Alpha Helix - Online Tutor, Practice Problems & Exam Prep

The alpha helix is a secondary protein structure characterized by a coiled conformation stabilized by hydrogen bonds between the backbone of amino acids. These bonds are nearly parallel to the helix's axis, distinguishing them from beta sheets. Right-handed alpha helices are more stable and common in nature, while left-handed variants are rare. The R groups of amino acids extend radially outward to minimize steric hindrance. The Ramachandran plot indicates that right-handed alpha helices occupy the bottom left quadrant, while left-handed ones are found in the upper right quadrant.

Alpha Helix

So now that we've talked about peptide bonds, primary protein structure, and Ramachandran plots, which remember can reveal secondary structures, let's talk about some of those secondary structures. We're going to start off by talking about the alpha helix. The alpha helix is a type of secondary protein structure. This is a type of secondary structure where the protein backbone takes on a coiled conformation. It has a coiled periodic spiral-like conformation like the ones that you've seen and you're already familiar with from your previous courses. You can see down here in our image, this coiled conformation that our backbone takes on. This spiral-like coiled conformation of the alpha helix is stabilized by hydrogen bonds. But these are not just any hydrogen bonds. These are very particular hydrogen bonds that form in the backbone of the alpha helix. The R group is not involved in stabilizing the alpha helix. It's all the backbone hydrogen bonds. The hydrogen bonds in the backbone can actually form between distant amino acid residues on the same chain. What you'll notice is that the backbone hydrogen bonds are nearly parallel to the axis of the alpha helix. If we take a look at our example below, what you'll see is that this helix has an axis, and the axis of the helix is going in this direction here. It's going up and down, and the hydrogen bonds, which are stabilizing the alpha helix here, are highlighted in yellow. Notice that these yellow hydrogen bonds, which I'll mark in red here, are almost parallel to the axis of the helix, which again, if I highlight the axis of the helix, it'll be down the center. You'll see that these lines, these hydrogen bonds are almost parallel, and you don't really see any hydrogen bonds that are perpendicular and go across sideways. That's not a feature of alpha helices. It's important to keep that in mind for alpha helices because when we get to beta sheets, that's going to be one of the distinguishing features, the direction of these hydrogen bonds. Again, these hydrogen bonds are parallel to the axis of the alpha helix. Your textbook and your professor might actually depict these alpha helices in different ways, so it's important to be able to recognize these different depictions. Alpha helices are normally depicted in a ribbon shape, but they can also be depicted in a cylinder shape. You can see that below in our example, where we have these alpha helix depictions. Over here on the left, what we have is our ribbon. This is the way that alpha helices are normally depicted, but you can also see that sometimes, you'll find alpha helices depicted as cylinders, and we'll see that in some of our examples as well. Again, over here, what you'll see is that we've got our hydrogen bonds that are stabilizing our alpha helix, and what you can also see is that these alpha helices can come together in a protein structure. You can see that we have two alpha helices in this protein structure. We'll talk more about protein, alpha helices, and protein structure in our next videos, and we'll get a little bit of practice, and then we'll continue our lesson. I'll see you guys in those practice videos.

Which of the following is true regarding the α-helices in the protein bacteriorhodopsin?

• A. Its α-helices involve multiple polypeptide chains to stabilize the coiled structures.
• B. Their spiral-like structure is stabilized primarily by backbone hydrogen bonds.
• C. Its α-helices are commonly depicted as cones pointing towards the c-terminal end.
• D. Along with its β-sheets, its α-helices define its tertiary level of protein structure.
• E. a & b.

Alpha Helix

So now that we've introduced the alpha helix, let's talk about the alpha helix screw sense. Essentially, the alpha helix screw sense is the difference between right-handed alpha helices and left-handed alpha helices. The right-handed alpha helix has a clockwise spin or twist of the alpha helix spiral, whereas the left-handed alpha helix has a counterclockwise spin or twist. We'll distinguish between these two in our example below. It's good to know that the right-handed alpha helix is much more stable and commonly found in proteins in nature. The left-handed alpha helix, on the other hand, is quite rare and not normally found in proteins in nature.

