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101-644: SYBR Green finds usage in several areas of biochemistry and molecular biology . It is used as a dye for the quantification of double stranded DNA in some methods of quantitative PCR . It is also used to visualise DNA in gel electrophoresis . Higher concentrations of SYBR Green can be used to stain agarose gels in order to visualise the DNA present. In addition to labelling pure nucleic acids, SYBR Green can also be used for labelling of DNA within cells for flow cytometry and fluorescence microscopy . In these cases RNase treatment may be required to reduce background from RNA in

202-628: 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

303-433: 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

404-467: A double displacement reaction , the anions and cations of two compounds switch places and form two entirely different compounds. These reactions are in the general form: AB + CD ⟶ AD + CB {\displaystyle {\ce {AB + CD->AD + CB}}} For example, when barium chloride (BaCl 2 ) and magnesium sulfate (MgSO 4 ) react, the SO 4 anion switches places with

505-434: A first-order reaction , which could be the disintegration of a substance A, is given by: Its integration yields: Here k is the first-order rate constant, having dimension 1/time, [A]( t ) is the concentration at a time t and [A] 0 is the initial concentration. The rate of a first-order reaction depends only on the concentration and the properties of the involved substance, and the reaction itself can be described with

606-736: A single displacement reaction , a single uncombined element replaces another in a compound; in other words, one element trades places with another element in a compound These reactions come in the general form of: A + BC ⟶ AC + B {\displaystyle {\ce {A + BC->AC + B}}} One example of a single displacement reaction is when magnesium replaces hydrogen in water to make solid magnesium hydroxide and hydrogen gas: Mg + 2 H 2 O ⟶ Mg ( OH ) 2 ↓ + H 2 ↑ {\displaystyle {\ce {Mg + 2H2O->Mg(OH)2 (v) + H2 (^)}}} In

707-623: A "vital force" and distinguished from inorganic materials. This separation was ended however by the synthesis of urea from inorganic precursors by Friedrich Wöhler in 1828. Other chemists who brought major contributions to organic chemistry include Alexander William Williamson with his synthesis of ethers and Christopher Kelk Ingold , who, among many discoveries, established the mechanisms of substitution reactions . The general characteristics of chemical reactions are: Chemical equations are used to graphically illustrate chemical reactions. They consist of chemical or structural formulas of

808-526: A characteristic half-life . More than one time constant is needed when describing reactions of higher order. The temperature dependence of the rate constant usually follows the Arrhenius equation : where E a is the activation energy and k B is the Boltzmann constant . One of the simplest models of reaction rate is the collision theory . More realistic models are tailored to a specific problem and include

909-557: A characteristic reaction rate at a given temperature and chemical concentration. Some reactions produce heat and are called exothermic reactions , while others may require heat to enable the reaction to occur, which are called endothermic reactions . Typically, reaction rates increase with increasing temperature because there is more thermal energy available to reach the activation energy necessary for breaking bonds between atoms. A reaction may be classified as redox in which oxidation and reduction occur or non-redox in which there

1010-399: 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

1111-434: 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,

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1212-406: 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

1313-468: 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

1414-399: A few molecules, usually one or two, because of the low probability for several molecules to meet at a certain time. The most important elementary reactions are unimolecular and bimolecular reactions. Only one molecule is involved in a unimolecular reaction; it is transformed by isomerization or a dissociation into one or more other molecules. Such reactions require the addition of energy in

1515-405: A fire-like element called "phlogiston", which was contained within combustible bodies and released during combustion . This proved to be false in 1785 by Antoine Lavoisier who found the correct explanation of the combustion as a reaction with oxygen from the air. Joseph Louis Gay-Lussac recognized in 1808 that gases always react in a certain relationship with each other. Based on this idea and

1616-404: 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

1717-438: A neutral radical . In the second case, both electrons of the chemical bond remain with one of the products, resulting in charged ions . Dissociation plays an important role in triggering chain reactions , such as hydrogen–oxygen or polymerization reactions. For bimolecular reactions, two molecules collide and react with each other. Their merger is called chemical synthesis or an addition reaction . Another possibility

1818-414: 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

1919-566: 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

2020-440: 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

2121-561: A study using the Ames test , which measures the ability of chemicals to cause mutations, when assayed at the same concentration SYBR Green I was on the order of 30 times less mutagenic than ethidium bromide. Biochemistry Biochemistry or biological chemistry is the study of chemical processes within and relating to living organisms . A sub-discipline of both chemistry and biology , biochemistry may be divided into three fields: structural biology , enzymology , and metabolism . Over

