Chapter 4: Chemical Composition in a Cell

Learning Objectives

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

• Identify and describe the major chemical compounds in cells
• Understand the structure and function of different biomolecules
• Explain the relationship between chemical structure and biological function
• Analyze the importance of water in biological systems

Overview

Living cells are composed of various chemical compounds that serve specific functions. The major categories include water, carbohydrates, proteins, lipids, and nucleic acids. Each class of compounds has unique structural features that determine their biological roles. Understanding these chemical components is essential for comprehending cellular processes and life functions.

Biochemical Classification

Water: The Universal Solvent

Water Molecule Structure

Properties of Water

Water is the most abundant compound in living organisms, typically making up 70-90% of cell mass.

Chemical Properties of Water

Biological Importance of Water

1. Solvent for Biochemical Reactions

   • Dissolves nutrients and waste products
   • Facilitates enzyme-substrate interactions
   • Provides medium for metabolic processes
   • Chemical Equation: $H_2O + \text{solute} \rightarrow \text{hydrated ions}$

2. Temperature Regulation

   • High specific heat maintains stable cellular temperatures
   • Evaporation (sweating, transpiration) provides cooling
   • Heat Capacity: $C_p = 4.18 \, J/g°C$ for water

3. Transport Medium

   • Blood plasma transports nutrients and oxygen
   • Plant vascular system transports water and minerals
   • Intracellular transport of materials

4. Structural Component

   • Provides turgor pressure in plant cells
   • Maintains shape and volume of cells

Did You Know? Water molecules can form hydrogen bonds that give water many of its unique properties. These bonds are crucial for the structure of DNA and proteins!

Carbohydrates: Energy and Structure

Types of Carbohydrates

Carbohydrates are organic compounds made of carbon, hydrogen, and oxygen atoms.

Monosaccharides

Key Monosaccharides:

• Glucose: Primary energy source for cells
• Fructose: Found in fruits, sweetest natural sugar
• Galactose: Component of milk sugar (lactose)

Structural Features:

• Formula: $C_6H_{12}O_6$ (glucose example)
• Ring structure in aqueous solutions
• Can exist as D-isomers (biologically active) or L-isomers

Disaccharides

Formation: Condensation reaction removes water, forms glycosidic bonds

Polysaccharides

Storage Polysaccharides:

• Starch: Plant energy storage (amylose and amylopectin)
• Glycogen: Animal energy storage (highly branched)

Structural Polysaccharides:

• Cellulose: Plant cell walls (β-glucose chains)
• Chitin: Fungal cell walls, arthropod exoskeletons

Comparison of Polysaccharides:

Proteins: The Molecular Machines

Protein Structure

Proteins are polymers made of amino acid monomers joined by peptide bonds.

Hierarchical Structure Levels

Amino Acids

General Structure:

• Central carbon with amino group (-N$H_2$), carboxyl group (-COOH), hydrogen, and R-group
• 20 different amino acids found in proteins
• R-group determines amino acid properties

Amino Acid Classification:

• Nonpolar: Hydrophobic (e.g., alanine, valine)
• Polar: Hydrophilic (e.g., serine, threonine)
• Charged: Acidic/basic (e.g., aspartic acid, lysine)

Protein Functions

Denaturation

Process: Loss of protein's 3D structure and function Causes:

• High temperatures
• Extreme pH values
• Heavy metals
• Organic solvents

Irreversibility: Most denaturation is irreversible Example: Cooking eggs - egg white proteins denature and solidify

SPM Exam Tip: Remember that enzymes are proteins and their function depends on their 3D structure. Denaturation destroys enzyme activity - this is a common exam topic!

Lipids: Energy Storage and Membranes

Lipid Structure

Lipids are hydrophobic molecules that include fats, oils, waxes, steroids, and phospholipids.

