enxyme test Flashcards
what is mean by kinetically favourbale
this means that the reaction will happen spontaneously, the free energy of the system is negative
what is meant by thermodynamically favorable
this means that the natural change in free energy is from high to low.
the products have slow energy and are more stable than in reactants
absolute vs group specificity
the pickiness of an enzyme. High specificity means that it can only bind to one type or very few substrates (that are alike).
group specificity means that an enzyme is able to bind to a larger group of enzymes that share similar characteristics
free energy
the measurement of energy that is able to do work in a system
transition state
a very high-energy intermediate where the substrate is no longer the reactant, but not yet the product. During this state, bonds are partially broken and formed
note at this stage an ES complex HAS NOT FORMED. rather its the state between the ES and the EP
free energy of activation
the difference between the reactant energy and the free energy of the transition state. This is the amount of energy that needs to be input into the system to allow the reaction to proceed
what is the purpose of an enzyme catalyst
make a reaction kinetically favorable by lowering the free energy of activation by stabilizing the transition state
what is the binding energy
the release of free energy when bonds are formed between the enzyme and substrate. enzymes lower the binding energy of a system.
what are the features of an active site?
1) comprised of many residues found @ different positions along the chain (folding)
2)very small
3) unique environment= specificity
4) has the ability to form weak interactions with substrates
5) the arrangement of residues in the active site contribute ti specificity too
what are cofactors why are they needed
nonprotein moles that bind to enzymes to increase their overall chemistry
they can be coenzymes or metals
what is a prosthetic group
a tightly bound cofactor to its enzyme
what is a coenzyme
they are cofactors derived from vitamins
what is a co substrate
a loosely bound cofactor to its enzyme
explain the induced model fit
the idea that the active site of an enzyme is not a rigid structure and is able to conform to the shape of the substrate upon binding. this model is much more dynamic
explain the lock and key model
the concept that each enzyme has an active site that is perfectly complementary to one substrate. it’s a perfect match
what is an apoenzyme
an enzyme without its co facotrs
what is a holoenzyme
an enzyme with its co factors
initial velocity
the rate of the reaction when time ~0
this is the slope of the curve
how does enzyme concentration impact intial vel
it doesn’t! substrate concentration impacts it. this is because enzyme conc is typically constant within a system
what needs to form before an rxn can be catalyzed
an ES complex
what are the assumptions for the MM plot
what is Vmax
the velocity of the reaction when ll enzymes are saturated
ES=Et, at this point generally [S]>km
note that Vmax directly depends on the [E]
what is Km
the concentration of S to REACH 1/2 Vmax. Note it is not = to 1/2Vmax
it is the [S] to allow for 1/2of the E to be occupied
what is the turnover number
the # of mole per unit time (rate) that product is made when enzymes are fully saturated (ES=Et)
this is Kcat=K2
what is Kcat/Km
this is the specificity constant used when [S]«Km and describes the affinity of a particular enzyme has for an enzyme
high values means that the sub and enzyme work well together, even at low concentrations
catalytic perfection
to the notion that all encounters a substrate has with a particular enzyme will result in product. it is the Kcat/Km value of which cannot go any hight (the rate of the reaction cannot increase with minimal amounts of moles)
temperature optimum
the temp at which an enzyme is functioning at peak efficientcy. Any hotter and the enzyme will become denatured
pH optimum
the Ph at which the enzyme functions the more effectively. Ph dictates the charge and ability for weak interactions to occur in the active site. this impacts the ability for the enzyme to interact with its substrate
pseudo-first-order reaction
a reaction that depends on the [S]
zero order reaction
a reaction that doesn’t depend n [S]
what is steady state kinetics
the idea that ES is constant through a period of a reaction. ES form ation= ES breakdown
on a burk plot… what is the Vo, the Km, Vmax, Km/Vmax
1/Vo=y
Km/Vmax=slope
-1/km=x int
1/Vmax= y int
what is the rate-limiting step of a reaction?
k1: the rate of the ES formation as products can only be made as fast a reactants collide
what is allostery
the regulation of an enzyme via the binding of effectors to effector sites. this in turn controls the abundance of biochemicals found within a system
feed forward activation
where the binding of an effector enhances the activity of an enzyme
feedback inhibition
where an inhibitor binds to an enzyme to repress activity, to stop catalyzing the committed step of a reaction.
what is the committed step of a pathway
generally, the first step of a pathway, where the catalysis of the substrate initiates the production of the final product.
this step is important as all intermediates are biologically useless, so all ‘ingredients’ to make product must be available.
what is a concerted reaction model for allosteric enzymes
this idea is that all active sites of an enzyme must be of the same conformation. Where the conversion to R from T will happen to all sites, vastly interrupting the RT equb.
this abides by the symmetry rule
what is the sequential reaction model for allosteric enzymes
the idea that active sites can be either R or T, though the conformation of one sight will influence the state of the neighboring sites.
