Nucleotides: the building blocks

Once DNA was known to be the genetic material, the next question was how its structure lets it store information and get copied. In biology, structure explains function, so the answer starts with the small parts DNA is made of.

DNA and RNA are nucleic acids

DNA (deoxyribonucleic acid) and its close relative RNA (ribonucleic acid) are both nucleic acids: long chains, or polymers, built from repeating units called nucleotides. Nucleic acids store, use, and pass on genetic information.

The name comes from two facts. DNA was first found in cell nuclei, and these molecules are acids: in water they release hydrogen ions (H⁺) and carry a negative charge.

Five levels of DNA structure

DNA is easiest to understand if you build it up in layers, each made from the one before.

Most bacteria have a genome made of one circular chromosome. A eukaryotic cell (a cell with a nucleus, like yours) has DNA in its nucleus, and also in its mitochondria and, in plants, its chloroplasts. Levels 1 to 3 come first; chromosomes appear at the end of the chapter.

The three parts of a nucleotide

Every nucleotide has the same three parts:

1. A phosphate group, a phosphorus atom surrounded by oxygen atoms.
2. A pentose, a sugar with five carbon atoms.
3. A nitrogen-containing base, a ring-shaped molecule made of carbon and nitrogen atoms.

Purines and pyrimidines

Five different bases occur in nucleotides, though each nucleotide carries only one. They fall into two groups by shape. Purines are bigger, with two fused rings. Pyrimidines are smaller, with a single ring.

So DNA uses A, G, C, and T, while RNA uses A, G, C, and U. Thymine and uracil are the swap. Since three bases are shared, the one part that always differs between a DNA nucleotide and an RNA nucleotide is the sugar.

Numbering the atoms

To describe how nucleotides connect, biologists number the atoms in each nucleotide. The carbons in the sugar get a prime mark (′) so they can’t be confused with atoms in the base, which are numbered without one.

The sugar carbons are 1′ (“one prime”) through 5′. Counting starts at the carbon just to the right of the oxygen atom in the sugar’s ring and goes clockwise. The 5′ carbon sticks out of the ring. Two attachment points are worth memorizing:

• The base attaches to the 1′ carbon.
• The phosphate group attaches to the 5′ carbon.

The 3′ carbon matters too, because that is where the next nucleotide will connect. Its role comes up in the next segment.

What “deoxy” means

Ribose and deoxyribose differ by a single oxygen atom. Ribose has a hydroxyl group (–OH) on its 2′ carbon. Deoxyribose has only a hydrogen there. The prefix deoxy- means “without oxygen,” so deoxyribose is simply ribose missing the oxygen at 2′.

Check yourselfA nucleotide contains ribose and uracil. Did it come from DNA or RNA, and would you need both clues to tell?

It came from RNA. Either clue alone is enough: ribose is the RNA sugar (DNA has deoxyribose), and uracil appears only in RNA (DNA has thymine instead).