AP Biology Chapter 8: Additional Notes:

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1 AP Biology Chapter 8: Additional Notes: I. Entropy(S) a. The entropy of an isolated system increases in the course of spontaneous change i. Examples of spontaneous change are cooling to the temperature of the surroundings (hot metal placed in cold water) and free expansion of a gas ii. Both of these processes increase entropy iii. Heat flow (q) stimulates disorderly motion in the surroundings iv. Work- stimulates uniform motion- does not change the degree of disorder and does not change entropy in the surroundings b. Thermodynamics focuses on change in entropy ds i. Change in the extent to which energy is dispersed in a disorderly manner depends on how much energy is transferred as heat ii. Molecular example: 1. Molecules in a system at high temperature are highly disorganized a. Small transfers of energy will result in small changes of disorder b. Sneezing in a busy street will go relatively unnoticed 2. However, molecules at a low temperature are not as disorganized a. Small transfers of energy will result in larger degree of disorder b. Sneezing in a library will be very disturbing 3. So, change in entropy when a given quantity of heat is transferred will be greater when it is transferred to a cold body versus being transferred into a warm body. 4. Change in entropy is inversely proportion to the change in temperature at which the transfer takes place c. Entropy is a state function: d. When energy leaves from a hot reservoir as heat, entropy decreases i. When that same energy enters a cold sink, entropy increases by a large amount ii. Overall increase in entropy, the process is spontaneous e. Two classes of processes summarized by the second law of thermodynamics i. Spontaneous- change that does not require work ii. Non- spontaneous- change that requires work f. Kelvin s definition:

2 II. III. i. No process is possible which the sole result is the absorption of heat from a reservoir and its complete conversion into work.. 1. example: it impossible to construct an engine in which heat is drawn from a hot reservoir and completely converted to work a. all heat engines have a hot source and a cold sink b. some heat is always discarded into a cold sink and not converted into work Conservation of Energy: a. First law of thermodynamics i. Total energy of an isolated system is constant ii. The law of entropy follows the law of conservation iii. Introduces internal energy (U): 1. Lets us asses whether change is permissible or not 2. Entropy identifies spontaneous change among those permissible changes Chapter 8.1: An introduction to metabolism: a. The Second Law of Thermodynamics: i. Heat (q): energy associated with random motion of atoms or molecules 1. When we eat food, only a small fraction is used for cellular processes a. Most is lost to the universe as heat b. This process in living organisms is unavoidable 2. A system can put heat to work only when there is a temperature difference that results from heat flowing from a warmer location to a cooler one a. If temperature is uniform, as is in living cells, the only use for heat energy is to warm the body 3. A consequence of loss of usable energy during energy transfer or transformation is that each such event makes the universe more disordered. b. Entropy: a measure of disorder or randomness i. Examples of increased energy: 1. Gradual decay of a building 2. Metal rusting ii. Entropy helps understand why certain processes occur 1. A process occurring on its own must increase the entropy of the universe a. These are spontaneous processes b. Can be very fast like an explosion c. Can be very slow like iron rusting 2. A process that can not occur on its own is non spontaneous a. Occurs only if energy is added to the system

3 IV. c. Chemistry of Life organized into metabolic pathways: i. A metabolic pathway begins with a specific molecule, which is altered through a series of defined steps resulting in a certain product. 1. Each step of the pathway is catalyzed by a specific enzyme 2. They manage the material and energy resources of the cell 3. Two types of pathways: a. Catabolic pathways: i. Breakdown pathways ii. Cellular respiration- glucose broken down in the presence of oxygen to carbon dioxide and water iii. Energy stored in glucose becomes available to do work of the cell 1. Example: membrane transport iv. Downhill pathway 4. Anabolic pathways: a. Builds more complicated molecules from more simple molecules by using up energy i. Biosynthetic pathways ii. Synthesis of proteins from amino acids iii. Uphill pathway 5. Energy released from the downhill catabolic pathway can be stored and then used to drive uphill anabolic pathways Chapter 18.2: The free- energy change of a reaction tells us whether the reaction occurs spontaneously. a. Free energy change: i. Gibbs free energy system: created by a Yale professor J. Willard Gibbs ii. Free energy measures the portion of a systems energy that can perform work when temperature and pressure are uniform through out the system iii. Allows biologists to predict which kinds of change can happen without help. iv. Very important in the study of metabolism v. Free Energy can be calculated: 1. ΔG = ΔH TΔS a. ΔH = change in enthalpy- equivalent to total energy of a biological system b. ΔS = change in entropy c. T = absolute temperature in Kelvin 2. ΔG can be used to predict whether the process will be spontaneous

