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biochemistry exam 2
| Term | Definition |
|---|---|
| enzymes | catalysts that accelerate the rate of a reaction in both forward and reverse directions (by the same factor) without being consumed, almost all are proteins |
| ribozymes | catalytically active RNA molecules |
| most important characteristics of enzymes | catalytic power and specificity |
| proteases | catalyze proteolysis, the hydrolysis of a peptide bond. most also catalyze the hydrolysis of an ester bond |
| enzyme specificity is due to | precise interaction of the enzyme and substrate |
| papain | proteolytic enzyme that cleaves any peptide bond |
| thrombin and trypsin | cleave only specific peptide bonds |
| 6 major classes of enzymes | oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases |
| oxidoreductases | oxidation-reduction |
| transferases | group transfer |
| isomerases | isomerization (intramolecular group transfer) |
| hydrolases | hydrolysis reactions (transfer of functional groups to water) |
| lyases | addition or removal of groups to form double bonds |
| ligases | ligation of two substrates at the expense of ATP hydrolysis |
| cofactors | small molecules that many enzymes require for catalytic activity |
| two main classes of cofactors | coenzymes and metal ions |
| coenzymes | small organic molecules often derived from vitamins |
| prosthetic groups | tightly bound coenzymes |
| holoenzyme | an enzyme with its cofactor |
| apoenzyme | an enzyme without its cofactor |
| first law of thermodynamics | the total energy of a system and its environment is constant |
| second law of thermodynamics | the total entropy of a system plus that of its surroundings always increases |
| system | part of universe you are studying |
| surroundings | all the rest of the universe outside the system |
| gibbs free energy (G) | the measure of energy capable of doing work |
| change in free energy (delta G) provides what info | provides information about spontaneity does NOT provide information about rate of reaction |
| if delta G is negative | reaction is spontaneous/exergonic/downhill |
| if delta G is zero | system is at equilibrium, no net change can take place |
| if delta G is positive | nonspontaneous/endergonic/uphill |
| delta G of a reaction depends on | only the free energy of the products minus the free energy of the reactants |
| how do enzymes affect delta G | THEY DONT, they only change reaction rate |
| delta G = delta G° + RT ln ([products]/[reactants]) | equation for free energy change delta G° = standard free energy change R = gas constant T = absolute temperature |
| competitive inhibition | inhibitor competes with substrate to bind to active site of enzyme PABA is an enzyme needed by bacteria medicine has created a mimic antibiotic that inhibits it competitively and kills the bacteria but does not harm us another example is chemotherapy |
| uncompetitive inhibition | inhibitor binds only to the enzyme-substrate complex once they are bound (near active site) |
| noncompetitive inhibition | the inhibitor binds either the free enzyme or ES complex (not at active site) |
| kinetics of competitive inhibitor | smaller dissociation constant (Ki) means inhibitor is more powerful Vmax not affected |
| competitive inhibition can be overcome by | sufficiently high substrate concentration (Vmax not affected, increasing apparent value of Km) |
| kinetics of uncompetitive inhibitor | lowers Vmax and lowers apparent Km inhibits catalysis (reaction happening) instead of preventing substrate binding cannot be overcome by addition of more substrate |
| kinetics of noncompetitive inhibitor | lowers concentration of functional enzyme apparent value of Vmax decreased Km unchanged cannot be overcome by increasing substrate concentration |
| slope of line weaver plot | Km/Vmax |
| X intercept of line weaver plot | -1/Km |
| Y intercept of line weaver plot | 1/Vmax |
| transition state analogs | inhibitors that resemble the transition state (best inhibitor) |
| transition state | stage in between substrate and product (when it is highly reactive) enzymes used to stabilize this state and help it move along better |
| types of reversible inhibitors | competitive, noncompetitive, uncompetitive |
| irreversible inhibitors | covalently bind to enzymes can help figure out reaction mechanism by showing which type of inhibitor makes reaction stop working |
