1. A polypeptide chain has a large percentage of acidic and basic amino acids in

Question

1. A polypeptide chain has a large percentage of acidic and basic amino acids in it. The R groups of these amino acids form ionic interactions, which helps the protein to maintain it’s structure. This particular polypeptide works well under an optimum pH of 7. Ignoring effects of strong acids and bases on peptide bonds, what will happen to the tertiary structure of the protein if you move it stomach acid, which has a pH of 1-2. Why? Be specific regarding what influence the pH will have on the bonds maintaining tertiary structure in the molecule. Include the amino acid charges of the acidic and basic amino acids at the acidic pH, as well as the concept of pK in your answer. Assume that acidic amino acids have a pK of approximately 4.7 and basic amino acids have a pK of approximately 10.

2. Ignoring peptide length (or lack thereof) where would this portion of a polypeptide be most likely to be found: On the inside or on the outside surface of a protein floating around in the cytoplasm? Explain

3. A mutation occurs in the SRC kinase such that the tyrosine on the loop over the active site is changed to aspartic acid. This mutation mimics phosphorylation.
a. knowing what you know about the properties of phosphate groups and aspartic acid, why does aspartic acid mimic phosphorylation?
b. What would be the implication of this mutation on the function of the SRC kinase?

Explanation / Answer

1. when the above mentioned polypeptide is placed in the stomach, which has a low pH, the structure and stability of the protein changes. usually, denaturation of protein occurs.

2. at low pH, the H+ ions will increase and hence more groups will be protonated. the acidic groups will become uncharged when protonated and the basic groups will be charged.

3. the charged groups will move towards the surface of the protein and the uncharged groups tend to move inwards. the structure changes. electrostatic interactions will occur within the medium and salt bridges may occur.

4. the pK values will be increased at low pH.

5. tyrosine kinase enzyme transfers phosphate group from ATP to a protein in a cell. whereas aspartate kinase enzyme catalyses phosphorylation of amino acid aspartate. but aspartate occurs mainly in plants and animals. so, mutation of SRC kinase may lead to cancer

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