Organik Kimya: Azot ve Fosfor Dünyası

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 groups we've discussed in the past few chapters include hydrogen and include oxygen and together these three elements carbon hydrogen and oxygen they make up 93 percent of the composition of the human body by weight now other elements and other atoms also contribute to biomolecules nitrogen comprises 3.2 percent of the body weight and phosphorus about 1%. And so in this chapter, our focus is to talk about nitrogen and phosphorus-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 Strecker and the Gabriel synthesis. And then last but not least, we'll focus 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. 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 the development of 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 communication, movement, and the list goes on. 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. protein to have its 3D structure known 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 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 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 carboxyl group. Alright, they have an amino group and a carboxyl 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 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 an alpha carbon attached to an amino group, a hydrogen, and a carboxyl 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 function of the amino acid. 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 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. Now, really, to be even more precise, we can group the 20 amino acids into five categories. We can do non-polar, non-aromatic, 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. are nonpolar, non-aromatic amino acids, they tend to have side chains that are saturated hydrocarbons. All right, so we're going to circle our nonpolar, non-aromatic amino acids. All right, now we do have these categories. These are good categories. I'm just further refining these categories. Nonpolar, non-aromatic amino acids, like we just said, they tend to have side chains that are... saturated hydrocarbons. So alanine, valine, all right, leucine, isoleucine, in addition to glycine, proline, sorry, yeah, glycine, proline, and methionine. So all the names that I have circled in green are non-polar, non-aromatic. Now for proline, It is cyclic, but with a secondary amine. All right. So this when 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 non-polar, non-aromatic category, especially as defined for the MCAT. All right. Now, what about aromatic amino acids? All right. Now, what you see here are OK, so we're going to choose a different color. We're going to do polar for our aromatic. I do want to quickly say that these three are obviously aromatic and we're going to circle them. They are 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, phenylalanine. All right, these are... our aromatic amino acids, tryptophan, phenylalanine, and tyrosine. Now, nonpolar amino acids, both non-aromatic and aromatic, these are nonpolar, by the way, all right? Regardless, non-aromatic and aromatic, they are nonpolar 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 circled nonpolar amino acids, both aromatic and non-aromatic, and nonpolar 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 serine, 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 or acidic amino acids. These are going to include only two amino acids and that's a aspartic acid and glutamic acid. All right, these are negatively charged or acidic amino acids. These amino acids have terminal carboxylate anions 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 histidine 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 red, purple, and black, are all hydroxychloroquine. hydrophilic and they tend to form hydrogen bonds with water and aqueous solution. Now with that being covered I do want to make a couple of notes. Like we said amino acids they have a carboxyl group and they have a basic group right when we talked about our general formula we have alpha carbon it's attached to a carboxyl group I'm going to just write it out an amino group a hydrogen and an R group. Now Now, the carboxyl group is, you know, their acidic carboxyl 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 carboxyl groups can take on negative charges by being deprotonated. Now, when an amino acid is put into a solution, solution, it will take on both charges, forming a dipolar ion, or in other words, zwitterion. 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 protonated. 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 carboxyl group, a hydrogen, and an R group. And so with its four different groups, this alpha carbon is a chiral center. There is only one exception to this from R20 amino acids, and that is going to be glycine. Glycine here is that alpha carbon has an amino group, a carboxyl group, and two hydrogens. And because it has two of the same group, hydrogen, glycine is an exception to the rule. It is not chiral, all right? It's the simplest amino acid, and it's an exception to the rule because it's our group is a hydrogen atom. So it has two hydrogen atoms at that alpha carbon, meaning that it is not chiral. All the other amino acids here are chiral at the alpha carbon, all right? Here in addition, all right, I just have these amino acids listed. listed in hydrophobic, hydrophilic, and amphipathic 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 your nonpolar amino acids, whether aromatic or non-aromatic, 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 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 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 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 carbohydrates, group 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 covalent bond called a peptide bond. And repeated over and over, this process yields a bond. polypeptide, a polymer of many amino acids linked 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 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 quaternary. 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 bonds. 