| types of irreversible inhibitors | group-specific reagents, affinity labels, mechanism based (suicide) |
| group-specific inhibitors | inhibit by reacting with specific side chains of the amino acids so they no longer work (inactivate enzyme) ex: DIPF |
| affinity labels | inhibit enzymes by being structurally similar to the substrate and covalently bonding to active-site residues ex: TPCK irreversible version of competitive inhibition |
| mechanism-based (suicide) inhibitors | bind to the enzyme as a substrate and creates a reactive intermediate that covalently modifies to inactivate the enzyme ex: penicillin inhibits formation of cell walls in bacteria |
| how to tell which enzyme has the highest affinity for substrate | lowest Km = highest affinity |
| how to tell which enzyme can convert the most substrate to product in a given period of time | highest Kcat |
| how to tell which enzyme has the highest catalytic efficiency | Kcat/Km |
| binding energy | free energy released in the formation of a large number of weak interactions between the enzyme and the substrate to lower activation energy when enzyme interacts with TS: binding energy released is greatest |
| purposes of binding energy | establishes substrate specificity increases catalytic efficiency |
| induced fit | process by which binding energy can also promote structural changes in both the enzyme and the substrate that facilitate catalysis (not lock and key) |
| covalent catalysis | the active site contains a reactive group that becomes temporarily covalently attached to a part of the substrate ex: proteolytic enzyme chymotrypsin, aspartate in EcoRV most enzymes have this, enzymes can fit into multiple categories |
| general acid-base catalysis | a molecule other than water acts as a proton donor or acceptor ex: histidine residues in chymotrypsin and carbonic anhydrase |
| delta G°' | free energy change at biochemical/standard conditions pH of 7 |
| K'eq | [products]/[reactants] when delta G =0 (at equilibrium) |
| what does larger Keq mean for delta G° | more negative |
| what causes actual delta G to differ from delta G°' | concentrations of reactants and products |
| enzymes change ___ of equilibrium but not ___ of equilibrium | speed of attainment (rate of reaction), position |
| equilibrium position is a function only of the | free energy difference between reactants and products |
| delta G+ | difference in free energy between the transition state and the substrate (transition state is unstable and has a lot of energy) activation energy enzymes accelerate reactions by decreasing this |
| enzymes facilitate the formation of the _____ | transition state no longer substrate but not yet product |
| catalysis by approximation | enzyme brings 2 substrates together along a single binding surface in a manner that enhances the reaction rate ex: carbonic anhydrase |
| metal ion catalysis | metal ions function catalytically, such as by direct coordination, stabilizing negative charges on reaction intermediates, or serving as a bridge between enzyme and substrate ex: myosin and kinesin |
| proteases | cleaves proteins by hydrolysis through breaking peptide bonds hydrolysis alone thermodynamically favorable but kinetically slow, proteases increase both |
| peptide bonds resistant to hydrolysis because | resonance structure of the peptide bond (partial double bond characteristic) requires more powerful nucleophile, protease makes it more susceptible to attack |
| chymotrypsin | protease that cleaves peptide bonds selectively on the C terminal end of large hydrophobic amino acids (methionine, trypsin, lysine, phenylalanine) covalent and acid-base catalysis by employing a powerful nuc to attack unreactive carbonyl C of substrate |
| what does serine have that makes it a powerful nucleophile | has OH group - catalytic triad (Ser, His, Asp) |
| what does DIPF do | inactivates chymotrypsin by modifying serine 195, which makes chymotrypsin irreversibly lose all activity -> suggests serine 195 plays a central catalytic role (is the active site) P-based agents that modify serine like DIPF can be toxins |
| chymotrypsin action steps | 2 steps: rapid step (burst) and slow step (steady state) linked by a covalently bound intermediate |
| catalytic triad of chymotrypsin | serine, aspartate, histidine at active site |
| makeup of chymotrypsin | contains 3 polypeptide chains linked by disulfide bonds singular catalytic triad at active site (includes serine 195) |
