The vast areas of applications for IoTs in future smart cities, smart transportation systems, and so on represent a thriving surface for several security attacks with economic, environmental and societal impacts. This survey paper presents a review of the security challenges of emerging IoT networks and discusses some of the attacks and their countermeasures based on different domains in IoT networks. Most conventional solutions for IoT networks are adopted from communication networks while noting the particular characteristics of IoT networks such as the nodes quantity, heterogeneity, and the limited resources of the nodes, these conventional security methods are not adequate. One challenge toward utilizing common secret key-based cryptographic methods in large-scale IoTs is the problem of secret key generation, distribution, and storage and protecting these secret keys from physical attacks. Physically unclonable functions (PUFs) can be utilized as a possible hardware remedy for identification and authentication in IoTs. Since PUFs extract the unique hardware characteristics, they potentially offer an affordable and practical solution for secret key generation. However, several barriers limit the PUFs' applications for key generation purposes. We discuss the advantages of PUF-based key generation methods, and we present a survey of state-of-the-art techniques in this domain. We also present a proof-of-concept PUF-based solution for secret key generation using resistive random-access memories (ReRAM) embedded in IoTs.