Organic structure and reactivity

Learn each group's polarity, H-bonding ability, and acidity/basicity. The carbonyl (C=O) family is central: aldehydes and ketones undergo nucleophilic addition; carboxylic acids and their derivatives undergo nucleophilic acyl substitution, with reactivity ordered anhydride > ester > amide (better leaving group = more reactive). Relative acidity is a recurring theme: carboxylic acids are acidic because the conjugate base (carboxylate) is resonance-stabilized — a direct payoff from resonance.

Assign R/S by Cahn–Ingold–Prelog priority (highest atomic number first); a molecule with n stereocenters has up to 2ⁿ stereoisomers. Enantiomers differ only in the direction they rotate plane-polarized light and in how they interact with other chiral things (enzymes, receptors) — which is why one enantiomer of a drug can be active and the other inert or harmful. Diastereomers (including cis/trans and meso compounds) differ in ordinary physical properties and can be separated by normal means. A meso compound has stereocenters but an internal mirror plane, so it's achiral overall. Double bonds carry their own configuration: cis/trans (or the CIP-based E/Z) — rank the groups on each sp² carbon; higher-priority groups on the same side = Z (zusammen), opposite sides = E (entgegen).

Curved arrows track electron flow from nucleophile to electrophile. SN2 is one concerted step (rate depends on both reactants, inversion of configuration, favored at unhindered carbons); SN1 goes through a carbocation (rate depends only on the substrate, racemization, favored by stable carbocations and polar protic solvents). The carbonyl carbon is the most common electrophile in biochemistry — nucleophilic addition for aldehydes/ketones, acyl substitution for acid derivatives (ester/amide formation and hydrolysis, the chemistry behind peptide and ester bonds). Nucleophile/electrophile is just Lewis acid–base language applied to carbon.

Amino acids combine an acidic carboxyl and a basic amino group with a variable side chain (their acid–base behavior and pI come straight from 5A); peptide bonds are amide linkages formed by condensation. Carbohydrates show stereochemistry in action (D/L sugars, anomers, glycosidic bonds). Lipids (fatty acids, triglycerides, phospholipids, steroids) are defined by hydrophobicity and drive membrane formation. Nucleotides carry the genetic information and energy currency (ATP). Because this material is tested in both science sections, it is among the highest-leverage content on the exam.

IR reports bond vibrations — the carbonyl ~1700 cm⁻¹ and a broad alcohol O–H (~3200–3550) are the workhorses; a carboxylic-acid O–H is even broader and extends down toward ~2500–3000, and an N–H sits near 3300. ¹H NMR gives the number of distinct H environments (chemical shift), how many H's each is (integration), and how many neighbors each has (splitting, the n+1 rule); a few shift anchors are worth memorizing (ppm): alkane 0–2, α-to-carbonyl 2–3, vinyl 5–7, aromatic 6–8, aldehyde 9–10, carboxylic-acid 10–12. Mass spectrometry gives the molecular ion (molecular weight) and fragments — a roughly 1:1 M/M+2 pair signals bromine, ~3:1 signals chlorine. UV–Vis absorption rises with conjugation (why pigments are colored).