Chapter VI

An introduction to metabolism

We can consider metabolism as the totality of the chemical reactions that take place in living organisms. Two key topics are emphasized: the energy transformations that underlie all chemical reactions and the role of enzymes in the different reactions that occur in a cell. Enzymes are biological catalysts that lower the activation energy of a reaction and thus greatly speed up metabolic processes. An enzyme is a three-dimensional protein molecule with an active site specific for its substrate. Intricate control and feedback mechanisms produce the metabolic integration necessary for life. The reactions in a cell either release or consume energy.

The following illustration summarizes some of the components of the energy changes within a cell.

The chemistry of life is organized into metabolic pathways

Metabolism includes the thousands of precisely coordinated, complex, efficient, and integrated chemical reactions in an organism. These reactions are ordered into metabolic pathways- sequenced and branching routes controlled by enzymes. Through these pathways the cell transforms and creates the organic molecules that provide the energy and material for life.

Catabolic pathways release the energy stored in complex molecules through the breaking down of these molecules into simpler compounds.

Anabolic pathways require energy to combine simpler molecules into more complicated ones. This energy is often supplied through energy coupling, the linking of catabolic and anabolic pathways in a cell. Energy is involved in all metabolic processes. Thus, the study of energy transformations, called bioenergetics, is central to the understanding of metabolism.

Organisms transform energy.

Energy has been defined as the capacity to do work, to move matter against an opposing force, to rearrange matter. Kinetic energy is the energy of motion, of matter that is moving. This matter does its work by transferring its motion to other matter. Potential energy is the capacity of matter to do work as a consequence of its location or arrangement. Chemical energy is a form of potential energy stored in the arrangement of atoms in molecules.

Energy can be converted from one form to another. Plants convert light energy (a form of kinetic energy) to the chemical energy in sugar, and cells release this potential energy to drive cellular processes.

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

Thermodynamics is the study of energy transformations. The first law of thermodynamics states that energy can be neither created nor destroyed. Energy can be transferred between matter and transformed from one kind to another, but the total energy of the universe is constant. According to this principle of the conservation of energy, chemical reaction that either require or produce energy are merely transforming a set amount of energy into a different form.

The second law of thermodynamics states that every energy transformation or transfer results in an increasing disorder within the universe. Entropy is used as a measure of disorder or randomness.

A system, such as a cell, may become more ordered, but it does so with an attendant increase in the entropy of its surroundings. A cell can use highly ordered organic molecules as a source of the energy needed to create and maintain its own organized structure, but it returns heat and the simple molecules of carbon dioxide and water to the environment.

In any energy transformation or transfer, some of the energy is converted to heat, a less-ordered kinetic energy. The quantity of energy in the universe may be constant, but its quality is not.

Organisms live at the expense of free energy

A spontaneous process is a change that occurs without the input of external energy and that results in greater stability, reflected as an increase in entropy.

Free Energy: A criterion for spontaneous change.

A measure of the instability of a system’s energy available to perform work when the system’s temperature is uniform. Free energy (G) depends on the total energy of a system (H) and its entropy (S), such that G = H- TS. Absolute temperature (°Kelvin, or 0°C + 273) is a factor because higher temperature increases random molecular motion, disrupting order and increasing entropy. The change in free energy during a reaction is represented by DG= DH - T DS. For a reaction to be spontaneous, the free energy of the system must decrese (-DG): the system must lose energy (decrease H), become more disordered (increase S), or both. An unstable system is rich in free energy and has a tendency to change spontaneously to a more stable stage, potentially performing work in the process.

Free Energy and Equilibrium At equilibrium in chemical reaction, the forward and backward reaction are proceeding at the same rate, and DG = 0 because there is no net free energy change. Moving toward equilibrium is spontaneous; the DG of the reaction is negative. To move away from equilibrium is nonspontaneous; energy must be added to the system. Metabolic disequilibrium is a necessity of life; a cell at equilibrium is dead.

Since many metabolic reactions are reversible, they have the potential to reach equilibrium, so the system can do no work. In cells, the products of some reactions become reactants for the next reaction in the metabolic pathway. For instance, during cellular respiration a steady supply of high energy reactants such as glucose and removal of low energy products such as CO2 and H2O, maintain the disequilibrium necessary for respiration to proceed.

Free Energy and Metabolism:

Exergonic reaction = A reaction that proceeds with a net loss of free energy.

Endergonic reaction = An energy-requiring reaction that proceeds with a net gain of free energy; a reaction that absorbs free energy from its surroundings.

