Functional groups in biological molecules

1. As we said last time, functional groups are needed in biological systems to have any sort of activity. Therefore, we will see that all biochemical ractions and many of the most important interactions between biological macromolecules involve functional groups.

2. First, were do we find functional groups in different biomolecules?

a) Carbohydrates (Polysaccharides): We have many hydroxyl (-OH) groups, as well as ketones (R-CO-R), and aldehydes (R-CO-H). Carbohydrates exist as open chains, or most commonly, as rings. The ring closes using up one hydroxyl and the aldehyde or ketone - we obtain another group familiar to you from organic chemistry: ketals and hemiketals. These rings can be classified as pyranoses and furanoses, depending on the number of atoms in the ring (6 or 5). One resembles pyran and the other one furan, which are ethers (R-O-R).

Although we'll see carbohydrates in more detail in the near future, two of the most important structuar features in these molecules are the presence of chiral (non-symetric) carbons in almost all centers, and of a carbon with two oxygen substituents, the anomeric carbon.

b) Amino Acids (Proteins): In amino acids we have at least two functional groups in the same molecule: An amine (-NH₂) and a carboxylic acid (-COOH). Depending on the side chain, we can also have imidazole rings, guanidino groups, hydroxyls, thiols, etc., etc. These side chains are crucial for protein activity.

Amino acids also contain chiral centers: the Ca carbon as well as some of the carbons in the side chains.

c) Fatty acids, with alkyl chains of different lenghts (C16, C18) which may or may not contain double bonds. These chains are terminated by a carboxylic acid (-COOH). Together with phosphate units (-O-PO₃^-) and tryglicerides, they make up lipids.

d) Nucleic Acids (DNA/RNA): This ones have two monomers that we saw above. A pentose (furanose), ribose (RNA) or deoxyribose (DNA), to which a phosphate unit (-O-PO₃^-) is attached. These parts are always the same in all molecules of DNA and RNA.

Apart from these common units, we have a base that attaches to the sugar moiety. The bases can be either purines (adenine, guanine) or pyrimidines (thymine, cytosine, uracil). These are the ones that change and make DNA and RNA the useful molecules they are.

a) Group transfer reactions: Transesterification, transamidation, transphosphorilation. A group attached to one molecule is transferred to a functional group in another molecule. The best example is the transfer of a phosphate unit in adenosine triphosphate (ATP) to a sugar to form a sugar-phosphate and adenosine diphosphate (ADP), or the transfer of an amino acid from one chain to another.

b) Oxidation-reduction. They usually involve the transfer of hydirde ion (H^-), and the conversion of C=O to C-OH, COOH to COH, etc., etc., or viceversa. In biological systems, oxidation and reductions usually occur with the aid of a co-factor in the enzyme. We will see how FAD/FADH (flavine adenine dinucleotide) and NAD/NADH (nicotinamide adenine nucleotide) act as electron and proton 'sinks' for these type of reactions. An example is the conversion of alcohol to acetic acid by alcohol dehydrogenase - The less we have of this enzyme, the more dopy we get after a beer...

c) Rearrangement (isomerization): The end result of these reactions is the relocation of a functional froup or fragment in a molecule. Many times we can disect them in the other types of reactions occuring 'intramolecularly' (i.e., within the same molecule). An example is the conversion of glucose-6-phosphate into fructose-6-phosphate by an isomerase. As we will see, the name of most enzymes is associated with the reaction they catalize.

d) C-C bond formation or cleavage: This ones deals almost exclusivelly with C-C bonds. As we saw, carbons are not really active in reactions, except when they are activated. These usually means that we have heteroatoms or electron withdrawing groups (Z) directly attached to that carbon that make it (or the bond it is involved in) very reactive. Usually, these C-C bonds are weaker because the electron density of the C-C bond is distributed towards the heteroatoms bonded to the carbons. As we will see, most of these reaction are aldol-type reactions (Knoevenagel, Perkins, etc., etc.). Examples are the formation of C-C bonds in the synthesis of fatty acids and sugars.

e) Condensation: Two groups come together, usually with loss of a water molecule. Examples are the elongation of a protein by formation of a peptide bond, or an oligosaccharide by formation of a glycosidic bond. Usually, we have to look how a water molecule can be formed with parts of the molecules we want to condense.

f) Hydrolysis: It is the substitution of a group by water, or one of its components. An example would be the hydrolysis of a peptide bond or glycosidic bond by water. You can consider it a very special case of group transfer reaction.

Common electrophiles are carbonyl groups of amides and aldehydes, protons (positive hydrogen atoms), and metals. Thing to keep in mind: Not all things that have a negative charge are good nucleophiles, and viceversa.

