Hello chemists Michele Glass here and we have two videos left in our chapter two video series. And we are continuing or finishing up here our organic macromolecules so remember organic means carbon hydrogen-based. Macromolecule means big molecule. And the two organic macromolecules we have left are the proteins which is the topic for this video and nucleic acid which is the topic for our final chapter 2 video. Now proteins as you can see I've given you that really cool smiley face with sunglasses because proteins are such a cool molecule. And really your body is just like a big complex sack of proteins, right? When we talk about our nucleic acids in the next video we'll see that these are our hereditary molecules. And really those hereditary molecules, that DNA molecule basically tells your cell how to make proteins. That's how significant proteins are. Now remember as we look at our macromolecules we need to pay attention to three things. You should be able to give the structure, examples, and functions for each. And so that's what we want to do with our proteins here so to begin with our protein structure we have our monomer which is called an amino acid. And so what we'll see is that this monomer this amino acid has a carbon at the center. And remember carbon can pair with four things so we can draw our dashed lines to represent those four possible covalent bonds. Now one of those is going to be an amino group. So this is one of the functional groups that we talked about. So here you're going to pair a nitrogen to a carbon and then you're going to pair two hydrogens to that nitrogen. And then we will have a hydrogen atom pairing with carbon and that central carbon will also pair with what we call a carboxyl group. So you're going to pair a carbon with a double bound oxygen and then also that same carbon is paired with a hydroxyl or OH group. So the name amino acid comes from our amino functional group which is the nitrogen with the two hydrogens bound. And the acid part of our name comes from the carboxyl or carboxylic acid group which is that carbon double bound oxygen and then also bound to the carbon is the OH or hydroxyl group. Now the fourth thing that's paired with the carbon is often described just with the letter R. And this is not representing an atom. This is actually representing what we can call the varying group. I'm just going to write varies for the R group. I like to think of it like in algebra where in algebra you have that X. And the X could be any number on the number line. R could be any atom or functional group. So this could be as simple as another hydrogen or this could be a really complex carbon hydrogen structure. Now there are 20 amino acids that make up the proteins of our body. Also that means there's 20 amino acids that make up the proteins that we eat the food that we eat. And so when we talk about this R group varying that there are 20 different variations this is the piece that's different when we talk about the difference between a tryptophan and a leucine amino acid. It has to do with that R group. And that's going to be important to the overall structure of the protein. Now you do want to be familiar with the structure of the amino acids so you do need to pay attention to this detail here. Now as we continue talking about our protein structure a very important piece of information for us is that the structure is linked to the function. The protein structure is linked to the function. And we're going to see a very complicated 3D structure. Let me put it down here actually with the proteins - very complicated 3D structure. When we talk about our proteins and that shape determines its ability to function well think about a key fitting into its lock. It has to fit perfectly, right? It has to fit perfectly all right. Now we have all these different kinds of chargers, right? So I have a charger that's special for my laptop. I have a different kind of charger that I use to charge my phone. I have another type of charger that I use to charge my smart watch. And then I have even another charger in my bag of chargers that I use to plug in my headphones, right? And what would be really nice is the universal charger where I could just plug it into anything and that will charge but that's not how it works. It's not how they fit. So only my headphone charger will only fit with my headphones. And my phone charger fits with my phone. And so forth, right? And so this is the complexity of protein shape and the significance of protein shape. Now just to give myself a little bit of room here I'm going to lay out I'm going to erase here my amino acid you need to keep that in your notes. And I'm gonna actually pause and draw it really tiny. Okay so I have my amino acid structure still here in my notes super tiny and what we're going to look at are the four levels of protein structure. Now instead of calling this like first level, second level, third level, we use the terms primary, secondary, tertiary, and quaternary. Now you can abbreviate the term primary, secondary, and so forth by using the number and then the degree symbol. So you're basically saying like the first degree, the second degree, the third degree, the fourth degree or primary, secondary, tertiary, and quaternary. And what this is telling us is as you build each layer of structure you're adding properties. You're adding complexity to the molecule. To begin the most basic primary structure to protein is going to be a chain of amino acids and so I like to abbreviate my amino acid with a "aa" and then I put a dash line in between and that is actually representing what we call a peptide bond. A peptide bond. So the bond between amino acids is called a peptide bond. Now you might hear the phrase peptide. I'm going to actually put that into the examples. Peptide is talking about really just a short strand short strand of amino acids. If you hear something called a polypeptide "poly-" means many so now we have more peptide bonds. And here the definition is something that's less than 100 amino acids. So we're not really going to see as much complexity in a 3D structure if we're just a short strand of amino acids or for a polypeptide less than 100 amino acids together. So that also tells you when we do talk about protein structure that primary level that chain of amino acids is greater than a hundred amino acids together, right? So we're talking about a really long strand. Now when we talk about the secondary level we have two choices here. We have what's called the alpha helix or what's called the beta pleated sheet. And let me grab a visual for us. Okay so here I have in my hand a pipe cleaner and I have a few beads strong on my pipe cleaner. Now I like to use this as my visual for protein structure. You can see it's becoming very frayed so it's a well-loved visual that I have. I am using these beads as my reminder that my protein structure at its primary level is those chain of amino acids. So I'm just stringing a few more beads onto my pipe cleaner just to really help remind and illustrate that point. So here I have my amino acids connected by peptide bonds. This is my primary or first degree level of protein structure. Okay so you need to fill in the blanks there pretend it's like fully covered with the beads with amino acids. And now we're ready for this secondary level of structure and what we see is that there are interactions that occur between the backbone of the amino acid. So this is talking about the backbone would be really talking about you know the amino, carboxyl, and