Cell Compartmentalization

The appearance of the eukaryotic cell is considered one of the most important events in the history of life. The evolution from the simpler structure of prokaryotic cells to eukaryotic ones included the acquisition of a nucleus, an endomembrane system, a cytoskeleton, and energetic organelles through endosymbiosis. These new features allowed complex compartmentalization of the cell leading to the more efficient performance of cellular reactions and processes. How and when these features came to be is still not well understood, although it is critical to understand how they gave rise to the great diversity of eukaryotic cell types and organisms, including humans.

Cell Compartmentalization Cell Compartmentalization

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Table of contents

    We will describe compartmentalization in eukaryotic cells, including some examples of compartments, the models that try to explain its origin, and the advantages and disadvantages that the presence of compartments has for cell function.

    Cell compartmentalization in biology

    In biology, cell compartmentalization refers to the presence of separated compartments inside the cell, with specific conditions that allow the simultaneous occurrence of diverse metabolic reactions and processes.

    Cell compartmentalization is a major characteristic feature of eukaryotic cells, which have several differentiated compartments formed by membrane-bounded organelles and internal membranes (Fig. 1). This allows the cell to perform more efficiently, diverse metabolic reactions in these specialized compartments.

    Cell compartmentalization Examples, Eukaryotic animal and plant compartmentalized cells StudySmarterFig. 1: Observe all the internal membranes and organelles that eukaryotic cells have, like the animal and plant cells pictured here, which represent separated cell compartments.

    Compare the internal compartmentalization of these cells to the prokaryotic cell in Fig. 3.

    Metabolic reactions and processes require specific local environments to take place, with the appropriate molecules, enzymes, and specific conditions, such as a different pH.

    Although compartmentalization and compartmentation are related words and have similar semantic meanings, in biology we always use compartmentalization to refer to the division of a cell into internal compartments, instead of compartmentation of cells.

    The cell membranes not only enclose the cell and the organelles that form the internal compartments, but also actively participate in their functions. The membrane controls the passage of material into and out of the cell and the organelles, and contains built-in enzymes with specific functions. The basic structure of most biological membranes is a double layer of phospholipids, where diverse proteins are embedded (Fig. 2). The composition of lipids and proteins varies according to the cell and organelle function.

    Cell Compartmentalization Examples, Phospholipid Bilayer of membrane StudySmarter

    Fig. 2: The cell membrane consists of a double layer of phospholipids, with a hydrophilic head and hydrophobic tail.

    Cell membranes are essential for cell organization and function; we discuss them in detail in our Plasma Membrane section.

    Although prokaryotes generally lack internal membranes and membrane-bounded organelles, they have internal regions where specific molecules and cell materials concentrate. There are some groups of prokaryotes with membrane delimited compartments or cell membrane invaginations, however, they mostly serve for material storage and are not as complex as in eukaryotes.

    Cell compartmentalization Examples, comparison to prokaryotic cell not compartmentalized StudySmarterFig. 3: Prokaryotic cells, like the bacteria pictured here, are not compartmentalized as eukaryotic cells (although cell materials and molecules can concentrate in some regions).

    Cell compartmentalization examples

    Basically, every component of the cell that has a distinctive function can be a compartment. Based on their main function and interrelations we can classify them into five groups, representing different cell compartmentalization examples:




    The double membrane-bounded organelle that contains the genetic material (chromosomes) in a eukaryotic cell and controls cellular activity. The nucleoplasm (the semi-solid fluid that fills the interior of the nucleus) and the cytosol are connected through the nuclear pores.


    The semifluid that fills the cell interior and contains ions, molecules, and all the organelles. It can be considered a different compartment as different reactions take place there (gene translation, first reactions of cellular respiration, etc.).

    The endomembrane system

    The network of membranes and organelles that work together by modifying, packaging, and distributing proteins and lipids inside a cell. It is composed of the outer membrane of the nuclear envelope, the endoplasmic reticulum, the Golgi apparatus, vesicles, vacuoles, lysosomes, and the plasma membrane. Transport vesicles move material between the system components, connecting them.


    The double membrane-bounded organelle that performs cellular respiration (uses oxygen to break down organic molecules and synthesize ATP).


    A group of organelles, including chloroplasts, found in photosynthetic eukaryotic cells. A chloroplast is a double-membrane organelle found in plants and algae that perform photosynthesis (synthesis of organic compounds from carbon dioxide, water, and solar energy).

    Table 1: Examples of cell compartments.

