How do amino acids form the intricate polypeptide chains found in proteins? It's a matter of chemistry. Join glycine, a special amino acid, as she sizes up the other amino acids.
Amino Acid Structure
We've seen again that amino acids are compounds where there's an amino group attached to a carbon, next to a carboxylic acid. And on the carbon, in between the amine group and the carboxylic acid carbon, there is typically a sidechain attached, except in glycine.
In this lesson, we'll be joining glycine as she goes on a search for a perfect peptide date.
'Hi! My name is glycine, and I'm an amino acid. The way you can tell that I'm an amino acid is that I have a carboxylic acid group, and then on the carbon next to my carboxylic acid carbon, I have an amine. Now, you might think that I look a little funny. You might have heard that amino acids usually have an r-group.
Structure of a typical amino acid
And, in this case, you might be right. My r-group is a hydrogen! Now, I think that makes me pretty special, and the reason that it makes me special is that I can be both a polar amino acid and a non-polar amino acid. I think that's pretty neat.
'Now, let's look at my profile. You can see that my name is glycine, and that my friends call me 'gly' or 'G' for short, and you can see my structure. You can also see what I look like at biological pH as well. At biological pH, the hydrogen on my carboxylic acid goes away, and the nitrogen gets an extra hydrogen. So, my chemical formula is the same, but I look a little bit different. So don't be alarmed when you see hydrogens popping on and off on other amino acids as we go meet them.
'Now, what I'm looking for is another amino acid that can help me turn the peptide that I'm already a part of. So please join me as I go and look at profiles of other amino acids looking for that perfect partner. I think I'll go check out some polar amino acids. Hmm, let's check out this one: aspartic acid. It has a two-carbon side chain and a carboxylic acid on it. It says that it's important for gluconeogenesis, which is important in biology and is pervasive in biosynthesis. That sounds like it has a pretty important job - I wonder if it gets paid well? One interesting fact about aspartic acid is that it's very active, catalytically, in proteins, and that carboxylic acid side chain is usually missing that hydrogen at biological pH, so it's a negative amino acid. I don't know how I feel about that. Let me go check out another one.
'Hmm. Glutamic acid. Looks an awful lot like aspartic acid, except it has three carbons. What else is this good at? Hmm. Glutamic acid is also important in metabolism, that sounds good. It's part of that MSG stuff, monosodium glutamate, not sure I'm so excited about that. And it's a neurotransmitter. Pretty cool, but I don't know if I want an amino acid that's so busy. Plus, it doesn't look like it's going to help me turn my peptide. Well, I don't know if I was the hugest fan of those negative amino acids, so maybe I'll go check out some positive polar amino acids.
Polar Positive Amino Acids
'Like this guy, arginine. It's got a 3-carbon chain with this funky looking guanidinium group on it, pretty cool. It's important in cell division. It can have many hydrogen bonds, which might be interesting structurally, but I don't know if it'll turn my peptide. Mmm. Not quite what I'm looking for.
'Here we have histidine. Histidine says that it's an essential amino acid with an imidazole functional group. It can do pi-stacking, which lets it interact with other amino acids, and it's really common in catalytic sites and enzymes. Pretty cool! Says that it's very responsive. The hydrogen on the imidazole ring is removed around a pH of six. Pretty cool, but maybe not what I'm looking for right now.
'Looks like there's one more polar positive amino acid, called lysine. Lysine is one of the essential amino acids, and it has this amine group. Pretty cool. That could be positively charged because it adds a hydrogen at biological pH. One cool, fun fact that lysine says about itself is that Jurassic Park's dinosaurs were altered so that they couldn't make it, so that they were dependent on the scientists in Jurassic Park for food. Pretty crazy stuff. I guess essential means that our body can't make these amino acids. That must mean that it's really important for us to eat these specific ones.
Polar Neutral Amino Acids
'Since those amino acids didn't work out, maybe I'll check out the polar neutral amino acids. Serine has a one-carbon side chain with a hydroxyl group on it, and is really active in biosynthesis of purines and pyrimidenes, which are in DNA. It also says that it has a lot of catalytic roles, including in the enzyme trypsin, and it can have post-translational, or after protein-making, modifications. Sounds pretty cool, but I'm not quite sure that that's going to do what I need it to.
'Maybe I'll check out threonine. Looks pretty similar. It has two carbons on its hydroxyl group. It can also be modified after the protein it's part of is made, and it can participate in hydrogen bonding. Doesn't say anything about turning a peptide, though. Probably not the right amino acid for me.
'Hmm. How about asparagine? It's an amino acid with two carbons, and has an amide on its side chain. It was initially isolated from asparagus juice. Asparagine is really good at hydrogen bonding with the peptide backbone. Hmm… it's nearing the beginning and end of helices; that might help me to turn my peptide a little bit. But maybe I'll keep looking and see if there's a better amino acid out there for me.
