Organic Molecules

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Although we don't like to think about it that much, we, like everything else in this universe, that's made up of or not made up of energy, we're made out of molecules. Scientists realised this a long time ago, but still wanted to think we're special. So they decided that we have 'organic molecules' while things like dirt, air, they're made out of metal, those are inorganic and we're special. Oops! Turns out we're not. We still have to follow the same rules as all those inorganic molecules. But we're still kind of stuck with this nomenclature so that we still talk about organic Chemistry and inorganic Chemistry. And we also wind up with some weirdly arbitrary definitions where things like carbon dioxide gas, even though it has got carbon in it, it's declared just an inorganic molecule. Because it turned out that all those organic molecules, what's the basic thing behind them, is that they're made out of carbon. And it's because carbon can form these long chains or these rings that give the great diversity of the organic molecules.

So you really need to know about organic molecules for the AP biology test. Both because, they will ask questions on it and because their properties underlie a lot of the basic properties or things that go on in Biology like proteins, specificity or membrane function.

So I'm going to begin with the simplest of the organic molecules, the carbohydrates and continue then with the fats and lipids. Third, I'll go through the proteins, very important topic and finish off with the nucleic acids.

As I go through these groups of organic molecules, I'll begin by mentioning some of the common examples to give you a context for what I'm talking about.

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Then I'll describe the monomers, the basic building blocks that can be joined together to form the larger molecules called polymers. Then I'll finish off by going through some of the major functions of each of the groups of organic molecules.

So to begin with the carbohydrates, you can probably already hopefully mention off some common examples of carbohydrates. These are things like glucose, fructose, lactose, cellulose, starch. You may notice that a lot of them all end with the word 'ose'. That's one of the tips that you can use to fake you're way through some parts of the AP Biology exam. Because if you see something that ends with 'ose' then it's a carbohydrate. You don't even need to know what it is. If you see the word amylose, it's a carbohydrate. So let's look at the monomers, the basic building blocks that are used to build the rest of the carbohydrates. The monomers of carbohydrates are called monosaccharides, where mono means one, saccha means sugar. So this means one sugar, or simple sugars.

The monosaccharides of the carbohydrates are typically groups of three to eight carbons joined together with a bunch of hydrogens, and OH groups, or hydroxyl groups they're called. So we can see here an example of ribose which is a five carbon sugar, and glucose which is a six carbon sugar. Now these five carbon or six carbon sugars, can very often not only be in these what are called straight chains, but they can manoeuvre and join to form ring structures. Let's take a look at what happens with glucose.

So you could see glucose has a group of six carbons and a linear form or straight chain form, or forming this ring structure, the hexagon shape. So if you are looking at a AP-Bio multiple choice test question and you see this hexagon shape, or pentagon shape for a five carbon sugar, you know it's a monosaccharide, a carbohydrate. So that's a big clue, just look for these multiple hexagons formed in long chains.

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When you're trying to form a disaccharide that's when you put two of them together. And here we see glucose plus glucose to form sucrose, a disaccharide. You know 'di' means two, di-sugar, two sugars put together. So glucose plus a fructose, forms a sucrose. Now you'll notice to get them to join, we need to pull off a hydroxide group, an OH from one, a hydrogen from the other, and that forms water. And we're left with this oxygen here forming the bond between those two. Because we're removing water to do this, this is called dehydration synthesis. So this is putting things together, 'de' remove, hydro-water, dehydration synthesis.

Can you guess what would happen if we were breaking it apart? You've got it, hydro means water. You may recall in other videos I've talked about lice meaning to split or break. Hydrolysis is if we ran this backwards, where we split this two consuming a water.

All of us you me, everybody, every human, has the enzyme that can break this bond to do that hydrolysis. There are some other sugars, if we put a glucose together with let's say fructose, if we put it together with a monosaccharide called galactose, we would form a molecule called lactose. You may have heard of that. Lactose is a sugar commonly found in milk. Again you need an enzyme to break that because while monosaccharides can be absorbed easily in your small intestine, disaccharides are too large to fit through the walls of the small intestine. So if you don't have that enzyme to break lactose, that lactose winds up in your large intestine. You may have heard of people who are lactose intolerant, which means they lack the enzyme, lactase enzyme, that is needed to break up lactose. So, some poor guy wanted to just eat some ice cream and later on he winds up having issues because instead of him absorbing the lactose sugar, all the wee beasties that are living inside of his large intestine they go 'uh yummy!' and they start going to town and he starts having issues.

