PT, Milne SB, Byrne MO, Xiang Y, Brown HA (2007). "Glycerophospholipid identification and quantitation by electrospray ionization mass spectrometry". Methods in Enzymology 432: 2157. doi:10.1016/S0076-6879(07)32002-8. PMID17954212. [18] van Holde and Mathews, p. 844. [19] Paltauf F (1994). "Ether lipids in biomembranes". Chemistry and Physics of Lipids 74 (2): 10139. doi:10.1016/0009-3084(94)90054-X. PMID7859340. [20] Merrill AH, Sandhoff K. (2002). "Sphingolipids: metabolism and cell signaling",in New Comprehensive Biochemistry: Biochemistry of Lipids, Lipoproteins,and Membranes, Vance, D.E. and Vance, J.E., eds. Elsevier Science, NY. Ch. 14. [21] Devlin, pp. 42122. [22] Hori T, Sugita M (1993). "Sphingolipids in lower animals". Prog. Lipid Res 32 (1): 2545. doi:10.1016/0163-7827(93)90003-F. PMID8415797. [23] Wiegandt H (1992). "Insect glycolipids". Biochimica et Biophysica Acta 1123 (2): 11726. PMID1739742. [24] Guan X, Wenk MR (2008). "Biochemistry of inositol lipids". Frontiers in Bioscience 13: 323951. doi:10.2741/2923. PMID18508430. [25] Bach D, Wachtel E (2003). "Phospholipid/cholesterol model membranes: formation of cholesterol crystallites". Biochim Biophys Acta 1610 (2): 18797. doi:10.1016/S0005-2736(03)00017-8. PMID12648773. [26] Stryer et al., p. 749. [27] Bouillon R, Verstuyf A, Mathieu C, Van Cromphaut S, Masuyama R, Dehaes P, Carmeliet G (2006). "Vitamin D resistance" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S1521-690X(06)00079-0). Best Practice & Research. Clinical Endocrinology & Metabolism 20 (4): 62745. doi:10.1016/j.beem.2006.09.008. PMID17161336. . [28] Russell DW (2003). "The enzymes, regulation, and genetics of bile acid synthesis". Annual Review of Biochemistry 72: 13774. doi:10.1146/annurev.biochem.72.121801.161712. PMID12543708. [29] Villinski JC, Hayes JM, Brassell SC, Riggert VL, Dunbar RB (2008). "Sedimentary sterols as biogeochemical indicators in the Southern Ocean". Organic Geochemistry 39 (5): 56788. doi:10.1016/j.orggeochem.2008.01.009. [30] Deacon J (2005). Fungal Biology. Cambridge, MA: Blackwell Publishers. p.342. ISBN1-4051-3066-0. [31] Kuzuyama T, Seto H (2003). "Diversity of the biosynthesis of the isoprene units". Natural Product Reports 20 (2): 17183. doi:10.1039/b109860h. PMID12735695. [32] Rao AV, Rao LG (2007). "Carotenoids and human health" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S1043-6618(07)00035-7). Pharmacological Research : the Official Journal of the Italian Pharmacological Society 55 (3): 20716. doi:10.1016/j.phrs.2007.01.012.
Lipid
PMID17349800. . [33] Brunmark A, Cadenas E (1989). "Redox and addition chemistry of quinoid compounds and its biological implications". Free Radical Biology & Medicine 7 (4): 43577. doi:10.1016/0891-5849(89)90126-3. PMID2691341. [34] Swiezewska E, Danikiewicz W (2005). "Polyisoprenoids: structure, biosynthesis and function" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S0163-7827(05)00022-6). Progress in Lipid Research 44 (4): 23558. doi:10.1016/j.plipres.2005.05.002. PMID16019076. . [35] Raetz CR, Garrett TA, Reynolds CM, Shaw WA, Moore JD, Smith DC Jr, Ribeiro AA, Murphy RC,Ulevitch RJ, Fearns C, Reichart D, Glass CK, Benner C, Subramaniam S, Harkewicz R, Bowers-Gentry RC, Buczynski MW, Cooper JA, Deems RA, Dennis EA (2006). "Kdo2-Lipid A of Escherichia coli, a defined endotoxin that activates macrophages via TLR-4". Journal of Lipid Research 47 (5): 1097111. doi:10.1194/jlr.M600027-JLR200. PMID16479018. [36] Walsh CT (2004). "Polyketide and nonribosomal peptide antibiotics: modularity and versatility". Science 303 (5665): 180510. doi:10.1126/science.1094318. PMID15031493. [37] Caffrey P, Aparicio JF, Malpartida F, Zotchev SB (2008). "Biosynthetic engineering of polyene macrolides towards generation of improved antifungal and antiparasitic agents" (http:/ / www. bentham-direct. org/ pages/ content. php?CTMC/ 2008/ 00000008/ 00000008/ 0003R. SGM). Current Topics in Medicinal Chemistry 8 (8): 63953. doi:10.2174/156802608784221479. PMID18473889. . Retrieved 2009-04-12. [38] Minto RE, Blacklock BJ (2008). "Biosynthesis and function of polyacetylenes and allied natural products" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S0163-7827(08)00015-5). Progress in Lipid Research 47 (4): 233306. doi:10.1016/j.plipres.2008.02.002. PMC2515280. PMID18387369. . Retrieved 2009-04-12. [39] Stryer et al., pp. 329331 [40] Heinz E.(1996). Plant glycolipids: structure, isolation and analysis. in Advances in Lipid Methodology - 3, pp. 211332 (ed. W.W. Christie, Oily Press, Dundee) [41] Stryer et al., pp. 33334. [42] van Meer G, Voelker DR, Feigenson GW (2008). "Membrane lipids: where they are and how they behave". Nature Reviews. Molecular Cell Biology 9 (2): 11224. doi:10.1038/nrm2330. PMC2642958. PMID18216768. [43] Feigenson GW (2006). "Phase behavior of lipid mixtures". Nature Chemical Biology 2 (11): 56063. doi:10.1038/nchembio1106-560. PMC2685072. PMID17051225. [44] Wiggins PM (1990). "Role of water in some biological processes". Microbiological Reviews 54 (4): 43249. PMC372788. PMID2087221. [45] Raschke TM, Levitt M (2005). "Nonpolar solutes enhance water structure within hydration shells while reducing interactions between them". Proceedings of the National Academy of Sciences U.S.A 102 (19): 677782. doi:10.1073/pnas.0500225102. PMC1100774. PMID15867152. [46] Brasaemle DL (December 2007). "Thematic review series: adipocyte biology. The perilipin family of structural lipid droplet proteins: stabilization of lipid droplets and control of lipolysis" (http:/ / www. jlr. org/ cgi/ content/ full/ 48/ 12/ 2547). J. Lipid Res 48 (12): 254759. doi:10.1194/jlr.R700014-JLR200. PMID17878492. . [47] Stryer et al., p. 619. [48] Wang X (2004). "Lipid signaling". Current Opinions in Plant Biology 7 (3): 32936. doi:10.1016/j.pbi.2004.03.012. PMID15134755. [49] Eyster KM (2007). "The membrane and lipids as integral participants in signal transduction". Advances in Physiology Education 31 (1): 516. doi:10.1152/advan.00088.2006. PMID17327576. [50] Hinkovska-Galcheva V, VanWay SM, Shanley TP, Kunkel RG (2008). "The role of sphingosine-1-phosphate and ceramide-1-phosphate in calcium homeostasis". Current Opinion in Investigational Drugs 9 (11): 1192205. PMID18951299. [51] Saddoughi SA, Song P, Ogretmen B (2008). "Roles of bioactive sphingolipids in cancer biology and therapeutics". Subcellular Biochemistry 49: 41340. doi:10.1007/978-1-4020-8831-5_16. PMC2636716. PMID18751921. [52] Klein C, Malviya AN (2008). "Mechanism of nuclear calcium signaling by inositol 1,4,5-trisphosphate produced in the nucleus, nuclear located protein kinase C and cyclic AMP-dependent protein kinase" (http:/ / www. bioscience. org/ 2008/ v13/ af/ 2756/ fulltext. htm). Frontiers in Bioscience 13: 120626. doi:10.2741/2756. PMID17981624. . [53] Boyce JA (2008). "Eicosanoids in asthma, allergic inflammation, and host defense" (http:/ / www. bentham-direct. org/ pages/ content. php?CMM/ 2008/ 00000008/ 00000005/ 0003M. SGM). Current Molecular Medicine 8 (5): 33549. doi:10.2174/156652408785160989. PMID18691060. . [54] Betowski J (2008). "Liver X receptors (LXR) as therapeutic targets in dyslipidemia". Cardiovascular Therapy 26 (4): 297316. doi:10.1111/j.1755-5922.2008.00062.x. PMID19035881. [55] Indiveri C, Tonazzi A, Palmieri F (October 1991). "Characterization of the unidirectional transport of carnitine catalyzed by the reconstituted carnitine carrier from rat liver mitochondria". Biochim. Biophys. Acta 1069 (1): 1106. doi:10.1016/0005-2736(91)90110-T. PMID1932043. [56] Parodi AJ, Leloir LF (April 1979). "The role of lipid intermediates in the glycosylation of proteins in the eucaryotic cell". Biochim. Biophys. Acta 559 (1): 137. doi:10.1016/0304-4157(79)90006-6. PMID375981. [57] Helenius A, Aebi M (2001). "Intracellular functions of N-linked glycans". Science 291 (5512): 236469. doi:10.1126/science.291.5512.2364. PMID11269317. [58] M. Nowicki and M. Frentzen (2005). "Cardiolipin synthase of Arabidopsis thaliana". FEBS Letters 579 (10): 21612165. doi:10.1016/j.febslet.2005.03.007. PMID15811335. [59] M. Nowicki (2006). "Characterization of the Cardiolipin Synthase from Arabidopsis thaliana" (http:/ / darwin. bth. rwth-aachen. de/ opus/ volltexte/ 2006/ 1629/ ). Ph.D. thesis, RWTH-Aachen University. .
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[60] Gohil VM, Greenberg ML (2009). "Mitochondrial membrane biogenesis: phospholipids and proteins go hand in hand" (http:/ / jcb. rupress. org/ cgi/ content/ full/ 184/ 4/ 469). Journal of Cell Biology 184 (4): 46972. doi:10.1083/jcb.200901127. PMC2654137. PMID19237595. . [61] Hoch FL (1992). "Cardiolipins and biomembrane function". Biochimica et Biophysica Acta 1113 (1): 71133. PMID10206472. [62] http:/ / www. elmhurst. edu/ ~chm/ vchembook/ 556steroids. html [63] Stryer et al., p. 634. [64] Chirala S, Wakil S (2004). "Structure and function of animal fatty acid synthase". Lipids 39 (11): 104553. doi:10.1007/s11745-004-1329-9. PMID15726818. [65] White S, Zheng J, Zhang Y (2005). "The structural biology of type II fatty acid biosynthesis". Annual Review of Biochemistry 74: 791831. doi:10.1146/annurev.biochem.74.082803.133524. PMID15952903. [66] Ohlrogge J, Jaworski J (1997). "Regulation of fatty acid synthesis". Annual Review of Plant Physiology and Plant Molecular Biology 48: 109136. doi:10.1146/annurev.arplant.48.1.109. PMID15012259. [67] Stryer et al., p. 643. [68] Stryer et al., pp. 73339. [69] Kuzuyama T, Seto H (2003). "Diversity of the biosynthesis of the isoprene units". Natural Product Reports 20 (2): 17183. doi:10.1039/b109860h. PMID12735695. [70] Grochowski L, Xu H, White R (2006). "Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate". Journal of Bacteriology 188 (9): 319298. doi:10.1128/JB.188.9.3192-3198.2006. PMC1447442. PMID16621811. [71] Lichtenthaler H (1999). "The 1-Dideoxy-D-xylulose-5-phosphate pathway of isoprenoid biosynthesis in plants". Annual Review of Plant Physiology and Plant Molecular Biology 50: 4765. doi:10.1146/annurev.arplant.50.1.47. PMID15012203. [72] Schroepfer G (1981). "Sterol biosynthesis". Annual Review of Biochemistry 50: 585621. doi:10.1146/annurev.bi.50.070181.003101. PMID7023367. [73] Lees N, Skaggs B, Kirsch D, Bard M (1995). "Cloning of the late genes in the ergosterol biosynthetic pathway of Saccharomyces cerevisiaea review". Lipids 30 (3): 22126. doi:10.1007/BF02537824. PMID7791529. [74] Stryer et al., pp. 62526. [75] Bhagavan, p. 903. [76] Russo GL (2009). "Dietary n-6 and n-3 polyunsaturated fatty acids: from biochemistry to clinical implications in cardiovascular prevention" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S0006-2952(08)00777-6). Biochemical Pharmacology 77 (6): 93746. doi:10.1016/j.bcp.2008.10.020. PMID19022225. . [77] Bhagavan, p. 388. [78] Riediger ND, Othman RA, Suh M, Moghadasian MH (2009). "A systemic review of the roles of n-3 fatty acids in health and disease". Journal of the American Dietetic Association 109 (4): 66879. doi:10.1016/j.jada.2008.12.022. PMID19328262. [79] Galli C, Ris P (2009). "Fish consumption, omega 3 fatty acids and cardiovascular disease. The science and the clinical trials". Nutrition and Health (Berkhamsted, Hertfordshire) 20 (1): 1120. PMID19326716. [80] Micha R, Mozaffarian D (2008). "Trans fatty acids: effects on cardiometabolic health and implications for policy". Prostaglandins, Leukotrienes, and Essential Fatty Acids 79 (35): 14752. doi:10.1016/j.plefa.2008.09.008. PMC2639783. PMID18996687. [81] Dalainas I, Ioannou HP (2008). "The role of trans fatty acids in atherosclerosis, cardiovascular disease and infant development". International Angiology: a Journal of the International Union of Angiology 27 (2): 14656. PMID18427401. [82] Mozaffarian D, Willett WC (2007). "Trans fatty acids and cardiovascular risk: a unique cardiometabolic imprint?". Current Atherosclerosis Reports 9 (6): 48693. doi:10.1007/s11883-007-0065-9. PMID18377789. [83] Astrup A, Dyerberg J, Selleck M, Stender S (2008). "Nutrition transition and its relationship to the development of obesity and related chronic diseases". Obesity Review 9 Suppl 1: 4852. doi:10.1111/j.1467-789X.2007.00438.x. PMID18307699. [84] Astrup A (2005). "The role of dietary fat in obesity". Seminars in Vascular Medicine 5 (1): 4047. doi:10.1055/s-2005-871740. PMID15968579. [85] Ma Y. et al (2006). "Low-carbohydrate and high-fat intake among adult patients with poorly controlled type 2 diabetes mellitus". Nutrition 22 (11-12): 11291136. doi:10.1016/j.nut.2006.08.006. PMC2039705. PMID17027229. [86] Astrup A (2008). "Dietary management of obesity". JPEN Journal of Parenteral and Enteral Nutrition 32 (5): 57577. doi:10.1177/0148607108321707. PMID18753397. [87] Beresford SA, Johnson KC, Ritenbaugh C, et al. (2006). "Low-fat dietary pattern and risk of colorectal cancer: the Women's Health Initiative Randomized Controlled Dietary Modification Trial". JAMA: the Journal of the American Medical Association 295 (6): 64354. doi:10.1001/jama.295.6.643. PMID16467233. [88] Howard BV, Manson JE, Stefanick ML, et al. (2006). "Low-fat dietary pattern and weight change over 7 years: the Women's Health Initiative Dietary Modification Trial" (http:/ / jama. ama-assn. org/ cgi/ pmidlookup?view=long& pmid=16391215). JAMA: the Journal of the American Medical Association 295 (1): 3949. doi:10.1001/jama.295.1.39. PMID16391215. . [89] Howard BV, Van Horn L, Hsia J, et al. (2006). "Low-fat dietary pattern and risk of cardiovascular disease: the Women's Health Initiative Randomized Controlled Dietary Modification Trial". JAMA : the Journal of the American Medical Association 295 (6): 65566. doi:10.1001/jama.295.6.655. PMID16467234. [90] "Fats and Cholesterol: Out with the Bad, In with the Good - What Should You Eat? - The Nutrition Source - Harvard School of Public Health" (http:/ / www. hsph. harvard. edu/ nutritionsource/ what-should-you-eat/ fats-full-story/ index. html). . Retrieved 2009-05-12.
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Bibliography
Bhagavan NV (2002). Medical Biochemistry (http://books.google.com/?id=vT9YttFTPi0C& printsec=frontcover). San Diego: Harcourt/Academic Press. ISBN0-12-095440-0. Devlin TM (1997). Textbook of Biochemistry: With Clinical Correlations (4th ed.). Chichester: John Wiley & Sons. ISBN0-471-17053-4. Stryer L, Berg JM, Tymoczko JL (2007). Biochemistry (6th ed.). San Francisco: W.H. Freeman. ISBN0-7167-8724-5. Van Holde KE, Mathews CK (1996). Biochemistry (2nd ed.). Menlo Park, Calif: Benjamin/Cummings Pub. Co. ISBN0-8053-3931-0.
External links
Introductory List of lipid-related web sites (http://www.cyberlipid.org/cyberlip/link0041.htm) Nature Lipidomics Gateway (http://www.lipidmaps.org/) - Round-up and summaries of recent lipid research Lipid Library (http://www.lipidlibrary.co.uk/) - General reference on lipid chemistry and biochemistry Cyberlipid.org (http://www.cyberlipid.org/) - Resources and history for lipids.
Molecular Computer Simulations (http://www.fos.su.se/~sasha/Lipid_membranes.html) - Modeling of Lipid Membranes Lipids, Membranes and Vesicle Trafficking (http://www.biochemweb.org/lipids_membranes.shtml) - The Virtual Library of Biochemistry and Cell Biology Nomenclature IUPAC nomenclature of lipids (http://www.chem.qmul.ac.uk/iupac/lipid/) IUPAC glossary entry for the lipid class of molecules (http://www.chem.qmul.ac.uk/iupac/class/lipid.html) Databases LIPID MAPS (http://www.lipidmaps.org/data/databases.html) - Comprehensive lipid and lipid-associated gene/protein databases. LipidBank (http://lipidbank.jp/) - Japanese database of lipids and related properties, spectral data and references. LIPIDAT (http://www.lipidat.tcd.ie/) - Database composed mainly of phospholipids and associated thermodynamic data. General ApolloLipids (http://www.apollolipids.org/) - Provides dyslipidemia and cardiovascular disease prevention and treatment information as well as continuing medical education programs National Lipid Association (http://www.lipid.org/) - Professional medical education organization for health care professionals who seek to prevent morbidity and mortality stemming from dyslipidemias and other cholesterol-related disorders.
Biological membrane
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Biological membrane
A biological membrane or biomembrane is an enclosing or separating membrane that acts as a selective barrier, within or around a cell. It consists of a lipid bilayer with embedded proteins that may constitute close to 50% of membrane content.[1] The cellular membranes should not be confused with isolating tissues formed by layers of cells, such as mucous and basement membranes.
Function
Membranes in cells typically define enclosed spaces or compartments in which cells may maintain a chemical or biochemical environment that differs from the outside. For example, the membrane around peroxisomes shields the rest of the cell from peroxides, and the cell membrane separates a cell from its surrounding medium. Most organelles are defined by such membranes, and are called "membrane-bound" organelles.
Cross section view of the structures that can be formed by phospholipids in aqueous solutions
Probably the most important feature of a biomembrane is that it is a selectively permeable structure. This means that the size, charge, and other chemical properties of the atoms and molecules attempting to cross it will determine whether they succeed in doing so. Selective permeability is essential for effective separation of a cell or organelle from its surroundings. Biological membranes also have certain mechanical or elastic properties. Particles that are required for cellular function but are unable to diffuse freely across a membrane enter through a membrane transport protein or are taken in by means of endocytosis.
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References
[1] Mark L. Latash (2007). Neurophysiological basis of movement. Human Kinetics Publishers. ISBN978-0-7360-6367-8.
von Heijne G, Rees D (August 2008). "Membranes: reading between the lines" (http://linkinghub.elsevier.com/ retrieve/pii/S0959-440X(08)00091-2). Curr. Opin. Struct. Biol. 18 (4): 4035. doi:10.1016/j.sbi.2008.06.003. PMID18634876.
External links
MeSH Membranes (http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=&term=Membranes)
Membrane protein
A membrane protein is a protein molecule that is attached to, or associated with the membrane of a cell or an organelle. More than half of all proteins interact with membranes.
Function
Biological membranes consist of a phospholipid bilayer and a variety of proteins that accomplish vital biological functions. Structural proteins are attached to microfilaments in the cytoskeleton which ensures stability of the cell. Cell adhesion molecules allow cells to identify each other and interact. Such proteins are involved in immune response, for example. Membrane enzymes produce a variety of substances essential for cell function. Membrane receptor proteins serve as connection between the cell's internal and external environments. Transport proteins play an important role in the maintenance of concentrations of ions. These transport proteins come in two forms: carrier proteins and channel proteins.
Crystal structure of Potassium channel KvAP. Calculated hydrocarbon boundaries of the lipid bilayer are indicated by red and blue dots.
[ [membrane cells]] are the is a biological membrane that separates the interior of all cells from the outside environment
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Main categories
Membrane proteins can be divided into several categories:[1] Integral membrane proteins which are permanently bound to the lipid bilayer Peripheral membrane proteins that are temporarily associated with lipid bilayer or with integral membrane proteins Lipid-anchored proteins bound to lipid bilayer bound through lipidated amino acid residues In addition, pore-forming toxins and many antibacterial peptides are water-soluble molecules, but undergo a conformational transition upon association with lipid bilayer and become reversibly or irreversibly membrane-associated. A slightly different classification is to divide all membrane proteins to integral and amphitropic.[2] The amphitropic are proteins that can exist in two alternative states: a water-soluble and a lipid bilayer-bound. The amphitropic protein category includes water-soluble channel-forming polypeptide toxins, which associate irreversibly with membranes, but excludes peripheral proteins that interact with other membrane proteins rather than with lipid bilayer.
Peripheral membrane proteins are temporarily attached either to the lipid bilayer or to integral proteins by a combination of hydrophobic, electrostatic, and other non-covalent interactions. Peripheral proteins dissociate following treatment with a polar reagent, such as a solution with an elevated pH or high salt concentrations. Integral and peripheral proteins may be post-translationally modified, with added fatty acid or prenyl chains, or GPI (glycosylphosphatidylinositol), which may be anchored in the lipid bilayer.
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Polypeptide toxins
Polypeptide toxins, such as colicins or hemolysins, and certain proteins involved in apoptosis, are sometimes considered a separate category. These proteins are water-soluble but can aggregate and associate irreversibly with the lipid bilayer and form alpha-helical or beta-barrel transmembrane channels.
Intracellular localization
Proteins are specifically targeted to many different types of biological membranes [4]
Membrane protein protruding out of the cell membrane are usually hydrophilic amino acids.[7] The structures of membrane proteins are stabilized by weak interactions and influenced by additional interactions with the solubilizing environment. The influence of the environment on membrane protein structures is especially significant. Despite the significant functional importance of membrane proteins, the structural biology has been particularly challenging as shown by the low number of membrane protein structures determined. Integral membrane proteins are present in a heterogeneous environment that poses major obstacles for existing structural methodologies. Many of the successful membrane protein structures are characterized by X-ray crystallography and are very large structures in which the interactions with the membrane mimetic environments can be anticipated to be small in comparison to those within the protein structures. The small domains are particularly sensitive to the influence of membrane mimetic environments, potentially leading to non-native structures. Fortunately, there are many sample preparation conditions that can be chosen for crystallization and for solution NMR. All membrane protein structural biology should be subjected to careful scrutiny; through a combination of structural methodologies it should be possible to achieve an understanding of the native functional state for membrane protein structures.[8]
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References
White, Stephen. General Principle of Membrane Protein Folding and Stability. Stephen White Laboratory Homepage. 10 Nov. 2009. web.
[1] Gerald Karp (2009). Cell and Molecular Biology: Concepts and Experiments (http:/ / books. google. com/ books?id=arRGYE0GxRQC& pg=PA128). John Wiley and Sons. pp.128. ISBN9780470483374. . Retrieved 13 November 2010. [2] Johnson JE, Cornell RB (1999). "Amphitropic proteins: regulation by reversible membrane interactions (review)". Mol. Membr. Biol. 16 (3): 217235. doi:10.1080/096876899294544. PMID10503244. [3] Lodish H, Berk A, Zipursky SL, et al. Molecular Cell Biology. 4th edition. New York: W. H. Freeman; 2000. [4] Classification of membrane proteins with known 3D structure to different membrane types (http:/ / opm. phar. umich. edu/ atlas. php) [5] Daley, Daniel. 2008,"The Assembly of Membrane Proteins into Complexes", Current Opinion in Structural Biology, 18:420-424. [6] White, Stephen. General Principle of Membrane Protein Folding and Stability. Stephen White Laboratory Homepage. 10 Nov. 2009. web. [7] White, Stephen. General Principle of Membrane Protein Folding and Stability. Stephen White Laboratory Homepage. 10 Nov. 2009. web. [8] Cross, Timothy, Mukesh Sharma, Myunggi Yi, Huan-Xiang Zhou (2010). "Influence of Solubilizing Environments on Membrane Protein Structures"
External links
TCDB (http://www.tcdb.org/) - Transporter Classification database Orientations of Proteins in Membranes (OPM) database (http://opm.phar.umich.edu/) 3D structures of integral and peripheral membrane proteins arranged in the lipid bilayer The Protein Data Bank of Transmembrane Proteins (http://pdbtm.enzim.hu/) 3D models of all transmembrane proteins currently in PDB. Approximate positions of membrane boundary planes were calculated for each PDB entry. List of transmembrane proteins of known 3D structure (http://blanco.biomol.uci.edu/ Membrane_Proteins_xtal.html) TransportDB (http://www.membranetransport.org/) Genomics-oriented database of transporters from TIGR Membrane PDB (http://www.mpdb.tcd.ie/) Database of 3D structures of integral membrane proteins and hydrophobic peptides with an emphasis on crystallization conditions Membrane targeting domains (MeTaDoR) (http://proteomics.bioengr.uic.edu/metador/MeTaDoR.html) Antimicrobial Peptide Database (http://aps.unmc.edu/AP/main.php) MeSH Membrane+proteins (http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=&term=Membrane+ proteins) The Human Membrane Proteome (http://www.biomedcentral.com/1741-7007/7/50) - A comprehensive article covering the transmembrane protein component of the human proteome
Cell membrane
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Cell membrane
The cell membrane or plasma membrane is a biological membrane that separates the interior of all cells from the outside environment.[1] The cell membrane is selectively permeable to ions and organic molecules and controls the movement of substances in and out of cells.[2] It basically protects the cell from outside forces. It consists of the lipid bilayer with embedded proteins. Cell membranes are involved in a variety of cellular processes such as cell adhesion, ion conductivity and cell signaling and serve as the attachment surface for several extracellular structures, including the cell wall, glycocalyx, and intracellular cytoskeleton.
Function
The cell membrane surrounds the cytoplasm of a cell and, in animal cells, physically separates the intracellular Illustration of a Eukaryotic cell membrane components from the extracellular environment. Fungi, bacteria and plants also have the cell wall which provides a mechanical support for the cell and precludes the passage of larger molecules. The cell membrane also plays a role in anchoring the cytoskeleton to provide shape to the cell, and in attaching to the extracellular matrix and other cells to help group cells together to form tissues. The membrane is differentially permeable and able to regulate what enters and exits the cell, thus facilitating the transport of materials needed for survival. The movement of substances across the membrane can be either passive, occurring without the input of cellular energy, or active, requiring the cell to expend energy in transporting it. The membrane also maintains the cell potential. The cell membrane thus works as a selective filter that allows only certain things to come inside or go outside the cell. To do so, the membrane employs a number of transport mechanisms: 1. Diffusion : Some substances (small molecules, ions) such as carbon dioxide (CO2), oxygen (O2), and water, can move across the plasma membrane by diffusion, which is a passive transport process. 2. Osmosis : Because the membrane acts as a barrier for certain molecules and ions, they can occur in different concentrations on the two sides of the membrane. Such a concentration difference across a semipermeable membrane can set up a osmotic flow for the solvent, in this case water. Water can thus be transported across the membrane by osmosis. 3. Mediated Transport : Nutrients such as sugars and materials of growth such as amino acid must enter the cell, and the waste of metabolism must leave. Such molecules are moved across the membrane by special proteins called transport proteins or permeases. Permeases form a small passageway through the membrane, enabling the solute
Cell membrane molecule to cross the phospholipid bilayer. Permeases are usually quite specific, recognizing and transporting only a limited group of chemical substances, often even only a single substance. 4. Endocytosis : Endocytosis is the process in which cells absorb molecules by engulfing them. The plasma membrane creates a small deformation inward, called an invagination, in which the substance to be transported is captured. The deformation then pinches off from the membrane on the inside of the cell, creating a vesicle containing the captured substance. Endocytosis is a pathway for internalizing solid particles (cell eating or phagocytosis), small molecules and ions (cell drinking or pinocytosis), and macromolecules. Endocytosis requires energy and is thus a form of active transport. 5. Exocytosis : Just as material can be brought into the cell by invagination and formation of a vesicle, the membrane of a vesicle can be fused with the plasma membrane, extruding its contents to the surrounding medium. This is the process of exocytosis. Exocytosis occurs in various cells to remove undigested residues of substances brought in by endocytosis, to secrete substances such as hormones and enzymes, and to transport a substance completely across a cellular barrier. In the process of exocytosis, the undigested waste-containing food vacuole or the secretory vesicle budded from Golgi apparatus, is first moved by cytoskeleton from the interior of the cell to the surface. The vesicle membrane comes in contact with the plasma membrane. The lipid molecules of the two bilayers rearrange themselves and the two membranes are, thus, fused. A passage is formed in the fused membrane and the vesicles discharges its contents outside the cell.
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Prokaryotes
Gram-negative bacteria have a plasma membrane and an outer membrane separated by a periplasmic space. Other prokaryotic species have only a plasma membrane. Prokaryotic cells are also surrounded by a cell wall composed of peptidoglycan (amino acid and sugar). Some eukaryotic cells also have cells walls, but none that are made of peptidoglycan.
Structure
Fluid mosaic model
According to the fluid mosaic model of S.J. Singer and G.L. Nicolson (1972), biological membranes can be considered as a two-dimensional liquid in which all lipid and protein molecules diffuse more or less easily.[3] Although the lipid bilayers that form the basis of the membranes do indeed form two-dimensional liquids by themselves, the plasma membrane also contains a large quantity of proteins, which provide more structure. Examples of such structures are protein-protein complexes, pickets and fences formed by the actin-based cytoskeleton, and potentially lipid rafts.
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Lipid bilayer
Lipid bilayers go through a self assembly process in the formation of membranes. The cell membrane consists primarily of a thin layer of amphipathic phospholipids which spontaneously arrange so that the hydrophobic "tail" regions are shielded from the surrounding polar fluid, causing the more hydrophilic "head" regions to associate with the cytosolic and extracellular faces of the resulting bilayer. This forms a continuous, spherical lipid bilayer. Forces such as Van der Waal, electrostatic, hyrdogen bonds, and noncovalent interactions, are all forces that contribute to the formation of the lipid bilayer. Overall, hydrophobic interactions are the major driving force in the formation of lipid bilayers.
Diagram of the arrangement of amphipathic lipid molecules to form a lipid bilayer. The yellow polar head groups separate the grey hydrophobic tails from the aqueous cytosolic and extracellular environments.
Lipid bilayers have very low permeability for ions and most polar molecules.The arrangement of hydrophilic heads and hydrophobic tails of the lipid bilayer prevent polar solutes (e.g. amino acids, nucleic acids, carbohydrates, proteins, and ions) from diffusing across the membrane, but generally allows for the passive diffusion of hydrophobic molecules. This affords the cell the ability to control the movement of these substances via transmembrane protein complexes such as pores and gates. Flippases and scramblases concentrate phosphatidyl serine, which carries a negative charge, on the inner membrane. Along with NANA, this creates an extra barrier to charged moieties moving through the membrane. Membranes serve diverse functions in eukaryotic and prokaryotic cells. One important role is to regulate the movement of materials into and out of cells. The phospholipid bilayer structure (fluid mosaic model) with specific membrane proteins accounts for the selective permeability of the membrane and passive and active transport mechanisms. In addition, membranes in prokaryotes and in the mitochondria and chloroplasts of eukaryotes facilitate the synthesis of ATP through chemiosmosis.
Membrane polarity
The apical membrane of a polarized cell is the surface of the plasma membrane that faces the lumen. This is particularly evident in epithelial and endothelial cells, but also describes other polarized cells, such as neurons. The basolateral membrane of a polarized cell is the surface of the plasma membrane that forms its basal and lateral surfaces. It faces towards the interstitium, and away from the lumen. "Basolateral membrane" is a compound phrase referring to the terms basal (base) membrane and lateral (side) membrane, Alpha intercalated cell which, especially in epithelial cells, are identical in composition and activity. Proteins (such as ion channels and pumps) are free to move from the basal to the lateral surface of the cell or vice versa in accordance with the fluid mosaic model.
Cell membrane Tight junctions that join epithelial cells near their apical surface prevent the migration of proteins from the basolateral membrane to the apical membrane. The basal and lateral surfaces thus remain roughly equivalent to one another, yet distinct from the apical surface.
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Membrane skeleton
The cytoskeleton is found underlying the cell membrane in the cytoplasm and provides a scaffolding for membrane proteins to anchor to, as well as forming organelles that extend from the cell. Indeed, cytoskeletal elements interact extensively and intimately with the cell membrane.[4] Anchoring proteins restricts them to a particular cell surface for example, the apical surface of epithelial cells that line the vertebrate gut and limits how far they may diffuse within the bilayer. The cytoskeleton is able to form appendage-like organelles, such as cilia, which are microtubule-based extensions covered by the cell membrane, and filopodia, which are actin-based extensions. These extensions are ensheathed in membrane and project from the surface of the cell in order to sense the external environment and/or make contact with the substrate or other cells. The apical surfaces of epithelial cells are dense with actin-based finger-like projections known as microvilli, which increase cell surface area and thereby increase the absorption rate of nutrients. Localized decoupling of the cytoskeleton and cell membrane results in formation of a bleb.
Composition
Cell membranes contain a variety of biological molecules, notably lipids and proteins. Material is incorporated into the membrane, or deleted from it, by a variety of mechanisms: Fusion of intracellular vesicles with the membrane (exocytosis) not only excretes the contents of the vesicle but also incorporates the vesicle membrane's components into the cell membrane. The membrane may form blebs around extracellular material that pinch off to become vesicles (endocytosis). If a membrane is continuous with a tubular structure made of membrane material, then material from the tube can be drawn into the membrane continuously. Although the concentration of membrane components in the aqueous phase is low (stable membrane components have low solubility in water), there is an exchange of molecules between the lipid and aqueous phases.
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Lipids
The cell membrane consists of three classes of amphipathic lipids: phospholipids, glycolipids, and cholesterols. The amount of each depends upon the type of cell, but in the majority of cases phospholipids are the most abundant.[5] In RBC studies, 30% of the plasma membrane is lipid. The fatty chains in phospholipids and glycolipids usually contain an even number of carbon atoms, typically between 16 and 20. The 16- and 18-carbon fatty acids are the most common. Fatty acids may be saturated or unsaturated, with the configuration of the double bonds nearly always cis. The length and the degree of unsaturation of fatty acid chains have a profound effect on membrane fluidity[6] as unsaturated lipids create a kink, preventing the fatty Examples of the major membrane phospholipids and glycolipids: phosphatidylcholine acids from packing together as tightly, (PtdCho), phosphatidylethanolamine (PtdEtn), phosphatidylinositol (PtdIns), thus decreasing the melting temperature phosphatidylserine (PtdSer). (increasing the fluidity) of the membrane. The ability of some organisms to regulate the fluidity of their cell membranes by altering lipid composition is called homeoviscous adaptation. The entire membrane is held together via non-covalent interaction of hydrophobic tails, however the structure is quite fluid and not fixed rigidly in place. Under physiological conditions phospholipid molecules in the cell membrane are in the liquid crystalline state. It means the lipid molecules are free to diffuse and exhibit rapid lateral diffusion along the layer in which they are present. However, the exchange of phospholipid molecules between intracellular and extracellular leaflets of the bilayer is a very slow process. Lipid rafts and caveolae are examples of cholesterol-enriched microdomains in the cell membrane. In animal cells cholesterol is normally found dispersed in varying degrees throughout cell membranes, in the irregular spaces between the hydrophobic tails of the membrane lipids, where it confers a stiffening and strengthening effect on the membrane.[2]
Cell membrane liposome is formed. These provide researchers with a tool to examine various membrane protein functions.
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Carbohydrates
Plasma membranes also contain carbohydrates, predominantly glycoproteins, but with some glycolipids (cerebrosides and gangliosides). For the most part, no glycosylation occurs on membranes within the cell; rather generally glycosylation occurs on the extracellular surface of the plasma membrane. The glycocalyx is an important feature in all cells, especially epithelia with microvilli. Recent data suggest the glycocalyx participates in cell adhesion, lymphocyte homing, and many others. The penultimate sugar is galactose and the terminal sugar is sialic acid, as the sugar backbone is modified in the golgi apparatus. Sialic acid carries a negative charge, providing an external barrier to charged particles.
Proteins
Proteins within the membrane are key to the functioning of the overall membrane. These proteins mainly transport chemicals and information across the membrane. Every membrane has a varying degree of protein content. Proteins can be in the form of peripheral or integral.
Type Integral proteins or transmembrane proteins Description Span the membrane and have a hydrophilic cytosolic domain, which interacts with internal molecules, a hydrophobic membrane-spanning domain that anchors it within the cell membrane, and a hydrophilic extracellular domain that interacts with external molecules. The hydrophobic domain consists of one, multiple, or a combination of -helices and sheet protein motifs. Covalently bound to single or multiple lipid molecules; hydrophobically insert into the cell membrane and anchor the protein. The protein itself is not in contact with the membrane. Attached to integral membrane proteins, or associated with peripheral regions of the lipid bilayer. These proteins tend to have only temporary interactions with biological membranes, and, once reacted the molecule, dissociates to carry on its work in the cytoplasm. Examples Ion channels, proton pumps, G protein-coupled receptor
G proteins
The cell membrane plays host to a large amount of protein that is responsible for its various activities. The amount of protein differs between species and according to function, however the typical amount in a cell membrane is 50%.[6] These proteins are undoubtedly important to a cell: Approximately a third of the genes in yeast code specifically for them, and this number is even higher in multicellular organisms.[5] The cell membrane, being exposed to the outside environment, is an important site of cell-cell communication. As such, a large variety of protein receptors and identification proteins, such as antigens, are present on the surface of the membrane. Functions of membrane proteins can also include cell-cell contact, surface recognition, cytoskeleton contact, signaling, enzymatic activity, or transporting substances across the membrane. Most membrane proteins must be inserted in some way into the membrane. For this to occur, an N-terminus "signal sequence" of amino acids directs proteins to the endoplasmic reticulum, which inserts the proteins into a lipid bilayer. Once inserted, the proteins are then transported to their final destination in vesicles, where the vesicle fuses with the target membrane.
