Mitochondria protein

Of the very few variations in the genetic code that we know of, most occur in mitochondrial DNA (mtDNA), which encodes only 10 to 20 proteins. Mitochondria have their own tRNAs, so their code variations do not affect the much larger cellular genome. 

The mitochondria also contain small quantities of DNA, as well as RNA and ribosomes. Mitochondrial DNA encodes the synthesis of certain specific inner cell membrane proteins. Mitochondria can also divide during cell replication. 

The total concentration of Mn in the liver cell is about 35 iM, about 1/1000th that of magnesium. Free Mn occurs at about 0.2 to 1.0 iM in the liver cell. Loosely bound and freely exchangeable Mn occur at about 12. iM, with the rest of the ion occurring tightly bound to proteins. Mitochondria contain a concentration of Mn equivalent to 300 iM, about 1/100th that of mitochondrial magnesium (Senior et al, 1980). 

Proteomics based on the 2-DE approach, of course, suffers from problems associated with the analysis of membrane proteins, so that such mitochondrial proteins are poorly represented on 2-D profiles. In addition, many mitochondrial proteins are more basic than cytosolic proteins, mitochondria are rich in low molecular weight (<10 kDa) proteins, and mitochondrial proteins are poorly described in databases (Lescuyer et al.,... 

In order to synthesise proteins, mitochondria require ribosomes, together with a full complement of tRNAs. To use all of the codons, making allowance for wobble in the third position of the codon, it would be expected that 32 different tRNAs would be required. Mitochondrial translation apparatus has been found not only to have slightly different codon usage (see Table 8.5) but also to use a more extensive wobble ( superwobble ) than the cytoplasmic system, and this enables them to incorporate all the amino acids with only 22 tRNAs. 

A small proportion of human DNA is mtDNA contained within mitochondria that is involved in making some of the mitochondrial proteins. Mitochondria are thought to be the ghosts of ancient bacterial cells that, millions of years ago, established a symbiotic relationship (endosymbiosis) with what are now known as eukaryotic cells. As would be expected, mtDNA has a circular, double-stranded structure similar to prokaryotic DNA (Fig. 63.4). mtDNA is inherited maternally. This is because the sperm cells do not contribute mitochondria to the egg during fertilisation. 

Formation of subunits by limited proteolysis of precursor proteins Proteinase cuts precursor protein Mitochondrion Assembly of cytochrome oxidase from cytosolic precursor protein and mitochondrial subunits Restriction of proteolysis to site of cytochrome oxidase assembly... 

An electrophoresis gel of the bovine heart complex is shown in Figure 21.14. The total mass of the protein in the complex, composed of 13 subunits, is 204 kD. Subunits I through III, the largest ones, are encoded by mitochondrial DNA, synthesized in the mitochondrion, and inserted into the inner membrane from the matrix side. The smaller subunits are coded by nuclear DNA and synthesized in the cytosol. 

The mitochondrion has an outer and an inner membrane (Figure 1). The outer membrane contains pores formed from a protein, porin, which allow exchange of molecules with molecular weights up to about 2,000 between the cytosol and the intermembrane space. The inner membrane is extensively invaginated to increase its surface area. It has a different lipid composition from the outer membrane and is rich in the acidic phospholipid cardiolipin (diphosphatidyl-glycerol) which is only found in animal cells in mitochondria. Cardiolipin confers good electrical insulating properties on the inner membrane which is impermeable... 

Mitochondria have their own DNA (mtDNA) and genetic continuity. This DNA only encodes 13 peptide subunits synthesized in the matrix that are components of complexes I, III, IV, and V of the respiratory chain. Most mitochondrial proteins are synthesized on cytoplasmic ribosomes and imported by specific mechanisms to their specific locations in the mitochondrion (see below). 

Mitochondria are unique organelles in man and higher animals in that they contain their own genome. Mitochondrial DNA (mtDNA) in humans is a small (16.5 kb), circular genome that encodes only 13 proteins, 22 transfer RNA (tRNA), and 2 ribosomal RNA (rRNA) molecules. mtDNA is inherited only from the mother and is present in multiple copies within one mitochondrion. 

Energy-linked transhydrogenase, a protein in the inner mitochondrial membrane, couples the passage of protons down the electrochemical gradient from outside to inside the mitochondrion with the transfer of H from intramitochondrial NADH to NADPH for intramitochondrial enzymes such as glutamate dehydrogenase and hydroxylases involved in steroid synthesis. 

Pathways are compartmentalized within the cell. Glycolysis, glycogenesis, glycogenolysis, the pentose phosphate pathway, and fipogenesis occur in the cytosol. The mitochondrion contains the enzymes of the citric acid cycle, P-oxidation of fatty acids, and of oxidative phosphorylation. The endoplasmic reticulum also contains the enzymes for many other processes, including protein synthesis, glycerofipid formation, and dmg metabolism. 

Not all the cellular DNA is in the nucleus some is found in the mitochondria. In addition, mitochondria contain RNA as well as several enzymes used for protein synthesis. Interestingly, mitochond-rial RNA and DNA bear a closer resemblance to the nucleic acid of bacterial cells than they do to animal cells. For example, the rather small DNA molecule of the mitochondrion is circular and does not form nucleosomes. Its information is contained in approximately 16,500 nucleotides that func-tion in the synthesis of two ribosomal and 22 transfer RNAs (tRNAs). In addition, mitochondrial DNA codes for the synthesis of 13 proteins, all components of the respiratory chain and the oxidative phosphorylation system. Still, mitochondrial DNA does not contain sufficient information for the synthesis of all mitochondrial proteins most are coded by nuclear genes. Most mitochondrial proteins are synthesized in the cytosol from nuclear-derived messenger RNAs (mRNAs) and then transported into the mito-chondria, where they contribute to both the structural and the functional elements of this organelle. Because mitochondria are inherited cytoplasmically, an individual does not necessarily receive mitochondrial nucleic acid equally from each parent. In fact, mito-chondria are inherited maternally. 

