Life/Citable Version

Molecules of living things

One set of organic molecules provides the material building blocks for living things: compounds of carbon, oxygen, nitrogen and hydrogen. Those often contain other elements, such as sulphur and phosphor. Organic molecules always have a primary backbone of carbon atoms. In cells, organic molecular species exist dissolved or in mixtures of colloidal aqueous solutions, never completely homogeneous, semi-comparmentalized by sheets of lipid and proteins, each pool having a different internal composition — different organelles. The material stuff of life consists of carbon chains, studded with other atoms, and arranged in lagoons of fat, water, and salts, of differing composition. The specific compositions determine the physico-chemical as well as the biological properties of the compartments: charge-distributions, with overall electric neutrality, mass distribution leading to molecular structures and functional properties, viscosity, and osmotic pressure - providing, among other things, the basis for the generation of electric fields and fluid and material shifts with the environment (alloutside the compartment).

Why does carbon hold the central place in forming living materials? The physical chemistry of carbon shows it can form many different type of bonds to other elements, and, even very easily, to itself, forming carbon-to-carbon bonds. Not only does carbon react with diverse atoms, but, due to its energy content and the number of electrons available to form bonds, carbon can form different types of (covalent) bonds. These covalent bonds vary in strength as well as in conformation but are all remarkably stable. The standard, most simple, bond carbon can form is that of a tetrahedron structure, of four single bonds (one shared electron each between carbon and four other atoms). Methane (carbon bonded with four hydrogens) has carbon shares 4 electrons, one to every single hydrogen, to form a pyramidal structure with carbon in its center and the hydrogen on its extremities, this tetrahedral structure of carbon atoms accounts for the hardness of diamonds. Some bonds involve more than one electron shared between two atoms, and for that reason are called double, and triple bonds; importantly, these different bonds exhibit three entirely different geometries. That means that if a double bond is reduced to a single bond, for example, that region of the molecule actually changes shape. The avidity for carbon to bond to itself accounts for the formation of organic macromolecules. Carbon atoms easily join into longer chains and and even closed rings; and small carbon molecules (like sugars, amino acids and nucleotides) easily join into huge macromolecules. Those macromolecules can derive stability from their environment by electrostatic interactions such as hydrogen-bridges, and so, though readily formed, do not necessarily dis-associate so easily.

Because of those properties of carbon, organic macromolecules can contain tremendous banks of information coded in their very structure. Not only can each of the constituent molecules forming a huge macromolecule be one of several categories of chemicals, like sugars or nucleotides, but each category contains several species (e.g., for nucleotides: adenine, thymine, guanine, cytosine, uracil). Various substitutions of elements, like the halogen for hydrogen, add to the possible combinations for different chain sequences, hence informational units. Even if a macromolecule contains the exact same number of the exact same constituent molecules as another macromolecule, the order, or sequence, of species vary, allowing exponential numbers of possibilites. The shapes of the bonding orbitals of at least some of the carbon bonds add yet additional dimensions of information; for example, in double bonds, species can be connected in one of two different orientations, called in organic chemistry cis or trans.

Macromolecules carry sufficiently large amounts of information to specify the molecular interactions that enable cells to grow, survive and reproduce. These molecules, are uniquely (or at least primarily) found in living things. They are are dynamic, but stable, because covalent bonds can be formed between carbon-containing molecules in several different ways. This means that, in changing from one type of carbon-to-carbon bond to another type, energy can be consumed or released without, in the process, destroying the molecule. Such changes not only affect free energy, but also affect the actual shape of the molecule, and side groups attached to it. Further, these reactions have low enough disassociation constants to be reversible. In this way, for at least some organic molecules, the "pulse of life" is represented at an atomic level. Are there any other ways to make complex molecules with similar versatility? Yes, by using silicon — carbon's close relative on the periodic table. But whereas the bonds of carbon are very stable at the temperatures that are compatible with life as we know it, silicon's Si-Si bonds are much more likely to disassociate. That is not true at much higher temperatures, and so it is possible to imagine biochemical reactions, more or less as we know them, occurring at, say, 400 degrees Celsius with silicon taking the place of carbon. The stuff of life, should it exist on other worlds, might be carbonic, or might conceivably be based on another element, such as silicon, depending on conditions.

Of all the atoms with a similar chemistry to carbon (e.g., silicon), carbon’s structure renders it uniquely capable not only of bonding stably with itself but also with the other atoms found in living things — and carbon abundance in the universe far exceeds alternative elements with carbon-like properties. The atoms binding with carbon in living things include especially hydrogen, oxygen, nitrogen and phosphorus, necessary for forming the sugars, amino acids and nucleotides that make up the appropriate sequences of macromolecules — nucleic acids, proteins, lipids, and polysaccharides — involved in the molecular-interaction networks of cells. Included among those networks of interactions are those that enable cells to import and transform energy and energy-rich matter from the environment. Carbon also enables its compounds to readily dissolve in or associate functionally with water, of which the earth has a great abundance, and whose unique chemical properties for a liquid allow carbon chemistry to exploit its own life-giving properties. Elsewhere in the universe, where conditions differ greatly from earth’s, other atoms may hold a central place in life. If they do, one would expect that they too would exhibit structures of such variation in size, shape, charge and composition, that their very existence provides ordered information.