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Enzymes and the active site

Enzymes as biological catalysts, activation energy, the active site, and environmental effects on enzyme activity.


As a kid, I wore glasses and desperately wanted a pair of contact lenses. When I was finally allowed to get contacts, part of the deal was that I had to take very, very good care of them, which meant washing them with cleaner every day, storing them in a sterile solution, and, once a week, adding a few drops of something called “enzymatic cleaner.” I didn’t know exactly what “enzymatic cleaner” meant, but I did learn that if you forgot you’d added it and accidentally put your contacts in your eyes without washing them, you were going to have burning eyes for a good fifteen minutes.
As I would later learn, all that “enzymatic” meant was that the cleaner contained one or more enzymes, proteins that catalyzed particular chemical reactions – in this case, reactions that broke down the film of eye goo that accumulated on my contacts after a week of use. (Presumably, the reason it stung when I got it in my eyes was that the enzymes would also happily break down eye goo in an intact eye.) In this article, we’ll look in greater depth at what an enzyme is and how it catalyzes a particular chemical reaction.

Enzymes and activation energy

A substance that speeds up a chemical reaction—without being a reactant—is called a catalyst. The catalysts for biochemical reactions that happen in living organisms are called enzymes. Enzymes are usually proteins, though some ribonucleic acid (RNA) molecules act as enzymes too.
Enzymes perform the critical task of lowering a reaction's activation energy—that is, the amount of energy that must be put in for the reaction to begin. Enzymes work by binding to reactant molecules and holding them in such a way that the chemical bond-breaking and bond-forming processes take place more readily.
_Image modified from "Potential, kinetic, free, and activation energy: Figure 5," by OpenStax College, Biology, CC BY 3.0._
To clarify one important point, enzymes don’t change a reaction’s G value. That is, they don’t change whether a reaction is energy-releasing or energy-absorbing overall. That's because enzymes don’t affect the free energy of the reactants or products.
Instead, enzymes lower the energy of the transition state, an unstable state that products must pass through in order to become reactants. The transition state is at the top of the energy "hill" in the diagram above.

Active sites and substrate specificity

To catalyze a reaction, an enzyme will grab on (bind) to one or more reactant molecules. These molecules are the enzyme's substrates.
In some reactions, one substrate is broken down into multiple products. In others, two substrates come together to create one larger molecule or to swap pieces. In fact, whatever type of biological reaction you can think of, there is probably an enzyme to speed it up!
The part of the enzyme where the substrate binds is called the active site (since that’s where the catalytic “action” happens).
Image modified from "Enzymes: Figure 2," by OpenStax College, Biology, CC BY 3.0.
Proteins are made of units called amino acids, and in enzymes that are proteins, the active site gets its properties from the amino acids it's built out of. These amino acids may have side chains that are large or small, acidic or basic, hydrophilic or hydrophobic.
The set of amino acids found in the active site, along with their positions in 3D space, give the active site a very specific size, shape, and chemical behavior. Thanks to these amino acids, an enzyme's active site is uniquely suited to bind to a particular target—the enzyme's substrate or substrates—and help them undergo a chemical reaction.

Environmental effects on enzyme function

Because active sites are finely tuned to help a chemical reaction happen, they can be very sensitive to changes in the enzyme’s environment. Factors that may affect the active site and enzyme function include:
  • Temperature. A higher temperature generally makes for higher rates of reaction, enzyme-catalyzed or otherwise. However, either increasing or decreasing the temperature outside of a tolerable range can affect chemical bonds in the active site, making them less well-suited to bind substrates. Very high temperatures (for animal enzymes, above 40 C or 104 F) may cause an enzyme to denature, losing its shape and activity.2
  • pH. pH can also affect enzyme function. Active site amino acid residues often have acidic or basic properties that are important for catalysis. Changes in pH can affect these residues and make it hard for substrates to bind. Enzymes work best within a certain pH range, and, as with temperature, extreme pH values (acidic or basic) can make enzymes denature.

