Ubiquitin is a highly conserved 76 amino acid protein which is a unique and versatile signalling molecule. Ubiquitin can be attached by an isopeptide bond between its C-terminal diglycine to a lysine residue of a target substrate. However, it can also bind to itself though one of its own seven lysine residues allowing the formation of different chain types. These chains act as signals for different pathways, such as DNA damage repair, and in particular lysine-48 chains signal for proteins to be degraded via the proteasome by the ubiquitin proteasome system (UPS). This allows cells to control the concentration of proteins which is important in triggering cellular events, such as cyclin levels in cell division. Whilst old and incorrect proteins need to be removed so they do not interfere with normal processes. In order to recognise and ubiquitinate substrates an enzyme cascade has evolved. Ubiquitin is transferred from an ubiquitin activation enzyme (E1) to an ubiquitin conjugating enzyme (E2). The E2 which along with a ubiquitin ligase (E3) ubiquitinates a specific substrate. Research has focused on the E3 ligases since they are responsible for identifying substrates. One important ligase is the anaphase promoting complex/cyclosome (APC/C) which is responsible for faithful segregation of chromosome during mitosis. Failure to regulate this process can lead to aneuploidy, one of the main causes of cancer. It is therefore important to understand the function and regulation of APC/C and the UPS. This work firstly shows that four S. pombe kinases, Ssp2, Ppk9, Kin1 and Chk1 all contain a kinase associated 1 (KA1) or KA2 domain which they use to interact specifically with APC/C when it contained an unphosphorylated form of a subunit called Cut9. Yeast two hybrid and native far Westerns demonstrated that the KA domains interact with the APC/C co activator Slp1. Phosphorylation assays showed that three of these kinases phosphorylated a ~30kDa band of the APC/C complex which was shown to be Mad2, an important subunit of the APC/C inhibitor complex the mitotic checkpoint complex (MCC). These finding suggest a new role for KA contain kinases as regulators of APC/C activity. Future studies to identify the residues of Mad2 which are phosphorylated by these kinases, as well as the binding site of Slp1 that the KA domains recognise, would provide a more detailed understanding of the molecular mechanisms involved in regulating APC/C activity. Secondly, this study investigated the role of the ubiquitin associated (UBA) domains in the S. pombe shuttle factor Rhp23. This protein can recognise the proteasome via an ubiquitin like (UBL) domain and ubiquitin chains via one of two UBA domains: an internal UBA1 and a C-terminal UBA2. To dissect the different functions of these two UBA domains point mutations were made that abolished the domains ability to recognise ubiquitin without altering the protein structure. The minimal domains and full length domains were tested in vitro and in vivo. These surprising results showed that the domains act differently in isolation when compared to the full length protein. They also demonstrate that the UBA1 domain is responsible for ubiquitin recognition in Rhp23, whilst the UBA2 domain appears to have little to no binding ability.