in chapter 6 we're now going to take our amino acids which we learned about in the last chapter and we're going to turn them into proteins so we're going to be looking at the three-dimensional structure of proteins and this video we're going to focus on what are the levels of of our three-dimensional structures and how do we form our secondary structure elements so let's look at first how we classify proteins we can classify proteins in two different ways the first is just a simple protein and a simple protein just means that it's composed entirely of amino acids that's all that you have in your structure our second type is going to be a conjugated protein now conjugated proteins are going to contain other groups in them so they could contain metal ions so if you recall I talked about how in my graduate work those were the type of proteins that I was interested in looking at is proteins that had Metals in them they could have co-actors so co-actors are going to be things like vitamins and that you would take they could have IDs or carbohydrates as well that are attached to them so an example of a type of conjugated protein would be he hemoglobin so hemoglobin has these heem prosthetic groups that are attached to it so they are not amino acids they are these other molecules that are inserted into your protein in order to make them work we also have two different other classifications of your protein and that's going to be whether it's a fibrous protein or a globular protein so a fibrous protein is going to be these long strands or sheets of polypeptides they're generally going to be hydrophobic they're going to have a lot of hydrophobic amino acids and be water insoluble they tend to be very strong but flexible proteins so the main examples of these are going to be keratin and collagen so um you're actually fairly familiar with proteins that are fibrous proteins so collagen is going to be in your nose and in your ears giving it the structure and rigidity so your nose and your ears are very strong but they're also fairly flexible keratin is in your fingernails so that's the protein that you'll find in your fingernails and in fact all of the cells in your body are going to be surrounded by these fibrous proteins so those Metallo enzymes that I was studying when I was a graduate student uh their purpose was to um eat up the fibrous proteins that are around cells so they're providing rigidity and structure to your entire body now globular proteins um as the name kind of implies are going to be just kind of bulk proteins so whereas the fibrous or long strands the globular are going to be more spherical or globular they tend to be water soluble because they're going to be dissolved in the cytool of your cells or outside of your C and they'll contain several secondary structure elements and we'll go through what those are and globular proteins are going to have a wide variety of function so where fibrous are more structural globular pretty much do everything else else that a protein might need to do so they may be enzymes regulatory proteins and more so here would be an example on the left we've got catalase which is a globular protein you can see it is just a discre discrete like roundish structure whereas keratin and collagen are these long strands of amino acids in this case carin's got two strands twisted around each other and col will have collagen will have three strands making it a little a little bit harder so proteins can have a ton of different functions in fact if you're thinking about something process that happens in the body most likely it's being done with the aid of a protein or more than one protein so if you need to catalyze a reaction that is done by a protein um the spe if it is catalyzing a reaction we call those enzymes and how you can recognize that a protein is an enzyme is that its name is going to end in Ace a s e so catalase for example we saw in the previous slide would be an enzyme they could be structural like keratin um or F fibrogen they could be transport proteins so in the case of hemoglobin it is transporting oxygen from one location to another location uh they could be transmembranes so they could be on the membrane part of your cell and allow things to go from the outside to the inside or the inside to the outside so toxins generally tend to be proteins as well so if we think about snake uh rattlesnake venom that is going to be a protein that is a toxin they could be responsible for contractile function so your movement so if your muscles are moving that is by actin and mein and those are proteins proteins also act as hormones so insulin for example is a protein that acts as a hormone they could be for storage so your seeds your eggs those are also protein and then your antibodies are also proteins so you can see that proteins have a lot of different functions and what their function is depends on their structure their three three-dimensional structure which is what this chapter is about let's go back to the very Basics so what are our levels of protein structure so up here at the top we have our primary structure of an amino or of a protein which is just the amino acid sequence so it is just saying tryptophan is next to Proline which is next to to another Proline which is next to a veine which is next to the ETC it's just telling us which amino acid is connected to which in the chain now this primary structure can then fold upon itself and typically you might have two cyes coming together to form a disulfite bond or you may have Alpha helixes that form or beta strands and beta sheets that form those are going to be your secondary structural elements um aside from the cinee uh the dinee linkage your secondary structure is held together by hydrogen bonds and we will see that as we're going through and looking at our secondary structure elements all right so it could be these Alpha heles Beta sheets it's just the protein kind of coming together a little bit more now the entire protein or primary sequence forming its final globular or um fibrous shape that is going to be our tertiary structure uh so this is just going to be a single strand of polypeptide that is doing this would be our tertiary structure so most proteins or a lot of proteins they will end at the tertiary structure they will not go any further but you could have multiple polypeptides that are going to come together so for example um in this protein we've got different subunits we've got an alpha subunit a beta subunit and you you can see these different colors that are indicating that we've got these two sub subunits that or these multiple subunits that are coming together in this case there are four subunits this is a hemoglobin protein which is four separate subunits so we had four different quantin structures that were independent polypeptides that are coming together to make this quinary structure so while the tertiary structure again is the final spot for a lot of proteins other proteins will need multiple tertiary structures to come together to make this quary structure in order to be fully fun functional so an example of this as we see in this picture is hemoglobin all right we're going to focus now just on our secondary structure so we've got um our really four different things that we're looking at in secondary structure Alpha Helix beta sheet and loops and turns so we'll talk about each of them in turn the first thing we need to talk about though is that remember when we are looking at our polypeptide chain uh as we are going down our chain we've got this amid Bond and we talked about how that amid bond is very rigid has double bond character and so what that means is that it is very rigid and planer so we've got a planer Bond here and we've got another planer Bond here which means even though we've got this long polypeptide chain each amino acid only has two bonds with free rotation around it in the polypeptide chain so if we're looking at the bond between the amid nitrogen and the alpha carbon so this is the alpha carbon that has the side chain and the alpha hydrogen on it uh this is going to be our thi Bond so this Bond will have free rotation the other bond that will have free rotation will be between the alpha carbon and the carbonal this will be our s Bond so we only have these two car or these two bonds that actually have rotation so we don't have an endless amount of possibilities for um how the protein can fold so if we know all of the FIB bonds and all of the c bonds in a pep polypeptide chain we actually know the entire structure of our backbone so we know all of our angles however even though we've got these two fi and cyons that can rotate in seemingly infinite combinations there actually isn't infinite combinations uh because if our our group or if our carbonal are are um both facing down then we're going to have steric hindrance so there's actually a fairly limited number of angles that our fi and our sigh Bond our fi and our sigh bonds can be able to rotate towards so these ramondin plots what they are is you can put in any polypeptide or any amino acid and it's going to tell you what are the possible fi and sight angles that this amino acid can form so anywhere where we've got this yellow means it is very unlikely that this amino acid will be able to form those F Insight angles so we have our fi angles on our x axis and our s angles on our y AIS any of the areas where we've got these white spots these are going to be very common angles for our amino acids to be able to form so we can plug in our different amino acids and it will tell us what is the most likely configuration that these am Amo acids will form so we can see over here we've got some beta strands we've got some Alpha hel uh left right-handed Alpha helices here left-handed Alpha helices here and so these just tell us the different possibilities um so it can help us determine what um secondary structural elements are present in our polypeptide by putting them into these ramondin plots and being able to see what is possible and what is not possible all right so the alpha helix the alpha Helix was first proposed as a theoretical construct by L uh paus lonus Pauling and Robert Corey in 1951 but it wasn't actually identified um until it was found in Keratin by Max perut and the alpha Helix is a very ubiquitous component for protein so almost every protein will have Alpha Helix in them and it stabilized completely by hydrogen bonds so this is an example here of a um Alpha Helix so here we can see it's a right-handed Alpha Helix which means it's going to turn to the right so here we have eliminated everything but our backbone so we've got our carbonal carbon here our Alpha carbon in black and then our nitrogen in blue again another carbonal carbon Alpha carbon nitrogen in blue and we can see it's kind of twisting around making a helix as we are twisting around this Alpha Helix it's going to take 3.6 residues or 3.6 amino acids to make a complete turn so going from one position all the way around back to that same position and then as we are going so from here to around here would be a complete turn so you can see we've gone through 1 2 three and then a little bit almost a full fourth but just 3.6 so um three and approximately 2/3 amino acids so from here to here would be a complete ter and then as we are going up this is going to have a pitch of about 1 and a half angstroms or 0.54 nanometers so that's just the height from one position to another position which means our pitch which is how much we rise per turn is going to be about 5.4 angstroms all right in this picture over here we can see the stabilization because now we're adding in our carbonal and we're adding in our hydrogens from our amids and so these yellow Dash lines these are going to be the hydrogen bonds that are going to be stabilizing our Alpha Helix uh so we can see here we've got a carbonal and that carbonal is making a hydrogen bond to this nitrogen hydrogen so this nitrogen hydrogen is going to be our hydrogen bond donor and then the carbonal would be our hydrogen bond acceptor and the hydrogen bonds are always formed from between between a um amino group and a carbonal that are four amino acids away in order to be able to give us this Alpha Helix one of the interesting things about the alpha Helix is because it has um it is twisting up is that it's actually going to have a dipole moment associated with it because all of the hydrogen bonds are going to be going in the same direction so we have our carbonal here that's going to be making a hydrogen bond with the nitrogen hydrogen that is above it so that nitrogen hydrogen um that nitrogen is going to have a very partial negative charge and the carbonal will have that partial positive charge that will give us a directionality where our inter terminal end is going to have a partial positive charge and our C terminal end will have a partial