Mitochondrial

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Electron micrograph of a mitochondrion showing its mitochondrial matrix and membranes

In cell biology, a mitochondrion (plural mitochondria) is a membrane-enclosed organelle that is found in most eukaryotic cells.^[1] Mitochondria are sometimes described as "cellular power plants," because they generate most of the cell's supply of ATP, used as a source of chemical energy. In addition to supplying cellular energy, mitochondria are involved in a range of other processes, such as cell signaling, cellular differentiation, apoptosis, as well as the control of the cell cycle and cell growth.^[2] The number of mitochondria in a cell varies widely by organism and tissue type. Many cells possess only a single mitochondrion, whereas others can contain several thousand mitochondria.^[3]^[4]

Although most of a cell's DNA is contained in the cell nucleus, the mitochondrion has its own independent genome. This DNA shows similarity to bacterial genomes, and, according to the endosymbiotic theory, mitochondria are descended from free-living prokaryotes. The word mitochondrion comes from the Greek μίτος or mitos, thread + χονδρίον or khondrion, granule.

Mitochondrion structure

A mitochondrion contains inner and outer membranes composed of phospholipid bilayers and proteins. The two membranes, however, have different properties. Because of this double-membraned organization, there are 5 distinct compartments within the mitochondrion. There is the outer membrane, the intermembrane space (the space between the outer and inner membranes), the inner membrane, the cristae space (formed by infoldings of the inner membrane), and the matrix (space within the inner membrane). Mitochondria range from 1 to 10 micrometers (μm) in size.

Outer membrane

Main article: Outer mitochondrial membrane

The outer mitochondrial membrane, which encloses the entire organelle, has a protein-to-phospholipid ratio similar to that of the eukaryotic plasma membrane (about 1:1 by weight). It contains numerous integral proteins called porins.

Intermembrane space

The intermembrane space is the space between the outer membrane and the inner membrane.

Inner membrane

See also Inner mitochondrial membrane

The inner mitochondrial membrane contains proteins with four types of functions: <ref name = "Alberts" />

Those that carry out the oxidation reactions of the respiratory chain.
ATP synthase, which makes ATP in the matrix.
Specific transport proteins that regulate the passage of metabolites into and out of the matrix.
Protein import machinery.

It contains more than 100 different polypeptides, and has a very high protein-to-phospholipid ratio (more than 3:1 by weight, which is about 1 protein for 15 phospholipids). In addition, the inner membrane is rich in an unusual phospholipid, cardiolipin. This phospholipid was originally discovered in beef hearts in 1942, and is usually characteristic of mitochondrial and bacterial plasma membranes.^[5] Unlike the outer membrane, the inner membrane does not contain porins, and is highly impermeable; almost all ions and molecules require special membrane transporters to enter or exit the matrix. In addition, there is a membrane potential across the inner membrane.

The inner mitochondrial membrane is compartmentalized into numerous cristae, which expand the surface area of the inner mitochondrial membrane, enhancing its ability to generate ATP. In typical liver mitochondria, for example, the surface area, including cristae, is about five times that of the outer membrane. Mitochondria of cells that have greater demand for ATP, such as muscle cells, contain more cristae than typical liver mitochondria.

Mitochondrial matrix

See also mitochondrial matrix

Image of cristae in rat liver mitochondrion

The matrix is the space enclosed by the inner membrane. The matrix is important in the production of ATP with the aid of the ATP synthase contained in the inner membrane. The matrix contains a highly-concentrated mixture of hundreds of enzymes, in addition to the special mitochondrial ribosomes, tRNA, and several copies of the mitochondrial DNA genome. Of the enzymes, the major functions include oxidation of pyruvate and fatty acids, and the citric acid cycle.<ref name = "Alberts" />

Mitochondria possess their own genetic material, and the machinery to manufacture their own RNAs and proteins. (See: protein synthesis). A published human mitochondrial DNA sequence revealed 16,569 base pairs encoding 37 total genes, 24 tRNA and rRNA genes and 13 peptide genes.^[6] The 13 mitochondrial peptides in humans are integrated into the inner mitochondrial membrane, along with proteins encoded by genes that reside in the host cell's nucleus.

