hello everybody my name is Iman welcome back to my YouTube channel today we're going to be covering chapter 10 for MCAT organic chemistry this chapter is titled nitrogen and phosphorus containing compounds now we've defined organic chemistry as the study of carbon containing molecules but as we've seen in the past few chapters carbon is not the only element that plays a role in organic molecules many of the functional grp groups we' we've discussed in the past few chapters include hydrogen and include oxygen and together together these three elements carbon hydrogen and oxygen they make up 93% of the composition of the human body by weight now other elements and other atoms also contribute to biomolecules nitrogen comprises 3.2% of the body weight and phosphorus about 1% and so in this chapter our focus is to talk about nitrogen and phosphorous containing compounds our objectives are the following first we're going to start by talking about amino acids peptides and proteins we'll cover their description and their properties then we'll move into discussing the synthesis of alpha amino acids here we'll cover the ster and the Gabriel synthesis and then last but not least we'll focus a a little bit on phosphorus containing compounds and talk about their description and their properties now before we do dive into those objectives I do just want to set the stage up by talking about proteins all right proteins include a diversity of structures that results in a wide range of functions proteins they account for more than 50% of the dry mass of most cells and they're instrumental in almost everything organisms do some proteins are going to speed up chemical reactions others are going to play a role in defense storage transport cellular Comm communication movement and the list goes on all right a human has tens of thousands of different proteins each with a specific structure and a specific function here what you see is myoglobin this is the first protein to have its 3D structure know know using x-ray crystallography myoglobin is a protein in heart and skeletal muscles and so when you exercise right your muscles they use up available oxygen myoglobin it has oxygen attached to it which provides extra oxygen for the muscles to keep at a high level of activity for a longer period of time now as diverse as proteins are they're all constructed from the same set of 20 amino acids linked in unbranched polymers and so here now we're going to turn our Focus to talking about the building blocks for proteins and those are amino acids amino acids they are dipolar molecules that are going to come together through a condensation reaction forming peptides and then large folded pepti peptide chains are considered proteins and our goal is to make that sentence really easy to understand and for that to be true we're going to have to cover all these um different parts we're going to have to discuss what are amino acids what are peptides and then lastly what are proteins and so of course we start with the basics like I said the building block for proteins that is amino acids all amino acids share a common structure an amino acid is an organic molecule with both an amino group and a carboxy group all right they have an amino group and a carboxy group attached to a single carbon we call this the alpha carbon the other two substituents of the alpha carbon are a hydrogen and then a side chain all right that we refer to as as the R Group all right so here is the general structure of amino acids all amino acids share this structure here what's variable is again that R Group different amino acids have different R groups that is how you distinguish between different amino acids however all of them have these three groups they all have a alpha carbon attached to an amino group a hydrogen and a carboxy group the only thing that differs is that variable R Group the R Group determines chemistry and function of that amino acid and the physical and chemical properties of the side chain this R side chain determines the unique characteristics of a particular amino acid and that as a consequence affects its functional role in a polypeptide now the amino acids are grouped according to the properties of their side chain so there are 20 common amino acids that you need to know for the MCAT that's not to say that there aren't more but we're only concerned about these two these 20 amino acids for the MCAT and what you notice is that you can group these amino acids based off of General properties like polar or non-polar aromatic or non-aromatic charged or uncharged all right now really to be even more precise we can group the 20 amino acids into five categories we can do non-polar nonaromatic aromatic polar negatively charged which is acidic and positively charged basic now here what we see in this category is that we have amino acids with a hydrophobic side chain all right so these are our non-polar amino acids our non-polar non aromatic amino acids they tend to have side chains that are saturated hydrocarbons all right so we're going to circle we're going to circle our nonpolar nonaromatic amino acids all right now we do have these categories these are good categories I'm just further refining these categories non-polar non-aromatic amuno acids like we just said they tend to have cines that are saturated hydrocarbons so Alan veine all right Lucine isol leucine in addition to glycine Proline sorry yeah glycine Proline and methio 9 so all the names that I have circled in green are nonpolar non aromatic now for Proline it is cyclic but with a secondary amine all right so this we talk about aromatic we're going to be very specific in our definition to the point that Proline is not included in the aromatic category but more so in our nonpolar non aromatic category especially as defined for the mcap all right now what about aromatic amino acids all right now what you see here are okay so we're going to choose a different color we're going to do polar for aromatic I do want to quickly say that these three are obviously aromatic