Higher Human Biology Unit 1 – Human Cells Section 6 – Metabolic Pathways

What can you remember? What are enzymes? They are biological catalysts that speed up chemical reactions What are enzymes? What type of molecules are enzymes? What are the two types of enzyme catalysed reactions? What is it called when an enzyme catalyses the reaction at the fastest rate? What can affect an enzymes activity? Describe how an enzyme works Globular Proteins Synthesis and Degradation Optimum Conditions pH, temperature and concentration Must mention active site, substrate and specificity

a - Metabolic Pathways We will be learning to… State what is meant by the term metabolic pathways State that metabolic pathways are integrated and controlled at each step by enzymes Identify metabolic pathways as having reversible , irreversible and alternative routes Describe the difference between anabolic and catabolic processes State that anabolic reactions require energy by building up large molecules from small molecules State that catabolic reactions release energy by breaking down large molecules into smaller molecules

What is Cell Metabolism? A cell’s daily operations are carried out by a series of biochemical reactions that take place within a cell. Reactions are turned on and off or sped up and slowed down according to the cells needs. The collective term for all the enzyme- catalysed chemical reactions that take place in a cell is the cells metabolism.

What are Metabolic Pathways? The cells metabolism is a series of integrated pathways that are catalysed and controlled by enzymes. A metabolic pathway is a sequence of reactions controlled by enzymes which change one metabolite into another. The metabolite produced at each stage, the product, is used as the substrate for the next stage of the pathway.

Types of Metabolic Pathways There are two types of enzyme-catalysed metabolic pathways: Anabolic – these bring about the synthesis of complex molecules from simpler building block molecules and as such require energy from the breakdown of ATP to ADP and the transfer of the phosphate to the substrate molecule. E.g. protein synthesis

Types of Metabolic Pathways There are two types of metabolic pathways: Catabolic – these bring about the breakdown of complex molecules to simpler ones, usually releasing energy and often producing building block molecules. The release of energy is used to add the phosphate group to ADP to form ATP. E.g. aerobic respiration.

Catabolic – Aerobic Respiration Anabolic – e.g. Protein synthesis Carbon Dioxide + Water e.g. Amino Acids ATP Energy Energy ENERGY TRANSFER Catabolic – Aerobic Respiration Anabolic – e.g. Protein synthesis Energy Energy Glucose + Oxygen ADP + Pi Protein molecule Respiration Protein Synthesis Catabolic Anabolic

Reversible and Irreversible Pathways As metabolic pathways are regulated by enzymes a pathway often contains reversible and irreversible steps. This allows the process to be closely regulated. In glycolysis, glucose is converted to pyruvate which is an intermediate metabolite at the start of respiration. Glucose diffusing into a cell from a high concentration outside to a low concentration inside is irreversibly converted to intermediate 1 by enzyme A. This process is of advantage to the cell because it maintains a low concentration of glucose inside the cell and therefore promotes continuous diffusion of glucose into the cell from the high concentration outside.

The conversion of intermediate 1 to intermediate 2 by enzyme B is reversible. If more intermediate 2 is formed than the cell requires for the next step then some can be converted back to intermediate 1 and used in an alternative pathway. The conversion of intermediate 2 to intermediate 3 by enzyme C is irreversible and is a key regulatory point in the pathway. Steps that are irreversible involve the addition of phosphate (phosphorylation)

Alternative Pathways Metabolic pathways can also contain alternative routes that allow steps in the pathway to be bypassed. The diagram shows a pathways from glucose via an intermediate, that bypasses the steps controlled by enzymes A, B and C but returns to glycolysis later in the pathway. This bypass is used when the cell has a plentiful supply of sugar.

b – Enzyme Control of Metabolic Pathways We will be learning to… Describe how metabolic pathways are controlled by the presence or absence of particular enzymes. State that the rate of the metabolic pathways are regulated by the rate of reaction of key enzymes Explain what induced fit enzymes are Describe the role of the active site of an enzyme in affecting the activation energy and affinity of the substrate and products for the active site during a reaction Explain the effect of substrate and product concentration on the direction and rate of enzyme reactions Describe the control of metabolic pathways through competitive, non- competitive and feedback inhibition of enzymes.

Presence or absence of enzymes In all cells, there is the potential for a huge range of enzyme- assisted reactions to take place. Control of the metabolic pathways of the cell is achieved by adjusting the activity of the enzymes which catalyse the reactions in the pathway. Each step in a metabolic pathway is driven by a specific enzyme. Each enzyme is coded for by at least one gene. If one enzyme is absent, the metabolic pathway stops. Metabolic pathways can therefore be regulated through gene expression.

Inborn Errors of Metabolism An example of control in a metabolic pathway by enzymes is in inherited diseases caused by a single gene mutation. These are known as inborn errors of metabolism. One example is phenylketonuria (PKU), which results from a mutation to the gene that codes for the enzyme that converts the amino acid phenylalanine into tyrosine.

Phenylalanine is an 'essential' amino acid and must be obtained from the diet. Tyrosine can be synthesised. The last three compounds in the pathway are all important neurotransmitters. People with PKU lack the enzyme phenylalanine dehydroxylase and cannot carry out the conversion of phenylalanine to tyrosine. A build-up of phenylalanine in the body will lead to intellectual disabilities and seizures unless its intake in proteins is controlled.

Enzyme Controlled Rate of reaction Genes for some enzymes are continuously expressed, leading to the permanent presence of these enzymes within cells. These enzymes are always present in the cell and their control involves regulation of their rate of reaction. There are many different ways in which gene expression is controlled. Enzymes may have their activity reduced or stopped, either temporarily or permanently, by different forms of inhibition. Alternatively, they may be 'switched on' by enzyme activators.

Lactose Metabolism in E- coli Some metabolic pathways are only required to operate under certain circumstances. To prevent resources being wasted, the genes that code for the enzymes controlling each of their stages are ‘switched on’ or ‘switched off ’ as required. Lactose is a sugar that it found in milk. It is made up of a molecule of glucose and galactose

Enzyme Induction in Lactose Metabolism in E- coli E.coli can only make use of the glucose for respiration if it is released from the galactose. The enzyme responsible for breaking up lactose is B – galactosidase. E.coli has a gene that codes for B – galactosidase but it only produces this enzyme when lactose is present. Somehow the gene that codes for B – galactosidase is switched on in the presence of lactose. The process of switching on a gene only when the enzyme that it codes for is needed is called enzyme induction.

Genetic Control Control of growth is under genetic control with genes being switched on and off at specific times. The enzyme ß- galactosidase could be regulated to ensure that :- the enzyme was only switched on when its substrate lactose was present. valuable raw materials were not wasted. valuable energy in the form of ATP was not wasted. Genes can work together to help regulate the production of an enzyme Structural gene is transcribed and translated into the enzyme ß- galactosidase which breaks down the sugar lactose Operator gene switches on the structural gene Regulator gene controls the functioning of the operator through the production of a ‘repressor protein’ All three genes working together are known as an operon

The production of the enzyme B – galactosidase by E. coli bacteria. In the absence of lactose (a sugar) the lactose digesting enzyme ‘B – galactosidase’ is not produced by the bacteria. But when lactose is present, the lactose digesting enzyme ‘B – galactosidase’ is produced.

Since the lactose sugar starts the production of the enzyme it is known as the inducer http://www.youtube.com/watch?v=oBwtxdI1zvk

Mutations of the Operon Genes 1. Regulator The repressor protein would be faulty or not made so the operator would be free to switch on the structural gene all the time. Therefore the enzyme would be made continuously. Therefore wasting resources and energy. Operator The operator would not be able to switch on the structural gene. Therefore the enzyme would not be made. Therefore cell could not use lactose as an energy source 3. Structural The enzyme would be faulty or not be made. Therefore cell could not use lactose as an energy source.

Induced Fit Enzymes Molecules need a certain minimum energy before a reaction will take place. The energy needed to allow a reaction to occur is called the activation energy. The presence of a catalyst ensures that the initial energy requirement for a reaction is lowered, therefore more molecules have this energy and the reaction takes place faster. Enzymes therefore allow reactions to occur very quickly and at temperatures low enough to sustain life (5-40˚C)

A catalyst is a substance that: lowers the activation energy required for a chemical reaction to proceed speeds up the rate of a chemical reaction takes part in the reaction but remains unchanged at the end of it.

For a reaction to take place, the substrate must collide with the enzyme and that the reaction takes place on the surface of the enzyme. The activity of enzymes depends on their flexible and dynamic shape. There is an affinity of substrate molecules for the active site of an enzyme; once in position there are two proposed theories of how enzymes work. 1 2

Induced Fit Hypothesis Active sites are not rigid but are flexible and dynamic. http://web.chem.ucsb.edu/~molvisual/ABLE/induced_fit/index.html

Active site affinity When the reaction involves two (or more) substrates, the shape of the active site determines the orientation of the reactants. This ensures that they are held together in such a way that the reaction between them can take place. First the active site holds the two reactants closely together in an induced fit. Then it acts on them to weaken chemical bonds that must be broken during the reaction. This process reduces the activation energy needed by the reactants to reach the transition state that allows the reaction to take place. Once the reaction has occurred, the products have a low affinity for the active site and are released. This leaves the enzyme free to repeat the process with new molecules of substrate.

Inhibition An inhibitor is a substance which slows down, or stops, the activity of an enzyme. Two different types of inhibition are Competitive - Can bind to the active site of the enzyme, thereby competing with the substrate. This prevents the substrate from binding. Non-competitive – binds to the enzyme at a different area (away from the active site), changing the shape of the enzyme and subsequently the active site.

