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The endomembrane system

The endoplasmic reticulum (ER), Golgi apparatus, lysosomes, and vacuoles. Vesicle exchange between compartments.


Let’s imagine you are a pancreatic cell. Your job is to secrete digestive enzymes, which travel into the small intestine and help break down nutrients from food. In order to carry out this job, you somehow have to get those enzymes shipped from their site of synthesis—inside the cell—to their place of action—outside the cell.
How are you going to make this happen? After a moment of panic in which you consider calling the postal service, you relax, having remembered: I have an endomembrane system!

What is the endomembrane system?

The endomembrane system (endo- = “within”) is a group of membranes and organelles in eukaryotic cells that works together to modify, package, and transport lipids and proteins. It includes a variety of organelles, such as the nuclear envelope and lysosomes, which you may already know, and the endoplasmic reticulum and Golgi apparatus, which we will cover shortly.
Although it's not technically inside the cell, the plasma membrane is also part of the endomembrane system. As we'll see, the plasma membrane interacts with the other endomembrane organelles, and it's the site where secreted proteins (like the pancreatic enzymes in the intro) are exported. Important note: the endomembrane system does not include mitochondria, chloroplasts, or peroxisomes.
Let's take a closer look at the different parts of the endomembrane system and how they function in the shipping of proteins and lipids.

The endoplasmic reticulum

The endoplasmic reticulum (ER) plays a key role in the modification of proteins and the synthesis of lipids. It consists of a network of membranous tubules and flattened sacs. The discs and tubules of the ER are hollow, and the space inside is called the lumen.

Rough ER

The rough endoplasmic reticulum (rough ER) gets its name from the bumpy ribosomes attached to its cytoplasmic surface. As these ribosomes make proteins, they feed the newly forming protein chains into the lumen. Some are transferred fully into the ER and float inside, while others are anchored in the membrane.
Inside the ER, the proteins fold and undergo modifications, such as the addition of carbohydrate side chains. These modified proteins will be incorporated into cellular membranes—the membrane of the ER or those of other organelles—or secreted from the cell.
If the modified proteins are not destined to stay in the ER, they will be packaged into vesicles, or small spheres of membrane that are used for transport, and shipped to the Golgi apparatus. The rough ER also makes phospholipids for other cellular membranes, which are transported when the vesicle forms.
Micrograph and diagram of the endoplasmic reticulum. Micrograph shows the rough ER as a series of membrane folds surrounding the nucleus. Diagram gives a 3D representation of rough ER and smooth ER along with the cell nucleus.
_Image credit: left, "The endomembrane system and proteins: Figure 2" by OpenStax College, Biology (CC BY 3.0), modification of work by Lousia Howard; right, modification of "Animal cell structure" by Mariana Ruiz, public domain_
Since the rough ER helps modify proteins that will be secreted from the cell, cells whose job is to secrete large amounts of enzymes or other proteins, such as liver cells, have lots of rough ER.

Smooth ER

The smooth endoplasmic reticulum (smooth ER) is continuous with the rough ER but has few or no ribosomes on its cytoplasmic surface. Functions of the smooth ER include:
  • Synthesis of carbohydrates, lipids, and steroid hormones
  • Detoxification of medications and poisons
  • Storage of calcium ions
In muscle cells, a special type of smooth ER called the sarcoplasmic reticulum is responsible for storage of calcium ions which are needed to trigger the coordinated contractions of muscle fibers.
There are also tiny "smooth" patches of ER found within the rough ER. These patches serve as exit sites for vesicles budding off from the rough ER and are called transitional ERstart superscript, 1, end superscript.

