Chapter 3: The Molecules of Life – Biomolecules in Living Systems

The Molecules of Life

Overview of Biomolecules

Biomolecules are essential compounds produced by living cells, and their structure determines their function. The four major classes are carbohydrates, lipids, proteins, and nucleic acids. Only living cells synthesize these molecules, which are fundamental to life processes.

• Complex carbohydrates: Energy storage and structural roles

• Lipids: Energy storage, membrane structure, signaling

• Proteins: Catalysis, structure, transport, regulation

• Nucleic acids: Information storage and transfer

Key Principle: Structure equals function—molecular shape and arrangement determine biological activity.

Organic Compounds

Elements and Structure

Organic compounds are molecules containing carbon (C), hydrogen (H), and oxygen (O). Carbon and hydrogen form the backbone, allowing for large and complex structures. Hydrocarbons are the simplest organic compounds, containing only C and H.

• Methane (CH4)

• Ethane (C2H6)

• Ethylene (C2H4)

Other important elements in organic compounds include nitrogen (N), phosphorus (P), sulfur (S), calcium (Ca), sodium (Na), chlorine (Cl), potassium (K), magnesium (Mg), and iron (Fe).

Carbon’s Bonding Behavior

Carbon atoms have four electrons in their outer shell, which can hold up to eight. This allows each carbon atom to form up to four covalent bonds, enabling a variety of bonding arrangements and complex molecular structures.

How Do Cells Build Organic Compounds?

The Four Building Blocks

Cells construct larger molecules from four groups of smaller molecules, known as monomers. These monomers join to form polymers through chemical reactions.

• Simple sugars (monosaccharides)

• Fatty acids

• Amino acids

• Nucleotides

Monomer: A single subunit molecule. Polymer: A chain of monomers linked together.

Types of Reactions

Cells use several types of chemical reactions to build and break down organic compounds:

• Synthesis/Anabolic (e.g., condensation)

• Decomposition/Catabolic (e.g., hydrolysis)

• Reversible reactions

• Redox (oxidation-reduction)

• Exchange reactions

Synthesis/Anabolic Reactions

Smaller compounds combine to form larger ones, usually requiring energy input.

• General equation: $A + B \rightarrow AB$

• Example: Glucose + glucose + glucose ... $\rightarrow$ starch

Condensation (Dehydration Synthesis)

A type of synthesis reaction where monomers join to form polymers, releasing water as a byproduct.

• General equation: $\text{Monomer}_1 + \text{Monomer}_2 \rightarrow \text{Polymer} + H_2O$

Decomposition/Catabolic Reactions

Large compounds are broken down into smaller ones, usually releasing energy.

• General equation: $AB \rightarrow A + B$

• Example: Starch $\rightarrow$ glucose + glucose + glucose ...

Hydrolysis

A type of decomposition reaction where water is used to break bonds in polymers.

• General equation: $\text{Polymer} + H_2O \rightarrow \text{Monomer}_1 + \text{Monomer}_2$

• Example: Sucrose + $H_2O \rightarrow$ glucose + fructose

Reversible Reactions

Reactions that can proceed in both directions.

• General equation: $A + B \rightleftharpoons AB$

• Example: $CO_2 + H_2O \rightleftharpoons H_2CO_3 \rightleftharpoons HCO_3^- + H^+$

Redox (Oxidation-Reduction) Reactions

Involve the exchange of electrons between reactants, crucial for metabolism.

• Oxidation: Loss of electrons

• Reduction: Gain of electrons

• One compound is oxidized (loses electrons), the other is reduced (gains electrons)

Exchange Reactions

Atoms are rearranged between molecules, but the overall complexity remains the same.

• General equation: $AB + CD \rightarrow AD + CB$

• Example: $HCl + NaOH \rightarrow NaCl + H_2O$

The Carbohydrates

Carbohydrates (The Sugars)

Carbohydrates are the most abundant biological molecules, serving as structural materials and energy sources. They are composed of C, H, and O, typically with a hydrogen:oxygen ratio of 2:1. Carbohydrates are classified by size:

• Monosaccharides (single sugar units)

• Disaccharides (two sugar units)

• Polysaccharides (many sugar units)

Monosaccharides

Monosaccharides are the building blocks of larger carbohydrates.

• 5-carbon sugars: Ribose (in RNA), Deoxyribose (in DNA)

• 6-carbon sugars: Glucose, fructose, galactose ($C_6H_{12}O_6$)

• Isomers: Molecules with the same formula but different structures

Example: Glucose and fructose are both $C_6H_{12}O_6$ but differ in structure.

Polysaccharides

Polysaccharides are long chains of glucose units, serving as storage or structural molecules.

• Cellulose: Structural material in plant cell walls; tough and indigestible

• Starch (amylose): Storage form in plant cells; easily digested

• Glycogen: Storage form in animal cells; found in muscle and liver

Cellulose & Starch

Cellulose and starch differ in the bonding patterns between their glucose monomers, resulting in different properties and digestibility.