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Variation
The cell membrane has different lipid and protein compositions in distinct types of cells and may have therefore specific names for certain cell types: Sarcolemma in myocytes Oolemma in oocytes Historically, the plasma membrane was also referred to as the plasmalemma.
Permeability
The permeability of a membrane is the ease with which molecules pass through it. These molecules are known as permeant molecules. Permeability depends mainly on the electric charge of the molecule and to a lesser extent the molar mass of the molecule. Due to the cell membrane's hydrophobic nature, electrically neutral and small molecules pass through the membrane easier than charged, large ones. The inability of charged molecules to pass through the cell membrane results in pH parturition of substances throughout the fluid compartments of the body.
References
[1] Kimball's Biology Pages (http:/ / users. rcn. com/ jkimball. ma. ultranet/ BiologyPages/ C/ CellMembranes. html), Cell Membranes [2] Alberts B, Johnson A, Lewis J, et al. (2002). Molecular Biology of the Cell (http:/ / www. ncbi. nlm. nih. gov/ books/ bv. fcgi?rid=mboc4. section. 1864) (4th ed.). New York: Garland Science. ISBN0-8153-3218-1. . [3] Singer SJ, Nicolson GL (Feb 1972). "The fluid mosaic model of the structure of cell membranes" (http:/ / www. sciencemag. org/ cgi/ content/ abstract/ 175/ 4023/ 720). Science 175 (4023): 72031. doi:10.1126/science.175.4023.720. PMID4333397. . [4] Doherty GJ and McMahon HT (2008). "Mediation, Modulation and Consequences of Membrane-Cytoskeleton Interactions" (http:/ / arjournals. annualreviews. org/ doi/ abs/ 10. 1146/ annurev. biophys. 37. 032807. 125912). Annual Review of Biophysics 37: 6595. doi:10.1146/annurev.biophys.37.032807.125912. PMID18573073. . [5] Lodish H, Berk A, Zipursky LS, et al. (2004). Molecular Cell Biology (4th ed.). New York: Scientific American Books. ISBN0716731363. [6] Jesse Gray, Shana Groeschler, Tony Le, Zara Gonzalez (2002). "Membrane Structure" (http:/ / www. bio. davidson. edu/ people/ macampbell/ 111/ memb-swf/ membranes. swf) (SWF). Davidson College. . Retrieved 2007-01-11.
External links
Lipids, Membranes and Vesicle Trafficking - The Virtual Library of Biochemistry and Cell Biology (http:// www.biochemweb.org/lipids_membranes.shtml) Cell membrane protein extraction protocol (http://www.westernblotting.org/protocol membrane extraction. htm) Membrane homeostasis, tension regulation, mechanosensitive membrane exchange and membrane traffic (http:// www.phys.unsw.edu.au/~jw/tension.html) 3D structures of proteins associated with plasma membrane of eukaryotic cells (http://opm.phar.umich.edu/ localization.php?localization=Eukaryotic plasma membrane) Lipid composition and proteins of some eukariotic membranes (http://opm.phar.umich.edu/atlas. php?membrane=Eukaryotic plasma membrane) (http://www.etap.org/demo/biology1/instruction3tutor.html)
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Carbohydrate structure
Carbohydrate
A carbohydrate (pronounced/krbhadret/) is an organic compound with the empirical formula Cm(H2O)n (where m could be different from n); that is, consists only of carbon, hydrogen, and oxygen, with a hydrogen:oxygen atom ratio of 2:1 (as in water). However, there are exceptions to this. One common example would be Lactose is a disaccharide found in milk. It consists of a molecule of D-galactose and a deoxyribose, a component of DNA, which molecule of D-glucose bonded by beta-1-4 glycosidic linkage. It has a formula of C12H22O11. has the empirical formula C5H10O4. Carbohydrates can be viewed as hydrates of carbon, hence their name. Structurally however, it is more accurate to view them as polyhydroxy aldehydes and ketones. The term is most common in biochemistry, where it is a synonym of saccharide. The carbohydrates (saccharides) are divided into four chemical groupings: monosaccharides, disaccharides, oligosaccharides, and polysaccharides. In general, the monosaccharides and disaccharides, which are smaller (lower molecular weight) carbohydrates, are commonly referred to as sugars.[1] The word saccharide comes from the Greek word (skkharon), meaning "sugar". While the scientific nomenclature of carbohydrates is complex, the names of the monosaccharides and disaccharides very often end in the suffix -ose. For example, blood sugar is the monosaccharide glucose, table sugar is the disaccharide sucrose, and milk sugar is the disaccharide lactose (see illustration). Carbohydrates perform numerous roles in living things. Polysaccharides serve for the storage of energy (e.g., starch and glycogen), and as structural components (e.g., cellulose in plants and chitin in arthropods). The 5-carbon monosaccharide ribose is an important component of coenzymes (e.g., ATP, FAD, and NAD) and the backbone of the genetic molecule known as RNA. The related deoxyribose is a component of DNA. Saccharides and their derivatives include many other important biomolecules that play key roles in the immune system, fertilization, preventing pathogenesis, blood clotting, and development.[2] In food science and in many informal contexts, the term carbohydrate often means any food that is particularly rich in the complex carbohydrate starch (such as cereals, bread, and pasta) or simple carbohydrates, such as sugar (found in candy, jams, and desserts).
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Structure
Formerly the name "carbohydrate" was used in chemistry for any compound with the formula Cm (H2O) n. Following this definition, some chemists considered formaldehyde (CH2O) to be the simplest carbohydrate, [3] while others claimed that title for glycolaldehyde.[4] Today the term is generally understood in the biochemistry sense, which excludes compounds with only one or two carbons. Natural saccharides are generally built of simple carbohydrates called monosaccharides with general formula (CH2O)n where n is three or more. A typical monosaccharide has the structure H-(CHOH)x(C=O)-(CHOH)y-H, that is, an aldehyde or ketone with many hydroxyl groups added, usually one on each carbon atom that is not part of the aldehyde or ketone functional group. Examples of monosaccharides are glucose, fructose, and glyceraldehydes. However, some biological substances commonly called "monosaccharides" do not conform to this formula (e.g., uronic acids and deoxy-sugars such as fucose), and there are many chemicals that do conform to this formula but are not considered to be monosaccharides (e.g., formaldehyde CH2O and inositol (CH2O)6).[5] The open-chain form of a monosaccharide often coexists with a closed ring form where the aldehyde/ketone carbonyl group carbon (C=O) and hydroxyl group (-OH) react forming a hemiacetal with a new C-O-C bridge. Monosaccharides can be linked together into what are called polysaccharides (or oligosaccharides) in a large variety of ways. Many carbohydrates contain one or more modified monosaccharide units that have had one or more groups replaced or removed. For example, deoxyribose, a component of DNA, is a modified version of ribose; chitin is composed of repeating units of N-acetyl glucosamine, a nitrogen-containing form of glucose.
Monosaccharides
Monosaccharides are the simplest carbohydrates in that they cannot be hydrolyzed to smaller carbohydrates. They are aldehydes or ketones with two or more hydroxyl groups. The general chemical formula of an unmodified monosaccharide is (CH2O) n, literally a "carbon hydrate." Monosaccharides are important fuel molecules as well as building blocks for nucleic acids. The smallest monosaccharides, for which n = 3, are dihydroxyacetone and D- and L-glyceraldehydes.
Classification of monosaccharides
The and anomers of glucose. Note the position of the hydroxyl group (red or green) on the anomeric carbon relative to the CH2OH group bound to carbon 5: they are either on the opposite sides (), or the same side ().
Monosaccharides are classified according to three different characteristics: the placement of its carbonyl group, the number of carbon atoms it contains, and its chiral handedness. If the carbonyl group is an aldehyde, the monosaccharide is an aldose; if the carbonyl group is a ketone, the monosaccharide is a ketose. Monosaccharides with three carbon atoms are called trioses, those with four are called tetroses, five are called pentoses, six are hexoses, and so on.[6] These two systems of classification are often combined. For example, glucose is an aldohexose (a six-carbon aldehyde), ribose is an aldopentose (a five-carbon aldehyde), and fructose is a ketohexose (a six-carbon ketone).
D-glucose is an aldohexose with the formula (CH2O)6. The red atoms highlight the aldehyde group, and the blue atoms highlight the asymmetric center furthest from the aldehyde; because this -OH is on the right of the Fischer projection, this is a D sugar.
Carbohydrate Each carbon atom bearing a hydroxyl group (-OH), with the exception of the first and last carbons, are asymmetric, making them stereo centers with two possible configurations each (R or S). Because of this asymmetry, a number of isomers may exist for any given monosaccharide formula. The aldohexose D-glucose, for example, has the formula (CH2O) 6, of which all but two of its six carbons atoms are stereogenic, making D-glucose one of 24 = 16 possible stereoisomers. In the case of glyceraldehydes, an aldotriose, there is one pair of possible stereoisomers, which are enantiomers and epimers. 1, 3-dihydroxyacetone, the ketose corresponding to the aldose glyceraldehydes, is a symmetric molecule with no stereo centers). The assignment of D or L is made according to the orientation of the asymmetric carbon furthest from the carbonyl group: in a standard Fischer projection if the hydroxyl group is on the right the molecule is a D sugar, otherwise it is an L sugar. The "D-" and "L-" prefixes should not be confused with "d-" or "l-", which indicate the direction that the sugar rotates plane polarized light. This usage of "d-" and "l-" is no longer followed in carbohydrate chemistry.[7]
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Disaccharides
Two joined monosaccharides are called a disaccharide and these are the simplest polysaccharides. Examples include sucrose and lactose. They are composed of two monosaccharide units bound together by a covalent bond known as a glycosidic linkage formed via a dehydration reaction, resulting in the loss of a hydrogen atom from one monosaccharide and a hydroxyl group from the other. The formula of unmodified disaccharides is C12H22O11. Although there are numerous kinds of disaccharides, a handful of disaccharides are particularly notable.
Sucrose, also known as table sugar, is a common disaccharide. It is composed of two monosaccharides: D-glucose (left) and D-fructose (right).
Sucrose, pictured to the right, is the most abundant disaccharide, and the main form in which carbohydrates are transported in plants. It is composed of one D-glucose molecule and one D-fructose molecule. The systematic name for sucrose, O--D-glucopyranosyl-(12)-D-fructofuranoside, indicates four things: Its monosaccharides: glucose and fructose Their ring types: glucose is a pyranose, and fructose is a furanose How they are linked together: the oxygen on carbon number 1 (C1) of -D-glucose is linked to the C2 of D-fructose. The -oside suffix indicates that the anomeric carbon of both monosaccharides participates in the glycosidic bond. Lactose, a disaccharide composed of one D-galactose molecule and one D-glucose molecule, occurs naturally in mammalian milk. The systematic name for lactose is O--D-galactopyranosyl-(14)-D-glucopyranose. Other notable disaccharides include maltose (two D-glucoses linked -1,4) and cellulobiose (two D-glucoses linked -1,4). disaccharides can be classified into two types.They are reducing and non-reducing disaccahrides if the functional group is present in bonding with another sugar unit it is called a reducing disaccharide or biose.
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Carbohydrate
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Nutrition
Foods high in carbohydrate include fruits, sweets, soft drinks, breads, pastas, beans, potatoes, bran, rice, and cereals. Carbohydrates are a common source of energy in living organisms; however, no carbohydrate is an essential nutrient in humans.[10] Carbohydrates are not necessary building blocks of other molecules, and the body can obtain all its energy from protein and fats.[11] [12] The brain fats contain 37.8 kilojoules (9 kilocalories) per gram. In the case of protein, this is somewhat misleading as only some amino acids are usable for fuel. Organisms typically cannot metabolize all types of carbohydrate to yield energy. Glucose is a nearly universal and accessible source of calories. Many organisms also have the ability to metabolize other monosaccharides and Disaccharides, though glucose is preferred. In Escherichia coli, for example, the lac operon will express enzymes for the digestion of lactose when it is present, but if both lactose and Grain products: rich sources of carbohydrates glucose are present the lac operon is repressed, resulting in the glucose being used first (see: Diauxie). Polysaccharides are also common sources of energy. Many organisms can easily break down starches into glucose, however, most organisms cannot metabolize cellulose or other polysaccharides like chitin and arabinoxylans. These carbohydrates types can be metabolized by some bacteria and protists. Ruminants and termites, for example, use microorganisms to process cellulose. Even though these complex carbohydrates are not very digestible, they may comprise important dietary elements for humans. Called dietary fiber, these carbohydrates enhance digestion among other benefits. Based on the effects on risk of heart disease and obesity, the Institute of Medicine recommends that American and Canadian adults get between 4565% of dietary energy from carbohydrates.[13] The Food and Agriculture Organization and World Health Organization jointly recommend that national dietary guidelines set a goal of 5575% of total energy from carbohydrates, but only 10% directly from sugars (their term for simple carbohydrates).[14]
Classification
Historically nutritionists have classified carbohydrates as either simple or complex, however, the exact delineation of these categories is ambiguous. Today, simple carbohydrate typically refers to monosaccharides and disaccharides and complex carbohydrate means polysaccharides (and oligosaccharides). However, the term complex carbohydrate was first used in slightly different context in the U.S. Senate Select Committee on Nutrition and Human Needs publication Dietary Goals for the United States (1977). In this work, complex carbohydrate were defined as "fruit, vegetables and whole-grains".[15] Some nutritionists use complex carbohydrate to refer to any sort of digestible saccharide present in a whole food, where fiber, vitamins and minerals are also found (as opposed to processed carbohydrates, which provide calories but few other nutrients). Some simple carbohydrates (e.g. fructose) are digested very slowly, while some complex carbohydrates (starches), especially if processed, raise blood sugar rapidly. The speed of digestion is determined by a variety of factors including which other nutrients are consumed with the carbohydrate, how the food is prepared, individual differences in metabolism, and the chemistry of the carbohydrate. The USDA's Dietary Guidelines for Americans 2005 dispensed with the simple/complex distinction, instead recommending fiber-rich foods and whole grains.[16] The glycemic index (GI) and glycemic load concepts have been developed to characterize food behavior during human digestion. They rank carbohydrate-rich foods based on the rapidity and magnitude of their effect on blood
Carbohydrate glucose levels. Glycemic index is a measure of how quickly food glucose is absorbed, while glycemic load is a measure of the total absorbable glucose in foods. The insulin index is a similar, more recent classification method that ranks foods based on their effects on blood insulin levels, which are caused by glucose (or starch) and some amino acids in food.
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Carbohydrate chemistry
Carbohydrate chemistry is a large and economically important branch of organic chemistry. Some of the main organic reactions that involve carbohydrates are: Carbohydrate acetalisation Cyanohydrin reaction Lobry-de Bruyn-van Ekenstein transformation Amadori rearrangement Nef reaction Wohl degradation KoenigsKnorr reaction
References
[1] Flitsch, SL & Ulijn, RV (2003). "Sugars tied to the spot." Nature 421: 219220 (http:/ / www. nature. com/ nature/ journal/ v421/ n6920/ pdf/ 421219a. pdf). [2] Maton, Anthea; Jean Hopkins, Charles William McLaughlin, Susan Johnson, Maryanna Quon Warner, David LaHart, Jill D. Wright (1993). Human Biology and Health. Englewood Cliffs, New Jersey, USA: Prentice Hall. pp.5259. ISBN0-13-981176-1. [3] John Merle Coulter, Charler Reid Barnes, Henry Chandler Cowles (1930), A Textbook of Botany for Colleges and Universities (http:/ / books. google. com. br/ books?id=WyZnVpCiTHIC& pg=PA375& dq=simplest+ carbohydrate)" [4] Carl A. Burtis, Edward R. Ashwood, Norbert W. Tietz (2000), Tietz fundamentals of clinical chemistry (http:/ / books. google. com/ books?id=l5hqAAAAMAAJ& q=simplest+ carbohydrate) [5] Matthews, C. E.; K. E. Van Holde; K. G. Ahern (1999) Biochemistry. 3rd edition. Benjamin Cummings. ISBN 0-8053-3066-6 [6] Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life (http:/ / www. phschool. com/ el_marketing. html). Boston, Massachusetts: Pearson Prentice Hall. ISBN0-13-250882-6. . [7] Pigman, Ward; Horton, D. (1972). "Chapter 1: Stereochemistry of the Monosaccharides". In Pigman and Horton. The Carbohydrates: Chemistry and Biochemistry Vol 1A (2nd ed.). San Diego: Academic Press. pp.167. [8] Pigman, Ward; Anet, E.F.L.J. (1972). "Chapter 4: Mutarotations and Actions of Acids and Bases". In Pigman and Horton. The Carbohydrates: Chemistry and Biochemistry Vol 1A (2nd ed.). San Diego: Academic Press. pp.165194. [9] N.A.Campbell (1996) Biology (4th edition). Benjamin Cummings NY. p.23 ISBN 0-8053-1957-3 [10] http:/ / www. ajcn. org/ content/ 75/ 5/ 951. 2. full [11] Is dietary carbohydrate essential for human nutrition? - Westman 75 (5): 951 - American Journal of Clinical Nutrition (http:/ / www. ajcn. org/ cgi/ content/ full/ 75/ 5/ 951-a) [12] A High-Protein, High-Fat, Carbohydrate-Free Diet Reduces Energy Intake, Hepatic Lipogenesis, and Adiposity in Rats - Pichon et al. 136 (5): 1256 - Journal of Nutrition (http:/ / jn. nutrition. org/ cgi/ reprint/ 136/ 5/ 1256?ijkey=ebf0450b5cf21e8d83dd43f62b5559254694f65f) [13] Food and Nutrition Board (2002/2005). Dietary Reference Intakes for Energy, Carbohydrate, Fiber, Fat, Fatty Acids, Cholesterol, Protein, and Amino Acids (http:/ / newton. nap. edu/ books/ 0309085373/ html). Washington, D.C.: The National Academies Press. Page 769 (http:/ / newton. nap. edu/ books/ 0309085373/ html/ 769. html). ISBN 0-309-08537-3. [14] Joint WHO/FAO expert consultation (2003). Diet, Nutrition and the Prevention of Chronic Diseases (http:/ / www. who. int/ hpr/ NPH/ docs/ who_fao_expert_report. pdf) (PDF). Geneva: World Health Organization. Pages 5556. ISBN 92-4-120916-X. [15] Joint WHO/FAO expert consultation (1998), Carbohydrates in human nutrition, chapter 1 (http:/ / www. fao. org/ docrep/ W8079E/ w8079e07. htm). ISBN 92-5-104114-8. [16] DHHS and USDA, Dietary Guidelines for Americans 2005, Chapter 7 Carbohydrates (http:/ / www. health. gov/ dietaryguidelines/ dga2005/ document/ html/ chapter7. htm)
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External links
Carbohydrates, including interactive models and animations (http://www2.ufp.pt/~pedros/bq/carb_en.htm) (Requires MDL Chime (http://www.mdl.com/products/framework/chime/)) IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN): Carbohydrate Nomenclature (http:// www.chem.qmw.ac.uk/iupac/2carb/) Carbohydrates detailed (http://www.cem.msu.edu/~reusch/VirtualText/carbhyd.htm) Complex And Simple Carbohydrates (http://evilcyber.com/nutrition/complex-and-simple-carbohydrates/) Explanation of the differences Carbohydrates and Glycosylation - The Virtual Library of Biochemistry and Cell Biology (http://www. biochemweb.org/carbohydrates.shtml) Functional Glycomics Gateway (http://www.functionalglycomics.org/), a collaboration between the Consortium for Functional Glycomics and Nature Publishing Group Wine Carbohydrates (http://www.wineclubwizard.com/wine-carbohydrates.html)
Polysaccharide
Polysaccharides are long carbohydrate molecules, of repeated monomer units joined together by glycosidic bonds. They range in structure from linear to highly branched. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit. Depending on the structure, these macromolecules can have distinct properties from their monosaccharide building blocks. They may be amorphous or even insoluble in water.[1] [2]
When all the monosaccharides in a polysaccharide are the same type, the polysaccharide is called a homopolysaccharide or homoglycan, but when more than one type of monosaccharide is present they are called heteropolysaccharides or heteroglycans. [3] [4] Examples include storage polysaccharides such as starch and glycogen, and structural polysaccharides such as cellulose and chitin. Polysaccharides have a general formula of Cx(H2O)y where x is usually a large number between 200 and 2500. Considering that the repeating units in the polymer backbone are often six-carbon monosaccharides, the general formula can also be represented as (C6H10O5)n where 40n3000.
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Structure
Natural saccharides are generally built of simple carbohydrates called monosaccharides with general formula (CH2O)n where n is three or more. A typical monosaccharide has the structure H-(CHOH)x(C=O)-(CHOH)y-H, that is, an aldehyde or ketone with many hydroxyl groups added, usually one on each carbon atom that is not part of the aldehyde or ketone functional group. Examples of monosaccharides are glucose, fructose, and glyceraldehyde[5] Polysaccharides are composed of long chains of monosaccharide units bound together by glycosidic bonds. Polysaccharides contain more than ten monosaccharide units. Definitions of how large a carbohydrate must be to fall into the categories polysaccharides or oligosaccharides vary according to personal opinion. Polysaccharides is an important class Amylose is a linear polymer of glucose mainly linked with (14) bonds. It can be made of biological polymers. Their function of several thousands of glucose units. It is one of the two components of starch, the other in living organisms is usually either being amylopectin. structure- or storage-related. Starch (a polymer of glucose) is used as a storage polysaccharide in plants, being found in the form of both amylose and the branched amylopectin. In animals, the structurally similar glucose polymer is the more densely branched glycogen, sometimes called 'animal starch'. Glycogen's properties allow it to be metabolized more quickly, which suits the active lives of moving animals. Cellulose and chitin are examples of structural polysaccharides. Cellulose is used in the cell walls of plants and other organisms, and is claimed to be the most abundant organic molecule on earth.[6] It has many uses such as a significant role in the paper and textile industries, and is used as a feedstock for the production of rayon (via the viscose process), cellulose acetate, celluloid, and nitrocellulose. Chitin has a similar structure, but has nitrogen-containing side branches, increasing its strength. It is found in arthropod exoskeletons and in the cell walls of some fungi. It also has multiple uses, including surgical threads. Polysaccharides also include callose or laminarin, chrysolaminarin, xylan, arabinoxylan, mannan, fucoidan and galactomannan.
Function
Nutrition
Polysaccharides are common sources of energy. Many organisms can easily break down starches into glucose, however, most organisms cannot metabolize cellulose or other polysaccharides like chitin and arabinoxylans. These carbohydrates types can be metabolized by some bacteria and protists. Ruminants and termites, for example, use microorganisms to process cellulose. Even though these complex carbohydrates are not very digestible, they may comprise important dietary elements for humans. Called dietary fiber, these carbohydrates enhance digestion among other benefits. The main action of dietary fiber is to change the nature of the contents of the gastrointestinal tract, and to change how other nutrients and chemicals are absorbed.[7] [8] Soluble fiber binds to bile acids in the small intestine, making them less likely to enter the body; this in turn lowers cholesterol levels in the blood.[9] Soluble fiber also attenuates the absorption of sugar, reduces sugar response after eating, normalizes blood lipid levels and, once fermented in the colon, produces short-chain fatty acids as byproducts with wide-ranging physiological activities (discussion below). Although
Polysaccharide insoluble fiber is associated with reduced diabetes risk, the mechanism by which this occurs is unknown.[10] Not yet formally proposed as an essential macronutrient, dietary fiber is nevertheless regarded as important for the diet, with regulatory authorities in many developed countries recommending increases in fiber intake.[7] [8] [11] [12]
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Storage polysaccharides
Starches
Starches are glucose polymers in which glucopyranose units are bonded by alpha-linkages. It is made up of a mixture of Amylose (1520%) and Amylopectin (8085%). Amylose consists of a linear chain of several hundred glucose molecules and Amylopectin is a branched molecule made of several thousand glucose units (every chain of 2430 glucose units is one unit of Amylopectin). Starches are insoluble in water. They can be digested by hydrolysis, catalyzed by enzymes called amylases, which can break the alpha-linkages (glycosidic bonds). Humans and other animals have amylases, so they can digest starches. Potato, rice, wheat, and maize are major sources of starch in the human diet. The formations of starches are the ways that plants store glucose.
Glycogen
Glycogen serves as the secondary long-term energy storage in animal and fungal cells, with the primary energy stores being held in adipose tissue. Glycogen is made primarily by the liver and the muscles, but can also be made by glycogenesis within the brain and stomach.[14] Glycogen is the analogue of starch, a glucose polymer in plants, and is sometimes referred to as animal starch, having a similar structure to amylopectin but more extensively branched and compact than starch. Glycogen is a polymer of (14) glycosidic bonds linked, with (16)-linked branches. Glycogen is found in the form of granules in the cytosol/cytoplasm in many cell types, and plays an important role in the glucose cycle. Glycogen forms an energy reserve that can be quickly mobilized to meet a sudden need for glucose, but one that is less compact than the energy reserves of triglycerides (lipids).
Schematic 2-D cross-sectional view of glycogen. A core protein of glycogenin is surrounded by branches of glucose units. The entire globular granule may contain [13] approximately 30,000 glucose units.
In the liver hepatocytes, glycogen can compose up to eight percent of the fresh weight (100120g in an adult) soon after a meal.[15] Only the glycogen stored in the
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liver can be made accessible to other organs. In the muscles, glycogen is found in a low concentration (one to two percent of the muscle mass). However, the amount of glycogen stored in the bodyespecially within the muscles, liver, and red blood cells[16] [17] [18] mostly depends on physical training, basal metabolic rate, and eating habits such as intermittent fasting. Small amounts of glycogen are found in the kidneys, and even smaller amounts in certain glial cells in the brain and white blood cells. The uterus also stores glycogen during pregnancy to nourish the embryo.[19] Glycogen is composed of a branched chain of glucose residues. It is stored in liver and muscles. It is an energy reserve for animals. A view of the atomic structure of a single branched strand of glucose units in a It is the chief form of carbohydrate stored glycogen molecule. in animal body. It is insoluble in water. It turns red when mixed with iodine. It also yields glucose on hydrolysis.
Structural polysaccharides
Arabinoxylans
Arabinoxylans are found in both the primary and secondary cell walls of plants and are the copolymers of two pentose sugars: arabinose and xylose.
Cellulose
The structural component of plants are formed primarily from cellulose. Wood is largely cellulose and lignin, while paper and cotton are nearly pure cellulose. Cellulose is a polymer made with repeated glucose units bonded together by beta-linkages. Humans and many other animals lack an enzyme to break the beta-linkages, so they do not digest cellulose. Certain animals such as termites can digest cellulose, because bacteria possessing the enzyme are present in their gut. Cellulose is insoluble in water. It does not change color when mixed with iodine. On hydrolysis, it yields glucose. It is the most abundant carbohydrate in nature.
Chitin
Chitin is one of many naturally occurring polymers. It forms a structural component of many animals, such as exoskeletons. Over time it is bio-degradable in the natural environment. Its breakdown may be catalyzed by enzymes called chitinases, secreted by microorganisms such as bacteria and fungi, and produced by some plants. Some of these microorganisms have receptors to simple sugars from the decomposition of chitin. If chitin is detected, they then produce enzymes to digest it by cleaving the glycosidic bonds in order to convert it to simple sugars and ammonia.
Polysaccharide Chemically, chitin is closely related to chitosan (a more water-soluble derivative of chitin). It is also closely related to cellulose in that it is a long unbranched chain of glucose derivatives. Both materials contribute structure and strength, protecting the organism.
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Pectins
Pectins are a family of complex polysaccharides that contain 1,4-linked -D-galactosyluronic acid residues. They are present in most primary cell walls and in the non-woody parts of terrestrial plants.
Acidic polysaccharides
Acidic polysaccharides are polysaccharides that contain carboxyl groups, phosphate groups and/or sulfuric ester groups.
Bacterial polysaccharides
Bacterial polysaccharides represent a diverse range of macromolecules that include peptidoglycan, lipopolysaccharides, capsules and exopolysaccharides; compounds whose functions range from structural cell-wall components (e.g., peptidoglycan), and important virulence factors (e.g., Poly-N-acetylglucosamine in S. aureus), to permitting the bacterium to survive in harsh environments (e.g., Pseudomonas aeruginosa in the human lung).[20] Polysaccharide biosynthesis is a tightly regulated, energy-intensive process and understanding the subtle interplay between the regulation and energy conservation, polymer modification and synthesis, and the external ecological functions is a huge area of research. The potential benefits are enormous and should enable for example the development of novel antibacterial strategies (e.g., new antibiotics and vaccines) and the commercial exploitation to develop novel applications.[21] [22]
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Aqueous solutions of the polysaccharide alone have a curious behavior when stirred. After stopping, the swirl continues due to momentum, then stops, and then reverses direction briefly. This recoil demonstrates the elastic effect of the polysaccharide chains previously streched in solution, returning to their relaxed state. Cell-surface polysaccharides play diverse roles in bacterial ecology and physiology. They serve as a barrier between the cell wall and the environment, mediate host-pathogen interactions, and form structural components of biofilms. These polysaccharides are synthesized from nucleotide-activated precursors (called nucleotide sugars) and, in most cases, all the enzymes necessary for biosynthesis, assembly and transport of the completed polymer are encoded by genes organized in dedicated clusters within the genome of the organism. Lipopolysaccharide is one of the most important cell-surface polysaccharides, as it plays a key structural role in outer membrane integrity, as well as being an important mediator of host-pathogen interactions. The enzymes that make the A-band (homopolymeric) and B-band (heteropolymeric) O-antigens have been identified and the metabolic pathways defined.[25] The exopolysaccharide alginate is a linear copolymer of -1,4-linked D-mannuronic acid and L-guluronic acid residues, and is responsible for the mucoid phenotype of late-stage cystic fibrosis disease. The pel and psl loci are two recently discovered gene clusters that also encode exopolysaccharides found to be important for biofilm formation. Rhamnolipid is a biosurfactant whose production is tightly regulated at the transcriptional level, but the precise role that it plays in disease is not well understood at present. Protein glycosylation, particularly of pilin and flagellin, is a recent focus of research by several groups and it has been shown to be important for adhesion and invasion during bacterial infection.[26]
References
[1] Varki A, Cummings R, Esko J, Freeze H, Stanley P, Bertozzi C, Hart G, Etzler M (2008). Essentials of glycobiology (http:/ / www. ncbi. nlm. nih. gov/ bookshelf/ br. fcgi?book=glyco2). Cold Spring Harbor Laboratory Press; 2nd edition. ISBN0-87969-770-9. . [2] Varki A, Cummings R, Esko J, Jessica Freeze, Hart G, Marth J (1999). Essentials of glycobiology (http:/ / www. ncbi. nlm. nih. gov/ books/ bv. fcgi?rid=glyco. TOC& depth=2). Cold Spring Harbor Laboratory Press. ISBN0-87969-560-9. . [3] IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006) " homopolysaccharide (homoglycan) (http:/ / goldbook. iupac. org/ H02856. html)". [4] IUPAC, Compendium of Chemical Terminology, 2nd ed. (the "Gold Book") (1997). Online corrected version: (2006) " heteropolysaccharide (heteroglycan) (http:/ / goldbook. iupac. org/ H02812. html)". [5] Matthews, C. E.; K. E. Van Holde; K. G. Ahern (1999) Biochemistry. 3rd edition. Benjamin Cummings. ISBN 0-8053-3066-6 [6] N.A.Campbell (1996) Biology (4th edition). Benjamin Cummings NY. p.23 ISBN 0-8053-1957-3 [7] "Dietary Reference Intakes for Energy, Carbohydrate, fiber, Fat, Fatty Acids, Cholesterol, Protein, and Amino Acids (Macronutrients) (2005), Chapter 7: Dietary, Functional and Total fiber." (http:/ / www. nal. usda. gov/ fnic/ DRI/ / DRI_Energy/ 339-421. pdf). US Department of Agriculture, National Agricultural Library and National Academy of Sciences, Institute of Medicine, Food and Nutrition Board. .
Polysaccharide
[8] Eastwood M, Kritchevsky D (2005). "Dietary fiber: how did we get where we are?". Annu Rev Nutr 25: 18. doi:10.1146/annurev.nutr.25.121304.131658. PMID16011456. [9] Anderson JW, Baird P, Davis RH et al. (2009). "Health benefits of dietary fiber". Nutr Rev 67 (4): 188205. doi:10.1111/j.1753-4887.2009.00189.x. PMID19335713. [10] Weickert MO, Pfeiffer AF (2008). "Metabolic effects of dietary fiber consumption and prevention of diabetes". J Nutr 138 (3): 43942. PMID18287346. [11] "Dietary reference values for carbohydrates and dietary fiber" (http:/ / www. efsa. europa. eu/ EFSA/ DocumentSet/ nda_op_drv_carbohydrates_draft_en_released for consultation,0. pdf?ssbinary=true). European Food Safety Authority. . [12] Jones PJ, Varady KA (2008). "Are functional foods redefining nutritional requirements?" (http:/ / article. pubs. nrc-cnrc. gc. ca/ ppv/ RPViewDoc?issn=1715-5312& volume=33& issue=1& startPage=118) (PDF). Appl Physiol Nutr Metab 33 (1): 11823. doi:10.1139/H07-134. PMID18347661. . [13] Page 12 in: (http:/ / books. google. dk/ books?id=SRptlOx7yj4C& printsec=frontcover& hl=en) Exercise physiology: energy, nutrition, and human performance By William D. McArdle, Frank I. Katch, Victor L. Katch Edition: 6, illustrated Published by Lippincott Williams & Wilkins, 2006 ISBN 0781749905, 9780781749909, 1068 pages [14] Anatomy and Physiology. Saladin, Kenneth S. McGraw-Hill, 2007. [15] Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life (http:/ / www. phschool. com/ el_marketing. html). Boston, Massachusetts: Pearson Prentice Hall. ISBN0-13-250882-6. . [16] Moses SW, Bashan N, Gutman A (December 1972). "Glycogen metabolism in the normal red blood cell" (http:/ / www. bloodjournal. org/ cgi/ pmidlookup?view=long& pmid=5083874). Blood 40 (6): 83643. PMID5083874. . [17] http:/ / jeb. biologists. org/ cgi/ reprint/ 129/ 1/ 141. pdf [18] Miwa I, Suzuki S (November 2002). "An improved quantitative assay of glycogen in erythrocytes". Annals of Clinical Biochemistry 39 (Pt 6): 6123. doi:10.1258/000456302760413432. PMID12564847. [19] Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life (http:/ / www. phschool. com/ el_marketing. html). Boston, Massachusetts: Pearson Prentice Hall. ISBN0-13-250882-6. . [20] Sutherland, I. W. (2002). Vandamme, E. J., Ed.. ed. Polysaccharides from Microorganisms, Plants and Animals, in: Biopolymers, Volume 5, Polysaccharides I: Polysaccharides from Prokaryotes. Weiheim Wiley VCH. pp.119. ISBN978-3-527-30226-0. [21] Ullrich M (editor) (2009). Bacterial Polysaccharides: Current Innovations and Future Trends. Caister Academic Press. ISBN978-1-904455-45-5. [22] Rehm BHA (editor). (2009). Microbial Production of Biopolymers and Polymer Precursors: Applications and Perspectives. Caister Academic Press. ISBN978-1-904455-36-3. [23] Viscosity of Welan Gum vs. Concentration in Water. http:/ / www. xydatasource. com/ xy-showdatasetpage. php?datasetcode=345115& dsid=80 [24] http:/ / www. xydatasource. com/ xy-showdatasetpage. php?datasetcode=45615& dsid=76& searchtext=polysaccharide [25] Guo H, Yi W, Song JK, Wang PG (2008). "Current understanding on biosynthesis of microbial polysaccharides". Curr Top Med Chem 8 (2): 14151. doi:10.2174/156802608783378873. PMID18289083. [26] Cornelis P (editor). (2008). Pseudomonas: Genomics and Molecular Biology (http:/ / www. horizonpress. com/ pseudo) (1st ed.). Caister Academic Press. ISBN978-1-904455-19-6. . .
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External links
Polysaccharide Structure (http://employees.csbsju.edu/hjakubowski/classes/ch331/cho/complexoligosacch. htm) Applications and commercial sources of polysaccharides (http://www.polysaccharidecenter.com) European Polysaccharide Network of Excellence (http://www.epnoe.eu)
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Metabolism
Overview of metabolism
Metabolism (from Greek: "metabol", "change" or Greek: metabolismos, "outthrow") is the set of chemical reactions that happen in the cells of living organisms to sustain life. 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 organic matter, for example to harvest energy in cellular respiration. Anabolism uses energy to construct components of cells such as proteins and nucleic acids.
The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, by a sequence of enzymes. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy and will not occur by themselves, by coupling them to spontaneous reactions that release energy. As enzymes act as catalysts they allow these reactions to proceed quickly and efficiently. Enzymes also allow the regulation of metabolic pathways in response to changes in the cell's environment or signals from other cells. The metabolism of an organism determines which substances it will find nutritious and which it will find poisonous. For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals.[1] The speed of metabolism, the metabolic rate, influences how much food an organism will require, and also affects how it is able to obtain that food. A striking feature of metabolism is the similarity of the basic metabolic pathways and components between even vastly different species.[2] For example, the set of carboxylic acids that are best known as the intermediates in the citric acid cycle are present in all known organisms, being found in species as diverse as the unicellular bacteria Escherichia coli and huge multicellular organisms like elephants.[3] These striking similarities in metabolic pathways are likely due to their early appearance in evolutionary history, and being retained because of their efficacy.[4] [5]
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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). As these molecules are vital for life, metabolic reactions either focus on making these molecules during the construction of cells and tissues, or breaking them down and using them as a source of energy, in the digestion and use of food. Many important biochemicals can be joined together to make polymers such as DNA and proteins. These macromolecules are essential.
