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Enzyme structure and function

Enzymes: what they are and what they do

Right now, as you read this, there are billions of chemical reactions happening inside your body. Although they happen at lightning speed inside cells, when these reactions are run inside test-tubes --- in a lab instead of a body --- they happen at a snail’s pace. What explains this difference in speed? What do our cells have, that a test-tube lacks? The answer is: enzymes!
Enzymes are life’s great facilitators. They create the conditions needed for biochemical reactions to happen fast. The general name that chemists use for a chemical entity that increases the speed of a reaction is a “catalyst.” Enzymes are biological catalysts--they catalyze the chemical reactions that happen inside living things.

The definition of catalysis

Consider a chemical reaction where a molecule A bonds with a molecule B to create a molecule A-B (A stuck to B). Under a given set of conditions --- the temperature the reaction occurs at, the pressure of the atmosphere, and the concentrations of the reactants A and B and the product A-B --- this reaction happens at a certain speed. For example, 3 A molecules and 3 B molecules become 3 A-B molecules each second.
To call something a catalyst for this reaction, two criteria have to be met : First, it must increase the speed of the reaction --- from 3 A-B’s made per second to 16A-B’s molecules made per second, for example. And second, it can’t be used up or altered in any permanent way by the reaction --- it still has to be there after the reaction is over. A catalyst speeds up a reaction, but isn’t consumed by it.
This second part of the catalyst definition is very important. If we imagine starting a camp-fire, which is essentially a chemical reaction between wood and oxygen, we could certainly speed the reaction up by dumping a huge bucket of gasoline on the fire. But we wouldn’t be catalyzing the fire reaction. The gasoline makes the reaction go faster --- as indicated by the charred eyebrows and singed hair of anybody trying this at home --- but it also gets used up. There’s no gasoline around after the fire is extinguished. In other words, gasoline on a fire is not a catalyst.

If gasoline isn’t a catalyst, what is?

One of the best everyday examples of a catalyst is the emissions control system in your car. The main part of this system, unsurprisingly, is called a catalytic converter. This device is a container with a series of small screens coated in precious metals --- platinum, rhodium, etc. These metals are catalysts for the conversion of nitric oxide --- a nitrogen atom bonded to an oxygen atom --- into nitrogen and oxygen. The metals in a catalytic converter speed up the creation of nitrogen and oxygen, and unlike gasoline on a fire, they aren’t used up in the process --- in theory, a catalytic converter should keep working long after the wheels on your car fall off!

How do catalysts work?

Most catalysts (including enzymes) work the same basic way, because most chemical reactions (including biochemical ones) work the same basic way.
As a good basic example, lets look at the nitric oxide reaction from the last section. What you have is the collision of two molecules of nitric oxide that results in the breakage of nitrogen-oxygen bonds and the creation of new nitrogen-nitrogen and oxygen-oxygen bonds.
If we were to dump a whole bunch of nitric oxide molecules into a normal jar (with no catalytic converter), and we were able to get an extreme close-up of what was going on at the molecular level, we would see millions of N-O molecules spinning and tumbling in space, smashing into each other and ricocheting off the walls of the jar at incredible speeds. The vast majority of the collisions between the N-O molecules wouldn’t result in any chemical reactions at all. Very, very few nitrogen or oxygen molecules would be created, whereas most ofthe nitric oxide molecules would just bounce off of each other. Why?

