Water makes up ~70% of the total mass of living things.

It is almost certain that life initially arose in an aqueous environment, although the exact steps from non-living to living remain the subject of on-going research and lively debate.

Some chemical background

A chemical compound is a substance composed of a specific type of molecule.

Molecules are composed of two or more atoms held together by chemical bonds.

A molecule of water contains one oxygen atom attached to two hydrogen atoms.

Molecules of carbon monoxide arranged on a platinum surface using a scanning tunneling microscope.

Molecules display emergent properties. They are more than the sum of their atoms.

An atom has an equal numbers of positively charged protons, located in its nucleus, and negatively charged electrons .

The atoms of different elements differ in the number of protons they contain. The number of protons in an atom is its atomic number.

The electrons move around the nucleus in what are known as orbitals.

The size of the atom is determined by its electron orbitals, the nucleus is very small compared to the atom as a whole.

Aside from hydrogen, atomic nuclei also contain uncharged particles known as neutrons. The number of neutrons in different atoms of the same element can vary.

Atoms with the same number of protons and different numbers of neutrons are isotopes of the same element.

Since electrons are so much less massive than protons and neutons, an atom's weight is determined primarily by the number of protons and neutrons in its nucleus.

An element's atomic weight reflects the proportions of its isotopes found in nature.

Some isotopes are stable, others are not. Unstable isotopes undergo a process known as radioactive decay .

In alpha-decay, two protons and two neutrons, a helium nucleus, are ejected from the unstable nucleus.

In beta-decay a neutron is transformed into a proton, which remains in the nucleus and an electron, a beta particle, which is ejected.

When the number of protons in the nucleus changes the atom changes from one element into another.

Atoms contain equal numbers of electrons and protons and are electricially neutral.

An atom can become charged if you either add or remove electrons. Charged atoms are called ions.

A positively charged ion is called an anion, a negatively charged ion, a cation.

Chemical bonds and electronegativity

The formation of a chemical bond between two atoms involve the sharing of electrons.

Two electrons, one from each atom, are involved for each bond formed. The shared electrons are located in the outer or valence electron orbitals of the atoms.

Each element has its own characteristic electronegativity. Electronegativity is a measure of how tightly the positively charged nucleus holds the atom's outer orbital electrons.

If the electronegativities of the two atoms in a bond are equal, then the electrons are shared equally between them and the bond is said to be non-polar.

If the electronegativities of the two bonded atoms are unequal then the electrons will shared unequally.

On average, the electrons will spend more of time around the more electronegative atom and less time around the less electronegative atom.

This leads to a negatively charged and a positively charged side to the bond. Such a bond is said to be polar.

In the most extreme case, one atom completely loses its electron to the other.

The atom that loses the electron becomes positively charged, while the atom that gains the electron becomes negatively charged.

The two ions are linked by what is known as an ionic bond.

To determine whether the bond between two atoms is polar or not, just subtract the electronegativities of the two atoms that make up the bond.

If the absolute value of the number is larger than about 0.5, the bond is considered polar.

A universal glue: van der Waals Interactions

All molecules interact with one another through what are known as van der Waals interactions.

These are weak electrical interactions that arise from movement of electrons around the positively charged nuclei.

This movement leads to the formation a weak and 'flickering' electrical field, a temporary dipole, around each molecule.

As two molecules approach, these electric fields interact and attract one another.

This attraction is strongest when two molecules are separated by what is known as their van der Waals radii.

As they get closer the attraction turns very rapidly into an increasingly stronger repulsion.

Each atom and each molecule has its own characteristic van der Waals surface.

This is the closest distance it can come to another other atom's van der Waals surface.

There are a number of ways to draw molecules, but the space-filling or van der Waals surface view is the most realistic.

What are the implications of bond polarity?

A polar bond is associated with a stable electrical field, known as a permanent dipole. This leads to electrostatic interactions between molecules.

These interactions, known as hydrogen bonds, are much stronger than van der Waals interactions.

We can see the consequences of these interactions by comparing the properties of molecules with and without polar bonds.

We will look at the temperatures of phase changes, that is the temperature at which a compound turns from a solid to a liquid, its melting point, and from liquid to gas, its boiling point.

These phase changes reflect how strongly the molecules of the compound interact with one another.

Compounds

Compared to compounds that contain the same number of electrons, water displays a number of anomalous behaviors.

For example, both its melting and boiling points are quite high compared to other molecules of similar weight.

We can measure the strength of this surface tension in various ways. The most obvious is the weight that it can support.

This paper clip floats on water.

Solubility

The surface tension of water has to be dealt with by all organisms. Some, like the water strider, use it to cruise along the surface of ponds.

The strider walks on the surface of the water because the surfaces of its feet do not get wet, they are hydrophobic.

Some molecules, like sugars or alcohols, readily dissolve in water, they are hydrophilic. Why do some molecules dissolve in water and others do not?

Think of water as a network with the links between the molecules formed by H-bonds.

To insert a molecule into this network you have to break some of the H-bonds between the water molecules.

If the molecule you are trying to insert can make H-bonds with the water molecules, then the net loss of H-bonds in the system is small.

The molecule acts like water and is soluble in water, it is hydrophilic.

Which molecule is water soluble?

On the other hand, if the molecule cannot make H-bonds, then the total number of H-bonds in the system will be decreased.

To maximize the number of H-bonds that can be made, the water molecules will arrange themselves in a shell.

This ordering of water molecules decreases the entropy or disorder of the system, it is unlikely to occur spontaneously.

Molecules that cannot make H-bonds with water are insoluble in water, and so are to referred to as hydrophobic.

As a general rule, the more polar bonds a molecule contains, the more hydrophilic it will be. The fewer the polar bonds, the more hydrophobic.

At the same time, the smaller the molecule, the smaller are the effects of inserting it in between water molecules.

The solubility of a molecule in water depends upon its size, shape and the number of polar bonds it contains.

This general rule also applies to macromolecules, such as lipids, carbohydrates, proteins, and nucleic acids.

When a macromolecule is dissolved in water, its structure is determined in large part by its interactions with water.

For example, proteins contain both hydrophilic and hydrophobic groups.

The hydrophobic groups will tend to be buried in the center of the molecule, minimizing their interactions with water. The hydrophilic groups tend to be on the outside, maximizing their interacting with water.