What Are Enzymes? - Structure and Location

Enzymes are a class of proteins - if you haven't checked out my hub exploring proteins, go back and check it out. Specifically, enzymes are globular (rather than fibrous) proteins that act as biological catalysts. This brings us onto the next question:

What are catalysts?

Put simply, catalysts speed up chemical reactions without being used up or chemically altered. Compared to industrial catalysts, enzymes are often many times faster. Enzymes are also specific to only one reaction and produce far fewer unwanted by-products. Biotechnologists are now being employed to find replacements for industrial catalysts. In fact, you probably use enzymes more than you realise - biological washing powders, bread, and beer are all products of enzyme applications

As discussed in the What are Proteins Series, Proteins have three (or sometimes four) levels of structure:

1. Primary structure - the order of amino acids in the chain
2. Secondary structure - how the chain initially folds into alpha helices or beta-pleated sheets
3. Tertiary structure - the 3d structure of the protein chain (usually has hydrophobic R-groups 'inside' the molecule and hydrophillic R-groups 'outside' the molecule)
4. (Quaternary structure - where several polypeptide chains bond together for a common purpose)

As biological catalysts, enzymes all share the following similarities:

• Their names all end in -ase
• Generally soluble in water
• All contain an 'Active Site'
• Activity is affected by temperature and pH
• They are specific (catalyse only one reaction)

The active site is the most important part of the enzyme, but is only a tiny proportion of the overall shape. In many cases, as few as 10 amino acids form the actual active site. Most of the amino acids are only there to maintain this tertiary structure. The active site is the area of the enzyme where catalytic activity occurs. In other words, the active site is the only part of the enzyme that 'does' anything.

Each unique enzyme has an equally unique active site. It is this shape that makes enzymes specific to one reaction. Only one substrate can fit into the shape of the active site. This is known as the Lock-and-Key hypothesis and will be dealt with later

Despite the huge variety of life on Earth, enzymes all share the same weaknesses - after all, they are all proteins. The secondary and tertiary structures of enzymes are all held in place by weak intermolecular interactions such as hydrogen bonds, disulphide bridges and van der Waal interactions. This raises common problems:

• Extreme heat and pH can break the bonds holding the shape in place - this is called denaturation and is a one way ticket.
• Low temperatures reduces the kinetic energy of the enzymes and substrate. This means the enzymes and substrate collide less frequently (if they don't bump into each other, a reaction cannot occur)
• Enzymes only work in close proximity to their substrate. In the case of digestive enzymes, somehow the food needs to be brought to the enzymes...or the other way round...

But, as said by Goldblum in Jurassic Park, Life finds a Way.

• Extremophiles survive in some very inhospitable environments - e.g. next to hydrothermic vents (high temperature) or in salt lakes (extremes of pH). The only way they survive is that they have adaptations to allow their enzymes to continue to function
• Endothermic animals (animals that make their own body heat) have spread to cover most environments across the world. Even if temperatures fall well below freezing, the warm body temperature allows enzymes to function at their best. It is no co-incidence that human enzymes perform best at 37.5°C
• Some organisms, like fungi, excrete enzymes onto their 'food' and then absorb the resulting soup. Fruit flys do the same - they vomit their digestive enzymes onto your food and then drink up the broth.
• Most organisms, ourselves included, have evolve specific structures where their food and enzymes meet. These are the digestive tracts seen in most higher animals.

Enzymes carry out the 'will' of DNA; it is through enzymes (and other proteins) that DNA controls all aspects of cellular life. Some specific examples of enzymatic roles are:

• Lysosomal enzymes in white blood cells (specifically phagocytes) to digest bacteria
• Catabolic catalysts help break down complex molecules into more simple ones
• Anabolic catalysts help build up complex molecules from more simple ones
• DNA ligase catalyses the addition of nucleotides to a DNA/RNA chain
• Helicases unzip the DNA molecule during DNA replication.

For now at least. This series continues with how enzymes work and some of the factors that effect the rate of reaction. Until then, take the quiz to see how much you have learnt! Please feedback and comment!