Unit 6: Mitochondria and Peroxisomes PDF

Unit 6. Mitochondria and peroxisomes. SECTION II: CELL STRUCTURE AND FUNCTION. INDEX 6.1. Mitochondria 6.2. Peroxisomes 2  A fundamental activity of all cells is to generate metabolic energy. Mitochondria...

Unit 6. Mitochondria and peroxisomes. SECTION II: CELL STRUCTURE AND FUNCTION. INDEX 6.1. Mitochondria 6.2. Peroxisomes 2  A fundamental activity of all cells is to generate metabolic energy. Mitochondria: Peroxisomes: Responsible for generating most of the Contain enzymes that are involved in various useful energy derived from the breakdown metabolic pathways, including fatty acid of lipids and carbohydrates. breakdown and photorespiration. 3  Proteins destined for the mitochondria and peroxisomes are synthesized on the free ribosomes of the cytosol, except for the membrane proteins of the peroxisome Proteins are imported into their target organelles in the form of complete polypeptide chains. Mitochondria also contain their own genomes, which include some genes that are transcribed and translated in the organelle itself. 4 9.1. Mitochondria Organization and function of mitochondria Genetic system of mitochondria Mitochondrial diseases Protein internalization and mitochondria formation Mitochondrial lipids 5 Organization and function of mitochondria They are responsible for generating most of the useful energy derived from the degradation of carbohydrates and fatty acids, which is converted into ATP by the oxidative phosphorylation process. Most mitochondrial proteins are encoded by the nuclear genome and translated on free cytoplasmic ribosomes, and are incorporated from the cytosol into the organelle due to specific directing signals. They contain their own DNA, which codes for tRNA, rRNA, and some mitochondrial proteins. 6  Mitochondria are surrounded by a double membrane system, consisting of an inner and an outer mitochondrial membrane separated by an intermembrane space. The inner membrane forms numerous folds (cristae) that extend into the interior (or matrix) of the organelle. The matrix and the inner membrane are the main functional compartments of the mitochondria. Mitochondria are dynamic organelles: they fuse (fusion) with each other and divide (fission). 7 The matrix contains the mitochondrial genetic system as well as the enzymes responsible for the central reactions of oxidative metabolism. The main source of metabolic energy in animal cells is the oxidative breakdown of glucose and fatty acids. The initial stages of glucose metabolism (glycolysis) occur in the cytoplasm, where glucose is converted to pyruvate. Pyruvate is transported into the mitochondria, where its complete oxidation to CO2 produces most of the usable energy in the form of ATP. This involves the initial oxidation of pyruvate to acetyl CoA, which is subsequently degraded to CO2 through the citric acid cycle. The oxidation of fatty acids also produces acetyl CoA. Therefore, the enzymes of the citric acid cycle (located in the mitochondrial matrix) have a central role in the oxidative degradation of both carbohydrates and fatty acids. 8  The oxidation of acetyl CoA to CO2 is coupled with the reduction of NAD + and FAD to NADH and FADH2 respectively. Most of the energy derived from oxidative metabolism is produced by the oxidative phosphorylation process, which takes place in the inner mitochondrial membrane. The high-energy electrons from NADH and FADH2 are transferred to molecular oxygen through a series of membrane transporters. The energy derived from these electron transfer reactions is converted into accumulated potential energy in the form of a proton gradient across the inner membrane, which is used to drive ATP synthesis. 9  The fundamental role of the inner mitochondrial membrane is reflected in: a) Increase of its surface by the folding of its cristae; b) It contains 70% proteins, which are involved in oxidative phosphorylation, as well as in the transport of metabolites between the cytosol and the mitochondria; c) It is impermeable to most ions and small molecules, ensuring it maintains the proton gradient that drives oxidative phosphorylation. The outer mitochondrial membrane is completely permeable to small molecules. It contains a series of proteins called porins, which form channels that allow the free passage of molecules smaller than 1000 daltons. That is why the composition of the intermembrane space is similar to that of the cytosol, with respect to ions and small molecules. 10 Genetic system of mitochondria Mitochondria are believed to have evolved from bacteria that developed a symbiotic relationship living inside larger cells (endosymbiosis). The mitochondrial genome is made up of circular DNA molecules, present in several copies per organelle. They vary considerably in size between different species. It encodes a small number of proteins, but they are essential for the oxidative phosphorylation system. It encodes all the rRNAs and the tRNAs necessary for the translation of mitochondrial genes. Other mitochondrial proteins are encoded by nuclear genes, and these are thought to have been transferred to the nucleus from an ancestral mitochondrial genome. 11  The genomes of human mitochondria and most other animals are only 16 Kb, while yeast (80 Kb) and plants (200 Kb) are substantially larger, although they are predominantly made up of non-coding sequences. The human mitochondrial genome encodes 13 proteins involved in electron transport and oxidative phosphorylation. These genes are transcribed and translated within the same mitochondria, which contain their own ribosomes and tRNA. Human mitDNA codes for 16S and 12S rRNA, and for 22 tRNAs involved in the translation of the proteins encoded by mitDNA. Nuclear genes encode all the proteins necessary for transcription and translation, including mitochondrial RNA polymerase, ribosomal proteins, and transcription factors. 