Question

What do enzymes do and how do they do it (this question is intentionally vague and open ended)?

Answer 1

Enzymes are biological molecules (typically proteins) that significantly speed up the rate of virtually all of the chemical reactions that take place within cells.

They are vital for life and serve a wide range of important functions in the body, such as aiding in digestion and metabolism.

Some enzymes help break large molecules into smaller pieces that are more easily absorbed by the body. Other enzymes help bind two molecules together to produce a new molecule. Enzymes are highly selective catalysts, meaning that each enzyme only speeds up a specific reaction.

The molecules that an enzyme works with are called substrates. The substrates bind to a region on the enzyme called the active site.

There are two theories explaining the enzyme-substrate interaction.

In the lock-and-key model, the active site of an enzyme is precisely shaped to hold specific substrates. In the induced-fit model, the active site and substrate don't fit perfectly together; instead, they both alter their shape to connect.

Whatever the case, the reactions that occur accelerate greatly — over a millionfold — once the substrates bind to the active site of the enzyme. The chemical reactions result in a new product or molecule that then separates from the enzyme, which goes on to catalyze other reactions.

Here's an example: When the salivary enzyme amylase binds to a starch, it catalyzes hydrolysis (the breakdown of a compound due to a reaction with water), resulting in maltose, or malt sugar.

Examples of specific enzymes

There are thousands of enzymes in the human body, here are just a few examples:

• Lipases - a group of enzymes that help digest fats in the gut.
• Amylase - helps change starches into sugars. Amylase is found in saliva.
• Maltase - also found in saliva; breaks the sugar maltose into glucose. Maltose is found in foods such as potatoes, pasta, and beer.
• Trypsin - found in the small intestine, breaks proteins down into amino acids.
• Lactase - also found in the small intestine, breaks lactose, the sugar in milk, into glucose and galactose.
• Acetylcholinesterase - breaks down the neurotransmitter acetylcholine in nerves and muscles.
• Helicase - unravels DNA.
• DNA polymerase - synthesize DNA from deoxyribonucleotides.

  The "lock and key" model was first proposed in 1894. In this model, an enzyme's active site is a specific shape, and only the substrate will fit into it, like a lock and key.

  This model has now been updated and is called the induced-fit model.

  In this model, the active site changes shape as it interacts with the substrate. Once the substrate is fully locked in and in the exact position, the catalysis can begin.

  The perfect conditions

  Enzymes can only work in certain conditions. Most enzymes in the human body work best at around 37°C - body temperature. At lower temperatures, they will still work but much more slowly.

  Similarly, enzymes can only function in a certain pH range (acidic/alkaline). Their preference depends on where they are found in the body. For instance, enzymes in the intestines work best at 7.5 pH, whereas enzymes in the stomach work best at pH 2 because the stomach is much more acidic.

  If the temperature is too high or if the environment is too acidic or alkaline, the enzyme changes shape; this alters the shape of the active site so that substrates cannot bind to it - the enzyme has become denatured.

  Cofactors

  Some enzymes cannot function unless they have a specific non-protein molecule attached to them. These are called cofactors. For instance, carbonic anhydrase, an enzyme that helps maintain the pH of the body, cannot function unless it is attached to a zinc ion.

  Inhibition

  To ensure that the body's systems work correctly, sometimes enzymes need to be slowed down. For instance, if an enzyme is making too much of a product, there needs to be a way to reduce or stop production.

  Enzymes' activity can be inhibited in a number of ways:

  Competitive inhibitors - a molecule blocks the active site so that the substrate has to compete with the inhibitor to attach to the enzyme.

  Non-competitive inhibitors - a molecule binds to an enzyme somewhere other than the active site and reduces how effectively it works.

  Uncompetitive inhibitors - the inhibitor binds to the enzyme and substrate after they have bound to each other. The products leave the active site less easily, and the reaction is slowed down.

• Irreversible inhibitors - an irreversible inhibitor binds to an enzyme and permanently inactivates it.

  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.

  

  Reaction coordinate diagram showing the course of a reaction with and without a catalyst. With the catalyst, the activation energy is lower than without. However, the catalyst does not change the ∆G for the reaction.

  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).

  

  A substrate enters the active site of the enzyme. This forms the enzyme-substrate complex.The reaction then occurs, converting the substrate into products and forming an enzyme products complex. The products then leave the active site of the enzyme.

  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 404040 ^{\circ}\text C∘Cdegrees, start text, C, end text or 104104104 ^{\circ}\text F∘Fdegrees, start text, F, end text) may cause an enzyme to denature, losing its shape and activity.^22squared

• 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.

• 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.

  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.

  

  Illustration of the induced fit model of enzyme catalysis. As a substrate binds to the active site, the active site changes shape a little, grasping the substrate more tightly and preparing to catalyze the reaction. After the reaction takes place, the products are released from the active site and diffuse away.

  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.