Introduction: Enzyme kinetics
Enzyme kinetics is the study of chemical reactions that are catalyzed by enzymes. In enzyme kinetics, you can learn about the catabolism mechanism, functions of metabolism, and how to control the activity of enzymes.
An enzyme is a protein that speeds up the chemical reaction occurring in the cell. In the reaction, the enzyme is not destroyed and can be used again and again. A single cell contains thousands of enzymes that are used in different kinds of chemical reactions. Basically, an enzyme is a biological catalyst that is an amino acid but it can also be an RNA. Enzymes play an important role in the cells because they control the reactions. Biological reactions become very slow without enzymes that are not good for sustaining life.
Our body can produce enzymes naturally, but they are also produced in food. Enzymes play several functions in the body. The main function of enzymes is they act as catalysts and speed up the biochemical reactions within the cell. A chemical reaction is the conversion of the substrates into products. The speed of the reaction increases when enzymes are present in the chemical reaction.
Read on to learn about the reasons why students feel enzyme kinetics is a difficult topic to learn. We can also provide a few techniques that can be helpful to learn tough topics like enzyme kinetics. By the end, we will convince you why a virtual lab simulation is important for students to learn the topic as well as for teachers to convey the concepts of enzyme kinetics.
Why enzyme kinetics can be tricky to learn
Some students find enzyme kinetics a difficult topic to learn because there are thousands of enzymes present within a cell. Here are a few reasons why enzyme kinetic can be problematic for students and even for teachers to teach.
1. It feels abstract:
As we cannot see the enzymes with the naked eye, so it may be hard for students to believe in the structure and functions of enzymes. Studies show that the location of the enzyme can be seen through an electron microscope. That’s why many students find studying enzyme kinetics tough to learn through textbooks.
2. It’s content-heavy:
In enzyme kinetics, students need to learn the reactions, and equations, and make different graphs that are very time-consuming and boring. Due to the heavy content of the topic, students do not like to learn about enzyme kinetics. Enzyme kinetics is a detailed topic, so it is complicated for some learners. Moreover, there are multiple terms that need to be remembered when learning about enzyme kinetics.
3. Difficult enzymes names:
Many students may find it tough to pronounce the names of enzymes. Some examples are Lactate dehydrogenase, Alanine transaminase, Acid phosphates, and Aspartate transaminase. There are several enzymes with different functions. Therefore, students may be afraid to read enzyme kinetics due to the complexity of the topic.
5 ways to make enzyme kinetics a more approachable topic to understand
Since you know the reasons that student face during learning enzyme kinetics. Here are 5 ways to make enzyme kinetics an exciting topic to understand.
1. People behind the science:
In 1913, Leonor Michaelis and Maud Menten worked on enzymatic reactions and proposed a Michalis-Menten Model. Leonor Michalis was a German biochemist, and Menten was a Canadian physician. Michaelis-Menten model is one of the best models in the history of enzyme kinetics. There are two assumptions of this model that are following:
An enzymatic reaction takes place in two steps. The first step is the binding of the enzyme with the substrate and the formation of the enzyme-substrate complex (ES). The other step is the separation of an enzyme from the end product.
After a short interval, the rate of formation of enzyme-substrate complex equals the rate of ES complex consumed. The two important terms in the Michaelis-Menten model are Vmax and Km. Vmax is the maximum rate of enzymatic reaction because all the active sites are bound with the substrate. Km is known as the Michaelis constant, showing the concentration of substrate when the enzymatic reaction rate is 50% of the Vmax.
According to the first assumption, there can be four kinds of enzymatic reactions that take place in the cell.
Formation of an enzyme-substrate complex from the enzyme and substrate
Detachment of enzyme-substrate complex into enzyme and substrate
Detachment of ES into enzyme and substrate
Formation of ES into enzyme and substrate.
