2.4 Enzymes

“Insufficient enzyme production is at the root of much “tummy trouble” in our country”. So claims an advert-laden website urging you to “Take Control of Your Health”. Is this right,? Is it an over-reaction? Is it a purely commercial ploy? How can the average punter respond to the proliferation of health messages, couched in seemingly impeccable scientific terminology?

This is a mega-problem: information overload affecting so many aspects of our modern lives. This blog can’t solve it, of course – better stop here if you’re looking for nutritional advice – but it can play a part. Worrying about getting the right balance of enzymes, vitamins, amino acids, trace elements and antioxidants might at least be helped, if you knew what the words signified! And these just add to the everyday dietary vocabulary of proteins, carbohydrates, fats and sugars. So over the coming months we’ll explore what these different species are and what they do for us. Enzymes make as good a starting point as any.

An immediate simplification is that all the substances mentioned above with one exception, are molecules; that is to say, they are tiny structures made up of a mixture of atoms, much as a necklace is made of beads. Some are huge, comprising thousands of atoms, some are tiny with just two or three. The exception is the trace elements which are simply single atoms our bodies need – calcium, magnesium or selenium, for example.

We probably come across the enzyme word first in relation to making cheese or beer or in biological detergent – a magical ingredient with the power to transform milk or grain or to remove stubborn stains. A drop of rennet, as the cheesemakers know will shift a tub of milk from swirling liquid to clumpy solid in no time. It doesn’t take much imagination to see that these are all processes of chemical change.

image courtesy of US Department of Agriculture

Enzymes seem to bring about chemical changes (or reactions, as they are known). In fact their specific role is to speed up chemical reactions that might otherwise be imperceptibly slow (like the rusting of iron). The technical term for any substance that can do this is “catalyst”: enzymes are biological catalysts.

You can see from the everyday examples we’ve mentioned why they are called biological – because they break up substances in milk and beer or destroying patches of blood and food on dirty clothing. Enzymes interact with biological substances – like the proteins in milk or blood and the carbohydrates in grain. But, of even greater significance to us and our bodies, enzymes are the tools that carry out the everyday actions that make us tick. They digest the molecules of our food, break down sugars to give us energy and enable our DNA to instruct the growth and maintenance of our tissues – and plenty more too.

So, enzymes can be thought of as tools and, just as in a well-equipped workshop, there are thousands of different types, each suited to a particular function. But in what way do they resemble tools – do they cut, drill and screw like tools in a workshop? And, how do they carry out their many functions anyway. Come to think of it, what are they actually made of – they can’t be the kind of metal or wooden objects we usually call tools?

At the most basic level, enzymes essentially cut and join together molecules – molecules of many different kinds. They do this by breaking or making bonds that hold molecules together. A molecule is simply a group of atoms held together by mutual attraction. The links between the atoms in a molecule are called bonds. Under normal condition these hold firm – that’s why our bodies, our furniture, our food stay roughly the same from day to day! But as we know, any of these can change over time – skin can age, furniture tarnish and food putrify. These are examples of slow chemical reactions in which bonds between atoms in molecules get broken or made. Enzymes make chemical transformations happen quickly – pretty important if you need to run from a bull, digest a meal or create a baby!

The ability of enzyme molecules to cut and paste other molecules is down to the way they are structured. The bulk of an enzyme is a pretty firm structure that remains steady throughout any action it takes. But a small part of it is more flexible and, in the right circumstances, can move slightly – like the jaws of a pair of pincers or arms of pair of tweezers. This small part, called for obvious reasons the ‘active site’, is not only  adjustable but is shaped very precisely to fit round just one specific type of target molecule.

It’s this specificity that is so crucial to the work of enzymes. It means, in effect that the active site of a given enzyme ‘recognises’ target molecules but is indifferent all other types. This can be represented diagrammatically with nominal shapes.

Image courtesy of domdomegg   

The red shape represents an enzyme molecule designed to split a specific smaller molecule into two parts. One example of such a process is the breaking up of long chain molecules of starch in food into smaller units by the enzyme amylase which is present in saliva. Other enzymes in the stomach act similarly on the long chain molecules of proteins in food.

As the small substrate molecule docks into the active site it triggers a small and momentary movement in the structure of the enzyme’s active site. This slight movement breaks one of the bonds between two adjacent atoms in the substrate.

The blue shape represents the molecule to be acted upon (often called the substrate). In our examples this might be a stretch of a starch or protein molecule. The important point is that the active site of the enzyme molecule is specifically shaped to interact only with one particular substrate.

As the small substrate molecule docks into the active site it triggers a small and momentary movement in the structure of the enzyme’s active site. This slight movement breaks one of the bonds between two adjacent atoms in the substrate.

The two pieces of the substrate separate and are released from the grip of the enzyme. The active site returns to its original state and the enzyme has completed its task of cleaving the starch, protein or whatever molecule.    

