Lecture 5: Introduction to Enzymes Flashcards
Collision Theory:
states that chemical reactions can occur when atoms, ions and molecules collide
Activation Energy
- energy needed to initiate a chemical reaction
- disrupts electronic configurations (to initiate the reaction)
Reaction rates
- the frequencies of collisions with sufficient energy to make chemical reactions occur
- can be increased by enzymes or by supplying thermal energy or pressure
- enzymes lower the activation energy but DO NOTalter their free energy changes
What happens to the delta G in an enzymatic reaction
it DOES NOT change!
Enzymes alter the activation energy only
Acceleration of chemical reaction by enzyme
A reaction could take years to happen (or basically never seem to happen)
an enzyme makes it occur within minutes or seconds
enzymes as biological catalysts
- each is specific for a biological reaction
- they act on specific molecules at the beginning of the reaction (substrates) and convert them into products
- turnover rate of 1 - 10,000 molecules/second –> but can be evern higher
Enzyme specificity
- there is usually only one enzyme for one reaction
lots of enzymes!
Importance of cofactors
- enzymes are proteins but many need nonprotein components (inorganic or organic) for catalytic activity
Definitiions of enzyme parts and cofactors
apoenzyme: protein part of the enzyme without cofactor
cofactor: prosthetic groups (tightly bound to an enzyme) or coenzymes (released from the enzymes active site during the reaction)
holoenzyme: apoenzyme + cofactor
apoenzyme
protein portion of an enzyme
inactove
cofactor
non-protein portion of an enzyme
activator
holoenzyme
whole enzyme
active
coenzyme
- small organiz molecules that transport chemical groups from one enzyme to another
- some are dietary precursors or vitamins (cannot be made in the body and must be acquired from diet, deficiency leads to disease)
- chemically altered as a consequence of enzyme action (usually due to group transfer)
Important thermodynamic properties of enzymatic reactions
* reaction is likely exergonic (- delta G), if it is endergonic (+ delta G) it mnust be coupled with an exergonic one
- free energy change between the products and reactants
- energy required to initiate the conversion of reactants into products (activation energy, Ea)
Free energy change, delta G
(+, -, 0 ?)
- reaction occurs spontaneously if its free energy change is negative
–> exergonic reaction = - delta G
–> endergonic - + delta G –> requires input of free energy
- system is at equilibrium if delta G = 0
* depends only on the free energy of the products (final state) and free energy of the reactants (initial state)
Delta G Equation for
A + B <–> C + D
Delta G0= standard free energy change
(delta G when each of reactants and products is at 1M)
R = 8.314 j/(mol x k)
T = temp in kelvin
use each concentration of reactants and products
delta G0 at equilibrium
K eq =
delta G = G0 + RT ln ([C][D]/[A][B])
0 = G0 + RT ln ([C][D]/[A][B])
G0 = - RT ln ([C][D]/[A][B])
- G0 / RT = ln ([C][D]/[A][B])
*10 to the power of each side
k eq= [C][D] / [A][B]
What do different Keq values mean
- “large” or positive exponents –> products favored, exergonic
- “small” or negative exponents –> reactants favored, endergonic
How do enzymes interact with equilibrium?
- they do not alter the equilibrium itself but alter its rate
- they lower the difference in free energy between the transition state and the substrate and thus facilitate the formation of the transition state
Enzyme effect on Ea and transition state?
- lower the energy required to get to the transition state
overall delta G of the reaction is UNCHANGED
enzyme substrate complex
- when enzymes come together with a substrate and promote the formation of the transition state
- substrate binds to active site on enzyme
How do enzymes lower activation energies?
- orient substrates correctly
- strain the substrate bonds (more easily broken)
- provide favorable microenvironment
- bond the substrate
*physically modify substrate
Lock and key model
- NOT accurate
- fits perfectly together from start
induced fit model
- ACCURATE
- more like a handshake
- enzyme and substrate come together and alter shape a little to fit
General enzyme mechanism
- substrate binds to active site
- enzyme facilitates the reaction
- product is released
- enzyme is NOT permanently changed and is recycled
- continues to react with other substrate molecules
What “shape” does the enzyme fit?
- the transition state
- when substrate first comes into contact it does not fit well
- enzyme then adjusts it/forces it to fit –> puts it in transition state
- then it is easier to break etc
Classifications of enzymes
- oxidoreductases
- transferases
- hydrolases
- lysases
- isomerases
- ligases
oxidoreductases
ox/red reactions
transferases
transfer of functional groups
hydrolases
hydrolysis reactions
lysases
group elimination to form double bonds
isomerases
isomerization
ligases
bond formation couples with ATP hydrolysis
michaelis menten model (process of reaction)
E + S <–> ES <–> E + P
enzyme + substrate
Ensyme substrate complex
Enzyme + product
* first step can be reversed
* second unlikely to reverse
behavior of mechaelis menten curve
- substrate is added to an enzyme, the reaction rapidly achieves steady state in which the rate at which the ES forms balances the rate at which it breaks fdown (fast at first, then slows to the max velocity)
- as substrate concentration increases, the steady state activity of a fixed conc of enzyme increases in a hyperbolic fashion to approach Vmax (max velocity) at which all the enzyme has formed a complex with the substrate
Km
substrate concentration that results in a reaction rate equal to one half of Vmax
- considered “when enzyme is wokring well”
- V0 and Vmax doesnt really show this (they are extremes)
- Vmax/2 is like the average between the two
michaelis menten equation
uses Km relate the initial velocity to the substrate conc [S] and Vmax
Initial velocity and substrate conc
The greater the concentration the greater the initial velocity
Vmax
Km is the [S] that yields a velocity of 1/2 Vmax
When [S] = Km then V0 = Vmax/2
Vmax is approached asymtotically
Lineweaver burke plot
- double reciprocal presentation of the michaelis mentedn equation
- y intercept is 1/Vmax
- x intercept is -1/Km
- slope = Km/Vmax
Lineweaver buke equation
Catalytic efficiency
Kcat = equivalent to the number of substrate molecules converted to product in a given unit of time on a single enzyme molecule when it is saturated with substrate
Kcat = Vmax /[ET}
ET = total enzyme concentration
* looks at saturated conditions
Catalytic efficiency equation
V0 = [ET] [S] Kcat /Km
when [S] is << Km the concentration of free enzyme is nearly equal to ET
Kcat/Km are limited by the rate E and S can diffuse togeher in an aq solution
Catalytic perfection
- Kcat/Km is around 108 or 109
- rate at which Enzyme and substrate can diffuse together in aqueaous solution
- about as fast as the two could come together
