The Unbreakable Enterprise Kernel Release 2 (UEK R2) is Oracle's second major release of its heavily tested and optimized operating system kernel for Oracle Linux 5 and Oracle Linux 6. It is based on the mainline Linux 3.0 version 3.0.36. See the initial Oracle Unbreakable Enterprise Kernel Release 2 Release Notes (https://oss.oracle.com/ol6/docs/RELEASE-NOTES-UEK2-en.html) for a detailed description of the differences between UEK R2 and the first version of the Unbreakable Enterprise Kernel, which was based on Linux 2.6.32.
The 2.6.39-400.109.1 release is the fourth quarterly driver update release, which also includes bug and security fixes.
The version number displayed by the kernel and on the RPM packages is 2.6.39. This was done to avoid potential breakage of certain low-level utilities of the Oracle Linux distribution (also known as the plumbing) that potentially cannot cope with the new 3.x version scheme. Regular Linux applications are usually neither aware of nor affected by Linux kernel version numbers.