Carbon cycle

From Wikipedia, the free encyclopedia

This diagram of the fast carbon cycle shows the movement of carbon between land, atmosphere, and oceans in billions of tons of carbon per year. Yellow numbers are natural fluxes, red are human contributions in billions of tons of carbon per year. White numbers indicate stored carbon.

The carbon cycle is the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of the Earth. Along with the nitrogen cycle and the water cycle, the carbon cycle comprises a sequence of events that are key to making the Earth capable of sustaining life; it describes the movement of carbon as it is recycled and reused throughout the biosphere.

The global carbon budget is the balance of the exchanges (incomes and losses) of carbon between the carbon reservoirs or between one specific loop (e.g., atmosphere <-> biosphere) of the carbon cycle. An examination of the carbon budget of a pool or reservoir can provide information about whether the pool or reservoir is functioning as a source or sink for carbon dioxide.

The carbon cycle was initially discovered by Joseph Priestley and Antoine Lavoisier, and popularized by Humphry Davy.^[1]

Relevance for the global climate

Carbon-based molecules are crucial for life on Earth, because it is the main component of biological compounds. Carbon is also a major component of many minerals. Carbon also exists in various forms in the atmosphere. Carbon dioxide (CO₂) is partly responsible for the greenhouse effect and is the most important human-contributed greenhouse gas.^[2]

In the past two centuries, human activities have seriously altered the global carbon cycle, most significantly in the atmosphere. Although carbon dioxide levels have changed naturally over the past several thousand years, human emissions of carbon dioxide into the atmosphere exceed natural fluctuations.^[2] Changes in the amount of atmospheric CO₂ are considerably altering weather patterns and indirectly influencing oceanic chemistry. Records from ice cores have shown that, although global temperatures can change without changes in atmospheric CO₂ levels, CO₂ levels cannot change significantly without affecting global temperatures. Current carbon dioxide levels in the atmosphere exceed measurements from the last 420,000 years and levels are rising faster than ever recorded,^[3] making it of critical importance to better understand how the carbon cycle works and what its effects are on the global climate.^[2]

Main components

Carbon pools in the major reservoirs on earth.^[2]

Pool	Quantity (gigatons)
Atmosphere	720
Oceans (total)	38,400
Total inorganic	37,400
Total organic	1,000
Surface layer	670
Deep layer	36,730
Lithosphere
Sedimentary carbonates	> 60,000,000
Kerogens	15,000,000
Terrestrial biosphere (total)	2,000
Living biomass	600 - 1,000
Dead biomass	1,200
Aquatic biosphere	1 - 2
Fossil fuels (total)	4,130
Coal	3,510
Oil	230
Gas	140
Other (peat)	250

The global carbon cycle is now usually divided into the following major reservoirs of carbon interconnected by pathways of exchange:

• The atmosphere
• The terrestrial biosphere
• The oceans, including dissolved inorganic carbon and living and non-living marine biota
• The sediments, including fossil fuels, fresh water systems and non-living organic material, such as soil carbon
• The Earth's interior, carbon from the Earth's mantle and crust. These carbon stores interact with the other components through geological processes

The carbon exchanges between reservoirs occur as the result of various chemical, physical, geological, and biological processes. The ocean contains the largest active pool of carbon near the surface of the Earth.^[2] The natural flows of carbon between the atmosphere, ocean, and sediments is fairly balanced, so that carbon levels would be roughly stable without human influence.^[4]

Atmosphere

Carbon in the earth's atmosphere exists in two main forms: carbon dioxide and methane. Both of these gases absorb and retain heat in the atmosphere and are partially responsible for the greenhouse effect. Methane produces a large greenhouse effect per volume as compared to carbon dioxide, but it exists in much lower concentrations and is more short-lived than carbon dioxide, making carbon dioxide the more important greenhouse gas of the two.^[5]
Carbon dioxide leaves the atmosphere through photosynthesis, thus entering the terrestrial and oceanic biospheres. Carbon dioxide also dissolves directly from the atmosphere into bodies of water (oceans, lakes, etc.), as well as dissolving in precipitation as raindrops fall through the atmosphere. When dissolved in water, carbon dioxide reacts with water molecules and forms carbonic acid, which contributes to ocean acidity. It can then be absorbed by rocks through weathering. It also can acidify other surfaces it touches or be washed into the ocean.^[6]

Human activity over the past two centuries has significantly increased the amount of carbon in the atmosphere, mainly in the form of carbon dioxide, both by modifying ecosystems' ability to extract carbon dioxide from the atmosphere and by emitting it directly, e.g., by burning fossil fuels and manufacturing concrete.^[2]

Terrestrial biosphere

The terrestrial biosphere includes the organic carbon in all land-living organisms, both alive and dead, as well as carbon stored in soils. About 500 gigatons of carbon are stored above ground in plants and other living organisms,^[4] while soil holds approximately 1,500 gigatons of carbon.^[7] 

 

Most carbon in the terrestrial biosphere is organic carbon, while about a third of soil carbon is stored in inorganic forms, such as calcium carbonate.^[8] Organic carbon is a major component of all organisms living on earth. Autotrophs extract it from the air in the form of carbon dioxide, converting it into organic carbon, while heterotrophs receive carbon by consuming other organisms.

A portable soil respiration system measuring soil CO₂ flux

Because carbon uptake in the terrestrial biosphere is dependent on biotic factors, it follows a diurnal and seasonal cycle. In CO₂ measurements, this cycle is often called a Keeling curve^{[citation needed]}. It is strongest in the northern hemisphere, because this hemisphere has more land mass than the southern hemisphere and thus more room for ecosystems to absorb and emit carbon.

Carbon leaves the terrestrial biosphere in several ways and on different time scales. The combustion or respiration of organic carbon releases it rapidly into the atmosphere. It can also be exported into the oceans through rivers or remain sequestered in soils in the form of inert carbon. Carbon stored in soil can remain there for up to thousands of years before being washed into rivers by erosion or released into the atmosphere through soil respiration. Between 1989 and 2008 soil respiration increased by about 0.1% per year.^[9] In 2008, the global total of CO₂ released from the soil reached roughly 98 billion tonnes, about 10 times more carbon than humans are now putting into the atmosphere each year. There are a few plausible explanations for this trend, but the most likely explanation is that increasing temperatures have increased rates of decomposition of soil organic matter, which has increased the flow of CO₂. The length of carbon sequestering in soil is dependent on local climatic conditions and thus changes in the course of climate change. From pre-industrial era to 2010, the terrestrial biosphere represented a net source of atmospheric CO₂ prior to 1940, switching subsequently to a net sink.^[10]

Oceans

Oceans contain the greatest quantity of actively cycled carbon in this world and are second only to the lithosphere in the amount of carbon they store.^[2] The oceans' surface layer holds large amounts of dissolved organic carbon that is exchanged rapidly with the atmosphere. The deep layer's concentration of dissolved inorganic carbon (DIC) is about 15% higher than that of the surface layer.^[11] DIC is stored in the deep layer for much longer periods of time.^[4] Thermohaline circulation exchanges carbon between these two layers.^[2]
Carbon enters the ocean mainly through the dissolution of atmospheric carbon dioxide, which is converted into carbonate. It can also enter the oceans through rivers as dissolved organic carbon. It is converted by organisms into organic carbon through photosynthesis and can either be exchanged throughout the food chain or precipitated into the ocean's deeper, more carbon rich layers as dead soft tissue or in shells as calcium carbonate. It circulates in this layer for long periods of time before either being deposited as sediment or, eventually, returned to the surface waters through thermohaline circulation.^[4]

