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Nucleic Acids

Contents

• Nucleic acid building blocks.
• Nucleic acids.

If you are just looking for pictures and editable SKC files of organic molecules, you may with to peruse the molecules index page first.

Nucleic acid building blocks

Nucleic acids are composed of nucleotide monomers, which themselves are built from a phosphate group, a sugar, and a nitrogenous base (or alkaloid). The bases are of two types, pyrimidines (single ringed) and purines (double ringed).

The pyrimidines thymine, uracil (only found in RNA, where it substitutes T) and cytosine are nitrogen heterocycles with a single ring. When conjugated to ribose, these are termed thymidine, uridine and cytidine. Here I have shown cytidine in its charged, protonated form (as it would exist at pH < 4.2), and the other two in their uncharged, but still protonated forms. At pH > pK_a for T and U, the proton indicated is lost, and the nitrogen receives a negative charge, which gets delocalized onto the adjacent carbonyl groups.

The purines adenine and guanine are nitrogen heterocycles with a double ring: their nucleosides are termed adenosine and guanosine. Both are shown below in their acid form. Guanosine has two dissociable protons: N¹ on guanosine can lose its proton and become negatively charged.

At pH 7, all five bases are uncharged.

It should be noted as an aside that bases are not just found in DNA, RNA and enzyme cofactors. We also use them as insecticides (pirimicarb), as antibiotics (sulfazidiazine) and as antivirals (more in a minute).

The roles of pyrimidines and purines are many and varied:

• Synthesis of RNA and DNA.
• Energy: ATP, GTP, UTP.
• Reducing power: NADH, NADPH.
• Other coenzymes: CoA, FAD, APS.
• Cell messengers: cAMP, cGMP.
• Excretion: uric acid is a purine.
• Drugs: caffeine is a purine.

Purines are synthesised a bit at a time on a ribose 'handle'.

Nucleotide metabolism requires folate cofactors (the C₁ metabolism, which also involves homocysteine, methionine, S-adenosylmethionine and S-adenosylhomocysteine and vitamin B­₁₂). These must be reduced by dihydrofolate reductase to tetrahydrofolate to accept methylene and formate groups. This enzyme is therefore a target for chemotherapy agents, e.g. methotrexate.

Base pairing is a consequence of hydrogen-bonding between the acceptors and donors on the bases molecules. There are three donor-acceptor pairs in the G≡C pairing, but only two in the A=T pairing. This means it is slightly more difficult to separate DNA strands containing a lot of G≡C pairs, and this property (the increased temperature required to 'melt' i.e. separate G≡C-rich DNA) has been used to classify bacteria.

The pK_a of the groups in the bases has an effect on the H-bonding between complementary bases in nucleic acids. Here you can see one of the three H-bonds between guanine and cytosine being disrupted by the addition of a proton (at low pH) to the middle N in the cytosine. This can potentially cause mutation.

The bases are also prone to spontaneous isomery (tautomery), regardless of the pH. Here, the minor tautomers of the four DNA bases are shown. The minor tautomer is usually present at about 0.01% and will H-bond to the 'wrong' base. This is the main reason that DNA polymerase has a proofreading enzyme function built in, to check for such short-lived mistakes.

The nucleoside inosine (a derivative of the purine base hypoxanthine), which is found in many tRNAs, is capable of forming several sorts of hydrogen bond, and can consequently pair with A, C and U in mRNA, leading to the phenomenon known as wobble: the ability of one tRNA to bond to more than one codon.

Nucleosides and nucleotides are combinations of a base with a sugar. A nucleoside is an N-glycoside formed between a base and a sugar (usually ribose or deoxyribose). A nucleotide is a phosphate ester of a nucleoside. DNA nucleotides are more stable to acid hydrolysis of the glycosidic bond, which is one reason that DNA has superceded RNA as the main genetic storage molecule: it is less prone to mutation.

Acyclovir (for cold sores) and AZT (an antiretroviral used in HIV therapy) are both nucleotide analogues, i.e. they are picked up by mistake by viral replicating enzymes, and this stops nucleic acid synthesis. They stop the synthesis because they lack the -OH group at position 3 of the (deoxy)ribose that normally allows the extension of the nucleic acid chain. Similar nucleotide analogues (dideoxynucleotides, ddNTPs) can be used to sequence DNA.

Nucleic acids

Nucleic acids are simply polymers of nucleotides: a bond is formed between the 5′ hydroxyl group on the (deoxy)ribose and the OH group on the phosphate attached to the 3′ position of the ribose. Nucleic acid sequences are conventionally written in the 5′ to 3′ direction. In the diagram below the 5′ end is at the top.

RNA differs from DNA in is bases (it has uracil, not thymine) and in the hydroxylation of carbon-2 in the ribose ring.

Why aren't our genomes made from RNA? Purines take up protons at low pH, making them good leaving groups at low pH. At low pH, the bond between base and ribose is readily hydrolysed. Hence both DNA and RNA are unstable at very low pH. However, RNA has the additional disadvantage that at high pH, the backbone of the RNA molecule is hydrolysed too! This is because the 2′ OH group is a good nucleophile, and readily attacks the phosphate group on the 3′ carbon to form a cyclic product that is unstable to hydrolytic (hydroxide ion) attack. The upshot is that the phosphate group is swapped between the two carbons, and the sugar phosphate backbone is broken. So RNA needs cosseting to stop it from falling apart in a way that DNA doesn't.

RNA viruses are the only organisms whose genomes are written in RNA, and they have a notoriously high mutation rate. The packaging of DNA into the nucleus of a eukaryote is quite detailed: this summary diagram may help if you don't want to go into as much detail:

Test yourself

1. 5-methylcytosine is a common cytosine derivative found in epigenetic alterations to DNA. Show how it can cause mutation by oxidative (hydrolytic) deamination.

   

2. Why are nucleosides useful in antiviral therapy?
3. Why must much greater care be taken in preparing samples for reverse-transcriptase PCR, than for conventional Taq polymerase PCR?
4. Describe the importance of pyrroles.
5. Compare and contrast purine and pyrimidine synthesis.
6. What chemicals do plants have at their disposal to attack potential herbivores?

Answers

Bibliography

• Bloomfield, V. A., Crothers, D. M. and Tinocco, I. J. (2000). Nucleic acids - structures, properties, and functions. University Science Book, Sausalito, California, USA
• Fasman, G. D. (editor) (1975). Handbook of biochemistry and molecular biology. 3rd edition.. CRC Press, Cleveland, Ohio, USA