Peptides and Amides

Spec Mapping — OCR A-Level Chemistry A (H432) Module 6.2.4 (b) — Amides and peptide bonds, covering: the structure of amides as $R\text{-CO-NR'R''}$ with classification into primary, secondary and tertiary by the substitution at nitrogen; nomenclature (drop -oic acid, add -amide; use N- prefix for nitrogen substituents); formation of amides from acyl chlorides + amine/NH₃ (nucleophilic addition-elimination, two equivalents of amine required); the peptide bond as an amide linkage between two α-amino acid residues; the building of dipeptides, tripeptides, polypeptides and proteins from amino acid monomers by condensation; acid hydrolysis of peptides (6 mol dm⁻³ HCl, prolonged reflux) yielding amino acid cations and base hydrolysis (NaOH reflux) yielding amino acid carboxylate salts; and the resistance of amides to hydrolysis explained by the delocalisation of the N lone pair into the C=O π system (refer to the official OCR H432 specification document for exact wording).

Amides are a class of carbonyl compounds in which the C=O carbon is bonded to nitrogen instead of oxygen (ester) or chlorine (acyl chloride). They are the single most important functional group in biology — every protein in every living thing is held together by peptide bonds, which are simply amide linkages between amino acid residues. The same chemistry also gives us nylon (Lesson 9), Kevlar (Lesson 9), paracetamol (an N-substituted amide), penicillin (with its strained β-lactam ring, an amide variant), and the headline anti-cancer drug Taxol (which contains both ester and amide linkages). Understanding amide chemistry therefore opens a door to large swathes of biology, materials science and pharmacology simultaneously.

This lesson covers the OCR A-Level Chemistry A (H432) specification point 6.2.4 (b): formation and hydrolysis of peptide bonds in amides and proteins. It builds directly on Lesson 5 (acyl chlorides — the cleanest amide synthesis), Lesson 6 (amines — the nucleophile) and Lesson 7 (amino acids — the building blocks of peptides), and feeds forward into Lesson 9 (condensation polyamides like nylon-6,6 and Kevlar) and Lesson 10 (hydrolysis of polymers, where the same chemistry is applied to industrial-scale plastics recycling). The unifying theme is the carbonyl in amides: less reactive than acyl chloride or ester, but still hydrolysable under harsh enough conditions.

1. Amides — Structure and Nomenclature

1.1 Structure

An amide has the general formula R–CONR'R'', where R, R' and R'' can be H or a carbon chain. The carbonyl carbon is bonded to:

An oxygen (=O)
A nitrogen (–NR'R'')
A carbon (R) or hydrogen

Classification of amides:

Type	Nitrogen substitution	Example
Primary (unsubstituted)	–NH₂	CH₃CONH₂ ethanamide
Secondary (N-substituted)	–NHR'	CH₃CONHCH₃ N-methylethanamide
Tertiary (N,N-disubstituted)	–NR'R''	CH₃CON(CH₃)₂ N,N-dimethylethanamide

Note that "primary/secondary/tertiary" for amides counts carbons on the nitrogen of the amide — the same convention as amines (and different from alcohols).

1.2 Nomenclature

Take the parent carboxylic acid name, drop -oic acid, and add -amide.
For N-substituted amides, prefix the name with N-methyl-, N-ethyl- etc. showing substituents on the nitrogen.

Formula	Name
HCONH₂	Methanamide
CH₃CONH₂	Ethanamide
CH₃CH₂CONH₂	Propanamide
CH₃CONHCH₃	N-methylethanamide
CH₃CON(CH₃)₂	N,N-dimethylethanamide

2. How Amides Form

Amides are made by reacting an amine (or ammonia) with a carbonyl compound that has a good leaving group. At A-Level you meet two routes:

2.1 Acyl chloride + amine (preferred)

As seen in Lesson 5:

$CH_3COCl + 2CH_3NH_2 \longrightarrow CH_3CONHCH_3 + CH_3NH_3^+Cl^-$

Fast, at room temperature.
Mechanism: nucleophilic addition-elimination.
Needs two equivalents of the amine: one to react, one to mop up HCl.

2.2 Carboxylic acid + amine (difficult)

$R-COOH + R'-NH_2 \longrightarrow R-CONHR' + H_2O$

In principle the same "condensation" you saw with esters, but it does not work at room temperature.
The amine is basic, the acid is acidic → they just form a salt (R-COO⁻ R'-NH₃⁺) rather than an amide.
Industrially, high temperatures (200 °C+) or activating reagents are needed.
Not tested directly by OCR, but a reminder that amides are best made from acyl chlorides.