Oceanic absorption of CO₂ is one of the most important forms of carbon sequestering limiting the human-caused rise of carbon dioxide in the atmosphere. However, this process is limited by a number of factors. Because the rate of CO₂ dissolution in the ocean is dependent on the weathering of rocks and this process takes place slower than current rates of human greenhouse gas emissions, ocean CO₂ uptake will decrease in the future.^[2] CO₂ absorption also makes water more acidic, which affects ocean biosystems. The projected rate of increasing oceanic acidity could slow the biological precipitation of calcium carbonates, thus decreasing the ocean's capacity to absorb carbon dioxide.^[12][13]

Geological carbon cycle

The geologic component of the carbon cycle operates slowly in comparison to the other parts of the global carbon cycle. It is one of the most important determinants of the amount of carbon in the atmosphere, and thus of global temperatures.^[14]

Most of the earth's carbon is stored inertly in the earth's lithosphere.^[2] Much of the carbon stored in the earth's mantle was stored there when the earth formed.^[15] Some of it was deposited in the form of organic carbon from the biosphere.^[16] Of the carbon stored in the geosphere, about 80% is limestone and its derivatives, which form from the sedimentation of calcium carbonate stored in the shells of marine organisms. The remaining 20% is stored as kerogens formed through the sedimentation and burial of terrestrial organisms under high heat and pressure. Organic carbon stored in the geosphere can remain there for millions of years.^[14]

Carbon can leave the geosphere in several ways. Carbon dioxide is released during the metamorphosis of carbonate rocks when they are subducted into the earth's mantle. This carbon dioxide can be released into the atmosphere and ocean through volcanoes and hotspots.^[15] It can also be removed by humans through the direct extraction of kerogens in the form of fossil fuels. After extraction, fossil fuels are burned to release energy, thus emitting the carbon they store into the atmosphere.

Human influence

Human activity since the industrial era has changed the balance in the natural carbon cycle. Units are in gigatons.^[4]

Since the industrial revolution, human activity has modified the carbon cycle by changing its component's functions and directly adding carbon to the atmosphere.^[2]

The largest and most direct human influence on the carbon cycle is through direct emissions from burning fossil fuels, which transfers carbon from the geosphere into the atmosphere. Humans also influence the carbon cycle indirectly by changing the terrestrial and oceanic biosphere.

Over the past several centuries, human-caused land use and land cover change (LUCC) has led to the loss of biodiversity, which lowers ecosystems' resilience to environmental stresses and decreases their ability to remove carbon from the atmosphere. More directly, it often leads to the release of carbon from terrestrial ecosystems into the atmosphere. Deforestation for agricultural purposes removes forests, which hold large amounts of carbon, and replaces them, generally with agricultural or urban areas. Both of these replacement land cover types store comparatively small amounts of carbon, so that the net product of the process is that more carbon stays in the atmosphere.

Other human-caused changes to the environment change ecosystems' productivity and their ability to remove carbon from the atmosphere. Air pollution, for example, damages plants and soils, while many agricultural and land use practices lead to higher erosion rates, washing carbon out of soils and decreasing plant productivity.

Higher temperatures and CO₂ levels in the atmosphere increase decomposition rates in soil, thus returning CO₂ stored in plant material more quickly to the atmosphere.^{[citation needed]}

However, increased levels of CO₂ in the atmosphere can also lead to higher gross primary production. It increases photosynthesis rates by allowing plants to more efficiently use water, because they no longer need to leave their stomata open for such long periods of time in order to absorb the same amount of carbon dioxide. This type of carbon dioxide fertilization affects mainly C3 plants, because C4 plants can already concentrate CO₂ effectively.^{[citation needed]}

Humans also affect the oceanic carbon cycle. Current trends in climate change lead to higher ocean temperatures, thus modifying ecosystems. Also, acid rain and polluted runoff from agriculture and industry change the ocean's chemical composition. Such changes can have dramatic effects on highly sensitive ecosystems such as coral reefs, thus limiting the ocean's ability to absorb carbon from the atmosphere on a regional scale and reducing oceanic biodiversity globally.

Nuclear chemistry

From Wikipedia, the free encyclopedia

Nuclear chemistry is the subfield of chemistry dealing with radioactivity, nuclear processes, such as nuclear transmutation, and nuclear properties.

It is the chemistry of radioactive elements such as the actinides, radium and radon together with the chemistry associated with equipment (such as nuclear reactors) which are designed to perform nuclear processes. This includes the corrosion of surfaces and the behavior under conditions of both normal and abnormal operation (such as during an accident). An important area is the behavior of objects and materials after being placed into a nuclear waste storage or disposal site.

It includes the study of the chemical effects resulting from the absorption of radiation within living animals, plants, and other materials. The radiation chemistry controls much of radiation biology as radiation has an effect on living things at the molecular scale, to explain it another way the radiation alters the biochemicals within an organism, the alteration of the biomolecules then changes the chemistry which occurs within the organism, this change in chemistry then can lead to a biological outcome. As a result, nuclear chemistry greatly assists the understanding of medical treatments (such as cancer radiotherapy) and has enabled these treatments to improve.

It includes the study of the production and use of radioactive sources for a range of processes. These include radiotherapy in medical applications; the use of radioactive tracers within industry, science and the environment; and the use of radiation to modify materials such as polymers.^[1]

It also includes the study and use of nuclear processes in non-radioactive areas of human activity. For instance, nuclear magnetic resonance (NMR) spectroscopy is commonly used in synthetic organic chemistry and physical chemistry and for structural analysis in macromolecular chemistry.

History

After the discovery of X-rays by Wilhelm Röntgen, many scientists began to work on ionizing radiation. One of these was Henri Becquerel, who investigated the relationship between phosphorescence and the blackening of photographic plates. When Becquerel (working in France) discovered that, with no external source of energy, the uranium generated rays which could blacken (or fog) the photographic plate, radioactivity was discovered. Marie Curie (working in Paris) and her husband Pierre Curie isolated two new radioactive elements from uranium ore. They used radiometric methods to identify which stream the radioactivity was in after each chemical separation; they separated the uranium ore into each of the different chemical elements that were known at the time, and measured the radioactivity of each fraction. They then attempted to separate these radioactive fractions further, to isolate a smaller fraction with a higher specific activity (radioactivity divided by mass). In this way, they isolated polonium and radium. It was noticed in about 1901 that high doses of radiation could cause an injury in humans. Henri Becquerel had carried a sample of radium in his pocket and as a result he suffered a high localised dose which resulted in a radiation burn[6] this injury resulted in the biological properties of radiation being investigated, which in time resulted in the development of medical treatments.

Ernest Rutherford, working in Canada and England, showed that radioactive decay can be described by a simple equation (a linear first degree derivative equation, now called first order kinetics), implying that a given radioactive substance has a characteristic "half-life" (the time taken for the amount of radioactivity present in a source to diminish by half). He also coined the terms alpha, beta and gamma rays, he converted nitrogen into oxygen, and most importantly he supervised the students who did the Geiger–Marsden experiment (gold leaf experiment) which showed that the 'plum pudding model' of the atom was wrong. In the plum pudding model, proposed by J. J. Thomson in 1904, the atom is composed of electrons surrounded by a 'cloud' of positive charge to balance the electrons' negative charge. To Rutherford, the gold foil experiment implied that the positive charge was confined to a very small nucleus leading first to the Rutherford model, and eventually to the Bohr model of the atom, where the positive nucleus is surrounded by the negative electrons.

In 1934 Marie Curie's daughter (Irène Joliot-Curie) and her husband were the first to create artificial radioactivity: they bombarded boron with alpha particles to make the neutron-poor isotope nitrogen-13; this isotope emitted positrons.^[2] In addition, they bombarded aluminium and magnesium with neutrons to make new radioisotopes.

Main areas

Radiochemistry is the chemistry of radioactive materials, where radioactive isotopes of elements are used to study the properties and chemical reactions of non-radioactive isotopes (often within radiochemistry the absence of radioactivity leads to a substance being described as being inactive as the isotopes are stable).

