Enzymes (and Proteins) Part 4: Enzyme Inhibitors

Enzyme Inhibitors

Enzyme inhibitors interact with the enzyme and prevent it from working properly. There are two types of enzyme inhibitors, competitive and non-competitive. The ways in which inhibitors effect enzymes, as you might have guessed, centered around the active site of the enzyme.
Inhibitors occur both naturally in the body (and are involved in regulating certain processes) and can be synthetically created too. Inhibitors are commonly used as drugs, as blocking enzyme activity can help remedy certain chemical imbalances or can be used to kill pathogens.

Competitive Inhibitors

These inhibitors compete with the substrate for the enzyme's active site. A competitive inhibitor will bind to a complementary active site of an enzyme, just like the substrate otherwise would, but will not react and will effectively block any substrates from binding to the enzyme. Their effects are usually temporary, after they have bound to the enzyme, they will unbind and the enzyme will be free to bind to the substrate again afterwards.

Non-Competitive Inhibitors

Rather than binding to the active site of an enzyme, non-competitive inhibitors bind to another part of the enzyme (called the allosteric site). This causes the shape of the active site to change, so the substrate shape is no longer complementary. Their effects are usually permanent- the enzyme, even after the inhibitor has left it, will still not function as it is effectively denatured.

Comparisons

Consider this: A scientist is measuring the rate of reaction of a mixture of competitive inhibitors, enzymes, and complementary substrates. What happens when he increases the concentration of substrates? 

Now consider the same experiment, but replace the competitive inhibitors with non-competitive ones.

Because competitive inhibitors and substrates compete for the active site, increasing the amount of substrate compared to the amount of competitive inhibitor will mean that substrates are far more likely to bind to the enzyme before the inhibitor can. Imagine you're in a room with 50 other people and some famous guy you want to shake hands with. The problem is the other people want his autograph. Its pretty damn likely those other people are going to get to react with this famous guy before you can bind to him and stop him doing anything useful. But imagine if there were just 5 other people. Your job would be much easier. This is basically simple collision theory stuff from GCSE.

Now imagine there are 10 famous guys, 1,000,000 other people and 10 of you. But what if you happen to have glue all over yourself and want to give him a great big hug rather than a hand shake? You have (conveniently) transformed into the human equivalent of a non-competitive inhibitor. "So what?" I hear you say, "If you increase the concentration of substrates then the rate of reaction will increase until the effect of the inhibitor is negligible, right?". Wrong. When working with non-competitive inhibitors, the rate of reaction will actually level off at a considerably lower rate than it would if there were no inhibitors at all. Why? In order to give the famous guy your hug, you don't have to compete for his active site (his hands I guess), so you can waltz right past everyone and stick to him all you want. You then prevent him signing further autographs, and can move on to the next famous guy you want to cover in glue. Essentially, Non-Comp Inhibs don't compete with the substrate for the active site, and render the enzyme useless, so the overall rate of the reaction will always end up lower than it otherwise would no matter the concentration of substrate.

Here is a graph to make things even clearer! (seriously though, try and explain the shape of each line, why they level off where they do, etc...)

Source: https://teaching.ncl.ac.uk/bms/wiki/index.php/Enzyme

Enzymes (and Proteins) Part 3

What affects how enzymes work?

Welcome to the final part on enzymes and proteins.

There are five factors which affect enzyme activity you need to know, perhaps three of which you will already be aware of.

pH and Temperature: Each of these factors operate in a similar fashion. Enzymes will have an optimum pH and temperature that they work most efficiently at (converting substrates into products at the highest rate). When looking at graphs pay attention to the variables given, any maximum/minimum points, how the graph changes, and the scale given. Here are some graphs now to help understand:

Be careful though, there are many different enzymes, and they all have slightly different optimum temperatures and pH. The enzymes in your body might have an optimum temperature of 37 degrees Celsius, but the enzymes of bacteria living in a hydrothermal vent would likely have an optimum temperature that is far higher.

The key points to understand here are:

• Enzymes have an optimum pH and temperature that they operate best at.
• The further away the temp./pH is from the optimum, the lower the enzyme activity is.
• Extremely high temperatures or an extreme pH value will denature an enzyme. As you can see from the temperature graph, this means that enzyme activity grinds to a halt. Why? A high temperature will damage the bonds in the enzyme, and cause it to change shape. As you might have guessed, this is bad news for the enzyme as it can no longer form E-S complexes- it ceases to function. So in short, to denature is to damage an enzyme causing it's shape to change so it can no longer function.

