Protein Degradation - Online Tutor, Practice Problems & Exam Prep

Protein degradation occurs primarily through two pathways: the ubiquitin-proteasome pathway and the lysosomal pathway. The ubiquitin-proteasome pathway involves tagging proteins with ubiquitin, targeting them for degradation by the proteasome, which breaks them down into short peptides using ATP. In contrast, the lysosomal pathway degrades proteins using lysosomal enzymes without the need for tagging. Regulation of protein degradation is crucial for maintaining cellular function, as it controls protein lifespans and removes misfolded proteins that could cause cellular damage.

Ubiquitin Proteasome Pathway

Hi, in this topic, we're going to be talking about protein degradation. One of the main ways that proteins are degraded is through what we call the ubiquitin-proteasome pathway. So what is the proteasome? The proteasome is actually a multi-subunit protein complex that is able to degrade proteins. So how does this happen? Well, proteins must be labeled with another protein called ubiquitin, and if proteins are labeled with the ubiquitin, that targets them to the proteasome for degradation. So what is ubiquitin? It's about 76 amino acids protein. It's found in all eukaryotic organisms. And in order to degrade proteins, proteins need to be labeled with at least one called mono-ubiquitination or two or more than one which is poly-ubiquitin proteins. So this pathway occurs in five steps. So get ready to write down these steps and sort of learn these steps, and it requires energy from ATP. So let's go through these steps together.

First, ubiquitin is activated by an E1, ubiquitin-activating enzyme. So in our image here, you can see E1 and here's ubiquitin and it becomes activated. So this is the activation to form this complex. Then, in step two, the activated ubiquitin then binds the E2, ubiquity-dating conjugating enzyme. So here we see this process happening. So this is step one and this is step two, and finally, after step two, you end up with E2 bound to ubiquitin.

Then for steps 3, 4, and 5 let me show you. The E2 complex with the ubiquitin is attached onto the E3 and is attached onto the target protein via the E3 ubiquitin ligase. So, we can see this here. We have our E2 and ubiquitin, the E3 comes in and attaches it to the protein that needs to be ubiquitinated. Now there is an important thing to realize about the E3 protein, and that each E3 recognizes a different substrate protein. So there's a ton of E3 proteins, each recognizing a different protein for ubiquitination. So E3 is responsible for selecting the protein that needs to be degraded. So this is going to be step three.

Once this complex is formed, the ubiquitinated substrate becomes recognized by the proteasome. And so you can see that this step can happen multiple times with multiple coordination. And once this happens, this is going to be step four. And the proteasome recognizes it. Then step five is the protein is unfolded and fed through the proteasome which is actually cylindrical, and the proteasome contains ATP-dependent proteinases which are enzymes that chop up proteins into short peptides. So the entire protein remains bound to the proteasome until it's entirely chopped up.

So what does the proteasome look like? In step five, remember that the protein is unfolded and fed through. So you can imagine there's this big complicated protein here. It's been labeled with ubiquitin UB and it gets targeted to the proteasome and it gets fed through this channel as a single, sort of unfolded polypeptide chain. And inside this channel is where the protein is bound and chopped into short peptides. So that is the ubiquitin-proteasome pathway of protein degradation. Now let's move on.

Lysosomal Pathway

Okay, in this video, we're going to be talking about the lysosomal pathway, which is another way that proteins are degraded in the cell. So the lysosome is a really important organelle because it can degrade proteins and it does this because the lumen in the lysosome, where the inside of the lysosome contains enzymes known as proteases, which are responsible for chopping up proteins. And so, there's this process called autophagy, and it's kind of a process of cell death or cell destruction. You may have heard of it before: cell eating. But all of these processes involve a lot of protein destruction and this protein destruction happens via lysosomes and autophagy. And you don't necessarily need to know much about ontology right now, but we will talk about it in future topics. And just sort of know that autophagy, the lysosome, is responsible for these kind of overarching protein degradation pathways like autophagy. And then the lysosomal pathway is kind of special in a way because it can really rapidly respond to nutrients and external signals. So proteins that are degraded by the lysosomal pathway don't need to be labeled; they just need to get into the lysosome, which can happen really quickly. So if we're looking at the lysosomal protein degradation here, we have a lysosome. This is going to be the lumen of the lysosome, the internal part of the lysosome, and we have a polypeptide chain here, and it is bound to some type of protease, which is responsible for breaking it up into its free amino acids and degrading the protein. So, now that's the lysosomal protein degradation pathway. So, now let's move on.

Degradation Regulation

So in this video, we're going to talk about protein degradation regulation. Protein degradation in and of itself can regulate the amount of protein in the cell at a certain time. Because if we degrade the protein, then it can no longer do its function. So, degradation is a form of protein regulation. There are really two reasons that protein needs to be regulated via degradation. The first is that proteins have lifespans, and those lifespans can vary from seconds to decades. But eventually, when the protein runs through its lifespan, it needs to be degraded. And if it isn't, that means that there aren't proper protein levels, and the protein levels are crucial for certain chemical reactions to occur. So, if you have too much or too little protein, the chemical reaction won't occur and that would be devastating.

