The evidence that supports the endosymbiotic theory includes:
1.    Mitochondria have a circular genome

Circular Genome of Mitochondria

2.    Mitochondria divide separately from the division of the cell itself and do so in a manner similar to binary fission.

Mitochondria divide independently of the cell.

3.    Mitochondria are enclosed within a double membrane

Mitochondria with double membrane.

4.    Mitochondria and bacteria are similar in size and shape.

Evidence that goes against these points:
1.    There are cases in which mitochondria don’t have circular genomes, but instead, have linear (or straight) genomes. In these particular cases, the DNA polymerase enzymes are unable to finish replicating all the way to the end of the genetic code; as such, with each progressive copy, it will result in shorter and shorter chromosomes (with missing genetic code). In eukaryotes, an enzyme by the name of telomerase exists that attaches extra DNA to the ends to prevent this shortening of the chromosomes. In linear mitochondrial chromosomes, the methods used to prevent this include hairpin loops and “self-priming to protein-assisted primer synthesis.” However, the problem comes about because the telomeric regions of the mitochondrial DNA lack a direct relation to nuclear telomeres in eukaryotes. In essence, the mitochondria use proteins and mechanisms that differ widely from eukaryotes in order to prevent this shortening of genetic code. As a result, it becomes difficult to connect the mitochondria with eukaryotic cells and infer an evolutionary relationship between the two based on the data suggesting differences in telomeres and mechanisms for end replication.

2.    Despite the claim that circular mitochondrial DNA replication is similar to bacterial binary fission, there are differences. The key components are more eukaryotic in nature than prokaryotic. Also, the replication of the circular mitochondrial DNA begins at the Displacement (D-) loop is different from bacterial DNA replication.

3.    While they are enclosed in a double membrane, there are differences in structure between the membranes of bacteria and mitochondria. Bacterial and mitochondria membranes share characteristics such as a cell wall with peptidoglycan and lipopolysaccharides, gram-staining and antibiotic sensitivity. However, the one issue that arises from this is that antibiotics are able to distinguish between the membranes of mitochondria and bacteria. This supports the notion that the membranes are structurally different (and able to be identified by agents such as antibiotics). It is difficult to try to change the fundamental components of a bacterial membrane and find an analogous counterpart in mitochondria membranes without changing the membrane integrity. This difference in membrane structure is another component that argues against the idea that mitochondria evolved from bacteria.

4.    For years, it has been argued that mitochondria and bacteria are similar in size and shape. However, recent findings have labeled mitochondria as “dynamic reticular structures.” Through electron micrographs, the mitochondria are portrayed as spheres. However, when the 3D model is viewed in detail, the actual structure of the mitochondria doesn’t resemble a sphere at all, but instead, resemble more of a bacillus shape.

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