Chapter 3 Bonds found in biological chemistry

Each electron orbital has a specific allocation of spaces available for electrons to fill (see Figure 2.3, p. 9). In the case of the outer orbitals, it is unusual to find all the spaces empty or full and one atom will seek out another compatible atom so that they can share their respective electrons and fill their outer orbitals. This arrangement creates great stability for the associated atoms, which is why, whenever possible, bonds are formed, between individual atoms.

Taking the examples of hydrogen and carbon used in Chapter 2 (Figure 2.3), it is possible to see that hydrogen:

However, carbon:

The final result of this union is that four hydrogen atoms attach themselves to one carbon atom, thus filling the outer orbitals of both the carbon and the hydrogens satisfying the needs of both elements (Figure 3.1).

Figure 3.1 Formation of methane, with additional diagrams showing some of the more common chemical representations of this molecule.

It is a matter of simple arithmetic to work out where this leads: a more complex molecule – ethane – can be formed from two carbon atoms and six hydrogen atoms Figure 3.2. The process can be continued to make an even longer compound called propane (Figure 3.3).

Figure 3.2 Formation of ethane and common chemical representations.

Figure 3.3 Formation of propane.

Note: as drawing chemicals out in this way can become complicated, there is a need for a method of abbreviation. Each figure, therefore, contains examples of various chemical shorthands used to represent these structures. This will enable you to become used to seeing them. Naming and representation will be covered in more detail in Chapter 5 ‘Nomenclature: representation of chemical structures and basic terminology’.

Covalent Bonds

Bonds, formed by completely equal sharing of electrons, such as the previous examples, are called covalent bonds. This principle of bond formation can be applied to other elements, such as oxygen, nitrogen and sulphur, to create various organic compounds that can be structural or part of the metabolic processes of a plant or animal.

Covalent bonds have set bond lengths and angles, dictated by the electron orbitals of the atoms that are bonding together. Each atom has a distinctive arrangement of electrons due to the:

• electrical field produced by the orbiting electrons

• distance the outer orbital is from the nucleus

• shape of the orbital (Figure 3.4), as mostly electrons do not move in a perfectly circular orbit around the nucleus.

Figure 3.4 Different shapes of electron clouds.

For a greater appreciation, blow up balloons of different shapes and arrange them as you see them in Figure 3.4. The different balloons are the accepted shapes of electron orbitals and the shape of the electrostatic force created by this orbital. Notice how it is possible to bend the orbital shown in B around the axis, but that in C the movement around the axis is restricted because the sides of the balloons push against one another limiting movement.

Electron clouds are not solid but are negatively charged (like similar poles on magnets), which means that they repel one another to a particular distance and therefore into a particular shape, as in the balloon experiment. Therefore, when several of these clouds are in close proximity, which is what occurs when several atoms bond to form a molecule, the molecule acquires a specific shape.

Naturally, the above is a very simplistic explanation of what really happens, but it is important at this stage to appreciate that chemistry, and therefore pharmacology, is three dimensional, and it is very necessary to starting thinking in three dimensions to gain a proper appreciation of pharmacology, as the three-dimensional concept is very important when considering how chemicals (substrates) fit into sites that activate physiological processes.

Each substrate and site has a specific shape and in many cases only certain molecules will be allowed to fit into the site, which may be on an enzyme, the surface of a cell or at a nerve ending (see Chapter 11 ‘Amino acids and proteins’, p. 85 and Chapter 19

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