Acid-Base Properties of Amino Acids

Investigate the pH-dependent protonation of amino acids.


  1. Create and optimize a glycine molecule (). Open Build Menu and select Add Hydrogens for pH... Choose different values of pH : 1,2,3,…,13 and note the effect of pH shift on electrical charge of glycine.
  2. In a new View, create a (Glutamic acid - Lysine) dipeptide using Build Menu > Insert > Peptides... Set pH to 3 and calculate the correspondent electrical charge of the dipeptide. Do the same for pH=7 and 13.

When performing a paper electrophoresis at these pHs, in which direction will the dipeptide move (anode or cathode) ?


  1. Glycine electrical charge according to pH shift:
    • pH<5: ; net charge =+1
    • 5≤pH<10: ; net charge =0
    • 10≤pH≤13: ; net charge =-1
  2. Glu-Lys dipeptide:
Net charge +1 -1 -2
Electrophoresis → cathode (−) → anode (+) →→ anode (+)

Further readings