Chapter 5: Metabolism and Enzymes

Learning Objectives

By the end of this chapter, you should be able to:

• Define metabolism and differentiate between anabolism and catabolism
• Explain the characteristics and mechanisms of enzyme action
• Identify factors that affect enzyme activity
• Understand the relationship between enzyme structure and function
• Apply enzyme knowledge to practical biological applications

Overview

Metabolism refers to all the biochemical reactions that occur within living organisms to maintain life. These reactions are catalyzed by enzymes, which are biological catalysts that speed up reactions without being consumed. Understanding metabolism and enzymes is crucial for comprehending how organisms obtain energy, build molecules, and maintain homeostasis.

Metabolism: The Biochemical Basis of Life

Definition and Scope

Metabolism is the sum of all biochemical reactions that occur in an organism to:

• Obtain energy from nutrients
• Synthesize necessary molecules
• Eliminate waste products
• Maintain cellular conditions

Anabolism vs. Catabolism

Metabolic pathways can be broadly classified into two categories:

Metabolic Pathways

Key Characteristics:

• Sequential: Reactions occur in specific sequences
• Enzyme-mediated: Each step catalyzed by specific enzymes
• Regulated: Controlled by feedback mechanisms
• Interconnected: Pathways often share intermediates

Major Metabolic Pathways:

1. Glycolysis: Breakdown of glucose to pyruvate

$$C_6H_{12}O_6 + 2ADP + 2P_i + 2NAD^+ \rightarrow 2CH_3COCOO^- + 2ATP + 2NADH + 2H^+$$

2. Citric Acid Cycle: Complete oxidation of acetyl-CoA

$$CH_3COCOO^- + 3NAD^+ + FAD + GDP + P_i \rightarrow 2CO_2 + 3NADH + FADH_2 + GTP$$

3. Oxidative Phosphorylation: ATP production

$$ADP + P_i \rightarrow ATP \quad (\text{using energy from } NADH \text{ and } FADH_2)$$

4. Photosynthesis: Carbon fixation and sugar synthesis

$$6CO_2 + 6H_2O + \text{light} \xrightarrow{\text{chlorophyll}} C_6H_{12}O_6 + 6O_2$$

5. Protein Synthesis: Assembly of amino acids into proteins

$$\text{Amino acids} + ATP \rightarrow \text{Proteins} + ADP + P_i$$

Did You Know? The human body carries out thousands of metabolic reactions simultaneously, all coordinated and regulated by enzymes. The metabolic rate can vary from about 70 watts (at rest) to over 2,000 watts (during intense exercise)!

Enzymes: Biological Catalysts

Characteristics of Enzymes

Enzymes are proteins (except for ribozymes, which are RNA-based) that catalyze biochemical reactions. Key characteristics include:

Enzyme Nomenclature

Naming Conventions:

• Most enzyme names end with -ase
• Often named after their substrate or reaction type
• Examples:
  • Lipase: Breaks down lipids
  • Protease: Breaks down proteins
  • Amylase: Breaks down starch
  • Catalase: Breaks down hydrogen peroxide

Enzyme Structure

Hierarchical Organization:

1. Primary Structure: Amino acid sequence
2. Secondary Structure: α-helices, β-sheets
3. Tertiary Structure: Overall 3D folding
4. Quaternary Structure: Multiple subunits (if applicable)

Active Site:

• Specific region where substrate binds
• Has complementary shape to substrate (lock-and-key model)
• Contains amino acids essential for catalysis

Mechanisms of Enzyme Action

The Lock-and-Key Model

Proposed by Emil Fischer in 1894:

• Enzyme active site is rigid and complementary to substrate
• Substrate fits perfectly into active site like key into lock
• Product formed and released
• Limitation: Doesn't explain enzyme flexibility

The Induced Fit Model

More accurate modern understanding:

• Active site is flexible and changes shape when substrate binds
• Conformational change enhances catalysis
• Better explains enzyme specificity and regulation

Enzyme-Substrate Complex Formation:

1. Substrate binding: Substrate approaches active site
2. Induced fit: Active site changes shape to bind substrate
3. Catalysis: Chemical reaction occurs
4. Product release: Products dissociate from active site
5. Enzyme regeneration: Enzyme returns to original conformation

Factors Affecting Enzyme Activity

Temperature Effects

Optimum Temperature: Temperature at which enzyme activity is maximum

Temperature Adaptation:

• Human enzymes: Optimum ~37°C (body temperature)
• Thermophilic bacteria: Optimum ~70-80°C (hot springs)
• Psychrophilic organisms: Optimum ~0-10°C (cold environments)

pH Effects

Optimum pH: pH at which enzyme activity is maximum

pH Examples in Human Body:

• Pepsin (stomach): Optimum pH ~2
• Trypsin (intestines): Optimum pH ~8
• Blood enzymes: Optimum pH ~7.4

Substrate Concentration Effects

Michaelis-Menten Kinetics:

• Low substrate: Activity increases linearly with concentration
• High substrate: Activity plateaus (enzyme saturation)
• Vmax: Maximum reaction rate when all enzyme active sites are occupied
• Km: Substrate concentration at half Vmax (measure of enzyme affinity)

Michaelis-Menten Equation:

$$v = \frac{V_{max}[S]}{K_m + [S]}$$

Where:

• $v$ = initial reaction velocity
• $V_{max}$ = maximum reaction velocity
• $[S]$ = substrate concentration
• $K_m$ = Michaelis constant

