I have a fascination in biology and have wondered how proteins designed to make certain molecules like DNA or ATP, etc., create the chemical bonds between the atoms when making it.
I understand that they don’t make them from scratch, they usual just “smash” two different molecules together, but still how are the bonds created?
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Okay so I’m going to start off by talking about energy levels. [This is a graph ](https://images.app.goo.gl/ezSTotb9KEEg1TFD9)of the energy states associated with an exothermic reaction, or a reaction that releases energy. We start with the reactants, which then form a transition state of higher energy, then they settle down into the lower energy products. The key here is that the transition state requires energy to be put in to reach, and we chemists call this the activation energy. Any catalyst, protein or not, works by reducing the amount of activation energy a reactions requires.
So what does this have to do with proteins? Well, the way protein enzymes work is by having a binding affinity not just to the reactants but to THEIR TRANSITION STATE; which means the reactants binding to the enzyme “prepares” the reactants for the upcoming reaction and makes it far easier for the desired reaction to happen. Sometimes, this is a simple as literally squishing two reactants close enough together that they react.
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