Waste Disposal In Cells

Waste Disposal In Cells

I just put my garbage out, the useless stuff I didn’t need anymore. Right after that I thought, Wait.. how do cells get rid of all the things they make? Turns out there is indeed a way for cells to do that – literally put out the garbage. All our cells are like little humans aren’t they? Living their own little life. And that’s what brings us to today’s topic – Waste Disposal In Cells.

Waste disposal in cells is done through 2 pathways:

  1. Lysosomes
  2. Proteasomes


Lysosomes are membrane bound organelles containing more than 40 different enzymes.


These enzymes include proteases (break down protein), lipases (break down lipids), nucleases (break down nucleotides of nucleic acids), glycosidases (break down glycosidic bonds in complex sugars), phosphatases (break down phosphate bonds) and sulfatases (break down sulphate bonds), just to name a few. Look at the diagram below to see a few other classes of enzymes present in lysosomes.


It is clear that lysosomes are very equipped to break down almost anything the cell needs to get rid of. Obviously, these enzymes must be kept separated from the rest of the cytoplasm, and this is done by the single layer of membrane. If the membrane is ruptured, the enzymes will escape and destroy the cell from the inside out! It would be like the plot of The Dark Knight Rises, where Bane releases all the prisoners (enzymes) of Blackgate Penitentiary (single layer of membrane), who then proceeded to destroy the city.

Lysosomal enzymes function best at an acidic pH of less than 5. Thus, all the lysosomal enzymes are collectively referred to as acid hydrolases. The fact that the enzymes function best at an acidic pH is actually a protective mechanism, in addition to the single layer of membrane. This is because if the enzymes to manage to escape the lysosome, they will be far less active at the higher pH of approximately 7.3, in the cytosol.


This pH of


Lysosomal enzymes are all originally synthesized in a structure within the cell known as the rough endoplasmic reticulum, alongside all other proteins. However, how do the enzymes become lysosomal enzymes?

The answer is a pathway known as the mannose-6-pathway recognition pathway. Within the rough endoplasmic reticulum, enzymes intended to become lysosomal enzymes are tagged with a carbohydrate known as mannose, depicted below.


From here, the mannose-enzyme complex is transported to the cis-Golgi Apparatus. Within the cis-Golgi Apparatus, the mannose within the mannose-enzyme complex is converted to mannose-6-phosphate by a two-step procedure, involving 2 enzymes.

Remember, the final goal is to somehow make the mannose, a mannose-6-phosphate. This is done by the addition of a phosphate group, in any way possible, and this is what the enzymes allow.

  1. The first step involves the addition of a phosphorylated amine sugar. The amine sugar is called N-acetylglucosamine (GlcNAc). Thus, the structure added to mannose is GlcNAc-P, where the “P” represents the phosphate group. This GlcNAc-P is transported to the lysosomal enzyme, bound to a structure known as UDP. The binding of GlcNAc-P and removal of UDP is catalyzed by the enzyme GlcNAc phosphotransferase. Just remember that GlcNAc-P is transferred to mannose, and thus the enzyme is a phosphotransferase of the GlcNAc variety.
  2. At this stage, the mannose sugar contains a GlcNAc-P. However, the goal is simply to have a “-P” attached, or just a phosphate group. Thus, the GlcNAc is removed by an enzyme known as the “uncovering” enzyme, UCE, a type of enzyme called a GlcNAc phosphoglycosidase, but the phosphate is left. This produces the final product, mannose-6-phosphate (M6P), that is attached to the enzyme.

Phew, that was a crazy number of chemicals I just typed out there, but don’t worry, it’s perfectly understandable. Let’s try and make this even clearer.

“Oh, wow!” I said, glancing at the PS4 bundle.

“If I bought it, I would get a PS4, plus two games, and it’s at a great price too! But I already have one of the games in the bundle…”

“That’s alright, I’ll get the bundle anyway, and maybe give one of my friends the game I already have.”

