before you attempt to describe something that is extremely complicated we must start with the basics what is the first way to describe the structure of a protein we always start the structure of the protein with something referred to as the primary structure all right now the primary structure by definition this is important for the exam by the way because they may ask you what is meant by the primary structure of the protein some books will just call it primary proteins by the way and the primary structure is basically described as a polypeptide chain made up of a sequence of amino acids now I'm drawing out two polypeptide chains one in red one in blue but if you can't distinguish the colors just know that that is one chain to the top and one chain at the bottom the reason why I'm calling them polypeptide chains is because each chain consists of amino acids linked together by peptide bonds and I've represented those amino acids in those uh as circular as those circular symbols you can see those amino acids like that and I'm also just throwing out the structure of the peptide bond as a reminder C double bond o and H those are the peptide bonds now I'm going to ask you a very simple question are these two polypeptide chains similar some of my students will say well no they're not similar they are different colors Let's ignore the color let's just look at the lines uh ignoring color assuming the color is the same are these two chains similar the answer is no these two chains are not similar they both have different primary structures the reason why they have different primary structures because well the length of the chain differs why does the length of the chain differ perhaps the chain at the top is made up of lesser amino acids linked together the chain at the bottom is made up of more amino acids linked together so right from the get-go you can see that the primary structure can be determined by the length of the polypeptide chain but it's not just determined by the length of the polypeptide chain another example I'm going to give you here is polypeptide chain a and polypeptide chain B if you notice polypeptide chain a is made up of four amino acids linked together chain B is also made up of four amino acids linked together but do they then have the same primary structure now the primary structure in this case is also different the reason why it's different is because even though the length may be the same they consist of different sequences of amino acid so it's not the primary structure of the protein is not just determined by its length it's also determined by what type of amino acids are put in that and that's what makes it a bit more complicated so from the primary structure we can then do the secondary structure I'm drawing out a long chain and that long chain is described as the primary structure now I want you to see what has happened to the long chain that same long chain has now started to form weird shapes within itself and the two weird shapes that I want you to focus on are the coilings and the foldings that have started to appear I've highlighted the coil and I've highlighted one fold that has happened so secondary structure of proteins are basically described as a poly peptide chain that has formed coils or folds within itself and then and here's where it becomes uh a little bit more complicated why does it start to form coils or Falls this is a very important question let's imagine a single straight polypeptide chain that's the primary structure and each of those circles are just amino acids now that same chain has now started to curve or coil now why does it curve a coil we start noticing bonds appearing between amino acids That was supposed to be far away from each other all right like for example amino acids that are not linked close to each other start to form hydrogen bonds which are represented in those dotted lines as a student in a levels you do have to explain why a secondary structure or how a secondary structure is formed now if you remember peptide bonds contain C double bond o and also NIH bonds or NH groups C double bond o and H if you also remember in my video on hydrogen bonding I did mention before that c double bond o usually carries a partially negative charge and NH usually carries a partially positive charge I'm drawing out a I've just highlighted that single portion over there where I've represented this amino acid one two three and four and we can see that the NH group has a partially positive charge and the C double bond o has a partially negative charge and lo and behold a hydrogen bond is formed between them and because a hydrogen bond is formed between them the amino acids sorry the polypeptide chain becomes curved and the hydrogen bond is the one that's causing this curve to happen so there are two types of secondary structure within a polypeptide chain that can fall number one it can form something called the alpha Helix and number two it can form a folding called the beta pleated sheet the reason why it's called the beta pleated sheet is because it looks like the folding of a paper when you're trying to make a paper fan uh that's a pleat a pleat is like a fold so it gives the illusion that it's the chain is folded in reality it's not um and most importantly for the exam they will represent the alpha Helix as a coil and they will represent the beta sheet or the beta pleated sheet S and L so what do how does that look like in reality if we were to just basically draw out two chains that's one polypeptide chain on the left and there's one polypeptide chain on the right uh the polypeptide chain on the left will form two alpha Helix as you can see there and the polypeptide chain on the right will form as you can see two beta pleated sheets and an alpha Helix that is represented as the two arrows and the coil so some chains May fold some chains May coil some chains may do a combination of both what determines uh we don't again we don't have to memorize which chain does what we just have to know that the primary structure is just a single chain and the secondary structure is just that same single chain but it starts to form coils or pleats and the coils or pleats are usually due to the formation of hydrogen bonds between the NH and C double bond o bonds that's basically it