Enzymes: A Biology Overview PDF

2. ENZYMES 1. Gibb’s Free Energy 2. Redox reactions 3. Activation energy 4. ATP catabolic and anabolic reactions 5. Enzymes 6. Rate of Enzyme controlled reactions (Enzyme kinetics) 7. Effect of pH and temperature on enzyme activity 8. Enzyme inhibition 9. Review enzymes 10.Metabolic pathways 11.End...

2. ENZYMES 1. Gibb’s Free Energy 2. Redox reactions 3. Activation energy 4. ATP catabolic and anabolic reactions 5. Enzymes 6. Rate of Enzyme controlled reactions (Enzyme kinetics) 7. Effect of pH and temperature on enzyme activity 8. Enzyme inhibition 9. Review enzymes 10.Metabolic pathways 11.End product inhibition We are slowly working our way through this, star3ng with proteins, then lipids, then carbohydrates and finally nucleic acids. We started the course with proteins, because everything in the cell is carried out by proteins. THEN we covered lipids, because the materials that make up a cell have to pass through lipid membranes –with the help of proteins. NEXT –we will cover carbohydrates because this is how the energy is transferred to the cell to move materials around (metabolism). Before star3ng on carbohydrates, we must learn about enzymes and energy transfer reac3ons. Enzymes are (mostly) proteins. NEXT – we will cover how these metabolic processes are governed by genes, which are nucleic acids. Genes determine which proteins are made, where and when. We have looked at protein structure We are now applying principles of protein structure to enzyme func3on.  1. Gibb’s Free Energy FIRST LAW OF THERMODYNAMICS Energy can be transferred or transformed, but can neither be created nor destroyed. SECOND LAW OF THERMODYNAMICS Every energy transfer results in an increase in entropy. G =Gibb’s Free Energy ΔG = ΔH - TΔS Energy total energy temperature x entropy available to do (enthalpy) work Gibbs free energy is the work that can be extracted from a closed system (one that can exchange heat and work with its surroundings, but not matter) at ^ixed temperature and pressure. Erwin Schrodinger (the quantum physicist), wrote a book in 1944 , ‘’What is Life?’’ He speculated that living cells must use processes that use energy to prevent the cell from breaking down and decaying. This reverses the 2nd Law of Thermodynamics which says that order à disorder (entropy). In order to reverse entropy, there must be a free ^low of energy through the system, so it must be an open system, with energy input and energy loss. Schrodinger was an Austrian quantum physicist, famous for the ‘’Cat in the box’’ Schrodinger said that thought experiment. p. 124 Sketches of most physical laws on a the History of large scale are due to Science, Bell & Marleau chaos on a small scale. For example, diffusion, which seems to be a highly ordered process, is in fact the consequence of random movements of molecule. The cat is simultaneously alive AND dead un;l you observe it, at which point its state is fixed to be alive OR dead. Fig. 6.4 2. Redox reactions If endergonic, the electrons move to a higher energy level If exergonic, electrons move to a lower energy level. Fig. 6.2 The electrons moved further away from C. Oxida3on = electron loss. The electrons moved The electrons were not completely lost (which would closer to O be ionisa3on), but they went closer to the O atom 3. Ac5va5on energy Fig. 6.5 Fig. 8.7 Campbell Fig. 6.6 4. ATP in catabolic and anabolic reactions  ADP ADP ATP ATP  METABOLISM = all the chemical reac3ons in the cell Break down big molecules Build up big molecules CATABOLIC ANABOLIC Fig. 6.7  p. 106 Sketches of the History of To make these Science, Bell & Marleau reactions go fast enough to counteract the progress towards entropy, all metabolic reactions are catalysed by ENZYMES. Pasteur thought that fermenta3on was caused by a vital force found only in living cells. Buchner showed in 1897 that non-living enzyme ( he called zymase) could carry out fermenta3on Lysozyme was the first enzyme to have its structure determined by Xray crystallography in 1965 3. Ac5va5on energy Fig. 6.5 5. Enzymes Fig. 6.8 This enzyme is LYSOZYME It is found in our tears and kills bacteria by hydrolysing complex sugars in peptidoglycan Lysozyme with substrate PDB ID 1LZB  Substrates bind to active sites. They can only ^it into the active site if they are the right shape When the substrate binds the enzyme, it forms an Enzyme- Substrate complex (ES) E + S à ESà E + P Proteins (enzymes) are not rigid – they ^lex to allow the substrate to bind. This is called INDUCED FIT The enzyme catalyses the reaction because the amino acid R groups interact with the substrate, and destabilises it, lowering the activation energy. Fig. 6.10 Fig. Pyruvate 6.11 dehydrogenase – a mul3enzyme complex 6. Rate of Enzyme controlled reactions (Enzyme kinetics) Reaction