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 into elements. such as alpha helices and beta pleated 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 pleated 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, ionic 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 And it can be an agglomeration of, it could be like, it could be an accumulation of alpha helices, different alpha helices bonded together or alpha helices and beta pleated sheets or different beta pleated 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 can think of the tertiary structure as now taking the words and forming sentences with them. All right, and then finally we have the quaternary structure. So this is present in proteins with 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 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 quaternary 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 quaternary 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, strecker and gabriel, and we're going to go ahead and start off with the strecker synthesis. In this Drucker synthesis, you're going to start off with an aldehyde, ammonium chloride, and potassium cyanide. Alright, 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, alright, we're going to talk about just step one, which is right up to here. The carbonyl oxygen in our... aldehyde, all right, is going to be protonated. And that is going to increase the electrophilicity of the carbonyl carbon. That means then, as you see here, ammonia can attack the carbonyl 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-anion from potassium 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 nitrile, a compound containing an amino group and a nitrile 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 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. 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 carbonyl. Now a water molecule attacks, leading to the creation of a molecule that has both an amine and a hydroxyl group on the same carbon. This amine is attacked by another equivalent of water. Alright, a carbonyl is formed kicking off ammonia and creating the carboxylic acid functionality. Alright. Now, all right, after that, this step is performed, this 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 carboxylic acid amino group. There's a hydrogen and our R group. Now, the second step is performed, by the way, in aqueous acid, and it can be accelerated. by the use of heat. So here we've seen the Strucker synthesis. It happens in two steps. And in the first step, we generate an amino nitrile. And then in the second step, we go from that amino nitrile and we generate an amino acid. Now, the starting material I'm going to highlight here in orange, the starting material for the Strucker synthesis is is a planar carbonyl-containing compound. All right? Therefore, the product of this pathway is going to be a racemic mixture. All right? The incoming nucleophiles, what that means is that they're equally able to attack from either side of the carbonyl. 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 Gabriel synthesis. So this is another way of synthesizing amino acids through the Gabriel synthesis, also known as the malonic ester synthesis. Now, in this method, Potassium phthalmide is reacted with diethyl bromomelanate. Now, phthalmide is acidic and it exists in solution as a nucleophilic anion. Diethyl bromomelanate, it contains a secondary carbon bonded to bromine, a good leaving group. So the setup should very much sound like an SN2 reaction. With phthalmide as the nucleophile and the secondary substrate carbon as the electrophile and bromine as the nucleophile. As the leaving group, this reaction generates the following product. Now, in the presence of base, this carbon is easily deprotonated. This carbon is easily deprotonated, so we get the following product now. Now, the molecule as a whole can then act as a nucleophile, attacking the substrate carbon of a molecule. bromoalkane. This is another example of an SN2 reaction. And so now we get the following product. Next, this molecule is hydrolyzed with a strong base and heat. And much like converting acyclic anhydride into a dioic acid, the thalmide moiety is removed as thalmic acid with two carboxylic acids. And the malonic ester is hydrolyzed to a dicarboxylic acid with an amine on the alpha carbon. Finally, the dicarboxylic acid, which is a 1,3-dicarbonyl, can be decarboxylated through the addition of acid and heat. And the loss of a molecule of carbon dioxide results in the formation of the complete amino acid. Alright, so those are the two methods of creating amino acids. Now, like the Strecker synthesis, the Gabriel synthesis starts with a planar molecule. Thus, the product is a racemic mixture. of L and D amino acids. All right, so now we've covered the two methods of creating amino acids, the Strecker synthesis and the Gabriel synthesis. Now we can move into our third objective, phosphorus-containing compounds. Now, phosphoric acid is an extremely important molecule biochemically. This molecule forms the high-energy bonds that carry the molecule. energy in adenosine triphosphate, ATP. Now in a biochemical context, phosphoric acid is often referred to as phosphate group or inorganic phosphate denoted as P of I. Now at physiological pH, inorganic phosphate includes molecules of both hydrogen phosphate and dihydrogen. phosphate. In addition to the energy carrying nucleotide phosphates, phosphorus is also found in the backbone of DNA in phosphodiester bonds linking the sugar moieties. 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 ester dimer of phosphate referred to as pyrophosphate and denoted as PPI. Now the hydraulic, the hydrolytic release of this molecule provides the energy for the formation of the new phosphodiester bond. Now pyrophosphate. is unstable in aqueous 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, H3PO4 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 acids are synthesized in many ways. In the lab, certain standardized mechanisms are used. We talked about the Strecker synthesis, which generates an amino acid from an aldehyde. An aldehyde is essentially mixed with ammonium chloride and potassium cyanide. The ammonia attacks the carbonyl carbon, generating an amine. The amine is then attacked by the cyanide. All right, it's attacked by the cyanide, generating an amino nitrile. The amino nitrile is then hydrolyzed by two equivalents of water, generating an amine. an amino acid in the end. All right. Then the Gabriel synthesis, it generates an amino acid from potassium phthalmide and diethyl bromomelanate and an alkyl halide. Now, phthalmide attacks the diethyl bromomelanate, generating a phthalmide malonic ester. This attacks an alkyl halide, adding an alkyl group to the ester. Then the product is hydrolyzed. creating phthalic acid with two carboxylic groups and converting the esters into carboxylic acids. One carboxylic acid of the resulting 1,3-dicarbonyl is removed by decarboxylation 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 of 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 pyrophosphate is released, and pyrophosphate can then be hydrolyzed 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 a buffer over a large range of pH values. All right. In the next video, we're going to tackle 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.

