Simplifying Microbiology One Post Every Saturday + Helpful Glossary

#9ii- Nature’s Tireless Catalysts: Enzymes

The proteins that move way faster than Usain Bolt are back!

I hope you all are doing well! I have been busy with my personal stuff, and finishing my piece for the Medium Writers Challenge Contest 2021 which is right here 😊 Thank you for your patience and your support.

This is the final part on enzymes where I will share with you the two theories on how enzymes interact with their substrates, the many factors that affect enzyme activity, and the different classes of enzymes.

In case you haven’t seen my previous enzymes post, make sure to check out 👉 Post #9i.

Now let's get on with it, shall we?

What’s Microbiology Without Theories?

I: Lock-and-Key Theory

All of you know by now that majority of enzymes in our bodies are globular (tertiary structure), and they sometimes contain metal ions in them to function normally. Tertiary structures have a super precise shape containing a region that is shaped specifically for its substrate to fit in. This region is called an active site.

A simplified diagram showing the lock-and-key theory at work. Here, the two substrates fit snugly into the respective active sites in an enzyme (yellow) to form an enzyme-substrate complex, and then into a product (red) with a free enzyme. The reaction can go either way as well where the enzyme can catalyse the change of the product to substrate. Source in caption.
Figure 1- A simplified diagram showing the lock-and-key theory at work. The reaction can go either way as well where the enzyme (yellow) can catalyse the change of the product (red) to substrate (red). Source- Advanced Biology, by Kent, 2nd Edn.

This theory states, the substrate fits right into the stiff active site of an enzyme, like a key being inserted into a lock, which forms the enzyme-substrate complex. The catch is, the substrate has to fit in the enzyme’s active site shaped specifically for it to undergo a catalytic reaction (See Fig. 1).

It does give an idea as to why enzymes must have a specific structure to interact with their substrates, and also why a small change in the amino acid sequence can affect its abilities.

However, it is not the most accurate explanation for enzyme activity, which takes us to our next theory!

II: Induced-Fit Theory

Now this one is a modified version of the previous theory, with a bit more scientific thought put into it, in my opinion.

In this model, you don’t need the extreme precision for a substrate to exactly fit inside the enzyme’s active site to start a reaction. The enzyme here will adopt an effective catalytic shape where the active site’s shape is altered a bit to get a tight grip on the substrate. In other words, the substrate affects the enzyme’s shape, like the shape of a glove is affected by the hand in it.

Induced fit theory featuring the enzyme hexokinase (blue), which catalyses the phosphorylation of glucose (gold). Source in caption.
Figure 2- Induced fit theory featuring the enzyme hexokinase (blue), which catalyses the phosphorylation of glucose (gold). Source- Advanced Biology, by Kent, 2nd Edn.

The distortion of the enzyme, in turn, distorts the substrate by breaking the bonds within it. This whole process makes the substrate unstable, reducing the potential energy, as well as the activation energy to fully complete the reaction.

After the reaction, the products are made and released from the enzyme as they no longer fit inside its active site. The elastic enzyme goes back to its original state, ready to take in more substrate.

Next up! Factors affecting enzyme activity.

What’s a Reaction Without Factors Affecting It?

For a reaction to run perfectly, one must be aware of the factors that affect them:

  • Enzyme specificity: Some are highly specific in that they catalyse only one reaction, like catalase, while others, such as lipases, can break down a variety of fats during digestion
  • Substrate concentration: The rate of an enzyme-catalysed reaction increases when substrate concentration increases until the reaction rate reaches its maximum (See Fig. 3)
Graph depicting a gradual increase in the substrate (X-axis) when there is (a) moderate enzyme concentration, and (b) high enzyme concentration. In curve (a), the max rate of reaction is lesser when compared to curve (b). Both curves plateau as they reach their maximum rates. Source in caption.
Figure 3- Graph depicting a gradual increase in the substrate (X-axis) when there is (a) moderate enzyme concentration, and (b) high enzyme concentration. In curve (a), the max rate of reaction is lesser when compared to curve (b). Both curves plateau as they reach their maximum rates. Source- Advanced Biology, by Kent, 2nd Edn.
  • Enzyme concentration: Rate of an enzyme-catalysed reaction increases when substrate concentration increases. This is only true as long as there is PLENTY of substrate, and no adjustments being made to the other factors, just like in Fig. 3 where the substrate concentration was elevated
  • Incubation time: The span of time during which an enzyme catalyses a reaction. At some point, the enzyme will denature, losing its ability to do its job as the incubation period becomes longer, causing the rate of reaction to drop
  • Temperature: The enzyme-catalysed reaction rate increases with an increase in temperature, thus eventually reaching its optimum temperature; going above the optimum will cause a reduction in the reaction rate since the enzyme gets denatured; e.g.: the optimum temperature for enzymes to work effectively in humans is ~37℃
  • Hydrogen ion concentration (pH): Enzymes have very narrow pH ranges to work in; like temperature, it needs an optimum pH to do great, and going above the optimum will destroy bonds (mainly hydrogen and ionic bonds) within the enzyme, resulting in its denaturation; e.g.: pepsin prefers an acidic pH, hence it is found in the stomach as it produces hydrochloric acid (HCl)

Some enzymes need help to reach their full potential by interacting with special non-proteins called co-factors. They come in two types:

  • Activators: Inorganic and are metal atoms, like, iron, zinc, or copper; may bind to the active site to make its shape more effective
  • Coenzymes: Organic and many are either vitamins or altered forms of vitamins; some transfer chemical groups, atoms or electrons to other enzymes; e.g.: nicotinamide adenine dinucleotide (NAD), a vitamin B3 derivative, transfers hydrogen in cellular respiration (See Fig. 4)

To Remember: There are co-factors that bind to their enzymes rather tightly and they are called prosthetic groups

Ball-and-stick model of NAD molecule in its oxidised form, that is, it can accept electrons. Source in caption.
Figure 4- Ball-and-stick model of NAD molecule in its oxidised form, that is, it can accept an electron. Source- By Ben Mills — Own work, Public Domain, https://commons.wikimedia.org/w/index.php?curid=48398247

Lastly, you have inhibitors that can affect an enzyme’s job, either in a good or bad way. In a bit more detail, inhibitors can reduce or even stop the enzyme from doing its work permanently.

There are two main categories of inhibitors:

  • Competitive: Has almost similar shape to that of the substrate to occupy the enzyme’s active site; adding more substrate can get reaction speed to normal; effect of this inhibition relies on how tightly the inhibitor and substrate binds to the enzyme; e.g.: Sulphonamide antibiotics work by competing against para-aminobenzoate (PAB), a compound used by nasty bacteria to make folic acid (See below equation)

↑Sulphonamide + PAB + Enzyme for folic acid production → ↑Sulphonamide : Enzyme complex + ↓↓folic acid + bacterial death

Make sure to have your medications as per your doctor’s and pharmacist’s advice to recover perfectly, and avoid antimicrobial resistant infections from happening!

Liquid mercury being poured from a glass beaker into a glass dish. Its elemental symbol is Hg. Source in caption.
Figure 5- Liquid mercury (symbol: Hg). Source- By Bionerd — Own work, CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=4972709
  • Non-competitive: A sneaky way in which the inhibitor binds to another site on the enzyme named the allosteric site (allosteric means ‘at another place’); causes change in active site’s shape; e.g.: heavy metals such as mercury and cadmium (See Fig. 5 and 6) are irreversible non-competitive inhibitors and are considered deadly; not always bad as it is involved in controlling the amount of product produced in a biological reaction termed as end-product inhibition (See Fig. 7)
A 99.99% pure cadmium crystal bar along with a smoothed 1 cm³ cube for comparison. Its elemental symbol is Cd. Source in caption.
Figure 6- A 99.99% pure cadmium (symbol: Cd) crystal bar along with a 1 cm³ cube for comparison. Source- By Alchemist-hp (talk) (www.pse-mendelejew.de) — Own work, FAL, https://commons.wikimedia.org/w/index.php?curid=10323830

To Reverse, or Not To Reverse?: Reversible inhibitors bind to the enzyme via weak breakable bonds like hydrogen bonds and once they detach, the enzyme can work normally. Whereas irreversible inhibitors bind using very strong covalent bonds which can’t be broken without ruining the entire enzyme, hence having a permanent effect. These two forms can be seen in both competitive and non-competitive inhibitors.