    A cell compartment usually contains the material and molecules required only for certain cellular processes. it can also maintain a specific proton concentration for a required pH environment.

    For example, the mitochondria contain the enzymes and substrates involved in the latter stages of cellular respiration, while the enzymes involved in the digestion of cellular debris and foreign materials are located within lysosomes.

    Origins of cell compartmentalization

    Compartmentalization in cells represented a major change from prokaryotic to eukaryotic cell structure, organization, and function. Still, being such an important event in cell evolution, the origins of cell compartmentalization are not well understood and this is currently a prolific field of research and discussion. While the endosymbiont bacterial origin of the mitochondrion and the chloroplast is now widely accepted, the development of cell compartments as the endomembrane system and the nucleus is more of a mystery.

    Cell compartmentalization Origins of cell compartmentalization, endosymbiosis theory StudySmarter

    Fig. 4: This diagram of the endosymbiotic theory falls under the late endosymbiosis models, which generally hypothesize that the archaeal host was already complex when it acquired a bacterial symbiont. Thus, according to these models, the development of internal membranes was somewhat previous to the endosymbiotic event.

    The endosymbiosis theory proposes that the mitochondrion originated when an ancestral archaeon host (or an organism closely related to archaea) engulfed an ancestral bacterium (related to modern alfa-proteobacteria) that was not digested and eventually evolved into the organelle. This process is known as endosymbiosis. In photosynthetic eukaryotes, a second event of endosymbiosis is thought to have happened. A lineage of the heterotrophic eukaryotes containing the mitochondrial precursor acquired an additional endosymbiont (probably a cyanobacterium, which is photosynthetic).

    For more information on mitochondria and chloroplast origin check our Endosymbiotic Theory article.

    Models of cell compartmentalization

    Many hypotheses propose different models for the evolutionary processes that led to the Last Eukaryote Common Ancestor (LECA), the last single-cell organism that possessed all the characteristic features of a eukaryotic cell and from which all modern eukaryotes originated.

    The debate revolves mostly around the sequence and timeline in which different compartments developed. An important issue is when the acquisition of the ancestral mitochondrial endosymbiont occurred and the level of complexity the ancestral archaeon host had at that time. This matters because depending on the order of occurrence, the origin and formation of the internal membranes and the way of acquiring and maintaining an endosymbiont might have been completely different.

    There is also another Last Common Ancestor... LUCA, the Last Universal Common Ancestor!

    A lot of studies in the last decades using new technologies have increased the available information on this subject, but ample and appealing evidence (such as for the endosymbiont origin of the mitochondrion and chloroplasts) for one model over the others does not yet exist. Interestingly, the components of eukaryotic membranes are mostly bacterial-related in origin, instead of archaean. However, this particular structure could have arisen both directly from the endosymbiont, or have an initial archaea origin that was later replaced by bacterial components.

    We can classify most of the existing models into two major groups, based on the proposed timing of the endosymbiosis event, the early-endosymbiosis models, and the late-endosymbiosis models:

    • The models that propose the early merging of an ancestral archaeon and an ancestral bacterium gave rise to the new eukaryote cell. The key point is that the archaeon host had a simple prokaryotic structure and the endosymbiosis event itself enhanced the development of internal membranes (thus these models are commonly under symbiogenesis). Some more recent models even suggest that the eukaryotic internal membranes formed from vesicles secreted by the ancestral mitochondrion itself into the host cytosol.

    Although endosymbiosis is thought to have occurred through phagocytosis (engulfment) of the ancestral bacterium by the archaeon host, this implied the host had the ability to do this. However, many authors have argued against it since no modern examples of phagocytosis in prokaryotes exist (a well-developed cytoskeleton allows modern eukaryotes to phagocyte). Nonetheless, a prokaryote can invade or parasite other prokaryotes. The fusion of two prokaryotes, instead of one engulfing another, is supported by new evidence of a few modern prokaryotes containing endosymbionts.

    • The models that suggest a late endosymbiosis propose that a proto-eukaryote evolved from an ancestral archaeon, developing a more complex structure before the endosymbiosis event. There are different proposals for the nature of this proto-eukaryote, but it would have had simpler forms of some of the modern eukaryote features (internal membranes and a cytoskeleton, some propose a nucleus too). These early features would have allowed an ancestral host to phagocyte a bacterial endosymbiont. The models assume that the internal membranes were formed by invaginations of the archaeon host cell membrane, and therefore they are commonly called autogenous models.

