Right, so Curious 6 is a bit of a big one and it's all about metabolic pathways. So within this, we want to, the first part Curious 6a, we want to be able to identify what is meant by the term metabolism. We need to look at the terms anabolism and catabolism and understand that within a metabolic pathway, we may have irreversible, reversible and alternative routes that we can identify.
So, first of all, metabolic pathways, as opposed to an enzyme reaction, a metabolic pathway is an integrated pathway. It's highly controlled and there's lots of enzyme catalyzed reactions, all integrated and interacting within a cell. The sample is shown here by the next carrier you will be familiar with.
the ins and outs of this. But this is basically showing respiration, which would be a classic metabolic pathway. We have got one enzyme reaction here, where we've got substrate and a product. However, the product of this part, this reaction here becomes a substrate for this reaction. And so it's integrated and each step is going to be controlled with an enzyme.
For the cell to function correctly, these pathways have to be integrated and they have have to be subject to control. There are two main metabolic pathways that we want to be aware of. Anabolic, which at Nat5 we would have considered them as a synthesis reaction.
So anabolic reactions will build up large molecules from smaller substrates and therefore will require energy. Catabolic at Nat5 we refer to as degradation. Here we are going to break down large molecules into smaller products and it will release energy. So if we have all the chemical reactions in the cell, we would refer to this as metabolism. It can be broken down into anabolism and catabolism.
Anabolism is the buildup or the synthesis of large molecules from small substrates, whereas a catabolic reaction is breaking down large molecules into small products. Cannibalism requires energy. whereas a catabolic reaction will release energy.
So that's one simple way that we could represent that information. Alternatively, sometimes you may see something like this, where you've got many small substrates are going to interact in the presence of energy to form one large, more complex product, and then vice versa for catabolic reactions, whereas a large substrate is broken down into smaller, simpler products, releasing energy. Sometimes you may see it in an alternative way, we should be reasonably familiar with this style of diagram after Nat 5. Here, an example of catabolic reaction is respiration, so we're taking glucose. In the presence of oxygen, we're going to release energy and then other products, conducts in water. The energy is released and it's going to be then used to help in an anabolic pathway, for example, the synthesis of proteins.
by the joining of individual amino acids with energy to form more complex proteins. Now metabolic pathways can have reversible, irreversible steps and alternative routes. So for example that is shown here which is trying to depict glycolysis, so the first part of respiration. So on this diagram we can see reversible and irreversible steps.
So the first part of glycolysis is irreversible. We've got glucose being converted to the first intermediate and then we're kind of locked in. This is an advantage to the cell because it's going to make sure that the intracellular glucose concentration is maintained at a low level.
It's going to be constantly broken down to form intermediate one and therefore it promotes continuous diffusion of glucose into the cell from an area of higher extracellular. higher concentration outside of the cell. So we're going to form intermediate one.
However, the conversion of the first intermediate to a second intermediate is reversible. So we can go back and forth between these two intermediate materials. If more intermediate two is required than what the cell actually needs, then some can be converted back to intermediate one. And you can then see an alternative pathway comes along. So if actually we've got too much intermediate 2 as a result of potentially having too much glucose we don't need to break any more down to form ATP intermediate 1 will be reproduced from intermediate 2. and in us and other mammals be converted to glycogen and in plants it will be converted to starch.
Now metabolic pathways have to be subject to control so they can be controlled by the presence or absence of enzymes and the regulation of the rate of reaction of key enzymes occurs. So let's have a little look about how enzymes work. Now at that five level we talked about the lock and key mechanism. Now we're going to slightly adapt that now. So in an enzyme molecule, we have got what is known as an active site.
So that polypeptide chain that emerges at the end of translation will undergo significant folding. And as a consequence of that folding, there is this area of active site. And that is reasonably complementary in structure to the shape of the substrate in that reaction.
Enzymes are specific because. of this complementarity that exists between the substrate and the active site. And substrates are chemically attracted to that active site. They're said to have an affinity for it.
However, this lock and key model is not quite telling us the full story. In fact, we now move to what's called the induced fit model. And this occurs when the active site will actually change shape.
So as you can see here, it's not perfect. There's a high affinity between the two molecules. However, it's not perfectly suited to the shape of that substrate.
There's a rounded area here, there's a squared off edge here. The active site will then change shape to benefit the substrate after the substrate binds and it locks on a very, very tight fit. The substrate molecules have a high affinity for the active site and the subsequent products that are formed after catalysis have got a low affinity.
for the active site and therefore will leave the active site. As a consequence of this, the enzyme will actually lower the energy required for that reaction. It will lower what is known as the activation energy, the energy that is required for that reaction to take place.
And that can be shown here. So if we have a reaction where we start with some reactants or substrates and we're going to end with products, there's a certain point where we've really got to put a bit of energy into that system to allow us to finally produce the products. And in the absence of an enzyme, the amount of energy required is quite high. So high, in fact, that the reaction would be unlikely to progress in the absence of an enzyme.
