Metabolic reactions are regulated in response to the cell’s needs. METABOLISM Metabolic reactions are regulated in response to the cell’s needs. AHL Topic 8.1 IB Biology Miss Werba

TOPIC 8 – HL MOLECULAR BIOLOGY 8.1 METABOLISM 8.2 CELL RESPIRATION 8.3 PHOTOSYNTHESIS J WERBA – IB BIOLOGY 2

THINGS TO COVER U.1 U.2 U.3 U.4 A.1 A.2 S.1 S.2 Statement Guidance Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions. U.2 Enzymes lower the activation energy of the chemical reactions that they catalyse. U.3 Enzyme inhibitors can be competitive or non-competitive. U.4 Metabolic pathways can be controlled by end-product inhibition. Study one specific example for competitive and non-competitive inhibition. A.1 End-product inhibition of the pathway that converts threonine to isoleucine. A.2 Use of databases to identify potential new anti-malarial drugs. S.1 Calculating and plotting rates of reaction from raw experimental results. S.2 Distinguishing different types of inhibition from graphs at specified substrate concentration. NOS 3.8 Developments in scientific research follow improvements in computing J WERBA – IB BIOLOGY 3

U.1 METABOLISM Metabolism: sum total of all chemical reactions in an organism. Metabolic pathways: consist of cycles or chains of enzyme- catalysed reactions. http://iws.collin.edu/biopage/faculty/mcculloch/1406/outlines/chapter%206/Ra79.JPG J WERBA – IB BIOLOGY 4

U.2 ACTIVATION ENERGY Activation energy: the initial input of energy needed to trigger a chemical reaction. J WERBA – IB BIOLOGY 5

U.2 ACTIVATION ENERGY Enzymes lower the activation energy of the chemical reactions that they catalyse. J WERBA – IB BIOLOGY 6

U.2 ACTIVATION ENERGY J WERBA – IB BIOLOGY 7

U.2 ACTIVATION ENERGY Due to the binding with the enzyme, the bonds in the substrate molecules are stressed (less stable). This lowers the overall energy level of the substrate molecules. This reduces the energy required to complete the reaction. J WERBA – IB BIOLOGY 8

U.3 ENZYME INHIBITORS Inhibitor: molecules that bind to an enzyme and slows down or stops the enzyme’s function. Enzyme inhibitors can be competitive or non-competitive. J WERBA – IB BIOLOGY 9

COMPETITIVE INHIBITORS U.3 COMPETITIVE INHIBITORS inhibitor and substrate are structurally similar inhibitor binds to the active site substrate cannot bind Examples: the inhibition of folic acid synthesis in bacteria by sulfonamide Prontosil™ (an antibiotic) the inhibition of enzyme-catalysed synthesis of fumerate by oxaloacetate in the Kreb’s Cycle J WERBA – IB BIOLOGY 10

COMPETITIVE INHIBITORS U.3 COMPETITIVE INHIBITORS Examples: Use of Antabuse to compete with the aldehyde oxidase enzyme in the hydrolysis of alcohol (increases nausea as a result of the buildup of intermediates, a good deterrent from drinking) J WERBA – IB BIOLOGY 11

NON-COMPETITIVE INHIBITORS U.3 NON-COMPETITIVE INHIBITORS inhibitor and substrate are not structurally similar inhibitor binds at an allosteric site (different to the active site) changes the shape of the active site substrate cannot bind Examples: cyanide inhibition of cytochrome oxidase (an enzyme in cellular respiration). J WERBA – IB BIOLOGY 12

NON-COMPETITIVE INHIBITORS U.3 NON-COMPETITIVE INHIBITORS Examples: Use of ACE inhibitors for controlling blood pressure ACE inhibitors inhibit Angiotensin Converting Enzymes They prevent high blood pressure due to vasoconstriction in the blood vessels. J WERBA – IB BIOLOGY 13

U.3 ENZYME INHIBITORS J WERBA – IB BIOLOGY 14

U.3 ENZYME INHIBITORS The higher the concentration of competitive inhibitors, the slower the rate of reaction. J WERBA – IB BIOLOGY 15

U.3 S.2 ENZYME INHIBITORS At higher substrate concentrations, the effect of a competitive inhibitor can be overcome. It therefore has no effect on maximum rate of reaction. J WERBA – IB BIOLOGY 16

U.3 S.2 ENZYME INHIBITORS Since a non-competitive inhibitor prevents the enzyme activity regardless of substrate concentration, it always reduces the max rate of reaction. J WERBA – IB BIOLOGY 17