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2222-431: 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 ),

2323-428: Is a sub-discipline of chemistry that involves the chemical reactions of unstable and radioactive elements where both electronic and nuclear changes can occur. The substance (or substances) initially involved in a chemical reaction are called reactants or reagents . Chemical reactions are usually characterized by a chemical change , and they yield one or more products , which usually have properties different from

2424-412: 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

2525-407: 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,

2626-444: Is another way to identify a synthesis reaction. One example of a synthesis reaction is the combination of iron and sulfur to form iron(II) sulfide : 8 Fe + S 8 ⟶ 8 FeS {\displaystyle {\ce {8Fe + S8->8FeS}}} Another example is simple hydrogen gas combined with simple oxygen gas to produce a more complex substance, such as water. A decomposition reaction

2727-424: 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

2828-559: Is endothermic at low temperatures, becoming less so with increasing temperature. Δ H ° is zero at 1855  K , and the reaction becomes exothermic above that temperature. Changes in temperature can also reverse the direction tendency of a reaction. For example, the water gas shift reaction is favored by low temperatures, but its reverse is favored by high temperatures. The shift in reaction direction tendency occurs at 1100 K . Reactions can also be characterized by their internal energy change, which takes into account changes in

2929-499: Is no oxidation and reduction occurring. Most simple redox reactions may be classified as a combination, decomposition, or single displacement reaction. Different chemical reactions are used during chemical synthesis in order to obtain the desired product. In biochemistry , a consecutive series of chemical reactions (where the product of one reaction is the reactant of the next reaction) form metabolic pathways . These reactions are often catalyzed by protein enzymes . Enzymes increase

3030-421: 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

3131-508: 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

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3232-427: Is released. Typical examples of exothermic reactions are combustion , precipitation and crystallization , in which ordered solids are formed from disordered gaseous or liquid phases. In contrast, in endothermic reactions, heat is consumed from the environment. This can occur by increasing the entropy of the system, often through the formation of gaseous or dissolved reaction products, which have higher entropy. Since

3333-537: Is that only a portion of one molecule is transferred to the other molecule. This type of reaction occurs, for example, in redox and acid-base reactions. In redox reactions, the transferred particle is an electron, whereas in acid-base reactions it is a proton. This type of reaction is also called metathesis . for example Most chemical reactions are reversible; that is, they can and do run in both directions. The forward and reverse reactions are competing with each other and differ in reaction rates . These rates depend on

3434-506: 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

3535-492: 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

3636-409: 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),

3737-413: Is used in retro reactions. The elementary reaction is the smallest division into which a chemical reaction can be decomposed, it has no intermediate products. Most experimentally observed reactions are built up from many elementary reactions that occur in parallel or sequentially. The actual sequence of the individual elementary reactions is known as reaction mechanism . An elementary reaction involves

3838-532: Is when a more complex substance breaks down into its more simple parts. It is thus the opposite of a synthesis reaction and can be written as AB ⟶ A + B {\displaystyle {\ce {AB->A + B}}} One example of a decomposition reaction is the electrolysis of water to make oxygen and hydrogen gas: 2 H 2 O ⟶ 2 H 2 + O 2 {\displaystyle {\ce {2H2O->2H2 + O2}}} In

3939-491: The Le Chatelier's principle . For example, an increase in pressure due to decreasing volume causes the reaction to shift to the side with fewer moles of gas. The reaction yield stabilizes at equilibrium but can be increased by removing the product from the reaction mixture or changed by increasing the temperature or pressure. A change in the concentrations of the reactants does not affect the equilibrium constant but does affect

4040-415: The atoms are rearranged and the reaction is accompanied by an energy change as new products are generated. Classically, chemical reactions encompass changes that only involve the positions of electrons in the forming and breaking of chemical bonds between atoms , with no change to the nuclei (no change to the elements present), and can often be described by a chemical equation . Nuclear chemistry

4141-501: 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: Chemical reaction A chemical reaction is a process that leads to the chemical transformation of one set of chemical substances to another. When chemical reactions occur,

