How is Km determined in an enzymatic reaction?
Draw the Michaelis-Menten reaction scheme. Identify the rate determining step and explain how the step is limiting. What kind of binding takes place during this step? Why is this beneficial?
Define KM using rate constants. Does a high KM refer to strong or weak binding?
How is Vmax determined in an enzymatic reaction?
How would one increase Vmax? Include the appropriate equation.
What is kcat? How is kcat determined in an enzymatic reaction? (with Vmax and enzyme concentration) How is kcat determined when substrate concentration is exceedingly low?
Draw an energy diagram demonstrating the energetic changes in an enzymatic reaction. Label completely. What does an enzyme do?
Draw a Michaelis-Menten Curve. What is the general shape? Identify where on the curve the reaction is first order and zero order. What does that mean?
Aspartate transcarbamoylase is an enzyme regulated through allosteric activators and inhibitors. The reaction below provides a brief overview of the role aspartate transcarbamoylase plays in the synthesis of pyrimidine trinucleotides.
What molecule represents the allosteric inhibitor? What happens when this molecule interacts with the enzyme? Where does it bind?
When the allosteric inhibitor binds, how does it affect KM and Vmax?
The introduction of an unknown molecule causes a change in substrate specificity, but does not appreciably change the maximum initial rate of production. Draw a Michaelis-Menten Curve demonstrating these changes. What kind of inhibitor is the molecule? Describe the inhibitor with respect to the intended substrate.
What causes this behavior? Be sure to include details regarding its shape and substrate specificity. Draw the corresponding Michaelis-Menten reaction scheme.
Draw the corresponding Lineweaver-Burk Plot with and without the inhibitor.
Pyruvate is converted into lactate when a cell is immersed in an anaerobic environment.
Is pyruvate being oxidized or reduced?
Nicotinamide adenine dinucleotide is the coenzyme used in this reaction. Is it being oxidized or reduced in this reaction? Why? What classification of enzyme is at work?
Draw the coenzyme as it appears as a reactant in the reaction above. What type of coenzyme is it (cosubstrate or prosthetic group)?
Enolpyruvate is converted to phosphoenolpyruvate through the reaction below:
Draw the adenine version of the trinucleotide required as a reactant.
What type of coenzyme is it (cosubstrate or prosthetic group)? What is the classification of enzyme used to facilitate this reaction?
What classification of enzyme facilitates the following reaction? Why?
a) Draw the three amino acids required to facilitate the catalytic triad reaction in a serine protease.
b) Draw a peptide molecule interacting with the catalytic triad appropriately.
c) Circle the attacking species (nucleophile) and draw an arrow to the site of nucleophilic attack.
d) Place a box around the residue responsible for acid-base catalysis. How is it used as a acid? How is it used as a base?
e) What is the oxyanion hole? What does it do? How does it affect the energy diagram?
f) What classification of enzyme is a serine protease? Where does the relevant compound come into the mechanism?
Draw a phosphatidylcholine glycerophospholipid with a C18:3 Δ9,12,15 at A1 and a C16 Δ5 at A2.
Show (in the structure above) which bond a A2 phospholipase would break. What classification of enzyme is this?
Draw a phosphatidylethanolamine glycerophospholipid attached to a trans, cis-Δ10,13-hexadecanoate at the A1 position and a cis,cis-Δ9-dodecadoate at the A2 position.
Show (in the structure above) which bond a A1 phospholipase would break.
Label each of the following: