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 (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, a 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 C, 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 and it might be possible to use this method to form radioactive imaging agents for PET imaging.
*H (tritium), the radioisotope of hydrogen, is 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.
*C, carbon-11 is usually produced by cyclotron bombardment of N with protons. The resulting nuclear reaction is .  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 B with deuterons. By rapid organic synthesis, the C compound formed in the cyclotron is converted into the imaging agent which is then used for PET.
*C, 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.
*F, fluorine-18 can be made by the reaction of neon with deuterons, Ne reacts in a (d,He) reaction. It is normal to use neon gas with a trace of stable fluorine (F). The F 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.