Chapter 11 Flashcards
enzymes differ from chemical catalysts in the following ways:
…: the rates of enzymatically catalyzed rxns are typically 10^6 to 10^12 times greater than those of the corresponding uncatalyzed rxns and are at least several orders of magnitude greater than those of the corresponding chemically catalyzed rxns
higher rxn rates
enzymes differ from chemical catalysts in the following ways:
…: enzymatically catalyzed rxns occur under relatively mild conditions: temperatures below 100 degrees C, atmospheric pressure, and nearly neutral pH. in contrast, efficient chemical catalysis often requires elevated temps and pressures as well as extremes of pH
milder rxn conditions
enzymes differ from chemical catalysts in the following ways:
…: enzymes have a vastly greater degree of specificity with respect to the identities of both their substrates (reactants)
and their products than do chemical catalysts; that is, enzymatic rxns rarely have side products
greater rxn specificity
enzymes differ from chemical catalysts in the following ways:
…: the catalytic activities of many enzymes vary in response to the concentrations of substances other than their substrates. the mechanisms of these regulatory processes include allosteric control, covalent modification of enzymes, and variation of the amounts of enzymes synthesized
capacity for regulation
an enzyme’s … or … name is convenient for everyday use and is often an enzyme’s previously used name. its … name is used when ambiguity must be minimized; it is the name of its substrate followed by a word ending in -ase specifying the type of rxn the enzyme catalyzes according to its major group classification
accepted; recommended; systematic
in general, a substrate-binding site consists of an indentation or cleft on the surface of an enzyme molecule that is complementary in shape ot the substrate –> …
moreover, the amino acid residues that form the binding site are arranged to specifically attract the substrate –> …
geometric complementarity; electronic complementarity
x-ray studies indicate that the substrate-binding sites of most enzymes are largely preformed but undergo some conformational change on substrate binding –> …
induced fit
Enzymes are highly specific both in binding chiral substrates and in catalyzing their reactions. This .. arises because enzymes, by virtue of their inherent chirality (proteins consist of only L-amino acids), form asymmetric active sites
stereospecificity
… molecule: can become chiral (e.g. citrate)
prochiral
nearly all enzymes that participate in chiral rxns are ..
.absolutely stereospecific
most enzymes are selective about the identities of the chemical groups on their substrates. –> …, a more stringent requirement than stereospecificity
geometric specificity
…: act as the enzymes’ “chemical teeth”; may be metal ions, such as Cu2+.
cofactors
cofactors may also be organic molecules known as…. some cofactors are only transiently associated with a given enzyme molecule, so that they function as …
coenzymes; cosubstrates
other cofactors, known as …, are permanently associated with their protein, often by covalent bonds
prosthetic groups
a catalytically active enzyme-cofactor complex is called a … the enzymatically inactive protein resulting from the removal of it’s cofactor is referred to as an …
holoenzyme; apoenzyme
in order to complete the catalytic cycle, the coenzyme must return
to its original state
for a transiently bound coenzyme (cosubstrate), the regeneration rxn may be catalyzed by a different enzyme. however, for a prosthetic group, regeneration occurs as part of the
enzyme rxn sequence
the point of highest free energy is called the … of the system
transition state
reactants generally approach one antoher along the path of minimum free energy, their so0called …
rxn coordinate
a plot of free energy vs. the rxn coordinate is called a … or …
transition state diagram; rxn coordinate diagram
the free energy of the transition state less that of the reactants is known as the …
free energy of activation
the greater the value of delta G for the transition state, the … the rxn rate. this is bc the larger delta G is the smaller the number of reactant molecules that have sufficient thermal energy to achieve the transition state free energy
slower
in a multistep rxn, the step with the highest transition state free energy acts as a ‘bottleneck’ and is therefore said to be the … step of the rxn
rate-determining
catalyss act by providing a rxn pathway with a transition state whose free energy is … than that in the uncatalyzed rxn
lower
a catalyst equally accelerates the … and … rxns
forward; reverse
an enzyme cannot alter …; it can only degrees … to allow the rxn to more quickly approach equilibrium (where the rates of the forward and reverse rxns are equal) than it would in the absence of a catlyst
delta Greaction; delta G transition state
enzymes reduce the free E of the transition state: that is, they … the transition state of the catalyzed rxn
stabilize
the types of catalytic mechanisms that enzymes use are:
- … catalysis
- … catalysis
- … catalysis
- … and … effects
- preferential binding of the …
acid-base covalent metal ion proximity; orientation transition state complex
… is a process in which proton transfer from an acid lowers the free E of a rxn’s transition state
general acid catalysis
a reaction may also be stimulated by … if its rate is increased by proton abstraction by a base. some rxn may be simultaneously subject to both processes; these are …
general base catalysis; concerted acid-base catalyzed rxns
the ability of enzymes to …around their substrates makes concerted acid-base catalysis a common enzymatic mechanism
arrange several catalytic groups
… accelerates rxn rates through the transient formation of a catalyst-substrate covalent bond
covalent catalysis
usually in covalent catalysis, the covalent bond is formed by the rxn of a nucleophilic group on the catalyst with an electrophilic group on the substrate, and hence this form of catalysis is often also called …
nucleophilic catalysis
steps of covalent catalysis:
- the nucleophilic rxn between the catalyst and the substrate to form a covalent bond