Proteins (also called polypeptides) Fibrous proteins and globular proteins Polysaccharides Polynucleotides Starch, glycogen and cellulose DNA and RNA
Lipids
Lipids are the most diverse group of biochemicals. Their main structural uses are as part of biological membranes such as the cell membrane, or as a source of energy.[7] Lipids are usually defined as hydrophobic or amphipathic biological molecules that will dissolve in organic solvents such as benzene or chloroform.[8] 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.[9] Several variations on this basic structure exist, including alternate backbones such as sphingosine in the sphingolipids, and hydrophilic groups such as phosphate in phospholipids. Steroids such as cholesterol are another major class of lipids that are made in cells.[10]
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Carbohydrates
Carbohydrates are aldehydes or ketones with many hydroxyl groups that can exist as straight chains or rings. Carbohydrates are the most abundant biological molecules, and fill numerous roles, such as the storage and transport of energy (starch, glycogen) and structural components (cellulose in plants, chitin in animals).[7] The basic carbohydrate units are called monosaccharides and include galactose, fructose, and most importantly glucose. Monosaccharides can be linked together to form polysaccharides in almost limitless ways.[11]
Nucleotides
The two nucleic acids, DNA and RNA are polymers of nucleotides, each nucleotide comprising a phosphate group, a ribose sugar group, and a nitrogenous base. Nucleic acids are critical for the storage and use of genetic information, through the processes of transcription and protein biosynthesis.[7] This information is protected by DNA repair mechanisms and propagated through DNA replication. Many viruses have an RNA genome, for example HIV, which uses reverse transcription to create a DNA template from its viral RNA genome.[12] RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can catalyze chemical reactions. Individual nucleosides are made by attaching a nucleobase to a ribose sugar. These bases are heterocyclic rings containing nitrogen, classified as purines or pyrimidines. Nucleotides also act as coenzymes in metabolic group transfer reactions.[13]
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.[14] This common chemistry allows cells to use a small set of metabolic intermediates to carry Structure of the coenzyme acetyl-CoA.The transferable acetyl group is bonded to chemical groups between different [13] the sulfur atom at the extreme left. reactions. These group-transfer intermediates are called coenzymes. Each class of group-transfer reaction is carried out by a particular coenzyme, which is the substrate 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.[15] One central coenzyme is adenosine triphosphate (ATP), the universal energy currency of cells. This nucleotide is used to transfer chemical energy between different chemical reactions. There is only a small amount of ATP in cells, but as it is continuously regenerated, the human body can use about its own weight in ATP per day.[15] 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.
Overview of metabolism A vitamin is an organic compound needed in small quantities that cannot be made in the cells. In human nutrition, most vitamins function as coenzymes after modification; for example, all water-soluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells.[16] Nicotinamide adenine dinucleotide (NADH), a derivative of vitamin B3 (niacin), is an important coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of dehydrogenases remove electrons from their substrates and reduce NAD+ into NADH. This reduced form of the coenzyme is then a substrate for any of the reductases in the cell that need to reduce their substrates.[17] 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.
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Catabolism
Further information: Catabolism Catabolism is the set of metabolic processes that break down large molecules. These include breaking down and oxidizing food molecules. The purpose of the catabolic reactions is to provide the energy and components needed by anabolic reactions. The exact nature of these catabolic reactions differ from organism to organism and organisms can be classified based on their sources of energy and carbon (their primary nutritional groups), as shown in the table below. Organic molecules are used as a source of energy by organotrophs, while lithotrophs use inorganic substrates and phototrophs capture sunlight as chemical energy. However, all these different forms of metabolism depend on redox reactions that involve the transfer of electrons from reduced donor molecules such as organic molecules, water, ammonia, hydrogen sulfide or ferrous ions to acceptor molecules such as oxygen, nitrate or sulfate.[27] In animals these reactions involve complex organic molecules being broken down to simpler molecules, such as carbon dioxide and water. In photosynthetic organisms such as plants and cyanobacteria, these electron-transfer reactions do not release energy, but are used as a way of storing energy absorbed from sunlight.[7]
Preformed molecules chemoElectron donor organic compound inorganic compound Carbon source organic compound inorganic compound organolithoheteroauto-
The most common set of catabolic reactions in animals can be separated into three main stages. In the first, large organic molecules such as proteins, polysaccharides or lipids are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to yet smaller molecules, usually acetyl coenzyme A (acetyl-CoA), which releases some energy. Finally, the acetyl group on the CoA is oxidised to water and carbon dioxide in the citric acid cycle and electron transport chain, releasing the energy that is stored by reducing the coenzyme nicotinamide adenine dinucleotide (NAD+) into NADH.
Digestion
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. Several common classes of enzymes digest these polymers. These digestive enzymes include proteases that digest proteins into amino acids, as well as glycoside hydrolases that digest polysaccharides into monosaccharides. Microbes simply secrete digestive enzymes into their surroundings,[28] [29] while animals only secrete these enzymes from specialized cells in their guts.[30] The amino acids or sugars released by these extracellular enzymes are then pumped into cells by specific active transport proteins.[31] [32]
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Energy transformations
Oxidative phosphorylation
Further information: Oxidative phosphorylation, chemiosmosis and mitochondrion In oxidative phosphorylation, the electrons removed from organic molecules in areas such as the protagon acid cycle are transferred to oxygen and the energy released is used to make ATP. This is done in eukaryotes by a series of proteins in the membranes of mitochondria called the electron transport chain. In prokaryotes, these proteins are found in the cell's inner membrane.[38] These proteins use the energy released from passing electrons from reduced molecules like NADH onto oxygen to pump protons across a membrane.[39] Pumping protons out of the mitochondria creates a proton concentration difference across the membrane and generates an electrochemical gradient.[40] This force drives protons back into the mitochondrion through the base of
Overview of metabolism an enzyme called ATP synthase. The flow of protons makes the stalk subunit rotate, causing the active site of the synthase domain to change shape and phosphorylate adenosine diphosphate turning it into ATP.[15]
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Anabolism
Further information: Anabolism Anabolism is the set of constructive metabolic processes where the energy released by catabolism is used to synthesize complex molecules. In general, the complex molecules that make up cellular structures are constructed step-by-step from small and simple precursors. Anabolism involves three basic stages. 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. Organisms differ in how many of the molecules in their cells they can construct for themselves. Autotrophs such as plants can construct the complex organic molecules in cells such as polysaccharides and proteins from simple molecules like carbon dioxide and water. Heterotrophs, on the other hand, require a source of more complex substances, such as monosaccharides and amino acids, to produce these complex molecules. Organisms can be further classified by ultimate source of their energy: photoautotrophs and photoheterotrophs obtain energy from
Overview of metabolism light, whereas chemoautotrophs and chemoheterotrophs obtain energy from inorganic oxidation reactions.
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Carbon fixation
Further information: Photosynthesis, carbon fixation and chemosynthesis Photosynthesis is the synthesis of carbohydrates from sunlight and carbon dioxide (CO2). In plants, cyanobacteria and algae, oxygenic photosynthesis splits water, with oxygen produced as a waste product. This process uses the ATP and NADPH produced by the photosynthetic reaction centres, as described above, to convert CO2 into glycerate 3-phosphate, which can then be converted into glucose. This carbon-fixation reaction is carried out by the enzyme RuBisCO as part of the Calvin Benson cycle.[51] Three types of photosynthesis occur in plants, C3 carbon fixation, C4 carbon fixation and CAM photosynthesis. These differ by the route that carbon dioxide takes to the Calvin cycle, with C3 plants fixing CO2 directly, while C4 and CAM photosynthesis incorporate the CO2 into other compounds first, as adaptations to deal with intense sunlight and dry conditions.[52]
Plant cells (bounded by purple walls) filled with chloroplasts (green), which are the site of photosynthesis
In photosynthetic prokaryotes the mechanisms of carbon fixation are more diverse. Here, carbon dioxide can be fixed by the Calvin Benson cycle, a reversed citric acid cycle,[53] or the carboxylation of acetyl-CoA.[54] [55] Prokaryotic chemoautotrophs also fix CO2 through the Calvin Benson cycle, but use energy from inorganic compounds to drive the reaction.[56]
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Proteins
Further information: Protein biosynthesis, amino acid synthesis Organisms vary in their ability to synthesize the 20 common amino acids. Most bacteria and plants can synthesize all twenty, but mammals can synthesize only eleven nonessential amino acids.[7] Thus, nine essential amino acids must be obtained from food. All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen is provided by glutamate and glutamine. Amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then transaminated to form an amino acid.[74] Amino acids are made into proteins by being joined together in a chain by peptide bonds. Each different protein has a unique sequence of amino acid residues: this is its primary structure. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a transfer RNA
Overview of metabolism molecule through an ester bond. This aminoacyl-tRNA precursor is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase.[75] 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.[76]
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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.[3] [103] This universal ancestral cell was prokaryotic and probably a methanogen that had extensive amino acid, nucleotide, carbohydrate and lipid [104] [105] metabolism. 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, Evolutionary tree showing the common ancestry of organisms from all three domains of life. Bacteria are colored blue, eukaryotes red, and archaea green. Relative positions of with pathways such as glycolysis and some of the phyla included are shown around the tree. the citric acid cycle producing their end products highly efficiently and in a [4] [5] minimal number of steps. Mutation changes that affect non-coding DNA segments may merely affect the metabolic efficiency of the individual for whom the mutation occurs.[106] 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.[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.[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.[113] Similar reduced metabolic capabilities are seen in endosymbiotic organisms.[114]
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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.[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.[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.[119] Using these techniques, a model of human metabolism has now been produced, which will guide future drug discovery and biochemical research.[120] These models are now being used in network analysis, to classify human diseases into groups that share common proteins or metabolites.[121] [122] Bacterial metabolic networks seem to be a striking example of bow-tie[123] [124] [125] organization, an architecture able to input a wide range of nutrients and produce a large variety of products and complex macromolecules using a relatively few intermediate common currencies. A major technological application of this information is metabolic engineering. Here, organisms such as yeast, plants or bacteria are genetically modified to make them more useful in biotechnology and aid the production of drugs such as antibiotics or industrial chemicals such as 1,3-propanediol and shikimic acid.[126] These genetic modifications usually aim to reduce the amount of energy used to produce the product, increase yields and reduce the production of wastes.[127]
Metabolic network of the Arabidopsis thaliana citric acid cycle. Enzymes and metabolites are shown as red squares and the interactions between them as black lines.
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History
Further information: History of biochemistry and history of molecular biology The term metabolism is derived from the Greek "Metabolismos" for "change", or "overthrow".[128] The history of the scientific study of metabolism spans several centuries and has moved from examining whole animals in early studies, to examining individual metabolic reactions in modern biochemistry. The first controlled experiments in human metabolism were published by Santorio Santorio in 1614 in his book Ars de statica medicina.[129] He described how he weighed himself before and after eating, sleep, working, sex, fasting, drinking, and excreting. He found that most of the food he took in was lost through what he called "insensible perspiration". In these early studies, the mechanisms of these metabolic processes had not been identified and a vital force was thought to animate living tissue.[130] In the 19th century, when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur concluded that fermentation was catalyzed by substances Santorio Santorio in his steelyard within the yeast cells he called "ferments". He wrote that "alcoholic balance, from Ars de statica medicina, fermentation is an act correlated with the life and organization of the yeast first published 1614 cells, not with the death or putrefaction of the cells."[131] This discovery, along with the publication by Friedrich Whler in 1828 of the chemical synthesis of urea,[132] notable for being the first organic compound prepared from wholly inorganic precursors, proved that the organic compounds and chemical reactions found in cells were no different in principle than any other part of chemistry. It was the discovery of enzymes at the beginning of the 20th century 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.[133] 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.[134] He discovered the urea cycle and later, working with Hans Kornberg, the citric acid cycle and the glyoxylate cycle.[135] [61] Modern biochemical research has been greatly aided by the development of new techniques such as chromatography, X-ray diffraction, NMR spectroscopy, radioisotopic labelling, electron microscopy and molecular dynamics simulations. These techniques have allowed the discovery and detailed analysis of the many molecules and metabolic pathways in cells.
References
[1] Friedrich C (1998). "Physiology and genetics of sulfur-oxidizing bacteria". Adv Microb Physiol 39: 23589. doi:10.1016/S0065-2911(08)60018-1. PMID9328649. [2] Pace NR (January 2001). "The universal nature of biochemistry". Proc. Natl. Acad. Sci. U.S.A. 98 (3): 8058. Bibcode2001PNAS...98..805P. doi:10.1073/pnas.98.3.805. PMC33372. PMID11158550. [3] Smith E, Morowitz H (2004). "Universality in intermediary metabolism" (http:/ / www. pnas. org/ cgi/ pmidlookup?view=long& pmid=15340153). Proc Natl Acad Sci USA 101 (36): 1316873. Bibcode2004PNAS..10113168S. doi:10.1073/pnas.0404922101. PMC516543. PMID15340153. . [4] Ebenhh O, Heinrich R (2001). "Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems". Bull Math Biol 63 (1): 2155. doi:10.1006/bulm.2000.0197. PMID11146883. [5] Melndez-Hevia E, Waddell T, Cascante M (1996). "The puzzle of the Krebs citric acid cycle: assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution". J Mol Evol 43 (3): 293303. doi:10.1007/BF02338838. PMID8703096. [6] Michie K, Lwe J (2006). "Dynamic filaments of the bacterial cytoskeleton". Annu Rev Biochem 75: 46792. doi:10.1146/annurev.biochem.75.103004.142452. PMID16756499.
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[7] Nelson, David L.; Michael M. Cox (2005). Lehninger Principles of Biochemistry. New York: W. H. Freeman and company. pp.841. ISBN0-7167-4339-6. [8] Fahy E, Subramaniam S, Brown H, Glass C, Merrill A, Murphy R, Raetz C, Russell D, Seyama Y, Shaw W, Shimizu T, Spener F, van Meer G, VanNieuwenhze M, White S, Witztum J, Dennis E (2005). "A comprehensive classification system for lipids" (http:/ / www. jlr. org/ cgi/ content/ full/ 46/ 5/ 839). J Lipid Res 46 (5): 83961. doi:10.1194/jlr.E400004-JLR200. PMID15722563. . [9] "Nomenclature of Lipids" (http:/ / www. chem. qmul. ac. uk/ iupac/ lipid/ ). IUPAC-IUB Commission on Biochemical Nomenclature (CBN). . Retrieved 2007-03-08. [10] Hegardt F (1999). "Mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase: a control enzyme in ketogenesis". Biochem J 338 (Pt 3): 56982. doi:10.1042/0264-6021:3380569. PMC1220089. PMID10051425. [11] Raman R, Raguram S, Venkataraman G, Paulson J, Sasisekharan R (2005). "Glycomics: an integrated systems approach to structure-function relationships of glycans". Nat Methods 2 (11): 81724. doi:10.1038/nmeth807. PMID16278650. [12] Sierra S, Kupfer B, Kaiser R (2005). "Basics of the virology of HIV-1 and its replication". J Clin Virol 34 (4): 23344. doi:10.1016/j.jcv.2005.09.004. PMID16198625. [13] Wimmer M, Rose I (1978). "Mechanisms of enzyme-catalyzed group transfer reactions". Annu Rev Biochem 47: 103178. doi:10.1146/annurev.bi.47.070178.005123. PMID354490. [14] Mitchell P (1979). "The Ninth Sir Hans Krebs Lecture. Compartmentation and communication in living systems. Ligand conduction: a general catalytic principle in chemical, osmotic and chemiosmotic reaction systems". Eur J Biochem 95 (1): 120. doi:10.1111/j.1432-1033.1979.tb12934.x. PMID378655. [15] Dimroth P, von Ballmoos C, Meier T (March 2006). "Catalytic and mechanical cycles in F-ATP synthases. Fourth in the Cycles Review Series". EMBO Rep 7 (3): 27682. doi:10.1038/sj.embor.7400646. PMC1456893. PMID16607397. [16] Coulston, Ann; Kerner, John; Hattner, JoAnn; Srivastava, Ashini (2006). "Nutrition Principles and Clinical Nutrition". Stanford School of Medicine Nutrition Courses. SUMMIT. [17] Pollak N, Dlle C, Ziegler M (2007). "The power to reduce: pyridine nucleotidessmall molecules with a multitude of functions". Biochem J 402 (2): 20518. doi:10.1042/BJ20061638. PMC1798440. PMID17295611. [18] Heymsfield S, Waki M, Kehayias J, Lichtman S, Dilmanian F, Kamen Y, Wang J, Pierson R (1991). "Chemical and elemental analysis of humans in vivo using improved body composition models". Am J Physiol 261 (2 Pt 1): E1908. PMID1872381. [19] Sychrov H (2004). "Yeast as a model organism to study transport and homeostasis of alkali metal cations" (http:/ / www. biomed. cas. cz/ physiolres/ pdf/ 53 Suppl 1/ 53_S91. pdf) (PDF). Physiol Res 53 Suppl 1: S918. PMID15119939. . [20] Levitan I (1988). "Modulation of ion channels in neurons and other cells". Annu Rev Neurosci 11: 11936. doi:10.1146/annurev.ne.11.030188.001003. PMID2452594. [21] Dulhunty A (2006). "Excitation-contraction coupling from the 1950s into the new millennium". Clin Exp Pharmacol Physiol 33 (9): 76372. doi:10.1111/j.1440-1681.2006.04441.x. PMID16922804. [22] Mahan D, Shields R (1998). "Macro- and micromineral composition of pigs from birth to 145 kilograms of body weight" (http:/ / jas. fass. org/ cgi/ reprint/ 76/ 2/ 506). J Anim Sci 76 (2): 50612. PMID9498359. . [23] Husted S, Mikkelsen B, Jensen J, Nielsen N (2004). "Elemental fingerprint analysis of barley (Hordeum vulgare) using inductively coupled plasma mass spectrometry, isotope-ratio mass spectrometry, and multivariate statistics". Anal Bioanal Chem 378 (1): 17182. doi:10.1007/s00216-003-2219-0. PMID14551660. [24] Finney L, O'Halloran T (2003). "Transition metal speciation in the cell: insights from the chemistry of metal ion receptors". Science 300 (5621): 9316. Bibcode2003Sci...300..931F. doi:10.1126/science.1085049. PMID12738850. [25] Cousins R, Liuzzi J, Lichten L (2006). "Mammalian zinc transport, trafficking, and signals" (http:/ / www. jbc. org/ cgi/ content/ full/ 281/ 34/ 24085). J Biol Chem 281 (34): 240859. doi:10.1074/jbc.R600011200. PMID16793761. . [26] Dunn L, Rahmanto Y, Richardson D (2007). "Iron uptake and metabolism in the new millennium". Trends Cell Biol 17 (2): 93100. doi:10.1016/j.tcb.2006.12.003. PMID17194590. [27] Nealson K, Conrad P (1999). "Life: past, present and future" (http:/ / rstb. royalsocietypublishing. org/ cgi/ pmidlookup?view=long& pmid=10670014). Philos Trans R Soc Lond B Biol Sci 354 (1392): 192339. doi:10.1098/rstb.1999.0532. PMC1692713. PMID10670014. . [28] Hse C, Finkelstein R (December 1993). "Bacterial extracellular zinc-containing metalloproteases" (http:/ / mmbr. asm. org/ cgi/ pmidlookup?view=long& pmid=8302217). Microbiol Rev 57 (4): 82337. PMC372940. PMID8302217. . [29] Gupta R, Gupta N, Rathi P (2004). "Bacterial lipases: an overview of production, purification and biochemical properties". Appl Microbiol Biotechnol 64 (6): 76381. doi:10.1007/s00253-004-1568-8. PMID14966663. [30] Hoyle T (1997). "The digestive system: linking theory and practice". Br J Nurs 6 (22): 128591. PMID9470654. [31] Souba W, Pacitti A (1992). "How amino acids get into cells: mechanisms, models, menus, and mediators". JPEN J Parenter Enteral Nutr 16 (6): 56978. doi:10.1177/0148607192016006569. PMID1494216. [32] Barrett M, Walmsley A, Gould G (1999). "Structure and function of facilitative sugar transporters". Curr Opin Cell Biol 11 (4): 496502. doi:10.1016/S0955-0674(99)80072-6. PMID10449337. [33] Bell G, Burant C, Takeda J, Gould G (1993). "Structure and function of mammalian facilitative sugar transporters". J Biol Chem 268 (26): 191614. PMID8366068. [34] Bouch C, Serdy S, Kahn C, Goldfine A (2004). "The cellular fate of glucose and its relevance in type 2 diabetes" (http:/ / edrv. endojournals. org/ cgi/ content/ full/ 25/ 5/ 807). Endocr Rev 25 (5): 80730. doi:10.1210/er.2003-0026. PMID15466941. .
215
Overview of metabolism
[35] Sakami W, Harrington H (1963). "Amino acid metabolism". Annu Rev Biochem 32: 35598. doi:10.1146/annurev.bi.32.070163.002035. PMID14144484. [36] Brosnan J (2000). "Glutamate, at the interface between amino acid and carbohydrate metabolism" (http:/ / jn. nutrition. org/ cgi/ content/ full/ 130/ 4/ 988S). J Nutr 130 (4S Suppl): 988S90S. PMID10736367. . [37] Young V, Ajami A (2001). "Glutamine: the emperor or his clothes?" (http:/ / jn. nutrition. org/ cgi/ content/ full/ 131/ 9/ 2449S). J Nutr 131 (9 Suppl): 2449S59S; discussion 2486S7S. PMID11533293. . [38] Hosler J, Ferguson-Miller S, Mills D (2006). "Energy transduction: proton transfer through the respiratory complexes". Annu Rev Biochem 75: 16587. doi:10.1146/annurev.biochem.75.062003.101730. PMC2659341. PMID16756489. [39] Schultz B, Chan S (2001). "Structures and proton-pumping strategies of mitochondrial respiratory enzymes". Annu Rev Biophys Biomol Struct 30: 2365. doi:10.1146/annurev.biophys.30.1.23. PMID11340051. [40] Capaldi R, Aggeler R (2002). "Mechanism of the F(1)F(0)-type ATP synthase, a biological rotary motor". Trends Biochem Sci 27 (3): 15460. doi:10.1016/S0968-0004(01)02051-5. PMID11893513. [41] Friedrich B, Schwartz E (1993). "Molecular biology of hydrogen utilization in aerobic chemolithotrophs". Annu Rev Microbiol 47: 35183. doi:10.1146/annurev.mi.47.100193.002031. PMID8257102. [42] Weber K, Achenbach L, Coates J (2006). "Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction". Nat Rev Microbiol 4 (10): 75264. doi:10.1038/nrmicro1490. PMID16980937. [43] Jetten M, Strous M, van de Pas-Schoonen K, Schalk J, van Dongen U, van de Graaf A, Logemann S, Muyzer G, van Loosdrecht M, Kuenen J (1998). "The anaerobic oxidation of ammonium". FEMS Microbiol Rev 22 (5): 42137. doi:10.1111/j.1574-6976.1998.tb00379.x. PMID9990725. [44] Simon J (2002). "Enzymology and bioenergetics of respiratory nitrite ammonification". FEMS Microbiol Rev 26 (3): 285309. doi:10.1111/j.1574-6976.2002.tb00616.x. PMID12165429. [45] Conrad R (1996). "Soil microorganisms as controllers of atmospheric trace gases (H2, CO, CH4, OCS, N2O, and NO)" (http:/ / mmbr. asm. org/ cgi/ pmidlookup?view=long& pmid=8987358). Microbiol Rev 60 (4): 60940. PMC239458. PMID8987358. . [46] Barea J, Pozo M, Azcn R, Azcn-Aguilar C (2005). "Microbial co-operation in the rhizosphere" (http:/ / jxb. oxfordjournals. org/ cgi/ content/ full/ 56/ 417/ 1761). J Exp Bot 56 (417): 176178. doi:10.1093/jxb/eri197. PMID15911555. . [47] van der Meer M, Schouten S, Bateson M, Nbel U, Wieland A, Khl M, de Leeuw J, Sinninghe Damst J, Ward D (July 2005). "Diel variations in carbon metabolism by green nonsulfur-like bacteria in alkaline siliceous hot spring microbial mats from Yellowstone National Park" (http:/ / aem. asm. org/ cgi/ pmidlookup?view=long& pmid=16000812). Appl Environ Microbiol 71 (7): 397886. doi:10.1128/AEM.71.7.3978-3986.2005. PMC1168979. PMID16000812. . [48] Tichi M, Tabita F (2001). "Interactive control of Rhodobacter capsulatus redox-balancing systems during phototrophic metabolism" (http:/ / jb. asm. org/ cgi/ pmidlookup?view=long& pmid=11591679). J Bacteriol 183 (21): 634454. doi:10.1128/JB.183.21.6344-6354.2001. PMC100130. PMID11591679. . [49] Allen J, Williams J (1998). "Photosynthetic reaction centers". FEBS Lett 438 (12): 59. doi:10.1016/S0014-5793(98)01245-9. PMID9821949. [50] Munekage Y, Hashimoto M, Miyake C, Tomizawa K, Endo T, Tasaka M, Shikanai T (2004). "Cyclic electron flow around photosystem I is essential for photosynthesis". Nature 429 (6991): 57982. Bibcode2004Natur.429..579M. doi:10.1038/nature02598. PMID15175756. [51] Miziorko H, Lorimer G (1983). "Ribulose-1,5-bisphosphate carboxylase-oxygenase". Annu Rev Biochem 52: 50735. doi:10.1146/annurev.bi.52.070183.002451. PMID6351728. [52] Dodd A, Borland A, Haslam R, Griffiths H, Maxwell K (2002). "Crassulacean acid metabolism: plastic, fantastic" (http:/ / jxb. oxfordjournals. org/ cgi/ content/ full/ 53/ 369/ 569). J Exp Bot 53 (369): 56980. doi:10.1093/jexbot/53.369.569. PMID11886877. . [53] Hgler M, Wirsen C, Fuchs G, Taylor C, Sievert S (May 2005). "Evidence for autotrophic CO2 fixation via the reductive tricarboxylic acid cycle by members of the epsilon subdivision of proteobacteria" (http:/ / jb. asm. org/ cgi/ pmidlookup?view=long& pmid=15838028). J Bacteriol 187 (9): 30207. doi:10.1128/JB.187.9.3020-3027.2005. PMC1082812. PMID15838028. . [54] Strauss G, Fuchs G (1993). "Enzymes of a novel autotrophic CO2 fixation pathway in the phototrophic bacterium Chloroflexus aurantiacus, the 3-hydroxypropionate cycle". Eur J Biochem 215 (3): 63343. doi:10.1111/j.1432-1033.1993.tb18074.x. PMID8354269. [55] Wood H (1991). "Life with CO or CO2 and H2 as a source of carbon and energy" (http:/ / www. fasebj. org/ cgi/ reprint/ 5/ 2/ 156). FASEB J 5 (2): 15663. PMID1900793. . [56] Shively J, van Keulen G, Meijer W (1998). "Something from almost nothing: carbon dioxide fixation in chemoautotrophs". Annu Rev Microbiol 52: 191230. doi:10.1146/annurev.micro.52.1.191. PMID9891798. [57] Boiteux A, Hess B (1981). "Design of glycolysis". Philos Trans R Soc Lond B Biol Sci 293 (1063): 522. Bibcode1981RSPTB.293....5B. doi:10.1098/rstb.1981.0056. PMID6115423. [58] Pilkis S, el-Maghrabi M, Claus T (1990). "Fructose-2,6-bisphosphate in control of hepatic gluconeogenesis. From metabolites to molecular genetics". Diabetes Care 13 (6): 58299. doi:10.2337/diacare.13.6.582. PMID2162755. [59] Ensign S (2006). "Revisiting the glyoxylate cycle: alternate pathways for microbial acetate assimilation". Mol Microbiol 61 (2): 2746. doi:10.1111/j.1365-2958.2006.05247.x. PMID16856935. [60] Finn P, Dice J (2006). "Proteolytic and lipolytic responses to starvation". Nutrition 22 (78): 83044. doi:10.1016/j.nut.2006.04.008. PMID16815497. [61] Kornberg H, Krebs H (1957). "Synthesis of cell constituents from C2-units by a modified tricarboxylic acid cycle". Nature 179 (4568): 98891. Bibcode1957Natur.179..988K. doi:10.1038/179988a0. PMID13430766.
216
Overview of metabolism
[62] Rademacher T, Parekh R, Dwek R (1988). "Glycobiology". Annu Rev Biochem 57: 785838. doi:10.1146/annurev.bi.57.070188.004033. PMID3052290. [63] Opdenakker G, Rudd P, Ponting C, Dwek R (1993). "Concepts and principles of glycobiology" (http:/ / www. fasebj. org/ cgi/ reprint/ 7/ 14/ 1330). FASEB J 7 (14): 13307. PMID8224606. . [64] McConville M, Menon A (2000). "Recent developments in the cell biology and biochemistry of glycosylphosphatidylinositol lipids (review)". Mol Membr Biol 17 (1): 116. doi:10.1080/096876800294443. PMID10824734. [65] Chirala S, Wakil S (2004). "Structure and function of animal fatty acid synthase". Lipids 39 (11): 104553. doi:10.1007/s11745-004-1329-9. PMID15726818. [66] White S, Zheng J, Zhang Y (2005). "The structural biology of type II fatty acid biosynthesis". Annu Rev Biochem 74: 791831. doi:10.1146/annurev.biochem.74.082803.133524. PMID15952903. [67] Ohlrogge J, Jaworski J (1997). "Regulation of fatty acid synthesis". Annu Rev Plant Physiol Plant Mol Biol 48: 109136. doi:10.1146/annurev.arplant.48.1.109. PMID15012259. [68] Dubey V, Bhalla R, Luthra R (2003). "An overview of the non-mevalonate pathway for terpenoid biosynthesis in plants" (http:/ / www. ias. ac. in/ jbiosci/ sep2003/ 637. pdf) (PDF). J Biosci 28 (5): 63746. doi:10.1007/BF02703339. PMID14517367. . [69] Kuzuyama T, Seto H (2003). "Diversity of the biosynthesis of the isoprene units". Nat Prod Rep 20 (2): 17183. doi:10.1039/b109860h. PMID12735695. [70] Grochowski L, Xu H, White R (May 2006). "Methanocaldococcus jannaschii uses a modified mevalonate pathway for biosynthesis of isopentenyl diphosphate" (http:/ / jb. asm. org/ cgi/ pmidlookup?view=long& pmid=16621811). J Bacteriol 188 (9): 31928. doi:10.1128/JB.188.9.3192-3198.2006. PMC1447442. PMID16621811. . [71] Lichtenthaler H (1999). "The 1-Ddeoxy-D-xylulose-5-phosphate pathway of isoprenoid biosynthesis in plants". Annu Rev Plant Physiol Plant Mol Biol 50: 4765. doi:10.1146/annurev.arplant.50.1.47. PMID15012203. [72] Schroepfer G (1981). "Sterol biosynthesis". Annu Rev Biochem 50: 585621. doi:10.1146/annurev.bi.50.070181.003101. PMID7023367. [73] Lees N, Skaggs B, Kirsch D, Bard M (1995). "Cloning of the late genes in the ergosterol biosynthetic pathway of Saccharomyces cerevisiaea review". Lipids 30 (3): 2216. doi:10.1007/BF02537824. PMID7791529. [74] Guyton, Arthur C.; John E. Hall (2006). Textbook of Medical Physiology. Philadelphia: Elsevier. pp.8556. ISBN0-7216-0240-1. [75] Ibba M, Sll D (2001). "The renaissance of aminoacyl-tRNA synthesis" (http:/ / www. molcells. org/ home/ journal/ include/ downloadPdf. asp?articleuid={A158E3B4-2423-4806-9A30-4B93CDA76DA0}). EMBO Rep 2 (5): 3827. doi:10.1093/embo-reports/kve095. PMC1083889. PMID11375928. . [76] Lengyel P, Sll D (1969). "Mechanism of protein biosynthesis". Bacteriol Rev 33 (2): 264301. PMC378322. PMID4896351. [77] Rudolph F (1994). "The biochemistry and physiology of nucleotides". J Nutr 124 (1 Suppl): 124S127S. PMID8283301. Zrenner R, Stitt M, Sonnewald U, Boldt R (2006). "Pyrimidine and purine biosynthesis and degradation in plants". Annu Rev Plant Biol 57: 80536. doi:10.1146/annurev.arplant.57.032905.105421. PMID16669783. [78] Stasolla C, Katahira R, Thorpe T, Ashihara H (2003). "Purine and pyrimidine nucleotide metabolism in higher plants". J Plant Physiol 160 (11): 127195. doi:10.1078/0176-1617-01169. PMID14658380. [79] Smith J (1995). "Enzymes of nucleotide synthesis". Curr Opin Struct Biol 5 (6): 7527. doi:10.1016/0959-440X(95)80007-7. PMID8749362. [80] Testa B, Krmer S (2006). "The biochemistry of drug metabolisman introduction: part 1. Principles and overview". Chem Biodivers 3 (10): 1053101. doi:10.1002/cbdv.200690111. PMID17193224. [81] Danielson P (2002). "The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans". Curr Drug Metab 3 (6): 56197. doi:10.2174/1389200023337054. PMID12369887. [82] King C, Rios G, Green M, Tephly T (2000). "UDP-glucuronosyltransferases". Curr Drug Metab 1 (2): 14361. doi:10.2174/1389200003339171. PMID11465080. [83] Sheehan D, Meade G, Foley V, Dowd C (November 2001). "Structure, function and evolution of glutathione transferases: implications for classification of non-mammalian members of an ancient enzyme superfamily" (http:/ / www. biochemj. org/ bj/ 360/ 0001/ bj3600001. htm). Biochem J 360 (Pt 1): 116. doi:10.1042/0264-6021:3600001. PMC1222196. PMID11695986. . [84] Galvo T, Mohn W, de Lorenzo V (2005). "Exploring the microbial biodegradation and biotransformation gene pool". Trends Biotechnol 23 (10): 497506. doi:10.1016/j.tibtech.2005.08.002. PMID16125262. [85] Janssen D, Dinkla I, Poelarends G, Terpstra P (2005). "Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities". Environ Microbiol 7 (12): 186882. doi:10.1111/j.1462-2920.2005.00966.x. PMID16309386. [86] Davies K (1995). "Oxidative stress: the paradox of aerobic life". Biochem Soc Symp 61: 131. PMID8660387. [87] Tu B, Weissman J (2004). "Oxidative protein folding in eukaryotes: mechanisms and consequences" (http:/ / www. jcb. org/ cgi/ content/ full/ 164/ 3/ 341). J Cell Biol 164 (3): 3416. doi:10.1083/jcb.200311055. PMC2172237. PMID14757749. . [88] Sies H (1997). "Oxidative stress: oxidants and antioxidants" (http:/ / ep. physoc. org/ cgi/ reprint/ 82/ 2/ 291. pdf) (PDF). Exp Physiol 82 (2): 2915. PMID9129943. . [89] Vertuani S, Angusti A, Manfredini S (2004). "The antioxidants and pro-antioxidants network: an overview". Curr Pharm Des 10 (14): 167794. doi:10.2174/1381612043384655. PMID15134565. [90] von Stockar U, Liu J (1999). "Does microbial life always feed on negative entropy? Thermodynamic analysis of microbial growth". Biochim Biophys Acta 1412 (3): 191211. doi:10.1016/S0005-2728(99)00065-1. PMID10482783.
