*Enzymes* – biochemistry (quiz 1/exam) – Flashcards
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what is an enzyme
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An enzyme is a *catalyst*-which *increases* the rate of the rxn by lowering the Ea
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What are most enzyme made up of?
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Most are golbular proteins *note* that some RNA (ribozymes and ribosomal RNA) do also catayze rxn
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Enzymes have the capability to do what?
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*excert kinetic control over thermodynamics* I.e. Enzymes have the ability to break down stable object, such as sugar and convert it into energy.
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Enzymes are agents of what function?
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The metabolic function E+S ES EP E+P
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Classify the enzyme: *Oxidoreductases*
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Transfer of electrons (H-atoms) (AKA- oxidation and reduction reaction) *Example*- alcohol dehydrogenase - convert alcohol to aldehydes
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Classify the enzyme: *Kinase*
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-kinase- it always add phosphate groups(beging or end) taken from ATP-->ADP
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Classify the enzyme: *Transferase*
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Group transfer Rxns; they move functional groups from one molecule to another *Example*- Alanine aminotransferase shuffles the alpha- amino between alanine & aspartate
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Classify the enzyme: *Hydrolases*
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Hydrolysis Rxns (transfer of functional groups to H2O); breaks single bonds by adding H2O *Example*-Phosphatases breaks oxygen-phosphorous bond of phosphate esters
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Classify the enzyme:*Lyase*
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Formation or Removal of a *double bond* w/ group transfer THESE INCLUDE: *amino groups, water, and* *ammonia* *example*-decarboxylase removes CO2 for alpha/beta- Keto acids
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Classify the enzyme:*Isomerase*
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Transfer of groups w/in molecules to yield *isomeric form* Functional groups changed w/in structure to form *isomers* (THINK mirror the structure is the same just conformed in a different manner to allow usage)
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Classify the enzyme: *Lygases*
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Formation of C-C,C-S, C-O, & C-N bonds by condensation Rxns coupled to cleavage of ATP or similar cofactors *Hydrolases is the breakdown bonds by adding H2O; while Lifases carries out the reverse Rxns removing element of H2O for functional groups to form a single bond* **Synthestases: is a subclass fo legates that uses hydrolysis of ATP to drive this formation.
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Exergonic reaction
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(Does not require energy) A process with a net release of free energy; sometimes may be spontaneous, but that does not mean it will occur rapidly *Example*- cellular respiration (catabolic process) which the energy is stored in glucose is released and used to generate ATP. (during paper is one to but you have to ignite it first)
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Endergonic reaction
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(needs energy) Absorbs energy from the surroundings; *this is MOST SYNTHESIS REACTIONS are endergonic) *Example*- photosynthesis uses light to drive the synthesis of CHO, in which energy is stored.
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What is an *Enzyme-substrate complex*?
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This is when the enzyme is bound to its substrate
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Enzymes act by binding to What
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substrates
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What is the Michales complex?
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It is the noncovalent enzyme substrate complex
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How do enzyme know which substrate to bind to ?
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Enzymes *selectively* recognize proper (correct) substrates over other molecules (each enzyme has a specific formation which the specific substrate can fit into) Enzymes have lots of activation sites but only specific substrates can bind to each one.
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What is an activation site
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The activation site is where the substrate can bind to the enzyme. (AKA active Site)
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Enzymes produce products in what *types of yields*
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They produce products in *very high yields- * often greater then 95%.
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What keep other substrates from binding to the enzyme?
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Specificity is controlled by structure - *the unique* fit of substrate with enzyme controls the selectivity for substrate and the product yield
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What is the term *induced fit* mean?
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When the substrate combines to the enzyme it may not fit perfectly; so the enzyme will conform around the substrate this is known as induced fit.
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Do enzymes affect equilibrium ?
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No they do not affect Delta G
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What slows the reaction face? what barrier must they overcome?
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Slow reactions face significant activation barriers (delta G) that are difficult to overcome durning the reaction
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How do enzymes lower the (delta) G barrier?
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Enzymes increase reactions rates (k) by lowering the (delta) G barriers
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What is related to the Equilibrium constant?
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The *OVERALL FREE ENERGY* change for a reaction, related to (delta) G (no plus)
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What is related to the rate constant?
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(delta) G with pluses, the *free energy of activation for a reaction*.
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What are two entrophally unfavorable reactants?
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*uncatalyzed biomolecular reactions* --*two free* reactants --> *single* restricted transition states conversion is entrophally unfavorable. *uncatalyzed unimolecular reactions* -- flexible reactant--> rigid transition state conversion is entrophally unfavorable for flexible reactants.
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What is entrophally favorable ?
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*catalyzed reaction* --Enzymes uses the binding energy of substrate to organize the reactant to a fairly rigid ES complex. *entropy cost is payed during binding* rigid reactant complex--> transition state is entrophally favorable.
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Rules of entropy lowest---> highest in solid liquid Gas
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Solid is generally low in entropy Liquid is a greater entropy Gas has the highest entropy
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The natural tendency of the universe is toward ______________ entropy, many chemical reactions have a _______ entropy (more spontaneous)
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The natural tendency of the universe is toward ___*maximum*__ entropy, many chemical reactions have a _*(+)*_ entropy (more spontaneous)
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Who proposed the *Enzymes bind transition state best*
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Linus Pauling
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*The Enzyme bind transition state* says?
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ÂșEnzyme active site are *complimentary* to the transition state of the reaction ÂșEnzymes bind transition state are better then substrates ÂșStronger/additional interaction w/ the transition states as compared to the lower activation barriers *the enzyme will bind to the molecule the it hits the barrier*
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define Kinetics:
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Is the study of the rate at which compounds react
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Name the factors that affect enzymatic reactions (5)
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ÂșEnzymes (are specific) ÂșSubstrate ( availability is important) ÂșEffectors (+/- work with cofactors) ÂșTempature (can speed up, slow down, or destroy enzymes) ÂșpH
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Rate/ velocity =
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V^0 and V^max
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Rate constant
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Km=1/2 Vmax
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What is assumed about the michaelil-menten equation
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Âș assume the formation of the ES complex Âș assume that the ES complex is in *rapid equilibrium* w/ a free enzyme
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What is important to know about the breakdown of the michaelil-menten equation
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The breakdown of the ES to form products is assumed to be *slower* than.... 1. formation ES 2.the breakdown of ES to reform E & S V(sub)0= _Vmax [s]_/Km + [S]
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Understanding Km
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-Km is constant -Km is a constant derived form rate constant -Km is under *true michaelil-menten* conditions -small Km= high affinity (tight bonding) -high Km= low affinity (weak bonding)
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Understanding Vmax
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-Vmax is constant -Vmax theoretical Maximal rate of the reaction (this is never achieved in real life) -to reach Vmax all enzyme molecules are highly bound w/ substrate
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Enzyme activity can be regulated by?
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Âș noncovalent Âș covalent modification Âș irreversible Âș reversible
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What is Kcat
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The turnover number
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catalytic efficiency
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An estimate of "how perfect" the enzyme is kcat/Km is an apparent second-order rate constant (rate is proportional to the product of two reactant concentrations) It measures how the enzyme performs when S is low The upper limit for kcat/Km is the diffusion limit - the rate at which E and S diffuse together
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Transition State
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The overall free energy change for a reaction DG, is related to the equilibrium constant (rate of fwd rxn= rate of the bwd rxn) The free energy of activation for a reaction DGâĄ, is related to the rate constant (?) It is extremely important to appreciate this distinction!