In what direction do inhibitors shift a sigmoidal curve? activators?
INH= right
Acti= left (less {s}needed to hit Vmax
what is a homotropic effect
the presence of substrate affects that allostery of the enzyme and disrupts the tP qub
what is a heterotropic effect
the influence regulators have on enzymes. Inhibitors stabilize the T while activators stabilize the R
what do allosteric enzymes do?
catalyze the commtted step of a reaction
what is the allosteric constant
Lo=T/R commonly 100:1
what is the threshold effect
the idea that allosteric enzyme are more sensitive to Km than MM w/ that same Vmax
less d[S] is needed to reach the same Vmax than MM
what are the 4 types of enzyme mechanisms?
Covalent catalysis
general acid base catalysis
metal ion catalysis
catalysis by approximation
what is covalent catalysis
the formation of at least one temporary covalent bond between the enzyme and substrate
what is general acid base catalysis
when an acid or basic residue in the active site is sed to facilitate the transfer of protons
what is metal ion catalysis
metal ions used as cofactors commonly to stabilize other molecules in the active site
what is catalysis by approximation
bringing two substrate close together in a proper orientation to increase the rate of reaction
what are irreversible inhibitors?
moels that become tightly bound to an enzyme and dissociate very slowly
may be covalent or non covalent
what are reversible inhibitors
moles that bind but are able to dissociated very quickly from an enzyme in the EIC
what are the types of reversbale inhibit
competitive
uncompetitive
noncompetitive
what are the types of irreversible inhibitor
group specific
affinity labels
suicide inhibit
transition state analogs
competitive inhibit
those that bind directly to the acitve site.
effects can be undone by increase [S]
Km inc but Vmax stays the same (as the [E] functional stays the same)
un competitive inhibit
a mole that binds to the ESI completely, after the ES has been formed. No product is formed
Both Km and Vmax dec
non competative inhibt
moles that bind to the enzyme or the ESI changing the conformation of the enzyme
no product is made
km stays the same while Vmax dec
group specific inhibition
bind to the side chains of AA, preventing the interaction with sub
affinity labels
moles that mimic the functional properties of a substrate but will covalently bond with enzyme and not let go
suicide inhibitors
the substrate is converted into a chemically reactive intermediate which remains bound to the enzyme via covalent bonding.
transition state analogs
moles that resemble the transition state of the substrate and there for bind tighter to the enzyme
what are the 7 major classes of enzymes
1) oxidoreductases
2) transferases
3) hyrdrolases
4) lyases
5)isomerases
6) transolcases
7) ligases
oxidoreductases
enzymes that cata oxidation-reduction reactions by transferring electrons between moles
transferases
transfer functional groups between moles
hydrolases
cleave moles by adding water
lysates
add moles or FG to double bonds or will removed moels to make double bonds
isomerases
move FG within the same mole
ligases
join moles together via using ATP
translocases
cata movement of ions or mole across membranes
what kind of mole is chymotrypsin
protease = protein tr over. chymotrypsin specifically does this via hydrolysis
chy cleaves on the carboxyl side of a bulky hydrophobic chain. this is because of a high specificity constant
what kind of curve are oxygen binding curves
sigmoidal bc of the cooperatvity of the multiple active sites on the subunits
how does the biding of oxygen affect the binding ability of the other sites
O2 into the 5th coord site on the heme group causes a structural change. the heme becomes planar and the aB group rotates 15deg. this induces R charter into the neighboring sites. a sequential like application
what regulates the release of O2 from hemoglobin
2,3 BPG. this mole bind to a pock of the T form (deoxY) and stabilizes it. this reduces O2 affinity
how does fetal hemoglobin differ from adult hemoglobin
the fetus gets their O2 from their mother. TF their hemoglobin has a very high affinity for O2 and a low affinity or 2.3 BPG. this is to ensure the fetus gets enough oxygen from the already limited supply.
what is the bhor affect
the regulation of O2 affinity through the present of CO2 and H+
what happens to O2 affinity with increased resp?
increase rep= ^CO2=^H+ in the blood. the lower the pH the lower the affinity hemoglobin has or oxygen. this is because hemo is trying to deliver more O2 to the muscles.
how does an abundance of H= allow from the decreased affinity of O2?
H+ stabilizes the deoxy. the H+ ion is ale to bind to redu=isude in the active site and form salt bridges between other residues.
specifically, the His146 is protenates at low pH and forms brings with Lys 40 and Asp 94
how does CO2 alone decrease O2 affinity??
CO2 reacts with terminal amono groups to form carbamate anions
these groups in hand can form salt brigdes between residues in the subunits, stabilizing the T form
what are the mutations that cause sickle cell
the B chain, Glu 6 is changed to Val 6. Val 6 is associated heavily with the Phe 85 and Leu 88 pocket (where O2 would bind) and reduces the binding ability with oxygen.
these cells aggregate together and can not bind to oxygen
