Question

A friend argues that redundancy of the genetic code (see Chapter 16 ) is due to wobble pairing. Explain why this isn't the case.

Short answer

Redundancy in the genetic code, referring to the fact that most amino acids are specified by multiple codons, is not solely due to the wobble pairing phenomenon. While wobble pairing does contribute to degeneracy by allowing non-standard base pairing at the third position, redundancy is also influenced by evolutionary pressures such as mutational robustness, error minimization, and modulation of gene expression and translation rates. These factors provide the organism with a balance of robustness, accuracy, and flexibility.

Step-by-step solution

Understanding Redundancy in the Genetic Code

Redundancy in the genetic code refers to the fact that a particular amino acid can be encoded by more than one nucleotide triplet (codon). This feature is also known as degeneracy. There are 64 possible codons, but only 20 amino acids are used in protein synthesis. As a result, most amino acids are specified by multiple codons, which can be considered "redundant" in the genetic code.

Define Wobble Pairing

Wobble pairing is a phenomenon first described by Francis Crick that allows non-standard base pairing between the third nucleotide in a codon and the base in the corresponding anticodon of a tRNA molecule. This non-standard base pairing contributes to the degeneracy of the genetic code, as the same tRNA molecule can recognize more than one codon due to flexibility in this third position, also known as the wobble position.

Addressing the Misconception

While it is true that wobble pairing contributes to the degeneracy of the genetic code, it is not the sole reason for redundancy. Firstly, some amino acids have multiple codons with different bases in all three positions, which cannot be solely explained by wobble pairing. Secondly, there are other factors, including the influence of evolutionary pressures such as mutational robustness and the need for a balance between flexibility and accuracy in translation, that also contribute to the redundancy of the genetic code. In other words, the genetic code has evolved to exhibit redundancy for various reasons beyond wobble pairing alone.

Explain the True Reasons Behind Genetic Code Redundancy

Redundancy in the genetic code can be seen as a product of evolution and adaptation. It allows for several benefits, including: 1. Mutational robustness: Redundant genetic codes can help protect an organism against harmful effects of mutations. If a mutation occurs in a gene but still results in a functional protein, the organism is less susceptible to negative consequences from the mutation. 2. Error minimization: Since multiple codons can code for the same amino acid, errors in translation might not necessarily result in a non-functional protein. This increases the efficiency and accuracy of protein synthesis. 3. Modulation of gene expression and translation rate: Redundancy allows for flexibility in the regulation of gene expression and protein synthesis. Different codons are recognized at different speeds by tRNA molecules, which can affect translation efficiency and response to cellular signals. In conclusion, redundancy in the genetic code is not solely due to the wobble pairing phenomenon. It has evolved as an essential feature of the genetic code, providing a combination of robustness, accuracy, and flexibility that benefits the organism.

Key concepts

Degeneracy of the Genetic Code

The genetic code is considered degenerate because several codons can encode for a single amino acid. This feature of the genetic code is prevalent as there are 64 possible codons, but only 20 amino acids required for protein synthesis. Different codons that specify the same amino acid are known as synonymous codons. This redundancy serves a significant biological purpose, including reduced severity of mutation effects.

For example, leucine can be encoded by six different codons: UUA, UUG, CUU, CUC, CUA, and CUG. This means if one base changes due to a mutation, it may still encode for leucine, thus not altering the protein's structure or function. This aspect of genetic code degeneracy highlights its importance in maintaining genetic and phenotypic stability across generations.

Wobble Pairing

Wobble pairing refers to the flexibility of base-pairing rules at the third position of a codon, where non-standard base pairings can occur. Francis Crick introduced this concept to explain why several codons can be recognized by a single tRNA molecule, expanding the genetic code's redundancy.

For instance, inosine (I) in the anticodon can pair with uracil (U), cytosine (C), or adenine (A) in the codon's third position. This wobble pairing means that tRNAs do not need to match every codon exactly but can still bring the correct amino acid to the ribosome, contributing to both translational efficiency and the degeneracy of the genetic code.

Mutational Robustness

Mutational robustness is the capability of an organism's genetic code to withstand and buffer mutations without exhibiting drastic changes in phenotype. This robustness is partly attributable to the redundancy of the genetic code. Synonymous mutations, those that do not change the amino acid sequence of a protein, are frequently neutral because of degeneracy.

As a protective measure, this redundancy ensures that a mutation on one codon may not alter the protein that is synthesized, thus protecting the organism from potential harmful effects. It is an evolutionary adaptation that contributes to the stability and survival of species.

Translation Efficiency

Translation efficiency refers to how swiftly and accurately a cell translates mRNA sequences into amino acid chains to form proteins. The degenerate nature of the genetic code influences translation efficiency in various ways. It allows for certain codons to be 'preferred' over others, based on their availability and the concentration of corresponding tRNA molecules.

Different organisms might exhibit bias towards certain codons, which can affect the speed of the translation process. For instance, 'rare' codons may slow translation, allowing proper protein folding. On the contrary, 'common' codons can be translated quickly, enhancing the rate of protein production. This modulation is crucial for cells to adapt to their metabolic needs and environmental conditions.