The bonds break when the molecules of the reactant have absorbed enough energy to make them unstable. and they are now in a state which is known as the transition state. So it's trying to get enough energy into that system to reach what's called the transition state. Enzymes will speed up the rate of reaction in metabolic pathway by lowering the activation energy needed by the reactants to form the unstable transition state, which is the prerequisite just before the products can be formed.
Okay, so in summary, an enzyme will lower the activation energy required for a biological reaction to proceed. It speeds up the rate of the reaction. It will take part in the reaction but remains unchanged at the end.
And it does so through this induced fit model. So let's have a look at this basic metabolic pathway here where we are converting metabolite W to Z through a controlled pathway involving three So some metabolic pathways are going to be reversible and the presence of a substrate or the absence removal of a product will drive the sequence of reactions in a particular direction. So if we have more metabolite W, it's likely to proceed faster. And if we have more metabolite Z, it's likely to proceed slower or indeed it may affect the direction. So let's have a look at how substrate concentration can impact the way a reaction could progress.
So substrate concentration increases, more substrate molecules are available to bind the enzyme active site. Now, this will continue for a period of time. So here's your substrate. You've got here's your enzyme, your active site and your substrate. And the substrate will bind.
You will have some product formed. However, as we increase the number of substrate molecules, more of the active sites are occupied and therefore we will have a faster rate of reaction. If we keep increasing substrate concentration, however, So many of these are just left floating around because there's simply not enough active sites to occupy.
So we are now at the point where we're limited by the enzyme concentration. So in graph form, this is how this looks. So here's the rate of reaction and substrate concentration along the bottom.
And as we increase the amount of substrate that's there, it binds the active sites and that keeps making more products. So the rate of reaction increases. However, as you reach a really high substrate concentration at this end of the graph, there's more substrate than there are active sites. So all the active sites are now occupied and you've reached the maximum rate of reaction at that particular enzyme concentration.
You could allow this to increase again if you then increased the enzyme concentration so that you have more active sites. So as substrate concentration increases, the rate of reaction will increase until a certain point where your enzyme concentration is now limiting the rate of reaction. Okay, so now let's look at how the concentration of the product can affect the rate of reaction. So this brings us to something called feedback inhibition. So you've worked all the way down your reaction here and you're finally building up lots and lots of metabolism.
But actually to continue with that and the presence of increasing metabolite Z concentration, it's kind of wasteful. This reaction is going to involve an input of ATP. Why would the cell be so wasteful to continue making more metabolite Z when it isn't required?
So it actually doesn't. And it goes through a process called feedback inhibition when in this particular example here, metabolite Z builds up to a critical threshold concentration. At that point, this end product Z will act by inhibiting an earlier enzyme, usually enzyme one in the reaction. So it stops it right at the beginning. There wouldn't be much point blocking it here because you're already on the way to making Z.
So you might as well stop at the beginning and allow metabolite W to be conserved. So metabolite Z will come up to enzyme one. It will bind to enzyme one and it will.
prevent further catalysis from that point. So how else can we control metabolic pathways? So maybe another reason why we want to slow something down and stop it working so well. And this can be done by different levels of inhibition. So we have competitive inhibitors, we've got non-competitive inhibitors, or this feedback inhibition that we've just seen.
To compare them, let's start with a competitive inhibitor. So in the normal way that an enzyme would work, you would have your enzyme, you've got your roughly complementary substrate that will bind to form an enzyme-substrate complex, and you will produce your products. However, in the presence of a competitive inhibitor, you're going to slow that rate of reaction, and this is going to work by competing for the active site. with the substrate.
So you can see that it's similarly shaped to the substrate and instead if there's enough competitive inhibitor molecules it's going to out-compete the substrate and it will manage to reach the active site and the substrate cannot bind. As a consequence there will be no product and there will be a build-up of substrate. So for a competitive inhibition is a similar similar structure, shape to the substrate and it will compete with the substrate for the active site itself.
So competitive inhibitors will bind at the active site preventing the substrate from binding. However, as you can imagine, if you want to out-compete the inhibitor, all you would really need to do is add some more substrate because therefore they're just competing with each other. If there's five of these and one of these, chances are... the substrate is going to get there first.
So we can overcome the effect of a competitive inhibitor by increasing substrate concentration. So let's now look at a non-competitive inhibitor. So again, we've got the same enzyme, we've got the same substrate, but the first thing to notice is a non-competitive inhibitor does not look anything like the substrate and therefore is not going to bind to the active site. So a non-competitive inhibitor will bind to the active site.
bind away from the active site it actually binds to a distinct site elsewhere on the enzyme When it does that, it's going to change the shape of the whole enzyme molecule and particularly, or most importantly, it's going to impact on the shape of that active site, which therefore is going to prevent the substrate from binding. Non-competitive inhibition cannot be reversed because of this. As soon as you've got an inhibitor bound, they're not competing for the same site, they're different, and inhibitor binds, changes the active site, renders it useless for reaction.
So the substrate cannot bind. We could add 10 times more substrate. It's still not going to be able to bind that altered form.