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Enzymes
Written by Tim Sheppard MBBS BSc. Last updated 9/11/10

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What is an enzyme?

An enzyme is a globular protein which acts as a biological catalyst. In other words, an enzyme is a biological molecule which speeds up the rate of a reaction. It's not like any normal catalyst which you can throw into a reaction and it will speed the whole thing up. Because it is a protein, a biological molecule, an enzyme is susceptible to various biological factors. That is to say, an enzyme won't always have that much of an effect.

If you take a substrate, S, which is supposed to turn into a product, P, then you might have to wait a while for the reaction to happen. The chances are, it's going to take so long that it just won't happen. The reaction won't be able to get past the first hurdle, so the substrate will either just stay in its normal state, or it will take a very long time to turn into the product.

An enyzme helps the substrate get over this first hurdle. The lock and key theory suggests that the substrate slots into the active site of the enzyme, and a reaction takes place which turns the substrate into its product. The enzyme remains the same, as it is a catalyst. The product then leaves the enzyme, and the reaction has been successful.

Enzymes are very important in the body because without them reactions often wouldn't take place. Every reaction shown in the metabolism section has a corresponding enzyme which ensures that the reaction happens. Although in equilibria the catalyst will speed up the reaction in both directions, sometimes one enzyme is more appropriate for one direction than the other. In the body, if a reaction needs to go both forwards and backwards, then one enyzme may be used for the forward reaction and another for the backwards reaction.

Although enzyme structure is essential, sometimes two different enzymes, each with slightly different structures, can catalyse the same reaction. This usually means that they catalyse the reaction in a different way. These are known as isoenzymes, and although their genetic coding (and therefore their structures) are different, they are capable of speeding up the same reaction.


What is a substrate?

A substrate is a substance which undergoes an enzyme-catalysed reaction. That is a complicated way of saying that a substrate is a reactant in a reaction which uses an enzyme. There is no real defining feature of a substrate which makes it a substrate, it's just important to realise that if a substance uses an enzyme in order to form a product, then it can be known as a substrate - and whenever a substrate is mentioned, we're talking about the chemical which goes into a reaction, and which is helped out by an enyzme.

If you see the reaction: A + B ⇒ C + B, then you can see that A changes into C but B stays the same. A, then, is the substrate, while B is the catalyst (which could be an enzyme) and C is the product.


What is an active site?

Remember that the protein is actually a really long chain of amino acids, strung together and forming a structure which depends upon the bonds (especially hydrogen bonds) between atoms in the molecule. Because this produces a globular protein with a tertiary structure, and this structure depends upon the order of the amino acids, then a specific shape is formed by the protein. This protein will be different from other proteins because other proteins have a different order in their amino acids, and therefore a different shape will be formed.

One specific part of the enzyme will have a shape which is complimentary to the substrate. This means that, in the same way that a glove is shaped to fit a hand, so the active site is shaped to fit the substrate. If there is a mutation in the DNA so that one of the bases is changed, then a different amino acid may appear in the protein. If this happens to be one of the amino acids in the section of the protein which forms the active site, then the active site may change shape, so it no longer fits the substrate. This in turn means that there may be no enzyme for a particular reaction in the body, and that can be catastrophic. Mutations in genes coding for enzymes are a cause of many diseases.

If you want to go into a bit more detail, then you might like to know that the active site isn't actually complimentary to the shape of the subtrate, as such. We actually look at the process as a whole. Generally speaking we can say that a substrate has to undergo a reaction to form a product, and on the way it will form some kind of intermediate. The image on the right represents this as a circle turning into a star, and a cross between the two in the middle.

An enzyme works because the active site is actually complimentary to the intermediate of the reaction. The substrate basically forms the intermediate and therefore is able to fit into the active site of the enzyme. The fact that the active site is complimentary to the intermediate 'encourages' the substrate to go through the reaction forming the intermediate. However, as it carries on the reaction to form the product, the shape of the product is no longer complimentary to the active site, and therefore the product is forced out of the active site, leaving both the product and the enzyme to do their own business - and allowing the enzyme to remain unchanged.

It's a very clever business, but it's also very complicated. All you really need to understand is that the active site is complimentary to the substrate, but understanding its relation to the intermediate helps to understand how the enyme works.

Importantly, like evolution, this is all theory. None of it has actually been proven because it's difficult for us actually to know. Unlike evolution, the lock and key theory is widely accepted because it combines plausibility with scientific evidence, but it's difficult to say for sure exactly how much enzyme function relates to complimentary substrates...