3. The Peptide Bond

3.1 What is a peptide bond?

When two amino acids link together, the –COOH of one reacts with the –NH₂ of another, eliminating water and forming an amide bond between them. This amide is called a peptide bond.

$H_2N-CHR_1-COOH + H_2N-CHR_2-COOH \longrightarrow H_2N-CHR_1-CO-NH-CHR_2-COOH + H_2O$

The product is a dipeptide. Repeating this process builds up a chain:

Dipeptide: 2 amino acids, 1 peptide bond.
Tripeptide: 3 amino acids, 2 peptide bonds.
Oligopeptide: a few amino acids.
Polypeptide or protein: many (often 50+) amino acids.

graph LR
  A[Amino acid 1 -COOH] --> C[Peptide bond -CO-NH-]
  B[Amino acid 2 H2N-] --> C
  C --> D[Dipeptide + H2O]

3.2 Drawing peptide bonds

You need to be able to spot and draw a peptide bond in a structural formula. The bond itself is the –CO–NH– linkage between two amino acid residues. Around it you will see the α-carbons of the two residues with their side chains R₁ and R₂.

Example — glycylalanine (a dipeptide from glycine + alanine):

The peptide bond is the CO–NH between them.

3.3 Proteins as polyamides

A protein is a polypeptide with (usually) dozens to thousands of amino acid residues strung together by peptide bonds. Because every bond in the backbone is a –CO–NH–, the entire protein backbone is a giant polyamide. The three-dimensional folding — α-helices, β-sheets, and the final "tertiary structure" — is held in place by hydrogen bonds, disulfide bridges, hydrophobic interactions and ionic bonds between side chains.

4. Hydrolysis of Peptides and Amides

Any amide can be broken back apart into its carboxylic acid (or amine) components by hydrolysis — just like an ester. But amides are much more resistant than esters because the C=O carbon is less electrophilic (the nitrogen lone pair donates into the carbonyl by resonance). Hydrolysis therefore needs harsh conditions.

4.1 Acid hydrolysis

$R-CONHR' + H_2O + HCl \longrightarrow R-COOH + R'-NH_3^+Cl^-$

Reagents: 6 mol dm⁻³ HCl, prolonged reflux (several hours), often at 100 °C or higher.
The amine is protonated and released as an ammonium salt.
The carboxylic acid is released in its free form.

For a peptide, acid hydrolysis breaks every peptide bond, releasing the constituent amino acids (each as their cation ⁺H₃N-CHR-COOH because of the acidic conditions).

4.2 Base hydrolysis

$R-CONHR' + NaOH \longrightarrow R-COO^-Na^+ + R'-NH_2$

Reagents: Aqueous NaOH, reflux.
The carboxylic acid is released as its sodium salt.
The amine is released in its free form.

For a peptide, base hydrolysis releases amino acids as carboxylate salts (H₂N-CHR-COO⁻ Na⁺). You would then acidify to get the free amino acids (in their zwitterionic form).

4.3 Comparison with ester hydrolysis

Feature	Ester hydrolysis	Amide hydrolysis
Speed	Minutes to hours	Hours to days
Temperature	Reflux in dilute acid/base	Reflux in concentrated acid/base
Why the difference	C=O is reactive	N lone pair donates into C=O, reducing reactivity
Biological role	Digestion of fats	Digestion of proteins (by proteases)

In the body, proteases (protein-cleaving enzymes) hydrolyse peptide bonds at body temperature and neutral pH — they catalyse the reaction that, without an enzyme, would require hours of boiling 6 M HCl.

5. Why Amides Are So Stable

Amides are far less reactive than acyl chlorides, esters or even carboxylic acids. Three reasons:

The nitrogen lone pair donates into the C=O by resonance. Electron density flows from N into the π* of C=O, partly filling the δ+ charge on C and making it less electrophilic.
The C–N bond has partial double bond character — which is why peptide bonds are essentially planar and cannot rotate freely.
The leaving group in hydrolysis (NH₂⁻ or the amine) is a poor leaving group compared to Cl⁻ or RO⁻.

This combination is what makes proteins chemically stable enough to build a body out of, while still being hydrolysable by enzymes when food needs to be digested.

graph LR
  A[Amide R-CO-NR'R''] --> B[N lone pair donates into C=O]
  B --> C[Less delta+ on C]
  C --> D[Resistant to nucleophiles]
  B --> E[C-N bond has partial double-bond character]
  E --> F[Peptide bond is planar, restricts protein shape]

6. From Dipeptides to Proteins — Building a Polypeptide Chain

A useful exam exercise is to predict the products of joining specific amino acids. Two amino acids can be linked in two orderings (with either's COOH reacting with the other's NH₂), giving two distinct dipeptides. For glycine + alanine:

Glycylalanine (gly-ala, abbreviated G-A): glycine's COOH reacts with alanine's NH₂. Sequence: H₂N-CH₂-CO-NH-CH(CH₃)-COOH.
Alanylglycine (ala-gly, A-G): alanine's COOH reacts with glycine's NH₂. Sequence: H₂N-CH(CH₃)-CO-NH-CH₂-COOH.