rate controlled by: Collisions between enzyme and substrate Binding ability of enzyme Therefore affected by Concentration Temperature pH Ionic concentration Other chemicals that interfere with enzyme shape  Fig. 6.12 7. Effect of pH and temperat ure on enzyme activity 8. Inhibition Fig. 6.13 9. Review Enzymes: Usually protein (sometimes RNA) Specific Can saturate Unchanged by reaction Work within a narrow range of optimal conditions. How enzymes work E+S ES E+P This is also true of carriers and active transport proteins COFACTOR = A substance that helps the enzyme carry out its reaction Can be non-protein e.g. zinc, iron. COENZYME = an organic cofactor that helps the enzyme carry out its reaction Examples 1. NAD+ 2. B vitamins LIGAND = a substrate  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Example of a cofactor: Fig. 8a (TEArt) Zinc in carbonic anhydrase draws electrons towards it, making the covalent bonds of the substrate H2O unstable. H H HIS HIS O O O– O Zn++ C HIS Zn C HIS O O– HIS HIS CO2 + H2O à HCO3- + H+ (This makes the blood acidic, which causes you to breathe faster to remove the CO2 from the blood)  Sometimes RNA can act like an enzyme*. An RNA enzyme is a RIBOZYME For example RIBOSOME is a ribozyme. Orange = RNA *this is why many people think that the ^irst protocells were RNA–based, because RNA can self replicate, transfer energy and act as an enzyme.. The Michaelis-Menten Maude Menten was a Canadian! But constant, Km, is a she had to go to Germany to study, rough measure of how because women were not allowed to well the enzyme binds do research in Canada the substrate Enzyme Kine5cs: Michaelis Menten equa5on Vmax 2 When the inhibitor binds ES complex e.g. ethanol binds NMDA receptor, so causes drunkenness  Non-compe33ve Inhibi3on: Lineweaver Burk plot (double reciprocal) Km is the same; Vmax is smaller, so 1/Vmax is bigger) Compe33ve Inhibi3on: Vmax is the same; Km is bigger, so 1/Km is smaller) Examples of competitive inhibition: Ethanol and methanol compete for the same active site on alcohol dehydrogenase. CO competes with O2 on heme group in haemoglobin Cocaine competes with dopamine on dopamine re-uptake receptor Examples of non-competitive inhibition: Silver, lead and mercury displace H in disulphide bridges. Strychnine inhibits the glycine receptor, which normally opens Cl- channels in nerve cells. à nerve cells fire too quickly àconvulsions and death. Penicillin binds to an allosteric site on DD-transpeptidase (the enzyme that makes peptidoglycan cross links in bacterial cell wall). Cyanide inhibits cytochrome c oxidase (see metabolism, later)  10. Metabolic pathways Enzymes are frequently associated with membranes. Membranes help compartmentalise the product from the substrate, so that reaction rate stays high. Membranes are very complex and dynamic structures. Membranes are where the action in a cell takes place. The membrane proteins are made in the Golgi. Sometimes enzymes are grouped together in a membrane where they can carry out a series of reactions in sequence Fig. 7.10 Freeman  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Fig. 6.14 Initial substrate Raven Enzyme1 Intermediate substrate A Enzyme2 Intermediate substrate B Enzyme3 You will see this type Intermediate of enzyme pathway substrate C when we do respira3on and Enzyme4 photosynthesis End product Metabolic Pathways evolved from end-product « backwards »… Cà Dà Eà F + àH G 11. End product inhibi3on  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 12. Oxidation and reduction with a cofactor (A 3C sugar) Fig. 8.3 (TEArt)Fig. 7.1 Energy-rich molecule Raven Enzyme H H NAD+ H Product NAD+ NAD+ NAD H 1. Enzymes that harvest hydrogen atoms have a 2. In an oxidation- binding site for NAD+ reduction reaction, NAD H located near another a hydrogen atom binding site. NAD+ and is transferred to 3. NADH then an energy-rich NAD+, forming diffuses away and molecule bind to NADH. is available to the enzyme. other molecules. The enzyme brings the molecule into contact with NAD+ This makes it easy for electron tansfer to happen. The elctrons move onto the NAD+ The molecule is OXIDISED The NAD+ is REDUCED ENZYMES what you should know 1. Draw and understand graph of activation energy 2. Know that oxidation = electron loss =energy loss = “H loss” 3. ATP involvement with catabolic and anabolic reactions 4. Induced ^it 5. E + S à ES à E + P 6. Factors controlling rate of Enzyme controlled reactions 7. Graphs showing effect of pH and temperature on enzyme activity 8. Difference between competitive, non---competitive inhibitors 9. What is an allosteric site 10. Enzyme rate graphs in presence of inhibitors 11. Why metabolic pathways are so long, and how they evolved to be that way 12. What is End product inhibition 13. Function of NADH as a cofactor