217
Overview of metabolism
[91] Demirel Y, Sandler S (2002). "Thermodynamics and bioenergetics". Biophys Chem 97 (23): 87111. doi:10.1016/S0301-4622(02)00069-8. PMID12050002. [92] Albert R (2005). "Scale-free networks in cell biology" (http:/ / jcs. biologists. org/ cgi/ content/ full/ 118/ 21/ 4947). J Cell Sci 118 (Pt 21): 494757. doi:10.1242/jcs.02714. PMID16254242. . [93] Brand M (1997). "Regulation analysis of energy metabolism" (http:/ / jeb. biologists. org/ cgi/ reprint/ 200/ 2/ 193). J Exp Biol 200 (Pt 2): 193202. PMID9050227. . [94] Soyer O, Salath M, Bonhoeffer S (2006). "Signal transduction networks: topology, response and biochemical processes". J Theor Biol 238 (2): 41625. doi:10.1016/j.jtbi.2005.05.030. PMID16045939. [95] Salter M, Knowles R, Pogson C (1994). "Metabolic control". Essays Biochem 28: 112. PMID7925313. [96] Westerhoff H, Groen A, Wanders R (1984). "Modern theories of metabolic control and their applications (review)". Biosci Rep 4 (1): 122. doi:10.1007/BF01120819. PMID6365197. [97] Fell D, Thomas S (1995). "Physiological control of metabolic flux: the requirement for multisite modulation". Biochem J 311 (Pt 1): 359. PMC1136115. PMID7575476. [98] Hendrickson W (2005). "Transduction of biochemical signals across cell membranes". Q Rev Biophys 38 (4): 32130. doi:10.1017/S0033583506004136. PMID16600054. [99] Cohen P (2000). "The regulation of protein function by multisite phosphorylationa 25 year update". Trends Biochem Sci 25 (12): 596601. doi:10.1016/S0968-0004(00)01712-6. PMID11116185. [100] Lienhard G, Slot J, James D, Mueckler M (1992). "How cells absorb glucose". Sci Am 266 (1): 8691. doi:10.1038/scientificamerican0192-86. PMID1734513. [101] Roach P (2002). "Glycogen and its metabolism". Curr Mol Med 2 (2): 10120. doi:10.2174/1566524024605761. PMID11949930. [102] Newgard C, Brady M, O'Doherty R, Saltiel A (2000). "Organizing glucose disposal: emerging roles of the glycogen targeting subunits of protein phosphatase-1" (http:/ / diabetes. diabetesjournals. org/ cgi/ reprint/ 49/ 12/ 1967. pdf) (PDF). Diabetes 49 (12): 196777. doi:10.2337/diabetes.49.12.1967. PMID11117996. . [103] Romano A, Conway T (1996). "Evolution of carbohydrate metabolic pathways". Res Microbiol 147 (67): 44855. doi:10.1016/0923-2508(96)83998-2. PMID9084754. [104] Koch A (1998). "How did bacteria come to be?". Adv Microb Physiol 40: 35399. doi:10.1016/S0065-2911(08)60135-6. PMID9889982. [105] Ouzounis C, Kyrpides N (1996). "The emergence of major cellular processes in evolution". FEBS Lett 390 (2): 11923. doi:10.1016/0014-5793(96)00631-X. PMID8706840. [106] C.Michael Hogan. 2010. Mutation. ed. E.Monosson and C.J.Cleveland. Encyclopedia of Earth. National Council for Science and the Environment. Washington DC (http:/ / www. eoearth. org/ article/ Mutation?topic=49496) [107] Caetano-Anolles G, Kim HS, Mittenthal JE (2007). "The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture". Proc Natl Acad Sci USA 104 (22): 935863. Bibcode2007PNAS..104.9358C. doi:10.1073/pnas.0701214104. PMC1890499. PMID17517598. [108] Schmidt S, Sunyaev S, Bork P, Dandekar T (2003). "Metabolites: a helping hand for pathway evolution?". Trends Biochem Sci 28 (6): 33641. doi:10.1016/S0968-0004(03)00114-2. PMID12826406. [109] Light S, Kraulis P (2004). "Network analysis of metabolic enzyme evolution in Escherichia coli". BMC Bioinformatics 5: 15. doi:10.1186/1471-2105-5-15. PMC394313. PMID15113413. Alves R, Chaleil R, Sternberg M (2002). "Evolution of enzymes in metabolism: a network perspective". J Mol Biol 320 (4): 75170. doi:10.1016/S0022-2836(02)00546-6. PMID12095253. [110] Kim HS, Mittenthal JE, Caetano-Anolles G (2006). "MANET: tracing evolution of protein architecture in metabolic networks". BMC Bioinformatics 19 (7): 351. doi:10.1186/1471-2105-7-351. PMC1559654. PMID16854231. [111] Teichmann SA, Rison SC, Thornton JM, Riley M, Gough J, Chothia C (2001). "Small-molecule metabolsim: an enzyme mosaic". Trends Biotechnol 19 (12): 4826. doi:10.1016/S0167-7799(01)01813-3. PMID11711174. [112] Spirin V, Gelfand M, Mironov A, Mirny L (June 2006). "A metabolic network in the evolutionary context: multiscale structure and modularity" (http:/ / www. pnas. org/ cgi/ pmidlookup?view=long& pmid=16731630). Proc Natl Acad Sci USA 103 (23): 87749. Bibcode2006PNAS..103.8774S. doi:10.1073/pnas.0510258103. PMC1482654. PMID16731630. . [113] Lawrence J (2005). "Common themes in the genome strategies of pathogens". Curr Opin Genet Dev 15 (6): 5848. doi:10.1016/j.gde.2005.09.007. PMID16188434. Wernegreen J (2005). "For better or worse: genomic consequences of intracellular mutualism and parasitism". Curr Opin Genet Dev 15 (6): 57283. doi:10.1016/j.gde.2005.09.013. PMID16230003. [114] Pl C, Papp B, Lercher M, Csermely P, Oliver S, Hurst L (2006). "Chance and necessity in the evolution of minimal metabolic networks". Nature 440 (7084): 66770. Bibcode2006Natur.440..667P. doi:10.1038/nature04568. PMID16572170. [115] Rennie M (1999). "An introduction to the use of tracers in nutrition and metabolism". Proc Nutr Soc 58 (4): 93544. doi:10.1017/S002966519900124X. PMID10817161. [116] Phair R (1997). "Development of kinetic models in the nonlinear world of molecular cell biology". Metabolism 46 (12): 148995. doi:10.1016/S0026-0495(97)90154-2. PMID9439549. [117] Sterck L, Rombauts S, Vandepoele K, Rouz P, Van de Peer Y (2007). "How many genes are there in plants (... and why are they there)?". Curr Opin Plant Biol 10 (2): 199203. doi:10.1016/j.pbi.2007.01.004. PMID17289424. [118] Borodina I, Nielsen J (2005). "From genomes to in silico cells via metabolic networks". Curr Opin Biotechnol 16 (3): 3505. doi:10.1016/j.copbio.2005.04.008. PMID15961036.
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Overview of metabolism
[119] Gianchandani E, Brautigan D, Papin J (2006). "Systems analyses characterize integrated functions of biochemical networks". Trends Biochem Sci 31 (5): 28491. doi:10.1016/j.tibs.2006.03.007. PMID16616498. [120] Duarte NC, Becker SA, Jamshidi N, et al. (February 2007). "Global reconstruction of the human metabolic network based on genomic and bibliomic data" (http:/ / www. pnas. org/ cgi/ pmidlookup?view=long& pmid=17267599). Proc. Natl. Acad. Sci. U.S.A. 104 (6): 177782. Bibcode2007PNAS..104.1777D. doi:10.1073/pnas.0610772104. PMC1794290. PMID17267599. . [121] Goh KI, Cusick ME, Valle D, Childs B, Vidal M, Barabsi AL (May 2007). "The human disease network". Proc. Natl. Acad. Sci. U.S.A. 104 (21): 868590. Bibcode2007PNAS..104.8685G. doi:10.1073/pnas.0701361104. PMC1885563. PMID17502601. [122] Lee DS, Park J, Kay KA, Christakis NA, Oltvai ZN, Barabsi AL (July 2008). "The implications of human metabolic network topology for disease comorbidity" (http:/ / www. pnas. org/ lookup/ pmid?view=long& pmid=18599447). Proc. Natl. Acad. Sci. U.S.A. 105 (29): 98809885. Bibcode2008PNAS..105.9880L. doi:10.1073/pnas.0802208105. PMC2481357. PMID18599447. . [123] Csete M, Doyle J (2004). "Bow ties, metabolism and disease". Trends Biotechnol. 22 (9): 44650. doi:10.1016/j.tibtech.2004.07.007. PMID15331224. [124] Ma HW, Zeng AP (2003). "The connectivity structure, giant strong component and centrality of metabolic networks". Bioinformatics 19 (11): 142330. doi:10.1093/bioinformatics/btg177. PMID12874056. [125] Zhao J, Yu H, Luo JH, Cao ZW, Li YX (2006). "Hierarchical modularity of nested bow-ties in metabolic networks". BMC Bioinformatics 7: 386. doi:10.1186/1471-2105-7-386. PMC1560398. PMID16916470. [126] Thykaer J, Nielsen J (2003). "Metabolic engineering of beta-lactam production". Metab Eng 5 (1): 5669. doi:10.1016/S1096-7176(03)00003-X. PMID12749845. Gonzlez-Pajuelo M, Meynial-Salles I, Mendes F, Andrade J, Vasconcelos I, Soucaille P (2005). "Metabolic engineering of Clostridium acetobutylicum for the industrial production of 1,3-propanediol from glycerol". Metab Eng 7 (56): 32936. doi:10.1016/j.ymben.2005.06.001. PMID16095939. Krmer M, Bongaerts J, Bovenberg R, Kremer S, Mller U, Orf S, Wubbolts M, Raeven L (2003). "Metabolic engineering for microbial production of shikimic acid". Metab Eng 5 (4): 27783. doi:10.1016/j.ymben.2003.09.001. PMID14642355. [127] Koffas M, Roberge C, Lee K, Stephanopoulos G (1999). "Metabolic engineering". Annu Rev Biomed Eng 1: 53557. doi:10.1146/annurev.bioeng.1.1.535. PMID11701499. [128] "Metabolism" (http:/ / www. etymonline. com/ index. php?term=metabolism). The Online Etymology Dictionary. . Retrieved 2007-02-20. [129] Eknoyan G (1999). "Santorio Sanctorius (15611636) founding father of metabolic balance studies". Am J Nephrol 19 (2): 22633. doi:10.1159/000013455. PMID10213823. [130] Williams, H. S. (1904) A History of Science: in Five Volumes. Volume IV: Modern Development of the Chemical and Biological Sciences (http:/ / etext. lib. virginia. edu/ toc/ modeng/ public/ Wil4Sci. html) Harper and Brothers (New York) Retrieved on 2007-03-26 [131] Dubos J. (1951). "Louis Pasteur: Free Lance of Science, Gollancz. Quoted in Manchester K. L. (1995) Louis Pasteur (18221895)chance and the prepared mind". Trends Biotechnol 13 (12): 511515. doi:10.1016/S0167-7799(00)89014-9. PMID8595136. [132] Kinne-Saffran E, Kinne R (1999). "Vitalism and synthesis of urea. From Friedrich Whler to Hans A. Krebs". Am J Nephrol 19 (2): 2904. doi:10.1159/000013463. PMID10213830. [133] Eduard Buchner's 1907 Nobel lecture (http:/ / nobelprize. org/ nobel_prizes/ chemistry/ laureates/ 1907/ buchner-lecture. html) at http:/ / nobelprize. org Accessed 2007-03-20 [134] Kornberg H (2000). "Krebs and his trinity of cycles". Nat Rev Mol Cell Biol 1 (3): 2258. doi:10.1038/35043073. PMID11252898. [135] Krebs HA, Henseleit K (1932). "Untersuchungen ber die Harnstoffbildung im tierkorper". Z. Physiol. Chem. 210: 3366. Krebs H, Johnson W (April 1937). "Metabolism of ketonic acids in animal tissues". Biochem J 31 (4): 64560. PMC1266984. PMID16746382.
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Further reading
Introductory Rose, S. and Mileusnic, R., The Chemistry of Life. (Penguin Press Science, 1999), ISBN 0-14-027273-9 Schneider, E. D. and Sagan, D., Into the Cool: Energy Flow, Thermodynamics, and Life. (University Of Chicago Press, 2005), ISBN 0-226-73936-8 Lane, N., Oxygen: The Molecule that Made the World. (Oxford University Press, USA, 2004), ISBN 0-19-860783-0 Advanced Price, N. and Stevens, L., Fundamentals of Enzymology: Cell and Molecular Biology of Catalytic Proteins. (Oxford University Press, 1999), ISBN 0-19-850229-X Berg, J. Tymoczko, J. and Stryer, L., Biochemistry. (W. H. Freeman and Company, 2002), ISBN 0-7167-4955-6 Cox, M. and Nelson, D. L., Lehninger Principles of Biochemistry. (Palgrave Macmillan, 2004), ISBN 0-7167-4339-6
Overview of metabolism Brock, T. D. Madigan, M. T. Martinko, J. and Parker J., Brock's Biology of Microorganisms. (Benjamin Cummings, 2002), ISBN 0-13-066271-2 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 0-19-855598-9 Nicholls, D. G. and Ferguson, S. J., Bioenergetics. (Academic Press Inc., 2002), ISBN 0-12-518121-3
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External links
biochemical families: prot nucl carb (glpr, alco, glys) lipd (fata/i, phld, strd, gllp, eico) amac/i ncbs/i ttpy/i
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Carbohydrate metabolism
Glycolysis
Glycolysis (from glycose, an older term[1] for glucose + -lysis degradation) is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO + H+. The free energy released in this process is used to form the high-energy compounds ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide).
Glycolysis overview
Glycolysis is a definite sequence of ten reactions involving ten intermediate compounds (one of the steps involves two intermediates). The intermediates provide entry points to glycolysis. For example, most monosaccharides, such as fructose, glucose, and galactose, can be converted to one of these intermediates. The intermediates may also be directly useful. For example, the intermediate dihydroxyacetone phosphate (DHAP) is a source of the glycerol that combines with fatty acids to form fat. It occurs, with variations, in nearly all organisms, both aerobic and anaerobic. The wide occurrence of glycolysis indicates that it is one of the most ancient known metabolic pathways.[2] It occur in the cytosol of the cell. The most common type of glycolysis is the Embden-Meyerhof-Parnas pathway (EMP pathway), which was first discovered by Gustav Embden, Otto Meyerhof and Jakub Karol Parnas. Glycolysis also refers to other pathways, such as the EntnerDoudoroff pathway and various heterofermentative and homofermentative pathways. However, the discussion here will be limited to the Embden-Meyerhof pathway. The entire glycolysis pathway can be separated into two phases[3] : 1. The Preparatory Phase - in which ATP is consumed and is hence also known as the investment phase 2. The Pay Off Phase - in which ATP is produced.
Overview
The overall reaction of glycolysis is:
D-[Glucose] + 2 [NAD]+ + 2 [ADP] + 2 [P]i 2 [Pyruvate] + 2 [NADH] + 2 H+ + 2 [ATP] + 2 H2O
The use of symbols in this equation makes it appear unbalanced with respect to oxygen atoms, hydrogen atoms, and charges. Atom balance is maintained by the two phosphate (Pi) groups:[4] each exists in the form of a hydrogen phosphate anion (HPO42-), dissociating to contribute 2 H+ overall
Glycolysis each liberates an oxygen atom when it binds to an ADP (adenosine diphosphate) molecule, contributing 2 O overall Charges are balanced by the difference between ADP and ATP. In the cellular environment, all three hydroxy groups of ADP dissociate into -O- and H+, giving ADP3-, and this ion tends to exist in an ionic bond with Mg2+, giving ADPMg-. ATP behaves identically except that it has four hydroxy groups, giving ATPMg2-. When these differences along with the true charges on the two phosphate groups are considered together, the net charges of -4 on each side are balanced. For simple anaerobic fermentations, the metabolism of one molecule of glucose to two molecules of pyruvate has a net yield of two molecules of ATP. Most cells will then carry out further reactions to 'repay' the used NAD+ and produce a final product of ethanol or lactic acid. Many bacteria use inorganic compounds as hydrogen acceptors to regenerate the NAD+. Cells performing aerobic respiration synthesize much more ATP, but not as part of glycolysis. These further aerobic reactions use pyruvate and NADH + H+ from glycolysis. Eukaryotic aerobic respiration produces approximately 34 additional molecules of ATP for each glucose molecule, however most of these are produced by a vastly different mechanism to the substrate-level phosphorylation in glycolysis.
Glycolysis
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The lower-energy production, per glucose, of anaerobic respiration relative to aerobic respiration, results in greater flux through the pathway under hypoxic (low-oxygen) conditions, unless alternative sources of anaerobically-oxidizable substrates, such as fatty acids, are found.
Glycolysis
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Sequence of reactions
Preparatory phase
The first five steps are regarded as the preparatory (or investment) phase, since they consume energy to convert the glucose into two three-carbon sugar phosphates[3] (G3P).
The first step in glycolysis is phosphorylation of glucose by a family of enzymes called hexokinases to form glucose 6-phosphate (G6P). This reaction consumes ATP, but it acts to keep the glucose concentration low, promoting continuous transport of glucose into the cell through the plasma membrane transporters. In addition, it blocks the glucose from leaking out the cell lacks transporters for G6P, and free diffusion out of the cell is prevented due to the charged nature of G6P. Glucose may alternatively be from the phosphorolysis or hydrolysis of intracellular starch or glycogen. In animals, an isozyme of hexokinase called glucokinase is also used in the liver, which has a much lower affinity for glucose (Km in the vicinity of normal glycemia), and differs in regulatory properties. The different substrate affinity and alternate regulation of this enzyme are a reflection of the role of the liver in maintaining blood sugar levels. Cofactors: Mg2+
D-Glucose (Glc)
-D-Glucose-6-phosphate (G6P)
ATP
H+ + ADP
G6P is then rearranged into fructose 6-phosphate (F6P) by glucose phosphate isomerase. Fructose can also enter the glycolytic pathway by phosphorylation at this point. The change in structure is an isomerization, in which the G6P has been converted to F6P. The reaction requires an enzyme, phosphohexose isomerase, to proceed. This reaction is freely reversible under normal cell conditions. However, it is often driven forward because of a low concentration of F6P, which is constantly consumed during the next step of glycolysis. Under conditions of high F6P concentration, this reaction readily runs in reverse. This phenomenon can be explained through Le Chatelier's Principle. Isomerization to a keto sugar is necessary for carbanion stabilization in the fourth reaction step (below).
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The energy expenditure of another ATP in this step is justified in 2 ways: The glycolytic process (up to this step) is now irreversible, and the energy supplied destabilizes the molecule. Because the reaction catalyzed by Phosphofructokinase 1 (PFK-1) is coupled to the hydrolysis of ATP, an energetically favorable step, it is, in essence, irreversible, and a different pathway must be used to do the reverse conversion during gluconeogenesis. This makes the reaction a key regulatory point (see below). This is also the rate-limiting step. Furthermore, the second phosphorylation event is necessary to allow the formation of two charged groups (rather than only one) in the subsequent step of glycolysis, ensuring the prevention of free diffusion of substrates out of the cell. The same reaction can also be catalyzed by pyrophosphate-dependent phosphofructokinase (PFP or PPi-PFK), which is found in most plants, some bacteria, archea, and protists, but not in animals. This enzyme uses pyrophosphate (PPi) as a phosphate donor instead of ATP. It is a reversible reaction, [5] increasing the flexibility of glycolytic metabolism. A rarer ADP-dependent PFK enzyme variant has [6] been identified in archaean species. Cofactors: Mg2+
Destabilizing the molecule in the previous reaction allows the hexose ring to be split by aldolase into two triose sugars, dihydroxyacetone phosphate, a ketone, and glyceraldehyde 3-phosphate, an aldehyde. There are two classes of aldolases: class I aldolases, present in animals and plants, and class II aldolases, present in fungi and bacteria; the two classes use different mechanisms in cleaving the ketose ring. Electrons delocalized in the carbon-carbon bond cleavage associate with the alcohol group. The resulting carbanion is stabilized by the structure of the carbanion itself via resonance charge distribution and by the presence of a charged ion prosthetic group.
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Triosephosphate isomerase rapidly interconverts dihydroxyacetone phosphate with glyceraldehyde 3-phosphate (GADP) that proceeds further into glycolysis. This is advantageous, as it directs dihydroxyacetone phosphate down the same pathway as glyceraldehyde 3-phosphate, simplifying regulation.
Pay-off phase
The second half of glycolysis is known as the pay-off phase, characterised by a net gain of the energy-rich molecules ATP and NADH[3] . Since glucose leads to two triose sugars in the preparatory phase, each reaction in the pay-off phase occurs twice per glucose molecule. This yields 2 NADH molecules and 4 ATP molecules, leading to a net gain of 2 NADH molecules and 2 ATP molecules from the glycolytic pathway per glucose.
The triose sugars are dehydrogenated and inorganic phosphate is added to them, forming 1,3-bisphosphoglycerate. The hydrogen is used to reduce two molecules of NAD+, a hydrogen carrier, to give NADH + H+ for each triose. Hydrogen atom balance and charge balance are both maintained because the phosphate (Pi) group actually exists in the form of a [4] hydrogen phosphate anion (HPO42-), which dissociates to contribute the extra H+ ion and gives a net charge of -3 on both sides.
D-1,3-bisphosphoglycerate (1,3BPG)
NAD+ + Pi
NADH + H+
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This step is the enzymatic transfer of a phosphate group from 1,3-bisphosphoglycerate to ADP by phosphoglycerate kinase, forming ATP and 3-phosphoglycerate. At this step, glycolysis has reached the break-even point: 2 molecules of ATP were consumed, and 2 new molecules have now been synthesized. This step, one of the two substrate-level phosphorylation steps, requires ADP; thus, when the cell has plenty of ATP (and little ADP), this reaction does not occur. Because ATP decays relatively quickly when it is not metabolized, this is an important regulatory point in the glycolytic pathway. ADP actually exists as ADPMg-, and ATP as ATPMg2-, balancing the charges at -5 both sides. Cofactors: Mg2+
1,3-bisphosphoglycerate (1,3-BPG)
3-phosphoglycerate (3-P-G)
ADP
ATP
3-phosphoglycerate (3PG)
2-phosphoglycerate (2PG)
Enolase next forms phosphoenolpyruvate from 2-phosphoglycerate. Cofactors: 2 Mg2+: one "conformational" ion to coordinate with the carboxylate group of the substrate, and one "catalytic" ion that participates in the dehydration.
2-phosphoglycerate (2PG)
phosphoenolpyruvate (PEP)
enolase (ENO)
Glycolysis
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A final substrate-level phosphorylation now forms a molecule of pyruvate and a molecule of ATP by means of the enzyme pyruvate kinase. This serves as an additional regulatory step, similar to the phosphoglycerate kinase step. Cofactors: Mg2+
phosphoenolpyruvate (PEP)
pyruvate (Pyr)
Regulation
Glycolysis is regulated by slowing down or speeding up certain steps in the glycolysis pathway. This is accomplished by inhibiting or activating the enzymes that are involved. The steps that are regulated may be determined by calculating the change in free energy, G, for each step. If a step's products and reactants are in equilibrium, then the step is assumed to not be regulated. Since the change in free energy is zero for a system at equilibrium, any step with a free energy change near zero is not being regulated. If a step is being regulated, then that step's enzyme is not converting reactants into products as fast as it could, resulting in a build-up of reactants, which would be converted to products if the enzyme were operating faster. Since the reaction is thermodynamically favorable, the change in free energy for the step will be negative. A step with a large negative change in free energy is assumed to be regulated.
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The change in free energy for each step of glycolysis estimated from the concentration of metabolites in an erythrocyte.
The change in free energy, G, for each step in the glycolysis pathway can be calculated using G = G' + RTln Q, where Q is the reaction quotient. This requires knowing the concentrations of the metabolites. All of these values are available for erythrocytes, with the exception of the concentrations of NAD+ and NADH. The ratio of NAD+ to NADH in the cytoplasm is approximately 1000 in the step 6, something that makes the oxidation of glyceraldehyde-3-phosphate more favourable. Using the measured concentrations of each step, and the standard free energy changes, the actual free energy change can be calculated. (Neglecting this is very common - the delta G of ATP hydrolysis in cells is not the standard free energy change of ATP hydrolysis quoted in textbooks).
fructose-1,6-bisphosphate4- dihydroxyacetone phosphate2- + glyceraldehyde-3-phosphate2- 23.9 dihydroxyacetone phosphate2- glyceraldehyde-3-phosphate2glyceraldehyde-3-phosphate2- + Pi2- + NAD+ 1,3-bisphosphoglycerate4- + NADH + H+ 1,3-bisphosphoglycerate4- + ADP3- 3-phosphoglycerate3- + ATP43-phosphoglycerate3- 2-phosphoglycerate32-phosphoglycerate3- phosphoenolpyruvate3- + H2O phosphoenolpyruvate3- + ADP3- + H+ pyruvate- + ATP47.56 6.30 -18.9 4.4 1.8 -31.7
From measuring the physiological concentrations of metabolites in an erythrocyte it seems that about seven of the steps in glycolysis are in equilibrium for that cell type. Three of the steps the ones with large negative free energy changes are not in equilibrium and are referred to as irreversible; such steps are often subject to regulation. Step 5 in the figure is shown behind the other steps, because that step is a side-reaction that can decrease or increase the concentration of the intermediate glyceraldehyde-3-phosphate. That compound is converted to dihydroxyacetone
Glycolysis phosphate by the enzyme triose phosphate isomerase, which is a catalytically perfect enzyme; its rate is so fast that the reaction can be assumed to be in equilibrium. The fact that G is not zero indicates that the actual concentrations in the erythrocyte are not accurately known.
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Biochemical logic
The existence of more than one point of regulation indicates that intermediates between those points enter and leave the glycolysis pathway by other processes. For example, in the first regulated step, hexokinase converts glucose into glucose-6-phosphate. Instead of continuing through the glycolysis pathway, this intermediate can be converted into glucose storage molecules, such as glycogen or starch. The reverse reaction, breaking down, e.g., glycogen, produces mainly glucose-6-phosphate; very little free glucose is formed in the reaction. The glucose-6-phosphate so produced can enter glycolysis after the first control point. In the second regulated step (the third step of glycolysis), phosphofructokinase converts fructose-6-phosphate into fructose-1,6-bisphosphate, which then is converted into glyceraldehyde-3-phosphate and dihydroxyacetone phosphate. The dihydroxyacetone phosphate can be removed from glycolysis by conversion into glycerol-3-phosphate, which can be used to form triglycerides.[9] On the converse, triglycerides can be broken down into fatty acids and glycerol; the latter, in turn, can be converted into dihydroxyacetone phosphate, which can enter glycolysis after the second control point.
Regulation
The three regulated enzymes are hexokinase, phosphofructokinase, and pyruvate kinase. The flux through the glycolytic pathway is adjusted in response to conditions both inside and outside the cell. The rate in liver is regulated to meet major cellular needs: (1) the production of ATP, (2) the provision of building blocks for biosynthetic reactions, and (3) to lower blood glucose, one of the major functions of the liver. When blood sugar falls, glycolysis is halted in the liver to allow the reverse process, gluconeogenesis. In glycolysis, the reactions catalyzed by hexokinase, phosphofructokinase, and pyruvate kinase are effectively irreversible in most organisms. In metabolic pathways, such enzymes are potential sites of control, and all three enzymes serve this purpose in glycolysis. Hexokinase In animals, regulation of blood glucose levels by the pancreas in conjunction with the liver is a vital part of homeostasis. In liver cells, extra G6P (glucose-6-phosphate) may be converted to G1P for conversion to glycogen, or it is alternatively converted by glycolysis to acetyl-CoA and then citrate. Excess citrate is exported to the cytosol, where ATP citrate lyase will regenerate acetyl-CoA and OAA. The acetyl-CoA is then used for fatty acid synthesis and cholesterol synthesis, two important ways of utilizing excess glucose when its [10] Yeast hexokinase B. PDB 1IG8 . concentration is high in blood. Liver contains both hexokinase and glucokinase; the latter catalyses the phosphorylation of glucose to G6P and is not inhibited by G6P. Thus, it allows glucose to be converted into glycogen, fatty acids, and cholesterol even when hexokinase activity is low.[11] This is important when blood glucose levels are high. During hypoglycemia, the glycogen can be converted back to G6P and then converted to glucose by the liver-specific enzyme glucose 6-phosphatase. This reverse reaction is an important role of liver cells to maintain blood sugars levels during fasting. This is critical for brain function, since the brain utilizes glucose as an energy source under most conditions.
Glycolysis Phosphofructokinase Phosphofructokinase is an important control point in the glycolytic pathway, since it is one of the irreversible steps and has key allosteric effectors, AMP and fructose 2,6-bisphosphate (F2,6BP). Fructose 2,6-bisphosphate (F2,6BP) is a very potent activator of phosphofructokinase (PFK-1), which is synthesised when F6P is phosphorylated by a second phosphofructokinase (PFK2). In liver, when blood sugar is low and glucagon elevates cAMP, PFK2 is phosphorylated by protein kinase A. The phosphorylation inactivates PFK2, and another domain on this protein becomes active as fructose 2,6-bisphosphatase, which converts F2,6BP back to F6P. Both Bacillus stearothermophilus phosphofructokinase. [12] glucagon and epinephrine cause high levels of cAMP in the liver. The PDB 6PFK . result of lower levels of liver fructose-2,6-bisphosphate is a decrease in activity of phosphofructokinase and an increase in activity of fructose 1,6-bisphosphatase, so that gluconeogenesis (in essence, "glycolysis in reverse") is favored. This is consistent with the role of the liver in such situations, since the response of the liver to these hormones is to release glucose to the blood. ATP competes with AMP for the allosteric effector site on the PFK enzyme. ATP concentrations in cells are much higher than those of AMP, typically 100-fold higher,[13] but the concentration of ATP does not change more than about 10% under physiological conditions, whereas a 10% drop in ATP results in a 6-fold increase in AMP.[14] Thus, the relevance of ATP as an allosteric effector is questionable. An increase in AMP is a consequence of a decrease in energy charge in the cell. Citrate inhibits phosphofructokinase when tested in vitro by enhancing the inhibitory effect of ATP. However, it is doubtful that this is a meaningful effect in vivo, because citrate in the cytosol is utilized mainly for conversion to acetyl-CoA for fatty acid and cholesterol synthesis. Pyruvate kinase This enzyme catalyzes the last step of glycolysis, in which pyruvate and ATP are formed. Regulation of this enzyme is discussed in the main topic, pyruvate kinase.
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Post-glycolysis processes
The overall process of glycolysis is: glucose + 2 NAD+ + 2 ADP + 2 Pi 2 pyruvate + 2 NADH + 2 H+ + 2 ATP + 2 H2O If glycolysis were to continue indefinitely, all of the NAD+ would be used up, and glycolysis would stop. To allow glycolysis to continue, organisms must be able to oxidize NADH back to NAD+.
Yeast pyruvate kinase. PDB 1A3W [15] .
Fermentation
One method of doing this is to simply have the pyruvate do the oxidation; in this process, the pyruvate is converted to lactate (the conjugate base of lactic acid) in a process called lactic acid fermentation: pyruvate + NADH + H+ lactate + NAD+
Glycolysis This process occurs in the bacteria involved in making yogurt (the lactic acid causes the milk to curdle). This process also occurs in animals under hypoxic (or partially-anaerobic) conditions, found, for example, in overworked muscles that are starved of oxygen, or in infarcted heart muscle cells. In many tissues, this is a cellular last resort for energy; most animal tissue cannot maintain anaerobic respiration for an extended length of time. Some organisms, such as yeast, convert NADH back to NAD+ in a process called ethanol fermentation. In this process, the pyruvate is converted first to acetaldehyde and carbon dioxide, then to ethanol. Lactic acid fermentation and ethanol fermentation can occur in the absence of oxygen. This anaerobic fermentation allows many single-cell organisms to use glycolysis as their only energy source.
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Anaerobic respiration
In the above two examples of fermentation, NADH is oxidized by transferring two electrons to pyruvate. However, anaerobic bacteria use a wide variety of compounds as the terminal electron acceptors in cellular respiration: nitrogenous compounds, such as nitrates and nitrites; sulfur compounds, such as sulfates, sulfites, sulfur dioxide, and elemental sulfur; carbon dioxide; iron compounds; manganese compounds; cobalt compounds; and uranium compounds.
Aerobic respiration
In aerobic organisms, a complex mechanism has been developed to use the oxygen in air as the final electron acceptor of respiration. First, pyruvate is converted to acetyl-CoA and CO2 within the mitochondria in a process called pyruvate decarboxylation. Second, the acetyl-CoA enters the citric acid cycle, also known as Krebs Cycle, where it is fully oxidized to carbon dioxide and water, producing yet more NADH. Third, the NADH is oxidized to NAD+ by the electron transport chain, using oxygen as the final electron acceptor. This process creates a "hydrogen ion gradient" across the inner membrane of the mitochondria. Fourth, the proton gradient is used to produce a large amount of ATP in a process called oxidative phosphorylation.
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Glycolysis in disease
Genetic diseases
Glycolytic mutations are generally rare due to importance of the metabolic pathway, this means that the majority of occurring mutations result in an inability for the cell to respire, and therefore cause the death of the cell at an early stage. However, some mutations are seen with one notable example being Pyruvate kinase deficiency, leading to chronic hemolytic anemia.
Cancer
Malignant rapidly-growing tumor cells typically have glycolytic rates that are up to 200 times higher than those of their normal tissues of origin. This phenomenon was first described in 1930 by Otto Warburg and is referred to as the Warburg effect. The Warburg hypothesis claims that cancer is primarily caused by dysfunctionality in mitochondrial metabolism, rather than because of uncontrolled growth of cells. A number of theories have been advanced to explain the Warburg effect. This high glycolysis rate has important medical applications, as high aerobic glycolysis by malignant tumors is utilized clinically to diagnose and monitor treatment responses of cancers by imaging uptake of 2-18F-2-deoxyglucose (FDG) (a radioactive modified hexokinase substrate) with positron emission tomography (PET).[16] [17] There is ongoing research to affect mitochondrial metabolism and treat cancer by reducing glycolysis and thus starving cancerous cells in various new ways, including a ketogenic diet.
Alzheimer's disease
Disfunctioning glycolysis or glucose metabolism in fronto-temporo-parietal and cingulate cortices has been associated with Alzheimer's disease,[18] probably due to the decreased amyloid (1-42) (A42) and increased tau, phosphorylated tau in cerebrospinal fluid (CSF) [19]
Alternative nomenclature
Some of the metabolites in glycolysis have alternative names and nomenclature. In part, this is because some of them are common to other pathways, such as the Calvin cycle.
This article 1 3 4 5 6 7 glucose fructose 6-phosphate fructose 1,6-bisphosphate Glc F6P F1,6BP fructose 1,6-diphosphate glycerone phosphate 3-phosphoglyceraldehyde PGAL, G3P, GALP,GAP,TP FBP, FDP, F1,6DP Alternative names dextrose Alternative nomenclature
1,3BPG glycerate PGAP, BPG, DPG 1,3-bisphosphate, glycerate 1,3-diphosphate, 1,3-diphosphoglycerate 3PG 2PG PEP glycerate 3-phosphate glycerate 2-phosphate PGA, GP
8 9
3-phosphoglycerate 2-phosphoglycerate
10 phosphoenolpyruvate
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11 pyruvate Pyr pyruvic acid
References
[1] [2] [3] [4] Webster's New International Dictionary of the English Language, 2nd ed. (1937) Merriam Company, Springfield, Mass. Romano AH, Conway T. (1996) Evolution of carbohydrate metabolic pathways. Res Microbiol. 147(6-7):448-55 PMID 9084754 Glycolysis - Animation and Notes (http:/ / pharmaxchange. info/ press/ 2011/ 09/ glycolysis-animation-and-notes/ ) Lane, A. N.; Fan, T. W. -M.; Higashi, R. M. (2009). "Metabolic acidosis and the importance of balanced equations". Metabolomics 5 (2): 163165. doi:10.1007/s11306-008-0142-2. [5] Reeves, R. E.; South D. J., Blytt H. J. and Warren L. G. (1974). "Pyrophosphate: D-fructose 6-phosphate 1-phosphotransferase. A new enzyme with the glycolytic function 6-phosphate 1-phosphotransferase". J Biol Chem 249 (24): 77377741. PMID4372217. [6] Selig, M.; Xavier K. B., Santos H. and Schnheit P. (1997). "Comparative analysis of Embden-Meyerhof and Entner-Doudoroff glycolytic pathways in hyperthermophilic archaea and the bacterium Thermotoga". Arch Microbiol 167 (4): 217232. PMID9075622. [7] Garrett, R.; Grisham, C. M. (2005). Biochemistry (3rd ed.). Belmont, CA: Thomson Brooks/Cole. p.584. ISBN0-534-49011-6. [8] Garrett, R.; Grisham, C. M. (2005). Biochemistry (3rd ed.). Belmont, CA: Thomson Brooks/Cole. pp.582583. ISBN0-534-49011-6. [9] Berg, J. M.; Tymoczko, J. L.; Stryer, L. (2007). Biochemistry (6th ed.). New York: Freeman. p.622. ISBN0-534-49011-6. [10] http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1IG8 [11] Voet D., and Voet J. G. (2004). Biochemistry 3rd Edition (New York, John Wiley & Sons, Inc.) [12] http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=6PFK [13] Beis I., and Newsholme E. A. (1975). The contents of adenine nucleotides, phosphagens and some glycolytic intermediates in resting muscles from vertebrates and invertebrates. Biochem J 152, 23-32. [14] Voet D., and Voet J. G. (2004). Biochemistry 3rd Edition (New York, John Wiley & Sons, Inc.). [15] http:/ / www. rcsb. org/ pdb/ explore/ explore. do?structureId=1A3W [16] "PET Scan: PET Scan Info Reveals ..." (http:/ / www. petscaninfo. com/ ). . Retrieved December 5, 2005. [17] "4320139 549..559" (http:/ / biogenomica. com/ PDFs/ PauwelsPETandHexokinase. pdf). . Retrieved December 5, 2005. [18] Hunt, A . et al.; Schonknecht, P; Henze, M; Seidl, U; Haberkorn, U; Schroder, J (2007). "Reduced cerebral glucose metabolism in patients at risk for Alzheimer's disease". Psychiatry Research: Neuroimaging 155 (2): 147154. doi:10.1016/j.pscychresns.2006.12.003. PMID17524628. [19] Hunt, A . et al.; Van Der Flier, WM; Blankenstein, MA; Bouwman, FH; Van Kamp, GJ; Barkhof, F; Scheltens, P (2008). "CSF and MRI markers independently contribute to the diagnosis of Alzheimer's disease". Neurobiology of Aging 29 (5): 669675. doi:10.1016/j.neurobiolaging.2006.11.018. PMID17208336.
External links
A Detailed Glycolysis Animation provided by [[IUBMB (http://www.iubmb-nicholson.org/swf/glycolysis. swf)]] ( Adobe Flash (http://get.adobe.com/flashplayer/) Required) The Glycolytic enzymes in Glycolysis (http://nist.rcsb.org/pdb/molecules/pdb50_1.html) at Protein Data Bank Glycolytic cycle with animations (http://www.wdv.com/CellWorld/Biochemistry/Glycolytic) at wdv.com Metabolism, Cellular Respiration and Photosynthesis - The Virtual Library of Biochemistry and Cell Biology (http://www.biochemweb.org/metabolism.shtml) at biochemweb.org notes on glycolysis (http://www.rahulgladwin.com/blog/2007/01/notes-on-glycolysis.html) at rahulgladwin.com The chemical logic behind glycolysis (http://www2.ufp.pt/~pedros/bq/glycolysis.htm) at ufp.pt Expasy biochemical pathways poster (http://www.expasy.org/tools/pathways/boehringer_legends.html) at ExPASy Mnemonic at medicalmnemonics.com 317 5468 (http://www.medicalmnemonics.com/cgi-bin/lookup. cfm?id1=317&id2=5468&id3=&id4=)
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Gluconeogenesis
Gluconeogenesis (abbreviated GNG) is a metabolic pathway that results in the generation of glucose from non-carbohydrate carbon substrates such as lactate, glycerol, and glucogenic amino acids. It is one of the two main mechanisms humans and many other animals use to keep blood glucose levels from dropping too low (hypoglycemia). The other means of maintaining blood glucose levels is through the degradation of glycogen (glycogenolysis).[1] Gluconeogenesis is a ubiquitous process, present in plants, animals, fungi, bacteria, and other microorganisms.[2] In animals, gluconeogenesis takes place mainly in the liver and, to a lesser extent, in the cortex of kidneys. This process occurs during periods of fasting, starvation, low-carbohydrate diets, or intense exercise and is highly endergonic. For example, the pathway leading from pyruvate to glucose-6-phosphate requires 4 molecules of ATP and 2 molecules of GTP. Gluconeogenesis is often associated with ketosis. Gluconeogenesis is also a target of therapy for type II diabetes, such as metformin, which inhibits glucose formation and stimulates glucose uptake by cells.[3]
Gluconeogenesis pathway with key molecules and enzymes. Many steps are the opposite of those found in the glycolysis.