5. Are biomolecules flexible? The obviuos answer is 'yes', but lets check out why. Last time we talked briefly about the bonds that carbon atoms make in macromolecules. They almost exclusively make single (s) bonds or double (p) bonds.

s bonds and their electron cloud have cylindrical symetry, so except for a relatively small torsional barrier, they can rotate - We call them rotatable bonds. Recall the torsional profile of ethane.

On the other hand, p bonds have two sub-like lobes, one above and below the plane of the bond (remember that p orbitals make these ones). Therefore, we cannot rotate around them - We would have to break and re-make the bond. There is a large torsional barrier.

We also have to keep in mind that we have some systems that have bonds with aromatic character (resonant structures - compare to benzene). These are in between single and double, and we therefore have limited rotation around them.

The take home message of all this mumbo-jumbo is that if we have single, rotatable bonds in a molecule, its structure will have several degrees of freedom - we can have a large number of rotamers (geometrical isomers) for each bond. Each one will have different energies depending on how much different atoms in the molecule butt against each other. These collection of 'possible' rotamers are called conformations.

Understanding conformations and conformational freedom (how much a molecule can flop around) is extremelly important in biochemistry. Almost all biomolecules have anywere from tenths to thousands of rotatable bonds, and therefore thousands of possible conformations. Only one (or a bunch of very similar ones) make the molecule useful or active - an enzyme, which has several rotatable bonds, and therefore many possible conformers, folds only into a favoured conformer which is active. The same goes for polysaccharides and DNA/RNA. The game of figuring out the active conformation of a biomolecule is a multi-billion dolar industry.

4. Do biomolecules have sides? As we mentioned before, many monomers (sugars, amino acids), present what is know as chiral centers. As you probably recall from organic chemistry, if a molecule has this type of atom, we cannot superimpose it with its mirror image. In other words, the molecule has no axes or planes of symmetry that allow us to obtain its mirror image by simply rotating it or flipping it around.

sp³-Hybridized carbon has the potential to be chiral. If we attach four different substituents to an sp³-hybridized carbon we end up with a chiral center. There are ways to view this, and rules to assign which enantiomer is which. One way are Fisher projections. Horizontal  bonds come towards the viewer, and vertical ones go backwards. Another way is with wedgy looking bonds. Solid (bolded) bonds come out to the fromt of the plane, and dashed bonds go backwards. The arrangement of the atoms around a chiral center is called its configuration. There are rules to determine the configuration of chiral centers, the Cahn-Ingold-Prelog rules, in which we prioritize the substituents of the chiral center:

a) We put the least heavy of the atoms (usually a proton) pointing back.

b) Then we assign numbers to the other substituents, using small numbers for large substituents. If the first atom is the same in two substituents, we go the next atom in the substituent.

c) Now we follow the direction of rotation from small to big numbers. If we move clockwise, we have an R configuration (rectus, right). Otherwise, we have an S (sinistrus, left), configuration.

In molecules with more than one stereocenter, we will have combination of chiralities. If we have two chiral carbons, we can have (R,R), (R,S), (S,R), or (S,S) combinations, which we call diastereomers. From these four diastereomers, we have two pairs of enantiomers, the (R,R) and (S,S) pair, and the (S,R) and (R,S) pair. While enantiomers have the same physical properties (except OR), diastereomers have different physical properties.

Now, since most biological macromolecules are made up of monomers which contain chiral centrers (amino acids, sugars, ribose and deoxy-ribose in RNA and DNA), biological macromolecules are chiral. This has very important consecuences in biochemistry, as all reaction catalyzed by a chiral enzyme (protein) will work only on one stereoisomer. For example, aspartame (L-aspartyl-L-phenylalanyl methyl ester) the stuff used in NutraSweet, is sweet. If we change the configuration of one stereocenter (L-aspartyl-D-phenylalanyl methyl ester), the taste is bitter.

Another example, drugs: Most drugs are not fantastic to take. In a drug with chiral centers, only one compound is active against the bug, but both are probably toxic. If possible the enantiomer/diastereomer recognized by the target is used as a drug to minimize side effects.

Another important concept in biochemistry is pro-chirality. If a carbon atom has two protons and two other (different) substituents, the only thing that we need to do to make it chiral is to change one of the protons for a third substituent. The two protons are called pro-chiral protons. Changing one will give rise to an S configuration (pro-S proton), and changing the other one would give us an R configuration (pro-R proton). Enzymes that work on pro-chiral carbons usually have a preference for the pro-S or the pro-R hydrogen (very important when designing drugs).

Another type of stereochemistry we will find in biomolecules occurs due to double bonds. Since we can not rotate them, we can have two stereoisomers depending on how the groups attached to the double bond are arranged. We have Z and E, or cis-trans isomerism. These type of isomers are not enantiomers, as we cannot superimpose mirror images of them. Also, they have markedly different physical properties.

Prepared by Guillermo Moyna, 1999.