MCAT Organic Chemistry Review: For MCAT 2015 (Graduate School Test Preparation) - P.J. Alaimo, Ph.D. 2015
Organic Chemistry Glossary
After each entry, the section number in MCAT Organic Chemistry Review where the term is discussed is given.
1,3-diaxial interaction
A destabilizing interaction between substituents that occupy axial positions on the same side of a cyclohexane ring. [Section 4.2]
achiral
A molecule that is superimposable on its mirror image. [Section 4.2]
aldehyde
A functional group where a carbonyl is attached to one carbon group and one hydrogen. [Section 6.1]
aldol condensation
A reaction in which the enolate anion of one carbonyl reacts with the carbonyl of another compound. [Section 6.1]
alkanes
Saturated hydrocarbons of the form CnH2n+2. [Section 3.3]
amphipathic
A molecule that is both hydrophilic and hydrophobic. [Section 6.3]
anomeric center
The orientation at the anomeric center distinguishes anomers from one another. [Section 4.2]
anomers
Epimers formed by ring closure. [Section 4.2]
anti conformation
A conformation in which the two largest groups are 180° apart. [Section 4.2]
axial
A substituent orientation on rings where the group is pointed up or down, perpendicular to the plane of the ring. [Section 4.2]
Benedict’s test
A test to detect aldehydes, ketones, and hemiacetals in sugars. [Section 7.3]
boiling point
The temperature at which a compound changes from a liquid into a gas. [Section 5.1]
Cahn-Ingold-Prelog rules
A set of rules for assigning absolute configuration to a stereocenter. [Section 4.2]
carbanions
Negatively charged species with a negative formal charge on carbon. [Section 4.2]
carbocations or carbonium ions
Positively charged species with a positive formal charge on carbon. [Section 4.2]
carbohydrate
A chain of hydrated carbon atoms with the molecular formula CnH2nOn. [Section 7.3]
chair conformation
The most stable conformation of cyclohexane. [Section 4.2]
chemical shift
The location of a resonance in a NMR spectrum. [Section 5.2]
chiral
A molecule that cannot be superimposed on its mirror image is chiral. Most frequently this refers to an sp3 hybridized carbon with four different groups attached to it. [Section 4.2]
cis
Substituents on the same side of a double bond or ring. [Section 4.2]
conformational isomers
Any compounds that have the same molecular formula and the same connectivity but that differ from one another by rotation about a σ bond. [Section 4.2]
constitutional isomers
Any compounds with the same molecular formula but whose atoms have different connectivity. [Section 4.2]
degree of unsaturation
A degree of unsaturation is either one ring or one π bond in a molecule. The degree of unsaturation can be calculated using the formula [(2n + 2) − x]/2, where n is the number of carbon atoms and x is the number of hydrogen atoms. [Section 4.1]
delocalized
Electron density that is spread over multiple atoms is said to be delocalized. [Section 4.1]
diastereomers
Stereoisomers that are not enantiomers. [Section 4.2]
disaccharide
Two monosaccharides bonded together. [Section 7.3]
distillation
A purification method based on a difference in boiling points. [Section 5.1]
disulfide bonds
A sulfur-sulfur bond between two cysteines that stabilizes protein structure. [Section 7.2]
(E)-alkenes
Alkenes where the two higher priority groups are on the opposite side of the double bond. [Section 4.2]
electron-donating groups
Groups that push (donate) electron density towards another functional group through σ or π bonds. [Section 4.2]
electron-withdrawing groups
Groups that pull (withdraw) electron density towards themseleves through σ or π bonds. [Section 4.2]
electrophiles
Electrophiles (“electron loving”) are electron-deficient and typically react with nucleophiles by accepting electrons. [Section 4.1]
enantiomers
Molecules that are mirror images and non-superimposable. [Section 4.2]
enolate ion
A resonance-stabilized anion resulting from the deprotonation of a carbon atom adjacent to a carbonyl functional group. [Section 6.1]
epimeric center
The stereocenter at which the configuration differs in epimers. [Section 4.2]
epimers
Diastereomers that differ in configuration at only one of many chiral centers. [Section 4.2]
equatorial
A substituent orientation on rings where the group is pointed away from the center of the ring. [Section 4.2]
extraction
A separation technique that relies on relative solubilities of the two solvents used. [Section 5.1]
gas chromatography
A method that separates compounds based on their volatilities. [Section 5.1]
gauche conformation
A conformation in which the two largest groups are 60° apart when viewed in a Newman projection. [Section 4.2]
geometric isomers
Diastereomers that differ in orientation of substituents around a ring or double bond. [Section 4.2]
glycosidic linkage
The bond between two saccharides. [Section 7.3]
half-chair conformation
