Enzymes and Metabolism

🟢 Lite — Quick Review (1h–1d)

Rapid summary of enzymes and metabolism for NABTEB biology.

Enzymes are biological catalysts — proteins that speed up chemical reactions without being used up in the process.

Key Properties of Enzymes:

• Catalyst: Speeds up reactions without being consumed
• Specific: Each enzyme acts on a specific substrate (lock and key model)
• Reusable: Enzymes are not used up in reactions
• Efficient: Can increase reaction rates by millions of times
• Temperature sensitive: Work best at optimal temperature (37°C for human enzymes)
• pH sensitive: Work best at optimal pH (pepsin: pH 2, trypsin: pH 8)

Enzyme Terms:

Term	Definition
Substrate	The molecule the enzyme acts upon
Active site	Region on enzyme where substrate binds
Product	The molecule(s) produced by the reaction
Denaturation	Loss of enzyme shape due to heat or extreme pH

Mechanism — Lock and Key Model:

• The enzyme’s active site has a specific shape
• Only the correct substrate can fit (like a key in a lock)
• The substrate binds, forming an enzyme-substrate complex
• The reaction occurs, products are released
• The enzyme is free to catalyse another reaction

Factors Affecting Enzyme Activity:

1. Temperature:

   • Below optimum: molecules move slowly, few collisions
   • At optimum: maximum activity (37°C for human enzymes)
   • Above optimum: enzyme denatures (permanent shape loss)

2. pH: Each enzyme has an optimum pH. Extreme pH causes denaturation.

3. Substrate concentration: Rate increases until all active sites are occupied (saturation)

4. Enzyme concentration: Rate increases proportionally (more active sites available)

5. Inhibitors: Substances that reduce enzyme activity

⚡ NABTEB Exam Tip: Competitive inhibitors compete with the substrate for the active site — increasing substrate concentration can overcome this. Non-competitive inhibitors bind elsewhere (allosteric site) and change the enzyme’s shape — increasing substrate concentration does NOT overcome this.

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🟡 Standard — Regular Study (2d–2mo)

For NABTEB students who want thorough understanding of enzymes.

Types of Enzyme Inhibition:

1. Competitive Inhibition:

• Inhibitor resembles substrate
• Competes for active site
• Can be overcome by increasing substrate concentration
• Example: Statins (cholesterol-lowering drugs) inhibit HMG-CoA reductase

2. Non-competitive Inhibition:

• Inhibitor binds to a site other than the active site (allosteric site)
• Changes enzyme shape, making active site less effective
• Cannot be overcome by increasing substrate
• Example: Cyanide inhibits cytochrome oxidase (stops cellular respiration)

3. Feedback Inhibition:

• End product of a metabolic pathway inhibits an earlier enzyme
• Prevents over-production of the end product
• Example: Isoleucine inhibits threonine deaminase (first enzyme in its own synthesis pathway)

Metabolism:

Metabolism = all chemical reactions in an organism (anabolism + catabolism)

Anabolism: Building up — synthesis of complex molecules from simpler ones

• Requires energy (endergonic)
• Examples: Photosynthesis, protein synthesis, glycogen synthesis

Catabolism: Breaking down — complex molecules broken into simpler ones

• Releases energy (exergonic)
• Examples: Cellular respiration, digestion, protein breakdown

Endoenzyme vs Exoenzyme:

Type	Description	Example
Endoenzyme	Secreted to act within the cell	Digestive enzymes in cytoplasm
Exoenzyme	Secreted outside the cell to act externally	Amylase (digests starch outside cell)

Co-factors and Prosthetic Groups:

Many enzymes require non-protein helpers:

• Co-factors: Metal ions (e.g., Zn²⁺, Mg²⁺, Fe²⁺) or organic molecules (coenzymes)
• Coenzymes: Organic molecules that carry specific atoms or groups (e.g., NAD⁺, FAD, Coenzyme A)
• Prosthetic groups: Permanently attached cofactors (e.g., haem in haemoglobin)

Vitamins as Enzyme Cofactors:

Vitamin	Coenzyme Form	Function
B1 (Thiamine)	Thiamine pyrophosphate	Decarboxylation
B2 (Riboflavin)	FAD, FMN	Electron carrier
B3 (Niacin)	NAD⁺	Hydrogen carrier
B5 (Pantothenic acid)	Coenzyme A	Acetyl group transfer
B6 (Pyridoxine)	Pyridoxal phosphate	Amino group transfer
B12 (Cobalamin)	Methylcobalamin	Methyl group transfer
C (Ascorbic acid)	—	Hydroxylation reactions

⚡ NABTEB Exam Tip: Enzyme names often end in “-ase” and indicate the substrate they act on:

• Amylase acts on amylose (starch)
• Lipase acts on lipids
• Protease acts on proteins
• Trypsin acts on proteins in the small intestine
• Pepsin acts on proteins in the stomach

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🔴 Extended — Deep Study (3mo+)

Comprehensive coverage of enzymes and metabolism for thorough NABTEB preparation.