Mitochondrial functions

Although it is well known that the mitochondria convert organic materials into cellular energy in the form of ATP, mitochondria play an important role in many metabolic tasks, such as:

Apoptosis-programmed cell death
Glutamate-mediated excitotoxic neuronal injury
Cellular proliferation
Regulation of the cellular redox state
Heme synthesis
Steroid synthesis

Some mitochondrial functions are performed only in specific types of cells. For example, mitochondria in liver cells contain enzymes that allow them to detoxify ammonia, a waste product of protein metabolism. A mutation in the genes regulating any of these functions can result in mitochondrial diseases.

Energy conversion

A dominant role for the mitochondria is the production of ATP, as reflected by the large number of proteins in the inner membrane for this task. This is done by oxidizing the major products of glycolysis: pyruvate and NADH that are produced in the cytosol. This process of cellular respiration, also known as aerobic respiration, is dependent on the presence of oxygen. When oxygen is limited, the glycolytic products will be metabolised by anaerobic respiration, a process that is independent of the mitochondria. The production of ATP from glucose has an approximately 13-fold higher yield during aerobic respiration compared to anaerobic respiration.^[7]

Pyruvate: the citric acid cycle

Main articles: pyruvate decarboxylation and citric acid cycle

Each pyruvate molecule produced by glycolysis is actively transported across the inner mitochondrial membrane, and into the matrix where it is oxidized and combined with coenzyme A to form CO₂, acetyl-CoA and NADH.

The acetyl-CoA is the primary substrate to enter the citric acid cycle , also known as the tricarboxylic acid (TCA) cycle or Krebs cycle. The enzymes of the citric acid cycle are located in the mitochondrial matrix, with the exception of succinate dehydrogenase, which is bound to the inner mitochondrial membrane. The citric acid cycle oxidizes the acetyl-CoA to carbon dioxide, and, in the process, produces reduced cofactors (three molecules of NADH and one molecule of FADH₂) that are a source of electrons for the electron transport chain, and a molecule of GTP (that is readily converted to an ATP).

NADH and FADH₂: the electron transport chain

Main articles: Electron transport chain and Oxidative phosphorylation

The redox energy from NADH and FADH₂ is transferred to oxygen (O₂) in several steps via the electron transport chain. These energy-rich molecules are produced within the matrix via the citric acid cycle, but are also produced in the cytoplasm by glycolysis; reducing equivalents from the cytoplasm can be imported via the malate-aspartate shuttle system of antiporter proteins or feed into the electron transport chain using a glycerol phosphate shuttle. Protein complexes in the inner membrane (NADH dehydrogenase, cytochrome c reductase and cytochrome c oxidase) perform the transfer and the incremental release of energy is used to pump protons (H⁺) into the intermembrane space. This process is efficient, but a small percentage of electrons may prematurely reduce oxygen, forming reactive oxygen species such as superoxide. This can cause oxidative stress in the mitochondria and may contribute to the decline in mitochondrial function associated with the aging process.^[8]

As the proton concentration increases in the intermembrane space, a strong electrochemical gradient is established across the inner membrane. The protons can return to the matrix through the ATP synthase complex, and their potential energy is used to synthesize ATP from ADP and inorganic phosphate (P_i). This process is called chemiosmosis, and was first described by Peter Mitchell^[9]^[10] who was awarded the 1978 Nobel Prize in Chemistry for his work. Later, part of the 1997 Nobel Prize in Chemistry was awarded to Paul D. Boyer and John E. Walker for their clarification of the working mechanism of ATP synthase.