How does temperature affect the activity of an enzyme?

Temperature is one of those marvellous things - once you understand that heat is simply more energy in the particles, you've understood the most complicated part. Well, almost anyway. The thing is, it doesn't really get that more complicated. The principles of temperature are pretty much the same for everything. So, when it says in the rates of reactions section that temperature increases reaction rate, you would be right in thinking that temperature also increases the activity of an enzyme.

It all relates to the movement of the particles again. You have your substrate whizzing about (lets assume everything is dissolved in solution) and you've also got your enzyme there as well. Well, ideally you'd like the enzyme molecules and substrate molecules to meet as many times as possible, because the more times they hit each other, the more likely it is that the substrate will slot into the active site, leading to the product being formed.

The higher the temperature, the more energy the molecules have, so they'll be moving more quickly, and are more likely to collide successfully. So, the higher the temperature, the greater the activity of the enzyme. As simple as that? Not quite.

The problem you get is that an enzyme is a biological molecule, and in the same way that we don't like temperatures to get too hot, enzymes don't respond well to high temperatures. When the temperature rises too much, proteins get denatured, which means that bonds between the functional groups of amino acids break, and the protein changes shape. This means that the enzyme's function, which relies so much on its shape, is lost, and the enzymes become useless. So, at a certain temperature, the enzymes stop working, and any further increase in temperature will not help the enzymes activity any more. In the body, this is often around 37ÂșC.

So as you increase temperature, the activity of an enzyme will increase, until you reach the optimum value. After that, any further increase in temperature will result in denaturation of the enzyme, and a steep drop in activity.


How does substrate concentration affect the activity of an enzyme?

If you want an enzyme to work best, then you need it to have as fast a turnover as possible. You need as many substrate molecules to meet up with that enzyme within a given time as possible. So, it makes sense that if there are more of the substrate molecules in a given space, the enzyme can meet up with more of them in a given time!

This is effectively what is happening when you alter the substrate concentration . The enzyme, busily going about its catalytic work, will simply hang around until a substrate molecule collides with it appropriately. In the same way that increasing the temperature increases the chances of a favourable collision, so increasing the substrate concentration increases the chances - because there are simply more substrate molecules kicking about!

Unfortunately this doesn't carry on forever. Eventually you reach an optimum value - let's say this is 4 molarity. If you increase the concentration of the substrate passed this point, it makes no difference. Why?

Well, it's all to do with the number of available sites. Yes, enzymes are kicking about, 'waiting' for substrate molecules to jump in so they can do their work. However, there's only so much work that each enzyme molecule can do. Eventually you'll reach a stage where there are more substrate molecules than there are enzyme molecules to work their magic - so, as the image hopefully shows, you've got too many substrate molecules for any extra to make any difference. If you raise the concentration any further, it will make no difference because there are no extra enzyme molecules to meet this supply.

This is, of course, assuming you keep everything the same except for the substrate concentration. So, increasing the substrate concentration increases the activity of the enzyme, up to a point, after which increasing the substrate concentration has no effect.


How does enzyme concentration affect the activity of an enzyme?

This effect is much like that of the concentration of substrate, and you might also guess from the section on rates of reactions that increasing concentration will tend to increase reaction rate. And again, there is an optimum value.

It's obviously not exactly the same this time, though. This time you're looking at the enzyme molecules. Each one of them is turning the substrate into the product as quickly as it possible can, but it takes a certain amount of time for the substrate to slot into the active site, undergo the change that it needs to undergo, and then leave the active site. The next substrate molecule can't come in until the first one has left, so there is a limit to how quickly the enzyme can do its stuff.

If you increase the enzyme concentration, there are more enzyme molecules kicking about in a given volume - so there's more enzyme molecules about to perform whatever task they have. More substrate molecules can be turned into the product - and this effect increases, the more you increase the enzyme concentration.

Of course, in the same way that substrate concentration eventually has no further effect, you finally reach a point where there are more enzyme molecules available to accept the substrate than there are substrate molecules. At this point, the enzyme has reached its optimum value, and the only way that enzyme concentration can make a difference now is if you increase the substrate concentration further.

Substrate concentration and enzyme concentration have a similar effect. Increasing the enzyme concentration increases the activity of the enzyme up to the optimum value, at which point increasing the enzyme concentration further has no effect unless substrate concentration is altered.


How does pH affect the activity of an enzyme?

