Organic Biochemistry Lecture Notes

Vocabulary practice flashcards covering basic principles of acids, bases, salts, and foundations of organic chemistry including functional groups and hybridization.

Arrhenius acid

A hydrogen-containing compound that produces $H^+$ ions in solution (adding water).

Arrhenius base

A hydroxide-containing compound that produces $OH^-$ (Hydroxide) ions in solution.

Ionization

The process in which individual positive and negative ions are produced from a molecular compound that is dissolved in solution (in water).

Dissociation

The process in which individual positive and negative ions are released from an ionic compound that is dissolved in solution.

Bronsted-Lowry Acid

A substance that can donate a proton ($H^+$ ion) to some other substance; a proton donor.

Bronsted-Lowry Base

A substance that can accept a proton ($H^+$ ion) from some other substance; a proton acceptor.

Conjugate Acid

The species that is formed when a base accepts a proton.

Conjugate Base

The product that is left behind (ion left) after an acid has donated its proton.

Acid Ionization Equilibrium

The state at which the rate of the forward reaction between acids and bases is equal to the rate of the product formation.

Amphiprotic Substance

A substance that can either lose or accept a proton and thus can function as either a Bronsted-Lowry Acid or a Bronsted-Lowry base, such as $H_2O$.

Monoprotic Acid

An acid that supplies one proton ($H^+$ ion) per molecule during an acid-base reaction.

Diprotic Acid

An acid that supplies two protons ($H^+$ ions) per molecule during an acid-base reaction.

Polyprotic Acid

An acid that supplies two or more protons ($H^+$ ions) during an acid-base reaction, including both diprotic and triprotic acids.

Strong Acid

An acid that transfers approximately $100 \text{\%}$ of its protons to water in an aqueous solution; its ionization equilibrium lies far to the right.

Acid Ionization Constant ($K_a$)

The equilibrium constant for the reaction of a weak acid with water where $K_a = \frac{[H_3O^+][A^-]}{[HA]}$.

Neutralization Reaction

The chemical reaction between an acid and a hydroxide base in which a salt and water are the products.

Self-ionization of Water

A process where water molecules in pure water interact with one another to form equal amounts of hydronium and hydroxide ions: $H_2O + H_2O \rightleftharpoons H_3O^+ + OH^-$.

Ion Production Constant for Water ($K_w$)

At $24\,^\circ\text{C}$, the product of the concentrations of hydronium and hydroxide ions, which must always equal $1.00 \times 10^{-14}$.

pH for a solution with whole number concentration

Calculated by $pH = -\log [H^+]$; for example, if $[H^+] = 1 \times 10^{-5}$, the pH is $5$.

Buffer

An aqueous solution containing substances that prevent major changes in solution pH when small amounts of acid or base are added to it.

Henderson-Hasselbalch Equation

An equation used to calculate the pH of a buffer: $pH = pK_a + \log \frac{[A^-]}{[HA]}$.

Organic Chemistry

The study of the compounds of carbon.

Structural Formula

A representation that shows the atoms in a molecule and the bonds that connect them.

Electronegativity (EN)

The intrinsic ability of an atom to attract the shared electrons in a covalent bond.

Addition Reaction

An organic reaction where two molecules combine to form a single product.

Elimination Reaction

An organic reaction where one molecule splits into two products.

Substitution Reaction

An organic reaction where parts from two molecules exchange with each other.

Hybridization

The mixing of different orbitals of a single atom to produce an equal number of hybrid orbitals of the same energy and identical properties.

Sigma ($\sigma$) Bond

A bond formed by the overlap of two hybrid orbitals through areas of maximum electron density at the tips of the lobes.

Pi ($\pi$) Bond

A bond formed by the overlap of two unhybridized, parallel p orbitals at the sides of the lobes.

sp3 Hybridization

Also called tetrahedral hybridization; involves combining one s orbital and three p orbitals to form four hybrid orbitals at angles of $109.5^\circ$.

sp2 Hybridization

Also called trigonal hybridization; involves combining one s orbital and two p orbitals to produce three orbitals directed toward the corners of an equilateral triangle at $120^\circ$.

sp Hybridization

Also known as diagonal hybridization; involves combining one s orbital and one p orbital at an angle of $180^\circ$.

Functional Group

An atom or group of atoms within a molecule that has similar chemical properties whenever it appears in various compounds.

Alkane

A hydrocarbon containing only carbon-carbon single bonds with the general formula $C_nH_{2n+2}$.

Constitutional Isomers

Compounds that have the same molecular formula but different structural formulas (different connectivity).

Cycloalkane

A cyclic hydrocarbon in which all carbons of the ring are saturated.

Alcohols

Compounds containing an $-OH$ (hydroxyl) group bonded to a tetrahedral carbon atom.

Thiol

A compound containing an $-SH$ (sulfhydryl) group, often associated with strong, unpleasant odors.

Carbonyl Group

A functional group common to aldehydes and ketones, consisting of a carbon-oxygen double bond ($C=O$).

Fischer Esterification

The reaction of a carboxylic acid with an alcohol in the presence of an acid catalyst to prepare an ester.

Saponification

The hydrolysis of an ester using a hot aqueous base to produce a carboxylic acid salt and an alcohol.

Aliphatic Amine

An amine in which all carbons bonded to nitrogen are derived from alkyl groups.

Kevlar

A polyaromatic amide (polyamide) made from an aromatic dicarboxylic acid and an aromatic diamine.