Nucleic Acids and Directionality

One monomer, two polymers

A nucleotide has three parts: a phosphate group, a five-carbon sugar, and a nitrogenous base. Change the sugar and you change the molecule.

• DNA — deoxyribose, double-stranded, bases A, T, C, G. Stable, used for long-term storage.
• RNA — ribose (an extra $-\text{OH}$), usually single-stranded, uses U instead of T. Less stable, used for short-lived working copies.

Purines (A, G) have two rings; pyrimidines (C, T, U) have one. A purine always pairs with a pyrimidine, so the helix keeps a constant width: A–T with two hydrogen bonds, G–C with three. DNA rich in G and C therefore takes more heat to separate.

Every strand has a direction

The carbons of the sugar are numbered $1'$ to $5'$. A phosphodiester bond joins the $3'$ hydroxyl of one nucleotide to the $5'$ phosphate of the next, so one end of a strand is a free $5'$ phosphate and the other a free $3'$ hydroxyl.

• The two strands of DNA are antiparallel: one runs $5'\to3'$ while its partner runs $3'\to5'$.
• Polymerases can only add a nucleotide to a free $3'$ end, so synthesis always runs $5'\to3'$.
• Ribosomes read mRNA $5'\to3'$ as well. By convention a written sequence is $5'\to3'$ unless labelled otherwise.

The order is the information

Nothing in the backbone carries meaning — it is identical everywhere. The information sits entirely in the sequence of bases, exactly as a protein's information sits in the sequence of amino acids.