The wobble hypothesis, introduced by Francis Crick, addresses the flexibility of the genetic code in relation to codon-anticodon pairing in protein synthesis. This hypothesis explains how the pairing between the third base of a codon and the corresponding base of an anticodon in tRNA is not as strict as the other two bases. The first two bases of the codon form standard Watson-Crick base pairs with the anticodon, but the third base can "wobble" and form non-standard base pairs. This wobble allows for a certain degree of variation or mismatch, enabling one tRNA molecule to recognize and bind to multiple codons that code for the same amino acid. For instance, the tRNA for Alanine can recognize and bind to GCU, GCC, and GCA codons, all of which code for Alanine. This flexibility contributes to the efficiency and accuracy of protein synthesis, as fewer tRNA species are needed to read all codons. It also provides a buffer against some mutations, as changes in the third nucleotide of a codon might not affect the amino acid sequence of the protein, thanks to the wobble base pairing.

The start codon AUG plays a critical role in the translation process. It not only signifies the beginning of a protein-coding sequence but also sets the reading frame for the ribosome. Translation occurs in a 5' to 3' direction along the mRNA, and the ribosome reads nucleotides in groups of three (codons). The AUG codon, which codes for the amino acid Methionine, is the signal for the ribosome to begin translating the mRNA into a protein. It is the point at which the ribosome assembles and starts reading the mRNA to synthesize the polypeptide chain. The correct identification of the start codon is crucial because if the ribosome starts translating at the wrong point, the entire sequence of amino acids will be incorrect, leading to a nonfunctional or harmful protein. In eukaryotes, the first AUG codon from the 5' end of the mRNA is typically chosen as the start site, although there are exceptions. This specificity and the vital role of the start codon in ensuring accurate protein synthesis underscore its importance in the genetic translation process.

Silent mutations, also known as synonymous mutations, occur when a change in the nucleotide sequence of a codon does not result in a change in the amino acid sequence of the protein. This phenomenon is possible due to the redundancy of the genetic code, where multiple codons can encode the same amino acid. For example, if a mutation changes the third nucleotide of the UCU codon (which codes for Serine) to UCC, UCA, or UCG, the encoded amino acid remains Serine. Thus, in protein synthesis, silent mutations generally do not affect the resulting protein's structure or function. However, it's important to note that while the amino acid sequence remains unchanged, silent mutations can still have an impact on the protein synthesis process. They can influence the efficiency and accuracy of translation by affecting mRNA stability and the speed of translation, as some tRNAs are more abundant or efficient than others. Additionally, in certain contexts, silent mutations might affect the regulation of gene expression or splicing mechanisms. Therefore, while silent mutations often do not alter the protein product directly, they can have subtle effects on the overall process of gene expression and protein synthesis.

A single codon does not code for more than one amino acid. The genetic code is specific and unambiguous, meaning each codon corresponds to only one amino acid. This specificity is crucial for the accurate translation of genetic information into proteins. The genetic code comprises 64 codons (61 codons for amino acids and 3 stop codons). Despite the redundancy, where multiple codons can specify the same amino acid, the reverse is not true; one codon cannot specify multiple amino acids. This rule is known as the 'one codon-one amino acid' rule. For instance, the codon AUG will always code for Methionine, and never for any other amino acid. The specificity of the genetic code ensures that proteins are synthesized correctly, as each codon precisely dictates the addition of a specific amino acid to the growing polypeptide chain. Any deviation from this rule would lead to ambiguity in protein synthesis, potentially resulting in nonfunctional or deleterious proteins.

A stop codon mutation can have significant effects on protein synthesis, leading to various cellular consequences. A stop codon (UAA, UAG, UGA) signals the termination of protein synthesis by prompting the release of the nascent polypeptide chain from the ribosome. If a mutation occurs in a codon that changes it to a stop codon (a process known as nonsense mutation), it can result in premature termination of translation. This leads to the production of a truncated protein that is often nonfunctional or unstable. Such premature termination can have serious implications, as the incomplete protein may lack critical functional domains, leading to loss of function or gain of harmful functions. Additionally, these truncated proteins can be rapidly degraded by the cell's quality control mechanisms, further reducing their functional availability. In some cases, these premature termination products can exert dominant-negative effects or interfere with normal cellular processes. On the other hand, if a stop codon is mutated into a sense codon (codon for an amino acid), this can result in the extension of the protein beyond its normal length. Such extended proteins can be nonfunctional or deleterious. Overall, mutations involving stop codons are often harmful and can be associated with various genetic disorders and diseases.