Lecture 9 Flashcards
(21 cards)
What is an enzyme?
An enzyme is a biological catalyst that speeds up a chemical reaction by lowering activation energy (ΔG‡) without being consumed in the reaction.
How do enzymes affect the Gibbs free energy (Delta G) of a reaction?
Enzymes do not affect DeltaG (the overall thermodynamics) but only lower the activation energy (Delta G‡) to speed up reaction rates.
What are the three fundamental questions of enzyme-catalyzed reactions?
Thermodynamics – What direction is favored?
Structural Changes – What happens to molecular bonds?
Kinetics – How fast does the reaction proceed?
What are the six major catalytic mechanisms enzymes use to speed up reactions?
1.Proximity & Orientation – Brings reactants close together in the right orientation.
2.Substrate Distortion – Strains bonds to favor reaction.
3.Electrostatic Catalysis – Stabilizes charge buildup in transition state.
4.Metal Ion Catalysis – Uses metal ions (e.g., Zn²⁺) to stabilize charges.
5.General Acid-Base Catalysis – Transfers protons to stabilize intermediates.
6.Covalent Catalysis – Forms temporary enzyme-substrate covalent bonds.
What are the two main models of enzyme-substrate interaction?
1.Lock and Key Model – Substrate fits perfectly into the enzyme like a key in a lock.
2.Induced Fit Model – The enzyme changes shape to accommodate the substrate.
Which model better explains enzyme catalysis?
The induced fit model, because it explains how enzymes stabilize the transition state to enhance the reaction.
What are the three key residues in the catalytic triad of serine proteases?
- Serine (Ser-195) – Acts as a nucleophile.
- Histidine (His-57) – General acid/base catalysis.
- Aspartate (Asp-102) – Stabilizes histidine via electrostatic interactions.
What catalytic mechanisms do serine proteases use?
Covalent Catalysis – Serine forms an acyl-enzyme intermediate.
General Acid-Base Catalysis – Histidine donates/accepts protons.
Electrostatic Catalysis – The oxyanion hole stabilizes the transition state.
How do acid proteases cleave peptide bonds?
They use two aspartic acid (Asp) residues to activate water for hydrolysis.
How do HIV protease inhibitors work?
Drugs like lopinavir & ritonavir bind to the active site, blocking substrate access and preventing viral maturation.
How do metalloproteases catalyze peptide bond hydrolysis?
They use Zn²⁺ to generate a strong nucleophile (OH⁻) that attacks the peptide bond.
What is the role of Glu-270 in carboxypeptidase A?
Acts as a general base catalyst to activate water and as a general acid catalyst to break the peptide bond.
What is the Michaelis-Menten equation?
v = (Vmax[S])/(Km + [S])
v = reaction velocity
Vmax = maximum reaction velocity
Km = Michaelis constant (substrate concentration at v = 1/2 Vmax)
What does a low Km indicate?
High enzyme-substrate affinity (less substrate needed to reach 1/2Vmax).
What is the steady-state assumption in Michaelis-Menten kinetics?
The concentration of the enzyme-substrate complex ([ES]) remains constant over the reaction.
What is kcat (turnover number)?
kcat = Vmax/[E]total
The number of substrate molecules converted to product per enzyme per second under saturation.
What is enzyme efficiency?
Measured by kcat/Km – the higher this value, the more efficient the enzyme.
What is a Lineweaver-Burk plot?
A double-reciprocal transformation of Michaelis-Menten:
1/v = (Km/Vmax[S]) + (1/Vmax)
Slope = Km / Vmax
Y-intercept = 1/Vmax
X-intercept = -1/Km
How do Michaelis-Menten and Lineweaver-Burk plots differ?
Michaelis-Menten Plot → Hyperbolic curve.
Lineweaver-Burk Plot → Linear plot (easier to estimate Km & Vmax).
What are the six major types of enzyme regulation?
- Zymogen Activation – Irreversible cleavage (e.g., chymotrypsinogen → chymotrypsin).
- Covalent Inhibition – Irreversible inhibitors (e.g., serpins blocking proteases).
- Reversible Phosphorylation – Kinases add phosphates, phosphatases remove them.
- Allosteric Regulation – Effectors bind to sites other than the active site.
- Modulator Protein Binding – Regulatory proteins influence enzyme activity.
- Targeted Degradation – Enzymes are broken down when no longer needed.
How does phosphorylation activate enzymes?
Adding a phosphate group induces conformational changes, activating or deactivating the enzyme.
