Introduction to Molecular Cell Biology Biocatalysts

1. Introduction to Molecular Cell BiologyBiocatalysts Dr. Fridoon Jawad Ahmad HEC Foreign Professor King Edward Medical University Visiting Professor LUMS-SSE

2. The Miracle Workers One of biggest miracles of life is that it can perform slow reactions and the ones requiring extreme conditions, quickly and at physiological conditions. N2(g) + 3H2(g) 2NH3(g) The reaction is carried out under conditions of 150-250 atmospheres (atm), 450-500 °C; resulting in a yield of 10-20% Nitrogenase N2 + 8H+ + 8e− + 16 ATP 2NH3 + H2 + 16ADP + 16 Pi

3. Energy and Energy Conversions Energy is the capacity to do work. Potential energy is the energy of state or position; it includes the energy stored in chemical bonds. Kinetic energy is the energy of motion (and related forms such as electric energy, light, and heat).

4. The Laws of Thermodynamics Living things, obey the laws of thermodynamics. 1) Energy cannot be created or destroyed. 2) The quantity of energy available to do work (free energy) decreases and unusable energy (associated with entropy) increases.

5. Free Energy (ΔG) total energy = usable energy + unusable energy H = G + TS (H = Enthalpy, G = free energy, T= absolute temperature, S = entropy) G = H – TS Absolute G, H or S can not be measured ΔG (reaction) = G (products) – G (reactants) Changes in free energy, total energy, temperature, and entropy are related by the equation. ΔG = ΔH – TΔS

6. ΔG of Combustion CH4 + 2O2 CO2 + 2H2O H = G + TS H = G + TS 500 = 400 + 100 300 = 100 + 200 G = H – TS G = H – TS 400 = 500 - 100 100 = 300 - 200 ΔG (reaction) = G (products) – G (reactants) - 300 = 100 - 400 ΔG = - 300 ΔH = - 200

7. ΔG of Reverse Reaction CO2 + 2H2O CH4 + 2O2 H = G + TS H = G + TS 300 = 100 + 200 500 = 400 + 100 G = H – TS G = H – TS 100 = 300 - 200 400 = 500 - 100 ΔG (reaction) = G (products) – G (reactants) 300 = 400 - 100 ΔG = 300 ΔH = 200 ΔS = - 100

8. Free Energy (ΔG) If ΔG is negative free energy is released If ΔG is positive free energy is required ΔH is the total amount of energy added In living systems magnitude and sign of ΔG can depend significantly on changes in entropy ΔS ΔS will be positive in hydrolysis

9. Hydrophobicity Counterintuitive ??? Water Molecules adjacent to hydrophobic molecule suffer restrictions in orientation as they form hydrogen bonds with other water molecules. Bonding (hydrogen) also reduces energy state.

10. Water Structure

11. Exergonic & Endergonic Reactions Exergonic reactions release free energy and have a negative ΔG. Endergonic reactions take up free energy and have a positive ΔG. Endergonic reactions proceed only if free energy is provided

12. Equilibrium in Reversible Reactions The change in free energy (ΔG) of a reaction determines its point of chemical equilibrium, at which the forward and reverse reactions proceed at the same rate. For exergonic reactions, the equilibrium point lies toward completion (the conversion of all reactants into products). ΔG = -1.7 kcal/mol @ 0.02M, 25C & pH 7

13. ATP Hydrolysis ATP (adenosine triphosphate) serves as an energy currency in cells. Hydrolysis of ATP releases a relatively large amount of free energy (-12 kcal/mol). Oxidation of Luciferin in fire flies is powered by ATP hydrolysis.

14. ATP Hydrolysis Is Coupled

15. Biological Catalysts are Enzymes Change in free energy (ΔG) is indicative of equilibrium point. The more negative ΔG is, the further the reaction proceeds towards completion. However ΔG does not tell us any thing about the rate of a reaction (the speed at which it moves towards equilibrium). Most Enzymes are proteins (ribozymes are RNA)

16. Activation Energy Exergonic although release energy however they are not generally spontaneous and proceed only after the reactants are pushed over the energy barrier by small amount of added energy (Activation Energy Ea e.g. CH4 + O2

17. Activation Energy Activation energy changes reactants into unstable molecules forms called transition-state species. At normal temperatures only few molecules have enough kinetic energy for this transformation. Enzymes lower the energy barrier.

18. Enzymes are Specific Reactants (substrates) bind the a particular (active) site of the respective enzyme. The specificity of this binding is a function of three-dimensional shape, structure and environment of its active site.

19. Enzymes Lower the Energy Barrier Enzymes Lower the Energy Barrier for both forward and reverse reaction. Equilibrium and ΔG are not changed by enzymes. 50% 600 poly arginine degradation by carboxypeptidase 7 years vs. half a second

20. How do Enzymes Work

21. How do Enzymes Work

22. Induced Fit Upon binding to substrate, some enzymes change shape, facilitating catalysis. The shape changes (Induced fitting) modify the active site and exposes/ aligns those regions that perform catalysis Water is exclusion at the active site results in transfer of Pi from ATP to glucose preventing APT hydrolysis to ADP The active site = the catalytic + binding sites

23. Helpers Cofactors: Inorganic ions (Cu, Zn & Fe) bound to some enzymes and are essential to their function. Coenzymes: Carbon containing molecules bind enzymes temporarily (by collision) and are chemically changed during reaction (like substrate). Prosthetic groups: non-protein component permanently bound to enzymes (heme group), without its prosthetic group apoprotein vs. holoprotein.

24. Cofactors and Coenzymes

25. Substrate Concentration

26. Enzyme Regulation Some factors can activate enzymes and other can deactivate them (inhibit their function). Irreversible inhibitors permanently inhibit enzymes function generally by modifying the active site

27. Reversible Inhibitors Competitive inhibiters are similar to the natural substrate (bind the active site) however they are different enough that no reaction is catalyzed. When their concentration is lower they come of the enzyme and enzyme can bind the substrate (ADH).

28. The Citric Acid Cycle

29. Reversible Inhibitors Noncompetitive inhibiters bind the enzyme at a a site other than active site and cause a conformational change that prevents enzyme from binding its substrate or slow the catalysis.

30. Feed Back/End Product Inhibition End product can serves as allosteric inhibitor of commitment step enzyme If sufficient amount of end product of a pathway is available in the environment

31. Allosteric Regulators Allostery (different shape) change in enzyme shape due to binding of a noncompetitive inhibiter. These enzymes exist in more than one shape and have multiple poly peptide chains. Allosteric regulator (AR) can be positive or negative. Enzymes catalyzing commitment step have AR

32. Physical Factors Influence Enzymes Fever?