Lecture 7: Enzymes Flashcards
Enzyme
Biocatalyst which speeds up a reaction without being changed. Has specificity and high catalytic power, accelerating reactions by a factor of 10^6 or more.
Cofactor
Small nonprotein molecule that binds and facilitates enzyme activity
Holoenzyme
Enzyme with its cofactor; active state
Apoenzyme
Enzyme without its cofactor; inactive state
What are examples of inorganic cofactors?
Metal ions (Mg2+, Zn2+, K+, etc.)
What are the types of organic cofactors?
Organic cofactors (aka coenzymes):
1. Co-substrates
2. Prosthetic groups
Co-substrate
Type of organic cofactor which binds loosely and is changed by the reaction (e.g. NAD+/NADH)
Prosthetic group
Organic cofactor which binds tightly and covalently, is not changed by the reaction (e.g. biotin)
Enzyme specificity factors and degrees
Enzymes catalyze 1 reaction or a set of closely related reactions, differing in degree of substrate specificity. Specificity is due to precise substrate interaction with the enzyme’s 3D structure.
How do enzymes function?
Enzymes lower activation energy of a reaction, providing an alternative kinetically advantageous path.
Where on the enzyme does catalysis occur? How?
The active site brings substrates/cofactors/enzyme close together in favorable orientations.
Equation for free energy in nonstandard conditions
ΔG = ΔGo’ + RT ln([products]/[reactants])
How does ΔG describe spontaneity?
ΔG < 0 for spontaneous, exergonic reactions
ΔG = 0 at equilibrium
ΔG > 0 for non-spontaneous endergonic reactions
Induced fit model
Induced fit says that the enzyme and substrate induce small conformational changes in each other to create an ideal catalytic fit. This explains both specificity and transition state stabilization, unlike the older rigid lock and key model.
Catalytic strategies for enzymes
- Binding energy of ES complex
- Covalent catalysis
- General acid-base catalysis
- Catalysis by approximation
- Metal ion catalysis
Binding energy of ES complex
Many weak interactions form between enzyme and substrate, releasing free energy (binding energy) used to facilitate formation of the transition state for maximum interactions, lowering the activation energy.
Covalent catalysis
Transient covalent bond forms between enzyme and substrate to catalyze reaction, usually involving nucleophilic attack
General acid-base catalysis
A non-H2O molecule acts as a proton donor/acceptor in catalysis
Catalysis by approximation
The enzyme aligns reactants and holds them together; proximity and orientation facilitates the reaction
Metal ion catalysis
Metal ions can:
1. Promote nucleophile formation
2. Act as electrophiles to stabilize negative charges on intermediates
3. Serve as enzyme-substrate bridges`
ΔG vs ΔGo’ or ΔGo at physiological concentrations
At nonequilibrium conditions, ΔG can be a different sign than ΔGo’; this is the basis for coupling reactions. If K’ < Keq, ΔG < 0.
How does reaction rate change based on changes in activation energy?
Small changes in the activation energy cause relatively very large changes in the overall reaction rate, e.g. an 80% (5X) decrease in activation energy causes a >100,000X increase in reaction speed
Free energy equation at standard conditions
ΔGo’ = -RT ln(Keq’)
