AP Biology 2.11 - Origins of Cell Compartmentalization

Here, we cover the basics of the Endosymbiotic Theory and the Origin of Cell Compartmentalization – section 2.11 of the AP Biology curriculum. We’ll start with a quick overview of evolution and some basic vocabulary needed to understand endosymbionts. Then, we’ll take a look at why compartmentalization is evolutionarily advantageous. After this short intro, we’ll dive head-first into the theory of symbiogenesis (endosymbiotic theory) and take a look at a large amount of evidence that supports this theory. For instance, we’ll see modern-day prokaryotes that appear to be evolving a nucleus, we’ll see how chloroplasts and mitochondria still retain circular DNA, and we’ll look at some of the biological macromolecules that are shared between organelles and modern bacterial cells!

Video Tutorial

The following video summarizes the most important aspects of this topic!

To watch more tutorial videos like this, please click here to see our full Youtube Channel!

Resources for this Standard

For Students & Teachers

For Teachers Only


Evolution is characterized by a change in the genetic makeup of a population over time and is supported by multiple lines of evidence.


Describe similarities and/or differences in compartmentalization between prokaryotic and eukaryotic cells.

Describe the relationship between the functions of endosymbiotic organelles and their free-living ancestral counterparts.


Membrane-bound organelles evolved from once free-living prokaryotic cells via endosymbiosis.

Prokaryotes generally lack internal membrane-bound organelles but have internal regions with specialized structures and functions.

Eukaryotic cells maintain internal membranes that partition the cell into specialized regions.

Membrane-bound organelles evolved from previously free-living prokaryotic cells via endosymbiosis.

2.11 Origins of Cell Compartmentalization Overview

The theory of evolution was widely rejected when it was first proposed. Not only did people doubt that humans were related to the Great Apes, but Charles Darwin himself had trouble connecting the complex life that humans live all the way to the first single-celled organism! But, science has come a long way since Darwin first traveled the oceans of the world aboard the H.M.S Beagle.

Now, using advanced microscopy, genetic science, and centuries of careful observation, we can easily connect the dots between humans and single-celled organisms. This overview covers the very beginning of that story – when cells first started to become compartmentalized and carry out complex functions. This is known as the Endosymbiotic Theory, and concepts from this theory will certainly be on the AP test! So, stick with us as we cover everything you need to know about the Origins of Cell Compartmentalization!

In this overview, we will be covering the information found in section 2.11 of the AP Biology Curriculum that focuses on the origins of cell compartmentalization. We will begin with some basics and vocabulary about evolution, then we will quickly review the benefits of compartments and the complexity that they create. After we review these things, we’ll dive into the Endosymbiotic Theory and see how organelles have evolved from free-living organisms. Finally, we’ll review the plethora of evidence that supports the theory.

If you have been following along with our AP Biology overviews, we’re going to switch gears now from the structures and functions of cells to the theories behind how cells evolved.

Before we dive into the complexities of the Endosymbiotic Theory, let’s cover some evolutionary basics and vocabulary. Evolution is a process that has been happening since the very first cells appeared on Earth around 2.3 Billion Years Ago! Evolution takes place because limited resources and a changing environment create a natural selection that allows some variations of a species to reproduce, while other variations are eliminated. In other words, only the organisms with sufficient adaptations are allowed to survive and reproduce the next generation, which slowly changes a population of organisms over time.

The fallacy that many people believe about evolution is that organisms at the bottom of the tree of life are less evolved than organisms at the top of the tree of life. While some forms of life are more complex than other forms, all of the organisms alive today have been evolving for the same amount of time.

The endosymbiotic theory looks at the very beginning of this journey when the first cells were starting to change due to the pressures of natural selection.

To fully understand the endosymbiotic theory, you also have to understand the concept of symbiosis. Symbiosis simply means that two species have a relationship, and there are three different kinds. In a mutualistic relationship, both species benefit. In a commensal relationship, one organism benefits while the other is unaffected. In a parasitic relationship, the parasite benefits while the other organism is harmed.

