Change in pH can have serious effects on the structure of a protein which ultimately changes the function of the protein. Changing pH can affect the charge of ionizable groups of amino acids. Amino acids make up polypeptide chains via peptide bonds. These peptide bonds are not affect by a change in pH, however the alpha amino group at the N-terminus of a polypeptide chain (the subunits of proteins), the alpha carboxyl group at the C-terminus of a polypeptide chain, and the ionizable R groups of acidic and basic amino acids, as well as the ionizable R groups of tyrosine and cysteine. pH is directly related to pKa, this is the amount of base require to react with half of the acid present. Which in this case means at which point the ionizable group will start to become primarily deprotonated. The alpha carboxyl group at the C-terminus has a pKa of 2.2, so whenever the pH is above around 3 every alpha carboxyl group will be deprotonated. The pH of a cell is 7 so most of the times the group has a negative charge. The alpha amino group at the N-terminus has a pKa of 9.5, so unless the pH goes above 9.5 this group will remain protonated with a positive charge which it almost always is in the cell. A lot of ionizable R groups have a pKa of around 6-10 so if the pH of a cell is significantly raised or lowered the R groups will become deprotonated or protonated. This will in turn affect the charges of these groups and disrupt the electrostatic interactions they are taking part in causing the protein to fold differently which alters the function of the protein.
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