Secondary Protein Structure - Online Tutor, Practice Problems & Exam Prep

Secondary protein structures arise from hydrogen bonding between amide hydrogens and carbonyl oxygens in peptide chains, forming two main patterns: alpha helices and beta pleated sheets. The alpha helix adopts a right-handed spiral shape, with 3.6 residues per turn, while the beta pleated sheet consists of adjacent beta strands in a zigzag formation, with hydrogen bonds stabilizing the structure. R groups extend above and below these structures, optimizing spatial arrangement. Understanding these formations is crucial for grasping protein functionality and interactions.

Secondary Protein Structure Concept 1

Now, when it comes to the secondary protein structure, we're going to say that this is the type of structure that results from hydrogen bonding of the atoms in the backbone of a protein. It involves the connection between the amide hydrogen of one peptide with the carbonyl oxygen of another. So if we take a look here at this image, we're going to say that this is our peptide chain 1, and this is our peptide chain 2. Here we have an amide, this NH group, because it's connected to a carbonyl. We just don't see it.

It's what's connected to it out of view. And this is our carbonyl oxygen. They will form a hydrogen bond with one another. Remember, hydrogen bonding is not actually bonding. It's an intermolecular force.

So we're going to show it and depict it through dashed bonds, so dashed lines. So that's one hydrogen bond. Here goes another amide nitrogen. Again, it's an amide because it's connected to this carbonyl here. So there goes the amide hydrogen, the carbon in the carbonyl oxygen.

So there goes another hydrogen bond. And here we just have two R groups. We don't specify what kind of R groups they are, so we don't know if hydrogen bonding would happen. So we don't do anything. So in this example, we have two sites where we see hydrogen bonding being used.

Alright. So just remember, it's this type of hydrogen bonding that exists, that happens, that helps to give us our secondary protein structure.

Secondary Protein Structure Example 1

Determine which of the following amino acid pairs could potentially perform hydrogen bonding between their respective R groups. So for a, we have glycine and serine together. Glycine has an H as its R group. Because of the presence of an H, there's no way that it could form hydrogen bonding with its R group with serine. So, this is out as a possibility.

Next, we have aspartic acid and glutamic acid. These are acidic amino acids. They possess carboxylic acids within their R groups. Because of this, they have the potential to hydrogen bond. So, we say that this could perform hydrogen bonding between their respective R groups.

Next, we have valine and leucine. These two represent non-polar amino acids. Their R groups are hydrocarbons. They're only composed of carbons and hydrogens, so they wouldn't be able to engage in hydrogen bonding with their R groups. So this is out.

Then finally, we have here aspartic acid again, and then we have arginine as our other amino acid. Aspartic acid is an acidic amino acid. Arginine is a basic amino acid. This one has the presence of an OH group in its acidic form, or we can say that it's a carboxyl group in its conjugate base form. Arginine can exist as a protonated amino group that has an H+ already on it, or it can exist in its neutral form.

Either way, because one is acidic and one is basic, they could engage in hydrogen bonding between their respective R groups. So this is also a possibility. In this case, we can say both b and d could engage in hydrogen bonding between their respective R groups. Right. So the answer again, here would be options b and d.

How many hydrogen bonding pairs are possible when the following two peptides interact? 

• A. 3
• B. 5
• C. 4
• D. 6
• E. 1

Alpha-Helix Concept 2

Secondary structures give rise to two types of repeating patterns. In this video, we're going to take a look at the alpha helix. Now, here we're going to say that the backbone of a single protein chain coils into a spiral-like staircase. If we take a look at the image to the right, we have our primary structure, which remember is just a sequence of amino acids depicted by these beads here that are connected to each other through peptide bonds. This chain interacts with itself and it coils to give us our first secondary structure, this alpha helix.

Here we can see that it becomes spiral-like. Now, there's a second structure, we're going to talk about that later on, but for right now, we're talking about the alpha helix. Now, when it comes to the alpha helix, we're going to say it's stabilized by hydrogen bonding between distant amino acids on the same chain. So again, this is just that one chain hydrogen bonding with itself to make this staircase. If we took a look here, here goes our chain that's coiled up.

And when it comes to hydrogen bonding, remember, it happens between the amide hydrogen and the carbonyl oxygen. So we'd have our hydrogen bond here connecting these two. We'd have another hydrogen bond here connecting these two. So here we're showing two places of hydrogen bond formation. This alpha helix can just be one or a region of a large polypeptide chain.

Here, if we take a look to the right, we've highlighted these two alpha helices here, this one and this one. And as you can see, they're just a small segment of the entire chain. The rest of the chain is larger than it and it's grayed out. So, again, a secondary structure is just the chain interacting with itself. In this case, it's hydrogen bonding with itself to help make this staircase.

This represents one of our first of two repeating patterns that help to make a secondary structure for a protein.

Secondary Protein Structure Example 2

Determine which of the following statements represents a secondary structure for a protein. Here, the creation of peptide bonds. Remember, the creation of peptide bonds helps to make the sequence of amino acids and the primary structure. The attractive force between the hydrogen atom of a peptide bond and the oxygen atom of another peptide bond. Alright.

So here, this makes the most sense because it's basically saying we have hydrogen bonding that's happening. This is one of the forces that helps to make the staircase and make our alpha helix. So option B is correct. The amide bond formation, the creation of the amino acid chain, this is saying the same thing as option A. We're talking about a primary structure when we're talking about peptide bonds or amide bond formation.

