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M.Ed., Stanford University
Winner of multiple teaching awards
Patrick has been teaching AP Biology for 14 years and is the winner of multiple teaching awards.
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.
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