Substrate Concentration/Enzyme Concentration: All this means is the amount of substrate present compared to the amount of enzyme. The concept is simple enough to grasp, but sometimes when asked to apply the idea certain questions can throw people. So let's say you begin with a large amount of substrate and just a few enzymes. Then repeat the experiment many times, keeping the amount of substrate the same but ever increasing the amount of enzymes.  Consider how the rate at which product molecules are produced changes from experiment to experiment. 

Try drawing a graph and see if it matches the following explanation... At first, as you increase the enzyme concentration the rate of reaction will also increase. This increase in rate of reaction will continue until there are so many enzymes present that adding more has no effect, as all the substrates can immediately form E-S complexes. So your graph should increase at a constant rate then curve off into a 'flat' line as the rate no longer changes.

Substrate concentration is a similar ball game. If you have a set number of enzymes, and then add more and 

more substrate you get a graph like this: 

  

www.rsc.org

  Adding more substrate to the enzymes present will  increase the rate of reaction up until the point where  all the enzymes are saturated with substrate  molecules. After this, the reaction occurs at it's  maximum rate as there physically aren't any more  enzymes present to bind to the excess substrate  molecules.

Tip: With graphs (or indeed with all questions, but especially graphs :P) reading the question properly, and not just going into "I-revised-this-50-times-let-me-pump-out-an-answer" machine mode, is more important than with other questions. Graphs may sometimes look like simple recall, but they will try and fool you. What I'm trying to get at here, is lets say they give you a specific context, or change a certain parameter. For instance, what would happen to our "Enzyme concentration" example, if rather than the amount of substrate being kept the same, it was in excess. The graph would not level off at all, you would simply draw a straight diagonal line between the x and y axis, because there would always be enough substrate molecules (if they were in excess) to satisfy the enzyme's never ending thirst for them- regardless of how many enzymes you throw in there.

Enzymes (and Proteins) Part 2

How Enzymes Work

Models of Enzyme Action

These are two simple models that help us understand the physical process of how an enzyme actually catalyses a reaction. Each model sets out how the enzyme interacts with the substrate molecule. There are two you need to know.

The Lock and Key Model

In this model, the substrate is said to fit into the enzyme like a lock into a key. This then transforms the substrate into the product molecule(s). This is actually now deemed outdated, and the more recent "induced fit" model (discussed later) is supposedly more accurate. However, the lock and key model is still useful in conveying the basic ideas of enzyme action. Here is a diagram to illustrate the process:

First the enzyme and substrate molecules must 'collide' (I'm sure you are all familiar with particle models from GCSE). They then bind and form the Enzyme substrate complex. It has been simple up until now. But how does the E-S complex split the substrate into two product molecules? Magic? Well, we will find out about that in the next model.

It is also worth noting a couple of things. First, notice how the enzyme remains 'unused' by the reaction and finishes the reaction unchanged. You can also apply your other knowledge of enzymes to each of the models. For instance, the shape of the substrate 'key' must be complementary to the Enzyme 'lock' as shown in the diagram. From the notes in part one you should be able to explain how the enzyme gets this specific shape.

The Induced Fit Model

The induced fit model follows pretty much the same idea as the lock and key model. An enzyme must first collide with a substrate molecule. However, here is the key difference. The enzyme and substrate are not complementary to begin with. When they try and bind, there are minute changes in the shapes of both which allow the E-S complex to form, allowing the substrate to react and form product molecules. So, the models are essentially the same, except in Induced Fit the shape of the enzyme and substrate must change to become complementary. 

The idea behind this (the magic part :P) is that the change in shape places certain stresses on the bonds in the substrate. This stress makes the bonds more inclined to form new ones and become product molecules. It is comparable to a situation where you have a child safe screw lid on a medicine pot. Normally to get the lid off (or to make the substrate react) you have to put in loads of effort (or energy). But if you have the technique and push down on the cap first, then you can unscrew it more easily by simply providing a different route. (Just like how the enzyme, by pushing in on the substrate molecule, provides an alternate route for the reaction making it require less energy and thus take less time). Okay, so not my best analogy, but you get the picture.

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!  

-Please post any comments, tips, or mistakes in the section below-