Acid base behaviour of amino acids

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Tasks

1. Create and optimize a glycine molecule (H₂N-CH₂-COOH). 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) ?

Solution

1. Glycine electrical charge according to pH shift:

• pH<5: NH₃⁺-CH₂-COO^- H⁺; net charge =+1
• 5≤pH<10: NH₃⁺-CH₂-COO^-; net charge =0
• 10≤pH≤13: NH₂-CH₂-COO^-; net charge =-1

2. Glu-Lys dipeptide:

pH
Net charge	+1	-1	-2
Electrophoresis	→ cathode (−)	→ anode (+)	→→ anode (+)

Further readings

• chemguide.co.uk: The acid-base behaviour of amino acids
• Wikipedia:Isoelectric point

Issues