hydrogen group, okay? Interactions remember means hydrogen bonding. So what we're going to see happening is either what's described as an alpha helix which looks like a spring. So I've taken my pipe cleaner and I've pulled it around my finger to make like a spring shape or a slinky shape. And then I'm going to just grab another one from my kit here and I'm going to represent the beta pleated sheet. So with beta pleated sheet you take your strand and you fold it up and you fold it down kind of in the same way maybe if you make a fan out of paper. So the beta pleated sheet is kind of folded like an accordion and the alpha helix is like a spring. And this has to do with interactions within the molecule within the backbone of that amino acid. So basically you have opposites attracting and likes repelling each other. And so you get this automatic folding. So you can see as your strand gets really long you're going to add to that complexity. You're going to add to that automatic folding that shows up. Now the tertiary level is really where you start to see hydrogen bonding and interactions with that R group. So the R group remember is that variable group. Some can be really long. Some can be just a hydrogen. They can be polar. They can be nonpolar. So you start to get like hydrophilic and hydrophobic interactions meaning any of those hydrophobic parts are going to fold up so they're in the interior of this strand of this protein, right? And hydrophilic parts fold out so that they're outside. And so that's happening...maybe this protein is consisting of two strands and that tertiary level of folding is happening with both. Now here's the thing that matters. Your environment plays a key role in how those proteins fold in that tertiary structure. So your temperature, your pH, your ion concentration, and salt, and water, and other factors can influence the folding of that protein. And it's only when that protein is like properly folded that it works perfectly. So there are protein shapes that are like less than optimal but still workable. If they're less than optimal they don't work as well as optimal, right? And so this is one of the reasons that your body homeostatically regulates factors such as temperature and pH. It's to help make sure "oh I want my proteins to fold up exactly right so that they work at their best." The fourth level of structure is a complex. So that's where maybe these two different strands come together to form that final 3D structure. Now what I've represented here I would call globular because it looks like a glob. So something like hemoglobin has the term globin which means like globular, right? And so hemoglobin would be a protein in your red blood cells that's a globular protein that helps to transport oxygen to your cells. Another type of quaternary structure is what can be described as fibrous. So here I didn't take the time to fully illustrate my secondary and tertiary structures but I am illustrating with my pipe cleaners my fiber structure by stranding them together and this is more like a fiber which is why it's called fibrous, right? So here we would see your structural proteins things like keratin which is making a hard protective covering in your integumentary system or collagen which is your super strong fibers and all kinds of connective tissues would be of that fibrous type. And so if we go back to our note taking we have our primary level as our chain of amino acids connected by peptide bond. We have our secondary level as alpha helix or beta pleated sheet and I illustrated those with pipe cleaners. Remember secondary level would be hydrogen bond within the molecule so I abbreviated hydrogen bond with H bond. And just to give myself plenty of room with your tertiary structure this is where you get hydrogen bonding or interactions between R groups and with the environment There's also what's called a disulfide bond which you'll see described in your textbook so that's just a little bit of a different kind of bond and we won't spend a whole lot of time talking about that. But it's good to note that your hydrogen bonds and your disulfide bonds are both involved in that tertiary structure. And then with the quaternary I like to talk about this as a complex. So this is where you get these multiple subunits coming together and essentially you can either have a globular complex or fibrous. When you're looking at your fibrous these are mostly involved in the structure of the body and very often these are hydrophobic so that means they're not soluble in water. Whereas your globular are going to be making up your enzymes we've talked about a little bit already. They're going to be involved in transport and then these are going to typically be your hydrophobic I mean excuse me hydrophilic water loving. to go into examples a little bit more we're going to have buffers and we talked about buffers as helping to regulate pH in the body. We said it can act as a temporary store for hydrogen ion. Remember if you can store something you can stick it in the cupboard but you can also take it out right. And this is because of that carboxylic acid an amino acid is a weak acid which weak acids make great buffers. Another example is collagen. Collagen is a fiber and it's going to be very strong and you're going to see this in like tendons, ligaments, you're going to see it lots and lots of places. Keratin is another important fiber that's going to be hard and very protective. And we see this in the integumentary system. So we're going to see this as part of the structure of our nails. This is making our nails hard. Our hair, the outer layer of our skin. Enzymes are going to be a super duper important let's highlight enzymes super duper important protein. Remember these are going to catalyze all chemical reactions. Remember a reaction in your body cannot happen without its particular enzyme. And so this is important for regulation. If you need to turn on a reaction in your cell you're going to have to kick up the production of that enzyme. If you want to turn off a reaction in your cell you just stop making that enzyme. So it's like a really nice on/off switch. Antibodies which are important in our defense against pathogens. Our neurotransmitters and we have hormones, I'm going to put these together partly because I'm running out of room, but also because they're both involved in communication. Neurotransmitters are being released by your neurons in your nervous system whereas hormones are released into the bloodstream that's part of your endocrine system function. We'll also see cell membrane receptors, channels which are also basically involved in communication. We'll learn about that more in the future. And then under functions I'm also going to add the word transport. We already mentioned hemoglobin as a protein that transports oxygen in your red blood cells and we'll see other examples of that as well. A lot of times we think about protein as providing energy for the body and that can be true, but in order to get energy for the body from the protein you have to break down your actual body structure. So you're going to start by breaking down skeletal muscle and go from there. So this is clearly less than optimal. It's much preferred to get it directly from your diet or from your adipose tissue reserves than it would be to break down your protein in order to produce energy. Okay that is it for proteins. We have one video left to finish up chapter two which is our nucleic acid video so stay tuned for that and as always take care of yourselves and each other