Reference Article: https://technet.microsoft.com/en-us/library/cc978012.aspx

Port 3268. This port is used for queries specifically targeted for the global catalog. LDAP requests sent to port 3268 can be used to search for objects in the entire forest. However, only the attributes marked for replication to the global catalog can be returned. For example, a user’s department could not be returned using port 3268 since this attribute is not replicated to the global catalog.

Port 389. This port is used for requesting information from the local domain controller. LDAP requests sent to port 389 can be used to search for objects only within the global catalog’s home domain. However, the requesting application can obtain all of the attributes for those objects. For example, a request to port 389 could be used to obtain a user’s department.

The Schema Manager is used to specify additional attributes (i.e ThumbnailPhoto, Department…) that should be replicated to each global catalog server. The attributes included in the global catalog are consistent across all domains in the forest.

Effect of Global Catalog When Searching Back Links and Forward Links

Some Active Directory attributes cannot be located specifically by finding a row in the directory database. A back link is an attribute that can be computed only by referencing another attribute, called a forward link. An example of a back-link attribute is the memberOf attribute on a user object, which relies on the group attribute members to derive its values. For example, if you request the groups of which a specific user is a member, the forward link members , an attribute of the group object, is searched to find values that match the user name that you specified.

Because of the way that groups are enumerated by the Global Catalog, the results of a back-link search can vary, depending on whether you search the Global Catalog (port 3268) or the domain (port 389), the kind of groups the user belongs to (global groups vs. domain local groups), and whether the user belongs to groups outside the local domain. Connecting to the local domain does not locate the user’s group membership in groups outside the domain. Connecting to the Global Catalog locates the user’s membership in global groups but not in domain local groups because local groups are not replicated to the Global Catalog