The structure of DNA and RNA

Building a nucleotide

DNA is a polymer, which is a long chain of repeating units. The unit is a nucleotide. Its length is counted in nucleotides, or, for a double helix, in base pairs (bp). For example, the bacteriophage ΦX174 has 5386 nucleotides. The bacteriophage lambda has 48502 base pairs. The bacterium Escherichia coli has $4.6 \times 10^6$ base pairs, and a human cell with one set of chromosomes has $3.3 \times 10^9$ base pairs.

A nucleotide has three parts.

1. A nitrogenous base. The purines have two rings: adenine (A) and guanine (G). The pyrimidines have one ring: cytosine (C), thymine (T) and uracil (U).
2. A pentose sugar, with five carbons, numbered $1'$ to $5'$ (said as "one prime"). It is deoxyribose in DNA and ribose in RNA.
3. A phosphate group.

Cytosine is in both DNA and RNA. Thymine is in DNA. Uracil is in RNA in its place.

A base and a sugar joined together make a nucleoside. Add a phosphate, and you have a nucleotide.

The name of the nucleoside depends on the base.

• Adenine: adenosine in RNA, deoxyadenosine in DNA.
• Guanine: guanosine in RNA, deoxyguanosine in DNA.
• Cytosine: cytidine in RNA, deoxycytidine in DNA.
• Uracil: uridine in RNA. It is not found in DNA.
• Thymine: deoxythymidine in DNA. It is not found in RNA.

Joining the nucleotides

Three kinds of bond hold a strand together.

• The N-glycosidic bond joins the base to the $1'$ carbon of the sugar.
• The phosphoester bond joins the phosphate to the $5'$ carbon of the sugar.
• The phosphodiester bond joins two nucleotides. The phosphate on the $5'$ carbon of one nucleotide is also linked to the $3'$ carbon of the next one. The phosphate is joined by two ester bonds, which is why it has this name.

This makes a sugar-phosphate backbone, with the bases pointing sideways. One end of the strand has a free phosphate on a $5'$ carbon, the 5′ end. The other end has a free OH on a $3'$ carbon, the 3′ end. A strand has a direction.

Chargaff's rules

Erwin Chargaff measured the bases of DNA from many species. He found that in every double-stranded DNA:

• the amount of A equals the amount of T, and the amount of G equals the amount of C;
• so the purines equal the pyrimidines, $\text{A} + \text{G} = \text{T} + \text{C}$.

But the ratio $\dfrac{\text{A} + \text{T}}{\text{G} + \text{C}}$ is not the same in every species. It is a mark of the species.

You should find that A and T stay equal, G and C stay equal, and the purines always equal the pyrimidines. A DNA with more G-C pairs has more hydrogen bonds.

The double helix

James Watson and Francis Crick published the model in 1953. They used the X-ray pictures that Rosalind Franklin and Maurice Wilkins had made, and the rules of Chargaff.

• Two strands wind round each other, in a right-handed helix.
• The strands are antiparallel. One runs 5′ to 3′, and the other runs 3′ to 5′.
• The sugar-phosphate backbones are outside. The bases are inside, stacked like the steps of a stair.
• A pairs with T by 2 hydrogen bonds. G pairs with C by 3 hydrogen bonds. A purine always pairs with a pyrimidine, and so every pair has the same width.
• The distance between two base pairs is 0.34 nm.
• In the textbook model there are 10 base pairs in each turn, so the pitch (the length of one turn) is $10 \times 0.34\ \text{nm} = 3.4\ \text{nm}$.

Careful measurements of DNA in water give 10.5 base pairs in a turn, and a pitch of about 3.6 nm. NCERT and most school books print 10 and 3.4 nm, and this course uses those values in all its sums.

RNA

RNA is also a polymer of nucleotides. It differs from DNA in four ways: the sugar is ribose, the base uracil takes the place of thymine, it is usually single stranded, and it is less stable. In RNA, A pairs with U. Where an RNA folds back on itself, as a tRNA does, short stretches pair like a double helix.

Try it in Python

The program makes the partner strand of a piece of DNA, and finds its G-C content and its hydrogen bonds.

Practise with new numbers

Common mistakes

• Saying that A pairs with G. A pairs with T (or with U in RNA). G pairs with C.
• Mixing up the bonds. A-T has 2 hydrogen bonds, G-C has 3.
• Applying Chargaff's rules to a single strand. A equals T only in a double helix.
• Saying that the strands run in the same direction. They are antiparallel.
• Writing thymine in RNA. RNA has uracil.

Remember these

• Nucleoside is base plus sugar. Nucleotide is base plus sugar plus phosphate.
• Bonds: N-glycosidic (base to sugar), phosphoester (sugar to phosphate), phosphodiester (between nucleotides).
• Chargaff: A equals T, G equals C, purines equal pyrimidines.
• Double helix: antiparallel, right-handed, 0.34 nm between base pairs, 10 base pairs in a turn, pitch 3.4 nm (NCERT).
• RNA: ribose, uracil, usually one strand.

Check yourself

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

1. What is the difference between a nucleoside and a nucleotide?

2. Name the bond that joins two nucleotides in a strand. Which two carbons does it join?

3. A sample of DNA has 22 per cent guanine. What per cent is adenine?

4. Why does a purine always pair with a pyrimidine?

5. Give three differences between DNA and RNA.

References

• NCERT (2023). Biology, Textbook for Class XII, chapter 5, Molecular Basis of Inheritance.
• Clark M. A. et al. (2018). Biology 2e, OpenStax, chapter 14, section 14.2, DNA Structure and Sequencing.
• Watson J. D. and Crick F. H. C. (1953). Molecular structure of nucleic acids. Nature, 171, 737 to 738.