Master of Science / Department of Chemistry / Ping Li / Biodegradable polyhydroxybutyrates (PHBs) produced by a wide range of bacteria have been considered as an ideal alternative to petroleum-based plastics. Two types of mechanistic probes have been synthesized in order to understand the mechanism of PHB synthases (PhaCs). The first type is oxo analogs in which the sulfur in the coenzyme A (CoA) thioester has been replaced with an oxygen atom. A series of 3-R-hydroxybutyryl oxo CoA analogs, (HB)[subscript]nOCoA (n = 1, 2 and 3), were synthesized chemoenzymatically in good yields. Two models involving covalent catalysis with Cys have been proposed for the chain elongation catalyzed by PhaCs. The first involves an active site composed of two monomers in which the growing hydroxybutyrate (HB) chain alternates between Cys on each monomer. The second involves noncovalent intermediates (HB)[subscript]nCoA (n ≥ 2). Here the substrate analog HBOCoA was successfully employed to trap the noncovalent intermediates in the reactions catalyzed by class III PhaC from Allochromatium Vinosum, which supports our preferred second mechanistic model. Furthermore, it is also the first time that a wild-type (wt) synthase was used to investigate the chain elongation models. The other type of mechanistic probes is 3-R-hydroxyalkyl CoA that was used to investigate the substrate specificity of PhaCs from different classes. Substrate availability has been a challenge to study PHB synthases in vitro. Starting with commercially available dimethyl S-malate, the intermediate S-ethyl 2-(oxiran-2-yl) acetate 23 was synthesized via a ring-opening reaction involving lactone 21 and trimethylsilyl iodide followed by an oxidation reaction involving silver oxide. The regiospecific ring-opening reaction of epoxide 23 with different organometallic reagents afforded a straightforward access to ethyl 3-R-hydroxybutanoates attached with a variety of side chains. The final CoA compounds were obtained through the thiotransesterification reaction between corresponding benzenethioesters and the thiol group in CoA. This synthetic approach provides a new avenue to modifications of alkyl groups in 3-R-hydroxyalkyl CoA in an efficient manner.