Difficulty: Introductory | Prerequisites: Part 1 of these study notes (Eukaryotic Cell Organelles), basic understanding of prokaryotic cells.
One of the most important questions in biology is how complex eukaryotic cells arose from simpler ancestors. The endosymbiotic theory, championed by Lynn Margulis in 1967, provides the leading explanation: mitochondria and chloroplasts were once independent prokaryotes that were engulfed by a host cell and became permanent internal partners. This topic sits at the intersection of cell biology, evolution, and microbiology. You should already know what mitochondria and chloroplasts do (from Part 1) before tackling how they got there.
Mitochondria descended from an ancient aerobic bacterium (likely an alpha-proteobacterium) and chloroplasts from an ancient cyanobacterium. Both were engulfed by ancestral host cells and, over billions of years, became obligate endosymbionts. The evidence is strong: double membranes, their own circular DNA, 70S ribosomes, and reproduction by binary fission all point back to their prokaryotic origins.
Endosymbiosis
A relationship in which one organism lives inside the cells of another, with both benefiting. In simple terms, one cell moves in with another and the arrangement becomes permanent.
Endosymbiotic theory
The hypothesis that mitochondria and chloroplasts originated as free-living prokaryotes that were engulfed by an ancestral eukaryotic (or proto-eukaryotic) cell. Over evolutionary time, the engulfed cells lost independence and became organelles.
Alpha-proteobacterium
The group of bacteria from which mitochondria are thought to have descended, based on DNA sequence comparisons.
Cyanobacterium
A photosynthetic bacterium (formerly called blue-green algae) from which chloroplasts are thought to have descended. Cyanobacteria were the first organisms to produce oxygen via photosynthesis.
Primary endosymbiosis
The original event in which a prokaryote was engulfed by a eukaryotic host cell and became an organelle. This accounts for mitochondria (once) and chloroplasts (in the ancestor of plants, green algae, and red algae).
Secondary endosymbiosis
A later event in which a eukaryote that already contained a chloroplast (via primary endosymbiosis) was itself engulfed by another eukaryote. This explains the extra membranes around chloroplasts in certain algae (e.g. brown algae, diatoms).
Endosymbiont gene transfer (EGT)
The process by which genes from the endosymbiont's genome were transferred to the host cell's nuclear genome over evolutionary time. This is why mitochondria and chloroplasts now depend on the nucleus for most of their proteins.
Cristae
The folds of the inner mitochondrial membrane, where the electron transport chain is located. Their shape echoes the infolded membranes seen in some modern aerobic bacteria.
Thylakoid
The internal membrane system of chloroplasts where the light reactions of photosynthesis occur. Structurally similar to the photosynthetic membranes found in modern cyanobacteria.
Endosymbiosis literally means "living together inside." In the context of cell evolution, it refers to a scenario in which a larger host cell engulfed a smaller prokaryotic cell. Rather than being digested, the engulfed cell survived inside the host and continued to function. Over hundreds of millions of years, the relationship became obligate: neither partner could survive without the other.
The engulfed cell provided a metabolic benefit to the host (aerobic respiration in the case of the mitochondrial ancestor, photosynthesis in the case of the chloroplast ancestor). In return, the host provided protection, nutrients, and a stable environment. Over time, many of the endosymbiont's genes migrated to the host nucleus, tying the two together permanently.
This is the section exams test hardest. Know these lines of evidence cold.
Mitochondria and chloroplasts are each surrounded by two membranes. The inner membrane is thought to derive from the engulfed prokaryote's own plasma membrane. The outer membrane is thought to derive from the host cell's membrane (the engulfing vesicle). No other organelle that was not once an independent cell has this double-membrane structure.
Both organelles contain their own small, circular DNA molecules, similar in form to bacterial chromosomes. This DNA is not associated with histones, just like prokaryotic DNA. The mitochondrial genome in humans encodes 37 genes (13 proteins, 22 tRNAs, 2 rRNAs). Most of the original endosymbiont genes have been transferred to the host nucleus over evolutionary time.
Mitochondria and chloroplasts have their own ribosomes, and these are 70S (the prokaryotic size), not 80S (the eukaryotic cytoplasmic size). The ribosomal RNA sequences are more closely related to bacterial rRNA than to cytoplasmic eukaryotic rRNA.
