Electron Transport Chain vs Oxidative Phosphorylation

	oxidative phosphorylation	electron transport chain
energy input / usage	utilizes products of the Krebs cycle	driven by the process of proton pumping by complexes I, III, and IV
phosphorylation / dephosphorylation	generates ATP from energy stored by the electron transport chain (ETS)	consumes NADPH & FADH2
proton pump	ultimately coupled to phosphorylation	electron transport is driven by the proximity of reduced and oxidized carriers generated by proton pumping
electron transport	complexes I, III, and IV pump protons coupled to proton pumping ... you don't get one without the other	electrons enter the chain only through NADH dehydrogenase and succinate dehydrogenase electron transport is driven by the proximity of reduced and oxidized carriers generated by proton pumping
chemiosmotic gradient	maintained in presence of substrate, and in absence of mitochondrial poisoning by chemicals such as cyanide ATP synthase protons do not reduce O2, which acts as an electron acceptor	ETS accepts energy from carriers in the matrix the ETS moves electrons because of the chemiosmotic gradient
ATP synthase	membrane-bound enzyme at final step in oxidative phosphorylation	follows from and is not part of the electron transport chain
ATP synthase activation	does not alter the chemiosmotic gradient	ETS maintains the gradient at a constant level ATP synthase activation increases the rate at which energy is removed from the gradient
O2 consumption	ATP is not needed for O2 consumption	O2 serves as an electron acceptor, so the electron transport chain drives O2 consumption

Adapted from here.

Enzymes Function Krebs Cycle

Enzyme	Function in Krebs cycle
pyruvate dehydrogenase	pyruvate + NAD+ + CoASH → acetyl-CoA + NADH + CO2 Provides acetyl-CoA for entry to cycle
citrate synthase	oxalacetate + acetyl–CoA → citrate + CoASH
aconitase	citrate isocitrate
isocitrate dehydrogenase	isocitrate + NAD+ → a-oxoglutarate NADH isocitrate + NADP+ → a-oxoglutarate NADH
a-ketoglutarate dehydrogenase	a-oxoglutarate + NAD+ + CoASH → succinyl-CoA + NADH + CO2
succinic thiokinase	succinyl-CoA + GTP (or ATP) + CoASH → succinyl-CoA + PPi + GMP (or AMP)
succinate dehydrogenase	succinate + FAD → fumarate + FADH2
fumarase	fumarate + H2O → L-malate
malate dehydrogenase	malate + NAD+ → oxalacetate + NADH + H+ malate + NADP+ → oxalacetate + NADPH + H+

Enzymes Cofactors of Krebs Cycle

Enzyme	Cofactors	Inhibitors	DG(kcal/mol)
citrate synthase			-9.1
aconitase		fluorocitrate	+1.6
isocitrate dehydrogenase	NADP+		-1.7
a-ketoglutarate dehydrogenase	NAD+, FAD, lipoate	arsenite	-8.8
succinic thiokinase	ATP	hydroxylamine	-2.1
succinate dehydrogenase	FAD, FeS group	malonate	0
fumarase		meso-tartrate	-0.9
malate dehydrogenase	NAD+	b-fluoroxalacetate fluoromalate	+6.7

Nitrogen cycle

Nitrification involves the oxidation of NH3 to NO3^- (nitrite), and is the opposite of denitrification. This is a two step process: 1. NH3 + O2 → NO2^- + 3H⁺ + 2e^- performed by autotrophic bacteria including the genus Nitrosomonas and Nitrosococcus. 2. NO2^- + H2O → NO3^- + 2H⁺ + 2e^- (oxidation of nitrite into nitrate) is chiefly performed by autotrophic bacteria of the genus Nitrobacter. Denitrification reduces the products of nitrification, and is performed by heterotrophic bacteria, including Pseudomonas sp. NO3 → NO2 → NO → N2O → N2 2NO3^- + 10e^- + 12H⁺ → N2 + 6H2O

