As we already said, proteins actually make up a majority portion of the membrane, and there are actually 6 different types that you can find, or 6 classifications if you will. You don't actually need to know what each type is and what it's all about. You just need to know that there are 6 types. Generally speaking, membrane proteins tend to have a few different functions. They'll act as receptors and signaling pathways. They'll act as channels, gates, and pumps to transport molecules across the membrane, and they'll act as enzymes generally speaking to catalyze lipid biosynthesis and to catalyze ATP synthesis. Now, the exterior amino acids, as in the amino acids on the exterior portion of a protein, tend to be polar and may have carbohydrates attached to them. So, these are the portions of the protein that interact with the aqueous environment that you see here. So, these tend to be polar amino acids. Now, the interior amino acids or amino acids that are inside the membrane in the protein, tend to be non-polar. So that's going to be, like these amino acids. This portion right here in purple, these, I'm just going to jump out of the image here. These are generally speaking going to be non-polar.
Now, it's worth noting that this polarity trend actually extends to the individual alpha helices of a protein too. So just for a moment here, pretend that we're looking, like a bird's eye view down under the surface of a particular protein channel, and it's made up of, or a particular protein, let's just say. And let's say that it's made up of like 6 alpha helices. And I'm sorry my drawing isn't perfect, but say these 6 alpha helices come together to make a particular protein. And what I mean to say that alpha helices have a polar and a nonpolar side is these exterior portions that I'm kind of highlighting in blue, those portions of the alpha helix are going to interact with the membrane, right? That's what they're touching. They're touching the membrane. So, those are going to tend to be non-polar amino acids. Whereas, the amino acids on the interior portions of these chains that I'm highlighting in red, those are going to be polar amino acids. And remember that each one of these is an alpha helix. And we're looking at it on a top-down level. So that means that if you were to think of the primary structure of this alpha helix and go amino acid to amino acid, you'd be alternating every few amino acids between polar and nonpolar amino acids. So it would be like 2 nonpolar then 2 polar then 2 nonpolar, then 2 polar, something like that. It wouldn't actually necessarily work out like I said right there. I'm just trying to illustrate the point.
Now, it's also important to note that phospholipids, that is, membrane phospholipids, can be associated with the interior portions of proteins as well as the exterior surfaces. So, of course, in an embedded protein, these portions, for example, what we see in dark blue here, those portions are going to be associated with the interior portion of the membrane and therefore, they're going to be associated with phospholipids, right? They're going to have hydrophobic interactions, kind of holding them together. But these interior portions that we see in light blue, those interior portions of the protein are also potentially can be associated with membrane phospholipids. That is to say membrane phospholipids can get into the insides of these proteins as well.
Now how do we know what part of the protein is going to be associated with the interior segment of the membrane and what parts of the protein are going to interact with the aqueous environment that surrounds the membrane? Well, we use something called hydropathy index to reveal what the hydrophobic and hydrophilic portions of the membrane are. Again, that's a hydropathy index. You can see an example of one right here. Basically, the way this works is amino acids in a protein are given like a sort of hydropathy rating and it's either a positive or a negative number, and that value dictates whether it's hydrophobic or hydrophilic. So positive values are hydrophobic, whereas negative values are hydrophilic. And you can see that we basically scan along the polypeptide and some regions like this are hydrophobic or they have a hydrophobic rating. So they're probably internal because they're made up of mostly hydrophobic amino acids. So they're probably going to exist in the hydrophobic internal environment of the membrane. Whereas, these portions that have a negative value are more likely to be external because they're more hydrophilic so they're more likely to associate with the aqueous environment.
So, you don't really need to know how to, how to, you know, precisely read a hydropathy index. You just need to have a general understanding of what it's showing. And just to be clear, these green markings on the image are showing the different regions of the protein and where it crosses through the membrane. You don't need to worry about any of that. You just need to know what the general values mean. You know, negative is hydrophilic, positive is hydrophobic, positive tends to be internal, negative tends to be external. Now, a couple of things to note before we move on. Tryptophan and tyrosine, boy, those guys always show up together, right? They always are appearing together, because they have similar properties obviously. And it turns out that they tend to be found right at the edge of the membrane in transmembrane proteins. So if we go back up to this image here, we see these trans you know, on All the way on the left, these two proteins here, these are transmembrane proteins, and basically, tyrosine and tryptophan, we would tend to find right at the edge of the membrane like where I'm marking in red here. So, they're most likely to find Tyrosine and tryptophan in a location like that. Also worth noting is that peripheral proteins are always attached to a fatty acid that's embedded in the membrane. We can see an example of this right here where we have this fatty acid and attached to it is this peripheral protein. With that, let's flip the page.
