Mitochondria Biogenesis, Gene Expression and Cellular Dynamics

Biological roles of mitochondria; morphology/appearance of mitochondria in cells and their dynamics. Structure/functions of mitochondrial membranes. Inner mitochondrial membrane (IMM) composition and permeability, electric potential properties. Transport processes across cell membranes. Mechanisms of mitochondrial biogenesis. Mitochondrial fusion and fission. Mitophagy. Contact sites between mitochondria and other organelles. Bioenergetics. Thermodynamic bases of chemical equilibrium. Stationary flux in a reaction sequence and thermodynamic force driving a reactive process. Redox processes and their thermodynamic relationships. The adenylate system: cellular energy charge and the concentration ratio of the adenylate pool. The adenylate system transfers and distributes energy from nutrient metabolism. ATP turnover in vivo. Redox coenzymes and the extraction/transfer of chemical energy in the cell. The OXidative PHOSphorylation (OXPHOS). Mitochondrial electron transport chain (ETC) complexes and carriers. The proton-motive force (Δp) generated by the ETC is the proton electrochemical potential across the IMM. Measuring the potentials in mitochondrial systems: use of fluorescent probes to estimate Δp from the IMM electrical potential (Δψ). The electrons move between redox centres by tunnel effect, allowing the complexes with multiple redox centres to direct electron transfers in a functional scheme. Redox reactions with the quinones/quinols in Complex II and III. The Q cycle. Superoxide formation in Complex III. Reactive oxygen species (ROS) generation in mitochondria and their detoxification by specific enzymes. “Not all ROS is evil”. COX catalytic cycle: redox-process coupled proton pumping generates the proton-motive force. The V complex or ATP synthase: rotational catalysis and models for coupling proton transfer and ATP synthesis. Subunit differences for ATP synthase from various organisms and dual-membrane organelles. Genomes in dual-membrane organelles. Mitochondrial DNA (mtDNA) evolution. Mammalian mtDNA. Genetic map of the human mtDNA. mtDNA packing in the nucleoid. mtDNA and maternal inheritance. A plausible mechanism to prevent exceptions to this almost inflexible rule. Biological reasons for uniparental inheritance of mtDNA and the ideal homoplasmy. The mitochondrial bottleneck in mammalian oogenesis. mtDNA mutation: heteroplasmy is a typical condition. mtDNA replication: alternative models. Mitochondrial transfer: cells share mitochondria by several mechanisms with relevant biological consequences. Mitochondrial proteome expression. Strand L and H transcription from HSP and LSP promoters: start, elongation, termination. Processing of primary transcripts from H and L strands. Nuclear genes coding for mitochondrial biogenesis components. Mitochondrial translation: mitoribosomes and translation cycle of a human mitoribosome. Import of cytoplasm-synthesized mitochondrial proteins: mitochondrial compartments and organizing complexes for nuclear-coded protein import. Coordinate expression of mitochondrial proteins: a kinetic study shows how the expression of the bigenomic system is synchronized. Assembly processes for multi-subunit protein OXPHOS complexes: Complex I. An almost complete model for the assembly pathway of Complex I. Super-complexes: the respirasome and its possible functional significance. Applying genome editing technologies to mitochondria: some perspectives for gene therapy of diseases caused by mtDNA mutations using ZFN (Zinc-Finger Nucleases) and (mito)TALEN (Transcriptional Activator-Like Effector Nucleases). Critical factors for utilizing CRISPR–Cas9 and –Cas12a systems in mtDNA editing: challenges in localizing guide RNAs into mitochondria and the issue of nuclease cleavage specificity. A new frontier of mtDNA editing CRISPR-free base editors, and their evolution. Local mitochondrial biogenesis in neuronal cells. Some experiments showing that mtDNA replication, mitochondrial fusion and fission occur in axons of peripheral neurons, wherein different organelles move RNA granules. mRNA for nuclear-encoded mitochondrial proteins reaches the neuron distal compartments, through late endosomes and ribonucleoprotein particles. Other studies indicate that, in neuronal axons or dendrites, RNA granules can move with lysosome by a tethering annexin. Some specific issues on mitochondrial and cellular energetics. Chemical energy transformed into heat: brown adipose tissue and its mechanisms, and other thermogenesis models. A brief discussion on reverse electron transport and Δp generation through ATP hydrolysis: some noteworthy exceptions. The Inhibitor Protein (IF1) blocking the hydrolytic activity on mitochondrial ATP synthase and its consequences. The Oligomycin Null-Point Test and its applications. Mitochondria and aging: an ever-growing issue in mitochondrial biology.