negative charge the other thing about Alpha Helix is the location of our side chains is going to be pointing out from the alpha Helix because of the way that our um Alpha Helix turns or spiral they're going to be pointed outwards and typically how these are are positioned is that amino acids that are polar will be on one side of our Alpha Helix and amino acids that are non-polar will typically have it their side chains on the other side and this is so that they can interact with each other or the protein effectively so to give you an example um here we'll have two um on this inside we'll have our hydrophobic um side chains on the outside we'll have have our hydrophilic side chains uh so our hydrophobic side chains are going to be having hydrophobic interactions with each other and so they are going to be connected to each other whereas our hydrophilic on the outside and so our hydrophilic will be able to interact with the water on the outside of these side chains and so you can see here we've got these hydrophobic interactions between the two alpha helices and then the hydrophilic will be on the outside all right so those are the alpha helices now let's at beta strands and beta sheets again these were also postulated by by Pauling and Corey um and they can be either parallel or anti-parallel let's look at what we mean by parallel and anti-parallel so here I have eliminated again the side chains just to give a more simplistic view we've got our uh in terminal over here so here would be our nitrogen our Alpha carbon our carbonal then our in uh our amino group so this would be making the am Bond our Alpha carbon or carbonal and so in this case we're going in Terminus to C Terminus the bottom strand down here is also going in Terminus to C Terminus uh we've got our our nitrogen uh carbon our carbonal and you can see they are parallel they line up so the the amid group the alpha carbon and the carbonal are all directly on top of each other so they are going in the same direction so these would be parallel beta sheets they held together by hydrogen bonds uh we can see we've got a hydrogen bond here between this amid nitrogen hydrogen and the carbonal so this is our donor and this is our acceptor and then we've got one going up so we've got our amid Bond donating to our uh carbonal this one's going down this one would be going up down and up with those hydrogen bonds so this would be our parallel configuration so this is our anti-parallel beta sheet and in this case we can see that we're going on our top strand is going in terminal to C terminal so we've got our Amid and our Alpha carbon carbonal amid Alpha carbon carbonal whereas the bottom sheet is going in the opposite direction um and so we can see that our hydrogen bonds here line up a little bit better because of this that makes the anti- parallel beta sheet more stable than the parallel uh beta sheet now these beta sheets are going to be able to um make these or I guess these technically are beta strands um and these are going to be beta sheets so they're going to be multiple beta strands connected to each other so we could have two to four two to 15 beta strands per beta sheet so we've got one beta strand a second a third and then a fourth so this would be four beta strands making this beta sheet and each strand is generally made up of about six amino acids and what you can see from this is that our amino acids are pointing up or they're pointing down from the sheets so here are two sheets here represented by these blue arrows this would be an anti-parallel because one's going One Direction one's going the other direction and then our amino acid side chains are pointing to the back or pointing towards the front of the beta sheets okay so loops and turns so Loops are going to be when you've just got a strand of amino acids that really has no defined structure they tend to be on the surface of proteins they tend to connect Alpha heles and beta sheets and they usually have hydrophilic residues in them so if you're looking at a protein structure and it doesn't look like it forms an alpha Helix it doesn't look like it form a forms a beta sheet it's probably going to be a loop and it's just generally an undefined structure in the protein a turn is going to be a loop that is very short and it's going to generally be less than five amino acids It could only be two or three and it's going to be connecting generally the sheets in um our beta sheets so a beta turn is going to be a very common element so let's take a little bit of a closer look at these beta turns so what this is going to do is allow our polypeptide to quickly change direction so you can think of it as a U-turn uh so here is an example using Proline we know that Proline side chain um is connected back upon itself and so because of that it's perfect for these turns and we can see we've got a hydrogen bond here and then we're quickly turning around so this would be one side of the beta sheet this would be going to the other side of the beta sheet this would be the turn connecting it so prolines are great for beta turns but also um glycines are because glycine side chain is a hydrogen and so it makes it not having that side chain makes it very easy for it to turn upon itself so you're not going to have any steric hindrance from that hydrogen so generally your carbonal carbon here um to the hydrogen bond that it's bonding to is about three residues away could be two could be four but generally three is The Sweet Spot there all right so I have this protein here as an example of what these elements might look like so obviously this is a pictorial representation of a protein uh but we can see all of those different um SE secondary structural elements in this protein so we can see here uh we've got our beta sheets and this is an anti-parallel beta sheet here we've got our Alpha Helix over here we have another Alpha Helix and then this part here that's just kind of randomly going around this is a loop we've got a little small Alpha Helix here in the back in this purple is another beta sheet um and then right up here connecting these these two beta strands in this beta sheet is going to be a turn so it kind of gives you an idea of once they're all together and this this would be a globular protein what it actually is going to be looking like so these pictures are generally focused on the backbone not on the side chains but just showing what the backbone of the protein is doing