Unit 4: Enzymes — Catalysis and Kinetics
How a protein bends the odds of a reaction, measures its own speed limit, and gets throttled by inhibitors and feedback.
10 topics · 35 questions
Each topic is a path, not a menu: work down it in order and every question builds on the one above. Click any of them to watch the answer draw itself.
Activation Energy and the Transition State
- How it worksHow does a reaction have to climb over an energy barrier at its transition state before it can reach its products?
- Common mistakeWhy doesn't a reaction's activation energy tell you anything about whether the reaction is spontaneous?
- Going furtherWhat happens to a reaction's rate when its activation energy barrier gets lowered?
Your turn1 of 2
A reaction has a large negative delta G, strongly favorable overall, but also a large activation energy barrier. A student argues that because the reaction is so thermodynamically favorable, its activation energy must be low too, since a strongly downhill reaction should have an easy path to get there. Why is this reasoning wrong?How an Active Site Stabilizes the Transition State
- How it worksHow does an enzyme's active site bind the transition state more tightly than it binds the substrate itself?
- How it worksWalk me through how straining a bound substrate toward its transition-state shape lowers the energy needed to react.
- Common mistakeWhy doesn't an enzyme speed up a reaction by adding energy to the molecules reacting?
- Going furtherWhat happens to an enzyme's rate enhancement when a mutation weakens its grip on the transition state specifically?
Your turn1 of 2
An enzyme binds its substrate only moderately well, yet it binds the fleeting, high-energy transition state of that substrate far more tightly. A student assumes tighter binding to the transition state must be a side effect with no real bearing on catalysis. Why does this tighter binding actually matter?Enzyme Specificity: Lock-and-Key Versus Induced Fit
- How it worksHow does an enzyme's active site reshape itself around a substrate in the induced-fit model?
- Common mistakeWhy isn't the lock-and-key model actually how most enzymes recognize their substrate?
- Going furtherWhat happens to an enzyme's specificity when induced fit lets its active site flex around several closely related substrates?
Your turn1 of 2
The lock-and-key model pictures an enzyme's active site as a rigid shape that a substrate simply drops into, unchanged, like a key into a lock. A student assumes this rigid picture is how most real enzymes actually recognize their substrates. What does the more accurate induced-fit model say instead?Cofactors and Coenzymes
- How it worksHow does a metal ion cofactor sitting in an active site help stabilize a build-up of negative charge during catalysis?
- Going furtherWhat happens to an enzyme's activity when its dietary vitamin-derived coenzyme runs short?
- Ties togetherHow does an enzyme's coenzyme rely on the same molecular-recognition chemistry that lets the enzyme recognize its own substrate?
Your turn1 of 2
An enzyme has a perfectly shaped active site for its substrate, yet without a small, non-protein helper molecule bound in that site, it catalyzes nothing at all. A student assumes an active site's shape alone should be enough for catalysis, since it already fits the substrate. Why might a cofactor still be essential?Michaelis-Menten Kinetics
- How it worksHow does an enzyme-substrate complex forming and breaking apart give rise to the Michaelis-Menten rate equation?
- Worked exampleFind the reaction velocity of an enzyme with a Vmax of 100 micromolar per minute and a Km of 5 millimolar at a substrate concentration of 5 millimolar.
- Common mistakeWhy doesn't an enzyme's rate keep climbing forever as you add more and more substrate?
- Going furtherWhat happens to an enzyme's velocity curve when you double the amount of enzyme in the reaction?
Your turn1 of 2
An enzyme has a Vmax of 137 micromolar per minute and a Km of 10 millimolar. Find its reaction velocity at a substrate concentration of 28 millimolar.Km and Vmax: What They Actually Measure
- How it worksHow does Km capture both how tightly an enzyme grips its substrate and how fast it lets the substrate go?
- Worked exampleFind the substrate concentration needed to reach 90 percent of Vmax for an enzyme with a Km of 2 millimolar.
- Common mistakeWhy isn't a low Km the same thing as a fast enzyme?
Your turn1 of 2
An enzyme has a Km of 7 millimolar. Find the substrate concentration needed to reach 79 percent of Vmax.Lineweaver-Burk Double-Reciprocal Plots
- How it worksHow does taking the reciprocal of both sides of the Michaelis-Menten equation turn a curve into a straight line?
- Worked exampleFind the y-intercept and x-intercept of a Lineweaver-Burk plot for an enzyme with a Vmax of 20 micromolar per minute and a Km of 4 millimolar.
- Going furtherWhat happens to a Lineweaver-Burk plot's slope and intercepts once the enzyme is mixed with a competitive inhibitor?
Your turn1 of 2
Find the y-intercept of a Lineweaver-Burk plot for an enzyme with a Vmax of 45 micromolar per minute.Competitive Inhibition
- How it worksHow does a competitive inhibitor block an enzyme by physically occupying the same active site as its normal substrate?
- Common mistakeWhy doesn't a competitive inhibitor change an enzyme's actual maximum speed, Vmax?
- Going furtherWhat happens to an enzyme's apparent Km when a competitive inhibitor gets added to the reaction?
- Ties togetherHow does an HIV protease inhibitor drug use the same competitive-inhibition chemistry as any molecule that merely resembles the natural substrate?
Your turn1 of 2
A competitive inhibitor raises an enzyme's apparent Km by a factor of 6.03 while Vmax stays unchanged. If the enzyme's true Km is 7 millimolar, find its apparent Km with the inhibitor present.Noncompetitive Inhibition
- How it worksHow does a noncompetitive inhibitor bind a site away from the active site and still shut catalysis down?
- Worked exampleFind an enzyme's apparent Vmax once a noncompetitive inhibitor cuts its uninhibited Vmax of 80 micromolar per minute in half.
- Common mistakeWhy doesn't adding more substrate reverse the effect of a noncompetitive inhibitor?
- Going furtherWhat happens to an enzyme's Lineweaver-Burk plot when a noncompetitive inhibitor is added instead of a competitive one?
Your turn1 of 2
A noncompetitive inhibitor cuts an enzyme's uninhibited Vmax of 114 micromolar per minute down to a fraction of 0.589 of its original value. Find the new apparent Vmax.Allosteric Regulation and Feedback Inhibition
- How it worksHow does an allosteric inhibitor binding away from the active site push an enzyme toward its low-activity shape?
- How it worksWalk me through how phosphorylating an enzyme can flip it between an active and an inactive conformation.
- Going furtherWhat happens to a whole metabolic pathway's output when its feedback-inhibited enzyme gets a mutation that blocks the regulatory site?
- Common mistakeWhy isn't allosteric feedback inhibition the same mechanism as competitive inhibition at the active site?
Your turn1 of 2
A ten-step metabolic pathway builds up its final product, and that final product then binds and shuts off the very first enzyme in the pathway, far upstream. A student assumes this must be wasteful, since the first enzyme is not directly involved in making the final product. Why is shutting off the first enzyme actually an efficient strategy?