Biological Molecules: Structure, Function, and Classification

Biological Molecules

Organic Molecules and Carbon

Most biologically related molecules contain carbon, making them organic molecules. Organic molecules are defined as compounds containing carbon, with some exceptions such as carbon dioxide, carbon monoxide, graphite, and diamonds. Living organisms can synthesize organic molecules, and carbon atoms serve as the most versatile building blocks due to their ability to form up to four covalent bonds.

• Carbon atom valence: 4

• Can bond to 2, 3, or 4 other atoms

Functional Groups

Functional groups are small characteristic groups of atoms frequently bonded to the carbon skeleton of organic molecules. They confer specific chemical and physical properties, determine reactivity, and behave consistently across different organic molecules.

• Determine chemical properties and reactivity

• Can be used to classify organic molecules

Seven general functional groups found in organic molecules:

1. Hydroxyl Group (-OH): Polar group; involved in condensation (dehydration) and hydrolysis reactions.

2. Carbonyl Group (-C=O): Polar group; if terminal, forms an aldehyde; if within the chain, forms a ketone.

3. Carboxyl Group (-COOH): Polar group; can donate a proton, making it acidic; involved in peptide bonds.

4. Amino Group (-NH2): Polar group; acts as a weak base; involved in peptide bonds.

5. Sulfhydryl Group (-SH): Nonpolar group; critical for stabilizing protein structure.

6. Phosphate Group (-PO4): Polar group; acts as an acid; links nucleotides; important in energy storage and transfer (e.g., ATP).

7. Methyl Group (-CH3): Nonpolar group; makes molecules more hydrophobic.

Synthesizing Organic Molecules: A Modular Approach

Monomers and Polymers

Biological molecules are assembled from smaller subunits called monomers. Monomers join to form polymers, which are chains of similar building blocks.

• Dehydration synthesis (condensation reaction): Forms polymers by removing a water molecule during covalent linkage.

• Hydrolysis: Breaks covalent bonds between monomers by adding water.

Equations:

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

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

Classes of Biological Macromolecules

There are four major classes of biological macromolecules:

Macromolecule Class	Monomers, Dimers, and Polymers	Examples
Carbohydrates	Sugars (Monosaccharides, Disaccharides)	Glucose, Sucrose, Glycogen, Cellulose
Lipids	Fatty acids, Triglycerides, Wax, Phospholipids, Steroids	Oils, Fat, Plant cuticle, Cholesterol
Proteins	Amino acids	Keratin, Silk
Nucleic Acids	Nucleotides	DNA, RNA

Carbohydrates

Structure and Classification

Carbohydrates are organic molecules made of sugars and their polymers. They serve as fuel and building material. Classified by the number of simple sugars:

• Monosaccharides: Simple sugars (e.g., glucose), ratio of C:H:O is typically 1:2:1

• Disaccharides: Two monosaccharides joined by glycosidic linkage

• Polysaccharides: Hundreds or thousands of monosaccharides joined

General structure:

• Each carbon has a hydroxyl group except one, which is a carbonyl group

• Monosaccharides with 5 or more carbons favor ring structures in aqueous solutions

Disaccharides

Disaccharides are formed by dehydration synthesis, joining two monosaccharides via a glycosidic bond.

Disaccharide	Monomers	Common Use
Maltose	Glucose + Glucose	Important in beer brewing
Lactose	Glucose + Galactose	Sugar present in milk
Sucrose	Glucose + Fructose	Table sugar, most common disaccharide

Polysaccharides

Polysaccharides are macromolecules formed by enzyme-mediated condensation reactions. They serve biological functions such as energy storage and structural support.

• Starch: Glucose polymer used for energy storage in plants

• Glycogen: Glucose polymer used for energy storage in animals

• Cellulose: Linear, unbranched glucose polymer; major component of plant cell walls; differs from starch in linkage type and three-dimensional structure; not digestible by most animals

• Chitin: Polymer of an amino sugar; forms exoskeleton of arthropods and cell walls of fungi

Proteins

Structure and Function

Proteins are polymers of amino acids arranged in a specific linear sequence and linked by peptide bonds. They are the molecular tools for most cellular functions and can make up 50% or more of cell dry weight.

• Functions: Structure, catalysis (enzymes), storage, transport, movement, hormones, immune defense, and more

Amino Acids

Amino acids are the monomer building blocks of proteins. Each consists of:

• A hydrogen atom

• A carboxyl group

• An amino group

• A variable "R" group (side chain) that determines properties

Classes of amino acids:

• Hydrophobic (nonpolar)

• Hydrophilic (polar)

Peptide Bonds

Peptide bonds are covalent bonds formed by dehydration synthesis, linking the carboxyl group of one amino acid to the amino group of another.

Equation:

• $\text{Amino Acid}_1 + \text{Amino Acid}_2 \rightarrow \text{Dipeptide} + H_2O$

Levels of Protein Structure

1. Primary structure: Sequence of amino acids; determined by genes; unique for each protein

2. Secondary structure: Regular coiling and folding of polypeptide backbone; stabilized by hydrogen bonds; major types are alpha helices and beta pleated sheets

3. Tertiary structure: Irregular contortion due to bonding/interactions between side chains (R groups); includes covalent linkages (disulfide bridges), hydrogen bonding, ionic bonds, and hydrophobic interactions

4. Quaternary structure: Results from interaction among several polypeptides (subunits) in a single protein

What Determines Protein Conformation?

The native conformation of a protein is dictated by its primary structure and the interactions that produce secondary, tertiary, and quaternary structures. Denaturation is the unfolding of a protein due to environmental changes, which disrupts weak interactions and can lead to loss of function.

*Additional info: The notes provide foundational knowledge for General Biology students, including definitions, examples, and structural details of major biological macromolecules and their functional groups. Equations and tables have been expanded for clarity and completeness.*