Think about this… As far as we know, cells can only come from other cells. Cell growth and reproduction are driven by the genetic molecule DNA, which is essentially creating clever new ways to replicate itself. If there were unlimited resources, cells might have remained exactly how they were when they first appeared somewhere between 1.6 and 2.3 billion years ago. But, since limited resources and competition drive natural selection, these cells slowly changed into more complex forms of life that could gather resources and exploit different niches of the environment. So, the diversity of life we see today is essentially a product of billions of years of organisms trying to maximize their reproductive success! Remember this fact as we start to dive into the endosymbiotic theory!

As we saw in section 2.10, compartmentalization in organisms creates the ability to carry out catabolic and anabolic reactions at the same time. In other words, if organisms can section off parts of their cells they can be much more efficient at gathering nutrients, growing, and reproducing. Since all organisms are in constant competition for resources, organisms that are able to compartmentalize their cells can reproduce more quickly.

While eukaryotic cells have many membrane-bound organelles that create different compartments, prokaryotic cells also have methods of compartmentalizing their cells. Prokaryotic cells not only create a chamber around themselves in the periplasmic space, but they can also compartmentalize different areas of their cytoplasm using proteins to complete anabolic and catabolic reactions in different areas.  Compartmentalization is an important component of the endosymbiotic theory!

So, what exactly is the endosymbiotic theory? Also known as symbiogenesis, this theory postulates that the common ancestor of all life on Earth was something similar to the prokaryotic cells that we see today. To protect its DNA and become more efficient through compartmentalization, this ancient prokaryote may have evolved the membranes of the nuclear envelope and endoplasmic reticulum. This is just the start of the endosymbiotic journey!

The real symbiosis occurred when this primitive eukaryotic cell encountered a much smaller, bacteria-like cell. Through the process of phagocytosis, this primitive eukaryote could have taken the bacterium into its cytoplasm.

Whereas this ingested bacterium would normally be digested by a lysosome, a mutation could have allowed the bacterial cell to survive and reproduce within the larger, primitive eukaryote. This is what likely led to the mitochondria that are seen in all eukaryotes today!

This situation could have been repeated with a photosynthetic bacterium, which likely evolved into the chloroplasts and other plastids used by algae and plants!

While we will get to the full list of evidence for the endosymbiotic theory in a minute, one of the most compelling pieces of evidence that these organelles were once free-living organisms comes from the fact that they both retain strands of circular DNA – much like modern-day bacterial cells! Though this genome is much smaller than a bacterial genome, it is assumed that the bacterial genome transferred some genes to the eukaryotic nucleus as the endosymbionts synchronized their cell division with the host cell, and lost other genes that were no longer essential for survival.

There is a large body of evidence that supports the endosymbiotic theory. However, this was not always the case. The theory was first presented in 1901 by a Russian biologist named Konstantin Mereschkowski. The theory went mostly unnoticed until the 1960’s when Evolutionary Biologist Lynn Margulis presented a large body of microbiological evidence.

One of the most important pieces of evidence is the similarities between various organelles and living bacteria. While evolution changes some organisms, it keeps others much the same as they were billions of years ago. For instance, the nucleus of eukaryotic organisms resembles the simple membranes formed in some Planctomycetes bacteria. Membranes like these could have easily evolved into the nuclear membrane and endoplasmic reticulum. Chloroplasts closely resemble cyanobacteria, commonly found in water all over the world. Mitochondrial are very similar to Rickettsial bacteria – a type of bacteria that cause Spotted Fever and Typhus when they infect humans.

Not only are these organelles and bacteria superficially related, but DNA evidence and similar biological macromolecules link them even further. For example, both mitochondria and bacterial cells have integral membrane proteins and lipids in their membranes that are nearly identical. Much like some cyanobacteria have a peptidoglycan cell wall, the chloroplasts of some eukaryotic algae species have retained this peptidoglycan cell wall.

The final piece of evidence supporting the endosymbiotic theory is present during cell division. Though eukaryotic cells divide via the process of mitosis, the mitochondria and chloroplasts in those cells divide through the process of binary fission. What’s more… if you artificially remove the chloroplasts or mitochondria from a cell, the cell has no way to reproduce those organelles – since the organelles house a large portion of their own DNA!