Water makes up approximately 70% of the total mass of living organisms.

It is quite likely that life arose in an aqueous environment, although the exact steps from non-living to living systems remains the subject of on-going research and lively debate.

The properties of water arise from the properties of water molecules, and they are the major determinant of how cells and their components are organized and how they function.  Water is also a reactant/product in many of the reactions that occur in living systems.

This means that to understand (i.e. make sense of) biological systems we need to know some basic chemistry. 

• On the graph above, what would "total energy" look like as a function of distance between atoms?
• Why do molecules begin to repel one another once they get closer than their van der Waals radii? 
• Under what conditions might the nuclei actually fuse together?
• Where does the energy released when a bond forms go?

Bond stability:  When atoms or molecules interact through van der Waals interactions, the bond energies are weak.   In a solution, molecules are moving rapidly.  The temperature of the system is a measure of their
average kinetic energy = 1/2 (average mass x average velocity²). 

Under the conditions where life exists, the kinetic energy of the average molecule is greater than the potential energy of van der Waals bonded atoms - so the bonded atoms are knocked part.  Only when many van der Waals interactions take place between two molecules is the bonded form stable. 

Covalent bonds: In van der Waals interactions, the atoms/molecules retain their hold on their electrons.  There are cases, however, where atoms come to "share" each other's electrons

This sharing, known as a covalent bond, produces a much stronger bond interaction (lower energy). 

This applet (made by ChemThink) will allow you to play with atoms and bonding.

just "jump through" the parts in the middle involving the periodic table.

When atoms form a bond, their van der Waals surfaces merge to produce a new molecular 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 (at least for our purposes).

• Consider two molecules that interact with their neighbors only through van der Waals interactions; how will the shape of a molecule affect its melting point or boiling point?
• Why do molecules begin to repel one another once they get closer than their van der Waals radii?

Polar covalent bonds & enhanced intermolecular interactions:

So far, we have been considering covalent bonds in which the sharing of electrons between the atoms involved is more or less equal.    The electronegativity of an atom is a measure of how tightly it holds onto its outer orbital electrons.

Each type of atom (element) has its own characteristic electronegativity,  If the electronegativities of the two atoms in a bond are equal or close, then the electrons are shared more or less 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 be shared unequally.

• Two molecules interact by van der Waals and H-bonds; how do their shapes influence the strength of the interactions?
• What determines if two molecules, bound together through non-covalent bonds, form a stable or unstable complex?

What are the implications of bond polarity?  We can see the consequences of bond polarity by comparing the properties of molecules with and without polar bonds.

For example CH₄(methane) and Ne (neon) have no polar bonds, whereas H₂O (water), NH₃ (ammonia), and FH (hydrogen fluoride) have three and one, respectively.  All five have the same number of electrons (10). 

Compounds

So why is water weird?   Well, in addition to the presence of polar covalent bonds, we have to consider the molecule's geometry.

Each water molecule can take part in four hydrogen bonds with neighboring molecules - it has two partially positive Hs and two partially negative sites on the O.

These sites of potential H-bonding are arranged in a nearly tetragonal geometry

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

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

As the strider walks on the surface of the water, the molecules of its feet do not form H-bonds with water molecules, they are hydrophobic.

Water soluble (hydrophilic) and insoluble (hydrophobic) behaviors: 

Some molecules, like sugars, alcohols,and most amino acids, dissolve readily 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, A, into this network you have to break some of the H-bonds between the water molecules.

If the A molecules can make H-bonds with water molecules, then the total net loss of H-bonds as the molecule enters the water is small.

Such molecules tend to be soluble in water – they are hydrophilic. 

Which molecule is more likely to be water soluble?

On the other hand, if A molecules cannot make H-bonds, then when these molecules are inserted into water the total number of H-bonds in the system decreases - the energy of the system increases (remember, bond forming lowers potential energy).

For both of these reasons, molecules that cannot make H-bonds with water are relatively insoluble in water - they are hydrophobic.

As a general rule, the more polar bonds a molecule contains, the more hydrophilic (water soluble) it will be; the fewer the polar bonds, the more water insoluble (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.

These general rules of molecular interactions with water apply to macromolecules, such as lipids, carbohydrates, proteins, and nucleic acids, which we will consider in greater detail later.

Most macromolecules 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 interactions with water.  Carbohydrates are an exception - they are almost exclusively hydrophilic and tend to adopt an extended structure in solution. 

• Why does the size of a molecule influence the molecule's solubility in water?
• Even with very water soluble molecules, such as sugars, there is a limit to the amount that can be dissolved in a specific volume of water -- what might limit solubility?
• Consider a macromolecule in which one side is hydrophilic and the other is hydrophobic. Can such a macromolecule be dissolved in water?  
• Sketch the interactions between water molecules and molecules of the macromolecule to support your answer. 

Because of the polar nature of their bonds, water molecules interact with ions, thereby making them soluble.

Take common table salt, NaCl, which normally exists as a crystalline solid. The bonds between the Na and Cl atoms are totally ionic - electrons are not shared, rather Na gives up an electron and becomes Na⁺, while Cl accepts the electron and becomes Cl^-. The solid is held together by electrostatic interactions (ionic bonds).

To remove a Na⁺ or a Cl^- ion from a salt crystal involves separating positive from negative charges.

In water, these charges are largely neutralized by interactions with the partially charged groups of the water molecules.

As salt dissolves, the Na⁺ and Cl^- ions become surrounded by a shell of oriented water molecules.

Water does the same thing to itself.

It stabilizes its own dissociation into OH^- (hydroxyl) and H⁺ ions.  

The H⁺ ion, a naked proton, does not exist as such, but is associated with water molecules, forming H₃O⁺, H₅O₂⁺ and larger ions.

In pure water, [OH^-] = [H⁺] and equal 10^-7 Molar.  That means that in a solution of pure water there are 10^-7 moles of OH^- and 10^-7 moles of H⁺ per liter.   

While these are small numbers small changes in the concentrations of OH^- and H⁺ have important effects in biological systems (see here).

You might want to brush up on the meaning of a Molar solution, the definition of pH, and what it means to be an acid or a base.

• You dissolve table salt in water - does the water become charged?
• Why is it easier to separate Na⁺ and Cl^- ions surrounded by water that it is to separate "naked" Na⁺ and Cl^- ions?