Where and how many times does encryption take place when we browse the internet?

I'm taking a cryptography course and what I've gathered so far is: PGP takes place at the application layer TLS takes place at the transport layer IPsec takes place in the network layer WPA2 Encryption takes place in the physical layer I understand the protocols and such but don't really get how they are used in practice. Do any one of the above protocols take place? Are they all used at the same time? For example say I'm sending an email to a friend. Will it first be encrypted with PGP by the application, then by TLS at the transport layer, then by IPsec in the network layer, and then by WPA2 in the physical layer? Or is any single one of the above done? Consider I'm sending an email over an HTTPS connection through a VPN and am connected to a router using WPA2. If encryption and decryption is happening multiple times is it safe to remove all but one of the above? If not what is the purpose of using each of them together?
http://dlvr.it/RzSy6h