Tripeptide aldehyde. Reversible competitive inhibitor of serine and cysteine proteases. Inhibits also phospholipase D and C activation in rat hepatocytes.
The malignant cells of this hepatocellular carcinoma (seen mostly on the right) are well differentiated and interdigitate with normal, larger hepatocytes (seen mostly at the left).
Supplementing the deficient protein in the blood doesn't fix the liver problems, since they're caused by defective alpha-1 antitrypsin building up in the hepatocytes.
Misfolded alpha-1 antitrypsin can aggregate and get stuck in the endoplasmic reticulum of the liver hepatocytes where it's made, causing some of those cells to die.
Frequently affected organs include the liver, where the bacterial toxins damage liver sinusoids and hepatocytes, causing bilirubin to spill into the bloodstream - which clinically translates as jaundice.
Ultimately the answer to this question is still unknown, what is known is that in patients with Reye's syndrome the mitochondria inside their liver cells, or hepatocytes, become damaged.
Whatever the case, as the hepatocytes die and the liver becomes dysfunctional, blood doesn't get filtered, and so it doesn't get the nitrogen-containing toxins filtered by the liver like it normally would.
Here's a pretty basic layout of the basic functional unit of the liver, you've got the portal vein and hepatic artery that combine into a sinusoid, which then goes into the central vein, and these are all lined with hepatocytes.