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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.
_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 ER1.

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.
_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 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.
_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.3 Plant vacuoles also function in water balance and may be used to store compounds such as toxins and pigments (colored particles).4

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 (H2O2) 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.

Want to join the conversation?

  • aqualine ultimate style avatar for user srija
    What's the difference between a vesicle and a vacuole?
    (39 votes)
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  • male robot hal style avatar for user ranmarmar
    "single-celled eukaryotes"?
    isn't that wrong ?
    (6 votes)
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  • starky sapling style avatar for user Bri Nielsen
    What's the difference between a lipid and a phospholipid? And why are proteins so important?
    (12 votes)
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    • aqualine ultimate style avatar for user Anna Leep
      A lipid is composed of glycerol and three fatty acid chains. A phospholipid has a phosphate group attached to it.

      And proteins are so important because they do all the key activities to make a functioning human. When an embryo is growing, it is because of proteins. When the muscles send and receive signals from the brain, it is because of proteins. When cuts heal, it is because of proteins. When we digest food, it is because of proteins. You get the idea. They essentially do everything to make you able to live.
      (38 votes)
  • aqualine sapling style avatar for user Erin Griffin
    i know there are vacuoles in plants and animals cells, are there any major differences between the two other than the size? location maybe. like characteristics or different functions? both vacuoles in each type of cell store energy.
    (9 votes)
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    • female robot grace style avatar for user bubolina.bon
      The central vacuole of a plant has a crucial role. As mentioned above, the water there pushes the cytoplasm outward against the cell wall. This creates hydrostatic pressure - turgor. The mechanism keeps the plant from wilting and plays a key role in the water balance. Generally this central vacuole has a lower pH, witch help digesting substances; it can also be used as a storage room - citruses have their juice in these vacuoles; it also keeps the cell wall rigid and thus keeps the plant in upright position and so on. It also pushes every other cell organelle against the wall and to the surface of the cell. This a very clever way to push the chloroplasts closer to light and ''promote'' photosynthesis. Animal cells do not have a cell wall (they can have a similar thing , called a cell cortex). So the vacuoles here play a more subordinate role - they still help with endo- and exocytosis. Also the are quite smaller than plant vacuoles and greater in number. And of course, there are some animal cells with no vacuoles at all. Hope that helps :)
      (18 votes)
  • aqualine ultimate style avatar for user Keith Harvey
    How do they know the chemical composition for certain structures? For example if it's a phospholipid bilayer or a certain protein, exc.
    (8 votes)
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  • purple pi purple style avatar for user Sindhu Gunturi
    Why is the inner membrane of the lysosome not affected by the enzymes present inside it?
    (4 votes)
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  • blobby green style avatar for user Victor W
    Why are mitochondria, choloroplasts, and peroxisomes not included in the endomembrane system?
    (5 votes)
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  • duskpin ultimate style avatar for user Laura Eggen
    Hey, everyone!
    I'm having a rather hard time grasping some of the concepts in this article; specifically, how are the "shipments" between organelles (I.E. the ER and the Golgi) made? What structure connects them? Or do they just sort of float over?
    I would appreciate some help on this. Thanks!
    (5 votes)
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  • winston default style avatar for user catzuswag
    Why is it that pathogens can't enter though the plasma membrane by passing the phospholipid bilayer but still enter organelles like lysosomes? Don't organelles have a phospholipid bilayer?
    (6 votes)
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    • blobby green style avatar for user DerpingDerp202
      The plasma membrane serves as a protective barrier for cells, consisting of a phospholipid bilayer that regulates the passage of molecules in and out of the cell. While this membrane is selectively permeable, pathogens such as bacteria and viruses cannot simply diffuse through it due to its structural integrity and the presence of various transport proteins that carefully regulate what enters and exits the cell. However, once inside the cell, pathogens can exploit various mechanisms to gain access to organelles like lysosomes, which also have a phospholipid bilayer. Lysosomes, though they possess a similar lipid bilayer structure, contain a unique set of membrane proteins and enzymes tailored for breaking down cellular waste and foreign invaders. Pathogens can be engulfed by the cell through processes like endocytosis, where the invader is enclosed within a vesicle and transported to the lysosome for degradation. Additionally, some pathogens may have evolved mechanisms to evade or exploit the cellular machinery, allowing them to breach lysosomal membranes or manipulate cellular processes to their advantage. Basically, while both the plasma membrane and lysosomal membranes consist of a phospholipid bilayer, the specific composition and functionality of lysosomes, along with cellular processes like endocytosis, enable pathogens to access and potentially exploit these organelles despite the protective barrier posed by the lipid bilayer.
      (2 votes)
  • orange juice squid orange style avatar for user Hubert
    If plant has no lysosomes, than how do they defend themselves from bacteria? Or bacteria simply do not attack plants?
    (4 votes)
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    • marcimus pink style avatar for user Adrija Roy
      Yes, bacteria do attack plants but plant cells have a different defense mechanism.

      They have proteins which defend the plant from being infected. If a pathogen attacks a plant cell, then the proteins first try to prevent the pathogen from entering the plant cell. If that strategy fails and the pathogen manages to enter the cell, then the cell(or cells) have to sacrifice themselves, i.e, they die and prevent the pathogen from spreading further into the plant.
      (5 votes)