| ***what does catalytic triad generate | histidine 57 alkoxide ion at ser195 that is a very powerful nucleophile |
| ***what happens if one of the catalytic triad is mutated | catalytic rate decreases |
| ***mechanism of catalytic triad | aspartate 102 orients histidine 57 (which acts as a base catalyst) so that it will take the proton from serine 195, which creates the alkoxide ion which cleaves a peptide bond (nucleophilic attack) all 3 very important for function |
| what is peptide hydrolysis intermediate stabilized by | oxyanion hole |
| peptide hydrolysis by chymotrypsin steps | substrate binds, serine nucleophilic attacks peptide carbonyl, tetrahedral intermediate collapses, amine component released, water binds, water nucleophilic attacks acyl-enzyme intermediate, tetrahedral intermediate collapse, carboxylic acid released |
| oxyanion hole | temporarily stabilizes unstable tetrahedral intermediates through hydrogen bond interactions that occur during chymotrypsin reaction and transition state that precedes the formation of the tetrahedral intermediate |
| specificity pocket (s1 pocket) | in chymotrypsin, pocket is deep and hydrophobic favors the binding of residues with long hydrophobic side chains because it can fit long uncharged side chains in it side chain binding positions the adjacent peptide bond for cleavage |
| what accounts for different specificities of proteases? | structural differences in specificity pocket have similar catalytic triads |
| how to be sure that the proposed mechanism for catalytic triad is correct | site-directed mutagenesis |
| ***site-directed mutagenesis | specifically mutate one of the amino acids to another one and see what happens to find the mechanism if catalytic activity is significantly lowered with mutation, shows that residue is important to mechanism (found all 3 are important to catalytic triad) |
| ***does mutated enzyme still work in mutagenesis? | yes, mutated enzyme is still better than no enzyme at all but is less efficient than non mutated enzyme |
| other major classes of peptide cleaving enzymes | cysteine, aspartyl, and metalloproteases not all proteases rely on activated serine at active site cysteine, aspartate, and metals can be used to generate a nucleophile |
| cysteine proteases | rely on a cys residue activated by a his residue to play the role of the nucleophile that attacks the peptide bond ex: papain that has a lot of commercial uses like meat preservation |
| aspartyl proteases | use a pair of asp residues at catalytic site that act together to allow a water molecule to attack the peptide bond ex: renin (role in regulation of blood pressure) and pepsin (digestive enzyme) |
| metalloproteases | use a bound metal ion (typically zinc) that activates water to perform nucleophilic attack on peptide carbonyl group |
| protease inhibitors | drugs that block protease activity |
| captopril | ACE inhibitor to regulate blood pressure |
| carbonic anhydrases | co2 + h2o -> release H+ and lowers pH which stabilizes the T state in blood convert co2 into bicarbonate ion and a protein in red blood cells dehydrate bicarbonate ion in the blood to form co2 for exhalation |
| what does the active site of human carbonic anhydrase II include | a zinc ion that is bound to four ligands: imidazole rings of three his residues water molecule (or hydroxide ion depending on pH) |
| how does this zinc complex facilitate carbon dioxide hydration | co2 + h20 -> h2co3, works with Zn and carbonic anhydrase |
| catalysis involves zinc activation of a ____ | water molecule at pH 8, reaction proceeds near its maximal rate (highest Kcat) as pH decreases, rate of reaction drops -> midpoint at pH 7 suggesting group loses a proton at pH 7 |
| what does zinc do to carbonic anhydrase | Zn decreases pKa of water which makes it lose a proton (makes it more acidic) and at neutral pH creates an OH nucleophile on carbonic anhydrase that attacks co2 to form the bicarbonate ion |
| carbonic anhydrase co2 binding site | adjacent to zinc site possesses a hydrophobic patch that serves as a binding site for co2 patches cause catalysis by approximation with co2 and something else |
| mechanism for hydration of carbon dioxide | Zn generates OH by facilitating release of H+ from water, co2 binds to the active site and is positioned to react with OH (nuc attack), OH attacks co2 which generates HCO3-, active site is regenerated with release of HCO3- and binding of h2o |