12 Biogenesis of the mitoribosome. The mitoribosome is composed of mitoribosomal proteins (MRPs) and RNAs, which are produced in the cytosol and mitochondria, respectively. The RNA components are derived from the transcription of mtDNA in nucleoids, followed by the RNA maturation in RNA granules. MRPs are synthesized by the 80S cytosolic ribosome and imported into the mitochondrial matrix through the mitochondrial import machinery (TOM and TIM proteins). Next, MRPs and rRNAs are assembled into the mitochondrial large subunit (mt-LSU) and the mitochondrial small subunit (mt-SSU). The complete 55S monosome is anchored to the inner mitochondrial membrane (IMM) and interacts with the translocase OXA1L. OMM-outer mitochondrial membrane. Lopez Sanchez, M.I.G.; Krüger, A.; Shiriaev, D.I.; Liu, Y.; Rorbach, J. Human Mitoribosome Biogenesis and Its Emerging Links to Disease. Int. J. Mol. Sci. 2021, 22, 3827. https://doi.org/10.3390/ijms22083827 13  The genetic code of mitDNA is slightly different from the universal genetic code used by eukaryotic and prokaryotic cells. 22 mitochondrial tRNAs are used in the translation of mitochondrial mRNAs, and in this case a single tRNA can recognize up to 4 codons (extreme form of “wobble”, the U in the anticodon pairs with any base in the third position of the codon). Furthermore, in the mitochondria some codons specify aa. other than those encoded by the universal code. 14 Mitochondrial diseases MitDNA can undergo mutations, which are generally The multiple copies of mtDNA contained in harmful to the organelle. Since almost all the the cells of an organism are often identical, mitochondria in the fertilized egg are supplied by the known as homoplasmy. However, when oocyte, germline mutations in mtDNA are transmitted there are mutations, the altered mtDNA by the mother. normally coexists, in different proportions, with the wild-type mtDNA, which is called heteroplasmy. 15 The proportion necessary for the disease to manifest varies depending on: the mutation the tissue the individual environmental factors physical exercise the nuclear genetic load itself In the most common mutations, the disease manifests itself at the cellular level if a threshold of 80-90% of mutated mitochondria is exceeded. The clinical phenotype depends on the ratio at the tissue level. Clinical spectrum of mitochondrial disease 16  Mitochondrial diseases have no cure Avoid transmisión to offspring Adoption Oocyte dnation Prenatal diagnosis Preimplantational diagnosis Mitochondrial replacement Mitochondrial replacement techniques They involve manipulation/destruction of embryos 17  Protein internalization and mitochondria formation Mammalian mitochondria contain about 1,500 proteins that are encoded by the nuclear genome of the cell: proteins required for the replication and expression of mtDNA, some mitochondrial proteins required for oxidative phosphorylation, and the enzymes involved in mitochondrial metabolism (acid cycle citric). The proteins encoded by the nuclear genes are synthesized by free ribosomes in the cytoplasm and transported as completed polypeptide chains. As the mitochondria have a double membrane system, protein import is more complex than in the case of a single phospholipid bilayer. Proteins directed to the mitochondrial matrix have to cross the outer and inner mitochondrial membrane, while other proteins have to be transported specifically to specific regions of the organelle (membranes, matrix, intermembrane space). There are several directing signals that will direct these proteins specifically to the different mitochondrial compartments. 18  The most studied leader sequences are the aminoterminal presequences. The presequences are made up of 15-55 positively charged aa. Proteins, through their presequences, bind to Tom complex, a protein complex on the surface of the mitochondria that directs their translocation through the outer membrane. These proteins are then transferred to a second protein complex in the inner membrane of the mitochondria , Tim23. Mitochondrial matrix proteins cross the inner membrane through Tim23 thanks to the electrochemical potential established across the inner mitochondrial membrane in electron transport. In contrast, proteins that contain a transmembrane sequence exit laterally from the Tim23 channel and insert into the inner membrane. Matrix processing peptidase (MPP) cleaves the presequence Protein entry into mitochondria requires chaperones. 19  Proteins can be targeted to the inner membrane not only by presequences Many of the inner membrane proteins are multipass transmembrane proteins that function as transporters to exchange ions and nucleotides between the mitochondria and the cytosol. These proteins do not contain presequences, but rather have multiple internal signals for introduction to the mitochondria. These proteins cross the outer membrane through the Tom complex, but instead of being transferred to Tim23, they are recognized by mobile cheperones (Tim9-Tim10) in the intermembrane space. These chaperones escort these proteins to the second translocase of the inner membrane (Tim22). The proteins are then partially translocated through Tim22 before internal transmembrane sequences cause them to exit the Tim22 pore laterally and insert into the inner membrane. 20  Other proteins in this membrane are encoded by the mitochondrial genome. These proteins are synthesized on the ribosomes of the mitochondrial matrix and target the Oxa1 translocase on the inner membrane. Proteins exit Oxa1 laterally to insert into the inner membrane. 