reaction-formation: see defense mechanism.

reaction, chemical: see chemical reaction.

reaction rate: see chemical reaction.

polymerase chain reaction (PCR), laboratory process in which a particular DNA segment from a mixture of DNA chains is rapidly replicated, producing a large, readily analyzed sample of a piece of DNA; the process is sometimes called DNA amplification.

The Process

In PCR, DNA (see nucleic acid) is immersed in a solution containing the enzyme DNA polymerase, unattached nucleotide bases (the subunits that DNA is composed of), and "primers," short sequences of nucleotides designed to bind with an end of the desired DNA segment. Two primers are used: one primer binds at one end of the desired segment on one of the two paired DNA strands, and the other primer binds at the other end but on the other strand. The solution is heated to break the bonds between the strands of the DNA. When the solution cools, the primers bind to the separated strands, and DNA polymerase quickly builds a new strand by joining the free nucleotide bases to the primers. When this process is repeated, a strand that was formed with one primer binds to the other primer, resulting in a new strand that is restricted solely to the desired segment. Thus the region of DNA between the primers is selectively replicated. Further repetitions of the process can produce billions of copies of a small piece of DNA in several hours.

Development and Applications

PCR was developed in 1985 by Kary B. Mullis, who was awarded the 1993 Nobel Prize in chemistry for his work. It is used in DNA fingerprinting and in medical tests to identify diseases from the infectious agent's DNA. In forensic use, the test can be used to compare two samples of DNA, usually by looking at matches (or mismatches) of six inherited traits (e.g., hair curliness) from each of the samples. Each trait is controlled by a single gene, each gene having at least two forms, or alleles, resulting in 21 combinations of these alleles, some of them very rare. A nonmatch conclusively excludes a suspect. PCR also is used in taxonomic classification to help show evolutionary relationships between organisms on the molecular level. It has the advantage of being able to be used even when only very small samples, such as tiny pieces of preserved tissue from extinct animals, are available.

chemical reaction, process by which one or more substances may be transformed into one or more new substances. Energy is released or is absorbed, but no loss in total molecular weight occurs. When, for example, water is decomposed, its molecules, each of which consists of one atom of oxygen and two of hydrogen, are broken down; the hydrogen atoms then combine in pairs to form hydrogen molecules and the oxygen atoms to form oxygen molecules. In a chemical reaction, substances lose their characteristic properties. Water, for example, a liquid which neither burns nor supports combustion, is decomposed to yield flammable hydrogen and combustion-supporting oxygen. In some reactions heat is given off (exothermic reactions), and in others heat is absorbed (endothermic reactions). Furthermore, the new substances formed differ from the original substances in the energy they contain. Chemical reactions are classified according to the kind of change that takes place. When a compound, which consists of two or more elements or groups of elements, is broken down into its constituents, the reaction is called simple decomposition. When two compounds react with one another to form two new compounds, the reaction is called double decomposition. In so-called replacement reactions the place of one of the elements in a compound is taken by another element reacting with the compound. When elements combine to form a compound, the reaction is termed chemical combination. Oxidation and reduction reactions are extremely important. Reversible reactions are those in which the chemical change taking place may be paralleled by another change back to the original substances. The rates at which chemical reactions proceed depend upon various factors, e.g., upon temperature, pressure, and the concentration of the substances involved and, sometimes, upon the use of a chemical called a catalyst. In some chemical reactions, such as that of photographic film, light is an important factor. The changes taking place in a chemical reaction are represented by a chemical equation. An element's activity, i.e., its tendency to enter into compounds, varies from one element to another.

chain reaction, self-sustaining reaction that, once started, continues without further outside influence. Proper conditions for a chain reaction depend not only on various external factors, such as temperature, but also on the quantity and shape of the substance undergoing the reaction. A chain reaction can be of various types, but nuclear chain reactions are the best known. A line of dominoes falling after the first one has been pushed is an example of a mechanical chain reaction; a pile of wood burning after it has been kindled is an example of a chemical chain reaction. In the latter case each piece of wood, as it burns, must release enough heat to raise nearby pieces to the kindling point. The wood, therefore, must be piled close enough together so that not too much heat is lost to the surrounding air. The conditions for a nuclear chain reaction can be understood by analogy. In the case of the fission of a nucleus, the reaction is begun by the absorption of a slow neutron. Each fission produces two or three fast neutrons. In order to sustain a chain reaction, a sample must be large enough to slow the neutrons so that one can be captured by another nucleus and produce a second fission. The sample must also be compact to prevent neutrons from escaping. The minimum quantity of a fissionable material necessary to sustain a nuclear chain reaction is called the critical mass. In a nuclear fission bomb, a chain reaction is started by forcing together two or more samples of fissionable material, each of less than critical mass, to form one sample of supercritical mass. The number of subsequent fissions produced by a single fission is always greater than one. The total number of fissions increases rapidly (exponentially) with time. In a fission reactor, the number of subsequent fissions for each fission must be exactly one. If the rate is less, the chain reaction will stop; if greater, it will soon grow out of control. In one type of fission reactor, a combination of fuel rods and control rods is moved in or out of a solid block of moderating material to control the reaction rate. In another type of reactor, the temperature of a liquid moderator controls the reaction. See also nuclear energy; nuclear reactor.

