hello class and welcome back so we're going to look at section 1.2 which is kind of a review of the functional groups and some of the terminology used in organic chemistry hopefully this will be a short video because a lot of this should be a little bit more recent and more fresh in your memory than the other concepts in chemistry from the general chemistry side okay so first is just a review of your functional groups the functional groups shown here so we're looking we'll move this up in table 1.2 these are your common functional groups that you're going to use in biochemistry so the table continues down you'll see both your oxygen containing molecules as well as your nitrogen containing molecules as these are going to be the most common functional groups in terms of reactivity to make larger molecules in biochemistry so take a look at table 1.2 review those for yourself you'll notice of course the alcohols the carboxylic acids so there's a lot of carbonyl chemistry in biochemistry um esters as an example of that we'll also see sulfur containing functional groups so dials disulfides thioesters then the nitrogen containing molecules the amino groups amides and phosphorus of course is another very common functional group in terms of the phosphates the phospho anhydrides and the phosphoesters you'll also see enols especially in glycolysis we'll take a look at those um in great detail so this isn't all-inclusive it's not going to include every single functional group that you are going to encounter in biochemistry but it provides a great foundation and a good start to the functional groups that we will be visiting throughout the semester and if you continue on to advanced biochem throughout the year the others as we encounter them we'll review them and name them but to get you started a great place to start reviewing if you aren't familiar with the chirality 2 app i highly recommend installing this in your somewhere on your device um so it's compatible with android as well as apple products and so let's we'll cruise over to my chirality2 app this is what the app looks like in your play store or app store and it does a lot of different functions so i'm going to switch over and then you can kind of see what this app looks like so this is what the chirality 2 app looks like it allows for a great review of functional groups chirality stereoisomers naming intermolecular forces etc so we're going to just go into number one which is functional groups on the bottom of the screen that you can't see it will give you the name of the molecule which is this is the bacon uh yep you should look that up later because that's totally cool okay so this is a drag and drop so we're just going to drag and drop some functional groups and i don't know we'll do some that are correct and some that are wrong and yes i am doing this wrong just to to show you what happens okay on the bottom of the screen that you can't quite see there is an arrow that you hit when you're done oops i forgot one so let's put a molecule there okay so if you get them right they turn green feed them wrong they turn red and then you can do a quick review of yourself for yourself what they are you push the green button and it gives you a fun fact about the bacon all right there you go so this is a great way to review you can um for yourself review them you can play games you can get competitive with friends a great kind of thing to to brush up on those functional groups okay so if you have the chirality app get familiar with it do a little review for yourself especially for before the first exam and then what you know moving on to the rest of the section really the understanding here of why functional groups are important these are so inherent to the organic reactions that are going to be taking place in a living organism so you have to remember that biochemistry is the study in the chemistry of life and life exists because of carbon chemistry therefore we start with a review of some of the gen chem principles because the guiding rules stay the same we're just applying them to a living organism as well as the organic chemistry the rules and the functional groups the chemistry that's happening is going to be the same and so much of the organic chemistry becomes an example in biochemistry which if you didn't like organic chemistry please do not lose all hope i really was not a fan as a student of organic chemistry but i fell in love with biochemistry right so understanding these functional groups and the chemistry gives that foundation to really take this into an organism to understand the biological molecules that are being built or broken down so we'll see these chemical reactions from these functional groups based on that organic chemistry that's happening happening okay the functional groups we already know give rise to intermolecular forces and the ability of a molecule to either be soluble or insoluble um dipole moments polarity types of concepts come from of course these functional groups and the atoms that are present in a molecule because biochemistry largely occurs in an aqueous system the way that these molecules are going to interact largely is going to be dependent on those functional groups and the polarity the dipole moments that they display so we'll see in the next section the role of water which plays a very important role in biological systems of course and the chemistry so there's a lot of acid-base chemistry in the next section so in understanding your functional groups not only do you want to be able to identify them name them but also know something about their chemistry knowing that a carboxylic acid acts as an acid that an amine is going to act as a base these are going to be the functional groups that have those properties and inside a biological system they're going to be important for an enzyme to carry out a reaction mechanism based on acid-base chemistry so within an enzyme and within a protein environment those functional groups are playing a critical role they're allowing a biological system to very quickly be able to respond to changing conditions you'll see conformational changes occur because of these non-covalent interactions that are going to be foundational for these biological molecules to interact so understanding for example reaction mechanisms within an enzyme environment within a protein right this is going to become from these functional groups that are going to be allowed to make and break bonds so for example