21  Proteins destined for the outer membrane or intermembrane space are also introduced into the mitochondria through the Tom complex Many of the outer membrane proteins (eg porins) are Barrel β proteins that cross the Tom complex into the intermembrane space. These proteins are recognized by the mobile chaperones Tim9-Tim10, and transported to a second translocon complex called the SAM complex, which mediates their insertion to the outer membrane. Other outer membrane proteins with a-helix transmembrane domains are inserted into the membrane by the outer membrane protein Mim1. Proteins destined for the intermembrane space are recognized by specific chaperones once the proteins have exited the Tom complex. 22  Mitochondrial lipids Most of the lipids in the mitochondrial membranes are imported from the cytosol. They are synthesized in the ER and transported to the mitochondria. Mitochondria also synthesize phosphatidylethanolamine from phosphatidylserine. The mitochondria also catalyze the synthesis of cardiolipin, a rare phospholipid containing four fatty acid chains. Cardiolipin is located on the inner membrane of the mitochondria, where it acts to enhance the efficiency of oxidative phosphorylation, in Structure of cardiolipin. part by restricting the flow of protons across the It is a rare double phospholipid found in the inner membrane. mitochondrial membrane. 23  Lipid transfer between the ER and mitochondria occurs at close contact points between the ER and mitochondrial membranes, and is mediated by ER membrane phospholipid transfer proteins, which extract individual molecules from the ER membrane. The lipid can then be transported through the aqueous environment of the cytosol, immersed in a hydrophobic binding site on the protein, and released when the complex reaches a new membrane. Lipids are exchanged between the outer and inner mitochondrial membranes at the points of contact Outer mitocondrial membrane between them. Phospholipid transfer proteins. They extract phospholipid molecules from the ER membrane to the mitochondrial outer membrane 24 6.2. Peroxisomes Peroxisome functions Assembly of peroxisomes 25  Peroxisomes contain enzymes involved in various metabolic reactions They are small organelles (0,1-1 mm) surrounded by a membrane. They contain enzymes involved in various metabolic reactions Human cells contain between 100 and 1000 peroxisomes depending on cell activity. They do not have their own genome. All its proteins are synthesized in free ribosomes in the cell cytoplasm, only some come from the ER (the membrane ones). They can be replicated by division, or generated by the cell de novo. While many mitochondrial proteins resemble those of prokaryotes, reflecting their endosymbiotic origin, peroxisome proteins resemble typical eukaryotic proteins. 26  Peroxisomes contain more than 50 different enzymes involved in different metabolic pathways. In peroxisomes, oxidative reactions are carried out producing hydrogen peroxide. Since hydrogen peroxide is harmful to the cell, peroxisomes contain catalase, which breaks down hydrogen peroxide, either by forming water and oxygen or by oxidizing another organic compounds. Oxidation of fatty acids in peroxisomes. In peroxisomes, oxidation of uric acid, amino acids, and some fatty acids occurs, especially branched and very long-chain fatty acids. Fatty acids are also oxidized in the mitochondria. Peroxisomes are also involved in the synthesis of plasmalogens, a family of phospholipids in which one of the hydrocarbon chains is linked to glycerol through an ether bond, instead of an ester bond. They are important components in the membranes of some tissues (heart and Structure of plasmalogen brain). 27  In peroxisome assembly, internal peroxisomal proteins come from free ribosomes in the cytosol; while most of the transmembrane proteins come from the ER. Transmembrane proteins include many involved in metabolite transport and others called peroxins or Pex proteins. Most internal proteins target peroxisomes by the simple aa sequence Ser-Lis-Leu at their carboxyl terminus, (peroxisome targeting signal 1, or PTS1).Other internal proteins have positioning signals at the amino terminus, which are made up of 9 aa (peroxisome targeting signal 2, or PTS2). 28 Import of peroxisomal matrix proteins The positioning signals PTS1 and PTS2 are recognized by the peroxins Pex5 and Pex7 respectively. These peroxins are cytosolic receptors. E.g. PTS1-Pex5. The Pex5/protein complex first binds to an anchor complex consisting of 3 other peroxins (Pex13, Pex14, and Pex17) on the peroxisomal membrane. The protein enters the vesicle. Later Pex5 is recycled. 29 Import of some peroxisomal membrane proteins Some peroxisomal membrane proteins are also synthesized on free ribosomes, instead of being transported from the ER. These proteins have a peroxisome membrane targeting signal (mPTS), recognized by Pex19. Pex19/cargo complexes are recognized by Pex3 and Pex16 on the peroxisome membrane, and cargo proteins are inserted into the lipid bilayer. Then Pex19 is recycled to the cytosol. 30 Formation of new peroxisomes by budding from the ER Peroxisomes can be formed by two different mechanisms: budding of vesicles from the ER; and by division and growth. Peroxisome transmembrane proteins form budding vesicles from a specialized region of the ER called the peroxisomal ER. The vesicles produced in the peroxisomal ER do not contain a protein coat, are induced by peroxins and do not previously pass through the Golgi apparatus. For the formation of peroxisomes, several vesicles containing different classes of peroxins are required. 31  Formation of new peroxisomes by growth and division of the old ones New peroxisomes are produced more rapidly from the division of existing peroxisomes. 32