H-B Woodlawn Biology - Jim’s Discussion Notes

AN INTRODUCTION TO METABOLISM

A. Metabolism, Energy, and Life

1. The chemistry of life is organized into metabolic pathways

· The totality of an organism’s chemical reactions is called metabolism.

· When heterotrophic organisms (like us) eat foods, our digestive system breaks down chemical bonds and convert the chemical energy into mechanical energy (work), stored energy (in our case, stored glycogen or stored body fat) and heat.

· Metabolic pathways alter molecules in a series of steps.

· Enzymes selectively accelerate each step.

· The activity of enzymes is regulated to maintain an appropriate balance of supply and demand.

· Catabolic pathways release energy by breaking down complex molecules to simpler compounds.

· This energy is stored in organic molecules until it needs to do work in the cell.

· Anabolic pathways consume energy to build complicated molecules from simpler compounds.

· The energy released by catabolic pathways is used to drive anabolic pathways.

· Energy is fundamental to all metabolic processes, and therefore to understanding how the living cell works.

· The principles that govern energy resources in chemistry, physics, and engineering also apply to bioenergetics, the study of how organisms manage their energy resources.

2. Organisms transform energy

· Energy is the capacity to do work - to move matter against opposing forces.

· Energy is also used to rearrange matter.

· Kinetic energy is the energy of motion.

· Objects in motion, photons, and heat are examples.

· Potential energy is the energy that matter possesses because of its location or structure.

· Chemical energy is a form of potential energy in molecules because of the arrangement of atoms.

· Energy can be converted from one form to another.

· For example, as a boy climbs a ladder to the top of the slide he is converting his kinetic energy to potential energy.

· As he slides down, the potential energy is converted back to kinetic energy.

· It was the potential energy in the food he had eaten earlier that provided the energy that permitted him to climb up initially.

· Cellular respiration and other catabolic pathways unleash energy stored in sugar and other complex molecules.

· This energy is available for cellular work.

· The chemical energy stored on these organic molecules was derived primarily from light energy by plants during photosynthesis.

· A central property of living organisms is the ability to transform energy.

3. The energy transformations of life are subject to two laws of thermodynamics

· Thermodynamics is the study of energy transformations.

· In this field, the term system indicates the matter under study and the surroundings are everything outside the system.

· A closed system, like liquid in a thermos, is isolated from its surroundings.

· In an open system energy (and often matter) can be transferred between the system and surroundings.

· Organisms are open systems.

· They absorb energy - light or chemical energy in organic molecules - and release heat and metabolic waste products.

· The first law of thermodynamics states that energy can be transferred and transformed, but it cannot be created or destroyed.

· Plants transform light to chemical energy; they do not produce energy.

· The second law of thermodynamics states that every energy transformation must make the universe more disordered.

· Entropy is a quantity used as a measure of disorder, or randomness.

· The more random a collection of matter, the greater its entropy.

· While order can increase locally, there is an unstoppable trend toward randomization of the universe.

· Much of the increased entropy of the universe takes the form of increasing heat which is the energy of random molecular motion.

· In most energy transformations, ordered forms of energy are converted at least partly to heat.

· Automobiles convert only 25% of the energy in gasoline into motion; the rest is lost as heat.

· Living cells unavoidably convert organized forms of energy to heat.

· The metabolic breakdown of food ultimately is released as heat even if some of it is diverted temporarily to perform work for the organism.

· Heat is energy in its most random state.

· Combining the two laws, the quantity of energy is constant, but the quality is not.

· Living organisms, ordered structures of matter, do not violate the second law of thermodynamics.

· Organisms are open systems and take in organized energy like light or organic molecules and replace them with less ordered forms, especially heat.

· An increase in complexity, whether of an organism as it develops or through the evolution of more complex organisms, is also consistent with the second law as long as the total entropy of the universe, the system and its surroundings, increases.

· Organisms are islands of low entropy in an increasingly random universe.

4. Organisms live at the expense of free energy

· Spontaneous processes are those that can occur without outside help.

· The processes can be harnessed to perform work.

· Nonspontaneous processes are those that can only occur if energy is added to a system.

· Spontaneous processes increase the stability of a system and nonspontaneous processes decrease stability.

· The concept of free energy provides a criterion for measuring spontaneity of a system.

· Free energy is the portions of a system’s energy that is able to perform work when temperature is uniform throughout the system.

