Chapter 8: Energy and Metabolism



Chapter 8: Energy and MetabolismDiscuss energy conversions and the 1st and 2nd law of thermodynamics. Be sure to use the terms work, potential energy, kinetic energy, and entropy.What are Joules (J) and calories (cal)?The laws of thermodynamics are sometimes stated as: In energy conversions, “You can’t win, and you can’t break even.” Explain.Differentiate between:anabolism and catabolismexergonic and endergonic reactionsWhy is ATP so darned important? What is a phosphorylated intermediate?How much ATP is in a cell at any given time?Why must cells keep a high ATP/ADP ratio?What are redox reactions used for in cells? How (generally) can you tell which of two similar compounds is reduced and which is oxidized? Give some examples of compounds commonly used in redox reactions in cells.What do enzymes do for cells, and how do they do it? Be sure to use the following terms: catalyst (or catalyze); activation energy, enzyme-substrate complex, active site, induced fitWhat are the four main things that enzymes do to lower activation energy?How are enzymes named (what suffixes indicate an enzyme)?Explain the terms cofactor, apoenzyme, and coenzyme.Discuss the effects of temperature and pH on enzyme activity.What is a metabolic pathway?How do cells regulate enzyme activity? Include the terms inhibitors, activators, allosteric site, and feedback inhibition; also, differentiate between irreversible and reversible inhibition and between competitive and noncompetitive inhibition.Chapter 8: Energy and Metabolism Why do organisms need energy? How do organisms manage their energy needs?Energy and thermodynamicsLiving organisms require energy to do work, any change in state or motion of matterenergy can be expressed in units of work (kJ) or heat energy (kcal); 1 kcal = 4.184 kJenergy can change forms (energy conversion)organisms carry out transformation in energy forms between potential energy (capacity to do work) and kinetic energy (energy of motion, actively performing work)organisms commonly use chemical bonds for storage and transfer of (potential) energywork is required for the processes of lifeTwo laws of thermodynamics describe the constraints on energy usageFirst law: the total amount of energy (+ matter) in a closed system remains constant (principle of conservation of energy)The universe is a closed systemLiving things are open systemsSecond law: in every energy conversion, some energy is converted to heat energy that is lost to the surroundings, and thus cannot be used for workAlso can be stated as: Every energy conversion increased the entropy of the universe.Energy converted to heat in the surroundings increases entropy (spreading of energy)Upshot: no energy conversion is 100% efficientJust to maintain their current state, organisms must get a constant influx of energy because of energy lost in conversionsMetabolic reactions include anabolism and catabolism, and involve energy transfersRecall that metabolism is the sum of chemical activities in a organismMetabolism can be divided into anabolism (anabolic reactions) and catabolism (catabolic reactions)anabolic reactions are processes that build complex molecules from simpler onescatabolic reactions are processes the break down complex molecules into simpler onesChemical reactions involve changes in chemical bonds and substance concentrations, along with changes in free energyfree energy = energy available to do work in a chemical reaction (such as: create a chemical bond)free energy changes depend on bond energies and concentrations of reactants and productsbond energy = energy required to break a bond; value depends on the bondleft undisturbed, reactions will reach dynamic equilibrium when the relative concentrations of reactants and products is correctforward and reverse reaction rates are equal; concentrations remain constantcells manipulate relative concentrations in many ways, so that equilibrium is rare for key reactionsexergonic reactions – the products have less free energy than reactantsthe difference in energy is released and is available to do workexergonic reactions are thermodynamically favored; thus, they are spontaneous, but not necessarily fast (more on activation energy later)catabolic reactions are usually exergonicATP + H2O ADP + Pi is highly exergonic in cellular conditionsendergonic reactions – the products have more free energy than the reactantsthe difference in free energy must be supplied (stored in chemical bonds)endergonic reactions are not thermodynamically favored, so they are not spontaneousan endergonic reaction is coupled with an exergonic reaction to provide the needed energy to drive an endergonic reactiontogether, the coupled reactions must have a net exergonic naturereaction coupling requires that the reactions share a common intermediate(s)EXAMPLE:A B (exergonic)C D (endergonic)Coupled: