Krdytkyu

I am learning about redundancy in genetics and I came across this statement in my textbook:

more than one codon for an amino acid means that some codons are redundant - the process of protein synthesis could function without them.

I understand that codons are used to make specific amino acids. Does the statement from my textbook mean that if there are two codons which code for the same amino acid that only one of the codons code for an amino acid and not both? I know the term reduntant means that in some cases - more than one codon can code for the same amino acid - but does it also mean that some codons are not used because another codon codes for the same amino acid?

Thanks

The textbook is asserting that translation could function without redundant codons, not that it does. In reality, all possible codons are used.

See this answer on the interchangeability of codons.

The term ‘redundant’ is not ideal in this respect, as that implies a redundancy in reality rather than theory, as @canadianer points out.

Redundancy and Degeneracy

However I would mention that there is another term more usually applied to the fact that certain amino acids are encoded by more than one codon — degeneracy.

There is a Wikipedia entry on Codon Degeneracy:

Degeneracy of codons is the redundancy of the genetic code, exhibited as the multiplicity of three-base pair codon combinations that specify an amino acid. The degeneracy of the genetic code is what accounts for the existence of synonymous mutations.

Although this definition may appear circular in that it refers to redundancy, I am fairly sure that historically degeneracy was one of the attributes listed for the genetic code (e.g. by Crick):

specific

non-overlapping

comma-less

degenerate

universal (no longer true)

I perceive the traces of this in the Nature Scitable entry for the genetic code.

Synonymous Codon Usage

Codons that code for the same amino acid are termed ‘synonymous’. An obvious follow-up to the question and answer in this post is on the lines of “Does it matter which synonymous codon is used? Are all used equally and is it the same in all organisms and genes?”. The answer is that synonymous codon usage is non-random in various different circumstances. This is a broad area, but the Wikipedia entry on Codon Usage Bias is one place to start. There is also a question on this topic on this list.

As David and canadianer pointed out, duplicate codons exist simply because there are 64 codons to encode 20 amino acids and three stop-codons. Even though using only one way to encode each amino acid is possible, in reality it doesn't happen. It seems that duplicate codons make translation more robust and resistant to translational misreading. There are four theories that explain existence of duplicate codons:

• Stereochemical theory


• Coevolution theory


• Error minimization theory


• Frozen accident hypothesis

They are not mutually exclusive and “Origin and evolution of the genetic code: the universal enigma” paper attempts to reconcile them:

Mathematical analysis of the structure and possible evolutionary
trajectories of the code shows that it is highly robust to
translational misreading but there are numerous more robust codes, so
the standard code potentially could evolve from a random code via a
short sequence of codon series reassignments. Thus, much of the
evolution that led to the standard code could be a combination of
frozen accident with selection for error minimization although
contributions from coevolution of the code with metabolic pathways and
weak affinities between amino acids and nucleotide triplets cannot be
ruled out. However, such scenarios for the code evolution are based on
formal schemes whose relevance to the actual primordial evolution is
uncertain. A real understanding of the code origin and evolution is
likely to be attainable only in conjunction with a credible scenario
for the evolution of the coding principle itself and the translation
system.

From my understanding the idea is that codons are grouped by a selection by physico-chemical properties of corresponding amino-acids so a random one nucleotide mutation wouldn't change properties or a corresponding amino-acids too dramatic.