There is an optimum value for lots of things. There is an optimum temperature for enzyme activity - there is an optimum speed for efficient fuel consumption in a car. In the same way, there is an optimum pH for each and every enzyme. At a pH above this optimum, the enzyme's activity will be reduced and therefore the reaction rate will be lowered; at a pH below this optimum, the enzyme's activity again will be reduced and lower reaction rates result.

The obvious question is, why? Why does changing the pH - changing the concentration of hydrogen ions in the solution - have such an affect on the enzyme?

To begin with we have to rethink the idea we have of the active site. It's not simply a case of the molecule forming a particular shape. Unfortunately it's a bit more complicated than that. When a substrate molecule slots into the active site of an enzyme, it doesn't just fit snuggly like a glove - although that is a reasonable simplification of it. Instead, the active site is made up of a series of groups of atoms which form temporary bonds to the substrate. These groups are the functional groups of the amino acids in the protein chain, and they have an important effect on the shape of the enzyme. If they're in a different order, the substrate won't temporarily bond to the enzyme, but the shape will also be different, so it's often easier just to think about it from the point of view of shape.

However, if we want to understand the effect of pH, we really need to be able to understand the way in which it is the position of the atoms that is important. This means that if the group changed - even if the shape stayed the same - the substrate may not be able to bond to the active site. This is what happens when the pH changes. If the pH increases, this means there are fewer hydrogen ions in solution. This can lead to reactions taking place that alter the functional groups of the amino acids, which in turn leads to the enzyme changing shape. Similarly if the pH decreases, there are more hydrogen ions in solution, leading to the possibility of hydrogen ions causing other group changes.

If the functional groups change, the shape will change, and the active site will no longer fit the substrate. This is what happens when pH changes. If the pH is changed sufficiently, the enzyme will be completely altered due to this effect, and it is said to be denatured. However, unlike the effect of extreme heat, which causes the enzyme to be irreparably damaged, denaturation due to pH change is reversible. Restore the pH to its original level, and the enzyme will return to its original capability.


What else affects the activity of an enzyme?

There are many things, as already shown, that affect enzyme rate. However, because they are biological molecules, they are sensitive to many, many things. It's not necessarily important to know exactly how everything in the world affects a particular enzyme, because enzymes tend to be used within controlled environments. However, it is sometimes interesting to know about enzyme function is regulated; because reaction rate is determined so much by the enzymes which speed it up, the body take full advantage of enzyme regulation when it wants to increase or decrease the rate of a reaction.

Covalent modification of enzymes (i.e. changing the bonds in some of the groups) will obviously have an affect. Often the body does this by adding or removing phosphate groups from the enzyme (particularly serine, threonine or tyrosine). When the body is making glycogen, it needs an enzyme called glycogen synthase; phosphorylating this enzyme decreases its activity. However, when the body is breaking down glycogen (because it needs the glucose), it needs an enzyme called glycogen phosphorylase, whose activity is increased by phosphorylation. In this case, phosphorylating enzymes is co-ordinated so less glycogen is produced and more is broken down (and similarly dephosphorylating the enzymes increases glycogen production and leads to less breaking down). What a clever design, hey?

If we're talking about adding of removing a phosphate group, it's worth noting that this itself is done by an enzyme. So one enzyme leads to another enzyme being phosphorylated. If an enzyme is responsible for causing another molecule to be phosphorylated, then it is often known as a kinase (e.g. hexokinase, the first enzyme involved in glycolysis).

Allosteric regulation, explained in more detail below, basically involves substances coming in and binding to other sites on the enzyme (not the active site). These substances can either increase or decrease the activity of the enzyme.

Enzyme synthesis (i.e. how much of the protein which makes up the enzyme is made) inevitably plays a huge role in how much affect an enzyme has on the system it's placed into. Ultimately this is controlling the concentration of the enzyme, but specifically in the body. This is also a slow effect - it can takes hours or days for a change in enzyme production to actually show any effect.

For instance, if the body receives a large amount of glucose, then this will increase the amount of production of a hormone called insulin. Insulin, as well as having many other affects, will increase the production of the enzymes glucokinase, phosphofructokinase and pyruvate kinase, which are all enzymes involved in metabolism. This is a long term response, so that the body can respond to a change in diet. Immediate responses to an increase in glucose are controlled differently.

Inhibition, where a substance inhibits or reduces enzyme activity, is obviously a way in which enzymes are regulated, and works slightly differently from allosteric regulation. It is dealt with next.


What is an inhibitor?

There are two types of inhibition, and it's probably easiest just to deal with each of them separately. These are competitive inhibition and non-competitive inhibition.

