Protein Motifs and Domains - Video Tutorials & Practice Problems
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Protein Motifs and Domains
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So now that we've introduced tertiary structure, we can talk about protein motifs and domains. So it turns out that tertiary protein structure actually includes the distribution of secondary structures such as alpha helices, beta strands, beta turns, and loops to make protein motifs and protein domains. And so just to get you guys oriented on the hierarchy of all of these terms and structures, we've got this image below. And so, of course, at the lowest level of the hierarchy, composition, as well as amino acid sequence, and the sequence is the particular order of amino acids from the n terminal n n to the c terminal n of a polypeptide chain. So then, what we have is our secondary structures, and we talked about multiple types of secondary structures including alpha helixes, beta sheets, and, loops and turns loops and beta turns. And so, then what we did was we jumped straight from secondary structure to tertiary structure. And now that we've got tertiary structure introduced, we can better understand this organization. So it turns out that secondary structures actually come together to form super secondary structures, which are also known as then, the domains are just independent folding units. And so together, the motifs and the domains, as you can see by this bracket here, they come together to form the tertiary structure which we know as the overall three d shape of the protein. And so, what we're going to first do is talk about the super secondary structures or the motifs, and then, once we're done talking about the motifs, we'll go and we'll talk about the protein domains. So, I'll see you guys in our next video where we'll talk about protein motifs.
2
concept
Protein Motifs and Domains
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Video transcript
So as we said in our previous video, motifs are also known as super secondary structures. And if you Google the definition of motif, what you'll find is that in the everyday language, it means a pattern, and that's really all a protein motif is. It's literally just a specific pattern and combination of secondary structures such as, for instance, alpha helices, beta strands, beta turns, and loops. And so, motifs can have varying functions or varying jobs in different proteins, and so they can, have different functions in proteins that include providing, strength, as well as creating binding sites for different molecules. And so it turns out that there are actually several 100 of known motifs. And so it's not likely that your professor is gonna want you to memorize all of them. So, there are a few common ones that you might wanna know, and so I've tried to provide those here. And so what you'll see is that we've got a helix loop helix motif, a coiled coil motif, motif, beta alpha beta motif, and a hairpin motif. And so in our example below, what we're going to do is label the, corresponding motifs. And so for our first motif here, what we have is the helix loop helix motif. And literally, this is just an alpha helix, so notice it's an alpha helix with a loop and another alpha helix. And that's exactly coiled coil. And so the coiled coil, what you'll see is is that it's a alpha helix, it's when you have 2 alpha helices that are actually winded up on one another. And so, remember that a single alpha helix is going to be an interchange structure, so it's going to be within 1 single polypeptide chain. And so, an alpha helix is different than a coiled coil because the alpha helix is a single, polypeptide chain, whereas the coiled coil is 2 polypeptide chains, 2 alpha helix structures that are winded up and twisted on one another. And this type of structure really does create a lot of strength. So, whenever you see coiled coil structures, you know that that protein is gonna provide a lot of strength. So the next motif that we have is the beta alpha beta motif. And so with this beta alpha beta motif, it's literally just a a beta strand connected to an alpha helix which is connected to another beta strand, so it's beta alpha beta, pretty straightforward. So then our last and final motif is the hairpin motif. And with the hairpin motif, it's literally just 2 beta strands going, in anti parallel direction that's looped together by a hairpin loop. So, it's a small little hairpin loop that connects 2, beta strands that are anti parallel, they're going in opposite directions. And so, these are some of the common motifs that you might want to try to commit to memory that your professor might try to ask you guys about. And so, we'll be able to get a little bit of practice in our practice video, so I'll see you guys there.
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Problem
Problem
Which of the following colored regions in the images below is not an example of a supersecondary structure?
A
Greek key.
B
β-meander.
C
βαβ unit.