4 a. ΔG = spontaneous reaction i. reaction must give up enthalpy (enthalpy must decrease) ii. or the reaction must give up order, so increase in TS iii. or both, decrease enthalpy and increase entropy b. every spontaneous reaction decreases the systems free energy b. Free energy, stability and equilibrium: i. ΔG = G final state G initial state 1. So ΔG can only be negative when free energy is lost during the change from initial state to final state ii. Unstable systems: have high G- tend to change to become more stable (low G) 1. Example: drop of dye is less stable than when it is distributed evenly through out the liquid 2. Example: a sugar molecule is less stable than the components its made of iii. These systems will move towards stability, unless something prevents it 1. State of maximum stability is equilibrium 2. Equilibrium and free energy: a. Most chemical reactions are reversible and will proceed until the forward and reverse reactions reach chemical equilibrium i. Chemical equilibrium- no further net change of products vs. reactants ii. As a reaction proceeds towards equilibrium, free energy of the mixture of reactants and products decreases iii. Free energy will increase as a reaction is pushed away from equilibrium 1. Maybe by removing some of the products iv. A system at equilibrium will have the lowest possible value of G v. Any change in the equilibrium will have a positive ΔG and will not be spontaneous vi. Systems never move away from equilibrium sponateously b. A system at equilibrium can not spontaneously change, there for it can not do work i. Only when the system is moving towards equilibrium can it perform work c. Free Energy and metabolism:

5 i. Exergonic reactions: energy outward- proceeds with a net release in free energy 1. Chemical mixture loses free energy(g decreases), ΔG is negative for an exergonic reaction. 2. Exergonic reactions are spontaneous reactions 3. The magnitude of the ΔG represents the maximum amount of work the reaction can perform(theoretical upper limit of available energy given that some will be lost as heat) 4. Example: reaction for cellular respiration: a. C6H12O6 + O2 è 6CO2 + 6H20 b. ΔG = kcal/mol, or kj/mol c. For each 180g of glucose broken down by respiration, 686 kcal/mol of energy is made available for work d. The products are the result of this free energy ii. Endergonic reaction: 1. Absorbs free energy from its surroundings 2. Stores free energy in molecules 3. ΔG is positive 4. Nonspontaneous reaction 5. The magnitude of ΔG is the amount of energy required to drive the reaction 6. Endergonic = uphill 7. The reverse process of cellular respiration = ΔG = +686kcal/mol V. Chapter 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions. a. Cell does work i. Mechanical: muscle contraction, movement of chromosomes ii. Transport: pumping substances across a membrane iii. Chemical: pushing endergonic reaction, synthesis of polymers from monomers b. The structure of hydrolysis and ATP: i. ATP- adenosine tri phosphate 1. Adenine 2. Ribose 3. Three phosphate groups ii. Bonds between phosphate groups can be broken by hydrolysis iii. ATP losing its terminal phosphate group to produce ADP and Pi releasing 7.3 kcal/mol of energy 1. Exergonic reaction iv. Phosphate bonds are often referred to as high energy phosphate bonds 1. Misleading

