Enzymes

ENZYMES

Enzymes are an incredibly important type of protein..so they get their own page!

Structure of an Enzyme

As diverse as enzymes are between and within organisms, they have a few things in common that allow us to discuss them as a whole group. Enzymes are always (in our class) proteins, so recall that they are polypeptides or chains of amino acids that take on their 3-dimensional shapes with interactions between the amino acids.

All enzymes have a particular 3-dimensional shape that is integral to their function (remember, structure determines function, so changing the shape changes the function). Often in cartoon representations, you will see that they have a specific shape 'missing' from them, almost as if they are missing a piece. This spot where it looks like something should fit in is known as the active site. This is where a particular molecule (enzymes are HIGHLY specific, so ONLY that one molecule) should fit. The molecule that will come in and bind to the enzyme at the active site is known as the substrate.

In reality, of course, enzymes are complexly shaped and in nearly no way resemble these oversimplifications. Enzymes and substrates, in reality, look more like this second image. This is more accurate, but far less useful for us, so you can rely on cartoons most of the time. When the substrate has bound to the enzyme, the entire structure can be referred to as the enzyme-substrate complex.

Enzyme Catalysis

What do all of these enzymes actually do, though? We have discussed how diverse and intimidating they can be, but what purpose do they serve? Well, just name it. Enzymes are the 'doers' of a cell. If you need a job done, it is an enzyme that will do it. Specifically, enzymes are crucial to chemical reactions within our cells that keep us alive. These chemical reactions are collectively referred to as an organism's metabolism.

Activation Energy

Some reactions will occur on their own without assistance (more on that later). However, many reactions need an input of additional energy to get underway. This is known as a reaction's activation energy - the energy that must be invested into a reaction for it to occur. Activation energy is basically a threshold that a system must surpass in order to undergo the chemical reaction.

Enzymes become incredibly useful because they catalyze these reactions, basically meaning that they lower the activation required for the reactions to occur.

Do not focus on the term free energy from the graph yet, observe the "transition state". This is effectively our activation energy. You can see that the system needs less energy to undergo the reaction because the 'hump' is lower when an enzyme is present (catalysis occurs).

Changing the Rate of a Reaction

As we've discussed, enzymes allow reactions to occur more easily via catalysis. This means that reactions will speed up with the help of an appropriate enzyme. However, the presence or absence of enzymes is not the only thing that can affect the rate of a reaction or the speed at which reactions occur.

In order to examine other factors that may impact the rate of a reaction, take a moment to familiarize yourself with how an enzyme does its job. As you can see in the diagram, the enzyme floats around a cell with its active site available. Once the appropriate substrate(s) bind, the enzyme undergoes a conformational change, or change of its shape, that instigates a chemical reaction, leading to the product(s) that are unique from the products (different color/shape in the diagram).

So that's how enzymes function, so let's see how we might speed up or slow down this process. The following are all factors that affect the rate of reactions:

A. Temperature

Temperature is the simplest of factors that affects the rate of a reaction. If you increase the temperature of the substance, particles will move faster. Faster particles are more likely to encounter the appropriate enzymes and undergo the chemical reaction. So, increasing temperature increases the rate of reaction. It should be noted, however, that there is a point at which rising temperature will actually have the opposite effect (more on that in a bit).

You can observe a graph much like the one shown for virtually all enzymes, but the temperatures at which you see the enzymes function will differ. Some enzymes can function at higher temperatures than others. But we will discuss that more with denaturation.

B. pH

Much like the temperature of a system, the pH of a system can also impact the rate of reactions. You will see a relatively similar graph for any enzyme as the one shown here.

However, again, these specific values will differ depending on the enzyme in question. Some enzymes can operate quite well in basic conditions and some in acidic conditions. Some have a wide range of values at which they can operate and some have a narrow range. You will never need to memorize any specific values at which an enzyme slows down - simply be able to interpret a graph such as this.

C. Changing Substrate Concentration

As we have seen, enzymes must come into physical contact with their substrates in just the right way (at the active site) and orientation in order to bond and catalyze the reaction.

