Amino acids and the central dogma of molecular biology. Amino and carboxyl groups, side chains, and zwitterions.
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Why would Nitrogen grab a proton (H+) from the environment if this atom is very eletronegative?(17 votes)
- The atom as a whole is not electronegative, if the carboxyl tail becomes negative by losing a H+ the amino head becomes positive by gaining a H+, to make a neutral molecule.(19 votes)
- How to calculate a molcular weight(5 votes)
- If dna codes for proteins, what codes for other types of substances?(5 votes)
- The other molecules like starch, glycogen, fatty acids... are much more simple by structure. They are build by enzymes which are more or less specific for this one reaction step only. Enzymes are proteins which are encoded in the genome. So the genes indirectly influence which carbohydrates ... are built.(15 votes)
- Shoudn't Serine have only one methyl bonded to hidroxy group and to alpha carbon? I'm sorry if I didn't name it right, English is not my mother language.(9 votes)
- Yes, well spotted! You are right that the structure of serine is incorrect in the video.
As you say, there should only be one methylene group (CH2) between the alpha carbon and the hydroxyl group.(7 votes)
- Hi! Just wondering, are all amino acids in our body zwitterions? And in what way is being a zwitterion important for an amino acid in terms of its function or property?(7 votes)
- All amino acids are capable of forming zwitterions, but this only happens at a specific pH value which is unique for each amino acid. Zwitterions are important for encouraging substances to dissolve in the water present in the body- this is important for a lot of things and allows the chemical reactions we need to occur.(6 votes)
- 1-Does every amino acid has D & L form ?
I mean glycine has no asymmetric carbon atom for example.
And does having a D form have something to do with being dextrorotatory? Or not?
2-Does every amino acid has an isoelectric point in which it will be called a “zwitterion” ?
3-Every amino acid (except for polar ones) is amphipathic right?
4-Proline is an iminic acid, what is special about it?(3 votes)
- 1) There are actually thousands of amino acids§, but of the ones commonly found in proteins all except glycine are chiral and so will have
L-are not related to the direction that light is rotated!
Excellent article on this here:
2) Yes, each amino acid will have an isoelectric point and will exist as a zwitterion at that pH.
3) Like many things, it is more a question of to what degree something is amphipathic rather than whether it is or is not amphipathic. That being said, I would agree that the amino acids with non-polar side-chains are the most strongly amphipathic.
4) Have you looked at the structure?
This is a good resource:
Proline's unique† ring structure means that it puts a "kink" in the polypeptide chain — this tends to break up secondary structures (e.g. alpha helices or beta-strands).
§Note: For more on the diversity of amino acids see:
†Note: None of the other standard amino acids share this feature.(4 votes)
- at 1.24 what does [TRNA] mean(4 votes)
- tRNA is Transfer RNA. RNA is a biological molecule, but it has several different types (mRNA, tRNA, rRNA) that perform different functions. tRNA is used in protein synthesis to match amino acids to their corresponding codon (nucleotide sequences).
The process that I'm referring to and how it happens is too much for me to describe here. For more information on tRNA and protein synthesis, go to this Khan Academy article.
Note: you might want to start at the beginning of the lesson to fully understand what is going on.(2 votes)
- At7:45Sal says that at physiologically normal pH levels (which are slightly alkaline) the amino acids get de-protonated. Just before this he introduce peptide bonds (which I can guess is going to be a dehydration synthesis step.) But we need that de-protonation to happen before that dehydration synthesis can happen. Does this explain why having blood that is slightly too acidic will inhibit protein synthesis?(4 votes)
- Yes, if acidic blood, than deprotonation and formation of zwitterion is impossible.
Not sure if that directly affects protein synthesis, but I know that affects the production of ATP (disfigures it) and you end up with less available energy.(2 votes)
- why does the side group get labeled "R"(3 votes)
- R is used as symbol to represent any hydrocarbon in general which is different in every amino acid(3 votes)
- If peptides are made of amino acids linked together by peptide linkages, the smallest peptide would be dipeptide? Is there a monopeptide?(2 votes)
- You are correct a peptide made of two amino acids is a dipeptide, this is the smallest peptide molecule. A monopeptide is just an amino acid as there are no peptide bonds needed!(4 votes)
- DNA gets a lot of attention as the store of our genetic information, and it deserves that. If we didn't have DNA, there would be no way of keeping the information that makes us us, and other organisms what those organisms are. And DNA has some neat properties, it can replicate itself, and we go into a lot of depth on that in other videos. So DNA producing more DNA, we call that, we call that replication, but just being able to replicate yourself on its own isn't enough to actually produce an organism. And to produce an organism, you somehow have to take that information in the DNA, and then produce things like a structural molecules, enzymes, transport molecules, signaling molecules, that actually do the work of the organism. And that process, the first step, and this is all a review that we've seen in other videos. The first step is to go from DNA to RNA, and in particular, messenger RNA. "Messenger RNA," and this process right over here, this is called transcription. "Transcription," we go into a lot of detail on this in other videos. And then you wanna go from that messenger RNA, it goes to the ribosomes and then tRNA goes and grabs amino acids, and they form actual proteins. So you go from messenger RNA, and then in conjunction, so this is all, this is in conjunction with tRNA and amino acids, so let me say "+tRNA," and "amino acids." And I'll write "amino acids" in, I'll write it in a brighter color, since that's going to be the focus of this video. So tRNA and amino acids, you're able to construct proteins. You are able to construct proteins, which are made up of chains of amino acids, and it's the proteins that do a lot of the work of the organism. Proteins, which are nothing but chains of amino acids, or they're made up of, sometimes multiple chains of amino acids. So you can image, I'm just going to, that's an amino acid. That's another amino acid. This is an amino acid. This is an amino acid, you could keep going. So these chains of amino acids, based on how these different, based on the properties of these