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Overview of protein structure

AP.BIO:
SYI‑1 (EU)
,
SYI‑1.B (LO)
,
SYI‑1.B.2 (EK)
,
SYI‑1.C (LO)
,
SYI‑1.C.1 (EK)
Primary, secondary, tertiary and quaternary protein structure. Beta pleated sheets and alpha helices.

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  • aqualine tree style avatar for user Lexie VanDall
    When talking about the interactions at the secondary level, () he refers to the second carbon as "the carbonyl carbon," but this is the carbon of the carboxyl group of the A.A. Is the name of the functional group changed once the Amino Acid has bonded? Is this just a mistake?
    (11 votes)
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  • piceratops sapling style avatar for user haekele
    I did not really the concept of primary, secondary, tertiary and quaternary structures
    (1 vote)
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    • orange juice squid orange style avatar for user N Peterson
      Primary proteins structure is simply the order of amino acids bound together by peptide bonds to make up a polypeptide chain.
      Secondary structure refers to the alpha helices and beta pleated sheets created by hydrogen bonding in portions of the polypeptide.
      Tertiary structure refers to the 3D folding of the polypeptide due to van-der-waals interactions, hydrophobic interactions, disulfide bridges, and ionic bonding between amino acid side chains.
      Quaternary structure involves positioning of multiple folded polypeptides into a protein.
      Doing a google image search for "levels of protein structure" could help you get a visualization.
      (26 votes)
  • aqualine ultimate style avatar for user Becky
    At Sal says that the bond is a hydrogen bond. Although the difference in electro negativity between nitrogen and hydrogen is large, the difference in electro negativity between carbon and oxygen is small. How is the bond between the hydrogen and oxygen still hydrogen bond.
    (5 votes)
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    • piceratops ultimate style avatar for user Just Keith
      You should probably review hydrogen bonding in the chemistry section. When, either in separate or the same molecule, you have a partially positively charged hydrogen come close to certain kinds of partially negatively charged groups, then you get an electrostatic attraction between the two groups. This is not a true bond, just an electrostatic attraction. Most of the time, the attraction will be between an H and N, O or F. There are a few other ways it can happen, but it is usually that way.

      As for what you mentioned about the electronegativity difference between O and C, please understand that electronegativity difference is a rule of thumb, not a strict law. There are many factors that go into determining how polarized a bond is. For example, it matters what else the atoms involved might be bonded to.

      But the difference in electronegativity of C and O is 0.89 which is sufficient to polarize a bond. And, note that there is a π bond between the C and O, which makes available additional electron density to O.
      (3 votes)
  • starky tree style avatar for user Leela
    I'm a bit confused by the secondary structure. Taking the beta-pleated sheet as an example, are there are two peptide chains involved, each one linked by hydrogen bonds? Or just one chain, which loops at the top or something? Thanks in advance :)
    (4 votes)
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  • starky ultimate style avatar for user Sir Ardent Inferno
    How does one decide how many poly peptide chains are present in a macroprotein. as all the amino acids will be connected in a convoluted manner,wouldn't it be very painful to differentiate b/w the two peptide chains ?
    (4 votes)
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    • female robot grace style avatar for user tyersome
      If you have a purified protein complex a very standard technique involves denaturing the protein in an anionic detergent (SDS). This (usually) results in all the individual proteins being separated and stretched out into negatively charged rods. The mixture is then dragged through a gel by applying an electric field. Because different proteins are usually different sizes they move at different rates through the gel. You then stain the gel with something that interacts with all proteins but not the gel. This gives you a series of bands. The number of different bands corresponds to the number of different proteins ...

      Note however, this can get very complicated, since there may be multiple copies of one or more identical proteins within a complex, some proteins may be of similar sizes, some proteins may have been broken down into smaller parts, you may have not completely purified your protein ...

