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Although we've spent a lot of time in this series looking at human-made organic chemicals, the term "organic chemistry" was originally used to describe molecules isolated from living things. In this episode of Crash Course Organic Chemistry, we're going back to our roots to learn more about the best synthetic chemists: living things. We'll look at the biochemical building blocks of life from the nitrogenous bases, sugars, and phosphate groups that make up DNA and RNA, to amino acids and lipids, and we'll learn how to convert between Fischer and Haworth projections of carbohydrates.

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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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. The term "organic chemistry" was first used to describe molecules isolated from living things. This was back in the 1800s, when some scientists thought that organic compounds had to be made biologically.

But in the past 47 episodes, we've seen plenty of examples of human-made chemicals. Like polymers and medicines. We explored some of the lab techniques and equipment that let us make new chemicals. And even worked through multi-step organic syntheses.

Despite all that, living things are arguably the best synthetic chemists, carrying out countless simultaneous organic reactions at mind-boggling speeds. So in this episode, we'll return to organic chemistry's origins to explore the chemical building blocks of life. 

[Intro music]

The organic chemicals that make up living things can be organized into four classes: carbohydrates, nucleic acids, lipids, and proteins. Carbohydrates can be sweet, like the table sugar we put in tea. But all the nomenclature might make you a little sour. So, let's get that out of the way first.

Most carbohydrates are molecules with this general formula. There's usually a 2:1 ratio of hydrogen atoms to oxygen. And the number of carbon atoms, the m subscript, ranges from 3 to 9. One way to refer to carbohydrates is by the number of carbons they contain. 

A carbohydrate with three carbon atoms is a triose, four a tetrose, five a pentose, six a hexose, and so on. We can also classify carbohydrates based on their functional group. Because they're either aldehydes or ketones. Of the trioses

 (02:00) to (04:00)


glyceraldehyde is an aldose because it contains an aldehyde, and dihydroxyacetone is a ketose, with that ketone on the central carbon.

Five-carbon pentoses and six-carbon hexoses mainly exist as cyclic hemiacetals in solution. As a reminder, hemiacetals form when one alcohol group adds to an aldehyde or ketone, and usually the equilibrium favors the aldehyde or ketone. But five- and six-membered ring hemiacetals are often more stable than the open-chain forms. We saw this with glucose in episode 29.

The six-membered ring form of a sugar is called a pyranose, named after the pyran ring which looks like this. Sugars can also form five-membered furanose rings. We met tetrahydrofuran in episode 28 as a good solvent for Grignard reactions. A really important carbohydrate that forms a furanose as its cyclic form is ribose, which we'll see again in nucleic acids.

These linear representations of carbohydrates are called Fischer projections. Sometimes, all the carbon atoms are drawn out and sometimes carbons are just shown as crossing lines. And, you can also show stereochemistry if you want. See, all the horizontal bonds are coming out of the screen, toward us.

Fischer projections are drawn so the highest-priority group is closest to the top of the diagram: the aldehyde of an aldose or the ketone of a ketose. Then, the -H and -OH groups are placed on specific sides of the chiral carbons.

If I build this with a model kit and point all of the horizontal bonds toward me, the carbon backbone starts to curl and form a ring. The structure isn't actually linear. So, even though it's a linear representation, we can use the Fischer projection to draw cyclic structures, too.

Before we start drawing rings, though, there's one more nomenclature thing to learn. If the -OH group on the bottommost chiral carbon of the Fischer projection is on the right, it's a D-sugar, with a capital "D". And if it's on the left, 

 (04:00) to (06:00)


it's an L-sugar. This "D" and "L" designation is named for the Latin "Dexter"and "Laevus", "right" and "left". So to sum all this nomenclature up, this ribose molecule is a pentose, because it has a five-carbon chain, an aldose, because there's an aldehyde on the top, and a D-sugar, because the -OH group on the bottommost chiral carbon is on the right. Sweet!

To really understand carbohydrate rings, let's do a quick chirality review. When a nucleophile attacks an aldehyde and a chiral carbon forms, it can attack either face of the trigonal planar aldehyde. In this simple example, if methoxide attacks from the front face, the alcohol gets pushed back into the screen. But, if methoxide attacks the back face, coming from behind screen, the alcohol gets pushed toward us. This is how we get a mixture of stereoisomers at the anomeric carbon in a carbohydrate ring.

The anomeric carbon was the carbonyl carbon and becomes sp3 hybridized when the linear carbohydrate closes to form a ring. We can show the ring closure on a Fischer projection by drawing a long bond from the highest-number chiral carbon to the anomeric carbon. Our new -OH group can be on either side of the Fischer projection.

A stable, five-membered ribose ring forms when D- or L- determining hydroxyl group forms a hemiacetal with the aldehyde at carbon-1. And to draw the ring form, we use a diagram called a Haworth projection. To start, we draw a five-membered ring and put the oxygen right at the top. Now, we need to look at the hydroxyl group attached to the highest-numbered chiral carbon again – the one that makes it a D-sugar or L-sugar. This is the -OH group that ends up in the ring, and it'll determine where the CH2OH group points on the Haworth.

If it's a D-sugar and the -OH is on the right, the CH2OH points up. That's what we have here. If it's the less common L-sugar and -OH is on the left, the CH2OH points down.

 (06:00) to (08:00)


And, remember, we don't have to write CH2OH every time. We can represent the carbon as a bent line, draw the hydroxyl group, and leave the two hydrogens off because they're implied. Much neater!

