All four nucleotides (A, T, G, and C) are made by sticking a phosphate group and a nucleobase to a sugar. The sugar in all four nucleotides is called deoxyribose. It’s a cyclical molecule—most of its atoms are arranged in a ring structure. The ring contains one oxygen and four carbons. A fifth carbon atom is attached to the fourth carbon of the ring. Deoxyribose also contains a hydroxyl group (-OH) attached to the third carbon in the ring.

The phosphate group is a phosphorous atom with four oxygen atoms bonded to it. The phosphorous atom in phosphate has a marked tendency to bond to other oxygen atoms (for instance, the oxygen atom sticking off the deoxyribose sugar of another nucleotide).

Each type of nucleotide has a different nucleobase stuck to its deoxyribose sugar.

The nucleotide monomers in a DNA polymer are connected by strong electromagnetic attractions called phosphodiester bonds. Phosphodiester bonds are part of a larger class of electromagnetic attractions between atoms that chemists refer to as covalent bonds.

In order to keep things organized, biochemists have developed a numbering system for talking about the molecular structure of nucleotides. These numbers are applied to the carbon atoms in the sugar, starting at the carbon immediately to the right of the oxygen in the deoxyribose ring, and continuing in a clockwise fashion: the numbers range from 1’ (“one prime”), identifying the carbon immediately to the right of the oxygen) all the way to 5’ (“five prime”), identifying the carbon that sticks off the fourth and final carbon in the deoxyribose ring.

The phosphodiester bonds that join one DNA nucleotide to another always link the 3’ carbon of the first nucleotide to the 5’ carbon of the second nucleotide. This forms a covalent bond between the oxygen sticking off the 3’ carbon of the first nucleotide, and the phosphorous atom in the phosphate group that sticks off the 5’ carbon of the second nucleotide. These bonds are called 3’-5’ phosphodiester bonds. Each time nucleotides are bound together, a water molecule is removed (or “lost”) through a process called dehydration synthesis. Many molecules rely on dehydration synthesis to assist with forming polymers.

Chromosomal DNA consists of two DNA polymers that make up a 3-dimensional (3D) structure called a double helix. In a double helix structure, the strands of DNA run antiparallel, meaning the 5’ end of one DNA strand is parallel with the 3’ end of the other DNA strand.

The nucleotides forming each DNA strand are connected by noncovalent bonds, called hydrogen bonds. Considered individually, hydrogen bonds are much weaker than a single covalent bond, such as a phosphodiester bond. But, there are so many of them that the two DNA polymers are very strongly connected to each other.

The hydrogen bonds that join DNA polymers happen between certain hydrogen atoms on one base (called hydrogen bond donors) and certain oxygen or nitrogen atoms on the base across from it (called hydrogen bond acceptors). Adenine (“A”) and Thymine (“T”) each have one donor and one acceptor, whereas Cytosine (“C”) has one donor and two acceptors, and Guanine (“G”) has one acceptor and two donors.

The A nucleotides are always hydrogen bonded to T nucleotides, and C nucleotides are always hydrogen bonded to G nucleotides. This selective binding is called complementary base pairing, and creates consistency in the nucleotide sequences of the two DNA polymers that join together to make a chromosome. This was first observed by Erwin Chargaff, who developed methods for counting nucleotides in DNA samples, and found that the percent of A nucleotides always equaled the percent of T nucleotides, and the percent of G nucleotides always equaled the percent of C nucleotides (within a margin of error). Now, we know that complementary base pairing can be explained by reference to hydrogen bonding between the donors and acceptors on the bases of each nucleotide: A nucleotides and T nucleotides have a match (one donor and one acceptor each), and C nucleotides and G nucleotides have a match (the former has one donor and two acceptors, while the latter has one acceptor and two donors).

Chromosomes are very long structures consisting of two DNA polymers, joined together by hydrogen bonds connecting complementary base pairs. A chromosome is divided into segments of double-stranded DNA called genes.