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102-607: SBGN is made up of three orthogonal languages for representing different views of biological systems: Process Descriptions , Entity Relationships and Activity Flows . Each language defines a comprehensive set of symbols with precise semantics, together with detailed syntactic rules regarding the construction and interpretation of maps. Using these three notations, a life scientist can represent in an unambiguous way networks of interactions (for example biochemical interactions). These notations make use of an idea and symbols similar to that used by electrical and other engineers and known as

204-628: A biological polymer , they undergo a process called dehydration synthesis . Different macromolecules can assemble in larger complexes, often needed for biological activity . Two of the main functions of carbohydrates are energy storage and providing structure. One of the common sugars known as glucose is a carbohydrate, 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 simplest type of carbohydrate

306-433: A carboxylic acid group, –COOH (although these exist as –NH 3 and –COO under physiologic conditions), a simple hydrogen atom , and a side chain commonly denoted as "–R". The side chain "R" is different for each amino acid of which there are 20 standard ones . It is this "R" group that makes each amino acid different, and the properties of the side chains greatly influence the overall three-dimensional conformation of

408-622: A chemical compound composed of more than one element, e.g. water (two hydrogen atoms and one oxygen atom; H 2 O). In the kinetic theory of gases , the term molecule is often used for any gaseous particle regardless of its composition. This relaxes the requirement that a molecule contains two or more atoms, since the noble gases are individual atoms. Atoms and complexes connected by non-covalent interactions , such as hydrogen bonds or ionic bonds , are typically not considered single molecules. Concepts similar to molecules have been discussed since ancient times, but modern investigation into

510-440: A plane , e.g. graphene ; or three-dimensionally e.g. diamond , quartz , sodium chloride . The theme of repeated unit-cellular-structure also holds for most metals which are condensed phases with metallic bonding . Thus solid metals are not made of molecules. In glasses , which are solids that exist in a vitreous disordered state, the atoms are held together by chemical bonds with no presence of any definable molecule, nor any of

612-565: A certain number of these atoms united by attraction to form a single molecule . In coordination with these concepts, in 1833 the French chemist Marc Antoine Auguste Gaudin presented a clear account of Avogadro's hypothesis, regarding atomic weights, by making use of "volume diagrams", which clearly show both semi-correct molecular geometries, such as a linear water molecule, and correct molecular formulas, such as H 2 O: In 1917, an unknown American undergraduate chemical engineer named Linus Pauling

714-399: A chemical theory of metabolism, or even earlier to the 18th century studies on fermentation and respiration by Antoine Lavoisier . Many other pioneers in the field who helped to uncover the layers of complexity of biochemistry have been proclaimed founders of modern biochemistry. Emil Fischer , who studied the chemistry of proteins , and F. Gowland Hopkins , who studied enzymes and

816-434: A component of DNA . A monosaccharide can switch between acyclic (open-chain) form and a cyclic form. The open-chain form can be turned into a ring of carbon atoms bridged by an oxygen atom created from the carbonyl group of one end and the hydroxyl group of another. The cyclic molecule has a hemiacetal or hemiketal group, depending on whether the linear form was an aldose or a ketose . In these cyclic forms,

918-406: A cyclic [ring] and planar [flat] structure) while others are not. Some are flexible, while others are rigid. 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 maybe saturated (no double bonds in

1020-399: A dimension of a few angstroms (Å) to several dozen Å, or around one billionth of a meter. Single molecules cannot usually be observed by light (as noted above), but small molecules and even the outlines of individual atoms may be traced in some circumstances by use of an atomic force microscope . Some of the largest molecules are macromolecules or supermolecules . The smallest molecule

1122-468: A few (around three to six) monosaccharides are joined, it is called an oligosaccharide ( oligo- meaning "few"). These molecules tend to be used as markers and signals , as well as having some other uses. Many monosaccharides joined form a polysaccharide . They can be joined in one long linear chain, or they may be branched . Two of the most common polysaccharides are cellulose and glycogen , both consisting of repeating glucose monomers . Cellulose

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1224-435: A graphical type of formula called a structural formula may be needed. Structural formulas may in turn be represented with a one-dimensional chemical name, but such chemical nomenclature requires many words and terms which are not part of chemical formulas. Molecules have fixed equilibrium geometries—bond lengths and angles— about which they continuously oscillate through vibrational and rotational motions. A pure substance