| proton shuttle | to shift equilibrium toward products: Zn-h2o must lose H+ to regenerate active form of carbonic anhydrase so it can attack co2. need something to take H+ away so it doesn't bind back to water molecule (buffer/proton shuttle): histidine |
| how is rate of co2 hydration by carbonic anhydrase affected by buffer concentration | rate increases as buffer concentration increases |
| difference in proton shuttle for large buffers | some large buffers are too big to fit in active site, so histidine 64 on carbonic anhydrase will act as temporary buffer and pick up proton and rotate out of active site to bind to real buffer can mutate his64 to see if it is the buffer |
| restriction endonucleases/enzyme | defense mechanism that bacteria have to degrade viral dna cleaves at a specific site called recognition sequences/sites meant to cleave invasive DNA but not host DNA that look very similar |
| bacteriophage | viral infection a bacterium can get |
| specificity of restriction enzymes | must cleave only DNA that contain recognition without cleaving DNA that lacks these sites (host) |
| how do restriction enzymes catalyze DNA cleavage | catalyze hydrolysis of bond between 3' O and P in DNA, leaving DNA strands with a free 3' OH group and 5' P group at cleavage site uses magnesium activated water |
| in-line displacement | reaction takes place by this incoming nucleophile attacks P atom, pentacoordinate transition state is formed nuc attacks P in middle and leaving group is across from nuc attack site |
| mechanism 1 for phosphodiester bond hydrolysis | theory: restriction enzymes cleave DNA through a covalent intermediate using a strong nuc 2 displacement reactions take place at P 2 sterochem inversions that result in no net inversion incorrect b/c they saw inversion in experiment results |
| mechanism 2 for phosphodiester bond hydrolysis | theory: restriction enzymes cleave DNA through direct hydrolysis 1 displacement reaction (nuc attack by water) taking place at P 1 inversion of stereochemistry that results in visible inversion proven correct by noticing inversion in experiment results |
| experiment to determine which mechanism is correct for phosphodiester bond hydrolysis (breaking) | EcoRV (restriction enzyme) cleaved at a recognition sequence was consistent with a direct nuc attack by water at P, showed no covalently bound intermediate needed resulted in inversion of stereochem, showing it's 1 step not 2 |
| what metal is required for DNA cleavage | magnesium ions position and activate water molecule for nuc attack on P in DNA backbone/phosphodiester bond |
| target sequence | the sequence the restriction enzyme will cleave |
| recognition site for restriction enzymes displays ___ | twofold rotational symmetry |
| binding of the restriction enzyme to the recognition sequence causes ___ | distortion in the DNA by introducing a kink which creates further contact with the enzyme, increasing the binding energy keeps P in phosphodiester bond and water/Mg close together non target DNA does not bend so it wont be cleaved |
| methylation | methyl group added by methylases to host DNA in recognition sequence to distinguish it from viral DNA, will prevent restriction enzymes from cleaving it because blocks formation of hydrogen bonds between DNA and restriction enzyme |
| why is enzyme activity regulation important | more efficient/ can save energy |
| four mechanisms of regulation | allosteric regulation, multiple forms of enzyme, reversible covalent modification, proteolytic activation |
| allosteric regulation | contain distinct regulatory sites and multiple functional sites can control activity by binding of small signal molecules cooperativity and feedback inhibition (ATCase) |
| multiple forms of enzyme | isozymes with differing Km and Vmax |
| reversible covalent modification | addition/removal of phosphoryl group |
| proteolytic activation | zymogens or proenzymes (blood clotting) |
| ATCase | catalyzes the first step in pyrimidine biosynthesis (aromatic group that composes the unique bases found in DNA and RNA |
| committed step | step in the pathway where the products of the reaction are committed to the ultimate synthesis of end products in the pathway (irreversible under cellular conditions and catalyzed by allosteric enzymes) |
| committed step in CTP formation | ATCase because only forward arrows after it is added (equilibrium cannot shift backwards after this) regulated with CTP/end product concentration (feedback loop) |
