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Enzymes and metabolism - chapter 7

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Queen's University
BIOL 102
Wayne Snedden

Enzymes & Metabolism • Sum total of all chemical reactions that occur within an organism • Also refers to specific chemical reactions at the cellular level Chemical reactions • 2 factors govern fate of a chemical reaction – Direction: Many cells use ATP to drive reactions in 1 direction – If the cells want to take a and b and make c and d and this into thermodynamically favorable, it has to put energy in. – Rate: Catalysts called enzyme can speed the reaction rate
 aA + bB ↔ cC + dD regulation speed, amount, direction.. different in different cells, different proteomes Energy • Ability to promote change • 2 forms – Kinetic- associated with movement – Potential- due to structure or location
 • Chemical energy- energy in molecular bonds high energy compounds can be converted to other things and exploited to do useful work. Two Laws of thermodynamics 1. First law
 - Law of conservation of energy
 - Energy cannot be created or destroyed 2. Second law -Transfer or transformation of energy from one form to another increases entropy or degree of disorder of a system - always an increase in entropy Entropy - a measure of the disorder that cannot be harnessed to do work H = G + TS • H= enthalpy or total energy • G= free energy or amount of energy 
for work • S= entropy or unusable energy • T= absolute temperature in Kelvin (K) Spontaneous reactions? • thermodynamically favoured
 • Not necessarily fast
 • Key factor is the free energy change ΔG = Δ H - T Δ S 'o Biochemistry uses ΔG : “standard” free energy change • specific conditions and concentrations was empirically determined… constant (the ‘Oshows this compared to a regular ΔG) A + B →C + D • Exergonic
ΔG <0 or negative free energy change – Spontaneous 'o • Endergonic
ΔG >0 or positive free energy change – Requires addition of free energy If A and B has more free energy, then ΔG is negative If C and D have more free energy, then ΔG is positive... Spontatneous vs non spontaneous… not literal. If it is exergonic then it is spontaneous, which says nothing about the speed of reaction. Still need to overcome activation barrier, then it can “begin”. Relative description of the amount of energy. If the cell needs C and D but its not spontaneous… how do we get there? We need to put energy in. One way is by burning something to create more energy. The products of ATP have much lower energy then the reactants. Not high energy bonds- high energy compound. ATP is much higher than ADP. Why is it energy rich? Involves the phosphate group. When the bonds are cleaved it releases (bunch of negative charges ready to “burst”, once it is liberated, you release the repulsion and you have more stable products. Breaking bonds doesn’t release bonds. Forming bonds releases energy. By forming the bonds in the new ADP you are creating usable energy) ATP is less stable than its products, however this doesn’t mean it will immediately react. It is pretty stable, but when an enzyme is driving it it can be accelerated to a much larger rate. ATP is not just blowing up all over the place Glucose + phosphate → glucose-phosphate + H2O ΔG'o = +3.3 Kcal/mole
 endergonic ATP + H2O → ADP + Pi ΔG'o = -7.3 Kcal/mole Exergonic Coupled reaction:
 Glucose + ATP → glucose-phosphate + ADP ΔG'o = -4.0 Kcal/mole
Overall (sum) exergonic -generally don’t see phosphate intermediate.. but this is how ATP works. Can calculate K’eq. reactions are set up under standards and allowed to be at equilibrium. We know these values. Why is this important? Equilibrium can be reached at different final concentrations, but this can then be calculated and put into formulas (doesn’t mean same amount of products on both sides…). ΔG = ΔG'o + Rln(Q) Q= [C] [D] /[A] [B] REAL CELL CONCENTRATION! Enzymes • A spontaneous reaction is not necessarily a fast reaction • Catalyst- speeds up the rate of reaction without being consumed • Enzymes- protein catalysts in living cells • May be multi-meric, complexes • Often highly regulated (various levels) - cells have to do things that are not favorable. It can link this to favorable ones (ie ATP) or manipulating relationship of product to substrates. This means we are “displacing from equilibrium”. Activation energy • Allows molecules to get close enough to cause bond rearrangement • Can now achieve transition state where bonds are stretched  •Enzymes are lowering the activation energy •Free energy doesn’t change, just how it gets there • (G) cant be changed, whether ATP is put in something without an enzyme or with it will still be brought to the same thing, just at a faster rate with enzymes •Rate can be controlled Overcoming activation energy • 2 common ways -large amounts of heat -using enzymes to lower activation energy (-small amounts of heat can now push reactants to transition state) Lowering activation energy • Straining bonds in reactants to make it easier to achieve transition state • Positioning reactants together to facilitate bonding • Changing local environment 
– Direct participation through very temporary bonding • Active site = where reaction takes place • Substrate(s) = reactant(s) that bind to active site • Enzyme-substrate complex formed when enzyme and substrate bind • Optimal temp, pH, etc. If you’re trying to design a drug that is better than the substrate- only things that will fit are things that are shaped the same way. High affinity and high specificity- trial and error is hard so you can figure out shape and custom design a drug to affect the productivity. Substrate binding • Enzymes have a high affinity and/or high degree of specificity for a substrate • Induced fit - interaction also involves conformational changes • Concepts exploited in pharmacology [High affinity= low Km. still has the same maximum speed, but in the high affinity it doesn’t need as much to get there. This gives it a lower Km. The enzyme with the lower Km will always get the substrate that it is competing for with one with a higher. Doesn’t matter if there are many substrates. Important when looking at metabolic pathways. Can exploit these principles in pharmacology, need to find something to outcompete, higher affinity. Km= Michaelis constant, Expressed in mM, uM, Km is substrate concentration at half max “speed”. ] **watch notes at time 20minutes from October 11 ) diagram about enzymes** Other requirements for enzymes • Prosthetic groups- small molecules (ion or organic) permanently attached to the enzyme • Cofactor-usually in organic ion that temporarily binds to enzyme (eg. Cu2+ in cytochrome oxidase, Zn2+ in ADH) • Coenzyme-organic molecule that participates in reaction but left unchanged afterward (eg. NADH, vitamins) Overview of metabolism • Chemical reactions occur in metabolic pathways many reactions is a pathway (one enzyme to the next, with slight modification until you get the desired results) • Each step is coordinated by a specific enzyme
 • Catabolic pathways: breakdown, exergonic
 takes in supplies from the body to break it down and make things • Anabolic pathways: synthesis, endergonic – Must be coupled to exergonic reaction
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