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You might think a self regulating factory sounds pretty unbelievable, but that’s pretty much exactly how our bodies work! Our bodies are full of regulatory mechanisms that keep all the organic molecules we need to live in balance. In this episode of Crash Course Organic Chemistry, we’ll look at the building blocks that form these biological polymers, including carbohydrates, proteins, and DNA!

Episode Sources:
Garrett, R. H., & Grisham, C. M. (2016). Biochemistry. Cengage Learning.
Appling, Dean R., Anthony-Cahill, Spencer J., Mathews, Christopher K.. (2016). Biochemistry: concepts and connections. Essex: Pearson.
PDB IDs (available at
• 1BNA, 6TNA, 3MQ7, 7BJK, 6EC0, 2D3H, 1UBQ, 1BBB, 3FGU

Series Sources:
Brown, W. H., Iverson, B. L., Ansyln, E. V., Foote, C., Organic Chemistry; 8th ed.; Cengage Learning, Boston, 2018.
Bruice, P. Y., Organic Chemistry, 7th ed.; Pearson Education, Inc., United States, 2014.
Clayden, J., Greeves, N., Warren., S., Organic Chemistry, 2nd ed.; Oxford University Press, New York, 2012.
Jones Jr., M.; Fleming, S. A., Organic Chemistry, 5th ed.; W. W. Norton & Company, New York, 2014.
Klein., D., Organic Chemistry; 1st ed.; John Wiley & Sons, United States, 2012.
Louden M., Organic Chemistry; 5th ed.; Roberts and Company Publishers, Colorado, 2009.
McMurry, J., Organic Chemistry, 9th ed.; Cengage Learning, Boston, 2016.
Smith, J. G., Organic chemistry; 6th ed.; McGraw-Hill Education, New York, 2020.
Wade., L. G., Organic Chemistry; 8th ed.; Pearson Education, Inc., United States, 2013.

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 (00:00) to (02:00)

You can review content from Crash Course Organic Chemistry with the Crash Course App, available now for Android and iOS devices.

Hi! I’m Deboki Chakravarti and welcome to Crash Course Organic Chemistry!

Imagine a huge factory that makes plushies. The factory is completely automatic, so when there’s enough material around, production begins. If we start to run out of plastic eyes, the machines that make the plushies send signals to the eye machines to manufacture more.

And if the ratio of noses to eyes is too high – no problem! The nose machine can slow down, or the eye machine can speed up. A self-regulating factory might sound a little unbelievable, but it’s exactly how our bodies work.

If we have plenty of food and nutrients, we go into manufacturing mode. When there's not enough, we break down energy storage molecules. We’re chock full of regulatory mechanisms that keep the ratios of the organic molecules we’re making constantly in balance.

So let's explore how building blocks like carbohydrates, nucleotides, and amino acids become the biological polymers that control our body-factory. First, I've got to mention lipids. Lipids are one of the four main biochemical building blocks, but they don’t form polymers.

Still, these hydrophobic molecules are critical to our factory. Some are hormones that send cellular signals that have powerful controls on manufacturing. Some form cell membranes that hold each mini-factory together.

And lipids are the major form of long-term energy storage. Triglycerides, stored in our fat cells, can be broken down to provide lots of energy, like when we’re on a long hike and haven’t eaten in awhile.

 (02:00) to (04:00)

Now, the focus of this episode is the three building blocks that can form polymers.

And carbohydrates provide another important type of energy storage to keep our factory powered. Let’s quickly recap carbohydrate structure from episode 48, by using the Haworth projection of galactose to draw its Fisher projection.

Galactose has six carbons, so we can set up a Fisher projection with six carbon atoms. Carbohydrates can be D or L, which is determined by the stereochemistry at the highest numbered chiral carbon. For galactose, this is carbon five, because carbon six has two hydrogens.

Since the group attached to the highest numbered chiral carbon – this CH2OH – is pointing up on the Haworth projection, it’s a D-sugar. On the Fisher projection, we need to put the hydroxyl group on the right side of carbon five. And let’s add the CH2OH group on carbon 6.

Looking at our Haworth, the anomeric carbon hydroxyl is on the same side as the carbon five substituent. They're BY each other, so this cyclic form is beta. This doesn’t really matter for our Fisher projection since it's the open form, but it's good to practice.

The anomeric carbon is carbon one, so this is an aldose – with an aldehyde at the top. Lastly, we need to fill in the rest of the groups: those pointing down on the Haworth are on the right hand side of the Fisher projection, and those pointing up go left. And we're done!

