Organic Chemistry 101: Biological Molecules

It is an organic compound with a backbone of at least 3 carbons, typically with a C:H:O ratio of 1:2:1. Carbohydrates consist of either aldehydes or ketones with other carbons in the chain bound to hydroxyl groups.

Exceptions to the 1:2:1 ratio exist for “deoxy” sugars, in which a hydroxyl group has been replaced by a hydrogen.

Fischer projection - straight-chain carbohydrates are often shown in this form.

On any Fischer projection, horizontal lines are considered to point out of the page (“wedges”), while vertical lines point into the page (“dashes”). Thus, this method can accurately convey stereochemistry.

Haworth projection - carbohydrates in the ring form are often shown in this manner.

The relative positions of substituents as “cis” or “trans” can be determined by whether they point upward or downward from the face of the ring.

• Aldoses are sugar molecules that contain a single aldehyde group.

• Ketoses contain a single ketone.

Note that both aldoses and ketoses are monosaccharides.

1. The compound is first classified as either an aldose or a ketose.

2. Next, the number of carbons is counted (di, tri, quatr, pent) and included after the aldo- or keto- prefix.

3. Finally, the -ose suffix, used to denote a carbohydrate, is attached to the name.

Note that there should be no spaces between the prefix, numerical identifier, and suffix.

aldopentose

This carbohydrate has an aldehyde group, which should be denoted by the prefix “aldo-.” As a five-carbon sugar, it should be named using the Greek term “pent.” Finally, the “-ose” suffix identifies the molecule as a carbohydrate.

They are named based on the number of members in the ring, its two main categories are:

• five-membered furanoses

• six-membered pyranoses

To denote a carbohydrate in the ring form, remove “-se” from the carbohydrate name and replace it with the suffix “-furanose” or “-pyranose,” as is appropriate.

pyranose

The carbohydrate has a six-membered ring form, so it is a pyranose. Five-membered rings are known as furanoses.

glucose

Glucose, a hexose, is the most common carbohydrate. Its Fischer projection can be identified by the orientation of its hydroxyl groups. From top to bottom, the -OH groups will be oriented either “right, left, right, right” (D-glucose) or “left, right, left, left” (L-glucose).

fructose

Fructose, a hexose, its Fischer projection can be identified by the orientation of its hydroxyl groups. From top to bottom, the -OH groups will be oriented either “left, right, right” (D-fructose) or “right, left, left” (L-fructose).

1. As aldoses (aldehyde-containing carbohydrates) or ketoses (ketone-containing carbohydrates)

2. As furanoses (five-membered rings) or pyranoses (six-membered rings)

3. As regular sugars (those with oxygen atoms bound to each carbon) or deoxy sugars (those missing one oxygen atom)

• monosaccharide is composed of one cyclic sugar subunit.

• disaccharide is composed of two cyclic sugars connected by a glycosidic linkage.

A polysaccharide, then, consists of more than two sugar subunits bound together.

1. glucose

2. fructose

3. galactose

Ribose and deoxyribose are also monosaccharides.

Monosaccharides can be connected by glycosidic linkages to form longer sugar chains.

1. sucrose

2. lactose

3. maltose

In general, disaccharides consist of two sugar subunits bound by a glycosidic linkage.

• Sucrose is composed of fructose and glucose

• Lactose is composed of glucose and galactose

• Maltose is composed of two glucose monomers

The absolute configuration of a straight-chain carbohydrate is determined by the chirality of the carbon stereocenter that is farthest from the carbonyl carbon.

In other words, the absolute configuration depends on the highest-numbered chiral carbon in the molecule.

Any carbohydrate depicted as a Fischer projection:

• is classified as a D sugar if the -OH on the highest-numbered chiral carbon is pointing to the right.

• is classified as an L sugar if that same -OH is instead pointing to the left.

TD configuration

Look at the -OH on the chiral carbon farthest from the carbonyl group. Since that -OH is pointing to the right on the Fischer projection, this must be a D sugar.

These are two molecules that differ in configuration at a single chiral carbon.

Epimers are a special type of diastereomer. They are especially important in relation to sugars.

These are epimers, since they differ in configuration at only one position: the third carbon from the carbonyl.

Like all epimers, these molecules are also diastereomers.

• 1 and 2 are epimers differing at the chiral carbon closest to the carbonyl. Like all epimers, they are also diastereomers.

• 2 and 3 are enantiomers, or nonsuperimposable mirror images of each other. They differ in configuration at all chiral centers.

• 1 and 3 are diastereomers, since they differ in configuration at 3 of 4 chiral carbons. Diastereomers are stereoisomers which differ at some (but not all) stereocenters.

• 1 and 2 are epimers differing at the chiral carbon closest to the carbonyl. Like all epimers, 1 and 2 are also diastereomers.

• 1 and 3 are epimers differing at the chiral carbon second from the carbonyl. Again, 1 and 3 are also diastereomers.

