KAPITOLA 7 Základy bioenergetiky termodynamika metabolických termodynamika metabolickýchprocesů makroenergetické sloučeniny makroenergetické sloučeniny biologické oxidace biologické oxidace

The cycling of carbon dioxide and oxygen between the autotrophic (photosynthetic) and the heterotrophic domains in the biosphere. The cycling of carbon dioxide and oxygen between the autotrophic (photosynthetic) and the heterotrophic domains in the biosphere. The flow of mass through this cycle is enormous; about 4x10 11 metric tons of carbon are turned over in the biosphere annually.

Koloběh uhlíku na Zemi atmosféra dýchání fotosyntéza Dolomity H2OH2OH2OH2O ropa - uhlí živiny mikroorganismyfosilace CO 2 dýchání

Milan Kodíček & Vladimír Karpenko: Biofysikální chemie, Academia, 2000

The cycling of nitrogen in the biosphere. The cycling of nitrogen in the biosphere. Gaseous nitrogen (N 2 ) makes up 80% of our atmosphere.

Energy relationships between catabolic and anabolic pathways. Catabolic pathways deliver chemical energy in the form of ATP, NADH, and NADPH. These are used in anabolic pathways to convert small precursor molecules into cell macromolecules.

Three types of nonlinear metabolic pathways: a)converging, catabolic b)diverging, anabolic and c)cyclic pathway, in which one of the starting materials (oxaloacetate) is regenerated and reenters the pathway. Acetate, a key metabolic intermediate, can be produced by the breakdown of a variety of fuels (a), can serve as the precursor for the biosynthesis of an array of products (b), or can be consumed in the catabolic pathway known as the citric acid cycle.

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Enzyme cofactors and coenzymes incorporating adenosine in their structure. The adenosine portion is shaded grey. Coenzyme A functions in acyl group transfer reactions. NAD + participates in hybride transfers. FAD, the active form of vitamine B 2 (riboflavin), participates in electron transfers. Another coenzyme incorporating adenosine in its structure is 5´- deoxyadenosylcobalamin, the active form of vitamin B 12. This coenzyme is involved in intramolecular group transfers between adjacent carbons.

The free energy of hydrolysis of thioesters is large relative to that of oxygen esters. The products of both types of hydrolysis reactions have about the same free-energy content (G), but the thioester has a higher free-energy content than the oxygen ester. Orbital overlap between the O and C atoms allows resonance stabilization in oxygen esters, but orbital overlap between S and C is poorer and little resonance stabilization occurs.

a)The deoxyribonucleotide units of DNA in free form at pH 7,0. In their free form these nucleotides are commonly abbreviated dAMP, dGMP, dTMP, and dCMP. b)The ribonucleotide units of RNAs. All abbreviations assume that the phosphate group is at the 5´position. The nucleoside portion of each molecule is depicted here in gray boxes.

ATP/ Adenosin-5´-trifosfát

ATP: Adenosintrifosfát

Flow of phosphate groups Flow of phosphate groups, represented by P, from high-energy phosphate donors via ATP to acceptor molecules (such as glucose and glycerol) to form their low-energy phosphate derivatives. This flow of phosphate groups, which is catalyzed by enzymes called kinases, proceeds with an overall loss of free energy under intracellular conditions. Hydrolysis of low-energy phosphate compounds releases P i, which has an even lower group transfer potential.

Hydrolysis of 1,3-bisphosphoglycerate. The direct product of hydrolysis is 3-phosphoglyceric acid, with an undissociated carboxylic acid group, but dissociation occurs immediately. This ionization and the resonance structures it makes possible stabilize the product relative to the reactants. Resonance stabilization of P i further contributes to the free-energy change.

Hydrolysis of phosphoenolpyruvate (PEP) Hydrolysis of phosphoenolpyruvate (PEP), catalyzed by pyruvate kinase, is followed by spontaneous tautomerization of the product. Tautomerization is not possible in PEP, and thus the product of hydrolysis is stabilized relative to the reactant. Resonance stabilization of P i also occurs.

Membrane/Oxidative phosphorylation Electron transports: NAD+/NADH (H-; 2H+, 2e) FAD/FADH2 (2xH; 2H+, 2e) Cytochromes (Fe2+/Fe3+; Cu+/Cu2+) Fe-S complexes (Rieske´s proteins) Chinol/Chinon

a)Nicotinamide adenine dinucleotide (NAD + ) and its phosphorylated analog NADP + undergo reduction to NADH or NADPH, accepting a hydride ion (two electrons and one proton) from an oxidizable substrate. The hydride ion may be added to either the front (A type) or the back (B type) of the planar nicotinamide ring b)The UV absorption spectra of NAD + and NADH. Reduction of the nicotinamide ring produces a new, broad absorption band with a maximum at 340 nm. The production of NADH during an enzyme-catalyzed oxidation can be conveniently followed by observing the appearance of the absorbance at 340 nm.

Flavin adenine dinucleotide (FAD) Flavin adenine dinucleotide (FAD) and its reduced forms. FAD accepts two hydrogen atoms (two electrons and two protons), both of which appear in flavin ring system of FADH 2. When FAD accepts only one hydrogen atom, the semiquinone, a stable free radical, is formed. The closely similar coenzyme flavin mononucleotide (FMN) consists of the structure above the broken line shown on the oxidized (FAD) structure.

Flavin adenine dinucleoside (FAD) Nicotinamide adenine dinucleoside (NAD+)

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Measurement of the standart reduction potential (E 0 ´ ) of a redox pair. Electrons flow from the test electrode to the reference electrode, or vice versa. The ultimate reference half-cell is the hydrogen electrode. The arbitrary electromotive force (emf) of this electrode is 0,00 V. At pH=7, E 0 ´ for the hydrogen electrode is -0,414 V. The direction of electron flow depends upon the relative electron "pressure" or potential of the two cells. A salt bridge containing a saturated KCl solution provides a path for counter-ion movement between the test cell and the reference cell. From the observed emf and the known emf of the reference cell, the emf of the test cell containing the redox pair is obtained. The cell that gains electrons has, by convention, the more positive reduction potential.

Data mostly from Loach, P.A. (1976) In Handbook of Biochemistry and Molecular Biology, 3rd edn (Fasman, G.D., ed), Physical and Chemical Data, Vol. I, pp , CRC Press, Cleveland, OH.