Enzymes: Videos & Practice Problems

Enzymes are specialized proteins or RNA that catalyze chemical reactions by lowering the activation energy required. They bind to specific substrates at their active sites, facilitating reactions that would otherwise take an impractically long time. Enzyme activity is regulated through mechanisms like feedback inhibition, allosteric regulation, and phosphorylation. Understanding these processes is crucial for grasping metabolic pathways and cellular functions, as enzymes play a vital role in maintaining life by accelerating necessary biochemical reactions.

Enzyme Basics

Hi. In this video, we're going to be talking about enzymes. So, enzymes are really crucial in cell biology, and a lot of biology, and they have super important functions, so we're going to spend a lot of time talking about what enzymes are, what they do, and how they work. So, first, what are enzymes? Well, enzymes can be protein or RNA, that essentially, their purpose is to reduce the energy necessary for a chemical reaction to occur. So, enzymes act on what's known as a substrate, which is just the molecule that an enzyme acts on, and it's highly specific. So, enzymes don't just go around speeding up reactions of anything. They are really specific to a single molecule or really just a couple of molecules that are very similar.

So, they act very similarly. And they also catalyze. That is another term that you are going to hear a lot about with enzymes. What that means is that they speed up the rate of, or increase the rate of a chemical reaction that the substrate needs to undergo. And so, they can actually speed up reactions, making them very fast. So, the number that's mentioned in the textbook is going to be 108 to 1013 times faster. So, what does that actually mean? Well, for a reaction that would take 3 to 300,000 years to happen by itself, an enzyme can actually make it happen in one single second. So, they really speed up chemical reactions, which you can imagine is very important because we can't wait around 300,000 years for a single chemical reaction to occur. We need them to happen now, and usually, we need them to happen repeatedly over the course of a lifetime.

So, we really need enzymes to speed up reactions. Now, they can work to speed up forward or reverse reactions, but essentially, for an enzyme to be considered an enzyme, it must meet three conditions. The first is that the enzyme cannot be consumed in the reaction. So, once the reaction takes place, the enzyme still needs to be present. They cannot be changed by the reaction, meaning that the enzyme stays the same before the reaction as it is after the reaction, so that it can be used again. It can't be used up, and it has to stay the same. And, the enzyme only affects the rate of the reaction and does not affect the free energy. So the free energy of the reaction stays the same. All the enzyme does is come in and make it happen faster.

So, if we are looking at an enzyme, here we can see this is the enzyme. And these here are substrates. And so the enzyme binds to the substrate and catalyzes some type of chemical reaction that the substrate needs to undergo. It speeds up that chemical reaction. So now, let's move on.

Activation Energy

So now let's talk a little bit about how enzymes speed up reactions. In order to do this, they must overcome what's known as the activation energy, which is the minimum amount of energy reactants must have before becoming products. This is needed in any type of reaction, including thermodynamically favorable ones where the delta G is negative. These don't necessarily need any help, but sometimes, they just take a really long time. They can take years to occur without help. Therefore, in cells and in life, enzymes come in and provide this energy boost to allow reactions to occur, even ones that would occur by themselves, but are just sort of slow about it.

There's another term that you may read about in your textbook, and that's actually metastable state. What that means is that these molecules or compounds are thermodynamically unstable. So, meaning that their delta G is negative, and they will eventually occur by themselves, but they usually won't. They actually stay in this metastable state for an extended period of time because they can't overcome this activation energy to produce the products. So if we're looking at this graph, this is an exergonic reaction, which means it's energy-releasing. ΔG here is going to be negative; it's going to be less than 0, because the free energy of the reactants is higher than the free energy of the products. We talked about activation energy, so what is that on this graph? Well, that's the peak you see here. Activation energy. Although this is an exergonic reaction, which is going to release energy as it changes from reactants to products, we still need to get over this energy hump right here, this activation energy to occur.

