Protonation & Deprotonation

CDESTY side chains & carboxylate

(Cysteine has an S & all the other ones have an O.)

HKR (Histidine, Lysine, Arginine) side chains & amino

(They all have N. Remember that NQ are NOT ionizable.)

• NH3+: +1
• COOH: 0
• R: N/A
• Total charge = +1

(non-ionizable amino acids: all hydrophobic + NQ)

• NH2: 0
• COO-: -1
• R: N/A
• Total charge = -1

(non-ionizable amino acids: all hydrophobic + NQ)

• NH3+: +1
• COOH: 0
• R: 0
• Total charge = +1

• NH2: 0
• COO-: -1
• R: -1
• Total charge = -2

• NH3+: +1
• COOH: 0
• R: +1
• Total charge: +2

• NH2: 0
• COO-: -1
• R: 0
• Total charge = -1

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

• 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)