1326-404: A molecule with a 5-membered ring, called glucofuranose . The same reaction can take place between carbons 1 and 5 to form a molecule with a 6-membered ring, called glucopyranose . Cyclic forms with a 7-atom ring called heptoses are rare. Two monosaccharides can be joined by a glycosidic or ester bond into a disaccharide through a dehydration reaction during which a molecule of water

1428-491: A network. It can be used to show all the molecular interactions taking place in a network of biochemical entities, with the same entity appearing multiple times in the same diagram. The SBGN Entity Relationship (ER) language allows to see all the relationships in which a given entity participates, regardless of the temporal aspects. Relationships can be seen as rules describing the influences of entities nodes on other relationships. The SBGN Activity Flow (AF) language depicts

1530-414: A protein. Some amino acids have functions by themselves or in a modified form; for instance, glutamate functions as an important neurotransmitter . Amino acids can be joined 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 carboxylic acid group. The resulting molecule

1632-566: A reducing end because of full acetal formation between the aldehyde carbon of glucose (C1) and the keto carbon of fructose (C2). Lipids comprise 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, open-chain aliphatic molecules, while others have ring structures. Some are aromatic (with

1734-401: A regular arrangement of molecules (as in a crystal). Microwave spectroscopy commonly measures changes in the rotation of molecules, and can be used to identify molecules in outer space. Infrared spectroscopy measures the vibration of molecules, including stretching, bending or twisting motions. It is commonly used to identify the kinds of bonds or functional groups in molecules. Changes in

1836-440: A study of the components and composition of living things and how they come together to become life. In this sense, the history of biochemistry may therefore go back as far as the ancient Greeks . However, biochemistry as a specific scientific discipline began sometime in the 19th century, or a little earlier, depending on which aspect of biochemistry is being focused on. Some argued that the beginning of biochemistry may have been

1938-431: Is a monosaccharide , which among other properties contains carbon , hydrogen , and oxygen , mostly in a ratio of 1:2:1 (generalized formula C n H 2 n O n , where n is at least 3). Glucose (C 6 H 12 O 6 ) is one of the most important carbohydrates; others include fructose (C 6 H 12 O 6 ), the sugar commonly associated with the sweet taste of fruits , and deoxyribose (C 5 H 10 O 4 ),

2040-402: Is a chemical bond that involves the sharing of electron pairs between atoms. These electron pairs are termed shared pairs or bonding pairs , and the stable balance of attractive and repulsive forces between atoms, when they share electrons, is termed covalent bonding . Ionic bonding is a type of chemical bond that involves the electrostatic attraction between oppositely charged ions, and

2142-455: Is a very simple type of chemical formula. It is the simplest integer ratio of the chemical elements that constitute it. For example, water is always composed of a 2:1 ratio of hydrogen to oxygen atoms, and ethanol (ethyl alcohol) is always composed of carbon, hydrogen, and oxygen in a 2:6:1 ratio. However, this does not determine the kind of molecule uniquely – dimethyl ether has the same ratios as ethanol, for instance. Molecules with

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2244-412: Is an energy source in most life forms. For instance, polysaccharides are broken down into their monomers by enzymes ( glycogen phosphorylase removes glucose residues from glycogen, a polysaccharide). Disaccharides like lactose or sucrose are cleaved into their two component monosaccharides. Glucose is mainly metabolized by a very important ten-step pathway called glycolysis , the net result of which

2346-407: Is an important structural component of plant's cell walls and glycogen is used as a form of energy storage in animals. Sugar can be characterized 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 ( aldose ) or keto form ( ketose ). If the joining of monomers takes place at such a carbon atom,

2448-424: 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 . Proteins can have structural and/or functional roles. For instance, movements of the proteins actin and myosin ultimately are responsible for

2550-435: Is composed of molecules with the same average geometrical structure. The chemical formula and the structure of a molecule are the two important factors that determine its properties, particularly its reactivity . Isomers share a chemical formula but normally have very different properties because of their different structures. Stereoisomers , a particular type of isomer, may have very similar physico-chemical properties and at

2652-479: Is derived from French molécule (1678), from Neo-Latin molecula , diminutive of Latin moles "mass, barrier". The word, which until the late 18th century was used only in Latin form, became popular after being used in works of philosophy by Descartes . The definition of the molecule has evolved as knowledge of the structure of molecules has increased. Earlier definitions were less precise, defining molecules as