All citric acid cycle intermediates, through conversion to oxaloacetate, amino acids other than lysine or leucine, and glycerol can also function as substrates for gluconeogenesis.[4] Transamination or deamination of amino acids facilitates entering of their carbon skeleton into the cycle directly (as pyruvate or oxaloacetate), or indirectly via the citric acid cycle. Whether fatty acids can be converted into glucose in animals has been a longstanding question in biochemistry.[6] It is known that odd-chain fatty acids can be oxidized to yield propionyl CoA, a precursor for succinyl CoA, which can be converted to
Catabolism of proteinogenic amino acids. Amino acids are classified according the [5] abilities of their products to enter gluconeogenesis: Glucogenic amino acids have this abilityKetogenic amino acids do not. These products may still be used for ketogenesis or lipid synthesis.Some amino acids are catabolized into both glucogenic and ketogenic products.
Gluconeogenesis pyruvate and enter into gluconeogenesis. In plants, specifically seedlings, the glyoxylate cycle can be used to convert fatty acids (acetate) into the primary carbon source of the organism. The glyoxylate cycle produces four-carbon dicarboxylic acids that can enter gluconeogenesis.[4] In 1995, researchers identified the glyoxylate cycle in nematodes.[7] In addition, the glyoxylate enzymes malate synthase and isocitrate lyase have been found in animal tissues.[8] Genes coding for malate synthase gene have been identified in other [metazoans] including arthropods, echinoderms, and even some vertebrates. Mammals found to possess these genes include monotremes (platypus) and marsupials (opossum) but not placental mammals. Genes for isocitrate lyase are found only in nematodes, in which, it is apparent, they originated in horizontal gene transfer from bacteria. The existence of glyoxylate cycles in humans has not been established, and it is widely held that fatty acids cannot be converted to glucose in humans directly. However, carbon-14 has been shown to end up in glucose when it is supplied in fatty acids.[9] Despite these findings, it is considered unlikely that the 2-carbon acetyl-CoA derived from the oxidation of fatty acids would produce a net yield of glucose via the citric acid cycle.[6] Glycerol, which is a part of the triacylglycerol molecule, can be used in gluconeogenesis.
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Location
In humans, gluconeogenesis is restricted to the liver and to a lesser extent the kidney.[10] In all species, the formation of oxaloacetate from pyruvate and TCA cycle intermediates is restricted to the mitochondrion, and the enzymes that convert PEP to glucose are found in the cytosol.[11] The location of the enzyme that links these two parts of gluconeogenesis by converting oxaloacetate to PEP, PEP carboxykinase, is variable by species: it can be found entirely within the mitochondria, entirely within the cytosol, or dispersed evenly between the two, as it is in humans.[11] Transport of PEP across the mitochondrial membrane is accomplished by dedicated transport proteins; however no such proteins exist for oxaloacetate.[11] Therefore species that lack intra-mitochondrial PEP, oxaloacetate must be converted into malate or asparate, exported from the mitochondrion, and converted back into oxaloacetate in order to allow gluconeogenesis to continue.[11]
Pathway
Gluconeogenesis is a pathway consisting of eleven enzyme-catalyzed reactions. The pathway can begin in the mitochondria or cytoplasm, depending on the substrate being used. Many of the reactions are the reversible steps found in glycolysis. Gluconeogenesis begins in the mitochondria with the formation of oxaloacetate through carboxylation of pyruvate. This reaction also requires one molecule of ATP, and is catalyzed by pyruvate carboxylase. This enzyme is stimulated by high levels of acetyl-CoA (produced in -oxidation in the liver) and inhibited by high levels of ADP. Oxaloacetate is reduced to malate using NADH, a step required for transport out of the mitochondria. Malate is oxidized to oxaloacetate using NAD+ in the cytoplasm, where the remaining steps of gluconeogenesis occur. Oxaloacetate is decarboxylated and phosphorylated to produce phosphoenolpyruvate by phosphoenolpyruvate carboxykinase. One molecule of GTP is hydrolyzed to GDP during this reaction. The next steps in the reaction are the same as reversed glycolysis. However, fructose-1,6-bisphosphatase converts fructose-1,6-bisphosphate to fructose 6-phosphate, requiring one water molecule and releasing one phosphate. This is also the rate-limiting step of gluconeogenesis. Glucose-6-phosphate is formed from fructose 6-phosphate by phosphoglucoisomerase. Glucose-6-phosphate can be used in other metabolic pathways or dephosphorylated to free glucose. Whereas free glucose can easily diffuse in and out of the cell, the phosphorylated form (glucose-6-phosphate) is locked in the cell, a mechanism by which
Gluconeogenesis intracellular glucose levels are controlled by cells. The final reaction of gluconeogenesis, the formation of glucose, occurs in the lumen of the endoplasmic reticulum, where glucose-6-phosphate is hydrolyzed by glucose-6-phosphatase to produce glucose. Glucose is shuttled into the cytosol by glucose transporters located in the membrane of the endoplasmic reticulum.
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Regulation
While most steps in gluconeogenesis are the reverse of those found in glycolysis, three regulated and strongly exergonic reactions are replaced with more kinetically favorable reactions. Hexokinase/glucokinase, phosphofructokinase, and pyruvate kinase enzymes of glycolysis are replaced with glucose-6-phosphatase, fructose-1,6-bisphosphatase, and PEP carboxykinase. This system of reciprocal control allow glycolysis and gluconeogenesis to inhibit each other and prevent the formation of a futile cycle. The majority of the enzymes responsible for gluconeogenesis are found in the cytoplasm; the exceptions are mitochondrial pyruvate carboxylase and, in animals, phosphoenolpyruvate carboxykinase. The latter exists as an isozyme located in both the mitochondrion and the cytosol.[12] The rate of gluconeogenesis is ultimately controlled by the action of a key enzyme, fructose-1,6-bisphosphatase, which is also regulated through signal transduction by cAMP and its phosphorylation. Most factors that regulate the activity of the gluconeogenesis pathway do so by inhibiting the activity or expression of key enzymes. However, both acetyl CoA and citrate activate gluconeogenesis enzymes (pyruvate carboxylase and fructose-1,6-bisphosphatase, respectively). Due to the reciprocal control of the cycle, acetyl-CoA and citrate also have inhibitory roles in the activity of pyruvate kinase. Global control of gluconeogenesis is mediated by glucagon (released when blood glucose is low); it triggers phosphorylation of enzymes and regulatory proteins by Protein Kinase A (a cyclic AMP regulated kinase) resulting in inhibition of glycolysis and stimulation of gluconeogenesis, thus bringing blood glucose levels up.[13]
References
[1] Silva, Pedro. "The Chemical Logic Behind Gluconeogenesis" (http:/ / www2. ufp. pt/ ~pedros/ bq/ gng. htm). . Retrieved September 8, 2009. [2] David L Nelson and Michael M Cox (2000). Lehninger Principles of Biochemistry. USA: Worth Publishers. pp.724. ISBN1-57259-153-6. [3] Hundal R, Krssak M, Dufour S, Laurent D, Lebon V, Chandramouli V, Inzucchi S, Schumann W, Petersen K, Landau B, Shulman G (2000). "Mechanism by Which Metformin Reduces Glucose Production in Type 2 Diabetes". Diabetes 49 (12): 20639. doi:10.2337/diabetes.49.12.2063. PMC2995498. PMID11118008. Free full text (http:/ / diabetes. diabetesjournals. org/ cgi/ reprint/ 49/ 12/ 2063)PDF(82KiB) [4] Garrett, Reginald H.; Charles M. Grisham (2002). Principles of Biochemistry with a Human Focus. USA: Brooks/Cole, Thomson Learning. pp.578, 585. ISBN0-03-097369-4. [5] Chapter 20 (Amino Acid Degradation and Synthesis) in: Denise R., PhD. Ferrier. Lippincott's Illustrated Reviews: Biochemistry (Lippincott's Illustrated Reviews). Hagerstwon, MD: Lippincott Williams & Wilkins. ISBN0-7817-2265-9. [6] Figueiredo, Luis F., Stefan Schuster, Christoph Kaleta, David A. Fell (2009). "Can sugars be produced from fatty acids? A test case for pathway analysis tools". Bioinformatics 25 (1): 152158. doi:10.1093/bioinformatics/btn621. PMID19117076. [7] Liu, F., et al. (1995). "Bifunctional glyoxylate cycle protein of Caenorhabditis elegans: a developmentally regulated protein of intestine and muscle". Developmental Biology 169 (2): 399414. doi:10.1006/dbio.1995.1156. PMID7781887. [8] Fyodor A Kondrashov, Eugene V Koonin, Igor G Morgunov, Tatiana V Finogenova, Marie N Kondrashova (2006). "Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation". Biology Direct 1: 31. doi:10.1186/1745-6150-1-31. PMC1630690. PMID17059607. [9] Weinman, E.O., et al. (1957). "Conversion of fatty acids to carbohydrate: application of isotopes to this problem and role of the Krebs cycle as a synthetic pathway". Physiol. Rev. 37 (2): 25272. PMID13441426. [10] Widmaier, Eric (2006). Vander's Human Physiology. McGraw Hill. pp.96. ISBN0-07-282741-6. [11] Voet, Donald; Judith Voet, Charlotte Pratt (2008). Fundamentals of Biochemistry. John Wiley & Sons Inc. p.556. ISBN978-0470-12930-2. [12] Chakravarty, K., Cassuto, H., Resef, L., & Hanson, R.W. (2005) Factors that control the tissue-specific transcription of the gene for phosphoenolpyruvate carboxykinase-C. Critical Reviews of Biochemistry and Molecular Biology, 40(3), 129-154. [13] http:/ / rpi. edu/ dept/ bcbp/ molbiochem/ MBWeb/ mb1/ part2/ gluconeo. htm - Gluconeogenesis, by Diwan. Cites no sources.
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External links
Overview at indstate.edu (http://themedicalbiochemistrypage.org/gluconeogenesis.html) Interactive diagram at uakron.edu (http://ull.chemistry.uakron.edu/Pathways/gluconeogenesis/index.html#) The chemical logic behind gluconeogenesis (http://homepage.ufp.pt/pedros/bq/gng.htm)
Glycogen
Glycogen is a molecule that serves as the secondary long-term energy storage in animal and fungal cells, with the primary energy stores being held in adipose tissue. Glycogen is made primarily by the liver and the muscles, but can also be made by glycogenesis within the brain and stomach.[2] Glycogen is the analogue of starch, a glucose polymer in plants, and is sometimes referred to as animal starch, having a similar structure to amylopectin but more extensively branched and compact than starch. Glycogen is a polymer of (14) glycosidic bonds linked, with (16)-linked branches. Glycogen is found in the form of granules in the cytosol/cytoplasm in many cell types, and plays an important role in the glucose cycle. Glycogen forms an energy reserve that can be quickly mobilized to meet a sudden need for glucose, but one that is less compact than the energy reserves of triglycerides (lipids).
Schematic 2-D cross-sectional view of glycogen. A core protein of glycogenin is surrounded by branches of glucose units. The entire globular granule may contain [1] approximately 30,000 glucose units.
In the liver hepatocytes, glycogen can compose up to eight percent of the fresh weight (100120g in an adult) soon after a meal.[3] Only the glycogen stored in the liver can be made accessible to other organs. In the muscles, glycogen is found in a low concentration (one to two percent of the muscle mass). However, the amount of glycogen stored in the bodyespecially within the muscles, liver, and red blood cells[4] [5] [6] mostly depends on physical training, basal metabolic rate, and eating
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habits such as intermittent fasting. Small amounts of glycogen are found in the kidneys, and even smaller amounts in certain glial cells in the brain and white blood cells. The uterus also stores glycogen during pregnancy to nourish the embryo.[7]
A view of the atomic structure of a single branched strand of glucose units in a glycogen molecule.
After a meal has been digested and glucose levels begin to fall, insulin secretion is reduced, and glycogen synthesis stops. When it is needed for energy, glycogen is broken down and converted again to glucose. Glycogen phosphorylase is the primary enzyme of glycogen breakdown. For the next 812 hours, glucose derived from liver glycogen will be the primary source of blood glucose to be used by the rest of the body for fuel. Glucagon is another hormone produced by the pancreas, which in many respects serves as a counter-signal to insulin. In response to insulin level below normal (when blood levels of glucose begin to fall below the normal range), glucagon is secreted in increasing amounts to stimulate glycogenolysis and gluconeogenesis pathways.
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Synthesis
Glycogen synthesis is, unlike its breakdown, endergonic. This means that glycogen synthesis requires the input of energy. Energy for glycogen synthesis comes from UTP, which reacts with glucose-1-phosphate, forming UDP-glucose, in a reaction catalysed by UDP-glucose pyrophosphorylase. Glycogen is synthesized from monomers of Glycogen Structure Segment UDP-glucose by the enzyme glycogen synthase, which progressively lengthens the glycogen chain with (14) bonded glucose. As glycogen synthase can lengthen only an existing chain, the protein glycogenin is needed to initiate the synthesis of glycogen. The glycogen-branching enzyme, amylo (14) to (16) transglycosylase, catalyzes the transfer of a terminal
Glycogen fragment of 6-7 glucose residues from a nonreducing end to the C-6 hydroxyl group of a glucose residue deeper into the interior of the glycogen molecule. The branching enzyme can act upon only a branch having at least 11 residues, and the enzyme may transfer to the same glucose chain or adjacent glucose chains.
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Breakdown
Glycogen is cleaved from the nonreducing ends of the chain by the enzyme glycogen phosphorylase to produce monomers of glucose-1-phosphate, which is then converted to glucose 6-phosphate by phosphoglucomutase. A special debranching enzyme is needed to remove the alpha(1-6) branches in branched glycogen and reshape the chain into linear polymer. The G6P monomers produced have three possible fates:
G6P can continue on the glycolysis pathway and be used as fuel. G6P can enter the pentose phosphate pathway via the enzyme Glucose-6-phosphate dehydrogenase to produce NADPH and 5-carbon sugars. In the liver and kidney, G6P can be dephosphorylated back to Glucose by the enzyme Glucose 6-phosphatase. This is the final step in the gluconeogenesis pathway.
References
[1] Page 12 in: (http:/ / books. google. dk/ books?id=SRptlOx7yj4C& printsec=frontcover& hl=en) Exercise physiology: energy, nutrition, and human performance By William D. McArdle, Frank I. Katch, Victor L. Katch Edition: 6, illustrated Published by Lippincott Williams & Wilkins, 2006 ISBN 0781749905, 9780781749909, 1068 pages [2] Anatomy and Physiology. Saladin, Kenneth S. McGraw-Hill, 2007. [3] Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life (http:/ / www. phschool. com/ el_marketing. html). Boston, Massachusetts: Pearson Prentice Hall. ISBN0-13-250882-6. . [4] Moses SW, Bashan N, Gutman A (December 1972). "Glycogen metabolism in the normal red blood cell" (http:/ / www. bloodjournal. org/ cgi/ pmidlookup?view=long& pmid=5083874). Blood 40 (6): 83643. PMID5083874. . [5] http:/ / jeb. biologists. org/ cgi/ reprint/ 129/ 1/ 141. pdf [6] Miwa I, Suzuki S (November 2002). "An improved quantitative assay of glycogen in erythrocytes". Annals of Clinical Biochemistry 39 (Pt 6): 6123. doi:10.1258/000456302760413432. PMID12564847. [7] Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life (http:/ / www. phschool. com/ el_marketing. html). Boston, Massachusetts: Pearson Prentice Hall. ISBN0-13-250882-6. . [8] Pedersen DJ, Lessard SJ, Coffey VG, et al. (July 2008). "High rates of muscle glycogen resynthesis after exhaustive exercise when carbohydrate is coingested with caffeine". Journal of Applied Physiology 105 (1): 713. doi:10.1152/japplphysiol.01121.2007. PMID18467543. [9] Post-exercise Caffeine Helps Muscles Refuel (http:/ / newswise. com/ articles/ view/ 542216/ ) Newswise, Retrieved on July 6, 2008.
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External links
Glycogen detection using Periodic Acid Schiff Staining (http://www.histochem.net/protocol periodic acid schiff.htm) Glycogen storage disease - McArdle's Disease Website (http://mcardlesdisease.org) MeSH Glycogen (http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=&term=Glycogen)
Outcome
The primary results of the Pathway are: The generation of reducing equivalents, in the form of NADPH, used in reductive biosynthesis reactions within cells. (e.g. fatty acid synthesis) Production of ribose-5-phosphate (R5P), used in the synthesis of nucleotides and nucleic acids. Production of erythrose-4-phosphate (E4P), used in the synthesis of aromatic amino acids. Aromatic amino acids, in turn, are precursors for many biosynthetic pathways, notably including the lignin in wood.
The Pentose Phosphate Pathway
Dietary pentose sugars derived from the digestion of nucleic acids may be metabolized through the pentose phosphate pathway, and the carbon skeletons of dietary carbohydrates may be converted into glycolytic/gluconeogenic intermediates. In mammals, the PPP occurs exclusively in the cytoplasm, and is found to be most active in the liver, mammary gland and adrenal cortex in the human. However, the pathway is absent in skeletal muscle tissue. The PPP is one of the three main ways the body creates molecules with reducing power, accounting for approximately 60% of NADPH production in humans. One of the uses of NADPH in the cell is to prevent oxidative stress. It reduces glutathione via glutathione reductase, which converts reactive H2O2 into H2O by glutathione peroxidase. If absent, the H2O2 would be converted to hydroxyl free radicals by Fenton chemistry, which can attack the cell. In a significant step, erythrocytes generate, through the pentose phosphate pathway, a large amount of NADPH used in the reduction of glutathione. Hydrogen peroxide is also generated for phagocytes in a process often referred to as a respiratory burst.[2]
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Phases
Oxidative phase
In this phase, two molecules of NADP+ are reduced to NADPH, utilizing the energy from the conversion of glucose-6-phosphate into ribulose 5-phosphate.
Oxidative phase of pentose phosphate pathway. glucose-6-phosphate (1), 6-phosphoglucono--lactone (2), 6-phosphogluconate (3), ribulose 5-phosphate (4).
6-phosphogluconolactonase
6-phosphogluconate dehydrogenase
Oxidative decarboxylation. NADP+ is the electron acceptor, generating another molecule of NADPH, a CO2, and ribulose 5-phosphate.
The overall reaction for this process is: Glucose 6-phosphate + 2 NADP+ + H2O ribulose 5-phosphate + 2 NADPH + 2 H+ + CO2
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Non-oxidative phase
transaldolase
transketolase
244
Regulation
Glucose-6-phosphate dehydrogenase is the rate-controlling enzyme of this pathway. It is allosterically stimulated by NADP+. The ratio of NADPH:NADP+ is normally about 100:1 in liver cytosol. This makes the cytosol a highly-reducing environment. An NADPH-utilizing pathway forms NADP+, which stimulates Glucose-6-phosphate dehydrogenase to produce more NADPH.
References
[1] Kruger NJ, von Schaewen A (June 2003). "The oxidative pentose phosphate pathway: structure and organisation" (http:/ / linkinghub. elsevier. com/ retrieve/ pii/ S1369526603000396). Curr. Opin. Plant Biol. 6 (3): 23646. doi:10.1016/S1369-5266(03)00039-6. PMID12753973. . [2] Immunology at MCG 1/cytotox (http:/ / www. lib. mcg. edu/ edu/ esimmuno/ ch1/ cytotox. htm) [3] Cappadoro M, Giribaldi G, O'Brien E, et al. (October 1998). "Early phagocytosis of glucose-6-phosphate dehydrogenase (G6PD)-deficient erythrocytes parasitized by Plasmodium falciparum may explain malaria protection in G6PD deficiency" (http:/ / bloodjournal. hematologylibrary. org/ cgi/ content/ full/ 92/ 7/ 2527). Blood 92 (7): 252734. PMID9746794. .
External links
The chemical logic behind the pentose phosphate pathway (http://www2.ufp.pt/~pedros/bq/ppp.htm) MeSH Pentose+Phosphate+Pathway (http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=& term=Pentose+Phosphate+Pathway) Pentose phosphate pathway Map - Homo sapiens (http://www.genome.jp/dbget-bin/ www_bget?path:hsa00030)
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Evolution
Components of the TCA cycle were derived from anaerobic bacteria and the TCA cycle itself may have evolved more than once.[6] Theoretically there are several alternatives to the TCA cycle, however the TCA cycle appears to be the most efficient.[7] If several alternatives independently evolved, they all undoubtedly rapidly converged to the TCA cycle.
Overview
The citric acid cycle is a key component of the metabolic pathway by which all aerobic organisms generate energy. Through catabolism of sugars, fats, and proteins, a two carbon organic product acetate in the form of acetyl-CoA is produced. Acetyl-CoA along with two equivalents of water (H2O) are consumed by the citric acid cycle producing two equivalents of carbon dioxide (CO2) and one equivalent of HS-CoA. In addition, one complete turn of the cycle converts three equivalents of nicotinamide adenine dinucleotide (NAD+) into three equivalents of reduced NAD+ (NADH), one equivalent of ubiquinone (Q) into one equivalent of reduced ubiquinone (QH2), and one equivalent each of guanosine diphosphate (GDP) and inorganic phosphate (Pi) into one equivalent of guanosine triphosphate (GTP). The NADH and QH2 that is generated by the citric acid cycle is in turn used by the oxidative phosphorylation pathway to generate energy rich adenosine triphosphate (ATP). One of the primary sources of acetyl-CoA are sugars that are broken down by glycolysis to produce pyruvate that in turn is decarboxylated by the enzyme pyruvate dehydrogenase generating acetyl-CoA according to the following reaction scheme: CH3C(=O)C(=O)O (pyruvate) + HSCoA + NAD+ CH3C(=O)SCoA (acetyl-CoA) + NADH + H+ + CO2 The product of this reaction, acetyl-CoA, is the starting point for the citric acid cycle. Below is a schematic outline of the cycle: The citric acid cycle begins with the transfer of a two-carbon acetyl group from acetyl-CoA to the four-carbon acceptor compound (oxaloacetate) to form a six-carbon compound (citrate). The citrate then goes through a series of chemical transformations, losing two carboxyl groups as CO2. The carbons lost as CO2 originate from what was oxaloacetate, not directly from acetyl-CoA. The carbons donated by acetyl-CoA become part of the oxaloacetate carbon backbone after the first turn of the citric acid cycle. Loss of the acetyl-CoA-donated carbons as CO2 requires several turns of the citric acid cycle. However, because of the role of the citric acid cycle in anabolism, they may not be lost, since many TCA cycle intermediates are also used as precursors for the biosynthesis of other molecules.[8] Most of the energy made available by the oxidative steps of the cycle is transferred as energy-rich electrons to NAD+, forming NADH. For each acetyl group that enters the citric acid cycle, three molecules of NADH are produced. Electrons are also transferred to the electron acceptor Q, forming QH2. At the end of each cycle, the four-carbon oxaloacetate has been regenerated, and the cycle continues.
Steps
Two carbon atoms are oxidized to CO2, the energy from these reactions being transferred to other metabolic processes by GTP (or ATP), and as electrons in NADH and QH2. The NADH generated in the TCA cycle may later donate its electrons in oxidative phosphorylation to drive ATP synthesis; FADH2 is covalently attached to succinate dehydrogenase, an enzyme functioning both in the TCA cycle and the mitochondrial electron transport chain in oxidative phosphorylation. FADH2, therefore, facilitates transfer of electrons to coenzyme Q, which is the final electron acceptor of the reaction catalyzed by the Succinate:ubiquinone oxidoreductase complex, also acting as an intermediate in the electron transport chain.[9]
Citric acid cycle The citric acid cycle is continuously supplied with new carbon in the form of acetyl-CoA, entering at step 1 below.[10]
Substrates 1 Oxaloacetate + Acetyl CoA + H2O Citrate Products Citrate + CoA-SH Enzyme Citrate synthase Reaction type Aldol condensation Comment irreversible, extends the 4C oxaloacetate to a 6C molecule
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Aconitase
Dehydration
reversible isomerisation
Hydration
Isocitrate dehydrogenase
Oxidation
Oxalosuccinate
Decarboxylation
Oxidative decarboxylation
irreversible stage, generates NADH (equivalent of 2.5 ATP), regenerates the 4C chain (CoA excluded)
substrate-level phosphorylation
[9]
Oxidation
uses FAD as a prosthetic group (FADFADH2 in the [9] first step of the reaction) in the enzyme, generates the equivalent of 1.5 ATP
Fumarate + H2O
L-Malate
Fumarase
Hydration
10 L-Malate + NAD+
Oxaloacetate + NADH + H+
Malate dehydrogenase
Oxidation
reversible (in fact, equilibrium favors malate), generates NADH (equivalent of 2.5 ATP)
Mitochondria in animals, including humans, possess two succinyl-CoA synthetases: one that produces GTP from GDP, and another that produces ATP from ADP.[11] Plants have the type that produces ATP (ADP-forming succinyl-CoA synthetase).[10] Several of the enzymes in the cycle may be loosely-associated in a multienzyme protein complex within the mitochondrial matrix.[12] The GTP that is formed by GDP-forming succinyl-CoA synthetase may be utilized by nucleoside-diphosphate kinase to form ATP (the catalyzed reaction is GTP + ADP GDP + ATP).[9]
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Products
Products of the first turn of the cycle are: one GTP (or ATP), three NADH, one QH2, two CO2. Because two acetyl-CoA molecules are produced from each glucose molecule, two cycles are required per glucose molecule. Therefore, at the end of two cycles, the products are: two GTP, six NADH, two QH2, and four CO2
Description The sum of all reactions in the citric acid cycle is: Reactants Acetyl-CoA + 3 NAD+ + Q + GDP + Pi + 2 H2O Pyruvate ion + 4 NAD+ + Q + GDP + Pi + 2 H2O Glucose + 10 NAD+ + 2 Q + 2 ADP + 2 GDP + 4 Pi + 2 H2O Products CoA-SH + 3 NADH + 3 H+ + QH2 + GTP + 2 CO2 4 NADH + 4 H+ + QH2 + GTP + 3 CO2 10 NADH + 10 H+ + 2 QH2 + 2 ATP + 2 GTP + 6 CO2
Combining the reactions occurring during the pyruvate oxidation with those occurring during the citric acid cycle, the following overall pyruvate oxidation reaction is obtained: Combining the above reaction with the ones occurring in the course of glycolysis, the following overall glucose oxidation reaction (excluding reactions in the respiratory chain) is obtained:
The above reactions are balanced if Pi represents the H2PO4- ion, ADP and GDP the ADP2- and GDP2- ions, respectively, and ATP and GTP the ATP3- and GTP3- ions, respectively. The total number of ATP obtained after complete oxidation of one glucose in glycolysis, citric acid cycle, and oxidative phosphorylation is estimated to be between 30 and 38. A recent assessment of the total ATP yield with the updated proton-to-ATP ratios provides an estimate of 29.85 ATP per glucose molecule.[13]
Regulation
Although pyruvate dehydrogenase is not technically a part of the citric acid cycle, its regulation is included here. The regulation of the TCA cycle is largely determined by substrate availability and product inhibition. NADH, a product of all dehydrogenases in the TCA cycle with the exception of succinate dehydrogenase, inhibits pyruvate dehydrogenase, isocitrate dehydrogenase, -ketoglutarate dehydrogenase, and also citrate synthase. Acetyl-coA inhibits pyruvate dehydrogenase, while succinyl-CoA inhibits succinyl-CoA synthetase and citrate synthase. When tested in vitro with TCA enzymes, ATP inhibits citrate synthase and -ketoglutarate dehydrogenase; however, ATP levels do not change more than 10% in vivo between rest and vigorous exercise. There is no known allosteric mechanism that can account for large changes in reaction rate from an allosteric effector whose concentration changes less than 10%.[14] Calcium is used as a regulator. It activates pyruvate dehydrogenase, isocitrate dehydrogenase and -ketoglutarate dehydrogenase.[15] This increases the reaction rate of many of the steps in the cycle, and therefore increases flux throughout the pathway. Citrate is used for feedback inhibition, as it inhibits phosphofructokinase, an enzyme involved in glycolysis that catalyses formation of fructose 1,6-bisphosphate,a precursor of pyruvate. This prevents a constant high rate of flux when there is an accumulation of citrate and a decrease in substrate for the enzyme. Recent work has demonstrated an important link between intermediates of the citric acid cycle and the regulation of hypoxia-inducible factors (HIF). HIF plays a role in the regulation of oxygen homeostasis, and is a transcription factor that targets angiogenesis, vascular remodeling, glucose utilization, iron transport and apoptosis. HIF is synthesized consititutively, and hydroxylation of at least one of two critical proline residues mediates their interaction with the von Hippel Lindau E3 ubiquitin ligase complex, which targets them for rapid degradation. This reaction is catalysed by prolyl 4-hydroxylases. Fumarate and succinate have been identified as potent inhibitors of prolyl hydroxylases, thus leading to the stabilisation of HIF.[16]
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References
[1] Lowenstein JM (1969). Methods in Enzymology, Volume 13: Citric Acid Cycle. Boston: Academic Press. ISBN0-12-181870-5. [2] Krebs HA, Weitzman PDJ (1987). Krebs' citric acid cycle: half a century and still turning. London: Biochemical Society. ISBN0-904498-22-0. [3] Lane, Nick (2009). Life Ascending: The Ten Great Inventions of Evolution. New York: W.W. Norton & Co. ISBN0-393-06596-0. [4] "The Nobel Prize in Physiology or Medicine 1937" (http:/ / nobelprize. org/ nobel_prizes/ medicine/ laureates/ 1937/ ). The Nobel Foundation. . Retrieved 2011-10-26. [5] "The Nobel Prize in Physiology or Medicine 1953" (http:/ / nobelprize. org/ nobel_prizes/ medicine/ laureates/ 1953/ ). The Nobel Foundation. . Retrieved 2011-10-26. [6] Gest H (1987). "Evolutionary roots of the citric acid cycle in prokaryotes". Biochem. Soc. Symp. 54: 316. PMID3332996. [7] Melndez-Hevia E, Waddell TG, Cascante M (September 1996). "The puzzle of the Krebs citric acid cycle: assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution". J. Mol. Evol. 43 (3): 293303. doi:10.1007/BF02338838. PMID8703096. [8] Wolfe RR, Jahoor F (February 1990). "Recovery of labeled CO2 during the infusion of C-1- vs C-2-labeled acetate: implications for tracer studies of substrate oxidation". Am. J. Clin. Nutr. 51 (2): 24852. PMID2106256. [9] Stryer L, Berg J, Tymoczko JL (2002). Biochemistry. San Francisco: W.H. Freeman. ISBN0-7167-4684-0. [10] Jones RC, Buchanan BB, Gruissem W (2000). Biochemistry & molecular biology of plants (1st ed.). Rockville, Md: American Society of Plant Physiologists. ISBN0-943088-39-9. [11] Johnson JD, Mehus JG, Tews K, Milavetz BI, Lambeth DO (October 1998). "Genetic evidence for the expression of ATP- and GTP-specific succinyl-CoA synthetases in multicellular eucaryotes". J. Biol. Chem. 273 (42): 275806. doi:10.1074/jbc.273.42.27580. PMID9765291. [12] Barnes SJ, Weitzman PD (June 1986). "Organization of citric acid cycle enzymes into a multienzyme cluster". FEBS Lett. 201 (2): 26770. doi:10.1016/0014-5793(86)80621-4. PMID3086126. [13] Rich PR (December 2003). "The molecular machinery of Keilin's respiratory chain". Biochem. Soc. Trans. 31 (Pt 6): 1095105. doi:10.1042/BST0311095. PMID14641005. [14] Voet D, Voet JG (2004). Biochemistry (3rd ed.). New York: John Wiley & Sons, Inc.. p.615. [15] Denton RM, Randle PJ, Bridges BJ, Cooper RH, Kerbey AL, Pask HT, Severson DL, Stansbie D, Whitehouse S (October 1975). "Regulation of mammalian pyruvate dehydrogenase". Mol. Cell. Biochem. 9 (1): 2753. doi:10.1007/BF01731731. PMID171557. [16] Koivunen P, Hirsil M, Remes AM, Hassinen IE, Kivirikko KI, Myllyharju J (February 2007). "Inhibition of hypoxia-inducible factor (HIF) hydroxylases by citric acid cycle intermediates: possible links between cell metabolism and stabilization of HIF". J. Biol. Chem. 282 (7): 452432. doi:10.1074/jbc.M610415200. PMID17182618. [17] Halarnkar PP, Blomquist GJ (1989). "Comparative aspects of propionate metabolism". Comp. Biochem. Physiol., B 92 (2): 22731. doi:10.1016/0305-0491(89)90270-8. PMID2647392. [18] The interactive pathway map can be edited at WikiPathways: "TCACycle_WP78" (http:/ / www. wikipathways. org/ index. php/ Pathway:WP78). . [19] http:/ / www. wikipathways. org/ index. php/ Pathway:WP78
External links
Citric acid cycle Animation (http://www.1lec.com/Biochemistry/How the Krebs Cycle Works/index. html)(flash required) An animation of the citric acid cycle (http://www.science.smith.edu/departments/Biology/Bio231/krebs. html) at Smith College Notes on citric acid cycle (http://www.rahulgladwin.com/blog/2007/01/notes-on-citric-acid-cycle-glyoxylate. html) at rahulgladwin.com Citric acid cycle variants (http://biocyc.org/META/NEW-IMAGE?object=TCA-VARIANTS) at MetaCyc Pathways connected to the citric acid cycle (http://www.genome.ad.jp/kegg/pathway/map/map00020.html) at Kyoto Encyclopedia of Genes and Genomes A more detailed tutorial animation (http://www.johnkyrk.com/krebs.html) at johnkyrk.com A citric-acid cycle self quiz flash applet (http://www.pitt.edu/AFShome/j/b/jbrodsky/public/html/1820/tca. htm) at University of Pittsburgh The chemical logic behind the citric acid cycle (http://www2.ufp.pt/~pedros/bq/tca.htm) The Krebs cycle song (http://www.science-groove.org/Now/) by Lynda Jones.
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Oxidative phosphorylation
Oxidative phosphorylation
Oxidative phosphorylation (or OXPHOS in short) is a metabolic pathway that uses energy released by the oxidation of nutrients to produce adenosine triphosphate (ATP). Although the many forms of life on earth use a range of different nutrients, almost all aerobic organisms carry out oxidative phosphorylation to produce ATP, the molecule that supplies energy to metabolism. This pathway is probably so pervasive because it is a highly efficient way of releasing energy, compared to alternative fermentation processes such as anaerobic glycolysis. During oxidative phosphorylation, electrons are transferred from electron The electron transport chain in the mitochondrion is the site of oxidative phosphorylation donors to electron acceptors such as in eukaryotes. The NADH and succinate generated in the citric acid cycle are oxidized, oxygen, in redox reactions. These releasing energy to power the ATP synthase. redox reactions release energy, which is used to form ATP. In eukaryotes, these redox reactions are carried out by a series of protein complexes within mitochondria, whereas, in prokaryotes, these proteins are located in the cells' inner membranes. These linked sets of proteins are called electron transport chains. In eukaryotes, five main protein complexes are involved, whereas in prokaryotes many different enzymes are present, using a variety of electron donors and acceptors. The energy released by electrons flowing through this electron transport chain is used to transport protons across the inner mitochondrial membrane, in a process called chemiosmosis. This generates potential energy in the form of a pH gradient and an electrical potential across this membrane. This store of energy is tapped by allowing protons to flow back across the membrane and down this gradient, through a large enzyme called ATP synthase. This enzyme uses this energy to generate ATP from adenosine diphosphate (ADP), in a phosphorylation reaction. This reaction is driven by the proton flow, which forces the rotation of a part of the enzyme; the ATP synthase is a rotary mechanical motor. Although oxidative phosphorylation is a vital part of metabolism, it produces reactive oxygen species such as superoxide and hydrogen peroxide, which lead to propagation of free radicals, damaging cells and contributing to disease and, possibly, aging (senescence). The enzymes carrying out this metabolic pathway are also the target of many drugs and poisons that inhibit their activities.
Oxidative phosphorylation
254
Within the inner mitochondrial membrane, the lipid-soluble electron carrier coenzyme Q10 (Q) carries [8] both electrons and protons by a redox cycle. This small benzoquinone molecule is very hydrophobic, so it diffuses freely within the membrane. When Q accepts two electrons and two protons, it becomes reduced to the ubiquinol form (QH2); when QH2 releases two electrons and two protons, it becomes oxidized back to the ubiquinone (Q) form. As a result, if two enzymes are arranged so that Q is reduced on one side of the membrane and QH2 oxidized
Reduction of coenzyme Q from its ubiquinone form (Q) to the reduced ubiquinol form (QH2).
Oxidative phosphorylation on the other, ubiquinone will couple these reactions and shuttle protons across the membrane.[9] Some bacterial electron transport chains use different quinones, such as menaquinone, in addition to ubiquinone.[10] Within proteins, electrons are transferred between flavin cofactors,[3] [11] ironsulfur clusters, and cytochromes. There are several types of ironsulfur cluster. The simplest kind found in the electron transfer chain consists of two iron atoms joined by two atoms of inorganic sulfur; these are called [2Fe2S] clusters. The second kind, called [4Fe4S], contains a cube of four iron atoms and four sulfur atoms. Each iron atom in these clusters is coordinated by an additional amino acid, usually by the sulfur atom of cysteine. Metal ion cofactors undergo redox reactions without binding or releasing protons, so in the electron transport chain they serve solely to transport electrons through proteins. Electrons move quite long distances through proteins by hopping along chains of these cofactors.[12] This occurs by quantum tunnelling, which is rapid over distances of less than 1.4109 m.[13]
255
Cytochrome bc1 complex Coenzyme Q10ox / Coenzyme Q10red Cytochrome bc1 complex Complex IV Complex IV Complex IV Conditions: pH = 7 [15] Cytochrome box / Cytochrome bred Cytochrome cox / Cytochrome cred Cytochrome aox / Cytochrome ared O2 / HO
Oxidative phosphorylation
256
Complex I or NADH-Q oxidoreductase. The abbreviations are discussed in the text. In all diagrams of respiratory complexes in this article, the matrix is at the bottom, with the intermembrane space above.
The reaction that is catalyzed by this enzyme is the two electron reduction by NADH of coenzyme Q10 or ubiquinone (represented as Q in the equation below), a lipid-soluble quinone that is found in the mitochondrion membrane:
The start of the reaction, and indeed of the entire electron chain, is the binding of a NADH molecule to complex I and the donation of two electrons. The electrons enter complex I via a prosthetic group attached to the complex, flavin mononucleotide (FMN). The addition of electrons to FMN converts it to its reduced form, FMNH2. The electrons are then transferred through a series of ironsulfur clusters: the second kind of prosthetic group present in the complex.[18] There are both [2Fe2S] and [4Fe4S] ironsulfur clusters in complex I. As the electrons pass through this complex, four protons are pumped from the matrix into the intermembrane space. Exactly how this occurs is unclear, but it seems to involve conformational changes in complex I that cause the protein to bind protons on the N-side of the membrane and release them on the P-side of the membrane.[22] Finally, the electrons are transferred from the chain of ironsulfur clusters to a ubiquinone molecule in the membrane.[16] Reduction of ubiquinone also contributes to the generation of a proton gradient, as two protons are taken up from the matrix as it is reduced to ubiquinol (QH2).