2. Learn about enzyme structure
Enzymes are proteins and typically have a globular tertiary structure. They have active sites where the substrate can attach to the enzyme. An active site is a small area with a specific structure that allows a substrate to attach and make an enzyme-substrate complex (ES complex). Enzymes and substrates attach with a weak bond that can break at the end of the reaction.
There are many factors that may affect the activity of enzymes. Enzymes need a specific pH and temperature to work effectively. If pH or temperature changes, it will alter the function of enzymes. If severe changes occur in pH or temperature, the shape of the active site may change and the enzyme becomes denatured. Enzyme denaturation means the enzyme is not able to perform its function and cannot attach to any substrate.
There are two main models according to the specific active sites for the enzymes.
Lock and key model
Induced fit model
Lock and key model: The lock and key model states that the active site of the enzyme and substrate have specific shapes that can fit with each other and do not require any change.
Induced fit model: According to induce fit model, when a substrate attaches to the active site of an enzyme then both can change their shapes to fit properly. Induce fit model is more acceptable as compared with the lock and key model.
A cofactor is a non-protein molecule that needs to be attached to some enzymes. Without cofactor, enzymes are present in the “apoenzyme form” which shows the inactivity of the enzymes. When the cofactor is added to the reaction, the enzyme becomes a “holoenzyme” and performs its function appropriately. So, cofactors are worked as “helper molecules” because they help the enzyme to initiate the performance. There are three types of cofactors; coenzymes, metal ions, and prosthetic groups.
For example, Alcohol hydrogenase (ADH) is an enzyme that needs a co-enzyme to complete the reaction. NAD+ is a co-enzyme that attaches with the alcohol hydrogenase (ADH), as shown in the figure, to complete the reaction and produce acetaldehyde. In this reaction, NAD+ accepts 2 electrons from the to make NADH.
Figure: An image from Labster’s enzyme kinetics simulation that shows an enzyme (Alcohol Dehydrogenase) with the substrates.
3. Use color diagrams
Since enzyme kinetics comprises enzymatic reactions and graphs. It is a unique way to understand a difficult topic because you can have a picture of the process in your mind. Color images can be helpful to understand the topic more appropriately.
For example, the image below shows a graph between the concentration of enzyme absorbance to the time consumed. With the help of these kinds of color diagrams, students can learn difficult topics like enzyme kinetics more quickly.
Figure: The image from the Labster’s enzyme kinetic simulation that shows the graph between the absorbance of the enzyme to time.
4. Basic knowledge of enzyme inhibitors
Enzyme inhibitors are molecules that temporarily or permanently slow down the activity of enzymes. There are 2 types of enzyme inhibitors.
Irreversible enzyme inhibitors
Reversible enzyme inhibitors
Irreversible enzyme inhibitors: These inhibitors make the covalent bond with an enzyme to permanently inactivate the enzyme.
Reversible enzyme inhibitors: These inhibitors make a non-covalent bond with the enzyme to temporarily decrease the acidity of the enzyme. The reversible enzyme inhibitors are further classified into three types; competitive inhibitors, mixed inhibitors, and uncompetitive inhibitors.
A competitive inhibitor is a type of reversible enzyme inhibitor in which the inhibitor competes with the substrate to attach to the active site of the enzyme. Mixed inhibitors can combine with both the enzyme as well as enzyme-substrate complex. Moreover, uncompetitive inhibitors can only attach to an enzyme-substrate complex.
5. Use virtual lab simulation
The conventional methods of teaching about enzyme kinetics through textbooks are not always interesting. In this advanced world, teachers may need to use a 3D simulation to convey the topic to the students.
Labster provides enzyme kinetics simulations that give you 3D animations about the topic. When students see 3D animation of enzyme kinetics at the molecular level, they will understand the topic more effectively. Moreover, Labster’s enzyme kinetics simulation enhances your knowledge related to the experimental design of enzyme kinetics, the Michaelis-Menten model, analysis of spectrometric data, and several types of inhibitors.