So now that we've talked about Alfa Helix and beta sheet secondary structures in this video, we're going to 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 Alfa Ulysses 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 hydro filic, amino acid residues. And so, by being on the surface of proteins that allows the Hydra Filic amino acid residues, Thio easily interact with their acquis 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 could imagine a protein that has a folded compact shape is going to change the backbone direction. Ah, 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 toe 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, um, of their large lengths of amino acids that cause changes and backbone direction without fixed internal hydrogen bonds so they do not use fix 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 four amino acid residues, and they cause abrupt changes and 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 poly peptide chain, and this probably peptide chain has an internal and an A C terminal end, and you'll see we have beta sheets, Alfa Hillis ease and Morva beta streets here or beta strands. And so notice that this beta strand is connected to this Alfa 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 four amino acids. So this is a large link of amino acids, causing a change in the backbone direction. So notice the backbone directions 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 four 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 on notice. Over here with Loop, there are no internal hydrogen bonds, and so over here in our image, on the far right, we have a single poly peptide chain that has ah bunch of secondary structures, and it has the yellow structures, which are beta sheets. It has the pink structures in here, which are Alfa Ulysses, and it has beta turns and loops, so notice that these Gracia 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 our 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 will be able to get some more practice with beta turns, and we'll talk about different types of beta turns that exists, 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
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5m
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So now that we know a little bit about beta turns and loops in this video, we're going to distinguish between two different types of beta turns type one beta turns and type two beta turns. Now it turns out that there's actually many different types of beta turns, but these air two of them or common types of beta turns that your professors likely gonna want you guys to know. And so both Type one and type two beta turns produce abrupt changes in the backbone direction. They both also contained a total of four amino acid residues, and they are both stabilized by hydrogen bonding. And so really, the main differences between type one and type two beta turns is that type one beta turns are even mawr common than type two beta turns, and they usually contain a pro lean amino acid residue, specifically at position number two of the turn and then type two beta turns. On the other hand, there gonna be less common, and they contain a glycerine amino acid residue, but specifically at position number three of the turn and so down below. In our example, we can visually distinguish between Type one beta, turn on the left and type two beta turn on the right and which will notice is that both type one and type two baited her and 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 two beta turn. So they both produce these abrupt changes and backbone direction and also noticed that they both contain four amino acid residues, as shown by these four blue squares in the back of each of the structures numbered 123 and four. And they are both also stabilized by hydrogen bonding, specifically between the first residue in the turn and the fourth residue in the turn between the Carbonnel Group and the Amino Group and the poly peptide backbone. Since we know that on Lee backbone hydrogen bonds stabilized secondary structures and type one and type two beta turns are a type of secondary structure, so we could see the hydrogen bonds forming Type one and the hydrogen bond forming and type two. And so again, the major differences between type one and type two beta turn is that Type one beta turn over. Here on the left is Mawr common, and it has a pro lean amino acid residue, specifically at position number two of the turn, as shown. So the P. R. O is the three letter code for polling, and the two is for position number two and then for Type two beta turns. Over here, they specifically have a glycerine amino acid residue at position number three of the turn. And so you might be wondering, How am I supposed to remember the differences between type one and type two 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 one and type two Beta turn is that Type one beta turn because it has a pro lean at Position two and pro leans three 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 12 punches, and so when I think of a type one beta turn. I literally think of one to peep. And so when I think of 12 p, I'm really thinking of the pro boxer, one to punching. And so the one here is a reminder for it's a type one beta turn the two is specifically for at position number two, and the P here is for the pro bowling amino acid residue, since we know that P is the one that air code for paroling, and so if you can remember 12 P, then you'll remember type one, uh, beta turn at position number two have a pro lean amino acid residue. And that's exactly what we're seeing over here now for type two beta turns. On the other hand, all you need to remember is to three G, 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 g you think of, uh, the goat whose Michael Jordan or LeBron James with the number 23. And that tells us that at with a type two with a type two beta, turn at position number three, there is a glazing amino acid residue. And so, essentially, if you can remember 12 P and 23 G, then you'll be able to remember the differences between type one and type two beta turns. So you can see that with this type 23 G here, that type two beta turns these over here at position number three. Up here they have a glycerine amino acid residue. So hopefully that will help you guys remember the differences between type one and type two 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 one and type two, and so we'll be able to get some practice utilizing these concepts and memory tools and our next couple of practice video. 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:
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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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So now that we've distinguished between type one and type two 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 Rama Condron plot. And that's actually a unique feature of loops and turns, because we know that with Alfa, he'll, Aziz and beta sheets were ableto pinpoint those fine side bond angles in tow very specific regions in the Rama Condron plot. So let's take a look at our example down below to refresh our memories. And so we know that we can split around a condom plot into four different quadrants and amino acid residues that are part of a beta sheet will have fine side bond angles that fall into the upper left hand quadrant of the Rama Condron plot. Whereas amino acids that are part of an alfa helix will have fine side bond angles that fall into the lower left hand quadrant of the Rama Condron plot. And so we're able to pinpoint beta sheets and Alfa Hillis ease toe very specific regions within the Rama Condron plot, but were not able to do the same with loops and turns because loops and turns are found in multiple regions of the Rama Condra plot. So let's take a look at an example of a Type two beta turn. And so it turns out that some of the fi and sigh bond angles of a type two beta turn actually lie outside of the expected permissible bond angles for most of the amino acid residues. But we know that glisten is an exception to this, because glazing can actually adopt a wide range of fine side bond angles because it has such a small, our group, it's literally just a hydrogen atom and that small, our group is able to avoid Starik Hindrance, which allows it to adopt a wide range of fine side bond angles and so it can easily adopt those find side bond angles that lie outside of the expected permissible angles. For most of the amino acids and from our pneumonic to three G, we know that type two beta turns specifically at position number three have a glazing amino acid residue, and so glazing is often the residue that's found in type two beta turns. And that's because it's one of the Onley amino acids that can actually adopt those find 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 two, um, beta turns have fine inside bond angles that fall into the upper left hand quadrant, as well as fine inside bond angles that fall into the lower right hand quadrant. And so we know that most amino acids are able to easily adopt the fine side bond angles required for type two beta turns that fall into the upper left. But not many amino acids have find side bond angles that are able to, um, uh, form in the lower right quadrant of the Rama Condra plot. But glazing is the exception. And so glazing, uh, is one of the Rama Condron 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 glazing is pretty easily able to adopt the type to find side bond angles in the upper left hand quadrant and It's also able to pretty easily adopt the type to beta turned bond angles and the lower right hand quadrant as well. And so again, that's why glazing is often the residue found in type two beta turns. And so, really, the major take away 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 Rama Condron plot. And so we'll be able to get some practice applying these concepts and 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.