AAMC FL1 BB#31

[663697]

Just wondering how enzymes alter the local pH. Tried googling it but no luck. Is it because any charged residues they may contain could become protonated/deprotonated?

Also, would a serine protease, for example, not alter the primary structure of the substrate? Wiki says it cleaves the peptide bond so I'm curious as to why this is incorrect

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[Nugester]

I'd imagine it is because enzymes have variable charged side groups, which would affect local pH. A & C are definitely out, leaving D. Enzymes lower the activation energy of reactions and I assume they are writing it as enzymes facilitating reactions between substrates, rather than directly participating in it. There are exceptions like you have pointed out so take it as you'd like.

 

[aldol16]

Just wondering how enzymes alter the local pH. Tried googling it but no luck. Is it because any charged residues they may contain could become protonated/deprotonated?

The environment of the active site is highly controlled by the enzyme and thus the enzyme can modulate pH in a variety of ways. I'll give only a few examples - these are by no means exhaustive. The active site could contain many fortuitously-positioned lysine residues that would want to ion-pair with negative charge. So say you have a carboxylic acid on your substrate - outside the active site, say the pKa is 2. Once it enters the active site where there's a lot of local positive charge, it's going to want to shed that proton more readily to become negatively charged - in other words, it has become more acidic and the pKa has lowered. Or the active site could contain many acidic residues that tend to deprotonate upon substrate binding, which would increase the [H+] in the local environment.

 

[nostra_damus]

I think the question is asking how the enzyme itself can regulate the reaction... the enzyme itself wouldn't be cleaving it's own peptide bonds

 

[danielsan1]

I think the question is asking how the enzyme itself can regulate the reaction... the enzyme itself wouldn't be cleaving it's own peptide bonds

The question says "substrate primary structure" not its own primary structure. So it seems with the present wording of the question, that enzymes such as proteases do indeed alter primary structure of their substrate.

 

[jmu29]

Ill give an example, Some enzymes have a metal ion at the active site and use h20 as a substrate and a histidine at the active site (proton shuttle). When the water gets “activated” to oh- histidine shuttles an h to the local environment. That h is “absorbed” by local base altering ph