Determining net charge on amino acids

[toothless rufus]

Hello! Anybody know how to determine the net charge on an amino acid using pKa and pH values? I thought it was "if pH<pKa, then will have protonated form" and "if pH>pKa, then will have unprotonated form". My biochem book doesn't explain at all how to solve this type of problem, and I have been unable to find a good resource on the net. even though it has several at end of chapter. Thanks!

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[bkpa2med]

I'm not sure, but I believe the more acidic, lower pH, the more positive. More alkaline, higher pH, the more negative. I can be wrong, just taking a shot from what I understand.

 

[Sol Rosenberg]

Hello! Anybody know how to determine the net charge on an amino acid using pKa and pH values? I thought it was "if pH<pKa, then will have protonated form" and "if pH>pKa, then will have unprotonated form". My biochem book doesn't explain at all how to solve this type of problem, and I have been unable to find a good resource on the net. even though it has several at end of chapter. Thanks!

What's the exact question? Your reasoning is correct -- If pH < pKa, "everything" will be in the protonated form. If pH > pKa, "everything" will be in the deprotonated form. For an individual amino acid, "everything" is composed of the following: Amino Group, Carboxyl Group, Side Chain. I don't remember the pKa values for all of the side-chains of amino acids, but I'll make up a problem for Lysine, whose side chain is a string of methylene groups with an amino group at the end (Therefore, its pKa is similar to the amino group on the alpha carbon of the amino acid): What is the net charge on Lysine in a solution of pH = 14?

Carboxyl Group has a pKa of about 5, so the Carboxyl group will be DEPROTONATED (-1 charge)
Amino Group has a pKa of about 9-10, so the Amino group will also be DEPROTONATED (0 charge)

Lysine's side-chain (amino group at the end of its side chain) has a pKa of about 9-10, so at pH = 14, it will be DEPROTONATED (0 charge)

Therefore, the net charge on Lysine at pH=14 is -1 + 0 + 0 = -1

By similar reasoning, at physiological pH, the net charge on Lysine is: -1 + 1 + 1 = +1

I doubt that you need to know the pKas of the side chains for the MCAT, but it's probably a good idea to at least know which side chains are charged at physiological pH (glutamate(-), aspartate(-), lysine(+), arganine(+),) and similarly which are acidic/basic (acidic = glutamate, aspartate, basic = lysine, arganine, AND histidine)

Hope that helps,

Jota

 

[toothless rufus]

Awesome! Thank you, Jota!

 

[NRAI2001]

What's the exact question? Your reasoning is correct -- If pH < pKa, "everything" will be in the protonated form. If pH > pKa, "everything" will be in the deprotonated form. For an individual amino acid, "everything" is composed of the following: Amino Group, Carboxyl Group, Side Chain. I don't remember the pKa values for all of the side-chains of amino acids, but I'll make up a problem for Lysine, whose side chain is a string of methylene groups with an amino group at the end (Therefore, its pKa is similar to the amino group on the alpha carbon of the amino acid): What is the net charge on Lysine in a solution of pH = 14?

Carboxyl Group has a pKa of about 5, so the Carboxyl group will be DEPROTONATED (-1 charge)
Amino Group has a pKa of about 9-10, so the Amino group will also be DEPROTONATED (0 charge)

Lysine's side-chain (amino group at the end of its side chain) has a pKa of about 9-10, so at pH = 14, it will be DEPROTONATED (0 charge)

Therefore, the net charge on Lysine at pH=14 is -1 + 0 + 0 = -1

By similar reasoning, at physiological pH, the net charge on Lysine is: -1 + 1 + 1 = +1

I doubt that you need to know the pKas of the side chains for the MCAT, but it's probably a good idea to at least know which side chains are charged at physiological pH (glutamate(-), aspartate(-), lysine(+), arganine(+),) and similarly which are acidic/basic (acidic = glutamate, aspartate, basic = lysine, arganine, AND histidine)

Hope that helps,

Jota

Nice and easy way to explain it.

If you want to know the exact ratios i think you have to use the Henderson Hassel Bach equation.

 

[shantster]

Nice and easy way to explain it.

If you want to know the exact ratios i think you have to use the Henderson Hassel Bach equation.

Yup, but that's way past the details for the MCAT. We don't need to know the pKas, but it probably is helpful to know that the N-terminal is NH3+ and the C terminal is COO- at physiological pH. As for the actual charge on the amino acids, the basic amino acids (argenine, lysine, and histidine) all are +1 and the acids (glutamate and aspartate) are both -1.