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59 Cards in this Set
- Front
- Back
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Enzymes can speed up a reaction by a factor of what?
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millions relative to an uncatalyzed reaction
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Proteins which serve as enzymes are usually what in nature?
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globular
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A catalyst enhances the what?
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rate of the reaction
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Is a catalyst permanently altered?
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no
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Specificity of the enzyme is achieved by what?
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the structure of the active site - its shape and charge distribution. (It optimally orients the substrate for reaction)
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The catalyst does what to the enzyme substrate complex?
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Brings the energy of it closer to the TS
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An enzyme speeds up a reaction by what?
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lowering the activation by changing the reaction pathway
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A catalyst alters what kind of energy?
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the free energy of activation (change in G double dagger). It doesn't alter the free energy (delta G) for the reaction equilibrium constant.
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Most enzymes are sensitive to what?
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temperature and pH, they cannot work outside their normal temp or pH range b/c they will be denatured
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Can a catalyst make an enderogonic reaction exergonic or vice versa?
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no
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lock and key model
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enzyme is assumed to be like a lock and the substrate like a key. the two are made to fit exactly. True for simple enzymes.
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Induced Fit Model
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assumes that the enzyme conformation can change to accommodate the substrate.
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What is the mechanism that might cause induced fit model?
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induced dipole - charges ccan rearrange eachother to be complementary for a reaction
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explain exosite model
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In order for the active site to be available the substrate must first bind to a interaction sites on the enzyme distant from the active site. This induces the enzyme and makes it available to bind at the active site, but also imposes additional specificity for target site.
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The international union of biochemistry (IUB) classifies and names enzymes according to what?
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the type of chemical reactions it catalyzes
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In the IUB enzymes are assigned what kind of names?
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four number class and systematic two part name and a shorted recommended name
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Oxidoreductases do what?
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catalyze redox reaction such as reductases or peroxidases. can't separate oxidation from reduction
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transferases do what?
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transfer a group from one molecule to another such as transaminases and transcarboxylases
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hydrolases do what?
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cleave bonds by adding water such as phosphatases,chymotripsin peptidases, serine proteases
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lyases do what?
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catalyze removal of groups to form double bonds or the reverse such as decarboxylase or synthases
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isomerases do what?
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catalyze intramolecular rearrangements such as epimerases, racemases or mutases
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ligases do what?
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bind two molecules together. many are called synthetases such as carboxylases
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any enzymes that ends with kinases uses what as cofactor?
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Mg
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kinetics is the field of chemistry that studies what?
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the rate and mechanism of a reaction
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How are rates measured?
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in terms of how many moles or reactant or product are changed per time period
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what is a mechanism?
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a detailed step-by-step description of how a reaction occurs at the molecular level
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how do you determine initial velocity?
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See notes
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What is a first order rate equation?
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See notes
- it is directly proportional to the substrate concentration |
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What is the rate equation
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Rate=k[S]^x
x = 0,1,2 usually |
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how are x and k determined
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experimentally
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Sometimes 2nd order reactions involve reactants such as water that are present in great excess and appear as what order? Such reactions are said to be what?
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1st order, pseudo-first-order
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in a zero order reaction the rate=?
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k
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Chymotripsin cleaves what kind of proteins and where?
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COOH ends of aromatic side chain AAs.
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At low substate concentrations what is the reaction order?
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first order
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As the concentration of substrate increases what does the order go to?
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zero order
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The Aspartate transcarbomoylase (ATCase)catalyzes the reaction between?
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aspartate and carbamoyl phosphate leading to the synthesis of nucleobases needed for DNA and RNA synthesis
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What kind of reaction curve does ATCase have? Why?
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sigmoidal curve b/c ATCase is an allosteric enzyme so with each binding of substrate additional binding becomes easier
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Why does chymotripsin have a hyperbolic curve?
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b/c it is a nonallosteric enzyme so no cooperative binding. once enzymes are bound it doesn't matter how much substrate you add
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Michaelis-Menten kinetics explains behavior for what kind of enzymes?
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non-allosteric
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When does Vmax occur for M-M kinetics?
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When the enzymes is saturated
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Rate of formation of ES equals rate of degradation when?
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at low P concentration
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A lower Km does what to an enzyme?
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increases its affinity for substrate
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An enzymes kinetic properties can be used to determine its what?
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catalytic efficiency
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what is the turnover number (Kcat)?
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it is equal to Vmax divided by the total enzyme concentration. it is the number of substrate molecules converted to product per unit time by an enzyme molecule under optimum conditions (saturated with substrate)
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Km (michaelis constant) is equal to what?
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the substrate concentration at 1/2 Vmax
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A lineweaver-burk plot for nonallosteric enzymes gives what kind of a line?
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straight line so it is better for determining Km. 1/V = Km/Vmax x 1/[S] + 1/Vmax
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what does a hydrophobic pocket in the enzyme do?
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it lowers the surrounding dielectric constant allowing electrostatic interaction between E and S
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When the substrate closely approaches the catalytic site with proper orientation the enzyme conformation probably changes to give what?
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a strained ES complex
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In acid base catalysis the enzyme side chains do what?
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act as proton donors and acceptors
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In covalent catalysis a nucleophillic side chain does what?
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forms an unstable covalent bond to the substrate
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The active site on chymotripsin (CT) involves what residues? How was this determined?
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it involves the serine 195 and the histidine 57 residue (CT is a serine protease). serine and histidine are close together in the active site. this was determined by labeling the serine with diisopropylfluorophosphate (DFP)
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What effect does histidine have on serine in chymotripsin?
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histidine acts as a general base catalyst and converts serine to its anion, making it a better nucleophile for attack at the carbonyl carbon to be hydrolyzed
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List four factors that affect enzyme activity
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1,physical factors - light, heat, pH, water
2.cofactors- vitamins, minerals, proteins 3.inhibitors- class or specific inhibitors 4.allsoteric regulators |
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Why are metals used as cofactors?
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Transition metals are often involved in catalysis b/c they
1. have a high positive charge density 2. act as lewis acids (accept e- pairs) 3. can mediate redox reactions (Fe3+/2+) 4. help polarize water molecules Eg.- Fe3+, Cu2+, C02+, Zn2+ |
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explain the mechanism of carbonic anhydrase
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1 step- nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide. 2 step- active site is regenerated by the ionization of the zinc-bound water molecule and the removal of a proton from the active site
2 forms active site- a high pH form that is active in hydration of carbon dioxide and a low pH form that is active in the dehydration of bicarbonate |
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what are coenzymes?
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organic molecules often derived form vitamins
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List some common vitamins used as coenzymes and their process
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1.Thiamine(B1) - TTP - Decarboxylation
2.Niacin - NAD(P)+ - Redox 3.Riboflavin(B2) - FAD, FMN - Redox 4.Pyridoxine(B6) - Pyridoxal P - amino transfer group 5.Folic acid - THF - one carbon transfer 6.Vit A - retinal - vision, growth 7. Vit K - Vit K - blood coagulation |
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Why is Vit K a necessary coenzyme in the carboxylation of glutamate residues to form gama- carboxyglutamate (Gla) residues?
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this reaction is catalyzed by Vit K dependent carboxylase. This is a critical part of the conversion of preprothrombin to prothrombin (factor II). The R group of Gla is a strong chelator of Ca+. The ion becomes coordinated between the two COO- components of the gama- carboxylgutamate.
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where does gama-carboxylation take place?
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in the lumen of the er
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