How amino acids form peptide bonds (peptide linkages) through a condensation reaction (dehydration synthesis).
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- Sorry if this seems like an awfully basic question, but why does O get a negative charge at4:01?(13 votes)
- Well oxygen is a very electronegative atom hence it can remain stable holding an additional electron/negative charge.(17 votes)
- Since the amino acid can be a zwitterion in physiological pHs and it is considered as 'neutral', why is it still called the amino 'acid' ?(7 votes)
- Amino acids have both, a amino (NH2) and a carboxy group (-COOH).
For naming it does not matter if the groups are protonated or not.(6 votes)
- Why on earth are these amino acids trading protons? Doesn't that change the element that the donor atom is? Don't they normally trade electrons?(3 votes)
- You are correct, you don't get protons leaving and joining the nuclei of atoms during chemical reactions — those would be nuclear reactions.
The "protons" Sal is talking about are hydrogen ions (
H⁺) – since the nucleus of most hydrogen atoms is just a single proton he is using them interchangeably.
While I agree this usage is imprecise it is quite widespread, so we just need to accept that when people are discussing (bio)chemistry if they say proton they usually mean
I suggest you rewatch this video and mentally substitute hydrogen ion when he says proton – it will make a lot more sense now. 😊
And yes, molecules also trade electrons.(14 votes)
- would water be considered a zwitter ion because of its polar bonds?(5 votes)
- I thought of that too, but my guess would be no.
A water molecule is considered polar because of electronegativity differences between the oxygen atom and the 2 hydrogen atoms. The oxygen atom "Hogs" the electrons from the covalent bond creating a partially negative side in the molecule while the other side becomes partially positive. At this point, the molecule is polar, additionally there are no formal charges.
In the case of the amino acids shown in the video above, we have an amino group which gained a proton from the solution and its net charge became + 1 (positive). On the other side, we have a carboxyl group which let go of a proton therefore gaining a -1 net charge (negative). Unlike the water molecule, these net charges are independent of each other. Just like any ionic compound, the charges are opposite and equal in magnitude and therefore cancel out. But this isn't an ionic compound! Rather we can look at it as an ion (Acting as a cation and anion simultaneously) with two opposite charges that cancel out, making it a zwitterion (hybrid ion)!
Water has no net charge to begin with, just an unequal distribution of electrons across the molecule.
Hopefully I am not misleading anyone, I'm just assuming this is the case.(7 votes)
- As Sal said at0:37that a peptide is nothing more than a chain of amino acids, he also said in the last video that amino acids is the main substance in formation of proteins. My question to you is that does that mean that a peptide is a protein?(3 votes)
- Many proteins are formed by not only one strand of amino acids, but many. These proteins are also called polypeptides. Therefore if a protein were to contain only one strand of amino acids it could be called a peptide as you have noticed. But since most proteins are not only composed of one chain you cannot call them a peptide, but a polypeptide.(5 votes)
- At7:22, 3 lone pairs of oxygen are shown while oxygen only contains 6 electrons in its valence shell. 2 electrons are used to form the bond with Carbon so how was the 3rd lone pair present?(3 votes)
- 3 lone pairs of electrons = 6 electrons
The covalent bond between carbon and oxygen has two electrons, one from the oxygen and one from the carbon.(4 votes)
- I'm confused, please help! At physiological pH, the amino group would be protonated because the pH is less than its pKa. This means the amino group is protonated and thus, does not have a lone pair. Without a lone pair at physiological pH, how on earth does the peptide bond form? There can be no nucleophilic attack by that Nitrogen because it doesn't have a lone pair at physiological pH.(4 votes)
- At1:27what does"net net" mean?
"So this lone pair goes to this carbonyl carbon, forms a bond, and then this hydrogen, this hydrogen, and this oxygen could be used net net to form a water molecule"(3 votes)
- According to Wiktionary:
net net (plural net nets)
(business) A true and final result, after more than the obvious subtractions and allowances.
