First for the protiens in cell membranes:

The polar amino acids will be exposed to either the exterior or interior of the cell or will line a channel between the two. The non-polar hydrophobic amino acids will be the pieces that anchor the protien to the membrane. Think function.

To seperate peptides (500 daltons ~ 5 amino acids) one can use an HPLC, reverse phase works best, using acidic buffers for basic compounds and basic buffers for acidic (negative charged) compounds. In general one should not use extreme pH's for protiens because one could denature them. At 500 daltons, there can be no structures that can be denatured by pH (just not enough there to have a structure).

There are other types of chromatography, ionic and affinity being likely choices. In ionic, on varies ion concentrations to purify compounds. In affinity chromatography, one relies on how well a compound sticks to the resin to purify. For your peptide, running your sample through a weak base ion echange resin while in, say, EtOAc (neutral) would likely get it to absorb on the resin while all the basic compounds where washed out, afterwards you would wash with EtOAc & 1-10% Acetic acid to remove your peptide.

Other methods include size exclusive chromatography - good for getting large compounds while leaving small ones in the resin. Dialysis is often used but is very slow and requires large volumes of solvent - good for crude seperations. Finally there is electroforisis (sp), which is how DNA finger prints are made.

Hope that helps.

"Q.How would you determine the size, and charge of a protein?"

Size is determined by two things mass (mass spec) and shape (x-ray crystolography).
Charge is determined by pH titration or estimated from counting acidic and basic groups.

"AM I right in thinking that size, charge, and active sites are the only things you can separate proteins by? "

No, solubility often works. Charge is misleading with protiens - they can form complexes with metals or other compounds which mask their charges. Also protiens form intra-molecular acid-base pairs (IE glutamatic acid and arginine) which also tie-up charges and give the protien its shape.