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Chapter 2 The Molecules of Life

PERSPECTIVE 2.1 Isotopes: Valuable Tools for the Study of Biological Systems

One important tool in the analysis of living cells is the use of isotopes, variant forms of the same element that have different atomic weights.The nuclei of certain elements can have greater or fewer neutrons than usual and thereby be heavier or lighter than is typical. For example, the most common form of the hydrogen atom contains 1 proton and 0 neutrons and has an atomic weight of 1 (1H). Another form, however, also exists in nature in very low amounts. This isotope, 2H (deuterium), contains 1 neutron. A third, even heavier isotope, 3H (tritium), is not found in nature but can be made by a nuclear reaction in which stable atoms are bombarded with high-energy particles.This latter isotope is unstable and gives off radiation (decays) in the form of rays or electrons, which can be very sensitively measured by a radioactivity counter. Once the atom has finished disintegrating, it no longer gives off radiation and is stable.

An important feature of radioactive isotopes is that their other properties are very similar to their non-radioactive counterparts. For example, tritium combines with oxygen to form water and with carbon to form hydrocarbons, and both molecules have biological properties very similar to their nonradioactive counterparts.The only difference is that the molecules containing tritium can be detected by the radiation they emit.

Isotopes are used in numerous ways in biological research.They are frequently added to growing cells in order to label particular molecules, thereby making them detectable. For example, tritiated thymidine (a component of DNA) added to growing bacteria will specifically label DNA and no other molecules.Tritiated uridine, a component of RNA, will label RNA. Isotopes are also used in medical diagnosis. For example, to evaluate proper functioning of the human thyroid gland, which produces the iodine containing hormone thyroxin, doctors often administer radioactive iodine and then scan the gland later to locate the gland and determine if the amount and distribution of the iodine in the gland is normal (figure 1).

Figure 1 Radioactive Isotopes (a) Physicians use scintillation counters such as this to detect radioactive isotopes. (b) A scan of the thyroid gland 24 hours after the patient receives radioactive iodine.

Bacteria often produce acids and, less commonly, bases when they degrade compounds to gain energy. To prevent drastic shifts in pH, which would be deleterious to growth of the organism, it is very common to add compounds called buffers to the growth medium that maintain the pH near neutrality. A common buffer is a mixture oftwo salts ofphosphoric acid, Na2HPO4 and NaH2PO4. These salts can combine chemically with the H+ ions of acids and the OH: of bases to produce neutral compounds, thereby maintaining the pH near neutrality.

Small Molecules in the Cell

All cells contain a variety of small organic and inorganic molecules, many of which occur in the form of ions. About 1% of the weight of a bacterial cell, once the water is removed (dry weight), is composed of inorganic ions, principally Na+ (sodium), K+ (potassium), Mg^+(magnesium), Ca2+ (calcium), Fe2+ (iron), Cl: (chloride), PO43: (phosphate), and SO42: (sulfate). Positively charged ions are required in minute amounts in order for certain enzymes to function. The negatively charged phosphate ion plays a key role in energy metabolism. This will be discussed in chapter 6.

The organic small molecules include compounds that have accumulated in the process of metabolism of sugars to supply the cell with energy. These are precursor metabolites, which are converted to the building blocks of large molecules, the macromolecules, which will be considered in the next section. The building blocks, also small molecules, include amino acids, purines and pyrimidines, and various sugars.

An especially important small organic molecule is adeno-sine triphosphate (ATP), the storage form of energy in the cell. The molecule is composed of the sugar ribose, the purine ade-

nine, and three phosphate groups, arranged in tandem (figure 2.11). This is an energy-rich molecule because two of the bonds which join the three phosphate molecules are readily broken with the release of energy. The breakage of the terminal high-energy bond of ATP results in the formation of adenosine diphosphate (ADP), inorganic phosphate, and the release of energy. The role of ATP in energy metabolism is covered more fully in chapter 6.

Macromolecules and Their Component Parts

Macromolecules are very large molecules (macro means "large") consisting of several thousand atoms each. The four major classes of biologically important macromolecules are proteins, poly-saccharides, nucleic acids, and lipids. These four groups of macromolecules differ from each other in their chemical struc-

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