It’s the same logic behind the M6P pathway. The mannose sugar needs to obtain a phosphate, and the only way it can do this is by obtaining phosphate through GlcNAc. So the mannose obtains a GlcNAc-P, and then gets rid of the GlcNAc so it just has the “-P” or the phosphate.

From here, the M6P-enzyme complex travels along the trans-Golgi Apparatus, towards M6P receptors, where the complex is loaded into an transport vesicle. At this stage, the M6P-enzyme complex remains bound to the M6P receptor which was also loaded into the transport vesicle.

This transport vesicle containing the M6P receptor and the M6P-enzyme complex travels to a structure called a late endosome and deposits the lysosomal enzymes within it. The pH within the late endosome is relatively low, usually around 6.0, and at this pH, the M6P receptor is able to dissociate from the lysosomal enzyme. This results in the M6P-enzymes becoming deposited in the endosome. Here, the phosphate is removed and the remaining product becomes the stored form of the lysosomal enzymes, whereby it is stored within the late endosome, now called a lysosome.

Meanwhile, M6P receptors move out of the lysosome in the form of an M6P transport vesicle from the lysosome, and move back to the trans-Golgi Apparatus, where M6P receptors reenter the Golgi Apparatus and can be reused. The entire cycle can be depicted in the diagrams below.


Mechanism of Action of Lysosome: 

There are 3 ways in which the lysosome can intake and break down products within the cell:

1) Material internalized by fluid-based pinocytosis and receptor-mediated endocytosis binds to a receptor on the cell surface and then forms a vesicle from the cell membrane of a cell. This vesicle binds to an early endosome, called a sorting endosome, located close to the cell membrane. The pH of the sorting vesicle is usually low, which encourages the dissociation of the receptor and the endocytosed products. The receptor then is loaded onto a recycling endosome which travels back to the cell membrane and lodges the receptor back into place. The early endosome, after giving off the recycling endosome, becomes a late endosome, containing the endocytosed products, It moves towards the Golgi Apparatus, where it fuses with lysosomes, where internalized    products are decomposed or broken down within the lysosome.


2) Senescent organelles and large, dysfunctional proteins are shuttled into lysosomes by a process known as autophagy. Autophagy occurs as the endoplasmic reticulum gives off a double layered vesicle that becomes progressively larger and surrounds the obsolete structures and organelles. This structure is called an autophagosome. This autophagosome fuses with a lysosome to form an autolysosome and all internalized structures are removed. Autophagy is very important in the process of atrophy, and therefore allows the cell to survive in times of low nutrient supply.


3) Phagocytosis, a process reserved for phagocytes (neutrophils and macrophages) involves the engulfing of a large amount of cellular debris and antigens, and surrounding them with a membrane, forming a phagosome. This phagosome then fuses with the lysosome to form a phagolysosome, in which the engulfed products are broken down.


Summary of Mechanism of Lysosomes:



Proteasomes are protein complexes located inside cells that are extremely important in the breakdown of damaged or unneeded proteins via proteolysis, reaction that breaks peptide bonds in proteins.

Structure of a Proteasome:

In structure, a proteasome is a cylindrical complex containing a “core” of 4 stacked rings forming a central pore. Each ring is composed of 7 distinct proteins. This core is called a 20S Proteasome.


As visible in the diagrams above, these guys have 2 inner beta rings, and 2 outer alpha rings.

It is the two beta rings that contain the active enzyme sites, and these sites are located towards the inside of the proteasome structure. Thus, structures must pass into the proteasome in order to be proteolytically cleaved.

The two alpha rings that are located on the outer part of the proteasome core, and these alpha rings form a gate that controls the movement of proteins into the proteasome, not allowing peptides longer than 4 amino acids into the interior of the 20S proteasome. These alpha sub-units are controlled by binding to “cap proteins” or regulatory proteins which are literal caps that seal the proteasome on the top and bottom. These caps only open when they are exposed to a particular structure, called ubiquitin, which will be described below.

This cap protein is called a 19S Proteasome, and consists of a 10S lid and a 9S base.


Together, both 19S and 20S proteasome form a 26S Proteasome which refers to the entire proteasome complex.


