Chapter 7 Flashcards
Apoenzyme
The protein portion, without its cofactors
Holoenzyme
An enzyme containing all its cofactors
Cofactors
Metal ions - inorganic
Coenzymes - organic
Prosthetic group
A cofactor which is covalently bound to the enzyme
Active site micro-environment contribution to catalysis:
Exclude excess water
Provide optimal orientation
Binding interactions between the substrate and the enzyme to create a transition state
Presence of catalytic functional groups
Michaelis-Menten assumptions
The concentration of ES is relatively constant after the initial reaction time.
The reaction must be considered early, before any appreciable amount of product has been generated.
The product release is a rapid step in the process.
Velocity of a rxn in relation to the rate constant
v = k[S]
What AA’s are phosphorylated by kinases?
Serine, Threonine, and Tyrosine
For competitive inhibitors
vmax remains the same, but Km increases
For uncompetitive inhibitors
vmax and Km decrease
For mixed inhibitors
decrease vmax, but can increase or decrease Km
For noncompetitive inhibitors
decrease vmax, but has no effect on Km
How to determine equation for no inhibition
It will have the lowest slope and y-intercept
Turn over number
Kcat.. Use this EQ to solve for it
Vmax = Kcat [E]t
Catalytic efficiency
aka specificity constant
Kcat/Km
High Km
Low affinity
Low Km
High affinity
two models to explain how the binding of
enzyme and substrate occurs
Lock and Key
Induced Fit
Substrate AKA
Reactant
Lock and Key Model
Substrate fits perfectly with the enzyme
Induced Fit Model
Enzyme is flexible to accommodate the ill fitting
substrate
Permits a much larger number of weaker
interactions between the substrate and enzyme
EX of an induced fit mechanism
Hexokinase
Critical Aspects of Enzyme Structure and Function
Enzymes bind to substrates with high affinity and
specificity
Substrate binding to the active site induces
changes in the enzyme
Enzyme activity is highly regulated in cells
Active sites AKA
Binding pockets
Modes of enzyme regulation
Bioavailability: Amount of enzyme
present in the cell
Catalytic efficiency: Quantitative measure of
enzyme activity
Organic catalysts vs enzymes
catalysts speed up reactions but not as fast as enzymes
Enzymes are highly specific where as catalysts are not
Enzymes alter the rates of reaction without changing
the ratio of:
substrates and products at equilibrium
6 Major groups of enzymes:
Oxidoreducatase Transferase Hydrolase Lyase Isomerase Ligase
Oxidoreducatase
Oxidation/reduction, Transfer of H or O atoms
Transferase
Transfer of functional group
Hydrolase
Formation of two products by hydrolyzing the substrate
Lyase
Cleavage of C-C, C-O and C-N and other bonds by means other than hydrolysis or oxidation
Isomerase
Intramolecular rearrangements, transfer of groups with in a molecule
Ligase
Formation on C-C, C-O, C-S and C-N bonds using ATP cleavage
3 ways enzymes increase the rate of a reaction:
They lower the activation energy by stabilizing the
transition state
They provide an alternate path for product
formation
They reduce entropy by orienting the substrates
appropriately for the reaction to occur
Physical and Chemical Properties of Active Sites
Hydrophobic regions and charged regions
Enzymes decrease the ____ of the reaction
Δ𝐺‡
Michaelis-Menten constant
Km = (k-1 + k2) / k1
Describes rates of breakdown and formation of ES
Catalytic efficiency of an enzyme is regulated by:
reversible and irreversible inhibition, allosteric
control, covalent modification, and proteolytic
processing
Reversible inhibition
Noncovalent bonding
Includes: Competitive, uncompetitive and mixed
Can be decreased by diluting the enzyme reaction
Irreversible inhibition
forms a covalent bond or very strong non-covalent bond
“suicide inhibitors” kill the enzyme
Not affected by enzyme dilution
Diisopropylfluorophosphate an example of:
Irreversible Inhibitor
Blocks protease and phospholipase enzymes
A Reversible Inhibitor ex
Malonate
Competes with succinate to bind to the active
site of succinate dehydrogenase
Type of inhibition that can be overcome by increasing [S]
Competitive
Competitive inhibition:
E + S –> E S –> E +P
II
EI
Uncompetitive inhibition:
E + S –> E S –> E +P
……………..II
……………..ESI
Mixed inhibition:
How do you know is it is noncompetitive or not?
E + S –> E S –> E +P
II…………..II
EI………….ESI
Ki = Ki’
Ki = K-i / Ki Ki' = K-i' = Ki'
EX of competitive inhibition:
Saquinavir
An HIV protease inhibitor
Mimics the natural Phe-Pro dipeptide substrate
Fxn of Saquinavir
HIV protease essential for processing of proteins in virus.
Without these proteins, viable viruses can not be released to cause further infection
Uncompetitive inhibitors bind to the:
enzyme-substrate complex and alters the active site conformation
Mixed inhibitors bind to sites unique from the _____
active site
Kcat =
K2
How do enzymes fxn so efficiently?
When S binds to active site on E they make and ES complex, While in the transition state, binding occurs which allows S to interacting with different AA’s in the active site, during these small weak interactions, energy is released, and it accumulates to make “binding energy” which is used to lower Ea
K(t)
Ae^(-Ea/Rt)
If Ea goes down, K(t) goes up which means Rate goes up!
Ea is the same as
Δ𝐺‡
