Introduction to Organic Chemistry

Vocabulary flashcards covering the key concepts, definitions, chemical conventions, and nomenclature rules from the introductory organic chemistry lecture.

Organic chemistry

The study of the fundamental concepts of molecular structure and reactivity of carbon-containing compounds.

11-cis-retinal

An organic compound that absorbs light and allows vision.

Serotonin

A human neurotransmitter.

Glucose oxidation

An energy-yielding oxidation reaction represented by the equation $C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + \text{energy}$.

ATP

A triphosphate–ribose–adenine molecule involved in energy transfer in the body.

Primary elements of organic chemistry

Hydrogen ($H$), carbon ($C$), nitrogen ($N$), and oxygen ($O$), highlighted as the most important elements in the organic chemist's periodic table.

Organic synthesis

The backbone of organic chemistry; a creative science focused on making $C-C$ and $C-X$ bonds, interconverting functional groups, and controlling stereochemistry.

Terodiline

An antispasmodic drug (spelled “antisplasmodic” in the lecture slides) used to introduce the concept of chemical synthesis.

Structure ↔ function/activity

The central relationship emphasised in organic chemistry connecting the molecular architecture of a compound to its chemical and biological action.

Palytoxin

A huge, complex natural product highlighted as an example of a very large organic molecule, contrasted with methane ($CH_4$).

Hydrocarbon framework

The carbon skeleton of an organic molecule that provides the structural base to which functional groups attach.

Functional groups

Specific groupings of atoms that determine how an organic molecule works chemically and biologically.

Alanine

An amino acid containing an amino group and a carboxylic acid group.

Lysine

An amino acid possessing an additional amino group compared with alanine.

Methionine

An amino acid characterized by containing an additional sulfide functional group.

Lidocaine

A local anaesthetic containing a tertiary amine; its free base is lipophilic (used topically) while its hydrochloride ($\text{HCl}$) salt is water-soluble (used for injectables).

Morphine sulfate

An opioid drug formulation featuring a tertiary amine converted into a sulfate or phosphate salt to enable injection and oral solutions.

Golden rule of drawing organic molecules

Be economical: be as realistic as possible, but do not include superfluous detail.

Linoleic acid

An 18-carbon carboxylic acid simplified in skeletal drawings to a zigzag framework with two $C=C$ bonds and a terminal $COOH$ group.

Skeletal formula

A molecular representation where each bend or line end is a carbon atom, carbon-bound hydrogens are implied, and heteroatoms/functional groups like $OH$, $NH_2$, and $O$ are written explicitly.

Deprotonation of leucine

The reaction in which leucine's carboxylic acid reacts with $OH^-$ to form carboxylate ($COO^-$) and $H_2O$.

Protonation of leucine

The reaction in which leucine's amine group reacts with $H_3O^+$ to form an ammonium ion ($NH_3^+$) and $H_2O$.

Curly arrows

Notational arrows in reaction mechanisms that show the movement of electron pairs.

Wedge-and-dash bonds

Conventions used in 2D structures to indicate 3D stereochemistry: solid wedges point towards you, hashed wedges point away from you, and plain lines lie in the plane.

Proprietary name

The commercial brand name of a pharmaceutical drug (e.g., Anadin).

Generic name

The officially recognized common name of a pharmaceutical compound (e.g., aspirin).

Trivial name

A traditional, non-systematic chemical name (e.g., acetylsalicylic acid).

Systematic (IUPAC) name

A standardized chemical name constructed of a prefix, parent, and suffix based on chemical structure (e.g., 2-acetoxybenzoic acid).

Suffix -ane

An IUPAC naming suffix designating a hydrocarbon with single carbon–carbon bonds.

Suffix -ene

An IUPAC naming suffix designating an organic compound containing a carbon–carbon double bond.

Suffix -yne

An IUPAC naming suffix designating an organic compound containing a carbon–carbon triple bond.

R-

A general abbreviation used in organic structures to represent a generic alkyl group.

Isopropyl

A branched three-carbon alkyl substituent with the formula $(CH_3)_2CH-$.

tert-Butyl

A branched four-carbon alkyl substituent with the formula $(CH_3)_3C-$.