2754-480: Is essential for the understanding of the chemical bond. The simplest of molecules is the hydrogen molecule-ion , H 2 , and the simplest of all the chemical bonds is the one-electron bond . H 2 is composed of two positively charged protons and one negatively charged electron , which means that the Schrödinger equation for the system can be solved more easily due to the lack of electron–electron repulsion. With

2856-421: Is not an essential element for plants. Plants need boron and silicon , but animals may not (or may need ultra-small amounts). Just six elements— carbon , hydrogen , nitrogen , oxygen , calcium and phosphorus —make up almost 99% of the mass of living cells, including those in the human body (see composition of the human body for a complete list). In addition to the six major elements that compose most of

2958-508: Is released. The reverse reaction in which the glycosidic bond of a disaccharide is broken into two monosaccharides is termed hydrolysis . The best-known disaccharide is sucrose or ordinary sugar , which consists of a glucose molecule and a fructose molecule joined. Another important disaccharide is lactose found in milk, consisting of a glucose molecule and a galactose molecule. Lactose may be hydrolysed by lactase , and deficiency in this enzyme results in lactose intolerance . When

3060-556: Is the diatomic hydrogen (H 2 ), with a bond length of 0.74 Å. Effective molecular radius is the size a molecule displays in solution. The table of permselectivity for different substances contains examples. The chemical formula for a molecule uses one line of chemical element symbols, numbers, and sometimes also other symbols, such as parentheses, dashes, brackets, and plus (+) and minus (−) signs. These are limited to one typographic line of symbols, which may include subscripts and superscripts. A compound's empirical formula

3162-506: Is the generic name of the family of biopolymers . They are complex, high-molecular-weight biochemical macromolecules that can convey genetic information in all living cells and viruses. The monomers are called nucleotides , and each consists of three components: a nitrogenous heterocyclic base (either a purine or a pyrimidine ), a pentose sugar, and a phosphate group. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The phosphate group and

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3264-617: Is the primary interaction occurring in ionic compounds . The ions are atoms that have lost one or more electrons (termed cations ) and atoms that have gained one or more electrons (termed anions ). This transfer of electrons is termed electrovalence in contrast to covalence . In the simplest case, the cation is a metal atom and the anion is a nonmetal atom, but these ions can be of a more complicated nature, e.g. molecular ions like NH 4 or SO 4 . At normal temperatures and pressures, ionic bonding mostly creates solids (or occasionally liquids) without separate identifiable molecules, but

3366-492: Is thought to be the reason why complex life appeared only after Earth's atmosphere accumulated large amounts of oxygen. In vertebrates , vigorously contracting skeletal muscles (during weightlifting or sprinting, for example) do not receive enough oxygen to meet the energy demand, and so they shift to anaerobic metabolism , converting glucose to lactate. The combination of glucose from noncarbohydrates origin, such as fat and proteins. This only happens when glycogen supplies in

3468-409: Is to break down one molecule of glucose into two molecules of pyruvate . This also produces a net two molecules of ATP , the energy currency of cells, along with two reducing equivalents of converting NAD (nicotinamide adenine dinucleotide: oxidized form) to NADH (nicotinamide adenine dinucleotide: reduced form). This does not require oxygen; if no oxygen is available (or the cell cannot use oxygen),

3570-529: The Avogadro constant using three different methods, all involving liquid phase systems. First, he used a gamboge soap-like emulsion, second by doing experimental work on Brownian motion , and third by confirming Einstein's theory of particle rotation in the liquid phase. In 1927, the physicists Fritz London and Walter Heitler applied the new quantum mechanics to the deal with the saturable, nondynamic forces of attraction and repulsion, i.e., exchange forces, of

3672-518: The block diagram . The simplicity of SBGN syntax and semantics makes SBGN maps suitable for use at the high school level. Some software support for SBGN is already available, mostly for the Process Description language. SBGN visualizations can be exchanged with the XML-based file format SBGN-ML. The SBGN Process Description (PD) language shows the temporal courses of biochemical interactions in

3774-479: The chemistry required for biological activity of molecules, molecular biology studies their biological activity, genetics studies their heredity, which happens to be carried by their genome . This is shown in the following schematic that depicts one possible view of the relationships between the fields: Molecule A molecule is a group of two or more atoms that are held together by attractive forces known as chemical bonds ; depending on context,

