LSM2106 Chap.5 Forms and Functions of Enzymes
Forms and Functions of Enzymes
What a catalyst does, and the three claims it cannot support
The fifth lecture turns to enzymes. A catalyst raises the rate at which a reaction approaches equilibrium. It does not move the equilibrium, it does not supply free energy, and it emerges from the reaction unchanged.
Most wrong answers on this topic assert one of those three, so holding them as explicit negatives is more useful than any definition.
The mechanism is transition-state stabilisation. A reaction passes through an arrangement of higher free energy than either reactant or product, and the rate depends on how many molecules reach it.
Lowering the energy of that arrangement raises the rate in both directions by the same factor, which is exactly why the equilibrium position is untouched.
An active site achieves it through four separable jobs: binding the substrate in a pocket complementary in shape and charge, orienting two substrates so that the reacting groups meet correctly, holding the transition state more tightly than the substrate, and supplying chemistry through side chains or a bound partner.
Specificity falls out of the first two, since a molecule bound at the wrong angle reacts slowly even when it is bound at all.
Partners, and the conditions under which activity is lost
Side chains supply acids, bases and nucleophiles but cannot carry electrons or one-carbon units, so enzymes needing those recruit a non-protein partner.
A cofactor is any such component, including a metal ion; a coenzyme is an organic one, and a loosely bound coenzyme released each cycle behaves as a co-substrate rather than as part of the enzyme. This course meets one such pair repeatedly, because its oxidised and reduced forms differ optically and the third practical is built on that difference.
The course materials note that many dehydrogenases linked to these carriers can be followed spectrophotometrically, and that enzymes without a convenient signal of their own can be measured by coupling their products to a reaction that such an enzyme catalyses.
Activity falls away on both sides of an optimum, and the two declines are different in kind.
Rising temperature increases rate until the non-covalent interactions holding the fold begin to fail, after which activity is lost because protein is lost, and cooling does not restore it. A narrow pH optimum instead implies ionisable groups that must be in particular protonation states, so activity returns when the pH does.
Naming which of the two a described profile shows, and saying that reversibility is the test, is what these questions are marked on.
What this chapter covers
- 01
Rate, equilibrium and the three properties a catalyst does not change
- 02
Transition-state stabilisation as the source of the rate increase
- 03
The four jobs of an active site and where specificity comes from
- 04
Cofactors, coenzymes and the co-substrate behaviour of a loosely bound carrier
- 05
Coupled assays and the condition that keeps them interpretable
- 06
Temperature and pH optima, and reversibility as the test that separates them
Separating a chemical effect from a structural one
- 2Account for the rising part of the temperature curve.
- 2Account for the fall, and say what is lost.
- 2Explain the narrow pH peak in terms of ionisable groups.
Key terms
- Transition state
- The highest-energy arrangement a reacting system passes through. An enzyme binds it more tightly than the substrate, which is what lowers the barrier.
- Activation barrier
- The free energy difference between reactant and transition state. It controls rate, and lowering it speeds forward and reverse reactions equally.
- Active site
- The pocket that binds substrate, orients it, stabilises the transition state and supplies catalytic chemistry from side chains or a bound partner.
- Cofactor
- Any non-protein component an enzyme requires for activity, including metal ions as well as organic molecules.
- Coenzyme
- An organic cofactor. When it binds loosely and is released after each cycle it behaves as a co-substrate rather than as a permanent part of the enzyme.
- Coupled assay
- Measurement of an enzyme with no convenient optical signal by joining its product to a second reaction that produces one, with the second reaction run in excess.
Forms and Functions of Enzymes FAQ
Does adding more enzyme shift the position of equilibrium?
No. A catalyst lowers the activation barrier for the forward and reverse directions by the same amount, so both rates rise by the same factor and the ratio at which they balance is unchanged. Adding enzyme to a mixture already at equilibrium produces no visible change at all; the activity would only show as a faster return to equilibrium after a disturbance.
What actually distinguishes a cofactor from a coenzyme?
A cofactor is the broader category and covers anything non-protein the enzyme needs, metal ions included. A coenzyme is specifically an organic cofactor. The further distinction worth making is how tightly it binds: one that stays attached through many cycles is part of the enzyme, while one released each cycle is consumed and replaced like a substrate.
Why must the second enzyme in a coupled assay be present in excess?
Because the assay reports the slowest step. If the coupling enzyme is not fast enough to consume the first product as it appears, the measured rate becomes a property of the coupling reaction rather than of the enzyme under study. Adding more of the coupling enzyme until the measured rate stops changing is the usual check.
Exam move
Write the three negatives about what a catalyst does not change on the first page of your notes and check every answer against them. Then rehearse the temperature and pH profiles as a pair, since questions almost always present one and expect you to distinguish it from the other. Finish by sketching a coupled assay and marking which reaction must be rate-limiting.
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