Isolate database performance on an instance I have SQL Server 2014 Standard Edition installed on a machine with two different users and two catalogs, each of them accessed by a different user (each user is strictly tied to his catalog).

Is it possible that a time consuming operation on a catalog slows down operations on the other? How can I avoid that?

The physical server machine has four cores assigned, so I assume SQL Server can use more than one of them, but I have not configured anything explicitly.
You're question is very broad.  But in general the answer is yes.  A single instance has to share resources across all databases unless configured specifically not to.
By default, SQL uses all available CPU's for all operations.  You can configure MAXDOP (max degree of parallelism) on the database so a single query will only have access to that many CPU's.
IO is another tricky issue.  Generally it's best to seperate your workloads on physical hardware whenever possible.  Logs, data and tempdb all on seperate physical storage.  In addition, if you are trying to create a seperation of resources for the databases, you can use filegroups to assign the objects or the entire database to a separate storage device.
There are many, many other answers but again.  The question of 'how can I avoid that?'(in terms of cross database resource allocation) is way too broad for a specific answer.  If you are looking at one aspect, say IO, or CPU usage, it's an easier, more specific answer.