Hello everybody, this is Biology 1310 and this is the first class video on the principles of organic chemistry. You might be asking why on earth are we starting with organic chemistry? Well, it's because the first chapter of the biology 1310 is about the principles of organic chemistry. chapter that will be taken up formally, Chapter 5 in the textbook, which is on biological macromolecules, is difficult to understand properly unless you have a sense of the basic principles of organic chemistry. Now, high school chemistry is virtually a requirement for admission to the science program at UPI, so I'm sure that almost all of you know the basics of chemistry, including the concept of atoms, electron orbitals, ionic interactions, and covalent bonds.
If you haven't taken high school chemistry, or if you feel you don't have a good grasp of these things, you will have to do some extra reading on your own, particularly chapter 2 and 3 of Campbell's book. biology and also go over the resources for those chapters in mastering biology if you got that resource. I've also posted links to some good basic chemistry tutorials in Khan Academy that you can find on the CourseMoodle site. Now that high school chemistry course you took may or may not have had some organic chemistry. Some do and some don't.
As I've mentioned it is vitally important that you understand certain concepts in organic chemistry. before going into the first topic in this course. So we will go over some key things in the online notes and the class video that you're watching now. You won't be examined on this material, at least not directly, but you won't get far in Chapter 5 without having a decent understanding of certain key concepts. Now, there are six points to be made in this class video.
The first is the covalent bond number of atoms and the resulting double bond. that can occur. The concept of electronegativity, and I want to emphasize that that is really important in cell biology.
The number of functional groups that can occur on organic compounds. The numbering of carbons that are on organic molecules. Organic chemistry shorthand. And the idea of alternate configurations of organic molecules. There's certainly much more to organic chemistry than this.
but these particular aspects of it will suffice for this biology course. So let's go to our first point, that being of covalent bond number and double bonds. Organic compounds are made up almost exclusively of the elements carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. A few other elements are needed in other sorts of bonds or as cofactors, but these six are the major ones. And what we are particularly interested in right now is the number of covalent bonds.
of covalent bonds that each of these elements will form. Carbon is involved in four covalent bonds in molecules, hydrogen in one, nitrogen in three, oxygen in two, phosphorus will either have three or five covalent bonds depending on the state that it's in, and sulfur is involved in two. When you're looking at organic compounds, or non-organic compounds for that matter, you need to be aware if each atom has the correct number of covalent bonds attached to it. This becomes particularly important to consider when you're looking at organic chemistry shorthand, and we'll see some more on that later.
This is figure 2.10 in your text, that is the Campbell text, and the key thing is that each atom in each part of the figure does have the correct number of covalent bonds. Each of these hydrogens all have one covalent bond because the hydrogen atoms have one empty spot in their single orbital which needs two electrons to be full. These oxygens have two covalent bonds because, as with hydrogen, the outer orbital requires more electrons to be full, two in the case of oxygen atoms, and carbons require four through covalent sharing to fill its outer orbital. This is part of the basic chemistry that I hope you're already familiar with.
with. What I want to emphasize in mentioning all of this is that in many important biological macromolecules, atoms and especially carbon atoms can form double bonds. So for example in this compound here which is called ethane, the two carbons are each involved in a double bond with the other carbon.
But every carbon does have one, two, three, four covalent bonds associated with it. One, two, three, four with this one as well. And this double bond comes about by sharing two pairs of valence electrons in the outer shell. Carbon is not the only one that can form double bonds though. Nitrogen can as well.
Again, nitrogen has one, two, three covalent bonds involved in it and some of it is part of a double bond. And oxygen can form double bonds as well as we saw in the other slide. Here are the covalent bonds that oxygen is involved in and you see it is both as a double bond. Now, what you're seeing in this depiction is a short section of what we refer to as a linear hydrocarbon, which are the major constituent of an important macromolecule known as a fatty acid.
