question: How mitochondria has stayed in our cells even after millions of years of reproduction?
comment: There is a lot of integration between mitochondria and cell, but as far as I know part of genes involved in oxidative phosphorylation are now located in the main nucleus, while some other genes are located in mitochondria own circular DNA. So mitochondria can't survive or reproduce outside eukaryotic cell.
passages: The ability for a mitochondrion to self-replicate is rooted in its evolutionary history. It is commonly thought that mitochondria descend from cells that formed endosymbiotic relationships with α-protobacteria, they have their own genome for replication. However, recent evidence suggests that mitochondria may have evolved without symbiosis. The mitochondrion is a key regulator of the metabolic activity of the cell, and is also an important organelle in both production and degradation of free radicals. It is reckoned that higher mitochondrial copy number (or higher mitochondrial mass) is protective for the cell.
   Section::::Genome.
  
  Mitochondria contain their own genome, an indication that they are derived from bacteria through endosymbiosis. However, the ancestral endosymbiont genome has lost most of its genes so that the mitochondrial genome (mitogenome) is one of the most reduced genomes across organisms.
   Bioinformatics analysis showed that [[amino acid composition of mitochondrial proteins correlate with longevity (long-living species are depleted in [[cysteine]] and [[methionine]]), linking mitochondria to the process of ageing. 
  
  By studying expression of certain [[genes]] in "[[C. elegans]]", "[[Drosophila]]", and mice it was found that disruption of ETC complexes can extend life – linking mitochondrial function to the process of ageing.
  
  Evidence supporting the theory started to crumble in the early 2000s.
   In sexual reproduction, mitochondria are normally inherited exclusively from the mother; the mitochondria in mammalian sperm are usually destroyed by the egg cell after fertilization. Also, most mitochondria are present at the base of the sperm's tail, which is used for propelling the sperm cells; sometimes the tail is lost during fertilization. In 1999 it was reported that paternal sperm mitochondria (containing mtDNA) are marked with ubiquitin to select them for later destruction inside the embryo. Some "in vitro" fertilization techniques, particularly injecting a sperm into an oocyte, may interfere with this.
   In the "Star Wars" franchise, microorganisms referred to as "midi-chlorians" give some characters the ability to sense and use the Force. George Lucas, director of the 1999 film "", in which midi-chlorians were introduced, described them as "a loose depiction of mitochondria". The non-fictional bacteria genus "Midichloria" was later named after the midi-chlorians of "Star Wars".
  
  As a result of the mitochondrion's prominence in modern American science education, the phrase "the mitochondria is the powerhouse of the cell" became an internet meme.
  
  Section::::See also.
  
  BULLET::::- Anti-mitochondrial antibodies
  
  BULLET::::- Chloroplast
  
  BULLET::::- Hydrogenosome
  
  BULLET::::- "Midichloria" bacterial genus
  
  BULLET::::- Mitochondrial metabolic rates
   The occurrence of programmed cell death in protists is possible, but it remains controversial. Some categorize death in those organisms as unregulated apoptosis-like cell death.
  
  Biologists had long suspected that mitochondria originated from bacteria that had been incorporated as endosymbionts ("living together inside") of larger eukaryotic cells. It was Lynn Margulis who from 1967 on championed this theory, which has since become widely accepted. The most convincing evidence for this theory is the fact that mitochondria possess their own DNA and are equipped with genes and replication apparatus.
   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.
  
  Section::::Cellular proliferation regulation.
   Eukaryotic cells typically have mitochondrial DNA; however, mitochondria that lack their own DNA have been found in a marine parasitic dinoflagellate from the genus "Amoebophyra". This microorganism, "A. cerati", has functional mitochondria that lack a genome. In related species, the mitochondrial genome still has three genes, but in "A. cerati" only a single mitochondrial gene — the cytochrome c oxidase I gene ("cox1") — is found, and it has migrated to the genome of the nucleus.
  
  Section::::Population genetic studies.
   Mitochondria are thought to be organelles that developed from endocytosed bacteria which learned to coexist inside our cells. These bacteria maintained their own DNA, the mitochondrial DNA (mtDNA), which codes for components of the electron transport chain (ETC). The ETC is found in the inner mitochondrial membrane and functions to produce energy in the form of ATP molecules. The process is called oxidative phosphorylation, because ATP is produced from ADP in a series of redox reactions. Electrons are transferred through the ETC from NADH and FADH to oxygen, reducing oxygen to water.
  
  Section::::Molecular basis.:ROS.
   Most mitochondrial function and biogenesis is controlled by nuclear DNA. Human mitochondrial DNA encodes 13 proteins of the respiratory chain, while most of the estimated 1,500 proteins and components targeted to mitochondria are nuclear-encoded. Defects in nuclear-encoded mitochondrial genes are associated with hundreds of clinical disease phenotypes including anemia, dementia, hypertension, lymphoma, retinopathy, seizures, and neurodevelopmental disorders.
  
  A study by Yale University researchers (published in the February 12, 2004 issue of the "New England Journal of Medicine") explored the role of mitochondria in insulin resistance among the offspring of patients with type 2 diabetes.
   Mitochondrial genomes have far fewer genes than the bacteria from which they are thought to be descended. Although some have been lost altogether, many have been transferred to the nucleus, such as the respiratory complex II protein subunits. 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 lost or transferred. 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.
   Section::::Genome.:Replication and inheritance.
   Madeleine L'Engle's 1973 science fantasy novel "A Wind in the Door" prominently features the mitochondria of main character Charles Wallace Murry, as being inhabited by creatures known as the farandolae. The novel also features other characters travelling inside one of Murry's mitochondria.
  
