The pKa represents the pH of the medium at which the zwitterionic amino acid assumes most stable ionic form due to structural stabilization. As the pKa is dependent upon the environmental factors of the solution around the amino acids, a change in their structure and localization can cause change in the pKa of the protein. Thus, the answers can be found as below:
Part A: Decrease (As the lysine is basic in nature, it will tend to stabilize the electrostatic interaction and weak interactions between the acidic amino acids and hydrogen bonds in the viscinity, thus lowering the pH and hence pKa of the protein)
Part B: Increase (As the carboxyl group is acidic in nature, removal of it will tend to increase the pKa since the basic amino acids will tend to accumulate more negative charge in their viscinity)
Part C: Increase (As glutamic acid is an acidic amino acid, its shift from outside to a non-polar site will prevents its ionization and hence the pKa will tend to shift from slightly acidic to slightly basic, hence increase)