Phosphate-handling enzymes

Class	Actions	Examples
Phosphorylases	Transfer of phosphate group from an inorganic phosphate to an acceptor (usually a sugar). Bacterial phosphorylases employ the same catalytic mechanisms as their plant and animal counterparts, but differ considerably in terms of their substrate specificity and regulation. That is, catalytic domains are highly conserved, while the regulatory sites are only poorly conserved. [s][r]	glycogen phosphorylase
Protein kinases	Transfer a phosphate group from a donor such as ATP to amino acid acceptors in proteins. Serve important roles in signal transduction.	protein kinase A, protein kinase C, protein tyrosine kinases (PTKs), cAMP-dependent protein kinase (AKAPs), MAP Kinase, receptor tyrosine kinases, (RTKs), Table RTKs, w Ca2+/calmodulin-dependent protein kinases, w Mos/Raf kinases, w Protein Kinase B, w Receptor-associated tyrosine kinases, w Histidine-specific protein kinases, w Aspartic acid/glutamic acid-specific protein kinases
Phosphatases	Remove, from amino acids, the phosphate groups attached by protein kinases. Serve important roles in signal transduction.	PP1 (α, β, γ1, γ2), PP2A, w calcineurin (PP2B), PP2C, PP4, PP5 tyrosine phosphatases (CD45)
Adenylyl (adenylate) cyclases	Convert ATP to the second-messenger cAMP plus pyrophosphate. Serve important roles in eukaryotic signal transduction.	ADCY1, ADCY2, ADCY3, ADCY4, ADCY5, ADCY6, ADCY7, ADCY8, ADCY9
Phospholipases, (phospholipases)	Hydrolyze specific ester bonds in phosphoglycerides or glycerophosphatidates, converting the phospholipids into fatty acids and other lipophilic substances. Participate in transmission of ligand-receptor induced signals from the plasma membrane to intracellular proteins, primarily protein kinase C (PKC), which is maximally active in presence of Ca2+ and diacylglycerol.	PLA1, PLA2, w Phospholipase A (PLA), w Phospholipase B (PLB), w Phospholipase C (PLC), Phospholipase D (PLD)
Phosphodiesterases	Catalyze the hydrolysis of phosphodiester bonds, and so degrade the cyclic nucleotides, second messengers cAMP and cGDP to 5'-nucleotide monophosphates (AMP, GMP) Important in regulation of signal transduction.	Enzymes of 10 identified phosphodiesterase families exist as homodimers with structural similarity, but differences with respect to selectivity for cyclic nucleotides, sensitivity for inhibitors and activators, physiological roles and tissue distribution.
DNA ligases	DNA ligase forms covalent phospodiester bonds between 3'-OH of one nucleotide and 5'-PO4 of another. DNA ligases are important research tools in recombinant DNA technology. 3'-phospodiesterase is important in repair of oxidative DNA damage.	DNA ligases I, II, III, IV

 Cell signaling  Receptor Tyrosine Kinases(RTK)  Second Messengers  Phosphate-handling Enzymes 

· adenylyl (adenylate) cyclase · cAMP-dependent protein kinase · CDKs · cyclin-dependent kinases · DAG · diacylglycerol · DNA ligases · ERKs · GPCRs · GPCR families · guanyl cyclase · inositol triphosphate · IP3 · MAP kinases · mitogen activated protein kinases · phosphatases · phosphodiesterases · phospolipases · phosphorylation · PKA · PKC · phospholipase C-gamma · protein kinase A · protein kinase C · protein tyrosine kinases (PTKs) · receptor tyrosine kinases · second messengers · signal transduction · two-component systems ·

Trophism

Organisms obtain their energy either as transducers of light energy (phototroph) or as consumers of inorganic (autotroph, lithotroph) or organic (heterotroph) substances.

Expasy Wall Chart

Above: the chart at Expasy is clickable by map location, clicking on the image above will call up the clickable chart. For enquiries on how to obtain a paper copy of the wall chart, please contact Roche Applied Science directly. Go to Cellular and Molecular Processes on Expasy, search Metabolic Pathways.