A fatty acid is simply a long chain of carbons and hydrogens like this, with a functional group known as a carboxyl at one end. We'll look at functional groups in a few minutes. Now, the one at the top is referred to as a saturated.
fatty acid. If you look at all the carbons they all have one, two, three, four covalent bonds. One, two, three, four, one, two, three, four, and so on.
But they're all single bonds and the bonds that are not involved in the connections to other carbons are all to hydrogen atoms. We refer to this as a saturated fatty acid because the fatty acid has as many hydrogens bonded in it as there could possibly be. I'm sure you've heard the term saturated fat before and this is what it's driving at.
Contrast to the molecule on the bottom where you've noticed that between these two carbons there is a double bond and therefore it's not quite as saturated with hydrogen's as the one on top. Note that both these carbons still have one two three four covalent bonds one two three, four, like that, there are no hydrogens here. So it's not completely saturated with hydrogen, and therefore it's referred to as an unsaturated fatty acid.
So the one on the top is a saturated fatty acid, and the one on the bottom is an unsaturated one, due to the fact that there is a double bond right here. This diagram is exactly like the one on the last slide, except it's a bit more realistic depiction of what fatty acids really look like. These are depicting a three-dimensional structure, even though it is a two-dimensional depiction. This is a bit more realistic of that three-dimensionality, and it really does fit with your scene here, but think of it this way for now.
The key thing is that the fatty acid really does have a zigzag. pattern like this and it's the result of the bonding structures of the carbons with the hydrogen's as you see over here. The zigzag pattern is very typical of a saturated fatty acid and when we look at the diagram that's coming up soon you'll see a zigzag pattern.
It is something that's very common in organic chemistry. Compare that to the one down here and you'll notice that the zigzag pattern goes goes along nicely until you get to the double bond. And what happens is when you get to that double bond in an unsaturated fatty acid, the regular zigzag configuration all of a sudden gets a bit disrupted.
And there can be a bend into the fatty acid. And that bend does have some very important functional consequences for fatty acids. We'll jump ahead to one figure in Chapter 5. specifically figure 510. What you're seeing here and here are fat molecules.
And the key thing about a fat molecule is that you have three long-chain fatty acids. Three here and three here. Note the zigzag pattern here. That is what I was talking about in the last slide. So these are just simply carbons and hydrogens.
Same as over here. with the hydrogens left out of the diagram for simplicity. We'll talk about that as well.
Note the zigzag pattern right here. This is a saturated fatty acid, and if you look at the space-filling diagram, the fatty acid turns out to be 9. and straight. When you get to the unsaturated fatty acid molecule, it goes along nice and straight until you get to that double bond, which is right here, and look what happens. The molecule bends.
That bend causes the fat to be a little bit more irregular in shape. Because of this, they push out a little bit, and there is more space between them. Therefore, at room temperature, fats with unsaturated fatty acids, which typically come from plant material tend to be a bit more fluid as you would see with this vegetable oil.
Note also that this diagram identifies this as being what's called a cis double bond. We will contrast these to trans double bonds when we consider lipids which is part of our first official topic on macromolecules. Saturated fats which we typically get from animal products tend to be nice and straight. They pack in together a little bit more regularly, and because there is less space between them, they show a greater tendency to be a semi-solid. So animal fats tend to be more like a solid at room temperature, and that's exactly what we see here in the case of butter.
We will see this critical effect of double bonds on organic molecules also when we look at the functionality of cellular membranes a little bit later in the course. Thank you. Now, our second point is on the concept of what is known as electronegativity.
This is from figure 2.11 in your text, and it depicts a molecule of water, two hydrogens and an oxygen. I think we're all familiar with that. Now there's a single covalent bond between this hydrogen and the oxygen, and between this hydrogen and oxygen. And it's the sharing of a single pair of electrons. I want you to notice that there are arrows that are pointing away from the hydrogen's and toward the oxygen.
And those arrows are a consequence of a property that all elements have which is called electronegativity. Electronegativity can be thought of as being a little bit greedy with the electrons. What happens is that the electrons in the covalent bond are not entirely equally shared between the oxygen and the hydrogen, but rather the electrons are pulled a little bit more closely to the oxygen than to the hydrogen.
