Organic Molecules and Functional Groups in General Biology

Organic Molecules in Biology

Introduction to Organic Molecules

Organic molecules are the foundation of biological systems, consisting mainly of carbon and hydrogen atoms. Their structure and functional groups determine their chemical properties and biological roles.

• Organic molecules contain mostly C-H and C-C bonds.

• Common elements: CHONPS (Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, Sulfur).

• Properties of carbon:

  • Carbon has 4 valence electrons.

  • Completes shell by covalent bonding (tetravalence).

  • Tetravalence allows for large molecules and diverse structures.

  • Tetravalence gives a 3-D shape to molecules.

• Shapes of molecules are important for their function.

Major Classes of Large Organic Molecules

Carbohydrates

Carbohydrates are organic molecules made of carbon, hydrogen, and oxygen, typically in a 1:2:1 ratio. They are polar and serve as energy sources and structural components.

• Example: Glucose (C6H12O6)

Proteins

Proteins are polymers of amino acids, which contain both amino and carboxyl groups. They are made of 20 different amino acids and have diverse functions, including catalysis, structure, and signaling.

• Part of a molecule is hydrophilic, and part is hydrophobic.

Lipids

Lipids are organic molecules with many C-H bonds and very little oxygen. They are mostly nonpolar and hydrophobic, serving as energy storage and membrane components.

Nucleic Acids

Nucleic acids (DNA and RNA) are made of polar nucleotides. Each nucleotide consists of a sugar, a nitrogenous base, and a phosphate group.

Carbon Skeletons

Structure and Diversity

Carbon skeletons are long chains of carbon atoms, which can vary in length, shape, and branching. They may contain double bonds and other elements, allowing for complex and diverse molecules.

• Example: C-C-C-C-C-C (hexane)

Hydrocarbons

Properties and Examples

Hydrocarbons are the simplest form of carbon skeletons, containing only carbon and hydrogen. They are major components of fossil fuels and are generally nonpolar and hydrophobic.

• Examples: Methane, ethane, propane, butane, pentane, hexane

Isomers

Definition and Types

Isomers are molecules with the same molecular formula but different structural arrangements, leading to different physical and chemical properties.

• The number of isomers increases with the size of the carbon skeleton.

• Double bonds can create isomeric forms.

Types of Isomers

• Geometric isomers (cis-trans isomers):

  • Different arrangements around a double bond.

  • Cis: same groups on the same side of the axis.

  • Trans: same groups on opposite sides of the axis.

  • Geometric isomers have different properties and affect biological processes.

• Structural isomers: Different connectivity of atoms.

Functional Groups in Organic Molecules

Overview

Functional groups are specific groups of atoms within molecules that confer particular chemical properties and reactivity. They are critical for the function of biological molecules.

Functional Group	Structure	Properties/Functions	Example
Carboxyl	-COOH	Acts as an acid, donates H+	Amino acids, fatty acids
Amino	-NH2	Acts as a base, accepts H+	Amino acids
Sulfhydryl	-SH	Forms disulfide bridges, stabilizes proteins	Cysteine (amino acid)
Phosphate	-PO4	Acidic, highly reactive, stores/releases energy	ATP, DNA, RNA, phospholipids
Methyl	-CH3	Nonpolar, hydrophobic, affects solubility	Methylated DNA

Additional Functional Groups

• Hydroxyl (-OH): Polar, forms hydrogen bonds, found in alcohols and sugars.

• Carbonyl (C=O): Found in aldehydes and ketones, affects reactivity.

Summary Table: Properties of Major Functional Groups

Group	Polarity	Acidity/Basicity	Biological Role
Carboxyl	Polar	Acidic	Protein structure, fatty acids
Amino	Polar	Basic	Protein structure
Sulfhydryl	Nonpolar	Neutral	Protein stabilization
Phosphate	Polar	Acidic	Energy transfer, nucleic acids
Methyl	Nonpolar	Neutral	Gene regulation, solubility

Key Equations and Concepts

• General formula for carbohydrates: $C_n(H_2O)_n$

• ATP hydrolysis (energy release): $ATP + H_2O \rightarrow ADP + P_i + \text{energy}$

Examples and Applications

• Glucose is a carbohydrate used for energy in cells.

• Proteins are made of amino acids and perform enzymatic and structural functions.

• Lipids form cell membranes and store energy.

• Nucleic acids store genetic information.

Additional info:

• Functional groups determine the solubility, reactivity, and interactions of organic molecules in biological systems.

• Isomerism increases molecular diversity and affects biological function.