A catalyst is something that speeds up a reaction without getting used up in the process. We talk about them a lot in biochemistry, and typically when we do so we’re talking about enzymes. Enzymes are biochemical catalysts – they’re often proteins, sometimes RNA, and sometimes a complex of protein + RNA – and they make it waaaaay more likely that a reaction will occur. They can do this by holding the substrate(s) (things that are going to react and/or change) in the optimal position to reaction, donating or holding onto protons (H⁺), or other tricks of the trade. And, at the end of the reaction, the enzyme is back to its old self and ready to do it again.
Enzymes don’t alter the start or end points of a reaction, but they can provide an easier path between them. If you look at a reaction diagram showing the free energy (ΔG) on the y-axis and the reaction course on the x-axis, it will look a bit like a rainbow. The higher the free energy, the more “uncomfy” the reaction. And the reason why it’s rainbow-shaped is because there’s usually an activation energy that’s required to get the reaction to a tipping point. If you imagine trying to break a stick, there’s that really awkward point for the stick when it’s super bent and straining and starting to break but still together. And that’s like the top of the rainbow – the transition point.
Your arms put in some energy to get the stick to start to snap and it’s a good thing that many reactions require some energy investment as well. If they didn’t, it’d be like fireworks going off in our cells all the time! But we don’t want our bodies to have to invest too much energy… Enter the enzyme. It lowers the activation energy that’s required to get the reaction to that tipping point – it kinda makes a shorter rainbow between the start of the rainbow and the pot of gold at the other end. It doesn’t tip the scales – so it catalyzes the reaction in both the forward and reverse directions (when you’re at the top of the rainbow you’re still just as likely to go either direction). But it can massively speed things up.
Imagine you have 2 RNA letters (nucleotides) floating around in a cell along with all sorts of other molecules. And you want those letters to link up. You’re probably gonna have to wait a long time – and you’d probably get some “wrong” reaction to occur before those letters even came into contact. But if you bring them together and hold them in the optimal position, stabilize their uncomfy transition state, etc. you can get them to link up. And do this over and over and over and over and over and…
So, enzymes are pretty awesome. And, in fact, a whole series of enzymes is involved in the step-wise manufacture of those nucleotides themselves!
But enzymes can also be pretty complicated. Our body’s main RNA polymerase, RNA Pol II, is actually made up of 12 protein subunits!
So, typically, although we use enzymes in vitro (“in a test tube”) for many purposes in the lab – like polymerase chain reaction (PCR) and in vitro transcription (IVT) which pieces together RNA letters based on a template – for many other purposes, such as building those building blocks, alternative catalysts are often used (and desirable) when possible. But then there are problems with selectivity & stereospecificity. This year’s Nobel Prize in Chemistry laureates found ways to get around this “stereochemistry” problem – in ways that are more environmentally-friendly than traditional synthesis routes. (but still no match for enzymes for more complicated reactions!) I was working on that post but realized I had too much to say about enzymes, so I thought I would do this ode to enzymes today.
If you want to know more about enzymes, see this past post which has a lot more detail http://bit.ly/enzymecatalysis
more about enzyme kinetics: https://bit.ly/maudmenten
more about ATP: https://bit.ly/ATPasenergymoney