#9i- Nature’s Tireless Catalysts: Enzymes

The proteins that move way faster than Usain Bolt!

You have made it through the Macromolecules of Life series! Brilliant! 🙌 Using this knowledge, you will be able to understand most of the complex machinery within our bodies and around us, including how infections happen, and how the immune system manages to fight them off.

This post shall be dedicated to one of the major classes of proteins called enzymes. They are what keeps us alive because of their ridiculous fast speeds of ramping up all biological reactions. My upcoming microbiology posts will involve a lot of enzymes and other classes of proteins, so I must talk about them pronto!

Note: There is a lot of must-knows about enzymes that I want to share, so I will be splitting this post into #9i and #9ii instead of piling it all in one post 😊

What are Enzymes?

Enzymes are protein molecules that act as catalysts in several biochemical reactions in all cells. These reactions sum up cellular metabolism, and there are two types of metabolism:

  • Catabolism: Large complex molecules → Smaller molecules + Energy
  • Anabolism: Simple small molecules + Energy → Large molecules

Reactions that take more energy than they release are endergonic. Others that release more energy than they take are exergonic. These words sure do sound similar to exothermic and endothermic reactions from chemistry! Can you tell me which one of the forms of metabolism is exergonic and endergonic? 👀

The enzymes are part of the seven classes of proteins mentioned below:

  • Enzymes: Bio-catalysts; e.g.: salivary amylase digests starch in our mouths
  • Structural proteins: Provides structure to the cell and body; example: collagen under our skin
  • Signal proteins: Messengers in the body; e.g.: insulin controls blood glucose levels
  • Contractile proteins: Promotes movement; e.g.: actin and myosin in our muscles
  • Storage proteins: Reservoir of nutrients for later use; e.g.: albumen, a.k.a., the egg white
  • Defensive proteins: Infection fighters; e.g.: antibodies in our blood
  • Transport proteins: Carry or allow passage of molecules; e.g.: haemoglobin carries oxygen in the blood

Fast Fact!: Any protein’s name ending with ‘-ase’ is an enzyme. Their names are usually a dead give-away to show which substrate they target followed by the term describing their job, like, kinase adds a phosphate group to their substrate.

Ribbon model of the human alpha salivary amylase enzyme bound to a calcium ion (pale khaki) and a chloride ion (green). Source in caption.
Figure 1- Ribbon model of the human alpha salivary amylase enzyme bound to a calcium ion (pale khaki) and a chloride ion (green). Source- By Own work. — From PDB entry 1SMD., Public Domain, https://commons.wikimedia.org/w/index.php?curid=1765675

You will definitely meet a lot of the proteins from all seven categories in future, so keep your eyes peeled 👀

Not sure what proteins are? Check Post #7 before you go any further! 😉

Now moving onto some chemistry behind as to why enzymes are actually needed.

From Reactants to Products

In the subject of biology, there will always be some chemistry and physics involved. Hence, I will be introducing you to the two laws of thermodynamics.

  • The First Law of Thermodynamics or The Law of Conservation of Energy states that energy can neither be created nor destroyed; it can only be changed from one form to another. In a situation where energy changes in an organism, the energy input = energy output.
  • The Second Law of Thermodynamics or The Law of Entropy is based on the assumption that the universe is becoming increasingly disordered. We and every other organism consume energy from our environment and release some of it as heat, which is a waste because not ALL the consumed energy was used for useful work. Therefore, this is considered entropy and it happens when organisms advance to increasing complexity. In other words, life and the universe want to be in a constant mess (that doesn’t mean your home or room should be a mess! 👀)

When you see a chemical reaction equation, you have the reactants always on the left and the products formed on the right, like the one below where two hydrogen molecules combine with a molecule of oxygen to give two molecules of water:

2H₂ + O₂ → 2H₂O

Do you know why this equation is balanced on both sides? It is to indicate that chemical reactions do not create or destroy matter.

Important Tip: It’s good practice to write a balanced chemical equation during your tests, exams, or whenever you can!

The above equation may look pretty simple and easy to perform at the lab, but this whole reaction can’t just happen out of thin air since these gas molecules are quite stable on their own. They definitely need an energy input to get some interaction to form between them and eventually create a product.

