Term
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Definition
| the totality of an organism's chemical reactions. an emergent property of life that arises from orderly interactions between molecules |
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Term
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Definition
| begins with a specific molecule, which is then alterned in a series of defined steps catalyzed by a specific enzyme, and results in a product |
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Term
| what does the metabolism do? |
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Definition
| as a whole, it manages the material and energy resources of a cell, releases energy by breaking down complex molecules |
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Term
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Definition
releasing energy which can then be used to do the work of the cell by the breakdown of complex molecules to simpler compounds.
Ex- cellular respiration |
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Term
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Definition
consume energy to build complicated molecules from simpler ones.
Ex- synthesis of an amino acid from simpler molecules, synthesis of proteins from amino acids |
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Term
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Definition
| the study of how energy flows through living organisms |
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Term
| Energy released from the _____ reactions of catabolic pathways can be stored and then used to drive the _____ reactions of anabolic pathways |
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Definition
| Energy released from the downhill reactions of catabolic pathways can be stored and then used to drive the uphill reactions of anabolic pathways |
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Term
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Definition
| the capacity to cause change, ability to rearrange a collection of matter |
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Definition
| energy associated with the relative motion of objects. the basis for moving objects being able to perform work by imparting motion to other mater |
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Definition
| aka heat, kinetic energy associated with the random movement of atoms or molecules |
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Definition
non-kinetic energy that matter possesses because of its location or structure
Ex- Water behind a damn has PE due to its elevation above sea level |
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Term
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Definition
| the potential energy available for release in a chemical reaction |
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Definition
| study of energy transformations that occur in a collection of matter |
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Definition
| unable to exchange either matter or energy with its surroundings |
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Term
| organisms are _____ systems |
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Definition
| organisms are open systems |
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Term
| first law of thermodynamics (AKA the principle of conservation of energy) |
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Definition
| energy of the universe is constant: energy can be transferred and transformed, but it cannot be created or destroyed. |
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Term
| Why can't organisms recycle their energy over and over again? |
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Definition
| during every energy transfer or transformation, some energy becomes unavailable to do work because it becomes converted to/lost as heat, which dissipates rapidly through the surroundings |
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Term
| when can a system put heat to work? |
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Definition
| a system can only put heat to work when there is a difference in temperature that results in the heat flowing from a warmer location to a cooler one |
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Term
| What is the only use for heat in a living cell? |
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Definition
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Term
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Definition
| a measure of disorder or randomness |
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Term
| second law of thermodynamics |
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Definition
| every energy transfer or transformation increases the entropy of the universe. although order can increase locally, there is an unstoppable trend toward randomization of the universe as a whole. For a process to occur spontaneously, it must increase the entropy of the universe. Energy transformations proceed spontaneously to convert matter from a more ordered, less stable form, to a less ordered, more stable form. |
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Term
| Where is most of the universe's entropy apparent? |
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Definition
| most of the universe's entropy is apparent in the increasing amounts of heat and less ordered forms of matter. |
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Term
| Increased entropy is evident in what in a system? |
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Definition
| increased entropy is evident in the physical disintegration of a system's organized structure. |
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Term
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Definition
| a process that can occur without an input of energy, increases the entropy of the universe. A "downhill" or energetically favorable process |
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Term
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Definition
| a process that is "up hill" and requires energy to be added to the system, it cannot occur on it's own |
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Term
| what forms does most energy flow into ecosystems in? |
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Definition
| most energy flows into ecosystem in the form of light or heat |
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Term
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Definition
energy that can perform work when the temperature and pressure are uniform throughout the system
G<0 --- a reaction can occur spontaneously
G=0 --- system is at equib, no net change
G>0 --- a rxn cant occur spontaneously, input of energy is needed |
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Term
| _______ processes decreases the system's free energy |
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Definition
| spontaneous decreases the system's free energy |
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Term
| what causes an increase in free energy? |
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Definition
| as a reaction is pushed away from equilibrium, it's free energy increases |
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Term
| when is G at it's lowest point? |
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Definition
| G is at it's lowest point when the system is in equilibrium |
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Term
| at what point can a system perform work? |
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Definition
| a system can only perform work when it's moving toward equilibrium. when the system is in equilibrium, it is not spontaneous and can't perform work. |