A + C B + D (overall exergonic)Actually: A + C I B + Dtypically, the exergonic reaction in the couple is ATP + H2O ADP + Pianabolic reactions are usually endergonicOne way that organisms manage their energy needs is to use ATP as a ready energy source for many reactions.ATP is the main energy currency in cellsRecall ATP (adenosine triphosphate) is a nucleotide with adenine base, ribose sugar, and a chain of 3 phosphate groupsThe last two phosphate groups are joined to the phosphate group chain by unstable bonds; breaking these bonds is relatively easy, and releases energy; thus:hydrolysis of ATP to ADP and inorganic phosphate (Pi) releases energyATP + H2O ADP + Pithe amount of energy released depends in part on concentrations of reactants and products, but is generally ~30 kJ/molIntermediates are involved when ATP hydrolysis is coupled to a reaction to provide energy; often these involve phosphorylated compounds, with the inorganic phosphate removed from ATP transferred onto another compound rather than being immediately releasedEXAMPLE:glucose + fructose sucrose + H2O (endergonic; requires ~27 kJ/mol)ATP + H2O ADP + Pi (provides ~30 kJ/mol)coupled:glucose + fructose + ATP + H2O sucrose + H2O + ADP + Pi simplified:glucose + fructose + ATP sucrose +ADP + Pi with intermediates:glucose + fructose + ATP + H2O glucose-P + fructose + ADP sucrose + H2O + ADP + Pi Thus, energy transfer in cellular reactions is often accomplished through transfer of a phosphate group from ATPMaking ATP involves an endergonic condensation reactionreverse of an exergonic reaction is always endergonicADP + Pi ATP + H2O (endergonic, usually requires more than ~30 kJ/mol)must be coupled with an exergonic reaction; typically from a catabolic pathway (more on that later)Overall, ATP is typically created in catabolic reactions and used in anabolic reactions, linking those aspects of metabolismCells maintain high levels of ATP relative to ADPmaximizes energy available from hydrolysis of ATPratio typically greater than 10 ATP: 1 ADPOverall concentration of ATP still very lowsupply typically only enough for a few seconds at bestinstability prevents stockpilingmust be constantly producedin a typical cell, the rate of use and production of ATP is about 10 million molecules per secondresting human has less than 1 g of ATP at any given time but uses about 45 kg per dayRedox reactions are used to harvest energy from some chemicals; the acceptors of that energy typically cannot be used directly as energy currency.Redox reactions are also used for energy transferElectrons can also be used for energy transferRedox reactions: recall reduction, gain electrons; oxidation, lose electrons; both occur simultaneously in cells (generally no free electrons in cells)Typically, the oxidized substance gives up energy with the electron, the reduced substance gains energy with the electronCommonly occur as a chain of redox reactions or electron transfers (more on electron transport chains later)As the electron is transferred to an acceptor molecule, it releases free energy that can be used for other chemical reactionsTypically, a proton is removed as well when an electron is removed from covalent molecules; thus, the equivalent of a hydrogen atom is transferredCatabolism typically involves removal of hydrogen atoms from nutrients (such as carbohydrates), and the transfer of the protons and electrons to intermediate electron acceptorsOne common intermediate acceptor is nicotinamide adenine dinucleotide (NAD+)Use XH2 to represent a nutrient molecule:XH2 + NAD+ X + NADH + H+Often, the reduced form is just called NADHReduced state stores energy, which is partially released as free energy when NADH is oxidizedThe free energy usually winds up being used to make ATPOther commonly used acceptors are NADP+, FAD, and cytochromesNADP+/NADPH – important in photosynthesisFAD/FADH2 – flavin adenine dinucleotideCytochromes – small iron-containing proteins; iron serves as electron acceptorEnzymes are a large part of the answer to how organisms manage their energy needs. Manipulation of reactions is essential to and largely defining of life, and enzymes manipulate the speed of reactions. Understanding life requires understanding how enzymes work.Enzymes regulate chemical reactions in living organismsAn enzyme is an organic molecule (typically a protein) that acts as a catalystcatalyst – substance that increases the rate of a chemical reaction without being consumed in the reaction (the catalyst recycles back to its original state)enzymes (catalysts) only alter reaction rate; thermodynamics still governs whether the reaction can occur – thus, enzymes only catalyze reactions that are occurring anywayEnzymes (catalysts) work by lowering the activation energy of a reactionall reactions have a required energy of activation (the energy required to break existing bonds) that