Much of the evidence for the endosymbiotic theory comes from the structure and handling of these organelles' genetic codes. Both mitochondria and plastids have DNA sequences in circles as that of bacteria. Their DNA also lacks histones (proteins that the DNA is wrapped around) which are present in eukaryotes and some archea. In addition, mitochondria and plastid transcription begin with the amino acid fMet (formyl-methionine) as in bacteria, not Met (methionine) as in eukaryotes.

Ribosome sizes are questionable evidence for the endosymbiotic theory. Bacteria usually have ribosomes of 70s (Svedberg units) and eukaryotes usually have around 80s in their cytoplasm. While the mitochondrial and plastid ribosomes are usually of around 70s, they do in fact vary among species from around 60s to 80s, thus overlapping both bacterial and cytoplasmic eukaryote ribosome sizes.

Other evidence for the endosymbiotic theory comes from the two membranes usually surrounding these organelles. The inner membrane belongs to that of the original bacteria and outer membrane presumably a result from the original engulfment. The outer membrane has approximately a 1:1 protein-lipid ratio by dry weight, similar to many eukaryotic cytoplasmic membranes, while the inner membrane (which is made of two layers) has approximately a 3:1, similar to many bacteria. These organelles and bacteria also both utilize electron transport enzymes lacking elsewhere in eukaryotes.

Some of the best evidence for the endosymbiotic theory however comes from bioinformatics. Phylogenetic analyses of various bacteria, mitochondria from various hosts from various kingdoms, and nuclear DNA from those hosts usually place mitochondria as most related to a group of bacteria known as proteobacteria, often placed closest to Rickettsia and other a-proteobacteria. The a-proteobacteria as a group are almost entirely symbiotic or parasitic which may have predisposed the mitochondrial ancestor to an existence within its host. Chloroplasts are most often placed next to cyanobacteria and both contain thylakoids and chlorophyll a; cyanobacteria are also involved in a number of symbioses including lichens and corals.

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