Enzymes as catalysts for reactions in biological systems; discussion of substrates, active sites, induced fit, and activation energy.
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- How does the ATP molecule work in the active site? Why is it there?(18 votes)
- ATP is known to be a perfect energy currency for various reasons. If you draw out an ATP molecule, you will notice that it has three phosphates sticking out of the molecule, held together by phosphoanhydride bonds. There is a fair amount of resonance but ultimately, this is fairly unstable and can easily break down to absorb/release energy.
Phosphates are negatively charged and parts of the protein (enzyme) have a very specific active site with charged amino acids. This allows the phosphates to find a positively charged binding site(36 votes)
- Why does the hexokinase need to be so big? Wouldn't it just need a few positive ions to draw the ATP's electrons away, and not need the rest of it?(7 votes)
- How would you get the positive ions to be in the correct places relative to the substrate?
How would you keep chemically similar substrates from being affected?
Metabolic reactions also need to be regulated — how would you do that?
Another factor to consider is that enzymes are evolved and therefore may seem poorly designed. This is, of course, because they aren't designed! The process of evolving a new enzyme usually starts with another enzyme that has a weak ability to do some new reaction and then by trial and error organisms with slightly more effective versions are selected. This necessarily leads to compromises.
With a lot of work and testing you could design a molecule that catalyzed the same reaction. You might even make one that was better in some ways, but this is much more difficult than you might expect.(15 votes)
- How does the enzyme Lipase breakdown lipids/fats in milk and why/how so are these reactions so greatly effected by temperature ?(10 votes)
- Also, enzymes are proteins, and proteins are affected by temperature and pH values. When the temperature is too high, or at extreme values of pH, the enzymes undergoes conformational change (ie. change in shape) of the active site, also known as denaturation. The substrates no longer fit into the shape of the active site to form an enzyme-substrate complex, so the rate of the enzymatic reaction decreases.(5 votes)
- I don't completely understand the idea that the reaction is releasing energy when the two molecules bond. Since two molecules are bonding it is an antibiotic reaction and that is an endergonic reaction so energy is being stored. Wouldn't the graph for the Gibbs free energy be increasing?(7 votes)
- I'm assuming that when you wrote "antibiotic" reaction you meant anabolic — if that is not correct, please leave a comment.
The reaction discussed in this video is the phosphorylation of glucose, which as Sal states is exergonic.
This is because during this reaction a high energy bond in ATP is broken and provides the energy for the new bond between phosphate and glucose. The new bond has a lower energy (is more stable) than the phosphoanhydride bond and so the net effect is a release of energy.
Does that help?(2 votes)
- I'm curious. How do/did scientists know that the proteins form these complex structures and with all the given elements (down to the atomic scale), if most research was done without electron microscopes? (or were they?)(5 votes)
- When they didn't have microscopes, they had magnifises. These are like a magnifying glass. But, they have am extra 5 layers to make it as powerful as a microscope.(3 votes)
- What factors increase enzymes work and what decrease they're work(2 votes)
- There are five factors affecting enzyme activity: enzyme concentration, substrate concentration, inhibitors, pH and temperature.(9 votes)
- How do scientists find out about enzymes? Im just curios to know this.(5 votes)
- Normally I would try to give you a specific answer, but the sources I looked at list so many names that I cannot specifically name one. So I recommend you to personally research it(3 votes)
- What happens if enzymes were allowed to operate at a maximum rate at all times?(3 votes)
- The enzymes would have an optimum production rate. They would be able to go through any metabolic reaction at a faster rate. However, by allowing them to always be in these rates, they might produce products the body might not need. This is why enzymes are not always operating in a maximum rate. This allows the body to maintain its homeostasis.(4 votes)
- Are enzymes something in your body that allows you to be/look young. How many enzymes do we have? Also is it true that honey can last for a long time because bees put their enzymes in it.(3 votes)
- Not sure about the honey part, but enzymes speed up chemical reactions. I'm pretty sure that enzymes don't have to do anything with looking young.(3 votes)
- Do ALL enzymes break things down?(2 votes)
- No, enzymes are catalyst of biological reactions meaning they speed up reactions of altering and affecting molecules in our bodies, but it does not have to be breakdown.
Digestive enzymes are known to break down molecules but here are some other functions:
IN DNA replication they unwind DNA, or synthesize DNA.