Why the nitric oxide molecules bounce off each other: a thought experiment

One way to visualize a molecule like nitric oxide is as two magnets stuck together. If you’ve ever played around with magnets, you know that in order for two to stick together, you need to align the “pole” of one --- all magnets have a north and a south pole --- with the opposite pole of the other: north to south, or south to north. You also know that if you try and align one pole of a magnet with the same pole of the other, the magnets will repel. Nitrogen and oxygen atoms are like magnets in this sense. If you align them in just the right way, so that the “north pole” of the nitrogen is right up next to the “south pole” of oxygen, they will stick together to form the molecule we call nitric oxide. Chemical “bonds” are really nothing more than attractions between atoms!
So let’s simplify things and think of oxygen atoms as red magnets and nitrogen atoms as blue magnets. And let’s make two rules about how these magnets behave. The first rule is that there is a mutual attraction between red magnets and blue magnets. This means that if you stick the north pole of a red magnet to the south pole of a blue magnet, they will stick together, just like you would expect with two magnets. The second rule is that there is a stronger mutual attraction between magnets of the same color: red to red, or blue to blue. What this means is that a red magnet will prefer to stick to another red magnet, and a blue magnet will prefer to stick to another blue magnet, if given the choice.
So those are the rules about how our magnets behave. Let’s consider what would happen when a red magnet stuck to a blue magnet collides with another red magnet stuck to a blue magnet. If the poles of the colliding magnets are lined up in the correct way, so that the north pole of one red magnet is contacting the south pole of the other red magnet, with the same happening for the blue magnets, what would happen? Since magnets of the same color are more strongly attracted to each other than they are to magnets of the opposite color, what you would get would be the “destruction” of the two red-blue “molecules” and the creation of one “red-red” molecule and one “blue-blue” molecule. But only if the alignment is correct! Otherwise, the “red-blue” molecules will bounce off each other, and no new molecules will be created.
This magnet thought experiment is a good approximation of what happens with real-life molecules like nitric oxide. If one N-O collides with another N-O, and they are in the exact right orientation, with N’s aligned with N’s and O’s aligned with O’s, the two N-O’s will go away and a new N-N and new O-O will be created in their place. But the alignment is key--nothing will happen without it.
This is where catalysts come in. They help with alignment. To see how, let’s return back to the magnet example. Imagine we’ve got a jar with a bunch of small red-blue magnet “molecules,” and imagine that we’re giving the jar a good shake, jostling the magnets around on the inside in a random way, with lots of collisions. Sometimes, two red-blue’s will bump into each other in the exact right alignment, and a red-red and a blue-blue will be created. But there are tons more incorrect alignments than there are correct ones, so colliding red-blues are more likely to just bounce off than they are to make new “molecules”. The odds favor nothing happening.
This is what happens with nitric oxide molecules in a jar, when no catalyst is present.
But now imagine that we add an extremely motivated and conscientious magic gnome to the inside of our jar, with the instructions that he is to grab a red-blue in each one of his hands, align them in the right way, and then smash them together. Adding this helpful gnome assistant will increase the rate at which red-reds and blue-blues are made, because achieving the right alignment is no longer a matter of random chance. We’ve now got someone on the inside, making sure that the alignments that we want are being created.
Catalysts are the real-life versions of our imaginary magic gnomes. A platinum screen sits inside a catalytic converter attracting nitric oxide molecules to it and aligning them in just the right way, so that when they collide, the N and O switch places, and nitrogen gas and oxygen gas are created. Catalysts make reactions fast by aligning reactants so that successful reactions are more likely!

Enzymes are biological catalysts

Enzymes are the catalysts involved in biological chemical reactions. They are the “gnomes” inside each one of us that take molecules like nucleotides and align them together to create DNA, or amino acids to make proteins, to name two of thousands of such functions. They are so important for life that scientists weren’t satisfied with calling them catalysts, and had to invent the fancy new name “enzyme” instead.