The same thing is happening here. Oxygen pulls them just a little bit closer. The electrons are fully shared.
It's a proper covalent bond, but they tend to spend a little bit more time closer to the oxygen than they do to the hydrogen. hydrogens. Now, because the electrons tend to be a little bit more over here than over here, or over here, the oxygen has a very weak but very distinct slight negative charge, and that's what this symbol over here is depicting. And the hydrogens have a very weak but distinct slight positive charge. Oxigens are slightly negative because of the unequal sharing and hydrogens are slightly positive again because of that unequal sharing this is referred to in chemistry as the molecule having a dipole and this unequal sharing of the electrons has a number of very very important consequences in organic chemistry and in cell biology now again electronegativity is the tendency of an element to pull electrons closer toward itself.
All elements have some degree of electronegativity, but some are stronger than others. In general, elements with a smaller atomic mass, as you see here in this abbreviated periodic table, are more electronegative, as are those with fuller outer valence shells. And because of that, they have a higher ionization energy.
The two two most electronegative atoms that are a common part of organic molecules are oxygen and nitrogen. And those are the two that we will consider as being electronegative for the balance of this discussion. So chant yourself to sleep with this idea, alright? Oxygen and nitrogen are electronegative.
The rest we're not going to worry about. But oxygen and nitrogen. You can remember that.
You're going to go a long way. It will put a lot of other things into place. So again, oxygen and nitrogen are electronegative.
Okay. There are other elements such as halogens that have high electronegativity, but halogens are really not a big part of organic molecules. Sulfur is a bit of an exception. We'll talk about sulfur later.
It's also important to note that carbon and hydrogen have nearly equal electronegativities. This is figure 9.3 in your text, and it depicts just one example of the very important consequences the concept of electronegativity has. Over here you see a molecule of methane, which is carbon and hydrogen.
Now carbon and hydrogen, as mentioned, have pretty much equal electronegativities. And you should notice that the sharing of the electrons here, these are the shared valence electrons, you should notice that the electrons... are depicted as being almost exactly smack in the middle between the carbon and the hydrogen.
And that depiction is not accidental. This type of bond is referred to as a non-polar bond. The electrons are shared equally between the hydrogen and the carbon.
To get from a polar bond to a non-polar bond like this, you have to put energy into it. And spoiler alert! alert, that energy comes from the sun.
Watch for it. So, bonds between carbons and hydrogens, and between carbons and carbons are non-polar bonds. Now, let's take methane, put it together with some oxygen.
Again, there's some non-polar bonds, and a little bit of a spark from a match. Now, everybody knows that methane burns, and it will release energy along with The reason that the energy is released is because the electrons in the methane go from a nonpolar state to a polar state in the carbon dioxide. Look at the position of the electrons in the carbon dioxide. The electrons are much, much closer to the highly electronegative oxygen than to the not-so-electronegative carbon. And that's referred to as a polar bond.
The same with water. They're much closer to the polar bond. to the highly electronegative oxygen than they are to the not so electronegative hydrogen.
Going from a nonpolar bond to a polar bond, like that, releases energy, often in the form of heat. In this reaction, methane becomes what is referred to as being oxidized. There are a number of definitions of the term oxidized and oxidation, but in this definition, it means that you've actually lost something.
And what the carbons have lost here is some proximity to the electrons. They've gone from equally shared to shared unequally, with the oxygen getting more proximity to them. So the carbon has lost some proximity to the electrons, and because they've lost something, that's called being oxidized. The oxygen is referred to as becoming reduced, and that term is a little bit counterintuitive.
Reduced in this case means that you've actually gained something. In this case here, the oxygen, because the electrons are equally shared here, but over here in carbon dioxide, the oxygen atoms now have greater proximity to the electrons compared to the not so electronegative atoms. carbon atom.