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Now what if we put a whole bunch of them together. Putting together a whole bunch of molecules together. You know from Math, poly means many, like polygons. Well a whole bunch of sugars put together is called a polysaccharide. Now, a couple of common polysaccarides include starch which is made of a group of glucoses joined together. Well there is another one called cellulose, which again is made out of a bunch of glucoses joined together. What's the difference is exactly how the glucoses are joined together. Notice here how this CH2OH group is always above the plane? Here it alternates, left right. We can break down starch. So if I sit here... my body can break down the starches that make up things like apples or potatoes, because I've got an enzyme called amylase. The proper name for starch is amylose. But to break cellulose, I would need a different enzyme. And it turns out almost nothing on this planet has the enzyme to break apart cellulose. So if I sat here and try to do this, instead of getting yummy nutrition, I get splinters in places I don't want splinters.

Who does have it? It's a few bacteria and a few single celled creatures called prototista. You may realise there is lots of things that eat cellulose, that eat wood. Well, what are those creatures? They are things like cows and termites. How do they get any nutrition from it? Inside their guts, they actually have colonies of these bacteria or these protista breaking down the cellulose for them and sharing the glucose that's coming out of that.

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Now, another example of a polysaccharide is a special polysaccharide called chitin, which is used only in fungi and in arthropods to make up their exoskeleton shells. And that leads into one of the major functions of carbohydrates. Carbohydrates are used for a lot of cellulose structures. The cellulose I mentioned before forms the structural outer cell wall of plants cells, while chitin is used to make the cell walls of fungi. It's also used to make the shells like I said of arthropods, things like the lobsters or bugs. The other major function of the carbohydrates is energy storage, whether it is starch or the simpler sugars glucose or the nice sugary sweet sucrose that we love on our cereal in the morning.

Carbohydrates aren't the only energy storage molecules, obviously fats are a big player in that. The lipids are a big group, ranging from the things that we may know like the triglycerides, which are fat. Which we're all familiar with, and some of us are a little bit too familiar. To things like the testosterone, which is a steroid hormone that has been screwing with your body since puberty. To the not so familiar, phospholipids. Now, as a group, unfortunately the fats and lipids don't have a common monomer like the carbohydrates do with the monosaccharides or the proteins do with the amino acids. So unfortunately, they are all grouped together not because of some common structure, but because a common behavior. They're all the rejects. That is because they don't dissolve well in water. They're called hydrophobic and that's because they don't have the ability to do what's called hydrogen bonding. Let's take a look first at one of the two major groups which are the triglycerides and phospholipids and they will have a common structure that we can see here.

You see this three carbon molecule there, that's a molecule called glycerol. The triglycerides, you can hear the 'glyc' and the phospholipids share this carbon-carbon-carbon chain.

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Now in the triglycerides, the fats attached to each of the carbons in the glycerol, you'll have these long chains of carbons with hydrogens on them. These are called fatty acids. wWereas with the phospholipids, you'll see the wiggly fatty acids here. But and on that third carbon, instead of having a fatty acid, you'll have a phosphate ion attached to it. Now, notice how each of these is kind of lined up and this little wiggly line there represents one of these carbon chains. Notice how this one is bent, that's because this is what's known as a saturated fatty acid, while this is an unsaturated fatty acid.

You may have seen food labels where they have to list the saturated versus unsaturated fats. And there is two kinds of unsaturated fats. There is trans fatty acid and cis fatty acids. All you need to know really on that is see how this one is bent, that's a cis fatty acid, that's good. If it was one of these triglycerides, if they had a bent one here, because those trans fatty acids stay in a straight line like these guys. And they cam make easy big stacks of triglycerides in your bloodstream clogging them. While the cis fatty acid is with their bend, they can't form bid clumps. So the cis fatty acids, those are good because they can help dissolve the big chunks of fat into smaller chunks of fat. A little bit of health issue there.

The other big group or structural group of the fats and lipids, are the steroid molecules. They have lots of different things attached to it but, all the steroids share this 1, 2, 3, 4 ring structure. And whatever is attached to the outsides of that, make it different from one to the next. In your body, all of the steroids hormones are made using the steroid core that you get from the cholesterol in your diet. So we always talk about cholesterol being bad.

