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Determining Net Charge of a Peptide quiz #1 Flashcards

Determining Net Charge of a Peptide quiz #1
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  • How do you determine the net charge of a peptide at a given pH?
    To determine the net charge of a peptide at a given pH, identify all ionizable groups (N-terminus, C-terminus, and any ionizable side chains), compare each group's pKa to the pH, assign the appropriate charge based on whether the conjugate acid or base form predominates, and sum the charges of all groups.
  • What is the first step in determining the net charge of a peptide at a given pH?
    Identify all ionizable groups in the peptide, including the N-terminus, C-terminus, and any ionizable side chains.
  • How do you decide if an ionizable group is charged or uncharged at a specific pH?
    Compare the pKa of the group to the pH; if pKa > pH, the conjugate acid form predominates (usually charged), and if pKa < pH, the conjugate base form predominates (may be neutral or charged).
  • Why is it important to use the correct set of pKa values when calculating peptide net charge?
    Because pKa values for amino acid residues in peptides can differ from those of free amino acids, and using the wrong set can lead to incorrect charge calculations.
  • How can the microenvironment of a peptide affect its net charge calculation?
    The microenvironment can shift the pKa values of ionizable groups, affecting whether they are charged or uncharged at a given pH.
  • Which groups in a peptide always have free ionizable alpha amino or alpha carboxyl groups?
    Only the first (N-terminus) and last (C-terminus) amino acid residues in a peptide chain have free ionizable alpha amino or alpha carboxyl groups.
  • In the example peptide with arginine, histidine, aspartic acid, and glutamine, which side chains are considered ionizable at pH 7.4?
    The side chains of arginine, histidine, and aspartic acid are considered ionizable at pH 7.4.
  • What is the net charge of the example peptide (arginine, histidine, aspartic acid, glutamine) at pH 7.4?
    The net charge is zero at pH 7.4 after summing the charges of all ionizable groups.
  • What charge does the N-terminus typically have at a pH below its pKa?
    The N-terminus is typically positively charged (NH3+) when the pH is below its pKa.
  • What is the general process for calculating the net charge of a peptide?
    Assign charges to each ionizable group based on their pKa and the solution pH, then sum all the charges to get the net charge.