3876-416: The essential amino acids . 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

3978-424: 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. Ingested proteins are usually broken up into single amino acids or dipeptides in

4080-549: The small intestine and then absorbed. They can then be joined to form new proteins. Intermediate products of glycolysis, the citric acid cycle, and the pentose phosphate pathway can be used to form 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 . Because they must be ingested, these are

4182-399: The " vital principle ") distinct from any found in non-living matter, and it was thought that only living beings could produce the molecules of life. In 1828, Friedrich Wöhler published a paper on his serendipitous urea synthesis from potassium cyanate and ammonium sulfate ; some regarded that as a direct overthrow of vitalism and the establishment of organic chemistry . However,

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4284-469: The Chemical Bond" in which he used quantum mechanics to calculate properties and structures of molecules, such as angles between bonds and rotation about bonds. On these concepts, Pauling developed hybridization theory to account for bonds in molecules such as CH 4 , in which four sp³ hybridised orbitals are overlapped by hydrogen 's 1s orbital, yielding four sigma (σ) bonds . The four bonds are of

4386-512: The N-terminal domain. The enzyme-linked immunosorbent assay (ELISA), which uses antibodies, is one of the most sensitive tests modern medicine uses to detect various biomolecules. Probably the most important proteins, however, are the enzymes . Virtually every reaction in a living cell requires an enzyme to lower the activation energy of the reaction. These molecules recognize specific reactant molecules called substrates ; they then catalyze

4488-489: The NAD is restored by converting the pyruvate to lactate (lactic acid) (e.g. in humans) or to ethanol plus carbon dioxide (e.g. in yeast ). Other monosaccharides like galactose and fructose can be converted into intermediates of the glycolytic pathway. In aerobic cells with sufficient oxygen , as in most human cells, the pyruvate is further metabolized. It is irreversibly converted to acetyl-CoA , giving off one carbon atom as

4590-481: The Wöhler synthesis has sparked controversy as some reject the death of vitalism at his hands. 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

4692-416: The amino group is removed from an amino acid, it leaves behind a carbon skeleton called an α- keto acid . Enzymes called transaminases can easily transfer the amino group from one amino acid (making it an α-keto acid) to another α-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

4794-434: The amount of energy gained from glycolysis (six molecules of ATP are used, compared to the two gained in glycolysis). Analogous to the above reactions, the glucose produced can then undergo glycolysis in tissues that need energy, be stored as glycogen (or starch in plants), or be converted to other monosaccharides or joined into di- or oligosaccharides. The combined pathways of glycolysis during exercise, lactate's crossing via

4896-878: The animals' needs. Unicellular organisms release the ammonia into the environment. Likewise, bony fish can release ammonia into the water where it is quickly diluted. In general, mammals convert ammonia into urea, via the urea cycle . 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 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 , so-called because of their prevalence in cellular nuclei ,

4998-441: The arrangements of electrons yield absorption or emission lines in ultraviolet, visible or near infrared light, and result in colour. Nuclear resonance spectroscopy measures the environment of particular nuclei in the molecule, and can be used to characterise the numbers of atoms in different positions in a molecule. The study of molecules by molecular physics and theoretical chemistry is largely based on quantum mechanics and

5100-464: The bloodstream to the liver, subsequent gluconeogenesis and release of glucose into the bloodstream is called the Cori cycle . Researchers in biochemistry use specific techniques native to biochemistry, but increasingly combine these with techniques and ideas developed in the fields of genetics , molecular biology , and biophysics . There is not a defined line between these disciplines. Biochemistry studies

5202-513: The body and are broken into fatty acids and glycerol, the final degradation products of fats and lipids. Lipids, especially phospholipids , are also used in various pharmaceutical products , either as co-solubilizers (e.g. in parenteral infusions) or else as drug carrier components (e.g. in a liposome or transfersome ). Proteins are very large molecules—macro-biopolymers—made from monomers called amino acids . An amino acid consists of an alpha carbon atom attached to an amino group, –NH 2 ,

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5304-539: The carbon chain) or unsaturated (one or more double bonds in the carbon chain). Most lipids have some polar character and are 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