Now, we've got to sprinkle in the rest of the -OH groups. The groups on the right in the Fischer projection point down below the ring on the Haworth projection. And the groups on the left in the Fischer point up on the Haworth. The drawings of alpha- and beta-ribose rings look slightly different.

In an alpha-ribose, our new -OH group and this CH2OH group are on opposite sides of the ring, away from each other. And, in a beta-ribose, the groups are on the same side of the ring, or by each other. And, we're done! Ribose is an important pentose. But these four carbohydrates are the most abundant hexoses in nature.

Glucose, galactose, and mannose all form six-membered pyranose rings as their most stable structure, while fructose usually forms a five-membered furanose ring. Let's practice by drawing a Haworth projection of alpha-D-glucose.

We need to start with a six-membered ring this time. And we place the oxygen atom in the upper right. And let's number our carbons. As before, the highest-number chiral carbon determines if the carbohydrate is D- or L-. It's on the right, so this is another D-sugar. And the CH2OH group points above the ring. Let's put it there and simplify the drawing.

Let's begin with carbon-2 to add the hydroxyl groups. Those on the right of the Fischer point down on the Haworth and vice versa. Lastly, we just have to make sure it's the alpha form, so we'll make the hydroxyl on carbon-1 point away from this group coming off of carbon-5. And that's it!

Since the Haworth shows groups that are above and below the ring, it maps really well onto the chair form. We place the substituents that point up on the Haworth in the positions on the chair that point above the ring. Like I mentioned, this is the D- form of glucose,

 (08:00) to (10:00)


but let's look at alpha-L-glucose for practice. The CH2OH group points below the ring on the Haworth projection and the stereochemistry of all the carbons are flipped. L-glucose is the enantiomer of D-glucose. And here's what its Fischer projection looks like.

[Sigh] That's all for carbohydrates for now. Onto nucleic acids! We briefly mentioned these structures in episode 42, the two DNA bases that link up because of a sun-caused pericyclic reaction. Both DNA and the closely related RNA are nucleic acids.

One building block is a nitrogenous base, which is a nitrogen heterocycle, a ring with more than one type of atom. These are categorized as single-ring structures called pyrimidines or double-ringed structures called purines. The pattern of double bonds in nitrogenous bases doesn't exactly match the chemicals pyrimidine and purine, because added groups can cause different tautomers of the structure to be favored. Remember, tautomers have different positions for double bonds and hydrogen atoms.

As we saw way, way back in episode 4, these tautomeric forms are what made it so hard to initially figure out DNA's structure. In DNA, the -NH groups of these bases link up with the anomeric carbon of a 2-deoxyribose sugar in a dehydration reaction. The "deoxy" in the name means there's no hydroxyl group on carbon-2 of ribose.

A nitrogenous base connected to a carbohydrate is called a nucleoside. I remember this has an "s" because it's just the sugar. Add a phosphate group and we get a nucleotide. I remember this has a "t" for total. This unit is the whole building block for DNA and RNA, too.

Like we mentioned, DNA uses deoxyribose as its sugar. That's why it's called DNA, for deoxyribonucleic acid. But in RNA, the sugar is just ribose, with the -OH at the


 (10:00) to (12:00)


2 position of the carbohydrate. It's short for ribonucleic acid. And the nitrogenous base uracil replaces thymine. That's it for now, but we'll revisit nucleic acids and see how they link up to form polymers and carry genetic messages.

Next, we have lipids. Our hydrophobic class of building blocks. They're made up of hydrocarbons with just a few polar groups. We've met a few examples in the series, like cholesterol, the sex hormone progesterone, and Vitamin D. In episode 31, we touched on fatty acids, which are carboxylic acids attached to long hydrocarbon chains.

They're pretty straightforward to draw, especially compared to some of the rings we've been dealing with. They can be saturated, which means they have no double bonds, or unsaturated, with double bonds. When fatty acids link up to a molecule of glycerol, we get triacylglycerols or triglycerides. These are the main form of fat we consume and also how we store it in our bodies.

We can replace one of the fatty acid chains in a triglyceride with a phosphate group to get a phospholipid, which is a component of cell membranes. This phosphate at the end carbon of a glycerol can be attached to a whole variety of R groups, depending on what types of cell the membrane belongs to.

Okay, really briefly, we've got one final building block to go. Amino acids contain an amine and a carboxylic acid, both connected to a central carbon atom, the alpha carbon. The alpha carbon also has a variable R group sticking out, called a side chain. Each of the twenty standard amino acids has it's own unique side chain.

There's some interesting stuff going on inside an amino acid molecule. Our blood and cells are slightly basic environments, above the pKa of a carboxylic acid, but below the pKa of the protonated amine. This causes the carboxylic acid to lose a proton, which the amine generously

 (12:00) to (13:15)


accepts, because of its basicity. This proton exchange creates both a positive and negative charge in the amino acid molecule, called a zwitterion. This whole "becoming charged" thing can also happen with side chains that contain carboxylic acids or amines.

In fact, we can classify the amino acids into four major groups based on their side chain properties. As we'll see in the next two episodes, amino acids determine the shape of a protein. And some side chains even let proteins cause chemical reactions. But, that's it for now.

In this episode, we converted between Fischer and Haworth projections of carbohydrates, linked nitrogenous bases, sugars, and phosphate groups to form the building blocks of DNA and RNA, reviewed lipid structures, and saw that amino acids form zwitterions and have side chains with specific properties. 

In the next episode, we'll join these building blocks together and take a closer look at biological polymers. Until then, thanks for watching this episode of Crash Course: Organic Chemistry. If you wanna help keep all Crash Course free for everybody, forever, you can join our community on Patreon.