Ubiquitination - Online Tutor, Practice Problems & Exam Prep

Ubiquitination is a crucial process where the small protein ubiquitin, consisting of 76 amino acids, is covalently attached to target proteins, primarily through lysine's R group. This ATP-dependent modification marks proteins for degradation by proteasomes, large complexes that break down proteins into peptides and amino acids. Ubiquitination regulates enzyme activity by decreasing cellular protein concentration, making it a vital mechanism in various cellular processes across eukaryotic organisms. Understanding this process is essential for grasping protein regulation and cellular dynamics.

Ubiquitination

In this video, we're going to introduce ubiquitination. So, ubiquitin is actually a small protein. It's actually a highly conserved and a very prevalent or ubiquitous small protein. And that's exactly where ubiquitin gets its name from because ubiquitin is so ubiquitous that it's pretty much found in every eukaryotic organism from yeast all the way up through humans. And so, ubiquitin, this small ubiquitous protein, only contains 76 amino acid residues. And so, ubiquitination is just a process that involves the covalent attachment of these ubiquitin peptides to a target protein. And so ubiquitination is also an energy intensive process or an ATP dependent process, which means that it utilizes energy in the form of ATP in order to covalently attach these ubiquitin peptides to the target protein.

And so if we take a look at our image down below in our example of ubiquitination, notice over here on the left hand side, we're showing you a target protein here. And these green circles with 'u's in them each represents a different ubiquitin peptide, each with 76 amino acid residues. And so we can go ahead and label these green 'u's as ubiquitin peptides. And so, of course, this arrow here represents the process of ubiquitination which we know is an ATP dependent process and so notice that it's utilizing ATP in order to covalently attach the target protein here with these ubiquitin peptides. Now it turns out that these ubiquitin peptides are covalently attached to the target protein, through the R-group of a lysine amino acid residue, which is the amino acid residue that is most susceptible to ubiquitination. And so, down below what we can say is that these ubiquitin peptides here are going to be covalently attached to our target protein, specifically through lysines, R-group.

And so, over here on the right hand side, we can get a better visualization of that idea. And so notice that our target protein is represented by this red structure here. The squiggly line represents the remainder of our large, red target protein. But notice that we're showing you that it's lysine's R-group, which we know lysine's R-group ends with an amino group at the end. That is most susceptible to ubiquitination. And so here we have the ubiquitin peptide and the carboxylate group of the ubiquitin peptide can interact with lysine's R-group and through a mechanism here, they are able to be covalently attached to each other. And so, this blue bond here represents the covalent attachment of the ubiquitin to the target protein through lysines R-group. And so, notice here that this bond right here is actually an amide linkage. Since we have a carbonyl group right here. And we, the carbonyl group is attached covalently to the nitrogen atom. So this is an amide linkage, and, you might think that because these are proteins, this is a protein and so is ubiquitin. Because these are proteins and this is an amide linkage, you might think that this is a peptide bond. But recall that peptide bonds are the ones that are in the backbone of the protein. Whereas, because this amino group right here is not part of the backbone, it's actually part of lysine's R-group, this is actually not a peptide bond. Instead, sometimes, it's referred to as an isopeptide bond. An isopeptide bond. Sometimes. But otherwise, you should be able to recognize this as an amide linkage.

Now, of course, what's important to note is that multiple ubiquitin peptides will actually link together to form a chain of ubiquitin peptides on the target protein. And we kind of already saw that before over here in the image on the right. Notice that we have a chain of ubiquitin peptides attached to our target protein and so through the same mechanism as up above, we're able to take another ubiquitin peptide and attach it covalently to the target protein in this ubiquitin molecule. So we form another bond right here, another covalent bond. So we're linking these ubiquitin peptides. And so in our next video, we're going to talk about exactly why it is that this ubiquitination process is a form of regulation of protein activity. And so, this here concludes our introduction to ubiquitination, and I'll see you guys in our next video.

Ubiquitination

So what exactly is the purpose of ubiquitination? Well, ubiquitination actually targets proteins. It marks proteins for degradation by a complex known as a proteasome. And so, what exactly are these proteasomes? Well, proteasomes are just large protein complexes themselves that are specialized for proteolytic activity. Essentially, these proteasomes are specialized for breaking down large proteins into tiny, tiny peptide fragments and free amino acids.

If we take a look at our image down below, notice that the first part of this image is exactly the same as in our last lesson video. We know that some proteins can be targeted for ubiquitination, which involves taking these ubiquitin peptides and linking them into a chain to the target protein, and this is an ATP or an energy-intensive process. In this video, we're learning that the ubiquitination of a protein targets that protein for degradation by a large protein complex known as a proteasome. The proteasome is for proteolytic activity; it will break down this targeted protein into tiny peptide fragments.

