BIOL 20A Tamkun (Topic 4 Enzymes & Metabolism)
BIOL 20A Tamkun (Topic 4 Enzymes & Metabolism) BIO 20A
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This 4 page Class Notes was uploaded by Holly Chen on Friday October 7, 2016. The Class Notes belongs to BIO 20A at University of California - Santa Cruz taught by John Tamkun in Fall 2016. Since its upload, it has received 5 views.
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Date Created: 10/07/16
Unit 4 - Enzymes & Cellular Metabolism Metabolism Basics • Metabolism - general term used for all chemical reactions involved in keeping a cell or organism alive. • Metabolic pathway: a molecule being altered in a series of steps with enzymes, resulting in a product. There are two general types: • Catabolic pathway: breaking down molecules to release the energy stored in chemical bonds. The energy will then be free to do work. • Anabolic pathways: synthesis of molecules, consumes energy. • Think of catabolic pathways as downhill and anabolic pathways as uphill. Energy & Thermodynamics • Energy - many definitions, but in this case, it’s the ability to cause change. • Kinetic energy - energy of motion. • Thermal energy - energy that comes from heat, which is the movement of particles. Faster movements generate more heat. • Potential energy - energy the matter has due to location or structure, includes the energy stored in chemical bonds. • Thermodynamics - the study of energy transformation. • 1st Law of Thermodynamics: • Energy can be transferred and transformed, but never created or destroyed. • Example: sunlight is converted into chemical energy by plants. That makes the plant an energy transformer, not energy producer. • 2nd Law of Thermodynamics: • Every energy transfer or transformation increases the entropy of the universe. • Entropy: a measure of disorder. • Example: a bear hunts for food is in motion, therefore the chemical energy from his last meal is being transferred into kinetic energy, producing heat and CO2 by movement and exhaling. This increases the disorder of the universe (not apparent to us). • Laws of thermodynamics allow the prediction of whether or not a reaction will occur spontaneously based on the change in free energy. • ΔG = G (products) - G(reactants) • ΔG =ΔH - TΔS • ΔH is the change in total energy whileΔS is entropy. • ΔG is based on the change in total energy and entropy decrease as the degree of randomness increases. • ΔG < 0 (negative) = energy released, exergonic reaction, spontaneous. • Energy released from exergonic reactions can be converted into other forms of energy. • Example: cellular respiration,ΔG = -686 kcal/mole, exergonic, spontaneous. • ΔG > 0 (positive) = energy consumed, endergonic reaction, not spontaneous. • Example: photosynthesis,ΔG = 686 kcal/mole therefore endergonic and not spontaneous. ATP(adenosine triphosphate) • ATP - contains sugar ribose, nitrogenous base adenine, and a chain of 3 phosphate groups bonded to it. • Cell’s 3 main work process: chemical work, transport work, mechanical work. • Universal energy currency of cells. • Stores chemical energy to do work. • Living organisms use it continuously, it’s a regenerating resource. • Chemical / energy coupling - using an exergonic process to drive an endergonic process. • Example: oxidation of glucose drives the synthesis ofATP. ATP Hydrolysis • All life depends on theATP cycle, it allows cells to maintain overall low entropy. • The bonds between the phosphate groups ofATP can is broken down by hydrolysis. • Extremely exergonic process. • ATP hydrolysis drives other endergonic reaction in cells. • Example: when the terminal phosphate bond is broken, triphosphate becomes diphosphate and yieldsADP. This is also an example of chemical coupling. How doesATP perform work? • Example: with help of specific enzymes, cell is able to release energy byATP hydrolysis to drive endergonic reactions. • Glutamic acid’s conversion to glutamine is not spontaneous (ΔG positive). • When coupled withATP hydrolysis occurs:ATP phosphorylates glutamic acid, making it unstable, ammonia displaces phosphate group, forms glutamine. • Glutamic acid to glutamineΔG = 3.4 kcal/mol • ATP hydrolysisΔG = -7.3 kcal/mol • Total reactionΔG = -3.9 kcal/mol • Chemical coupling results in the process being spontaneous. How to cells control spontaneous exergonic reactions? • Spontaneous reactions can occur very slowly. • Reactants must be converted to high energy intermediates before being converted into products. • This creates an energy barrier (activation energy is very large). • This is where enzymes come in. Enzymes • Catalyst - a chemical agent that will speed up reactions without being consumed. • Enzyme - a macromolecule that acts as a catalyst. • Enzymes reduces activation energy. • Does not changeΔG • Enzymes can’t force endergonic reaction, exergonic chemical coupling still required. • Specialized to catalyze specific reactions. • An average cell contains thousands of different enzymes. • Without enzymes and enzyme regulations, chemical reactions would happen all over the place, or take too long, or not happen at all. • Cells regulate metabolic pathway by regulating enzyme activity. Substrate Specificity • Substrate - the reactant in which the enzyme operates on. • Overall process: • Enzyme + substrate —> enzyme substrate complex —> enzyme + products. • Each enzyme is specific and can only recognize its specific substrate. • Example: sucrase will act only on sucrose and will not bind to any other disaccharides. • If there are big temperature or pH changes, the enzyme will denature and lose it’s ability to function. • Each enzyme works best at a specific temperature and pH. Enzyme Structure • Active site - a “pocket” on the surface of the enzyme where the catalysis occurs. • Usually formed by a few amino acids. • Rest of the molecule provides framework that determines size and shape of the active site. • Recent studies found active sites change subtly in equilibrium with small differences in free energy for each shape. This is because the shape that best fit the substrate isn’t always the shape with the lowest energy. • Substrate - the reactant in which enzymes operates on. It’s held to the active site usually by weak hydrogen bonds and ionic bonds. • Substrate and active site interact like lock and key. How to Enzymes work? 1. Substrate enters active site. 2. Enzyme alters its shape so the active site folds around the enzyme (induced fit). 3. Substrates are held in the active site through weak bonds such as hydrogen or ionic bonds. 4. Substrate is converted into products. 5. Products released from active site. 6. Active site is now free for new substrates to enter. Factors that regulate of EnzymeActivity • Amounts of enzymes in the cell • Phosphorylation of S/T/Y residues. • Binding of small molecules: • Competitive inhibitors will bind to the active site and compete with substrate. • Non competitive inhibitors, also known as allosteric effectors, will bind to the enzyme away from the active site, which will alter the structure and activity of the enzyme.