Induced fit

The matching between an enzyme's active site and the substrate isn’t just like two puzzle pieces fitting together (though scientists once thought it was, in an old model called the “lock-and-key” model).
Instead, an enzyme changes shape slightly when it binds its substrate, resulting in an even tighter fit. This adjustment of the enzyme to snugly fit the substrate is called induced fit.
Image modified from "Enzymes: Figure 2," by OpenStax College, Biology, CC BY 3.0.
When an enzyme binds to its substrate, we know it lowers the activation energy of the reaction, allowing it to happen more quickly. But, you may wonder, what does the enzyme actually do to the substrate to make the activation energy lower?
The answer depends on the enzyme. Some enzymes speed up chemical reactions by bringing two substrates together in the right orientation. Others create an environment inside the active site that's favorable to the reaction (for instance, one that's slightly acidic or non-polar). The enzyme-substrate complex can also lower activation energy by bending substrate molecules in a way that facilitates bond-breaking, helping to reach the transition state.
Finally, some enzymes lower activation energies by taking part in the chemical reaction themselves. That is, active site residues may form temporary covalent bonds with substrate molecules as part of the reaction process.
An important word here is "temporary." In all cases, the enzyme will return to its original state at the end of the reaction—it won't stay bound to the reacting molecules. In fact, a hallmark property of enzymes is that they aren't altered by the reactions they catalyze. When an enzyme is done catalyzing a reaction, it just releases the product (or products) and is ready for the next cycle of catalysis.

Explore outside of Khan Academy

Do you want to learn more about the effect of temperature on enzyme function? Check out this interactive image from LabXchange.
Do you want to learn more about the effect of pH on enzyme function? Check out this interactive image from LabXchange.
LabXchange is a free online science education platform created at Harvard’s Faculty of Arts and Sciences and supported by the Amgen Foundation.

Want to join the conversation?

  • hopper jumping style avatar for user joshua721
    What would happen if the shape of the enzyme's active site were changed?
    (27 votes)
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    • piceratops seedling style avatar for user Angie
      If the active site were changed, possibly by a large change in temperature or pH, the enzyme would most likely not be able to catalyze the same reactions. This is because temperature and pH can denature (or change) and enzyme's shape and therefore make it unable to bind with the same specifically shaped substrates as before.
      (22 votes)
  • blobby green style avatar for user vildaya
    Which type of bond exists between enzyme and the substrate in enzyme substrate complex?
    (13 votes)
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  • leafers tree style avatar for user Faith Ho
    How do inhibitors stop enzyme activities?
    (3 votes)
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    • spunky sam blue style avatar for user bart0241
      There are four different kinds of inhibitors; competitive inhibitors, noncompetitive inhibitors (allosteric inhibitors), irreversible inhibitors, and feedback inhibitors.

      Competitive inhibitors compete with the substrates of an enzyme at its active site. When they bind to the active site of the enzyme, they prevent the enzyme from breaking or creating molecules.

      Noncompetitive inhibitors, also known as allosteric inhibitors, do not compete with substrates for the active site. Rather they bind to a different area on the enzyme. This area is known as the allosteric site. When the inhibitor binds to the allosteric site, it causes a conformational shape change, preventing the enzyme's substrates from attaching to it. Thus preventing the breakdown or formation of a molecule.

      Irreversible inhibitors have two forms; irreversible competitive inhibitors or irreversible noncompetitive inhibitors. These inhibitors either bind to the active or allosteric site of an enzyme.