Heat production

Under certain conditions, protons can re-enter the mitochondrial matrix without contributing to ATP synthesis. This process is known as proton leak or mitochondrial uncoupling and is due to the facilitated diffusion of protons into the matrix. This process results in the unharnessed potential energy of the proton electrochemical gradient being released as heat. The process is mediated by a proton channel called thermogenin, or UCP1.^[11] Thermogenin is a 33kDa protein first discovered in 1973.^[12] Thermogenin is primarily found in brown adipose tissue, or brown fat, and is responsible for non-shivering thermogenesis. Brown adipose tissue is found in mammals, and is at its highest levels in early life and in hibernating animals. In humans, brown adipose tissue is present at birth and decreases with age.^[11]

Storage of calcium ions

The concentrations of free calcium in the cell can regulate an array of reactions and is important for signal transduction in the cell. Mitochondria store calcium, a process that is one important event for the homeostasis of calcium in the cell. Release of this calcium back into the cell's interior can initiate calcium spikes or waves. These events coordinate processes such as neurotransmitter release in nerve cells and release of hormones in endocrine cells.

Mitochondrial dysfunction and disease

With their central place in cell metabolism, damage and dysfunction in mitochondria is an important factor in a wide range of human diseases. These diseases include schizophrenia, Bipolar disorder, dementia, Alzheimer's disease, Parkinson's disease, epilepsy, strokes, heart disease, retinitis pigmentosa, and diabetes.^[13]^[14] The common thread linking these seemingly-unrelated conditions is cellular damage causing oxidative stress and the accumulation of reactive oxygen species. These oxidants then damage the mitochondrial DNA, resulting in mitochondrial dysfunction and cell death.^[14]

Mutations in mitochondrial DNA can also be inherited, causing genetic disorders such as dominant optic atrophy, Friedreich's ataxia, hereditary spastic paraplegia, and Wilson's disease.^[15] Environmental influences may also interact with hereditary predispositions and cause mitochondrial disease; an example of this is the possible role of pesticide exposure in causing some individuals to develop Parkinson's disease.^[16]^[17]

Origin

Main article: Endosymbiotic theory

As mitochondria contain ribosomes and DNA, and are formed only by the division of other mitochondria, it is generally accepted that they were originally derived from endosymbiotic prokaryotes. Studies of mitochondrial DNA, which is often circular and employs a variant genetic code, show that their ancestor, the so-called proto-mitochondrion, was a member of the Proteobacteria.^[18] In particular, the pre-mitochondrion was probably related to the rickettsias, although the exact position of the ancestor of mitochondria among the alpha-proteobacteria remains controversial. The endosymbiotic hypothesis suggests that mitochondria descended from specialized bacteria (probably purple non-sulfur bacteria) that somehow survived endocytosis by another species of prokaryote or some other cell type, and became incorporated into the cytoplasm. The ability of symbiont bacteria to conduct cellular respiration in host cells that had relied on glycolysis and fermentation would have provided a considerable evolutionary advantage. Similarly, host cells with symbiotic bacteria capable of photosynthesis would also have an advantage. In both cases, the number of environments in which the cells could survive would have been greatly expanded.

This relationship developed at least 2 billion years ago, and mitochondria still show some signs of their ancient origin. Mitochondrial ribosomes in mammals are the 70S (bacterial) type, in contrast to the 80S ribosomes found elsewhere in the cell.<ref name=O'Brien>O'Brien TW (2003 Sep). "Properties of human mitochondrial ribosomes.". IUBMB Life. 55 (9): 505-13. .

A few groups of unicellular eukaryotes lack mitochondria: the microsporidians, metamonads, and archamoebae.^[19] These groups appear as the most primitive eukaryotes on phylogenetic trees constructed using rRNA information, suggesting that they appeared before the origin of mitochondria. However, this is now known to be an artifact of long branch attraction — they are apparently derived groups and retain genes or organelles derived from mitochondria (e.g., mitosomes and hydrogenosomes).<ref name="mitosomes" /> There are no primitively amitochondriate eukaryotes, and so the origin of mitochondria may have played a critical part in the development of eukaryotic cells.