  The 1995 horror fiction novel "Parasite Eve" by Hideaki Sena depicts mitochondria as having some consciousness and mind control abilities, attempting to use these to overtake eukaryotes as the dominant life form. This text was adapted into an eponymous film, video game, and video game sequel all involving a similar premise.
   Section::::Structure.:Intermembrane space.
   Some of these differences should be regarded as pseudo-changes in the genetic code 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, the codon in the processed RNA was discovered to be the UGG codon, consistent with the standard genetic code for tryptophan. Of note, the arthropod mitochondrial genetic code has undergone parallel evolution within a phylum, with some organisms uniquely translating AGG to lysine.
  
  Section::::Genome.:Evolution and diversity.
   Section::::Function.: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 can transiently store calcium, a contributing process for the cell's homeostasis of calcium.
   Entities undergoing uniparental inheritance and with little to no recombination may be expected to be subject to Muller's ratchet, the inexorable accumulation of deleterious mutations until functionality is lost. Animal populations of mitochondria avoid this buildup through a developmental process known as the mtDNA bottleneck. The bottleneck exploits stochastic processes in the cell to increase in the cell-to-cell variability in mutant load as an organism develops: a single egg cell with some proportion of mutant mtDNA thus produces an embryo where different cells have different mutant loads. Cell-level selection may then act to remove those cells with more mutant mtDNA, leading to a stabilisation or reduction in mutant load between generations. The mechanism underlying the bottleneck is debated, with a recent mathematical and experimental metastudy providing evidence for a combination of random partitioning of mtDNAs at cell divisions and random turnover of mtDNA molecules within the cell.
   In 1967, it was discovered that mitochondria contained ribosomes. In 1968, methods were developed for mapping the mitochondrial genes, with the genetic and physical map of yeast mitochondrial DNA being completed in 1976.
  
  Section::::Origin and evolution.
   In total, the mitochondrion hosts about 3000 different types of proteins, but only about 13 of them are coded on the mitochondrial DNA. Most of the 3000 types of proteins are involved in a variety of processes other than ATP production, such as porphyrin synthesis. Only about 3% of them code for ATP production proteins. This means most of the genetic information coding for the protein makeup of mitochondria is in chromosomal DNA and is involved in processes other than ATP synthesis. This increases the chances that a mutation that will affect a mitochondrion will occur in chromosomal DNA, which is inherited in a Mendelian pattern. Another result is that a chromosomal mutation will affect a specific tissue due to its specific needs, whether those may be high energy requirements or a need for the catabolism or anabolism of a specific neurotransmitter or nucleic acid. Because several copies of the mitochondrial genome are carried by each mitochondrion (2–10 in humans), mitochondrial mutations can be inherited maternally by mtDNA mutations which are present in mitochondria inside the oocyte before fertilization, or (as stated above) through mutations in the chromosomes.
   Section::::Function.
  
  The most prominent roles of mitochondria are to produce the energy currency of the cell, ATP (i.e., phosphorylation of ADP), through respiration, and to regulate cellular metabolism. The central set of reactions involved in ATP production are collectively known as the citric acid cycle, or the Krebs cycle. However, the mitochondrion has many other functions in addition to the production of ATP.
  
  Section::::Function.:Energy conversion.
   Acetyl-CoA, on the other hand, derived from pyruvate oxidation, or from the beta-oxidation of fatty acids, is the only fuel to enter the citric acid cycle. With each turn of the cycle one molecule of acetyl-CoA is consumed for every molecule of oxaloacetate present in the mitochondrial matrix, and is never regenerated. It is the oxidation of the acetate portion of acetyl-CoA that produces CO and water, with the energy thus released captured in the form of ATP.
   Section::::Structure.:Inner membrane.
  
  The inner mitochondrial membrane contains proteins with five types of functions:
  
  BULLET::::1. Those that perform the redox reactions of oxidative phosphorylation
  
  BULLET::::2. ATP synthase, which generates ATP in the matrix
  
  BULLET::::3. Specific transport proteins that regulate metabolite passage into and out of the mitochondrial matrix
  
  BULLET::::4. Protein import machinery
  
  BULLET::::5. Mitochondrial fusion and fission protein
   Nuclear and mitochondrial DNA are thought to be of separate evolutionary origin, with the mtDNA being derived from the circular genomes of the bacteria that were engulfed by the early ancestors of today's eukaryotic cells. This theory is called the endosymbiotic theory. Each mitochondrion is estimated to contain 2–10 mtDNA copies. In the cells of extant organisms, the vast majority of the proteins present in the mitochondria (numbering approximately 1500 different types in mammals) are coded for by nuclear DNA, but the genes for some, if not most, of them are thought to have originally been of bacterial origin, having since been transferred to the eukaryotic nucleus during evolution.
   It contains more than 151 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). The inner membrane is home to around 1/5 of the total protein in a mitochondrion. In addition, the inner membrane is rich in an unusual phospholipid, cardiolipin. This phospholipid was originally discovered in cow hearts in 1942, and is usually characteristic of mitochondrial and bacterial plasma membranes. Cardiolipin contains four fatty acids rather than two, and may help to make the inner membrane impermeable. Unlike the outer membrane, the inner membrane doesn't contain porins, and is highly impermeable to all molecules. Almost all ions and molecules require special membrane transporters to enter or exit the matrix. Proteins are ferried into the matrix via the translocase of the inner membrane (TIM) complex or via Oxa1. In addition, there is a membrane potential across the inner membrane, formed by the action of the enzymes of the electron transport chain.
   Section::::Function.:Energy conversion.:Heat production.
  