Both organelles replicate by dividing in two (binary fission), using a mechanism similar to bacterial cell division, including the use of an FtsZ ring (a protein homologous to the bacterial division protein). They are not made from scratch by the cell; new mitochondria come only from existing mitochondria, new chloroplasts from existing chloroplasts.
Mitochondria and chloroplasts are approximately the same size as typical bacteria (1 to 10 micrometres).
When you build evolutionary trees (phylogenies) using the DNA sequences of mitochondria, they cluster most closely with alpha-proteobacteria. Chloroplast DNA sequences cluster with cyanobacteria. This is the genetic smoking gun: the organelles share a recent common ancestor with specific groups of living bacteria.
The mitochondrial ancestor was likely an alpha-proteobacterium, an aerobic (oxygen-using) bacterium capable of efficient energy extraction via oxidative phosphorylation.
The scenario runs roughly as follows:
An ancestral host cell (possibly an archaeon or an early eukaryote) lived in an environment where oxygen was becoming more abundant, thanks to cyanobacterial photosynthesis.
The host cell engulfed an aerobic bacterium. This may have begun as a predator-prey or parasitic relationship.
The engulfed bacterium was not digested. Instead, it continued to carry out aerobic respiration inside the host, supplying ATP.
Over time, gene transfer from the endosymbiont to the host nucleus made the bacterium dependent on the host for many proteins. The relationship became permanent.
The result: mitochondria, present in virtually all eukaryotic lineages today.
Mitochondrial DNA is inherited maternally in most organisms (the egg contributes the cytoplasm, including mitochondria; sperm mitochondria are typically destroyed after fertilisation). This maternal inheritance pattern is used in population genetics and forensic science to trace maternal lineages.
Chloroplasts trace back to an ancient cyanobacterium, a prokaryote that carried out oxygenic photosynthesis (splitting water, releasing O2).
The story parallels the mitochondrial one:
An early eukaryotic cell (one that already had mitochondria) engulfed a photosynthetic cyanobacterium.
The cyanobacterium survived inside the host and continued to photosynthesise, supplying the host with sugars.
Gene transfer to the nucleus made the cyanobacterium dependent on the host. The result: the chloroplast.
This primary endosymbiotic event gave rise to the plant and green algae lineage (Viridiplantae) and the red algae lineage (Rhodophyta). The internal thylakoid membranes of chloroplasts closely resemble the photosynthetic membranes of modern cyanobacteria, and chloroplast DNA sequences nest within the cyanobacterial phylogenetic tree.
Modern cyanobacteria are still free-living today, which gives researchers a direct comparison point. The pigments (chlorophyll a, phycocyanin), the oxygen-evolving complex, and the thylakoid membrane architecture are strikingly similar between free-living cyanobacteria and chloroplasts.
Primary endosymbiosis explains how the first chloroplasts arose. But some algal lineages have chloroplasts wrapped in three or four membranes, not two. This is explained by secondary endosymbiosis.
In secondary endosymbiosis, a eukaryote that already had a chloroplast (from primary endosymbiosis) was itself engulfed by another eukaryote. The engulfed eukaryote was reduced over time to little more than its chloroplast, now wrapped in additional membranes from the secondary host.
Examples include brown algae, diatoms, and euglenids, whose chloroplasts have three or four bounding membranes. In a few cases (e.g. certain dinoflagellates), tertiary endosymbiosis has occurred, with an algae already containing a secondary chloroplast being engulfed again.
This is not usually examined in depth at the BIO 101 level, but knowing that it exists helps you understand why not all chloroplasts look the same across the tree of life.
Mitochondrial DNA analysis is used in forensic science and genealogy to trace maternal ancestry (since mtDNA is maternally inherited and does not recombine).
The antibiotic sensitivity of mitochondrial and chloroplast ribosomes (70S, like bacteria) explains why certain antibiotics (e.g. chloramphenicol) can have toxic side effects in humans: they can inhibit mitochondrial protein synthesis as well as bacterial protein synthesis.
Understanding endosymbiosis has influenced genetic engineering: scientists can target genes to the chloroplast genome in crop plants, taking advantage of the organelle's own transcription and translation machinery to produce desired proteins at high levels.