- the withdrawal of electrons fromt he rxn center by the now … catalyst
- the elimination of the catalyst, a rxn that is essentially the reverse of stage 1
electrophilic
the nucleophilicity of a substance is closely related to its …
basicity
the more stable the covalent bond formed, the less easily it can … in the final steps of a rxn
decompose
nearly one third of all known enzymes require metal ions for catalytic activity.–> …
metalloenzymes
metal ions participate in the catalytic process in three major ways:
by binding to substrates to .. them properly for rxn
by mediating … rxns through reversible changes in the metal ion’s oxidation state
by electrostatically stabilizing or shielding …
orient; oxidation-reduction; negative charges
metal ions are often much more effective catalysts than protons bc metal ions can be present in high concentrations at … and may have charges greater than …
neutral pH; +1
… and …: reactants must come together with the proper spatial relationship for a rxn to occur
proximity; orientation
by simply binding their substrates, enzymes facilitate their catalyzed rxns in 4 ways:
enzymes bring substrates into contact with their .. and, in rxns with more than one substrate, with each other. however, such proximity effects alone can enhance rxn rates by no more than a factor of ~5
catalytic groups
by simply binding their substrates, enzymes facilitate their catalyzed rxns in 4 ways:
enzymes bind their substrates in the … for rxn. enzymes aligh their substrates and catalytic groups so as to optimize reactivity
proper orientation
by simply binding their substrates, enzymes facilitate their catalyzed rxns in 4 ways:
charged groups may help stabilize the transition state of the rxn–> …
the charge distribution around the active sites of enzymes may also guide polar substrates toward their binding site
electrostatic catalysis
by simply binding their substrates, enzymes facilitate their catalyzed rxns in 4 ways:
enzymes freeze out the relative … and … motions of their substrates and catalytic groups. this effect can promote rate enhancements of up to ~10^7
translational; rotational
an enzyme may bind the … of the rxn it catalyzes with greater affinity than its substrates/products
transition state
enzymes that preferentially bind the transition state structure increase its … and therefore proportionally increase the …
concentration; reaction rate
if an enzyme preferentially binds its transition state, then it can be expected that …, stable molecules that geometrically and electronically resemble the transition state, are potent inhibitors of the enzyme
transition state analogs
… is an enzyme that destroys bacterial cell walls. it does so by hydrolyzing the beta 1,4 glycosidic linkages from N-acetylmuramic acid to N-acetylglucosamine in cell wall peptidoglycan
lysozyme
the most striking feature of lysozyme’s catalytic site is a prominent …, the substrate-binding site, that traverses one face of the molecule
cleft
the rxn catalyzed by lysozyme, the hydrolysis of a …, is the conversion of an … to a …
glycoside; acetal; hemiacetal
the delta-lactone analog of (NAG)3 is a transition state analog of lysozyme since this compound’s … ring has the half chair conformation that geometrically resembles the proposed … of the substrate’s D ring
lactone; oxonium ion transition state
in the catalytic mechanism of lysozyme, … in its protonated form acts as an acid catalyst to cleave the polysaccharide substrate between its … and …r ings, and … in its anionic state forms a covalent bond to … of the … ring
Glu 35; D; E; Asp 52; C1; D
diverse and widespread group of proteolytic that have a common catalytic mechanism involving a reactive Serine residue: …
serine proteases
a diagnostic test for the presence of the active site Ser of serine proteases is its reaction with … (DIPF) which irreversibly inactivates the enzyme
diisopropylphosphofluoridate
DIPF reacts only with Ser 195 of …, thereby demonstrating that this residue is the enzyme’s …
chymotrypsin; active site Ser
…: a substrate analog bearing a reactive group specifically binds at the enzyme’s active site, where it reacts to form a stable covalent bond with a nearby susceptible group. the affinity labeled group can be subsequently isolated and labeled
affinity labeling
serine proteases contain a …-…-… catalytic triad near a binding pocket that helps determine the enzymes’ substrate specificity
Ser-His-Asp
catalysis in the serine proteases occurs through acid-base catalysis, covalent catalysis, proximity and orientation effects, electrostatic catalysis, and by preferential transition state binding in the ..
oxyanion hole
synthesis of pancreatic enzymes as inactive … protects the pancreas from self-digestion. these are activated by specific …
zymogens; proteolytic cleavages
the great similarities among chymotrypsin, trypsin, and elastase indicate that these proteins arose through duplications of an ancestral … gene followed by the … evolution of the resulting enzymes
serine protease; divergent
…: nature seems to have independently discovered the same catalytic mechanism several times
convergent evolution
much of chymotrypsin’s catalytic power derives from its preferential binding of the …
transition state
the tetrahedral intermediate of chymotrypsin catalysis decomposes to a …
acyl-enzyme intermediate
process by which serine proteases cleave polypeptides:
- general base catalysis and nucleophilic attack to form …
- general acid catalysis aids breakdown of the tetrahedral intermediate to the .. intermediate
- … product is released and replaced by …
- general base catalysis and nucleophilic attack occurs again to form tetrahedral intermediate
- general acid catalysis breakdown of tetrahedral intermediate to the … product and the …
tetrahedral intermediate
acyl-enzyme intermediate
amine; water
carbonyl; active enzyme
this preferential binding of the transition state (…) over the enzyme-substrate complex or the acyl-enzyme intermediate is responsible for much of the catalytic efficiency of serine proteases
tetrahedral intermediate;
….: unusually short and strong H bonds where the H atom becomes more or less equally shared between the donor and acceptor, bc the groups have similar pKas
low-barrier hydrogen bonds