Mitochondrial genome

One mitochondrion can contain 2-10 copies of its DNA.^[20] As in prokaryotes, there is a very high proportion of coding DNA, and an absence of repeats. Mitochondrial genes are transcribed as multigenic transcripts, which are cleaved and polyadenylated to yield mature mRNAs. Not all necessary proteins, however, are encoded by the mitochondrial genome; most are coded by genes in the cell nucleus and imported to the mitochondrion.^[21] Unlike their nuclear cousins, mitochondrial genes are small, and many chromosomes are circular, conforming to the bacterial pattern. In humans, mitochondrial genes lack introns,^[21] yet other Eukaryotic mitochondrial DNA has 1-37 of them.

While slight variations on the standard code had been predicted earlier,^[22] none were discovered until 1979, when researchers studying human mitochondrial genes discovered they used an alternative code. Many slight variants have been discovered since,^[23] including various alternative mitochondrial codes,^[24] Further, the AUA, AUC, and AUU are each allowable start codons.

Exceptions to the universal genetic code (UGC) in mitochondria
Organism	Codon	Standard	Novel
Mammalian	AGA, AGG	Arginine	Stop codon
	AUA	Isoleucine	Methionine
	UGA	Stop codon	Tryptophan
Drosophila	AGA, AGG	Arginine	Serine
	AUA	Isoleucine	Methionine
	UGA	Stop codon	Tryptophan
Yeast	AUA	Isoleucine	Methionine
	UGA	Stop codon	Tryptophan
	CUA, CUC, CUG, CUU	Leucine	Threonine
Higher plant	UGA	Stop codon	Tryptophan
Higher plant	CGG	Arginine	Tryptophan

Pseudo changes in the DNA genetic code are also seen due to the phenomenon of RNA editing, which is common in mitochondria. In higher plants it was thought that CGG encoded for tryptophan and not arginine; however, it was discovered that the processed RNA from these genes does have the UGG codon, consistent with the universal genetic code. ^[25]

Mitochondrial genomes have many fewer genes than do the related eubacteria from which they are thought to be descended. Although some have been lost altogether, many have been transferred to the nucleus. This is thought to be relatively common over evolutionary time. A few organisms, such as the Cryptosporidium, actually have mitochondria that lack any DNA, presumably because all their genes have been either lost or transferred.^[26] In Cryptosporidium, the mitochondria have an altered ATP generation system that renders the parasite resistant to many classical mitochondrial inhibitors such as cyanide, azide, and atovaquone.^[26]

Replication and gene inheritance

See also: mitochondrial genome

Mitochondria replicate their DNA and divide mainly in response to the energy needs of the cell; in other words, their growth and division is not linked to the cell cycle. When the energy needs of a cell are high, mitochondria grow and divide. When the energy use is low, mitochondria are destroyed or become inactive. At cell division, mitochondria are distributed to the daughter cells more or less randomly during the division of the cytoplasm. Mitochondria divide by binary fission similar to bacterial cell division. Unlike bacteria, however, mitochondria can also fuse with other mitochondria.

Mitochondrial genes are not inherited by the same mechanism as nuclear genes. At fertilization of an egg by a sperm, the egg nucleus and sperm nucleus each contribute equally to the genetic makeup of the zygote nucleus. In contrast, the mitochondria, and therefore the mitochondrial DNA, usually comes from the egg only. The sperm's mitochondria enters the egg, but are almost always destroyed and do not contribute their genes to the embryo.^[27] Paternal sperm mitochondria are marked with ubiquitin to select them for later destruction inside the embryo.^[28] The egg contains relatively few mitochondria, but it is these mitochondria that survive and divide to populate the cells of the adult organism. Mitochondria are, therefore, in most cases inherited down the female line.