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It's bad on high levels but if you didn't have a certain level of cholesterol on your diet, you couldn't make testosterone and oestrogen and all the other steroid hormones that you need in order to maintain homeostasis and be healthy.

So what are the functions of fats and lipids? Well they are pretty wide ranging. They range from, obviously the energy storage of the triglycerides, the fats. But fat does more than just store energy. It also provides insulation. Both against heat loss and electrical insulation in your brain provided by a special fat called myelin. They also help protect and cushion against shock, whether it's the fat in your derrière or the pads of fat behind your eyes. So that when you're going jogging eyeballs aren't bounce around and popping. There are also of course those steroid hormones testosterone and oestrogen that I mentioned before, forming signalling compounds in your body. And then those phospholipids that I mentioned previously, they form the cell membrane. And it's their chemical behavior that gives the cell membrane a lot of its properties.

The last fat that you may see mentioned on the AP exam, would be the waxes. I mean again because the waxes are hydrophobic, they prevent the movement of water across them. And that's why we have waxes in our ears to help prevent our eardrums from drying out, or plants will have a waxy cuticle. That a word to remember, to get that extra little point there in the essay about leaf structure. The waxy cuticle prevents water loss at the surface of leaves.

So while carbohydrates and fats are really good at storing energy and they form some important structural parts of the cell, it's the proteins that are the real work forces of the cell. What are some proteins you may have heard? Well there is keratin. The stuff that makes up finger nails or hair. There is enzymes like the lactase enzyme that we mentioned before, amylase. There is myosin. It's one of the two major contractors or proteins found in muscles.

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So these are some common proteins or another one that you may see on the AP exam, will be albumen, which is that egg white protein. So what are the basic building blocks or monomers of proteins? There are structures called amino acids. Let's take a look at one amino acid.

All amino acids and there is roughly 20 of them, share a common structure. They have a central carbon that's often called the alpha carbon. On one end, you'll have an amino group. And in some textbooks, depending on the pH that the solution is at, you may see 3 Hydrogens instead of the two here. On the other end you'll have the carboxyl group, which again may have lost that hydrogen depending on the pH.

Down of the alpha carbon, you'll find a single hydrogen by itself. And then up here you'll find one of 20 different possible R-groups. I'm not going to have you take a look at all of them, you can easily find those in your textbook. But let's take a quick look at some of the various R-groups. And it's the R-groups that make each amino acid unique. Now I've often thought of amino acids kind of like train cars. There's box cars, flat cars, passenger cars, dinning cars. But all train cars share a common structure the wheel base, the axils and etcetera. And that's kind of like the amino carboxyl group with the alpha carbon and it's hydrogen.

What makes each train car unique, is what on top whether it's a group of carbons, that's a passenger car or if it's a big flat platform with some tie downs that's a flat car. And it's these R-groups here that make each one unique.

To join them together, much like how you join train cars together, what you do is you'll take an OH group off a carboxyl of one peptide, or amino acid. Peptide is an old name for amino acids. And you'll rip off a hydrogen from the amino of the next amino acid. And by doing that, we pull out a water, and now we've joined together our two amino acids. They call the bond that holds the two amino acids together, between the amino of one, and the carboxyl group of the other, they call that a peptide bond.

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Again, because the old name of the amino acids was peptides, that's also why an amino acid chain which is a group these all hook together, is sometimes called a polypeptide.

Now, when scientists were first starting to study proteins, they run into a problem. Remember those R groups are extremely variable, and they have different chemistries. Some of them are negatively charged, some of them are positively charged. Some of them are non polar or hydrophobic R groups. And so they all start to form up into these really complicated tangled up masses.

And initially when scientists were first studying this, they just couldn't make sense of it. It'd be kind of like if I handed one of the Lord of the Rings books to a kindergarten. So what I'm going to do is, I'm going to take you through the different levels of structure, because initially, the only thing that scientists could figure out was, the different amino acids in the chain that makes up the protein. They couldn't figure out anything beyond that. Just like the kindergarten over the Lord of the Rings book, all he could figure out was the sequence of letters. If you asked him what's it about? No idea. So let's take a quick look at a video from YouTube that takes us all through four layers of a structure of a protein.

