What Is the Genetic Code?
Before we can understand what degeneracy of the genetic code means, we must first understand some basics about the genetic code.
A gene is a segment of DNA that codes for a protein. A gene in DNA is encoded as a sequence of nucleotides. There are four different kinds of nucleotides: adenine, guanine, cytosine, and thymine. When DNA is transcribed into mRNA, thymine is replaced by uracil, but otherwise the sequence of nucleotides stays the same.
A protein, meanwhile, consists of a sequence of amino acids. To get from mRNA to protein, there must be a translation system between nucleotides and amino acids. The genetic code is what we call that translation system.
What is Degeneracy?
In the genetic code, three nucleotides code for one amino acid. With four nucleotides, there are 64 possible combinations of three nucleotides. Each is called a codon.
However, only 20 different amino acids are used to make proteins. Since every codon must be used for something to have a working code, this means that at least some of the amino acids must have multiple codons. The term "degenerate" simply refers to the fact that the translation from nucleotide codons to amino acids isn't one to one. Some parts of the genetic code are redundant.
How Genetic Code Degeneracy Works
To get more specific about how translation works, let's talk about tRNA.
A tRNA molecule is a small strip of nucleotides folded into a series of loops. One end, called the anticodon end, matches up with a codon in the mRNA. Adenine matches with uracil, guanine matches with cytosine, and vice versa.
The other end is attached to an amino acid. As protein synthesis occurs, tRNA molecules take turns matching up to the mRNA codons and transferring their amino acids to the forming polypeptide chain that will eventually become a protein.
There are a lot of different kinds of tRNA molecules – not just one per codon, or one per amino acid, as you might expect. Some amino acids associate with only one tRNA, while others associate with several – each with a different anticodon. Some tRNA molecules have anticodons that can match up with multiple codons – this phenomenon is known as wobble. And some tRNA molecules have the same anticodon and same amino acid, but different nucleotides in other areas, indicating that they come from different tRNA genes.
About Base Pair Wobble
Normally, adenine matches up to uracil, and guanine matches up to cytosine. Wobble is where the third nucleotide in a codon can match up with more than one first nucleotide in the tRNA's anticodon. For example, if the tRNA's first nucleotide is a G, it can match with either C or U in the third codon position. tRNA can also occasionally have the nucleotide inosine in its anticodon, which matches up with U, C, or A.
In summary, the amount of degeneracy for a given amino acid is the sum of two parts:
- number of codons that each match only one tRNA with one anticodon
- number of codons that match the same tRNA due to wobble
The total amount of degeneracy of the genetic code, then, would be the degeneracy of every amino acid combined.
References and Credits
Griffiths, Anthony J.F., Jeffrey H. Miller, David T. Suzuki, Richard C. Lewontin, and William M. Gelbart. 1993. An Introduction to Genetic Analysis 5th ed. W.H. Freeman and Company.
Genetic code table from Wikipedia.