Metabolic pathways and their control

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Metabolic pathways

Right, all the reactions that happen in a body. No easy way of putting this. Voila!




It's OK, don't panic. Metabolic pathways are the routes from chemical to chemical that represent their various reactions inside cells, catalysed by enzymes. Enzymes are proteins that enable a much faster reaction - catalysts. These pathways cover the making and breaking of all compounds. They cover the energy-producing processes that use oxygen and glucose to make ATP (adenosine triphosphate, the cellular energy currency), the breaking down of sugars, fats and proteins from food, the building of new enzymes, the constant breaking down of waste products and creation of maintenance molecules for energy and the many functions in the body, etc.

These metabolic pathways are integrated and controlled so that connections exists between pathways, with checkpoints that can be self-regulating to ensure the right rate of reaction is taking place. Some simpler chemicals are recycled in some pathways, while others are introduced to the system from the outside e.g. through food and drink, as well as removed from the system e.g. excretion.

The pathways which use up energy to carry out their reactions are called anabolic, while those that release energy are catabolic. Anabolic pathways are biosynthetic as they assemble larger molecules from smaller units, hence requiring energy. Catabolic pathways break down larger molecules into their constituent building blocks, releasing energy. Chemical bonds contain energy, so breaking them releases it, while creating them requires it.




These pathways can have reversible steps where a reaction can go backwards or forwards to break down or assemble a chemical again, or irreversible steps where the broken down compound, or the newly synthesised molecule, cannot be undone and will have to follow one or more of the possible forward-looking routes. Speaking of routes, some compounds have multiple alternative routes they can take.

For example, glucose can undergo glycolysis as the first step towards cellular respiration to produce energy through ATP, or become a building block for glycogen in the liver for storage. Circumstances such as blood sugar levels, food intake and activity will determine which pathway is taken.


Membranes

The surface compartments formed by cellular plasma membranes is what enables the maintenance of metabolic pathways. The high surface area to volume ratio of small compartments means that molecules can quickly reach high concentrations and reaction rates.



We can now explore the structure of plasma membranes, specifically in the context of the fluid-mosaic model. Phospholipids have a hydrophilic (water loving) head, and hydrophobic (water repelling) tails. This results in the formation of a phospholipid bilayer (double layer), which forms the basis for the plasma membrane.


The name of fluid-mosaic model comes from:

Fluid = the arrangement of proteins contained in the membrane is always changing
Mosaic = the proteins present are spread around in a mosaic-like fashion.



It's pretty isn't it? The proteins are crucial to cell communication as well as the selective permeability of the membrane. The glycoprotein (sugars/carbohydrates attached to a protein) side chains act as receptorsLipid soluble stuff such as vitamins A, D and K, as well as oxygen and carbon dioxide, can pass freely though the membrane. Cholesterol can be part of the membrane to restrict the movement of other components.

Protein pumps embedded in the membrane help transport any molecules or ions that can't make it straight through the membrane without help, while enzymes embedded in the membrane carry out reactions on the side of the membrane towards the inside of the cell e.g. breaking down a molecule into two products.

The main properties of molecules that determine how they may be transported across a membrane are solubilitysize and charge.




Large molecules can't cross the membrane, charged molecules also can't, and naturally, lipid-repelling (or water-attracting) molecules can't. Conversely, small molecules can cross the membrane barrier, alongside molecules with no charge (nonionised) as well as lipophilic (hydrophobic) molecules.

It's important to understand the role of microvilli. These are elongations of plasma membrane which increase the surface area available for reaction or absorption.




The presence of certain enzymes on the plasma membrane will determine which reactions take place in a cell, and how fast. Reaction rate regulation takes place when intracellular or extracellular signal molecules such as adrenaline bind to receptors on the membrane. Enzymatic cascades trigger resulting cellular metabolic pathways and events such as gene expression or suppression, and the secretion of certain molecules.


Enzymes

Enzymes are proteins which catalyse (speed up) metabolic reactions. Like all other catalysts (e.g. in chemistry), enzymes achieve this by lowering the activation energy (energy needed for a reaction to occur) of a reaction, by forming an enzyme-substrate complex.



This can be described by the lock and key, and induced fit models of enzyme action. The lock and key model is based on complementary shapes between the enzyme and substrate. The substrate fits into the enzyme.




