Chemistry for Biology: you can never know too much! Part 1

Unit 16 of the Applied Science BTEC qualification is entitled "Chemistry for Biology Technicians". The overview and justification provided by the course designers and monitors contains some important observations.

"Biology technicians ... may look after a variety of animals, plants and other organisms or prepare tissue slides in human anatomy and pathology laboratories." 

"Technicians carry out microbiological tests on water or pathology specimens, work in infection control, investigate blood smears, make vaccines, grow cell cultures and carry out biochemical tests and DNA analysis."

These roles have historically been the preserve of technicians, but as you will know from your placements, Quality Assurance and auditing (samples and notes) is possibly the main responsibility of many Hospital Technicians, in conjunction with use of a growing number of automated sample analysis instruments. In other words, what you do in a laboratory will continue to evolve and so it is essential that you understand fundamental principles more than specific techniques. After all, when I trained for my PhD, I used equipment that is long since obsolete and the technical staff too.


"Biological processes work because of the underlying chemical processes."

This is much more important! And this is why we need to focus on the areas of chemistry that are indispensable and provide you with a fundamental platform for laboratory work that will be enduring. 

"If learners understand the units of concentration, they will feel more confident that they are making up a solution or diluting it correctly."

"If learners understand the nature of chemical bonding, they will understand why certain solvents are used in processing tissue samples."

"Knowing more about chemical formulae enables learners to identify the correct chemicals to use. Understanding about rates of reaction and equilibrium allows learners to see why standard laboratory protocols may have timed steps."

Agreed! So let's identify the key aspects of Chemistry for Biologists. Let's begin with the aims and objectives of this unit, with more advanced topics to follow in other Chemistry Units. I am using Linus Pauling's classic Text as my general source with contemporary knowledge taken from the research literature.

1. Understanding the laws of thermodynamics, in particular the relationship between enthalpy and bond making and breaking.

2. Understanding how rates of reaction are affected by varying the reaction conditions

3. Understanding the key features of equilibrium processes

4. Understand the structure and properties of simple organic molecules

Let's take a look at (1) Thermodynamics, specifically energy and enthalpy.

Enthalpy. The term comes from a combination of a Greek prefix and a verb: "en" (within) and "thalpein" (to heat). There are two fundamental laws of thermodynamics (Greek for heat and power, originally hyphenated and then combined: this word has only been in use for 150 years). I like Linus Pauling's definition:

"The change in energy accompanying change of a system from an initial state to a final state is determined exactly by the initial state and the final state, and is independent of the path by way of which this change is effected"

So the enthalpy of a system (H) is defined by the equation:

1.             H = E + P.V

where E is the internal energy and P is pressure and V is volume. A nice little addition to the First Law (sometimes referred to as the law of "Conservation of Energy") is Hess's Law which states that:

The heat of any reaction ΔH∘f for a specific reaction is equal to the sum of the heats of reaction for any set of reactions which in sum are equivalent to the overall reaction. 

So if there are 2, 3, 5 or even 10 steps between a given set of reactants (eg Glucose and ATP) and a product (eg Pyruvate) then the enthalpy value is the same. So, by understanding the first law of thermodynamics, provides a framework for the energy calculations you will have come across in the Biochemistry Unit, which of course underpins our whole appreciation of nutrition and energy metabolism. For the more chemically minded, I like this Chem Wiki site on Hess's Law.


Endothermic (heat extracting) and exothermic (heat releasing) reactions. The easiest way to appreciate the concept of enthalpy, is to monitor the temperature change accompanying the solvation (dissolving) of ionic compounds in water. The two most commonly used examples are Calcium Chloride and Ammonium Nitrate. We shall carry out this experiment and you will use this to help with the assignments. (What vessel will you use for these experiments? See equations 1, above).

And now I am going to jump to (4), leaving (2) and (3) for Part 2.

Bonding. By choosing Linus Pauling's text for my Blog, I have in fact chosen the Mr. Bond of Chemistry. Or as Linus Pauling might have said, "The name's Bond. Linus Bond". Maybe not! Anyway back to the serious stuff. The attractive forces that sometimes occur between two elements in a molecule is referred to as a bond or an interaction. I like to think of bonds and interaction on a scale of affinities (or interaction energies). Ionic bonds, such as those between alkali metals and halides (eg NaCl) arise owing to the "spare" electron in the Na element that sits comfortably in the Cl atom, which is electron deficient. As Sarah said, the Chlorine steals an electron from the Sodium, thereby creating an ionic compound. Covalent bonds also arise as a consequence of electron reorganization, but for example in the case of Ethanol, (write the formula out), we have C-H, C-O, C-C and O-H bonds to consider. If you think of the simplest situation in which two hydrogen nuclei (1 proton each) are stabilised by a single electron (write out the chemical formula). I say simple, but try telling that to Schroedinger in 1925, or worse still, me in my first University Chemistry class in Sheffield in 1977!. The point is that it is the sharing of an electron that is critical. Covalent bonds achieve their stability by reducing the conflict between the two positive nuclei (in this case two single protons). Schroedinger derived a simple equation, but one that combines a series of complex mathematical and quantum elements: a little like the subatomic composition of an element such as Carbon. We now understand that covalent bonds are the product of electron sharing in such a way as to provide two otherwise repulsive nuclei, with a favourable energy state: subatomic contentment. However, an appreciation of the role of electrons in the context of nuclear interactions is critical for all areas of Science. Think in terms of reactivity in chemistry (eg organic synthesis), biology (eg enzyme catalysed metabolic pathways) or in physics (eg nuclear power). We have already considered the complex enzyme catalysed reaction in which Glutamate Dehydrogenase "supervises" the reversible redox reaction between Glutamate and NAD+. (See earlier Blog). This is a perfect example of why Biologists must appreciate the chemistry of bonds, valency and electrons!conversion. We shall look at some Bond energies and geometries, to try and firm up your understanding of these concepts in the lab sessions.

I want to add to the concept of ionic and covalent bonding, the Hydrogen Bond and Hydrophobic Interactions. These phenomena lie on my spectrum of interactions and are less fixed than ionic and covalent bonds, although an important aspect of H-bond theory incorporates some simple geometry. The Hydrogen Bond is possibly one of the most important (certainly the most talked about) interactions in Biochemistry. However, the hydrophobic interaction, in which two molecules prefer each other's company and not that of water (or a similarly "polar" environment). The Hydrogen Bond is nicely understood in the context of the structure of DNA which you can read about here. However, the hydrophobic interaction is in my view just as important in Biology. For example, as a protein begins to emerge from the ribosome, it "samples" a set of shapes which minimise its energy. It may combine with water (forming polar interactions, some of which may be Hydrogen Bonds), but often there is a great tendency for the hydrophobic "elements" of the primary structure (eg leucines, alanines, tryptophans etc) to associate with each other, to avoid the water or the polar groups. This is in fact believed to be the "driver" behind the first phase of protein folding. What could be more important! 

This Blog is intended to support your work towards the Unit 16 assignments and I shall follow this with Part 2 in which I try and distill the concepts underpinning reaction kinetics and redox phenomena and the associated equations But don't forget, your enzyme reaction classes provided you with considerable insight into the factors that can affect the rate of a chemical reaction.