Chemistry Clarification: hydrophobic/hydrophilic, acidic/basic, polar/nonpolar, +/- charged

[mmktiger]

Hi!

1. I am looking for some clarification of the relationship between these concepts.

hydrophobic/hydrophilic
non-polar/polar
negatively charged/positively charged
acidic/basic

I understand that a molecule can be any of the above. But I am wondering how these are related. From my current understanding:

Hydrophobic molecules are non-polar (since water is polar)
Hydrophilic molecules are polar (since water is polar)

Acidic molecules are typically positively charged (electron acceptor)
Basic molecules are typically negatively charged (electron donor)

2. How does the environment surrounding an animo acid affects its pKa value?

From my current understanding:

Hydrophobic/negative/basic environment, pka would be increased (increased chance of amino acid being protonated).
Hydrophilic/positive/acidic environment, pka would be decreased (increased chance of amino acid being deprotonated).

I am unsure of these concepts and hope that someone can provide some clarification and tell me if my current understanding is right or lacking.

Thank you!

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[aldol16]

Hydrophobic molecules are non-polar (since water is polar)
Hydrophilic molecules are polar (since water is polar)

Good.

Acidic molecules are typically positively charged (electron acceptor)
Basic molecules are typically negatively charged (electron donor)

There's no typical charge for either acids or bases. It really depends on the acid. So phosphoric acid or sulfuric acid or citric acid, etc. are uncharged and then after they deprotonate, they become negatively charged as the conjugate base. The only rule is that you have to remember conservation of charge.

Hydrophobic/negative/basic environment, pka would be increased (increased chance of amino acid being protonated).
Hydrophilic/positive/acidic environment, pka would be decreased (increased chance of amino acid being deprotonated).

So if a residue is in an environment with either no charge or negative charge, it will want to reduce repulsion and pair like-charges, so it will want to be protonated if the conjugate base is negative (e.g. Asp, Glu). So to remain protonated, you must raise the pKa. But if you have a basic residue that's already positive (Lys, Arg, sometimes His), then it will want to deprotonate to lose the charge, aka become more acidic. That means the pKas of those aminos acids would be lowered in that environment.

You can flip the argument for a positively-charged environment.

The only caveat is that in the hydrophobic core of a protein, ionized side chains can exist but they must be ion-paired with an opposite charge (salt bridge) or stabilized by buried and ordered water molecules.

 

[mmktiger]

Good.



There's no typical charge for either acids or bases. It really depends on the acid. So phosphoric acid or sulfuric acid or citric acid, etc. are uncharged and then after they deprotonate, they become negatively charged as the conjugate base. The only rule is that you have to remember conservation of charge.



So if a residue is in an environment with either no charge or negative charge, it will want to reduce repulsion and pair like-charges, so it will want to be protonated if the conjugate base is negative (e.g. Asp, Glu). So to remain protonated, you must raise the pKa. But if you have a basic residue that's already positive (Lys, Arg, sometimes His), then it will want to deprotonate to lose the charge, aka become more acidic. That means the pKas of those aminos acids would be lowered in that environment.

You can flip the argument for a positively-charged environment.

The only caveat is that in the hydrophobic core of a protein, ionized side chains can exist but they must be ion-paired with an opposite charge (salt bridge) or stabilized by buried and ordered water molecules.

For the last part of your post:
Is it only the positive/negative charge nature of the environment that affects pKa? Is pKa affected if the amino acid is near acidic/basic amino acids or in a hydrophilic/hydrophobic environment?

 

[aldol16]

Is it only the positive/negative charge nature of the environment that affects pKa? Is pKa affected if the amino acid is near acidic/basic amino acids or in a hydrophilic/hydrophobic environment?

Well, you're asking basically the same thing. Just because two acids are next to each other don't tell you anything meaningful. The fact that one is deprotonated and negatively charged tells you that the other one probably doesn't want to be negatively charged either by Coulomb's law unless there's a stabilizing salt bridge.