Enzymes come in here to really reduce the amount of activation energy necessary for a reaction to occur. So, how do enzymes do this? Well, there are two potential ways of overcoming the activation energy. The bad way is just to increase the heat. An increase in heat is going to increase kinetic energy, and therefore, make reactions happen faster. But, unfortunately, we would all die because we would all overheat. So, obviously, that's not a good way to do this. Now, the second way of overcoming activation energy is the good way, and that is using an enzyme that will lower the activation energy.

How do enzymes work? Well, they bind to what's known as the transition state form of the reactant. So here we have our reactant, our two reactants. You have one here, and you have our products, which look different because some type of chemical reaction has occurred. The transition state is going to be this state here, where it's sort of in between the reactant and the product. The activation energy that is required to get to this point is fairly high. And this transition state is fairly unstable. At any time it can go this way or it can go this other way. What an enzyme does, and here is an enzyme, it comes in right here and it binds to the transition state, and it stabilizes it, so that it can overcome the activation energy and proceed to the product. That is how an enzyme works to reduce the activation energy and promote the formation of the products in a reaction.

So now let's move on.

Substrate Interactions

So now, let's talk about enzyme and substrate interactions. Enzyme and substrate interactions are actually responsible for regulating the actual reaction that is occurring. One way to promote enzyme substrate interaction is through diffusion, which is the passive movement of substrates throughout the cytoplasm. In order for an enzyme and substrate to work, they have to interact with each other. They have to be close together in the cell. For instance, if I'm the enzyme and you're the substrate, we're not going to interact if we are far apart. But, if we were in a cell, I could diffuse over to where you are. We could interact, and the chemical reaction could move forward. Diffusion is a major way that enzymes and substrates come into contact with each other.

In a cell, molecules are dynamic. A molecule in a cell takes 115 of a second to travel 10 micrometers. The average cell diameter is 15 micrometers. So in 115 of a second, a single molecule can move nearly two-thirds the diameter of the cell. This means that enzymes are impacted by about 500000 random collisions each second, leading to the possibility of thousands of substrate reactions every second due to these interactions and diffusion within the cytoplasm.

Once an enzyme and substrate have found each other, they interact in the active site, a groove in the enzyme where the substrate binds, and the reaction takes place. Usually, the shape or the bonds are complementary between the substrate and the enzyme. The binding site is typically not on the surface but is instead buried inside the enzyme to isolate the substrate from other chemical reactions in the cytosol or other environments.

The enzyme-substrate interaction models include the lock and key model and the induced fit model. In the lock and key model, the enzyme and substrate shapes fit together perfectly, akin to a key in a lock. With the induced fit model, the enzyme and substrate initially don’t fit perfectly; however, a conformational change in the enzyme occurs, enabling them to fit together and allowing the chemical reaction to occur.

Enzymes can also interact with other molecules known as cofactors or coenzymes, depending on whether they are inorganic or organic. Binding these facilitators helps the reaction take place. Cofactors can also be referred to as prosthetic groups in some texts, which is another term for the same facilitating components. Let's now proceed to discuss these interactions further.

Enzyme Regulation

Okay. So now we're going to talk about enzyme regulation. Enzyme catalysis is highly regulated, which makes sense because enzymes speed up chemical reactions. So, we don't want enzymes speeding up reactions that we don't want to take place. They have to be regulated. There are many different ways that enzymes are regulated. I'm only going to mention a few here, and we'll talk about more later in the course. But these are just three that are mentioned in your textbook and are good to know conceptually about how enzymes are regulated:

The first is feedback inhibition. That's when a product of one pathway inhibits the enzyme involved in its synthesis. So if you have an enzyme acting on this to produce some other type of product here, and that product can come back up here and inhibit the enzyme. This feedback inhibition can stop enzyme catalysis when enough of the product has been made. That's one way of regulation.

