Part three of this module we're going to get into proteins. Proteins are polymers like carbohydrates. They have monomer building blocks. The monomers that compose proteins are called amino acids. Amino acids all have this general shape where they have a central carbon and then that carbon has four bonds.
One bond will be just to a simple hydrogen atom. Another will be to an amino group, a third to a carboxyl group, and then the fourth bond will be to something called an R group or an R side chain. And these R side chains, you can think of that R as just standing as like a variable, because the R side chains are going to be what differentiates different amino acids from each other.
So all amino acids are going to have this same top part. and then the r side chain will be different depending on which of the 20 amino acids in our body that we are talking about um functionally we're not even really going to get into what proteins do because function of a protein or function of proteins is so diverse proteins essentially do everything in our body anything that you think of as like a cell activity or cell physiology That's almost always being carried out by, at least in part, by one or more proteins. So, you know, different functions for different proteins will come up throughout the semester and all throughout as you learn more and more about biology.
For this unit, we're just going to focus on the structure of proteins. As I mentioned, there are 20 different types of amino acids. All of them are shown in these tables here. And I'm not going to ask you to memorize the structure of these amino acids or anything like that, but you should understand the significance of the structural makeup of the different R side chains.
So for example, if a protein is made up of lots of valine, alanine, isoleucine, all of these R groups, are made up of all carbons and hydrogens so all those r groups are very non-polar therefore you can make assumptions about what that protein does or where in the cell that protein is likely located if it's non-polar that means it's hydrophobic and maybe if that's the case it might be say embedded in the membrane so while i'm not going to ask you to memorize the structure of these you should under understand the significance of the structure because um the you know all amino acids have the amino group and carboxyl group which have a charge and are therefore have some polarity but the r group uh or the r groups of all the amino acids are what's going to actually determine how the protein behaves so even though you know a protein might be made up of lots of amino and carboxyl groups if the r groups of all those amino acids are nonpolar, then the protein will be nonpolar. And we'll kind of talk about why that is in the next slide. I lied.
We're going to talk about why amino and carboxyl groups don't create polarity in the protein on the next slide. Before that, we're going to get into just some naming conventions for proteins. So short proteins made up of typically fewer than 20 amino acids are called peptides.
or oligopeptides. Peptides and oligopeptides are really important for cell-to-cell communication. Some of our hormones, those that are not composed of lipids, are generally going to be composed of peptides. And then when you link more amino acids together, that's what creates a polypeptide or, you know, the terms polypeptide and protein are often used.
kind of interchangeably. Other than the hormones and some smaller signaling molecules, most of the proteins in our body are polypeptides. The bond that links the amino acids together are called peptide bonds. So here we have one amino acid linked to another amino acid, and we're going to remove water, another dehydration reaction, to form a bond. between this new amino acid.
And hey, I was right. We are going to talk about significance of carboxylamino groups here because when this dehydration reaction happens it forms a peptide bond between the carboxyl group of one molecule carboxyl group and the amino group of the next amino acid so when this bond forms down here The carboxyl group no longer has its charge. The amino group no longer has its charge. So any sort of polarity that would be caused by these functional groups is gone because this bonding has happened to make the larger protein. What's sort of left or available to influence the protein's activity are these R groups and we'll kind of we'll go into more detail on this next.
So when it comes to protein structure, there are multiple layers, for lack of a better term. The primary structure of a protein is exactly what I was just talking about. Amino acids linked together by peptide bonds.
So here we have a carboxyl group and an amino group, and then highlighted in blue. is the peptide bond. And so linking all of these amino acids, right, each amino acid is in this pink rectangle, and you can see each one is linked to the next by a peptide bond between its carboxyl group and the amino group of the next amino acid.
Just this level of bonding, this string of amino acids, this is the primary structure. Now these peptide bonds are polar covalent bonds. and they are nearby lots of other polar covalent bonds involving hydrogen so for example right we have this bond here and that is right near uh say this hydrogen attached to a nitrogen so by Creating this primary structure of the protein, we have generated dipoles.
