As small devices are being integrated to the Internet, there is a growing interest toward technologies enabling this integration. Internet Engineering Task Force (IETF) has been developing technologies such as 6LoWPAN, 6TiSCH to reliably include small devices into the Internet. The goal of these efforts is to create the next generation Internet where the small devices can communicate with each other over the Internet without complex network gateways. This new concept, which is expected to connect billions of small devices to each other over the Internet, is called the Internet of Things (IoT). In this new global network, billions of small devices will be the source and the destination of a large portion of the Internet traffic. The Internet enabled embedded devices will have to face the security challenges of this new global network with limited resources. In this study, the protocols and mechanisms for securing IoT networks is analaysed at each layer of the protocol stack outlining challenges and possible solutions. Furthermore, the steps necessary for enabling a secure and dependable IoT is presented from the perspective of new protocols such as IETF 6LoWPAN and 6TiSCH.