[minimal]

Ok, the question is general across alkaloids but if it needs to be specific please reference it to serotonin.

As far as I know, the general theory is that they are not water soluble in plant/fruit/other biological material, due to the fact that if they were, every time it would rain/get water they would effectively be washed away.  Also as far as I know they are basic.  Now, I was under the impression that things of an acidic or basic nature were generally polar, is it just the case that they are slightly polar because of their basic nature but not enough to be water soluble?
Anyways, so you acidify the solution to make them polar, add organic solvent to remove membrane lipids and such, then basify the solution to return the alkaloid to its initial state.
My question arises here...apparently the final step involves adding another organic solvent in order to have the alkaloid move into that layer...but if they are not polar should they not form a precipitate/crystallize before you add the final step of organic solvent? And if they are slightly miscible, would not boiling off the solution yield your product?  If you were to cool the entire solution (but not freeze), would you expect your alkaloid to crystallize then?
Another question referring to an earlier step...lets say when you acidified the solution earlier you used acetic acid.  Then, when you add a base (NaOH), would that not create an acetic acid/acetate layer and an H20 layer?  Would your alkaloid dissolve/not dissolve evenly throughout both?  If you were able to boil off solution to yield your alkaloid, would you want to boil off both layers?
Also, with so many compounds occurring in cells, I find it hard to comprehend the fact that you're left with just the alkaloid, would you not also yield serious amounts of proteins?
Thanks for the help

[shelanachium]

1 Alkaloids are contained inside the plant cells, therefore they will no more wash away in rain than other water-soluble cell contents like carbohydrates and proteins.

2 Free-base alkaloids may have only one basic group among a great deal of hydrophobic groups. Steroids mostly contain polar groups but are not water-soluble because of the large hydrocarbon frameworks to which these are attached; but they are not basic so cannot be converted into cations to enhance their water-solubility. Alkaloids can.

3 Acidification followed by extraction with organic solvent indeed removes lipids and leaves the alkaloids as cations in the aqueous layer. But also in the aqueous layer will be carbohydrates and proteins, in much larger quantities than the alkaloids.

4 So adding base produces the free alkaloids which are soluble in organic solvents, whilst the proteins and carbohydrates are not - both bristle with highly polar groups even if uncharged, so largely remain in the water. It does not matter if the alkaloids precipitate from the aqueous phase at this stage, they will soon dissolve in a water-immiscible organic solvent if the mixture is strongly shaken.

The organic solvent will now contain the alkaloids with relatively little of anything else. Leave out the alkalise-then-organic-solvent extraction step and you will indeed end up with a gooey mixture of all sorts of stuff!