Why enzymes are so important

The big reason enzymes are important to life is because cellular energy is a precious resource. To see how enzymes help preserve this resource, and how such preservation matters to living things, let’s return again to our magnet thought experiment.
We already saw that adding a magic gnome speeds up the production of red-red and blue-blue “molecules.” Another way to get the same speed increase would be to shake the jar harder. This wouldn’t do anything for alignment, like the gnome, but it would increase the total number of collisions between red-blues that happen every second --- shaking harder jostles everything around quicker. This increase in the total number of collisions per second would increase, just as a matter of probability, the number of correctly aligned collisions too. So, in the end, shaking the jar harder --- much harder, perhaps --- would result in an increase in the speed of red-red and blue-blue production too, just like adding a gnome and keeping the shaking of the jar the same.
Think about the pro’s and con’s of these two strategies. By just shaking the jar harder, you choose to do the work yourself and forego the services of the gnome. You get the same end-result, but it requires more energy expenditure on your part. If you use the gnome, you get to save this energy for other purposes: you can shake the jar lightly, and the gnome takes care of the rest. If you have lots of energy to burn, or if you are very strong and shaking the jar harder is child’s play, the energy savings associated with using the gnome might not mean much to you. But what if energy is in short supply, and you don’t have much to waste on shaking the jar harder? Or what if you have lots of energy available, but you have to do a lot of work to obtain it? Or, maybe you have extra energy, but you want to spend it on doing other important things. In any of these three cases, the added savings you get from using the gnome to do the work might make a world of difference.
Let’s think about how this logic applies to living things. It’s a bit subtle, but if you can make the connections, you’ll understand something very profound about the nature of what it means to be alive. Pretty cool for a few minutes effort!
Consider a rabbit in a field. This rabbit has millions and millions of cells, all of which have billions and billions of chemical reactions going on, every second of every day that the rabbit is alive.
In order to maintain the conditions needed for these reactions to occur, the rabbit’s cells need to “burn energy.” The rabbit eats grass. The grass gets converted to simple sugars. The simple sugars get converted to fuel molecules. Cells “burn” these molecules, like a car “burns” gasoline. Burning fuel molecules releases energy, and this energy increases the speed with which molecules travel inside cells. A cell burning energy has the same effect on the molecules inside it as shaking our imaginary jar has on the red and blue magnets inside it. In both cases, work is being done that results in more collisions happening, which in turn results in more reactions happening.
Over millions of years of evolution, the rabbit’s cells have been fine-tuned to burn a certain, relatively constant amount of energy. With the help of enzymes, this amount of energy is just enough --- not too much, and not too little --- to get molecules moving fast enough to react in the ways that the rabbit needs in order to go on living. The energy released from burning the fuel molecules drives the molecules around at a certain speed, and the enzymes make sure that the molecules are aligned in just the right way so that the right kinds of collisions happen.
If we kept everything the same, but just took the enzymes away, the chemical reactions going on inside the rabbit’s cells would all start to happen at much slower rates. The molecules would be moving around with the same speed, but the collisions would be totally random: you’d have to wait longer for the “right” sort of collisions to occur.
This is a huge problem for the rabbit, because most of what it does depends on the speed of the chemical reactions in its cells. If it’s in a field, having some grass for lunch, and it spots an owl in the sky, it has to react to this threat in a split second. If the chemical reactions that drive the mechanical actions of its hopping muscles are slowed down even a little bit, the rabbit will go from eating lunch to being lunch.
This gets to the point of why enzymes are so very important for life. Think of them as the optimal solution to an equation with two separate variables. On the one hand, you have the requirement for everything to happen inside the rabbit's body very rapidly—this is how it evades predators, beats other rabbits to food sources, and reproduces. On the other hand, you have the limitation imposed on the rabbit by the environment and its own body. There aren’t unlimited amounts of food available for it to eat. It often has to travel long distances to access this food. It has to process the food into usable fuel for its cells. It has to efficiently dispose of the heat generated when it burns the fuel. In short: the rabbit needs the speedy reactions associated with burning lots of energy, but it can’t burn too much because energy isn’t free: in fact, it’s very hard to come by, and there are costs associated with using it.
Enzymes are the perfect solution to this problem. They allow for the fast reactions a rabbit needs, without the associated increase in energy expenditure that is required when enzymes aren’t present.
If you take a second to think about all the advantages a regular rabbit has against an imaginary rabbit with no enzymes, you will begin to understand how these miraculous devices came about in the first place. Somewhere in the depths of history, a tiny single cell organism, through the actions of random chance, developed a prehistoric enzyme, which allowed some chemical reaction that happened inside the organism to happen just a little faster than the same reaction in its neighboring organisms. This slight advantage made our tiny organism just a touch better at reproducing, and the rest, as they say, is history. The descendants of the original pioneering organism retained this advantage and quickly multiplied. Other chance occurrences created other new enzymes, and new and better adapted forms of life, eventually culminating, over millions and millions of years, in our rabbit, reacting to the owl in the sky in and bounding to safety, just in the knick of time.

Want to join the conversation?

  • male robot hal style avatar for user Jake Robertson
    In the example with the "O's" (oxygens) and "N's" (nitrogens), why does each atom want to be with an atom identical to itself more than it wants to be with an opposite atom? If two NO molecules crashed into each other, and the bond broke, wouldn't it be equally likely for the atoms to come back together to form NO as they originally were?
    (13 votes)
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    • winston default style avatar for user michael henderson
      First off I'll be honest, I didn't actually read this article, I scanned it to see if i needed to read it. To answer your question : Well atoms don't specifically want to pair with themselves or a different atom for that matter, this just an example to help understand enzyme activity. From what I'm aware of, atoms, specifically their electrons like to be in a low energy state, this is analogous to how we all like to hit the snooze button in bed rather than get up and start moving in the mornings.
      For example in the case of NO, O2 and N2 are lower energy states, in other words energy is released when forming O2 or N2 but energy is required to create NO, it is an endothermic reaction. This energy requirement means that the O2 and N2 states are more favourable, just like your bed is as opposed to work or school.

