Enzymes Mechanism

 Have you ever noticed how - when learning more about a science topic - we can get so interested 

that we start to discover favorites? Favorite dinosaur? I’ve found quite a few opinions there. 

Favorite animal? I’m a little obsessed. Favorite  flower? Well, sometimes a little too obvious. 

Of course, you can always get a 
little more unique. Favorite protist? 

Favorite amino acid? Your favorite nitrogenous base? 

I’m a little saddened that no one has yet asked me those three above nor have they asked me 

what I’ve been waiting to be asked, and yet have often volunteered, what is your favorite enzyme? 

ATP synthase is mine, but it’s a hard choice, because there are a ton of fascinating enzymes! 

We already have an intro video about enzymes, but this video topic is about to go into 

a little more: enzyme examples, cofactors and coenzymes, inhibitors, and feedback inhibition! 

Enzyme examples are important, because without learning about some real-life examples, 

it’s kind of hard to connect to how 
important they are to living things. 

Let’s start with some fascinating 
enzyme examples in the human body. 

A great place to focus on: digestion. Many enzymes focus on breaking down certain biomolecules. 

You remember the four biomolecules: 
carbohydrates, lipids, proteins, nucleic acids. 

These biomolecules are found in your food; you’ve got to break those biomolecules down in digestion. 

Amylase is an example of an enzyme that breaks down carbohydrates, and one action 

location is in the mouth. Amylase can break the glycosidic linkages in starch (which is 

a large carbohydrate), into smaller carbohydrates. Lipase is an example of an enzyme that breaks down 

lipids, and one action location is in the small intestine. Lipase can break the ester bonds found 

in triglycerides, which are a type of lipid, into their building blocks: fatty acids and glycerol. 

Pepsin and trypsin are some examples of enzymes that break down proteins. An action location 

for pepsin is in the stomach and an action location of trypsin is in the small intestine. 

These enzymes break the peptide bonds in proteins. Pepsin breaks proteins down into peptides. 

You even have nucleases that break down nucleic acids: that’s DNA and RNA. And yes, 

DNA and RNA can be found in your food. Nucleases break down phosphodiester bonds 

found in connected DNA and RNA and 
helps break them into nucleotides. 

By the way, once all of these biomolecules are broken down into smaller pieces, there are even 

more digestive enzymes that can break them down even more. But it’s not just digestion. 

You can name any human body 
system: excretory system, 

respiratory system, circulatory system: 
and you’ll find there are enzymes involved. 

These enzymes might break down or build up the substances that they act upon which is needed by 

different body systems. And while you’re at it, realize that enzymes are not just for humans. 

Enzymes are found in all living organisms, like this venus fly trap here. Beyond the 

three domains of living organisms, you’ll even find some types of enzymes in viruses! 

Ok so moving on. What’s next on our list? Oh, yes, cofactors and coenzymes. So just a quick review 

from our main enzyme video: this is an enzyme here and we have our active site and a substrate that 

could fit in the active site for the enzyme to act upon. It’s an enzyme-substrate complex when 

the substrate is bonded in this active site, and there is likely induced fit where the active site 

actually changes its shape slightly for an ideal fit- an enzyme substrate hug. But the thing is 

enzymes often don’t do it all alone, and they tend to have cofactors, which tend to be inorganic like 

zinc or iron - or coenzymes, which tend to be organic like many vitamins. Cofactors 

and coenzymes may be permanent or temporary, which often depends on how they’re bonded. 

A cofactor or coenzyme may sit in this active site here. It helps the bonding of the enzyme 

and substrate so that it can work at its best and sometimes it won’t work at all without them. 

An example of a cofactor or coenzyme? You know when we’ve mentioned DNA polymerase, 

an enzyme in DNA replication? It often 
has a zinc ion as a cofactor to help. 

There are also inhibitors. They might 
be reversible or not reversible – a lot 

of that depends on how they bond. They 
may be competitive or noncompetitive. 

Competitive inhibitors tend to sit right there in the active site, blocking a substrate from being 

able to bind. The substrates are competing with the competitive inhibitor for binding. 

Noncompetitive inhibitors bind to some other area of the enzyme, somewhere that isn’t the 

active site. This can be referred to as an 
allosteric site, a site on the enzyme that 

isn’t the active site. When the noncompetitive inhibitor binds on the allosteric site, 

the enzyme has a shape change. 
If the substrate still binds,  

the enzyme’s active site might 
not function well. Or at all. 

You know inhibitors might sound like a bad thing. But inhibitors can be harmful or 

they can be helpful. Some examples. You might remember DDT from our biomagnification video. 

It can act as an inhibitor for certain enzymes in the human body and can cause health issues. But 

understand that our body also uses inhibitors all the time to control a lot of biological 

processes. It’s called feedback inhibition. This is a hypothetical example here but 

let’s say that enzyme 1 converts a substrate A to an intermediate B. Then enzyme 2 converts B to C. 

Then enzyme 3 converts C to a final product D. These enzymes are all working in a pathway here. 

But what if you have enough product 
D now. It’s the ultimate product, 

but you have enough, and it’s wasteful to keep producing it or maybe it’s even harmful 

to make too much. Well product D might also be a noncompetitive inhibitor for enzyme 1. 

Stopping enzyme 1 from working, which will stop the process. Again, this could be reversible or 

it could be that more enzyme 1s are produced in the body if this needs to start up again. 

So to recap: we explored some real life enzyme examples, talked about cofactors and coenzymes, 

inhibitors, and feedback inhibition. But 
one last thing. We’re big on asking why: 

what is the significance of learning this? 

So we know that enzymes are ubiquitous – love that word – and they are critical for understanding 

biological processes. They’re also important to understand because many of the medications 

we use to treat diseases and disorders act on enzymes. One example –high blood pressure. It can 

be harmful to your organs and blood vessels. One class of blood pressure medications is the class 

of ACE inhibitors. ACE inhibitors work by blocking angiotensin-converting enzymes. When inhibited, 

these enzymes can’t convert angiotensin to angiotensin II. Angiotensin II can be 

involved with raising blood pressure so by blocking the enzyme that helps produce it, 

it can lower blood pressure -there’s some more complexity with this to explore. By the way, 

it’s not just the human body: medications can act on enzymes in microbes that might make us sick. 

An example: Penicillin. Penicillin is an 
antibiotic, but it works by inhibiting the enzyme 

transpeptidase - which prevents many types of bacteria from being able to build their cell wall. 

Well, that’s it for the Amoeba Sisters, 
and we remind you to stay curious.