Enzyme Concentration Effects

Direct Relationship:

• At constant substrate concentration, reaction rate increases with enzyme concentration
• Linear relationship until substrate becomes limiting

Inhibitor Effects

Types of Inhibition:

Enzyme Regulation and Control

Allosteric Regulation

Mechanism: Molecules bind to allosteric sites (not active sites) causing conformational changes

Characteristics:

• Can be inhibitory or activating
• Allows for fine-tuning of metabolic pathways
• Important in feedback inhibition

Feedback Inhibition

Mechanism: End product of pathway inhibits an early enzyme

• Purpose: Prevents overproduction of metabolites
• Example: ATP inhibits phosphofructokinase in glycolysis

Coenzyme and Cofactor Requirements

Coenzymes: Organic molecules required for enzyme activity

• Examples: NAD⁺, FAD, coenzyme A
• Often act as carriers of electrons or chemical groups
• Formula examples: NAD⁺ + 2H → NADH + H⁺

Cofactors: Inorganic molecules required for enzyme activity

• Examples: M$g^2$⁺, Z$n^2$⁺, F$e^2$⁺
• Often act as enzyme activators
• Important for metalloenzymes

SPM Exam Tip: When explaining enzyme inhibition, always distinguish between competitive and non-competitive inhibition. Competitive inhibition can be overcome by increasing substrate concentration, while non-competitive cannot. This is a common exam question!

Practical Applications of Enzymes

Industrial Applications

Food Industry:

• Pectinases: Fruit juice clarification
• Amylases: Bread making, syrup production
• Proteases: Cheese production, meat tenderizing

Detergents:

• Proteases: Remove protein stains
• Lipases: Remove fat stains
• Amylases: Remove carbohydrate stains

Medical Applications:

• Diagnostic tests: Enzyme-linked assays
• Therapeutic enzymes: Streptokinase (clot dissolution)
• Drug development: Enzyme inhibitors as medications

Enzyme Technology

Immobilized Enzymes:

• Enzymes attached to solid supports
• Advantages: Reusability, stability, continuous production
• Applications: Biosensors, bioreactors

Enzyme Engineering:

• Protein engineering to improve enzyme properties
• Applications: Thermostable enzymes, specific catalysts

Laboratory Investigation of Enzymes

Catalase Experiment

Materials: Liver extract, hydrogen peroxide, test tubes Procedure:

1. Add liver extract to $H_2O_2$ solution
2. Measure oxygen production (bubbling)
3. Test effects of temperature, pH, inhibitors

Expected Results:

• Positive control: Rapid bubbling (oxygen production)
• Temperature effects: Reduced activity at extreme temperatures
• pH effects: Reduced activity at non-optimal pH

Catalase Reaction:

$$2H_2O_2 \xrightarrow{\text{catalase}} 2H_2O + O_2$$

Amylase Investigation

Materials: Amylase solution, starch solution, iodine Procedure:

1. Mix amylase with starch at different temperatures
2. At intervals, test for starch with iodine
3. Measure starch breakdown rate

Measurement: Color change from blue-black (starch present) to brown (starch absent)

Amylase Reaction:

$$(C_6H_{10}O_5)_n + nH_2O \xrightarrow{\text{amylase}} nC_6H_{12}O_6$$

Practice Tips for SPM Students

Key Concepts to Master

1. Metabolic pathways: Understand anabolism vs. catabolism
2. Enzyme characteristics: Catalytic nature, specificity, denaturation
3. Factors affecting enzymes: Temperature, pH, concentration, inhibitors
4. Regulation mechanisms: Feedback inhibition, allosteric control

Experimental Skills

1. Design enzyme experiments with controlled variables
2. Interpret enzyme kinetics graphs (Michaelis-Menten)
3. Calculate reaction rates from experimental data
4. Identify independent and dependent variables in enzyme studies

Problem-Solving Strategies

1. Graph analysis: Understand Vmax, Km, and their changes with inhibitors
2. Experimental design: Identify controlled variables and expected outcomes
3. Application questions: Relate enzyme knowledge to real-world scenarios

Environmental and Health Connections

Enzyme Deficiencies

• Phenylketonuria (PKU): Missing enzyme for phenylalanine metabolism
• Lactose intolerance: Deficiency in lactase enzyme
• Albinism: Deficiency in tyrosinase enzyme

Environmental Impact on Enzymes

• Temperature changes affect enzyme activity in climate change scenarios
• Pollutants can inhibit enzymes in aquatic organisms
• pH changes due to acid rain affect enzyme function

Medical Applications

• Drug design: Many drugs target specific enzymes
• Diagnostic tests: Enzyme levels indicate disease states
• Enzyme replacement therapy: Treatment for genetic disorders

Summary

• Metabolism encompasses all biochemical reactions in living organisms
• Anabolism builds complex molecules using energy
• Catabolism breaks down molecules to release energy
• Enzymes are biological catalysts that speed up metabolic reactions
• Enzyme activity is affected by temperature, pH, substrate concentration, and inhibitors
• Understanding enzymes is essential for medicine, industry, and biotechnology

Related Topics

• Chapter 3: Movement of Substances Across Plasma Membrane
• Chapter 4: Chemical Composition in Cells
• Chapter 6: Cell Division
• Chapter 9: Nutrition and the Human Digestive System