Enzymes are biological catalysts that play a HUGE role in the chemical reactions that happen around us! The reason why they are so important is because without them, the metabolic processes in our cells won't occur at rates that are fast enough to sustain life! According to Dr. Richard Wolfenden from the University of North Carolina at Chapel Hill, most chemical reactions that occur in nature do not happen without the presence of enzymes because the amount of activation energy that the reactants need to overcome is too great! Without these biological catalysts, reactions that are required to create the building blocks of DNA and RNA will take approximately 78 million years. This means that without enzymes, there would be no life at all!
A. Enzymes are classified into 6 different categories:
These enzymes are normally globular proteins and the sequences of the amino acids ultimately determine the catalytic activity of the enzymes themselves. If you take a look at Figure 2, you will notice that in order for reactants to become products, they need to overcome a high energy transition state. The reason why enzymes are so important is because an uncatalyzed reaction requires a higher activation energy than a catalyzed reaction. Because enzymes can lower the activation energy, reactants won't have to overcome such a high activation energy to become products and thus the rate of the reaction will increases.
If enzymes are so great, you would think that we can just add any kind of enzymes to a substrate and they would bind right? Nope. That's not the case at all. The reason why enzymes won't just bind to any substrates that are being thrown at them is because of their specificity - which makes them particularly picky and won't just bind to any substrates that are dilly-dallying around. ;)
B. SUBSTRATE BINDING: Now, in order to catalyze (speed up the rate of) a reaction, substrates need to bind to enzymes at the active site - a location in the enzyme in which substrates can attached to during chemical reactions. We call this enzyme/substrate compound the enzyme-substrate complex (as seen in Figure 3). When substrates find the active site, ionic interactions, covalent bonds, and hydrogen bonding help stabilizes the spatial arrangement between the enzyme and its substrate. Once the substrate attaches to the active site, the enzyme helps converts it into a product and the product is then released from the active site.
The two different theories that explain the interaction between substrates and enzymes are: The lock and key theory and the induced fit model. In a lock and key theory, enzymes don't have to alter their structure in order for the substrate to bind to its active site. In the induced fit model, however, the binding of substrates to enzymes cause a small amount of free energy to be released. The enzyme starts to alter their conformational structure so that it will increase its affinity to the substrate. In a way, we can say that the binding of the substrate to the active site induces a conformational change in the enzyme so that the enzyme's affinity to the substrate increases (as seen in Figure 4).
C. MECHANISMS OF CATALYSIS: For the most part, enzymes require non-protein molecules called cofactors or coenzymes in order to work properly. Both of them tend to be small in size and are kept at low concentrations so that they can be recruited only when needed. The differences between cofactors and coenzymes are that: 1) Cofactors are inorganic molecules or ions (ie: Fe2+ and Mg2+). Enzymes without cofactors are inactive and are called apoenzymes; 2) Coenzymes include organic groups like NAD+, FAD, Coenzyme A, as well as water-soluble and fat-soluble vitamins. Enzymes with cofactors and coenzymes help create conjugated enzymes called holoenzymes. In the real world, deficiencies in vitamin cofactors can result in diseases that can be life-threatening. For instance, a deficiency in thiamine - a cofactor that is involved in cellular communication and metabolism - can result in Wernicke-Korsakoff syndrome. Patients who suffer from this disorder can have neurological problems and in severe cases, are unable to form new memories.
D. CONTROL OF ENZYME ACTIVITY: The concept of enzyme kinetics can be explained using the Michaelis-Menten Equation, where v is the rate of the reaction, [E] is the concentration of both of the enzymes, [S[ is the concentration of the substrate, [P] is the concentration of the product, and Km is a constant that measures the affinity of the enzyme to its substrate. It is important to remember that changes in enzyme concentration does not affect Km. Higher concentrations of enzymes will result in the reaction to reach the 1/2 Vmax at lower concentration of substrates; while lower concentrations of enzymes will require high concentrations of substrates to reach 1/2 Vmax. If we are comparing 2 different enzymes, just remember that enzymes with lower Km values will require a lower concentration of substrates to be half-saturated while those with higher Km values will require a higher concentrations of substrates to be half-saturated. This means that enzymes with lower Km values have a higher affinity for enzymes and those with higher Km values have a lower affinity for their substrates!
1) COOPERATIVITY: There are certain enzymes, however, that show an S-shaped (sigmoidal) instead of a normal hyperbola. These enzymes are considered to be "cooperative" or "allosteric" enzymes because they have multiple subunits and active sites. Binding of a substrate can cause it to transition from a low-affinity tense state (T) to a high-affinity relaxed state (R). On the other hand, the loss of substrates can cause the enzymes to convert from a relaxed state (R) to a tense state (T). Due to the fact that these enzymes show cooperative kinetics, they often act as regulatory enzymes and are subjected to activation and inhibition.
