For an amino acid, it's a little tricky because there are always at least two acidic/basic functional groups due to the backbone of the structure. The phrase "pH > pKa" makes no sense applied to an amino acid, because there are multiple pKas for multiple acidic/basic groups-- which one are you referring to? In general though, when pH > pKa for a certain functional group, it doesn't necessarily mean that the group is 100% deprotonated-- it just means that there's more of the deprotonated form in solution. Recall that the equation you can use to figure this out quantitatively for a weak acid is pH=pKa + log (A-/HA). Notice that if pH>pKa, then log(A-/HA) must be a positive term, meaning that [A-] > [HA] in solution.
What you might be trying to think of is when pH > pI of the amino acid, where pI refers to the isoelectric point (the pH at which the amino acid is electrically neutral). In this case, majority of amino acid in solution would be negatively charged, since the pH is basic relative to it's "balance point," the pI.