Another way of regulation is allosteric regulation, and that's when some type of small molecule actually binds to a regulatory site on the enzyme. When it does that, it binds to the enzyme, it can change the shape or structure, and that can affect the binding of the substrate or its ability to speed up reactions. Generally, it usually inhibits the reaction moving forward. That's one way enzymes are regulated.

Finally, another way is through phosphorylation. Phosphorylation occurs when there's an addition of a phosphate group. This actually has the ability to inhibit or activate enzyme activity. If we're going to look at just an example of regulation, we see here that there is an enzyme and a substrate. And you can see that the active site is right here. Normally, the enzyme is going to bind the substrate and then release products. But there can be all of this regulation that occurs in this process. For instance, this product here, this red one, can come back and bind to the enzyme and block substrate binding; that would be feedback inhibition. There can be some type of binding site of something else, some cofactor here, which blocks substrate binding. So that would be allosteric regulation. And then you can add phosphorylation, which is going to be a little difficult to draw. So I'll just put here, phosphate group. And that phosphorylation can actually stimulate or inhibit the enzyme substrate binding and the reaction that occurs. So now let's move on.

Which of the following is not one of the three major conditions of enzymes?

• A. Enzymes cannot be consumed by a reaction
• B. Enzymes cannot be changed by a reaction
• C. Enzymes do not effect the rate of the reaction, only the free energy
• D. Enzymes do not effect the free energy of the reaction, only the reaction rate

Answer: (C)

Here’s what students ask on this topic:

What are enzymes and how do they function in biological reactions?

Enzymes are specialized proteins or RNA molecules that act as catalysts in biological reactions. They function by lowering the activation energy required for a reaction to occur, thereby speeding up the reaction. Enzymes are highly specific, meaning they only act on particular substrates. The substrate binds to the enzyme's active site, forming an enzyme-substrate complex. This interaction stabilizes the transition state and reduces the activation energy, allowing the reaction to proceed more quickly. Importantly, enzymes are not consumed or altered in the reaction, so they can be used repeatedly.

How do enzymes lower activation energy in chemical reactions?

Enzymes lower the activation energy of chemical reactions by stabilizing the transition state of the reactants. They achieve this by binding to the transition state form of the reactant at their active site. This binding reduces the energy required to reach the transition state, making it easier for the reaction to proceed to the product stage. By lowering the activation energy, enzymes increase the rate of the reaction without being consumed or permanently altered in the process.

What are the different models of enzyme-substrate interaction?

There are two primary models of enzyme-substrate interaction: the lock and key model and the induced fit model. In the lock and key model, the enzyme's active site is perfectly complementary to the substrate's shape, allowing them to fit together precisely. In the induced fit model, the enzyme's active site is not initially a perfect fit for the substrate. Instead, the binding of the substrate induces a conformational change in the enzyme, allowing a better fit and facilitating the reaction. Both models explain how enzymes achieve specificity and catalysis.

What are the main mechanisms of enzyme regulation?

Enzyme activity is regulated through several mechanisms to ensure that reactions occur only when needed. The main mechanisms include feedback inhibition, allosteric regulation, and phosphorylation. Feedback inhibition occurs when the product of a reaction pathway inhibits an enzyme involved in its synthesis. Allosteric regulation involves the binding of a small molecule to a regulatory site on the enzyme, causing a conformational change that affects enzyme activity. Phosphorylation involves the addition of a phosphate group, which can either activate or inhibit the enzyme's activity. These regulatory mechanisms are crucial for maintaining cellular homeostasis.

What is the role of cofactors and coenzymes in enzyme activity?

Cofactors and coenzymes are non-protein molecules that assist enzymes in catalyzing reactions. Cofactors can be inorganic ions like Mg²⁺ or Fe²⁺, while coenzymes are organic molecules, often derived from vitamins. These molecules bind to the enzyme and help stabilize the enzyme-substrate complex or participate directly in the chemical reaction. By facilitating the proper orientation of the substrate or participating in the reaction, cofactors and coenzymes enhance the enzyme's catalytic efficiency.