Organic Molecules: Carbon, Isomerism, and Functional Groups (Lecture Notes)

Vocabulary flashcards covering core concepts from the lecture notes on carbon chemistry, isomerism, and functional groups.

Carbon

Element with 6 protons and 6 electrons; has 4 valence electrons; central to organic molecules; forms covalent bonds and can make up to four bonds.

Valence electrons

Electrons in the outermost shell; carbon has 4 valence electrons, enabling diverse covalent bonding.

Covalent bond

Bond formed by sharing electrons; carbon predominantly forms covalent bonds, not ionic bonds.

Ionic bond

Bond formed by transfer of electrons; carbon does not readily form ionic bonds.

Organic compound

Compounds that contain carbon, typically with covalent bonds; basis of biology.

CHNOPS

Six most common elements in living systems: Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), Phosphorus (P), Sulfur (S) — the others often accompany carbon in biomolecules.

Single C–C bond

A covalent bond between two carbons; allows rotation around the bond and provides flexibility to organic molecules.

Carbon backbone

The carbon chain or framework that forms the main structure of organic molecules.

Hydrocarbon (CH bonds)

Contain only hydrogen and carbon; form flexible chains due to single C–C bonds.

Rotation around single bonds

Single bonds (like C–C) permit rotation, contributing to the flexibility of molecules.

Covalent backbone as molecular backbone

Carbon’s ability to bond with itself and other elements creates long chains and complex structures.

C=C double bond

A double bond between two carbons; restricts rotation and leads to planarity; each carbon is sp2 hybridized.

Bond angles in single bonds (tetrahedral)

109.5° angles around carbon when bound to four atoms (tetrahedral geometry).

Tetrahedron

Molecular geometry around carbon with four single bonds forming a tetrahedral shape.

Bond angles with C=C bonds

Around a double-bonded carbon, bond angles are about 120°, and the C=C plane is typically flat.

Planarity of C=C

Atoms involved in a C=C bond lie in the same plane due to the double bond’s rigidity.

Rotation about C=C bonds

Rotation around double bonds is restricted because the π bond locks the orientation.

Isomer

Compounds with the same molecular formula but different structures.

Structural isomer

Isomers with the same formula but different covalent bonding arrangements.

Stereoisomer

Isomers with the same covalent bonds but different spatial arrangement of atoms.

Cis isomer

A stereoisomer where substituents are on the same side of a C=C bond; no rotation about the double bond.

Trans isomer

A stereoisomer where substituents are on opposite sides of a C=C bond; rotation is restricted.

Enantiomer

Mirror-image stereoisomers that cannot be superimposed; organisms often use only one form.

D- and L- nomenclature

Descriptors for enantiomer configuration; biological systems commonly favor one form (often D or L, depending on context).

R- and S- configuration

Alternative descriptors for stereocenters indicating absolute configuration.

Functional group

Atoms or groups of atoms covalently bonded to a carbon skeleton that determine reactivity and properties.

Hydroxyl group (-OH)

Polar group found in alcohols; often increases solubility in water.

Carbonyl group (C=O)

Polar group found in aldehydes and ketones; contributes to reactivity of carbohydrates and other compounds.

Carboxyl group (-COOH)

Weakly acidic group found in amino acids and fatty acids; can donate a proton.

Amino group (-NH2)

Weakly basic group found in amino acids; can accept protons.

Sulfhydryl group (-SH)

Thiols; found in some amino acids; can form disulfide bonds; noted as nonpolar in these notes.

Phosphate group (-OPO3H2)

Weakly acidic group found in phospholipids and nucleic acids (DNA/RNA); important in energy transfer (e.g., ATP).

Methyl group (-CH3)

Nonpolar, hydrophobic group found in lipids and membrane components; influences molecular properties.

Rotation around C–C bonds

Single bonds allow rotation, contributing to conformational flexibility of carbon chains.

Shape and chemistry of carbon compounds

Carbon’s bonding versatility (single, double, triple) and bond angles determine molecular shape, reactivity, and function.