Protonation & Deprotonation

  1. when protonated have a formal charge of 0 & when deprotonated have a formal charge of -1
    CDESTY side chains & carboxylate

    (Cysteine has an S & all the other ones have an O.)
  2. when protonated have a formal charge of +1 & when deprotonated have a formal charge of 0
    HKR (Histidine, Lysine, Arginine) side chains & amino

    (They all have N. Remember that NQ are NOT ionizable.)
  3. Calculate the charge on a fully protonated non-ionizable free amino acid
    • NH3+: +1
    • COOH: 0
    • R: N/A
    • Total charge = +1

    (non-ionizable amino acids: all hydrophobic + NQ)
  4. Calculate the charge on a fully deprotonated non-ionizable free amino acid
    • NH2: 0
    • COO-: -1
    • R: N/A
    • Total charge = -1

    (non-ionizable amino acids: all hydrophobic + NQ)
  5. Calculate the charge on a fully protonated CDESTY free amino acid
    • NH3+: +1
    • COOH: 0
    • R: 0
    • Total charge = +1
  6. Calculate the charge on a fully deprotonated CDESTY free amino acid
    • NH2: 0
    • COO-: -1
    • R: -1
    • Total charge = -2
  7. Calculate the charge on a fully protonated HKR free amino acid
    • NH3+: +1
    • COOH: 0
    • R: +1
    • Total charge: +2
  8. Calculate the charge on a fully deprotonated HKR free amino acid
    • NH2: 0
    • COO-: -1
    • R: 0
    • Total charge = -1
  9. Which amino acids do NOT exist as a zwitterion at a pH of 7.40?
    DEKR

    • DE will have an overall charge of -1
    • KR will have an overall charge of +1

    zwitterion: sum of formal charges in a molecule is 0 (the neutral state). All the other 16 amino acids will have a charge of 0 at a pH of 7.40
  10. Determine the protonated:deprotonated ratios of each ionizable functional group for the free amino acid Lysine.
    • pH is set to 7.40.
    • If pH > pKa, expect more deprotonated.
    • If pH < pKa, expect more protonated.
    • Add exponent value |pH-pKa| to the 10.

    alpha COO- pKa = 2.20. pH > pKa. 1:10^5.2 (prot:deprot)

    alpha NH3+ pKa = 9.40. pH < pKa. 10^2:1 (prot:deprot)

    Lys R group pKa = 10.50. pH < pKa. 10^3.1:1 (prot:deprot)
Author
sophathida
ID
350541
Card Set
Protonation & Deprotonation
Description
Protonated, deprotonated
Updated