Students often think endosymbiosis was a single, sudden event. In reality, it was a gradual process spanning millions of years, during which gene transfer, loss of autonomy, and co-adaptation occurred incrementally.
Students sometimes say "the mitochondrion is a bacterium." It was derived from a bacterium but is no longer one. It has lost the vast majority of its original genes and cannot survive outside the host cell.
A common error is thinking that chloroplasts evolved from mitochondria, or that both came from the same ancestor. They arose from two separate endosymbiotic events: mitochondria from an alpha-proteobacterium, chloroplasts from a cyanobacterium.
Some students assume all eukaryotes have chloroplasts. Only photosynthetic eukaryotes (plants and algae) do. All eukaryotes (with very few exceptions) have mitochondria.
Be able to list and explain all six lines of evidence for endosymbiosis (double membrane, circular DNA, 70S ribosomes, binary fission, size, phylogenetics).
Know which prokaryotic group gave rise to mitochondria (alpha-proteobacteria) and which gave rise to chloroplasts (cyanobacteria).
Be prepared to explain why mitochondrial DNA is inherited maternally.
Understand what endosymbiont gene transfer is and why mitochondria and chloroplasts now depend on the host nucleus.
If asked to "describe the evidence that supports endosymbiosis," structure your answer around the six evidence categories, not as a vague narrative.
True or false: Chloroplasts have their own DNA, but mitochondria do not. (Answer: False. Both have their own circular DNA.)
Fill in the blank: Mitochondria are thought to have evolved from an ancient ______. (Answer: alpha-proteobacterium.)
True or false: The inner membrane of a mitochondrion is believed to derive from the engulfed bacterium's own plasma membrane. (Answer: True.)
Fill in the blank: Mitochondrial ribosomes are ______S, the same size as bacterial ribosomes. (Answer: 70S.)
True or false: Secondary endosymbiosis explains why some algal chloroplasts have more than two membranes. (Answer: True.)
Q: List four lines of evidence supporting the endosymbiotic origin of mitochondria.
A: (1) Mitochondria have a double membrane, consistent with engulfment. (2) They contain their own circular DNA, similar to bacterial chromosomes. (3) Their ribosomes are 70S, the prokaryotic size. (4) They reproduce by binary fission, like bacteria. Additional evidence includes their bacteria-like size and phylogenetic placement with alpha-proteobacteria.
Q: Why do mitochondria and chloroplasts depend on the nucleus for most of their proteins, if they were once independent organisms?
A: Over evolutionary time, most of the endosymbiont's genes were transferred to the host cell's nuclear genome (endosymbiont gene transfer). The proteins encoded by those genes are now synthesised on cytoplasmic ribosomes and imported into the organelle. This gene transfer made the endosymbiont dependent on the host.
Q: A student says "chloroplasts evolved from mitochondria." Correct this statement.
A: Chloroplasts and mitochondria evolved from two separate endosymbiotic events involving different prokaryotes. Mitochondria descended from an alpha-proteobacterium (aerobic), and chloroplasts descended from a cyanobacterium (photosynthetic). They are not derived from each other.
Q: Explain why some antibiotics that target bacterial ribosomes can also harm human cells.
A: Human mitochondria contain 70S ribosomes, the same type found in bacteria. Antibiotics that target 70S ribosomes (e.g. chloramphenicol) can therefore inhibit mitochondrial protein synthesis as well, leading to side effects, particularly in tissues with high energy demands such as bone marrow and the liver.
Q: What is secondary endosymbiosis, and what physical evidence for it can be observed in certain algae?
A: Secondary endosymbiosis is an event in which a eukaryote containing a chloroplast (from primary endosymbiosis) was engulfed by a second eukaryote. The physical evidence is the presence of three or four membranes around the chloroplast in groups such as brown algae and diatoms, reflecting the extra membranes from the secondary engulfment.
Endosymbiosis connects to evolution (how major cellular innovations arose), to genetics (maternal inheritance of mitochondrial DNA, gene transfer between genomes), and to ecology (the cyanobacterial oxygenation of Earth's atmosphere, which made aerobic life possible). It also links back to Part 1's material on organelle structure: every structural feature of mitochondria and chloroplasts you learned there (double membrane, own DNA, 70S ribosomes) is also a piece of evidence for their endosymbiotic origin.
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