different amino acids, and how the protein takes shape and how it might interact with its surrounding, these proteins can serve all sorts of different functions. Anything from part of your immune system, antibodies, they can serve as enzymes, they can serve as signaling hormones, like insulin. They're involved in muscle contraction. Actin and myosin, we actually have a fascinating video on that. Transport of oxygen. Hemoglobin. So proteins, the way at least my brain of it, is they do a lot of the work. DNA says, well, what contains the information, but a lot of the work of organism is actually done, is actually done by the proteins. And as I just said, the building blocks of the proteins are the amino acids. So let's focus on that a little bit. So up here are some examples of amino acids. And there are 20 common amino acids, there are a few more depending on what organism you look at, and theoretically there could be many more. But in most biological systems, there are 20 common amino acids that the DNA is coding for, and these are two of them. So let's just first look at what is common. So, we see that both these, and actually all three of this, this is just a general form, you have an amino group. You have an amino group, and this where, this is why we call it an "amino," an amino acid. So you have an amino group. Amino group right over here. Now you might say, "well, it's called an amino acid," "so where is the acid?" And that comes from this carboxyl group right over here. So that's why we call it an acid. This carboxyl group is acidic. It likes to donate this proton. And then in between, we have a carbon, and we call that the alpha carbon. We call that the alpha carbon. Alpha carbon, and that alpha carbon is bonded, it has a covalent bond to the amino group, covalent bond to the carboxyl group, and a covalent bond to a hydrogen. Now, from there, that's where you get the variation in the different amino acids, and actually, there's even some exceptions for how the nitrogen is, but for the most part, the variation between the amino acids is what this fourth covalent bond from the alpha carbon does. So you see in serine, you have this, what you could call it an alcohol. You could have an alcohol side chain. In valine right over here, you have a fairly pure hydrocarbon, hydrocarbon side chain. And so in general, we refer to these side chains as an R group, and it's these R groups that play a big role in defining the shape of the proteins, and how they interact with their environment and the types of things they can do. And you can even see, just from these examples how these different sides chains might behave differently. This one has an alcohol side chain, and we know that oxygen is electronegative, it likes to hog electrons, it's amazing how much of chemistry or even biology you can deduce from just pure electronegativity. So, oxygen likes to hog electrons, so you're gonna have a partially-negative charge there. Hydrogen has a low electronegativity relative to oxygen, so it's gonna have its electrons hogged, so you're gonna have a partially positive charge, just like that, and so this has a polarity to it, and so it's going to be hydrophilic, it's going to, at least this part of the molecule is going to be able to be attracted and interact with water. And that's in comparison to what we have over here, this hydrocarbon side chain, this has no polarity over here, so this is going to be hydrophobic. So this is going to be hydrophobic. And so when we start talking about the structures of proteins, and how the structures of proteins are influenced by its side chains, you could image that parts of proteins that have hydrophobic side chains, those are gonna wanna get onto the inside of the proteins if we're in an aqueous solution, while the ones that are more hydrophilic will wanna go onto the outside, and you might have some side chains that are all big and bulky, and so they might make it hard to tightly pack, and then you might have other side chains that are nice and small that make it very easy to pack, so these things really do help define the shape, and we're gonna talk about that a lot more when we talk about the structure. But how do these things actually connect? And we're gonna go into much more detail in another video, but if you have... If you have serine right over here, and then you have valine right over here, they connect through what we call peptide bonds, and a peptide is the term for two or more amino acids connected together, so this would be a dipeptide, and the bond isn't this big, I just, actually let me just, let me draw it a little bit smaller. So... That's serine. This is valine. They can form a peptide bond, and this would be the smallest peptide, this would be a dipeptide right over here. "Peptide," "peptide bond," or sometimes called a peptide linkage. And as this chain forms, that polypeptide, as you add more and more things to it, as you add more and more amino acids, this is going to be, this can be a protein or can be part of a protein that does all of these things. Now one last thing I wanna talk about, this is the way, the way these amino acids have been drawn is a way you'll often see them in a textbook, but at physiological pH's, the pH's inside of your body, which is in that, you know, that low sevens range, so it's a pH of roughly 7.2 to 7.4. What you have is this, the carboxyl group right over here, is likely to be deprotonated, it's likely to have given away its hydrogen, you're gonna find that more likely than when you have... It's gonna be higher concentrations having been deprotonated than being protonated. So, at physiological conditions, it's more likely that this oxygen has taken both of those electrons, and now has a negative charge, so it's given, it's just given away the hydrogen proton but took that hydrogen's electron. So it might be like this, and then the amino group, the amino group at physiological pH's, it's likely to actually grab a proton. So nitrogen has an extra loan pair, so it might use that loan pair to grab a proton, in fact it's physiological pH's, you'll find a higher concentration of it having grabbed a proton than not grabbing a proton. So, the nitrogen will have grabbed a proton, use its loan pairs to grab a proton, and so it is going to have... So it is going to have a... It is going to have a positive charge. And so sometimes you will see amino acids described this way, and this is actually more accurate for what you're likely to find at physiological conditions, and these molecules have an interesting name, a molecule that is neutral even though parts of it have charge, like this, this is called a zwitterion. That's a fun, fun word. Zwitterion. And "zwitter" in German means "hybrid," and "ion" obviously means that it's going to have charge, and so this has hybrid charge, even though it has charges at these ends, the charges net out to be neutral.