Triglycerides (Fats and Oils)

Structure:

• Glycerol backbone + 3 fatty acids
• Ester bonds formed through condensation reactions

Types of Fatty Acids:

• Saturated: No double bonds (e.g., butter, coconut oil)
• Unsaturated: One or more double bonds (e.g., olive oil, fish oil)

Comparison:

Phospholipids

Structure: Glycerol + 2 fatty acids + phosphate group Function: Major component of cell membranes Amphipathic Nature:

• Hydrophilic head (phosphate portion)
• Hydrophobic tails (fatty acid portions)

Steroids

Structure: Four fused carbon rings Examples:

• Cholesterol: Membrane component, precursor for hormones
• Hormones: Testosterone, estrogen, cortisol
• Vitamin D: Calcium absorption

Lipid Functions

Nucleic Acids: Genetic Information

DNA (Deoxyribonucleic Acid)

Structure:

• Double helix with two antiparallel strands
• Sugar: deoxyribose
• Nitrogenous bases: Adenine (A), Thymine (T), Cytosine (C), Guanine (G)
• Base pairing: A-T, G-C Function: Stores genetic information

RNA (Ribonucleic Acid)

Structure:

• Single-stranded
• Sugar: ribose
• Nitrogenous bases: Adenine (A), Uracil (U), Cytosine (C), Guanine (G) Types and Functions:
• mRNA: Carries genetic code from DNA to ribosomes
• tRNA: Transfers amino acids during protein synthesis
• rRNA: Component of ribosomes

Genetic Code

Triplet Code: Three consecutive bases code for one amino acid Codons: mRNA triplets that specify amino acids Start/Stop Signals: AUG (start), UAA, UAG, UGA (stop)

Chemical Interactions in Cells

Bond Types in Biological Molecules

Chemical Reactions in Cells

Types of Reactions:

• Synthesis: Building complex molecules (anabolic)
• Decomposition: Breaking down molecules (catabolic)
• Exchange: Rearranging atoms
• Reversible: Can proceed in both directions

Enzyme-Catalyzed Reactions:

• Enzymes lower activation energy
• Specific to particular substrates
• Not consumed in reactions

Did You Know? A single human cell contains about 10,000 different proteins, each with a specific 3D structure and function. The diversity comes from different combinations of just 20 amino acids!

Laboratory Techniques for Chemical Analysis

Biochemical Tests

Chromatography

Principle: Separation based on solubility differences Applications:

• Separating plant pigments
• Identifying amino acids
• DNA sequencing

Practice Tips for SPM Students

Memorization Strategies

1. Create comparison tables for different biomolecule types
2. Use flashcards for amino acid structures and properties
3. Practice drawing molecular structures with proper bonding
4. Memorize test results for biochemical tests

Conceptual Understanding

1. Relate structure to function (e.g., protein 3D structure determines enzyme activity)
2. Understand hydrogen bonding in water and biomolecules
3. Apply knowledge to experimental scenarios and problem-solving

Exam Preparation

1. Focus on energy relationships between different biomolecules
2. Practice calculation problems involving concentrations and solutions
3. Review laboratory techniques and their applications

Environmental and Health Connections

Nutrition and Health

• Carbohydrate intake affects blood sugar levels
• Protein quality impacts muscle development and immune function
• Lipid types influence cardiovascular health
• Water balance affects cellular function and overall health

Environmental Impact

• Water pollution affects cellular processes in aquatic organisms
• Chemical contaminants can denature proteins and disrupt cellular functions
• Nutrient cycles involve biochemical transformations in ecosystems

Summary

• Water is essential as a solvent, temperature regulator, and transport medium
• Carbohydrates provide energy and structural support
• Proteins serve diverse functions including enzymatic, structural, and regulatory roles
• Lipids provide energy storage and form cellular membranes
• Nucleic acids store and transmit genetic information
• Understanding chemical composition is fundamental to understanding life processes

Related Topics

• Chapter 1: Introduction to Biology
• Chapter 2: Cell Biology and Cell Organization
• Chapter 3: Movement of Substances Across Plasma Membrane
• Chapter 5: Metabolism and Enzymes