Competitive Inhibition In competitive inhibition, a molecule that matches a similar shape to the substrate. It competes for the active site of the enzyme and effectively reduces the concentration of the available enzyme. The inhibitor attaches temporarily to the active site, blocking the substrate from attaching. This type of inhibition can be reversed by increasing the concentration of the substrate. At high concentration, there is a greater likelihood of a substrate molecule attaching to an active site than an inhibitor molecule.

Competitive Inhibitors The effect of a competitive inhibitor is reduced if the substrate concentration is increased.

Non-Competitive Inhibition An inhibitor molecule binds to the enzyme at a different area (away from the active site). This changes the shape of the enzyme and active site. As a result, the catalytic efficiency of the enzyme is reduced and the shape of the active site may be altered so much that the reaction cannot occur at all. Increasing substrate concentration will not increase the rate of reaction.

Non competitive inhibitors are not influenced by change in substrate concentration. https://www.youtube.com/watch?v=PILzvT3spCQ

Feedback (End Product) Inhibition Metabolic pathways can be controlled by feedback inhibition. When the product of a series of enzymatic reactions, for example an amino acid, starts to accumulate in the cell, it can inhibit the action of the first enzyme involved in its synthesis. Further action of the enzyme is halted. This is called feedback inhibition. As the level of the end product drops, the inhibition is removed and the pathway will proceed. Feedback inhibition prevents a wasteful build-up of product occurring.

The end product binds to an enzyme that catalyses a reaction early in the pathway. ‘Feedback’ or ‘end point’ inhibition is another way in which metabolic pathways can be regulated. It is an example of ‘negative feedback’ control and helps avoid wasteful overproduction of products. http://highered.mheducation.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/0072437316/120070/bio10.swf::Feedback%20Inhibition%20of%20Biochemical%20Pathways

Now I can….. a – Metabolic Pathways State what is meant by the term metabolic pathways State that metabolic pathways are integrated and controlled at each step by enzymes Identify metabolic pathways as having reversible , irreversible and alternative routes Describe the difference between anabolic and catabolic processes State that anabolic reactions require energy by building up large molecules from small molecules State that catabolic reactions release energy by breaking down large molecules into smaller molecules

Word Definition Metabolite these are intermediates and products of metabolism Activation Energy input of energy required to start a chemical reaction Active Site region on an enzyme molecule where the substance binds Anabolic method of pathways that consume energy in synthesis of complex molecules Catabolic metabolic activity that releases energy in breakdown reactions Competitive Inhibition slowing of reaction rate due to the presence of a substance resembling the substrate Feedback Inhibition enzyme inhibition caused by the presence of an end product of a metabolic pathway Induced Fit change to an enzyme's active site brought about by its substrate Metabolic Pathway enzyme-controlled sequence of chemical reactions in a cell Non-Competitive Inhibition enzyme inhibition caused by a substance that permanently alters the active site of the enzyme Product substance resulting from an enzyme-catalysed reaction Substrate substance on which an enzyme works Signal Molecule molecule that brings about changes in a cell's metabolism

Now I can….. b – Enzyme Control of Metabolic Pathways Describe how metabolic pathways are controlled by the presence or absence of particular enzymes. State that the rate of the metabolic pathways are regulated by the rate of reaction of key enzymes Explain what induced fit enzymes are Describe the role of the active site of an enzyme in affecting the activation energy and affinity of the substrate and products for the active site during a reaction Explain the effect of substrate and product concentration on the direction and rate of enzyme reactions Describe the control of metabolic pathways through competitive, non- competitive and feedback inhibition of enzymes.

Higher Human 2017 – A Q4 C

Higher Human 2016 – A Q4 B

Higher Human 2017 Q2

Give an account of enzymes under the following headings: (i) Factors affecting activity (7) (ii) Activation of enzymes (3)

(i) Factors affecting activity Enzymes are catalysts/speed up metabolism/chemical reactions/lower activation energy affected by: (each with a brief description) temperature: a rise in temperature causes an increase in activity up to an optimum/point, thereafter a decline. (or graph) pH: a change in pH causes an increase in activity up to an optimum/point, thereafter a decline (or graph) 4 Denaturing - change in enzyme structure with high temp/pH change 5 Inhibitors - slows up/stops enzyme activity 6 competitive - attach to active site (labelled diagram OK) 7 non-competitive - other part of enzyme, distorts active site 8 Substrate concentration, with explanation/graph 9 Enzyme concentration, with explanation/graph   (ii) Activation of enzymes 10 Definition of activation 11 Vitamins/minerals/change in pH activate enzymes 12 Vitamins/minerals act as co-enzymes/co-factors 13 Co-factor/co-enzyme enables substrate to fit active site (diagram) 14 Any example of/or reason for need for activation. eg activation of trypsin eg prevention of digestion of cells producing the enzyme

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