The document discusses various application layer protocols including SMTP, POP3, IMAP4, DNS, and FTP, detailing their functions, characteristics, and commands. SMTP is highlighted for its role in sending emails, while POP3 and IMAP4 are explained as protocols for retrieving emails, with IMAP4 offering more advanced features. Additionally, the document covers DNS for domain name resolution and FTP for file transfers, emphasizing their respective port numbers and operational modes.