'Hmm. How about this one, glutamine. It looks pretty similar to asparagine; maybe it will help. It has three carbons instead of two, and is able to regulate the acid/base balance in kidneys, and can do nitrogen donation when making part of DNA. It's also able to hydrogen bond, and is more flexible than asparagine, which actually means it's worse at forming helices. Definitely not the amino acid for me.
'Well, I didn't have much luck with those hydrophilic polar amino acids, so maybe I'll try out some hydrophobic non-polar amino acids, like alanine, which is the second most abundant amino acid. That's pretty impressive. It has a single carbon on its side chain and it's pretty non-reactive - that might be good. It's involved in energy metabolism, but it doesn't really do anything to the structure of the protein, or to the peptide.
'Maybe I'll try valine. Hmm. Valine is also non-polar, and it has three carbons in its side chain. It says that it's named after the herb valerian, which is a sedative. Not quite sure clumping is what I'm going for, though it is essential.
'Hmm. Maybe there's this one, isoleucine. It was discovered in hemoglobin, and has a branched carbon chain as well, but doesn't do much for my structure.
'Same for this leucine - it can be used in making sterols in the liver, and can stimulate protein synthesis in the muscles. It's also the most common amino acid, with its 4-carbon side chain, but it doesn't really do a lot for my structure.
'These carbon side chains don't seem to be doing very much. Maybe I should branch out a little bit and look at something like this essential amino acid, methionine. This is pretty cool. It looks like it has an ether with a sulfur instead of an oxygen in its side chain. It's also non-polar, and it's involved in making other amino acids. Again, it's really non-polar and doesn't seem to do much structurally.
'Well, let's check out this guy, he has a bigger side chain. Phenylalanine has a benzyl group, which is this big, funny-looking ring. It's really good at doing pi-stacking interactions with similar amino acids, and it can be converted to tyrosine. It's an essential amino acid, which is pretty cool, but I don't know that it's going to turn my peptide, although it might help stabilize it.
'Hmm. Maybe tyrosine will behave a little bit differently, since it has this hydroxyl group on that ring. Tyrosine was isolated from a milk protein, and it can have phosphorus added to it, and it can participate in hydrogen bonding. Sounds like it's a pretty active amino acid, and it's even involved in some enzymatic reactions, but I don't know if it's the peptide-turning amino acid for me.
'Here we have tryptophan, which is another essential amino acid. This is the one that we associate with turkey day, and being really tired after eating Thanksgiving dinner. Initially it wasn't found in turkey, though; it was apparently found in milk proteins. Serotonin, which is an important neurotransmitter, is made from tryptophan, and it can participate in pi-stacking, and it has this funky indole functional group. I don't know that it will help me turn my peptide, though.
'I feel like I've gone through polar and non-polar amino acids, but I still haven't found my peptide-turning amino acid. That's kind of a problem. I wonder if there are any others?
Special Amino Acids
'Wait a second… there are other special amino acids of the 20. Like me! I'm a special amino acid! Maybe one of them is my perfect peptide-turning match.
'Well let's check this guy out: cysteine. Cysteine has a sulfhydryl or thiol group on its side chain, and it can do things like bond with cystines in other peptide chains to form disulfide bonds, which are incredibly important, structurally. Now, this is what I'm talking about - getting much closer to what I'm looking for. It's a hydrophobic group, which is OK by me, and it's really good at binding metal ions.
Chemical structures of three special amino acids
'Well, that sounds promising, but I might keep looking. There's one more amino acid that I can check out. There's this one called proline. It's a little bit funny looking in that it's a secondary amine, and it's a little bit rigid, but it's able to be the edge of a beta strand, or start an alpha helix. It forms its own helices in collagen, which is what makes up our cartilage in our ears, and, it loses less energy when folding. It tends to be found in turns and is solvent-exposed. Hmm. All of this sounds really good to me! I think that proline is going to be my peptide date. Thanks for helping me pick out my new date, and helping me figure out how to turn my peptide.'
To summarize, we've learned that amino acids can fall into many different categories. Amino acids, generally, can be polar, non-polar, or special amino acids. Polar amino acids can be broken down into negatively charged, positively charged, and neutral amino acids, while non-polar amino acids can be broken down into aliphatic and aromatic amino acids.
There are three different special amino acids: proline, cysteine, and glyciene.
Glycine is special because it does not have a side chain. Proline is special because it has a secondary amine, which means that there are two carbons attached to its amine nitrogen. Finally, cysteine is unusual because it contains a sulfur atom, which helps in forming disulfide bonds, which are important in protein structure.
We've also revisited amino acid structure. We've seen, again, that amino acids are compounds where there's an amino group attached to a carbon next to a carboxylic acid, and on the carbon, in-between the amine group and the carboxylic acid carbon, there is typically a side chain attached, except in glycine.