D
Type I β-turn
E
Helix-loop-helix
4
concept
Protein Motifs and Domains
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3m
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Video transcript
So now that we've talked about protein motifs, we can focus on protein domains. And so, domains are really just combinations of motifs. And so, again, motifs are just patterns and combinations of secondary structures and domains are combinations of motifs, so you can see how that hierarchy builds up on itself. And really, the interesting thing about domains is that they are independently folding units. So they have the ability to independently fold from the rest of the protein. And also, domains have the potential about domains is that they are literally an extension to the peptides backbone. And so, domains can be found on a single poly peptide chain. One single polypeptide chain could have multiple domains because literally a domain is just the an extension to the peptide backbone. Mode. So it's really important not to get domains confused with subunits. And so subunits over here is really a term that we're gonna talk more about when we get to quaternary structure a little later in our course. But subunits are completely separate polypeptide chains and their backbones are not connected. But again, domains are literally just an extension to the peptides backbone. Backbone. And so, they are very different terms, and it's important to point that out now just to make sure that you're starting to get that, make that realization. And so again, we'll revisit this term subunits when we get to quaternary structure later in our course. Now, another very important thing to notice about domains is that they're often grouped according to the structural and functional characteristics that they have. And so, scientists can actually learn a lot about, they can learn a lot from domains. So say a scientist finds a brand new protein that they know nothing about, and within this brand new protein, a scientist recognizes a smaller, particular domain within that big protein and that domain that they recognize, they've studied that domain in another protein and they've learned a lot about that domain. And so, by knowing this particular domain that's in this new protein, that can reveal some of the functions that this new protein has. And so, that's, why it's very important and critical to study a protein's domains. And so in our example below, what we're gonna do is circle the 3 most obvious domains in the figure. And so in this figure down below, this is literally one single polypeptide chain that is completely folded up. And so, we've colored the different domains that make it pretty easy to see. So what you'll see is that we've got one domain in the back over here in purple, we've got another domain in the middle here in green, and then we've got our last domain over here in blue. And so, what you can see is that even though this is a single polypeptide chain, it has these independently folding units. And so, if you were to cut off, say, this, purple section over here from the rest of the chain, this, section, because it's its own domain, we would expect it to still fold properly. And the same goes for all of these other domains here, so these are the 3 domains. And so, this concludes our lesson on protein motifs and domains and we'll be able to get some practice in our practice video. So I'll see you guys there.
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Problem
Problem
Which of the following statements concerning a Cas9 endonuclease's protein domains is true?
A
They are a form of its secondary structure.
B
They have only been found in eukaryotic proteins.
C
All its domains consist of separate polypeptide subunits.
D
They retain their shape when separated from the protein.
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Problem
Problem
Which of the following is true concerning the motifs and domains of proteins?
A
Many domains make up a motif.
B
Every polypeptide chain is limited to one domain.
C
Separate proteins with similar domains are likely to have a similar function.
D
All domains of a protein have the same function.
7
Problem
Problem
Appropriately label the domains of the membrane embedded protein in the figure below.
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8
Problem
Problem
The structure of an immunoglobulin G (antibody) molecule is shown schematically below. The black solid lines depict individual polypeptides and so there are four polypeptides in the quaternary structure of this molecule. Each of the spheres represents a stretch of about 100 amino acids folded independently of the rest of the polypeptide and performs a specific function in the molecule. Therefore, each sphere was given its own individual name (VH, CH1, CH2, etc.). Without knowing any additional details, you can predict that there must be TWELVE ___________________ in this molecule.
A
α-helices.
B
Domains.
C
Subunits.
D
Motifs.
9
Problem
Problem
What is the main difference between an endonuclease's domains and its subunits?
A
Its domains are composed mostly of the α-helix, while subunits contain both α-helices and β-sheets.
B
Its subunits are separate polypeptide chains, while its domains constitute a part of a polypeptide chain.
C
Its domains do not have secondary structure, whereas its subunits have do.
D
Its domains are stabilized by hydrogen bonds, while its subunits are stabilized by disulfide bonds.