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 groups we've discussed in the past few chapters include hydrogen and include oxygen and together these three elements carbon hydrogen and oxygen they make up 93 percent of the composition of the human body by weight now other elements and other atoms also contribute to biomolecules nitrogen comprises 3.2 percent of the body weight and phosphorus about 1%. And so in this chapter, our focus is to talk about nitrogen and phosphorus-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 Strecker and the Gabriel synthesis. And then last but not least, we'll focus 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. 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 the development of 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 communication, movement, and the list goes on. 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. protein to have its 3D structure known 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 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 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 carboxyl group. Alright, they have an amino group and a carboxyl 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 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 an alpha carbon attached to an amino group, a hydrogen, and a carboxyl 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 function of the amino acid. 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 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. Now, really, to be even more precise, we can group the 20 amino acids into five categories.

We can do non-polar, non-aromatic, 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.

are nonpolar, non-aromatic amino acids, they tend to have side chains that are saturated hydrocarbons. All right, so we're going to circle our nonpolar, non-aromatic amino acids. All right, now we do have these categories.

These are good categories. I'm just further refining these categories. Nonpolar, non-aromatic amino acids, like we just said, they tend to have side chains that are... saturated hydrocarbons.

So alanine, valine, all right, leucine, isoleucine, in addition to glycine, proline, sorry, yeah, glycine, proline, and methionine. So all the names that I have circled in green are non-polar, non-aromatic. Now for proline, It is cyclic, but with a secondary amine. All right. So this when 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 non-polar, non-aromatic category, especially as defined for the MCAT.

All right. Now, what about aromatic amino acids? All right. Now, what you see here are OK, so we're going to choose a different color. We're going to do polar for our aromatic.

