Chemistry IV: Organic Chemistry and Biomolecules
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Organic chemistry is the chemistry of carbon compounds, and it is the foundation of biochemistry and pharmacology (Clayden et al., 2012).
Basic Concepts
- Nomenclature (IUPAC): longest chain, lowest locants, alphabetical substituents.
- Isomerism: structural (chain, position, functional group) and stereoisomerism (geometrical cis/trans or E/Z, and optical). Chirality is vital in biology: amino acids in proteins are L-forms, and sugars are D-forms; the enantiomers of a drug can have very different effects.
- Reactive species: free radicals, nucleophiles, electrophiles; inductive and resonance effects.
Reactions of Main Classes
| Class | Typical reactions |
|---|---|
| Alkanes | Free-radical substitution (initiation, propagation, termination) |
| Alkenes | Electrophilic addition; Markovnikov's rule; test with bromine water (decolourized) |
| Benzene and arenes | Electrophilic substitution (nitration, halogenation, Friedel-Crafts); delocalized electrons |
| Halogenoalkanes | Nucleophilic substitution (S_N1, S_N2) and elimination |
| Alcohols | Oxidation (primary to aldehyde to acid; secondary to ketone; tertiary resists); dehydration; esterification |
| Phenols | Weakly acidic; electrophilic substitution; violet colour with FeCl₃ (phenol is an antiseptic) |
| Aldehydes and ketones | Nucleophilic addition; Tollens' and Fehling's tests; 2,4-DNP test; iodoform test |
| Carboxylic acids and derivatives | Acidity, esterification, acid chlorides, amides, hydrolysis |
| Amines | Basicity; reaction with acid chlorides; diazonium salts and azo dyes |
Organic Chemistry of Biomolecules
| Biomolecule | Chemical link |
|---|---|
| Carbohydrates | Polyhydroxy aldehydes or ketones; glycosidic bonds (acetal links); reducing sugars react with Benedict's reagent |
| Amino acids and proteins | An amine and a carboxylic acid on the same carbon; zwitterions; peptide (amide) bonds; hydrolysis by acid or enzymes |
| Lipids | Triglycerides are esters; saponification gives soap; unsaturation (C=C double bonds) and hydrogenation |
| Nucleotides | Sugar, phosphate, and nitrogenous base joined by phosphodiester bonds |
| Drugs | Aspirin (an ester of salicylic acid), paracetamol (an amide with a phenol group), and antibiotics contain familiar functional groups |
Study Method
Make a reaction map, learn the mechanisms with curved arrows, practise naming and drawing structures daily, use flash cards for reagents and conditions, and solve multi-step synthesis problems.
Common Mistakes
- Memorizing reactions without mechanisms.
- Misplacing curly arrows.
- Naming compounds from the wrong chain.
CHAPTER 19