Biochem Enzymes Lecture 1 Flashcards
These are proteins which catalyze biochemical reactions
Enzymes
The structure of enzymes are essential to their
Catalytic activity
Is the MW of enzymes variable?
Yes, vary from 12,000 to 1,000,000+
Some enzymes require and additional chemical component to function, called a
Cofactor
Cofactors tend to be one or more ___
They can also be a complex organic or metalloorganic molecule, called a
Or they can be both a
inorganic ions (Fe2+, Mg2+, Mn2+, Zn2+)
(coenzyme
Metal ion and a coenzyme
How are enzymes classified?
According the the type of reaction that they catalyze
Many enzymes ar enamed by addding _____ to the name describing their activity
“ase”
What does an enzyme do?
Provides an environment that speeds up a given reaction
This is the term describing a pocket on the enzymes where the enzymes-catalyzed reaction occurs
The surface of the above location is lined with _____ that help bind the substrate and catalyze its chemical transformation
Active Site
AA residues
This is the term describing the molecule that is bound in the active site and acted upon by the enzyme
Substrate
Does a reaction affect the equilibrium of a reaction? Yes or no?
No
What does an enzyme affect about a reaction?
The reaction rate
In a reaction diagram, the equilibrium between S and P reflects the difference in ____ of their ground states
Free energies
E + S → ES → EP → E + P
If the free energy of the ground state, P is lower than that of S, ΔG is _____ and the equilibrium favors ___ formation
Negative
P formation
Does a favorable equilibrium mean a fast conversion of products?
No.
The difference between energy levels of the ground state and the transition state is the ________ or ΔG‡
Activation energy
A higher activation energy means a faster/slower reaction?
Slower reactions
Catalysts increase reaction rates by lowering….
ΔG‡
This is the term describing the transient chemical species of a raection
Reaction Intermediates
This is the term describing the step in an enzymatic reaction with the highest activation energy, it determines the overall reaction rate
Rate-limiting step
E + S → ES → EP → E + P
In the above reaction, the reaction rate is determined by the concentration of ___ and
What is the equation, then, for the rate of the reaction (V)?
What order is it?
What is the unit for the rate constant, k?
Reaction [S] and the rate constant, K
V=k[S]
First order
s^-1
If a reaction is dependent upon two different compounds, S1 and S2, k is a _______ rate constant with units ____
What would the rate equation be then
Second Order
M-1s-1
V=k[S1][S2]
What is the equation that describes how the rate constant and activation energy are related?
k=(kT/h)e ^-ΔG‡/RT
k=Boltzmann constant and h is Planck’s constant
What helps to lower activation energies?
Weak, noncovalent interactions between substrate and enzyme
What are the weak interaction between E and S in ES complexes?
H-bonds
Hydrophobic interactions
Ionic Interactions
Some of these weak interactions occur in the reaction transition state and stabilize the transition state
The energy obtained from an enzyme substrate interaction is the _____
Binding energy, ΔG
The binding energy is used by enzymes to to increase/lower the activation energies of reactions?
Lower the activation energies
The binding energy can be used to lower substrate _______ or to cause a ___ change in the enzymes
Entropy
Conformational Change (induced fit)
To successfully catalyze reactions, the enzye must be complementary the reaction ___ state
Weak interactions formed in the transition state make the major contribution to ____
Transition state
Catalysis
Figure 6-5 describes how the free energy changes that occur depending upon how the enzyme interacts with the substrate
When the enzyme fits tightly to the substrate, is the substrate more or less difficult to move to the transition state?
What about when the enzyme fits well with the transition state?
More difficult because the substrate is stabilized
The substrate is destabilized and catalysis readily proceeds
Fig 6-6 shows how the binding energy (ΔGB) lowers the activation energy.
The free energy released by the formation of weak interactions between E and S in the transition states partially offsets the __ energy for the reaction
Activation energy
Binding energy also gives an enzyme its ______ for a particular substrate
Specificity
Enzymes tend to be large. Why?
They provide functional groups located in specific positions to maximize multiple weak interactions in the transition state.
The binding energy holds substrates in the proper orientation to react. This lowers the ____
entropy
Enzyme-substrate interactions replace virtually all of the ______ bonds between the substrate and water
H-bonds
Binding energy compensates kinetically or thermodynamically for the electron redistribution the substrate undergoes in order to react?
Thermodynamically
Binding energy may be used to cause a conformation change in the enzyme itself when the substrate binds. This is called an ___
It changes the alignment of specific ___ groups
It also is important in the formation of additional ______ interactions in the transition state
Induced fit
Functional
Weak interactions
Additional catalytic mechanisms involve transient ____ interactions with a substrate or group transfer to or from a substrate
Covalent
Different from the weak contributions found with the binding energy just discussed
When there is no catalyst present, unstable, charged intermediates formed in many biochemical reactions tend to break down immediately to form reactants (and products will not be formed)
These charged intermediates can be stabilized by _____ to form a species that breaks down readily to products (instead of reactants)
Proton transfer
This is acid-base catalysis that uses only the H+ or OH- ions present in water
This is acid-base catalysis of proton transfers facilitated by other classes of molecules
Specific Acid-Base catalysis
General Acid-Base Catalysis
For nonenzymatic reactions in aqueous solutions, weak organic acids or bases can be proton _____ in addition to water
Donors
In an enzyme’s active site, amino acid side chains can act as proton ____ and _____
Rate enhancements of ___ to ___ are observed
donors and acceptors
10^2 to 10^5
________ are the most common biochemical reactions
Proton transfers
This type of catalysis involves the formation of a transient covalent bond between an enzyme and substrate
In the uncatalyzed hydrolysis of an A-B bond
In the presence of a covalent catalyst (an enzyme with nucleophile X)
Covalent Catalysis
?
?
Catalysis occurs when the newer pathway has a HIGHER/LOWER energy than the uncatalyzed reaction
Where do the nucleophiles come from?
Lower
AA side chains
Functional groups of some enzyme cofactors
This type of catalysis is ionic interactions between an enzyme bound metal and a substrate
It can orient the ___ for reaction
Or stabilize the ____
Metal Ion Catalysis
Substrate
Transition state
Metals are involved in ______ reactions
about 1/3 of all known enzymes require metal ions for activity
Oxidation/reduction
In sum, most enzymes use a combination of catalytic strategies or one catalytic strategy?
What two processes does chemotrypsin use?
A combination
Covalent and general acid-base catalysis
