Nucleotides and nucleic acids

Well, time to get to the final class of molecules we will talk about in this course. These are the nucleotides and nucleic acids. In my humble opinion and regarding their structure, these molecules are grossly overated. There are thousands of molecules out there that have a lot nicer, more complicated, andcooler structures, and are more interestiong to study. However, we cannot forget that the ultimate function of nucleic acids is to pass genetic information, i.e., they are the templates for everything else that will be done.

Apart from this central 'scripting of life' function, nucleotides and nucleic acids have other functions. Among other things, they are used for:

- We have talked over and over again about adenosin triphosphate (ATP), which is the token used for energy transfer (not storage) in all living systems. Other nucletides (uridine triphosphate and guanosine triphosphate - UTP amd GTP) are also used for energy transfer.

- Many molecules with nucleotide components are used by cells to give out signals about chores to do around the cell. One of them is cyclic adenosine monophosphate (cAMP). cAMP does many things around the cells, among them, triggering the comsumption og glycogen (generation of D-glucose-6-phosphate), which makes us get hyper. If you have an addiction to caffeine, take a look at how similar these two molecules are, and you may be able to come up with a chemical reason for your caffeine jitters.

-Many nucleotides/nucleic acids are used as part of larger molecules to form important coofactors, like flavine adenine dinuclotide (FAD), nicotinamide adenine dinucleotide (NAD), etc., etc. We'll look at these with some detail below.

Nucleotides

Nucleotides consist of two parts: A base and a sugar, linked together by an N-glycosidic bond. The base can take two major forms, that of a purine or of a pyrimidine:

The numbering will be important later, and it follows the numbering scheme of heterocycles. There are 5 major bases that we will see. These are adenine, (A), guanine (G), cytosine (C), thymine (T), and uracil (U):

As most heterocyclic compounds, bases are pretty funky molecules. Although there are many natural sources for similar bases (xanthines), they are made from scratch by the organisms that use them. This means that these molecules connect all organisms in the very early stages of evolution. The same goes for DNA and RNA - They are the same in all organisms, so they link all evolution at a certain point in time - Everything came from a primordial bug that already made DNA and RNA. Pretty spooky.

In any case, the bases are highly congujated rings. If you analyze them, you will recognize that almost all the carbons are in sp² hybridization, and form part of congujated systems. Even those that are sp³ (like the N9 in purines) are sharing their electron to form aromatic systems. Other nitrogens are either sp² or form part of amide bonds (partial sp² character). This means that this molecules will absorb UV-visible radiation, will be flat or almost flat, and they are pretty non-polar (except for the exocyclic amines in A and C).

Furthermore, since they have clouds of p-electrons, they will form favourable p-p stacking interactions with one another. This, as we will see later on, is a very important force that stabilizes polynucleotides like DNA and RNA. The bases will place on top of one another due to the favourable p-p stacking interactions, increasing the stability of the molecules they form part of.

Finally, the functional groups of the bases, carbonyls (C=O) and amines (-NH₂) and amides (NH-CO), will participate in h-bonds. These h-bonds can be to water, or more importantly, between them - The second important interaction in molecules like DNA or RNA:

As we will see later, h-bonding will be between A and T or U, and G and C. Another property of the bases is they can form tautomers (not the same as resonant forms). We can have in many of them keto-enol equilibria:

The position of the equilibria (that is, which form will predominate) will depend on the pH of the solution (if in aqueous solution). In phisyological conditions (than is, pH = 7), the ones drawn at the top will predominate.

Apart from the bases, we have two possible sugars to which the bases are linked. These are cyclic aldopentoses (furanoses). One of them is ribose, and the other is ribose that lost the 2-position hydroxyl, deoxyribose:

Now, what about the numbering in the sugar part? We add the 'primes' to distinguish the carbons of the sugar from the carbons of the base, but use the numbering scheme of sugars: C1' is the anomeric carbon, and C5' is the other end, the one with the achiral hydroxyl. The base and the sugar form the nucleoside. Note that the N-glycosidic bond is always b in nucleosides. Furthermore, the connection is between C1' of the sugar and N9 of the base in purines or N1 in pyrimidines:

If we add the last components, which are phosphates, we get the nucleotides. Consistent with the precense or absence of the 2'-OH, we will have ribonucleotide or deoxynucleotides. As we will see later, the first ones form part of ribonucleic acid (RNA), and the latter are part of deoxyribonucleic acid (DNA):

To name the nucleic acids, we can use the '-ylic acid' termination (adenylic acid, guanylic acid, cytidylic acid, etc.), or just call them nucloside monophosphates, disphosphates, or triphosphates, like adenosine monophosphate.

