Bases, nucleosides and nucleotides

Four letters, three parts

A page of text is built from letters. DNA stores the instructions of a cell using only four letters, the four bases. The chain that carries the letters is built from two other parts. So every unit of DNA and RNA has three parts:

1. A nitrogenous base.
2. A five-carbon sugar.
3. A phosphate group.

The sugars

The sugar of RNA is ribose. The sugar of DNA is 2-deoxyribose, which has an H in place of the $\text{-}\text{OH}$ on carbon 2. That is the only difference, but it makes DNA more stable. In nucleic acids we number the carbons of the sugar 1′, 2′, 3′, 4′ and 5′ (say "one prime"), to keep them apart from the numbering of the base. Both sugars are in the furanose ring form, with the ring oxygen between C-1′ and C-4′.

The bases

There are five bases, in two families:

• Purines have two fused rings: adenine (A) and guanine (G).
• Pyrimidines have one ring: cytosine (C), thymine (T) and uracil (U).

DNA has A, G, C and T. RNA has A, G, C and U. Thymine is uracil with a methyl group on C-5.

Nucleoside and nucleotide

A base joins to the sugar through a bond from C-1′ of the sugar to N-9 of a purine, or to N-1 of a pyrimidine. This is an N-glycosidic bond. The base and sugar together make a nucleoside.

A phosphate group joined to the C-5′ hydroxyl group of the sugar as an ester makes a nucleotide.

• Adenine (A): the nucleoside is adenosine in RNA and deoxyadenosine in DNA. The RNA nucleotide is adenosine monophosphate (AMP).
• Guanine (G): guanosine and deoxyguanosine. The RNA nucleotide is guanosine monophosphate (GMP).
• Cytosine (C): cytidine and deoxycytidine. The RNA nucleotide is cytidine monophosphate (CMP).
• Thymine (T): found in DNA only, as thymidine (deoxythymidine).
• Uracil (U): found in RNA only, as uridine. The nucleotide is uridine monophosphate (UMP).

Adenosine triphosphate, ATP, has three phosphates in a chain. It is the energy carrier of the cell. Removing the last phosphate by hydrolysis releases about $30.5\ \text{kJ/mol}$ under standard conditions.

Joining nucleotides into a strand

The 3′ hydroxyl group of one nucleotide forms an ester with the phosphate on the 5′ carbon of the next nucleotide. The result is a phosphodiester linkage. It has a phosphate group joined by two ester bonds, one to each sugar. Repeating this gives a polynucleotide.

• The backbone is a chain of sugar and phosphate, one after the other. The bases stick out from it.
• Every phosphate carries a negative charge at neutral pH, so DNA is a polyanion.
• A strand has direction. One end has a free 5′ phosphate, the 5′ end. The other end has a free 3′ hydroxyl group, the 3′ end. We write a sequence from 5′ to 3′.
• A strand of $n$ nucleotides has $n - 1$ phosphodiester linkages.

On complete hydrolysis, DNA gives phosphoric acid, 2-deoxyribose, and the four bases A, G, C and T. RNA gives phosphoric acid, ribose, and A, G, C and U. Partial hydrolysis gives nucleotides and nucleosides.

DNA and RNA compared

• Sugar: 2-deoxyribose in DNA, ribose in RNA.
• Bases: A, G, C and T in DNA. A, G, C and U in RNA.
• Strands: two strands, in a double helix, in DNA. Usually one strand in RNA.
• Main job: DNA stores the genetic information. RNA copies it and builds proteins.

Chargaff's rules

Erwin Chargaff measured the bases in DNA from many species. He found two rules for double-stranded DNA:

• The amount of adenine equals the amount of thymine, and the amount of guanine equals the amount of cytosine.
• So the purines equal the pyrimidines: A + G = T + C.

The ratio (A + T) to (G + C) differs from one species to the next, but A = T and G = C always hold. The next lesson explains why.

Set 12 base pairs and 6 G-C pairs. Now make all 12 pairs G-C. The number of hydrogen bonds goes from 30 to 36. The melting temperature rises, because more heat is needed to separate the strands. This simple rule works for very short stretches only. Long DNA melts at a temperature that also depends on the salt in the water.

Practise with new numbers

Try it in Python

The program builds the partner of a strand. It then counts the G-C and A-T pairs and the hydrogen bonds of the duplex.

Common mistakes

• Mixing up nucleoside and nucleotide. A nucleoside has no phosphate. A nucleotide has one or more.
• Putting thymine in RNA. RNA has uracil.
• Forgetting that a strand has direction. 5′ and 3′ are not the same end.
• Counting the linkages as the number of nucleotides. A strand of $n$ nucleotides has $n - 1$ phosphodiester linkages.

Remember these

• A nucleotide is base + sugar + phosphate. A nucleoside is base + sugar.
• DNA: deoxyribose with A, G, C, T. RNA: ribose with A, G, C, U. Purines: A and G. Pyrimidines: C, T and U.
• Nucleotides are joined by 3′ to 5′ phosphodiester linkages. A strand runs 5′ to 3′.
• Chargaff: A = T, G = C, and purines equal pyrimidines.

Check yourself

Try each one on your own first. If you are stuck, open a hint. Then check with Show the answer.

1. Name the two bases that are purines, and the three that are pyrimidines.

2. What is the difference between adenosine and adenosine monophosphate?

3. A DNA strand has 30 nucleotides. How many phosphodiester linkages does it have?

4. Which sugar differs between DNA and RNA, and where?

References

• Nelson and Cox, Lehninger Principles of Biochemistry, 8th edition, Chapter 8 (Nucleotides and Nucleic Acids).
• NCERT Chemistry for Class 12, Part II, the chapter Biomolecules (nucleic acids: chemical composition).
• OpenStax, Organic Chemistry, Chapter 28 (Biomolecules: Nucleic Acids).