Mitochondria are eukaryotic organelles with a multitude of functions including biosynthesis of molecules and cellular regulation. Most prominently though is their role in energy conversion which culminates with the production of ATP, the universal molecular unit of currency. This is done through several metabolic pathways, including the pyruvate dehydrogenase bridging reaction, the citric acid cycle and the oxidative phosphorylation. In the latter pathway, electrons are transferred from electron carriers formed in the previous pathways and shuttled trough a chain of protein complexes (complex I – complex IV) via the mobile electron carriers coenzyme Q and cytochrome c. Collectively this is known as the respiratory chain. This process harnesses energy from the transferred electrons to translocate protons across the mitochondrial inner membrane, forming an electrochemical gradient that the ATP synthase uses to generate ATP. In this thesis we study parts of these metabolic pathways both structurally and functionally, using a combination of cryo-EM, biochemistry and cell biology. In the first project we used cryo-EM to solve the structure of the pyruvate dehydrogenase complex of E. coli, gaining new insight into how the flexible lipoyl-domain interacts with the active site of the core of the complex. We could determine that this interaction is mediated through electrostatic interaction formed between an acidic patch of amino acids of the lipoyl-domain and positively charged amino acids on the core. In the second project we again employed cryo-EM, this time to solve the structure of the yeast respiratory supercomplex, and for the first time we could obtain a near-atomic resolution structure of how complex III and complex IV in yeast interact with each other to form respiratory supercomplexes. Two forms of these higher order assemblies exist in the respiratory chain of yeast (CIII₂/CIV and CIII₂/CIV₂), which assembles very differently compared to the mammalian CI/CIII₂/CIV respirasome. The main interaction point of the yeast supercomplexes occurs between the subunits Cor1 and Cox5a. Through selective point mutations, we were able to disrupt this interaction and effectively hinder supercomplex formation in yeast. Using biochemistry and cell biology on such disrupted cells, we could determine that supercomplexes form to facilitate better diffusion of cytochrome c between the individual complexes of the supercomplex. In the third project we look at how manganese toxicity impacts the respiratory chain in yeast on a molecular level. By combining proteomics, biochemistry and metal analyses, we found that manganese overload causes mismetalation of Coq7, an essential subunit of the coenzyme Q synthesis pathway, which causes a loss of the electron carrier between complex II and complex III. This loss of coenzyme Q could be restored when cells were augmented with Coq7 overexpression, which restored functional respiration and prevented age-related cell death.