Competitive Inhibition is where the inhibitor is a molecule which has a similar shape to the molecule which is supposed to be binding to the active site. In the case of enzymes, a competitive inhibitor may have the same shape as that of the substrate, but it doesn't react in the same way. Rather than turning into the product, it simply uses up time and prevents the substrate from getting to the active site. It blocks the way.

Non-competitive Inhibition is the kind that is shown in the animation, and exists when a molecule binds to a different site on the protein, rendering it inactive. Sometimes it does this before the substrate reaches the active site, sometimes afterwards, but in either case it stops the protein doing its job, and prevents a product being formed.

In both competitive and non-competitive inhibition, it is possible to have both reversible and irreversible inhibitors. As the name suggests, a reversible inhibitor does not have a permanent affect - it will stop the protein doing what it is supposed to do, but it will move off again and allow the protein to function later on; an irreversible inhibitor, on the other hand, permanently renders the protein inactive, so it will have to be replaced by a brand new one - the inhibitor will not budge. For example, there is a protein on the edge of the cells of the stomach which pumps the acid into it; an inhibitor called omeprazole permanently blocks the pump, making it useless. For acid to be pumped into the stomach from that cell, a new pump would have to be produced; of course, there are millions of these pumps in the stomach, so it won't stop acid pumping altogether!

If there is an inhibitor about, then changing the concentration of substrate won't change the rate of the reaction in the same way as before. The problem you have is that something is stopping the enzyme doing its job properly, and so although increasing the substrate concentration does increase the reaction rate, it simply cannot do so to the same extent.

The way in which the situation differs depends upon which kind of inhibitor you're using. If the inhibitor is non-competitive (that is, it's acting on a site other than the active site, then the rise in reaction rate in comparison to substrate concentration (as shown in the image) will be the same shape but squashed. Due to the inhibition, the enzyme simply cannot achieve the same level of activity; the optimum substrate concentration will still be the same because it will require the same concentration of substrate to fill all of the active sites on the enzymes, but it won't produce the same level of activity because it's all being inhibited.

A competitive inhibitor is slightly different because this time you do have some hope of reaching the normal level of enzyme activity. At low substrate concentrations, there will be a comparitively large proportion of inhibitor molecules floating about - that is, you may have 2 substrate molecules and 4 inhibitor molecules for 5 enzymes. Obviously the inhibitor molecules are more likely to get into the active sites. However, if you increase the concentration of substrate molecules, you may have 7 substrate molecules and 4 inhibitor molecules for 5 enzymes. This time the substrate molecules are more likely to get into the active sites - but you'll still have some inhibition.

Eventually you'll have so many substrate molecules that the inhibitor molecules are much, much less likely to get into the active sites, and so the substrate molecules will fill the active sites. This is effectively the same situation you had when the optimum substrate concentration was achieved before - all the active sites are filled with substrate, so the enzyme is doing the best job it can.

The difference with a competitive inhibitor in comparison to a non-competitive inhibitor is that, if all the active sites are filled with substrate, there's no inhibition going on, and therefore the maximum reaction rate will be achieved. So, it is possible to overcome the effect of a competitive inhibitor, but you have to get a much higher substrate concentration than usual.

As shown in the image, this produces an optimum value for the substrate concentration that is higher than you would get if you didn't have a competitive inhibitor there.

The issue of inhibition is obviously quite a complicated one, but with a little bit of study it can be easily understood. With enzymes, you always have to try and picture what's going on - what is occupying the active site, and is it supposed to be there? What kind of inhibitor are you dealing with, and will increasing the substrate concentration replace the inhibitor molecules?


What is allosteric regulation?

Allosteric regulation is different from inhibition for two main reasons: the first is that allosteric regulation can be both positive and negative; the second is the allosteric regulation does not simply activate or inactivate - it regulates, so the enzyme isn't necessarily switched on or off.

As has been shown above, an enzyme has more than just its active site. In the case of allosteric regulation, we consider three of an enzyme's possible sites. One is obviously the active site - the site which the substrate slots into. The other two are for the allosteric regulators, positive and negative.

Rather than being positively or negatively charged, we mean positive and negative in the same sense as when they are used in everyday language - so 'positive' as in encouraging, and 'negative' as in discouraging. A positive regulator will bind to its binding site on the enzyme and encourage the enzyme in its interaction with the substrate. A negative regulator will bind to its binding site on the enzyme and discourage the enzyme, making it less effective at turning the substrate into its product.


Further Reading