Are the commas optional?

No. You need both.

Eats shoots and leaves.

Eats, shoots and leaves.

I feel better now.

Fortunately, she has been around too long to be so easily confused.

Glad you were able to get out of your system.

"whose mother is a teacher" is in commas because it's a clause that's not critical to the point of the sentence which is is that Johnathon is my best friend. Another example:

That blue house on the corner, which was renovated last year, is the house where I grew up.