· The free energy (G) in a system is related to the total energy (H) and its entropy (S) by this relationship:

· G = H - TS, where T is temperature in Kelvin units.

· Increases in temperature amplify the entropy term.

· Not all the energy in a system is available for work because the entropy component must be subtracted from the maximum capacity.

· What remains is free energy.

· Free energy can be thought of as a measure of the stability of a system.

· Systems that are high in free energy—compressed springs, separated charges—are unstable and tend to move toward a more stable state, one with less free energy.

· Systems that tend to change spontaneously are those that have high energy, low entropy, or both.

· In any spontaneous process, the free energy of a system decreases.

· We can represent this change in free energy from the start of a process until its finish by:

· D G = G _{final state} - G _{starting state}

· Or D G = D H - T D S

· For a system to be spontaneous, the system must either give up energy (decrease in H), give up order (decrease in S), or both.

· D G must be negative.

· The greater the decrease in free energy, the greater the maximum amount of work that a spontaneous process can perform.

· Nature runs “downhill.”

· A system at equilibrium is at maximum stability.

· In a chemical reaction at equilibrium, the rates of forward and backward reactions are equal and there is no change in the concentration of products or reactants.

· At equilibrium D G = 0 and the system can do no work.

· Movements away from equilibrium are nonspontaneous and require the addition of energy from an outside energy source (the surroundings).

· Chemical reactions can be classified as either exergonic or endergonic based on free energy.

· An exergonic reaction proceeds with a net release of free energy and D G is negative.

· The magnitude of D G for an exergonic reaction is the maximum amount of work the reaction can perform.

· For the overall reaction of cellular respiration:

· C₆H₁₂O₆ + 6O₂ -> 6CO₂ + 6H₂O

· D G = -686 kcal/mol

· Through this reaction 686 kcal have been made available to do work in the cell.

· The products have 686 kcal less energy than the reactants.

· An endergonic reaction is one that absorbs free energy from its surroundings.

· Endergonic reactions store energy.

· D G is positive.

· Reactions are nonspontaneous.

· If cellular respiration releases 686 kcal, then photosynthesis, the reverse reaction, must require an equivalent investment of energy.

· D G = + 686 kcal / mol.

· Photosynthesis is steeply endergonic, powered by the absorption of light energy.

· Reactions in closed systems eventually reach equilibrium and can do no work.

· A cell that has reached metabolic equilibrium has a D G = 0 and is dead!

· Metabolic disequilibrium is one of the defining features of life.

· Cells maintain disequilibrium because they are open with a constant flow of material in and out of the cell.

· A cell continues to do work throughout its life.

· A catabolic process in a cell releases free energy in a series of reactions, not in a single step.

· Some reversible reactions of respiration are constantly “pulled” in one direction as the product of one reaction does not accumulate, but becomes the reactant in the next step.

· Sunlight provides a daily source of free energy for the photosynthetic organisms in the environment.

· Nonphotosynthetic organisms depend on a transfer of free energy from photosynthetic organisms in the form of organic molecules.

5. ATP powers cellular work by coupling exergonic reactions to endergonic reactions

· A cell does three main kinds of work:

· Mechanical work, beating of cilia, contraction of muscle cells, and movement of chromosomes.

· Transport work, pumping substances across membranes against the direction of spontaneous movement.

· Chemical work, driving endergonic reactions such as the synthesis of polymers from monomers.

· In most cases, the immediate source of energy that powers cellular work is ATP.

· ATP (adenosine triphosphate) is a type of nucleotide consisting of the nitrogenous base adenine, the sugar ribose, and a chain of three phosphate groups.

· The bonds between phosphate groups can be broken by hydrolysis.

· Hydrolysis of the end phosphate group forms adenosine diphosphate [ATP -> ADP + P_i] and releases 7.3 kcal of energy per mole of ATP under standard conditions.

· In the cell D G is about -13 kcal/mol.

· While the phosphate bonds of ATP are sometimes referred to as high-energy phosphate bonds, these are actually fairly weak covalent bonds.

· They are unstable, however, and their hydrolysis yields energy because the products are more stable.

· The phosphate bonds are weak because each of the three phosphate groups has a negative charge.

· Their repulsion contributes to the instability of this region of the ATP molecule.

· In the cell the energy from the hydrolysis of ATP is coupled directly to endergonic processes by transferring the phosphate group to another molecule.