      Another set of techniques using mass-spectroscopy is often used, but I'm not going to try to explain that here!
      (4 votes)
  • purple pi purple style avatar for user Jonathan Locke
    Why is it called a beta-pleated sheet? Why is it called an alpha helix? (thanks!)
    (3 votes)
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    • ohnoes default style avatar for user kristin
      Wikipedia says it is called a beta-pleated sheet because beta strands (which are stretches of polypeptide chains) form a twisted pleated sheet.
      i'm sure someone else will be willing to look through the mile long list of search results about alpha helices for you.
      (3 votes)
  • starky sapling style avatar for user Mohammed Tazwar
    What causes a polypeptide to take on a alpha-helix shape or a beta-pleated sheet shape?
    (2 votes)
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  • piceratops sapling style avatar for user haekele
    Which carbon do we call an alpha carbon
    (2 votes)
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  • orange juice squid orange style avatar for user Adric Northam
    why does it say that there is only 4 pep-tide chains in the hemoglobin molecule? in the middle of the yellow part there's orange. so wouldn't that be 5?
    (2 votes)
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  • blobby green style avatar for user Alfred Sugarman
    What is a protein domain?
    (2 votes)
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Video transcript

- [Voiceover] We've already spent a lot of time talking about proteins, and how they do a huge variety of things in biological systems, anything from acting as hormones to antibodies to providing structures in cells, signaling mechanism, a whole series of things and their ability to do all of those things in living systems comes out, it's a by-product of their structure, so what we want to talk about in this video is protein, protein structure, and to just get a high-level appreciation for protein structure, this is a hemoglobin molecule right over here, and this hemoglobin molecule, it's made out of four polypeptide chains. Two of them have 141 amino acids, two of them have 146 amino acids, for a total of 574, 574 amino acids. But you see, they don't just go into some random configuration, they come into a configuration that is really good for doing what hemoglobin does, and that is being a transporter for oxygen, being a transporter for oxygen within red blood cells. So how do proteins like hemoglobin, there's many, many other types of proteins that do many, many other types of things. How do they get their structure? Well, one way to think about it is, there's different layers of the structure, or there's different degrees of structure. The first degree of the structure we can call the primary structure. Primary structure, and this is really just the sequence of the amino acids. When we talk about the translation step, when we go from mRNA and we go to a ribosome and the tRNA brings the amino acids and puts them, and starts linking them together, it's setting up the primary, it's setting up the primary structure. The DNA, the information in DNA, that's essentially what it's coding. It's coding for what order do we put the different amino acids in, so this is just the order, the order, order of, of the amino, of the amino acids. Now the next level of structure, this is just the order, this is how we form our polypeptide, but how does a polypeptide start getting bent into these shapes to be able to do the different things that it needs to do? Well the second, the second order of our structure, or I could say the secondary structure, secondary structure, this is due to interactions of the peptide backbone. Due to interactions, interactions of the backbone of the peptide, of the peptide backbone, and I have some examples of that. I have some examples of that right over here. You see, right over here, we have a bunch of, we have a polypeptide chain. We have a bunch of amino acids that are bonded with the peptide bonds. This is a, this is a peptide bond over here. This is a, this is between the carbonyl carbon and the nitrogen, another peptide bond between the carbonyl carbon and the nitrogen, another peptide bond. And this chain, this polypeptide chain, you can imagine maybe it goes down here, maybe it goes around, maybe it comes back, who knows? But we see that when it comes back, we still are going from nitrogen to carbonyl carbon, polypeptide linkage, nitrogen, carbonyl carbon, peptide linkage, but what you see happening is, from these two chains, the backbones are interacting. I actually didn't even explicitly even draw the side chains. I just put an "R" here for the different side chains, but you see how they're interacting. Right over here, we have nitrogen. Nitrogen is electronegative. It would hog the electrons from the hydrogen, so the hydrogen's going to have a partially positive charge. Oxygen is electronegative. It's going to hog the electrons from the carbon, so it's going to have a partially negative charge, and so this hydrogen, this oxygen, they're going to be attracted to each other. This is a hydrogen bond, our good, old friend the hydrogen bond. Same thing is going to happen over here, same thing is going to happen over here. And so these two chains, these can form kind of this sheet, in fact