Organic Molecules: Carbon, Isomerism, and Functional Groups (Lecture Notes)
Carbon and the Chemistry of Carbon
Organic compounds are defined as organic compounds - have at least one carbon atom covalently bound to another carbon atom or to hydrogen. Organic molecules are largely organized around Carbon.
Carbon basics:
Carbon has 6 protons and 6 electrons; valence electrons = 4. The other 2 electrons occupy its first energy level.
Carbon doesn’t seek out electrons nor readily give them up, so it does not readily form ionic bonds. Therefore, carbon almost always shares electrons, forming covalent bonds.
Can form up to 4 covalent bonds.
Diversity of organic compounds:
>5 million identified to date.
Variety arises because carbon tends to bond to other carbons, hydrogen, nitrogen, oxygen, phosphorus, and sulfur — CHNOPS.
Carbon as a molecular backbone:
Carbon works as a molecular backbone for forming long chain molecules.
Building macromolecules: carbon chains form the backbone of biological polymers.
Single vs multiple bonds:
Single C–C bonds allow rotation around them and lend flexibility to most biological molecules.
Double or triple bonds (C=C, C≡C) can form in carbon frameworks and alter geometry.
Carbon chains can branch as well.
Shapes and bonding geometry:
The four bonds carbon can form result in bond angles of 109.5^ ext{°}, forming a tetrahedral geometry (a pyramid with a triangular base).
If carbon forms a double bond (C=C), the bonds are formed at about 120^ ext{°} apart, and the C=C is in the same plane; rotation about C=C bonds is restricted.
Isomerism basics:
Isomers are molecules with the same molecular formula but different arrangements.
Rotation and bond arrangements give rise to different shapes and properties.
Isomerism in Organic Molecules
Bonding behavior of Carbon and isomerism:
Molecules with the same molecular formula can have different structures (isomers) due to variations in covalent bonding or spatial arrangement.
2 main types of isomers:
Structural isomers (also called constitutional isomers) - Substances with the same molecular formula that differ in the covalent arrangement of atoms.
Stereoisomers - Substances with the same order of covalent bonds, but the spatial arrangement of atoms is different.
Stereoisomer subtypes:
Cis–trans (geometric) isomers:
Associated with compounds that have C–C double bonds.
No rotation about the double bonds; the other substituents attached to the carbons are fixed in relation to each other.
Cis = same side; trans = opposite sides.
Enantiomers:
Substances that are mirror images of each other that cannot be superimposed on each other.
Typically, only one form of an enantiomer pair is found or used by organisms.
Notation can be D/L (d/l) or R/S for absolute configuration.
Important concept:
Small chemical differences between isomers can have huge biological consequences.
Functional Groups
Functional groups determine the most reactive properties and functions of organic molecules; they are groups of atoms covalently bonded to a carbon backbone that impart characteristic properties different from C–H bonds.
The properties of major classes of organic compounds (carbohydrates, lipids, proteins) are determined by functional groups.
Common functional groups (with examples and characteristics):
Hydroxyl group (-OH)
Polar, found in alcohols.
Example formula: -OH
Carbonyl group (C=O)
Polar, found in aldehydes and ketones.
Example formula: C=O
Carboxyl group (-COOH)
Weakly acidic, found in amino acids.
Example formula: -COOH
Amino group (-NH_2)
Weakly basic, found in amino acids.
Example formula: -NH_2
Sulfhydryl group (-SH) – Thiol
Non-polar, found in amino acids.
Example formula: -SH
Phosphate group (-PO4H2)
Weakly acidic, found in phospholipids and nucleic acids (DNA/RNA), Polar.
Example formula: -PO4H2
Methyl group (-CH_3)
Non-polar (hydrophobic), found in lipids and membrane components of cells.
Example formula: -CH_3
Contextual notes:
These groups alter polarity, acidity/basicity, reactivity, solubility, and interactions with other molecules.
The presence and arrangement of functional groups help explain the properties and behavior of carbohydrates, lipids, proteins, and nucleic acids.
CHNOPS and Relevance
CHNOPS stands for Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur.
These elements are the backbone and key components of most biological molecules.
The diversity of organic matter arises from the ways these elements bond to carbon and to each other, forming a vast array of structures and functions.
Connections to Foundational Principles and Real-World Relevance
Valence and octet concept underpin covalent bonding patterns and molecular geometry.
Tetrahedral and sp2 geometries govern the 3D shape of molecules, which in turn affects reactivity, polarity, and interactions with biological systems.
Isomerism explains why compounds with identical formulas can have drastically different properties and biological roles.
Functional groups determine chemical reactivity, polarity, acid/base behavior, and participation in biochemical pathways.
The carbon backbone’s versatility explains the vast diversity of biomolecules (carbohydrates, lipids, proteins, nucleic acids) and their functions in cells and organisms.
Formulas and Notation Summary (quick reference)
Valence electrons of carbon: 4
Bond angles in tetrahedral geometry: 109.5^ ext{°}
Bond angle in C=C double bonds: 120^ ext{°}
Methyl group: -CH_3
Hydroxyl: -OH
Carbonyl: C=O
Carboxyl: -COOH
Amino: -NH_2
Sulfhydryl: -SH
Phosphate: -PO4H2
Methyl: -CH_3
Common core elements: ext{C, H, N, O, P, S} (CHNOPS)