5406-490: 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

5508-651: The causes and cures of diseases . Nutrition studies how to maintain health and wellness and also the effects of nutritional deficiencies . In agriculture, biochemists investigate soil and fertilizers with the goal of improving crop cultivation, crop storage, and pest control . In recent decades, biochemical principles and methods have been combined with problem-solving approaches from engineering to manipulate living systems in order to produce useful tools for research, industrial processes, and diagnosis and control of disease—the discipline of biotechnology . At its most comprehensive definition, biochemistry can be seen as

5610-507: The contraction of skeletal muscle. One property many proteins have is that they specifically bind to a certain molecule or class of molecules—they may be extremely selective in what they bind. Antibodies are an example of proteins that attach to one specific type of molecule. Antibodies are composed of heavy and light chains. Two heavy chains would be linked to two light chains through disulfide linkages between their amino acids. Antibodies are specific through variation based on differences in

5712-484: The development of fast digital computers, approximate solutions for more complicated molecules became possible and are one of the main aspects of computational chemistry . When trying to define rigorously whether an arrangement of atoms is sufficiently stable to be considered a molecule, IUPAC suggests that it "must correspond to a depression on the potential energy surface that is deep enough to confine at least one vibrational state". This definition does not depend on

5814-587: The discovery and detailed analysis of many molecules and metabolic pathways of the cell , such as glycolysis and the Krebs cycle (citric acid cycle), and led to an understanding of biochemistry on a molecular level. Another significant historic event in biochemistry is the discovery of the gene , and its role in the transfer of information in the cell. In the 1950s, James D. Watson , Francis Crick , Rosalind Franklin and Maurice Wilkins were instrumental in solving DNA structure and suggesting its relationship with

5916-492: The discovery of the first enzyme , diastase (now called amylase ), in 1833 by Anselme Payen , while others considered Eduard Buchner 's first demonstration of a complex biochemical process alcoholic fermentation in cell-free extracts in 1897 to be the birth of biochemistry. Some might also point as its beginning to the influential 1842 work by Justus von Liebig , Animal chemistry, or, Organic chemistry in its applications to physiology and pathology , which presented

6018-511: The dynamic nature of biochemistry, represent two examples of early biochemists. The term "biochemistry" was first used when Vinzenz Kletzinsky (1826–1882) had his "Compendium der Biochemie" printed in Vienna in 1858; it derived from a combination of biology and chemistry . In 1877, Felix Hoppe-Seyler used the term ( biochemie in German) as a synonym for physiological chemistry in the foreword to

6120-550: The electrons from high-energy states in NADH and quinol is conserved first as proton gradient and converted to ATP via ATP synthase. This generates an additional 28 molecules of ATP (24 from the 8 NADH + 4 from the 2 quinols), totaling to 32 molecules of ATP conserved per degraded glucose (two from glycolysis + two from the citrate cycle). It is clear that using oxygen to completely oxidize glucose provides an organism with far more energy than any oxygen-independent metabolic feature, and this

6222-426: The enzyme can be regulated, enabling control of the biochemistry of the cell as a whole. The structure of proteins is traditionally described in a hierarchy of four levels. The primary structure of a protein 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

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6324-469: The enzyme complexes of the respiratory chain, an electron transport system transferring the electrons ultimately to oxygen and conserving the released energy in the form of a proton gradient over a membrane ( inner mitochondrial membrane in eukaryotes). Thus, oxygen is reduced to water and the original electron acceptors NAD and quinone are regenerated. This is why humans breathe in oxygen and breathe out carbon dioxide. The energy released from transferring

6426-448: The first issue of Zeitschrift für Physiologische Chemie (Journal of Physiological Chemistry) where he argued for the setting up of institutes dedicated to this field of study. The German chemist Carl Neuberg however is often cited to have coined the word in 1903, while some credited it to Franz Hofmeister . It was once generally believed that life and its materials had some essential property or substance (often referred to as

6528-539: The flow of information between biochemical entities in a network. It omits information about the state transitions of entities and is particularly convenient for representing the effects of perturbations, whether genetic or environmental in nature. Work on defining a set of symbols to describe interactions and relationships of molecules was pioneered by Kurt Kohn at the National Cancer Institute with his Molecular Interaction Maps (MIM). The development of SBGN

6630-463: 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 forms a full acetal with the C4-OH group of glucose. Saccharose does not have

6732-525: 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 (ATP), the primary energy-carrier molecule found in all living organisms. 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. Glucose

