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62 Cards in this Set
- Front
- Back
• Metabolism
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the totality of an organism’s chemical reactions
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• Metabolic pathway
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begins with a specific molecule which is then altered in a series of defined steps which results in a certain product→ enzymes catalyze each step in the pathway
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• Catabolic pathways
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metabolic pathways that release energy by breaking down complex molecules into simpler compounds
o Cellular respiration |
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• Anabolic pathways
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consume energy to build complicated molecules from simpler ones (aka biosynthetic pathways)
o Ex: Synthesis of proteins from amino acids |
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• Bioenergetics
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study of how organisms manage their energy resources
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• Energy
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capacity to cause change
• Energy can be used to do work (move matter against opposing forces) |
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• Kinetic energy
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energy in movement
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• Heat/Thermal energy
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kinetic energy associated with the random movements of atoms or molecules
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• Potential energy
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→ energy due to position/structure
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• Chemical energy
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potential energy available for release in a chemical reaction
o Reactants in catabolic RXNS are high in chemical energy |
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• Thermodynamics
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study of the energy transformations that occur in a collection of matter
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• System
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the matter under study
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• Surroundings
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→ the rest of the universe and everything outside the system
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• Closed system
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the matter under study is isolated from its surroundings
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• Open system
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energy and matter can be transferred between the system and its surroundings
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• First law of thermodynamics
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→ the energy of the universe is constant
o Energy cannot be created or destroyed o Aka principle of conservation of energy |
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• Second law of thermodynamics
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every energy transfer or transformation increases the entropy of the universe. In order for a process to occur spontaneously it must increase the entropy of the universe
o Most energy in an energy transfer becomes unusable energy (heat) so some energy is “lost” o The loss of usable energy during energy transfer makes the universe more disordered |
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o Entropy
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measure of disorder or randomness
o The more randomly arranged a collection of matter is the greater its entropy o There is an unstoppable trend toward randomization of the universe as a whole • Examples of increasing entropy-→ buildings decay, people age, a burning log • In order for a process to occur on its own (without energy) it must increase the entropy of the universe • Living systems increase the entropy of their surroundings |
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• Spontaneous
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processes that occur without an input of energy
o Things roll downhill |
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• Nonspontaneous
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processes that require energy
o Things cannot roll uphill |
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• Living systems increase the entropy of their surroundings
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• Organisms take in organized forms of matter and energy from their surroundings and replace them with less ordered forms
o Ex: animal eats food and breaks the food down into CO2 and H20 (small molecules that store less chemical energy than the food did) o Depletion of chemical energy is accounted for by heat generated during metabolism • Evolution of biological order is consistent with the laws of thermodynamics o Its true that organisms evolved from simpler organisms to more ordered organisms o The entropy of individual organisms decreased b/c of evolution o BUT the total entropy of the universe increased- so it fits with the laws of thermodynamics |
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• Energy flows into an ecosystem in the form of ___ and leaves in the form of ___
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LIGHT
HEAT |
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• Gibbs free energy equation
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o ΔG = ΔH – TΔS
• ΔG= G final state – G initial state o G=Free energy o H=change in enthalpy (aka total energy) o S=change in entropy o T=absolute temperature in Kelvin (K= Celcius + 273) |
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• Processes with a negative G
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are spontaneous
• Every spontaneous process decreases the system’s free energy (b/c G is negative) |
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Processes with positive G
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• Positive and zero G reactions require energy
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Which systems tend to have a higher/lower G?
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• Unstable systems (higher G) tend to change to become more stable (lower G)
o Ex: glucose tends to break down into monomers • Systems will move toward greater stability (equilibrium) |
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• Equilibrium
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state of maximum stability
o Reactions proceed to a point where the forward and backward reactions occur at the same rate (said to have reached equilibrium- no further net change in relative concentration of products/reactants) o Free energy of reactants/products mixture decreases as something moves towards equilibrium o Free energy increases when the reaction gets pushed away from equilibrium Systems NEVER spontaneously move away from equilibrium • Processes are spontaneous and can preform work only as they’re moving towards equilibrium |
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• Exergonic reaction
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proceeds with a net release of free energy
o Delta G is negative b/c it loses free energy o Exergonic RXNs occur spontaneously b/c delta G is negative o Magnitude of delta G for an exergonic reaction represents the maximum amount of work the RXN can perform cellular respiration is exergonic |
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• Endergonic reaction
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→ absorbs free energy from its surroundings
o Delta G is positive because it gains energy o These reactions are nonspontaneous o Magnitude of delta G is the quantity of energy needed to drive the RXN synthesizing proteins is endergonic |
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• If a RXN is exergonic in one direction
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than its reverse reaction is endergonic (and vis versa)
o If this isn’t true than the reaction can’t be reversible |
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• Delta G for cellular respiration
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-686 kcal/mol
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• Types of work that a cell does
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o Mechanical work→ movement
o Transport work→ actively transporting things across the membrane o Chemical work→ synthesizing polymers with the help of energy |
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• Energy coupling
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use of an exergonic process to drive an endergonic one
o The way cells manage their energy resources to do work o ATP is responsible for mediating most energy coupling in cells o ATP acts as the immediate source of energy that powers cellular work |
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• ATP
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o Ribose sugar, adenine, and three phosphate groups
o Bonds between phosphate groups in ATP’s tail can be broken by hydrolysis o Becomes ADP when it loses a phosphate group o Delta G of ATP→ADP reaction is -7.3 kcal/mol |
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How does ATP generate energy?
