Chapter 3: The Chemistry of Organic Molecules – General Biology Study Notes

3.1 Organic Molecules

Introduction to Organic Molecules

Organic molecules are fundamental to all living organisms, containing both carbon and hydrogen atoms. The diversity of organic molecules arises from the versatile bonding properties of carbon.

• Organic molecules contain both carbon and hydrogen atoms.

• Four major classes of organic molecules (biomolecules): Carbohydrates, Lipids, Proteins, Nucleic Acids.

• Functions of biomolecules include energy storage, structural support, catalysis, and information storage.

The Carbon Atom

Carbon's unique ability to form four covalent bonds makes it the backbone of organic chemistry.

• Carbon has 6 electrons: 2 in the first shell, 4 in the outer shell.

• Forms stable bonds with C, N, H, O, P, S.

• Can create single, double, triple bonds, and ring structures.

• Branching increases molecular complexity.

Carbon Skeleton and Functional Groups

The carbon skeleton forms the backbone of organic molecules, while functional groups determine their chemical properties.

• Functional groups are clusters of atoms that confer specific chemical reactivity and polarity.

• Example: Replacing H with -OH in ethane forms ethanol, changing it from hydrophobic to hydrophilic.

Inorganic vs. Organic Molecules

Organic molecules are distinguished by the presence of both carbon and hydrogen, while inorganic molecules may lack this combination.

Group	Structure	Compound	Significance
Hydroxyl	-OH	Alcohols	Present in sugars, some amino acids
Carbonyl	-CO	Aldehyde/Ketone	Present in sugars
Carboxyl	-COOH	Carboxylic acid	Present in amino acids, fatty acids
Amino	-NH2	Amine	Present in amino acids
Sulfhydryl	-SH	Thiols	Present in some amino acids
Phosphate	-PO4	Organic phosphates	Present in nucleotides, phospholipids

The Biomolecules of Cells

Biomolecules are typically polymers made from repeating monomer units, except for lipids.

• Monomer: Single repeating unit.

• Polymer: Molecule composed of many monomers.

• Example: Amino acids (monomers) form proteins (polymers).

• Lipids are not true polymers; they have two types of subunits.

Category	Subunits (Monomers)	Polymer
Carbohydrates	Monosaccharide	Polysaccharide
Lipids	Glycerol and fatty acids	Fat
Proteins	Amino acids	Polypeptide
Nucleic acids	Nucleotide	DNA, RNA

Synthesis and Degradation of Biomolecules

Biomolecules are assembled and broken down by specific chemical reactions.

• Dehydration reaction: Joins monomers by forming covalent bonds and releasing water.

• Hydrolysis reaction: Breaks covalent bonds by adding water, splitting polymers into monomers.

• Enzymes catalyze these reactions, increasing their rate without being consumed or altered.

Equations:

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

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

3.2 Carbohydrates

Introduction to Carbohydrates

Carbohydrates are essential biomolecules that serve as energy sources and structural materials.

• Composed of carbon, hydrogen, and oxygen in a 1:2:1 ratio.

• Types: Monosaccharides, Disaccharides, Polysaccharides.

Monosaccharides

Monosaccharides are the simplest carbohydrates, consisting of a single sugar molecule.

• Backbone of 3 to 7 carbon atoms.

• Examples: Glucose (C6H12O6), Fructose, Galactose.

• Hexoses: Six-carbon sugars (e.g., glucose).

• Pentoses: Five-carbon sugars (e.g., ribose, deoxyribose).

Disaccharides

Disaccharides are formed by joining two monosaccharides via dehydration synthesis.

• Examples: Lactose (galactose + glucose), Sucrose (glucose + fructose), Maltose (glucose + glucose).

• Lactose intolerance results from lack of the enzyme lactase.

Equation:

• $\text{Glucose} + \text{Glucose} \xrightarrow{\text{dehydration}} \text{Maltose} + H_2O$

Polysaccharides: Energy-Storage and Structural Molecules

Polysaccharides are polymers of monosaccharides, serving as energy storage and structural components.

• Starch: Energy storage in plants.

• Glycogen: Energy storage in animals.

• Cellulose: Structural component in plant cell walls; most abundant organic molecule.

• Chitin: Found in fungal cell walls and animal exoskeletons.

• Peptidoglycan: Found in bacterial cell walls; monomers contain amino acid chains.