and we're going to circle them they are also considered they're also considered hydrophobic side chains so that's an important thing to keep in mind all right so now our aromatic amino acids they are going to include tryptophan tyrosine phenol alanine all right these are our aromatic amino acids tryptophan phenol alanine and tyrosine now nonpolar amino acids both non-aromatic and aromatic these are non-polar by the way all right regardless non-aromatic and aromatic they are non-polar amino acids the ones that we've circled so far in this pink category and that means they're also hydrophobic and these two as well by the way all right they are hydrophobic and they tend to be sequestered in the interior of proteins so so far all right we've CED CED nonpolar amino acids both aromatic and non-aromatic and non-polar amino acids are hydrophobic and they tend to be sequestered in the interior of proteins now what about polar what about polar amino acids let's talk about that polar amino acids they tend to have terminal groups containing oxygen nitrogen or sulfur and so these are going to include molecules like 309 asparagine glutamine and cysteine all right so the ones that we've circled in red these are polar amino acids all right now another group we want to talk about is negatively charged or acidic amino acids so negatively charged all right or acidic amino acids these are going to include only two amino acids and that's aspartic acid and GL glutamic acid all right these are negatively charged or acidic amino acids these amino acids have terminal carboxy anion in their R Group and then last but not least our final group is going to be positively charged or basic amino acids all right these are going to include all right arginine histadine and lysine all right so these positively charged basic amino acids have a proteinated amino group as you notice in their R groups polar acidic and basic amino acids all the ones that we've talked about in or in red purple and black are all hydrophilic and they tend to form hydrogen bonds with water and aquous solution now with that being covered I do want to make a couple of notes like we said amino acids they have a carboxy group and they have a basic group right when we talked about our general formula we have a alpha carbon it's attached to a carboxy group I'm going to just write it out an amino group a hydrogen and an R Group now the carboxy group is this you know their acidic carboxy group and their basic amino group they have those two these amino acids are amphoteric molecules that is they can act as both acids and bases in different conditions now amino acids can take on a positive charge by being protonated and carboxy groups can take on negative charges by being deprotonated now when an AM Meo acid is put into a solution it will take on both charges forming a dipolar ion or in other words zwitter ion so how an amino acid acts depends on the pH of the environment so what that means is in basic Solutions the amino acids can become fully deprotonated and in acidic Solutions it can become fully proteinated now when we talked about the basic structure of amino acids all right this Alpha carbon has four different groups attached to it an amino group a carboxy group a hydrogen and an R Group and so with its four different groups this Alpha carbon is a chyal center there is only one exception to this from R20 amino acids and that is going to be glycine glycine here's that Alpac carbon has an amino group a carboxy group and two hydrogens and because it has two of the same group hydrogen glycine is an exception to the rule it is not chyal all right it's the simplest amino acid and it's an exception to the rule because it's R Group is a hydrogen atom so it has two hydrogen atoms at that Alpha carbon meaning that it is not chyal all the other amino acids here are chyal at the alpha at the alpha carbon all right here in addition all right I just have these amino acids listed in a in in hydrophobic hydrophilic and tic empathic sorry um categories for you in addition to the categories we talked about here it's just important to understand hydrophilic and hydrophobic and while we did Define you know your um non-polar amino acids whether aromatic or non-aromatic tend to they they tend to fall under the hydrophobic category and then your polar negative and positively charged amino acids tend to fall under the hydrophilic category some do fall under the amphipathic category though as as well and I have those listed here now with that now that we know the basic structure of amino acids and we know they're the building blocks of of of proteins let's dive into that a little more all right we said that amino acids are the building blocks of proteins but then how do we get higher order structure where do we start all right and where we want to start here is is by working through the logic of if we know the basic structure of our amino acids right we've talked about individual amino acids what if we have a linear sequence of amino acids and then how do we have binding between amino acids those are two important questions we need to be able to answer if we want to build up to talking about proteins now when two amino acids are positioned so that their carboxy group um uh of on one amino acid is adjacent to the amino group of another amino acid they can become joined by a dehydration reaction so with the removal of water they can form a bond between these two amino acids the result is a coent bond called a peptide bond and repeated over and over this process yields a polypeptide a polymer of many amino acids link by peptide bonds all right now this is really important to understand all right that we have these amino acids they can undergo reactions to form peptide bonds between each other all right the molecules these bonds have are the base units of proteins so with that how do we build up to proteins all right how do we build up to proteins so let's work through through that we said proteins are complex molecules that play a critical role in our body