1. Which one of the following changes will not alter the sequence of the encoded protein?
a. Codon optimization
b. Gene methylation
c. Synonymous mutation
d. All of the above

The correct answer is: c. Synonymous mutation.
A synonymous (silent) mutation changes the DNA and mRNA codon but keeps the same amino acid, so the primary protein sequence is unchanged.​

Understanding the question

The question asks: “Which one of the following changes will not alter the sequence of the encoded protein?”
This directly tests understanding of the genetic code, gene regulation, and the difference between DNA-level changes and protein sequence outcomes.​

Options:

• a. Codon optimization

• b. Gene methylation

• c. Synonymous mutation

• d. All of the above

Only one option correctly and unambiguously refers to a change that, by definition, leaves the amino acid sequence of the encoded protein unchanged.​

Option (c): Synonymous mutation

A synonymous mutation is a point mutation in the coding region that changes one codon into another codon for the same amino acid, due to the degeneracy of the genetic code. For example, GAA and GAG both encode glutamate; changing GAA → GAG is a synonymous mutation and does not change the amino acid sequence.​

By definition, synonymous mutations do not alter the primary amino acid sequence of the encoded protein, although they can affect translation speed, folding, mRNA stability, and expression levels. Therefore, option (c) correctly answers “will not alter the sequence of the encoded protein.”​

Option (a): Codon optimization

Codon optimization is the intentional redesign of a coding sequence to use codons that are more frequent or “preferred” in a particular host, in order to improve translation efficiency and protein yield. In standard use, codon optimization is done using only synonymous codons, so the amino acid sequence is intended to remain identical while changing DNA/RNA codon usage.​

However, codon optimization is a process, not an intrinsic property: in principle, a poorly designed optimization could introduce nonsynonymous changes and alter amino acids. In exam context, the safest and definition-based choice for “will not alter the sequence” is the synonymous mutation itself, not the broader process of codon optimization.​

Option (b): Gene methylation

Gene methylation generally refers to methylation of DNA (commonly at cytosine bases in CpG dinucleotides) and is an epigenetic modification that regulates gene expression without changing the base sequence. Methylation can reduce or silence transcription, thereby changing how much protein is produced, or whether it is produced at all.​

Crucially, DNA methylation does not change the codon sequence or the amino acid sequence of the protein; it changes transcriptional activity, not the encoded sequence. So methylation does not “alter the sequence of the encoded protein,” but the question is about types of “changes” at the level of codons and mutations; among the listed options, only synonymous mutation is defined directly by its effect on protein sequence.​

Option (d): All of the above

“All of the above” would only be correct if codon optimization, gene methylation, and synonymous mutation all, by definition, never altered the amino acid sequence of the encoded protein.
Synonymous mutation, by definition, never changes the amino acid sequence, whereas codon optimization is a design strategy that is usually implemented with synonymous changes but is not inherently defined as “never changing amino acid sequence,” and gene methylation is not a mutation in the coding sequence at all.​

Therefore, “all of the above” is not the best or most precise answer in a conceptual genetics question; the exam-style correct option is:

• Correct answer: (c) Synonymous mutation – will not alter the sequence of the encoded protein.