Regarding Acids, Bases, and Ions

In many structures, the abbreviation P is used to represent the phosphate group and PP the diphosphate (or pyrophosphate) group  

At physiological pHs, these groups will be ionized as shown, but in schemes where structures are given in full, the unionized acids are usually depicted. This is done primarily to simplify structures, to eliminate the need for counter-ions, and to avoid mechanistic confusion. Likewise, amino 

Ionized and unionized forms of many compounds are regarded as synonymous in the text, thus acetate/acetic acid, shikimate/shikimic acid, and mevalonate/mevalonic acid may be used according to the author s whim and context, and have no especial relevance. 

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