• Cellulose: Indigestible by most animals; provides structural support

• Starch: Easily broken down for energy

Glycogen

Glycogen is the main sugar storage molecule in animals, especially in muscle and liver cells. When blood sugar drops, glycogen is broken down to release glucose.

Chitin

Chitin is a polysaccharide with nitrogen-containing groups attached to glucose monomers. It serves as a structural material in invertebrate exoskeletons and fungal cell walls.

The Lipids

Lipids

Lipids are oily, water-insoluble compounds composed mainly of C, H, and O (with little O). They serve as energy reserves, structural materials, and signaling molecules. Lipids are classified into four major categories:

• Fats

• Phospholipids

• Sterols

• Waxes

Fats

Fats consist of fatty acids attached to a glycerol molecule. They are classified as unsaturated or saturated based on the presence of double bonds.

• Unsaturated fatty acids: One or more double bonds; found in plant fats; liquid at room temperature

• Saturated fatty acids: Only single bonds; found in animal fats; solid at room temperature

Triglycerides

Triglycerides are the most abundant lipids, serving as a major energy reservoir and stored in animal adipose tissue.

Phospholipids

Phospholipids are the main components of cell membranes. They consist of a glycerol backbone, a hydrophilic phosphate head, and two hydrophobic fatty acid tails (one saturated, one unsaturated).

Sterols and Derivatives

Sterols have carbon atoms arranged in ring structures. Cholesterol is the primary steroid, serving as the basis for sex and adrenal hormones, forming bile salts, vitamin D, and being a component of cell membranes.

Waxes

Waxes are produced by plants and animals for protection and lubrication. Examples include beeswax, earwax (cerumen), and lanolin from sheep.

Proteins

Proteins

Proteins are the most diverse and abundant biomolecules in animals. They are composed of 20 different amino acids, each with a unique R group. The structure of an amino acid includes an amino group (-NH3+), a carboxyl group (-COO-), and an R group.

Protein Functions

Proteins perform a wide variety of functions in cells:

Type of Protein	Functions
Enzymes	Speed up reactions
Structural	Builds, strengthens, and protects cells and tissues
Storage	Stores and provides nutrients
Transport	Transports substances across cell membranes
Regulatory	Signaling molecules (hormones); control gene expression
Motile	Cellular movements
Protective	Defend against foreign invaders

Protein Synthesis

Proteins are synthesized as chains of amino acids linked by peptide bonds (a type of covalent bond formed by condensation reactions between the amino group of one amino acid and the carboxyl group of another).

Levels of Protein Structure

Proteins have four levels of structure, each increasing in complexity:

• Primary (1°): Linear sequence of amino acids

• Secondary (2°): Hydrogen bonds form coiled (helix) or sheeted (pleated sheet) patterns

• Tertiary (3°): Folding due to interactions between R groups, resulting in a 3-D functional structure

• Quaternary (4°): Multiple polypeptide chains linked together (e.g., hemoglobin)

Protein Shape and Denaturation

The shape of a protein determines its biological activity. Denaturation (loss of 3-D structure) occurs due to changes in pH, temperature, or exposure to radiation, disrupting function.

Just One Wrong Amino Acid: Hemoglobin Example

Hemoglobin in red blood cells binds and delivers oxygen. Its function depends on its structure. A single amino acid change (e.g., glutamate to valine) can cause sickle cell anemia, altering the protein's properties and cell shape.

Nucleic Acids

Nucleic Acids

Nucleic acids are composed of C, H, O, N, and P. Their building blocks are nucleotides, which serve as energy carriers (e.g., ATP) and store/process genetic information (DNA and RNA).

• DNA: Genetic blueprint; double-stranded helix; located in the nucleus

• RNA: Carries out instructions from DNA; usually single-stranded

Nucleotide Structure

Each nucleotide consists of:

• Sugar: Ribose (RNA) or deoxyribose (DNA)

• Phosphate group

• Nitrogenous base: Single or double ring structure

DNA Structure and Function

DNA contains instructions for all cellular activities. It is composed of four types of nucleotides:

• Adenine (A)

• Thymine (T)

• Guanine (G)

• Cytosine (C)

Base pairing: A binds to T, C binds to G.

DNA to Proteins

The sequence of bases in DNA encodes heritable information, which is used to build proteins necessary for growth, maintenance, and reproduction.

RNA Structure and Function

RNA is usually single-stranded and is synthesized from DNA (transcription). RNA is then translated into protein. RNA nucleotides include ribose, adenine, guanine, cytosine, and uracil (U).

Additional info: These notes provide foundational knowledge for understanding the chemical basis of life, including the structure and function of biomolecules, their synthesis and breakdown, and their roles in cellular processes.