Nucleotides, DNA and RNA

What DNA and RNA are made of

A grain of rice, a drop of blood and a leaf all carry instructions for building a living thing. The instructions are written in two kinds of long molecules called nucleic acids. They are DNA and RNA.

A nucleic acid is a polymer. Its units, the monomers, are nucleotides. Thousands or even millions of them join in a row, so a nucleic acid is also called a polynucleotide.

One nucleotide

Each nucleotide has three parts.

• A nitrogenous base: a ring-shaped compound that holds nitrogen.
• A pentose sugar: a sugar with five carbon atoms.
• A phosphate group.

There are five bases. Adenine and guanine are purines, which have two rings. Cytosine, thymine and uracil are pyrimidines, which have one ring.

The sugar is ribose in RNA and deoxyribose in DNA. Deoxyribose has one oxygen atom fewer than ribose, which is where its name comes from.

A base joined to a sugar is a nucleoside. The nucleosides are adenosine, guanosine, cytidine, uridine and thymidine. When a phosphate group is added to the sugar of a nucleoside, the result is a nucleotide. The nucleotides are adenylic acid, guanylic acid, cytidylic acid, uridylic acid and thymidylic acid.

Keep the two names straight with one rule. Base plus sugar is a nucleoside. Base plus sugar plus phosphate is a nucleotide.

How DNA and RNA differ

• Sugar: DNA has deoxyribose; RNA has ribose.
• Bases: DNA has adenine, guanine, cytosine and thymine. RNA has uracil in place of thymine.
• Shape: DNA is usually a double strand. RNA is usually a single strand.

RNA comes in three main kinds, called messenger, transfer and ribosomal RNA. All three help the cell to build proteins.

The double helix

The structure of DNA was worked out by James Watson and Francis Crick. They used X-ray pictures taken by Maurice Wilkins and Rosalind Franklin. Their model is the double helix.

• DNA is made of two polynucleotide strands wound round each other, like a twisted ladder.
• The backbone of each strand, the sides of the ladder, is a chain of sugars and phosphates.
• The bases point inwards and meet in the middle. Each pair of bases is a rung.
• The two strands are antiparallel: they run in opposite directions.
• Adenine pairs with thymine by two hydrogen bonds. Guanine pairs with cytosine by three hydrogen bonds.
• A purine always pairs with a pyrimidine, so every rung has the same width.

The helix turns as it climbs. One full turn is called the pitch. It is 3.4 nm long and holds about 10 base pairs. So neighbouring base pairs are 0.34 nm apart. One nanometre, written nm, is a billionth of a metre.

Chargaff's rules

Erwin Chargaff measured the bases in the DNA of many living things. His results are now called Chargaff's rules.

• The amount of adenine equals the amount of thymine.
• The amount of guanine equals the amount of cytosine.
• So the purines, adenine plus guanine, equal the pyrimidines, thymine plus cytosine.

The ratio of adenine plus thymine to guanine plus cytosine differs from one species to another. The pairing of bases explains the rules. Every adenine has a thymine opposite it, and every guanine has a cytosine opposite it.

You should find that with $30$ per cent adenine, thymine is also $30$ per cent, and guanine and cytosine are $20$ per cent each. A piece of $1000$ base pairs is $340$ nm long, makes $100$ turns, and has $2400$ hydrogen bonds. More guanine and cytosine means more hydrogen bonds, so that DNA is held together more firmly.

Try it in Python

The program writes the partner of a short strand and counts the bases in both strands together.

You should see adenine and thymine at $35$ per cent each, and guanine and cytosine at $15$ per cent each. With the new strand, adenine and thymine are $8$ per cent each, and guanine and cytosine are $42$ per cent each. The pairs always match.

Practise with new numbers

Common mistakes

• Pairing adenine with guanine. Adenine pairs with thymine, and guanine pairs with cytosine. A purine always pairs with a pyrimidine.
• Giving every pair two hydrogen bonds. Adenine and thymine have two; guanine and cytosine have three.
• Putting thymine in RNA. RNA has uracil in its place.
• Mixing up the two names. A nucleoside has no phosphate group. A nucleotide has one.
• Drawing the two strands in the same direction. They are antiparallel.

Remember these

• A nucleotide is a base, a pentose sugar and a phosphate group. A nucleoside has no phosphate.
• Purines: adenine and guanine. Pyrimidines: cytosine, thymine and uracil.
• DNA: deoxyribose and thymine, usually double. RNA: ribose and uracil, usually single.
• Double helix: antiparallel strands; A with T by two bonds, G with C by three; pitch $3.4$ nm; $10$ base pairs a turn.
• Chargaff: adenine equals thymine, and guanine equals cytosine.

Check yourself

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

1. What are the three parts of a nucleotide?

2. Which bases of DNA are purines, and which are pyrimidines?

3. Give two differences between DNA and RNA.

4. In a DNA sample, $35$ per cent of the bases are cytosine. What per cent is adenine?

5. How far apart are neighbouring base pairs in the helix?