· This molecule is now phosphorylated.

· This molecule is now more reactive.

· ATP is a renewable resource that is continually regenerated by adding a phosphate group to ADP.

· The energy to support renewal comes from catabolic reactions in the cell.

· In a working muscle cell the entire pool of ATP is recycled once each minute, over 10 million ATP consumed and regenerated per second per cell.

· Regeneration, an endergonic process, requires an investment of energy: D G = 7.3 kcal/mol.

B. Enzymes

1. Enzymes speed up metabolic reactions by lowering energy barriers

· A catalyst is a chemical agent that changes the rate of a reaction without being consumed by the reaction.

· An enzyme is a catalytic protein.

· Enzymes regulate the movement of molecules through metabolic pathways.

· Chemical reactions between molecules involve both bond breaking and bond forming.

· To hydrolyze sucrose, the bond between glucose and fructose must be broken and then new bonds formed with a hydrogen ion and hydroxyl group from water.

· Even in an exergonic reaction, the reactants must absorb energy from their surroundings, the free energy of activation or activation energy (E_A), to break the bonds.

· This energy makes the reactants unstable, increases the speed of the reactant molecules, and creates more powerful collisions.

· In exergonic reactions, not only is the activation energy released back to the surroundings, but even more energy is released with the formation of new bonds.

· Activation energy is the amount of energy necessary to push the reactants over an energy barrier.

· At the summit the molecules are at an unstable point, the transition state.

· The difference between free energy of the products and the free energy of the reactants is the D G.

· For some processes, the barrier is not high and the thermal energy provided by room temperature is sufficient to reach the transition state.

· In most cases, E_A is higher and a significant input of energy is required.

· A spark plug provides the energy to energize gasoline.

· Without activation energy, the hydrocarbons of gasoline are too stable to react with oxygen.

· The laws of thermodynamics would seem to favor the breakdown of proteins, DNA, and other complex molecules.

· However, in the temperatures typical of the cell there is not enough energy for a vast majority of molecules to make it over the hump of activation energy.

· Yet, a cell must be metabolically active.

· Heat would speed reactions, but it would also denature proteins and kill cells.

· Enzymes speed reactions by lowering E_A.

· The transition state can then be reached even at moderate temperatures.

· Enzymes do not change D G.

· It hastens reactions that would occur eventually.

· Because enzymes are so selective, they determine which chemical processes will occur at any time.

2. Enzymes are substrate specific

· A substrate is a reactant that binds to an enzyme.

· When a substrate, or substrates, binds to an enzyme, the enzyme catalyzes the conversion of the substrate to the product.

· Sucrase is an enzyme that binds to sucrose and breaks the disaccharide into fructose and glucose.

· The active site of an enzyme is typically a pocket or groove on the surface of the protein into which the substrate fits.

· The specificity of an enzyme is due to the fit between the active site and that of the substrate.

· As the substrate binds, the enzyme changes shape leading to a tighter induced fit, bringing chemical groups in position to catalyze the reaction.

3. The active site is an enzyme’s catalytic center

· In most cases substrates are held in the active site by weak interactions, such as hydrogen bonds and ionic bonds.

· R groups of a few amino acids on the active site catalyze the conversion of substrate to product.

· A single enzyme molecule can catalyze thousands or more reactions a second.

· Enzymes are unaffected by the reaction and are reusable.

· Most metabolic enzymes can catalyze a reaction in both the forward and reverse direction.

· The actual direction depends on the relative concentrations of products and reactants.

· Enzymes catalyze reactions in the direction of equilibrium.

· Enzymes use a variety of mechanisms to lower activation energy and speed a reaction.

· The active site orients substrates in the correct orientation for the reaction.

· As the active site binds the substrate, it may put stress on bonds that must be broken, making it easier to reach the transition state.

· R groups at the active site may create a conducive microenvironment for a specific reaction.

· Enzymes may even bind covalently to substrates in an intermediate step before returning to normal.

· The rate that a specific number of enzymes converts substrates to products depends in part on substrate concentrations.

· At low substrate concentrations, an increase in substrate speeds binding to available active sites.

· However, there is a limit to how fast a reaction can occur.

· At some substrate concentrations, the active sites on all enzymes are engaged, called enzyme saturation.

· The only way to increase productivity at this point is to add more enzyme molecules.