Two-carbohydrate disaccharides form through an overall dehydration reaction, which results in a new covalent bond between the two rings. We name this bond based on the stereochemistry of the anomeric carbon and the carbons that are involved in the bond. For example, when galactose links up with glucose, we get lactose – the sugar in milk that some people can't break down so well.

In other words, they have lactose-intolerance.

 (04:00) to (06:00)

In this Haworth projection, we can see galactose is in its beta conformation, and it's connected through its anomeric carbon, which is in the beta form.

Then, we use the anomeric carbon stereochemistry, and the linked carbon atoms, starting with the lowest number. And we put this information together to get a beta-1,4-glycosidic bond.

When two glucose molecules link up, we get maltose. The linkage here is an alpha-1,4-glycosidic bond, which I like to show with these curved lines. Sometimes you’ll see slightly angled bonds in the drawing, and sometimes full-on bends.

But that can be confusing and look like extra carbons! Now if we take maltose and add hundreds more alpha-1,4-glycosidic bonds with more D-glucose, we make the polysaccharide amylose. Amylose is one of the two components of starch, the main energy storage molecules in plants.

These polymers can pack pretty tightly together for easy storage. The other part of starch is amylopectin, which has some alpha-1,6-glycosidic bonds sprinkled in. As you can see from its bulkier structure, this polymer takes up more storage space in the plant.

But it's also easier for humans to digest! In fact, the amylopectin structure is really similar to glycogen, the energy storage molecule in animals. Glycogen helps power our muscles, because it’s quickly broken down to glucose.

And in this 3D model, we can see the structure curls around – it’s much more complex than the linear representations we often use. Glycogen is also stored in the liver, where it can break down quickly into glucose in order to keep the main factory server – our brain – up and running. This regulation is the reason we don’t go into a coma if we skip lunch, or why folks with diabetes and other liver-impairing conditions have to monitor their blood glucose!

So if our brain is the central server, each cell in our body is like a room of the factory, with its own computer in the nucleus: the polymer DNA.

 (06:00) to (08:00)

The building blocks of DNA are nucleotides, which are made up of a pyrimidine or purine nitrogenous base, a deoxyribose sugar, and a phosphate group.

Like usual, to talk about these molecules and name bonds, we label the atoms in each of the ring structures. The nitrogenous bases get plain old numbers, and the positions of the carbohydrate are given numbers with prime symbols, starting with the anomeric carbon of ribose.

Counting around the deoxyribose ring, here are the 1-prime, 2-prime, 3-prime, 4-prime, and 5-prime carbons. Nucleotides also polymerize by an overall dehydration reaction that links the phosphate of one to the 3-prime hydroxyl group of another ribose. This makes up the backbone of DNA, which is repeating sugar-phosphate-sugar-phosphate linkages.

Basically, the 3-prime and 5-prime carbons of two sugars are linked through a phosphate, so we call this end of DNA the 5-prime-end, and this end the 3-prime-end. The order of covalently-linked nucleotides in the backbone is the primary structure of DNA. We usually write out the DNA sequence of a strand using one-letter codes that correspond to the nitrogenous base: A, T, G, or C.

But, DNA in our cell nuclei isn't single-stranded! In the secondary structure, two DNA strands bond together to form the familiar double helix. Nucleotides can only hydrogen bond in specific pairings: A to T, and G to C.

And to form those bonds, the DNA strands have to line up in opposite directions – one has the 3-prime position of the carbohydrate facing up and runs 3-prime to 5-prime, and the other runs 5-prime to 3-prime. We can see this hydrogen bonding really well in the 3D structure of DNA, where atoms are marked using colors instead of letters!

 (08:00) to (10:00)

Nitrogen is blue, oxygen is red, sulfur is yellow, phosphorus is orange, and carbon can be any color but is often gray or black.

Notice the red and orange of the sugar-phosphate backbone along the outer edge of the double-helix, and the blue and red of the nitrogenous base pairs holding the two DNA strands together in hydrogen bonds. Each DNA strand's sequence of nitrogenous base letters encodes messages that can tell our cell factory which plushies – well, proteins – to make.

Specifically, DNA is used as the template to make another biological polymer called RNA, which helps our bodies pass on these encoded messages. Remember that an RNA strand is very similar to a DNA strand, except that 2-deoxyribose is replaced with ribose, and uracil replaces thymine in the nitrogenous bases. And there are different kinds of RNA that do lots of different things.