Radiation chemistry

Radiation chemistry is the study of the chemical effects of radiation on matter; this is very different from radiochemistry as no radioactivity needs to be present in the material which is being chemically changed by the radiation. An example is the conversion of water into hydrogen gas and hydrogen peroxide.

Chemistry for nuclear power

Radiochemistry, radiation chemistry and nuclear chemical engineering play a very important role for uranium and thorium fuel precursors synthesis, starting from ores of these elements, fuel fabrication, coolant chemistry, fuel reprocessing, radioactive waste treatment and storage, monitoring of radioactive elements release during reactor operation and radioactive geological storage, etc. ^[3]

Study of nuclear reactions

A combination of radiochemistry and radiation chemistry is used to study nuclear reactions such as fission and fusion. Some early evidence for nuclear fission was the formation of a short-lived radioisotope of barium which was isolated from neutron irradiated uranium (¹³⁹Ba, with a half-life of 83 minutes and ¹⁴⁰Ba, with a half-life of 12.8 days, are major fission products of uranium). At the time, it was thought that this was a new radium isotope, as it was then standard radiochemical practice to use a barium sulfate carrier precipitate to assist in the isolation of radium.[7]. More recently, a combination of radiochemical methods and nuclear physics has been used to try to make new 'superheavy' elements; it is thought that islands of relative stability exist where the nuclides have half-lives of years, thus enabling weighable amounts of the new elements to be isolated. For more details of the original discovery of nuclear fission see the work of Otto Hahn.^[4]

The nuclear fuel cycle

This is the chemistry associated with any part of the nuclear fuel cycle, including nuclear reprocessing. The fuel cycle includes all the operations involved in producing fuel, from mining, ore processing and enrichment to fuel production (Front end of the cycle). It also includes the 'in-pile' behaviour (use of the fuel in a reactor) before the back end of the cycle. The back end includes the management of the used nuclear fuel in either a spent fuel pool or dry storage, before it is disposed of into an underground waste store or reprocessed.

Normal and abnormal conditions

The nuclear chemistry associated with the nuclear fuel cycle can be divided into two main areas, one area is concerned with operation under the intended conditions while the other area is concerned with maloperation conditions where some alteration from the normal operating conditions has occurred or (more rarely) an accident is occurring.

Reprocessing

Law

In the United States it is normal to use fuel once in a power reactor before placing it in a waste store. The long term plan is currently to place the used civilian reactor fuel in a deep store. This non-reprocessing policy was started in March 1977 because of concerns about nuclear weapons proliferation. President [Jimmy Carter] issued a [Presidential directive] which indefinitely suspended the commercial reprocessing and recycling of plutonium in the United States. This directive was likely an attempt by the United States to lead other countries by example, but many other nations continue to reprocess spent nuclear fuels. The Russian government under President Vladimir Putin repealed a law which had banned the import of used nuclear fuel, which makes it possible for Russians to offer a reprocessing service for clients outside Russia (similar to that offered by BNFL).

PUREX chemistry

The current method of choice is to use the PUREX liquid-liquid extraction process which uses a tributyl phosphate/hydrocarbon mixture to extract both uranium and plutonium from nitric acid. This extraction is of the nitrate salts and is classed as being of a solvation mechanism. For example, the extraction of plutonium by an extraction agent (S) in a nitrate medium occurs by the following reaction.

Pu⁴⁺_aq + 4NO₃⁻_aq + 2S_organic --> [Pu(NO₃)₄S₂]_organic

A complex bond is formed between the metal cation, the nitrates and the tributyl phosphate, and a model compound of a dioxouranium(VI) complex with two nitrates and two triethyl phosphates has been characterised by X-ray crystallography.^[5]

When the nitric acid concentration is high the extraction into the organic phase is favoured, and when the nitric acid concentration is low the extraction is reversed (the organic phase is stripped of the metal). It is normal to dissolve the used fuel in nitric acid, after the removal of the insoluble matter the uranium and plutonium are extracted from the highly active liquor. It is normal to then back extract the loaded organic phase to create a medium active liquor which contains mostly uranium and plutonium with only small traces of fission products. This medium active aqueous mixture is then extracted again by tributyl phosphate/hydrocarbon to form a new organic phase, the metal bearing organic phase is then stripped of the metals to form an aqueous mixture of only uranium and plutonium. The two stages of extraction are used to improve the purity of the actinide product, the organic phase used for the first extraction will suffer a far greater dose of radiation. The radiation can degrade the tributyl phosphate into dibutyl hydrogen phosphate. The dibutyl hydrogen phosphate can act as an extraction agent for both the actinides and other metals such as ruthenium. The dibutyl hydrogen phosphate can make the system behave in a more complex manner as it tends to extract metals by an ion exchange mechanism (extraction favoured by low acid concentration), to reduce the effect of the dibutyl hydrogen phosphate it is common for the used organic phase to be washed with sodium carbonate solution to remove the acidic degradation products of the tributyl phosphate.

New methods being considered for future use

The PUREX process can be modified to make a UREX (URanium EXtraction) process which could be used to save space inside high level nuclear waste disposal sites, such as Yucca Mountain nuclear waste repository, by removing the uranium which makes up the vast majority of the mass and volume of used fuel and recycling it as reprocessed uranium.

The UREX process is a PUREX process which has been modified to prevent the plutonium being extracted. This can be done by adding a plutonium reductant before the first metal extraction step. In the UREX process, ~99.9% of the Uranium and >95% of Technetium are separated from each other and the other fission products and actinides. The key is the addition of acetohydroxamic acid (AHA) to the extraction and scrub sections of the process. The addition of AHA greatly diminishes the extractability of Plutonium and Neptunium, providing greater proliferation resistance than with the plutonium extraction stage of the PUREX process.

Adding a second extraction agent, octyl(phenyl)-N, N-dibutyl carbamoylmethyl phosphine oxide(CMPO) in combination with tributylphosphate, (TBP), the PUREX process can be turned into the TRUEX (TRansUranic EXtraction) process this is a process which was invented in the USA by Argonne National Laboratory, and is designed to remove the transuranic metals (Am/Cm) from waste. The idea is that by lowering the alpha activity of the waste, the majority of the waste can then be disposed of with greater ease. In common with PUREX this process operates by a solvation mechanism.

As an alternative to TRUEX, an extraction process using a malondiamide has been devised. The DIAMEX (DIAMideEXtraction) process has the advantage of avoiding the formation of organic waste which contains elements other than Carbon, Hydrogen, Nitrogen, and Oxygen. Such an organic waste can be burned without the formation of acidic gases which could contribute to acid rain. The DIAMEX process is being worked on in Europe by the French CEA. The process is sufficiently mature that an industrial plant could be constructed with the existing knowledge of the process. In common with PUREX this process operates by a solvation mechanism.[8][9]

Selective Actinide Extraction (SANEX). As part of the management of minor actinides it has been proposed that the lanthanides and trivalent minor actinides should be removed from the PUREX raffinate by a process such as DIAMEX or TRUEX. In order to allow the actinides such as americium to be either reused in industrial sources or used as fuel the lanthanides must be removed. The lanthanides have large neutron cross sections and hence they would poison a neutron driven nuclear reaction. To date the extraction system for the SANEX process has not been defined, but currently several different research groups are working towards a process. For instance the French CEA is working on a bis-triaiznyl pyridine (BTP) based process.

Other systems such as the dithiophosphinic acids are being worked on by some other workers.
This is the UNiversal EXtraction process which was developed in Russia and the Czech Republic, it is a process designed to remove all of the most troublesome (Sr, Cs and minor actinides) radioisotopes from the raffinates left after the extraction of uranium and plutonium from used nuclear fuel. [10][11] The chemistry is based upon the interaction of caesium and strontium with poly ethylene oxide (poly ethylene glycol) [12] and a cobalt carborane anion (known as chlorinated cobalt dicarbollide) . The actinides are extracted by CMPO, and the diluent is a polar aromatic such as nitrobenzene. Other dilents such as meta-nitrobenzotrifluoride and phenyl trifluoromethyl sulfone [13] have been suggested as well.

