What does a kinase do in terms of electrons? (use citric acid cycle as an example)

Answer 1

So a Kinase catalyzes the Phosphorylation of a protein.

Phosphorylation is the addition of a phosphate group onto a protein/molecule.

Usually, what happens is:

An electronegative ion (ex: a lone pair of electrons on an oxygen) attacks the Phosphorous group which, in the case of ATP, then kicks off an oxygen it was previously bound to.

However, the kinase isn't the one doing the reaction, it is the catalyst.

As a catalyst, it speeds up the reaction by making it less energetically taxing. It essentially stabilizes the reaction.

So how does it do this?

Two ways:

It either "holds" or orients the substrate so that the reaction can more easily take place.

Or, which is what I think is what your question is getting at, the Kinase uses positively charged residues to stabilize the transition state throughout the reaction. It does this by creating electrostatic bonds with the phosphorus.

In the case of the citric acid cycle, we have pyruvate dehydrogenase kinase stabilizes the conversion of pyruvate to oxaloacetate.