Oxidative phosphorylation
257
In some eukaryotes, such as the parasitic worm Ascaris suum, an enzyme similar to complex II, fumarate reductase (menaquinol:fumarate oxidoreductase, or QFR), operates in reverse to oxidize ubiquinol and reduce fumarate. This allows the worm to survive in the anaerobic environment of the large intestine, carrying out anaerobic oxidative phosphorylation with fumarate as the electron acceptor.[26] Another unconventional function of complex II is seen in the malaria parasite Plasmodium falciparum. Here, the reversed action of complex II as an oxidase is important in regenerating ubiquinol, which the parasite uses in an unusual form of pyrimidine biosynthesis.[27]
In mammals, this metabolic pathway is important in beta oxidation of fatty acids and catabolism of amino acids and choline, as it accepts electrons from multiple acetyl-CoA dehydrogenases.[30] [31] In plants, ETF-Q oxidoreductase is also important in the metabolic responses that allow survival in extended periods of darkness.[32]
Oxidative phosphorylation
258
As only one of the electrons can be transferred from the QH2 donor to a cytochrome c acceptor at a time, the reaction mechanism of complex III is more elaborate than those of the other respiratory complexes, and occurs in two steps called the Q cycle.[36] In the first step, the enzyme binds three substrates, first, QH2, which is then oxidized, with one electron being passed to the second substrate, cytochrome c. The two protons released from QH2 pass into the intermembrane space. The third substrate is Q, which accepts the second electron from the QH2 and is reduced to Q.-, which is the ubisemiquinone free radical. The first two substrates are released, but this ubisemiquinone intermediate remains bound. In the second step, a second molecule of QH2 is bound and again passes its first electron to a cytochrome c acceptor. The second electron is passed to the bound ubisemiquinone, reducing it to QH2 as it gains two protons from the mitochondrial matrix. This QH2 is then released from the enzyme.[37] As coenzyme Q is reduced to ubiquinol on the inner side of the membrane and oxidized to ubiquinone on the other, a net transfer of protons across the membrane occurs, adding to the proton gradient.[3] The rather complex two-step mechanism by which this occurs is important, as it increases the efficiency of proton transfer. If, instead of the Q cycle, one molecule of QH2 were used to directly reduce two molecules of cytochrome c, the efficiency would be halved, with only one proton transferred per cytochrome c reduced.[3]
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Organization of complexes
The original model for how the respiratory chain complexes are organized was that they diffuse freely and independently in the mitochondrial membrane.[17] However, recent data suggest that the complexes might form higher-order structures called supercomplexes or "respirasomes."[49] In this model, the various complexes exist as organized sets of interacting enzymes.[50] These associations might allow channeling of substrates between the various enzyme complexes, increasing the rate and efficiency of electron transfer.[51] Within such mammalian supercomplexes, some components would be present in higher amounts than others, with some data suggesting a ratio between complexes I/II/III/IV and the ATP synthase of approximately 1:1:3:7:4.[52] However, the debate over this supercomplex hypothesis is not completely resolved, as some data do not appear to fit with this model.[17] [53]
Oxidative phosphorylation
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Glycerol-3-phosphate dehydrogenase DHAP / Gly-3-P Pyruvate oxidase Lactate dehydrogenase D-amino acid dehydrogenase Glucose dehydrogenase Succinate dehydrogenase Ubiquinol oxidase Nitrate reductase Nitrite reductase Dimethyl sulfoxide reductase Trimethylamine N-oxide reductase Fumarate reductase Acetate + Carbon dioxide / Pyruvate Pyruvate / Lactate 2-oxoacid + ammonia / D-amino acid Gluconate / Glucose Fumarate / Succinate Oxygen / Water Nitrate / Nitrite Nitrite / Ammonia DMSO / DMS TMAO / TMA Fumarate / Succinate
As shown above, E. coli can grow with reducing agents such as formate, hydrogen, or lactate as electron donors, and nitrate, DMSO, or oxygen as acceptors.[56] The larger the difference in midpoint potential between an oxidizing and reducing agent, the more energy is released when they react. Out of these compounds, the succinate/fumarate pair is unusual, as its midpoint potential is close to zero. Succinate can therefore be oxidized to fumarate if a strong oxidizing agent such as oxygen is available, or fumarate can be reduced to succinate using a strong reducing agent such as formate. These alternative reactions are catalyzed by succinate dehydrogenase and fumarate reductase, respectively.[58] Some prokaryotes use redox pairs that have only a small difference in midpoint potential. For example, nitrifying bacteria such as Nitrobacter oxidize nitrite to nitrate, donating the electrons to oxygen. The small amount of energy released in this reaction is enough to pump protons and generate ATP, but not enough to produce NADH or NADPH
Oxidative phosphorylation directly for use in anabolism.[59] This problem is solved by using a nitrite oxidoreductase to produce enough proton-motive force to run part of the electron transport chain in reverse, causing complex I to generate NADH.[60]
[61]
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Prokaryotes control their use of these electron donors and acceptors by varying which enzymes are produced, in response to environmental conditions.[62] This flexibility is possible because different oxidases and reductases use the same ubiquinone pool. This allows many combinations of enzymes to function together, linked by the common ubiquinol intermediate.[57] These respiratory chains therefore have a modular design, with easily interchangeable sets of enzyme systems. In addition to this metabolic diversity, prokaryotes also possess a range of isozymes different enzymes that catalyze the same reaction. For example, in E. coli, there are two different types of ubiquinol oxidase using oxygen as an electron acceptor. Under highly aerobic conditions, the cell uses an oxidase with a low affinity for oxygen that can transport two protons per electron. However, if levels of oxygen fall, they switch to an oxidase that transfers only one proton per electron, but has a high affinity for oxygen.[63]
This phosphorylation reaction is an equilibrium, which can be shifted by altering the proton-motive force. In the absence of a proton-motive force, the ATP synthase reaction will run from right to left, hydrolyzing ATP and pumping protons out of the matrix across the membrane. However, when the proton-motive force is high, the reaction is forced to run in the opposite direction; it proceeds from left to right, allowing protons to flow down their concentration gradient and turning ADP into ATP.[64] Indeed, in the closely related vacuolar type H+-ATPases, the same reaction is used to acidify cellular compartments, by pumping protons and hydrolysing ATP.[68] ATP synthase is a massive protein complex with a mushroom-like shape. The mammalian enzyme complex contains 16 subunits and has a mass of approximately 600 kilodaltons.[69] The portion embedded within the membrane is called FO and contains a ring of c subunits and the proton channel. The stalk and the ball-shaped headpiece is called F1 and is the site of ATP synthesis. The ball-shaped complex at the end of the F1 portion contains six proteins of two different kinds (three subunits and three subunits), whereas the "stalk" consists of one protein: the subunit, with the tip of the stalk extending into the ball of and subunits.[70] Both the and subunits bind nucleotides, but only the subunits catalyze the ATP synthesis reaction. Reaching along the side of the F1 portion and back into the membrane is a long rod-like subunit that anchors the and subunits into the base of the enzyme. As protons cross the membrane through the channel in the base of ATP synthase, the FO proton-driven motor rotates.[71] Rotation might be caused by changes in the ionization of amino acids in the ring of c subunits causing electrostatic interactions that propel the ring of c subunits past the proton channel.[72] This rotating ring in turn drives the rotation of the central axle (the subunit stalk) within the and subunits. The and subunits are prevented from rotating themselves by the side-arm, which acts as a stator. This movement of the tip of the subunit within the ball of and subunits provides the energy for the active sites in the subunits to undergo a cycle of movements that produces and then releases ATP.[2]
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This ATP synthesis reaction is called the binding change mechanism and involves the active site of a subunit cycling between three states.[73] In the "open" state, ADP and phosphate enter the active site (shown in brown in the diagram). The protein then closes up around the molecules and binds them loosely the "loose" state (shown in red). The enzyme then changes shape again and forces these molecules together, with the active site in the resulting "tight" state (shown in pink) binding the newly produced ATP molecule with very high affinity. Finally, the active site cycles back to the open state, releasing ATP and binding more ADP and phosphate, ready for the next cycle.
Mechanism of ATP synthase. ATP is shown in red, ADP and
In some bacteria and archaea, ATP synthesis is driven by the phosphate in pink and the rotating subunit in black. movement of sodium ions through the cell membrane, rather than the movement of protons.[74] [75] Archaea such as Methanococcus also contain the A1Ao synthase, a form of the enzyme that contains additional proteins with little similarity in sequence to other bacterial and eukaryotic ATP synthase subunits. It is possible that, in some species, the A1Ao form of the enzyme is a specialized sodium-driven ATP synthase,[76] but this might not be true in all cases.[75]
These reactive oxygen species and their reaction products, such as the hydroxyl radical, are very harmful to cells, as they oxidize proteins and cause mutations in DNA. This cellular damage might contribute to disease and is proposed as one cause of aging.[78] [79] The cytochrome c oxidase complex is highly efficient at reducing oxygen to water, and it releases very few partly reduced intermediates; however small amounts of superoxide anion and peroxide are produced by the electron transport chain.[80] Particularly important is the reduction of coenzyme Q in complex III, as a highly reactive ubisemiquinone free radical is formed as an intermediate in the Q cycle. This unstable species can lead to electron "leakage" when electrons transfer directly to oxygen, forming superoxide.[81] As the production of reactive oxygen species by these proton-pumping complexes is greatest at high membrane potentials, it has been proposed that mitochondria regulate their activity to maintain the membrane potential within a narrow range that balances ATP production against oxidant generation.[82] For instance, oxidants can activate uncoupling proteins that reduce membrane potential.[83] To counteract these reactive oxygen species, cells contain numerous antioxidant systems, including antioxidant vitamins such as vitamin C and vitamin E, and antioxidant enzymes such as superoxide dismutase, catalase, and peroxidases,[77] which detoxify the reactive species, limiting damage to the cell.
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Inhibitors
There are several well-known drugs and toxins that inhibit oxidative phosphorylation. Although any one of these toxins inhibits only one enzyme in the electron transport chain, inhibition of any step in this process will halt the rest of the process. For example, if oligomycin inhibits ATP synthase, protons cannot pass back into the mitochondrion.[84] As a result, the proton pumps are unable to operate, as the gradient becomes too strong for them to overcome. NADH is then no longer oxidized and the citric acid cycle ceases to operate because the concentration of NAD+ falls below the concentration that these enzymes can use.
Compounds Cyanide Carbonmonoxide Azide Oligomycin CCCP 2,4-Dinitrophenol Rotenone Malonate and oxaloacetate Use Poisons Effect on oxidative phosphorylation Inhibit the electron transport chain by binding more strongly than oxygen to the FeCu center in cytochrome c [85] oxidase, preventing the reduction of oxygen.
Antibiotic Inhibits ATP synthase by blocking the flow of protons through the F subunit.[84] o Poisons Ionophores that disrupt the proton gradient by carrying protons across a membrane. This ionophore uncouples [86] proton pumping from ATP synthesis because it carries protons across the inner mitochondrial membrane.
Pesticide Prevents the transfer of electrons from complex I to ubiquinone by blocking the ubiquinone-binding site.[87] Competitive inhibitors of succinate dehydrogenase (complex II). [88]
Not all inhibitors of oxidative phosphorylation are toxins. In brown adipose tissue, regulated proton channels called uncoupling proteins can uncouple respiration from ATP synthesis.[89] This rapid respiration produces heat, and is particularly important as a way of maintaining body temperature for hibernating animals, although these proteins may also have a more general function in cells' responses to stress.[90]
History
Further information: History of biochemistry and History of molecular biology The field of oxidative phosphorylation began with the report in 1906 by Arthur Harden of a vital role for phosphate in cellular fermentation, but initially only sugar phosphates were known to be involved.[91] However, in the early 1940s, the link between the oxidation of sugars and the generation of ATP was firmly established by Herman Kalckar,[92] confirming the central role of ATP in energy transfer that had been proposed by Fritz Albert Lipmann in 1941.[93] Later, in 1949, Morris Friedkin and Albert L. Lehninger proved that the coenzyme NADH linked metabolic pathways such as the citric acid cycle and the synthesis of ATP.[94] For another twenty years, the mechanism by which ATP is generated remained mysterious, with scientists searching for an elusive "high-energy intermediate" that would link oxidation and phosphorylation reactions.[95] This puzzle was solved by Peter D. Mitchell with the publication of the chemiosmotic theory in 1961.[96] At first, this proposal was highly controversial, but it was slowly accepted and Mitchell was awarded a Nobel prize in 1978.[97] [98] Subsequent research concentrated on purifying and characterizing the enzymes involved, with major contributions being made by David E. Green on the complexes of the electron-transport chain, as well as Efraim Racker on the ATP synthase.[99] A critical step towards solving the mechanism of the ATP synthase was provided by Paul D. Boyer, by his development in 1973 of the "binding change" mechanism, followed by his radical proposal of rotational catalysis in 1982.[73] [100] More recent work has included structural studies on the enzymes involved in oxidative phosphorylation by John E. Walker, with Walker and Boyer being awarded a Nobel Prize in 1997.[101]
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References
[1] Mitchell P, Moyle J (1967). "Chemiosmotic hypothesis of oxidative phosphorylation". Nature 213 (5072): 1379. doi:10.1038/213137a0. PMID4291593. [2] Dimroth P, Kaim G, Matthey U (1 January 2000). "Crucial role of the membrane potential for ATP synthesis by F(1)F(o) ATP synthases" (http:/ / jeb. biologists. org/ cgi/ reprint/ 203/ 1/ 51). J. Exp. Biol. 203 (Pt 1): 519. PMID10600673. . [3] Schultz B, Chan S (2001). "Structures and proton-pumping strategies of mitochondrial respiratory enzymes". Annu Rev Biophys Biomol Struct 30: 2365. doi:10.1146/annurev.biophys.30.1.23. PMID11340051. [4] Rich PR (2003). "The molecular machinery of Keilin's respiratory chain" (http:/ / www. biochemsoctrans. org/ bst/ 031/ 1095/ bst0311095. htm). Biochem. Soc. Trans. 31 (Pt 6): 1095105. doi:10.1042/BST0311095. PMID14641005. . [5] Porter RK, Brand MD (1995). "Mitochondrial proton conductance and H+/O ratio are independent of electron transport rate in isolated hepatocytes". Biochem. J. 310 ((Pt 2)): 37982. PMC1135905. PMID7654171. [6] Mathews FS (1985). "The structure, function and evolution of cytochromes". Prog. Biophys. Mol. Biol. 45 (1): 156. doi:10.1016/0079-6107(85)90004-5. PMID3881803. [7] Wood PM (1983). "Why do c-type cytochromes exist?". FEBS Lett. 164 (2): 2236. doi:10.1016/0014-5793(83)80289-0. PMID6317447. [8] Crane FL (1 December 2001). "Biochemical functions of coenzyme Q10" (http:/ / www. jacn. org/ cgi/ content/ full/ 20/ 6/ 591). Journal of the American College of Nutrition 20 (6): 5918. PMID11771674. . [9] Mitchell P (1979). "Keilin's respiratory chain concept and its chemiosmotic consequences". Science 206 (4423): 114859. doi:10.1126/science.388618. PMID388618. [10] Sballe B, Poole RK (1999). "Microbial ubiquinones: multiple roles in respiration, gene regulation and oxidative stress management" (http:/ / mic. sgmjournals. org/ cgi/ reprint/ 145/ 8/ 1817. pdf) (PDF). Microbiology (Reading, Engl.) 145 (Pt 8): 181730. PMID10463148. . [11] Johnson D, Dean D, Smith A, Johnson M (2005). "Structure, function, and formation of biological iron-sulfur clusters". Annu Rev Biochem 74: 24781. doi:10.1146/annurev.biochem.74.082803.133518. PMID15952888. [12] Page CC, Moser CC, Chen X, Dutton PL (1999). "Natural engineering principles of electron tunnelling in biological oxidation-reduction". Nature 402 (6757): 4752. doi:10.1038/46972. PMID10573417. [13] Leys D, Scrutton NS (2004). "Electrical circuitry in biology: emerging principles from protein structure". Curr. Opin. Struct. Biol. 14 (6): 6427. doi:10.1016/j.sbi.2004.10.002. PMID15582386. [14] Boxma B, de Graaf RM, van der Staay GW, et al. (2005). "An anaerobic mitochondrion that produces hydrogen". Nature 434 (7029): 749. doi:10.1038/nature03343. PMID15744302. [15] Medical CHEMISTRY Compendium. By Anders Overgaard Pedersen and Henning Nielsen. Aarhus University. 2008 [16] Hirst J (2005). "Energy transduction by respiratory complex Ian evaluation of current knowledge" (http:/ / www. biochemsoctrans. org/ bst/ 033/ 0525/ 0330525. pdf) (PDF). Biochem. Soc. Trans. 33 (Pt 3): 5259. doi:10.1042/BST0330525. PMID15916556. . [17] Lenaz G, Fato R, Genova M, Bergamini C, Bianchi C, Biondi A (2006). "Mitochondrial Complex I: structural and functional aspects". Biochim Biophys Acta 1757 (910): 140620. doi:10.1016/j.bbabio.2006.05.007. PMID16828051. [18] Sazanov L.A., Hinchliffe P. (2006). "Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus". Science 311 (5766): 14301436. doi:10.1126/science.1123809. PMID16469879. [19] Efremov R.G., Baradaran R., & Sazanov L.A., (2010) The arcdhitecture of respiratory complex I, Nature 465, 441-445 [20] Baranova EA, Holt PJ, Sazanov LA (2007). "Projection structure of the membrane domain of Escherichia coli respiratory complex I at 8 A resolution". J. Mol. Biol. 366 (1): 14054. doi:10.1016/j.jmb.2006.11.026. PMID17157874. [21] Friedrich T, Bttcher B (2004). "The gross structure of the respiratory complex I: a Lego System". Biochim. Biophys. Acta 1608 (1): 19. doi:10.1016/j.bbabio.2003.10.002. PMID14741580. [22] Hirst J (January 2010). "Towards the molecular mechanism of respiratory complex I". Biochem. J. 425 (2): 32739. doi:10.1042/BJ20091382. PMID20025615. [23] Cecchini G (2003). "Function and structure of complex II of the respiratory chain". Annu Rev Biochem 72: 77109. doi:10.1146/annurev.biochem.72.121801.161700. PMID14527321. [24] Yankovskaya V., Horsefield R., Tornroth S., Luna-Chavez C., Miyoshi H., Leger C., Byrne B., Cecchini G. et al. (2003). "Architecture of succinate dehydrogenase and reactive oxygen species generation". Science 299 (5607): 700704. doi:10.1126/science.1079605. PMID12560550. [25] Horsefield R, Iwata S, Byrne B (2004). "Complex II from a structural perspective". Curr. Protein Pept. Sci. 5 (2): 10718. doi:10.2174/1389203043486847. PMID15078221. [26] Kita K, Hirawake H, Miyadera H, Amino H, Takeo S (2002). "Role of complex II in anaerobic respiration of the parasite mitochondria from Ascaris suum and Plasmodium falciparum". Biochim. Biophys. Acta 1553 (12): 12339. doi:10.1016/S0005-2728(01)00237-7. PMID11803022. [27] Painter HJ, Morrisey JM, Mather MW, Vaidya AB (2007). "Specific role of mitochondrial electron transport in blood-stage Plasmodium falciparum". Nature 446 (7131): 8891. doi:10.1038/nature05572. PMID17330044. [28] Ramsay RR, Steenkamp DJ, Husain M (1987). "Reactions of electron-transfer flavoprotein and electron-transfer flavoprotein: ubiquinone oxidoreductase". Biochem. J. 241 (3): 88392. PMC1147643. PMID3593226. [29] Zhang J, Frerman FE, Kim JJ (2006). "Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool". Proc. Natl. Acad. Sci. U.S.A. 103 (44): 162127. doi:10.1073/pnas.0604567103. PMC1637562.
Oxidative phosphorylation
PMID17050691. [30] Ikeda Y, Dabrowski C, Tanaka K (25 January 1983). "Separation and properties of five distinct acyl-CoA dehydrogenases from rat liver mitochondria. Identification of a new 2-methyl branched chain acyl-CoA dehydrogenase" (http:/ / www. jbc. org/ cgi/ reprint/ 258/ 2/ 1066). J. Biol. Chem. 258 (2): 106676. PMID6401712. . [31] Ruzicka FJ, Beinert H (1977). "A new iron-sulfur flavoprotein of the respiratory chain. A component of the fatty acid beta oxidation pathway" (http:/ / www. jbc. org/ cgi/ reprint/ 252/ 23/ 8440. pdf) (PDF). J. Biol. Chem. 252 (23): 84405. PMID925004. . [32] Ishizaki K, Larson TR, Schauer N, Fernie AR, Graham IA, Leaver CJ (2005). "The Critical Role of Arabidopsis Electron-Transfer Flavoprotein:Ubiquinone Oxidoreductase during Dark-Induced Starvation". Plant Cell 17 (9): 2587600. doi:10.1105/tpc.105.035162. PMC1197437. PMID16055629. [33] Berry E, Guergova-Kuras M, Huang L, Crofts A (2000). "Structure and function of cytochrome bc complexes". Annu Rev Biochem 69: 100575. doi:10.1146/annurev.biochem.69.1.1005. PMID10966481. [34] Crofts AR (2004). "The cytochrome bc1 complex: function in the context of structure". Annu. Rev. Physiol. 66: 689733. doi:10.1146/annurev.physiol.66.032102.150251. PMID14977419. [35] Iwata S, Lee JW, Okada K, et al. (1998). "Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex". Science 281 (5373): 6471. doi:10.1126/science.281.5373.64. PMID9651245. [36] Trumpower BL (1990). "The protonmotive Q cycle. Energy transduction by coupling of proton translocation to electron transfer by the cytochrome bc1 complex" (http:/ / www. jbc. org/ cgi/ reprint/ 265/ 20/ 11409. pdf) (PDF). J. Biol. Chem. 265 (20): 1140912. PMID2164001. . [37] Hunte C, Palsdottir H, Trumpower BL (2003). "Protonmotive pathways and mechanisms in the cytochrome bc1 complex". FEBS Lett. 545 (1): 3946. doi:10.1016/S0014-5793(03)00391-0. PMID12788490. [38] Calhoun M, Thomas J, Gennis R (1994). "The cytochrome oxidase superfamily of redox-driven proton pumps". Trends Biochem Sci 19 (8): 32530. doi:10.1016/0968-0004(94)90071-X. PMID7940677. [39] Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa-Itoh K, Nakashima R, Yaono R, Yoshikawa S. (1996). "The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A". Science 272 (5265): 113644. Bibcode1996Sci...272.1136T. doi:10.1126/science.272.5265.1136. PMID8638158. [40] Yoshikawa S, Muramoto K, Shinzawa-Itoh K, et al. (2006). "Proton pumping mechanism of bovine heart cytochrome c oxidase". Biochim. Biophys. Acta 1757 (910): 11106. doi:10.1016/j.bbabio.2006.06.004. PMID16904626. [41] Rasmusson AG, Soole KL, Elthon TE (2004). "Alternative NAD(P)H dehydrogenases of plant mitochondria". Annual review of plant biology 55: 2339. doi:10.1146/annurev.arplant.55.031903.141720. PMID15725055. [42] Menz RI, Day DA (1996). "Purification and characterization of a 43-kDa rotenone-insensitive NADH dehydrogenase from plant mitochondria" (http:/ / www. jbc. org/ cgi/ content/ full/ 271/ 38/ 23117). J. Biol. Chem. 271 (38): 2311720. doi:10.1074/jbc.271.38.23117. PMID8798503. . [43] McDonald A, Vanlerberghe G (2004). "Branched mitochondrial electron transport in the Animalia: presence of alternative oxidase in several animal phyla". IUBMB Life 56 (6): 33341. doi:10.1080/1521-6540400000876. PMID15370881. [44] Sluse FE, Jarmuszkiewicz W (1998). "Alternative oxidase in the branched mitochondrial respiratory network: an overview on structure, function, regulation, and role". Braz. J. Med. Biol. Res. 31 (6): 73347. doi:10.1590/S0100-879X1998000600003. PMID9698817. [45] Moore AL, Siedow JN (1991). "The regulation and nature of the cyanide-resistant alternative oxidase of plant mitochondria". Biochim. Biophys. Acta 1059 (2): 12140. doi:10.1016/S0005-2728(05)80197-5. PMID1883834. [46] Vanlerberghe GC, McIntosh L (1997). "Alternative oxidase: From Gene to Function". Annual Review of Plant Physiology and Plant Molecular Biology 48: 70334. doi:10.1146/annurev.arplant.48.1.703. PMID15012279. [47] Ito Y, Saisho D, Nakazono M, Tsutsumi N, Hirai A (1997). "Transcript levels of tandem-arranged alternative oxidase genes in rice are increased by low temperature". Gene 203 (2): 1219. doi:10.1016/S0378-1119(97)00502-7. PMID9426242. [48] Maxwell DP, Wang Y, McIntosh L (1999). "The alternative oxidase lowers mitochondrial reactive oxygen production in plant cells" (http:/ / www. pnas. org/ cgi/ content/ full/ 96/ 14/ 8271). Proc. Natl. Acad. Sci. U.S.A. 96 (14): 82716. doi:10.1073/pnas.96.14.8271. PMC22224. PMID10393984. . [49] Heinemeyer J, Braun HP, Boekema EJ, Kouril R (2007). "A structural model of the cytochrome C reductase/oxidase supercomplex from yeast mitochondria". J. Biol. Chem. 282 (16): 122408. doi:10.1074/jbc.M610545200. PMID17322303. [50] Schgger H, Pfeiffer K (2000). "Supercomplexes in the respiratory chains of yeast and mammalian mitochondria". EMBO J. 19 (8): 177783. doi:10.1093/emboj/19.8.1777. PMC302020. PMID10775262. [51] Schgger H (2002). "Respiratory chain supercomplexes of mitochondria and bacteria". Biochim. Biophys. Acta 1555 (13): 1549. doi:10.1016/S0005-2728(02)00271-2. PMID12206908. [52] Schgger H, Pfeiffer K (2001). "The ratio of oxidative phosphorylation complexes I-V in bovine heart mitochondria and the composition of respiratory chain supercomplexes" (http:/ / www. jbc. org/ cgi/ content/ full/ 276/ 41/ 37861). J. Biol. Chem. 276 (41): 378617. doi:10.1074/jbc.M106474200. PMID11483615. . [53] Gupte S, Wu ES, Hoechli L, et al. (1984). "Relationship between lateral diffusion, collision frequency, and electron transfer of mitochondrial inner membrane oxidation-reduction components". Proc. Natl. Acad. Sci. U.S.A. 81 (9): 260610. doi:10.1073/pnas.81.9.2606. PMC345118. PMID6326133. [54] Nealson KH (1999). "Post-Viking microbiology: new approaches, new data, new insights". Origins of life and evolution of the biosphere: the journal of the International Society for the Study of the Origin of Life 29 (1): 7393. doi:10.1023/A:1006515817767. PMID11536899.
265
Oxidative phosphorylation
[55] Schfer G, Engelhard M, Mller V (1999). "Bioenergetics of the Archaea". Microbiol. Mol. Biol. Rev. 63 (3): 570620. PMC103747. PMID10477309. [56] Ingledew WJ, Poole RK (1984). "The respiratory chains of Escherichia coli". Microbiol. Rev. 48 (3): 22271. PMC373010. PMID6387427. [57] Unden G, Bongaerts J (1997). "Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors". Biochim. Biophys. Acta 1320 (3): 21734. doi:10.1016/S0005-2728(97)00034-0. PMID9230919. [58] Cecchini G, Schrder I, Gunsalus RP, Maklashina E (2002). "Succinate dehydrogenase and fumarate reductase from Escherichia coli". Biochim. Biophys. Acta 1553 (12): 14057. doi:10.1016/S0005-2728(01)00238-9. PMID11803023. [59] Freitag A, Bock E (1990). "Energy conservation in Nitrobacter". FEMS Microbiology Letters 66 (13): 15762. doi:10.1111/j.1574-6968.1990.tb03989.x. [60] Starkenburg SR, Chain PS, Sayavedra-Soto LA, et al. (2006). "Genome Sequence of the Chemolithoautotrophic Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Nb-255" (http:/ / aem. asm. org/ cgi/ content/ full/ 72/ 3/ 2050?view=long& pmid=16517654). Appl. Environ. Microbiol. 72 (3): 205063. doi:10.1128/AEM.72.3.2050-2063.2006. PMC1393235. PMID16517654. . [61] Yamanaka T, Fukumori Y (1988). "The nitrite oxidizing system of Nitrobacter winogradskyi". FEMS Microbiol. Rev. 4 (4): 25970. PMID2856189. [62] Iuchi S, Lin EC (1993). "Adaptation of Escherichia coli to redox environments by gene expression". Mol. Microbiol. 9 (1): 915. doi:10.1111/j.1365-2958.1993.tb01664.x. PMID8412675. [63] Calhoun MW, Oden KL, Gennis RB, de Mattos MJ, Neijssel OM (1993). "Energetic efficiency of Escherichia coli: effects of mutations in components of the aerobic respiratory chain" (http:/ / jb. asm. org/ cgi/ reprint/ 175/ 10/ 3020. pdf) (PDF). J. Bacteriol. 175 (10): 30205. PMC204621. PMID8491720. . [64] Boyer PD (1997). "The ATP synthasea splendid molecular machine". Annu. Rev. Biochem. 66: 71749. doi:10.1146/annurev.biochem.66.1.717. PMID9242922. [65] Van Walraven HS, Strotmann H, Schwarz O, Rumberg B (1996). "The H+/ATP coupling ratio of the ATP synthase from thiol-modulated chloroplasts and two cyanobacterial strains is four". FEBS Lett. 379 (3): 30913. doi:10.1016/0014-5793(95)01536-1. PMID8603713. [66] Yoshida M, Muneyuki E, Hisabori T (2001). "ATP synthasea marvellous rotary engine of the cell". Nat. Rev. Mol. Cell Biol. 2 (9): 66977. doi:10.1038/35089509. PMID11533724. [67] Schemidt RA, Qu J, Williams JR, Brusilow WS (1998). "Effects of Carbon Source on Expression of Fo Genes and on the Stoichiometry of the c Subunit in the F1Fo ATPase of Escherichia coli". J. Bacteriol. 180 (12): 32058. PMC107823. PMID9620972. [68] Nelson N, Perzov N, Cohen A, Hagai K, Padler V, Nelson H (1 January 2000). "The cellular biology of proton-motive force generation by V-ATPases" (http:/ / jeb. biologists. org/ cgi/ reprint/ 203/ 1/ 89). J. Exp. Biol. 203 (Pt 1): 8995. PMID10600677. . [69] Rubinstein JL, Walker JE, Henderson R (2003). "Structure of the mitochondrial ATP synthase by electron cryomicroscopy". EMBO J. 22 (23): 618292. doi:10.1093/emboj/cdg608. PMC291849. PMID14633978. [70] Leslie AG, Walker JE (2000). "Structural model of F1-ATPase and the implications for rotary catalysis". Philos. Trans. R. Soc. Lond., B, Biol. Sci. 355 (1396): 46571. doi:10.1098/rstb.2000.0588. PMC1692760. PMID10836500. [71] Noji H, Yoshida M (2001). "The rotary machine in the cell, ATP synthase" (http:/ / www. jbc. org/ cgi/ content/ full/ 276/ 3/ 1665). J. Biol. Chem. 276 (3): 16658. doi:10.1074/jbc.R000021200. PMID11080505. . [72] Capaldi R, Aggeler R (2002). "Mechanism of the F(1)F(0)-type ATP synthase, a biological rotary motor". Trends Biochem Sci 27 (3): 15460. doi:10.1016/S0968-0004(01)02051-5. PMID11893513. [73] Gresser MJ, Myers JA, Boyer PD (25 October 1982). "Catalytic site cooperativity of beef heart mitochondrial F1 adenosine triphosphatase. Correlations of initial velocity, bound intermediate, and oxygen exchange measurements with an alternating three-site model" (http:/ / www. jbc. org/ cgi/ reprint/ 257/ 20/ 12030). J. Biol. Chem. 257 (20): 120308. PMID6214554. . [74] Dimroth P (1994). "Bacterial sodium ion-coupled energetics". Antonie Van Leeuwenhoek 65 (4): 38195. doi:10.1007/BF00872221. PMID7832594. [75] Becher B, Mller V (1994). "Delta mu Na+ drives the synthesis of ATP via an delta mu Na(+)-translocating F1F0-ATP synthase in membrane vesicles of the archaeon Methanosarcina mazei G1". J. Bacteriol. 176 (9): 254350. PMC205391. PMID8169202. [76] Mller V (2004). "An exceptional variability in the motor of archaeal A1A0 ATPases: from multimeric to monomeric rotors comprising 613 ion binding sites". J. Bioenerg. Biomembr. 36 (1): 11525. doi:10.1023/B:JOBB.0000019603.68282.04. PMID15168615. [77] Davies K (1995). "Oxidative stress: the paradox of aerobic life". Biochem Soc Symp 61: 131. PMID8660387. [78] Rattan SI (2006). "Theories of biological aging: genes, proteins, and free radicals". Free Radic. Res. 40 (12): 12308. doi:10.1080/10715760600911303. PMID17090411. [79] Valko M, Leibfritz D, Moncol J, Cronin MT, Mazur M, Telser J (2007). "Free radicals and antioxidants in normal physiological functions and human disease". Int. J. Biochem. Cell Biol. 39 (1): 4484. doi:10.1016/j.biocel.2006.07.001. PMID16978905. [80] Raha S, Robinson B (2000). "Mitochondria, oxygen free radicals, disease and ageing". Trends Biochem Sci 25 (10): 5028. doi:10.1016/S0968-0004(00)01674-1. PMID11050436. [81] Finkel T, Holbrook NJ (2000). "Oxidants, oxidative stress and the biology of ageing". Nature 408 (6809): 23947. doi:10.1038/35041687. PMID11089981. [82] Kadenbach B, Ramzan R, Wen L, Vogt S (May 2009). "New extension of the Mitchell Theory for oxidative phosphorylation in mitochondria of living organisms". Biochim. Biophys. Acta 1800 (3): 205212. doi:10.1016/j.bbagen.2009.04.019. PMID19409964.
266
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[83] Echtay KS, Roussel D, St-Pierre J, et al. (January 2002). "Superoxide activates mitochondrial uncoupling proteins". Nature 415 (6867): 969. doi:10.1038/415096a. PMID11780125. [84] Joshi S, Huang YG (1991). "ATP synthase complex from bovine heart mitochondria: the oligomycin sensitivity conferring protein is essential for dicyclohexyl carbodiimide-sensitive ATPase". Biochim. Biophys. Acta 1067 (2): 2558. doi:10.1016/0005-2736(91)90051-9. PMID1831660. [85] Tsubaki M; Yoshikawa, Shinya (1993). "Fourier-transform infrared study of cyanide binding to the Fea3-CuB binuclear site of bovine heart cytochrome c oxidase: implication of the redox-linked conformational change at the binuclear site". Biochemistry 32 (1): 16473. doi:10.1021/bi00052a022. PMID8380331. [86] Heytler PG (1979). "Uncouplers of oxidative phosphorylation". Meth. Enzymol.. Methods in Enzymology 55: 46242. doi:10.1016/0076-6879(79)55060-5. ISBN9780121819552. PMID156853. [87] Lambert AJ, Brand MD (2004). "Inhibitors of the quinone-binding site allow rapid superoxide production from mitochondrial NADH: ubiquinone oxidoreductase (complex I)" (http:/ / www. jbc. org/ cgi/ content/ full/ 279/ 38/ 39414). J. Biol. Chem. 279 (38): 3941420. doi:10.1074/jbc.M406576200. PMID15262965. . [88] Dervartanian DV, Veeger C. (November 1964). "Studies on succinate dehydrogenase. I. Spectral properties of the purified enzyme and formation of enzyme-competitive inhibitor complexes". Biochim. Biophys. Acta 92: 23347. PMID14249115. [89] Ricquier D, Bouillaud F (2000). "The uncoupling protein homologues: UCP1, UCP2, UCP3, StUCP and AtUCP". Biochem. J. 345 Pt 2 (2): 16179. doi:10.1042/0264-6021:3450161. PMC1220743. PMID10620491. [90] Boreck J, Vercesi AE (2005). "Plant uncoupling mitochondrial protein and alternative oxidase: energy metabolism and stress". Biosci. Rep. 25 (34): 27186. doi:10.1007/s10540-005-2889-2. PMID16283557. [91] Harden A, Young WJ. (1906). "The alcoholic ferment of yeast-juice". Proc. R. Soc. (Lond.) B (77): 40520. doi:10.1098/rspb.1906.0029. [92] Kalckar HM (1974). "Origins of the concept oxidative phosphorylation". Mol. Cell. Biochem. 5 (12): 5563. doi:10.1007/BF01874172. PMID4279328. [93] Lipmann F, (1941). "Metabolic generation and utilization of phosphate bond energy". Adv Enzymol 1: 99162. [94] Friedkin M, Lehninger AL. (1 April 1949). "Esterification of inorganic phosphate coupled to electron transport between dihydrodiphosphopyridine nucleotide and oxygen" (http:/ / www. jbc. org/ cgi/ reprint/ 178/ 2/ 611). J. Biol. Chem. 178 (2): 61123. PMID18116985. . [95] Slater EC. (1953). "Mechanism of Phosphorylation in the Respiratory Chain". Nature 172 (4387): 9758. doi:10.1038/172975a0. PMID13111237. [96] Mitchell P. (1961). "Coupling of Phosphorylation to Electron and Hydrogen Transfer by a Chemi-Osmotic type of Mechanism". Nature 191 (4784): 1448. Bibcode1961Natur.191..144M. doi:10.1038/191144a0. PMID13771349. [97] Milton H. Saier Jr. "Peter Mitchell and the Vital Force" (http:/ / www-biology. ucsd. edu/ ~msaier/ transport/ petermitchell/ MitchellFrame-1. html). . Retrieved 2007-08-23. [98] Mitchell, Peter (1978). "David Keilin's Respiratory Chain Concept and Its Chemiosmotic Consequences" (http:/ / nobelprize. org/ nobel_prizes/ chemistry/ laureates/ 1978/ mitchell-lecture. pdf) (Pdf). Nobel lecture. Nobel Foundation. . Retrieved 2007-07-21. [99] Pullman ME, Penefsky HS, Datta A, and Racker E. (1 November 1960). "Partial Resolution of the Enzymes Catalyzing Oxidative Phosphorylation. I. Purification and Properties of Soluble, Dinitrophenol-stimulated Adenosine Triphosphatase" (http:/ / www. jbc. org/ cgi/ reprint/ 235/ 11/ 3322). J. Biol. Chem. 235 (11): 33229. PMID13738472. . [100] Boyer PD, Cross RL, Momsen W (1973). "A New Concept for Energy Coupling in Oxidative Phosphorylation Based on a Molecular Explanation of the Oxygen Exchange Reactions". Proc. Natl. Acad. Sci. U.S.A. 70 (10): 28379. doi:10.1073/pnas.70.10.2837. PMC427120. PMID4517936. [101] "The Nobel Prize in Chemistry 1997" (http:/ / nobelprize. org/ nobel_prizes/ chemistry/ laureates/ 1997/ ). Nobel Foundation. . Retrieved 2007-07-21.
