all right hi youtubes mr lim here again and this is the second video on tertiary structures of proteins okay so uh tertiary structures of proteins remember what we are combining side groups or have talking about interactions between the side groups of amino acids not the peptide bonds of the amino acids which differentiates it from secondary structures okay so dipole-dipole dipole-dipole interactions are formed when two side chains of amino acids which are polar but not polar enough for hydrogen bonding create a force holding them together okay so serine and methionine is an example of this methionine the side group i'm not going to draw the rest of it but the side group is made up of ch2ch2 s ch3 so this would have a generally a negative end that sulfur okay and then a side group of the uh meth irony no we did that the serine would be a c with a ch2 oops ch2 and then an oh okay and so that negative ends that positive end so this positive end here all right the positive end on the hydrogen and the negative end on that oxygen but the positive end of that hydrogen would form a dipole dipole bond with the negative end of that sulfur and then hold that together it's not very generally a very strong one but it does exist so therefore we have to learn about it okay these interactions are quite weak but a large number of them can do their thing all right dispersion forces so also known as hydrophobic forces so the idea is that side groups are either polar or non-polar or a mix of the two okay and so here are some non-polar side groups okay so you have the the amino acid end part of it and then the part in blue is the non-polar parts okay so all of them are just made out of carbons and hydrogens they're all generally non-polar so the idea is that some proteins need to be soluble in non-polar substances and some need to be soluble in polar substances and so if you need to have a power protein but it's in a non-polar solvent so like in fats the non-polar side groups will be found on the exterior of the protein so remember here we have our protein and it's all folded into a particular shape but your non-polar which will be in blue side groups might be here all the non-polar side groups okay all the non-polar side groups will be on the outside of your protein and this is a spherical thing but you know all the non-polar things will be on the outside and all the polar side groups will be on the inside okay so all your polar side groups will be on the inside sticking together in the pole in the um polar end all right so that's if you want it to be uh uh in a non-polar solvent like a lipid bilayer right but however if you need to be in a polar solvent like water it'll be the opposite so here's your folded protein okay and then all of the polar side groups will be on the outside all of the polar side groups will be on the outside interacting with the water polar side grips on the outside and all of the non-polar side groups would be on the inside trying to stay away from the water okay so over non-polar side groups on the inside okay and so by having this uh you keep the you maximize the interactions which are best suited for that okay so the hydrophobic and hydrophilic nature of the side groups can provide a significant amount of force to keep the protein in correct shape so i generally um the the non-polar stuff generally sits on the inside for polar soluble proteins and they all kind of sit in the inside and they hold together because they don't want to be accessed by the water on the outside right and then finally the tertiary structures right so the tertiary structure we have uh ionic interactions as the last one so certain amino acids have side groups that can be changed into ions due to functional groups on the side groups so in other words anything with an amine or a carboxylic acid can be turned into a um ion all right so uh aspartic acid is an example with lysine okay so there's the aspartic acid side group or side chain right oh actually that's the lysine one sorry and then the aspartic acid one is here okay and so this one forms the c-o-o minus that forms nh3 plus and so therefore they're going to have an ionic interaction between there the positive and the negative thing there electrostatic attraction there okay so that's going to perform there alternatively you could even have a sodium ion interacting with the aspartic acid okay so the aspartic acid is a ch2 c o o minus okay and so there'll be an interaction between the sodium ion and the carboxylate part of that side group okay assuming that it's lost its hydrogen there um these ions can interact with other ions or other or or other ionic side chains to perform various roles such as uh one ion can have uh ionic interactions of another a number of amino acids in the same protein or over multiple proteins to ensure that they stay together so what that means is that instead of this um being a negative and a positive what it might be is that okay here's my iron ion like in hemoglobin okay and then you have a whole bunch of this is one carboxylate ion from one part of the chain from one part of the chain and here's it from another part of the chain another carboxylate ion from one of the side groups and then effectively that has an ionic interaction that has an ionic direction and therefore these two side chains are held together okay and so that one ion can hold together things that are quite far apart and that's what happens with most of the ions there the hemoglobin is one iron ion holding together like four heme units all into one area to hold it all together and doing its thing all right or you can just have um two a positive end and a negative end holding everything together for that part okay but this one's quite more fun but anyway that's the idea the ionic charged parts hold stuff together and therefore they can't break apart and everything gets held together holding it into shape that's it