So while they're still sharing the electrons, they've actually gained something. The same happens in water. The oxygen atoms are reduced and the hydrogen atoms are oxidized. So the idea of a polar bond versus a non-polar bond is very very important and the terms oxidation versus reduction are also very important and believe me we're going to come back to this again and again and again this is figure 2.14 in your text and this is depicting another extremely important consequence of electronegativity which is the Formation of the hydrogen bond.
Now this is a water molecule up here and as you can see the oxygen is slightly negative and the hydrogens are slightly positive because of the highly electronegative oxygen. Down here there's an ammonia. molecule. The same sort of thing is going on. Nitrogen is also highly electronegative.
Therefore, in ammonia, the hydrogens are slightly positive and the nitrogen is slightly negative. Now, when you have ammonia in water, there will be a slight attraction between the nitrogen atoms of ammonia and the hydrogen atoms of water. This is a very slight attraction that is a class of interaction called a dipole-dipole interaction. And I should point out that this is not a covalent bond.
Okay. that's really important to understand. And this very slight attraction is one of the most important forces in all of life science.
The weak attraction between the slightly positive hydrogen and the slightly negative nitrogen is called a hydrogen bond. It is virtually impossible to overstate the importance of hydrogen bonds in life science. in life science. As we shall see going forward, hydrogen bonds show up in virtually every molecular system that is of any significance to cell biology.
Hydrogen bonds will be formed between any molecules that are polar, and the way we define it being polar is basically that they contain oxygen and nitrogen. And hydrogen bonds are not only formed between ammonia and water. They can also be formed between two water molecules. The slightly negative oxygen of water, hydrogen bonding to the slightly positive hydrogens of water.
Arguably, the most important hydrogen bond system is between the water molecules themselves. In fact, some of the most important properties of water come from the fact that they form so many hydrogen bonds between them. Hydrogen bonds are responsible for the wetting capabilities of water, its ability to absorb heat, and its ability to absorb water.
to create surface tension on the surface of any pool of water. Again, it is really important to keep in mind that hydrogen bonds are not covalent bonds. They are weak interactions that are constantly being formed and broken at speeds that we can scarcely begin to imagine, but their transient nature does not diminish the importance that they have.
Electronegativity and the capacity for water to form hydrogen bonds is key to the ability of water to dissolve things among water molecules, a phenomenon known as solubility. For something to be soluble in water, it either needs to be polar in that it must contain some electronegative atoms themselves, themselves. Simple table sugar is a good example of this as we shall see. Or it must be able to be dissociated into ions such as table salt with the ions bearing a proper positive and negative charge, not a weak one. The dissociated sodium and chlorine ions each attract a shell of hydration of water molecules around them.
That shell of hydration is caused entirely by hydrogen bonds. bonds. In this figure, we see a biological macromolecule, specifically a protein, that has also attached a large number of water molecules around it. This would be known as a soluble protein, and most of the proteins that we find in cellular systems tend to be soluble. The reason that this protein is soluble will become clear in a moment, but what you should notice, though, is that the water molecules form hydrogen bonds with the macromolecule.
Water is also a little unusual in that when it transitions from a liquid into a solid, it actually becomes less dense. You can see this when you see an ice cube floating in a glass of water. The reason this occurs is that with lower amounts of thermal energy, and thus less movement of the water molecules, the hydrogen bonds are not formed and broken as quickly, thus allowing the hydrogen bonds to become more stable. form a regular structure. The temperature that this happens is of course zero degrees Celsius.
The fact that ice is less dense than liquid water is extremely important. The world would be a very, very different place if ice sank in water rather than floated. By the way, the two pages immediately before Chapter 2 in the Campbell textbook has a really, really nice depiction of the properties of water as it pertains to living systems. And you will see that hydrogen bonds play a really big role in that.
Okay, we've talked a lot about electronegativity, and we're not finished yet, folks. There's still a real... important part here.