Absorption of fission products on surfaces

Another important area of nuclear chemistry is the study of how fission products interact with surfaces; this is thought to control the rate of release and migration of fission products both from waste containers under normal conditions and from power reactors under accident conditions. It is interesting to note that, like chromate and molybdate, the ⁹⁹TcO₄ anion can react with steel surfaces to form a corrosion resistant layer. In this way, these metaloxo anions act as anodic corrosion inhibitors. The formation of ⁹⁹TcO₂ on steel surfaces is one effect which will retard the release of ⁹⁹Tc from nuclear waste drums and nuclear equipment which has been lost before decontamination (e.g. submarine reactors lost at sea). This ⁹⁹TcO₂ layer renders the steel surface passive, inhibiting the anodic corrosion reaction. The radioactive nature of technetium makes this corrosion protection impractical in almost all situations. It has also been shown that ⁹⁹TcO₄ anions react to form a layer on the surface of activated carbon (charcoal) or aluminium.^[6][14]. A short review of the biochemical properties of a series of key long lived radioisotopes can be read on line.[15]

⁹⁹Tc in nuclear waste may exist in chemical forms other than the ⁹⁹TcO₄ anion, these other forms have different chemical properties.[16]

Similarly, the release of iodine-131 in a serious power reactor accident could be retarded by absorption on metal surfaces within the nuclear plant.^[7]

Spinout areas

Some methods first developed within nuclear chemistry and physics have become so widely used within chemistry and other physical sciences that they may be best thought of as separate from normal nuclear chemistry. For example, the isotope effect is used so extensively to investigate chemical mechanisms and the use of cosmogenic isotopes and long-lived unstable isotopes in geology that it is best to consider much of isotopic chemistry as separate from nuclear chemistry.

Kinetics (use within mechanistic chemistry)

The mechanisms of chemical reactions can be investigated by observing how the kinetics of a reaction is changed by making an isotopic modification of a substrate, known as the kinetic isotope effect. This is now a standard method in organic chemistry. Briefly, replacing normal hydrogen (protons) by deuterium within a molecule causes the molecular vibrational frequency of X-H (for example C-H, N-H and O-H) bonds to decrease, which leads to a decrease in vibrational zero-point energy. This can lead to a decrease in the reaction rate if the rate-determining step involves breaking a bond between hydrogen and another atom.^[8] Thus, if the reaction changes in rate when protons are replaced by deuteriums, it is reasonable to assume that the breaking of the bond to hydrogen is part of the step which determines the rate.

Uses within geology, biology and forensic science

Cosmogenic isotopes are formed by the interaction of cosmic rays with the nucleus of an atom. These can be used for dating purposes and for use as natural tracers. In addition, by careful measurement of some ratios of stable isotopes it is possible to obtain new insights into the origin of bullets, ages of ice samples, ages of rocks, and the diet of a person can be identified from a hair or other tissue sample. (See Isotope geochemistry and Isotopic signature for further details).

Biology

Within living things, isotopic labels (both radioactive and nonradioactive) can be used to probe how the complex web of reactions which makes up the metabolism of an organism converts one substance to another. For instance a green plant uses light energy to convert water and carbon dioxide into glucose by photosynthesis. If the oxygen in the water is labeled, then the label appears in the oxygen gas formed by the plant and not in the glucose formed in the chloroplasts within the plant cells.
For biochemical and physiological experiments and medical methods, a number of specific isotopes have important applications.

• Stable isotopes have the advantage of not delivering a radiation dose to the system being studied; however, a significant excess of them in the organ or organism might still interfere with its functionality, and the availability of sufficient amounts for whole-animal studies is limited for many isotopes. Measurement is also difficult, and usually requires mass spectrometry to determine how much of the isotope is present in particular compounds, and there is no means of localizing measurements within the cell.

• H-2 (deuterium), the stable isotope of hydrogen, is a stable tracer, the concentration of which can be measured by mass spectrometry or NMR. It is incorporated into all cellular structures. Specific deuterated compounds can also be produced.
• N-15, the stable isotope of nitrogen, has also been used. It is incorporated mainly into proteins.

• Radioactive isotopes have the advantages of being detectable in very low quantities, in being easily measured by scintillation counting or other radiochemical methods, and in being localizable to particular regions of a cell, and quantifiable by autoradiography. Many compounds with the radioactive atoms in specific positions can be prepared, and are widely available commercially. In high quantities they require precautions to guard the workers from the effects of radiation—and they can easily contaminate laboratory glassware and other equipment. For some isotopes the half-life is so short that preparation and measurement is difficult.

By organic synthesis it is possible to create a complex molecule with a radioactive label that can be confined to a small area of the molecule. For short-lived isotopes such as ¹¹C, very rapid synthetic methods have been developed to permit the rapid addition of the radioactive isotope to the molecule. For instance a palladium catalysed carbonylation reaction in a microfluidic device has been used to rapidly form amides^[9] and it might be possible to use this method to form radioactive imaging agents for PET imaging.[17]

• ³H, Tritium, the radioisotope of hydrogen, it available at very high specific activities, and compounds with this isotope in particular positions are easily prepared by standard chemical reactions such as hydrogenation of unsaturated precursors. The isotope emits very soft beta radiation, and can be detected by scintillation counting.

• ¹¹C, Carbon-11 is usually produced by cyclotron bombardment of ¹⁴N with protons. The resulting nuclear reaction is ¹⁴N(p,α)¹¹C.^[10] Additionally, Carbon-11 can also be made using a cyclotron; boron in the form of boric oxide is reacted with protons in a (p,n) reaction. Another alternative route is to react ¹⁰B with deuterons. By rapid organic synthesis, the ¹¹C compound formed in the cyclotron is converted into the imaging agent which is then used for PET.

• ¹⁴C, Carbon-14 can be made (as above), and it is possible to convert the target material into simple inorganic and organic compounds. In most organic synthesis work it is normal to try to create a product out of two approximately equal sized fragments and to use a convergent route, but when a radioactive label is added, it is normal to try to add the label late in the synthesis in the form of a very small fragment to the molecule to enable the radioactivity to be localised in a single group. Late addition of the label also reduces the number of synthetic stages where radioactive material is used.

• ¹⁸F, fluorine-18 can be made by the reaction of neon with deuterons, ²⁰Ne reacts in a (d,⁴He) reaction. It is normal to use neon gas with a trace of stable fluorine (¹⁹F₂). The ¹⁹F₂ acts as a carrier which increases the yield of radioactivity from the cyclotron target by reducing the amount of radioactivity lost by absorption on surfaces. However, this reduction in loss is at the cost of the specific activity of the final product.

Nuclear magnetic resonance (NMR)

NMR spectroscopy uses the net spin of nuclei in a substance upon energy absorption to identify molecules. This has now become a standard spectroscopic tool within synthetic chemistry. One major use of NMR is to determine the bond connectivity within an organic molecule.

NMR imaging also uses the net spin of nuclei (commonly protons) for imaging. This is widely used for diagnostic purposes in medicine, and can provide detailed images of the inside of a person without inflicting any radiation upon them. In a medical setting, NMR is often known simply as "magnetic resonance" imaging, as the word 'nuclear' has negative connotations for many people.

Gene

From Wikipedia, the free encyclopedia

Chromosome (107 - 1010 bp) DNA Gene (103 - 106 bp ) Function A gene is a segment of DNA that encodes function. A chromosome consists of a long strand of DNA containing many genes. A human chromosome can have up to 500 million base pairs of DNA with thousands of genes.

A gene is a locus (or region) of DNA that encodes a functional RNA or protein product, and is the molecular unit of heredity.^{[1][2]:Glossary} The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic traits. Most biological traits are under the influence of polygenes (many different genes) as well as the gene–environment interactions. Some genetic traits are instantly visible, such as eye colour or number of limbs, and some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that comprise life.

