THE STRUCTURE OF NUCLEIC ACID CHAINS
Nucleotides are joined together in DNA and RNA by phosphate ester bonds between the phosphate component of one nucleotide and the sugar component of the next nucleotide. An ester bond is a bond which occurs between a Carbon atom and an Oxygen atom.
More and more nucleotides can be added on by the same process of forming ester bonds until an immense chain is formed. But no matter how long a polynucleotide chain is, one end of the nucleic acid molecule always has a free -OH group on the sugar at the Carbon known as C3' (called the 3' end) and the other end of the molecule always has a phosphoric acid group at C5' (the 5' end). The Carbons get this name from a counting system illustrated in the next diagram.
Beginning from the "right-hand" side of the sugar, count the Carbons....1', 2', 3' (where the phosphate group of the next nucleotide in a series can be linked via a chemical bond), 4', 5' (where the phosphate group of the previous nucleotide is linked via a chemical bond).
This "counting system" allows the strand of nucleic acid to be oriented: the 5' end of the molecule always ends with a phosphate and the 3' end of the strand always ends with a sugar. You may be wondering why we don't just call the 5' end the "top" of the DNA or RNA molecule and the 3' end the "bottom" of the molecule. But in order to name something the "top", we're assuming that that end of the molecule is "up".
But how can you assume this in a cell?
YOU CAN'T! Remember that cells don't have specific orientations and that the nucleic acid within the cells is tightly wrapped and coiled around special proteins in the nucleus. So the terms "top" and "bottom" or "left" and "right" are pretty useless in this situation. Any nucleotides in between the 3' and 5' nucleotides would be involved in phosphodiester bonds. These nucleotides on the ends of each strand have a "free" end which is not involved in such a bond.
Click here to see one interpretation of the general structure of the nucleic acid DNA. The phosphate groups joined to sugar groups form what is known as the "backbone" of a nucleic acid molecule. The bases are attached to the sugars at a different point than the phosphate groups to form this generalized structure. The shape of DNA (a double-stranded molecule) is often referred to as a "double helix" or "twisted ladder" with the sugar-phosphate backbone forming the sides of the ladder and the nitrogen bases forming the rungs of the ladder in the middle.
The sequence of nucleotides in a chain is described by starting at the 5' end and identifying the bases in the order that they are linked together. Rather than write the full name of each nucleotide or each base, however, it's quicker and easier to use the simple one-letter abbreviations of the bases: A for Adenine, G for guanine, C for cytosine, T for thymine (and U for uracil in RNA). So, to describe a sequence of DNA, you might write something like -T-A-G-G-C-T-.
In the coming sections of this tutorial and in lecture, you will learn that the exact structure of a protein depends on the sequence in which the individual amino acids are connected. The same is true with nucleic acids; the exact structure of a nucleic acid molecule depends on the sequence in which individual nucleotides are connected. We'll return to this concept later in the tutorial.