While I have no idea why Sal keeps using this business jargon in this video, the sentences make sense (and are correct) if you just ignore those words.(3 votes)
- I've watched the video 3 times,tried to draw dot & cross diagrams & still can't get my head around the electrons moving around,because to fill the outer shell there should be 8 http://www.gcsescience.com/Ammonia-Molecule.gif but if the 2Hydrogens are bonded to Nitrogen there are 7 electrons in the outer shell.Where is Sal getting 2 lone pair.How can oxygen already have 2 lone pairs at3:52when it usually have 6 electrons in its outer shell? https://proxy.duckduckgo.com/iu/?u=http%3A%2F%2Fmontessorimuddle.org%2Fwp-content%2Fuploads%2F2012%2F02%2FOxygen-shells.png&f=1(3 votes)
- There are two hydrogens and one carbon bonded to the amino nitrogen, which has one lone pair of electrons. The amino nitrogen has essentially the same electronic configuration as ammonia.
The oxygen at3:52isn't an isolated atom — it is part of the hydroxide leaving group. If you do your diagrams correctly you will see it has 8 outer shell electrons, two came from the the bond that was between the oxygen and the carbonyl carbon, two are shared with the hydrogen, and the remaining four are the two lone pairs that were already present when the oxygen was part of the carboxyl group.
Does that help?
If you want to understand this better, I strongly encourage you to work through the Organic Chemistry material on KhanAcademy.
However, you will probably benefit from starting by working through the regular Chemistry material first:
That may look like a lot of work, but you've probably watched many of the videos already under "Chemistry of life". A deep understanding of chemistry is essential to anyone interested in modern biological sciences or medicine, so I really encourage you to take the time to work though all of the chemistry material.(3 votes)
- Hello! When you form proteins in the ribosomes, is the energy required to form a peptide bond between two amino acids from the breaking of the bond between the amino acid and the tRNA molecule? If so, does this make it an overall energy neutral reaction? Or is ATP still required in addition to this?(3 votes)
- Good question. 😊
The bond in the aminoacyl-tRNA is higher energy than the peptide bond, so there is no new energy input required to form the peptide bond — the energy came from hydrolyzing ATP to AMP plus PPᵢ (pyrophosphate) during the binding of the amino acid to the tRNA.
However, a GTP is hydrolyzed to ensure that the correct aminoacyl-tRNA binds to the mRNA-ribosome complex and another is used to move the ribosome along the mRNA by one codon.
This discussion does a reasonable job of explaining the energetics of this process:
- [Voiceover] So I've got two arbitrary amino acids here. We recognize the telltale signs of an amino acid. We have an amino group right over here that gives us the amino and amino acid. We have a carboxyl group right over here. This is the acid part of an amino acid. And in between we have a carbon, and we call that the alpha carbon. And that alpha carbon is gonna be bonded to a hydrogen and some type of a side chain, and we're just gonna call this side chain R1, and then we're gonna call this side chain R2. And what we're gonna concern ourselves with in this video is, how do you take two amino acids and form a peptide out of them? And just as a reminder, a peptide is nothing more... than a chain of amino acids. And so, how do you take these two amino acids and form a dipeptide like this? A dipeptide would have two amino acids. That would be the smallest possible peptide, but then you could keep adding amino acids and form polypeptides. And a very high-level overview of this reaction is that this nitrogen uses its lone pair to form a bond with this carbonyl carbon right over here. So this lone pair goes to this carbonyl carbon, forms a bond, and then this hydrogen, this hydrogen, and this oxygen could be used net net to form a water molecule... that's let go from both of these amino acids. So this reaction, you end up with the nitrogen being attached to this carbon, and a release of a water molecule. And because you have the release of this water molecule, this type of reaction, and we've seen it many other times with other types of molecules, we call this a condensation reaction, or a dehydration synthesis. So condensation... condensation reaction or dehydration synthesis. We saw this type of reaction when we were putting glucoses together, when we were forming carbohydrates. Dehydration synthesis. But whenever I see a reaction like this, it's somewhat satisfying to just be able to do the counting and say, "All right, this is gonna bond "with that, we see the bond right over there, "and I'm gonna let go of an oxygen and two hydrogens, "which net net equals H2O, equals a water molecule." But how can we actually imagine this happening? Can we push the electrons around? Can we do a little bit of high-level organic chemistry to think about how this happens? And that's what