Enzyme Catalysis
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73 Terms
What is the range of catalytic power of enzymes?
10^4 to 10^17
What do enzymes stabilize to lower activation energy?
Transition State
How does proximity help catalysis?
enzymes hold substrate close to functional groups of enzyme (substrate or cofactor)
Why does increasing effective concentration increase reaction rate?
substrates collide more often
How does orientation help catalysis?
Enzymes align substrates in the optimal position for reaction
How does orientation increase enzyme activity?
reduces random movement and positions
What provides the energy needed to orient substrates?
binding energy of substrate to enzyme
What two things increase reaction rate?
Proximity + Orientation
What are the four major enzyme catalytic strategies?
Electrostatic, Acid-base, Covalent, Metal Ion
What is the main purpose of electrostatic catalysis?
Stabilize charges that develop in the transition state
What type of charge does the transition state usually have?
Usually negative (anionic), but sometimes positive (cationic)
Why are electrostatic interactions stronger inside enzyme active sites?
active site has a low dielectric constant because water is excluded
How does a low dielectric constant affect catalysis?
It strengthens charge interactions and stabilizes the transition state
How does transition state stabilization affect activation energy?
lowers it
What molecule acts as the catalyst in specific acid catalysis?
H+
What determines the rate of specific acid catalysis?
pH
How do you increase reaction rate in Specific Acid Catalysis?
lower pH
Does buffer concentration affect specific acid catalysis?
No, only pH matters
What molecule acts as the catalyst in specific base catalysis?
OH-
What determines the rate of specific base catalysis?
pH
How do you increase reaction rate in Specific Base Catalysis?
increase pH
Does buffer concentration affect specific base catalysis?
No
What is general acid catalysis?
A weak acid partially donates a proton to the substrate to stabilize the transition state
What determines the rate of general acid catalysis at constant pH?
Weak acid concentration
What is general base catalysis?
A weak base partially removes a proton from the substrate to lower activation energy
What determines the rate of general base catalysis at constant pH?
Weak base concentration
What is the difference between specific and general acid catalysis?
Specific uses H⁺ only; general uses a weak acid
What is the difference between specific and general base catalysis?
Specific uses OH⁻ only; general uses a weak base
In General Catalysis, what increases the rxn rate?
increasing buffer
Why is uncatalyzed keto-enol tautomerization slow?
The transition state develops high-energy carbanion character
How does general acid catalysis help keto-enol tautomerization?
Proton donation reduces carbanion character and stabilizes the transition state
How does general base catalysis help keto-enol tautomerization?
Proton abstraction helps delocalize negative charge
Why is concerted general acid-base catalysis more effective?
removes AND donates protons, stabilizing TS
What form must a general base be in to function?
deprotonated
When is a general base inactive?
at a pH below pKa
What form must a general acid be in to function?
protonated
When is a general base inactive?
at a pH above pKa
When does an enzyme using both general acid and base catalysis have maximum activity?
above GB pKa and below GA pKa
What type of catalysis does RNase A use?
Concerted general acid-base catalysis
What is RNase A’s function?
Digests RNA into nucleotides
What amino acid acts as the general base in RNase A?
His-12
What does His-12 do in RNase A?
Removes a proton from the 2'-OH group
What amino acid acts as the general acid in RNase A?
His-119
What does His-119 do in RNase A?
Donates a proton to the leaving group
What intermediate forms during RNase A catalysis?
2’,3’-cyclic intermediate
What is covalent catalysis?
Formation of a temporary covalent bond between enzyme and substrate
What is another name for covalent catalysis?
Nucleophilic catalysis
What type of reaction usually forms enzyme-substrate covalent intermediates?
Nucleophilic substitution reactions
What must the enzyme nucleophile be compared to the substrate nucleophile?
A better nucleophile
What must the enzyme leaving group be compared to the substrate leaving group?
A better leaving group
Which amino acids can act as nucleophiles in covalent catalysis?
Lys, Arg, Asp, Glu, Ser, Thr, Tyr, His, Cys
What is a Schiff base?
An imine bond formed when an amine attacks a carbonyl
What amino acid usually forms Schiff bases?
Lysine
What are the steps of Schiff base catalysis?
Nucleophilic attack by amine
Electron withdrawal by protonated imine
Water attack releases enzyme
What is a metalloenzyme?
An enzyme that binds a metal cofactor tightly
What is a metal-activated enzyme?
An enzyme that binds a metal weakly
Why are metals good electrophilic catalysts?
They stabilize developing negative charges
How do metals activate water molecules?
They increase water acidity, allowing hydroxide formation at physiological pH
Why do metals function in redox reactions?
multiple oxidation states
What reaction does carbonic anhydrase catalyze?
CO2 + H2O → HCO3-
Where is carbonic anhydrase found in high concentration?
red blood cells
What metal does carbonic anhydrase use?
Zn2+
How is Zn²⁺ coordinated in carbonic anhydrase?
3 His and 1 H2O
How does Zn²⁺ activate water?
polarizes water and lowers its pKa from 14 to 7
Why is lowering water’s pKa important?
allows formation of Zn-OH, a strong nucleophile
What attacks CO₂ in carbonic anhydrase?
Zn-OH
What is the role of His-64 in carbonic anhydrase?
transfers/removes protons to regenerate the active Zn-OH⁻ form
Which catalytic mechanism involves transition state charge stabilization?
Electrostatic catalysis
Which catalytic mechanism forms a temporary enzyme-substrate bond?
Covalent catalysis
Which catalytic mechanism uses proton transfer?
Acid-base catalysis
Which catalytic mechanism uses cofactors like Zn²⁺?
Metal ion catalysis
What is the most important target of enzyme stabilization?
Transition state
Does substrate binding alone explain enzyme catalysis?
No. Enzymes must stabilize the transition state and provide catalytic mechanisms.