it's called, this is called a beta-pleated sheet. Beta-pleated, beta-pleated sheet. Now, over here, I have also constructred a beta-pleated sheet but you might notice the difference. This one went from the nitrogen to the alpha carbon, this is the alpha carbon over here, to the carbonyl carbon, nitrogen, alpha carbon, carbonyl carbon, and this one was also going in the same direction, nitrogen, alpha carbon, carbonyl carbon, nitrogen, alpha carbon, carbonyl carbon, so this is a parallel beta-pleated sheet. These, both of these side chains that are interacting, sorry, both of these backbones that are interacting are going in the same direction, so we would just call this one, we would just call this one a parallel beta-pleated sheet. Now this one, they're parallel, but what we see going on, we go nitrogen, alpha carbon, carbonyl carbon, nitrogen, alpha carbon, carbonyl carbon, that's on the left side, but on the right side, we're going carbonyl carbon, alpha carbon, nitrogen. Carbonyl carbon, alpha carbon, nitrogen. We're going in the opposite direction. In fact, even to construct this, I copy and pasted this but I rotated it around. You can see that I've actually drawn it upside down, and so here, we have these two things, you still have the hydrogen bonds between these, between these partially positive ends of these, of this bond, this nitrogen-hydrogen bond, at the hydrogen end, and this partially negative charge of the oxygen. You still see, you still have these hydrogen bonds, but, and these backbones are parallel, but they are going in different directions. They are, so we would say these are anti, these are anti-parallel beta-pleated sheets. So, anti, anti-parallel beta-pleated sheets. So this is another form of a secondary structure. Now this over here, we see, we see that the backbone is going in this, it's going in this, in this helical structure, and we have, essentially, hydrogen bonds between the different layers of the helices, or between the different layers of the helix, I should say. So, over here, this oxygen is partially negative, partially negative charge. This hydrogen, partially positive charge, so I have a hydrogen bond. I could have a hydrogen bond over here, and so that's what gives this a helical, a helical structure, and we would call this an alpha, an alpha helix, so these interactions between the backbone, between the backbone, the peptide backbone, that's the secondary structure. That's the secondary structure of a protein. Now, we're not done yet because you could imagine these side chains have something to say. Some of these side chains are hydrophobic, so they would want to kind of pull that part into, kind of, away from, if it's in water, away from the outside. Some of these side chains might form hydrogen bonds with other side chains, so they, those would interact in certain ways. You could have side chains that form, actually, disulfide bonds, actually covalent bonds with other side chains, and we're gonna go into a lot more detail of that in a future video but the, the third, I guess, the third form of structure, and we'll call that the tertiary structure, the tertiary structure, this is due to interactions of side chains, so, due to side chain, due to side chain interactions. Due to side chain interactions. And so you can imagine, you know, if, let's say I have this, you know, this thing over here, maybe, maybe I have a bunch of hydrophobic, hydrophobic side chains right over here. I'm just drawing them as "R" but let's just assume they're hydrophobic and let's say that the H2O is out here, they might, and we'd have to think in three dimensions, but they might want to get away from the H2O, and likewise, you can maybe have hydrophilic side chains, maybe polar side chains might be on, might be on the outside. You might have a situation where, where one side chain, let's call it R1 and another side chain R2, maybe they form hydrogen bonds with each other. Maybe they have an ionic bond with each other, so there's a bunch of different types of side chain interactions that we could actually think about, and we'll go into more depth in that in a future video. Now, any protein that's made up of a single polypeptide is only going to have primary structure, secondary structure and tertiary structure, but if we're dealing with something like hemoglobin, that's made up of more than one polypeptide, then we're going to talk about quaternary structure. So, quaternary, quaternary, quaternary structure, quaternary structure, and this is all about how the different polypeptide chains come together to form the larger, to form the larger complex, so, multiple, multiple, I guess you could say, interactions or arrangement of multiple chains together. So, arrangement, arrangement of multiple, multiple, in the case of hemoglobin we had four, multiple peptide, peptide chains. So hopefully that gives you an appreciation, and this is a fascinating thing. Protein structure is a fascinating area, in fact, there are so many permutations, so how you can, how you can actually construct proteins, that if we understand that better, we'll be able to, much better be able to go from DNA, to be able to translate to primary structure, and then to really figure out how proteins work, what they do, how they can be fixed, how they can maybe provide other functions, so it's a fascinating, fascinating field of study.