• 2 and 3 are diasteromers, as they differ at two of their three stereocenters (the chiral carbons one and two positions away from the carbonyl). Diastereomers are stereoisomers that differ at one or more, but not all, stereocenters.

These are diastereomers, a broad term for stereoisomers that are not enantiomers.

Specifically, these molecules cannot be enantiomers since they do not have opposite configurations at all of their chiral carbons. They also are not epimers, which only differ in configuration at one position.

In the straight-chain form, the -OH on the chiral carbon farthest from the carbonyl acts as a nucleophile and attacks the carbonyl carbon. This forms a cyclic structure.

In the proccess, the attacking hydroxyl loses its proton and the carbonyl oxygen becomes protonated.

This is called the anomeric carbon. Its stereochemical configuration is another way by which carbohydrates are classified.

Abpve, the anomeric carbon is bound to a hydroxyl group and to the oxygen member of the ring. It derives from the carbonyl carbon in the straight-chain form.

It is the only carbon that is bound to two oxygen atoms.

For this reason, all anomeric carbons are part of another functional group: acetals and hemiacetals (or ketals and hemiketals).

It is a functional group that is derived from a carbonyl compound. It consists of two -OR groups bound to the same carbon.

Conventionally, "acetal" has referred to compounds derived from aldehydes, while "ketal" refers to those derived from ketones.

It is formed when an aldehyde is reacted with two equivalents of alcohol compounds. The -OH acts as the nucleophile and attacks the aldehyde carbon, as shown below.

• The carbon on an acetal is bound to two -OR groups.

• The carbon on a hemiacetal is bound to one -OR and one -OH.

"Hemi-" means "half," so a hemiacetal is simply a half-formed acetal. In other words, it is the product of a carbonyl compound and a single alcohol.

This is a hemiacetal. It contains a single carbon (the anomeric carbon) bound to one -OR and one -OH group.

The molecule shown is cyclic glucose, a pyranose.

This is an acetal. It contains a single carbon (the anomeric carbon) bound to two -OR groups. Often, the hemiacetal functionality on a monosaccharide becomes an acetal to form a glycosidic linkage.

The molecule shown is maltose, a disaccharide composed of two glucose subunits.

In a Haworth projection:

• the -OH on the alpha anomer is trans to the carbon substituent on the ring

• the -OH on the beta anomer is cis to the carbon substituent on the ring

It is the equilibration of alpha and beta anomers in solution. During this process, the optical rotation of the mixture changes.

Mutarotation occurs due to the opening and closing of carbohydrate rings. When the carbohydrate opens, its carbonyl group can then be attacked from a different side, forming either the alpha or beta anomer.

alpha linkage

The nomenclature is determined by the anomeric carbon participating in the linkage. Here, the left carbohydrate's anomeric carbon is linked to the right carbohydrate via an oxygen atom. Since the configuration of the left anomeric carbon is alpha, this is an alpha linkage.

Glycosidic linkages are broken via hydrolysis.

As a nucleophile, water can attack the anomeric carbon in the linkage; the other carbohydrate will act as the leaving group. This reaction is a specific example of the hydrolysis of an acetal.

The aldehyde group on an aldose can be oxidized to a carboxylic acid, as can the terminal carbon.

Tollen's reagent can only react with the aldose's aldehyde group. In contrast, nitric acid can oxidize both the aldose aldehyde and the terminal carbon to carboxylic acids.

polyalcohol

The aldehyde or ketone group will be reduced to a hydroxy group. The existing hydroxy groups will not be reduced further.

These detect the presence of reducing sugars. These are carbohydrates that can act as reducing agents; in other words, they can oxidize themelves.

It produces a dark red precipitate. The reagent involved is a mixture of sodium citrate, sodium carbonate, and copper sulfate pentahydrate.

It yields a silver mirror-like product. The reagent involved is a mixture of ammonia and silver nitrate.

These contain metal ions, which can be reduced by compounds that are prone to oxidation. Reducing sugars are examples of such compounds.

The metal ion in Benedict's test is Cu2+, while that in Tollens' test is Ag+.

These contains hemiacetals (or hemiketals). Since they contain an -OH group, they can further oxidize when that -OH is replaced by an -OR.

Note that reducing sugars do not reduce themselves - they oxidize, thus acting as reducing agents! In a straight-chain form, aldehydes are the classic marker of a reducing sugar, as they can easily oxidize to carboxylic acids.

Molecule B is a reducing sugar. Unlike Molecule A, it contains a hemiacetal group, and is thus able to further oxidize.

Molecule B is maltose, a disaccharide. Molecule A is sucrose and is also a disaccharide.

ester

All of the carbohydrate's free hydroxyl groups are able to act as nucleophiles. They attack the carbonyl carbon of the anhydride, resulting in acylation at those positions.