For example, the appropriately-named messenger RNA carries information from the nucleus into the main cellular compartment. And transfer RNA are single stranded polymers, but they fold up on themselves in really incredible shapes. They carry amino acids to help assemble them into the factory’s machines... proteins!

Proteins, which can also be called polypeptides, form the machines that fabricate all of the parts of our plushies. But they can also provide the structural support for the factory by forming filaments that give a cell its shape. Sometimes they can even transmit signals between the outside and inside of the cell, and so much more!

Individual amino acids undergo an overall dehydration reaction to form peptide bonds – the name for the amide bond in a protein. The order of amino acids in a protein strand, like in DNA, is called the primary structure. And amino acids have one letter codes too.

We’ll just show them on screen, though, because there's 20 of them… not just 4. The backbone is the part of the protein chain that doesn't include the side chains.

 (10:00) to (12:00)

And the primary structure folds up in two main ways to make the secondary structure of the protein, with hydrogen bonds forming between these backbone atoms.

Here’s what the hydrogen bonding looks like in two components of the secondary structure, one is alpha helices and the other is beta sheets. Sometimes the secondary structure largely determines what a protein does, like some structural proteins in spider silk.

Small amino acids pack into beta-sheets, and the hydrogen bonds made across the strand backbone are close and strong. Other structural proteins, like the collagen in our connective tissue and the keratin that makes up our hair and fingernails, rely on helical secondary structures to give them strength. When a polypeptide folds up into more than just a single continuous alpha helix or beta sheet, the overall 3D shape is its tertiary structure.

Here, side chain interactions begin to play a role – both in the shape and what these protein machines can do. Let’s check out these four main side chain interactions from weakest to strongest. In most proteins, hydrophobic side chains cluster together in the center of the protein, to avoid mixing with water.

This weak interaction is called the hydrophobic effect, and these side chains make hydrophobic interactions. Next is hydrogen bonding – but, remember, we're talking about between the side chains instead of the backbone this time. Polar amino acids have side chains with partial positive and partial negative charges that can form hydrogen bonds.

And polar amino acids with side chains near the protein surface can hydrogen bond with water. Getting stronger, our third interaction involves full charges. Two ionized side chains can form an ionic interaction or salt bridge.

For example, the negatively charged carboxylate side chain of aspartate can ionically interact with the positively charged arginine side chain. The fourth main interaction that contributes to the tertiary structure is actually pretty strong: it’s a covalent bond that can form between the sulfur atoms of two cysteine side chains, called a disulfide bond.

 (12:00) to (14:00)

So those interactions stabilize the tertiary structure of a single protein.

But a protein has quaternary structure if multiple protein chains – or even multiple protein molecules – cluster together, making the same interactions we just mentioned. Quaternary structure is important in the regulation of some enzymes, the proteins that catalyze chemical reactions that make or break down organic molecules.

Enzymes can be incredible at their jobs. Some can speed up reactions 10 million times compared to the uncatalyzed reaction rate. In other words, shape changes in the quaternary structure are one way our plushie-making machines can communicate with each other to speed up or slow down production rates.

And enzymes really are like little machines – they bind a reactant in an active site, where the chemical reaction takes place. There, carefully positioned side chains of the amino acids that point into the active site get to work. By that I mean, those side chains allow an enzyme to do acid- and base-catalyzed reactions in a gentler way.

For example, negatively charged side chains and some with amines accept protons – acting as bases. While others can donate protons – acting as acids. Some side chains can even act as nucleophiles to speed up a chemical reaction.

So while you’re sitting there thinking about organic chemistry – or maybe adorable plushies – your own molecular factory is hard at work doing the organic chemistry that keeps you going. Thanks to some pretty amazing biological polymers. In this episode, we learned: Lipids don’t form biological polymers but are important, Carbohydrates can link up to form disaccharides and polysaccharides, DNA and RNA carry messages to direct protein production, and proteins have many functions, like enzymes, the organic chemists of the cell.

 (14:00) to (14:30)

In the next – and final – episode we’ll see how stopping a bacterial enzyme in its tracks can improve human health, as we finish our penicillin synthesis and take a look at medicinal chemistry.

Until then, thanks for watching this episode of Crash Course Organic Chemistry. If you want to help keep all Crash Course free for everybody, forever, you can join our community on Patreon.