2) FEEDBACK REGULATION: Enzymes are normally subjected by products in a process called feedback regulation. While it is true that some enzymes may be regulated by feed-forward regulation, most enzymes are regulated by a process called negative feedback (feedback inhibition). These can either increase enzyme-substrate affinity or reduce/inactivate the activity at the active site. Now, you may ask yourself, "Why do we need negative feedback? Isn't the whole point of catalytic reactions is to create more products instead of inhibiting more from being created?" The answer is simple. Imagine this, our body is constantly trying to maintain homeostasis (maintain equilibrium). If we have enough of one product, we want to turn off the pathway so that it will prevent more from being created.
There are 4 types of reversible inhibition: Competitive, noncompetitive, mixed, and uncompetitive.
a. Competitive Inhibition: This is pretty straightforward. If you don't want a certain substrate to bind to the active site, all you need to do is add a competitive substrate (inhibitor) with a similar structure so that it will bind to the active site instead. This inhibition can be overcome if we add more substrate so that the concentration of substrates is higher than the concentration of inhibitors. Because the addition of tons of competitive inhibitors can outcompete the inhibitor, the Vmax value is not affected and the Km value increases. ***Remember that enzymes with higher Km values have lower affinity to their substrates because we require higher concentration of substrates to reach 1/2 Vmax in the presence of the inhibitor.
b. Noncompetitive Inhibition: This is different from competitive inhibition because the inhibitor binds to the allosteric site instead of the active site. Because the inhibitor binds to a non-catalytic region, the two molecules are not competing for the same site and the inhibition is thus considered as noncompetitive. Once the inhibitor binds to the allosteric site, the active site of the enzyme will go through a conformational change that will prevent new substrates from binding to the enzyme. Therefore, we cannot add more substrates to overcome this type of inhibition! Even though noncompetitive inhibitors don't affect the Km value, they do decrease the value of Vmax because less enzymes are available to bind to substrates. Takeaway from this: Enzymes that go through conformation changes due to competitive inhibitors will decrease the number of enzymes that are available to bind to substrates.
c. Mixed Inhibition: Similar to noncompetitive inhibition, mixed inhibitors bind to the allosteric sites instead of the active sites. Interestingly, they have the ability to bind to an enzyme or to an enzyme-substrate complex. If the inhibitor binds to an enzyme, it increases the Km value. If it binds to a complex, however, it lowers the Km value by increasing the enzyme's ability to bind to the substrate.
d. Uncompetitive Inhibition: Uncompetitive inhibitors are unique because they only bind to allosteric sites on enzyme-substrate complexes. This lowers the Km and Vmax values, which means that the enzyme's affinity to its substrate will increase and decrease the number of enzymes that are available to react.
e. Irreversible Inhibition: Unlike reversible inhibitions, in irreversible inhibitions, the active site is either unavailable for a long time or the enzyme is permanently altered and substrates can no longer bind to the active sites. The only way to overcome this is to synthesize more enzymes through transcription and translation.
3) REGULATED ENZYMES: These enzymes are often parts of biological pathways like glycolysis and the Kreb Cycle. There are 3 different types of regulated enzymes: Allosteric enzymes, covalently modified enzymes, and zymogens.
a. Allosteric Enzymes: These enzymes have multiple binding sites and alternate between an active and inactive form.
b. Covalently Modified Enzymes: Enzymes that can be activated or deactivated by phosphorylation, dephosphorylation, or glycosylation.
c. Zymogens: Enzymes that are secreted in its inactive form and are activated by cleavage. An example of trypsin, which is an enzyme that is released from the pancreas. It is secreted as trypsiniogen because without being controlled, this enzyme will digest the organ itself.
B. IMMUNE SYSTEM: The high degree of protein variability allows for a key feature of the adaptive (or acquired) immune system, the production of antibodies. An antibody is a type of protein that has a unique and very specific binding site that will readily bind its target, called an antigen, such that its target is inactivated or tagged for immune response.
C. MOTORS: A motor protein can perform mechanical work by coupling exergonic (energy releasing) ATP hydrolysis to a conformational change that allows for interaction with the protein's target substrate. Muscle contraction, for example, is achieved through a process of the motor protein myosin binding and releasing its microfilament (actin) substrate. Myosin also acts on microfilaments of the cytoskeleton to generate cellular movement.
Two other types of motor proteins, kinesins and dyneins, act on microtubules and play a role in transport within the cell. Kinesin walks microtubule "tracks" to deliver cellular cargo (e.g. chromosomes during mitosis, vesicles), generally in an antegrade direction (center to periphery). Dynein is used in retrograde cargo transport in the axons of neurons, and is capable of sliding microtubules in relation to one another, generating the movement of cilia and flagella.
Let's do a quick recap! Basically, we have learned that enzymes:
I'm Linh - a science geek who loves experimenting and tinkering with recipes! I hope that this blog brings more ideas into your kitchens! Happy eating folks! XOXO