Hello.

Having in mind that this is my first post here, I'd like to say hello to everyone on this site.

My name is Krzysiek, I'm 21 and currently studying first year of medicine.

 

Right now I'm preparing for my first biochemistry exam.

I'm using "Harper's Biochemistry", but the author's language ain't making it easy to understand
This is the only paragraph that mentions the acid-base catalysis:

"Acid-base catalysis can be either specific

or general. By "specific" we mean only

protons (H3O+) or OH- ions. In specific

acid or specific base catalysis, the rate

of reaction is sensitive to changes

in the concentration of protons but

independent of the concentrations of other

acids (proton donors) or bases (proton acceptors)

present in solution or at the active site.

Reactions whose rates are responsive to all the

acids or bases present are said to be

subject to general acid or general base catalysis."

For me it is so unclear!

So, as far as I know only the H+ and OH- ions decide whether a particular compound is acidic or not. So how come "the rate of reaction is sensitive to changes in the concentration of protons but independent of the concentrations of other acids"? If there are other acids in the solution automatically the concentration of H+ ions increases and this is what the "specific" mechanism is sensitive to. I mean, in my opinion the presence of other acids induces the change of H+ concentration, so it's impossible that the "specific" catalysis won't be affected...

Can someone please put this Harper's paragraph in a simpler language with regards to my reflections? Thanks in advance

I did a little Googling, as I found the paragraph you posted to be odd and it made very little sense to me. I came across this video:

 

 

It seems they are referring to specific as involving strong acids or bases, where there is full dissociation prior to the rate determining step, and general as involving weak acids or bases, where proton transfer occurs during the RDS. Way to use standard terminology, biochemistry!

 

Also, there are other types of acids and bases not covered by this definition. Specifically, Lewis acids and bases. They are not referencing these, however.

If an aqueous reaction speeds up as the concentration of protons is increased, then it is subject to specific acid catalysis. If a reaction speeds up as the concentration of a buffering species is increased at constant pH, then general acid (or general base) catalysis may be occurring (but nucleophilic catalysis would need to be ruled out before one could conclude that it was IIUC). The key is that if one raises the concentration of a buffer then one does not change the pH (to a very good first approximation), yet the reaction speeds up. Therefore, the weak acid or weak base component of the buffer must be the catalytic species.

 

William P. Jencks' Catalysis in Chemistry and Enzymology has a good discussion (all of Chapter 3), despite its being an older book. Many enzymes use a histidyl residue to perform general acid or general base catalysis; these include chymotrypsin and ribonuclease A. General acid and general base catalysis may be more important for enzymes than in organic synthesis, because much biochemistry takes place near neutral pH, where both protons and hydroxide ion are in very low concentration.

Edited November 16, 201510 yr by BabcockHall

It is my understanding that proton transfer may be, but need not be, concerted with the bond breaking or bond forming between heavy atoms. However the reading I have done so far has not addressed this point explicitly.