Cell metabolism

Metabolism encompasses the integrated and controlled pathways of enzyme catalysed reactions within a cell Metabolism The word “metabolism” refers to all the chemical reactions occurring in a cell. Reactions are usually part of a series called a metabolic pathway, where the product of one reaction is the reactant of the next reaction in the sequence. Each reaction in a metabolic pathway is controlled by its own enzyme. Metabolic pathways. Anabolic (energy requiring) and catabolic (energy releasing) pathways — can have reversible and irreversible steps and alternative routes. Metabolic pathways involve biosynthetic processes (anabolism) and the breakdown of molecules (catabolism) to provide energy and building blocks. Synthetic pathways require the input of energy; pathways that break down molecules usually release energy. Anabolic and catabolic pathways Catabolic pathways are those involving breakdown of larger molecules to smaller molecules to provide energy or molecules to be used as building blocks for larger molecules. These pathways release energy Anabolic pathways involve synthesis of larger molecules from smaller ones. These pathways require energy to be used.

Most metabolic reactions are reversible and the presence of a substrate or the removal of a product will drive a sequence of reactions in a particular direction. Substance A Substance B Most metabolic reactions are reversible, the direction that the reactions proceeds depending on the concentration of the reactants and products e.g. in this reaction A high concentration of A and a low concentration of B, will lead to A being changed to B. A low concentration of A and a high concentration of B will lead to the reaction going in the opposite direction with B being changed to A. Metabolic pathways are controlled by the presence or absence of particular enzymes in the metabolic pathway Each reaction in a metabolic pathway is controlled by a particular enzyme. If this enzyme is present, the reaction occurs and the pathway proceeds. If the enzyme is absent, the reaction cannot occur and the pathway stops.

Regulation can be controlled by intra- and extracellular signal molecules. Role of signal molecules Genes control the production of proteins including enzymes. The production of enzymes can depend on signal molecules either inside the cell or in the environment. Some signal molecules switch on the gene for the enzyme while others affect the actual enzyme itself. Lactose metabolism in E.coli The bacterium E. coli produces the enzyme galactosidase which converts the milk sugar lactose to glucose and galactose. The enzyme is only produced when the bacterium has lactose available as a food. This prevents unnecessary energy being used to produce the enzyme when it is not needed. Two scientist, Jacob and Monod suggested how the presence of lactose led to the gene for β galactosidase being switched on. (This is called the Jacob-Monod hypothesis)

Jacob-Monod hypothesis 3 genes involved Structural gene – codes for production of the enzyme Operator gene – switches on the structural gene Regulator gene – Codes for a repressor protein that blocks the operator gene preventing it from switching on the structural gene When no lactose is present: 1.Regulator gene codes for production of the repressor protein 2.Repressor protein binds to the operator gene 3.The operator gene cannot switch on the structural gene 4.The enzyme is not produced When lactose is present: 1.Regulator gene codes for production of the repressor protein 2.Lactose binds to the repressor protein preventing it from binding to the operator gene 3.The operator gene can now switch on the structural gene 4.The structural gene produces the enzyme In this case lactose is a signal molecule leading to production of the enzyme.

Genes for some enzymes are continuously expressed. These enzymes are always present in the cell and their control involves regulation of their rate of reaction. Some enzymes are always present in cells, e.g. those that control glycolysis reactions. The genes that code for production of such enzymes are always switched on. The rate of the reactions controlled by these enzymes can be regulated in a number of ways, e.g. Feedback inhibition by an end product (described in a later slide) Effect of signal molecules, e.g. adrenaline binds to liver cell receptors and acts as a signal molecule triggering the activation of the enzyme that converts glycogen to glucose

Activation energy. The role of the active site in lowering the activation energy of the transition state Activation energy and transition state The energy required to break chemical bonds in reactants and begin a chemical reaction is called the activation energy. When the reactants have absorbed enough energy to break the bonds and make the molecules unstable they are said to be in a transition state and the reaction can now occur. Enzymes are biological catalysts which lower the activation energy and allow reactions to occur fast enough at the temperatures found in living cells and organisms. How enzymes work Enzymes are proteins. Part of an enzyme molecule, called the active site, has a shape that is complementary to the substrate molecule. An enzyme is specific to its substrate which fits onto the active site – the substrate shows affinity for the active site.

Induced fit. The role of the active site in orientating reactants and the release of products with low affinity for the active site. Induced fit The active site of an enzyme alters its shape slightly to ensure the active site fits very closely around the substrate molecule. This is called the induced fit and increases the chance of the reaction taking place. This is summarised below. Orientation of reactants When the reaction involves two or more substrates, the shape of the active site determines the orientation of the reactants ensuring that they are held in the correct position for the reaction to occur. Low affinity of products for the active site When the reaction has occurred, the products have a low affinity for the active site and are released leaving the enzyme free to bind to another substrate.

The effects of substrate concentration on the rate of enzyme reactions. Effect of substrate concentration on the rate of an enzyme reaction The graph shows the effect of substrate concentration on enzyme activity: Rate of enzyme controlled reaction Substrate concentration As substrate concentration increases rate of reaction increases because more and more substrate molecules join to enzyme active sites and are changed to product molecules. Eventually, increasing substrate concentration does not increase the rate of reaction because at this point all the enzyme active sites are occupied by substrate molecules and any more substrate molecules added cannot find an active site – at this point the enzyme concentration is the limiting factor for the reaction

The effects of substrate and end product concentration on the direction of enzyme reactions. Many enzyme controlled reactions are reversible, e.g. Substance A Substance B The direction taken by this reaction depends on the concentration of the substrate (A) and end product (B) Where there is a high concentration of substrate, the reaction proceeds A B Where the concentration of end product is high the reaction B A occurs

Enzymes often act in groups or as multi-enzyme complexes. Multi-enzyme complexes Enzymes often act in groups or multi-enzyme complexes. DNA polymerase and RNA polymerase are parts of multi-enzyme complexes.

Control of metabolic pathways through competitive (binds to active site), non-competitive (changes shape of active site) and feedback inhibition (end product binds to an enzyme that catalyses a reaction early in the pathway). Competitive inhibition can be reversed by increasing substrate concentration Inhibitors Metabolic pathways can be affected by inhibitors – an inhibitor will decrease the rate of an enzyme controlled reaction. Competitive inhibitor A competitive inhibitor is a substance whose molecule has a similar shape to the substrate molecule and competes with it for the enzyme active sites. Enzyme molecule Substrate molecule Substrate molecule fits onto active site Inhibitor molecule has similar shape to substrate molecule Inhibitor can also bind to active site and so competes with substrate

Non-competitive inhibitors A non-competitive inhibitor is able to bind to the enzyme at a site different from the active site (this is called an allosteric site. In doing so it results in the shape of the active site being changed so that the substrate can no longer bind to it. Enzyme molecule Substrate molecule Non-competitive inhibitor molecule Non-competitive inhibitor molecule binds to allosteric site and changes the shape of the active site so that the substrate will no longer bind

Feedback inhibition by an end product The diagram represents how end product inhibition works: Substance A Substance B Substance C End product Enzyme 1 Enzyme 2 Enzyme 3 As the concentration of the end-product builds up, some of it binds to and inhibits enzyme 1. In this way the pathway is slowed and production of the end product reduced