| feedback inhibition | inhibition of an enzyme by the end product of the pathway ex: ATCase inhibition by CTP important because ensures pathway intermediates are not needlessly formed when end product is abundant (efficiency/conserve energy) |
| what kind of inhibitor is CTP | allosteric (doesn't bind to active site of ATCase, inhibits rate b/c molecule cannot be cooperative and bind) |
| what kind of kinetics does ATCase display | sigmoidal kinetics (allosteric, shows cooperativity) does not obey michaelis-menten kinetics |
| how are subunits organized in ATCase | catalytic and regulatory sites on separate polypeptide chains 6 catalytic/active sites and 6 regulatory (c6r6) 2 catalytic trimers stacked and three regulatory dimers link them significant contact between these subunits, Zn ion critical for interact |
| ***how active sites of ATCase were found | ATCase crystallized in presence of PALA (bisubstrate analog) that resembles an intermediate along the catalysis pathway PALA is a potent competitive inhibitor of ATCase (competes for active site) PALA resembles both subunits (carbonyl phosphate and asp) |
| ***conformations of ATCase | T state and R state PALA binding causes structural changes (allosteric) that convert less active T state to more active R state. exists in equilibrium between the state s |
| allosteric coefficient (L) | ratio of concentration of enzyme in the T state to enzyme in the R state -> L= T/R |
| when is ATCase in T state vs R state | T state (tense): more in this state when no substrate present R state (relaxed): more in this state when substrate present (catalysis will occur) |
| T state | has a low affinity for substrate, has low catalytic activity, is favored in the absence of substrate |
| R state | has higher affinity for substrate, is the most active form, is favored upon binding of substrate |
| homotropic effects | cooperative (subunits cooperating with each other) effects of substrates on allosteric enzymes act on enzyme ACTIVE sites, generate the sigmoidal curve, impact ATCase activity by altering T/R ratio |
| limiting modes for cooperativity | ATCase has concerted mechanism (all or none) for allosteric enzymes (entire enzyme converted from T into R) most other allosteric enzymes exhibit features of both concerted and sequential model |
| sigmoidal curve for ATCase | composite of 2 michaelis-menten curves: less active T state with high Km more active R state with low Km |
| what do allosteric regulators influence/control in terms of ATCase | T-R equilibrium in T state when bound to CTP do not bind to active site, bind to regulatory subunits causing shift between T and R |
| which state does CTP stabilize when bound to the regulatory site of ATCase | favors the T state decreases net enzyme activity increases L |
| which state does substrate binding to ATCase favor | stabilizes R state |
| what is the allosteric activator of ATCase | ATP |
| ***kinetics of ATCase and its allosteric affectors | CTP (inhibitor) favors T state, shifts right (decrease enzyme activity) ATP (activator) favors R state, shifts left (increase enzyme activity) |
| where do ATCase's allosteric affecters bind | regulatory site, NOT active site |
| heterotrophic effects | effects of non-substrate molecules on allosteric enzymes binds at sites other than the active site shift the Km alters T/R ratio and impacts ATCase |
| Isozymes | enzymes that differ in amino acid sequence that catalyze the same reaction (encoded in different genes but have same substrate) typically display different kinetic parameters or respond to different regulatory molecules |
| lactate dehydrogenase | tetrameric protein that catalyzes a step in anaerobic glucose metabolism and glucose synthesis humans have two isozymic polypeptide chains: H protein in heart muscle and M protein in skeletal muscle isozyme content varies by tissue type |
| why study enzyme kinetics | understand catalytic mechanism, find effective inhibitors, understand regulation of activity |
| kinetics | the study of reaction rates |
| how is reaction rate measured | mix enzyme and substrate, then measure formation of product over time or disappearance of reactant over time |
| first order reaction | when velocity of reaction is directly proportional to reactant concentration V= k[A] |
| second order reaction | more than one concentration in velocity reaction V= k[A]^2 or V=k[A][B] |
| Vo | initial rate of reaction (the instant substrate and enzyme mix) |
