Indole-3-acetic acid

Indole-3-acetic acid is a naturally occurring auxin and plant hormone. Its structure combines an indole ring system with an acetic acid side chain; the neutral molecule has formula ${\mathrm{C}}_{10}{\mathrm{H}}_9\mathrm{N}{\mathrm{O}}_2$. Its chemical identity is more specific than the functional class auxin, which also includes other compounds.^[ref]

A transport experiment illustrates the difference between applying a signal and delivering it to the responsive cells. Work on Arabidopsis thaliana localized AUX1 within the root apex and connected its function to uptake and redistribution of indole-3-acetic acid. A membrane-permeable synthetic analogue, naphthaleneacetic acid, could bypass the mutant's uptake defect in a gravitropism assay.^[ref]

Concentration and total amount must also be distinguished. In an illustrative homogeneous solution, $1\mathrm{mL}$ at $1\mu \mathrm{mol}{\mathrm{L}}^{-1}$ contains $1\mathrm{nmol}$ of solute by $n=cV$. That calculation specifies an inventory; it does not establish the intracellular concentration, spatial distribution or growth response. Those require measurements of transport and biological activity.

Indole-3-acetate is the conjugate base of indole-3-acetic acid, formed by loss of a proton from its carboxylic acid group. ChEBI records molecular formula ${\mathrm{C}}_{10}{\mathrm{H}}_8\mathrm{N}{\mathrm{O}}_2^{-}$ and charge $-1$. The uncharged acid and its anion have related chemical roles but are distinct protonation forms.^[ref]

Write the acid as $\mathrm{HA}$ and indole-3-acetate as ${\mathrm{A}}^{-}$:For a dilute two-form model, the Henderson-Hasselbalch equation gives $r=[{\mathrm{A}}^{-}]/[\mathrm{HA}]=10^{\mathrm{pH}-\mathrm{p}{K}_a}$, and the anion fraction is $r/(1+r)$. At pH equal to $\mathrm{p}{K}_a$, the two fractions are equal. One pH unit above it gives $10/11\approx 90.9\%$ anion, while one unit below gives $1/11\approx 9.1\%$. This is a symbolic calculation relative to the acid dissociation constant, not a claim of a newly measured numerical $\mathrm{p}{K}_a$.

The fraction does not specify the total amount. A hypothetical100-nanomole pool in the90.9percent case contains about90.9 nanomoles of indole-3-acetate and9.1 nanomoles of acid. Specifying pH alone would not determine that pool size, a transport rate or a growth response to auxin.