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Enzyme Catalysis

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pebebane's version from 2017-09-21 01:46

enzyme classification, power & specifity

Question Answer
range of mass of enzymes10 kDa - over 1000 kDa
enzyme suffix-ase
classification number formatEC.n1.n2.n3.n4
in classifying enzymes, n1 representstype of reaction (6 classes)
in classifying enzymes, n4 representssubstrate
for _________ enzymes, n1 = 1oxidoreductases
for _________ enzymes, n1 = 2transferases
for _________ enzymes, n1 = 3hydrolases
for _________ enzymes, n1 = 4lyases
for _________ enzymes, n1 = 5isomerases
for _________ enzymes, n1 = 6ligases
6 classes of enzymes(1) oxidoreductases
(2) transferases
(3) hydrolases
(4) lyases
(5) isomerases
(6) ligases
Once They Have Laughed I Laugh
fxn of oxidoreductase (n= _________)1, catalyzes transfer of electrons from reductant (e- donor) to oxidant (e- acceptor)
fxn of transferases (n= _________)2, catalyzes transfer of functional group from one molecule to another
fxn of hydrolases (n= _________)3, catalyzes cleavage of bond by addition of water
fxn of lyases (n= _________)4, catalyzes breaking of bond by means other than hydrolysis/oxidation
fxn of isomerases (n= _________)5, catalyzes rearrangement of isomers
fxn of ligases (n= _________)6, catalyzes joining of 2 large molecules
enzymes accelerate reactions by a factor of at least 10^6
define cofactorsmall, non-protein molecules that bind to enzymes & facilitate catalysis
enzyme + cofactorholoenzyme (active)
enzyme - cofactorapoenzyme (inactive)
inorganic cofactorsmetals (Zn2+, Mg2+, K+, Mn)
cofactor for carbonic anyhdraseZn2+
cofactor for hexokinaseMg2+
organic cofactors are derived fromvitamins
define coenzymeorganic cofactor
types of coenzymes(1) co-substrate (2) prosthetic group
define co-substrateloosely bound organic cofactor, changed by reaction
co-substrates (are/not) changed by reaction
prosthetic groups (are/not) changed by the reaction
co-substrates - changed
prosthetic gr. - not changed
define prosthetic grouptightly bound organic cofactor, unchanged by reaction
co-substrate are (loose/tightly) bound,
prosthetic groups are (loose/tightly) bound
co-substrates - loosely bound
prosthetic groups - tightly/covalently bound
NAD+ is a (co-substrate / prosthetic group) for what enzyme?copsubstrate for lactate dehydrogenase
FAD is a (co-substrate / prosthetic group) for what enzyme?prosthetic group for monoamine oxidase
how many different types of reactions does a single enzyme usually catalyze?just one rxn or one group of related rxns
proteases are (more/less) specific than other enzymesless - more diverse
what property of an enzyme determines its specificity?3D structure
papain, a ________ cleavesprotease - any peptide bond
trypsin, a ________ cleavesprotease - peptide bond on carboxyl side of K and R
thrombin, a _______ cleavesprotease - R-G bond in particular sequences
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thermodynamics

Question Answer
free energy change is (in/dependent) of pathindependent
formula for free energy change of a reactiondG = G(products) - G(reactants)
ΔG (does/not) inform rate & (does/not) inform specificitydoes NOT give info on rate
& DOES give info on sponteneity
if ΔG < 0spontaneous & exergonic
define exergonicyields energy
define endergonicrequires energy input
if ΔG = 0equilibrium (no net change)
if ΔG > 0not spontaneous
& endergonic
what is K'(eq)?equilibrium constant under standard conditions
what is ΔG(o')?standard free energy change
what are the conditions of ΔG(o')?T = 25C
P = 1 atm
[X] = 1M
pH = 7
at equilibrium conditions, ΔG(o') formulaΔG(o') = -RT ln([C][D] / [A][B]) = -RT ln K'(eq)
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if ΔG(o') < 0, then K'(eq) ___ 1 and : K >1, products are favored
Question Answer
if ΔG(o') > 0, then K'(eq) ___ 1 andK <1, reactants are favored
K' eq = [products]/[reactants] = [C][D]/[A][B]
criterion for spontaneityΔG < 0
if K > 1product favored
if K < 1 reactants favored
if K = 1equilibrium
ΔG formulaΔG = ΔG(o') + RT ln ([products]/[reactants])
can a reaction be spontaneous if ΔG(o') is positive?YES, because if RT ln ([products]/[reactants]) is very negavite, then ΔG will still be negative
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transition state