6834-515: The 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 convicted of murder with DNA evidence, which led to the growth of forensic science . More recently, Andrew Z. Fire and Craig C. Mello received the 2006 Nobel Prize for discovering

6936-464: The heavenly bodies. The viewpoint of Leucippus and Empedocles, along with the aether, was accepted by Aristotle and passed to medieval and renaissance Europe. In a more concrete manner, however, the concept of aggregates or units of bonded atoms, i.e. "molecules", traces its origins to Robert Boyle 's 1661 hypothesis, in his famous treatise The Sceptical Chymist , that matter is composed of clusters of particles and that chemical change results from

7038-448: The human body, humans require smaller amounts of possibly 18 more. The 4 main classes of molecules in biochemistry (often called biomolecules ) are carbohydrates , lipids , proteins , and nucleic acids . Many biological molecules are polymers : in this terminology, monomers are relatively small macromolecules that are linked together to create large macromolecules known as polymers. When monomers are linked together to synthesize

7140-581: The hydrogen molecule. Their valence bond treatment of this problem, in their joint paper, was a landmark in that it brought chemistry under quantum mechanics. Their work was an influence on Pauling, who had just received his doctorate and visited Heitler and London in Zürich on a Guggenheim Fellowship . Subsequently, in 1931, building on the work of Heitler and London and on theories found in Lewis' famous article, Pauling published his ground-breaking article "The Nature of

7242-463: The last decades of the 20th century, biochemistry has become successful at explaining living processes through these three disciplines. Almost all areas of the life sciences are being uncovered and developed through biochemical methodology and research. Biochemistry focuses on understanding the chemical basis which allows biological molecules to give rise to the processes that occur within living cells and between cells, in turn relating greatly to

7344-735: The laws governing their structure and properties. In practice, however, this distinction is vague. In molecular sciences, a molecule consists of a stable system ( bound state ) composed of two or more atoms. Polyatomic ions may sometimes be usefully thought of as electrically charged molecules. The term unstable molecule is used for very reactive species, i.e., short-lived assemblies ( resonances ) of electrons and nuclei , such as radicals , molecular ions , Rydberg molecules , transition states , van der Waals complexes , or systems of colliding atoms as in Bose–Einstein condensate . Molecules as components of matter are common. They also make up most of

7446-458: The liver are worn out. The pathway is a crucial reversal of glycolysis from pyruvate to glucose and can use many sources like amino acids, glycerol and Krebs Cycle . Large scale protein and fat catabolism usually occur when those suffer from starvation or certain endocrine disorders. The liver regenerates the glucose, using a process called gluconeogenesis . This process is not quite the opposite of glycolysis, and actually requires three times

7548-404: The mass of a neutral carbon-12 ( C isotope ) atom. For network solids , the term formula unit is used in stoichiometric calculations. For molecules with a complicated 3-dimensional structure, especially involving atoms bonded to four different substituents, a simple molecular formula or even semi-structural chemical formula may not be enough to completely specify the molecule. In this case,

7650-448: The minerals that make up the substance of the Earth, sand, clay, pebbles, rocks, boulders, bedrock , the molten interior , and the core of the Earth . All of these contain many chemical bonds, but are not made of identifiable molecules. No typical molecule can be defined for salts nor for covalent crystals , although these are often composed of repeating unit cells that extend either in

7752-537: The nature of molecules and their bonds began in the 17th century. Refined over time by scientists such as Robert Boyle , Amedeo Avogadro , Jean Perrin , and Linus Pauling , the study of molecules is today known as molecular physics or molecular chemistry. According to Merriam-Webster and the Online Etymology Dictionary , the word "molecule" derives from the Latin " moles " or small unit of mass. The word

7854-440: The nature of the interaction between the atoms, but only on the strength of the interaction. In fact, it includes weakly bound species that would not traditionally be considered molecules, such as the helium dimer , He 2 , which has one vibrational bound state and is so loosely bound that it is only likely to be observed at very low temperatures. Whether or not an arrangement of atoms is sufficiently stable to be considered

7956-517: The oceans and atmosphere. Most organic substances are molecules. The substances of life are molecules, e.g. proteins, the amino acids of which they are composed, the nucleic acids (DNA and RNA), sugars, carbohydrates, fats, and vitamins. The nutrient minerals are generally ionic compounds, thus they are not molecules, e.g. iron sulfate. However, the majority of familiar solid substances on Earth are made partly or completely of crystals or ionic compounds, which are not made of molecules. These include all of