    Cell compartmentalization advantages

    Cell compartmentalization probably gave many benefits to early eukaryotes as they evolved in an incredible variety of organisms (unicellular and multicellular) with an equal variety of cell types and functions. The advantages of cell compartmentalization probably allowed eukaryotes to compete for resources in a different way than prokaryotes, and to exploit new resources as well.



    Increased surface for energy production

    Prokaryotes can only synthesize ATP in their cell membrane. Eukaryotes can contain hundreds of energy-producing compartments (mitochondria).

    Increased cell size

    The boost in energy production and a more complex internal transportation system (vesicles from the internal membranes) might have lifted some restrictions for early eukaryotic cells to grow in size.

    Simultaneous occurrence of otherwise incompatible metabolic reactions and processes

    Higher efficiency due to reduced loss of intermediate products (they can be transported and used immediately where required), isolation of toxic by-products, and enzymes with different local environment requirements can work at the same time.

    Greater regulation of gene expression

    On the other hand, Transcription and translation occur simultaneously in prokaryotes.

    Table 2: Some advantages that compartments can give to eukaryotic cells compared to prokaryotic ones.

    However, prokaryotes have existed for longer than eukaryotes and, even if all prokaryotes have a similar basic morphology, they are incredibly diverse in the way they obtain energy, the places they inhabit, and they reproduce extremely fast.

    Thus, we should see these differences as distinct ways to exist, both with advantages and disadvantages depending on the circumstances, but in the end, both types have been successful at living and thriving on earth.

    Disadvantages of cell compartmentalization

    While eukaryotic cells can be more efficient in some activities because they perform several reactions at the same time in different compartments, they also need more control checkpoints and regulatory mechanisms, thus slowing some processes compared to prokaryotes. Some disadvantages of cell compartmentalization in eukaryotic cells are the following:

    • More energy requirements to maintain a bigger cell with more complex biological components and organelles.
    • Slower cell division.
    • Gene expression takes more time.

    Cell Compartmentalization - Key takeaways

    • Membranes and membrane-bound organelles in eukaryotic cells compartmentalize specific metabolic processes and enzymatic reactions.
    • Prokaryotes generally lack internal membranes and membrane-b organelles but have internal regions where specific molecules and cell material concentrate.
    • Mitochondria and chloroplasts evolved from once free-living prokaryotic cells through endosymbiosis.
    • Models that propose an endosymbiosis event early in eukaryote origin suggest that the endosymbiosis event itself enhanced the development of internal membranes in an ancestral archaeon or archaeon-related host.
    • Models that propose an endosymbiosis event late in eukaryote origin suggest that a proto-eukaryote evolved from an ancestral archaeon, developing a more complex structure before the endosymbiosis event.


    1. Heidi McBride, Mitochondria and endomembrane origins, Current Biology - Guest Editorial, 2018.
    2. Dave Speijer, Zombie ideas about early endosymbiosis: Which entry mechanisms gave us the “endo” in different endosymbionts? BioEssays, 2021.
    3. Zimmer C. On the origin of eukaryotes. Science, 2009.
    4. Fig. 4: Serial endosymbiosis (https://commons.wikimedia.org/wiki/File:Serial_endosymbiosis.svg) by Kelvinsong (https://commons.wikimedia.org/wiki/User:Kelvin13), under CC BY-SA 3.0 License
    Frequently Asked Questions about Cell Compartmentalization

    What is the name of a cell that has compartmentalization?

    A cell that has complex compartmentalization is called a eukaryotic cell.

    How does compartmentalization organize a cell's functions?

    Compartmentalization organizes a cell's functions by providing specialized compartments with specific internal conditions and material required for particular reactions and processes.

    What is compartmentalization in cells?

    Compartmentalization in cells is the separation of the cell interior in distinct compartments with specific local conditions that allow the simultaneous occurrence of diverse metabolic reactions and processes. In eukaryotic cells, a system of internal membranes and organelles generate compartmentalization.

    What causes cell compartmentalization?

    A system of internal membranes and membrane bound organelles causes the compartmentalization of eukaryotic cells.

    What is the purpose of compartmentalization in a eukaryotic cell?

    The purpose of compartmentalization in a eukaryotic cell is increasing cell efficiency by allowing the simultaneous occurrence of otherwise incompatible metabolic reactions and processes. 

    Test your knowledge with multiple choice flashcards

    The function of internal membranes is only to physically delimit the organelles that form the internal compartments

    Which of the following are the most debatable aspects about the origin of the different eukaryotic compartments?

    Which of the following statements is false regarding cell organization and function in prokaryotes?

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