So now that we've talked about alpha helix and beta sheet secondary structures, in this video we're gonna talk about another type of secondary structure. The beta turns and loops. So beta turns and loops are a type of non repetitive secondary structure. And by non repetitive, all we mean is that they don't have that same repetitive periodic structure that alpha helices and beta sheets have. But beta turns and loops do cause the peptide backbone to change directions. And so beta turns and loops are usually found on the surface of proteins with hydrophilic amino acid residues. And so by being on the surface of proteins, that allows the hydrophilic amino acid residues to easily interact with their aqueous environment that most proteins are sitting in. And also beta turns and loops, they allow for the proteins to take on a folded compact shape. And that's because you can imagine a protein that has a folded compact shape is going to change the backbone direction a lot. Otherwise, it would continue in one direction and it would not have a compact shape. And so, thankfully to beta turns and loops that allow for changes in backbone direction, that allows us to have proteins that have folded compact shapes. Now down below, we're going to distinguish between the loops and beta turns. And so loops are essentially large links of amino acid, of there are large links of amino acids that cause changes in backbone direction without fixed internal hydrogen bonds. So, they do not use fixed internal hydrogen bonds. Now, beta turns on the other hand, which are also known as reverse turns, they are small loops, which have less than 4 amino acid residues, and they cause abrupt changes in backbone direction. And they're able to do that because they're stabilized by fixed internal hydrogen bonds unlike the loops. And so down below in our example, we're going to identify all the loops and beta turns in the figures. And so with our first figure over here on the left, notice we have a single polypeptide chain, and this polypeptide chain has an n terminal n and a c terminal n. And you'll see we have beta sheets, alpha helices, and more beta sheets here, or beta strands. And so notice that this beta strand is connected to this alpha helix here via a loop. And we know that it's a loop because it has 20 amino acids in it, which is greater than 4 amino acids. So this is a large link of amino acids causing a change in the backbone direction. So notice the backbone direction is going in this direction here and then it's changing through this loop. So this is a loop here. And so in our next example over here, notice what we have is a beta turn and we know that this is a beta turn because we can see that the backbone is abruptly changing directions. It's doing a quick u-turn. And, we have a small link of amino acids here, less than 4 amino acids, and we can see that it's stabilized by this hydrogen bond here, an internal hydrogen bond, and so, that's a way to identify as a beta turn as well. And notice over here with the loop, there are no internal hydrogen bonds. And so over here in our image on the the far right, we have a single polypeptide chain that has a bunch of secondary structures in it. It has the yellow structures, which are beta sheets, it has the pink structures in here, which are alpha helices, and it has beta turns and loops. So notice that these grayish links here of long amino acids are the loops, so those are our loops that are causing changes in the backbone direction. And then these blue, these shorter blue, structures that you see throughout are our beta sheets and that's because they're causing abrupt changes in backbone direction with a small amount of amino acid residues. So we can label them as beta turns. And so moving forward, we'll be able to get some more practice with beta turns, and we'll talk about different types of beta turns that exist. So I'll see you guys in those videos.
2
Problem
Problem
Which of the following options contains a true statement about protein turns & loops?
A
Loops & turns can interact with other proteins & the environment.
B
Loops are short links causing abrupt changes in direction & extend only from β strands.
C
Loops and turns usually contain hydrophilic residues located on the interior of proteins.
D
Loops exposed to an aqueous environment are usually composed of hydrophobic amino acids.
