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

4. Protein Structure

Peptide Bond


Peptide Bond

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so, up until this point, we've really only talked about amino acids as free individual amino acids, and we haven't talked much about their ability toe link together to form long proteins. But we're gonna begin that discussion in this video by talking about peptide bonds, so recall that free amino acids can actually be linked together via peptide bonds. And so all a peptide bond really is is just an AM I'd covalin linkage between neighboring amino acids in a poly peptide chain and recall that an am I'd is just when you have a carbonnel group that is linked to a nitrogen atom. And so, really, this is what an am I is. And this is what a peptide bond is. And so it turns out that the total number of peptide bonds is actually just one less than the total number of amino acids in a chain, and we'll see how that works down below. In our example now, peptide bond formation is actually an undergone IQ process, and recall and organic processes are ones that require energy, and they require ATP. And so the name of this, um, and organic reaction that forms peptide bonds is called a dehydration synthesis reaction, and the reason it's called dehydration is because, literally, the molecule is dehydrated because it loses water during the peptide bond formacion. And so hydraulics is here is actually the complete opposite reaction. It's the complete opposite reaction, and so instead of being end organic, it's actually an ex organic process. And instead of forming peptide bonds, it actually cleaves or breaks down peptide bonds. And so, in our example below, What we're gonna do is talk about peptide, bond, formacion and peptide bond breakdown. And we're also gonna circle all of the Alfa carbons, which can be symbolized like this, and recalled that the Alfa Carbon is just the central carbon atom oven amino acid. So let's take a look at this example and which will notice is over here on the far left. What we have is our dehydration synthesis reaction, and so this is again going to be for peptide bond formation. And so over here on the far right, what we have is the complete opposite reaction of hydrology, sis, and recall that hydraulic sis is specifically for peptide bond cleavage or for peptide bond breakdown, and notice that these arrows are going in opposite directions. And so let's first talk about dehydration synthesis. Then we'll talk about hydraulics. ISS. So over here, what we have is, uh, to free amino acids. We have one free amino acid here, and we have another one over here. And so notice that they're Alfa carbons are right in the center. So we have an Alfa Carbon here, which is linked to its our group. And then we also have an Alfa Carbon over here, which is again linked to this our group and you should recognize these are groups are group of just a hydrogen is, of course, going to be a glazing amino acid. And the our group of a metal group is going to be an Allen in amino acid. And so now that we've identified these alfa carbons and these amino acids, what we can see is that during a dehydration synthesis reaction, what happens is the car boxful group of the glazing interacts with the amino group of the Allan E, and what they do is they form a water molecule, and that's why it's being dehydrated and in the process of dehydrating them all What? Um, the molecule in forming a water. A peptide bond is made in the peptide bond is shown here in red. And so this is our peptide bond and which will notice is that the peptide bond is indeed an am I linkage because we have our Carbonnel group and the Carbonnel Group is linked to a nitrogen atoms. So this is an M I linkage. And an easy way to be able to find a peptide bond is to just look for the Carbonnel Group. Once you find the Carbonnel group in the backbone, then you know that the bond to the nitrogen linking the Carbonnel group is going to be the peptide bond. And so again, we can label these Alfa carbons here. So we have the Alfa Carbon here and we could circle them. So we have the circled Alfa carbons, and here we have an Alfa Carbon as well, so we could circle it. So we have all the Alfa Carbon circle and you can see that these two amino acids, glazing and aligning, are linked together via Covalin Peptide bond. A my linkage. So now let's talk about hydraulics and again, Hydraulic. This is gonna be the complete opposite reaction. So we're gonna take this peptide bond here and we're going to instead of dehydrated, we're going toe add water to it. So we're gonna add water. And what that's gonna do is initiate the, uh, peptide bond cleavage reaction. And so notice that the arrow again is going in the opposite direction here. And so basically, what happens is we break down this die peptide, which has two amino acids in it, and we form these two separate amino acids up above. And so this process here is going to be an extra gone IQ process. So that means that it happened spontaneously. So this is an extra chronic process, whereas over here, with the peptide bond formation, it's actually an end organic process, so it requires energy or ATP in order for the peptide bond to form. And so, uh, notice that when we have two amino acids, so we have two amino acids in this chain. We have one over here and one over here. But even though we have two amino acids, we only have one peptide bonds. So the number of peptide bonds is always gonna be one less than the number of amino acids in the protein. And so what we have here in the middle is a free energy diagram. So what we have is the free energy of the system on the Y axis and the reaction coordinate on the X axis or the time that passes as the reaction progresses. And so down here, what we have our reactant. And so what we have are two separate amino acids. They're not linked by a peptide bond, their free amino acids. And up here, what we have is a, um a peptide ah, small die peptide with two amino acids. And these two amino acids are linked by a peptide bond, which is in red right here. And so what I want you to know is that the formation of this peptide bond so going from here up over to this process over here is an end organic reaction, like we said earlier. And so because it's an organic, it requires energy input. And the opposite process, essentially of going from this peptide bond and breaking it down into two separate amino acids is actually an extra chronic process. So it's spontaneous. So you might be wondering if it's a spontaneous reaction. Why is it that it's possible for peptide bonds to be stable? How is it that proteins can be stable? And why isn't that all the proteins just break down into their amino acids quickly? And the reason is that it is an extra chronic process. But the reason that it happens very, very slowly is because of this energy barrier. So there's a big energy barrier between the peptide bond here and, um, the barrier here. So there's a big energy barrier that makes hydraulics ISS happen very, very slowly. So even though it is X organic, as you can see by the energy difference between the reactant and the product, here it is x organic. But, uh, there's a huge energy barrier that makes it slow, and that energy barrier allows peptide bonds to be relatively stable. And so, um, this concludes our lesson on peptide bonds and peptide bond formation and break down and we'll see you guys in our practice videos. We'll we'll be able to practice these concepts. I'll see you guys there

Considering that peptide bond hydrolysis is exergonic, how is the stability of a peptide bond accounted for?


Highlight the peptide bonds in the figure below & circle all the α-carbons. How many peptide bonds are there?


Which of the following best represents the backbone atom arrangement of two peptide bonds?