Genes can acquire mutations in their sequence, leading to different variants, known as alleles, in the population. These alleles encode slightly different versions of a protein, which cause different phenotype traits. Colloquial usage of the term "having a gene" (e.g., "good genes," "hair colour gene") typically refers to having a different allele of the gene. Genes evolve due to natural selection or survival of the fittest of the alleles.

The concept of a gene continues to be refined as new phenomena are discovered.^[3] For example, regulatory regions of a gene can be far removed from its coding regions, and coding regions can be split into several exons. Some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. Therefore, a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulation of gene expression.^[4][5]

History

Gregor Mendel

Discovery of discrete inherited units

The existence of discrete inheritable units was first suggested by Gregor Mendel (1822–1884).^[6] From 1857 to 1864, he studied inheritance patterns in 8000 common edible pea plants, tracking distinct traits from parent to offspring. He described these mathematically as 2ⁿ combinations where n is the number of differing characteristics in the original peas. Although he did not use the term gene, he explained his results in terms of discrete inherited units that give rise to observable physical characteristics. This description prefigured the distinction between genotype (the genetic material of an organism) and phenotype (the visible traits of that organism). Mendel was also the first to demonstrate independent assortment, the distinction between dominant and recessive traits, the distinction between a heterozygote and homozygote, and the phenomenon of discontinuous inheritance.

Prior to Mendel's work, the dominant theory of heredity was one of blending inheritance, which suggested that each parent contributed fluids to the fertilisation process and that the traits of the parents blended and mixed to produce the offspring. Charles Darwin developed a theory of inheritance he termed pangenesis,^[7] which used the term gemmule to describe hypothetical particles that would mix during reproduction. Although Mendel's work was largely unrecognized after its first publication in 1866, it was 'rediscovered' in 1900 by three European scientists, Hugo de Vries, Carl Correns, and Erich von Tschermak, who claimed to have reached similar conclusions in their own research.^[8]

The word gene is derived (via pangene) from the Ancient Greek word lγένος (génos) meaning "race, offspring".^[9] Gene was coined in 1909 by Danish botanist Wilhelm Johannsen to describe the fundamental physical and functional unit of heredity,^[10] while the related word genetics was first used by William Bateson in 1905.^[11]

Discovery of DNA

Advances in understanding genes and inheritance continued throughout the 20th century. Deoxyribonucleic acid (DNA) was shown to be the molecular repository of genetic information by experiments in the 1940s to 1950s.^[12][13] The structure of DNA was studied by Rosalind Franklin using X-ray crystallography, which led James D. Watson and Francis Crick to publish a model of the double-stranded DNA molecule whose paired nucleotide bases indicated a compelling hypothesis for the mechanism of genetic replication.^[14][15] Collectively, this body of research established the central dogma of molecular biology, which states that proteins are translated from RNA, which is transcribed from DNA. This dogma has since been shown to have exceptions, such as reverse transcription in retroviruses. The modern study of genetics at the level of DNA is known as molecular genetics.

In 1972, Walter Fiers and his team at the University of Ghent were the first to determine the sequence of a gene: the gene for Bacteriophage MS2 coat protein.^[16] The subsequent development of chain-termination DNA sequencing in 1977 by Frederick Sanger improved the efficiency of sequencing and turned it into a routine laboratory tool.^[17] An automated version of the Sanger method was used in early phases of the Human Genome Project.^[18]

Modern evolutionary synthesis

The theories developed in the 1930s and 1940s to integrate molecular genetics with Darwinian evolution are called the modern evolutionary synthesis, a term introduced by Julian Huxley.^[19] 

Evolutionary biologists subsequently refined this concept, such as George C. Williams' gene-centric view of evolution. He proposed an evolutionary concept of the gene as a unit of natural selection with the definition: "that which segregates and recombines with appreciable frequency."^[20]:24 In this view, the molecular gene transcribes as a unit, and the evolutionary gene inherits as a unit. Related ideas emphasizing the centrality of genes in evolution were popularized by Richard Dawkins.^[21][22]

Molecular basis

The chemical structure of a four base pair fragment of a DNA double helix. The sugar-phosphate backbone chains run in opposite directions with the bases pointing inwards, base-pairing A to T and C to G with hydrogen bonds.

DNA

The vast majority of living organisms encode their genes in long strands of DNA (deoxyribonucleic acid). DNA consists of a chain made from four types of nucleotide subunits, each composed of: a five-carbon sugar (2'-deoxyribose), a phosphate group, and one of the four bases adenine, cytosine, guanine, and thymine.^[2]:2.1

Two chains of DNA twist around each other to form a DNA double helix with the phosphate-sugar backbone spiralling around the outside, and the bases pointing inwards with adenine base pairing to thymine and guanine to cytosine. The specificity of base pairing occurs because adenine and thymine align form two hydrogen bonds, whereas cytosine and guanine form three hydrogen bonds. The two strands in a double helix must therefore be complementary, with their sequence of bases matching such that the adenines of one strand are paired with the thymines of the other strand, and so on.^[2]:4.1

Due to the chemical composition of the pentose residues of the bases, DNA strands have directionality. One end of a DNA polymer contains an exposed hydroxyl group on the deoxyribose; this is known as the 3' end of the molecule. The other end contains an exposed phosphate group; this is the 5' end. The two strands of a double-helix run in opposite directions. Nucleic acid synthesis, including DNA replication and transcription occurs in the 5'→3' direction, because new nucleotides are added via a dehydration reaction that uses the exposed 3' hydroxyl as a nucleophile.^[23]:27.2

The expression of genes encoded in DNA begins by transcribing the gene into RNA, a second type of  nucleic acid that is very similar to DNA, but whose monomers contain the sugar ribose rather than deoxyribose. RNA also contains the base uracil in place of thymine. RNA molecules are less stable than DNA and are typically single-stranded. Genes that encode proteins are composed of a series of three-nucleotide sequences called codons, which serve as the "words" in the genetic "language". The genetic code specifies the correspondence during protein translation between codons and amino acids. The genetic code is nearly the same for all known organisms.^[2]:4.1

Chromosomes

Fluorescent microscopy image of a human female karyotype, showing 23 pairs of chromosomes . The DNA is stained red, with regions rich in housekeeping genes further stained in green. The largest chromosomes are around 10 times the size of the smallest.^[24]

The total complement of genes in an organism or cell is known as its genome, which may be stored on one or more chromosomes. A chromosome consists of a single, very long DNA helix on which thousands of genes are encoded.^[2]:4.2 The region of the chromosome at which a particular gene is located is called its locus. Each locus contains one allele of a gene; however, members of a population may have different alleles at the locus, each with a slightly different gene sequence.

