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In class when we're studying enzymes like amylase or protease it only works well when you're using it to break down compounds like polysaccharides. I'm just curious but why is it not possible for enzymes to work efficiently in a reverse reaction? I mean a formula like
$\ce{amino\ acid + amino\ acid + energy<=>H2O + protein}$
does imply that our reaction can go both ways , right? But why is it that the enzyme favors the catabolic reaction?
Reactions have their set equilibrium constants, which are determined by the free energy of the reactants involved, and this cannot be changed by catalysts, including enzymes. Let's look at your example of peptide bond formation between two amino acids A and B,
A + B + energy $\leftrightharpoons$ H$_2$O + AB
This reaction might proceed in both directions; the rates of forward and reverse reactions depend on the free energy of A,B and the dipeptide AB, as well as how much "energy" we are talking about in the left-hand side. Let's ignore the energy term to start with, and just consider
A + B $\leftrightharpoons$ H$_2$O + AB
As it turns out, this reaction is not favorable: the $ \Delta G$ is about 10 kJ / mol (it depends a bit on which amino acids we're talking about). So this reaction goes in the reverse direction; dipeptides actually spontaneously decompose in water. But the rate of this reaction is very slow, because the peptide bond is quite stable. We say that there is an "energy barrier" between the substrates and products. Catalysts, including enzymes, lower this barrier, which increases the rate of reaction in both directions. It is physically impossible for enzymes to change the equilibrium by catalysis alone. There are plenty of enzymes that catalyze the above reaction, causing peptides to break down rapidly (peptidases, for example trypsin).
But enzymes don't just provide catalysis: an important role of enzymes is to couple two (or more) reactions together, so that a favorable one can drive an unfavorable one. This is how we obtain the "energy" term in the first reaction. The most common mechanism is to couple the unfavorable reaction to ATP hydrolysis,
ATP + H$_2$O $\leftrightharpoons$ ADP + P$_i$
which itself is highly favorable ($\Delta G$ around 40-50 kJ / mol). The coupled reaction is then
A + B + ATP + $\leftrightharpoons$ AB + ADP + P$_i$
which is now both favorable (due to ATP) and fast (due to catalysis). This is pretty much what ribosomes do (well, the actual mechanism is much more complex, but the principle is the same).
So, catalysts cannot change the equilibrium of a given reaction, but enzymes can couple reactions together to come up with something that is favorable. This is a central theme in biochemistry, allowing cells to drive reactions in the desired direction; but there is always a "price" to pay, often in the currency of ATP.