must be supplied in some way before the reaction can proceed; also, reactants must come togethercatalysts greatly reduce the activation energy requirement, making it easier for a reaction to occuroften, this reduction in activation energy is due to in part to the enzyme holding reactants (substrates) close together, which also reduces the reliance on random collisionsEnzymes lower activation energy by forming a complex with the substrate(s)the ability to form an enzyme-substrate complex is highly dependent on the shape of the enzymethe site where the substrate(s) binds to the enzyme is called the active sitewhen the enzyme-substrate complex forms, there are typically shape changes in the enzyme and substrate(s) – this is called induced fitthe enzyme-substrate complex is typically very unstable and short-lived; it breaks down into released product(s) and a free enzyme that is ready to be reusedoverall:enzyme +substrate(s) ES complex enzyme + product(s)the reduction in activation energy is due primarily to four things:an enzyme holds reactants (substrates) close together in the right orientation for the reaction, which reduces the reliance on random collisionsan enzyme may put a “strain” on existing bonds, making them easier to breakan enzyme provides a “microenvironment” that is more chemically suited to the reactionsometimes the active site of the enzyme itself is directly involved in the reaction during the transition statesEnzyme namesmany names give some indication of substratemost enzyme names end in –ase (example: sucrase)some end in –zyme (example: lysozyme)some traditional names are less indicative of enzyme function (example: pepsin)Enzymes are generally highly specificoverall shape as well as spatial arrangements in the active site limit what enzyme-substrate complexes can readily formthe amount of specificity depends on the particular enzymeexample of high specificity: sucrase splits sucrose, not other disaccharidesexample of low specificity: lipase splits variety of fatty acids from glycerolenzymes are classified by the kind of reaction they catalyzeMany enzymes require cofactors to functionapoenzyme + cofactor active enzyme (bound together)alone, an apoenzyme or a cofactor has little if any catalytic activitycofactors may or may not be changed by the reactioncofactors can be organic or inorganicorganic examples (coenzymes): ATP, NADH, NADPH, FADH2typically changed by the catalyzed reactioninorganic examples metal ions like Ca2+, Mg2+, Fe3+, etc.typically not changed by the catalyzed reactionmost vitamins are coenzymes or part of coenzymes, or are used for making coenzymesEnzymes are most active under optimal conditionseach enzyme has an optimal temperaturemost effective as a catalyst at the optimal temperaturerate of drop-off in effectiveness away from optimal temperature depends on the enzymehigh temperatures tend to denature enzymeshuman enzymes have temperature optima near human body temperature (37°C)each enzyme has an optimal pHagain, most effective at the optimum; drop-off variesextremes of pH tend to denature enzymesa particular organism shows more variety in enzyme pH optima than in temperature optima, but most of its enzymes will still be optimal at the pH normally found in the cytosol of its cellsMetabolic pathways use organized “teams” of enzymesthe products of one reaction often serve as substrates for the next reactionremoving products (by having them participate the “next reaction”) improves reaction ratemultiple metabolic pathways exit in cells, overlapping in some areas and diverging in othersCells can regulate enzyme activity to control reactionsincrease substrate amount increase reaction rate (up to saturation of available enzyme molecules)increase enzyme amount increase reaction rate (as long as substrate amount > enzyme amount)compartmentation of the enzyme, substrate, and products can help control reaction rateinhibitors and activators of enzymesinhibitors reduce or eliminate catalytic activityactivators allow or enhance catalytic activitysometime, this uses an allosteric site – a receptor site on an enzyme where an inhibitor or activator can binda common example of allosteric control is feedback inhibition, where the last product in a metabolic pathway binds to an allosteric site of an enzyme in an early step of the pathway (often the first) and inhibits activity of the enzymeirreversible inhibition – enzyme is permanently inactivated or destroyed; includes many drugs and toxinsreversible inhibition – if inhibitor is removed, the enzyme activity can be recoveredcompetitive inhibition – inhibitor is similar in structure to a substrate; competes with substrate for binding to the active sitenoncompetitive inhibition – binds at allosteric site, alters enzyme shape to make active site unavailable ................
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