The Golgi apparatus

When vesicles bud off from the ER, where do they go? Before reaching their final destination, the lipids and proteins in the transport vesicles need to be sorted, packaged, and tagged so that they wind up in the right place. This sorting, tagging, packaging, and distribution takes place in the Golgi apparatus (Golgi body), an organelle made up of flattened discs of membrane.
Micrograph of the Golgi apparatus showing a series of flattened membrane discs in cross-section
_Image credit: "The endomembrane system and proteins: Figure 3" by OpenStax College, Biology (CC BY 3.0), modification of work by Lousia Howard_
The receiving side of the Golgi apparatus is called the cis face and the opposite side is called the trans face. Transport vesicles from the ER travel to the cis face, fuse with it, and empty their contents into the lumen of the Golgi apparatus.
As proteins and lipids travel through the Golgi, they undergo further modifications. Short chains of sugar molecules might be added or removed, or phosphate groups attached as tags. Carbohydrate processing is shown in the diagram as the gain and loss of branches on the purple carbohydrate group attached to the protein.
Image showing transport of a membrane protein from the rough ER through the Golgi to the plasma membrane. The protein is initially modified by the addition of branching carbohydrate chains in the rough ER; these chains are then trimmed back and replaced with other branching chains in the Golgi apparatus. The protein, with its final set of carbohydrate chains, is then transported to the plasma membrane in a transport vesicle. The vesicle fuses with the plasma membrane, its lipids and protein cargo becoming part of the plasma membrane.
_Image modified from "The endomembrane system and proteins: Figure 1" by OpenStax College, Biology (CC BY 3.0), modification of work by Magnus Manske_
Finally, the modified proteins are sorted (based on markers such as amino acid sequences and chemical tags) and packaged into vesicles that bud from the trans face of the Golgi. Some of these vesicles deliver their contents to other parts of the cell where they will be used, such as the lysosome or vacuole. Others fuse with the plasma membrane, delivering membrane-anchored proteins that function there and releasing secreted proteins outside the cell.
Cells that secrete many proteins—such as salivary gland cells that secrete digestive enzymes, or cells of the immune system that secrete antibodies—have many Golgi stacks. In plant cells, the Golgi apparatus also makes polysaccharides (long-chain carbohydrates), some of which are incorporated into the cell wall.


The lysosome is an organelle that contains digestive enzymes and acts as the organelle-recycling facility of an animal cell. It breaks down old and unnecessary structures so their molecules can be reused. Lysosomes are part of the endomembrane system, and some vesicles that leave the Golgi are bound for the lysosome.
Lysosomes can also digest foreign particles that are brought into the cell from outside. As an example, let's consider a class of white blood cells called macrophages, which are part of the human immune system. In a process known as phagocytosis, a section of the macrophage’s plasma membrane invaginates—folds inward—to engulf a pathogen, as shown below.
Diagram of phagocytosis, in which the phagosome generated by engulfment of a particle fuses with a lysosome, allowing digestion of the particle.
_Image credit: modified from "The endomembrane system and proteins: Figure 4" by OpenStax College, Biology (CC BY 3.0)_
The invaginated section, with the pathogen inside, pinches off from the plasma membrane to form a structure called a phagosome. The phagosome then fuses with a lysosome, forming a combined compartment where digestive enzymes destroy the pathogen.


Plants cells are unique because they have a lysosome-like organelle called the vacuole. The large central vacuole stores water and wastes, isolates hazardous materials, and has enzymes that can break down macromolecules and cellular components, like those of a lysosome.cubed Plant vacuoles also function in water balance and may be used to store compounds such as toxins and pigments (colored particles).start superscript, 4, end superscript

Lysosomes vs. peroxisomes

One point that can be confusing is the difference between lysosomes and peroxisomes. Both types of organelles are involved in breaking down molecules and neutralizing hazards to the cell. Also, both usually show up as small, round blobs in diagrams.
However, the peroxisome is a different organelle with its own unique properties and role in the cell. It houses enzymes involved in oxidation reactions, which produce hydrogen peroxide (start text, H, end text, start subscript, 2, end subscript, start text, O, end text, start subscript, 2, end subscript) as a by-product. The enzymes break down fatty acids and amino acids, and they also detoxify some substances that enter the body. For example, alcohol is detoxified by peroxisomes found in liver cells.
Importantly, peroxisomes—unlike lysosomes—are not part of the endomembrane system. That means they don't receive vesicles from the Golgi apparatus. You can learn more about how proteins are shipped to the peroxisome in the article on protein targeting.

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