If dipoles are present and hydrogens are around, that generally means we're going to form hydrogen bonds. And those hydrogen bonds are what make up the secondary structure. So the hydrogen bonding between amino acids can occur or generally occurs in two major patterns.
there are these beta pleated sheets or alpha helices so either the um string of amino acids tend to like stack on top of each other that's what you're seeing with the beta pleated sheet or they form this spiral structure uh called the alpha helix so both primary structure and secondary structure are formed due to the interactions between you amino groups and carboxyl groups. The next level of structure, tertiary structure, is now going to be dependent on the specific types of R groups. So with tertiary structure, we may have multiple beta pleated sheets or multiple alpha helices all connected together.
And the way that those alpha helices, beta pleated sheets connect is dependent on which amino acids are there. to form different types of interactions. So the common interactions that form tertiary structure between R groups are disulfide bridges, these are bonds between two sulfur atoms, hydrogen bonding, van der Waals interactions, and ionic interactions.
So depending on which type of amino acids you have and which, you know, the R group of one might attract the R group of another, depending on the makeup of those amino acids that'll influence the overall structure of the protein and then finally we have quaternary structure not every protein has a quaternary structure in this case it's just the same type of interaction we see with tertiary structures but they are being formed between multiple tertiary structures so like here is one protein with four subunits. So each of these individual subunits is its own tertiary structure and it just so happens that they form together creating a quaternary structure. So primary and secondary structure are held together by the polar covalent bonds or peptide bonds and the hydrogen bonds that they form.
Tertiary quaternary structure held together by interactions between R groups and depending on the biochemical makeup of those R groups, the interactions can vary. The formation of that tertiary structure is often called protein folding. And same with the formation of the secondary structure, because primary structure is just linking the amino acids together.
Everything else is that now chain of amino acids kind of folding in on itself and changing shape. And a process called denaturing can break down that protein folding without actually breaking the peptide bonds themselves. So in that case, the protein will unfold.
It'll go down to its base primary structure. But once that denaturing agent is gone, the protein can kind of refold itself and return to its tertiary. secondary tertiary and or quaternary structure this is significant because protein shape and protein structure has a huge implication on the protein's activity or its ability to do its job often denatured proteins are inactive common ways to denature a protein are changes in ph so making something really acidic or really basic. Changing, you know, adding solute, making something more polar or more non-polar.
And maybe the most common are changes in temperature. So when you fry an egg and that egg white goes from being translucent to being this like white opaque color, that is because you are denaturing a protein. in these egg whites.
And so when the protein heats up, it unfolds and the heat causes it to take on a new shape. And that new shape is what creates this solid white color versus the more translucent translucent white of an uncooked egg. So that's just like a common example of denaturation.
But denaturation can happen in all sorts of settings including in your body which is why kind of maintaining a like a healthy body temperature and maintaining a neutral pH in our blood is really important for our overall physiology. An example of why protein structure is so important is highlighted by a condition called sickle cell anemia. Sickle cell anemia is going to come up a lot this semester and next.
It's kind of a go-to example for a lot of different biological concepts. So here's the first. With people of sickle cell anemia, a single amino acid is changed in a protein called hemoglobin.
So here this amino acid is changed into a valine. And as a result, hemoglobin, which is a protein that carries oxygen in our red blood cells, changes shape. That causes our red blood cells to change shape. And instead of being this nice flat round disc, they form this kind of crescent or sickle shape. These sickle-shaped red blood cells cannot move through our blood vessels easily.
and will often kind of catch on the walls of our blood vessels and start to accumulate and eventually form a clot. This can be really painful for people suffering from sickle cell anemia and it can and often will lead to death if it's not treated or like really carefully monitored. So just the simple change of one single amino acid has this huge impact on the shape of the protein. And because the shape of the protein has changed now, you know, it's a matter of literally life and death.