We're beginning our new unit now on the molecules of life, also called organic compounds. And so today we're going to talk first of all about some of the basic things about carbon compounds in general. And then we'll spend some time on a couple of different videos talking about the different classes of the organic molecules.
So here are the vocabulary terms that will be appropriate to learn in this unit. You can see here you can pause the video if you need to and write down the terms, but we'll be referring to these terms. throughout the notes as we go through these are more or less in the order in which they will appear in the notes so pause the video take a picture whatever you need to do write the words down as we see them in the notes will be in red and also remember that the things that you really need to make sure you write down in your notes are the purple things so organic compounds like it says here on the screen they're molecules that contain carbon the reason they're called organic is because because people who study these things first thought that they were only found or made by organisms.
We've since learned that isn't true, but that's how they got their name originally. We talked some about carbon in our last unit when we talked about the basic chemistry information, and the thing that's interesting about carbon is it lets it make very large and complex molecules. Since each carbon atom is able to share electrons in four covalent bonds, remember the added...
The valence level or the outer energy level here can hold up to eight electrons. Carbon has four. It would really love to have eight to feel complete. Carbon very often shares its electrons with other atoms. And so it can share up to four pairs of electrons to make those four covalent bonds.
And covalent bonds are very strong, so that's really good because it makes nice strong compounds. Not only can it bond to other elements, it can bond to other carbon atoms to make chains or rings of carbon atoms, which is really important. to the basic structure of organic molecules. So we've got a lot of different kinds of molecules that get formed with this basic substance that makes up the backbone basically of all of these organic molecules. There are some organic molecules that have only hydrogen and carbon, so we call those hydrocarbons, which makes sense, hydro for hydrogen and carbon.
Things like methane, butane, gasoline, other kinds of fuels like that are hydrocarbons. Now you can see in the pictures here that we have different kinds of formulas that you can see. Here's a structural formula.
Remember as we talked about before each one of these lines represents a shared pair of electrons. Whenever you see a structural formula like that and you see the lines that means one shared pair of electrons, one from the carbon, one from the hydrogen. If you see a double line that means the two shared pairs of electrons, a triple line would mean three shared pairs of electrons and so forth.
This is another kind of model. This is a ball and stick model. This shows you more or less the three-dimensional shape of the molecule. In the case of methane, which is what this is, methane is like natural gas. It shows the three-dimensional tetrahedral structure that forms from the bonds between the atoms in the molecule.
This is a space-filling molecule, a model to show you more or less how much space is taken up by the different... by the different atoms in the molecule. One thing to realize is that that carbon in this case, just hydrocarbons, don't make polar bonds. These are non-polar covalent bonds. There are some instances that are polar bonds but these particular elements, carbon and hydrogen, are not as electronegative as something like oxygen so they don't have an unequal sharing of the electrons and therefore we don't get that polar bond that we saw in the water molecule.
Here are some examples of carbon bonds. This just shows you the molecule. This is the molecular formula and the structural formula, the bond stick and the space filling model. You can see how many electrons are shared.
This particular one here has two carbons and six hydrogens. This is called ethane. Ethane has this arrangement right here.
It has each carbon has four covalent bonds. One covalent bond here between two carbon atoms. This is another molecule that is similar but not the same.
Notice this is ethane. This one is called ethene and it only has four carbons but the carbon atoms are double bonded to each other so that represents two shared pairs of electrons but still if you count each carbon has one two three four and one two three four bonds. Ethine which is another variant of this has a triple bond between the two carbons so they share three pairs of electrons together. and only one pair with the hydrogens. So those are slightly different versions of a very similar molecule.
Notice we have a two carbon backbone and it has different arrangements of the hydrogens attached to it and the bonds between the carbon atoms. Now those are called there are some times when you have the same chain or skeleton. There can be different shapes. There's branches like you see over here. These are just a plain chain as you see in ethane and propane.
Butane is here like this, but you can also have isobutane which has a branch there. That's a different kind of structure. It shows the location of the double bonds can be different and we name them differently because of that.