Mitochondrial DNA is inherited maternally. What makes mitochondrial diseases particularly interesting from a genetic point of view is that the mitochondrion has its own DNA (mtDNA) and its own transcription and translation processes. The mtDNA encodes only 13 polypeptides nuclear DNA (nDNA) controls the synthesis of 90-95% of all mitochondrial proteins. All known mito-chondrially encoded polypeptides are located in the inner mitochondrial membrane as subunits of the respiratory chain complexes (Fig. 42-3), including seven subunits of complex I the apoprotein of cytochrome b the three larger subunits of cytochrome c oxidase, also termed complex IV and two subunits of ATPase, also termed complex V. 

In spite of the variety of appearances of eukaryotic cells, their intracellular structures are essentially the same. Because of their extensive internal membrane structure, however, the problem of precise protein sorting for eukaryotic cells becomes much more difficult than that for bacteria. Figure 4 schematically illustrates this situation. There are various membrane-bound compartments within the cell. Such compartments are called organelles. Besides the plasma membrane, a typical animal cell has the nucleus, the mitochondrion (which has two membranes see Fig. 6), the peroxisome, the ER, the Golgi apparatus, the lysosome, and the endosome, among others. As for the Golgi apparatus, there are more precise distinctions between the cis, medial, and trans cisternae, and the TGN trans Golgi network) (see Fig. 8). In typical plant cells, the chloroplast (which has three membranes see Fig. 7) and the cell wall are added, and the lysosome is replaced with the vacuole. 

A variety of protein import pathways into the vacuole are known (Burd et al., 1998 Bryant and Stevens, 1998). It includes the sorting from the Golgi apparatus, endocytosis, autophagy (where a part of the cytoplasm such as a mitochondrion is engulfed into a newly formed vacuole and is degraded), direct import from the cytosol, and the vacuolar inheritance from the mother cell. Of these, the pathways from the Golgi... 

Ered Sanger, a double Nobel Prize winner, sequenced the human mitochondrial genome back in 1981. This genome codes for 13 proteins and the mitochondrion possesses the genetic machinery needed to synthesize them. Thus, the mitochondria are a secondary site for protein synthesis in eukaryotic cells. It turns out that the 13 proteins coded for by the mitochondrial genome and synthesized in the mitochondria are critically important parts of the complexes of the electron transport chain, the site of ATP synthesis. The nuclear DNA codes for the remainder of the mitochondrial proteins and these are synthesized on ribosomes, and subsequently transported to the mitochondria. 

It is important to appreciate that this principle of coupling-in-series underlies all biochemical pathways or processes, e.g. glycolysis, generation of ATP in the mitochondrion, protein synthesis from amino acids or a signal transduction pathway. Indeed, despite the fundamental importance of signalling pathways in biochemistry, a thermodynamic analysis of such a pathway has never been done, but the principles outlined above must apply even to signalling pathways. 

Figure 7.8 Comparison of oxygen transport from lung to a cell and then into a mitochondrion with fatty acid transport from an adipocyte to a cell and then into the mitochondria in various tissues/ organs. Fatty add is transported in blood bound to albumin, oxygen is transported in blood bound to haemoglobin. Fatly add is transported within the cell attached to the fatty acid-binding protein (BP), oxygen is transported within a cell attached to myoglobin (Mb). Alb represents albumin, Hb haemoglobin.

This zinc-dependent enzyme [EC 3.4.24.59] of the peptidase M3 family catalyzes the hydrolysis of a peptide bond such that there is a release of an N-terminal octa-peptide at the second stage of processing of some proteins imported into the mitochondrion. The natural substrates are precursor proteins that already have been processed by the mitochondrial processing peptidase. 

Oxidizible substrates from glycolysis, fatty acid or protein catabolism enter the mitochondrion in the form of acetyl-CoA, or as other intermediaries of the Krebs cycle, which resides within the mitochondrial matrix. Reducing equivalents in the form of NADH and FADH pass electrons to complex I (NADH-ubiquinone oxidore-ductase) or complex II (succinate dehydrogenase) of the electron transport chain, respectively. Electrons pass from complex I and II to complex III (ubiquinol-cyto-chrome c oxidoreductase) and then to complex IV (cytochrome c oxidase) which accumulates four electrons and then tetravalently reduces O2 to water. Protons are pumped into the inner membrane space at complexes I, II and IV and then diffuse down their concentration gradient through complex V (FoFi-ATPase), where their potential energy is captured in the form of ATP. In this way, ATP formation is coupled to electron transport and the formation of water, a process termed oxidative phosphorylation (OXPHOS). 

In this model, cellular stress mediates the release of cytochrome C from the mitochondrion. The proapoptotic proteins Bax and BH3 proteins support the release of cytochrome C, while the antiapoptotic Bcl2 protein has an inhibitory effect. Cytosolic cytochrome C binds to the cofactor Apaf 1, which then associates via its CARD motif with procaspase 9 to a complex termed apopto-some. In this complex, procaspase 9 is processed to the mature caspase which subsequently activates downstream effector caspases and commits the cell to death. 

Protein trafficking has been extensively studied in fungi and mammals, and a number of elaborate machines have been described that specifically import certain proteins into typical eukaryotic organelles such as the nucleus, the endoplasmic reticulum and the mitochondrion. 

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