| what happens when reaction velocity vs substrate concentration is in equilibrium | rate of reaction cannot keep increasing because amount of enzyme is constant and all that is being added is substrate, and all enzymes are occupied (no more free enzymes for added substrate to bind to) so reaction rate reaches its max |
| enzymatic catalysis first step | formation of enzyme substrate complex (ES complex) |
| michaelis-menten kinetics | concentrations of intermediates within a steady-state system (increasing amount of substrate with constant amount of enzyme) remain the same even though the concentrations of substrate and products are changing |
| steady state assumption | rate of formation of ES = rate of breakdown of ES note: enzymes are not used up in reactions |
| how does MM model change at Vo | there is negligible product formation at Vo so there is no backwards reaction |
| Km | michaelis constant, substrate concentration that yields 1/2 Vmax (half of active sites are full) -> significant catalysis can happen is independent of enzyme and substrate concentrations depends on buffer pH and concentrations of reactants or products |
| michaelis-menten equation | Vo = Vmax ([S]/([S]+Km)) |
| what can Km compare | mutant and wild type of the SAME enzyme, cannot compare between different enzymes |
| what does higher Km mean | enzyme requires more substrate and has lower binding affinity |
| what does lower Km mean | enzyme requires less substrate and has higher binding affinity |
| what does Km value depend on | particular substrate and environmental conditions such as pH, temperature, and ionic strength |
| alcohol dehydrogenase | converts ethanol into acetaldehyde in the liver excessive acetaldehyde in blood causes symptoms |
| aldehyde dehydrogenase | converts acetaldehyde to acetate 2 types on most people, low Km and high Km low Km deactivated in some people, causing them to feel symptoms quicker (high Km cannot process all, so some ends up in blood) |
| lineweaver burke equation | double-reciprocal of michaelis menten equation, yields straight line plot |
| Kcat | rate of catalysis or turnover number of enzyme (number of substrate molecules converted into product per second) |
| Kcat/Km | measure of catalytic efficiency because it takes into account the rate of catalysis and nature of enzyme substrate interaction highest Kcat/Km is enzyme that is most efficient |
| sequential reactions | all substrates must bind to the enzyme before any product is released 2 types: ordered and random |
| double displacement (ping pong) reactions | one or more products are released before all substrates bind the enzyme |
| ordered sequential reaction | substrates bind the enzyme in a defined sequence |
| random sequential | the order of the addition of substrates then release of products is random (products still cannot be released before all substrates bind) |
| double-displacement (ping-pong) reactions | one or more products are released before all substrates bind to the enzyme (no order at all) |
| what kind of enzymes do not obey michaelis-menten kinetics | allosteric - they have a sigmoidal curve (only hyperbolic curves work) has cooperative binding and more subunits |
| what kind of curves obey michaelis menten kinetics? | hyperbolic, NOT sigmoidal |
| covalent modification | covalent attachment of a modifying functional group to an enzyme, regulates enzyme activity most are reversible |
| protein kinases | catalyze the phosphorylation of protein substrates by attaching a phosphoryl group to a ser, thr, or tyr residue ATP is the most common phosphoryl group donor will add to the amino acid they are named after (ex: serine kinase adds to serine) |
| what is regulated by reversible phosphorylation | only intracellular proteins |
| protein phosphatases | catalyze the removal of phosphoryl groups attached to proteins by hydrolyzing the bond attaching the phosphoryl group |
| the reactions catalyzed by kinases and phosphatases are ___ under cellular conditions | irreversible take place at negligible rate in the absence of enzymes |
| what does phosphorylation do | effective means of regulating the activity of target proteins ATP is donor |
| why is phosphorylation highly effective | high free energy, adds 2 negative charges so electrostatic interactions are altered, can form 3+ H bonds, kinetics can be adjusted to meet cellular needs, can amplify signals, ATP is cellular currency ex: PKA (protein kinase A) |