Sometimes they're in a ring type structure that can have either single bonds or double bonds. Oftentimes when you see a ring structure like this you'll see in a structural formula just the ring. It's assuming that you realize that since it only shows single lines between the carbons understood to be at the angles here that each one is bonded to two hydrogens as well. When you see the double bonds you should realize that this carbon is double bonded to that carbon and it has only one hydrogen there in each one. Two compounds that have the same chemical formula but different structural formulas are called isomers.
Here we have isomers of butane you see butane has C4H8 H10 I'm sorry and isobutane if you count up the carbons and the hydrogen you'll find that it's the same formula C4H10 but they're arranged differently those are called isomers and that has an effect on the way the compound reacts in various kinds of chemical reactions there are also special groups of atoms that can be attached to the carbon skeleton. These are called functional groups. And functional groups affect the way the compound reacts or how it functions.
A lot of these groups, not all of them, but a lot of them are polar. And that makes them hydrophilic and water-soluble. There are a few that are non-polar. But most of the ones that we'll be talking about will be polar.
And so that leads to polarity, which affects the shape of the molecule as well. Polar interactions, hydrogen bonding, and so forth can occur. So hydrogen bonding doesn't occur just with water molecules.
It can occur with other molecules that have polar bonds. Here we have some important functional bonds, and we'll talk about several of them here. You need to be able to recognize these. You don't necessarily have to know always what they appear in, although there are some characteristic things that you will need to know about some of these. A hydroxyl group, remember we talked about the hydroxide ion.
that OH ion is present in bases, well if it's attached to another molecule it's called a hydroxyl group and we find the hydroxyl group in alcohols and also in sugars okay and it shows you here is the group and here it shows you in an alcohol molecule this molecule here is ethyl alcohol or ethanol another group that you find is a carbonyl group. The carbonyl group is a carbon double bonded to an oxygen Since we know that oxygen is very electronegative and has a strong attraction to the electrons, you can tell that anything that's going to have oxygen is going to have some polarity to it. The carbonyl group can be found at the end of a chain or in the middle of a chain.
In the case of sugars, or in the case of any of these really, if you find it at the end of a chain, it's called an aldehyde, and in the middle it's called a ketone. You do not necessarily have to know that, and you're not going to really be asked to identify. whether it's an aldehyde or a ketone, but that's one thing that we use to differentiate different things.
So when you talk about something like formaldehyde, it's going to have this group on the end. A carboxyl group has a C double-bonded to an oxygen, and then it also bonded to an OH. We often see it like this, COOH, or COO, sometimes we call it.
When you see it in a structural formula, it's often like this. This is a carboxylic acid, which means that it's got the carboxyl group. then the rest of the molecule here makes an acid. It can easily be ionized because, again, we've got polarity here, so we can lose that hydrogen ion, hydrogen proton ion to another molecule, and that'll leave that negatively charged there. And so since it donates hydrogens to the solution, then it would be an acid.
An amino group, NH2, acts as a base, and it acts as a base by picking up a hydrogen ion. And so if it could pick up that hydrogen ion from that carboxyl group, and here you'd have the ionized form, so this is an amino group. A phosphate group is PO4.
There are lots of different phosphates we'll talk about in lots of different kinds of things. They're found in lots of different kinds of molecules. An example of one right here is adenosine triphosphate.
It has three phosphate groups attached to it, and that's really important when we talk about energy transfer from one place to another in cells. A methyl group is one of the nonpolar groups. A methyl group is like methane with one of the hydrogens removed, and when it's attached to the rest of the chain, it makes something called a methylated compound. And it's nonpolar, so it doesn't mix with water very well at all.
So here's just another diagram showing you the kind of a summary of all of these functional groups. This table is from your book in Chapter 3, so you can look at that and see those if you need to look back at those. But these are important ones that we'll see over and over again in lots of different compounds we talked about.
So hydroxyl, carbonyl, carboxyl, amino, phosphate, and methyl. You should be able to recognize those when you see them. So the reason these groups are called functional groups is because they affect the function of the molecule. When you change functional groups on a compound, it can change the whole different thing, whole different way it reacts in the organism.