(helicase and DNA POlymerase).(5 votes)
- There are all sorts of reactions in biological systems that are energetically favorable, but they're still not going to happen quickly or even happen on their own, and the phosphorylation of glucose is an example of that. We go into some detail into that on the video on coupled reactions, and I think we actually called that The Phosphorylation of Glucose 6-Phosphate, but it's super important because by putting the phosphate group on a glucose, it's ready to be the input to a whole series of biological mechanisms, it allows the glucose to be tagged so it's going to be hard for it to escape the cell again, and it's fairly straightforward mechanism, where you have a lone pair of electrons on this hydroxyl group right over here, and then it attempts to, if it's in the right configuration, it could form a bond with the phosphorus in the phosphate group. Now, the reason why it doesn't happen on its own, even though it's energetically favorable, once you form the bond, you have, electrons are gonna be able to go to a lower energy state. So it has a negative delta G. If this is the molecules before the reaction, this is how much free energy they have before the reaction, after the reaction, they have less free energy, they have been able to release energy, so this is something that we would consider to be spontaneous, but for the reaction to happen, you need a little bit of energy to be put into the system. We call this our activation energy. You might say, "Well, why is that?" Well, we have electrons that want to form a bond with this phosphorus, but this phosphorus is surrounded by negative charges. This oxygen right over here has a negative charge. This oxygen right over here has a negative charge, and as you can imagine, electrons don't like being around other electrons, like charges repel each other, so in order for this reaction to occur, or for it to occur more frequently, it has to be catalyzed. A catalyst is anything that makes a reaction happen faster, or even allows the reaction to happen at all, and when we talk about catalysts in biological systems, we're typically talking about, we're typically talking about Enzymes. Enzymes. And the way that an Enzyme might catalyze this reaction, we actually talk about it, and when we talk about coupled reactions, it'll maybe can provide some positive charges. It could provide some positive charges around these negative charges to pull them further away to create space so that you can actually have the reaction proceed, and so what an Enzyme would do, it would make this curve, instead of having this hump on it, the curve would more like this, so that the reaction can just proceed. But what are these Enzymes? These things that can maybe, it could place some interesting charge that can allow the reaction to happen a certain way, it might bend the molecules in a certain way to expose some bonds, it might have a more acidic or basic environment that might be more favorable for the reaction. What are these seemingly magical things? Well, at a very high level, they tend to be these protein complexes, plus or minus a few other things, so you can view them as proteins and maybe sometimes, they'll be multiple polypeptide chains put together, they might have some other ions associated with them, but for the most part, they are proteins, and the molecules that are going to react, that are going to bind to the proteins, we call these the Substrates. So these, and this reaction, (mumbles) glucose and the ATP, these are going to be the Substrates. So you can imagine the Enzyme that does this, and the general term for the Enzyme that helps phosphorylate a sugar molecule like this, we call it hexokinase. So it might be this crazy-looking, this crazy-looking protein, we're gonna take better looks at this in a few moments, but the ATP might bind to it right over there. ATP is one of the Substrates, and then the glucose might bind to it right over there, and so these two Substrates bind, and the area where all of this is going on, we call that the Active Site. So the Active Site, because that's where all the action is, the Active Site. And often, when you have the Substrates bind, they're able to interact with the protein to make the fit even stronger, to make it even more, more suitable for the reaction to take place, and so the whole protein might bend a little bit to kind of lock these two in place a little bit more, and we call that Induced fit. Induced fit. And so, where would these positive charges come from? Well these would be things that are the side chains of the different amino acids on the actual, on the polypeptide chain on the protein, and it could even be other ions that get involved, in fact, in particular, to facilitate the phosphorylation of glucose, a magnesium ion might be involved to help draw some positive charge away, but there's other positively charged groups that help draw charge away so that the reaction is more likely to occur. So that's what enzymes are, and they tend to be optimally working in certain pH environments or certain temperatures. In general, the higher temperatures allow more interactions, things are bumping around more, but if temperatures get a little bit too high, the protein or the Enzyme might stop working, it might denature, it might lose its actual structure. And what I want now give you an appreciation for is how beautiful and complex these structures are. You should appreciate what I'm showing you. These are in your cells! These are in your, look at your hand, look at everything around you, there's a lot of this stuff going on inside of you, so hopefully it gives an appreciation for the complexity of you as a biological system, but frankly, all biological systems. So this right over here, this is a visualization of a hexokinase, one variety of it, and just to get a sense of scale, this is a glucose molecule, and this right over here is an ATP, and so they will bind, these are the two Substrates, they will bind at the Active Site. You might have the Induced fit, where this fits around it. It draws some charge away, it might bend the molecules in a certain way so that they're more likely to interact, bring these things close together, and so you're gonna have the reaction occur and then once the reaction occurs, they're not gonna want to bind to the Substrates anymore. I guess you could say the products, at that point, and then they're gonna let go of them, and then the Enzyme has a change, and that's an important property of an Enzyme. It's not like it just has one use and it goes away, it can keep doing this over and over and over again. One Enzyme will do this many, many, many, many, many times in its actual life. And so now what I want to show you is a little three-dimensional visualization that I got from a website, so let me go get that. Go ahead and pause my recording so I could get to this little simulation or this model, and this is actually a hexokinase as well, and hexokinase is come into, in a bunch of different varieties, but this is a pretty neat thing to look at and this has been visualized differently, and when you look up protein images on the web, or anywhere, you'll see them sometimes with these ball and stick models, sometimes you'll see them in these space-filling model, sometimes you'll see them with this kind of, where you the very structures, and you notice the alpha helices here that we studied when we talked about protein structures, and you can also see some beta sheets, but this gives you an appreciation of the binding sites and how these things might interact. This right over here, that is a molecule of ATP, and then right next to it, I believe, if I'm looking at that right, that is a molecule of glucose, and notice they have bound, they are the two Substrates, they have bound at the Active Site, and now, they can interact with each other, the Enzyme, the hexokinase in this case, can help facilitate the reaction that we care about, the phosphorylation of glucose. So hopefully, images like this, and like this, give you an appreciation for how complex and how beautiful these things actually are.