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Further reading
Introductory Nelson DL; Cox MM (2004). Lehninger Principles of Biochemistry (4th ed.). W. H. Freeman. ISBN0-7167-4339-6. Schneider ED; Sagan D (2006). Into the Cool: Energy Flow, Thermodynamics and Life (1st ed.). University of Chicago Press. ISBN0-226-73937-6. Lane N (2006). Power, Sex, Suicide: Mitochondria and the Meaning of Life (1st ed.). Oxford University Press, USA. ISBN0-19-920564-7. Advanced Nicholls DG; Ferguson SJ (2002). Bioenergetics 3 (1st ed.). Academic Press. ISBN0-12-518121-3. Haynie D (2001). Biological Thermodynamics (1st ed.). Cambridge University Press. ISBN0-521-79549-4. Rajan SS (2003). Introduction to Bioenergetics (1st ed.). Anmol. ISBN8-126-11364-2.
Oxidative phosphorylation Wikstrom M (Ed) (2005). Biophysical and Structural Aspects of Bioenergetics (1st ed.). Royal Society of Chemistry. ISBN0-85404-346-2.
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External links
General resources Animated diagrams illustrating oxidative phosphorylation (http://www.wiley.com/legacy/college/boyer/ 0470003790/animations/electron_transport/electron_transport.htm) Wiley and Co Concepts in Biochemistry ATP synthase - the rotary engine in the cell (http://www.res.titech.ac.jp/~seibutu/) Brief introduction, including videos of microscope images of the enzyme rotating, at Tokyo Institute of Technology On-line biophysics lectures (http://www.life.uiuc.edu/crofts/bioph354/) Antony Crofts, University of Illinois at Urbana-Champaign Structural resources Animations of the ATP synthase (http://nature.berkeley.edu/~hongwang/Project/ATP_synthase/) Hongyun Wang and George Oster, University of California, Berkeley PDB molecule of the month: ATP synthase (http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/ pdb72_1.html) Cytochrome c (http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/ pdb36_1.html) Cytochrome c oxidase (http://www.rcsb.org/pdb/static.do?p=education_discussion/ molecule_of_the_month/pdb5_1.html) Interactive molecular models at Universidade Fernando Pessoa: NADH dehydrogenase (http://www2.ufp.pt/~pedros/anim/2frame-ien.htm) succinate dehydrogenase (http://www2.ufp.pt/~pedros/anim/2frame-iien.htm) Coenzyme Q - cytochrome c reductase (http://www2.ufp.pt/~pedros/anim/2frame-iiien.htm) cytochrome c oxidase (http://www2.ufp.pt/~pedros/anim/2frame-iven.htm)
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Photosynthesis
Photosynthesis
Photosynthesis (English pronunciation: /fotosnss/; from the Greek - [photo-], "light," and [synthesis], "putting together", "composition") is a chemical process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight.[1] Photosynthesis occurs in plants, algae, and many species of bacteria, but not in archaea. Photosynthetic organisms are called photoautotrophs, since they can create their own food. In plants, Composite image showing the global distribution of photosynthesis, including both algae, and cyanobacteria, oceanic phytoplankton and vegetation photosynthesis uses carbon dioxide and water, releasing oxygen as a waste product. Photosynthesis is vital for all aerobic life on Earth. In addition to maintaining normal levels of oxygen in the atmosphere, photosynthesis is the Overall equation for the type of photosynthesis that occurs in plants source of energy for nearly all life on earth, either directly, through primary production, or indirectly, as the ultimate source of the energy in their food,[2] the exceptions being chemoautotrophs that live in rocks or around deep sea hydrothermal vents. The rate of energy capture by photosynthesis is immense, approximately 100terawatts,[3] which is about six times larger than the power consumption of human civilization.[4] As well as energy, photosynthesis is also the source of the carbon in all the organic compounds within organisms' bodies. In all, photosynthetic organisms convert around 100115 petagrams of carbon into biomass per year.[5] [6] Although photosynthesis can happen in different ways in different species, some features are always the same. For example, the process always begins when energy from light is absorbed by proteins called photosynthetic reaction centers that contain chlorophylls. In plants, these proteins are held inside organelles called chloroplasts, while in bacteria they are embedded in the plasma membrane. Some of the light energy gathered by chlorophylls is stored in the form of adenosine triphosphate (ATP). The rest of the energy is used to remove electrons from a substance such as water. These electrons are then used in the reactions that turn carbon dioxide into organic compounds. In plants, algae and cyanobacteria, this is done by a sequence of reactions called the Calvin cycle, but different sets of reactions are found in some bacteria, such as the reverse Krebs cycle in Chlorobium. Many photosynthetic organisms have adaptations that concentrate or store carbon dioxide. This helps reduce a wasteful process called photorespiration that can consume part of the sugar produced during photosynthesis.
Photosynthesis The first photosynthetic organisms probably evolved about 3500 [7] million years ago, early in the evolutionary history of life, when all forms of life on Earth were microorganisms and the atmosphere had much more carbon dioxide. They most likely used hydrogen or hydrogen sulfide as sources of electrons, rather than water.[8] Cyanobacteria appeared later, around 3000 [9] million years ago, and drastically changed the Earth when they began to oxygenate the atmosphere, beginning about 2400 [10] million years ago.[11] This new atmosphere allowed the evolution of complex life such as protists. Eventually, no later than a billion years ago, one of these protists formed a symbiotic relationship with a cyanobacterium, producing the ancestor of many plants and algae.[12] The chloroplasts in modern plants are the descendants of these ancient symbiotic cyanobacteria.[13]
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Overview
Photosynthetic organisms are photoautotrophs, which means that they are repositories of energy, they are able to synthesize food directly from carbon dioxide, water, and using energy from light. They accrue it as part of their potential energy. However, not all organisms that use light as a source of energy carry out photosynthesis, since photoheterotrophs use organic compounds, rather than carbon dioxide, as a source of carbon.[2] In plants, algae and cyanobacteria, photosynthesis releases oxygen. This is called oxygenic photosynthesis. Although there are some differences between oxygenic photosynthesis in plants, algae and cyanobacteria, the overall process is quite similar in these organisms. However, there are some types of bacteria that carry out anoxygenic photosynthesis, which consumes carbon dioxide but does not release oxygen. Carbon dioxide is converted into sugars in a process called carbon Photosynthesis changes sunlight into chemical fixation. Carbon fixation is a redox reaction, so photosynthesis needs energy, splits water to liberate O2, and fixes CO2 into sugar. to supply both a source of energy to drive this process, and the electrons needed to convert carbon dioxide into a carbohydrate, which is a reduction reaction. In general outline, photosynthesis is the opposite of cellular respiration, where glucose and other compounds are oxidized to produce carbon dioxide, water, and release chemical energy. However, the two processes take place through a different sequence of chemical reactions and in different cellular compartments. The general equation for photosynthesis is therefore: 2n CO2 + 2n DH2 + photons 2(CH2O)n + 2n DO Carbon dioxide + electron donor + light energy carbohydrate + oxidized electron donor In oxygenic photosynthesis water is the electron donor and, since its hydrolysis releases oxygen, the equation for this process is:
Photosynthesis 2n CO2 + 4n H2O + photons 2(CH2O)n + 2n O2 + 2n H2O carbon dioxide + water + light energy carbohydrate + oxygen + water Often 2n water molecules are cancelled on both sides, yielding: 2n CO2 + 2n H2O + photons 2(CH2O)n + 2n O2 carbon dioxide + water + light energy carbohydrate + oxygen Other processes substitute other compounds (such as arsenite) for water in the electron-supply role; the microbes use sunlight to oxidize arsenite to arsenate:[14] The equation for this reaction is: CO2 + (AsO33) + photons (AsO43) + CO [15] carbon dioxide + arsenite + light energy arsenate + carbon monoxide (used to build other compounds in subsequent reactions) Photosynthesis occurs in two stages. In the first stage, light-dependent reactions or light reactions capture the energy of light and use it to make the energy-storage molecules ATP and NADPH. During the second stage, the light-independent reactions use these products to capture and reduce carbon dioxide. Most organisms that utilize photosynthesis to produce oxygen use visible light to do so, although at least three use infrared radiation.[16]
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Chloroplast ultrastructure: 1. outer membrane 2. intermembrane space3. inner membrane (1+2+3: envelope) 4. stroma (aqueous fluid) 5. thylakoid lumen (inside of thylakoid) 6. thylakoid membrane 7. granum (stack of thylakoids) 8. thylakoid (lamella) 9. starch 10. ribosome 11. plastidial DNA 12. plastoglobule (drop of lipids)
In plants and algae, photosynthesis takes place in organelles called chloroplasts. A typical plant cell contains about 10 to 100 chloroplasts. The chloroplast is enclosed by a membrane. This membrane is composed of a phospholipid inner membrane, a phospholipid outer membrane, and an intermembrane space between them. Within the membrane is an aqueous fluid called the stroma. The stroma contains stacks (grana) of thylakoids, which are the site of photosynthesis. The thylakoids are flattened disks, bounded by a membrane with a lumen or thylakoid space within it. The site of photosynthesis is the thylakoid membrane, which contains integral and peripheral membrane protein complexes, including the pigments that absorb light energy, which form the photosystems. Plants absorb light primarily using the pigment chlorophyll, which is the reason that most plants have a green color. Besides chlorophyll, plants also use pigments such as carotenes and xanthophylls.[20] Algae also use chlorophyll, but various other pigments are present as phycocyanin, carotenes, and xanthophylls in green algae, phycoerythrin in red algae (rhodophytes) and fucoxanthin in brown algae and diatoms resulting in a wide variety of colors. These pigments are embedded in plants and algae in special antenna-proteins. In such proteins all the pigments are ordered to work well together. Such a protein is also called a light-harvesting complex.
Photosynthesis Although all cells in the green parts of a plant have chloroplasts, most of the energy is captured in the leaves. The cells in the interior tissues of a leaf, called the mesophyll, can contain between 450,000 and 800,000 chloroplasts for every square millimeter of leaf. The surface of the leaf is uniformly coated with a water-resistant waxy cuticle that protects the leaf from excessive evaporation of water and decreases the absorption of ultraviolet or blue light to reduce heating. The transparent epidermis layer allows light to pass through to the palisade mesophyll cells where most of the photosynthesis takes place.
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Light reactions
In the light reactions, one molecule of the pigment chlorophyll absorbs one photon and loses one electron. This electron is passed to a modified form of chlorophyll called pheophytin, which passes the electron to a quinone molecule, allowing the start of a flow of electrons down an electron transport chain that leads to the ultimate reduction of NADP to NADPH. In addition, this creates a proton gradient across the chloroplast membrane; its Light-dependent reactions of photosynthesis at the thylakoid membrane dissipation is used by ATP synthase for the concomitant synthesis of ATP. The chlorophyll molecule regains the lost electron from a water molecule through a process called photolysis, which releases a dioxygen (O2) molecule. The overall equation for the light-dependent reactions under the conditions of non-cyclic electron flow in green plants is:[21] 2 H2O + 2 NADP+ + 3 ADP + 3 Pi + light 2 NADPH + 2 H+ + 3 ATP + O2 Not all wavelengths of light can support photosynthesis. The photosynthetic action spectrum depends on the type of accessory pigments present. For example, in green plants, the action spectrum resembles the absorption spectrum for chlorophylls and carotenoids with peaks for violet-blue and red light. In red algae, the action spectrum overlaps with the absorption spectrum of phycobilins for red blue-green light, which allows these algae to grow in deeper waters that filter out the longer wavelengths used by green plants. The non-absorbed part of the light spectrum is what gives photosynthetic organisms their color (e.g., green plants, red algae, purple bacteria) and is the least effective for photosynthesis in the respective organisms.
Photosynthesis
273
Z scheme
In plants, light-dependent reactions occur in the thylakoid membranes of the chloroplasts and use light energy to synthesize ATP and NADPH. The light-dependent reaction has two forms: cyclic and non-cyclic. In the non-cyclic reaction, the photons are captured in the light-harvesting antenna complexes of photosystem II by chlorophyll and other accessory pigments (see diagram at right). When a chlorophyll molecule at the core of the photosystem II reaction center obtains sufficient excitation energy from the adjacent antenna pigments, an electron is transferred to the primary electron-acceptor molecule, pheophytin, through a process called photoinduced charge separation. These electrons are shuttled through an electron transport chain, the so-called Z-scheme shown in the diagram, that initially functions to generate a chemiosmotic potential across the membrane. An ATP synthase enzyme uses the chemiosmotic potential to make ATP during photophosphorylation, whereas NADPH is a product of the terminal redox reaction in the Z-scheme. The electron enters a chlorophyll molecule in Photosystem I. The electron is excited due to the light absorbed by the photosystem. A second electron carrier accepts the electron, which again is passed down lowering energies of electron acceptors. The energy created by the electron acceptors is used to move hydrogen ions across the thylakoid membrane into the lumen. The electron is used to reduce the co-enzyme NADP, which has functions in the light-independent reaction. The cyclic reaction is similar to that of the non-cyclic, but differs in the form that it generates only ATP, and no reduced NADP (NADPH) is created. The cyclic reaction takes place only at photosystem I. Once the electron is displaced from the photosystem, the electron is passed down the electron acceptor molecules and returns to photosystem I, from where it was emitted, hence the name cyclic reaction.
Water photolysis
The NADPH is the main reducing agent in chloroplasts, providing a source of energetic electrons to other reactions. Its production leaves chlorophyll with a deficit of electrons (oxidized), which must be obtained from some other reducing agent. The excited electrons lost from chlorophyll in photosystem I are replaced from the electron transport chain by plastocyanin. However, since photosystem II includes the first steps of the Z-scheme, an external source of electrons is required to reduce its oxidized chlorophyll a molecules. The source of electrons in green-plant and cyanobacterial photosynthesis is water. Two water molecules are oxidized by four successive charge-separation reactions by photosystem II to yield a molecule of diatomic oxygen and four hydrogen ions; the electron yielded in each step is transferred to a redox-active tyrosine residue that then reduces the photoxidized paired-chlorophyll a species called P680 that serves as the primary (light-driven) electron donor in the photosystem II reaction center. The oxidation of water is catalyzed in photosystem II by a redox-active structure that contains four manganese ions and a calcium ion; this oxygen-evolving complex binds two water molecules and stores the four oxidizing equivalents that are required to drive the water-oxidizing reaction. Photosystem II is the only known biological enzyme that carries out this oxidation of water. The hydrogen ions contribute to the transmembrane chemiosmotic potential that leads to ATP synthesis. Oxygen is a waste product of light-dependent reactions, but the majority of organisms on Earth use
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Light-independent reactions
The Calvin Cycle
In the light-independent or dark reactions the enzyme RuBisCO captures CO2 from the atmosphere and in a process that requires the newly formed NADPH, called the Calvin-Benson Cycle, releases three-carbon sugars, which are later combined to form sucrose and starch. The overall equation for the light-independent reactions in green plants is:[21] 3 CO2 + 9 ATP + 6 NADPH + 6 H+ C3H6O3-phosphate + 9 ADP + 8 Pi + 6 NADP+ + 3 H2O To be more specific, carbon fixation produces an intermediate product, which is then converted to the final carbohydrate products. The carbon skeletons produced by photosynthesis are then variously used to form other organic compounds, such as the building material cellulose, as precursors for lipid and amino acid biosynthesis, or as a fuel in cellular respiration. The latter occurs not only in plants but also in animals when the energy from plants gets passed through a food chain. The fixation or reduction of carbon dioxide is a process in which carbon dioxide combines with a five-carbon sugar, ribulose 1,5-bisphosphate Overview of the Calvin cycle and carbon fixation (RuBP), to yield two molecules of a three-carbon compound, glycerate 3-phosphate (GP), also known as 3-phosphoglycerate (PGA). GP, in the presence of ATP and NADPH from the light-dependent stages, is reduced to glyceraldehyde 3-phosphate (G3P). This product is also referred to as 3-phosphoglyceraldehyde (PGAL) or even as triose phosphate. Triose is a 3-carbon sugar (see carbohydrates). Most (5 out of 6 molecules) of the G3P produced is used to regenerate RuBP so the process can continue (see Calvin-Benson cycle). The 1 out of 6 molecules of the triose phosphates not "recycled" often condense to form hexose phosphates, which ultimately yield sucrose, starch and cellulose. The sugars produced during carbon metabolism yield carbon skeletons that can be used for other metabolic reactions like the production of amino acids and lipids.
Photosynthesis
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Photosynthesis In water Cyanobacteria possess carboxysomes, which increase the concentration of CO2 around RuBisCO to increase the rate of photosynthesis. This operates by carbonic anhydrase, producing hydrocarbonate ions (HCO3), which are then pumped into the carboxysome, before being processed by a different carbonic anhydrase to produce CO2.[27] Pyrenoids in algae and hornworts also act to concentrate CO2 around rubisco.[28]
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Transfer of electrons in photochemical reactions (thylakoid membranes) picosecond to nanosecond Electron transport chain and ATP synthesis (thylakoid membranes) Carbon fixation and export of stable products microsecond to millisecond millisecond to second
Efficiency
Plants usually convert light into chemical energy with a photosynthetic efficiency of 36%.[29] Actual plants' photosynthetic efficiency varies with the frequency of the light being converted, light intensity, temperature and proportion of carbon dioxide in the atmosphere, and can vary from 0.1% to 8%.[30] By comparison, solar panels convert light into electric energy at an efficiency of approximately 620% for mass-produced panels, and above 40% in laboratory devices.
Evolution
Early photosynthetic systems, such as those from green and purple sulfur and green and purple nonsulfur bacteria, are thought to have been anoxygenic, using various molecules as electron donors. Green and purple sulfur bacteria are thought to have used hydrogen and sulfur as an electron donor. Green nonsulfur bacteria used various amino and other organic acids. Purple nonsulfur bacteria used a variety of nonspecific organic molecules. The use of these molecules is consistent with the geological evidence that the atmosphere was highly reduced at that time. Fossils of what are thought to be filamentous photosynthetic organisms have been dated at 3.4 billion years old.[31] [32]
Plant cells with visible chloroplasts (from a moss, Plagiomnium affine)
The main source of oxygen in the atmosphere is oxygenic photosynthesis, and its first appearance is sometimes referred to as the oxygen catastrophe. Geological evidence suggests that oxygenic photosynthesis, such as that in cyanobacteria, became important during the Paleoproterozoic era around 2 billion years ago. Modern photosynthesis
Photosynthesis in plants and most photosynthetic prokaryotes is oxygenic. Oxygenic photosynthesis uses water as an electron donor, which is oxidized to molecular oxygen (O2) in the photosynthetic reaction center.
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Discovery
Although some of the steps in photosynthesis are still not completely understood, the overall photosynthetic equation has been known since the 19th century. Jan van Helmont began the research of the process in the mid-17th century when he carefully measured the mass of the soil used by a plant and the mass of the plant as it grew. After noticing that the soil mass changed very little, he hypothesized that the mass of the growing plant must come from the water, the only substance he added to the potted plant. His hypothesis was partially accurate much of the gained mass also comes from carbon dioxide as well as water. However, this was a signaling point to the idea that the bulk of a plant's biomass comes from the inputs of photosynthesis, not the soil itself.
Photosynthesis Joseph Priestley, a chemist and minister, discovered that, when he isolated a volume of air under an inverted jar, and burned a candle in it, the candle would burn out very quickly, much before it ran out of wax. He further discovered that a mouse could similarly "injure" air. He then showed that the air that had been "injured" by the candle and the mouse could be restored by a plant. In 1778, Jan Ingenhousz, court physician to the Austrian Empress, repeated Priestley's experiments. He discovered that it was the influence of sunlight on the plant that could cause it to revive a mouse in a matter of hours. In 1796, Jean Senebier, a Swiss pastor, botanist, and naturalist, demonstrated that green plants consume carbon dioxide and release oxygen under the influence of light. Soon afterward, Nicolas-Thodore de Saussure showed that the increase in mass of the plant as it grows could not be due only to uptake of CO2 but also to the incorporation of water. Thus, the basic reaction by which photosynthesis is used to produce food (such as glucose) was outlined. Cornelis Van Niel made key discoveries explaining the chemistry of photosynthesis. By studying purple sulfur bacteria and green bacteria he was the first scientist to demonstrate that photosynthesis is a light-dependent redox reaction, in which hydrogen reduces carbon dioxide. Robert Emerson discovered two light reactions by testing plant productivity using different wavelengths of light. With the red alone, the light reactions were suppressed. When blue and red were combined, the output was much more substantial. Thus, there were two photosystems, one absorbing up to 600nm wavelengths, the other up to 700 nm. The former is known as PSII, the latter is PSI. PSI contains only chlorophyll a, PSII contains primarily chlorophyll a with most of the available chlorophyll b, among other pigment. These include phycobilins, which are the red and blue pigments of red and blue algae respectively, and fucoxanthol for brown algae and diatoms. The process is most productive when absorption of quanta are equal in both the PSII and PSI, assuring that input energy from the antenna complex is divided between the PSI and PSII system, which in turn powers the photochemistry.[6] Robert Hill thought that a complex of reactions consisting of an intermediate to cytochrome b6 (now a plastoquinone), another is from cytochrome f to a step in the carbohydrate-generating mechanisms. These are linked by plastoquinone, which does require energy to reduce cytochrome f for it is a sufficient reductant. Further experiments to prove that the oxygen developed during the photosynthesis of green plants came from water, were performed by Hill in 1937 and 1939. He showed that isolated chloroplasts give off oxygen in the presence of unnatural reducing agents like iron oxalate, ferricyanide or benzoquinone after exposure to light. The Hill reaction is as follows: 2 H2O + 2 A + (light, chloroplasts) 2 AH2 + O2 where A is the electron acceptor. Therefore, in light, the electron acceptor is reduced and oxygen is evolved. Samuel Ruben and Martin Kamen used radioactive isotopes to determine that the oxygen liberated in photosynthesis came from the water. Melvin Calvin and Andrew Benson, along with James Bassham, elucidated the path of carbon assimilation (the photosynthetic carbon reduction cycle) in plants. The carbon reduction cycle is known as the Calvin cycle, which ignores the contribution of Bassham and Benson. Many scientists refer to the cycle as the Calvin-Benson Cycle, Benson-Calvin, and some even call it the Calvin-Benson-Bassham (or CBB) Cycle. Nobel Prize-winning scientist Rudolph A. Marcus was able to discover the function and significance of the electron transport chain. Otto Heinrich Warburg and Dean Burk discovered the I-quantum photosynthesis reaction that splits the CO2, activated by the respiration.[43] Louis N.M. Duysens and Jan Amesz discovered that chlorophyll a will absorb one light, oxidize cytochrome f, chlorophyll a (and other pigments) will absorb another light, but will reduce this same oxidized cytochrome, stating the two light reactions are in series.
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Photosynthesis
279
Factors
There are three main factors affecting photosynthesis and several corollary factors. The three main are: Light irradiance and wavelength Carbon dioxide concentration Temperature.
At constant temperature, the rate of carbon assimilation varies with irradiance, initially increasing as the irradiance increases. However, at higher irradiance, this relationship no longer holds and the rate of carbon assimilation reaches a plateau. At constant irradiance, the rate of carbon assimilation increases as the temperature is increased over a limited range. This effect is seen only at high irradiance levels. At low irradiance, increasing the temperature has little influence on the rate of carbon assimilation. These two experiments illustrate vital points: First, from research it is known that, in general, photochemical reactions are not affected by temperature. However, these experiments clearly show that temperature affects the rate of carbon assimilation, so there must be two sets of reactions in the full process of carbon assimilation. These are, of course, the light-dependent 'photochemical' stage and the light-independent, temperature-dependent stage. Second, Blackman's experiments illustrate the concept of limiting factors. Another limiting factor is the wavelength of light. Cyanobacteria, which reside several meters underwater, cannot receive the correct wavelengths required to cause photoinduced charge separation in conventional photosynthetic pigments. To combat this problem, a series of proteins with different pigments surround the reaction center. This unit is called a phycobilisome.
Photosynthesis 2 glycolate + ATP 3-phosphoglycerate + carbon dioxide + ADP + NH3 The salvaging pathway for the products of RuBisCO oxygenase activity is more commonly known as photorespiration, since it is characterized by light-dependent oxygen consumption and the release of carbon dioxide.
280
References
[1] Smith, A. L. (1997). Oxford dictionary of biochemistry and molecular biology. Oxford [Oxfordshire]: Oxford University Press. p.508. ISBN0-19-854768-4. "Photosynthesis the synthesis by organisms of organic chemical compounds, esp. carbohydrates, from carbon dioxide using energy obtained from light rather than the oxidation of chemical compounds." [2] D.A. Bryant & N.-U. Frigaard (2006). "Prokaryotic photosynthesis and phototrophy illuminated". Trends Microbiol 14 (11): 48896. doi:10.1016/j.tim.2006.09.001. PMID16997562. [3] Nealson KH, Conrad PG (1999). "Life: past, present and future". Philos. Trans. R. Soc. Lond., B, Biol. Sci. 354 (1392): 192339. doi:10.1098/rstb.1999.0532. PMC1692713. PMID10670014. [4] "World Consumption of Primary Energy by Energy Type and Selected Country Groups, 19802004" (http:/ / www. eia. doe. gov/ pub/ international/ iealf/ table18. xls) (XLS). Energy Information Administration. July 31, 2006. . Retrieved 2007-01-20. [5] Field CB, Behrenfeld MJ, Randerson JT, Falkowski P (1998). "Primary production of the biosphere: integrating terrestrial and oceanic components". Science 281 (5374): 23740. doi:10.1126/science.281.5374.237. PMID9657713. [6] Photosynthesis, McGraw-Hill Encyclopedia of Science and Technology, Vol. 13, 2007 [7] http:/ / toolserver. org/ ~verisimilus/ Timeline/ Timeline. php?Ma=3500 [8] Olson JM (2006). "Photosynthesis in the Archean era". Photosyn. Res. 88 (2): 10917. doi:10.1007/s11120-006-9040-5. PMID16453059. [9] http:/ / toolserver. org/ ~verisimilus/ Timeline/ Timeline. php?Ma=3000 [10] http:/ / toolserver. org/ ~verisimilus/ Timeline/ Timeline. php?Ma=2400 [11] Buick R (2008). "When did oxygenic photosynthesis evolve?". Philos. Trans. R. Soc. Lond., B, Biol. Sci. 363 (1504): 273143. doi:10.1098/rstb.2008.0041. PMC2606769. PMID18468984. [12] Rodrguez-Ezpeleta, Naiara; Henner Brinkmann, Suzanne C Burey, Batrice Roure, Gertraud Burger, Wolfgang Lffelhardt, Hans J Bohnert, Herv Philippe, B Franz Lang (2005-07-26). "Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes" (http:/ / www. ncbi. nlm. nih. gov/ pubmed/ 16051178). Current Biology: CB 15 (14): 13251330. doi:10.1016/j.cub.2005.06.040. ISSN0960-9822. PMID16051178. . Retrieved 2009-08-26. [13] Gould SB, Waller RF, McFadden GI (2008). "Plastid evolution". Annu Rev Plant Biol 59: 491517. doi:10.1146/annurev.arplant.59.032607.092915. PMID18315522. [14] Anaerobic Photosynthesis, Chemical & Engineering News, 86, 33, August 18, 2008, p. 36 [15] Kulp TR, Hoeft SE, Asao M, Madigan MT, Hollibaugh JT, Fisher JC, Stolz JF, Culbertson CW, Miller LG, Oremland RS (2008). "Arsenic(III) fuels anoxygenic photosynthesis in hot spring biofilms from Mono Lake, California". Science 321 (5891): 96770. doi:10.1126/science.1160799. PMID18703741. [16] "Scientists discover unique microbe in California's largest lake" (http:/ / www. bio-medicine. org/ biology-news/ Scientists-discover-unique-microbe-in-Californias-largest-lake-203-1/ ). . Retrieved 2009-07-20. [17] Tavano CL, Donohue TJ (2006). "Development of the bacterial photosynthetic apparatus". Curr. Opin. Microbiol. 9 (6): 62531. doi:10.1016/j.mib.2006.10.005. PMC2765710. PMID17055774. [18] Mullineaux CW (1999). "The thylakoid membranes of cyanobacteria: structure, dynamics and function". Australian Journal of Plant Physiology 26 (7): 671677. doi:10.1071/PP99027. [19] Sener MK, Olsen JD, Hunter CN, Schulten K (2007). "Atomic-level structural and functional model of a bacterial photosynthetic membrane vesicle". Proc. Natl. Acad. Sci. U.S.A. 104 (40): 157238. doi:10.1073/pnas.0706861104. PMC2000399. PMID17895378. [20] Campbell, Neil A.; Brad Williamson; Robin J. Heyden (2006). Biology: Exploring Life (http:/ / www. phschool. com/ el_marketing. html). Boston, Massachusetts: Pearson Prentice Hall. ISBN0-13-250882-6. . [21] Raven, Peter H.; Ray F. Evert, Susan E. Eichhorn (2005). Biology of Plants, 7th Edition. New York: W.H. Freeman and Company Publishers. pp.124127. ISBN0-7167-1007-2. [22] "Yachandra Group Home page" (http:/ / www. lbl. gov/ ~vkyachan/ index. html). . [23] Pushkar Y, Yano J, Sauer K, Boussac A, Yachandra VK (2008). "Structural changes in the Mn4Ca cluster and the mechanism of photosynthetic water splitting". Proc. Natl. Acad. Sci. U.S.A. 105 (6): 187984. doi:10.1073/pnas.0707092105. PMC2542863. PMID18250316. [24] L. Taiz, E. Zeiger (2006). Plant Physiology (4 ed.). Sinauer Associates. ISBN978-0878938568. [25] Sage, Rowan; Russell Monson (1999). "16" (http:/ / books. google. com/ ?id=H7Wv9ZImW-QC& pg=PA551). C4 Plant Biology. pp.551580. ISBN0126144400. . [26] Dodd, A. N.; Borland, AM; Haslam, RP; Griffiths, H; Maxwell, K (2002). "Crassulacean acid metabolism: plastic, fantastic". Journal of Experimental Botany 53 (369): 56980. doi:10.1093/jexbot/53.369.569. PMID11886877. [27] Badger, M. R.; Price, GD (2003). "CO2 concentrating mechanisms in cyanobacteria: molecular components, their diversity and evolution". Journal of Experimental Botany 54 (383): 60922. doi:10.1093/jxb/erg076. PMID12554704.
Photosynthesis
[28] Badger, Murray R.; Andrews, T. John; Whitney, S.M.; Ludwig, Martha; Yellowlees, David C.; Leggat, W.; Price, G. Dean (1998). "The diversity and coevolution of Rubisco, plastids, pyrenoids, and chloroplast-based CO2-concentrating mechanisms in algae". Canadian Journal of Botany 76 (6): 1052. doi:10.1139/cjb-76-6-1052. [29] Chapter 1 Biological energy production">Miyamoto K. "Chapter 1 Biological energy production" (http:/ / www. fao. org/ docrep/ w7241e/ w7241e05. htm#1. 2. 1 photosynthetic efficiency). Renewable biological systems for alternative sustainable energy production (FAO Agricultural Services Bulletin 128). Food and Agriculture Organization of the United Nations. . Retrieved 2009-01-04. [30] Govindjee, What is photosynthesis? (http:/ / www. life. uiuc. edu/ govindjee/ whatisit. htm) [31] Photosynthesis got a really early start (http:/ / www. newscientist. com/ article/ mg18424671. 600-photosynthesis-got-a-really-early-start. html), New Scientist, 2 October 2004 [32] Revealing the dawn of photosynthesis (http:/ / www. newscientist. com/ article/ mg19125654. 200-revealing-the-dawn-of-photosynthesis. html), New Scientist, 19 August 2006 [33] Venn AA, Loram JE, Douglas AE (2008). "Photosynthetic symbioses in animals". J. Exp. Bot. 59 (5): 106980. doi:10.1093/jxb/erm328. PMID18267943. [34] Rumpho ME, Summer EJ, Manhart JR (2000). "Solar-Powered Sea Slugs. Mollusc/Algal Chloroplast Symbiosis". Plant Physiol. 123 (1): 2938. doi:10.1104/pp.123.1.29. PMC1539252. PMID10806222. [35] Muscatine L, Greene RW (1973). "Chloroplasts and algae as symbionts in molluscs". Int. Rev. Cytol. 36: 13769. doi:10.1016/S0074-7696(08)60217-X. PMID4587388. [36] Rumpho ME, Worful JM, Lee J et al. (2008). "Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica". Proc. Natl. Acad. Sci. U.S.A. 105 (46): 1786717871. doi:10.1073/pnas.0804968105. PMC2584685. PMID19004808. [37] Douglas SE (1998). "Plastid evolution: origins, diversity, trends". Curr. Opin. Genet. Dev. 8 (6): 65561. doi:10.1016/S0959-437X(98)80033-6. PMID9914199. [38] Reyes-Prieto A, Weber AP, Bhattacharya D (2007). "The origin and establishment of the plastid in algae and plants". Annu. Rev. Genet. 41: 14768. doi:10.1146/annurev.genet.41.110306.130134. PMID17600460. [39] Raven JA, Allen JF (2003). "Genomics and chloroplast evolution: what did cyanobacteria do for plants?". Genome Biol. 4 (3): 209. doi:10.1186/gb-2003-4-3-209. PMC153454. PMID12620099. [40] "Cyanobacteria: Fossil Record" (http:/ / www. ucmp. berkeley. edu/ bacteria/ cyanofr. html). Ucmp.berkeley.edu. . Retrieved 2010-08-26. [41] Herrero A and Flores E (editor). (2008). The Cyanobacteria: Molecular Biology, Genomics and Evolution (1st ed.). Caister Academic Press. ISBN978-1-904455-15-8. [42] Plotkin, M.; Hod, I.; Zaban, A.; Boden, S. A.; Bagnall, D. M.; Galushko, D.; Bergman, D. J. (2010). "Solar energy harvesting in the epicuticle of the oriental hornet (Vespa orientalis)". Naturwissenschaften 97 (12): 1067. Bibcode2010NW.....97.1067P. doi:10.1007/s00114-010-0728-1. PMID21052618. [43] Otto Warburg Biography (http:/ / nobelprize. org/ nobel_prizes/ medicine/ laureates/ 1931/ warburg. html). Nobelprize.org (1970-08-01). Retrieved on 2011-11-03.
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Further reading
Books
Asimov, Isaac (1968). Photosynthesis. New York, London: Basic Books, Inc.. ISBN0-465-05703-9. Bidlack JE; Stern KR, Jansky S (2003). Introductory plant biology. New York: McGraw-Hill. ISBN0-07-290941-2. Blankenship RE (2008). Molecular Mechanisms of Photosynthesis (2nd ed.). John Wiley & Sons Inc. ISBN0-470-71451-4. Govindjee (1975). Bioenergetics of photosynthesis. Boston: Academic Press. ISBN0-12-294350-3. Govindjee Beatty JT,Gest H, Allen JF (2006). Discoveries in Photosynthesis. Advances in Photosynthesis and Respiration. 20. Berlin: Springer. ISBN1-4020-3323-0. Gregory RL (1971). Biochemistry of photosynthesis. New York: Wiley-Interscience. ISBN0-471-32675-5. Rabinowitch E, Govindjee (1969). Photosynthesis. London: J. Wiley. ISBN0-471-70424-5. Reece, J, Campbell, N (2005). Biology. San Francisco: Pearson, Benjamin Cummings. ISBN0-8053-7146-X.
Photosynthesis
282
Papers
Evolutionary relationships among photosynthetic prokaryotes : implications regarding the origin of photosynthesis. (http://www.ncbi.nlm.nih.gov/pubmed/10361294) Origin and early evolution of photosynthesis. (http://www.ncbi.nlm.nih.gov/pubmed/11538390) Photosystem II: evolutionary perspectives (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1693113/ ?tool=pmcentrez)
External links
A collection of photosynthesis pages for all levels from a renowned expert (Govindjee) (http://www.life.uiuc. edu/govindjee/linksPSed.htm) In depth, advanced treatment of photosynthesis, also from Govindjee (http://www.life.uiuc.edu/govindjee/ paper/gov.html) Science Aid: Photosynthesis (http://scienceaid.co.uk/biology/biochemistry/photosynthesis.html) Article appropriate for high school science Metabolism, Cellular Respiration and Photosynthesis The Virtual Library of Biochemistry and Cell Biology (http://www.biochemweb.org/metabolism.shtml) Overall examination of Photosynthesis at an intermediate level (http://www.chemsoc.org/networks/learnnet/ cfb/Photosynthesis.htm) Overall Energetics of Photosynthesis (http://www.life.uiuc.edu/govindjee/photosynBook.html) Photosynthesis Discovery Milestones (http://www.juliantrubin.com/bigten/photosynthesisexperiments.html) experiments and background The source of oxygen produced by photosynthesis (http://bcs.whfreeman.com/thelifewire/content/chp08/ 0802001.html) Interactive animation, a textbook tutorial Jessica Marshall (2011-03-29). "First practical artificial leaf makes debut" (http://news.discovery.com/earth/ artificial-leaf-technology-solar-110329.html). Discovery News. Photosynthesis Light Dependent & Light Independent Stages (http://www.biology-innovation.co.uk/pages/ plant-biology-ecology/photosynthesis/) Khan Academy, video introduction (http://www.khanacademy.org/video/photosynthesis?playlist=Biology)
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Lipid metabolism
Fatty acid synthesis
Fatty acid synthesis is the creation of fatty acids from acetyl-CoA and malonyl-CoA precursors through action of enzymes called fatty acid synthases. It is an important part of the lipogenesis process, which - together with glycolysis - stands behind creating fats from blood sugar in living organisms.
