Physical Chemistry for General Biochemistry — Lecture Notes Flashcards

Vocabulary-style flashcards covering functional groups, stereochemistry, thermodynamics, reactions, and key biochemical principles from the lecture notes.

Functional group

A specific group of atoms within a molecule that largely determines its chemical reactivity (e.g., hydroxyl, carbonyl, amine).

Chiral center

A carbon atom bonded to four different substituents, creating non-superimposable mirror images.

R configuration

Absolute configuration around a chiral center designated by CIP rules; 'R' indicates clockwise arrangement after priority ordering.

S configuration

Absolute configuration around a chiral center designated by CIP rules; 'S' indicates counterclockwise arrangement.

Stereoisomer

Molecules with the same connectivity and formula but different spatial arrangement.

Enantiomer

A pair of non-superimposable mirror-image stereoisomers.

Diastereomer

Stereoisomers that are not mirror images of each other.

Geometric isomer

Isomers around a double bond that differ in the spatial arrangement of substituents (cis/trans).

Cis isomer

Substituents on the same side of a double bond.

Trans isomer

Substituents on opposite sides of a double bond.

Conformation

Spatial arrangement of atoms resulting from rotation about single bonds; includes staggered/anti forms.

Steric hindrance

Interference caused by bulky groups that affects reactivity or conformations.

Methyl group

A -CH3 substituent attached to a carbon framework.

Ethyl group

A -CH2-CH3 substituent (C2H5).

Ether

R-O-R' functional group linking two carbon groups via an oxygen.

Imidazole

Five-member aromatic ring with two nitrogens; important in biology (e.g., histidine).

Acetyl

Acetyl moiety: -CO-CH3 group.

Guanidinium

Positively charged group (often in arginine): (H2N-C(=NH)-NH2)+.

Sulfhydryl

-SH group (thiol), important in disulfide bond formation.

Hydroxyl

-OH group; a common polar functional group.

Carbonyl

C=O group found in aldehydes and ketones.

Aldehyde

R-CHO, carbonyl carbon at the end of a carbon chain.

Ketone

R-CO-R', internal carbonyl group.

Ester

R-CO-O-R' functional group linking carbonyl to an alkoxy group.

Amide (Amido)

R-CO-NR'R''; carbonyl attached to nitrogen.

Phosphoryl

P=O group in phosphate-containing compounds.

Phosphoanhydride

P-O-P linkage (e.g., in ATP) with high energy but stable backbone.

Anhydride

R-CO-O-CO-R' linkage between two carbonyls; energy-rich in some contexts.

Disulfide

R-S-S-R'; bond between two sulfur atoms linking cysteine residues.

Enol

Tautomeric form of a carbonyl compound with C=C–OH.

Imine (Schiff base)

C=N bond formed from amine and carbonyl condensation.

Iminium ion

Protonated imine; positively charged intermediate.

Nucleophilic attack

Attack by a nucleophile on an electrophile to form a bond.

Phosphodiester bond

Backbone linkage between nucleotides via phosphate ester bonds.

Hydrogen bond

Weak attraction between a donor H (attached to electronegative atom) and an acceptor electronegative atom.

Ionic interaction

Electrostatic attraction between charged groups (e.g., salt bridges).

Van der Waals forces

Weak attractions/repulsions from transient dipoles between atoms.

Hydrophobic effect

Aggregation of nonpolar groups in water to reduce ordered water; increases entropy.

Hydrophilic

Molecules or groups that readily dissolve in water (polar/charged).

Hydrophobic

Nonpolar molecules or groups that do not dissolve well in water.

Amphipathic

Molecules with both polar (water-loving) and nonpolar (water-fearing) regions.

Osmosis

Movement of water across a semipermeable membrane due to solute differences.

Osmotic pressure

Pressure required to prevent osmosis; related to solute concentration.

Colligative properties

Properties that depend on particle number, not identity (vapor pressure lowering, boiling point elevation, freezing point depression, osmotic pressure).

Activation energy

Energy barrier that must be overcome for a reaction to proceed.

Transition state

High-energy, unstable arrangement at the peak of the reaction coordinate.

Rate-limiting step

Slowest step in a pathway, with the highest activation energy.

Enzyme

Biological catalyst that lowers activation energy and speeds reactions without changing the overall equilibrium.

Coupled reactions

Pairing an energetically unfavorable reaction with a favorable one to drive the process.

ATP hydrolysis

ATP + H2O → ADP + Pi; highly exergonic, provides cellular energy.

∆G (Gibbs free energy)

Change in free energy; negative for spontaneous processes; state function.

∆G° (standard free energy change)

Free energy change under standard conditions; relates to Keq and ∆G.

Keq (equilibrium constant)

Ratio of product to reactant activities at equilibrium; predicts spontaneity.

Q (mass-action ratio)

Ratio of product to reactant activities at a given moment; distance from equilibrium.

Equilibrium

Condition where forward and reverse reaction rates are equal; ΔG = 0.

Dynamic steady state

Non-equilibrium cellular state with ongoing flux and energy input to maintain stability.

Homeostasis

Maintenance of internal conditions despite external changes; requires energy.

Phenyl Group

An organic functional group characterized by a benzene ring attached to a larger molecular structure, often influencing chemical reactivity and physical properties.

∆G is < 0 for…

spontaneous reactions

∆G is > 0 for…

nonspontaneous reactions

∆G is zero at…

equilibrium