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4242-454: The contact process in the 1880s, and the Haber process was developed in 1909–1910 for ammonia synthesis. From the 16th century, researchers including Jan Baptist van Helmont , Robert Boyle , and Isaac Newton tried to establish theories of experimentally observed chemical transformations. The phlogiston theory was proposed in 1667 by Johann Joachim Becher . It postulated the existence of

4343-416: 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

4444-424: 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

4545-549: 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

4646-471: The stoichiometry , the number of atoms of each species should be the same on both sides of the equation. This is achieved by scaling the number of involved molecules (A, B, C and D in a schematic example below) by the appropriate integers a, b, c and d . More elaborate reactions are represented by reaction schemes, which in addition to starting materials and products show important intermediates or transition states . Also, some relatively minor additions to

4747-558: The transition state theory , the calculation of the potential energy surface , the Marcus theory and the Rice–Ramsperger–Kassel–Marcus (RRKM) theory . In a synthesis reaction, two or more simple substances combine to form a more complex substance. These reactions are in the general form: A + B ⟶ AB {\displaystyle {\ce {A + B->AB}}} Two or more reactants yielding one product

4848-399: 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,

4949-481: The 17th century, Johann Rudolph Glauber produced hydrochloric acid and sodium sulfate by reacting sulfuric acid and sodium chloride . With the development of the lead chamber process in 1746 and the Leblanc process , allowing large-scale production of sulfuric acid and sodium carbonate , respectively, chemical reactions became implemented into the industry. Further optimization of sulfuric acid technology resulted in

5050-555: The 2Cl anion, giving the compounds BaSO 4 and MgCl 2 . Another example of a double displacement reaction is the reaction of lead(II) nitrate with potassium iodide to form lead(II) iodide and potassium nitrate : Pb ( NO 3 ) 2 + 2 KI ⟶ PbI 2 ↓ + 2 KNO 3 {\displaystyle {\ce {Pb(NO3)2 + 2KI->PbI2(v) + 2KNO3}}} According to Le Chatelier's Principle , reactions may proceed in

5151-512: 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

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5252-489: 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

5353-481: 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

5454-416: 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

5555-434: 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

5656-878: 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 ,

5757-408: The atomic theory of John Dalton , Joseph Proust had developed the law of definite proportions , which later resulted in the concepts of stoichiometry and chemical equations . Regarding the organic chemistry , it was long believed that compounds obtained from living organisms were too complex to be obtained synthetically . According to the concept of vitalism , organic matter was endowed with

5858-427: The best characteristic for PCR methods. The second best was TOPhBu, which is close in values to Sybr Green. SYBR Green I is marketed as a replacement for ethidium bromide , a potential human mutagen , as both safer to work with and free from the complex waste disposal issues of ethidium bromide. However any small molecule capable of binding DNA with high affinity is a possible carcinogen , including SYBR Green. In

5959-464: 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

6060-513: 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 ,

6161-539: 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

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6262-490: 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

6363-651: 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

6464-403: The cells. A comprehensive Study of Thiazole-Orange-Based DNA Dyes were published, involving SYBR Safe, SYBR Green, PicoGreen, SYTO-16, SYTO-9 and a new derivative TOPhBu. Here, the synthesis of these compounds are published and characterised spectro-scopically to quantify their fluorescence enhancement upon binding to double-stranded DNA. The ability of the dyes to detect DNA at low concentrations

6565-528: The concentration and therefore change with the time of the reaction: the reverse rate gradually increases and becomes equal to the rate of the forward reaction, establishing the so-called chemical equilibrium. The time to reach equilibrium depends on parameters such as temperature, pressure, and the materials involved, and is determined by the minimum free energy . In equilibrium, the Gibbs free energy of reaction must be zero. The pressure dependence can be explained with

6666-507: 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

6767-587: 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

6868-492: 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

6969-511: 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

7070-550: 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

7171-455: The entropy term in the free-energy change increases with temperature, many endothermic reactions preferably take place at high temperatures. On the contrary, many exothermic reactions such as crystallization occur preferably at lower temperatures. A change in temperature can sometimes reverse the sign of the enthalpy of a reaction, as for the carbon monoxide reduction of molybdenum dioxide : This reaction to form carbon dioxide and molybdenum

7272-405: The entropy, volume and chemical potentials . The latter depends, among other things, on the activities of the involved substances. The speed at which reactions take place is studied by reaction kinetics . The rate depends on various parameters, such as: Several theories allow calculating the reaction rates at the molecular level. This field is referred to as reaction dynamics. The rate v of