Question Answer
enzymes cannot change what aspect of a reaction?equilibrium
equilibrium of a reaction depends solely on ΔG value
how can enzymes change a reaction (generally)? changing the path to accelerate attainment of equilibrium
X‡ transition state (S --> X‡ --> P)
transitory S-P structure in transition state has (higher/lower) free energy & is (more/less) stable than S & Phigher free energy, lower stability
formula for difference in free energy between transition state & substrate∆G(‡) = G(X‡) − G(S)
∆G(‡)activation energy = difference in energy between transition state & substrate
how do enzymes accelerate reactions?lowering ∆G(‡) & facilitating formation of X‡
enzymes facilitate the formation of X‡
a 20% decrease in ∆G(‡) (increases/decreases) rxn rate by 10-foldincreases (takeaway = small decrease in ∆G(‡) --> greater increase in rxn rate)
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active site

Question Answer
how large are catalytic groups?2-3 residues
ES complexinteraction of enzyme & substrate
where do enzyme & substrate interact?active site
active site of the enzyme is the region most responsible for lowering ∆G(‡)
active sites are often free ofwater
active sites are a (large/small) percentage of the whole enzyme moleculesmall
where do cofactors bind?active site
how do enzymes bind substrates?multiple weak interactions (electrostatic, van der Waals, H-bonds)
most amino acids in an enzyme function toprovide scaffolding for 3D structure of active site
define binding energyfree energy released during formation of weak interactions between substrate & enzyme
- represents lowering of activation energy
_________ energy represents lowering of activation energy by the enzymebinding energy
when is the max binding energy released?when enzyme facilitates formation of transition state
maximum binding energy requiresclose contact between E & S
2 models for E-S binding(1) lock & key, (2) induced fit
describe lock & key model
who came up with the lock & key model?Fischer, 1890
in ______ model, unbound enzyme has rigid active sitelock & key
in ______ model, unbound enzyme has flexible active siteinduced fit
_________ model explains specificity both lock & key and induced fit models
_________ model explains stabilization of transition stateONLY induced fit, not lock & key
in ______ model, substrate has shape complementary to active sitelock & key
in ______ model, substrate has shape arbitrary to shape of active siteinduced fit
experimental data support what model of E-S binding?induced fit - enzyme changes shape and becomes complementary to substrate shape
what determines whether the transition state collapses into S or P?G
how is binding energy released?formation of many weak interactions between E & S
mechanism for substrate specificitycorrect substrate --> more interactions --> increased binding energy
how is binding energy used by enzy,e>to distort substrate into conformation approximating transition site
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catalytic strategies