These are structural isomers with the same molecular formula but different connectivity — they would chromatograph differently, react with chiral enzymes differently, and have different biological properties. Tripeptides allow $3! = 6$ orderings; tetrapeptides $4! = 24$ . A typical 100-amino-acid protein has $20^{100} \approx 10^{130}$ possible sequences, which is more than the number of atoms in the visible universe.

By convention, peptide sequences are read from the N-terminus (the end with the free –NH₂) to the C-terminus (the end with the free –COOH). In G-A above, glycine is the N-terminus and alanine the C-terminus.

6.1 Protein structure levels

OCR does not require the detail, but the four levels of protein structure are:

Primary structure — the linear sequence of amino acid residues, joined by peptide bonds. This is the chemistry of this lesson.
Secondary structure — local folding into α-helices or β-pleated sheets, held together by hydrogen bonds between the backbone C=O of one residue and the backbone N–H of another four residues away (α-helix) or in an adjacent strand (β-sheet).
Tertiary structure — the three-dimensional folding of the whole polypeptide chain into a compact shape, stabilised by side-chain interactions (hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic clustering).
Quaternary structure — assembly of multiple polypeptide subunits (e.g. haemoglobin has four — two α and two β chains).

The chemistry of the peptide bond is what makes all these higher structures possible: the planarity of the bond restricts rotation and forces the chain into specific local geometries; the C=O and N–H groups are perfectly placed to form repeating hydrogen-bond patterns.

Synoptic Links

Synoptic Links — Connects to:

ocr-alevel-chemistry-carbonyls-polymers-spectroscopy / acyl-chlorides (Lesson 5 — the cleanest amide synthesis is acyl chloride + amine; the nucleophilic addition-elimination mechanism reappears here).

ocr-alevel-chemistry-carbonyls-polymers-spectroscopy / amines (Lesson 6 — the basic / nucleophilic amine is one half of the peptide bond; the same chemistry that lets an amine attack an acyl chloride lets an amino acid's NH₂ attack the next amino acid's activated COOH).

ocr-alevel-chemistry-carbonyls-polymers-spectroscopy / amino-acids-chirality (Lesson 7 — peptides are built from α-amino acid monomers, each contributing one C=O and one N–H to the backbone).

ocr-alevel-chemistry-carbonyls-polymers-spectroscopy / condensation-polymers (Lesson 9 — nylon-6,6 and Kevlar are polyamides whose chemistry is the polymeric version of the peptide bond explored here).

ocr-alevel-chemistry-carbonyls-polymers-spectroscopy / hydrolysis-and-comparison-of-polymers (Lesson 10 — hydrolysis of polyamides reuses the same acid/base hydrolysis chemistry from this lesson, scaled to long chains).

ocr-alevel-chemistry-carbonyls-polymers-spectroscopy / chromatography (Lesson 12 — TLC with ninhydrin staining identifies amino acids after peptide hydrolysis, a common A-Level exam pattern).

ocr-alevel-chemistry-carbonyls-polymers-spectroscopy / esters-esterification-hydrolysis (Lesson 4 — amide hydrolysis is a slower, harsher cousin of ester hydrolysis; the comparison is mark-scheme territory).

Practical Activity Group anchor: PAG 6 — Synthesis of an organic solid. The bench-scale preparation of paracetamol (an N-substituted amide of 4-aminophenol + ethanoic anhydride) is a classic PAG 6 amide synthesis exercise: the reaction is essentially the acyl chloride / anhydride + amine mechanism from this lesson. Students stir the mixture, isolate the product by filtration after the reaction has cooled, recrystallise from water, dry, and determine yield + melting point as quality controls. The melting point of pure paracetamol is 168-170 °C, allowing students to assess purity by mp comparison.

Specimen question modelled on the OCR H432 paper format

Question (9 marks): A dipeptide is formed from glycine ( $NH_2CH_2COOH$ ) and alanine ( $NH_2CH(CH_3)COOH$ ).

(a) Draw the structural formula of the dipeptide glycylalanine (gly-ala), clearly identifying the peptide bond. (2 marks)

(b) Explain how the dipeptide can be hydrolysed back to free amino acids. State the reagents and conditions, and predict the products under (i) acidic conditions and (ii) basic conditions. (4 marks)

Lesson 8: Peptides and Amides