In this AP Biology Crash Course, we will review what you need to know about enzymes for the AP Biology exam. We will cover what enzymes are, how enzymes work, some factors that affect how they work, and finally an example of an AP Bio question about enzymes.
What are Enzymes?
Enzymes are proteins that catalyze chemical reactions. Molecules at the beginning of the chemical reactionary process are called substrates, and these are converted into products. Enzyme kinetics, or Michaelis-Menten kinetics, investigate how enzymes bind substrates and turn them into products. The amount of substrate needed to reach a given rate of reaction is the Michaelis-Menten constant. Almost all metabolic processes require enzymes to occur at the proper rate.
Some chemical reactions take a lot of energy to start. The amount of energy needed to kick off a chemical reaction is called its activation energy. Enzymes help the chemical reaction reach the activation energy by lowering the amount of energy needed to overcome it.
French chemist Anselme Payen discovered the first recognized enzyme, diastase, in 1833. Louis Pasteur also noticed when studying a mixture of sugar, alcohol, and yeast, something was happening to ignite the fermentation process. The word “enzyme” was first used by a German physiologist in 1877 named Wilhelm Kuhne.
As you may have learned in your AP Biology course, an enzyme’s primary structure is nothing more than a long sequence of amino acids that bond with one another. Short-range interactions (secondary) between amino acids can be alpha-helix or beta sheet. Alphas look like spirals, and betas look like flat, wavy sheets.
The long-range interactions (tertiary) are when amino acids interact with other amino acids a long way down the strand, and as they fold over, they form a globular structure. The quaternary structure is when one globular strand interacts with other tertiary pieces. When bonds are formed at this level, they are often hydrogen bonds, but sometimes it is two hydrophobic pieces interacting, or even ionic bonds. Alternatively, when an enzyme is unfolded, it’s referred to as being denatured.
Enzymes are quite large relative to their substrates, yet only a small portion of the structure is involved in the reaction; that part is referred to as the catalytic site. This site is located next to a binding site where residues orient the substrates. These two sites together are referred to as the active site.
In order for an enzyme to work, it must be activated by the binding of another molecule. Activators can either be cofactors or coenzymes; cofactors are small, inorganic chemicals, and coenzymes are organic compounds. Both of these activators bind to the active site but are not considered substrates. When they bind to the active site, there is often a conformation change. A conformation change is a change in the enzyme’s configuration or shape. The change in shape alters the active site and allows the substrate to bind.
How Do Enzymes Work?
Enzymes are extremely selective about which substrates they are able to bind to. Related to the specificity of enzyme and substrate bonding, Emil Fischer proposed the lock and key model where the two would have complementary geometric forms. Daniel Koshland suggested that these complementary geometric pieces can actually shift and can even be reshaped by their interactions with substrates. This new discovery led to the induced fit model.
The induced fit model refers to the ability for the substrate and enzyme to modify their shape in order to fit together. After the enzyme and substrate have bound to each other, the enzyme will work to lower the activation energy of the chemical reaction.
In order to understand how enzymes work, we should review activation energy and Gibbs free energy. Using the Gibbs free energy models, we can see that the energy of the reactants is lower than the activation energy. The activation energy (delta G) is the amount of energy that is needed to make this reaction move forward. When the reaction is catalyzed by an enzyme, the amount of activation is greatly reduced, making that hump easier for the reactants to get over.
Enzymes are able to lower the activation energy of a chemical reaction by making changes to the transition state of the reaction. By stabilizing the transition state, the reaction will move toward the transition state more easily. Without an enzyme, the transition state is often not energetically favorable. The enzyme will alter the transition state in order to make it more favorable and to move the reaction forward. Similarly, the enzyme can lower the energy of the transition state, which will allow the reaction to move forward.
Inhibitors bind to an enzyme to decrease its activity. The prevention of substrate-enzyme binding is a form of regulation. Negative feedback is an example of a time when inhibitors are important. If the body has produced too much of the final products of a reaction, those final products can feedback to the reaction and prevent the enzyme and substrate from binding. In essence, in negative feedback, the end products are telling the body to stop creating them.
There are two types of inhibition that are used for regulation, competitive and non-competitive. In competitive inhibition, the inhibitor binds directly to the active site, effectively completely blocking access from the substrate.
