Module 6, L2 Flashcards
What are the most common types of reaction mechanisms?
- Acid/Base– most common
- Covalent/nucleophilic reaction
- Metal catalysis
- Reaction by proximity
What is the importance of the Michaelis-Menten constant?
The michaelis-menten constant shows us the binding affinity of an enzyme to a substrate, where a low Km illustrates tighter binding/higher affinity.
What is the Lineweaver-Burke Plot most useful for?
It is most useful for calculating the Vmax and Km of an enzyme.
What type of inhibitor would be the best competitive inhibitor?
One that will mimic the transition state structure will be the best competitive inhibitor since it will have the tightest binding.
What is acid/base reaction mechanism?
This mechanism involves protons being extracted or donated. Includes:
- General base Catalysis: extracts protons– glutamate, aspartate and histidine
- General acid catalysis: donates protons– histidine, glutamic acids and aspartic acid
Ex: Asp 102 function as general base to remove proton from Hist 57, then His 57 is a general base to remove proton on Ser 195 so it can function as nucleophile.
What is covalent/nucleophilic reaction mechanism?
Covelent reaction is a nucleophilic attack from an electron rich nucelophile to an electron deficient center
Nucelophiles= O-, Nitrogen and sulfur
Electrophiles= Carbonyl and phosphate centers (most common), metals, and protons
What is metal catalysis reaction mechanism?
Metals in the active site activate or lower the pKa of water so it becomes a strong base (commonly Zn and Mg)
Ex: Carbonic anhydrase allows zinc to attack/activate water. This molecule can then attack CO2 where Zn stabilizes the intermediate via electrostatic interactions.
What is reaction by proximity reaction mechanism?
involves enzyme binding two substrates, their closeness to eachother and exclusion of water is what facilitates the reaction.
Ex: Kinases catalyze phosphate transfer this way, the kinase sequesters substrate and ATP, preventing simple hydrolysis of ATP.
What is the Michaelis-Menten Equation/curve? Know what the variables stand for!
The Michaelis-Menten Equation/curve shows the rate of enzymes and how tightly bound they are to a substrate.
- The curve is hyperbolic where the steepness indicates tightness of binding to substrates and plateau is the maximum velocity of the enzyme (Vmax)
- K1= rate of formation of ES
- K2= K-1= breakdown of ES (Enzyme + Product)
- Vmax= [E] * K2 * [Substrate]
What is the one thing that the Michaelis-Menten Equation/curve can’t solve for and why?
B/c Vmax is never really attained, it is difficut to find the Km based on the Michaelis-Menten equation/curve.
What is the Lineweaver-Burke plot and how is it different/similar to Michaelis-Menten equation/curve?
Lineweaver-Burke plot is similar to Michaelis-Menten, but it is the double reciprocal of the Michaelis-Menten curve
- on the graph when it crosses the Y-axis = 1/Vmax
- when it crosses the X-axis= -1/Km
What is the Lineweaver-Burke plot useful for?
it is useful to determine Vmax and Km as well as determining enzyme inhibitor type
List the different types of inhibitors
- Competitive inhibitor
- Uncompetitive inhibitor
- Noncompetitive inhibitor
What is competitive inhibition and how does it look on a graph? How is Km and Vmzx affected?
Competitive inhibition is where inhibitor binds to active site and will directly compete with substrate.
- It can resemble the reactant, product or transition state intermediate
- When this inhibitor is present the Km is shifted to the right, meaning the Km INCREASES
- Vmax is unaffected as increasing substrate can allow the reaction to be catalyzed– SO the inhibited plot and uninhibited plot will intersect at y-axis
What is uncompetitive inhibition and how does it look on a graph? How is Km and Vmax affected?
Uncompetitive inhibitors binds to the ES complex to form an ESI complex, by binding to the adjacent site.
- When plotted in Line-weaver Burke plot, the line is to the left and parallel to no-inhibitor line; therefore, both Km and Vmax DECREASES