These kinds of enzyme – ones that break bonds between atoms – are crucially important for our bodies. As you can imagine they play an especially important role in digestion. Our diets contain a huge variety of different substances – many types of protein and carbohydrates for example.  Most of the molecules in food are large and complex, often in the form of very long chains of atoms. These need to be broken down into the smaller units of which they are composed in order to pass through the lining of our intestines into the blood stream so they can be circulated to where they are needed. A great menagerie of specific enzymes do this for us (and our fellow creatures).

Other kinds of enzyme play an equally crucial role in the opposite process: building up new molecules from the food we eat and air we breathe. These types of enzymes forge new bonds between atoms rather than cleave old ones. They are responsible, for example, for putting together the links between the units that make up each DNA molecule. This has to be done every time a new cell is created, as we grow or need to maintain and repair tissue. 

In the diagram an enzyme called DNA polymerase (because it extends the DNA polymer) – the green blob – is attached to a single strand of the DNA double helix – the blue thread. By forging new bonds between atoms it is able to extend the second thread of the double helix (in yellow). In this way one strand of the DNA double helix acts as a template for building the second one. This is the basis for growth and reproduction: the DNA double helix splits in two and then the enzyme enables two new double helices to be built on each of the old single ones.

Before leaving this extraordinary topic, we should take look at what an enzyme is as well as what it does. Perhaps the most remarkable property is its structure – the combination of a relative rigid backbone and a highly variable active site region. Enzymes are simply protein molecules. That means they are blobs (technically ‘globular’) made out of a long chain molecule that is wrapped up.

Enzymes, like all protein molecules are rather like a long necklace made of hundreds or thousands of beads. But rather than existing as a long thing, like a necklace on a neck, they are compacted like a necklace held in the palm of a hand.

Minute electrical attractions keep various stretches of the chain in firm contact with other parts of the chain – as though a few beads in a necklace were magnetic.

In the diagram of a typical enzyme each little sphere represents an atom. You can see how they cluster together, though in this kind of model the long chain structure is not clear.

In this diagram the individual atoms are not shown but the twists and turns of the chain in a typical enzyme structure are clear. The thin purple thread represents the chain of atoms of which the enzyme is composed. In some places it is twisted, apparently randomly, like spaghetti. But in other places it is constrained into a rigid sub-structure. In the brown parts, the thread adopts a strict helical structure and in the blue parts adjacent stretches of the thread are held firmly together in a sheet like sub-structure. These two aspects of the structure give the enzyme its overall firm shape.   (Image courtesy of the European Bioinformatics Institute)

Equipped as we now are with an idea of what enzymes are and what they do, let’s look back at how they deploy their magic to make cheese from milk and beer from grain. Milk is a rich mixture of many types of chemical, including proteins, sugars, fats, and minerals and plentiful water. An enzyme capable of cutting up a protein is added to milk to make cheese. A common source of one such enzyme (rennet) is an animal’s stomach, where it helps the animal digest milk. Vegetarian cheeses use plant-based enzymes.

Whatever the source, the enzyme breaks a bond between atoms in one of the main milk proteins (caseinogen), resulting in a crucially different one  with similar name (casein). Molecules of the former dissolve happily in the watery mixture of milk, but those of its descendent, casein, do not. As a result they precipitate out as a gel-like substance we call curd. In a gel the molecules connect up in a kind of grid; this traps most of the fat molecules and calcium atoms within the milk.

Gel produced by casein molecules. Scanning Electron Microscope image courtesy of Peter Hristov

Together with other cheesemaking processes, the action of enzymes result in the separation of the curds from the watery whey, making the cheeses we know and love

Enzymes play a role in two different stages of the beermaking process. In the early stage of mashing, naturally occurring enzymes in the grain convert some of the carbohydrates known as starches (these are a particular type of carbohydrate with long chain molecules) into smaller molecules, mainly sugars. In contrast to cheesemaking, the enzymes in beer-making are breaking bonds between atoms of a carbohydrate rather than a protein  –  but the principle is much the same as for the breaking of bonds in milk proteins in cheesemaking.

In beer making however, enzymes from a different source play an additional role at a later stage – fermentation, in which the alcohol is produced. These enzymes are not ‘naturally occurring’, but are normal components of the yeast cells that are deliberately added to the sugary mix. Yeast is the name given to a particular type of tiny living cell. Like other living cells, yeast cells can break bonds in the molecules of sugars such as glucose and fructose. In the process known as fermentation, molecules of ethanol (the common alcohol present in beer) and carbon dioxide are the products of the fermentation of sugars.

This exploration of the structure and function of enzymes has revealed something of what they are and what they do. It’s explained how important they are in the everyday functioning of our bodies (and indeed of all living things) and in the particular processes of cheesemaking and brewing. It hasn’t really had anything useful to say about the health claims of enzyme products. Sorry to disappoint. It’s purpose has been to portray something of the nature and role of enzymes as just one of the many families of molecules that make us tick. Later we’ll look into other families – sugars, carbohydrates, vitamins – and find out just what they are, to help us judge the claims of the food supplements industry.

© Andrew Morris 6th August 2019