Non-competitive inhibition, also known as allosteric inhibition, is when the inhibitor binds to a different part of the enzyme but induces a change in the active site to prevent binding by the substrate. The binding often changes the shape or charge of the binding site, preventing the substrate from being able to bind. The other way to inhibit is to bond. These processes all help to regulate rates of enzyme activity.
Factors that Affect Enzyme Activity
Enzyme activity is affected by many factors, including temperature and pH. An increase in temperature increases the rate at which the molecules in a system move. This increase in temperature will allow the substrates and enzymes to locate each other more quickly. However, there is a point at which the enzyme will become denatured due to the higher temperature, adding stress to its bonds. Many enzymes operate at an ideal temperature called the optimum temperature.
pH can also affect an enzymes activity. pH controls the balance between positively and negatively charged amino acids. Ionic interactions are important to hold the enzymes together. Most enzymes have an optimum pH between 6 and 8.
Now that we have covered the topic of enzymes, let’s explore a real life example. At this point in your studies, you may have come across an enzyme called DNA polymerase (if you haven’t please check out AP Biology Crash Course Review: DNA Replication). DNA polymerase is an enzyme that catalyzes the chemical reaction of deoxynucleoside triphosphate plus DNA to diphosphate and DNA (plus the nucleotide).
In this reaction, the enzyme breaks a phosphate bond from the deoxynucleoside triphosphate and uses that energy to add the nucleotide base to the DNA molecule. Without DNA polymerase, this process would not be able to occur because it is energetically unfavorable to catalyze. If this process could not occur, our cells would not be able to replicate and repair. This would result in death of the organism.
AP Biology Question
Now that we have reviewed the information you need to know about enzymes for the AP Biology exam, here is an example of a multiple choice question you could see:
Which of the following is characteristic of enzymes?
A. They lower the energy of activation of a reaction by binding the substrate.
B. They raise the energy of activation of a reaction by binding the substrate.
C. They lower the amount of energy present in the substrate.
D. They raise the amount of energy present in the substrate.
What did you pick? If you chose A you are correct! Enzymes lower activation energy when they bind to the substrate and alter the transition state. If you had trouble with this question, go back through and read this review. If you have any questions, let us know in the comment section!
In nearly every chemical reaction of life, enzymes are used. Dr. Richard Wolfenden recently found that if enzymes were removed, the biological reactions necessary to life would take 2.3 billion years to spontaneously occur. Clearly, enzymes are a necessary part of life!
In this AP Biology Crash Course Review, we went over the general structure of an enzyme and its activation site. We then reviewed what exactly enzymes do and how they do it. We then reviewed different types of activation and inhibition molecules. Finally, we wrapped up with an example of a real life enzyme and why it is important to survival.
The AP Bio exam will likely have questions about enzymes on it. Do you feel prepared? Let us know!
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Have you ever stopped think that why is it you eat food? I mean yeah everybody can tell you if you don't eat, you don't have the energy or building materials you need to make your body. But stop to think about that for a moment. If I need to grow some hair, unless I go down to a barber shop and start snacking off of the floor, how the heck does the food I eat become human hair? For that matter, how does sugar become energy?
Well, it turns out all these processes are helped along by the special molecules called enzymes. In order to get this, let’s focus in on the structure and function of these enzymes. Then I’ll take a look with you about the various factors that influence how enzymes work. Whether it’s the three factors that I mentioned in the AP Biology Lab on enzymes, that often is in the essay portion. Or those helper molecules called co-enzymes or cofactors that help enzymes do their job.
When you’re studying enzymes, a really good model to use to help you figure it out, are a pair of scissors. For example, if you’re trying to tear a piece of paper in half, by grabbing it on the sides and trying to rip it right down in the middle, you try and try, and it’s nearly impossible. Sometimes you can get it to rip right here, but unless you are a lot stronger than me, you can’t get it to rip in the middle.
On the other hand I use this pair of scissors and give it a little snip, easy. Now were the scissors used up in doing this? No. I can keep doing it over and over again and again and same thing with enzymes. They don’t get used up by the chemical reactions they help. With that same pair of scissors work however, if a co-enzyme provided me a tree branch, nope. Why not? It’s the shape. On the other hand, if I had a chain saw, it goes through easily. That same chain saw though on a piece of paper, I can’t make paper do this with a chain saw. What’s the difference? It’s the shape.
