Chapter 3: The Molecules of Cells – Structure and Function of Organic Molecules

Introduction to Organic Compounds

Overview

Organic molecules are the foundation of life, forming the structure and function of cells. This chapter explores the chemistry of carbon-based molecules and the four major classes of biological macromolecules: carbohydrates, lipids, proteins, and nucleic acids.

• Organic compounds are molecules containing carbon atoms bonded to other elements, especially hydrogen, oxygen, and nitrogen.

• The shape of a molecule determines its function in biological systems.

• Examples: Methane (CH4), Stearic acid (lipid), Glycine (amino acid), Glucose (carbohydrate).

Carbon and Organic Compounds

Properties of Carbon

• Carbon atoms can form four covalent bonds, allowing for a diversity of stable structures (chains, rings, branches).

• Hydrocarbons are molecules containing only carbon and hydrogen.

• Structural diversity includes straight chains, branched chains, and rings.

Isomers

Isomers are molecules with the same molecular formula but different structures and properties.

• Examples: Butane and isobutane (C4H10), 1-butene and 2-butene (C4H8).

• Isomerism is important for biological function and diversity.

Chemical Groups and Functional Groups

Functional Groups

Functional groups are specific groups of atoms within molecules that determine the chemical properties and reactions of those molecules.

Chemical Group	Examples
Hydroxyl (-OH)	Alcohols
Carbonyl (C=O)	Sugars
Carboxyl (-COOH)	Carboxylic acids
Amino (-NH2)	Amines, amino acids
Phosphate (-PO4)	ATP, DNA
Methyl (-CH3)	DNA, nonpolar molecules

• Hydroxyl group: Polar, found in alcohols.

• Carbonyl group: Found in sugars, can be at the end (aldehyde) or within (ketone) a carbon skeleton.

• Carboxyl group: Acts as an acid, found in amino acids and fatty acids.

• Amino group: Acts as a base, found in amino acids.

• Phosphate group: Important in energy transfer (ATP) and nucleic acids.

• Methyl group: Nonpolar, affects molecular shape and function.

Monomers, Polymers, and Macromolecules

Polymer Formation and Breakdown

• Monomers are small building-block molecules.

• Polymers are long chains of monomers linked by covalent bonds.

• Macromolecules are large polymers essential for life (carbohydrates, proteins, nucleic acids).

• Dehydration reaction: Joins monomers by removing a water molecule.

• Hydrolysis: Breaks polymers into monomers by adding water.

Equation for Dehydration Synthesis:

$ext{Monomer}_1 + ext{Monomer}_2 ightarrow ext{Polymer} + H_2O$

Equation for Hydrolysis:

$ext{Polymer} + H_2O ightarrow ext{Monomer}_1 + ext{Monomer}_2$

Four Types of Organic Compounds

Overview

• Carbohydrates – energy and structural support

• Lipids – energy storage, membranes, hormones

• Proteins – structure, enzymes, transport, defense

• Nucleic acids – genetic information

Carbohydrates

Structure and Function

• Composed of carbon, hydrogen, and oxygen (CH2O).

• Functions: energy source, energy storage, structural support.

Simple Sugars (Monosaccharides)

• General formula: (CH2O)n

• Examples: Glucose, Fructose

• Glucose and fructose are isomers (same formula, different structure).

Disaccharides

• Formed by joining two monosaccharides via dehydration reaction.

• Example: Sucrose (glucose + fructose), Maltose (glucose + glucose)

Polysaccharides (Complex Carbohydrates)

• Long chains of monosaccharides.

• Examples: Starch (plant energy storage), Glycogen (animal energy storage), Cellulose (plant cell walls), Chitin (exoskeletons of arthropods).

• Animals can digest starch and glycogen but not cellulose due to differences in glycosidic bonds.

Lipids

Structure and Function

• Hydrophobic molecules, not true polymers.

• Functions: energy storage (more efficient than carbohydrates), insulation, membrane structure, hormones.

Types of Lipids

• Fats (Triglycerides): Glycerol + 3 fatty acids. Used for long-term energy storage.

• Saturated fatty acids: No double bonds, solid at room temperature (e.g., butter).

• Unsaturated fatty acids: One or more double bonds, liquid at room temperature (e.g., olive oil).

• Phospholipids: Major component of cell membranes; two fatty acids + glycerol + phosphate group.

• Steroids: Four fused carbon rings (e.g., cholesterol, sex hormones).

Health Implications

• High intake of saturated and trans fats is linked to increased health risks.

• Unsaturated fats are generally healthier for the cardiovascular system.

Proteins

Structure and Function

• Polymers of amino acids (20 types).

• Functions: structural (collagen), contractile (muscle), enzymes, transport, hormones, antibodies, toxins.

Protein Structure

1. Primary structure: Amino acid sequence.

2. Secondary structure: Local coiling or folding (alpha helix, beta sheet).

3. Tertiary structure: Overall 3D shape.

4. Quaternary structure: Association of multiple polypeptide subunits.

Peptide Bonds

• Amino acids are linked by peptide bonds formed via dehydration reactions.

Properties

• Determined by the R group (side chain) of each amino acid.

• Amino acids can be hydrophobic or hydrophilic.

Hydrophobic	Hydrophilic
Leucine (Leu)	Serine (Ser), Aspartic acid (Asp)

Nucleic Acids

Structure and Function

• Polymers of nucleotides.

• Each nucleotide consists of a phosphate group, a five-carbon sugar (ribose or deoxyribose), and a nitrogenous base.

Nitrogenous Bases

• Adenine (A)

• Thymine (T) – DNA only

• Uracil (U) – RNA only

• Cytosine (C)

• Guanine (G)

DNA (Deoxyribonucleic Acid)

• Double-stranded helix with complementary base pairing (A-T, C-G).

• Stores genetic information; genes are segments of DNA that code for proteins.

RNA (Ribonucleic Acid)

• Single-stranded.

• Acts as a messenger, carrying instructions from DNA for protein synthesis (transcription and translation).

• Varies by cell type and function.

Summary Table: Major Classes of Biological Molecules

Class	Monomer	Polymer	Function
Carbohydrates	Monosaccharide	Polysaccharide	Energy, structure
Lipids	Fatty acid, glycerol	Triglyceride, phospholipid, steroid	Energy storage, membranes, hormones
Proteins	Amino acid	Polypeptide	Structure, enzymes, transport, defense
Nucleic acids	Nucleotide	DNA, RNA	Genetic information

Key Concepts for Exam Preparation

• Understand the structure and function of each class of biological macromolecule.

• Be able to identify functional groups and their properties.

• Know the processes of dehydration synthesis and hydrolysis.

• Recognize the importance of molecular shape and isomerism in biological function.

Example: The difference between glucose and fructose is the arrangement of atoms, making them isomers with different properties (e.g., sweetness).

Example: Cellulose and starch are both polymers of glucose, but only starch can be digested by humans due to the type of glycosidic bonds.

Additional info: Understanding the chemistry of life is foundational for all further study in biology, including metabolism, genetics, and cell structure.