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Basic Biochemistry

To arrive at the molecules of life and understand their structure and function, we must consider the most common elements, such as Hydrogen, Oxygen, Carbon, and Nitrogen, and how they bond to each other to create molecules.

Chemical bonds, partial charges and molecular behavior

Molecules are created when atoms form chemical bonds. This can happen when the atoms share pairs of electrons, or when positive and negative charges attract each other, or in more complex ways in metals.

Let's look specifically at electron sharing. A basic example is the hydrogen molecule, composed of two hydrogen atoms, which is denoted either as H2 or as H-H. Each hydrogen atom contributes exactly one electron to the bond.

Atoms of other elements (such as Carbon, Oxygen, and Nitrogen) typically have more electrons that they can share. Consider another very common molecule, water: H2O or H-O-H. The O atom contributes six electrons to the bond, compared to the H atoms which contribute one electron each. This creates the chemical bonds between each H atom and the O atom. The O atom will now be surrounded by 8 electrons, making the structure of the water molecule chemically stable and the bonds strong.

However, although the number of positive and negative charges within the molecule are exactly matched, they are not electrically balanced. The O atom tends to attract the negative electrons more towards itself, creating a slight imbalance with respect to the H atoms. Therefore in the single-bonded H-O unit, the O end carries a partial negative charge, while the H end carries a partial positive charge. Such units and molecules that have this slight charge imbalance are said to be "polar."

Polar molecules and partially charged units influence molecular behavior and cause molecules to interact with each other in specific ways. Polar molecules form weak and therefore fleeting chemical bonds. These are commonly known as hydrogen bonds, because most often they involve the partially positively charged H ends. The prototype is of course the hydrogen bond between two water molecules, responsible for many of the special properties of water.

Molecular Reactivity

Earth life is carbon based, in that carbon-carbon and carbon-hydrogen bonds dominate in the molecules of life. However, such molecules are quite inert and unreactive. To make them reactive at typical Earthly temperatures they need "heteroatoms" ("hetero" is Greek for "different"). Oxygen, Nitrogen, Sulphur and Phosphorus typically play such a role.

All life on Earth is built by a small set of "polymers" - large chains of basic molecular or atomic units. Proteins and nucleic acids are two families of key "biopolymers," all based on carbon. Proteins are polymers that play a structural role, as well as being "catalysts." Catalysts help start chemical reactions. Nucleic acids can store and transfer hereditary information; they are the genetic molecules.

Carbon's properties make it a very versatile element when it comes to forming the molecules that are important to life. It can form several different types of chemical bonds, it can form bonds which are weak and ones that are strong, and it forms a number of stable compounds.

The chemical properties of Silicon (Si) are most similar to those of Carbon, hence its place in the periodic table of the elements (same column, just one row below). Si is therefore a possible alternative for alien life: silicon-based life instead of our carbon-based life. However, despite being most similar, silicon's bonding properties are not equivalent - the variety of polymers that can be put together from silicon is very limited. More importantly, the temperature ranges for carbon and silicon-based chemistry are different. The temperature range for carbon reactivity is much better matched to liquid water.


Liquid water is essential to life on Earth. You are about 60% water by weight. That water is used to dilute and remove waste, and to transport nutrients throughout your body, among other things. Plants are similarly are composed of largely water, which they use for nutrient acquisition and transport, to aid gas exchange, and for photosynthesis. All life that we know of uses water to perform its basic functions.

What makes H2O so special?

First, the temperature range of the liquid phase of water (0? to 100? Celsius) is wide enough to allow for plenty of molecular reactivity in the interactions of the biopolymers. Within this temperature range, carbon bonds are stable, yet reactions can have fast rates. Second, H2O is a very polar molecule, which allows many different charge-based processes to occur. For example, small polar molecules arrange themselves in predictable ways depending on whether their partially charged end is hydrophobic (water-repellant) or hydrophilic (attracted to water). Larger polar molecules get some of their shapes for the same reason. Liquid water is always a source of positive electrical charges (hydrogen ions) to contribute to reactions. Finally, liquid water has high specific heat (a lot of energy is needed to raise its temperature). Because of that property, temperature fluctuations of water are minimized, making water a very stable medium (friendly environment for chemical reactions).

Can we imagine alien life, i.e., a biochemistry, that is not dependent on liquid water? The answer is a tentative "yes," though no medium known today even comes close to water as a supportive environment for life. For example, imagining environments colder than Earth would make us examine liquid ammonia (or the more common, ammonia-water mixture). Colder still, at -180 C, are the lakes and rivers on Titan, made of liquid ethane and methane. But in all these low-temperature cases we can't imagine easily the catalysts that would speed up chemical reactions to rates that are fast enough to sustain the coordinated networks that are needed for life. At warmer temperatures we would encounter nonpolar organic liquids as a medium, which would make them behave in ways that are less supportive to life. The impurities needed to create some polarity in these liquids are difficult to imagine. Water remains the best and most abundant medium nature seems to offer.

Солнечная система и ее тайны