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Term
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Definition
| a chemical reaction that proceeds with a net release of free energy, because the chemical mixture loses free energy, they occur spontaneously. |
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| what represents the maximum amount of work the reaction can perform |
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Definition
| the magnitude of delta G represents the maximum amount of work a reaction can perform |
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Term
| what does the energy stored in bonds mean? |
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Definition
| the potential energy that can be released when new bonds are formed after the original bonds break, as long as the products are of lower free energy than the reactants |
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Term
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Definition
| a chemical reaction that absorbs free energy from its surroundings. this kind of reaction essentially stores free energy in molecules and are not spontaneous |
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Term
| what is one of the defining features of life? |
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Definition
| cells can never be at equilibrium because cells at equilibrium can do no work, cells that have reached metabolic equilibrium is dead. |
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Term
| what is the key to maintaining a lack of equilibrium is cellular respiration? |
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Definition
| the key to maintaining a lack of equilibrium is that the product of a reaction does not accumulate but instead becomes a reactant in the next step; finally waste products are expelled from the cell. |
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Term
| what are the three main kinds of work? |
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Definition
| chemical, transport, mechanical |
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Term
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Definition
| the pushing of endergonic reactions that would not occur spontaneously |
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Term
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Definition
| the pumping of substances across membranes against the direction of the spontaneous movement |
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Term
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Definition
| the ways cells manage their energy resources by the using an exergonic process to drive an endergonic one |
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Term
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Definition
| adenosine triphosphate. powers cellular work by energy coupling, most energy coupling is mediated by ATP. it's bonds can be broken by hydrolysis, creating inorganic phosphate, energy, and ADP |
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Term
| how does ATP drive chemical work? |
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Definition
| ATP drives chemical work by coupling and ATP hydroloysis |
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Term
| how does ATP drives transport and mechanical work? |
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Definition
| ATP hydrolysis causes changes in the shapes and binding affinities of proteins either directly by phosphorylation or indirectly via noncovalent binding of ATP and its hydrolytic products |
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Term
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Definition
| the regeneration of ATP by the addition of inorganic phosphate to ADP (phosphorlate). the free energy to phosphorylate ADP comes from the exergonic breakdown reactions in the cell. the regeneration of ATP is an endergonic process |
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Term
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Definition
| a macromolecle acts as a catalyst, provides metabolic regulation that speeds up chemical reactions and prevents the metabolic pathways from getting congested |
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Term
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Definition
| a chemical agent that speeds up a reaction without being consumed by the reaction |
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Term
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Definition
| the initial investment of energy for starting a reaction, the energy required to contort the reactant molecules so the bonds can break. often supplied in the form of thermal energy |
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Term
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Definition
| when molecules have absorbed enough energy for the bonds to break, the reactants are in an unstable condition. |
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Term
| why do cells use catalysis instead of heat to speed up reactions? |
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Definition
1. heat denatures proteins and kills cells
2. heat would speed up all the reactions, not just those that are needed |
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Term
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Definition
| enzymes cannot change delta G of a reaction of make an endergonic reaction exergonic |
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Term
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Definition
| the reactant an enzyme acts on |
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Term
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Definition
| when an enzyme is bound to its substrate, while in this state the catalytic action of the enzyme coverts the substrate to the product |
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Term
| where does the specificity of a enzyme come from? |
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Definition
| the specificity of an enzyme comes from its shape, which is a result of its amino acid sequence |
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Term
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Definition
| a restricted region of the enzyme molecule that actually binds to the substrate, typically a pocket or groove on the face of the enzyme where catalysis occurs. formed by a few of the enzymes amino acids. |
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Term
| describe an enzyme's shape. |
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Definition
| enzymes do not have a stiff structure, they 'dance' between subtly different shapes in dynamic equilibrium, with a slight difference in free energy for each 'pose' |
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Term
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Definition
| the result of an enzyme's shape change once the substrate enters the active site. the induced fit brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction |
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Term
| what determines whether an enzyme will catalyze the forward or reverse reaction? |
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Definition
| an enzyme will catalyze a reverse or a forward reaction depending on the relative concentrations of the reactants and products, which affects whether the reaction has a negative delta g or not |
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Term
| what mechanisms do enzymes use to lower activation energy and speed up a reaction |
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Definition
1. acting as a template for the substrate orientation
2. stressing the substrates and stabilizing the transition state
