[brasarehot]

How do you know just by looking at chemical structures, which are intermediates and which are transition states?
(Ex: Serine protease mechanism. Transition states = tetrahedral intermediates, Intermediate = Acyl-enzyme intermediate)
I'm so confused when you draw peaks, how high to draw them, if transition peak 1 is higher/lower than transition peak 2.
Any websites that are very helpful?

[Potla]

I think, intermediates are isolable and transition states are not independent structures.
While drawing transition states, you use dotted lines, whereas intermediates have all lines concrete. It's either a carbocation, or a carbanion, or a free radical. Transition states only have partial charges, and it shows making and breaking of bonds. It's cannot be separated from the system.
In energy diagrams, the transition states are the peaks and the intermediates are the vales (where the compound can "rest"). If a transition state is more stable, it means that its activation energy is less and it can occur at a faster rate compared to another one having a higher activation energy.
I am sorry that I don't know anything beyond this, and will be glad if someone rectifies the errors in this post.

[Babcock_Hall]

The tetrahedral intermediate in the serine protease mechanism is thought to be a true intermediate, although a high energy one.  The acylenzyme is also an intermediate but it is lower in energy, to the best of my understanding.  Intermediates occur at the minima of an energy diagram, and transition states occur at the maxima.  Sometimes compounds that are labeled as transition state analogs in biochemistry (such as the peptidyl trifluoromethylketones) might be a little misleadingly named.  Perhaps one should call them reaction-coordinate analogs.