So how does a protein get degraded when its lifespan is up? I mean, it's not that it just turns 80 and, um, its heart fails because that doesn't make any sense for a protein. What usually happens for a protein is that a protein contains something like an internal degradation signal, and this degradation signal is hidden until it's time to be degraded, and then when it's time to be degraded, something happens in the cell which triggers the release of the signal, and then something like ubiquitin, for instance, can bind to this region and target it for degradation.

Now, a second reason for regulation is that proteins occasionally misfold and that can be devastating to the cell when they do this. Abnormally folded proteins or misfolded proteins can actually aggregate in the cell and cause disease, which we obviously don't want. So we need proteins to be able to degrade over time, either when they're misfolded or when their time is up so that they don't wreak havoc in the cell. How this would happen for the protein lifespan is, for instance, some type of conformational change. So you have this one protein here. A conformational change occurs here, which changes the conformation but also releases an internal degradation signal which before was hidden and now is released, and then ubiquitin can bind. And that can target the protein for degradation when its lifespan is up. So now let's move on.

Which of the following is not associated with protein degradation?

• A. Ubiquitin-proteasome pathway
• B. Lysosomal pathway
• C. 5' Cap
• D. N-terminal degradation signal

Which protein is responsible for attaching a ubiquitin molecule onto a protein to target it for degradation?

• A. E1 ubiquitin activation enzyme
• B. E2 ubiquitin conjugating enzyme
• C. E3 ubiquitin ligase
• D. E4 ubiquitin attachase

Before entering the proteasome the protein marked for degradation is unfolded.

• A. True
• B. False

What is the name of the signal released by some proteins when they can be degraded?

• A. Ubiquitin binding signal
• B. N-terminal degradation signal
• C. C-terminal degradation signal
• D. Proteosome signal

Here’s what students ask on this topic:

What is the ubiquitin-proteasome pathway in protein degradation?

The ubiquitin-proteasome pathway is a primary mechanism for protein degradation in cells. It involves tagging proteins with ubiquitin, a 76-amino acid protein found in all eukaryotic organisms. This tagging process, known as ubiquitination, targets the proteins for degradation by the proteasome, a multi-subunit protein complex. The pathway occurs in five steps: activation of ubiquitin by an E1 enzyme, transfer to an E2 enzyme, attachment to the target protein by an E3 ligase, recognition by the proteasome, and finally, degradation into short peptides using ATP. This pathway is crucial for regulating protein levels and removing damaged or misfolded proteins.

How does the lysosomal pathway degrade proteins?

The lysosomal pathway degrades proteins using lysosomal enzymes within the lysosome, an organelle containing a variety of hydrolytic enzymes. Unlike the ubiquitin-proteasome pathway, proteins do not need to be tagged for degradation. Instead, they are transported into the lysosome, where enzymes such as proteases break them down into amino acids. This pathway is particularly responsive to nutrient levels and external signals, allowing for rapid degradation of proteins. It also plays a role in processes like autophagy, where cellular components are engulfed and degraded to recycle nutrients and maintain cellular homeostasis.

Why is protein degradation important for cellular function?

Protein degradation is crucial for maintaining cellular function for several reasons. First, it regulates protein levels within the cell, ensuring that proteins are available in the right amounts for various biochemical reactions. Second, it removes damaged or misfolded proteins that could aggregate and cause cellular damage or disease. Proteins have varying lifespans, and their degradation prevents the accumulation of old or non-functional proteins. Additionally, degradation pathways like the ubiquitin-proteasome and lysosomal pathways help in recycling amino acids, which can be reused for new protein synthesis, thus maintaining cellular homeostasis.

What roles do E1, E2, and E3 enzymes play in the ubiquitin-proteasome pathway?

In the ubiquitin-proteasome pathway, E1, E2, and E3 enzymes play distinct roles in the ubiquitination process. E1, the ubiquitin-activating enzyme, initiates the process by activating ubiquitin in an ATP-dependent manner. E2, the ubiquitin-conjugating enzyme, then receives the activated ubiquitin from E1. Finally, E3, the ubiquitin ligase, facilitates the transfer of ubiquitin from E2 to the target protein. E3 enzymes are crucial because they recognize specific substrate proteins, ensuring that only proteins destined for degradation are tagged. This specificity is vital for the regulation and maintenance of cellular protein levels.

How does protein misfolding affect cellular health, and how is it managed?

Protein misfolding can have severe consequences for cellular health, as misfolded proteins can aggregate and disrupt cellular functions, potentially leading to diseases such as Alzheimer's and Parkinson's. Cells manage misfolded proteins through degradation pathways like the ubiquitin-proteasome and lysosomal pathways. Misfolded proteins are recognized and tagged with ubiquitin, targeting them for degradation by the proteasome. Alternatively, they can be transported to lysosomes for degradation. This process helps maintain protein quality control, preventing the accumulation of toxic protein aggregates and ensuring cellular homeostasis.