18

END-PRODUCT INHIBITION when the product of a pathway acts as an inhibitor of the pathway a form of non-competitive inhibition temporarily changes the shape of the active site prevents a large build-up of products J WERBA – IB BIOLOGY 19

END-PRODUCT INHIBITION J WERBA – IB BIOLOGY 20

END-PRODUCT INHIBITION A.1 END-PRODUCT INHIBITION Example: End-product inhibition of the pathway that converts threonine to isoleucine. J WERBA – IB BIOLOGY 21

END-PRODUCT INHIBITION A.1 END-PRODUCT INHIBITION Example: Isoleucine (Ile) is an amino acid that is used in the biosynthesis of proteins. It as a non-polar, amino acid which is essential in humans, meaning the body cannot synthesize it, and must be ingested in our diet. There are a series of reactions needed to convert threonine to isoleucine. It is regulated by allosteric inhibition. J WERBA – IB BIOLOGY 22

END-PRODUCT INHIBITION A.1 END-PRODUCT INHIBITION Five enzymes catalyze the steps in the pathway. The end product of the pathway, isoleucine, acts as an inhibitor of the first enzyme of the pathway, threonine deaminase. Isoleucine is an allosteric deactivator (non- competitive inhibitor) of the enzyme threonine deaminase. The pathway is then turned off when isoleucine concentrations are high. J WERBA – IB BIOLOGY 23

END-PRODUCT INHIBITION A.1 END-PRODUCT INHIBITION If the concentration of isoleucine later falls as a result of its use in cell synthesis, isoleucine is released from the threonine deaminase enzymes and the pathway will resume. J WERBA – IB BIOLOGY 24

Developments in scientific research follow improvements in computing NOS.3.8 BIOINFORMATICS Developments in scientific research follow improvements in computing Developments in bioinformatics, such as the interrogation of databases, have facilitated research into metabolic pathways. J WERBA – IB BIOLOGY 25

A.2 BIOINFORMATICS Bioinformatics is an approach where multiple research teams can add info to a database enabling other groups to search/use the database. Example: Databases have been used to identify potential new anti-malarial drugs. J WERBA – IB BIOLOGY 26

BIOINFORMATICS Example: Malaria is caused by the Plasmodium falciparum pathogen. Mosquitoes are used as a host, as are humans. There is increasing resistance to the current anti-malarial drugs. In one study, using bioinformatics, ~300,000 chemicals were screened against both the resistant and non-resistant pathogens. J WERBA – IB BIOLOGY 27

BIOINFORMATICS Example: 19 new chemicals that inhibit the enzymes normally targeted by anti-malarial drugs were found. 15 additional chemicals that bind to malarial proteins were also identified – can help with locating the pathogen J WERBA – IB BIOLOGY 28

CALCULATING & PLOTTING RATES OF REACTION Rate of reaction can be calculated using either of the following formulae: Rate of Reaction (s-1) = 1 / time taken (s) OR Rate of Reaction (cm3s-1) = volume change / time taken J WERBA – IB BIOLOGY 29

S.1 METABOLISM Q1. An investigation was carried out which measured the volume of carbon dioxide released over time. Calculate the rate of reaction. J WERBA – IB BIOLOGY 30

METABOLISM Q2. Which is correct for the non-competitive inhibition of enzymes? J WERBA – IB BIOLOGY 31

METABOLISM Q3. Consider the metabolic pathway shown below. If there is end-product inhibition, which product would inhibit which enzyme? J WERBA – IB BIOLOGY 32

METABOLISM Q4. Discuss factors that affect enzyme activity. (9 marks) J WERBA – IB BIOLOGY 33

METABOLISM A1. 1.25 cm3 s-1 A2. D A3. D J WERBA – IB BIOLOGY 34

METABOLISM A4. at low temperatures, rate of reaction increases as temperature increases (or vice versa); more kinetic energy / faster movement of molecules means more collisions between enzyme / active site and substrate; optimum temperature is temperature at which rate of enzyme-catalyzed reaction is fastest; at high temperatures enzymes are denatured and stop working; denatured means change of structure in enzyme / protein resulting in loss of its biological properties / no longer can carry out its function; too much kinetic energy / vibrations breaks bonds that give enzyme specific shape; optimum pH is one at which rate of enzyme-catalyzed reaction is fastest; rate of reaction reduced as increase or decrease pH (from optimum); strong acids and alkalis can denature enzymes; affect (weak, ionic, hydrogen) bonds that hold enzyme in specific shape; at low substrate concentrations, as increase concentration get increase in rate of reaction; more chance of collision between substrate and enzyme / active site; at high substrate concentration, have no change in rate as increase concentration; all active sites occupied; J WERBA – IB BIOLOGY 35