Enzymes (and Proteins) Part 1

What Are Enzymes?

I'm sure every A-level biologist has heard the term "Biological catalysts" used to describe enzymes. But what does this mean, and what exactly are enzymes?
Biological Catalysts: This simply means that enzymes speed up chemical reactions within our body without being 'used up' themselves. In AS biology this is often in the context of the digestive system, but more on that later.
Here are some other useful terms:
Substrate: A molecule that binds with an enzyme to be catalysed. It is the 'reactant' that will be catalysed by the enzyme to become usually one or two 'product' molecules.
Active Site: The part of the enzyme that the substrate binds to. This will be better illustrated in a picture further on in the post.
Enzyme-Substrate Complex: If you are ever in doubt during an enzyme question, then throw this phrase in. Heck, throw it in twice! When the substrate binds to the enzyme, they form an enzyme-substrate complex. This is just a fancy name for the intermediate phase where the enzyme actually catalyses the substrate before releasing the products.

The Structure of Enzymes

Enzymes are proteins. This means that they all have primary, secondary, tertiary (and sometimes quaternary) structures. (This is something you might be familiar with from elsewhere in Unit 1). I will explain what these terms mean below for those who don't already know. But before you skip ahead! If you already know protein structure- consider this little problem: Examiners often ask why enzymes are specific to their substrate molecules. If you can answer this then feel free to skip. If not I suggest you read this next bit...

Primary Structure: (remember these structures apply to all proteins, not just enzymes)

The only difference between each type of amino acid is the "R" group

A long sequence of amino acids.
Is the order of amino acids important? Yes, incredibly so, as it determines the final shape and function of the protein later on. I will go into more detail about amino acids and how they form proteins later, but for the moment it is useful to understand that each type of amino acid has a different R group which is what distinguishes it from other amino acids. The atoms in these R groups and the order which the amino acids join together will determine everything about how the protein functions.

Secondary Structure

The folding of the amino acid chain into a certain shape.
There are two shapes you should know of, the alpha helix and the beta-pleated sheet as shown below. These specific shapes are caused by hydrogen bonding between the amino acids.

Alpha Helix

Pleated blinds illustrate the beta-pleated
sheet shape nicely.

Tertiary Structure

The folded and coiled amino acid chains fold even further.
This gives the tertiary shape. Imagine you are holding a curly phone cord. That shows the secondary structure. Now imagine bending it around on itself until you have some horrible knotted mess. That is your tertiary structure. But what magic causes this? As hinted at earlier, this is due to complex interactions between atoms and ions in the amino acids, namely:

• Hydrogen bonds between polar R-groups
• Ionic bonds between charged R-groups
• Hydrophobic interactions between non-polar R-groups
• Disulphide bonds in amino acid chains where sulphate atoms are present

Don't worry about the polar, charged and  non-polar stuff too much, that's just some extra detail to aid the understanding of any chemistry students here. I'd suggest following this link for a more detailed explanation of the interactions in tertiary structures.

Quaternary Structure: This is like getting your phone cord, your auntie's phone cord and your neighbour's phone cord and tangling all of them together. Only proteins with multiple amino acid chains (e.g. haemoglobin) have a quaternary structure and it is simply the shape that they make when they all coil together.

And that's it for protein/enzyme structure,

...but I still hear some of you asking why many enzymes are specific to just one substrate.

This is all to do with the tertiary structure of the enzyme. If the tertiary structure is like the final shape of the enzyme, then guess what the tertiary structure determines. That's right, the shape of the active site! If every type of enzyme has a unique primary structure, giving it a unique tertiary structure then only a substrate with a shape specific to the enzymes will fit (forming that E-S comlpex!). Only one specific key can fit into a certain lock. This idea is key to understanding (note understanding, you can still learn some of the later ideas, but this phenomenon helps understand them) many ideas at A level surrounding enzymes. For example; how inhibitors work, why enzymes can be denatured and so forth. If you're clever I reckon you could work some of that out for yourself.

Part 2 of my posts on 'Enzymes' will cover all the graphs and models of enzyme action. That will be the real 'meat' of the enzymes topic and cover how they actually work. Until then, thanks for reading and I hope this has been useful!  

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