Enzyme function

Enzyme function


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Enzyme function

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A low Km means the enzyme has a (high/low) affinity for its substrate.  


Content Reviewers:

Rishi Desai, MD, MPH

Enzymes are proteins that play a major role in the biochemical reactions happening every moment inside our bodies - everything from digesting a bowl of ramen noodles to flexing your muscles in front of a mirror.

Enzymes act as catalysts - meaning that they speed up the rate at which these biochemical reactions happen.

So instead of waiting months to years for a reaction to happen, it can happen in seconds - which is essential for life to happen.

Imagine trying to digest a single bowl of ramen for a year - you’d die of hunger before you could do it!

Every biochemical reaction has a substrate and a product - so let’s put them on this graph called a reaction coordinate diagram.

The X axis shows how a reaction progresses, while the Y axis shows the energy level at the different points along the reaction.

In the beginning, we’ve got the substrate - let’s call it A - with a fair amount of free energy.

At the end of it, there’s the product - or B, which ranks lower energy-wise.

The energy of the product minus the energy of the substrate is called the energy of the reaction, also known as Gibbs free energy, or ΔG.

Because lower energy states are preferred, a reaction spontaneously occurs when the product has a lower free energy than the substrate - so a negative ΔG.

So let’s say we’re looking at one such spontaneously occurring reaction, but between going from the substrate to the product there’s an intermediate transition step that has a really high energy state.

The amount of extra energy the substrate requires to get to the transition state - so the height of the upslope - is called the activation energy - or a ΔG‡ plus plus.

As soon as it enters the transition state, the molecule is highly unstable - and wants to go to a more stable lower-energy molecule

It either goes back to being a substrate or to being a product.

If it’s a substrate once again, it can go back up to the transition state if there’s enough activation energy once more, but if it becomes a product then it needs even more energy to get back to the transition state.

That’s why over time, with millions of molecules doing this, the majority of substrate turns into product.

Now, without an enzyme, the substrate might eventually harness enough activation energy to enter the transition state - but enzymes help speed things up quite a bit.

Enzymes are proteins that are folded in a particular way, so that they have a pocket called the active site on their surface.

When enzymes get involved in a reaction, the substrate binds to the active site, and together they form an enzyme-substrate complex, and that helps stabilize the transition state.

So enzymes decrease that extra energy requirement for the reaction - graphically turning our mountain into a hill.

Consider this analogy.

Imagine a little boy who’s nervous about getting a vaccine - he’s the substrate, and he turns into a vaccinated child - that’s the product.

The transition state is where the needle goes in, and as you can imagine - the boy might get really anxious and upset - a highly energetic and uncomfortable state.

In this scenario, enzymes are like adults who hold the boy and calm him down, reducing the anxiety or energy level of the transition state and making the whole thing happen faster.

Fortunately, enzymes don’t get used up in the process.

They attach to the substrate until it turns into the product and then release the product.

As soon as they’re done, they find another substrate.

What’s more is that enzymes and substrates are like biochemical soulmates - each enzyme is specifically designed for a particular type of substrate.

For example, amylase is an enzyme in your saliva that specifically helps break down large carbohydrates - into smaller sugar molecules that are then further broken down by other enzymes.

Now, the rate at which enzymes catalyse biochemical reactions is called enzyme kinetics, and there are two graphical ways to look at this.

The first, is the Michaelis Menten graph which has the concentration of the substrate, or [S], on the X axis, and the speed, or velocity of the reaction or V, which is how much product is formed over time, on the Y axis.

If there’s a fixed amount of enzyme, the velocity of the reaction increases as more substrate is added - that is, until all the active sites on all of the enzyme become saturated.

At this point, adding more substrate won’t do a thing, because there’s no more enzyme to bind it - so the speed of the reaction plateaus.

The point where the curve flattens out corresponds to the maximum velocity, or Vmax, on the Y axis.

Now we can determine Km - which is the concentration of substrate at which the speed of the reaction is exactly half the maximum velocity.

So we look at the Y axis, find what half of Vmax is, then we go parallel to the X axis until we reach our reaction curve.

From there, we go straight down towards the X axis - and Km will be equal to that substrate concentration.

The reason that Km is worth figuring out is that it inversely reflects enzyme affinity - if Km is low, only a little substrate is needed for the reaction to skyrocket up to half of its maximum rate, so we’re looking at an enzyme with high affinity.

On the other hand, if Km is high, then it takes a lot of substrate to get the reaction to go at half the maximum rate - so the enzyme has low affinity for its substrate.