An example of a really big, important example that you're probably a little more familiar with than others would be the difference between estradiol, which is estrogen, and testosterone. Notice they've got the same fused ring structure here. You see all these different rings attached to each other, but look at the different functional groups. Now they've got the hydroxyl and the methyl up here at this end. but look at testosterone it's got a methyl group right here and it's got the carbonyl group on this end whereas the estrogen or estradiol is missing this methyl group on this on this carbon and instead of an oxygen double bonded there it now has a hydroxyl group very similar in structure they're both hormones but they cause very different reactions in the organism that they occur in now there are four classes of organic molecules and we're going to talk about each one of these in turn this is just basically the background okay the four classes of organic molecules are carbohydrates lipids proteins and nucleic acids these are all gigantic molecules called macromolecules and they're all made up of smaller subunits the smaller subunits we call monomers and when you put them together they make a polymer and so we're going to talk about the monomers and the polymers in the future lessons on the different kinds of organic compounds So that you'll know, we'll talk about the monomers of carbohydrates and the monomers of lipids and of proteins and nucleic acids.
And then the big molecules that they make when they put together again are called polymers. How in the world do you think they're put together? They're put together by a method called dehydration synthesis. Now if you think to what you know dehydration means, dehydration means removing water from something. The monomers in organic compounds are covalently bonded by this reaction called dehydration or dehydration synthesis.
So all of these monomers, every single one of them is going to have a hydroxyl group at one end of a molecule, and another one is going to have a hydrogen at the other end. When you bind two of them together, one of them loses a hydroxyl group, the other one loses a hydrogen group. Hydrogen and hydroxide together make water, and then that causes an open place there where the two molecules, smaller molecules, can join together, and that forms a covalent bond. then it produces water so you're removing water to synthesize or to make something here's how it works okay here's that here's one monomer and here's another notice this one has they both have a hydroxyl group on one end and a hydrogen on the other since these are the ones that are close together they're gonna they're they're gonna be drawn together there's gonna be an enzyme that will help this if we remove the hydroxyl group and the hydrogen group here together those make water and then we can bond this to this and now we have a longer polymer And when we're making some of these gigantic molecules, this happens over and over and over again. We have some of these molecules that are thousands of subunits long, thousands and thousands of them.
Now, sometimes you have to break them down. For instance, when you eat your food, you're breaking down the complex molecules in the food in your digestive system. And the way that's done is by an opposite kind of reaction called hydrolysis.
Hydro means water. Lysis means break or split apart and so what we're doing now is we're going to add water back and split those molecules apart. It's pretty much the opposite reaction of dehydration synthesis.
This is exactly how your food is broken down in your digestive system produce the nutrients that can then circulate through your blood and be used by your cells. So here we have our longer polymer and we have an enzyme that assists this activity as well. And it's going to add water back in, so the hydroxyl group is going to be added to one part of the molecule and a hydrogen to the other part, and then we have our two parts that we started with.
Here's a little video to show you how this works. Here we have two sugars, and we're going to take a hydroxide off of one and a hydrogen off the other and make water and bond those together. And this forms something called a glycosidic bond, which is what you call it when sugars join together. And this makes a... more complex sugar called a disaccharide.
And then hydrolysis does exactly the opposite. It takes that off and then you have your two monosaccharides. Same type process.
Now we have lots and lots of different kinds of macromolecules made from, like it says here, about 40 to 50 commonplace things that are put together. There are a few others that are a little bit more rare, but generally speaking, 40 to 50 common parts that can be put together to make lots and lots of different kinds of molecules. This variety or this difference of all these different kinds of compounds that can be made is what makes all the different organisms of the world unique.
So every... species is different from every other even individuals within the same species are unique from every other one. The monomers though can be used by any organism in any place to make the component parts that they are going to need and that's what's really interesting and cool about organic molecules. We're going to end this lesson here and the next lesson will be about sugars.