Water and ammonia form hydrogen bonds because they are polar. That is, they have electronegative atoms that give one side of the molecule a slight positive charge and the other a slight negative charge. Any molecule that contains electronegative atoms, and remember, what are they? Oxygen and nitrogen! and to a lesser extent sulfur, just a bit.
They have the capacity to be polar and form hydrogen bonds with water and other things. The reason that soluble proteins are soluble is because many of the basic structural units of a protein, known as the amino acids, we'll talk about amino acids when we consider proteins, have electronegative atoms in a crucial position. This figure from chapter 5 in your textbook shows six of the 20 amino acids used to make proteins in cellular systems. They are the polar amino acids. And the reason that they are polar is because they are electronegative atoms.
Oxygen, oxygen, oxygen, nitrogen, oxygen, and like that. In specific parts known as the side chains. The side chains are shown here in green.
Thank you. We'll consider the structure of amino acids and proteins in more detail in the next section of the course. But for now, I want you to take note of the fact that there are electronegative atoms in those places.
And that is what makes them polar and allows them to form hydrogen bonds. Now, one other thing. You may have heard the terms hydrophilic and hydrophobic.
Hydrophilic means that it attracts water, and hydrophobic means that it repels water away. Polar molecules attract water so polar molecules are called hydrophilic and nonpolar molecules, the ones that don't have electronegative atoms, will tend to be hydrophobic. We'll use those terms quite a bit in what's coming up as well. Okay, we're done with electronegativity finally.
Well, we're not done with it because, believe me, it's going to be a big topic going forward. But we can go on to our third point here. The third point to be made about organic molecules...
concerns their versatility, which is a consequence of the nature of the carbon atom and the various things that can be bonded to it. Indeed, organic chemistry is the study of carbon-based compounds. It's no particular accident that that living organisms are carbon-based. For one thing, they're able to form up to four covalent bonds with other elements.
This is the simplest organic compound called methane. It is simply a carbon atom bonded to four hydrogen atoms. Unfortunately, I'm trying to show you a three-dimensional object on a two-dimensional plane, but there you go. The key thing to appreciate though is that the four More bonds emanating from the carbon atom are spread out with every angle between every two bonds being approximately 109 degrees. And that gives a lot of room to form some really novel structures.
This shows you just some of the things you can build with just a few carbons and hydrogens. Each of the structures have very distinct chemical properties. And again, they're all just carbon and hydrogen. But organic compounds are more than just carbon.
than just carbons and hydrogens. What really gives organic molecules their versatility are the various functional groups that you'll find on them. In this depiction of a molecule of glucose, down here on the bottom left, you'll see that five of the six carbon atoms have what's called an OH group bonded to it.
And that OH group is referred to as a hydroxyl. Hydroxyls are one of the seven functional groups that are very important. in organic chemistry.
I want you to be familiar these seven. I'm not going to go into a lot of detail about what functionalities these groups give to organic molecules, and you'll get more of that as you go through your course in organic chemistry. But for the purposes of this course, you...
you should be able to recognize them and place them in some sort of context. The hydroxyl group is typically associated with alcohols, as you see here in the chemical formula for ethanol. So, that in glucose, five of the six carbons have a hydroxyl group. We'll come back to that when we look at the saccharides.
The second group that you should be able to recognize is called the carboxyl group. It is comprised of a carbon double bonded to an oxygen and then also bonded to an OH. Carboxyl groups are found on organic acids such as acetic acid, which is the acid you get in, say, lemon juice.
And it's... any aqueous solution, which of course is what we find in the cellular environment, that hydrogen will dissociate as any acid will. And we will see the carboxyl group on a number of organic compounds coming up.
The third group that you should be familiar with is called the carbonyl group. It looks a little bit like a carboxyl group, except that it's not necessarily found at the end of an organic compound. And what it is at the end, it does not have have an OH group bonded to it. When a carbonyl group is found at the end of an organic compound, it is referred to as an aldehyde. In the diagram of linear glucose, let me just go back to that.
