Modifying Base Permissions in SharePoint Online

Hi, 

I am new to SharePoint and trying to understand the security model of SharePoint 2013. As far as I understand, Base Permissions in SharePoint cannot be modified either via UI or via APIs. However, Permissions levels (combination of base permissions) can be modified either ways. 

If the Base Permissions can really be modified, how can it be done using the REST APIs?

Thanks,

Vibhuti