Secondary Protein Structure - Video Tutorials & Practice Problems
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Secondary Protein Structure Concept 1
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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. We're going to say it involves the connection between the amide hydrogen of one peptide with the carbon oxygen of another. So if we take a look here at this image, we're gonna say that this is our peptide chain one and this is our peptide chain too. Here, we're going to say we have this is an aide here, this n age group because it's connected to a carbon you. We just don't see it. It's what's connected to it out of view. And this is our carbon oxygen. They will form a hydrogen bomb with one another. Remember, hydrogen bonding is not actually bonding. It's an intermolecular force. So we're gonna 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 carbon here. So there goes the amide hydrogen, the carbon and the carbon oxygen. So there goes another H bond. And here we just have two R groups, we don't specify what kind of art groups they are. So we don't know if hydrogen bonding would happen. So we don't do anything. So in this example, we'd have two sites where we see hydrogen bonding being used, right? So just remember it's this type of hydrogen bonding that exists, that happens, that helps to give us our secondary protein structure.
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example
Secondary Protein Structure Example 1
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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 Cine 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 Siri. So this is out as a possibility. Next, we have aspartic acid and glutamic acid. These are acidic amino acids. They possess carbolic 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 the respective R groups. Next, we have valle and Lucy, these two represent nonpolar amino acids. There are 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 or as are other amino acid. Aspartic acid is an acidic amino acid. Arginine or 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 or arginine. It can exist as a prod as a amino group that has an H plus already on it or 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.
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Problem
Problem
How many hydrogen bonding pairs are possible when the following two peptides interact?
A
3
B
5
C
4
D
6
E
1
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concept
Alpha-Helix Concept 2
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Secondary structures give rise to two types of repeating patterns. In this video. We're gonna 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 gonna talk about that later on. But right now we're talking about the alpha helix. Now, when it comes to the alpha helix, we're gonna 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, eagles are chain that's coiled up. And when it comes to hydrogen bonding, remember it happens between the amide hydrogen and the carbon 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, 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 or a protein.
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example
Secondary Protein Structure Example 2
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Determine which of the Fong statements represents a secondary structure for a protein. The creation of peptide bonds. Remember, creation of peptide bonds helps to make the sequence of amino acids and the primary structure, the attractive force between the H atom of a peptide bond and the oxygen atom of a peptide bond. All right. So here this makes the most sense because it's basically saying we have hydrogen mining that's happening. This is one of the forces that helps to make the staircase make our alpha helis. So B is correct the amidon formation, the creation of amino acid chain. This is saying the same thing as option A. We're talking about a primary structure and we're talking about Hep tide bonds or amide bond formation ionic bomb formation between the R side chains of alanine and Bailey or Valley. 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 need even need to go into the discussion of what kind of R groups these two amino acids have. Can they even do ionic bond interactions? That doesn't matter. We know that ionic bond formation was not one of the criteria to help make this staircase when it comes to the alpha helix and secondary structures of a protein. So here only option B is the correct answer.
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concept
Alpha Helix Spiral Shape Concept 3
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Now, when it comes to the alpha helix, we can see that it adopts an optimal shape. You were going to say that the spiral like staircase adopts a right handed or clockwise shape. This is basically just how the staircase uh twists and turns. Which direction does it take? We'd say that this is a right handed or clockwise direction ie shape. Now, here we're gonna say that the hydrogen bonds lie within the helis. So remember we have hydrogen bondings that are helping to stabilize this structure. So we show these dotted lines that are helping to create this 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 body that's happening in between. And then here we have our, our groups, the spacing, they can't be inside of the staircase or the helix, they'd be represented outside of it. So we'd have in our group here here and all of these places. Now, in addition to this, we can say that the hydrogen bonding of the amide hydrogen and the carbon oxygen happens more residues further on the humans. 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. OK. This is gonna become important because they could ask you questions in terms of how many turns would you have if you have this many number of residue 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.
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example
Secondary Protein Structure Example 3
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Here, it says, what is the maximum number of turns for an alpha helix that contains 72 residues? All right. So we have 72 residues within this question. I remember we have a conversion factor. Our conversion factor says that for every one turn, we have 3.6 residues involved, we're gonna use this to help us find our answer. We wanna cancel out residue. So we put that on the bottom. So we have 3.6 residues here on the bottom. And that's where 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 terms. So here, this would mean that our answer would have to be option D when he turns.
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concept
Beta-Pleated Sheet Concept 4
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So now remember that secondary structures give rise to two repeating patterns. Here, we're gonna 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 gonna talk about a beta hated sheet as another secondary structure. Now, the name pleaded it's because of their zig zag 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 a hydrogen bonding happening here here here and here. So I basically hydrogen and also here and that looks and here. So these are all our spots of hydrogen bonding. I 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 this chain, these two chains that are hydrogen bond to each other, they kind of reside. If you look at it like on she on a folded 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's our groups, our 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 gonna say the R groups, they're gonna extend above or below to 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 we have beta sheets.
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example
Secondary Protein Structure Example 4
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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, right? So here we never talked about interchanging between alpha and beta. We talked about these being two possible repeating patterns. Also, we talked about them being key features of secondary structure. OK. So this would be wrong for those two reasons. Their interior is characterized by hydrogen bonding between amide hydrogens and carbonel oxygens. We've seen this, that's what's allowing these two portions of these chains to interact with each other. So here, their interiors characterized by our side chains interactions know 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
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Problem
Problem
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.
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