3
concept
Beta Turns
Video duration:
5m
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Video transcript
So now that we know a little bit about beta turns and loops, in this video we're going to distinguish between 2 different types of beta turns. Type 1 beta turns and type 2 beta turns. Now, it turns out that there's actually many different types of beta turns, but these are 2 of the more common types of beta turns that your Professor is likely going to want you guys to know. And so both type 1 and type 2 beta turns produce abrupt changes in the backbone direction. They both also contain a total of 4 amino acid residues and they are both stabilized by hydrogen bonding. And so really the main differences between type 1 and type 2 beta turns is that type 1 beta turns are even more common than type 2 beta turns, and they usually contain a proline amino acid residue specifically at position number 2 of the turn. And then type 2 beta turns on the other hand, they're going to be less common and they contain a glycine amino acid residue, but specifically at position number 3 of the turn. And so down below in our example, we can visually distinguish between type 1 beta turn on the left and type 2 beta turn on the right. And what you'll notice is that both type 1 and type 2 beta turn produce an abrupt change in the backbone direction. And so over here, you can see that the backbone direction is starting off in this direction and then it very quickly changes direction and does a u-turn and now it's going in the opposite direction. And the same applies for Type 2 Beta turn, so they both produce these abrupt changes in backbone direction. And also notice that they both contain 4 amino acid residues, as shown by these 4 blue squares in the back of each of the structures, numbered 1, 2, 3, and 4, and they are both also stabilized by hydrogen turn between the carbonyl group and the amino group in the polypeptide backbone. Since we know that only backbone hydrogen bonds stabilize secondary structures and type 1 and type 2 beta terms are a type of secondary structure. So we can see the hydrogen bonds forming in type 1 and the hydrogen bond forming in type 2. And so again, the major differences between type 1 and type 2 beta turn is that type 1 beta turn over here on the left is more common and it has a proline amino acid residue specifically at position number 2 of the turn as shown. So the p r o is the 3 letter code for proline and the 2 is for position number 2. And then for type 2 beta turns over here, they specifically have a glycine amino acid residue at position number 3 of the turn. And so you might be wondering, how am I supposed to remember the differences between type 1 and type 2 beta turn? That's really, really specific. And so I can tell you something that I came up with that helps me remember the differences between type 1 and type 2 beta turn, is that type 1 beta turn, because it has a proline at position 2, and proline's 3 letter code is pro, p r o. Whenever I think of pro, I think of a pro boxer. And what do pro boxers do? They throw 1, 2 punches. And so, when I think of a type 1 beta turn, I literally think of 1, 2 p. And so when I think of 12 p, I'm really thinking of the pro boxer 12 punching. And so, the one here is, a reminder for it's a type 1 beta turn. The 2 is specifically for at position number 2, and the p here is for the proline amino acid residue, since we know that p is the one letter code for proline. And so if you can remember 12 p, then you'll remember type 1, beta turn at position number 2 have a proline amino acid residue and that's exactly what we're seeing over here. Now, for type 2 beta turns on the other hand, all you need to remember is 23g And, really, what this is referring to is that the g of basketball is like the GOAT of basketball. The greatest of all time. And so when you think of the g of basketball, you think about either LeBron James or Michael Jordan. And their jerseys had the number 23 on them. And so, essentially when you think of 23 gs, you think of the GOAT, who's Michael Jordan or LeBron James with the number 23 and that tells us that at, with a type 2 with a type 2 beta turn, at position number 3, there is a glycine amino acid residue. And so, essentially, if you can remember 12p and 23 gs, then you'll be able to remember the differences between type 1 and type 2 beta turns. So you can see that with this type, 23 gs here, that type 2 beta turns, these over here, at position number 3, up here, they have a glycine amino acid residue. So, hopefully that'll help you guys remember the differences between type 1 and type 2 beta turns, and you guys can now go tell all of your friends, hey, I know a great way to remember the differences between type type 1 and type 2. And so we'll be able to get some practice utilizing these concepts and memory tools in our next couple of practice videos. So I'll see you guys there.
4
Problem
Problem
In the peptide below, circle the individual amino acid residues indicating the most likely positions for β-turns:
Video duration:
2m
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5
Problem
Problem
Which of the following statements is true regarding β-turns?
A
Only Type I β-turns are stabilized by hydrogen bonds, not Type II β-turns.
