Respiration, Metabolism and Enzyme Kinetics

Plant metabolic enzymes and reactions

Questions on plant metabolism usually test whether you can pair an enzyme with the reaction it catalyses, so each enzyme should be learned together with its substrate, product and cofactor or electron donor. Cinnamate-4-hydroxylase is a cytochrome P450 monooxygenase that hydroxylates cinnamic acid to p-coumaric acid. The deamination of L-phenylalanine to cinnamic acid is a different step, catalysed by phenylalanine ammonia-lyase, and the two must not be confused. Glycerate kinase phosphorylates glycerate to 2-phosphoglycerate with ATP, whereas the interconversion of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate is catalysed by triose phosphate isomerase. PEP carboxylase fixes bicarbonate onto phosphoenolpyruvate to give oxaloacetate, the primary carboxylation step of C_4 plants, while glycolate oxidase converts glycolate and O_2 into glyoxylate and H_2O_2 during photorespiration. Nitrate reductase reduces nitrate to nitrite using NAD(P)H as the electron donor, which is the first step of nitrate assimilation. Malic enzymes catalyse the oxidative decarboxylation of malate to pyruvate, CO_2 and a reduced pyridine nucleotide. The NAD-dependent form yields NADH, while the NADP-dependent form yields NADPH and operates in C_4 and CAM plants. Malate dehydrogenase, which forms oxaloacetate, and fumarase, which forms fumarate, are separate enzymes and do not belong to this group.

Alternative respiratory pathways in plant mitochondria

Plant mitochondria contain non-phosphorylating routes that run alongside the classical electron transport chain. Type II NAD(P)H dehydrogenases oxidise NADH or NADPH and pass electrons to ubiquinone without pumping protons, so they bypass Complex I. Alternative oxidase reduces O_2 directly from the ubiquinol pool, bypassing Complexes III and IV, and it is not inhibited by cyanide. A general principle is that a compound which blocks one enzyme is tolerated when the organism possesses a parallel enzyme that uses the same substrate and gives the same product. Rotenone binds the ubiquinone-binding site of Complex I and stops NADH oxidation through that complex, but plant NAD(P)H dehydrogenases are insensitive to it, so electron flow continues and the plant survives. Plant Complex I remains rotenone-sensitive, which explains why the compound is toxic to insects and fish.

Fermentation pathways and CO2 production

Fermentation regenerates NAD+ from NADH without a respiratory chain, and whether CO_2 is released depends on the pathway. In alcoholic fermentation, pyruvate is decarboxylated by pyruvate decarboxylase to acetaldehyde and CO_2, and acetaldehyde is then reduced to ethanol. Yeast performs this process, so wine brewing and bread leavening both release CO_2, which makes the dough rise. In homolactic fermentation, pyruvate is reduced directly to lactate by lactate dehydrogenase, so no CO_2 is produced. Lactobacillus carries out this pathway in yogurt, where lactose is converted to lactic acid. Cheese ripening by fungi such as Penicillium depends mainly on the proteolysis and lipolysis of the milk curd, and it is not a CO_2-generating fermentation of the yeast type. Useful rule: if the question asks about the release of CO_2, check whether pyruvate is decarboxylated before the reduction step.