Edited by simon
2025-12-04 03:22 · Updated content
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Enzymes & Chemical Reactions in Biology
Catalysts • Activation Energy • Substrates • Products • Yeast Examples • Microscopy Limits
Enzymes are essential for life. They make chemical reactions fast enough to sustain metabolism, growth, DNA replication, signaling, and every biological process.
This page introduces what enzymes are, how they work, what factors affect their activity, and why they are crucial in organisms like yeast and onion cells.
1. What Are Enzymes?
Enzymes are biological catalysts — proteins (and a few RNAs) that speed up chemical reactions without being consumed.
They:
- reduce activation energy
- increase reaction speed by up to 10⁶–10¹⁵ times
- are highly specific (each enzyme performs one reaction)
- are essential for all cellular processes
Without enzymes, nearly all reactions in the cell would occur far too slowly to support life.
2. How Enzymes Work
2.1. Substrate → Product
Enzymes bind specific molecules called substrates, convert them to products, and release them.
Example:
Sucrase converts sucrose → glucose + fructose.
2.2. Active Site
The active site is the region where:
- substrate binds
- reaction occurs
- products form
Active sites have precise shapes, charges, and chemical environments.
2.3. Lock-and-Key vs. Induced Fit
Two classic models:
Lock-and-Key
Substrate fits perfectly into enzyme.
Induced Fit
Enzyme changes shape slightly when substrate binds — more accurate model.
3. What Enzymes Do in Cells
Everything.
Here are major classes of enzyme functions:
1) Metabolism
- glycolysis (hexokinase, pyruvate kinase)
- fermentation (alcohol dehydrogenase)
- respiration (mitochondrial enzymes)
2) DNA & RNA Processing
- DNA polymerase
- RNA polymerase
- helicases
- ligases
3) Protein Processing
- proteases
- chaperones (folding helpers)
4) Membrane Transport
Pump enzymes like:
- ATP synthase
- proton pumps (H⁺-ATPase)
5) Cell Signaling
Kinases & phosphatases:
- add/remove phosphate groups
- regulate pathways like TOR, AMPK, MAPK
4. Enzymes in Yeast
Yeast enzymes are some of the most studied in biology.
4.1. Fermentation enzymes
- Pyruvate decarboxylase
- Alcohol dehydrogenase
These convert sugars → ethanol + CO₂.
4.2. TOR pathway enzymes
Regulate growth, aging, and nutrient sensing.
4.3. SIR2 (yeast sirtuin)
Important for chromatin stability and longevity.
4.4. Mitochondrial enzymes
Involved in respiration and ROS regulation.
4.5. Cell cycle enzymes
Cyclins and CDKs control budding and division.
5. Enzymes in Plant Cells (e.g., Onion)
Onion cells contain enzymes for:
- cell wall construction (cellulases, pectinases)
- metabolism
- stress response
- DNA/RNA synthesis
- antioxidant defense (catalase, peroxidases)
These are not visible, but their effects shape the cell.
6. Factors That Affect Enzyme Activity
6.1. Temperature
- Too low → slow
- Optimal → fast
- Too high → denatured (unfolded)
Yeast enzymes work best at 30°C.
6.2. pH
Each enzyme has an optimal pH.
Examples:
- stomach enzymes: pH 2
- yeast cytoplasm: pH ~7
6.3. Substrate concentration
More substrate → faster reaction (until enzyme saturation).
6.4. Enzyme concentration
More enzyme → faster reaction.
6.5. Inhibitors
Reduce enzyme activity.
Types:
- competitive
- noncompetitive
- allosteric regulators
6.6. Cofactors and Coenzymes
Some enzymes require:
- metal ions (Mg²⁺, Zn²⁺)
- vitamins (NAD⁺, FAD, biotin)
NAD⁺ is crucial for yeast SIR2 (aging enzyme).
7. Enzyme Kinetics (Simplified)
Basic reaction rate relationship:
Rate = Vmax [S] / (Km + [S])
Where:
- Vmax = maximum rate
- Km = affinity of enzyme for substrate
- [S] = substrate concentration
You don’t need the math to do experiments, but the concepts are useful.
8. Can You See Enzymes Under a Microscope?
No.
Enzymes are tiny — around 3–10 nm, far below the 200 nm resolution limit of optical microscopes.
Visible only indirectly:
- bubbling from yeast fermentation (CO₂ from enzymes)
- budding rate (enzyme-regulated metabolism)
- onion plasmolysis (transport proteins + enzymes)
- color changes in reactions (with indicators)
To see enzymes directly, you need:
- X-ray crystallography
- electron microscopy
- fluorescence tagging
- cryo-EM
None of these are possible with a standard light microscope.
9. Everyday Examples of Enzymes
9.1. In your kitchen
- yeast fermentation → bread rising
- lactase in lactose-free milk
- amylase in saliva (breaks starch)
9.2. In your body
- DNA polymerase copying your DNA right now
- ATP synthase making ATP in your mitochondria
- digestive enzymes breaking food
- catalase removing hydrogen peroxide
9.3. In your home lab
- yeast transforming glucose into ethanol
- peroxidase in plants (visible with chemical tests)
- enzymes degrading onion tissue during preparation
10. Summary Table: Types of Enzymes
| Enzyme Type | Function | Example | Visible Under Microscope? |
|---|---|---|---|
| Metabolic | ATP production | Hexokinase | No |
| Polymerases | DNA/RNA synthesis | DNA polymerase | No |
| Proteases | Protein degradation | Trypsin | No |
| Kinases | Add phosphates | MAPK | No |
| Phosphatases | Remove phosphates | PP2A | No |
| Synthases | Build molecules | ATP synthase | No |
| Isomerases | Rearrange atoms | PPIase | No |
| Dehydrogenases | Oxidation/reduction | Alcohol dehydrogenase | No |
11. Quick Beginner Summary
- Enzymes are protein catalysts that speed up reactions.
- They bind substrates at the active site and convert them to products.
- Temperature, pH, and concentration affect activity.
- Yeast rely heavily on enzymes for fermentation and aging pathways.
- Enzymes are too small to see under optical microscopes; only their effects are visible.
- Nearly every cellular process depends on enzymes — metabolism, DNA replication, signaling, stress response, and growth.