Enzymes: Functions and Kinetics Flashcards
Define a catalyst
A catalyst lowers the activation energy of a reaction and, most importantly, is regenerated at the end of the reaction. It is in the products and the reactants.
Indicate the main function of enzymes.
The main function of an enzyme is to lower the activation energy of a reaction. It facilitates the chemical reaction by increasing the rate. Enzymes ONLY act on the kinetics NOT the thermodynamics. They also tend to be very specific in terms of what they bind to.
Define ΔG and indicate when this term predicts a spontaneous chemical reaction with the release of energy.
ΔG is defined as the change in Gibbs Free Energy for a reaction. ΔG = Gproducts - Greactants - ΔG indicates a spontaneous reaction with the release of energy
Indicate whether or not ΔG predicts the rate of the reaction.
NO! Spontaneity has nothing to do with the rate or kinetics. It refers to the thermodynamics of the reaction.
Draw the graph showing how G changes during a chemical reaction in the absence of a catalyst.
Define “transition state” and draw on the graph the ΔG of activation and the ΔG of reaction for an uncatalyzed reaction.
Transition State: In going from substrate to product, there is a large increase in G. This corresponds to the formation of a high energy intermediate that involves unfavorable changes in the bond angles and electron redistribution. This intermediate is referred to as the transition state. The intermediate could decay back to the reactant or proceed forward to product. If the reaction was uncatalyzed, very few molecules would have the energy to make it over the hump. However, enzymes stabilize the transition state and lowers its energy making the reaction possible.
Increase rate by 10^6 – 10^14 – fold.
Describe the function of the active site.
The active site serves to 1) bind substrate and 2) catalyze the chemical reaction.
Describe the type of reaction that is catalyzed by carboxypeptidase A (CPA), and indicate whether or not this reaction could occur without an enzyme.
The type of reaction that is catalyzed by carboxypeptidase A (CPA) is a degradation reaction or hydrolysis that cleaves the C-terminal end of the protein. This protein is synthesized in the pancreas and delivered to the small intestine lumen. It plays a major role in digestion. This reaction may occur without an enzyme via hydrolysis, however, it would not occur quickly enough to be useful or make the amino acids available to the body before death would result. Thus this enzyme is essential for digestion.
Describe the role of the hydrophobic pocket and the salt bridge in recognizing and binding the C-terminal residue of a peptide substrate.
The role of the hydrophobic pocket and the salt bridge is to provide specificity and orient the substrate correctly.
Explain the role of the water molecule that is bound to the active site zinc ion of CPA.
The role of the water molecule is to carry out the hydrolysis reaction.
In very general terms, explain how the zinc ion and certain amino acids in the active site can stabilize the transition state.
The amino acid Glu270 strips a hydrogen from water, creating a free hydroxyl group to attack the peptide carbonyl bond. Then, the zinc serves to bind the carbonyl’s oxygen in the peptide. Then, Glu270 transfers the proton to the NH to break the peptide bond. This shows that the whole protein or enzyme is important and that even distant amino acids in the protein help maintain a proper orientation of active site residues for stabilizing the transition state. The enzyme helps to “speed up” this reaction or in a way, force it to occur when it otherwise would not have.
Indicate whether or not enzyme amino acids located at a distance from the active site are important for substrate binding and catalysis.
They are
List the six main reaction types catalyzed by enzymes and briefly describe their functions.
- Oxidoreductase: moves electrons, hydrogens, or oxygens from one substrate to another.
- Transferases: Transfer a chemical group from one molecule to another.
- Hydrolases: Use water to cleave
- Lyases: Cleave bonds (-C-C-, -C-N-, or –C-O-) or sometimes make them (Synthase)
- Isomerases: Move a group or a double bond
- Ligases: Join atoms together, usually using ATP. (sythetases)
Induced Fit
The substrate itself can induce conformational changes. The whole protein is involved in the enzymatic reaction.
Oxidoreductase
moves electrons, hydrogens, or oxygens from one substrate to another.
Transferases
Transfer a chemical group from one molecule to another
Hydrolases
Use water to cleave
Draw a graph of the initial rate versus substrate concentration.
Write out the Michaelis-Menten equation with kcat and total enzyme concentration included.
v = kcat [Eo] [S] / Km + [S]
Correlate various regions of the Michaelis-Menten plot with simplified versions of the Michaelis-Menten equation.
Draw Michaelis-Menton plots and Lineweaver-Burk plots for enzyme alone and enzyme with a competitive inhibitor present.
Draw Michaelis-Menton plots and Lineweaver-Burk plots for enzyme alone and enzyme with a noncompetitive inhibitor present.
Discuss how the term (1 + [I]/Ki) leads mathematically to Km(apparent) or Vmax (apparent) for competitive and noncompetitive inhibitors, respectively.
This term is always going to be greater than 1 because it is “1 + x”. It leads to the apparent because it is multiplying Km by this value greater than 1 giving a higher Km for a competitive inhibitor and Vmax is divided by it giving a lower Vmax for the noncompetitive inhibitor.