      Yep :) ! this is actually what happens in most cases. Reactions can move in both directions and its called equilbria, all reactions are just random collisions really and depending on the circumstances, (temperature, pressure, concentrations of products and reactants), they tend to favour different outcomes. So dependent on the conditions 2NO may form N2, O2 or just reform 2NO like you suggested, but with the use of an enzyme we can sort of "tweek" the reaction to get more of the products we want, (in this case N2 and O2), by lowering the energy required for our preferred reaction to take place.

      I hope I haven't babbled and this helps in some way :)
      (94 votes)
  • blobby green style avatar for user leezhang.hotlays
    Great article. One problem. The magic gnome doesn't look like a gnome.
    (42 votes)
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  • leaf blue style avatar for user Katie Finamore
    How does structure lead to specific function of an enzyme?
    (4 votes)
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    • leafers seed style avatar for user mistyanderson817
      Primary structure of a protein, i.e. the order that amino acids are bound together in a line, has everything it needs in order to tell the protein how to fold up into secondary and tertiary structure. Once that folding and 3D structure is formed, amino acid residues that were not close together in the primary structure, are now close together in the 3D structure. This means that they will have weak interactions among themselves. This further holds the 3D structure in place and in some cases forms Quaternary structure. The arrangement of amino acid residues determines the shape of the active site where the substrate will bind. This is what causes an enzyme to have specificity for a substrate. Think about it logically. Different confirmations of various shaped and sized amino acid residues coming together would form various shapes/sizes of clefts or crevices (active site). Therefore, only certain sized and shaped substrates could fit and bind there. The particular substrate-enzyme complex (what is formed when a substrate binds to an enzyme's active site) has a certain function or makes a certain end product. Soooooo, if that particular enzyme did not have its correct molecular architecture (3D shape), the correct substrate could not bind to the correct active site/enzyme and therefore, the correct product could not be made. This would mean that the particular enzyme with the wrong structure might bind the wrong substrate and create no product OR create a product that is not favorable in the particular reaction or environment that it is in. Does that make sense?
      (17 votes)
  • aqualine seed style avatar for user Madeline Ryan
    Who wrote this article and when?
    (8 votes)
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  • piceratops seedling style avatar for user Harsh Pandey
    What are the nucleic acids that behave like enzymes are known as?
    (4 votes)
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  • leafers sapling style avatar for user Anthony Lanauze
    Explain how the structure of an enzyme relates to how well the function catalyzes chemical reactions.
    (4 votes)
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  • blobby green style avatar for user 12xz
    If vitamins are considered coenzymes because they are organic and FAD is a vitamin-derivative, shouldn't FAD be considered a coenzyme as well?
    (1 vote)
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  • blobby green style avatar for user srajam23
    what is a substrate and how does it connect with this lesson
    (2 votes)
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  • blobby green style avatar for user Jade
    What are the structure of active centers for simple and conjugated enzymes?
    (2 votes)
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  • blobby green style avatar for user kmarmelo24
    What are the various structures of an enzyme?
    (1 vote)
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    • eggleston blue style avatar for user Soefae
      Enzymes can be described at four levels: primary, secondary, tertiary, and quaternary. 

      1. The primary structure of an enzyme is the linear sequence of amino acids in its polypeptide chain(s), which are linked by peptide bonds.

      2. The secondary structure refers to the local folded structures that form within a polypeptide due to interactions between atoms in the backbone of the chain. The most common types of secondary structures are 1) alpha helices: A right-handed coil resulting from hydrogen bonding between the carbonyl oxygen of one amino acid and the amide hydrogen of another and 2) beta sheets (β-sheets): Sheets formed by linking two or more parallel or antiparallel polypeptide chains through hydrogen bonds.

      3. The tertiary structure is the overall three-dimensional shape of a single polypeptide chain, which is stabilized by various interactions between the side chains (R groups) of the amino acids, such as hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bonds (covalent bonds between cysteine residues). The tertiary structure creates the specific shape and chemical environment necessary for substrate binding and catalysis.

      4. The quaternary structure exists in enzymes that consist of more than one polypeptide chain, known as subunits. The arrangement and interaction of these subunits form the quaternary structure.
      (1 vote)