      Feedback inhibitors are the end products of reactions. They interfere with the enzyme that helped produce them. They bind to the allosteric site of the enzyme changing the shape of the enzyme. They usually help in regulating and coordinating the products of an enzyme.
      (28 votes)
  • piceratops seed style avatar for user ANNIE OMOREGIE
    what exactly are activated co enzymes
    (4 votes)
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    • old spice man green style avatar for user Matt B
      (Activated) Coenzymes are small molecules. They cannot by themselves catalyze a reaction but they can help enzymes to do so. Enzymes are biological catalyst that do not react themselves but instead speed up a reaction.
      So, a coenzyme activates the enzyme to speed up a (biological) reaction.
      (19 votes)
  • primosaur ultimate style avatar for user Izabela Muller
    Can you give me an example of a catalyst that is not an enzyme?
    Many thanks!
    (5 votes)
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  • blobby green style avatar for user Kaja
    Hi, I think there's a mistake in the text. Or perhaps I don't understand it. There's written "Instead, enzymes lower the energy of the transition state, an unstable state that products must pass through in order to become reactants". Products become reactants? Isn't it supposed to be the other way around? That reactants become products. I don't know.
    (8 votes)
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    • ohnoes default style avatar for user tfeng1822
      When a reaction is catalyzed, generally it splits up the reaction into 2 steps. For example, if the reaction A + B -> AB is catalyzed, the reaction would be something like A + cat -> Acat then Acat + B -> AB + cat. So, what the text is saying is the activation energy of A + cat -> Acat (the transition state) is less than A + B -> AB, and that the product (Acat) becomes the reactant for the second step (Acat + B -> AB + cat), which gives the desires product. So, catalyzes such as enzymes generally split a reaction into steps, whose activation energies are less than the uncatalyzed reaction. Unfortunately, this was not specified in the text.
      (2 votes)
  • blobby green style avatar for user kredo.hosted
    enzymes have an active site that does all the actual work. but what is the function of the rest of the molecule? why it still exists? what is the evolutionary role of it?
    (5 votes)
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    • piceratops seed style avatar for user RogerP
      In general terms, the rest of the enzyme molecule is there to ensure that the active site contains the right amino acids in exactly the right orientation relative to one another.

      Let's say that the active site needs three specific amino acids lined up in a very defined way. The rest of the molecule provides a framework (scaffolding, if you like) that ensures the active site is properly set up. Without this framework there would be no way of fixing the key amino acids into the correct positions.

      Also, the critical amino acids may be a long way apart from one another in the primary sequence of the protein and are only brought together through the secondary and tertiary structuring of the protein.

      What's more, with the induced fit model, the rest of the molecule can be involved in changing the confirmation of the enzyme. Related to this is enzyme regulation where modification of an amino acid remote from the active site can control the activity of the enzyme. Furthermore, in some enzymes there is a second binding site and when something, such as an inhibitor, binds to that site it changes the shape of the active site, also controlling the enzyme.
      (7 votes)
  • leaf green style avatar for user Farooq Ahmad Khan
    Rather than the environmental pH. Does the pH of the substrate also causes a change in it's active site?
    (2 votes)
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    • aqualine ultimate style avatar for user Lydia
      Okay, so pH is actually defined based on the concentration of H+ in a given volume. So the substrate doesn't have a pH. Many molecules of the substrate dissolved in water do have a pH, but an individual molecule? Nah. The substrate does have different polarities (positive and negative charged areas) but the enzyme is built to handle that. These differently charged regions help the substrate lock in place.
      (9 votes)
  • starky ultimate style avatar for user Greacus
    How does RNA catalyze a reaction?
    (5 votes)
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    • duskpin ultimate style avatar for user Derrick Liang
      RNA molecules that can function as enzymes are known as ribozymes. RNA can have 3 dimensional structure because it can hydrogen-bond with itself and form loops. Some of the bases in the RNA have special functional groups which can add specificity to the shape. The RNA can also hydrogen-bond with other nucleic acids to create an even more specific shape.

      One example ribosomal RNA, which can catalyze the translation of mRNA in ribosomes. In ribosomes, rRNA and proteins come together and form a space for messenger RNA to be read and for transfer RNA to bond to the ribosome and attach the correct amino acid. The specific shape of the rRNA allow the mRNA to be translated properly.
      (4 votes)
  • blobby green style avatar for user zaainabkhan7
    How do enzymes enable chemical reaction to take place rapidly ?
    (3 votes)
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    • old spice man green style avatar for user Matt B
      They offer an alternative reaction pathway that has a lower activation energy i.e. less energy is required for the reaction to occur. Therefore, more particles will have the required energy, and more particles can react at the same time, thus increasing the reaction speed.
      (5 votes)