knowing that carboxylic acids and alcohols can react to make an ester at the same time esters can undergo a hydrolysis back to a carboxylic acid and an alcohol those reaction mechanisms that making in the breaking of a bond in a biological system has to happen inherently very quickly so these reactions that are occurring because of these organic functional groups it's very important to not only you know you're not just memorizing these groups you're understanding the rules of chemistry that they can go through to make and break bonds at the molecular level and that this is going to happen at a very fast very fast pace such that it allows the reaction to occur such that life can exist when we look at reaction mechanisms they are not just for organic chemistry we use them extensively in biochemistry to understand the way that an enzymatic reaction occurs why is that important well if we understand how a reaction occurs and if we understand a transition state that's going to be involved in the mechanism it allows for us to be able to control the enzyme and therefore control a reaction and control the amount of reactants and products that are going to be available in the biological system this is the basis for much of the pharmaceutical industry understanding for example why a certain reaction whether an enzyme is present or not in a system can lead to disease uh at the rate of a reaction the formation of the products that can also lead to diseases allows us to create a molecule that can interact with an enzyme sometimes better than the substrate the starting material that reactant can and therefore it can control the product that's being made and therefore we can control a disease so understanding these reaction mechanisms that's why they are important in biochemistry when you look at a reaction mechanism so a versus b for example in this figure notice what the reactants are and what the products are of course in any chemical reaction notice if the arrow is a forward only or if it's a reversible reaction we also want to take a look at what type of reaction it is and what intermediates might be you know in play in terms of that reaction when you look at the organic reaction mechanism shown in b so now we're looking specifically at a mechanism how do we know well we have arrows right and so when you see these arrows in organic chemistry they mean the same in biochemistry we're looking at a flow of of electrons and you'll notice these arrows always go from the electron dense starting material wherever we have our electrons and go towards the here we're looking at a nucleophilic attack so we're looking at and i don't want you to just use electrophile or nucleophile without understanding what they mean so keep in mind here's a nucleophile that's our hydroxyl group is and it's a hydroxide because it has a charge is going to do a nucleophilic attack so this is our nucleophile it's nucleophilic seeking and because it's electron dense you will never see electrophilic attack right so an electrophile is going to be something that does not have electrons or it has you know less electrons than our nucleophile so our nucleophile is always going to do the nucleophilic attack the electron flow and the arrows always go from the electron rich source to that electrophile the electron deficient so that's why we'll never see electrophilic attack these are always nucleophilic attacks so the hydroxide is going to attack the carbon here that's going to be our electrophile and we're going to have a rearrangement and we'll lose that alkyl alkyl halide group so the halide is going to come off then with the electrons and we'll have this transition state that occurs we know that it's a transition state well in a couple of ways first you'll notice that we're showing some intermediate bonds being formed between the hydroxyl group that's coming on to the carbon and we still have a group that's leaving we have the halide that is going to be leaving so we have a transition that's occurring as these have kind of a partial bond being made so you'll notice like carbon does not make five bonds in biochemistry just like it didn't make five bonds in organic chemistry our product that is being made at the end we lose that substitution product the halide is our leaving group and the transition state also has that double hash mark so that's another kind of indication just like in organic chemistry that we have a transition state that's occurring in biochemistry in terms of enzyme reaction mechanisms and we'll take a look at these in more detail further on in the semester but here you're now looking at what's happening in the active site of an enzyme for an enzyme so these are our proteins that have catalytic ability they are going to catalyze almost i mean nearly all of the reactions that are catalyzed in a biological system are being carried out by enzymes an enzyme reaction mechanism is going to be shown in the same way as the organic reaction mechanism the electron source we're drawing an arrow from that electron source or from the nucleophile and here you can see that we have an ion of an ester is going to attack a hydrogen and abstracted to make a carboxylic acid this is going to undergo a rearrangement reaction and then we'll see in this rearrangement reaction we're going to extract a hydrogen over from our nitrogen pyrrole group and so overall while the enzymatic reaction mechanism may look a little bit more complicated the overall steps and the the general rules for an organic reaction mechanism are going to stay the same the end of this section takes a look at polymers which we already know are going to be a larger more extensive uh organic molecule so we're looking at something like in chains or that might have branches off so in terms of polymers our macromolecules in biochemistry are going to of course be our proteins which are going to have a peptide or amide backbone as carboxylic acids are going to react with amine nitrogens and another example of this is also going to be our lipids so we'll see the polymers the larger molecules are going to be built up of the smaller building blocks and we'll see a variety of different polymers in terms of the biological chemistry and we'll get into those further on in the course okay start reviewing your organic functional groups look over not only their names and their structures but i also want you to look over and review the chemistry the chemical properties of those groups hope that helps