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Current time:0:00Total duration:9:58

Overview of protein structure

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SYI‑1.C.1 (EK)

Video transcript

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 byproduct 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 up have 146 amino acids for a total of 574 574 amino acids but you see that they don't just go into some random configuration they come into an into a configuration that is really good for doing what hemoglobin does and that is being a transporter for oxygen being a transporter 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 there's different layers of the structure or there's different degrees of structure the first degree of the structure we could 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 and we go to a ribosome and the tRNA brings the amino acids and puts then starts linking them together it's setting up the primary it's setting up the primary structure the the DNA the information in DNA that's essentially what it's coding its coding for well 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 the shape to be able to do the different things that it needs to do well the second the second order of our structure I could say the part 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 pep 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 other peptide bond and this this chain this polypeptide chain you could imagine maybe it goes down here maybe goes around maybe it comes back who knows but we see that it 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 explicitly even draw the side chains I just said 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 these two chains these can form kind of this sheet in fact it's called this is called a beta pleated sheet beta beta pleated beta pleated sheet now over here I've also constructed 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 this is a this is a parallel beta pleated sheet these both of these both of these side chains that are interacting are sorry both of these backbones that are interacting are going in the same direction so we would just call this one we would cut 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 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 with the hydrogen end and that's partially negative charge at the oxygen you still see you still have these hydrogen bonds but and these backbones are parallel but they're 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 that the bat we see that the backbone is going in this it's going in this in this helical structure and the and we have essentially hydrogen bonds between the different layers of the HeLa C's orbit 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 can 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 and alpha helix so these interactions between the backbone between the backbone the pot the pepper 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 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 with other side chains and we're going to go into a lot more detail that in a future video but the the third I guess the third form of structure we'll call that the tertiary structure the tertiary structure this is due to interactions of side chains so due to side side chain due to side chain interactions due to side chain interactions and so you could 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 are but let's just assume they're hydrophobic and let's say that the 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 could maybe have hydrophilic side chains may be 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 it will 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 kua 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 for multiple peptide peptide chains so hopefully that gives you an appreciation this is a fascinating thing protein structure is a fascinating area in fact there's so many permutations so how you can how you can actually construct proteins and if we understand that better we'll be able to much better be able to go from DNA to be able to translate the 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
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