Microbial Metabolism and Its Importance PDF

Microbial Metabolism and Its Importance Metabolism is the total of all chemical reactions in the cell and is divided into two parts – catabolism – anabolism  Catabolism fueling reactions energy-conserving reactions provide ready source or reducing power (electrons)...

Microbial Metabolism and Its Importance Metabolism is the total of all chemical reactions in the cell and is divided into two parts – catabolism – anabolism  Catabolism fueling reactions energy-conserving reactions provide ready source or reducing power (electrons) generate precursors for biosynthesis Anabolism the synthesis of complex organic molecules from simpler ones requires energy from fueling reactions 2  Types of work carried out by organisms energy – capacity to do work or to cause particular changes chemical work – synthesis of complex molecules transport work – take up of nutrients, elimination of wastes, and maintenance of ion balances mechanical work – movement of organisms or cells and movement of internal structures  Energy currency of cells ATP – used to transfer energy from cell’s energy- conserving systems to the systems that carry out cellular work  The Cell’s Energy Cycle Guanosine 5’-triphosphate, cytosine 5’- triphosphate and uridine 5’-triphosphate also supply some energy  First law of Thermodynamics Energy cannot be created or destroyed; it can be changed from one form to another. Example Chemical energy in food is converted to chemical energy in ATP and then converted to mechanical energy of muscle contraction.  Second Law of Thermodynamics Energy cannot be changed from one form into another without a loss of usable energy. Examples 25% of chemical energy of gasoline is converted to move a car; rest is lost as heat. When muscles convert chemical energy in ATP to mechanical energy, some is lost as heat.  Entropy Measure of randomness or disorder Organized/usable forms of energy have low entropy; unorganized/less stable forms have high entropy. Energy conversions result in heat and therefore the entropy of the universe is always increasing.  Free Energy In a reaction A + B C + D, A and B are reactants and C and D are products. Free energy (G) is the amount of energy that is free to do work after a chemical reaction. Change in free energy is noted as G; A negative  G means that products have less free energy than reactants; the reaction occurs spontaneously. A B, G X Y  Exergonic Reactions Have a negative  G and energy is released. Endergonic Reactions Have a positive  G; products have more energy than reactants; such reactions can only occur with an input of energy. Reversible reactions Have a free energy difference near zero; such a reaction is at equilibrium. A⇌B  Chemical Equilibrium Equilibrium consider the chemical reaction A+ B C+D – reaction is at equilibrium when rate of forward reaction = rate of reverse reaction Equilibrium Constant (Keq) – expresses the equilibrium concentrations of products and reactants to one another  Standard Reduction Potential (E0) Equilibrium constant for an oxidation- reduction reaction A measure of the tendency of the reducing agent to lose electrons more negative E0  better electron donor more positive E0  better electron acceptor  The greater the difference between the E0 of the donor and the E0 of the acceptor  the more negative the Go´  Oxidation-Reduction Reactions and Electron Carriers many metabolic processes involve oxidation-reduction reactions (electron transfers) electron carriers are often used to transfer electrons from an electron donor to an electron acceptor  Oxidation-Reduction (Redox) Reactions transfer of electrons from a donor to an acceptor – reducing agent or reductant = electron donor – oxidizing agent or oxidant = electron acceptor can result in energy release, which can be conserved and used to form ATP  Electron Carriers NAD – nicotinamide adenine dinucleotide NADP – nicotinamide adenine dinucleotide phosphate  Electron Carriers FAD – flavin adenine dinucleotide FMN – flavin mononucleotide – riboflavin phosphate riboflavin  Electron Carriers coenzyme Q (CoQ) – a quinone – also called ubiquinone  Biochemical Pathways Enzymes can be linked together to form pathways Pathways can be varied – Linear – Cyclic – Branching Pathways often overlap/feed into each other – Creates complex networks – Dynamic pathways can be used to monitor changes in metabolite levels (flux)  Enzymes protein catalysts – have great specificity for the reaction catalyzed and the molecules acted on catalyst – substance that increases the rate of a reaction without being permanently altered substrates – reacting molecules products – substances formed by reaction Structure and Classification of Enzymes some enzymes are composed solely of one or more polypeptides some enzymes are composed of one or more polypeptides and nonprotein components  Enzyme Structure apoenzyme – protein component of an enzyme cofactor – nonprotein component of an enzyme prosthetic group – firmly attached coenzyme – loosely attached holoenzyme = apoenzyme + cofactor The Mechanism of Enzyme Reactions a typical exergonic reaction A + B → ES(ABt )→ C + D transition-state complex – resembles both the substrates and the products Activation Energy – Energy Required To Form Transition- State Complex without enzyme with enzyme enzyme speeds up reaction by lowering Ea  HOW ENZYME LOWER ENERGY OF ACTIVATION By increasing concentrations of substrates at active site of enzyme By orienting substrates properly with respect to each other in order to form the transition-state complex Interaction of Enzyme and Substrate  Effect of [substrate] rate increases as [substrate] increases no further increase occurs after all enzyme molecules are saturated with substrate  Effect of pH and Temperature each enzyme has specific pH and temperature optima denaturation – loss of enzyme’s structure and activity when temperature and pH rises too much above optima  Enzyme Inhibition competitive inhibitor –directly competes with binding of substrate to active site noncompetitive inhibitor –binds enzyme at site other than active site; changes enzyme’s shape so that it becomes less active Competitive Inhibition of Enzyme Activity  Ribozymes Thomas Cech and Sidney Altman discovered that some RNA molecules also can catalyze reactions Examples – catalyze peptide bond formation – self-splicing – involved in self-replication  Regulation of Metabolism Important for conservation of energy and materials Maintenance of metabolic balance despite changes in environment Three major mechanisms – metabolic channeling – regulation of the synthesis of a particular enzyme (transcriptional and translational) – direct stimulation or inhibition of the activity of a critical enzyme  Metabolic Channeling Differential localization of enzymes and metabolites Compartmentation – differential distribution of enzymes and metabolites among separate cell structures or organelles – can generate marked variations in metabolite concentrations  Post-Translational Regulation of Enzyme Activity Two important reversible control measures – allosteric regulation – covalent modification  Allosteric Regulation enzyme inactive – allosteric can’t bind substrate enzyme enzyme effector catalyzes binding alters reaction shape of active site Figure 8.21  Covalent Modification of Enzymes reversible addition or removal of a chemical group alters enzyme activity  Feedback Inhibition also called end product inhibition inhibition of one or more critical enzymes in a pathway regulates entire pathway – pacemaker enzyme catalyzes the slowest or rate- limiting reaction in the pathway each end product regulates its own branch of the pathway each end product isoenzymes – regulates the different initial enzymes that pacemaker catalyze same enzyme reaction