Here is that video I was talking about at YouTube. Let's make it bigger so it's easier to see. Now all these little balls here, those are amino acids. So let's go ahead and we'll put them together, and that's what a ribosome does. Is it builds a peptide bond between each one. Now let's pause it here.

This sequence of amino acids and these are all just the abbreviations of the real amino acids names. If I went along and I rattled off each amino acid in sequence, that's what's called primary structure or one, the first level of structure. That's the simplest thing. That's again like that kindergarten who's saying, "The first letter is T, the next letter is H, then E then a space." Again ,it doesn't tell you what the protein can do but it does tell you some information.

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If we let it continue though, let's go ahead and start it up, the video again. You'll see that the R-groups of the amino acids start to interact with each other, and they start bending and whopping portions of it in space. Well let's pause it here. This is called the secondary structure.

The secondary structure is what's going on? What are the interactions? Well I see this part of the chain here, is in parallel with that part of the chain over there, and again over here and here. And then this area here start to spiral up. After some hard work, scientists started being able to figure out, "Okay, we know that all these areas here, all the R-groups are all say negative and positive." They'll start curling towards each other and that may form a spiral. That's called the secondary or second level of structure.

And that's kind of like, if a third grader read Lord of the Rings. He might say, "Look in this chapter, they are fighting oh it's cool and then in this chapter, photos winding again." Again he doesn't really know about the big grand sweep theme of the book that he's reading, but he can tell what's going on in small sections.

Let's start that up again and we'll look at the third level or the tertiary structure of a protein. So again this is the alpha helix, that's called a Beta pleated sheet. That parallel ripple effect. Now you can see some of these lines here represent the hydrogen bonds, and other forms of bonds that are helping hold it in its shape. Let's pause it here, the tertiary structure.

The tertiary or third level of structure is the 3D shape of the protein. That's kind of like what the heck happened in that novel? If you read Fellowship of the Rings, then you know what happened. And that's something that a high school kid can do with a novel. They can get a great idea of what's going on in the book. This took scientists a lot of scientists a lot of time to figure out. And it's only after investing years or decades of effort, that they can figure out the 3D or tertiary shape of a protein.

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Nowadays however with modern computers, this kind work can be done pretty quickly. Instead of a year or decade, it could take as short as a couple of months, or even faster.

Now with a lot of proteins, that's it. You've figured out it's three dimensional shape, that tells you what kind of molecules can it fit to, how does it interact with other things. But some proteins are actually made out of more than one chain of amino acids. And again we can still see here's the chain. Now, some proteins are made out of multiple chains. And here we see those ones coming in. Let's pause it real quick before it goes to the end. And we can see the yellow chain has to fit onto this blue guy, the red one has to go in there. And that's, again if I go to to the Lord of the Rings, that is not a single novel. It's actually a trilogy. And if you just read Fellowship of the Rings, and you thought, "That's it? You know what's the heck, they are just going off in different directions. What's up with that?" You need to know how those Fellowship of the rings fit in amongst the other two books for you to really understand what's going on.

So again, there's the four layer of structure within a protein. There is the primary structure, that's the sequence of amino acids from start to end of a chain. As you relax in tension, you'll find that some parts will spiral other parts will bend and that's the tertiary level structure. When you finally let go the chain, it'll wrap itself into some complicated shape, and that's the tertiary structure. If that chain happens to be put together with other polypeptide, or amino acid chains, that's what is called the quaternary structure.

So now you know how proteins are put together. What are some of their functions? It's actually a lot easier to just ask what don't they do. Some proteins obviously make up those enzymes that I've mentioned before, lactase enzyme, amylase enzyme there is a very important enzyme in photosynthesis called RuBisCo enzyme or Ribulose or bisphosphate carboxylase.

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They make up structural things like I mentioned hair is made out of keratin. They form important components of the cytoskeleton. They form protein hormones, some of the signals that are used between your various cells. They form channels in the cell membrane to allow stuff to go in or out of the cell. They form antibodies to help your immune system. They form receptor proteins, also embedded in the membrane, to help your cells communicate one to the other. So that gives you a sense of the broad range of what proteins can do.

So how do your cells know how to build those incredibly complex proteins? That's where nucleic acids come in. Now you may have heard of some of the nucleic acids such as DNA of course, but there is also RNA and ATP. The monomers of nucleic acids are molecules called nucleotides. Let's take a look.