| what does epinephrine do to the body | induces fight or flight response in muscles triggers formation of cAMP which activates PKA |
| allosteric regulation of PKA | in absence of cAMP R and C subunits are in an inactive complex binding of 2 cAMP to each R subunit causes complex to separate into R2 subunit and 2 active C subunits |
| zymogens (proenzymes) | inactive precursor of activating inactive folded forms of some enzymes, requires specific peptide bond cleavage to activate (proteolytic cleavage) |
| proteolytic cleavage | does not require an energy source and is irreversible ex: blood clotting, digestive enzymes |
| release of zymogens | synthesized in pancreas stored inside membrane-bound granules released into duodenum when cell receives a hormonal signal or nerve impulse |
| what activates chymotripsinogen | proteolytic cleavage (precursor of chymotrypsin) |
| what happens if trypsin is activated by accident | generated by trypsinogen, activates other zymogens if is activated by accident (you haven't eaten anything) then it will digest your digestive system unless there is something to protect us from this (inhibitors) |
| inhibitors | important to stop proteases from doing processes when they aren't supposed to, like when activated on accident ex: trypsin activated on an empty stomach, will trigger activation of other zymogens prematurely -> pancreatitis |
| alpha1-antitrypsin | protects tissues from digestion by elastase (inhibits it) blocks action of target enzymes by binding nearly irreversibly to active sites deficiency causes excess elastase -> damages alveolar wall by digesting connective tissues -> emphysema |
| enzymatic cascade | a series of zymogen activations amplifies the signal at each step used to achieve a rapid response |
| hemostasis | process of blood clot formation and dissolution factor 10 converted to active form |
| two pathways to initiate blood clotting cascades | intrinsic pathway and extrinsic pathway lead to common end point |
| intrinsic pathway | activated by exposure of anionic surfaces upon rupture of the endothelial lining of the blood vessels (damaged surface) |
| extrinsic pathway | initiated when trauma exposes tissue factor (TF), an integral membrane glycoprotein (appears to be most crucial in blood clotting) |
| fibrin | smooth clot at first, needs crosslinks with factor 13a activated from a chain reaction of thrombin to fibrin then factor13A |
| what vitamin is needed to clot blood | vitamin K essential for synthesis of prothrombin and other clotting factors |
| what type of drug blocks blood clotting pathway | anticoagulants ex: warfarin |
| 4 domains of prothrombin | gla domain, 2 kringle domains, serine protease domain |
| what must prothrombin bind to in order to be converted to thrombin | Ca 2+ binding to gla domain that anchors the zymogen to platelets after injury brings prothrombin close to factor Xa and factor Va that catalyze its conversion into thrombin (proximity to injury) |
| what initiates fibrin clot formation | cleavage of fibrinogen by thrombin (irreversible activation proteolytic cleavage) |
| true or false: Enzymes bind the transition state better than the reaction products | true |
| Consider the reaction A→B in a cell at 37°C. At equilibrium, the concentrations of A and B are 30μM and 0.3μM, respectively. What is the value of Keq for this reaction? | 0.01 |
| When ΔG°' for a reaction is positive is the reaction endergonic or exergonic and is it spontaneous? | we don't know without knowing the concentrations of the reactants and products |
| true or false: All known enzymes are proteins. | false, some are RNA |
| true or false: Enzymes increase the activation energy for the conversion of substrate to product | false |
| true or false: Enzymes decrease the ΔG of the reaction they catalyze | false |
| Vmax, the maximum velocity, of an enzyme-catalyzed reaction is | dependent on the amount of enzyme present, which is why it is normally held constant on the graph |
| If the enzyme concentration is 5μM, the substrate concentration is 5 nM, and KM is 5 μM | most of the enzymes won't have the substrate bound (a lot more enzyme than substrate is present) |
| which type of inhibitor keeps Vmax constant | competitive |
| which type of inhibitor decreases Vmax | uncompetitive and noncompetitive |
| when will the enzyme be inhibited by its own substrate | when too much substrate compared to enzyme |
