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Concepts of Metabolism Chapter 8 Energy Needs • Organisms need constant supply of energy • Plants supply themselves and almost all other living organisms with basic molecules needed for life • Use energy stored in new molecules to drive life-sustaining processes • Chemical reactions make up complex process of metabolism Chemical Reactions • Rearrangement of atoms from initial positions to new positions in other molecules • Biochemical reactions – Reactions in living organisms • Plant cells synthesize complex compounds from carbon, hydrogen, oxygen, nitrogen, and smaller amounts of sulfur and phosphorus Basic molecules used for production of other Function molecules in cell Water (H2O) Primarily a solvent Source of most of the hydrogen atoms and some of the oxygen atoms in organic molecules Carbon dioxide (CO2) Primary source of carbon Major source of oxygen Ammonium (NH4+) Primary source of nitrogen in proteins and nucleic acids Nitrate (NO3-) Primary source of nitrogen in proteins and nucleic acids Sulfate (SO42-) Source of sulfur found in some amino acids Phosphate (PO43-) Incorporated in nucleotides Chemical Reactions • Involve rearrangement of atoms • Breaking and re-forming of covalent bonds – Breaking requires stretching or bending of bonds • Potential energy – Stored energy that can be used to stretch or break bonds Chemical Reactions • Kinetic energy – Energy of motion – Average kinetic energy of mixture depends on temperature – The greater the temperature, the faster the molecules are moving • Activation energy – Energy barrier that must be overcome so reaction can proceed Chemical Reactions A+BC+D Substrates or reactants Have potential energy in respective bonds Collisions of A and B increase potential energy High energy state called activated complex Products Catalysts • Rate of chemical reaction is important • Ways to speed a reaction – Increase concentrations of substrates • Increases probability that pairs of substrate molecules will meet – Increase temperature • Increases probability that substrate molecules will have enough kinetic energy to form activated complex • Not practical in living cells • Denatures proteins Catalysts • Catalysts – Better strategy than increased temperature • Increased heat harms cellular components – Not used up or formed as reaction proceeds – Work by forming temporary complex with one or more substrates • Attaches to substrate with reversible bonds • Formation distorts bonds of complex so further bond bending or stretching requires less energy Enzymes • • • • • • Biological catalysts Work only on one set of substrates Catalyze one type of reaction Primarily made of protein molecules 3-D shape Has active site into which substrate molecule fits Enzymes • H bonds hold substrate in active site • While in active site, bonds of substrate become distorted • Distortion of substrate makes it susceptible to reaction catalyzed by enzyme Enzymes • Ways substrate bonds become distorted in active site – Pulling substrate into misfitting groove distorts substrate’s shape – Active site may change shape once substrate is present – Electrical charges in active site push and pull electrons of substrate – Functional groups (side chains of amino acids) in active site react (temporarily) with substrate Enzymes • Enzyme activity – May depend entirely on protein structure – Some enzymes cannot function without nonprotein cofactors (coenzymes) • Examples of cofactors – Metal ions such as Fe2+, Fe3+ – Organic molecules without metal ions Enzymes – Ways cofactors attach to enzymes • Covalent bonds • Loosely bound and easily removed from enzyme protein – Cofactors often able to accept or donate electrons in oxidation-reduction reactions – Trace elements that serve as cofactors in plants • Iron, copper, molybdenum Enzymes – Bio-organic cofactors common in plants • Riboflavin, thiamin, niacin, pantothenic acid • Cannot be synthesized by humans • Humans must obtain these from plants that we consume Plant Enzyme Activities • Easy to detect examples • Darkening of apple fruit after cutting or biting – Action of enzyme polyphenol oxidase on chemicals released from cells • Softening of tomato fruit as it ripens – Action of enzymes on polysaccharides in cell wall – Cellulase – acts on cellulose – Polygalacturonase – acts on pectin Plant Enzyme Activities • Papain – Enzyme from papaya – Digest protein in fruit as it ripens – Can be extracted from fruit and used to tenderize meat before cooking Control of Reaction Rates • Synthesis of enzyme catalyzing particular reaction when and only when reaction is needed – Slow and crude method of control – Example • Formation and germination of seeds Control of Reaction Rates • Regulation