The high-energy intermediate conformation of cyclohexane as it converts from one chair conformation into the other. [Section 4.2]
hybrid orbitals
Hybrid orbitals are a mathematical combination of atomic orbitals centered on the same atom. The total number of orbitals is conserved in their formation (i.e., the number of atomic orbitals equals the number of hybrid orbitals). [Section 4.1]
hydrophilic
Literally “water loving.” [Section 7.4]
hydrophobic
Literally “water fearing.” [Section 7.4]
imine formation
A reaction between an aldehyde or ketone and a primary amine to form an imine. [Section 6.1]
inductive effect
The sharing of electrons through σ bonds. [Section 4.2]
infrared spectroscopy
A method that detects the vibrations of covalent bonds and can differentiate their frequencies, which is related to the type of bond. [Section 5.2]
isomers
Any compounds that have the same molecular formula. [Section 4.2]
ketone
A functional group in which a carbonyl is attached to two carbon groups. [Section 6.1]
lipase
Enzymes that hydrolyze fats. [Section 7.4]
lipids
Oily or fatty substances that are part of cellular membranes (phospholipids), can store energy as triglycerides (in adipose cells), and can serve as the building block for steroid hormones (cholesterol). [Section 7.4]
lipid bilayer
A double layer of lipids where the polar groups line the outside and the non-polar tails compose the inside. [Section 7.4]
localized
Electrons that are confined to one orbital, either a bonding orbital or a lone-pair orbital. [Section 4.1]
melting point
The temperature at which a compound changes from a solid into a gas. [Section 5.1]
meso
A molecule that contains chiral centers and an internal plane of symmetry. [Section 4.2]
monosaccharide
Literally a “single sweet unit”, also known as a simple sugar (e.g., fructose, glucose, etc.). [Section 7.3]
mutarotation
Interconversion between anomers. [Section 7.3]
nucleophile
Nucleophiles (“nucleus loving”) have an unshared pair of electrons or a π bond and react with electrophiles by donating these electrons. [Section 4.1]
nucleotides
The building blocks of nucleic acids. [Section 7.5]
oligosaccharide
Several monosaccharides bonded together. [Section 7.3]
optically active
Compounds that rotate the plane of polarized light are optically active. A pair of enantiomers will rotate the plane of polarized light in equal, but opposite directions. [Section 4.2]
peptide bond
The bond that links amino acids together formed between the carboxyl group of one amino acid and the amino group of another. [Section 7.2]
pi (π) bonds
A π bond consists of two electrons localized above and below a nodal plane; π bonds are formed from overlap of two unhybridized p orbitals on adjacent atoms. [Section 4.1]
polysaccharide
Many monosaccharides bonded together. [Section 7.3]
protease
A protein enzyme that performs proteolysis. [Section 7.2]
proteolysis
Hydrolysis of a protein by another protein. [Section 7.2]
racemic mixture
An equal mixture of two enantiomers is said to be racemic; racemic mixtures do not rotate the plane of polarized light because one enantiomer cancels out the rotation of the other. [Section 4.2]
resonance
The sharing of electrons through π bonds. [Section 4.2]
ring strain
Instability due to deviation of bond angles from optimal geometry. [Section 4.2]
saponification
The hydrolysis of esters by treatment with a basic solution. [Section 6.3]
saturated
A molecule is saturated if it contains no π bonds and no rings. [Section 4.1]
sigma (σ) bonds
A σ bond consists of two electrons localized between two nuclei; σ bonds are formed by overlap of two hybridized orbitals. [Section 4.1]
stereoisomers
Any compounds with the same molecular formula and connectivity that differ only in the spatial arrangement of atoms, are known as stereoisomers. Note that if the compounds only differ by rotation around a sigma bond they are not stereoisomers but conformational isomers. [Section 4.2]
tautomers
Readily interconvertible constitutional isomers. [Section 6.1]
thin-layer chromatography (TLC)
A rapid technique used to separate compounds based on their polarity. [Section 5.1]
trans
Substituents on opposite sides of a double bond. [Section 4.2]
twist boat conformation
The local energy minimum for cyclohexane as it converts from one chair conformation to the other. [Section 4.2]
unsaturated
A molecule is unsaturated if it contains at least one π bond or ring. [Section 4.1]
van der Waals forces
A general term for intermolecular forces, often used to describe London dispersion forces: forces between temporary dipoles formed in nonpolar molecules formed because of a temporary asymmetric electron distribution. [Section 5.1]
wavenumber
The reciprocal of wavelength, expressed in reciprocal centimeters (cm−1). [Section 5.2]
(Z)-alkenes
Alkenes where the two high priority groups are on the same side of the double bond. [Section 4.2]
zwitterion
A molecule with both positive and negative formal charges. [Section 7.1]