Matrix space

Most of the NADH used in electron transport is produced in the mitochondrial matrix space, an appropriate site because NADH is oxidized by Complex I on the matrix side of the inner membrane. Furthermore, the inner mitochondrial membrane is impermeable to NADH. Recall, however, that NADH is produced in glycolysis by glyceraldehyde-3-P dehydrogenase in the cytosol. If this NADH were not oxidized to regenerate NAD, the glycolytic pathway would cease to function due to NAD limitation. Eukaryotic cells have a number of shuttle systems that harvest the electrons of cytosolic NADH for delivery to mitochondria without actually transporting NADH across the inner membrane (Figures 21.33 and 21.34). 

This process occurs in the mitochondria, organelles present in the cells of all multicellular organisms (see Figs 6.8 and 6.26). Mitochondria have two membranes. The invaginations of the internal membrane into the inner space of the organelle (matrix space) are termed crests (from the Latin, cristae). 

P. Mitchell (Nobel Prize for Chemistry, 1978) explained these facts by his chemiosmotic theory. This theory is based on the ordering of successive oxidation processes into reaction sequences called loops. Each loop consists of two basic processes, one of which is oriented in the direction away from the matrix surface of the internal membrane into the intracristal space and connected with the transfer of electrons together with protons. The second process is oriented in the opposite direction and is connected with the transfer of electrons alone. Figure 6.27 depicts the first Mitchell loop, whose first step involves reduction of NAD+ (the oxidized form of nicotinamide adenosine dinucleotide) by the carbonaceous substrate, SH2. In this process, two electrons and two protons are transferred from the matrix space. The protons are accumulated in the intracristal space, while electrons are transferred in the opposite direction by the reduction of the oxidized form of the Fe-S protein. This reduces a further component of the electron transport chain on the matrix side of the membrane and the process is repeated. The final process is the reduction of molecular oxygen with the reduced form of cytochrome oxidase. It would appear that this reaction sequence includes not only loops but also a proton pump, i.e. an enzymatic system that can employ the energy of the redox step in the electron transfer chain for translocation of protons from the matrix space into the intracristal space. 

The energy obtained by oxidation of the substrate with oxygen through the electron transport chain is thus accumulated as a difference in the electrochemical potential for H+ between the intracristal and matrix spaces. 

This can be used in several ways. H+-ATPase plays a key role in oxidative phosphorylation (ATP synthesis) as it transfers protons back into the matrix space with simultaneous synthesis of ATP (with temporary enzyme phosphorylation, cf. page 451). 

Fig. 32. Packing relations and steric fit of the 26 acetic acid (1 1) clathrate (isomorphous with the corresponding propionic acid clathrate of 26)1U- (a) Stereoscopic packing illustration acetic acid (shown in stick style) forms dimers in the tunnel running along the c crystal axis of the 26 host matrix (space filling representation, O atoms shaded), (b) Electron density contours in the plane of the acetic acid dimer sa First contour (solid line) is at 0.4 eA" while subsequent ones are with arbitrary spacings of either 0.5 and 1 eA 3. Density of the enclosing walls comes from C and H atoms of host molecules.

Mitochondria are the centers for oxidative phosphorylation and the respiratory centers of all cells. While usually aerobic, some mitochondria (e.g. in some bacteria), are known that function anaerobically. These organelles occur ubiquitously in the neuron and its processes (Figs 1-4, 1-6). Their overall shape may change from one type of neuron to another but their basic morphology is identical to that in other cell types. Mitochondria consist morphologically of double-membraned sacs surrounded by protuberances, or cristae, extending from the inner membrane into the matrix space [7]. 

Bovine heart cytochrome bci (PDB 1BE3 and PDB IBGY) as studied by Iwata et al. exists as a dimer in the asymmetric unit cell. Each monomer consists of 11 different polypeptide subunits (SU) with a total of -2165 amino acid residues and a molecular mass of -240 kDa. The protein subunits of the complex occupy three separate regions (1) the intermembrane space (p side) occupied by cytochrome Ci (subunit 4, SU4), the iron-sulfur protein (ISP, SU5) and subunit 8 (2) the transmembrane region occupied by cytochrome b (SU3), the transmembrane helices of cytochrome Ci and the ISP, and subunits 7,10, and 11 and (3) the matrix space (n side) occupied by two large core proteins (subunits 1 and 2) as well as subunits 6 and 9. Subunit 8 is often called the hinge protein and is thought to be essential for proper complex formation between cytochrome c (the exit point for some bci complex electrons) and... 