As a result, adding more enzymes and/or more substrates will increase the rate of reaction because enzymes will be binding to substrates more often. There is a point, however, where increasing the concentration further has no effect known as the point of saturation.

D. Inhibitors

Inhibitors are a class of molecule that inhibit, or restrain, enzymes from doing their job properly or as effectively as normally. Sometimes cells release these purposefully in order to slow down the rates of reactions, which we will discuss more with gene regulation. Other times, they simply exist in the same area as the substrate and get in the way. There are two ways in which inhibitors can affect the efficiency or effectiveness of enzymes: competitively and non-competitively.

1. Competitive Inhibitors

Competitive inhibitors are molecules that resemble the intended substrate, and so will often take over the active site of an enzyme, preventing the enzyme from catalyzing its reaction. In this diagram, the competitive inhibitor's shape is very similar to the part of the substrate that enters the active site, so it will occasionally bind and block the substrate, slowing down the rate of the reaction.

2. Non- Competitive Inhibitors

Non-competitive inhibitors also lessen an enzyme's ability to do its job (catalyze a reaction), but it does so without interacting with the active site. The active site, you'll recall, is where the substrate binds. So non-competitive inhibitors do not have to resemble the substrate.

These inhibitors bind to an entirely separate site on the enzyme. When a non-competitive inhibitor does so, the enzyme's shape is altered so that it can no longer bind to the substrate and catalyze the chemical changes properly. Remember, enzymes move in 3-dimensions in order to catalyze these reactions, so the inhibitors will often get in the way or make the enzyme unable to move with the same flexibility as before, preventing them from doing their job.

Allosteric regulation

Allosteric Regulation is the modulation of an enzyme’s activity via the binding of an effector molecule (ligand) to a site other than the enzyme’s active site (an allosteric site)

Allosteric binding causes a conformational change in the enzyme’s structure which affects the enzyme’s affinity for the substrate. Non-Competitive Inhibition is a type of Allosteric regulation

Comparing Competitive vs. Non-Competitive Inhibitors

Both kinds of inhibitors inhibit (slow down) the rate of reaction, but in general, non-competitive inhibitors are much better at doing so. In this graph, you can see that the rate of reaction, V, is significantly lower than a normal enzyme with non-competitive inhibitors present. However, competitive inhibitors only slow down the rate of reaction slightly. You do not need to know any of these variables, just understand the graph knowing that V represents the rate of reaction.

Feedback inhibition

Involves the use of a reaction product to regulate its own further production. The cell responds to the abundance of specific products by slowing down production during anabolic or catabolic reactions. Such reaction products may inhibit the enzymes that catalyzed their production through the mechanisms described above.

Co Factors and Co- Enzymes

Many enzymes don’t work optimally, or even at all, unless bound to other specific non-protein helper molecules, either temporarily through ionic or hydrogen bonds or permanently through stronger covalent bonds. Two types of helper molecules are cofactors and coenzymes. Binding to these molecules promotes optimal conformation and function for their respective enzymes. Cofactors are inorganic ions such as iron (Fe++) and magnesium (Mg++). One example of an enzyme that requires a metal ion as a cofactor is the enzyme that builds DNA molecules, DNA polymerase, which requires a bound zinc ion (Zn++) to function. Coenzymes are organic helper molecules, with a basic atomic structure made up of carbon and hydrogen, which are required for enzyme action. The most common sources of coenzymes are dietary vitamins

Denaturing an Enzyme

Remember Enzymes are proteins so they also denature just like all proteins

We have spent a lot of time exploring what factors might affect the efficiency of an enzyme. As we have seen, enzymes have ranges of pH, temperature, etc. that they can function within. If the environmental conditions change too much, enzymes will denature. Effectively, the enzymes will no longer be able to function properly because their structure has been compromised. If the environment gets too acidic, an enzyme will denature. However, this will also happen if it gets too basic. If the temperature gets too high, all of those hydrogen bonds that maintain the enzyme's tertiary structure will break, causing the enzyme to flop over uselessly.

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