The majority of eukaryotic genes are stored on a set of large, linear chromosomes. The chromosomes are packed within the nucleus in complex with storage proteins called histones to form a unit called a nucleosome. DNA packaged and condensed in this way is called chromatin.^[2]:4.2 The manner in which DNA is stored on the histones, as well as chemical modifications of the histone itself, regulate whether a particular region of DNA is accessible for gene expression. In addition to genes, eukaryotic chromosomes contain sequences involved in ensuring that the DNA is copied without degradation of end regions and sorted into daughter cells during cell division: replication origins, telomeres and the centromere.^[2]:4.2 Replication origins are the sequence regions where DNA replication is initiated to make two copies of the chromosome. Telomeres are long stretches of repetitive sequence that cap the ends of the linear chromosomes and prevent degradation of coding and regulatory regions during DNA replication. The length of the telomeres decreases each time the genome is replicated and has been implicated in the aging process.^[25] The centromere is required for binding spindle fibres to separate sister chromatids into daughter cells during cell division.^[2]:18.2

Prokaryotes (bacteria and archaea) typically store their genomes on a single large, circular chromosome. Similarly, some eukaryotic organelles contain a remnant circular chromosome with a small number of genes.^[2]:14.4 Prokaryotes sometimes supplement their chromosome with additional small circles of DNA called plasmids, which usually encode only a few genes and are transferable between individuals. For example, the genes for antibiotic resistance are usually encoded on bacterial plasmids and can be passed between individual cells, even those of different species, via horizontal gene transfer.^[26]

Whereas the chromosomes of prokaryotes are relatively gene-dense, those of eukaryotes often contain regions of DNA that serve no obvious function. Simple single-celled eukaryotes have relatively small amounts of such DNA, whereas the genomes of complex multicellular organisms, including humans, contain an absolute majority of DNA without an identified function.^[27] This DNA has often been referred to as "junk DNA". However, more recent analyses suggest that, although protein-coding DNA makes up barely 2% of the human genome, about 80% of the bases in the genome may be expressed, so the term "junk DNA" may be a misnomer.^[5]

Structure and function

Regulatory sequence Regulatory sequence Enhancer /silencer Promoter 5'UTR Open reading frame 3'UTR Enhancer /silencer Proximal Core Start Stop Terminator Transcription DNA Exon Exon Exon Intron Intron Post-transcriptional modification Pre- mRNA Protein coding region + 5' cap + Poly-A tail Translation Maure mRNA Protein The structure of a eukaryotic protein-coding gene. Regulatory sequence controls when and where expression occurs for the protein coding region (red). Promoter and enhancer regions (yellow) regulate the transcription of the gene into a pre-mRNA which is modified to add a 5' cap and poly-A tail (grey) and remove introns. The mRNA 5' and 3' untranslated regions (blue) regulate translation into the final protein product. Polycistronic operon Regulatory sequence Regulatory sequence Enhancer /silencer Operator Promoter 5'UTR ORF UTR ORF 3'UTR Enhancer /silencer Start Stop Start Stop Terminator Transcription DNA RBS Protein coding region RBS Protein coding region Translation mRNA Protein The structure of a prokaryotic operon of protein-coding genes. Regulatory sequence controls when expression occurs for the multiple protein coding regions (red). Promoter, operator and enhancer regions (yellow) regulate the transcription of the gene into an mRNA. The mRNA untranslated regions (blue) regulate translation into the final protein products.

The Thestructure of a gene consists of many elements of which the actual protein coding sequence is often only a small part. These include DNA regions that are not transcribed as well as untranslated regions of the RNA.

Firstly, flanking the open reading frame, all genes contain a regulatory sequence that is required for their expression. In order to be expressed, genes require a promoter sequence. The promoter is recognized and bound by transcription factors and RNA polymerase to initiate transcription.^[2]:7.1 A gene can have more than one promoter, resulting in mRNAs that differ in how far they extend in the 5' end.^[28] Promoter regions have a consensus sequence, however highly transcribed genes have "strong" promoter sequences that bind the transcription machinery well, whereas others have "weak" promoters that bind poorly and initiate transcription less frequently.^[2]:7.2 Eukaryotic promoter regions are much more complex and difficult to identify than prokaryotic promoters.^[2]:7.3

Additionally, genes can have regulatory regions many kilobases upstream or downstream of the open reading frame. These act by binding to transcription factors which then cause the DNA to loop so that the regulatory sequence (and bound transcription factor) become close to the RNA polymerase binding site.^[29] For example, enhancers increase transcription by binding an activator protein which then helps to recruit the RNA polymerase to the promoter; conversely silencers bind repressor proteins and make the DNA less available for RNA polymerase.^[30]
The transcribed pre-mRNA contains untranslated regions at both ends which contain a ribosome binding site, terminator and start and stop codons.^[31] In addition, most eukaryotic open reading frames contain untranslated introns which are removed before the exons are translated. The sequences at the ends of the introns, dictate the splice sites to generate the final mature mRNA which encodes the protein or RNA product.^[32]

Many prokaryotic genes are organized into operons, with multiple protein-coding sequences that are transcribed as a unit.^[33][34] The products of operon genes typically have related functions and are involved in the same regulatory network.^[2]:7.3

Functional definitions

Defining exactly what section of a DNA sequence comprises a gene is difficult.^[3] Regulatory regions of a gene such as enhancers do not necessarily have to be close to the coding sequence on the linear molecule because the intervening DNA can be looped out to bring the gene and its regulatory region into proximity. Similarly, a gene's introns can be much larger than its exons. Regulatory regions can even be on entirely different chromosomes and operate in trans to allow regulatory regions on one chromosome to come in contact with target genes on another chromosome.^[35][36]

Early work in molecular genetics suggested the model that one gene makes one protein. This model has been refined since the discovery of genes that can encode multiple proteins by alternative splicing and coding sequences split in short section across the genome whose mRNAs are concatenated by trans-splicing.^[5][37][38]

A broad operational definition is sometimes used to encompass the complexity of these diverse phenomena, where a gene is defined as a union of genomic sequences encoding a coherent set of potentially overlapping functional products.^[11] This definition categorizes genes by their functional products (proteins or RNA) rather than their specific DNA loci, with regulatory elements classified as gene-associated regions.^[11]

Gene expression

In all organisms, two steps are required to read the information encoded in a gene's DNA and produce the protein it specifies. First, the gene's DNA is transcribed to messenger RNA (mRNA).^[2]:6.1 Second, that mRNA is translated to protein.^[2]:6.2 RNA-coding genes must still go through the first step, but are not translated into protein.^[39] The process of producing a biologically functional molecule of either RNA or protein is called gene expression, and the resulting molecule is called a gene product.

Genetic code

Schematic of a single-stranded RNA molecule illustrating a series of three-base codons. Each three-nucleotide codon corresponds to an amino acid when translated to protein

The nucleotide sequence of a gene's DNA specifies the amino acid sequence of a protein through the genetic code. Sets of three nucleotides, known as codons, each correspond to a specific amino acid.^[2]:6 Additionally, a "start codon", and three "stop codons" indicate the beginning and end of the protein coding region. There are 64 possible codons (four possible nucleotides at each of three positions, hence 4³ possible codons) and only 20 standard amino acids; hence the code is redundant and multiple codons can specify the same amino acid. The correspondence between codons and amino acids is nearly universal among all known living organisms.^[40]

Transcription

Transcription produces a single-stranded RNA molecule known as messenger RNA, whose nucleotide sequence is complementary to the DNA from which it was transcribed.^[2]:6.1 The mRNA acts as an intermediate between the DNA gene and its final protein product. The gene's DNA is used as a template to generate a complementary mRNA. The mRNA matches the sequence of the gene's DNA coding strand because it is synthesised as the complement of the template strand. Transcription is performed by an enzyme called an RNA polymerase, which reads the template strand in the 3' to 5' direction and synthesizes the RNA from 5' to 3'. To initiate transcription, the polymerase first recognizes and binds a promoter region of the gene. Thus, a major mechanism of gene regulation is the blocking or sequestering the promoter region, either by tight binding by repressor molecules that physically block the polymerase, or by organizing the DNA so that the promoter region is not accessible.^[2]:7

In prokaryotes, transcription occurs in the cytoplasm; for very long transcripts, translation may begin at the 5' end of the RNA while the 3' end is still being transcribed. In eukaryotes, transcription occurs in the nucleus, where the cell's DNA is stored. The RNA molecule produced by the polymerase is known as the primary transcript and undergoes post-transcriptional modifications before being exported to the cytoplasm for translation. One of the modifications performed is the splicing of introns which are sequences in the transcribed region that do not encode protein. Alternative splicing mechanisms can result in mature transcripts from the same gene having different sequences and thus coding for different proteins. This is a major form of regulation in eukaryotic cells and also occurs in some prokaryotes.^[2]:7.5[41]