End-product inhibition, a phenomenon where the end-product (green) produced at the end of a metabolic pathway involving several enzymes, goes to an enzyme (usually the first one, in this case). It binds to enzyme E1’s (yellow) allosteric site causing the active site to change shape so it cannot accept anymore substrate (red) as there is sufficient product. This is a great example of reversible non-competitive inhibition. Source in caption.
Figure 7- End-product inhibition, a phenomenon where the end-product (green) produced at the end of a metabolic pathway involving several enzymes, goes to an enzyme (usually the first one, in this case). It binds to enzyme E1’s (yellow) allosteric site causing the active site to change shape so it cannot accept anymore substrate (red) as there is sufficient product. This is a great example of reversible non-competitive inhibition. Source- Advanced Biology, by Kent, 2nd Edn.

Can’t Have Microbiology Without Classification!

You are almost there! I am glad that you are able to understand some of this which is a great effort on your part 👏 Now onto the last bit — the six major enzyme classes, because you gotta find some way to keep things a bit organised since there are several thousand enzymes being found and even synthesised!

The classification was established in 1964 by the International Union of Biochemistry based on the kind of job an enzyme does. See the list right below!:

  • Oxidoreductases: Catalyse redox reactions by shifting electrons, hydrogen, or oxygen from one molecule to another; e.g.: alcohol dehydrogenase
  • Transferases: Catalyse transfer of a chemical group from one molecule to another; e.g.: aminotransferase
  • Hydrolases: Catalyse the splitting of a large molecule into two molecules as products in the presence of water, therefore it is a hydrolytic reaction; e.g.: lactase
  • Lysases: Catalyse the inclusion of a chemical group across a double bond in a molecule; e.g.: pyruvic decarboxylase
  • Isomerases: Catalyse the change of one compound's isomer to another isomer by rearranging that very compound; e.g.: phosphoglucomutase
  • Ligases: Catalyse the bond formation between two compounds which requires energy from hydrolysis of ATP (Adenosine triphosphate) to ADP (Adenosine diphosphate); e.g.: aminoacyl-tRNA synthase

Phew! That was a long one but I am happy that you made it through 👍 There is a lot more to enzymes, however, this amount of knowledge will help you to explore my future posts with ease and perhaps guess which enzyme falls into which of the six major classes judging by the reaction they catalyse 👀

I will be taking a 1 month-ish break from this work till I get a bit antsy to make more posts for you all. Till then, happy sciencing and take care of yourselves! 😄👍

Don’t forget to leave a comment, or subscribe/follow me for more simplified microbiology! 😊

Glossary

pH- A scale to measure how acidic (below 7), and how high basic/alkaline (above 7) the substance is; 7 is neutral pH, like clean water

Redox- A reaction where oxidation and reduction occurs simultaneously

Isomer- Molecules or polyatomic ions that have an identical chemical formula and number of elements, but have a slightly different arrangement of atoms in space

Sources

  • Chapter 3: Metabolic Reactions, Section 3.2: How Enzymes Work. From the textbook Advanced Biology, by Michael Kent, 2nd Edn.
  • Chapter 3: Metabolic Reactions, Section 3.3: Factors Affecting Enzymes (1). From the textbook Advanced Biology, by Michael Kent, 2nd Edn.
  • Chapter 3: Metabolic Reactions, Section 3.4: Factors Affecting Enzymes (2). From the textbook Advanced Biology, by Michael Kent, 2nd Edn.
  • Chapter 3: Metabolic Reactions, Section 3.5: Classification of Enzymes. From the textbook Advanced Biology, by Michael Kent, 2nd Edn.
  • Me remembering stuff from my school and university lectures

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Treveni Mukherjee

Treveni Mukherjee

A University of Leeds alumna with an Integrated Masters degree in Microbiology taking a break from science 😄