Enzymes & Catalysis – Key Concepts

Enzyme = biological catalyst.
- Catalyst definition
- Speeds a reaction (increases rate constant k).
- Not consumed during the reaction cycle (can be reused indefinitely).
- Analogy: A factory machine stamping envelopes; it would be pointless if the machine self-destructed after one envelope.
Enzymes solve all three roadblocks in one stroke:
1. Lower the activation energy \left(\Delta G^\ddagger\right), increasing speed.
2. Possess a highly structured active site ⇒ same product every cycle.
3. Are expressed only in required tissues, compartments, or moments, keeping chemistry confined.
Naming convention: Most enzyme names end with “-ase” (lactase, protease, DNA-polymerase, etc.).

Enzymes can drive a reaction that is possible in principle but too slow or energetically uphill.
- If external energy is supplied (e.g.
  ATP hydrolysis, coupled redox), the car can be "pushed uphill".
They cannot force a reaction that violates the laws of chemistry/physics.
- Car metaphor:
- Gravity will let a car roll downhill (spontaneous).
- You can fuel the car to drive uphill (non-spontaneous but feasible).
- You cannot make the car sprout wings and fly (chemically impossible).

Enzymes are substrate-specific.
- Example: Lactase hydrolyzes only lactose, not glucose or sucrose.
Complex pathways use multiple sequential enzymes, much like an automobile assembly line:
1. Frame
2. Seats
3. Body panels
4. Engine …
- Each “station” ≡ separate enzyme performing one precise transformation.
Environmental narrowness
- Optimal pH, temperature, ionic milieu differ per enzyme (e.g.
  pepsin works at stomach pH \approx 2; trypsin at intestinal pH \approx 8).

Active Site
- 3-D pocket where the chemistry actually happens.
- Substrate(s) bind via complementary shape & charge.
Induced-Fit Model
- Binding is dynamic: enzyme and substrate mutually distort to achieve a snug, reaction-ready alignment.

Anabolic (Synthetic) Reactions
- Problem: Two molecules rarely collide in perfect orientation.
- Solution: Enzyme binds both, holding them with complementary charges ((+ / -)) so they are pre-aligned ⇒ faster bond formation.
Catabolic (Degradative) Reactions
- Analogy: Snapping a stick across a fulcrum.
- Enzyme provides "leverage"—applies strain at the exact bond to be broken, lowering the energy barrier for cleavage.

Apoenzyme = protein portion alone (inactive).
- Story: Campus bought microscopes with European plugs—useless until adapters arrived.
Cofactor = non-protein helper that completes the enzyme.
- Two classes
1. Coenzymes (organic) → almost always vitamins or their derivatives.
  - Examples: B-vitamins, folate, vitamin C.
2. Inorganic ions → minerals (Fe$^{2+}$, Zn$^{2+}$, Mg$^{2+}$, Cl$^-\,$…).
Holoenzyme = apoenzyme + required cofactor(s) ⇒ fully functional catalyst.
Key physiological examples
- Hemoglobin needs Fe$^{2+}$ as its mineral cofactor; iron deficiency ⇒ anemia, ↓O$_2$ transport.
- Vitamin C is a coenzyme for collagen biosynthesis; deficiency ⇒ scurvy (weak connective tissue).

Nutritional deficiencies (vitamin or mineral) manifest as enzyme malfunctions, not merely “missing nutrients.”
Drug design & toxicology exploit enzymatic specificity—e.g.
ACE inhibitors block one enzyme in renin–angiotensin cascade, lowering blood pressure but (ideally) sparing others.
Enzyme localization explains tissue vulnerability:
- Pancreatic leaks release proteases, digesting self-tissue ⇒ pancreatitis.
- Genetic absence of lactase causes lactose intolerance—undigested lactose ferments in the colon, causing cramps and gas.

Transit time for hemoglobin O$_2$ loading/unloading: 0.25\,\text{s}.
Activation energy symbol: \Delta G^\ddagger.
Enzyme + Cofactor equation: \text{Apoenzyme} + \text{Cofactor} \longrightarrow \text{Holoenzyme}.