Chapter 8: Introduction to Metabolism

1. Chapter 8: Introduction to Metabolism I. Energy and the Cell A. Energy – the capacity to perform work (Bioenergetics = the study of how energy flows through living organisms) 1. Kinetic energy – energy that is actually doing work a. movement, heat, light 2. Potential energy – stored energy matter possesses as a result of its location or arrangement a. electrons of an atom, molecules in a cell (due to arrangement) b. Chemical energy – potential energy of molecules (does the work of the cell)

2. B. Two laws that govern energy conversion 1. First Law of Thermodynamics – “ Conservation of Energy” a. energy of the universe is constant (nrg can be transferred and transformed, but it can be neither created nor destroyed) 2. Second Law of Thermodynamics – “Entropy” a. Every energy transfer or transformation increases the entropy of the universe b. entropy – measure of disorder or randomness c. Examples: decay of an unmaintained building. Increasing amount of heat (nrg of random molecular motion)

3. C. Chemical reactions store or release energy 1. Catabolic pathway – 2. Anabolic pathway – 3. Endergonic reaction – requires a net input of energy a. yield products rich in potential energy – stored in covalent bonds of the products b. photosynthesis (CO2 + H2O + sunlight  glucose + O2) 4. Exergonic reaction – chemical reaction that releases energy a. wood burning b. cellular respiration 5. Energy coupling – using energy released from exergonic rxns to drive essential endergonic rxns a. ATP molecules are key to this

4. b. ATP • Covalent bonds between 2nd and 3rd phosphate are unstable • As phosphate is removed, energy is released and ATP becomes ADP. (exergonic)

5. The cell couples this exergonic rxn with an endergonic rxn by using the third phosphate group as an energy shuttle • Phosphorylation – transfer of a phosphate group to a molecule • This energizes the molecule, enabling it to perform work • This is called the “phosphorylated intermediate”

6. II. How Enzymes work A. Enzymes speed up metabolic rxns by lowering the energy barriers B. Energy barrier is the Activation energy (EA) – the energy required to break bonds in the reactants 1. Chemical rxn involves both bond breaking and bond forming 2. Reactants absorb energy to break bonds, energy is released when the new bonds are formed 3. Activation energy is essential to life a. proteins, DNA, and other complex molecules have the potential to decompose spontaneously they don’t because of temperature of cells (heat can kill cells, so they must use somethings else to drive the rxn….enzymes)

7. Exergonic or endergonic?

9. C. Enzymes are substrate-specific 1. Substrate – reactant an enzyme acts on 2. While the enzyme and substrate are joined the catalytic action of the enzyme converts the substrate to the product 3. Enzymes are very specific a. proteins with a unique 3-D shape b. only the “active site” binds to the substrate c. Induced fit – as substrate enters active site, it induces the enzyme to change its shape slightly to fit more snugly (enhances ability to catalyze by bringing chemical groups into better positions to react)

11. Substrate Active Site

12. D. Active site is an enzyme’s catalytic center 1. Substrate held to active site by H-bonds and ionic bonds 2. R-groups of amino acids of active site catalyze reaction 3. products released and enzyme free to pick up another substrate a. one enzyme can act on 1000 substrate molecules per second (some faster) 4. How do they lower EA? a. provide template for two substrates to come together and react b. may stress the substrate, stretching and bending bonds c. provide microenvironment conducive to reaction (pH) d. direct participation

13. E. Physical and Chemical environment can affect enzyme’s activity 1. Temperature and pH a. optimal vs. denaturation 2. Cofactors – nonprotein helpers (may be permanent residents to enzyme or bind loosely) a. some are inorganic (metals) b. some are organic = coenzymes (vitamins) 3. Enzyme Inhibitors (poisons, antibiotics) a. Competitive inhibitors – block substrate from entering active site b. Noncompetitive inhibitors – bind to another part of the enzyme causing it to change shape and therefore unreceptive to substrate

15. F. Not all inhibitors are bad 1. Allosteric Regulation – noncompetitive inhibitors a. Allosterically regulated enzymes are made from 2 or more polypeptide chains, each subunit having its own active site b. Entire complex ocillates between two conformational states (active and inactive) c. Inhibitor/activator binds to allosteric site – this controls rates of reactions in metobolic pathways 2. Feedback Inhibition a. switching off of a metabolic pathway by its end-product, which acts as an inhibitor of an enzyme in the pathway 3. Cooperativity a. one substrate molecule primes an enzyme to accept additional substrate molecules

16. Allosteric Regulation