or redox

Any chemical reaction in which electrons are transferred. Addition of hydrogen or electrons is reduction, and removal of hydrogen or electrons is oxidation (originally applied to combination with oxygen but now including transfer of hydrogen or electrons). The processes always occur simultaneously: one substance is oxidized by the other, which it reduces. The conditions of the substances before and after are called oxidation states, to which numbers are given and with which calculations can be made. (Valence is a similar but not identical concept.) The chemical equation that describes the electron transfer can be written as two separate half reactions that can in theory be carried out in separate compartments of an electrolytic cell (see electrolysis), with electrons flowing through a wire connecting the two. Strong oxidizing agents include fluorine, ozone, and oxygen itself; strong reducing agents include alkali metals such as sodium and lithium.

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Amount of heat that must be added or removed during a chemical reaction to keep all substances involved at the same temperature. If it is positive (heat must be added), the reaction is endothermic; if it is negative (heat is given off), the reaction is exothermic. Accurate heat of reaction values are needed for proper design of equipment used in chemical processes; they are usually estimated from compiled tables of thermodynamics data (heats of formation and heats of combustion of many known materials). The activation energy is unrelated to the heat of reaction.

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Speed at which a chemical reaction proceeds, in terms of amount of product formed or amount of reactant consumed per unit of time. The reaction rate depends on the nature of the reacting substances and the type of chemical change, as well as temperature and pressure, especially if gases are involved. In general, the reactions of ions occur very rapidly, but those in which covalent bonds are formed or broken are slower. Catalysts usually accelerate reaction rates. The prediction, measurement, and interpretation of reaction rates are subjects of the branch of chemistry known as chemical kinetics. Seealso mass action, law of.

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Any chemical process in which substances are changed into different ones, with different properties, as distinct from changing position or form (phase). Chemical reactions involve the rupture or rearrangement of the bonds holding atoms together (see bonding), never atomic nuclei. The total mass and number of atoms of all reactants equals those of all products, and energy is almost always consumed or liberated (see heat of reaction). The speed of reactions varies (see reaction rate). Understanding their mechanisms lets chemists alter reaction conditions to optimize the rate or the amount of a given product; the reversibility of the reaction and the presence of competing reactions and intermediate products complicate these studies. Reactions can be syntheses, decompositions, or rearrangements, or they can be additions, eliminations, or substitutions. Examples include oxidation-reduction, polymerization, ionization (see ion), combustion (burning), hydrolysis, and acid-base reactions.

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Laboratory technique used to make numerous copies of specific DNA segments quickly and accurately. These are needed for various experiments and procedures in molecular biology, forensic analysis (DNA fingerprinting), evolutionary biology (to amplify DNA fragments found in ancient specimens), and medicine (to diagnose genetic disease or detect low viral counts). Invented by Kary Mullis, PCR requires a DNA template (as little as one molecule) to copy, nucleotides to build the copies, and the enzyme DNA polymerase to catalyze the formation of bonds between the nucleotide monomers. Each three-step cycle (separating the two strands of the DNA double helix, marking the ends of the segment to be copied, and catalyzing the formation of bonds), which takes only minutes to complete, doubles the number of DNA strands present in the reaction medium. Repetition of this cycle many times results in an exponential increase in the amount of DNA.

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Chemical reaction initiated by absorption of energy in the form of visible (light), ultraviolet, or infrared radiation. Primary photochemical processes occur as an immediate result, and secondary processes may follow. The most important example is photosynthesis. Vision depends on photochemical reactions that occur in the eye (see retina; rhodopsin). In photographic film and paper, light activates their silver salts to a state that is easy to reduce to metallic silver grains during development. Bleaching of laundry, tanning of human skin, formation of Earth's ozone layer, and many industrial reactions are also photochemical. Certain air pollutants (see smog) become more reactive and form noxious compounds in photochemical reactions.

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Process yielding products that initiate further processes of the same kind. Nuclear chain reactions are a series of nuclear fissions initiated by neutrons produced in a preceding fission. A critical mass, large enough to allow more than one fission-produced neutron to be captured, is necessary for the chain reaction to be self-sustaining. Uncontrolled chain reactions, as in an atomic bomb, occur when large numbers of neutrons are present and the reactions multiply very quickly. Nuclear reactors control their reactions through the careful distribution of the fissionable material and insertion of neutron-absorbing materials.

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