Ubiquitination - Video Tutorials & Practice Problems
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1
concept
Ubiquitination
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Video transcript
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, our 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 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 other otherwise, you should be able to recognize this as an amide linkage. Now, of course, what's important to note is that it's, multiple ubiquitin peptides will actually link together to form a chain of ubiquitin peptides on the target protein. And we kinda 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, 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.
2
concept
Ubiquitination
Video duration:
3m
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Video transcript
So what exactly is the purpose of ubiquitination? Well, ubiquitination actually targets proteins. So 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. And so essentially, what we're saying is that these proteasomes are specialized for breaking down large proteins into tiny, tiny peptide fragments and free amino acids. And so, if we take a look at our image down below, notice that the first part of this image here is exactly the same as was in our last lesson video. And so, we know that some proteins can be targeted for ubiquitination, which is essentially taking these ubiquitinpeptides peptides here and linking them into a chain, to the target protein and this is an ATP or an energy intensive process. And so here in this video, what we're learning is that ubiquitination of a protein actually targets that protein for degradation by a large protein complex known as a proteasome. And so the proteasome is for proteolytic activity. So it's going to break down this, targeted protein here into tiny tiny peptide fragments. And so over here, what we have is the degraded protein and so the ubiquitin peptides here can actually be recycled and reused to target another protein protein. And so, as the name ubiquitination suggests, this is a very ubiquitous process. So it occurs in pretty much every single eukaryotic organism from yeast all the way up to humans themselves. And so, this ubiquitination process is a process of post translational modifications. And so it's going to regulate enzymes activities. And so that's because ubiquitination is actually going to lead to the decrease in cellular protein concentration. Since it marks proteins for degradation and so therefore, ubiquitination can actually decrease an enzyme's activity or initial reaction velocity, V not And so that makes ubiquitination a very ubiquitous form of enzymatic regulation. Now, ubiquitination is so ubiquitous that it's pretty much capable of regulating virtually every single cellular process in our cells, which is amazing and shows why ubiquitination is worth studying and understanding. And so this here concludes our lesson on ubiquitination and how it targets proteins for degradation. And so we'll be able to apply the concepts that we've learned here and some practice problems moving forward. So I'll see you guys in our next video.
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Problem
Problem
_________ 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.
4
Problem
Problem
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.
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Problem
Problem
Ligation of a ubiquitin peptide's ______________ charged carboxylate group to the R-group of a target protein's ___________ residue forms a(n) _____________ bond.