8058-410: The reaction between them. By lowering the activation energy , the enzyme speeds up that reaction by a rate of 10 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

8160-411: The rearrangement of the clusters. Boyle argued that matter's basic elements consisted of various sorts and sizes of particles, called "corpuscles", which were capable of arranging themselves into groups. In 1789, William Higgins published views on what he called combinations of "ultimate" particles, which foreshadowed the concept of valency bonds . If, for example, according to Higgins, the force between

8262-546: The regularity of repeating unit-cellular-structure that characterizes salts, covalent crystals, and metals. Molecules are generally held together by covalent bonding . Several non-metallic elements exist only as molecules in the environment either in compounds or as homonuclear molecules, not as free atoms: for example, hydrogen. While some people say a metallic crystal can be considered a single giant molecule held together by metallic bonding , others point out that metals behave very differently than molecules. A covalent bond

8364-413: The ring usually has 5 or 6 atoms. These forms are called furanoses and pyranoses , respectively—by analogy with furan and pyran , the simplest compounds with the same carbon-oxygen ring (although they lack the carbon-carbon double bonds of these two molecules). For example, the aldohexose glucose may form a hemiacetal linkage between the hydroxyl on carbon 1 and the oxygen on carbon 4, yielding

8466-559: The role of RNA interference (RNAi) in the silencing of gene expression . Around two dozen chemical elements are essential to various kinds of biological life . Most rare elements on Earth are not needed by life (exceptions being selenium and iodine ), while a few common ones ( aluminum and titanium ) are not used. Most organisms share element needs, but there are a few differences between plants and animals . For example, ocean algae use bromine , but land plants and animals do not seem to need any. All animals require sodium , but

8568-405: The same atoms in different arrangements are called isomers . Also carbohydrates, for example, have the same ratio (carbon:hydrogen:oxygen= 1:2:1) (and thus the same empirical formula) but different total numbers of atoms in the molecule. The molecular formula reflects the exact number of atoms that compose the molecule and so characterizes different molecules. However different isomers can have

8670-404: The same atomic composition while being different molecules. The empirical formula is often the same as the molecular formula but not always. For example, the molecule acetylene has molecular formula C 2 H 2 , but the simplest integer ratio of elements is CH. The molecular mass can be calculated from the chemical formula and is expressed in conventional atomic mass units equal to 1/12 of

8772-405: The same length and strength, which yields a molecular structure as shown below: The science of molecules is called molecular chemistry or molecular physics , depending on whether the focus is on chemistry or physics. Molecular chemistry deals with the laws governing the interaction between molecules that results in the formation and breakage of chemical bonds, while molecular physics deals with

8874-568: The same time different biochemical activities. Molecular spectroscopy deals with the response ( spectrum ) of molecules interacting with probing signals of known energy (or frequency , according to the Planck relation ). Molecules have quantized energy levels that can be analyzed by detecting the molecule's energy exchange through absorbance or emission . Spectroscopy does not generally refer to diffraction studies where particles such as neutrons , electrons, or high energy X-rays interact with

8976-517: The smallest particles of pure chemical substances that still retain their composition and chemical properties. This definition often breaks down since many substances in ordinary experience, such as rocks , salts , and metals , are composed of large crystalline networks of chemically bonded atoms or ions , but are not made of discrete molecules. The modern concept of molecules can be traced back towards pre-scientific and Greek philosophers such as Leucippus and Democritus who argued that all

9078-585: The structure of cells and perform many of the functions associated with life. The chemistry of the cell also depends upon the reactions of small molecules and ions . These can be inorganic (for example, water and metal ions) or organic (for example, the amino acids , which are used to synthesize proteins ). The mechanisms used by cells to harness energy from their environment via chemical reactions are known as metabolism . The findings of biochemistry are applied primarily in medicine , nutrition and agriculture . In medicine, biochemists investigate

9180-476: The study of structure). Some combinations of amino acids will tend to curl up in a coil called an α-helix or into a sheet called a β-sheet ; some α-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