3. providing a favorable microenvironment
4. participation directly in the catalytic reaction |
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Term
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Definition
| the rate of the reaction is determined by the speed at which the active site converts substrate to product. the only way to increase the rate of product formation is to add more enzyme |
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Term
| the rate of a reaction is party a function of the ________ of the substrate |
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Definition
| the rate of a reaction is partly a function of the initial concentration of the substrate |
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Term
| what factors can affect the efficiency of an enzyme? |
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Definition
| temperature, pH, and affecting chemicals |
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Term
| what is the optimal pH range of most enzymes? |
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Definition
| the optimal pH values for most enzymes falls between 6-8 |
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Term
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Definition
| nonprotein helpers for catalytic activity (i.e. enzyme helpers). they tightly bind to the enzyme as either as permanent residents or loosely and reversibly along with the substrate |
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Term
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Definition
| an organic cofactor, such as vitamins |
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Term
| if the inhibitor ataches to the enzyme by _____, inhibition is usually irreversible |
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Definition
| if the inhibitor attaches to the enzyme by covalent bonds, the inhibition is usually irreveresible |
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Term
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Definition
| reversible inhibitors that resemble the normal substarte molecule and compete for admission into the active site. they reduce the productivity of enzymes by blocking substrates from entering active sites. can be overcome by increasing the concentration of substrate so that as active sites become available |
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Term
| noncompetitive inhibitors |
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Definition
| do not directly compete with the substrate, impede enzymatic reactions by binding to another part of the enzyme which causes the enzyme molecule to change its shape in such a way that the active site becomes less effective at catalyzing the conversion of substrate to product |
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Term
| how does a cell regulate it's metabolic pathways? |
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Definition
| either by switching on and off the genes that encode specific enzymes, or by regulating already existing enzymes |
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Term
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Definition
| when a protein's function at one site is affected by the binding of a regulatory molecule to a separate site causing inhibition or stimulation of an enzyme's activity |
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Term
| describe the structure of most allosterically regulated enzymes. |
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Definition
| these enzymes are usually comprised of two or more polypeptide chain subunits with their own active sites. the structure as a whole is oscillating between two shapes, one being catalytically active and the other inactive. a shape change in one subunit triggers a shape change in all other subunits of the enzyme |
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Term
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Definition
| binds to a regulatory site and stabilizes the functional shape |
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Term
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Definition
| binds to an enzyme and stabilizes its inactive form |
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Term
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Definition
| when a substrate binds to an active site in a multiunit enzyme, thus triggering a shape change throughout the enzyme and increasing the catalytic activity of all other active sites. this amplies the response of the enzyme to substrates |
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Term
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Definition
| when a metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts earlier in the pathway. prevents the cell from wasting chemical resources |
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Term
| function of cellular structures in regards to metabolic pathways |
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Definition
| cellular structures help bring order to metabolic pathways |
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Term
| a greater work capacity exists in a system that has ____ free energy and ____ stability |
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Definition
| a greater work capacity exists in a system with more free energy and less stability |
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Term
| in a spontaneous change... |
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Definition
1. free energy (G) decreases
2. system becomes more stable
3. the released free energy can be harnessed to do work |
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Term
| a system with low free energy and more stability has a _____ work capacity |
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Definition
| a system with low free energy and more stability has a lower work capacity |
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Term
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Definition
| adenosine triphosphate is comprised of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups |
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Term
| how does ATP drive endergonic reactions? |
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Definition
| ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule |
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Term
| phosphorylated intermediate |
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Definition
| the molecule that receives a phosphate group from the phosphorylation of ATP |
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Term
| how does the active site lower an activation energy barrier |
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Definition
1. orienting substrates correctly
2. straining substrate bonds
3. providing a favorable microenvironment
4. covalently bonding to the substrate |
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Term
| enzymatic-reaction process |
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Definition
1. substrates enter active site
2. substrates are held in active site by weak interactions
3. active site can lower activation energy and speed up a reaction
4. substrates are converted to products
5. products are released
6. active site is once again available for new substrate molecules |
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Term
| how do we get new enzymes? |
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Definition
| enzymes are proteins encoded by genes, so when there's a genetic malfunction (mutation) that leads to changes in amino acid composition of an enzyme. this can result in changes in substrate specificity, which under new environmental conditions might actually be favored to the original enzyme. |
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