The Induced-Fit Model:

More accurate than lock and key — the enzyme’s active site is not rigid:

1. Substrate approaches enzyme
2. Enzyme’s active site adjusts to fit the substrate perfectly (induced fit)
3. Enzyme-substrate complex forms
4. Reaction occurs
5. Products are released
6. Enzyme returns to original shape

This model explains why enzymes are so specific and efficient.

Enzyme Kinetics — Michaelis-Menten:

The rate of an enzyme-catalysed reaction follows this pattern: $$v = \frac{V_{\max}[S]}{K_m + [S]}$$

Where:

• $v$ = reaction rate
• $V_{\max}$ = maximum rate (all active sites occupied)
• $[S]$ = substrate concentration
• $K_m$ = Michaelis constant (substrate concentration at which $v = V_{\max}/2$)

Effects of Inhibitors on Kinetics:

Inhibitor Type	Effect on $V_{\max}$	Effect on $K_m$
Competitive	Unchanged	Increased
Non-competitive	Decreased	Unchanged

Mechanism of Catalysis:

Enzymes speed up reactions by:

1. Lowering activation energy: Reducing the energy barrier
2. Orientating substrates: Bringing reacting molecules together in the right orientation
3. Straining bonds: Distorting the substrate molecule
4. Providing alternative pathways: Creating a lower-energy reaction route

Metabolic Pathways:

Chemical reactions in cells are organised into pathways:

Example: Glycolysis Glucose → Glucose-6-phosphate → Fructose-6-phosphate → … → Pyruvate (Each step catalysed by a different enzyme)

Metabolic Co-factors:

NAD⁺ (Nicotinamide adenine dinucleotide):

• Carries hydrogen atoms (2H) from one reaction to another
• NAD⁺ + 2H → NADH + H⁺
• Used in: glycolysis, Krebs cycle, fermentation

FAD (Flavin adenine dinucleotide):

• Similar to NAD⁺ but carries 2H from one specific reaction
• FAD → FADH₂ → used in electron transport chain

ATP as Energy Currency:

Adenosine triphosphate stores and transfers chemical energy: $$ATP \rightarrow ADP + P_i + \text{energy}$$ $$ADP + P_i + \text{energy} \rightarrow ATP$$

ATP is:

• Generated in mitochondria (cellular respiration) and chloroplasts (photosynthesis)
• Used for: muscle contraction, active transport, biosynthesis, cell division
• Not stored in large amounts — must be regenerated continuously

Photosynthesis (Anabolism): $$6CO_2 + 6H_2O \xrightarrow{\text{light}} C_6H_{12}O_6 + 6O_2$$

• Light reactions: Occur in thylakoid membranes; produce ATP and NADPH; split water, release O₂
• Calvin cycle: Occurs in stroma; uses ATP and NADPH to fix CO₂ into glucose

Chemosynthesis: Some bacteria obtain energy from inorganic molecules: $$\text{Nitrifying bacteria: } NH_3 + O_2 \rightarrow HNO_2 + H_2O + \text{energy}$$ Energy is used to synthesise organic compounds from CO₂

Enzyme Cofactors — Detailed Roles:

Cofactor	Function	Deficiency
Iron (Fe²⁺/Fe³⁺)	Part of haem; electron transport	Anaemia
Zinc (Zn²⁺)	Carbonic anhydrase; stabilise protein structure	Growth retardation
Magnesium (Mg²⁺)	Chlorophyll; ATP activation	Muscle weakness
Manganese (Mn²⁺)	Photosynthetic oxygen evolution	Bone abnormalities
Copper (Cu²⁺)	Cytochrome oxidase; electron transport	Anaemia, neurological problems
Selenium (Se)	Glutathione peroxidase (antioxidant)	Muscle disorders

⚡ NABTEB Quick Reference:

• Enzymes: protein catalysts; speed up reactions; not consumed
• Lock and key / Induced-fit model: substrate fits active site
• Denaturation: heat or extreme pH destroys enzyme shape
• Competitive inhibitor: competes at active site; overcome by more substrate
• Non-competitive inhibitor: binds elsewhere; cannot be overcome
• Anabolism: building up; requires energy
• Catabolism: breaking down; releases energy
• $K_m$: substrate concentration at half $V_{\max}$
• Coenzymes: NAD⁺, FAD, CoA carry atoms/groups
• Vitamins: precursors to coenzymes
• ATP: cell’s energy currency
• Photosynthesis: anabolism; $6CO_2 + 6H_2O \rightarrow C_6H_{12}O_6 + 6O_2$
• Temperature: enzymes denature above optimum