Paying your employer's national insurance and pension out of your personal allowance

Dear all, I recently started a MC Individual Fellowship at Imperial College. In my financial statement of allowance payments, it is clarified that every month I need to pay (i) a national insurance and (ii) a pension for my employer. The total of these two items is around 1000 GBP per month, more or less half for each item. Although I have asked around, I have not been able to understand why one needs to pay for your employer's national insurance and pension out of your personal allowance. I ask this considering that the university receives extra money per month for the administrative purposes of handling you around... Does anyone can explain this to me? Many thanks, Fernando