Let’s take a closer look at what enzymes are. Enzymes are proteins catalysts. Now what does that mean? Protein catalysts are enzymes that can put together or tear apart other molecules, without being used up in the process. So a catalyst, what it does is, it lowers the activation energy required for a chemical reaction to occur. Now with enzymes, they’re highly specific in what they can work on, and that’s because of their shape. They only affect one particular kind of molecule and that’s called their substrate.
Now, the part of the enzyme that actually fits to the substrate, is called the active side. If we take a look at this, you can see here this is the active site of the enzyme and this is the substrate, the molecule that is going to be working on. Notice the precise match up to this. That’s called the Lock and Key Hypothesis. That’s the old model. The new model now is called the Induced Fit model.
If we take a look at that, you can see the active site is close to the right shape and not quite as the enzyme gets closer and closer, it starts to cause the active site to change shape, until it precisely fits. But this causes a strain on the enzyme which alternately causes a strain on the substrate. It helps it break things apart.
Now if it’s an enzyme that breaks things apart, that’s called the digestive or catabolic enzymes. That’s what our scissor model represents. If it’s putting molecules together, if we just reverse the arrows here, that would be called an anabolic enzyme. If you want a model for that, think of a stapler. Now what is it again that allows us to work? It’s the precise three dimensional shape. Now can I cut with any part of the enzyme? No, I can’t cut just by working my hand on this. I have to put my fingers right here in the active site. It’s the same thing for an enzyme.
Now what is it that gives it that precise shape? That’s called the tertiary structure of a protein. If we take a look at this protein here and you watch it rotate, these precise shapes here are what give it that three dimensional shape.
The term to toss out in the middle of an enzyme essay is tertiary structure. If you want to gain another point, what cause the tertiary structure? It's the interactions between the different parts of the enzymes. With the R-groups of each amino acid forming hydrogen bonds. That’s a magic word to use in the essay to get the point. It’s the hydrogen bonds between the different R groups of the enzyme. That’s the basic idea of how an enzyme works.
On the AP test, they love to ask questions about the AP lab number six. That’s all about enzymes. Now in a enzyme lab, what they do is they fool around with the pH, the temperature and the concentration of substrate involved around an enzyme. Then they look to see how does that affect the rate of how that enzyme can work. So I’m going to go through this; the enzymes response to pH, their responses to temperature. If we fool around the concentration of substrate and then I’ll address some of the other factors that could influence this.
So with pH, if you recall, the tertiary, a 3D shape of an enzyme is what gives it it’s ability to match up to the substrate with its active site. Now you’ve got to remember, this is a way to earn points. It’s the hydrogen bonding between those R groups of the amino acid chain that makes it the protein, that gives it the high specificity.
If we start fooling around with the pH and you should know that pH is the concentration of hydrogen ions in the solution, we start changing the number of hydrogen ions that are around that enzyme. Then that’ll change the shape of the active site and so it won’t work so well. So when we’re looking at an enzyme, you’ll notice most enzymes, if you have to guess will have an optimal pH at around 7 or 8. What that means is that, that’s the normal operating pH of that enzyme.
So if I was talking about an enzyme in a bloodstream which usually has a pH around 7.4, it should be optimized to work best at pH 7.5 or so.
If I get away from that, either making it more acidic or more basic, then that starts changing the shape of the enzyme. So it stops working so well. Just like if I took my scissors and I started bending the shape of the blade, so that they didn’t match up very well, they won’t cut very well. When you get outside, too far out, it stops working entirely. That’s called being denatured. That’s a good word to use in the essay. That will get you another point when it’s no longer in its natural shape.
Now what’s this curve over here? This could be an enzyme that’s located in say your stomach juices. Because since that’s highly acidic, they need to have an optimal pH of around 2. So they would be natured if though they wound up in your blood. Now what about temperature? Temperature it’s kind of the same. In that, every enzyme will have an optimal pH, but instead of having that standard Bell Curve, what you’ll see is, as you increase the temperature, that gives more energy for the chemical reactions to occur.
So you’ll see a steady increase in the rate of that enzyme’s ability to do its job. When you get past its optimal temperature, eventually you get so much heat energy that those R groups are no longer able to hold on to each other, because those hydrogen bonds. Remember that. Those hydrogen bonds get overwhelmed. Just like if I’m cutting away at this and I get so hot that it overheats, and eventually it’ll melt and be denatured. There is that point.