6 2. The release of energy comes from the chemical change to a state of lower free energy 3. Phosphate bonds are unstable and relatively weak c. How ATP Performs Work: i. ATP hydrolyzed in a test tube will release enough energy to heat the surrounding water ii. Hydrolysis of the phosphate groups in ATP is especially exergonic, because the resulting orthophosphate group is greatly stabilized by multiple resonance structures, making the products (ADP and Pi) much lower in energy than the reactant (ATP). The negative charge density associated with the three adjacent phosphate units of ATP also destabilizes the molecule, making it higher in energy. Hydrolysis relieves some of these electrostatic repulsions as well, liberating useful energy in the process. iii. In an organism this same heat released can be beneficial 1. Shivering uses ATP hydrolysis to generate heat during muscle contraction iv. Phosphorylation: transferring a terminal phosphate group from ATP to another molecule 1. Couples the energy of ATP hydrolysis directly to endergonic processes 2. Coupling of exergonic and endergonic reactions creates a phosphorylated intermediate which is more reactive and less stable than the original unphosphorylated molecule v. The Regeneration of ATP: 1. ATP is a renewable resource 2. Can be regenerate by adding a phosphate group to ADP 3. The energy required comes from catabolic reactions of the cell a. 7.3 kcal/mol b. endergonic c. non spontaneous 4. ATP cycle: a. Shuttling of inorganic phosphate and energy b. Couples the cell s energy yielding (exergonic) reactions to the energy consuming (endergonic) reactions c. 10 million molecules of ATP consumed and regenerated per second per cell i. any where from 10 to 100 trillion cells in the human body

7 VI. Chapter 8.4: Enzymes speed up metabolic reactions by lower energy barriers. a. Spontaneous process may take too long to occur: i. Example: sucrose dissolved in water will sit for years at room temperature with no hydrolysis 1. Adding sucrose will hydrolyze sucrose in a matter of seconds b. Catalyst: a chemical agent that speeds up a reaction without being consumed by the reaction i. Enzyme: is a catalytic protein ii. Ribozymes: biological catalysts made from RNA c. The activation energy barrier: i. Reactions involve bond making and bond forming 1. Changing the molecule involves contorting the starting molecule into a highly unstable state before the reaction can proceed a. Energy must be absorbed ii. Free energy of activation (activation energy- EA): 1. Amount of energy needed to push the reactants over the energy barrier so the downhill portion of the reaction can occur 2. Energizing (activation) is the uphill reaction a. Free energy is increasing 3. Transition state: where the reactants are in an unstable state a. Bond breaking phase 4. Downhill reaction is the bond forming phase a. Free energy is being lost iii. Activation energy is often supplied in the form of heat absorbed by the reactant molecules 1. Comes from the surroundings 2. Bonds will break when enough heat energy has been absorbed a. Absorption of thermal energy speeds up the molecules so they collide more often and more forcefully b. Thermal agitation makes the bonds more likely to break iv. Some reactions, there is enough energy at room temperature to overcome the activation barrier 1. Most cases, activation energy is so high and the transition state is rarely reached that the reaction will hardly proceed at all. a. Must add heat to start the reaction b. Example: combustion of gasoline d. How Enzymes lower activation energy barrier:

8 i. Proteins, DNA and other complex molecules have high free energy and can spontaneously decompose 1. Law of thermodynamics favors their breakdown a. Heat speeds the reaction of the breakdown of macromolecules by pushing these molecules to the transition state b. Typically the temperature of the cell allows these molecules to persist c. But, high temperature denatures proteins d. So enzymes must be used to lower activation energy so the downhill process can proceed. i. Does not change free energy e. Enzyme / substrate complex- and substrate specificity i. Substrate- the reactant an enzyme acts on ii. Enzyme- substrate complex: an enzyme bound to a substrate(s) 1. Enzyme then converts the substrate to the product iii. Active site: specific region of enzyme that binds to the substrate 1. Restricted region 2. Pocket or groove on the surface of the substrate 3. Few amino acids make up the active site while the rest of the enzyme provides a frame work that determines the configuration of the active site 4. Enzyme specificity determines the compatibility with the substrate 5. As substrate enters the active site, chemical processes cause the active site to slightly reconfigure to allow the enzyme substrate complex to form iv. Induced fit: brings chemical groups of the active site into position that enhance their ability to catalyze the chemical reaction f. Catalysis in the Enzyme s Active Site: g. Effects of Local Conditions on Enzyme Activity: i. Effects of Temperature and ph:: 1. Temperature: as T increases the rate of the enzymatic reaction also increases to a point because the substrate collide with the active sites more frequently. a. At some temperature the enzymes will start to break down (denature) i. Thermal agitation disrupts the hydrogen bonds, ionic bonds and other weak interactions that stabilize the active conformation ii. Each enzyme has an optimal temperature at which its reaction rate is greatest.