and their function is determined by their structure so it's really important that we do understand their structure their structure is organized into four distinct levels all right and they can vary at each level it's what determines their function but those levels are primary secondary tertiary and quinary all right so let's explore each of these levels we start off with the primary structure the primary structure of a protein is just going to be its amino acid sequence linked by peptide bond so it's just going to look like amino acids linked together like you see in the image the sequence is determined by our DNA blueprint it's crucial because that dict you know these polypeptide sequences this primary structure is important because it dictates the higher levels of structure that give proteins its functions think of the primary structure as the alphabet all right in a sentence each letter must be in its proper place to make sense then we move into secondary structure this involves the folding or coiling of the polypeptide chain that into elements such as Alpha helices and beta plated sheets these structures are going to be stabilized by hydrogen bonds between the backbone constituents of the amino acids the alpha Helix is a right-handed coil while the beta pleed sheet is formed by linking two or more strands sitting side by side the secondary structure we can think of as taking that alphabet and now forming a word with it all right if we're trying to build an analogy here then we can move into our tertiary structure the tertiary structure is a three-dimensional folding pattern of a protein due to side chain interactions so this can include hydrophobic interactions hydrogen bonds ion I IC bonds disulfate Bridges the tertiary structure is essential for the protein's functionality because it forms the unique shape that's necessary for the protein to form its specific tasks and it can be an um it can be an acclamation of um it could be like it could be an accumulation of alpha heles different Alpha helices binded together or Alpha helices and beta ple she or different beta pleed sheets that come together and so we can think about the tertiary structure sorry guys I had a little bit of a brain fart there all right we could think of the tertiary structure as now taking the words and forming sentences with them all right and then finally we have the quinary structure so this is present in proteins with M multiple polypeptide chains or subunits and these subunits come together to form a functional protein complex so in our example at the beginning all right you know we saw myoglobin we said that this is a protein right and we we can look at that or we can look at even hemoglobin this is a classic example hemoglobin it has four subunits that are working together to transport oxygen throughout the body all right and so the qu quinary structure is really vital for the function of proteins that operate in a more complex and coordinated fashion and so here we can think about taking many sentences and now forming paragraphs with them and so now we've covered the structure of proteins the complexity of structures by covering primary secondary tertiary and quinary structures here in objective two we're going to talk about synthesis of alpha amino acids we're going to talk about two specific synthesis Pathways streker and Gabriel and we're going to go ahead and start off with the the ster synthesis now in the ster synthesis you're going to start off with an aldah ammonium chloride and pottassium cyanide all right so those are your starting materials and here we're going to see how they are used throughout the pathway and what we end up with now to start all right the we're going to talk about just step one which is right up to here all right the carbonal oxygen in our alide all right is going to be protonated and that is going to increase the electrophilicity of the carbonal carbon that means then as you see here ammonia can attack the carbonal carbon and what we form is going to be an amine now the amine carbon is also susceptible to nucleophilic addition and so what we're going to notice is that at some point the CN minus annion from pottassium cyanide is going to attack all right forming a nitrile group and then the final molecule at the end of Step One is going to be an amino nital a compound containing an amino group and a nital group all right so that's step one all right we have protonation we have a nucleophilic attack then we have a couple of rearrangements we have we have um reforming a double bond and losing a leaving group right this water molecule here then we have another nucleophilic attack done by our CN group in our potassium Cyanide and then we end up with this group an amino nitrile a compound that contains an amino group group and a nitrile group now we can move into step two in step two that nitrile nitrogen is protonated again increasing the electrophilicity of the nitrile carbon all right this is similar to protonating the oxygen of a carbonal now a water molecule attacks leading to the creation of a molecule that has both an amine and a hydroxy group on the same carbon this amine is attacked by another equivalent of water all right a carbonal is formed kicking off ammonia and creating the carboxilic acid functionality all right now all right after that this step is performed uh the step ends with this following molecule all right what does this look like this looks like an amino acid here's our Alpha carbon we have carboxilic acid amino group there's a hydrogen and our R Group now the second step is performed by the way in aquous acid and it can be accelerated by the use of heat all right by the use of heat so here we've seen the struer synthesis it happens in two steps and in the first first step we generate an amino nitr and then in the second step we go from that Amino nitr and we generate an amino acid now the starting material I'm going to highlight here in Orange the starting material for the ster synthesis is a planer carbonal containing compound all right