Now what is this orange one? That represents an enzyme perhaps from some kind of bacteria that lives in hot volcanic pools. So it will have an optimal pH at much higher temperature.
Now, before I go into how things respond to change in their substrate concentration, I want to give you a model that you know of, that will demonstrate responses to pH and temperature. And that’s egg whites. If you take a look at egg white, it’s not white. What color is it when it comes out of the egg? It’s clear. What is that? Albumin is the name of the protein that makes up egg white. Albumin is actually this long chain that gets wound up into a tight little ball.
Now if I take a model of albumin say this. This looks normal. If I start to heat it up though, it starts to unwind.
Why? What was keeping it in the shape here? Some weak frictional effects and the bending of the metal that’s inside the pipe cleaners. But if I start doing this, that’s like heating up the albumin. You’ll notice that it unwinds. Just like if you cook the clear albumin, that ball unwinds and starts to form a thick tangled mat that becomes a solid, instead of being the little balls that can roll all over your hands. The same thing with pH. If I alter the pH, it unwinds. That’s how you can take vinegar, add it to albumin and it’ll start to form this white mass. So that’s how pH and temperature are affected.
Let’s take a look at substrate concentration. Obviously, the more substrate you give to an enzyme, the more it can do its reaction. But eventually you get to a point where you level off on this. Just like if I go back into my scissor model. If somebody hands me one piece of paper per minute, I can do one paper torn in half per minute. Two, two paper torn per minute, but if you give me a million pieces of paper, I can’t work that fast sorry. So I’ll level off and that’s basically how the official standard response is on the lab. So if you learn this, you’ll do well.
Now we’ve talked about how enzymes normally respond to things like temperature, pH and the amount of substrate. Now let’s take a look at some other molecules that influence enzyme behaviors. Those are things called cofactors and co-enzymes. These are essentially helper molecules that help the enzyme do its job. Now a number of these cofactors fall under the category of what are called negative regulators. That means that they slow down the enzyme. They stop it from doing its doing. That’s called inhibition.
Now some of them are competitive inhibitors. That’s where, here is the enzyme and the substrate. Notice this little red, guy lands in the active site and blocks it. If I go to my scissor model, let’s imagine I put something in here.
Now paper can’t get in, because my hand’s blocking that. It’s competitive, because it’s competing for the active site, inhibition. On the other hand you can have the inhibitor land on a different site. That’s called allosteric factors. If we take a look at that, here’s the substrate and its active site. Notice this allosteric site. If the inhibitor molecule comes into there, it changes the shape of the substrate. You should know that allosteric sites, allo- means other or separate. -ste refers to shape like stereo is 3D sound. So this allosteric site, when the inhibitor molecule lands on it, gives the enzyme an alternate shape that no longer fits. If I put my fingers like this or I warp a piece of paper around this, then the enzyme can’t open up.
Now there can be positive regulators or activators. These might be things that help it open up. Magnesium ions are a common cofactor that are positive regulators for many enzymes. That’s pretty much it. Just to highlight them, there’s other coenzymes. ATP is an example of a coenzyme. I could be that. I provide the energy for my enzyme. That’s it, pretty simple, cofactors and coenzymes.
There you go. You now know everything you need to know about enzymes to do well in the AP Biology exam. They’re protein catalysts that are highly specific in what they can work on due to their tertiary or 3D shape. You know that the three major factors that they’re going to ask about in lab questions are their responses to pH, temperature and the amount of substrate. With pH and temperature, you know that they’ll have some optimum based on what is their normal environment. Whereas, with the concentration of the substrate, the enzyme will tend to increase its rate until it levels off, when it’s completely saturated. You also know that there are helper molecules called coenzymes or cofactors. They help enzymes do their job.
One last trick I’m going to let you in on, to help you do better on the multiple choice and the essay portion, is the ending -ase, a-s-e typically means enzyme. So what that means is that, if you’re in a multiple choice question and they say, so which one of these molecules is a protein? Look for the one that ends in –ase. If you see that, you know it’s a protein.
Similarly in the essays, whenever you’re describing some molecular process, and you need an enzyme and you don’t know the name, invent it. Take the name of the molecule it’s working on like lactose, remove the -ose that means carbohydrates, slap in that –ase, that means protein enzyme and you’ve got lactase. Guess what? That’s the actual name. Even if you’re not right, you may trick the reader into thinking that you are right or that you know more than he and you’ve got yourself the point. There you go.