Now, you may be wondering about the R groups in the alpha helix. The R groups are excluded from the alpha helix structure and are normally not shown; however, it's important to understand that the R groups are still present. In an alpha helix, the R groups of amino acids point radially outward, away from the alpha helix axis to minimize steric hindrance. If the R groups pointed towards the center of the alpha helix, they would be very crowded, causing significant steric hindrance between these R groups, resulting in an unstable structure. So, the radial orientation of the R groups is an essential aspect of the alpha helix structure, which will also be demonstrated in our example below.

In our example, we discuss the alpha helix screw sense. A practical way to distinguish between right-handed and left-handed alpha helices is literally by using your hands. If you position your thumb upwards along the axis of the helix, the way your fingers curl represents the helix's twisting direction. For instance, if using the left hand, the fingers curl outward and away, indicative of a left-handed alpha helix. Conversely, using the right hand results in the fingers curling in the opposite direction, typical of a right-handed alpha helix. Right-handed alpha helices are much more common and stable. In our previous videos discussing the Ramachandran plot, we noted that alpha helices are found in the bottom left quadrant. However, the left-handed alpha helix falls in the upper right region, as shown in the Ramachandran plot, highlighting its rarity in nature. The Ramachandran plot helps distinguish the formation of different secondary structures.

On the far right, we present the R groups of each amino acid residue in an alpha helix with a green ball. Note that all the R groups point radially outward from the alpha helix axis, further emphasizing their orientation to minimize steric hindrance. This is a crucial feature to remember about alpha helices.

This concludes our lesson on the alpha helix. We will continue to explore the alpha helix and its various components in upcoming lessons, but for now, we will transition to some practical exercises. I look forward to seeing you in the practice video.

Which of the following statements about α-helices is false?

• A. Alpha helices of the Ribonuclease A enzyme are stabilized by hydrogen bonding of the peptide backbone.
• B. Hemoglobin proteins predominantly contain left-handed α-helices.
• C. The R groups of amino acids residues in an α-helix extend radially outward (away from helix center).
• D. α-helix hydrogen bonds of the enzyme citrate synthase are roughly parallel to the axis of the α-helix.

Here’s what students ask on this topic:

What is an alpha helix in protein structure?

An alpha helix is a type of secondary protein structure characterized by a coiled conformation. This spiral-like structure is stabilized by hydrogen bonds between the backbone of amino acids, specifically between the carbonyl oxygen of one amino acid and the amide hydrogen of another, four residues down the chain. These hydrogen bonds are nearly parallel to the helix's axis. The R groups of the amino acids extend radially outward to minimize steric hindrance. Right-handed alpha helices are more stable and commonly found in nature, while left-handed helices are rare.

How are alpha helices stabilized?

Alpha helices are stabilized by hydrogen bonds that form between the backbone atoms of the amino acids. Specifically, the hydrogen bond forms between the carbonyl oxygen of one amino acid and the amide hydrogen of another amino acid that is four residues away. These hydrogen bonds are nearly parallel to the axis of the helix, providing structural stability. The R groups of the amino acids point outward, reducing steric hindrance and further contributing to the stability of the alpha helix.

What is the difference between right-handed and left-handed alpha helices?

The difference between right-handed and left-handed alpha helices lies in the direction of their twist. A right-handed alpha helix has a clockwise twist and is more stable and commonly found in nature. In contrast, a left-handed alpha helix has a counterclockwise twist and is rare. The stability of the right-handed helix is due to its favorable steric interactions and hydrogen bonding patterns. The Ramachandran plot shows right-handed helices in the bottom left quadrant, while left-handed helices appear in the upper right quadrant.

Where are the R groups located in an alpha helix?

In an alpha helix, the R groups of the amino acids are located radially outward from the helix's central axis. This outward orientation minimizes steric hindrance, allowing the helix to maintain its stable structure. The R groups do not participate in the hydrogen bonding that stabilizes the helix; instead, they extend away from the backbone, reducing crowding and potential clashes between side chains.

How can you distinguish between right-handed and left-handed alpha helices using your hands?

To distinguish between right-handed and left-handed alpha helices using your hands, you can use the thumb rule. For a right-handed helix, point your right thumb along the axis of the helix; your fingers will curl in the direction of the helix's twist (clockwise). For a left-handed helix, point your left thumb along the axis; your fingers will curl in the opposite direction (counterclockwise). This simple method helps visualize the helical twist and differentiate between the two types.