Alpha Amino Acid Polarity

[Infinity Plus]

Hey guys I just have some problems with Amino Acid polarities that I was hoping you guys could clarify. When they give you a bunch of amino acids and then they ask you which one will adsorb to the polar stationary phase most (i.e-which amino acid is most polar) what is the best way to differentiate their polarities? Like I know that it is the Z groups that cause the polarity of the molecule but sometimes I can't tell which Z group is more polar.

[jgoudie]

You are correct in looking at the Z-group.  Base polarity on that part of the molecule and apply your normal polarity rules.
- symmetrical -less polar.
- More OH's more polar.
- Longer the group less polar it is (to an extent, you need to weigh up if the long group still has some OH's some where.
- NH2's = polar
- Cystine - polar, but will not hydrogen bond so less so than OH/NH2.

These are some general ideas, we will see what other have to say.

Hey guys I just have some problems with Amino Acid polarities that I was hoping you guys could clarify. When they give you a bunch of amino acids and then they ask you which one will adsorb to the polar stationary phase most (i.e-which amino acid is most polar) what is the best way to differentiate their polarities? Like I know that it is the Z groups that cause the polarity of the molecule but sometimes I can't tell which Z group is more polar.

[Infinity Plus]

You are correct in looking at the Z-group.  Base polarity on that part of the molecule and apply your normal polarity rules.
- symmetrical -less polar.
- More OH's more polar.
- Longer the group less polar it is (to an extent, you need to weigh up if the long group still has some OH's some where.
- NH2's = polar
- Cystine - polar, but will not hydrogen bond so less so than OH/NH2.

These are some general ideas, we will see what other have to say.

Thank you so much!

[Aurelian]

Note that this will be influenced by the pH of the solution which makes up your mobile phase. For example, if you have a really basic solution with lots of deprotonating OH^- ions, then a lysine residue is going to mainly have an -NH₂ at the end of its Z group. However, if the solution is really acidic then lysine will be mainly protonated an have a positive charge (with the Z group ending in -NH₃⁺). Hence potentially charged amino acids will interact with the stationary phase differently at different pHs.

Normally I would consider this point to be outside the VCE chem course, but since they've merged U3 and U4 this year, there's no reason why a question involving this idea couldn't be asked (the concept being a combination of U3 biochemistry and U4 equilibrium acid/base chemistry).

[lzxnl]

What I don't get is...how is cysteine polar? Sulfur has pretty much the same electronegativity as carbon, so saying S-H bonds are polar is like saying C-H are polar.

[Mao]

What I don't get is...how is cysteine polar? Sulfur has pretty much the same electronegativity as carbon, so saying S-H bonds are polar is like saying C-H are polar.

This is the fault of the "electronegativity theory". It doesn't work very well, you see.

C-H bonds *are* polar. The problem is, since C only has 4 valence electrons, it doesn't really form any compounds where it has a lone pair, and so the polarity is always more or less cancelled out due to the geometry, e.g. CH4 has the four polar C-H bonds but cancels out to a net dipole of 0.

As for the S-H bond, S is in the same group as O. Its bond geometry will give lone pairs of electrons. It therefore has a large polarity like an O-H bond, but slightly weaker than O-H.

[lzxnl]

Ah. Ok. That makes sense. Thanks ^_^