4. Protein Structure
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So now that we've talked about peptide bonds, primary protein structure and Rama Condron plots, which remember can reveal secondary structures, let's talk about some of those secondary structures, and we're going to start off by talking about the Alfa Helix. So the Alfa Helix is again a type of secondary protein structure. And really, this is a type of secondary structure where the protein backbone takes on a coiled confirmation. And it has a coiled, periodic spiral like confirmation, like the ones that you've seen and you're already familiar with from your previous courses. So you can see down here in our image this coiled confirmation that our backbone takes on. And so, really, the spiral, like coiled confirmation of the Alfa helix is stabilized by hydrogen bonds. But it's not any hydrogen bonds thes air. Very particular hydrogen bonds thes air hydrogen bonds that form in the backbone of the Alfa Helix. So the our group is not involved in stabilizing the Alfa helix. It's all the backbone hydrogen bonds, and so the hydrogen bonds in the backbone can actually formed between distant amino acid residues on the same chain. And so what you'll notice is that the backbone, hydrogen bonds are actually nearly parallel. They're nearly parallel to the axis of the Alfa Helix. And so if we take a look at our example down below, which will see is that this helix here has an axis in the axis of the helix is pretty much going in this direction here. And so it's going up and down. And the hydrogen bonds, which are stabilizing the Alfa Helix here are in yellow, highlighted here and notice that thes yellow hydrogen bonds, which I'll mark and read here. They're pretty much almost parallel to the axis of the helix, which again, if I had, like, the axis of the Helix, it'll be down the center. You'll see that these lines thes hydrogen bonds are almost parallel, and you don't really see any hydrogen bonds that air perpendicular and go across sideways. That's not a feature of health. Alfa Helix is so it's important to keep that in mind for Alfa Hillis is because when we get to beta sheets, that's going to be one of the distinguishing features, the direction of these hydrogen bonds. And so again, these hydrogen bonds are parallel to the axis of the Alfa helix. And so your textbook and your professor might actually depict these Alfa. He looks. He's in different ways, and so it's important to be able to recognize these different depictions. And so Alfa Ulysses are normally depicted in a ribbon shape, but they can be also depicted in a cylinder shape and so you can see that down below in our example where we have these Alfa helix depictions. And so over here on the left, what we have is our ribbon. So this is the way that Alfa Healy Cesaire normally depicted. But you can also see that sometimes you'll find Alfa Helix is depicted as cylinders, and we'll see that in some of our examples as well. So again, over here, what you'll see is that we've got our hydrogen bonds that are stabilizing our alfa helix, and what you can also see is that these Alfa Healy sees they can come together in a protein structure so you can see that we've got to Alfa. He'll sees in this protein structure, and so we'll talk more about protein structure, um, Alfa jealousies and protein structure and our next videos, and we'll get a little bit of practice and then we'll continue our lessons. So I'll see you guys in those practice videos
Which of the following is true regarding the α-helices in the protein bacteriorhodopsin?
Its α-helices involve multiple polypeptide chains to stabilize the coiled structures.
Their spiral-like structure is stabilized primarily by backbone hydrogen bonds.
Its α-helices are commonly depicted as cones pointing towards the c-terminal end.
Along with its β-sheets, its α-helices define its tertiary level of protein structure.
a & b.
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So now that we've introduced the Alfa Helix, let's talk about the Alfa Helix screw sense. And really, all the Alfa Helix screw Sense is talking about is the difference between right handed Alfa jealousies and left handed Alfa Hillis ease. And the right handed Alfa Helix just has a clockwise spin or twist of the Alfa helix spiral, whereas the left handed Alfa Helix has a counter clockwise spin or twist of the Alfa Helix spiral. And we'll distinguish between those two down our example below. Now it's good to know that the right handed Alfa Helix is actually much more stable and because it's much more stable, it's also much more commonly found and proteins that are in nature. And the left handed Alfa Helix is actually pretty rare, and it's not normally found in proteins that are in nature. Now you may be wondering where the are groups for the Alfa Helix, and it turns out that the are groups are actually, uh, excluded from the Alfa Helix structure, and they're normally not shown. But it's important to know that they are groups are still there and how they actually face. And so the are groups of amino acids in an Alfa helix actually point outwards. They point radia Lee outwards away from the Alfa Helix Center or the Alfa Helix axis. And so they do that in order to minimize the amount of Starik hindrance that they encounter. And so if the our groups were all pointing towards the center of the Alfa Helix, then there would be very, very crowded. There would be a lot of Starik hindrance between these are groups, and that would not be a very stable structure. And so the our groups face outwards, and so we'll be able to see that in our example down below as well. So over here in our example, we'll talk about the Alfa Helix crew sense and a good way to be able to distinguish between the right handed and left handed Alfa Ulysses is just literally by using your hands. And so if you use your thumb on, put your thumb up the, uh, the axis of the helix, then the way that your fingers curl are gonna be the way that the helix is twisting. So notice that this person here is using their left thumb here up the helix and noticed that their fingers are curling outwards in a way like that. Or you could think of it out or going from his palm up like this. That's the way that his fingers air current. And that's really the way that this is curling here outwards in a way like this, and it keeps going, and it's outwards in a way like that. So this is a left handed Alfa helix because of that. And so if you use your right handed right hand and do the same thing, notice this person's right thumb is going up and notice. It goes from his palm and then his fingers curled this way. And that's what's happening here. His fingers. The Alfa helix is curling that way goes back around and it's curling in the opposite direction. And so this is a right handed Alfa helix, and again the right handed Alfa Ulysses are much more common and much more stable. And in our previous videos of the Rama Condron plot, we know that the Alfa jealousies are found in the bottom left quadrant of a Rama Condron plot. And so over here, what we have is our Rama Condron plot where we have the fi angles on the bottom and the Sai angles on the side over here of the Rama Condra plot. And so our Alfa he leases are found in the bottom left quadrant somewhere over here in this region. And that's what we see here that we have our right handed Alfa Helix falls into this bottom left region, which is great. We already knew that from our previous videos. But the left handed Alfa Helix, as you can see, falls up here in the upper right region of the Rama Condron plot so you can see that the left handed helix is actually very rare and it's not normally found in nature. So it's important to recognize that they're actually found in different regions of the Rama condom plot. And again, the Rama Condron plot can be used to distinguish between the formation of different secondary structures. And so that's all we're trying to get from this graph here. Now, over here on the far right, what you'll see is that we're representing the are groups of each amino acid residue in an Alfa helix with this green ball that's shown here and so notice that all of the R groups are pointing radial e outwards from the axis of the Alfa Helix. So again, the axis of the Alfa helix is going right down the center like this and the are groups notice they don't point towards. They're not going inside of the Alfa Helix. They're pointing away radial e outwards away from the Alfa Helix center toe. Minimize stare, Kendrick's. So that's another important feature to keep in mind for the Alfa Hillis ease. So this concludes our lesson on the Alfa Helix, and we'll talk more about the Alfa Helix and different components of it in our different lessons. But for now, we'll get a little bit of practice, so I'll see you guys in that practice video.
Which of the following statements about α-helices is false?
Alpha helices of the Ribonuclease A enzyme are stabilized by hydrogen bonding of the peptide backbone.
Hemoglobin proteins predominantly contain left-handed α-helices.
The R groups of amino acids residues in an α-helix extend radially outward (away from helix center).
α-helix hydrogen bonds of the enzyme citrate synthase are roughly parallel to the axis of the α-helix.