Over here, we have the degraded protein, and the ubiquitin peptides can be recycled and reused to target another protein. As the name ubiquitination suggests, this is a very ubiquitous process. It occurs in pretty much every single eukaryotic organism, from yeast all the way up to humans. This ubiquitination process is a form of post-translational modifications. It is going to regulate enzymes' activities, leading to the decrease in cellular protein concentration since it marks proteins for degradation. Therefore, ubiquitination can decrease an enzyme's activity or initial reaction velocity, \(V_0\). This makes ubiquitination a very ubiquitous form of enzymatic regulation.

Ubiquitination is so ubiquitous that it is capable of regulating virtually every single cellular process in our cells, which is amazing and shows why ubiquitination is worth studying and understanding. This concludes our lesson on ubiquitination and how it targets proteins for degradation. We will be able to apply the concepts that we have learned here in some practice problems moving forward. I'll see you guys in our next video.

_________ involves covalent attachment of peptides leading to _________ of the target protein by ________.

• A. Ubiquitination ; Activation ; Proteasome.
• B. Glycosylation ; Degradation ; Ribosome.
• C. Ubiquitination ; Degradation ; Proteome.
• D. Ubiquitination ; Degradation ; Proteasome.
• E. Acetylation ; Activation ; Proteasome.

Which of the following is true regarding protein ubiquitination?

• A. Ubiquitin tagged proteins are usually degraded in the cell.
• B. Ubiquitin is a ubiquitous, small nucleotide.
• C. Covalent attachment of ubiquitin usually occurs via the R groups of methionine amino acid residues.
• D. Ubiquitin links to the target protein only via hydrogen bonds.
• E. Only a and c are true.
• F. All of the above are true.
• G. None of the above are true.

Ligation of a ubiquitin peptide's ______________ charged carboxylate group to the R-group of a target protein's ___________ residue forms a(n) _____________ bond.

• A. Neutrally ; Histidine ; Hydrogen.
• B. Negatively ; Leucine ; Isopeptide.
• C. Positively ; Lysine ; Ionic.
• D. Positively ; Lysine ; Disulfide.
• E. Negatively; Lysine ; Hydrogen.
• F. Negatively ; Lysine ; Isopeptide.

Here’s what students ask on this topic:

What is ubiquitination and why is it important?

Ubiquitination is a process where the small protein ubiquitin, consisting of 76 amino acids, is covalently attached to target proteins, primarily through the R group of lysine residues. This ATP-dependent modification marks proteins for degradation by proteasomes, which are large complexes that break down proteins into peptides and amino acids. Ubiquitination is crucial because it regulates enzyme activity by decreasing cellular protein concentration, thereby controlling various cellular processes. This regulation is essential for maintaining cellular homeostasis and responding to cellular stress, making ubiquitination a vital mechanism in eukaryotic organisms.

How does ubiquitination target proteins for degradation?

Ubiquitination targets proteins for degradation by attaching ubiquitin molecules to the target protein, forming a polyubiquitin chain. This process is ATP-dependent and involves the covalent attachment of ubiquitin to lysine residues on the target protein. Once ubiquitinated, the protein is recognized by proteasomes, large protein complexes specialized for proteolytic activity. The proteasome degrades the ubiquitinated protein into small peptide fragments and free amino acids, which can be recycled by the cell. This mechanism ensures the removal of damaged or unneeded proteins, maintaining cellular function and homeostasis.

What role do proteasomes play in ubiquitination?

Proteasomes play a critical role in ubiquitination by degrading ubiquitinated proteins. Once a protein is tagged with ubiquitin, it is recognized and bound by the proteasome, a large protein complex with proteolytic activity. The proteasome then unfolds and translocates the ubiquitinated protein into its core, where it is broken down into small peptide fragments and free amino acids. These degradation products can be recycled by the cell. Proteasomes ensure the removal of damaged, misfolded, or excess proteins, thereby regulating protein quality and quantity within the cell.

What is the significance of lysine residues in ubiquitination?

Lysine residues are significant in ubiquitination because they serve as the primary attachment points for ubiquitin molecules. The R group of lysine contains an amino group that forms a covalent bond with the carboxylate group of ubiquitin, creating an amide linkage. This specific attachment is crucial for the formation of polyubiquitin chains, which signal the target protein for degradation by proteasomes. The ability of lysine residues to form these covalent bonds makes them essential for the ubiquitination process and subsequent protein regulation.

How does ubiquitination regulate enzyme activity?

Ubiquitination regulates enzyme activity by marking specific proteins for degradation, thereby decreasing their cellular concentration. This reduction in protein levels can directly affect the activity of enzymes, as fewer enzyme molecules are available to catalyze reactions. By controlling the degradation of enzymes and other regulatory proteins, ubiquitination can modulate various cellular processes, including cell cycle progression, DNA repair, and signal transduction. This post-translational modification ensures that enzyme activity is tightly regulated in response to cellular needs and environmental conditions.