4. A cell’s physical and chemical environment affects enzyme activity

· The three-dimensional structures of enzymes (almost all proteins) depend on environmental conditions.

· Changes in shape influence the reaction rate.

· Some conditions lead to the most active conformation and lead to optimal rate of reaction.

· Temperature has a major impact on reaction rate.

· As temperature increases, collisions between substrates and active sites occur more frequently as molecules move faster.

· However, at some point thermal agitation begins to disrupt the weak bonds that stabilize the protein’s active conformation and the protein denatures.

· Each enzyme has an optimal temperature.

· Because pH also influences shape and therefore reaction rate, each enzyme has an optimal pH too.

· This falls between pH 6 - 8 for most enzymes.

· However, digestive enzymes in the stomach are designed to work best at pH 2 while those in the intestine are optimal at pH 8, both matching their working environments.

· Many enzymes require nonprotein helpers, cofactors, for catalytic activity.

· They bind permanently or reversibly to the enzyme.

· Some inorganic cofactors include zinc, iron, and copper.

· Organic cofactors, coenzymes, include vitamins or molecules derived from vitamins.

· The manners in which cofactors assist catalysis are diverse.

· Binding by some molecules, inhibitors, prevent enzymes from catalyzing reactions.

· If binding involves covalent bonds, then inhibition is often irreversible.

· If binding is weak, inhibition may be reversible.

· If the inhibitor binds to the same site as the substrate, then it blocks substrate binding via competitive inhibition.

· If the inhibitor binds somewhere other than the active site, it blocks substrate binding via noncompetitive inhibition.

· Binding by the inhibitor causes the enzyme to change shape, rendering the active site unreceptive (at worst) or less effective at catalyzing the reaction.

· Reversible inhibition of enzymes is a natural part of the regulation of metabolism.

C. The Control of Metabolism

1. Metabolic control often depends on allosteric regulation

· In many cases, the molecules that naturally regulate enzyme activity behave like reversible noncompetitive inhibitors.

· These molecules often bind weakly to an allosteric site, a specific receptor on the enzyme that is not the active site.

· Binding by these molecules can either inhibit or stimulate enzyme activity.

· Most allosterically regulated enzymes are constructed of two or more polypeptide chains.

· Each subunit has its own active site and allosteric sites are often located where subunits join.

· The whole protein oscillates between two conformational shapes, one active, one inactive.

· Some allosteric regulators, activators, stabilize the conformation that has a functional active site.

· Other regulators, inhibitors, stabilize the conformation that lacks an active site.

· As the chemical conditions in the cell shift, the pattern of allosteric regulation will shift as well.

· In many cases both inhibitors and activators are similar enough in shape that they compete for the same allosteric sites.

· These molecules may be products and substrates of a metabolic pathway.

· For example, some catabolic pathways have allosteric sites that are inhibited when ATP binds and activated when AMP binds.

· When ATP levels are low, AMP levels are high, and the pathway is turned on until ATP levels rise, AMP levels fall and inhibition by ATP dominates.

· One of the common methods of metabolic control is feedback inhibition in which a metabolic pathway is turned off by its end product.

· The end product acts as an inhibitor of an enzyme in the pathway.

· When the product is abundant the pathway is turned off, when rare the pathway is active.

· In enzymes with multiple catalytic subunits, binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits, a process called cooperativity.

· This mechanism amplifies the response of enzymes to substrates, priming the enzyme to accept additional substrates.

2. The localization of enzymes within a cell helps order metabolism

· Structures within the cell bring order to metabolic pathways.

· A team of enzymes for several steps of a metabolic pathway may be assembled together as a multienzyme complex.

· The product from the first can then pass quickly to the next enzyme until the final product is released.

· Some enzymes and enzyme complexes have fixed locations within the cells as structural components of particular membranes.

· Others are confined within membrane-enclosed eukaryotic organelles.

· Both methods concentrate enzymes for efficiency.

3. The theme of emergent properties is manifest in the chemistry of life: a review

· With each increase in levels of structural order, new properties emerge in addition to those of the component parts.

· The unusual behavior of water emerges from interactions of water molecules.

· The arrangement of carbon skeletons and functional groups underlies the properties of organic molecules.

· Small organic molecules assemble into larger molecules that gain additional functionality and properties.

· Metabolism is a concerted interplay of thousands of different kinds of molecules in the cell.