of catalytic activity of already existing enzymes – Lower affinity of active site for substrate or its catalytic efficiency once substrate has been found • Enzyme inhibited – Increase affinity of active site for substrate or its catalytic efficiency • Enzyme activated Metabolic Pathways • Series of linked reactions in a cell • Making complex molecules requires a series of steps • Product of first reaction is substrate for second reaction, product of second reaction is substrate for third reaction, and so on • Each reaction requires a different enzyme Metabolic Pathways • Intermediates – Products of reactions other than final product of a series • Intermediary metabolism – Collection of all the metabolic pathways in cells Metabolic Pathways Linked Reactions • Form complex network • Branch point – One intermediate is used as substrate by several separate enzymes to produce different products • Anabolic reactions – Reactions that produce subunits of functional or structural molecules – Predominant type of reaction in meristems Linked Reactions • Catabolic reactions – Reactions that break down damaged or unwanted molecules into their component parts – Catabolic reactions predominate in cells of ripening fruit Concentration of Compound • Often controls its production in a cell • Feedback inhibition • Efficient way to control formation of end product – Shut off activity of first enzyme in pathway to restrict formation of final product – Branch point enzyme (1st enzyme) of pathway has regulatory site – Final product serves as its inhibitor – Keeps concentration of product constant Concentration of Compound Role of Free Energy • Free energy determines direction of reversible reaction • A+BC+D – Overall reaction eventually reaches state of equilibrium • Rates of forward and reverse reactions become equal • Concentrations of substrates and products become constant Role of Free Energy • Factors determining reaction direction – Initial concentrations of substrates and products in reaction’s mixture – Relative stability of bonds in substrate and products – Number of substrates and products that participate in reaction – Temperature Role of Free Energy • Free energy – Greater the concentration of substrates in a reaction’s mixture, the greater their free energy – More stable the bonds of the substrate, the lower their free energy – More independent molecules included in the substrates, the lower their free energy ** above statements also apply to products of a reaction Role of Free Energy • Reactions that proceed forward spontaneously – Lose free energy – Downhill reactions • Reaction that shows no change in free energy is at equilibrium Role of Free Energy • Reactions associated with increase in free energy will not occur spontaneously – Need source of free energy to proceed – Uphill reactions Role of Free Energy – Examples of uphill reactions • Combination of amino acids into a single protein • Synthesis of RNA or DNA • Reduction of carbon-containing molecules to form hydrocarbon chain in lipid molecules • Movement of flagella • Separation of chromosomes during mitosis Coupled Reactions • Reactions that must occur together • Examples – Oxidation-reduction reactions • One compound is oxidized • Another compound is reduced • Neither reaction occurs by itself Coupled Reactions – Transfer of phosphate group • One compound loses phosphate group through hydrolysis reaction (requires addition of components of water) • Another compound gains phosphate group through condensation reaction (produces water) • Change in free energy of overall reaction equals sum of changes in free energy of partial reactions Reactions That Run Most of the Cell’s Machinery • Hydrolysis of ATP • Oxidation of NADH and NADPH Hydrolysis of ATP • ATP – adenosine triphosphate • Adenine + ribose + three phosphates – Phosphate linkages are unstable – Can be split apart by hydrolysis to form ADP + phosphate • High energy compound or energy carrier • Hydrolysis occurs spontaneously • Releases free energy of 7-12 kcal per mole of ATP Oxidation of NADH and NADPH • NADH – nicotinamide adenine dinucleotide • NADPH – nicotinamide adenine dinucleotide phosphate • Both are coenzymes • Reactive part of molecule is nicotinamide functional group – Humans obtain this from food because we cannot synthesize nicotinamide (niacin) Oxidation of NADH and NADPH • Plant cells synthesize niacin – Use it to make NADH and NADPH • NADPH – Reduced form of molecule – Can donate electrons • NAD+ – Oxidized form of molecule Oxidation of NADH and NADPH • Oxidation of NADH by oxygen gas releases 52 kcal per mole of free energy • Oxidation of NADH coupled to formation of 2 to 3 molecules of ATP • Oxidation of NADPH used to synthesize fatty acids and some amino acids