I wanna do here. I'm not gonna do a formal reaction mechanism, but really get a sense of what's going on. Well, nitrogen, as we said, has got this lone pair, it's electronegative. And this carbon right over here, it's attached to two oxygens, oxygens are more electronegative. The oxygens might hog those electrons. And so this nitrogen might wanna do what we call in organic chemistry a nucleophilic attack on this carbon right over here. And when it does that, if we were doing a more formal reaction mechanism, we could say, "Hey, well, maybe one "of the double bonds goes back, "the electrons in it go back to this oxygen, "and then that oxygen would have a negative charge." But then that lone pair from that double bond could then reform, and as that happens, this oxygen that's in the hydroxyl group will take back both of these electrons. Would take back both of those electrons, and now it's going to have an extra lone pair. Let me do that by erasing this bond and then giving it an extra lone pair. It already had two lone pairs, and then when it took that bond, it's gonna have a third lone pair. And then it's going to have a negative charge. And now you could imagine it's going to grab a hydrogen proton someplace. And now it could just grab any hydrogen proton, but probably the most convenient one would be this one, because if this nitrogen is going to use this lone pair to form a bond with carbon, it's going to have a positive charge, and it might wanna take these electrons back. So you could imagine where one of these lone pairs is used to grab this hydrogen proton, and then the nitrogen can take these electrons, can take these electrons back. So hopefully you didn't find this too convoluted, but I always like to think, what could actually happen here? And so you see, this lone pair of electrons from the nitrogen forms this orange bond with the carbon. Let me do that in orange color if I'm going to call it an orange bond. It forms this orange bond. What we call this orange bond, we could call this a peptide bond, or a peptide linkage. Peptide bond, sometimes called a peptide... peptide linkage. And then we have the release of a water molecule. And so you have this oxygen is this oxygen, and you could imagine that this hydrogen is this hydrogen, and this hydrogen is this hydrogen right over here, and so net net it all works out. Now when I first saw this reaction, I was like, "OK, that kind of makes sense." Except for the fact that in physiological pHs, amino acids don't tend to be in this form. In physiological pHs, you are more likely to find this form of the amino acids, to find them as zwitterions. Zwitterions. Let me write down that word. It's a fun word to say. And it's one word, but I'm gonna write the two parts of the word in different colors so you can see. It's a zwitterion. So what does that mean? Well, zwitter in German means hybrid. It's a hybrid ion. It's an ion, it has charge on different ends of it, parts of the molecule have charge, but when you net 'em out, it is neutral. Parts are charged, but is neutral overall. And so at physiological pHs, the amino, the nitrogen end of the amino acid, tends to grab an extra proton, becomes a positive charge, and the carboxyl group tends to let go of a proton and has a negative charge. And this is actually going to be in equilibrium with the forms that we just saw before, but at physiological pHs, it will actually tend to the zwitterion form. And so how do you get from this form to form a peptide bond? Well, you could imagine this character over here, after giving its hydrogen protons, has an extra lone pair. So it's got one lone pair, two lone pairs, and then it's got, I'll do the extra lone pair in, I'll do the extra loan pair in purple. It's got an extra lone pair. Well, maybe it could use an extra lone pair to either grab a proton from the solution or maybe just for accounting convenience we could say, "Well, maybe just bumps in the right way "to grab this proton and then allows the nitrogen... "to take back these electrons." And if it did that, well, then you're getting, at least when you're looking at this carboxyl group and this amino group, you're going to get to the form that we just saw. If this gets a hydrogen here, this is gonna become a hydroxyl, and if this nitrogen takes back these two electrons from this pair, then it's just going to be NH2. So it's going to be, at least this part of the molecules, are gonna be just what we started with up here, and so you could imagine how you get back to the peptide linkage which we have right over here. This is the peptide linkage. And then the only difference between the resulting peptide that I have in this reaction, I guess you could say, in the previous one, is this is a zwitterion. The zwitterion form, where this carboxyl group... having donated its proton to the solution, and over here the nitrogen, this nitrogen, has taken a proton from the solution, so it has a net neutral charge, even though you do have a charge at either end. So hopefully you found that fun.