Some nucleotides and their functions

Before diving into RNA and DNA, we will analyze some smaller molecules that contain nucleotides which are important prosthetic groups, energy trasfer, or siganling agents. The first one we will look at is adenosine triphosphate (ATP), which is the molecule used for transfer of energy in all living things. Using what we just learned

All the energy-yielding processes, such as metabolic oxidation of sugars or fatty acids and photosynthesis, give in the end ATP. The key is the formation of ATP from ADP (adenosine diphosphate), which is a reaction with a DG > O:

This means that it is unfavourable, and we therefore need to couple it to burning fuels. In any event, once we have ATP made, we can use it to provide energy to a variety of processes. One thing we have to keep in mind, is that we don't just burn it like wood, we couple it to the other reaction, which usually meant that we transfer a phosphate, a reaction with a DG < O (the reverse of the above).

Since the hydrolysis of the phosphoester bond has a DG < O, we can couple the reaction not only to transfer of phosphate, but many times we will see ADP involved in the transfer of other molecules:

ATP and ADP are the most ubiquitous (widely spread) nuclotides in organisms due to their role as energy transfer molecules. Another one that is also important is flavin adenine dinuclotide (FAD), in which adenosine is linked through two phosphate units to a riboflavin moiety;

The black molecule is adenosine dinucleotide. The red is ribitol, and the blue flavin. This molecule (together with NAD and NADP, which we won't see) are involved in oxidation-reduction reactions. The flavine portion has a the equivalent of quinone which can accept the equivalent of the dreaded 'H-' (hydride) specie, and go into the equivalent of a hydroquinone:

The overall reaction if FAD + 2H + 2e^- G FADH₂. You will see this over and over and over when you study metabolism. Finally, another important molecule is coenzyme A, which also contains adenosine, but this time phosphorylated at C3':

The molecule is also composed of pantothenic acid residue (in red) and a b-mercaptoethylamine moiety (in blue). This molecule is involved in all reactions involving transfer of acetyl residues, like fatty acid and polyketide biosynthesis. The acetyl group is charged to the thiol residue of the pantotheine 'arm', and then transferred to the recipient molecule:

Now, there are other molecules that contain nucleosides, but we have to start with DNA and RNA, and you will most likely see this in metabolism.

DNA and RNA

Now we will start analyzing how nucleotides can form polymers that will ultimately be DNA and RNA. As with any other polymer, we will call them polynucleotides if the molecule has more than 50 of them. Otherwise they will be called oligomers.

Two nucleotides can join using the phosphate residue that is clinging to the C5' position of one of them and the free C3'-OH from the other. If we use ribonucleotides, we get RNA, and if we use deoxyribonucleotides we get DNA:

These polymers have numerous phosphate groups, whose pK is approximately 0. Thus, at pH 7 (physiological conditions), they will be ionized. We therefore call the polymer poly- or oligonucleic acid to indicate this.

The negative charges on the oxygen of the phosphates and the hydroxyls of the sugar make the non-base part of the molecule pretty polar and water soluble. Furthermore, either in RNA or DNA, this 'backbone' won't change at all, pretty much like the backbone of peptides did not change. Therefore, it looks like a chain from which different bases come out.

Now, despite that the bases have groups which can (and will) h-bond, they are far less polar than the backbone of the polunucleotide. This will have important implications on the secondary and tertiary structure of DNA and RNA polymers.

Since writing this every time we refer to DNA or RNA is pretty tedious, we can use a shorthand notation. We represent the phosphodiester bond as a 'P' in a circle, and a vertical line for the sugar. The base is on top of the vertical line, and in a diagonal we represent the C5' and C3' poistions, which link the different nucleotides.

In this drawing, the C5' end is to the left, and the C3' end to the left. It is very important to recognize this ends in a polymer strand, because they are the places from which the polymer will grow, and they give the DNA/RNA strand a direction. This is important when analyzing the secondary structure of these molecules.

Another simple way of representing the structure of a DNA strand is by simply puting together the initials of the base one next to the other, from C5' to C3', precede by a p (pentadeoxyribose), and ending with an '-OH'. For the pentamer shown above:

Next time we will keep at it with DNA and RNA...

Prepared by Guillermo Moyna, 1999.