| true or false: Group specific reagents such as DIPF are reversible inhibitors | false, they are irreversible |
| true or false: Reversible inhibitors always bind to the active site of the enzyme | false, only competitive does |
| true or false: Methotrexate is an irreversible inhibitor which binds covalently to the active site of the enzyme. | false, reversible competitive |
| true or false: Suicide inhibitors can be used to treat diseases such as Parkinson and depression. | true penicillin is an example |
| true or false: In non-competitive inhibition, an inhibitor binds only to the ES complex | false, can bind to free enzyme or ES complex |
| how to find Km of an enzyme using chart of Vo and [S] | find 1/2 of highest Vo shown then look at the corresponding [S] |
| If you were attempting to design a new drug for the treatment of a disease by interfering with enzyme activity in the disease-causing organism, which type of inhibitor would likely be the MOST effective? | a transition-state analog that is an irreversible inhibitor |
| true or false: enzymes increase the rate of a chemical reaction | true |
| true or false: in acid-base catalysis, amino acids such as Histidine can act as proton donors or acceptors | true |
| true or false: in acid-base catalysis, This strategy is used by enzymes, such as carbonic anhydrase. | true |
| true or false: in acid-base catalysis, This strategy is used by enzymes, such as chymotrypsin | true |
| true or false: in acid-base catalysis, Metal ions are usually not required for this catalytic strategy | true |
| true or false: in acid-base catalysis, In this strategy, water can be used as the donor or acceptor of protons | false |
| true or false: Chymotrypsin binds its substrate with a deep hydrophilic s1 pocket | false, the pocket is hydrophobic |
| true or false: Catalytic triad of chymotrypsin include a serine, histidine, and arginine | false |
| true or false: Tetrahedral intermediate is stabilized by interacting with the oxyanion hole | true |
| true or false: During catalysis, chymotrypsin only uses covalent catalysis | false, it also uses acid-base catalysis |
| true or false: Chymotrypsin is a metalloprotease. | false |
| Binding of a water molecule to the zinc ion in carbonic anhydrase induces: | lowering of pKa for water, which leads to formation of a zinc-bound hydroxide ion. |
| What do trypsin, subtilisin, and elastase have in common? | All contain a catalytic triad at the active site. |
| true or false: Isozymes catalyze different reactions. | false |
| true or false: Isozymes have the same amino acid sequence. | false |
| true or false: Isozymes have identical regulatory properties. | false |
| true or false: Isozymes act on the same substrate | true |
| true or false: ATCase is an example of an isozyme | false |
| true or false regarding restriction endonucleases: They are produced by viruses to digest the bacterial genome | false |
| true or false regarding restriction endonucleases: They cleave phosphodiester bonds using a direct hydrolytic reaction | true |
| true or false regarding restriction endonucleases: They require Zn2+ ions for catalysis. | false |
| true or false regarding restriction endonucleases: The host DNA is protected by the addition of phosphoryl groups to specific Adenines. | false |
| true or false regarding restriction endonucleases: High specificity of restriction enzymes is due to decreased binding energy with distorted DNA | false |
| If the allosteric coefficient for ATCase increases from 1000 to 1500, the rate of the Ncarbamoylaspartate formation: | decreases and the curve shifts to the right |
| The allosteric effectors of ATCase are: | ATP and CTP |
| Which regulatory mechanism provides a connection between the energy status of the cell and metabolism regulation? | Phosphorylation |
| The enzyme chymotrypsin is produced in the pancreas initially as a _____, and gets activated by _____ . | zymogen; irreversible proteolytic cleavage. |
| true or false regarding phosphorylation: Both intracellular and extracellular proteins can be regulated by phosphorylation. | false |
| true or false regarding phosphorylation: Kinases add phosphoryl groups to serine, threonine, and tyrosine residues. | true |
| true or false regarding phosphorylation: Phosphorylation always inactivates proteins. | false |
| true or false regarding phosphorylation: Phosphoryl group donor is CTP | false |
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emw24geneseo