20S proteasomes can also associate with another type of regulatory protein, known as an 11S Proteasome, which contains 11 sub-units rather than the 19 sub-units of the 19S proteasome. The 11S proteasome promotes the disintegration of small polypeptides, but not large proteins. It is very important for producing small peptides via breakdown that bind to the Major Histocompatability Complex (MHC) of macrophages, and thus plays a crucial role in the immune system.

And just in case you guys are wondering, here’s how a 26S proteasome looks from the top (The cap in this one is an 11S cap, evidently very small).

Mechanism of Action of a Proteasome:

The mechanism is simple. Any protein marked for degradation has a 76 amino acid protein known as ubiquitin attached onto it. Remember that the protein marked for degradation must move towards the inside of the proteasome, where all the enzymatically active sites of the beta rings of the proteasome are located.

There is a lot of ubiquitin located within the cell, after all, it is called ubiquitin because it is ubiquitous! Thus, ubiquitin must undergo several priming reactions before it can attach to the protein.

First, ubiquitin is primed by an ATP dependent E1 activating enzyme. The activated ubiquitin is then transferred to an E2 ubiquitin conjugating enzyme, which simply acts as an escort to transfer activated ubiquitin to the third enzyme, E3 ubiquitin ligase, usually referred to as simply ubiquitin ligase, an extremely specific protein that determines whether or not ubiquitination will continue.

The tagging of the protein ubiquitin, is catalyzed by an enzyme known as ubiquitin ligase. Once a single ubiquitin is bound to the protein, it is a signal for multiple ubiquitin molecules to bind to the protein. This creates a polyubiquitin complex, recognized by the 19S and 11S proteasome or cap proteins.

This polyubiquitin chain is highly folded, and thus, is first unfolded, then funneled through the proteasome, where it is broken down and degraded by the enzymatic action of the Beta chains in the proteasome core.

Proteasomes digest the protein into much smaller peptides, usually between 6 to 12 amino acids long. These peptides, if unusable, are released from the cell by exocytosis, thus disposing of the protein waste in the cell. If usable however, the amino acids themselves may be individually obtained from the peptides and recycled.

Of course, you can’t forget why proteasome need to come into action in the first place. They play an extremely important role in apoptosis, atrophy and the removal of stressed proteins that have folded incorrectly or are dysfunctional. They effectively “clean up” the cell of proteins that are not functioning at maximum efficiency.

That’s all guys! Here are, as usual some extra resources for you guys.


Mannose-6-Pathway Explained (5:53)

Lysosomes in Detail (24:43)

Ubiquitin Proteasome System (6:14)


1. Which one of the following is not a mechanism of action of lysosomes?

A. Phagocytosis

B. Ubiquitin-Proteasome System

C. Receptor-mediated endocytosis

D. Autophagy

2. Which of the following is true regarding proteasomes?

A. The 20S proteasome consists of 2 inner alpha rings and 2 outer beta rings.

B. The 11S proteasome is important in breaking down very large proteins to small peptides

C. The Alpha rings of the 20S proteasome are associated with “cap proteins”

D. The “lid” of the 19S proteasome contains 9 sub-units.

3. Which of the following proteins demonstrates the highest specficity in the proteasome-ubiquitin system?

A. E1 ubiquitin activating enzyme

B. E2 ubiquitin conjugating enzyme

C. E3 ubiquitin ligase


4. A 40 year old female with chronic congestive heart failure has a productive cough with a rust colored sputum. Cytology shows numerous hemosiderin -laden macrophages. Which of the following organelles within the macrophage can explain this?

A. Lysosome

B. Ribosome

C. Golgi Apparautus

D. Endoplasmic Reticulum


[Why A for number 4? Heterophagocytosis requires that endocytosed material are fused with a lysosome and broken down. In congestive heart failure, there is extravasation (squeezing out) of RBCs or red blood cells into alveoli of the lungs, where macrophages present break down hemoglobin in the RBCs to produce a brown, iron rich pigment, hemosiderin.]

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