9 ii. Effects of ph: 1. Each enzyme also has an optimal ph at which it is most active a. Optimal range for most enzymes is between a ph of 6-8, i. Exception: pepsin is a stomach acid acid that functions at a ph of At a higher ph it exists as pepsinogen, but converts to pepsin when stomach ph drops to 2 ii. Exception: trypsin: an enzyme that exists in the small intestine operates at an optimal ph of 8 b. The enzyme becomes more ineffective the farther the ph moves from the optimal conditions i. It can denature if the ph becomes too acidic or basic iii. Cofactors: 1. Cofactors are non- protein helpers that may be tightly or loosely bound to the enzyme a. Can be inorganic such as: Zn, Fe, Cu b. Can be organic: is so it is called a coenzyme i. Vitamins 2. Cofactors function in various ways, but ultimately function in catalysis iv. Enzyme inhibitors: 1. Specific chemicals can inhibit specific enzymes 2. Competitive inhibitors: a. Reduce the productivity of enzymes by blocking substrates from entering active sites i. Can be overcome by increasing the concentration of the substrate 3. Non competitive inhibitors: a. Do not directly compete with the substrate to bind to the enzyme, they instead impede enzymatic reactions by binding to another part of the enzyme. i. Cause a conformational change of the enzyme so substrate no longer fits the active site 4. Toxins and poisons are irreversible enzyme inhibitors a. Sarin- nerve gas i. Binds to the R- group of serine which is found in the active site of

10 acetylcholoinesterase- an enzyme important to the nervous system b. DDT(dichlorodiphenyltrichloroethane): insecticide that is toxic to many animals specially weakening the eggs shell of birds of prey., i. also inhibit the nervous system c. Penicillin- blocks the active site of an enzyme that many bacteria use to make cell walls. VII. Chapter 8.5: Regulation of Enzyme activity helps control metabolism: a. Allosteric Regulation of Enzymes: i. A term used to describe a proteins function when one site is affected by the binding of a regulatory molecule to a separate site 1. may inhibit or stimulate enzyme activity b. Allosteric activation and inhibition: i. Most allosterically regulated enzymes are constructed from two or more polypeptide chains or subunits. 1. Oscillates between catalytic state and inactive state 2. Allosteric site- regulatory site 3. Involves an activator or inhibitor 4. Binding involves conformational change in one subunit which is transmitted to all other subunits ii. The products of ATP hydrolysis can play a major role in balancing the flow of traffic between anabolic and catabolic pathways by their effects on key enzymes. 1. ATP will bind to several catabolic enzymes allosterically, lower their affinity for substrate and thus inhibiting their activity 2. ADP will function as an activator of the same enzymes. c. Co- operativity: allosteric activation i. A substrate molecule binding to one active site may stimulate the catalytic powers of multi- subunit enzyme by affecting the other active sites 1. If an enzyme has two or more subunits, a substrate molecule causing induced fit in one subunit can trigger the same favorable conformational change in all the other subunits 2. This mechanism amplifies the response of enzymes to substrates. One substrate molecule primes an enzyme to accept additional substrate molecules more readily. d. Feed back inhibition: i. A metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway.

11 1. ATP allosterically inhibits an enzyme in an ATP generating pathway.

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