Ionic bond formation between the R side chains of alanine and valine. So here, this has nothing to do with a secondary structure. We never talked about ionic bond formation, so this would not work. Also, we don't even need to go into the discussion of what kind of R groups these two amino acids have. Can they even engage in ionic bond interactions?

That doesn't matter. We know that ionic bond formation was not one of the criteria to help make the staircase when it comes to the alpha helix and secondary structures of a protein. So here, only option B is the correct answer.

Alpha Helix Spiral Shape Concept 3

Now, when it comes to the alpha helix, we can say that it adopts an optimal shape. Here, we're going to say that the spiral-like staircase adopts a right-handed or clockwise shape. This is basically just how the staircase twists and turns. Which direction does it take? We'd say that this is a right-handed or clockwise direction, that is, a clockwise shape. Now, here we're going to say that the hydrogen bonds lie within the helix. So remember, we have hydrogen bonding that is helping to stabilize this structure. So, we show these dotted lines that are helping to create the staircase, and the amino acid R-groups lie outside the helix because of spacing.

So if we take a look at these two images, we'd say here that this represents our right-handed alpha helix; we have our hydrogen bonding that's happening in between. And then here, we have our R-groups. As for spacing, they can't be inside of the staircase or the helix; they'd be represented outside of it. So we'd have an R-group here, here, and in all of these places. Now, in addition to this, we can say that the hydrogen bonding of the amide hydrogen and the carbonyl oxygen happens for residues further along the helix.

Now, what is the result of this? Well, the result is that for every one turn of the helix, it contains an average of 3.6 residues. This is going to become important because they could ask you questions in terms of how many turns you would have if you have this many number of residues or if you have this many number of residues, how many theoretical turns could your alpha helix possess? Right. So, there's a connection for every one turn; there are 3.6 residues on average. Right. So, keep this in mind when we talk about alpha helices, their optimal shapes, and the number of residues per turn.

Secondary Protein Structure Example 3

Here it says, what is the maximum number of turns for an alpha helix that contains 72 residues? Alright. So we have 72 residues within this question. Now remember, we have a conversion factor. Our conversion factor says that for every one turn, we have 3.6 residues involved.

We're going to use this to help us find our answer. We want to cancel out residues, so we put that on the bottom. So we have 3.6 residues here on the bottom, and that's for every one turn that's on top. Here, my residues will cancel out, and at the end, I'd have my number of turns. So my end amount will come out to be 20 turns.

So here, this would mean that our answer would have to be option d, 20 turns.

Beta-Pleated Sheet Concept 4

So now remember that secondary structures give rise to two repeating patterns. Here, we're going to talk about the second pattern, which is called our beta pleated sheet. Now, here, this is a secondary structure consisting of two or more beta strands oriented side by side. If we take a look at the right, we see that again, our primary structure comes from the connecting of amino acids in a sequence through peptide bonds. We know that it can give our alpha helix as a secondary structure.

But now we're going to talk about a beta pleated sheet as another secondary structure. Now the name pleated, it's because of their zigzag pattern. If we take a look here, sheet. If we really visualize this, we have our two peptide chains that are hydrogen bonding to one another. Remember, here we have hydrogen bonding happening here, here, here, and here.

So I've basically hydrogen and also here, and that looks, and here. So these are all our spots of hydrogen bonding. Got all of them. Yes. So this is all our sites of hydrogen bonding that connects these two peptide chains to one another, and we can see that these chains that are hydrogen bonding to each other, they kind of reside if you look at it like on a full piece of paper.

That's what we talk about pleated, the zigzagging pattern. Think of paper being folded. The way the two chains orient themselves because of this hydrogen bonding, because of this way the beta strands orient themselves side by side gives us this depiction of a sheet. Now, here, we're talking about the chains, but remember there are R groups. R groups, because of spacing, can't be in the interior.

That's where hydrogen bonding is occurring. So what they do is they orient themselves above and below this sheet. So we're going to say the R groups, they're going to extend above or below the beta sheet. So here we have the R groups on top, so they're above the sheet, and then we have these R groups on the bottom below the sheet. And this all has to do with spacing and taking the optimal shape when it comes to these peptide chains.

Right. So remember, we have our primary structure. The primary structure leads to our secondary structure. This is happening to create two different types of possible shapes where we have alpha helices and beta sheets.

Secondary Protein Structure Example 4

Which of the following statements is true of beta sheets? Interchanging between an alpha helix and a beta sheet is a key feature of a primary structure. Alright. So here, we never talked about interchanging between alpha and beta. We talked about these being 2 possible repeating patterns.

Also, we talked about them being key features of secondary structure. K. So this would be wrong for those two reasons. Their interior is characterized by hydrogen bonding between amide hydrogens and carbonyl oxygens. We've seen this.

That's what allowing these two portions of these chains to interact with each other. So here, their interior is characterized by r-side chains interactions. No. The r groups orient themselves above and below the sheet. That's what happens when we do these beta sheets in terms of our secondary structure of proteins.

The r-side chains extend inward to ensure greater packing of the peptides. It's the opposite. The r groups take up space and optimally, we want them to be oriented on the outside. So here, the only answer that is correct would have to be option b.

Which of the following statements is true in regard to the peptide strand shown?

• A. The β-sheet defines the primary structure of the peptide strand.
• B. The C-Terminal end possesses an α-helix. 
• C. Along with its α-helix counterpart, the β-sheet is mainly stabilized by backbone hydrogen bonds. 
• D. The α-helix and the β-sheet are connected together through an ionic bond.