The induced fit model: (the enzyme changes shape to "hug" the substrate)



The enzyme's shape is not exactly matched to the substrate, but it is able to accommodate the substrate with a close enough shape into an enzyme-substrate complex and carry out catalysing that reaction. Here is a video of an enzyme catalysing a reaction between two molecules into one molecule. This is different to the above scenario in the diagrams, where one molecule is broken down into two molecules.



Substrate affinity as well as orientation contribute to the interaction with the enzyme active site towards the formation of a substrate-enzyme complex. Far from being an isolated event, catalysis by enzymes often takes place in groups of enzymes, such as in the aforementioned cascades inside cells, or in multi-enzyme complexes. These are clusters of more than one enzyme that execute a function in unison e.g. cleaving mRNA, where the different components of the complex do different things. One might provide the structural attachment to the substrate, while the other contains the specific active site where cleaving occurs.

In metabolic pathways, reaction rates can be determined by the relative concentration of substrates and products of a reaction or series of reactions. The substrate presence can drive the reactions to continue for as long as there is substrate available, or alternatively the reactions could continue for as long as the product is being removed, in order to maintain a constant level.





Feedback inhibition is when the presence of a threshold amount of product signals the reaction(s) to halt.


Inhibitors

Inhibitors are molecules which interfere with the substrate binding to the active site of an enzyme, slowing down or stopping the reaction. These may be reversible or non-reversible inhibitors. The reversible inhibitors can be competitive or non-competitive.

Competitive inhibitors have a similar 3D shape to the substrate, hence they can bind to the active site of the enzyme, preventing the substrate from doing so. It's easy to picture:




The competitive inhibitors compete (as you'd expect) with the substrate for the active sites of the enzymes. If more substrate is added, then the inhibitors' effect will be diminished. This is what the graph looks like (make sure you can recall this):




Non-competitive inhibitors on the other hand bind to the enzyme at a site (allosteric site) away from the active site. All good? No, because that results in the enzyme's shape changing. This means the substrate can no longer bind to the active site. Unlike the case of competitive inhibitors, changing the substrate concentration will not have an effect on the rate of reaction. Here is a comparison diagram (learn this):




If you're a video sort of person, here is a nice one:



Substrate and enzyme concentration

This topic is a matter of common sense. However, you must use A level language. Here it goes.

Common sense version: More substrate results in more reactions, so rate of reaction goes up. Of course, when all enzymes are working all the time, adding even more substrate will not increase the rate of reaction, unless more enzymes are added.




A level language version: The higher the substrate concentration, the faster the rate of reaction until the enzymes are working as fast as possible. This is when all the active sites are filled all the time. From this point, the only way to increase the rate any further is to add more enzyme.




If on the other hand we have excess substrate, adding increasing amounts of enzyme will allow the rate of reaction to increase linearly. What would happen if there were a limited amount of substrate instead? The reaction rate would fall off a cliff as soon as the substrate has been used up.




No matter how much enzyme we add, the substrate is no longer present so the reaction rate halts, and no more product can be made. In this case, the initial increase in reaction rate is slower (not linear) compared to the unlimited substrate graph. This is because the substrate is increasingly used up and the reaction rate increases ever more slowly before it stops and drops.

Being able to measure the initial rate of enzyme activity is useful in finding out whether a certain substance acts as an enzyme at all (by observing if adding it to a substrate depletes the substrate or creates a product over time), the efficiency of enzyme activity and hence the affinity of that enzyme to the tested substrate.

For example, we can have two test tubes, one with a lot of starch and one with a lot of lactose (a lot relative to the enzyme we're about to add; a lot is termed excess substrate). A lot might be 100 or 1,000 starch or lactose molecules for 1 enzyme molecule. We might need to experiment to actually find out how fast the reaction takes place if at all.

We then add an equal amount of enzyme to both starch and lactose tubes and detect how much there is left every minute, or 10 seconds or 5 minutes (again, depending on how fast we expect anything to happen, and that depends on the temperature, etc.). 

The results might show that our enzyme doesn't affect the amount of starch, but completely breaks down the lactose within 12 minutes. The enzyme has high affinity to lactose, hey it might be lactase!

Overall, enzymes catalyse a huge range of both intracellular reactions such as breaking down glycogen to release more glucose for energy, and extracellular reactions such as breaking down environmental components in soil by releasing the enzymes out of the body - this is a form of nutrition in some fungi.

Final tip: you should be aware of the lock and key versus induced fit models. The induced fit model is better because it suggests the enzyme changes shape slightly to accommodate the shape of the substrate. This is beneficial if the enzyme is perhaps fluctuating in shape due to change in temperature for example.

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