(a)
(b)
284
Reacts priming acetyl-ACP with chain extending malonyl-ACP.
(c)
3-ketoacyl-ACP synthetase
(d)
3-ketoacyl-ACP reductase
(e)
3-hydroxyacyl-ACP dehydrase
Removes water
(f)
Enoyl-ACP reductase
Regulation Acetyl-CoA is formed into malonyl-CoA by acetyl-CoA carboxylase, at which point malonyl-CoA is destined to feed into the fatty acid synthesis pathway. Acetyl-CoA carboxylase is the point of regulation in saturated straight-chain fatty acid synthesis, by both phosphorylation and allosteric regulation. Regulation by phosphorylation occurs mostly in mammals, while allosteric regulation occurs in most organisms. Allosteric control occurs as feedback inhibition by palmitol-CoA and activation by citrate. When there are high levels of palmitol-CoA, the final product of saturated fatty acid synthesis, it allosterically inactivates acetyl-CoA carboxylase to prevent a build up of fatty acids in cells. Citrate acts to activate acetyl-CoA carboxylase under high levels, because high levels indicate there is enough acetyl-CoA to feed into the Krebs cycle and produce energy.[3] De Novo Synthesis in Humans In humans, fatty acids are predominantly formed in the liver and lactating mammary glands, and, to a lesser extent, the adipose tissue. Most acetyl-CoA is formed from pyruvate by pyruvate dehydrogenase in the mitochondria. Acetyl-CoA produced in the mitochondria is condensed with oxaloacetate by citrate synthase to form citrate, which is then transported into the cytosol and broken down to yield acetyl-CoA and oxaloacetate by ATP citrate lyase. Oxaloacetate in the cytosol is reduced to malate by cytoplasmic malate dehydrogenase, and malate is transported back into the mitochondria to participate in the Citric acid cycle.[4]
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Desaturation
Unsaturated fatty acids are essential components to prokaryotic and eukaryotic cell membranes. These fatty acids primarily function in maintaining membrane fluidity.[5] They have also been associated with serving as signaling molecules in other processes such as cell differentiation and DNA replication.[5] There are two pathways organisms use for desaturation: Aerobic and Anaerobic. Anaerobic Desaturation Many bacteria use the anaerobic pathway for synthesizing unsaturated fatty acids. This pathway does not utilize oxygen and is dependent on enzymes to insert the double bond before elongation utilizing the normal fatty acid synthesis machinery. In Escherichia coli, this pathway is well understood. FabA is a -hydroxydecanoyl-ACP dehydrase- it is specific for the 10 carbon saturated fatty acid synthesis intermediate (-hydroxydecanoyl-ACP). FabA catalyzes the dehydration of -hydroxydecanoyl-ACP causing the release of water and insertion of the double bond between C7 and C8 counting from the methyl end. This creates the trans-2-decenoyl intermediate. The trans-2-decenoyl intermediate can either be shunted to the normal saturated fatty acid synthesis pathway by FabB, where the double bond will be hydrolyzed and the final product will be a saturated fatty acid, or FabA will catalyze the isomerization into the Synthesis of unsaturated fatty acids via anaerobic cis-3-decenoyl intermediate. desaturation FabB is a -ketoacyl-ACP synthase which elongates and channels intermediates into the mainstream fatty acid synthesis pathway. When FabB reacts with the cis-decenoyl intermediate the final product after elongation will be an unsaturated fatty acid.[6] The two main unsaturated fatty acids made are Palmitoleoyl-ACP (16:17) and cis-vaccenoyl-ACP (18:17).[7] Most bacteria that undergo anaerobic desaturation contain homologues of FabA and FabB.[8] Clostridia are the main exception; they have a novel enzyme, yet to be identified, that catalyzes the formation of the cis double bond.[7] Regulation This pathway undergoes transcriptional regulation by FadR and FabR. FadR is the more extensively studied protein and has been attributed bifunctional characteristics. It acts as an activator of fabA and fabB transcription and as a repressor for the -oxidation regulon. FabR, conversely, acts as a repressor for the transcription of fabA and fabB.[6]
Fatty acid synthesis Aerobic Desaturation Aerobic desaturation is the most widespread pathway for the synthesis of unsaturated fatty acids. It is utilized in all eukaryotes and some prokaryotes. This pathway utilizes desaturases to synthesize unsaturated fatty acids from full length saturated fatty acid substrates.[9] All desaturases require oxygen and reducing equivalents acquired from the electron transport chain. Desaturases are specific for the double bond they induce in the substrate. In Bacillus subtilis, the desaturase, 5-Des, is specific for inducing a cis-double bond at the 5 position.[5] [9] Saccharomyces cerevisiae contains one desaturase, Ole1p, which induces the cis-double bond at 9.[5] Regulation In B. subtilis, this pathway is regulated by a two-component system: DesK and DesR. DesK is a membrane associated kinase and DesR is a Synthesis of unsaturated fatty acids via aerobic transcriptional regulator of the des gene.[5] [9] The regulation responds desaturation to temperature; when there is a drop in temperature this gene is upregulated. Unsaturated fatty acids decrease the fluidity of the membrane and stabilize it under lower temperatures. DesK is the sensor protein that when there is a decrease in temperature, will autophosphorylate. DesK-P will transfer its phosphoryl group to DesR. Two DesR-P proteins will dimerize and bind to the DNA promoters of the des gene and recruit RNA polymerase to begin transcription.[5] [9] Pseudomonas aeruginosa Generally, both anaerobic and aerobic unsaturated fatty acid synthesis will not occur within the same system, however Pseudomonas aeruginosa and Vibrio ABE-1 are exceptions.[10] [11] [12] While, P. aeruginosa primarily undergoes anaerobic desaturation, it also undergoes two aerobic pathways. One pathway utilizes a 9 desaturase (DesA) that catalyzes a double bond formation in membrane lipids. Another pathway uses two proteins, DesC and DesB, together to act as a 9 desaturase which inserts a double bond into a saturated fatty acid-CoA molecule. This second pathway is regulated by repressor protein, DesT. DesT is also a repressor of fabAB expression for anaerobic desaturation when in presence of exogenous unsaturated fatty acids. This functions to coordinate the expression of the two pathways within the organism.[11] [13]
286
287
Valine primer
Leucine primer
Isoleucine primer
The branched-chain fatty acid synthesizing system uses -keto acids as primers. This system is distinct from the branched-chain fatty acid synthetase which utilizes short-chain acyl-CoA esters as primers.[14] -keto acid primers are derived from the transamination and decarboxylation of valine, leucine, and isoleucine to form 2-methylpropanyl-CoA, 3-methylbutyryl-CoA, and 2-Methylbutyryl-CoA, respectively.[15] 2-methylpropanyl-CoA primers derived from valine are elongated to produce even-numbered iso-series fatty acids such as 14-methyl-pentadecanoic (isopalmitic) acid, and 3-methylbutyryl-CoA primers from leucine may be used to form odd numbered iso-series fatty acids such as 13-methyl-tetradecanoic acid. 2-Methylbutyryl-CoA primers from isoleucine are elongated to form anteiso-series fatty acids containing an odd number of carbon atoms such as 12-Methyl tetradecanoic acid.[16] Decarboxylation of the primer precursors occurs through the branched-chain -keto acid decarboxylase (BCKA) enzyme. Elongation of the fatty acid follows the same biosynthetic pathway in Escherichia coli used to produce straight-chain fatty acids where malonyl-CoA is used as a chain extender.[17] The major end products are 12-17 carbon branched-chain fatty acids and their composition tends to be uniform and characteristic for many bacterial species.[16] BCKA decarboxylase and relative activities of -keto acid substrates The BCKA decarboxylase enzyme is composed of two subunits in a tetrameric structure (A2B2) and is essential for the synthesis of branched-chain fatty acids. It is responsible for the decarboxylation of -keto acids formed by the transamination of valine, leucine, and isoleucine and produces the primers used for branched-chain fatty acid synthesis. The activity of this enzyme is much higher with branched-chain -keto acid substrates than straight-chain substrates, and in Bacillus species its specificity is highest for the isoleucine-derived -keto--methylvaleric acid, followed by -ketoisocaproate and -ketoisovalerate.[16] [17] The enzymes high affinity toward branched-chain
Fatty acid synthesis -keto acids allows it to function as the primer donating system for branched-chain fatty acid synthetase.[17]
Substrate BCKA activity CO2 Produced (nmol/min mg) 19.7 12.4 7.4 4.9 Km (M) <1 <1 <1 51.1 Vmax (nmol/min mg) 17.8 13.3 5.6 15.2
288
Factors affecting chain length and pattern distribution -keto acid primers are used to produce branched-chain fatty acids that are generally between 12 and 17 carbons in length. The proportions of these branched-chain fatty acids tend to be uniform and consistent among a particular bacterial species but may be altered due to changes in malonyl-CoA concentration, temperature, or heat-stable factors (HSF) present.[16] All of these factors may affect chain length, and HSFs have been demonstrated to alter the specificity of BCKA decarboxylase for a particular -keto acid substrate, thus shifting the ratio of branched-chain fatty acids produced.[16] An increase in malonyl-CoA concentration has been shown to result in a larger proportion of C17 fatty acids produced, up until the optimal concentration (20M) of malonyl-CoA is reached. Decreased temperatures also tend to shift the fatty-acid distribution slightly toward C17 fatty-acids in Bacillus species.[14] [16]
289
References
[1] Dijkstra, Albert J., R. J. Hamilton, and Wolf Hamm. "Fatty Acid Biosynthesis." Trans Fatty Acids. Oxford: Blackwell Pub., 2008. 12. Print. [2] "Fatty Acids: Straight-chain Saturated, Structure, Occurrence and Biosynthesis." Lipid Library - Lipid Chemistry, Biology, Technology and Analysis. Web. 30 Apr. 2011. <http://lipidlibrary.aocs.org/lipids/fa_sat/index.htm>. Mechanism of the synthesis of Tuberculostearic acid
[3] Diwan, Joyce J. "Fatty Acid Synthesis." Rensselaer Polytechnic Institute (RPI) :: Architecture, Business, Engineering, IT, Humanities, Science. Web. 30 Apr. 2011. <http://rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/fasynthesis.htm>. [4] Ferre, P.; F. Foufelle (2007). "SREBP-1c Transcription Factor and Lipid Homeostasis: Clinical Perspective" (http:/ / content. karger. com/ ProdukteDB/ produkte. asp?Aktion=ShowFulltext& ArtikelNr=100426& Ausgabe=232805& ProduktNr=224036). Hormone Research 68 (2): 7282. doi:10.1159/000100426. PMID17344645. . Retrieved 2010-08-30. "this process is outlined graphically in page 73" [5] Aguilar, Pablo S, and Diegode Mendoza. "Control of fatty acid desaturation: a mechanism conserved from bacteria to humans." Molecular microbiology 62.6 (2006):1507-14. [6] Feng, Youjun, and John ECronan. "Complex binding of the FabR repressor of bacterial unsaturated fatty acid biosynthesis to its cognate promoters." Molecular microbiology 80.1 (2011):195-218. [7] Zhu, Lei, et al. "Functions of the Clostridium acetobutylicium FabF and FabZ proteins in unsaturated fatty acid biosynthesis." BMC microbiology 9(2009):119. [8] Wang, Haihong, and John ECronan. "Functional replacement of the FabA and FabB proteins of Escherichia coli fatty acid synthesis by Enterococcus faecalis FabZ and FabF homologues." Journal of biological chemistry 279.33 (2004):34489-95. [9] Mansilla, Mara C, and Diegode Mendoza. "The Bacillus subtilis desaturase: a model to understand phospholipid modification and temperature sensing." Archives of microbiology 183.4 (2005):229-35. [10] Wada, M, N. Fukunaga, and S. Sasaki. "Mechanism of biosynthesis of unsaturated fatty acids in Pseudomonas sp. strain E-3, a psychrotrophic bacterium." Journal of bacteriology 171.8 (1989):4267-71. [11] Subramanian, Chitra, Charles ORock, and Yong-MeiZhang. "DesT coordinates the expression of anaerobic and aerobic pathways for unsaturated fatty acid biosynthesis in Pseudomonas aeruginosa." Journal of bacteriology 192.1 (2010):280-5. [12] Morita, N, et al. "Both the anaerobic pathway and aerobic desaturation are involved in the synthesis of unsaturated fatty acids in Vibrio sp. strain ABE-1." FEBS letters 297.1-2 (1992):9-12. [13] Zhu, Kun, et al. "Two aerobic pathways for the formation of unsaturated fatty acids in Pseudomonas aeruginosa." Molecular microbiology 60.2 (2006):260-73. [14] Kaneda, Toshi. "Iso- and Anteiso-Fatty Acids in Bacteria: Biosynthesis, Function, and Taxonomic Significance." Microbiological Reviews 55.2 (1991): 288-302 [15] "Branched-chain Fatty Acids, Phytanic Acid, Tuberculostearic Acid Iso/anteiso- Fatty Acids." Lipid Library - Lipid Chemistry, Biology, Technology and Analysis. Web. 01 May 2011. http:/ / lipidlibrary. aocs. org/ lipids/ fa_branc/ index. htm. [16] Naik, Devaray N., and Toshi Kaneda. "Biosynthesis of Branched Long-chain Fatty Acids by Species of Bacillus: Relative Activity of Three -keto Acid Substrates and Factors Affecting Chain Length." Can. J. Microbiol. 20 (1974): 1701-708. [17] Oku, Hirosuke, and Toshi Kaneda. "Biosynthesis of Branched-chain Fatty Acids in Bacillis Subtilis." The Journal of Biological Chemistry 263.34 (1988): 18386-8396. [18] Christie, William W. "Fatty Acids: Natural Alicyclic Structures, Occurrence, and Biochemistry." The AOCS Lipid Library. 5 Apr. 2011. Web. 24 Apr. 2011. <http://lipidlibrary.aocs.org/lipids/fa_cycl/file.pdf>. [19] Ratledge, Colin, and John Stanford. The Biology of the Mycobacteria. London: Academic, 1982. Print. [20] Kubica, George P., and Lawrence G. Wayne. The Mycobacteria: a Sourcebook. New York: Dekker, 1984. Print.
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External links
Overview (http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/fasynthesis.htm) at Rensselaer Polytechnic Institute Overview (http://web.indstate.edu/thcme/mwking/lipid-synthesis.html#synthesis) at Indiana State University
Lipogenesis
Lipogenesis is the process by which acetyl-CoA is converted to fats. The former is an intermediate stage in metabolism of simple sugars, such as glucose, a source of energy of living organisms. Through lipogenesis, the energy can be efficiently stored in the form of fats. Lipogenesis encompasses the processes of fatty acid synthesis and subsequent triglyceride synthesis (when fatty acids are esterified with glycerol to form fats).[1] The products are secreted from the liver in the form of very-low-density lipoproteins (VLDL).
Lipogenesis Acetyl-CoA carboxylase Insulin affects ACC in a similar way to PDH. It leads to its dephosphorylation which activates the enzyme. Glucagon has an antagonistic effect and increases phosphorylation, deactivation, thereby inhibiting ACC and slowing fat synthesis. Affecting ACC affects the rate of acetyl-CoA conversion to malonyl-CoA. Increased malonyl-CoA level pushes the equilibrium over to increase production of fatty acids through biosynthesis. Long chain fatty acids are negative allosteric regulators of ACC and so when the cell has sufficient long chain fatty acids, they will eventually inhibit ACC activity and stop fatty acid synthesis. AMP and ATP concentrations of the cell act as a measure of the ATP needs of a cell and as ATP levels get low it activates the ATP synthetase which in turn phosphorylates ACC. When ATP is depleted, there is a rise in 5'AMP. This rise activates AMP-activated protein kinase, which phosphorylates ACC, thereby inhibits fat synthesis. This is a useful way to ensure that glucose is not diverted down a storage pathway in times when energy levels are low. ACC is also activated by citrate. This means that, when there is abundant acetyl-CoA in the cell cytoplasm for fat synthesis, it proceeds at an appropriate rate. Note: Research now shows that glucose metabolism (exact metabolite to be determined), aside from insulin's influence on lipogenic enzyme genes, can induce the gene products for liver's pyruvate kinase, acetyl-CoA carboxylase, and fatty acid synthase. These genes are induced by the transcription factors ChREBP/Mlx via high blood glucose levels[3] and presently unknown signaling events. Insulin induction is due to SREBP-1c, which is also involved in cholesterol metabolism.
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Lipogenesis
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References
[1] Kersten S (April 2001). "Mechanisms of nutritional and hormonal regulation of lipogenesis". EMBO Rep. 2 (4): 2826. doi:10.1093/embo-reports/kve071. PMC1083868. PMID11306547. [2] Elmhurst College. "Lipogenesis" (http:/ / www. elmhurst. edu/ ~chm/ vchembook/ 623acetylCoAfate. html). . Retrieved 2007-12-22. [3] Work from Howard Towle, Catherine Postic, and K. Uyeda.
Acetyl-CoA carboxylase
Acetyl-CoA carboxylase
Identifiers EC number CAS number 6.4.1.2
[1] [2]
9023-93-2
[7]
PDB structures RCSB PDB [9] PDBe [10] PDBsum [11] Gene Ontology AmiGO [12] / EGO [13] Search PMC articles
[14]
601557
NM_198839 Q13085
[20]
Acetyl-CoA carboxylase
293
Other data EC number Locus 6.4.1.2
[21] [22]
Chr. 17 q21
200350
EC number Locus
6.4.1.2
[21] [28]
Chr. 12 q24.1
Acetyl-CoA carboxylase (ACC) is a biotin-dependent enzyme that catalyzes the irreversible carboxylation of acetyl-CoA to produce malonyl-CoA through its two catalytic activities, biotin carboxylase (BC) and carboxyltransferase (CT). ACC is a multi-subunit enzyme in most prokaryotes and in the chloroplasts of most plants and algae, whereas it is a large, multi-domain enzyme in the endoplasmic reticulum of most eukaryotes. The most important function of ACC is to provide the malonyl-CoA substrate for the biosynthesis of fatty acids.[29] The activity of ACC can be controlled at the transcriptional level as well as by small molecule modulators and covalent modification. The human genome contains the genes for two different ACCs[30] ACACA[31] and ACACB.[32]
Structure
Prokaryotes and plants have multi-subunit ACCs composed of several polypeptides encoded by distinct genes. Biotin carboxylase (BC) activity, biotin carboxyl carrier protein (BCCP), and carboxyl transferase (CT) activity are each contained on a different subunit. The stoichiometry of these subunits in the ACC holoenzyme differs amongst organisms.[29] Humans and most eukaryotes have evolved an ACC with CT and BC catalytic domains and biotin carboxyl carrier domains on a single polypeptide. ACC functional regions, starting from the N-terminus to C-terminus are the biotin carboxylase (BC), biotin binding (BB), carboxyltransferase (CT), and ATP-binding (AB). AB lies within BC. Biotin is covalently attached through an amide bond to the long side chain of a lysine reside in BB. As BB is between BC and CT regions, biotin can be easily translocate to both of the active sites where it is required. In mammals where two isoforms of ACC are expressed, the main structural difference between these isoforms is the extended ACC2 N-terminus containing a mitochondria targeting sequence.[29]
Acetyl-CoA carboxylase
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Acetyl-CoA carboxylase
295
Acetyl-CoA carboxylase
296
Mechanism
The overall reaction of ACAC(A,B) proceeds by a two-step mechanism.[33] The first reaction is carried out by BC and involves the ATP-dependent carboxylation of biotin with bicarbonate serving as the source of CO2. The carboxyl group is transferred from biotin to acetyl CoA to form malonyl CoA in the second reaction, which is catalyzed by CT.
The reaction mechanism of ACAC(A,B).The color scheme is as follows: enzyme, coenzymes, substrate names, metal ions, phosphate, and carbonate
In the context of the active site, the reaction proceeds with extensive interaction of the residues Glu296 and positively charged Arg338 and Arg292 with the substrates.[34] Two Mg2+ are coordinated by the phosphate groups on the ATP, and are required for ATP binding to the enzyme. Bicarbonate is deprotonated by Glu296, although in solution, this proton transfer is unlikely as the pKa of bicarbonate is 10.3. The enzyme apparently manipulates pKas to facilitate the deprotonation of bicarbonate. The pKa of bicarbonate is decreased by its interaction with positively charged side chains of Arg338 and Arg292. Furthermore, Glu296 interacts with the side chain of Glu211, an interaction that has been shown to cause an increase in the apparent pKa. Following deprotonation of bicarbonate, the oxygen of the bicarbonate acts as a nucleophile and attacks the gamma phosphate on ATP. The carboxyphosphate intermediate quickly decomposes to CO2 and PO43-. The PO43- deprotonates biotin, creating an enolate, stabilized by Arg338, that subsequently attacks CO<sub>2</sub> resulting in the production of carboxybiotin.[34] The carboxybiotin translocates to the carboxytransferase (CT) active site, where the carboxyl group is transferred to acetyl-CoA. In contrast to the BC domain, little is known about the reaction mechanism of CT. A proposed mechanism is the release of carbon dioxide from biotin, which subsequently abstracts a proton from the methyl group from acetyl CoA carboxylase. The resulting enolate attacks CO2 to form malonyl CoA. In a competing mechanism, proton abstraction is concerted with the attack of acetyl CoA.
Function
The function of ACAC is to regulate the metabolism of fatty acids. When the enzyme is active, the product, malonyl-CoA is produced which is a building block for new fatty acids and can inhibit the transfer of the fatty acyl group from acyl CoA to carnitine with carnitine acyltransferase, which inhibits the beta-oxidation of fatty acids in the mitochondria. In mammals, two main isoforms of ACC are expressed, ACC1 and ACC2, which differ in both tissue distribution and function. ACC1 is found in the cytoplasm of all cells but is enriched in lipogenic tissue, such as adipose tissue and lactating mammary glands, where fatty acid synthesis is important.[35] In oxidative tissues, such as the skeletal muscle and the heart, the ratio of ACC2 expressed is higher. ACC1 and ACC2 are both highly expressed in the liver where both fatty acid oxidation and synthesis is important.[36] The differences in tissue distribution indicate that
Acetyl-CoA carboxylase ACC1 maintains regulation of fatty acid synthesis whereas ACC2 mainly regulates fatty acid oxidation.
297
Regulation
The regulation of mammalian ACC is complex, in order to control two distinct pools of malonyl CoA that direct either the inhibition of beta oxidation or the activation of lipid biosynthesis.
Mammalian ACC1 and ACC2 are regulated transcriptionally by multiple promoters which mediate ACC abundance in response to the cells nutritional status. Activation of gene expression through different promoters results in alternative splicing; however, the physiological significance of specific ACC isozymes remains unclear.[36] The sensitivity to nutritional status results from the control of these promoters by transcription factors such as SREBP1c, controlled by insulin at the transcriptional level, and ChREBP, which increases in expression with high carbohydrates diets.[37] [38] Through a feedforward loop, citrate allosterically activates ACC.[39] Citrate may increase ACC polymerization to increases enzymatic activity; however, it is unclear if polymerization is citrate's main mechanism of increasing ACC activity or if polymerization is an artifact of in vitro experiments. Other allosteric activators include glutamate and other dicarboxylic acids.[40] Long and short chain fatty acyl CoAs are negative feedback inhibitors of ACC.[41] Phosphorylation can result when the hormones glucagon or epinephrine bind to cell surface receptors, but the main cause of phosphorylation is due to a rise in AMP levels when the energy status of the cell is low, leading to the activation of the AMP-activated protein kinase (AMPK). AMPK is the main kinase regulator of ACC, able to phosphorylate a number of serine residues on both isoforms of ACC.[42] On ACC1, AMPK phosphorylates Ser79, Ser1200, and Ser1215. On ACC2, AMPK phosphorylates Ser218.[43] Protein kinase A also has the ability to phosphorylate ACC, with a much greater ability to phosphorylate ACC2 than ACC1. However, the physiological significance of protein kinase A in the regulation of ACC is currently unknown. Researchers hypothesize there are other ACC kinases important to its regulation as there are many other possible phosphorylation sites on ACC.[44] When insulin binds to its receptors on the cellular membrane, it activates a phosphatase to dephosphorylate the enzyme; thereby removing the inhibitory effect.
Control of Acetyl CoA Carboxylase. The AMP regulated kinase triggers the phosphorylation of the enzyme (thus inactivating it) and the phosphatase enzyme removes the phosphate group.
Clinical implications
At the juncture of lipid synthesis and oxidation pathways, ACC presents many clinical possibilities for the production of novel antibiotics and the development of new therapies for diabetes, obesity, and other manifestations of metabolic syndrome.[45] Researchers aim to take advantage of structural differences between bacterial and human ACCs to create antibiotics specific to the bacterial ACC, in efforts to minimize side effects to patients. Promising results for the usefulness of an ACC inhibitor include the finding that ACC2 -/- mice (mice with no expression of ACC2) have continuous fatty acid oxidation, reduced body fat mass, and reduced body weight despite an increase in food consumption. ACC2 -/- mice are also protected from diabetes.[46] It should be noted that mutant mice lacking ACC1 are embryonically lethal. However, it is unknown whether drugs targeting ACCs in humans must be specific for ACC2.[47]
Acetyl-CoA carboxylase
298
References
[1] [2] [3] [4] [5] [6] [7] [8] [9] http:/ / www. chem. qmul. ac. uk/ iubmb/ enzyme/ EC6/ 4/ 1/ 2. html http:/ / toolserver. org/ ~magnus/ cas. php?language=en& cas=9023-93-2& title= http:/ / www. ebi. ac. uk/ intenz/ query?cmd=SearchEC& ec=6. 4. 1. 2 http:/ / www. brenda-enzymes. org/ php/ result_flat. php4?ecno=6. 4. 1. 2 http:/ / www. expasy. org/ enzyme/ 6. 4. 1. 2 http:/ / www. genome. ad. jp/ dbget-bin/ www_bget?enzyme+ 6. 4. 1. 2 http:/ / biocyc. org/ META/ substring-search?type=NIL& object=6. 4. 1. 2 http:/ / priam. prabi. fr/ cgi-bin/ PRIAM_profiles_CurrentRelease. pl?EC=6. 4. 1. 2 http:/ / www. rcsb. org/ pdb/ search/ smartSubquery. do?smartSearchSubtype=EnzymeClassificationQuery& Enzyme_Classification=6. 4. 1. 2 [10] http:/ / www. ebi. ac. uk/ pdbe-srv/ view/ search?EC_number=6. 4. 1. 2& id_type=EC_number& id_value=6. 4. 1. 2& search_type=advanced [11] http:/ / www. ebi. ac. uk/ thornton-srv/ databases/ cgi-bin/ enzymes/ GetPage. pl?ec_number=6. 4. 1. 2 [12] http:/ / amigo. geneontology. org/ cgi-bin/ amigo/ go. cgi?query=GO:0003989& view=details [13] http:/ / www. ebi. ac. uk/ ego/ DisplayGoTerm?id=GO:0003989& format=normal [14] http:/ / www. ncbi. nlm. nih. gov/ entrez/ query. fcgi?db=pubmed& term=6. 4. 1. 2%5BEC/ RN%20Number%5D%20AND%20pubmed%20pmc%20local%5Bsb%5D [15] http:/ / www. ncbi. nlm. nih. gov/ entrez/ query. fcgi?db=pubmed& term=6. 4. 1. 2%5BEC/ RN%20Number%5D [16] http:/ / www. ncbi. nlm. nih. gov/ entrez/ query. fcgi?db=gene& amp;cmd=retrieve& amp;dopt=default& amp;list_uids=31& rn=1 [17] http:/ / www. genenames. org/ data/ hgnc_data. php?hgnc_id=84 [18] http:/ / www. ncbi. nlm. nih. gov/ omim/ 601557 [19] http:/ / genome. ucsc. edu/ cgi-bin/ hgTracks?Submit=Submit& position=NM_198839& rn=1 [20] http:/ / www. uniprot. org/ uniprot/ Q13085 [21] http:/ / www. genome. jp/ dbget-bin/ www_bget?enzyme+ 6. 4. 1. 2 [22] http:/ / omim. org/ search?index=geneMap& search=17q21 [23] http:/ / www. ncbi. nlm. nih. gov/ entrez/ query. fcgi?db=gene& amp;cmd=retrieve& amp;dopt=default& amp;list_uids=32& rn=1 [24] http:/ / www. genenames. org/ data/ hgnc_data. php?hgnc_id=85 [25] http:/ / www. ncbi. nlm. nih. gov/ omim/ 200350 [26] http:/ / genome. ucsc. edu/ cgi-bin/ hgTracks?Submit=Submit& position=NM_001093& rn=1 [27] http:/ / www. uniprot. org/ uniprot/ O00763 [28] http:/ / omim. org/ search?index=geneMap& search=12q24. 1 [29] Tong L (August 2005). "Acetyl-coenzyme A carboxylase: crucial metabolic enzyme and attractive target for drug discovery". Cell. Mol. Life Sci. 62 (16): 1784803. doi:10.1007/s00018-005-5121-4. PMID15968460. [30] Brownsey RW, Zhande R, Boone AN (November 1997). "Isoforms of acetyl-CoA carboxylase: structures, regulatory properties and metabolic functions". Biochem. Soc. Trans. 25 (4): 12328. PMID9449982. [31] Abu-Elheiga L, Jayakumar A, Baldini A, Chirala SS, Wakil SJ (April 1995). "Human acetyl-CoA carboxylase: characterization, molecular cloning, and evidence for two isoforms". Proc. Natl. Acad. Sci. U.S.A. 92 (9): 40115. doi:10.1073/pnas.92.9.4011. PMC42092. PMID7732023. [32] Widmer J, Fassihi KS, Schlichter SC, Wheeler KS, Crute BE, King N, Nutile-McMenemy N, Noll WW, Daniel S, Ha J, Kim KH, Witters LA (June 1996). "Identification of a second human acetyl-CoA carboxylase gene" (http:/ / www. biochemj. org/ bj/ 316/ 0915/ bj3160915. htm). Biochem. J.. 316 ( Pt 3): 91522. PMC1217437. PMID8670171. . [33] Lee CK, Cheong HK, Ryu KS, Lee JI, Lee W, Jeon YH, Cheong C (August 2008). "Biotinoyl domain of human acetyl-CoA carboxylase: Structural insights into the carboxyl transfer mechanism". Proteins 72 (2): 61324. doi:10.1002/prot.21952. PMID18247344. [34] Chou CY, Yu LP, Tong L (April 2009). "Crystal structure of biotin carboxylase in complex with substrates and implications for its catalytic mechanism". J. Biol. Chem. 284 (17): 116907. doi:10.1074/jbc.M805783200. PMC2670172. PMID19213731. [35] Kim TS, Leahy P, Freake HC (August 1996). "Promoter usage determines tissue specific responsiveness of the rat acetyl-CoA carboxylase gene". Biochem. Biophys. Res. Commun. 225 (2): 64753. doi:10.1006/bbrc.1996.1224. PMID8753813. [36] Barber MC, Price NT, Travers MT (March 2005). "Structure and regulation of acetyl-CoA carboxylase genes of metazoa". Biochim. Biophys. Acta 1733 (1): 128. doi:10.1016/j.bbalip.2004.12.001. PMID15749055. [37] Field F. J., Born E., Murthy S. and Mathur S. N. (December 2002). "Polyunsaturated fatty acids decrease the expression of sterol regulatory element binding protein-1 in CaCo-2 cells: effect on fatty acid synthesis and triacylglycerol transport.". Biochem. J. 386 (Pt 3): 85564. doi:10.1042/BJ20020731. PMC1223029. PMID12213084. [38] Ishii S, Iizuka K, Miller BC, Uyeda K (October 2004). "Carbohydrate response element binding protein directly promotes lipogenic enzyme gene transcription". Proc Natl Acad Sci USA 101 (44): 15597602. doi:10.1073/pnas.0405238101. PMC524841. PMID15496471. [39] Martin DB, Vagelos PR (June 1962). "The Mechanism of Tricarboxylic Acid Cycle Regulation of Fatty Acid Synthesis". J Biol Chem 237: 178792. PMID14470343.
Acetyl-CoA carboxylase
[40] Boone AN, Chan A, Kulpa JE, Brownsey RW (April 2000). "Bimodal Activation of Acetyl-CoA Carboxylase by Glutamate". J Biol Chem 275 (15): 1081925. doi:10.1074/jbc.275.15.10819. PMID10753875. [41] Faergeman NJ, Knudsen J (April 1997). "Role of long chain fatty acyl-CoA esters in the regulation of metabolism and in cell signalling". Biochem J. 323 (Pt 1): 112. PMC1218279. PMID9173866. [42] Park SH, Gammon SR, Knippers JD, Paulsen SR, Rubink DS, Winder WW (June 2002). "Phosphorylation-activity relationships of AMPK and acetyl-CoA carboxylase in muscle". J. Appl. Physiol. 92 (6): 247582. doi:10.1152/japplphysiol.00071.2002. PMID12015362. [43] Hardie DG (February 1992). "Regulation of fatty acid and cholesterol metabolism by the AMP-activated protein kinase". Biochim. Biophys. Acta 1123 (3): 2318. PMID1536860. [44] Brownsey RW, Boone AN, Elliott JE, Kulpa JE, Lee WM (April 2006). "Regulation of acetyl-CoA carboxylase". Biochem. Soc. Trans. 34 (Pt 2): 2237. doi:10.1042/BST20060223. PMID16545081. [45] Corbett JW, Harwood JH (November 2007). "Inhibitors of mammalian acetyl-CoA carboxylase". Recent Patents Cardiovasc Drug Discov 2 (3): 16280. doi:10.2174/157489007782418928. PMID18221116. [46] L Abu-Elheiga, M M Matzuk, K A Abo-Hashema, S J Wakil (March 2001). "Continuous Fatty Acid Oxidation and Reduced Fat Storage in Mice Lacking Acetyl-CoA Carboxylase 2". Science 291 (5513): 26136. doi:10.1126/science.1056843. PMID11283375. [47] Lutfi Abu-Elheiga, Martin M Matzuk, Parichher Kordari, WonKeun Oh, Tattym Shaikenov, Ziwei Gu, Salih J Wakil (August 2005). "Mutant Mice Lacking Acetyl CoA Carboxylase are Embryonically Lethal". Proc Natl Acad Sci 102 (34): 12116. doi:10.1073/pnas.0505714102. PMC1189351. PMID16103361.
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Further reading
Voet, Donald; Voet, Judith G. (2004). Biochemistry (3rd ed.). Wiley. ISBN0-471-19350-x. edited by (2000). Buchanan, Bob B.; Gruissem, Wilhelm; Jones, Russell L.. eds. Biochemistry and molecular biology of plants. American Society of Plant Physiologists. ISBN0-943088-37-2. Levert K, Waldrop G, Stephens J (2002). "A biotin analog inhibits acetyl-CoA carboxylase activity and adipogenesis". J. Biol. Chem. 277 (19): 1634750. doi:10.1074/jbc.C200113200. PMID11907024.
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The formula for the above is: RCOO- + CoA + ATP + H2O RCO-CoA + AMP + PPi + 2H+ This two-step reaction is freely reversible and its equilibrium lies near 1. To drive the reaction forward, the reaction is coupled to a strongly exergonic hydrolysis reaction: the enzyme inorganic pyrophosphatase cleaves the pyrophosphate liberated from ATP to two phosphate ions. Thus the net reaction becomes: RCOO- + CoA + ATP + H2O RCO-CoA + AMP + 2Pi + 2H+
301
-oxidation
Once inside the mitochondria, the -oxidation of fatty acids occurs via four recurring steps: 1. 2. 3. 4. 5. Oxidation by FAD, Hydration, Oxidation by NAD+, Thiolysis, The final product is acetyl-CoA, the entry molecule for the citric acid cycle.
Beta oxidation
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 generate Acetyl-CoA, the entry molecule for the Citric Acid cycle. The beta oxidation of fatty acids involve three stages: 1. Activation of fatty acids in the cytosol 2. Transport of fatty acids into mitochondria (carnitine shuttle) 3. Beta oxidation proper in the mitochondrial matrix
Schematic demonstrating mitochondrial fatty acid beta-oxidation and effects of long-chain 3-hydroxyacyl-coenzyme A dehydrogenase deficiency, LCHAD deficiency
Fatty acids are oxidized by most of the tissues in the body. However, the brain can hardly utilize fatty acids for energy requirements, while erythrocytes and adrenal medulla cannot use them at all.
Beta oxidation
302
L--hydroxyacyl CoA
Oxidation by NAD+: The third step is the oxidation of L--hydroxyacyl CoA by NAD+. This converts the hydroxyl group into a keto group.
-ketoacyl CoA
Thiolysis: The final step is the cleavage of -ketoacyl CoA by the thiol group of another molecule of CoA. The thiol is inserted between C-2 and C-3.
-ketothiolase
An acetyl CoA molecule, and an acyl CoA molecule that is two carbons shorter
This process continues until the entire chain is cleaved into acetyl CoA units. The final cycle produces two separate acetyl CoAs, instead of one acyl CoA and one acetyl CoA. For every cycle, the Acyl CoA unit is shortened by two carbon atoms. Concomitantly, one molecule of FADH2, NADH and acetyl CoA are formed.
Beta oxidation
303
Oxidation in peroxisomes
Fatty acid oxidation also occurs in peroxisomes, when the fatty acid chains are too long to be handled by the mitochondria. However, the oxidation ceases at octanyl CoA. It is believed that very long chain (greater than C-22) fatty acids undergo initial oxidation in peroxisomes which is followed by mitochondrial oxidation. One significant difference is that oxidation in peroxisomes is not coupled to ATP synthesis. Instead, the high-potential electrons are transferred to O2, which yields H2O2. The enzyme catalase, found exclusively in peroxisomes, converts the hydrogen peroxide into water and oxygen. Peroxisomal -oxidation also requires enzymes specific to the peroxisome and to very long fatty acids. There are three key differences between the enzymes used for mitochondrial and peroxisomal -oxidation: 1. -oxidation in the peroxisome requires the use of a peroxisomal carnitine acyltransferase (instead of carnitine acyltransferase I and II used by the mitochondria) for transport of the activated acyl group into the peroxisome. 2. The fi