Question

Investigators purify a protein produced by yeast grown under standard growth conditions. They incubate the protein with trypsin and sequence the peptides produced using mass spectrometry. One of the detected peptides, called peptide X, has the sequence Ala-Ser-Ala-Gly-Lys-Glu-Leu-Ile-Phe- Gln. The investigators then isolate the same protein, but this time from yeast grown under the stress of ultraviolet irradiation. When the sample is analyzed, a peptide with the mass of peptide \(X\) is no longer found. Instead, detection reveals a new peptide with the same sequence, except for an amino acid that replaces Ser and has a molecular mass of 167 Da. The investigators conclude that the protein has been altered in response to stress, and that the serine residue in the analyzed peptide has been modified. An unmodified series residue has a molecular mass of \(87 \mathrm{Da}\). What modification might account for the change in the peptide's mass?

Short answer

The serine residue is likely phosphorylated, adding a mass of 80 Da.

Step-by-step solution

Identify Original and New Mass

First, identify the molecular mass of the original serine residue, which is given as 87 Da. The new molecular mass with the modification is given as 167 Da in the stressed condition.

Calculate Mass Difference

Determine the mass difference caused by the modification by subtracting the original serine mass from the new mass: \( 167 \text{ Da} - 87 \text{ Da} = 80 \text{ Da} \).

Identify Possible Modifications

Research common post-translational modifications that result in an added mass of approximately 80 Da. One well-known modification that adds 80 Da is phosphorylation, where a phosphate group is added.

Conclude the Likely Modification

Based on the calculated mass difference of 80 Da and common modifications, the likely modification occurring to the serine residue in response to the stress condition is phosphorylation.

Key concepts

Protein Phosphorylation

Protein phosphorylation is a crucial post-translational modification where a phosphate group is added to a protein. This usually occurs on serine, threonine, or tyrosine residues. The addition of a phosphate group can significantly alter the protein's function by affecting its activity, interaction with other molecules, and localization within the cell.

Phosphorylation is a reversible process, controlled by a balance between kinase enzymes that add phosphate groups and phosphatase enzymes that remove them. This reversible nature allows cells to dynamically respond to changes and regulate processes such as cell growth, differentiation, and apoptosis.

In the context of the exercise, the serine residue in peptide X gains a phosphate group, increasing its mass by about 80 Da. This change suggests the protein is responding to ultraviolet stress by altering its phosphorylation state, reflecting a shift in cellular environment and activating stress response mechanisms.

Mass Spectrometry

Mass spectrometry is a powerful analytical technique used to identify the composition and mass of molecules. In biology, it is particularly useful for studying proteins and peptides. The method involves ionizing chemical compounds to generate charged molecules and measuring their mass-to-charge ratios.

Peptide sequencing through mass spectrometry allows researchers to identify changes in proteins, such as post-translational modifications. For example, as seen in the exercise, mass spectrometry detected a change in peptide X's mass, helping to identify phosphorylation as a stress-induced modification.

The application of mass spectrometry in this context enables precise detection of molecular changes, providing insights into how proteins respond to different conditions, such as stress, and highlighting alterations that may impact biological functions.

Yeast Stress Response

Yeast, like many organisms, has developed strategies to cope with stress. The yeast stress response is a collection of changes at the cellular and molecular levels that help the organism adapt to adverse conditions.

Exposing yeast to ultraviolet irradiation, as in the exercise, triggers a stress response involving various protective mechanisms. Changes in protein phosphorylation, like those seen in peptide X, are part of this response. Such modifications can lead to altered protein functions, assisting yeast in adapting to damage or stress by adjusting metabolic activities and repairing cellular components.

This ability to reprogram proteins rapidly through post-translational modifications allows yeast to survive and thrive even under challenging environmental conditions. Understanding these mechanisms not only provides insights into basic cellular processes but also has implications for fields like biotechnology and stress physiology.