The atom: The smallest unit of pharmacology

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Chapter 2 The atom

The smallest unit of pharmacology

Chapter contents

What is an atom? 7
The structure of an atom 9
The electron is the key to pharmacology 9

To achieve a confident working knowledge of pharmacology you need a sound understanding of the structure, and therefore the function, of the basic unit of chemistry: the atom.

What is an Atom?

• An atom is the smallest complete unit that cannot be broken up by chemical means. It has chemical properties in its own right.
• Atoms of exactly the same composition behave in exactly the same way in chemical reactions.
• These identical atoms are called elements (later in the text, this term will be used interchangeably with atom).
• Different atoms or elements can combine with each other to form chemical compounds, which can be relatively small, like a water molecule, or extremely large and complex, like the DNA helix.

Atoms consist of (Figure 2.1):

• a nucleus
• electrons orbiting around the nucleus.
image

Figure 2.1 Composition of an atom. Overall charge is neutral as the negative charge of the electron orbiting around the nucleus is neutralized by the positive charge of the proton in the nucleus.

The Nucleus

The nucleus is made up of protons and neutrons:

• Protons have a positive charge.
• Neutrons have no charge.

For the level of pharmacology covered in this book, the presence of neutrons is acknowledged here for completeness but they will not be discussed any further.

The Electrons

Like moons around a planet, electrons orbit around the nucleus (Figure 2.2). The space in which they move around the nucleus is therefore called an orbital.

image

Figure 2.2 The general atomic structure without the details of the composition of the nucleus. From now on the nucleus will be represented without differentiation of protons or neutrons.

How are Electrons Arranged Around the Nucleus?

Convention dictates that each orbital has a fixed number of available slots that can be filled until they reach capacity. Once an orbital becomes filled, the electrons start to fill the available slots in the next, higher orbital (the next orbital away from the nucleus). In this way, the bigger the atom, the more electrons it will have, and the more orbitals these electrons will need to fill (or occupy) around the nucleus, as can be seen in Figure 2.3.

image

Figure 2.3 Demonstrating atoms of different sizes have different orbitals.

It is important not to think of electron orbitals as being two dimensional; in fact, they can take several different three-dimensional paths around the nucleus. For simplicity’s sake, however, the atomic structure is kept to a circular two-dimensional shape in diagrams, as this is accepted convention.

The Structure of an Atom

An atom always seeks stability. So, under normal conditions, the number of electrons orbiting around the nucleus exactly equals the number of protons in the nucleus:

Number of electrons=Number of protons

The Electron is the Key to Pharmacology

Usually, protons in the nucleus remain tightly bound to the nucleus. This means they have to stay where they are and will take part in a reaction only under extreme conditions, e.g. in the presence of bombardment by high-energy particles such as a radioactive reaction. As this is not a chemical reaction, it is not relevant to pharmacology. Electrons, however, are not so tightly bound and it does not take too much energy to encourage the electrons to take part in different chemical reactions:

• Electrons interacting with other atoms (which is what happens in bonding) can form more complex structures (molecules) (Chapter 3 ‘Bonds found in biological chemistry’, p. 11 and Chapter 4 ‘Bonds continued’, p. 21).
• Electrons can also shift in position to an unoccupied orbit at a higher level, rather like a ball being kicked from flat ground to a level higher up a slope. The return of the electron (the ball rolling back down the slope) to its original position releases valuable energy that can be harnessed and used by a biological organism. This is what happens in photosynthesis (Figure 2.4, Chapter 9 ‘Carbohydrates’, p. 63).
• Electrons can also be traded like currency between specialized molecules to create energy (this happens in units in the cell called mitochondria which contain special molecules to do this, in a process called oxidative phosphorylation). This is similar to having water flowing down a hill and having small water wheels positioned at intervals to take advantage of the energy the movement of the water creates (Figure 2.5)
• Under certain circumstances, electrons can also be made to take part in reactions that should not occur and are detrimental to the function of human tissue. These aberrant molecules are called free radicals (see Chapter 7 ‘Free radicals’, p41).
image

Figure 2.4 Showing the movement of an electron in photosynthesis.

image

Figure 2.5 Analogy showing how electron transfer creates energy and how this can be harnessed.

From these few examples it is possible to see the important role electrons have to play in pharmacology.

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