3.3 Lipids

Introduction to Lipids

Lipids are diverse, nonpolar molecules that are insoluble in water and serve multiple biological functions.

• Functions: Long-term energy storage, structural components, heat retention, cell communication, protection.

• Types: Fats, Oils, Phospholipids, Steroids, Waxes.

Type	Functions	Human Uses
Fats	Energy storage, insulation	Butter, lard
Oils	Energy storage in plants	Cooking oils
Phospholipids	Plasma membrane component	Food additive
Steroids	Membrane component, hormones	Medicines
Waxes	Protection, water loss prevention	Candles, polishes

Triglycerides: Long-Term Energy Storage

Triglycerides, also known as fats and oils, are composed of one glycerol and three fatty acids.

• Formed by dehydration synthesis.

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

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

• Trans fats: At least one bond in trans configuration; associated with negative health effects.

Phospholipids: Membrane Components

Phospholipids are essential for cell membrane structure, forming a bilayer in aqueous environments.

• Structure: One glycerol, two fatty acids (nonpolar, hydrophobic), one phosphate group (polar, hydrophilic).

• In water, phospholipids form a bilayer with hydrophilic heads facing outward and hydrophobic tails inward.

• Kinks in fatty acid tails maintain membrane fluidity.

Steroids and Waxes

Steroids and waxes are specialized lipids with distinct structures and functions.

• Steroids: Four fused carbon rings; examples include cholesterol, testosterone, estrogen.

• Waxes: Long-chain fatty acids bonded to alcohols; solid, waterproof, protective.

3.4 Proteins

Introduction to Proteins

Proteins are polymers of amino acids, crucial for cellular structure and function.

• Linked by peptide bonds.

• Comprise up to 50% of cell dry weight.

• Polypeptides fold into specific shapes for function.

Functions of Proteins

• Metabolism: Enzymes catalyze biochemical reactions.

• Support: Structural proteins (e.g., keratin, collagen).

• Transport: Carrier proteins move substances.

• Defense: Antibodies fight pathogens.

• Regulation: Hormones regulate cellular processes.

• Motion: Contractile proteins enable movement.

Amino Acids: Protein Monomers

There are 20 common amino acids, each with a unique R group.

• General structure: $\text{H}_2\text{N}-\text{CHR}-\text{COOH}$

• R group determines properties and function.

Protein Structure and Folding

Proteins have up to four levels of structure, each critical for function.

• Primary: Linear sequence of amino acids.

• Secondary: Alpha helices and beta sheets stabilized by hydrogen bonds.

• Tertiary: Three-dimensional folding due to interactions among R groups.

• Quaternary: Association of multiple polypeptide chains.

• Denaturation disrupts protein function.

Protein Folding Diseases

• Chaperone proteins assist in proper folding.

• Defects can lead to diseases (e.g., Alzheimer's, cystic fibrosis).

• Prions: Misfolded proteins causing transmissible spongiform encephalopathies (TSEs), e.g., mad cow disease.

3.5 Nucleic Acids

Introduction to Nucleic Acids

Nucleic acids are polymers of nucleotides, essential for genetic information storage and transfer.

• Two types: DNA (deoxyribonucleic acid), RNA (ribonucleic acid).

• DNA stores genetic information; RNA is involved in protein synthesis and gene regulation.

Structure of a Nucleotide

• Three components: phosphate group, pentose sugar, nitrogenous base.

• DNA bases: adenine, guanine, cytosine, thymine.

• RNA bases: adenine, guanine, cytosine, uracil.

Structure of DNA and RNA

• DNA: Double-stranded helix, sugar-phosphate backbone, complementary base pairing (A-T, G-C).

• RNA: Single-stranded, sugar-phosphate backbone, uracil replaces thymine.

• Complementary base pairing ensures accurate replication and transcription.

	DNA	RNA
Sugar	Deoxyribose	Ribose
Bases	A, G, T, C	A, G, U, C
Strands	Double	Single
Helix	Yes	No

ATP (Adenosine Triphosphate)

ATP is a nucleotide that serves as the primary energy currency of the cell.

• Composed of adenine, ribose, and three phosphate groups.

• Hydrolysis of ATP releases energy for cellular work:

$\text{ATP} + H_2O \rightarrow \text{ADP} + P_i + \text{energy}$

• ATP hydrolysis is coupled to energetically unfavorable reactions.

Additional info: ATP is essential for processes such as muscle contraction, active transport, and biosynthesis.