9282-683: The sugar of each nucleotide bond with each other to form the backbone of the nucleic acid, while the sequence of nitrogenous bases stores the information. The most common nitrogenous bases are adenine , cytosine , guanine , thymine , and uracil . The nitrogenous bases of each strand of a nucleic acid will form hydrogen bonds with certain other nitrogenous bases in a complementary strand of nucleic acid. Adenine binds with thymine and uracil, thymine binds only with adenine, and cytosine and guanine can bind only with one another. Adenine, thymine, and uracil contain two hydrogen bonds, while hydrogen bonds formed between cytosine and guanine are three. Aside from

9384-410: The term may or may not include ions that satisfy this criterion. In quantum physics , organic chemistry , and biochemistry , the distinction from ions is dropped and molecule is often used when referring to polyatomic ions . A molecule may be homonuclear , that is, it consists of atoms of one chemical element , e.g. two atoms in the oxygen molecule (O 2 ); or it may be heteronuclear ,

9486-652: The ultimate particle of oxygen and the ultimate particle of nitrogen were 6, then the strength of the force would be divided accordingly, and similarly for the other combinations of ultimate particles. Amedeo Avogadro created the word "molecule". His 1811 paper "Essay on Determining the Relative Masses of the Elementary Molecules of Bodies", he essentially states, i.e. according to Partington 's A Short History of Chemistry , that: The smallest particles of gases are not necessarily simple atoms, but are made up of

9588-400: The understanding of tissues and organs as well as organism structure and function. Biochemistry is closely related to molecular biology , the study of the molecular mechanisms of biological phenomena. Much of biochemistry deals with the structures, functions, and interactions of biological macromolecules such as proteins , nucleic acids , carbohydrates , and lipids . They provide

9690-409: The universe is composed of atoms and voids . Circa 450 BC Empedocles imagined fundamental elements ( fire ( [REDACTED] ), earth ( [REDACTED] ), air ( [REDACTED] ), and water ( [REDACTED] )) and "forces" of attraction and repulsion allowing the elements to interact. A fifth element, the incorruptible quintessence aether , was considered to be the fundamental building block of

9792-432: The vaporization/sublimation of such materials does produce separate molecules where electrons are still transferred fully enough for the bonds to be considered ionic rather than covalent. Most molecules are far too small to be seen with the naked eye, although molecules of many polymers can reach macroscopic sizes, including biopolymers such as DNA . Molecules commonly used as building blocks for organic synthesis have

9894-425: The waste product carbon dioxide , generating another reducing equivalent as NADH . The two molecules acetyl-CoA (from one molecule of glucose) then enter the citric acid cycle , producing two molecules of ATP, six more NADH molecules and two reduced (ubi)quinones (via FADH 2 as enzyme-bound cofactor), and releasing the remaining carbon atoms as carbon dioxide. The produced NADH and quinol molecules then feed into

9996-474: The α-keto acid skeleton, and then an amino group is added, often via transamination . The amino acids may then be linked together to form 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 tactics have evolved in different animals, depending on

10098-700: Was initiated by Hiroaki Kitano , supported by a funding from the Japanese New Energy and Industrial Technology Development Organization . The meeting that initiated development of the Systems Biology Graphical Notation took place on February 11–12, 2006, at the National Institute of Advanced Industrial Science and Technology (AIST), in Tokyo, Japan. The first specification of SBGN Process Description language – then called Process Diagrams –

10200-516: Was learning the Dalton hook-and-eye bonding method , which was the mainstream description of bonds between atoms at the time. Pauling, however, was not satisfied with this method and looked to the newly emerging field of quantum physics for a new method. In 1926, French physicist Jean Perrin received the Nobel Prize in physics for proving, conclusively, the existence of molecules. He did this by calculating

10302-522: Was released on August 23, 2008 (Level 1 Version 1). Corrections of the document were released on September 1, 2009 (Level 1 Version 1.1), October 3, 2010 (Level 1 Version 1.2) and February 14, 2011 (Level 1 Version 1.3). The first specification of SBGN Entity relationship language was released on September 1, 2009 (Level 1 Version 1). Corrections of the document were released on October 6, 2010 (Level 1 Version 1.1) and April 14, 2011 (Level 1 Version 1.2). The first specification of SBGN Activity Flow language

10404-465: Was released on September 1, 2009. SBGN editors work in developing coherent specification documents. Below is a list of former SBGN editors and dates active: Biochemical Biochemistry or biological chemistry is the study of chemical processes within and relating to living organisms . A sub-discipline of both chemistry and biology , biochemistry may be divided into three fields: structural biology , enzymology , and metabolism . Over

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