7373-426: 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

7474-469: 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

7575-406: The equilibrium position. Chemical reactions are determined by the laws of thermodynamics . Reactions can proceed by themselves if they are exergonic , that is if they release free energy. The associated free energy change of the reaction is composed of the changes of two different thermodynamic quantities, enthalpy and entropy : Reactions can be exothermic , where Δ H is negative and energy

7676-448: 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

7777-448: The form of heat or light. A typical example of a unimolecular reaction is the cis–trans isomerization , in which the cis-form of a compound converts to the trans-form or vice versa. In a typical dissociation reaction, a bond in a molecule splits ( ruptures ) resulting in two molecular fragments. The splitting can be homolytic or heterolytic . In the first case, the bond is divided so that each product retains an electron and becomes

7878-407: The forward or reverse direction until they end or reach equilibrium . Reactions that proceed in the forward direction (from left to right) to approach equilibrium are often called spontaneous reactions , that is, Δ G {\displaystyle \Delta G} is negative, which means that if they occur at constant temperature and pressure, they decrease the Gibbs free energy of

7979-463: 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

8080-479: 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

8181-515: 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

8282-448: 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

8383-463: 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

8484-458: 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

8585-513: The rates of biochemical reactions, so that metabolic syntheses and decompositions impossible under ordinary conditions can occur at the temperature and concentrations present within a cell . The general concept of a chemical reaction has been extended to reactions between entities smaller than atoms, including nuclear reactions , radioactive decays and reactions between elementary particles , as described by quantum field theory . Chemical reactions such as combustion in fire, fermentation and

8686-404: The reactants on the left and those of the products on the right. They are separated by an arrow (→) which indicates the direction and type of the reaction; the arrow is read as the word "yields". The tip of the arrow points in the direction in which the reaction proceeds. A double arrow (⇌) pointing in opposite directions is used for equilibrium reactions . Equations should be balanced according to

8787-421: The reactants. Reactions often consist of a sequence of individual sub-steps, the so-called elementary reactions , and the information on the precise course of action is part of the reaction mechanism . Chemical reactions are described with chemical equations , which symbolically present the starting materials, end products, and sometimes intermediate products and reaction conditions. Chemical reactions happen at

8888-410: 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

8989-457: The reaction can be indicated above the reaction arrow; examples of such additions are water, heat, illumination, a catalyst , etc. Similarly, some minor products can be placed below the arrow, often with a minus sign. Retrosynthetic analysis can be applied to design a complex synthesis reaction. Here the analysis starts from the products, for example by splitting selected chemical bonds, to arrive at plausible initial reagents. A special arrow (⇒)

9090-477: The reaction. They require less energy to proceed in the forward direction. Reactions are usually written as forward reactions in the direction in which they are spontaneous. Examples: Reactions that proceed in the backward direction to approach equilibrium are often called non-spontaneous reactions , that is, Δ G {\displaystyle \Delta G} is positive, which means that if they occur at constant temperature and pressure, they increase

9191-688: The reduction of ores to metals were known since antiquity. Initial theories of transformation of materials were developed by Greek philosophers, such as the Four-Element Theory of Empedocles stating that any substance is composed of the four basic elements – fire, water, air and earth. In the Middle Ages , chemical transformations were studied by alchemists . They attempted, in particular, to convert lead into gold , for which purpose they used reactions of lead and lead-copper alloys with sulfur . The artificial production of chemical substances already

9292-413: 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

9393-559: 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

9494-585: 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

9595-476: 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

9696-683: 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

9797-400: 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

9898-425: 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

9999-474: 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

10100-456: Was a central goal for medieval alchemists. Examples include the synthesis of ammonium chloride from organic substances as described in the works (c. 850–950) attributed to Jābir ibn Ḥayyān , or the production of mineral acids such as sulfuric and nitric acids by later alchemists, starting from c. 1300. The production of mineral acids involved the heating of sulfate and nitrate minerals such as copper sulfate , alum and saltpeter . In

10201-399: Was evaluated using two new metrics, absolute fluorescence enhancement (AFE) and relativefluorescence enhancement (RFE). They were tested in qPCR experiments showing some important differences in the sensitivity and qPCR efficiency, which facilitate the DNA marker selection for analytical purposes. This study showed that Sybr Green exhibits the highest fluorescence enhancement (AFE) and provided

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