A third, clearer explanation of the electron transfer, proton translocation cycle is given by Saratse. Each ubiquinol (QH2) molecule can donate two electrons. A hrst QH2 electron is transferred along a high-potential chain to the [2Fe-2S] center of the ISP and then to cytochrome Ci. From the cytochrome Cl site, the electron is delivered to the attached, soluble cytochrome c in the intermembrane space. A second QH2 electron is transferred to the Qi site via the cytochrome b hemes, bL and bn. This is an electrogenic step driven by the potential difference between the two b hemes. This step creates part of the proton-motive force. After two QH2 molecules are oxidized at the Qo site, two electrons have been transferred to the Qi site (where one ubiquinone (Qio) can now be reduced, requiring two protons to be translocated from the matrix space). The net effect is a translocation of two protons for each electron transferred to cytochrome c. Each explanation of the cytochrome bci Q cycle has its merits and its proponents. The reader should consult the literature for updates in this ongoing research area. 

The tricarboxylic acid cycle not only takes up acetyl CoA from fatty acid degradation, but also supplies the material for the biosynthesis of fatty acids and isoprenoids. Acetyl CoA, which is formed in the matrix space of mitochondria by pyruvate dehydrogenase (see p. 134), is not capable of passing through the inner mitochondrial membrane. The acetyl residue is therefore condensed with oxaloacetate by mitochondrial citrate synthase to form citrate. This then leaves the mitochondria by antiport with malate (right see p. 212). In the cytoplasm, it is cleaved again by ATP-dependent citrate lyase [4] into acetyl-CoA and oxaloacetate. The oxaloacetate formed is reduced by a cytoplasmic malate dehydrogenase to malate [2], which then returns to the mitochondrion via the antiport already mentioned. Alternatively, the malate can be oxidized by malic enzyme" [5], with decarboxylation, to pyruvate. The NADPH+H formed in this process is also used for fatty acid biosynthesis. 

NADH oxidation via complex I takes place on the inside of the membrane—i. e., in the matrix space, where the tricarboxylic acid cycle and 3-oxidation (the most important sources of NADH) are also located. O2 reduction and ATP formation also take place in the matrix. 

Mitochondria are bacteria-sized organelles (about 1 X 2 im in size), which are found in large numbers in almost all eukaryotic cells. Typically, there are about 2000 mitochondria per cell, representing around 25% of the cell volume. Mitochondria are enclosed by two membranes—a smooth outer membrane and a markedly folded or tubular inner mitochondrial membrane, which has a large surface and encloses the matrix space. The folds of the inner membrane are known as cristae, and tube-like protrusions are called tubules. The intermembrane space is located between the inner and the outer membranes. 

Hydrocarbons yield more energy upon combustion than do most other organic compounds, and it is, therefore, not surprising that one important type of food reserve, the fats, is essentially hydrocarbon in nature. In terms of energy content the component fatty acids are the most important. Most aerobic cells can oxidize fatty acids completely to C02 and water, a process that takes place within many bacteria, in the matrix space of animal mitochondria, in the peroxisomes of most eukaryotic cells, and to a lesser extent in the endoplasmic reticulum. 

Quantitatively the major constituents of the matrix space are a large number of proteins. These account for about 56% by weight of the matrix material and exist in a state closer to that in a protein crystal than in a true solution.19-203 Mitochondrial membranes also contain proteins, both tightly bound relatively nonpolar intrinsic proteins and extrinsic proteins bound... 

Where within the mitochondria are specific enzymes localized One approach to this question is to see how easily the enzymes can be dissociated from mitochondria. Some enzymes come out readily under hypotonic conditions. Some are released only upon sonic oscillation, suggesting that they are inside the matrix space. Others, including the cytochromes and the flavoproteins that act upon succinate and NADH, are so firmly embedded in the inner mitochondrial membranes that they can be dissociated only through the use of non-denaturing detergents. 