therefore the product of this pathway is going to be a rasmic mixture all right the UN that the incoming nucleophiles what that means is that they're equally able to attack from either side of the carbonal and so what that means at the end is that we can generate both L and D amino acids from this process fantastic now we can talk about the Str the the Gabriel synthesis so this is another way of synthesizing amino acids through the Gabriel synthesis also known as the malonic Esther synthesis now in this method potassium thide is reacted with DL bromomalonate nalide is acidic and it exists in solution as a nucleophilic annion dyl bromomalonate it contains a secondary carbon bonded to bromine a good leing group so the setup should very much sound like an sn2 reaction with phide as the nucleophile and the secondary substrate carbon as the electrophile and bromine as the as the leaving group this reaction generates the following product all right now in the presence of Base this carbon is easily deprotonated this carbon is easily deprotonated so we get the following product now all right now the molecule as a whole can then act as a nucleophile attacking the substrate carbon of a bromo alane this is another example of an sn2 reaction and so now we get the following product next this molecule is hydrolized with a strong base and heat and much like converting a cyclic anhydride into a dioic acid the thide mo mo is removed as thalmic acid with two carboxilic acids and the milanic is hydrolized to a dicarboxylic acid with an amine on the alpha carbon finally the dicarboxylic acid which is a 13 dicarbon can be decarbox through the addition of acid and Heat and the loss of a molecule of carbon uh of carbon dioxide results in the formation of the complete amino acid all right so those are the two methods of creating amino acids now like the streker synthesis the Gabriel synthesis starts with a planer molecule thus the product is a rasmic mixture of L and D amino acids all right so now we've covered the two methods of creating amino acids the ster synthesis and the gabrial synthesis now we can move into our third objective phosphorus containing compounds now phosphor uh phosphoric acid is an extremely important molecule biochemically this molecule forms the high energy bonds that carry energy in adenosine triphosphate ATP now in a biochemical context phosphoric acid is often referred to as phosphate group or inorganic pH phosphate denoted as P of I now at physiological pH inorganic phosphate includes molecules of both hydrogen phosphate all right and dihydrogen phosphate in addition to the energy carrying nucleotide phosphates phosphorus is also found in the backbone of DNA in phosphodiester bond bonds linking the sugar moities of the nucleotides like you see right here all right when a new nucleotide is joined to a growing strand of DNA by DNA polymerase it releases an esterer of phosphate referred to as pyrro phosphate and denoted as PPI all right now the hydraulic the the hydratic release of this molecule provides the energy for the formation of the new phospho diaster Bond okay now phos pyrophosphate is unstable in aquous solution and it is hydrolyzed to form two molecules of inorganic phosphate which can then be recycled to form high energy Bonds in ATP or for other purposes nucleotides like ATP GTP and those in DNA are going to be referred to as organic phosphates due to the presence of the phosphate groups bonded to carbon containing molecules now one last thing that we want to cover here is that phosphoric acid all right H3 P4 has three hydrogens each of those hydrogens has a unique PKA the wide variety in PKA values allows phosphoric acid to act as a buffer over a large range of pH values all right those are the main points that we needed to cover for this chapter I want to summarize them all right just to Encompass the main points we said biologically amino acids are synthesized in many ways in the labs certain standardized mechanisms are used we talked about the ster synthesis which generates an amino acid from an alahh an alahh is essentially mixed with ammonium chloride and potassium cyanide the ammonia attacks the carbonal carbon generating an amine the amine is then attacked by the cyanide all right it's attacked by the cyanide generating an amino nitril the amino nital is then hydrolized by two equivalent of water generating an amino acid in the end all right then the Gabriel synthesis it generates an amino acid from potassium pomide and diethyl bromomalonate and an alkal haly now pomide attacks the diethyl bromomalonate generating a pide malonic Esther this Attacks An alkal halide adding an alkal group to the Esther then the product is hydrolized creating pic pathol acid with two carboxilic groups and converting the Esters into carboxilic acids one carboxilic acid of the resulting 13 dicarbon is removed by decarbox for us to form our amino acid then for phosphorus containing compounds we don't need to know too much for the MCAT we said that phosphorus is found in inorganic phosphate which is a mixture a buffered mixture of hydrogen phosphate and dihydrogen phosphate phosphorus is found in the backbone of DNA which uses phosphodiester Bonds in forming these bonds a pyrro phosphate is released and pyrro phosphate can then be hydrolized to two inorganic phosphates phosphate bonds are high energy because of large negative charges in adjacent phosphate groups and because of resonance stabilization of those phosphates organic phosphates are carbon containing compounds that have a phosphate group notable examples include ATP GTP or DNA and then as a last point we said phosphoric acid has three hydrogens each with a unique PKA and this wide variety in PKA values allows phosphoric acid to act as as a buffer over a large range of pH values all right in the next video we're going to tackle a pro a practice problem set let me know if you have any questions comments concerns down below other than that good luck happy studying and have a beautiful beautiful day future doctors