I do want to quickly say that these three are obviously aromatic and we're going to circle them. They are 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, phenylalanine. All right, these are...

our aromatic amino acids, tryptophan, phenylalanine, and tyrosine. Now, nonpolar amino acids, both non-aromatic and aromatic, these are nonpolar, by the way, all right? Regardless, non-aromatic and aromatic, they are nonpolar 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 circled nonpolar amino acids, both aromatic and non-aromatic, and nonpolar 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 serine, 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 or acidic amino acids. These are going to include only two amino acids and that's a aspartic acid and glutamic acid. All right, these are negatively charged or acidic amino acids. These amino acids have terminal carboxylate anions 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 histidine 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 red, purple, and black, are all hydroxychloroquine. hydrophilic and they tend to form hydrogen bonds with water and aqueous solution.

Now with that being covered I do want to make a couple of notes. Like we said amino acids they have a carboxyl group and they have a basic group right when we talked about our general formula we have alpha carbon it's attached to a carboxyl group I'm going to just write it out an amino group a hydrogen and an R group. Now Now, the carboxyl group is, you know, their acidic carboxyl 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 carboxyl groups can take on negative charges by being deprotonated. Now, when an amino acid is put into a solution, solution, it will take on both charges, forming a dipolar ion, or in other words, zwitterion. 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 protonated. 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 carboxyl group, a hydrogen, and an R group. And so with its four different groups, this alpha carbon is a chiral center.

There is only one exception to this from R20 amino acids, and that is going to be glycine. Glycine here is that alpha carbon has an amino group, a carboxyl group, and two hydrogens. And because it has two of the same group, hydrogen, glycine is an exception to the rule.

It is not chiral, all right? It's the simplest amino acid, and it's an exception to the rule because it's our group is a hydrogen atom. So it has two hydrogen atoms at that alpha carbon, meaning that it is not chiral. All the other amino acids here are chiral at the alpha carbon, all right?

Here in addition, all right, I just have these amino acids listed. listed in hydrophobic, hydrophilic, and amphipathic 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 your nonpolar amino acids, whether aromatic or non-aromatic, 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 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 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 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 carbohydrates, group 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 covalent bond called a peptide bond. And repeated over and over, this process yields a bond.

polypeptide, a polymer of many amino acids linked 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 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 quaternary. 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 bonds. 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 into elements.

such as alpha helices and beta pleated 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 pleated 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, ionic 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 And it can be an agglomeration of, it could be like, it could be an accumulation of alpha helices, different alpha helices bonded together or alpha helices and beta pleated sheets or different beta pleated 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 can think of the tertiary structure as now taking the words and forming sentences with them. All right, and then finally we have the quaternary structure.

So this is present in proteins with 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 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 quaternary 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 quaternary 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, strecker and gabriel, and we're going to go ahead and start off with the strecker synthesis. In this Drucker synthesis, you're going to start off with an aldehyde, ammonium chloride, and potassium cyanide.

Alright, 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, alright, we're going to talk about just step one, which is right up to here. The carbonyl oxygen in our...

aldehyde, all right, is going to be protonated. And that is going to increase the electrophilicity of the carbonyl carbon. That means then, as you see here, ammonia can attack the carbonyl 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-anion from potassium 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 nitrile, a compound containing an amino group and a nitrile 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 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. 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 carbonyl. Now a water molecule attacks, leading to the creation of a molecule that has both an amine and a hydroxyl group on the same carbon.

This amine is attacked by another equivalent of water. Alright, a carbonyl is formed kicking off ammonia and creating the carboxylic acid functionality. Alright.

Now, all right, after that, this step is performed, this 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 carboxylic acid amino group. There's a hydrogen and our R group. Now, the second step is performed, by the way, in aqueous acid, and it can be accelerated.

by the use of heat. So here we've seen the Strucker synthesis. It happens in two steps.

And in the first step, we generate an amino nitrile. And then in the second step, we go from that amino nitrile and we generate an amino acid. Now, the starting material I'm going to highlight here in orange, the starting material for the Strucker synthesis is is a planar carbonyl-containing compound. All right? Therefore, the product of this pathway is going to be a racemic mixture.