This maternal inheritance of mitochondrial DNA is seen in most organisms, including all animals. However, mitochondria in some species can sometimes be inherited through the father. This is the norm among certain coniferous plants, although not in pines and yew trees.^[29] It has been suggested to occur at a very low level in humans.^[30]

Uniparental inheritance means that there is little opportunity for genetic recombination between different lineages of mitochondria, although a single mitochondrion can contain 2-10 copies of its DNA.^[20] For this reason, mitochondrial DNA usually is thought of as reproducing by binary fission; what recombination that takes place is to maintain genetic integrity rather than to maintain diversity. However, there are several studies showing evidence of recombination in mitochondrial DNA. The enzymes necessary for recombination clearly are present in mammalian cells.^[32] Further, evidence suggests that animal mitochondria can undergo recombination.^[33] The data are a bit more controversial in humans, although, indirect evidence exists.^[34]^[35] If recombination does not occur, the whole mitochondrial DNA sequence represents a single haplotype, which makes it useful for studying the evolutionary history of populations.

The uniparental inheritance of mitochondria is thought to result in intragenomic conflict, such as seen in the petite mutant mitochondria of some yeast species. It is possible that the evolution of separate male and female sexes is a mechanism to resolve this organelle conflict.

Use in population genetic studies

Main article: Human mitochondrial genetics

The near-absence of genetic recombination in mitochondrial DNA makes it a useful source of information for scientists involved in population genetics and evolutionary biology. Because all the mitochondrial DNA is inherited as a single unit, or haplotype, the relationships between mitochondrial DNA from different individuals can be represented as a gene tree. Patterns in these gene trees can be used to infer the evolutionary history of populations. The classic example of this is in human evolutionary genetics, where the molecular clock can be used to provide a recent date for mitochondrial Eve.^[36] This is often interpreted as strong support for a recent modern human expansion out of Africa.^[37] Another human example is the sequencing of mitochondrial DNA from Neanderthal bones. The relatively large evolutionary distance between the mitochondrial DNA sequences of Neanderthals and living humans has been interpreted as evidence for lack of interbreeding between Neanderthals and anatomically-modern humans.^[38]

However, mitochondrial DNA reflects the history of only females in a population, and so may not represent the history of the population as a whole. For example, mitochondrial studies will not pick up if dispersal is primarily undertaken by males. This can be partially overcome by the use of patrilineal genetic sequences, if they are available (in mammals the non-recombining region of the Y-chromosome provides such a source). In a broader sense, only studies that also include nuclear DNA can provide a comprehensive evolutionary history of a population; as a result, genetic recombination means that these studies can be difficult to analyze.

Fiction

The midi-clorians of the Star Wars universe are fictional life-forms inside cells that provide the Force. George Lucas took inspiration from the endosymbiotic theory.
Madeleine L'Engle's novel A Wind in the Door posits fictional "farandolae," which are to mitochondria what mitochondria are to cells.
In Hideaki Sena's novel Parasite Eve (and the video game based on it), mitochondria are independent organisms, using animals and plants as a form of "transportation," causing a major biological disaster when they decide to set themselves free.

References

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External links

"For Arthropod Mitochondria, Variety in the Genetic Code Is Standard" at PLoS — Public Library of Science
Mitochondria Atlas at University of Mainz
Mitochondria Research Portal at mitochondrial.net
Mitochondria: Architecture dictates function at cytochemistry.net
Mitochondria links at University of Alabama
Mitochondrion Reconstructed by Electron Tomography at San Diego State University
Review of evidence addressing whether mitochondria form cellular networks or exist as discrete organelles at ELSO
Video Clip of Rat-liver Mitochondrion from Cryo-electron Tomography at wadsworth.org
Information on Mitochondrial Diseases at circuitblue.com
Mitochondria and Aging at circuitblue.com
3D structures of proteins from inner mitochondrial membrane at University of Michigan
3D structures of proteins associated with outer mitochondrial membrane at University of Michigan

Function and structure

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Cristae (singular crista) are the internal compartments formed by the inner membrane of a mitochondrion. They are studded with proteins, including ATP synthase and a variety of cytochromes. The maximum surface for chemical reactions to occur within the mitochondria.
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liver is an organ present in vertebrates and some other animals. It plays a major role in metabolism and has a number of functions in the body, including glycogen storage, decomposition of red blood cells, plasma protein synthesis, and detoxification.
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