Translation

Protein coding genes are transcribed to an mRNA intermediate, then translated to a functional protein. RNA-coding genes are transcribed to a functional non-coding RNA. (PDB: 3BSE, 1OBB, 3TRA )

Translation is the process by which a mature mRNA molecule is used as a template for synthesizing a new protein.^[2]:6.2 Translation is carried out by ribosomes, large complexes of RNA and protein responsible for carrying out the chemical reactions to add new amino acids to a growing polypeptide chain by the formation of peptide bonds. The genetic code is read three nucleotides at a time, in units called codons, via interactions with specialized RNA molecules called transfer RNA (tRNA). Each tRNA has three unpaired bases known as the anticodon that are complementary to the codon it reads on the mRNA. The tRNA is also covalently attached to the amino acid specified by the complementary codon. When the tRNA binds to its complementary codon in an mRNA strand, the ribosome attaches its amino acid cargo to the new polypeptide chain, which is synthesized from amino terminus to carboxyl terminus. During and after synthesis, most new proteins must folds to their active three-dimensional structure before they can carry out their cellular functions.^[2]:3

Regulation

Genes are regulated so that they are expressed only when the product is needed, since expression draws on limited resources.^[2]:7 A cell regulates its gene expression depending on its external environment (e.g. available nutrients, temperature and other stresses), its internal environment (e.g. cell division cycle, metabolism, infection status), and its specific role if in a multicellular organism. Gene expression can be regulated at any step: from transcriptional initiation, to RNA processing, to post-translational modification of the protein. The regulation of lactose metabolism genes in E. coli (lac operon) was the first such mechanism to be described in 1961.^[42]

RNA genes

A typical protein-coding gene is first copied into RNA as an intermediate in the manufacture of the final protein product.^[2]:6.1 In other cases, the RNA molecules are the actual functional products, as in the synthesis of ribosomal RNA and transfer RNA. Some RNAs known as ribozymes are capable of enzymatic function, and microRNA has a regulatory role. The DNA sequences from which such RNAs are transcribed are known as non-coding RNA genes.^[39]

Some viruses store their entire genomes in the form of RNA, and contain no DNA at all.^[43][44] Because they use RNA to store genes, their cellular hosts may synthesize their proteins as soon as they are infected and without the delay in waiting for transcription.^[45] On the other hand, RNA retroviruses, such as HIV, require the reverse transcription of their genome from RNA into DNA before their proteins can be synthesized. RNA-mediated epigenetic inheritance has also been observed in plants and very rarely in animals.^[46]

Inheritance

Inheritance of a gene that has two different alleles (blue and white). The gene is located on an autosomal chromosome. The blue allele is recessive to the white allele. The probability of each outcome in the children's generation is one quarter, or 25 percent.

Organisms inherit their genes from their parents. Asexual organisms simply inherit a complete copy of their parent's genome. Sexual organisms have two copies of each chromosome because they inherit one complete set from each parent.^[2]:1

Mendelian inheritance

According to Mendelian inheritance, variations in an organism's phenotype (observable physical and behavioral characteristics) are due in part to variations in its genotype (particular set of genes). Each gene specifies a particular trait with different sequence of a gene (alleles) giving rise to different phenotypes. Most eukaryotic organisms (such as the pea plants Mendel worked on) have two alleles for each trait, one inherited from each parent.^[2]:20

Alleles at a locus may be dominant or recessive; dominant alleles give rise to their corresponding phenotypes when paired with any other allele for the same trait, whereas recessive alleles give rise to their corresponding phenotype only when paired with another copy of the same allele. For example, if the allele specifying tall stems in pea plants is dominant over the allele specifying short stems, then pea plants that inherit one tall allele from one parent and one short allele from the other parent will also have tall stems. Mendel's work demonstrated that alleles assort independently in the production of gametes, or germ cells, ensuring variation in the next generation. Although Mendelian inheritance remains a good model for many traits determined by single genes (including a number of well-known genetic disorders) it does not include the physical processes of DNA replication and cell division.^[47][48]

DNA replication and cell division

The growth, development, and reproduction of organisms relies on cell division, or the process by which a single cell divides into two usually identical daughter cells. This requires first making a duplicate copy of every gene in the genome in a process called DNA replication.^[2]:5.2 The copies are made by specialized enzymes known as DNA polymerases, which "read" one strand of the double-helical DNA, known as the template strand, and synthesize a new complementary strand. Because the DNA double helix is held together by base pairing, the sequence of one strand completely specifies the sequence of its complement; hence only one strand needs to be read by the enzyme to produce a faithful copy. The process of DNA replication is semiconservative; that is, the copy of the genome inherited by each daughter cell contains one original and one newly synthesized strand of DNA.^[2]:5.2
After DNA replication is complete, the cell must physically separate the two copies of the genome and divide into two distinct membrane-bound cells.^[2]:18.2 In prokaryotes (bacteria and archaea) this usually occurs via a relatively simple process called binary fission, in which each circular genome attaches to the cell membrane and is separated into the daughter cells as the membrane invaginates to split the cytoplasm into two membrane-bound portions. Binary fission is extremely fast compared to the rates of cell division in eukaryotes. Eukaryotic cell division is a more complex process known as the cell cycle; DNA replication occurs during a phase of this cycle known as S phase, whereas the process of segregating chromosomes and splitting the cytoplasm occurs during M phase.^[2]:18.1

Molecular inheritance

The duplication and transmission of genetic material from one generation of cells to the next is the basis for molecular inheritance, and the link between the classical and molecular pictures of genes. Organisms inherit the characteristics of their parents because the cells of the offspring contain copies of the genes in their parents' cells. In asexually reproducing organisms, the offspring will be a genetic copy or clone of the parent organism. In sexually reproducing organisms, a specialized form of cell division called meiosis produces cells called gametes or germ cells that are haploid, or contain only one copy of each gene.^[2]:20.2 The gametes produced by females are called eggs or ova, and those produced by males are called sperm. Two gametes fuse to form a diploid fertilized egg, a single cell that has two sets of genes, with one copy of each gene from the mother and one from the father.^[2]:20
During the process of meiotic cell division, an event called genetic recombination or crossing-over can sometimes occur, in which a length of DNA on one chromatid is swapped with a length of DNA on the corresponding sister chromatid. This has no effect if the alleles on the chromatids are the same, but results in reassortment of otherwise linked alleles if they are different.^[2]:5.5 The Mendelian principle of independent assortment asserts that each of a parent's two genes for each trait will sort independently into gametes; which allele an organism inherits for one trait is unrelated to which allele it inherits for another trait. This is in fact only true for genes that do not reside on the same chromosome, or are located very far from one another on the same chromosome. The closer two genes lie on the same chromosome, the more closely they will be associated in gametes and the more often they will appear together; genes that are very close are essentially never separated because it is extremely unlikely that a crossover point will occur between them. This is known as genetic linkage.^[49]

Molecular evolution

Mutation

DNA replication is for the most part extremely accurate, however errors (mutations) do occur.^[2]:7.6 The error rate in eukaryotic cells can be as low as 10⁻⁸ per nucleotide per replication,^[50][51] whereas for some RNA viruses it can be as high as 10⁻³.^[52] This means that each generation, each human genome accumulates 1–2 new mutations.^[52] Small mutations can be caused by DNA replication and the aftermath of DNA damage and include point mutations in which a single base is altered and frameshift mutations in which a single base is inserted or deleted. Either of these mutations can change the gene by missense (change a codon to encode a different amino acid) or nonsense (a premature stop codon).^[53] Larger mutations can be caused by errors in recombination to cause chromosomal abnormalities including the duplication, deletion, rearrangement or inversion of large sections of a chromosome. Additionally, the DNA repair mechanisms that normally revert mutations can introduce errors when repairing the physical damage to the molecule is more important than restoring an exact copy, for example when repairing double-strand breaks.^[2]:5.4
When multiple different alleles for a gene are present in a species's population it is called polymorphic. Most different alleles are functionally equivalent, however some alleles can give rise to different phenotypic traits. A gene's most common allele is called the wild type, and rare alleles are called mutants. The genetic variation in relative frequencies of different alleles in a population is due to both natural selection and genetic drift.^[54] The wild-type allele is not necessarily the ancestor of less common alleles, nor is it necessarily fitter.

