Chapter 5 Directions and Rates of Biochemical Processes
Key Questions What factors determine which way a reaction will go? What factors determine the rate of a chemical reaction? How do enzymes work? How can cells modify the activity of enzymes?
Work and Energy Work: movement of an object against a force Work can be stored as potential energy: in a spring or battery Examples: lifting something against gravity, winding a spring Energy: ability to do work; ability to promote change 2 forms: Kinetic- associated with movement, rock falling or muscle contracting Potential- due to structure or location, can be gravitational, electrical, chemical Chemical energy- energy in molecular bonds Kinetic energy of molecules is heat
Thermodynamics Rules of chemical energy change Used to predict the conversion of energy from one form to another Determines the direction of the changes First law: The total amount of energy in any process stays constant Law of conservation of energy Energy cannot be created or destroyed Energy may change form from chemical to kinetic Ex. Doing a pushup; Muscles contract (work); Energy from ATP becomes kinetic energy of movement and heat Second law: entropy (chaos, disorder) continually increases in the universe Transfer or transformation of energy from one form to another increases entropy or degree of disorder of a system
Energy and Chemical Reaction Chemical reactions: one substance is changed into another, release & store energy Reactants: molecules entering into the chemical reaction Products: changed molecules at the end of the reaction Free energy of activation: Energy is needed to initiate the reaction between molecules Activation Energy: Initial input of energy to start reaction Allows molecules to get close enough to cause bond rearrangement Can now achieve transition state where bonds are stretched Overcoming activation energy 2 common ways Large amounts of heat Using enzymes to lower activation energy
Energy and Chemical Reaction Chemical reactions: one substance is changed into another, release & store energy Exergonic reaction: Energy released from the reactants during the reaction Energy released due to reactions breaking down complex molecules into simpler molecules called catabolic reactions ( 分解代謝 ). Endergonic reactions: Energy added to products during the reaction. DO NOT occur spontaneously Anabolic reactions ( 合成代謝 ) are endergonic reactions that use energy to build complex molecules from simpler molecules. Making bonds can store potential chemical energy
Direction of Reactions Chemical reactions usually go in the direction that releases heat Heat is energy that is not available to do work Energy input is required to reverse these reactions 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) Energy in a system that is available to do work Change in free energy determines direction Energy transformations involve an increase in entropy Entropy - a measure of the disorder that cannot be harnessed to do work
Entropy Measure of disorder Second law of thermodynamics, implies that disorder will increase Going from ordered state to disordered releases energy to do work Going from disorder to order requires energy Concentration and Entropy Movement of molecules from concentrated to less concentrated increases entropy, releases energy
Equilibrium and Free Energy Exergonic ΔG = Δ H - T Δ S ΔG<0 or negative free energy change Spontaneous Occur without input of additional energy Not necessarily fast Key factor is the free energy change Endergonic ΔG>0 or positive free energy change Requires addition of free energy Not spontaneous
Sources of Free Energy Breaking of unstable bonds and formation of stable bonds G of product lower than G of reactants High energy bonds unstable Hydrolysis of ATP ΔG = -7.3 kcal/mole Reaction favors formation of products Energy liberated can drive a variety of cellular processes
Cells use ATP hydrolysis Coupled Reactions An endergonic reaction can be coupled to an exergonic reaction Endergonic reaction will be spontaneous if net free energy change for both processes is negative Glucose + phosphate glucose-phosphate + H 2 O ΔG = +3.3 Kcal/mole endergonic ATP + H 2 O ADP + P i ΔG = -7.3 Kcal/mole exergonic Coupled reaction: Glucose + ATP glucose-phosphate + ADP ΔG = -4.0 Kcal/mole exergonic
Enzymes Act as Catalysts Catalyst- agent that speeds up the rate of a chemical reaction without being consumed during the reaction Enzymes can accelerate reactions as much as 1016 over uncatalyzed rates! Ex.: Urease catalyzed rate: 3x10 4 /sec Uncatalyzed rate: 3x10-10 /sec Ratio is 1x10 14! Pepsin (protein digestion in stomach) works best at ph2; too much food dilutes acid, inhibits digestion Vinegar (acetic acid) denatures proteins in bacteria, killing them, preserving food (pickles, herring)
Enzymes Features Catalyst- agent that speeds up the rate of a chemical reaction without being consumed during the reaction Enzymes- protein catalysts in living cells, speed up chemical reactions Do not affect free energy, cannot reverse a reaction Bind to reacting molecules (substrates) at the active site Binding is reversible (100,000 times per second) Binding is specific only do 1 kind of reaction Active site - location where reaction takes place Substrate- reactants that bind to active site Enzyme-substrate complex formed when enzyme and substrate bind Each enzyme has optimum conditions: temperature, ph, salt concentration High temperatures denature proteins ph influences 3-D structure of protein Salt can interfere with binding of substrates Prosthetic groups - small molecules permanently attached to the enzyme Cofactor - usually inorganic ion that temporarily binds to enzyme Coenzyme - organic molecule that participates in reaction but left unchanged afterward
Enzymes Lower Activation Energy of a Reaction Enzyme binds to substrate with non-covalent bonds Holds substrate in position for reaction Distorts substrate into a transition state Enzyme is unchanged at the end of a reaction 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
Enzyme Mechanism Substrate binding Enzymes have a high affinity or high degree of specificity for a substrate Used the example of a lock and key for substrate and enzyme binding Induced fit - interaction also involves conformational changes
Regulation Factors that Affect Enzyme Activity Enzyme s activity is sensitive to the change in their 3-dimensional shape. Temperature and ph are two factors that may make enzyme to lose its shape or denature. (antifreeze protein, hot spring protein) The 3-D shape of an enzyme can also be affected by the binding of specific chemicals called activators (facilitate chemical reactions) and inhibitors (turnoff chemical reactions). Steric inhibitors bind to active site and prevent substrate from binding; can be overcome by increasing substrate concentration Allosteric (non-competitive) inhibitors bind at another site, change shape of enzyme; some are reversible Enzyme activity within an organism is often regulated by inhibitors under the process called negative feedback End-product inhibition