In eukaryotic cells, electron transport and oxidative phosphorylation occur in mitochondria. Mitochondria have both an outer membrane and an inner membrane with extensive infoldings called cristae (fig. 14.2). The inner membrane separates the internal matrix space from the intermembrane space between the inner and outer membranes. The outer membrane has only a few known enzymatic activities and is permeable to molecules with molecular weights up to about 5,000. By contrast, the inner membrane is impermeable to most ions and polar molecules, and its proteins include the enzymes that catalyze oxygen consumption and formation of ATP. The role of mitochondria in 02 uptake, or respiration, was demonstrated in 1913 by Otto Warburg but was not fully confirmed until 1948, when Eugene Kennedy and Albert Lehninger showed that mitochondria carry out the reactions of the TCA cycle, the transport of electrons to 02, and the formation of ATP. 

NADH dehydrogenase is oriented in the inner membrane so that its binding site for NADH faces inwardly toward the matrix space (see fig. 14.8). This orientation is... 

In eukaryotes, most of the reactions of aerobic energy metabolism occur in mitochondria. An inner membrane separates the mitochondrion into two spaces the internal matrix space and the intermembrane space. An electron-transport system in the inner membrane oxidizes NADH and succinate at the expense of 02, generating ATP in the process. The operation of the respiratory chain and its coupling to ATP synthesis can be summarized as follows ... 

A suspension of mitochondria is incubated with pyruvate, malate, and l4C-labeled triphenylmethyl-phosphonium [TPP] chloride under aerobic conditions. The mitochondria are rapidly collected by centrifugation, and the amount of l4C that they contain is measured. In a separate experiment, the volume of the mitochondrial matrix space was determined so that the concentration of TPP cation in the matrix can be calculated. The internal concentration is found to be 1,000 times greater than that in the external solution. 

These organelles are the sites of energy production of aerobic cells and contain the enzymes of the tricarboxylic acid cycle, the respiratory chain, and the fatty acid oxidation system. The mitochondrion is bounded by a pair of specialized membranes that define the separate mitochondrial compartments, the internal matrix space and an intermembrane space. Molecules of 10,000 daltons or less can penetrate the outer membrane, but most of these molecules cannot pass the selectively permeable inner membrane. By a series of infoldings, the internal membrane forms cristae in the matrix space. The components of the respiratory chain and the enzyme complex that makes ATP are embedded in the inner membrane as well as a number of transport proteins that make it selectively permeable to small molecules that are metabolized by the enzymes in the matrix space. Matrix enzymes include those of the tricarboxylic acid cycle, the fatty acid oxidation system, and others. 

In mammalian cells, some 1% of the total cellular DNA is found in the mitochondria. This DNA is double stranded, circular, and small, with a molecular weight of about 10 million, which is in the same range as that of viral DNAs. Some four to ten molecules of DNA per mitochondrion, along with some ribosomes, are found in the matrix space. DNA replication, transcription, and synthesis of some mitochondrial proteins take place in the matrix space. This protein synthesis very much resembles that of bacteria. The mitochondrial genetic code differs from the "universal" genetic code (Chapter 12) used for nuclearly encoded proteins and bacteria. The reasons for this are unknown. 

The mitochondrial Ca2+ pool plays a second role in cellular Ca2+ homeostasis by serving as a sink for Ca2+ during times of excessive Ca2+ uptake by the cell. Under this circumstance, the non-ionic calcium pool in the matrix space can increase 10-fold or more, thereby protecting the cell from Ca2+ intoxication. This mechanism provides a temporary device by which the cell can protect itself, but in the long term only by regulating Ca2+ fluxes across the plasma membrane can the cell maintain Ca2+ homeostasis [14]. 

The two TOM-TIM23 pathways—the conservative sorting and stop-transfer pathways—differ in that the former posits a process in which the inner membrane protein is first fully imported into the matrix space and then inserted into the inner membrane from the matrix side using the Oxalp complex (Hell et al., 2001 Stuart and Neupert, 1996). This process is conservative in an evolutionary sense, since the prokaryotic ancestor of present-day mitochondria presumably inserted all their inner membrane proteins from the cytoplasmic (i.e., matrix) side of the membrane. 

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