Most mutations within genes are neutral, having no effect on the organism's phenotype (silent mutations). Some mutations do not change the amino acid sequence because multiple codons encode the same amino acid (synonymous mutations). Other mutations can be neutral if they lead to amino acid sequence changes, but the protein still functions similarly with the new amino acid (e.g. conservative mutations). Many mutations, however, are deleterious or even lethal, and are removed from populations by natural selection. Genetic disorders are the result of deleterious mutations and can be due to spontaneous mutation in the affected individual, or can be inherited. Finally, a small fraction of mutations are beneficial, improving the organism's fitness and are extremely important for evolution, since their directional selection leads to adaptive evolution.^[2]:7.6

Sequence homology

A sequence alignment, produced by ClustalO, of mammalian histone proteins

Genes with a most recent common ancestor, and thus a shared evolutionary ancestry, are known as homologs.^[55] These genes appear either from gene duplication within an organism's genome, where they are known as paralogous genes, or are the result of divergence of the genes after a speciation event, where they are known as orthologous genes,^[2]:7.6 and often perform the same or similar functions in related organisms. It is often assumed that the functions of orthologous genes are more similar than those of paralogous genes, although the difference is minimal.^[56][57]

The relationship between genes can be measured by comparing the sequence alignment of their DNA.^[2]:7.6 The degree of sequence similarity between homologous genes is called conserved sequence. Most changes to a gene's sequence do not affect its function and so genes accumulate mutations over time by neutral molecular evolution. Additionally, any selection on a gene will cause its sequence to diverge at a different rate. Genes under stabilizing selection are constrained and so change more slowly whereas genes under directional selection change sequence more rapidly.^[58] The sequence differences between genes can be used for phylogenetic analyses to study how those genes have evolved and how the organisms they come from are related.^[59][60]

Origins of new genes

Evolutionary fate of duplicate genes

The most common source of new genes in eukaryotic lineages is gene duplication, which creates copy number variation of an existing gene in the genome.^[61][62] The resulting genes (paralogs) may then diverge in sequence and in function. Sets of genes formed in this way comprise a gene family. Gene duplications and losses within a family are common and represent a major source of evolutionary biodiversity.^[63] Sometimes, gene duplication may result in a nonfunctional copy of a gene, or a functional copy may be subject to mutations that result in loss of function; such nonfunctional genes are called pseudogenes.^[2]:7.6

De novo or "orphan" genes, whose sequence shows no similarity to existing genes, are extremely rare. Estimates of the number of de novo genes in the human genome range from 18^[64] to 60.^[65] Such genes are typically shorter and simpler in structure than most eukaryotic genes, with few if any introns.^[61] Two primary sources of orphan protein-coding genes are gene duplication followed by extremely rapid sequence change, such that the original relationship is undetectable by sequence comparisons, and formation through mutation of "cryptic" transcription start sites that introduce a new open reading frame in a region of the genome that did not previously code for a protein.^[66][67]

Horizontal gene transfer refers to the transfer of genetic material through a mechanism other than reproduction. This mechanism is a common source of new genes in prokaryotes, sometimes thought to contribute more to genetic variation than gene duplication.^[68] It is a common means of spreading antibiotic resistance, virulence, and adaptive metabolic functions.^[26][69] Although horizontal gene transfer is rare in eukaryotes, likely examples have been identified of protist and alga genomes containing genes of bacterial origin.^[70][71]

Genome

The genome is the total genetic material of an organism and includes both the genes and non-coding sequences.^[72]

Number of genes

Representative genome sizes for plants (green), vertebrates (blue), invertebrates (red), fungus (yellow), bacteria (purple), and viruses (grey). An inset on the right shows the smaller genomes expanded 100-fold.^{[73][74][75][76][77][78][79][80]}

The genome size, and the number of genes it encodes varies widely between organisms. The smallest genomes occur in viruses (which can have as few as 2 protein-coding genes),^[81] and viroids (which act as a single non-coding RNA gene).^[82] Conversely, plants can have extremely large genomes,^[83] with rice containing >46,000 protein-coding genes.^[84] The total number of protein-coding genes (the Earth's proteome) is estimated to be 5 million sequences.^[85]

Although the number of base-pairs of DNA in the human genome has been known since the 1960s, the estimated number of genes has changed over time as definitions of genes, and methods of detecting them have been refined. Initial theoretical predictions of the number of human genes were as high as 2,000,000.^[86] Early experimental measures indicated there to be 50,000–100,000 transcribed genes (expressed sequence tags).^[87] Subsequently, the sequencing in the Human Genome Project indicated that many of these transcripts were alternative variants of the same genes, and the total number of protein-coding genes was revised down to ~20,000^[80] with 13 genes encoded on the mitochondrial genome.^[78] Of the human genome, only 1–2% consists of protein-coding genes,^[88] with the remainder being 'noncoding' DNA such as introns, retrotransposons, and noncoding RNAs.^[88][89]

Essential genes

A schematic view of essential genes in lysine biosynthesis of different bacteria. The same protein may be essential in one species but not another.

Essential genes are the set of genes thought to be critical for an organism's survival.^[90] This definition assumes the abundant availability of all relevant nutrients and the absence of environmental stress. Only a small portion of an organism's genes are essential. In bacteria, an estimated 250–400 genes are essential for Escherichia coli and Bacillus subtilis, which is less than 10% of their genes.^[91][92][93] Half of these genes are orthologs in both organisms and are largely involved in protein synthesis.^[93] In the budding yeast Saccharomyces cerevisiae the number of essential genes is slightly higher, at 1000 genes (~20% of their genes).^[94] Although the number is more difficult to measure in higher eukaryotes, mice and humans are estimated to have around 2000 essential genes (~10% of their genes).^[95]

Housekeeping genes are critical for carrying out basic cell functions and so are expressed at a relatively constant level (constitutively).^[96] Since their expression is constant, housekeeping genes are used as experimental controls when analysing gene expression. Not all essential genes are housekeeping genes since some essential genes are developmentally regulated or expressed at certain times during the organism's life cycle.^[97]

Genetic and genomic nomenclature

Gene nomenclature has been established by the HUGO Gene Nomenclature Committee (HGNC) for each known human gene in the form of an approved gene name and symbol (short-form abbreviation), which can be accessed through a database maintained by HGNC. Symbols are chosen to be unique, and each gene has only one symbol (although approved symbols sometimes change). Symbols are preferably kept consistent with other members of a gene family and with homologs in other species, particularly the mouse due to its role as a common model organism.^[98]

Genetic engineering

Comparison of conventional plant breeding with transgenic and cisgenic genetic modification.

 

Genetic engineering is the modification of an organism's genome through biotechnology. Since the 1970s, a variety of techniques have been developed to specifically add, remove and edit genes in an organism.^[99] Recently developed genome engineering techniques use engineered nuclease enzymes to create targeted DNA repair in a chromosome to either disrupt or edit a gene when the break is repaired.^{[100][101][102][103]} The related term synthetic biology is sometimes used to refer to extensive genetic engineering of an organism.^[104]
Genetic engineering is now a routine research tool with model organisms. For example, genes are easily added to bacteria^[105] and lineages of knockout mice with a specific gene's function disrupted are used to investigate that gene's function.^[106][107] Many organisms have been genetically modified for applications in agriculture, industrial biotechnology, and medicine.

For multicellular organisms, typically the embryo is engineered which grows into the adult genetically modified organism.^[108] However, the genomes of cells in an adult organism can be edited using gene therapy techniques to treat genetic diseases.