If a chemical process is exergonic, the reverse process must be endergonic. For example: For each mole of glucose oxidized in the exergonic process of cellular respiration, 2870 KJ are released, so (DG= - 2870 KJ/mol or 686 Kcal/mol) Joule = 0.239cal calorie = 4.184J

In cellular metabolism, endergonic reaction are driven by coupling them to reactions with a greater negative free energy (exergonic). ATP plays a critical role in this energy coupling.

ATP powers cellular work by coupling exergonic to endergonic reactions. ATP is the immediate source of energy that drives most cellular work, which includes: Mechanical work, Transport work, and Chemical work.

The Structure and Hydrolysis of ATP.

ATP (adenosine triphosphate) consists of the nitrogenous base adenine bonded to the sugar ribose, which is connected to a chain of three phosphate groups. This triphosphate tail is unstable; ATP can be hydrolyzed to ADP (adenosine diphosphate) and an inorganic phosphate molecule (Pi). The reaction releases energy (exergonic); 7.3 Kcal (31KJ) of energy per mole of ATP when measured under standard conditions. The DG of the reaction in the cell is estimated to be closer to - 13Kcal/mol, about 77% more than under standard conditions.

How ATP Performs Work?

In a cell, the free energy released from the hydrolysis of ATP is used to transfer the phosphate group to another molecule, producing a phosphorylated intermediate that is more reactive. The phosphorylation of other molecules by ATP forms the basis for almost all cellular work. The molecule acquiring the phosphate (phosphorylated or activated intermediate) becomes more reactive.

 

Regeneration of ATP:

ATP is continually regenerated by the cell. A cell regenerates ATP at a phenomenal rate; ( 107 molecules used and regenerated /sec/cell). The formation of ATP from ADP and Pi is endergonic, with a DG of + 7.3 Kcal/mol (standard conditions). Cellular respiration (the catabolic processing of glucose and other organic molecules) provides the energy for the regeneration of ATP. Plants can also produce ATP using light energy.

Enzymes speed up metabolic reaction by lowering energy barriers:

Free energy change indicates whether a reaction will occur spontaneously; but does not give information about the speed of reaction. A chemical reaction will occur spontaneously if it releases free energy -DG; but it may occur too slowly to be effective in living cells.

Biochemical reactions require enzymes to speed up and control reaction rates.

Catalyst = Chemical agent that accelerates a reaction without being permanently changed in the process, so it can be used over and over.

Enzymes = Biological catalysts, which are usually proteins.

Before a reaction can occur, the reactants must absorb energy to break chemical bonds. This initial energy investment is the activation energy.

Free energy of activation (Activation energy) = Amount of energy that reactant molecules must absorb to start a reaction (EA). This is the energy that must be absorbed by reactants to reach the unstable transition state, in which bonds are more fragile and likely to break, and from which the reaction can proceed.

The EA barrier is essential to life because it prevents the energy-rich macromolecules of the cell from decomposing spontaneously. For metabolism to proceed in a cell, however, EA must be reached. Heat, a possible source of activation energy in reactions, would be harmful to the cell and would also speed metabolic reaction indiscriminately. Enzymes are able to lower EA for specific reactions so that metabolism can proceed at cellular temperatures. Enzymes do not change DG for a reaction. DG for the overall reaction is the difference in free energy between products and reactants. In an exergonic reaction the free energy of the products is less than reactants. Even though a reaction is energetically favorable, there must be an initial investment of activation energy (EA). The breakdown of biological macromolecules is exergonic. However, these molecules react very slowly at cellular temperatures because they cannot absorb enough thermal energy to reach transition state. Enzymes, Lower EA, so the transition state can be reached at cellular temperatures and do not change the nature of a reaction (DG), but only speed up a reaction that would have occurred anyway.

Enzymes are substrate-specific:

Enzymes are specific for a particular substrate, and that specificity depends upon the enzyme’s three-dimensional shape. An enzyme binds to its substrate and catalyzes its conversion to product. The substrate is held in the active site by hydrogen or ionic bonds, crating an enzyme-substrate complex. The side chains (R groups) of some of the surrounding amino acids in the active site facilitate the conversion of substrate to product. The product then leaves the active site, and the enzyme is released in original form and can bind immediately with another substrate molecule. Active site = Restricted region of an enzyme molecule which binds to the substrate. Is usually a pocket or groove on the protein’s surface. Formed with only a few of the enzyme’s amino acids. Active site determines enzyme specificity which is based upon a compatible fit between the shape of an enzyme’s active site and the shape of the substrate. As substrate binds to the active site, it induces the enzyme to change its shape. ®this brings its chemical groups into positions that enhance their ability to interact with the substrate and catalyze the reaction. Enzymes can catalyze reactions involving the joining of two reactants by providing active sites in which the substrates are bound closely together and properly oriented. The rate at which an enzyme molecule works partially depends on the concentration of its substrate. The speed of a reaction will increase with increasing substrate concentration up to the point at which all enzyme molecules are saturated with substrate molecules and working at full speed.

