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Biochemistry

Learn the toughest concepts covered in Biochemistry with step-by-step video tutorials and practice problems by world-class tutors

4. Protein Structure
1

concept

Protein Folding

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So now that we've covered the infants and experiment in this video, we're going to talk about protein folding. So protein folding actually has many different contributing factors. But it heavily relies on non co Vaillant interactions such as the hydrophobic effect, and we'll be able to see that down below in our example of protein folding. Now recall from our previous lesson on the infants and experiment that the final protein confirmation ultimately depends on the primary level of protein structure or the amino acid composition and the amino acid sequence. And that's because the primary level of protein structure dictates all of the other levels of protein structure and the final protein confirmation. And so, generally, the way that protein folding works is that it leads to non polar hydrophobic amino acids found on the interior of the protein and polar hydrophobic. I'm sorry, hydro filic, polar amino acids found on the perimeter of the protein, and so we can see that down below in our example. So on the left over here, what we have is an unfolded poly peptide chain, and the black line here represents the peptide backbone. Now each of these red balls represents hydrophobic amino acid residues that are non polar so we can put hydrophobic amino acid residues. And then the blue balls over here represent hydro filic, amino acid residues that are polar. And so this is our unfolded poly peptide chain. But after it undergoes protein folding noticed that the tendency is for the non polar hydrophobic amino acid residues that Aaron red to be tucked away into the interior because their water fearing. And so what initiates the clumping of all of these hydrophobic amino acid residues is the hydrophobic effect. And so the Hydra Filic polar amino acid residues are likely to be found on the perimeter of the protein because they want to interact with the acquis water environment that's surrounding the protein. And so over here in our image on the right, essentially what we have our our 20 amino acids and the likelihood that of where we'll find these proteins after protein folding in terms of being on the inside of the protein or on the outside of the protein. And so in this dotted box over here we have our neutral amino acid residues. And then on the outside of the box, we have are charged amino acid residues at physiological pH. And so within our neutral amino acid residues, we've broken them up into non polar and polar amino acid groups. And so notice that we don't have our aromatic amino acid group. And that's because we've taken our aromatic amino acids, phenylalanine, tyrosine and trip to fan, and we've distributed them amongst the non polar and the polar groups. So notice that trip to Fan and Fennel Allen in our part of the non polar group and tire seen as part of the Polar group. And so we know that for are non polar amino acids are no Monica's Gavle limp and Soto add in trip to fan and fennel al inning. We can say that our buddy Gavin, who's limping away on crutches, away from the water he's not limping away slowly, he's limping away way fast, and so if we add way fast, gaveling way fast, then that will help us. Remember that trip to Fan and Fino Allen and can be grouped as non polar and the non polar amino acids are hydrophobic and because they're hydrophobic, they're going toe. Want to get away from the water, the acquis environment that surrounds the protein. And so they're going to be tucked into the interior of the protein, just like we see over here with these red hydrophobic residues. Now to go to the opposite extreme over here with the charged amino acids, The charged amino acids are going to be the most polar, and that's because they have full charges at physiological pH and the pneumonic to remember those is dragons eat nights riding horses. And so we've got our negatively charged and are positively charged amino acids. And they are very, very hydro filic or very, very water loving. And so they interact with these water molecules that are surrounding them. And so, in order to better interact with the water molecules that are surrounding the protein, they associate themselves on the outside of the protein or on the perimeter of the protein. So these charged amino acids are the ones that are most likely to be found on the perimeter of the protein. Now in the middle. Here we have our polar amino acids, and our polar amino acids are not charged. They are neutral at physiological pH, but they're still polar, just not as polar as the charge ones and because they're still polar, they're actually somewhat hydro Filic. So they have a little bit of, um, tendency to associate with water, but not as strongly as the charge one. So for that reason, the polar amino acids are likely to be found either on the inside of the protein or on the outside of the protein and pretty much an equal amount. And so they're pretty much gonna be distributed throughout our protein and the pneumonic to remember the polar amino acids is just saying his team crafts, new quilts and the why here for tire scene could be added to our demonic by saying, Sanders, team crafts, new quilts yearly. And so again, these amino acids here are somewhat hydro filic and could be distributed throughout our protein. And so this year concludes our lesson on protein folding and how the amino acids can. We can expect to find the amino acids distributed throughout our protein, and so we'll be able to get some practice with these concepts and our next practice video. So I'll see you guys there
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Problem

Which of the following is the greatest contributor to spontaneous protein folding?

3

concept

Protein Folding

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So now that we've covered the basics of protein folding, we could talk about Leventhal's paradox. And so this guy, Cyrus Leventhal, actually disproved the popular belief that protein folding was a random trial and error process where the protein would have to test all of its possible confirmations before it could actually achieve its final native confirmation. And so all 11 thought did was he made a pretty simple realization. He realized that testing all the possible confirmations would simply take way too long. And he knew that protein folding was super fast and was a non random process, not a random process. And what that means is that protein folding must have predictable folding pathways. And so today scientists are able to actually predict the folding pathways for some small proteins in this field is actually growing as we speak today. And so, like we said earlier, protein folding is super fast, and really, it has to do with the cooperative stepwise interactions between amino acids that makes the protein folding so fast. So they speed up the protein folding and thes cooperative stepwise interactions, pretty much act like protein folding shortcuts and so, in our example below What we have is an image for a Leventhal's paradox. And so what you'll see is on the far left. Over here. What we have is our unfolded protein, which has, Ah, 100 amino acids in it, a. A represents amino acids. And then on the far right. What we have is our native protein structure. And so, again, before $11 paradox, the popular belief was that the protein, the unfolded protein, would have to randomly test all of its possible confirmations and a random trial and error process until it achieved its native structure. And so you can see all of these different folding pathways and possibilities testing all the random confirmations. Now again, Leventhal just made a pretty simple realization. So he calculated that for a protein with 100 amino acids, um, the time that it would take for it to explore all of its possible confirmations was 10 to the 27th years, which is a massive massive number in a huge, huge amount of time. And so, um, it's predicted that the age of the entire universe is just 10 to the ninth years, so the time that it would take for ah, protein with 100 amino acids to explore. All of its possible confirmations is way longer than the length or the age of the entire universe. So there's no way that it could take that long for it to test for it to achieve its native confirmation. And today we know that it takes the actual time for a protein to fold into. Its native confirmation is actually less than one second, so that's a drastic, a massive difference in time. And so, of course. What that means is that there has to be a predictable folding pathway that can be achieved to reach the native structure. And again, this pathway is dictated by cooperative stepwise interactions between amino acids. And so this concludes our lesson on $11 paradox, and we'll be able to get more practice with these concepts in our practice video. So I'll see you guys there
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Problem

Draw each amino acid & determine which is most likely found in the blue regions of the folded protein below?

5
Problem

Which of the following occurs when myoglobin folds into its native conformation?

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Problem

In general, which option contains the major cooperative interactions driving spontaneous protein folding?

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