I have a biochem exam this week so I have been using my thirty minutes of writing each day to go further in depth with topics that I don’t fully understand and want to get a better grasp on. I went to a review session for it to try and help me with some of the topics and one of the questions that the SI asked us really confused me. She asked if the pKa of an amino acid could change and then said the answer to the question was no. She started to explain why it was no then said the question didn’t make sense and scrapped it all together. I made a note of it and tried to figure it out when I got back home. It turns out that in fact the pKa of amino acids can be altered. That is the pKa of the R-group. The pKa’s get altered when a neighboring R-group, which is ionizable, has a similar pKa. This means that the R-groups will be similarly protonated at similar pH levels which means that they will have similar charges. This will cause the R-groups to repel each other and can alter the folding of a protein which will alter the structure. So if an amino acid like glutamic acid (pKa of 4.25) is located close to aspartic acid (pKa of 3.86) they will have the same negative charge at around the same pH. If they are in a cell at physiological pH of 7 they will both be fully deprotonated and have negative charges, this will cause the two groups to repel. Since aspartic acid has a lower pKa it will become deprotonated first and in an effort to prevent repulsion the pKa of glutamic acid will be raised so it doesn’t acquire a negative charge from deprotonation. This helps maintain protein structure.
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