AP Biology 2.10 - Compartmentalization

Here, we take a look at section 2.10 of the AP Biology Curriculum: Cell Compartmentalization. We’ll start with an overview of the metabolism, and see how it is broken down into both catabolic processes and anabolic processes. Then, we’ll see why the cell needs to create different compartments with lipid bilayers and organelles to effectively separate these components of metabolism to ensure homeostasis and carry out the functions of life. Finally, we’ll take a look at how a cell creates a specialized compartment or organelle, and we will look at some specific examples of how the catabolism and anabolism of different biological macromolecules are separated!

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Resources for this Standard

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Cells have membranes that allow them to establish and maintain internal environments that are different from their external environments.


Describe the membrane-bound structures of the eukaryotic cell.

Explain how internal membranes and membrane-bound organelles contribute to compartmentalization of eukaryotic cell functions.


Membranes and membrane-bound organelles in eukaryotic cells compartmentalize intracellular metabolic processes and specific enzymatic reactions.

Internal membranes facilitate cellular processes by minimizing competing interactions and by increasing surface areas where reactions can occur.

2.10 Compartmentalization Overview

Have you ever wanted to start a band, but your parents made you practice in the garage because your siblings were trying to do their homework in their bedrooms? This is beneficial for both groups because the garage has a good environment for making great music, while your siblings can study in the quiet privacy of their bedrooms. This works because houses are compartmentalized. One room creates an environment that is good for some activities, while other rooms create different environments for different activities.

Cells work through the same principle of compartmentalization. The metabolic reactions of catabolism (or breaking substances down) must be separated from the metabolic reactions of anabolism (or building new substances). Much like the rooms of your house, these reactions must take place in different physical locations that have the right environment. Compartmentalization concepts will definitely be present on the AP test. So, stick with us as we cover everything you need to know about cellular compartmentalization.

An organism’s metabolism is formed from two separate components: catabolism and anabolism. Catabolic reactions break down large macromolecules into smaller molecules and release energy in the process. Anabolic reactions are using that energy to create larger biomolecules. To understand why cells need compartments, you need to understand why these two types of reactions cannot happen in the same physical space.

Let’s consider one, very simple reaction: the synthesis of a fatty acid. Fatty acids are created by a protein called Fatty Acid Synthase, which is located in the cytoplasm of cells. This massive protein complex is made of dozens of individual proteins that complete various reactions to synthesize a fatty acid molecule. Another protein, called the Mitochondrial Trifunctional Protein, breaks down fatty acids in the mitochondrial matrix. This protein cuts apart the fatty acid molecule into usable pieces. If you were to place both of these proteins into the same test tube with some fatty acids, nothing would get done because these proteins would constantly be undoing the work of the other protein. This is why compartmentalization is necessary.

Think about this… the idea of compartmentalization being efficient is not limited to cells. In fact, your entire body is compartmentalized. Each organ carries out a different function, allowing your body to be more efficient than if all your cells completed the same tasks. But, we also know that compartmentalization makes other aspects of human life more efficient. In a business, different departments are created to complete different tasks. This makes each department more efficient since they can focus on fewer tasks.

We also compartmentalize entire cities for the sake of efficiency. We live in some buildings, work in others, use some for entertainment, and some are reserved for specific functions like hospitals or waste processing plants. Try to remember the benefits of compartmentalization as we continue through this lesson!

In eukaryotic cells, compartmentalization is created by the use of a series of internal membranes. These membranes surround the nucleus, create the folds of the endoplasmic reticulum and Golgi complex, and surround organelles like chloroplasts and mitochondria. For example, let’s consider a mitochondrion.

A mitochondrion is an organelle surrounded by not one, but TWO membranes. The reactions taking place in the mitochondrion are breaking down substances to create ATP energy through catabolic reactions. These organelles can use glucose, amino acids, or fatty acids to create ATP. So, if these reactions were allowed to take place in the cytoplasm of the cell, the cell would not be able to complete the anabolic reactions it needs to combine glucose, amino acids, and fatty acids into large biological macromolecules like storage carbohydrates, proteins, or phospholipids.

You should also notice that many of these reactions happen right on the inner mitochondrial membrane. So, the membrane not only separates these reactions from the rest of the cell, but the many folds of the inner mitochondrial membrane produce a massive surface area for these reactions to take place! In mitochondria and chloroplasts, the space between the inner and outer membranes also makes a place where an ion gradient can be established, providing energy for ATP synthase to create new ATP molecules without affecting the pH or water balance of the rest of the cell.

These basic principles of compartmentalization – of separating important catabolic and anabolic reactions and creating a large surface area for reactions to occur – is true of all the membranes within a cell!

It is no coincidence that cells form specialized compartments. In fact, there are two mechanisms that create compartmentalization and keep the compartments of cells fully functional.  The first process is the anabolic processes of the metabolism that create and distribute new biological macromolecules. These molecules are tagged and distributed to specific parts of the cell.

For instance, a protein needed on the cell membrane will be created in the endoplasmic reticulum distributed to the cell membrane, while a protein needed in the cytosol will be created and distributed in the cytosol. Mitochondria and chloroplasts even have their own DNA and synthesize many of the substances they need. In this way, the anabolism produces and distributes molecules that create specialized compartments.

The second process that creates and maintains compartments with different enzymes and metabolites is the process of cellular division. Right before cell division starts to take place, all of the organelles within the cell are duplicated. Therefore, when the cell divides, each new cell has a full set of fully-functional compartments and organelles that already have the enzymes and structures needed to continue their important work within the cell.

These two processes ensure that every compartment in the cell is loaded up with the enzymes and metabolites that will create a specific environment for the important biological reactions that will be carried out in each compartment!

The last benefit of compartmentalization is that the reactions of catabolism and anabolism are physically separate, so they can operate simultaneously. There are many situations where this is beneficial.

The most obvious of these situations happens in a plant cell, where chloroplasts are rapidly creating glucose while the mitochondria are busy breaking glucose down. The chloroplasts are completing an anabolic process, whereas the mitochondria are engaging in a catabolic process. If these processes were not separated, the cell would become much less efficient. Being separated allows the chloroplasts to produce glucose as long as the sun is shining, while the mitochondria can slowly provide ATP for the cell from this glucose store – even at night when the sun is no longer shining!

But, this is just one example of how compartmentalization helps separate catabolic and anabolic processes. In fact, compartmentalization is important for each of the 4 types of biological macromolecules. Nucleic acids like mRNA can be continuously produced and exported by the nucleus while DNA and RNA from other organisms are digested down to individual nucleotides in a food vacuole. The cell can simultaneously create new phospholipids in the endoplasmic reticulum, while it recycles old ones in the cytoplasm. Likewise, the cell can simultaneously be destroying proteins while it makes new ones for different purposes or be creating storage carbohydrates while the mitochondria are using glucose to create ATP energy!

So, in essence, compartmentalization is incredibly important because it allows cells to carry out many reactions at the same time. This helps cells react and survive quickly changing environmental conditions and survive long enough to reproduce!