Induced fit = Change in the shape of an enzyme’s active site, which is induced by the substrate. The active site is an enzyme’s catalytic center:

Steps in the Catalytic Cycle of Enzymes:

1 Substrate binds to the active site forming an enzyme-substrate complex. Substrate is held in the active site by weak interactions. 2 Induced fit of the active site around the substrate. Side chains of a few amino acids in the active site catalyze the conversion of substrate to product. 3 Product departs active site and the enzyme emerges in its original form. Since enzymes are used over and over, they can be effective in very small amounts.

A cell’s chemical and physical environment affects enzyme activity:

Each enzyme has optimal environmental conditions. Optimal temperature allows the greatest number of molecular collisions without denaturing the enzyme.

Enzyme reaction rate increases with increasing temperature. Kinetic energy of reactant molecules increases with rising temperature, which increases substrate collisions with active sites. Beyond the optimal temperature, reaction rate slows. The enzyme denatures when increased thermal agitation of molecules disrupts weak bonds that stabilize the active conformation.

Optimal pH range for most enzymes is pH6-8. Some enzymes operate best at more extremes of pH, such as pepsin which has an optimal pH of 2.

Cofactors = Small nonprotein molecules that are required for proper enzyme catalysis. They may be inorganic, such as various metal atoms, or organic molecules called coenzymes ( e.g. most vitamins).

Enzyme Inhibitors

Certain chemicals can selectively inhibit enzyme activity.

ð Inhibition may be irreversible if the inhibitor attaches by covalent bonds.

ð Inhibition may be reversible if the inhibitor attaches by weak bonds.

Competitive inhibitors = Chemicals that resemble an enzyme’s normal substrate and compete with it for the active site.

ð Block active site from the substrate. ð If reversible, the effect of these inhibitors can be overcome by increased substrate concentration.

Noncompetitive inhibitors = Enzyme inhibitors that do not enter the enzyme’s active site, but bind to another part of the enzyme molecule. ð Causes enzyme to change its shape so the active site cannot bind substrate. ð May act as metabolic poisons ( e.g. DDT, many antibiotics). ð Selective enzyme inhibition is an essential mechanism in the cell for regulating metabolic reactions.

Allosteric Regulation Molecules that inhibit or activate enzyme activity may bind to an Allosteric Site = Specific receptor site on some part of the enzyme molecule other than the active site. ð Most enzymes with allosteric sites have tow or more polypeptide chains, each with its own active site. Allosteric sites are often located where the subunits join. ð Allosteric enzymes have tow conformations, one catalytically active and the other inactive.

ð Binding of an activator to an allosteric site stabilizes the active conformation.

ð Binding of an inhibitor (noncompetitive inhibitor) to an allosteric site stabilizes the inactive conformation. Enzyme activity changes continually in response to changes in the relative proportions of activators and inhibitors ( e.g. ATP/ADP).

ð Subunits may interact so that a single activator or inhibitor at one allosteric site will affect the active sites of the other subunits.

Cooperativity Substrate molecules themselves may enhance enzyme activity. Cooperativity = The phenomenon where substrate binding to the active site of one subunit induces a conformational change that enhances substrate binding at the active sites of the other subunits.

Metabolic order emerges from the cell’s regulatory systems and structural organization. Metabolic pathways are regulated by controlling enzyme activity.

Feedback inhibition = Regulation of a metabolic pathway by its end product, which inhibits an enzyme early in the, or within the pathway. You have an example in the book: (Threonine Isoleucine). This prevents the cell from wasting chemical resources by synthesizing more products than is necessary.

Structural Order and Metabolism

Specialized cellular compartments may contain high concentrations of the enzymes and substrates needed for a particular pathway. Also, some enzymes have fixed locations in the cell because they are incorporated into the membranes of cellular compartments. Dissolved enzymes and their substrates may be localized within organelles such as chloroplasts and mitochondria.