There we go. There's a carbonyl group and this makes it an aldehyde sugar. We'll talk about that in a bit. And the carbonyl group is found internal to the molecule. it's referred to as a ketone.
Aldehydes tend to be somewhat volatile and aromatic. In biology, an aldehyde that you're likely to be familiar with is formaldehyde, which is a very, very good preservative for biological specimens. Among the properties of the ketones are the tendency to be good solvents.
Acetone is a really important one and is used particularly in organic chemistry labs. The fourth group that you should... be familiar with is called the amino group and it is a derivative of ammonia and is normally found in an ionized form with an additional hydrogen ion and this technically it's a base there are amino groups in a number of important biological macromolecules and you're most likely familiar with the building blocks of proteins the amino acids and this is where they get their name the fifth group that you should be familiar with is called the sulfide hydral group. And the key significance of the sulfhydryl group is on one particular amino acid known as cysteine.
And cysteines allow proteins to form very strong covalent links to stabilize protein structure. We'll be looking very closely at this when we consider the proteins in chapter 5. The sixth group that you should be familiar with is the phosphate group. Phosphate groups show up in a number of important biological macromolecules, including the nucleotides which make up nucleic acids like DNA and RNA, and also ATP, which is the universal mediator of energy in cellular systems. And the final group that you should recognize is a methyl group.
The methyl group, as you can imagine from its name, is a derivative of methane. and it is often added to nucleic acids in order to protect them from degradation by certain enzymes. DNA that has had methyl groups added to it is also called methylated DNA.
The fourth point to be made in our basic understanding of organic molecules is that on every organic molecule, the carbon atoms that make up the organic molecules are numbered. Now this, again, is a linear form of glucose, and note that all the six carbons are given a number from one to six. The numbering system is very important in describing the chemical structure of organic compounds and of naming them.
Here is just one example of a reasonably simple organic compound that uses that numbering system. There is an OH group which makes an alcohol and carbon number one, an amino group on carbon number two, and this is referred to as a phenyl group. which is on carbon number three, which would be right here. We'll get more into that later. The numbering and naming of organic molecules is subject to rules set out by the International Union of Pure and Applied Chemistry, or IUPAC.
And I will leave it to your organic chemistry course to give you a fuller understanding of how this works. But for the purposes of biological macromolecules in this course, we do kind of need to know it at the fundamental level. A key thing to knowing the number of each carbon in the organic molecule is to look for the one that has given the number one position.
A rather over simplified but largely correct way to do this is to look for the terminal carbon at the end of the organic compound that is the most distinctive. In this depiction of linear glucose, you see that almost all of the carbons have a hydroxyl. group attached to them. But this carbon is distinctive in that it is the only one that has a carbonyl.
Therefore, this end of the molecule is more distinctive than that end. And since this terminal carbon is on the most distinctive side, we call this the number one carbon. Okay? And you number it from there. And again, the way I'm describing this is rather oversimplified.
but its basic elements are largely correct. Why does it matter? In biological macromolecules, and especially in the nucleic acids, by the way, there are a number of references to bonds and modifications of particular carbon atoms.
What you see on the left of this figure from your textbook is a cyclic or ring form of glucose. It is formed when a number one carbon is bonded to the number five carbon. carbon on glucose, thus forming a ring, with the number 6 carbon sticking out as a type of side chain.
The numbers on the various carbons are the same as when they were in the linear form. Therefore this carbon that was bearing the carbonyl in the linear form is still number 1, this is still number 2, number 3, and so on. The importance of this will become particularly clear when we consider the nucleic acids. This figure also brings to the fifth point that I want to make, which concerns organic chemistry shorthand.
When depicting organic molecules, carbons are often left out entirely and are just replaced by angles. And here are some examples of this convention. This one I showed you earlier is when you have a long chain saturated fatty acid.
Each angle in the zigzag is a carbon atom. atom. Note also that only two bonds seem to be connected to each of these carbons, and when this occurs you should assume that the other two bonds for that carbon are taken up with hydrogens, which are also often emitted in these shorthand depictions. This one on the bottom I showed you a little earlier as an example of a compound that requires the numbering system for proper description and naming.