All right? The incoming nucleophiles, what that means is that they're equally able to attack from either side of the carbonyl. 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 Gabriel synthesis.

So this is another way of synthesizing amino acids through the Gabriel synthesis, also known as the malonic ester synthesis. Now, in this method, Potassium phthalmide is reacted with diethyl bromomelanate. Now, phthalmide is acidic and it exists in solution as a nucleophilic anion. Diethyl bromomelanate, it contains a secondary carbon bonded to bromine, a good leaving group. So the setup should very much sound like an SN2 reaction.

With phthalmide as the nucleophile and the secondary substrate carbon as the electrophile and bromine as the nucleophile. As the leaving group, this reaction generates the following product. Now, in the presence of base, this carbon is easily deprotonated.

This carbon is easily deprotonated, so we get the following product now. Now, the molecule as a whole can then act as a nucleophile, attacking the substrate carbon of a molecule. bromoalkane. This is another example of an SN2 reaction. And so now we get the following product.

Next, this molecule is hydrolyzed with a strong base and heat. And much like converting acyclic anhydride into a dioic acid, the thalmide moiety is removed as thalmic acid with two carboxylic acids. And the malonic ester is hydrolyzed to a dicarboxylic acid with an amine on the alpha carbon. Finally, the dicarboxylic acid, which is a 1,3-dicarbonyl, can be decarboxylated through the addition of acid and heat. And the loss of a molecule of carbon dioxide results in the formation of the complete amino acid.

Alright, so those are the two methods of creating amino acids. Now, like the Strecker synthesis, the Gabriel synthesis starts with a planar molecule. Thus, the product is a racemic mixture. of L and D amino acids. All right, so now we've covered the two methods of creating amino acids, the Strecker synthesis and the Gabriel synthesis.

Now we can move into our third objective, phosphorus-containing compounds. Now, phosphoric acid is an extremely important molecule biochemically. This molecule forms the high-energy bonds that carry the molecule. energy in adenosine triphosphate, ATP.

Now in a biochemical context, phosphoric acid is often referred to as phosphate group or inorganic phosphate denoted as P of I. Now at physiological pH, inorganic phosphate includes molecules of both hydrogen phosphate and dihydrogen. phosphate. In addition to the energy carrying nucleotide phosphates, phosphorus is also found in the backbone of DNA in phosphodiester bonds linking the sugar moieties.

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 ester dimer of phosphate referred to as pyrophosphate and denoted as PPI. Now the hydraulic, the hydrolytic release of this molecule provides the energy for the formation of the new phosphodiester bond. Now pyrophosphate.

is unstable in aqueous 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, H3PO4 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 acids are synthesized in many ways. In the lab, certain standardized mechanisms are used. We talked about the Strecker synthesis, which generates an amino acid from an aldehyde. An aldehyde is essentially mixed with ammonium chloride and potassium cyanide.

The ammonia attacks the carbonyl carbon, generating an amine. The amine is then attacked by the cyanide. All right, it's attacked by the cyanide, generating an amino nitrile.

The amino nitrile is then hydrolyzed by two equivalents of water, generating an amine. an amino acid in the end. All right. Then the Gabriel synthesis, it generates an amino acid from potassium phthalmide and diethyl bromomelanate and an alkyl halide. Now, phthalmide attacks the diethyl bromomelanate, generating a phthalmide malonic ester.

This attacks an alkyl halide, adding an alkyl group to the ester. Then the product is hydrolyzed. creating phthalic acid with two carboxylic groups and converting the esters into carboxylic acids. One carboxylic acid of the resulting 1,3-dicarbonyl is removed by decarboxylation 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 of 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 pyrophosphate is released, and pyrophosphate can then be hydrolyzed 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 a buffer over a large range of pH values.

All right. In the next video, we're going to tackle 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.

Transcript for:Organik Kimya: Azot ve Fosfor Dünyası

Transcript for:
Organik Kimya: Azot ve Fosfor Dünyası