Enzymes 1 - catalysis 09/16 Spencer Flashcards
what is a common suffix attached to enzyme names
-ase
in enzyme classification numbers of the form EC.n1.n2.n3.n4, what does n1 refer to?
type of reaction (6 possible)
1 - oxidoreductase (oxidation/reduction)
2 - transferase (transfer of functional group)
3 - hydrolase (cleaves by hydrolysis)
4 - lyase (add or remove groups to form double bond)
5 - isomerase (intramolecular group transfer)
6 - ligase (covalently join molecules with energy from ATP hydrolysis)
what is an oxidoreductase enzyme
catalyzes an oxidation/reduction reaction
what is a transferase enzyme
catalyzes the transfer of a functional group from one molecule to another
what is a hydrolase enzyme
catalyzes cleavage of bonds by hydrolysis, the addition of water
what is a lyase enzyme
catalyzes addition or removal of a functional group to form a double bond
what is an isomerase enzyme
catalyzes the transfer of a functional group from one part of a molecule to another part of the same molecule
what is a ligase enzyme
catalyzes the covalent joining of molecules with energy from the hydrolysis of ATP
A- + B A + B- what class of enzyme is involved
oxidoreductase
AX + B A + BX what class of enzyme is involved
transferase
AB + H2O AOH + BH what class of enzyme is involved
hydrolase
XABY A=B + XY what class of enzyme is involved
lyase
D-A L-A (D-A and L-A are isomers) what class of enzyme is involved
isomerase
X + Y + ATP XY + ADP + Pi what class of enzyme is involved
ligase
in enzyme classification numbers of the form EC.n1.n2.n3.n4, what do n2 and n3 refer to?
some details of the enzyme reaction, we are not required to know these details
in enzyme classification numbers of the form EC.n1.n2.n3.n4, what does n4 refer to?
the substrate of the enzyme reaction
how much do enzymes increase physiologic reaction rates?
by a factor of 10^6 or more
uncatalyzed reaction rates are not consistent with life
enzyme cofactor
small non-protein molecules that bind and facilitate catalytic activity of enzymes
what are two types of enzyme cofactors
inorganic cofactors (metals) organic cofactors or coenzymes (from vitamins)
what are inorganic cofactors?
metals that bind and facilitate catalytic activity of enzymes
what are organic cofactors?
coenzymes derived from vitamins that bind and facilitate catalytic activity of enzymes
what are 2 types of organic cofactors?
co-substrate (loose, changed by rxn) prosthetic group (tight, not changed by rxn)
map the kinds of enzyme cofactors together
cofactor
______|______
inorganic organic
(metals) (coenzymes)
(vitamin derived)
_______|_______
co-substrate prosthetic group
(loose, changed) (tight, unchanged)
a coenzyme is another name for…
an organic co-factor
vitamin derived
what is a co-substrate
organic cofactor that is bound loosely and changed by the reacton
what is a prosthetic group
an organic cofactor that is bound tightly and unchanged by the reaction
holoenzyme
active enzyme with cofactor
apoenzyme
non-active enzyme without cofactor
active enzyme with cofactor =
holoenzyme
non-active enzyme without cofactor =
apoenzyme
T/F enzymes are highly specific to the reactions they catalyze
true - (to some varying degrees, e.g. cleaving peptide bonds vs only cleaving peptide bonds between R and G)
∆G refers to…
change in (Gibbs) free energy
T/F ∆G of a reaction is dependent on the path that is followed in converting reactants to products (e.g. transition state energies)
false - ∆G is dependent only on G products - G reactants
T/F ∆G is concerned only with initial state of reactants and final state of products
true
what does ∆G tell you about the rate of a reaction?
nothing. no info on rate, only spontaneity
∆G < 0
spontaneous reaction
∆G > 0
non-spontaneous reaction
∆G = 0
reaction at equilibrium (no net change)
what is ∆G for a spontaneous reaction
< 0
what is ∆G for a non-spontaneous reaction
> 0
how do you calculate ∆G for a given temperature?
∆G = ∆Go + RT ln (products/reactants) ∆Go = ∆G @ standard conditions
what are temperature, pressure, concentration, and pH at standard reaction conditions?
T = 298 K (room temp) P = 1 atm [X] = 1 M pH = 7
how can you calculate ∆Go (∆G @ standard conditions) for a reaction at equilibrium conditions?
∆Go = -RT ln Keq Keq = [products]/[reactants]
Keq =
equilibrium constant
[products]/[reactants]
Keq > 1 favors the..
products
Keq < 1 favors the…
reactants
if ∆Go is negative, is the reaction spontaneous?
not necessarily. reaction is spontaneous at standard conditions but at different conditions, ∆G may be non-spontaneous
T/F enzymes alter equilibrium
false - enzymes only accelerate the attainment of equilibrium by catalyzing the reaction
what is the activation energy of a reaction?
∆G transition state - ∆G reactants
how is reaction velocity related to activation energy?
lower activation energy, greater reaction velocity
T/F small changes in activation energy can result in large changes in reaction velocity
true
what is a catalytic group in an enzyme
a group of 2-3 residues in an active site that participate directly in the making or breaking of bonds
what is the active site of an enzyme
region that binds substrates and cofactors and contains catalytic groups that participate in the making / breaking of bonds
describe the general characteristics of an enzyme active site with respect to:
- 3D shape
- % of enzyme
- substrate binding interactions
- specificity of binding
- 3D shape usually cleft with unique microenvironment (e.g. H2O excluded)
- small % of total enzyme volume
- binds substrate with many weak interactions (electrostatic, van der Waals, H-bonds)
- controls binding specificity with orientation of atoms in the site
how does an enzyme lower activation energy?
numerous weak enzyme-substrate interactions and eventually formation of the transition state release free energy (binding energy)
what is the binding energy of an enzyme?
the free energy released (equivalent to the lowering of activation energy) by numerous weak interactions and eventually transition state formation between enzyme and substrate
why does maximum binding energy require close contact between enzyme and substrate?
many of the interactions contributing to binding energy are weak, short-range interactions - more interactions = greater release of energy and lower activation energy
which enzyme-substrate binding model accounts for specificity but not for stabilization of transition state?
lock & key
rigid, does not account for conformational change / flexibility
which enzyme-substrate binding model accounts both for specificity and for stabilization of transition state?
induced fit
enzyme has flexible active site that becomes complementary to substrate shape
in induced fit model of enzyme-substrate binding, which is flexible.. enzyme or substrate?
enzyme
4 catalytic strategies of enzymes
covalent catalysis
acid-base catalysis
metal ion catalysis
catalysis by approximation
describe covalent enzyme catalysis
a reactive group (usually a powerful nucleophile) in the active site makes a temporary covalent attachment to the substrate during the reaction
describe general acid-base enzyme catalysis
an enzyme or substrate residue becomes an H+ donor or acceptor
describe 3 mechanisms of metal ion enzyme catalysis
metal ions can:
- promote nucleophile formation
- act as electrophiles and stabilize neg charge
- serve as enzyme-metal-substrate bridge
describe enzyme catalysis by approximation
enzyme brings two distinct substrates together in the right conformation so they can react with one another
what amino acid residues make up the catalytic triad in chymotrypsin and what kind of catalysis do they facilitate?
asp, his, ser
asp makes his a better base
his accepts an H+ from ser (basic catalysis)
ser becomes a good electrophile (covalent catalysis)