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• Release of energy during ATP hydrolysis comes from the chemical change to a state of lower free energy NOT from the phosphate bonds
phosphorylation |
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• Why does ATP have energy
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all three phosphate groups are negatively charged and they repel each other and have potential energy
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• Phosphorylation
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the transfer of a phosphate group from ATP to a reactant
o The recipient of the phosphate group is said to be phosphorylated o Phosphorylation makes the reactant unstable and thus more reactive • The whole process is spontaneous and exergonic |
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Regeneration of ATP
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• Adding a phosphate group to ADP regenerates ATP
• Free energy required to phosphorylate ADP comes from exergonic break down reactions in the cell • ATP reactions are reversible so the reaction from ADP→ATP makes 7.3 kcal/mol o Reaction from ATP→ ADP loses 7.3 kcal/mol • ADP→ATP reaction is not spontaneous- that’s why you need cellular respiration |
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• Catalyst
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chemical agent that speeds up a reaction without being consumed by the reaction
organisms use catalysts to provide the activation energy (not heat) |
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• Enzyme
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catalytic protein
• Enzymes catalyze a reaction by lowering activation energy barrier which enables the reactant molecules to absorb enough energy to reach the transition state • Enzymes don’t change the delta G of a RXN- they can’t make an endergonic reaction exergonic • Enzymes speed up reactions that would happen even without the enzyme • Enzymes determine which chemical reactions will go on in a cell at any particular time • Enzymes always catalyze the reaction in the direction of equilibrium |
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• Activation energy
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amount of energy needed to start a reaction- energy required to contort the reactants so the bonds can change
o Amount of energy needed to push the reactants over an energy barrier often comes in the form of heat o Absorption of thermal energy increases the speed of the reactant molecules so they collide more often o Thermal agitation makes the bonds more likely to break • Activation energy provides a barrier that determines the rate of the reaction o Reactants must absorb enough energy to reach the top of the activation energy barrier o If the activation energy is low the reaction will proceed more often |
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• Transition state
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the state when the reactants are ready to start reacting→ when the reactants have absorbed the required amount of activation energy
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• Substrate
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reactant an enzyme acts on
• Enzymes are very specific to their substrates • Specificity of an enzyme results from its shape |
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• Active site→
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region where the enzyme bonds to the substrate
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o Induced fit
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brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction
• The active site changes shape to accommodate the substrate |
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• Steps in how enzymes work
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o Substrate enters active site
o Enzyme changes shape so its active site embraces the substrates (induced fit) o Substrate held in active site by weak bonds like hydrogen bonds and ionic bonds o Active site (and R groups of its amino acids) lower activation energy and speed up RXN o Substrates are converted into products o Products are released o Active site is now available for new substrates |
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• Ways that enzymes lower activation energy and speed up RXN
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o Active site provides a template for substrates to come together in the proper orientation
o Active site clutches the bound substrates and stresses the chemical bonds that must be broken in the RXN- distorting the substrate makes it approach the transition state faster o Active site provides a microenvironment that is more conducive to the reaction→ the active site might have an acidic or basic environment for example o The active site could directly participate in the chemical RXN |
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• An enzyme is saturated when
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it’s working the fastest that it can- when the substrate concentration exceeds the enzyme’s capability of processing substrate
o When an enzyme population is saturated the only way to make it go faster is to add more enzyme |
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o Optimal conditions
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enzymes work under certain specific conditions
o Temp and PH influence enzyme activity o Enzymes don’t work at very high temps b/c they get denatured o Generally, High temps (up to a certain point) and neutral PH’s help enzymes work better o Digestive enzymes work better at acidic PH’s |
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Cofactors
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non protein helpers for catalytic activity- bind to enzymes to help enzymes out
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• Coenzyme
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cofactors made out of organic molecules (C, H, O, N)
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• Competitive Inhibitors
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resemble the normal substrate molecule and compete for admission into the active site to inhibit enzyme productivity
o Reduces productivity by blocking active site |
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• Noncompetitive inhibitors
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impede enzymatic reactions by binding to another part of the enzyme- causes the enzyme to change shape which makes its active site less productive
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• Selective inhibition
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cells naturally regulate enzyme activity by making enzyme inhibitors- essential to the control of cellular metabolism
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• Allosteric regulation
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any case in which a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site
o Like noncompetitive inhibitors o Can result in stimulation or inhibition of enzyme activity |
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Allosteric enzymes
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o composed of multiple sub units and has two conformational states (one active and one inactive)
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o Allosteric site/Regulatory site
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the area where the inhibiting or activating regulatory molecule binds to
o A single activator or inhibitor molecule that binds to one regulatory site will affect the active sites of all subunits |
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o Activator
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bonds with the allosteric site to trigger the active part of the enzyme
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o Inhibitor
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bonds with the allosteric site to trigger the inactive part of the enzyme
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• ATP and allosteric enzymes
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• ATP binds to catabolic enzymes allosterically and lowers its affinity for substrate and thus inhibiting its activity
• ADP binds to catabolic enzymes and serves as an activator (a major function of catabolism is to generate ATP) • Allosteric enzymes help regulate the generation of ATP→ if there’s too much ATP the ATP will bind allosterically and slow the catabolic enzymes down…if there’s too much ADP the ADP will bond allosterically and speed up the catabolic enzymes o Allosteric enzymes control the rate of key reactions in metabolic pathways |
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• Cooperativity
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→ substrate molecule binding to one active site may stimulate the catalytic powers of a multi subunit enzyme by affecting other active sites
o A substrate molecule causing induced fit in one subunit can trigger the same favorable conformational change in the other sub units o Helps to amplify the response of enzymes to substrates |
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• Feedback inhibition
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common method of metabolic control, a metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway
o High concentration of product inhibits the reaction from going faster o The reaction operates according to how much product is needed o Ex: as isoleucine accumulates it slows down its own synthesis by allosterically inhibiting the enzyme for the first step of the metabolic pathway o Prevents the cell from synthesizing too much product |