B
Type II β-turns have a Pro residue at position #2 of the turn.
C
Type I β-turns have a Gly residue at position #4 of the turn.
D
Type II β-turns have a Gly residue at position #3 of the turn.
6
concept
Beta Turns
Video duration:
4m
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Video transcript
So now that we've distinguished between type 1 and type 2 beta turns, in this video we're going to talk about beta turn bond angles. And so the bond angles for loops and turns are actually found in multiple regions of the Ramachandran plot. And that's actually a unique feature of loops and turns because we know that with alpha helices and beta sheets, we're able to pinpoint those phi inside bond angles into very specific regions in the Ramachandran plot. So let's take a look at our example down below to refresh our memories. And so we know that we can split a Ramachandran plot into 4 different quadrants. And amino acid residues that are part of a beta sheet will have phi and psi bond angles that fall into the upper left hand quadrant of the Ramachandran plot, whereas amino acids that, are part of an alpha helix will have phi and side bond angles that fall into the lower left hand quadrant of the Ramachandran plot. And so we're able to pinpoint beta sheets and alpha helices to very specific regions within the Ramachandran plot. But we're not able to do the same with loops and turns because loops and turns are found in multiple regions of the rama Chandra plot. So let's take a look at an example of a type 2 beta turn. And so it turns out that some of the phi and psi bond angles of a type 2 beta turn actually lie outside of the expected permissible bond angles for most of the amino acid residues. But we know that glycine is an exception to this because glycine can actually adopt a wide range of phi and side bond angles. Because it has such a small r group. It's literally just a hydrogen atom. And that small r group is able to avoid steric hindrance, which allows it to adopt a wide range of phi and side bond angles. And so it can easily adopt those phi and side bond angles that lie outside of the expected permissible angles for most of the amino acids. And from our mnemonic, 23 3g, we know that type 2 beta turns, specifically at position number 3, have a glycine amino acid residue. And so, glycine is often the residue that's found in type 2 beta turns and that's because it's one of the only amino acids that can actually adopt those phi and side bond angles that lie outside of the expected permissible angles. And so if we take a look at our example down below, what we'll see is that type 2 beta turns have phi and side bond angles that fall into the upper left hand quadrant, as well as phi and side bond angles that fall into the lower right hand quadrant. And so we know that most amino acids are able to easily adopt the phi and side bond angles angles required for type 2 beta turns that fall into the upper left, but not many amino acids have fine side bond angles that are able to form in the lower right quadrant of the Ramachandran plot, but glycine is the exception and so, glycine is, one of the Ramachandran plot has a Ramachandran plot that is very unique because it essentially has permissible bond angles in every region of the Ramachandran plot except for the middle region here. And so you can see that glycine is pretty easily able to adopt the type 2, phi and side bond angles in the upper left hand quadrant, and it's also able to pretty easily adopt the type 2 beta turn bond angles in the lower right hand quadrant as well. And so again, that's why glycine is often the residue found in type 2 beta turns. And so really the major takeaway from this video is the fact that the fine side bond angles for residues that fall into loops and turns are found in multiple regions of the Ramachandran plot. And so we'll be able to get some practice, applying these concepts in our next practice video. So I'll see you guys there.
7
Problem
Problem
If the phi & psi angles of loop regions are plotted, where do they tend to fall on the Ramachandran plot below?
A
The area labeled in green.
B
The area labeled in blue.
C
The area labeled in grey.
D
All the above.
8
Problem
Problem
Which of the following statements is correct?
A
Loops and turns are usually found tucked away on the interior of folded proteins.
B
An α-helix peptide backbone located in the interior of a protein will H-bond to R-groups of other residues.
C
In extended fibrous proteins that are elongated, we would expect to find numerous β-turns & loops.
D
Tightly compact spherical/globular proteins tend to have more β-turns than elongated fibrous proteins.
E
A membrane-embedded α-helix is likely rich in Asp residues.