Boulder analogy of increasing the potential energy (moving boulder to the peak of the hump) to bypass the energy barrier (hump) and create the result, a fast-rolling boulder. Source in caption.
Figure 2- Boulder analogy of increasing the potential energy (moving boulder to the peak of the hump) to bypass the energy barrier (hump) and create the result, a fast-rolling boulder. Source- Advanced Biology, by Kent, 2nd Edn.

What’s actually getting in between the hydrogen and oxygen molecules from forming water is the energy barrier, which needs to be surpassed with a sufficient amount of energy, termed activation energy, required to start a chemical reaction. The energy barrier is like a steep hill where the little man is struggling to push the boulder to the peak and let it roll downhill, real fast (See Fig. 2).

Not to forget that the boulder at the peak signifies the two reactants forming an intermediate or the transition state. This state is unstable as it has a lot of energy.

This leads us to enzymes that can help surpass the energy barrier at a cost of less activation energy in a biochemical reaction to get to that transition state and eventually form a stable product.

How do Enzymes Really do the Thing? 👀

First things first, enzymes are organic catalysts that speed up biological reactions. Only one enzyme takes part in catalysing a single reversible reaction, unlike the inorganic catalysts, such as palladium, which is used in hydrogenation reaction where vegetable oil changes into solid margarine (✨the more you know!✨) and other many reactions in factories and labs.

Secondly, they are highly specific to one substrate and are rather picky with their working conditions. Inorganic catalysts can work happily in many reactions under different conditions.

In the end, just a few molecules of an enzyme can get the job done very quickly.

Now that’s Hella Fast!: At 0℃, a single molecule of catalase enzyme can catalyse 50,000 reactions of breaking down hydrogen peroxide into water and hydrogen gas in 1 second. But at 37℃ (human body temperature), it can complete 600,000 reactions alone in a single second! Normally, an enzyme molecule catalyses an average of 1000 reactions per second, which is still pretty damn fast!

A ribbon model of the enzyme catalase comprising a mix of peptide chains (lilac) alpha helices (red), and some beta sheets (blue). Source in caption.
Figure 3- A ribbon model of the enzyme catalase comprising a mix of peptide chains (lilac), alpha helices (red), and some beta sheets (blue). Source- By Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute — http://www.ebi.ac.uk/pdbe-srv/view/images/entry/7cat600.png, displayed on http://www.ebi.ac.uk/pdbe-srv/view/entry/7cat/summary, Public Domain, https://commons.wikimedia.org/w/index.php?curid=5860387

Remember, enzymes (and inorganic catalysts) are not part of the products, but involved in their making at greater speeds.

Okay, back to how enzymes get the job done in the following simple steps:

A graph showing that the enzyme helps reduce the activation energy to form the products by first forming a stable enzyme-substrate complex. Hence forming a smaller curve compared to the reaction having no of the enzyme’s assistance. Source in caption.
Figure 5- A graph showing that the enzyme helps reduce the activation energy to form the products by first forming a stable enzyme-substrate complex. Source- Advanced Biology, by Kent, 2nd Edn.
  • Enzyme binds to substrate
  • Substrate binds real tight with the enzyme to reach a more stable intermediate or transition state, forming the enzyme-substrate complex
  • Product is formed, and enzyme is released

As you can see, enzymes can help form a much stable intermediate state with the substrate by decreasing the activation energy to form the product(s) faster (See Fig. 4).

Now that’s plenty of science for now! In the next post, I will continue the two theories on enzyme-substrate complexes, various factors that affect enzyme activity, and the different enzyme classes as Post #9ii.

Thank you for your patience and your support! 🙌 Make sure to clap and subscribe for more awesome microbiology 😊

Glossary

Entropy- A term commonly used in thermodynamics to mean disorder or randomness in a system

Molecules- A combination of an atom with one or more atoms via chemical bonds

Sources

  • Chapter 3: Metabolic Reactions, Section 3.1: Energy and Metabolism. From the textbook Advanced Biology, by Michael Kent, 2nd Edn.
  • Chapter 3: Metabolic Reactions, Section 3.2: How Enzymes Work. From the textbook Advanced Biology, by Michael Kent, 2nd Edn.
  • Me remembering stuff from my school and university lectures

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