Question Answer
4 catalytic strategiescovalent catalysis
general acid-base catalysis
metal ion catalysis
catalysis by approximation
define covalent catalysisactive site contains reactive group that covalently bonds substrate during rxn
active groups in covalent catalysis are usuallystrong nucleophiles
example of covalent catalysisserine residue in active site of chymotrypsin
serine residue in active site of chymotrypisin is an example ofcovalent catalysis
mechanism for covalent catalysis by serine in chymotrypsinO of serine becomes strong nucleophile --> carbonyl C of target peptide bond
define general acid-base catalysismolecule other than water becomes proton donor or acceptor
example of general acid-base catalysishistidine residue in active site of chymotrypsin
histidine residue in active site of chymotrypsin is an example ofgeneral base catalysis
mechanism for general acid-base catalysis by histidine in chymotrypsinhistidine accepts proton from serine hydroxyl group (which is then a strong nucleophile)
3 catalytic functions of metal ions(1) promote nucleophile formation
(2) act as electrophiles
(3) serve as bridge between E & S
how do metal ions promote formation of nucleophiles?direct coordination
example of metal ion promoting formation of nucleophileZn2+ and carbonic anhydrase (Zn2+ coordinates with O-H2 and allows deprotonation)
Zn2+ and carbonic anhydrase is an example ofmetal ion promoting formation of nucleophile
how do metal ions act as electrophiles?by stabilizing negative charge on rxn intermediate
example of metal ion acting as an electrophileMg2+ and EcoRV endonuclease
Mg2+ and EcoRV endonuclease is an example ofmetal ion acting as an electrophile
example of metal ion forming bridge between E & SMg2+ stabilizes ATP in active site of myosin
Mg2+ for myosin & ATP is an example ofmetal ion forming bridge between E & S
define catalysis by approximationenzyme brings together 2 substrates at a common binding surface
example of catalysis by approximationcarbonic anhydrase binding CO2 & H2O at adjacent sites to facilitate rxn
carbonic anhydrase binding CO2 & H2O is an example ofcatalysis by approximation
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chymotrypsin

Question Answer
where does chymotrypsin act in the body?small intestines - digestive enzyme that breaks down proteins & polypeptides
what class of enzyme is chymotrypsin?hydrolase class, n=3
chymotrypsin catalyzes what rxn?cleavage of peptide bonds by hydrolysis
hydrolysis of peptide bonds is thermodynamically (un/favorable) and kinetically (un/favorable)thermo - favorable
kinetic - unfavorable
why does hydrolysis of peptide bonds need an enzyme?partial double bond character of peptide bond --> very slow rxn
what bond does chymotrypsin break?(scissile) bond between C & N of peptide bond
define scissile bondbond that an enzyme breaks
specificity of chymotrypsin (what does it break?)cleaves peptide bonds
carboxyl side of...
- aromatics (WYF)
- large hydrophobics (M)
features of active sitespecificity pocket (S1), oxyanion hole, catalytic triad
describe specificity sitedeep pocket lined with hydrophobic residues
- aromatic & long hydrophobic side chains fit inside
- positioned for cleavage
how is protein positioned for cleavage?S1 pocket bonds with side chain
describe oxyanion holeH-bonds link 2 NH groups in main chain with (-)O of intermediate
function of oxyanion holestabilize tetrahedral intermediate
function of specificity siteonly fits aromatic & large hydrophobic side chains
catalyic triadser195, his57, asp102
function of his57general base catalysis (accepts proton from ser195)
function of ser195covalent catalysis (forms alkoxide - strong Nu - when his57 takes its proton)
function of asp102neutralization of charge (electrostatically stabilizes)
withdrawal of H from ______ toward ______ creates a strong nucleophilefrom ser195 --> his57 to make serine an alkoxide (O-)
what part of chymotrypsin attacks the peptide bond?O- of deprotonated serine --> carbonyl C of peptide bond
the oxyanion hole stabilizes what O-?the carbonyl O of the peptide bond, when the oxyanion attacks and pushes double bond electrons onto it
tetrahedral intermediate is made when _____ binds to peptide carbonyl Cser195
first stage of catalysis by chymotrypsinacylation
in the acyl-enzyme intermediate, the new N-terminus is bound toHis57
in the acyl-enzyme intermediate, the new C-terminus is bound toSer195
what are the intermediates & products of acylation (stage _________)?stage 1
enzyme-substrate complex
--> tetrahedral intermediate
--> acyl-enzyme
what are the intermediates & products of deacylation (stage _________)?stage 2
acyl-enzyme
--> tetrahedral intermediate
--> enzyme-product complex --> enzyme & product
what is substrate 2, and when does it bind?water, binds after N-terminus detaches
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