All nucleotides share a common structure. They have a phoshate group attached to a central five carbon sugar. And then they have some kind of nitrogenous or nitrogen carrying base over here. And that five carbon sugar can be deoxyribose in the case of DNA, or ribose in RNA.

Now in another separate episode, I went far more in depth into the structure of DNA. And I recommend that you watch it if you're kind of unclear on that. But I want to make sure that we go over the basics of it. Now then nitrogenous base that I mentioned before comes in four varieties. With DNA, if you take a look at that, you'll see that the four kinds are thymine, cytosine. You notice each of those only has a single ring, whereas adenine and guanine they're double ring structures. Those are called purines these are called pyrimidines.

With DNA and RNA, there is pretty much the same bases. The one difference is instead of thymine in RNA, they use a molecule called uracil. How do you remember that? Just think, 'You are correct'. Again in case you missed that, that means uracil is in RNA that's the correct answer.

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Now to join the nucleotides again, you do that dehydration synthesis process. And what will happen is, you'll wind up forming long chains. What you're doing is you're popping off an OH group from the corner of the sugar here, and you're joining it to a hydrogen that you rip off of the phosphate of the next nucleotide. So you'll start to form a long strand with the sugars and the phosphates forming the backbone of this and the nitrogenous bases sticking out like this. With RNA, that's it.

RNA is generally single stranded molecule. But DNA, of course you've heard of the double helix. With DNA, you actually form a second strand. Notice how the pentagon is now pointing downwards, that's called anti-parallel. Mention that during an AP Biology essay on the structure of the DNA, and you got yourself another point.

You'll see that between adenine and thymine, you'll see two hydrogen bonds. Whereas between guanine and cytosine, those dash lines are the three hydrogen bonds that form between them. And if you can remember, two hydrogen bonds between A and T, three hydrogen bonds between guanine and cytosine, you got yourself another point.

So it's always A to T, G to C. Remember that and you're pretty good to go for DNA structure. Now what are the functions of the nucleic acids. Well everybody hopefully knows that DNA is the holder of your genetic information and RNA helps in that transmission of the genetic, or the inheritance abilities. But the one thing that a lot of people forget is that ATP, the energy currency of the cell is also a nucleotide. How is it different? It just has three phosphates in it instead of the normal one in the other nucleotides.

Here's a memory trick that'll help you learn these four different kinds of organic molecules. And it's a memory trick that you can also use to help learn any kind of categorical knowledge. And it's taking advantage of a former memory that you have, that you use all the time.

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It's the one that you use to remember, for example, where did you park your car? Very few of you will pull out your flashcards and cram to remember that. No. You just walk in the mall and an hour later, you walk out and there you are at your car. What you do, is you visualise each of these different categories into a different location and when you study them, turn and look in that area and visualize them being there. Then during a test, all you can do is just turn and look. Now make sure that you're not memorizing your location on your partners or tablemate's paper, because your teacher may not like that.

So what you do is, look over here and think that where those carbohydrates are those energy storing and structural molecules made out of monosaccharides getting joined together into the disaccharide, or even longer chains called polysaccharides. Next to them is that hydrophobic reject group of the organic molecules called the fats and lipids. Those include remember, the triglycerides and phospholipids used in that glycerol and fatty acid stuff to make them up, which are involving things like making fat or phospholipids in the membrane. Or the steroid core fats that are used for things like waxes and hormones.

Over here, we have the proteins. Now remember, the proteins are the ones with that incredibly complex structure, where you hook the individual monomers called amino acids, together to form long chains, the simple structure of the chain is called the primary structure. As you let it begin to coil up a little bit, that secondary structure it's three dimensional shape, its tertiary structure. And if an actual protein is made out of multiple chains, how those multiple chains fit together is called its quaternary structure. And again those proteins, they form enzymes, they form membrane channels and hormones. They make all sorts of things in the cell.

The last category way over here is the nucleic acids; the DNAs and RNA. And you recall of course, they are made of nucleotides joined together in strands with DNA requiring two strands to form the double helix.

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You use this tricks and you'll be better able to put this stuff together. And remember, it's not how hard you study, it's how smart you study. You put your time into being efficient, and that allows you to spend the time doing the things you really want to do like watching Desperate House Wives.