MCB 150 Frequently Asked Questions

Proteins and Enzymes

Positively charged R-groups are categorized as basic. When discussing the electrochemical gradient in a more recent lecture, the area of more positive charged has a lower pH. This indicates that this area is more ACIDIC. Why does a higher concentration of H+ make the intermembrane space more acidic? Also, how does this compare to the positively charged R-groups mentioned above in the earlier lecture on proteins?

The intermembrane space (IMS) is a more acidic environment than the matrix because of the fact that there are more protons in there. pH is a measurement of the concentration of hydrogen ions, or H+, or protons, whatever you want to call them. With regard to basic amino acids, remember one of the first instances I gave in class of the difference between chemistry and biology. In chemistry, a base is a proton acceptor. In biology, that acceptor either will have already accepted that proton, or it will not have, depending on the cellular conditions. And under normal physiological conditions in a cell, a basic amino acid side chain WILL have already accepted the proton it is capable of accepting. And since we've already established that protons are positively-charged, what is the consequence of gaining a proton in terms of your overall charge? If you were neutral, you're now positive, and this is the case for the side chains we refer to as basic.

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