In the case of this particular carbon there are three three bonds emanating one, two, three, so you would assume there would be one additional hydrogen atom involved. In the case of this carbon right here, right on that angle, there are one, two, three, four bonds coming out of it, so you see that there would be no hydrogens involved in that one. This figure in the middle is taken from one you'll see in a little while when we consider the carbohydrates. Each of these rings is a glucose molecule and this has been a very common way to depict a six carbon ring form sugar in short.
Note that the hydroxyl groups have been omitted as well. Even the number six carbons have been omitted. The main thing to take out of this though is that in organic chemistry shorthand angles are carbons. Sometimes you might have to fill in a few other blanks by just remembering those rules. The sixth and final point that I want to make in this consideration of the basics of organic chemistry is that many organic compounds can be found in isomeric forms.
That is, they have the same chemical formula but are bonded differently so that the chemical properties have changed, sometimes in really substantial ways and sometimes in minor ways, yet all are biologically relevant. There are three levels that we need to mention. The first level is referred to as a structural isomer. This is where you have two compounds that have the same chemical formula, but the bonding framework is noticeably different. The example given in the textbook, figure 4.5, is that of butane and isobutane, where one form is linear and the other form is branched.
You can see that in butane, none of the carbons is bonded to all of the other three carbons, while in isobutane, one of the carbons is bonded to all of the other three carbons. And that's what we mean by a very different bonding framework. The second and third levels are types of what we call stereoisomers. Stereoisomers have the same bonding framework, whereby the same things are bonded to the same things, but just in slightly different orientations. There are two types of stereoisomers.
two types of this. What is depicted here are called enantiomers. Enantiomers are stereoisomers that are mirror images of each other and can be superimposed as such.
Often they become referred to as the left-handed or the right-handed form. Also the L form and the D form. There are a couple of others as well but this is enough for now. What is depicted here is the two isomer of the amino acid alanine.
Remember this is a three-dimensional object, okay, keep that in mind. Suppose you place both forms of the amino acid side by side such that the carboxyl group is sticking up and the methyl group is sticking out towards you. In one enantiomer the hydrogen would be on the left and in the other enantiomer the hydrogen is on the right.
Again mirror images of each other. The reason The reason this is important is because in biological systems, the L-form of amino acids are the only ones that are used in the synthesis of proteins. There are some minor exceptions to this, but for the most part it is correct. And just to drive that point home, I really like this figure and he's a great actor too.
The third level are the cis-trans or geometric isomers. It is the other type of steroid. isomer in that the basic bonding framework is the same but there is a change in orientation at at least one position such that the isomers cannot be considered mirror images of each other. A very important example of this is shown in the ring structures of glucose which you see on the bottom here.
The isomerization concerns the position of the hydroxyl around the number one carbon. The two-dimensional depiction you see here here, in what's called alpha glucose, the hydroxyl is pointed down. While in what's called beta glucose, the hydroxyl is pointed up and away from the number 2 carbon, which is right here.
These depictions are not scientifically precise in that these are three-dimensional structures, not two-dimensional, but it does reflect a very real difference in the position of the hydroxyl on the number one carbon. The reason that is important is because making a polymer of alpha glucose gives you a very different product than making a polymer of beta glucose. Polymers of alpha glucose give you starch, while polymers of beta glucose give you cellulose.
I'm sure most of you can appreciate the biological difference between those two. Okay, that's it for our consideration of the fundamentals of organic chemistry. We'll deal with more of this when we gather, and you should now be ready for a section on the biological macromolecules, okay?
I just want to remind you that I I'm not going to test you on this directly, but only in the context of what's coming up in the course. So for chapter five onward, and this will naturally wind its way in. And it's only in the context of the course that this material is actually going to show up on any sort of exams that I give you.
OK, so thanks for listening to this first one and bye for now.