MHT-CET Chemistry · Biomolecules

Amino Acids, Peptides and Proteins

Alpha-amino acids carry an amino group and a carboxyl group on the same carbon and differ in the side chain R, which sets the class (acidic, basic, neutral) and the three- and one-letter code; they join through peptide (amide) bonds — n residues, n minus 1 bonds — into fibrous or globular proteins whose alpha-helix has 3.6 residues per turn.

All Biomolecules notes MHT-CET Chemistry strategy

Why this matters

27 PYQs, none HARD. Seventeen are the amino acids themselves — pick the acidic, basic, neutral or essential one from three-letter codes (asked nine times), the one-letter symbol, the side chain of serine or alanine, sulphur in methionine, the heterocyclic ring of histidine, the achiral glycine, the zwitterion; ten are peptides and proteins — how many bonds link n amino acids, glycylalanine, myosin as the fibrous one among globular proteins (asked six times), 3.6 residues per turn, pepsin. Two cards.

Concept 1 of 2

The Amino Acids by Side Chain: Class, Code and the Essential Ones

Intuition

Every alpha-amino acid is

\text{H}_2\text{N-CH(R)-COOH}

; only R changes. If R carries a second COOH the acid is ACIDIC (aspartic, glutamic); if R carries a second basic nitrogen it is BASIC (lysine, arginine, histidine); everything else is neutral. Glycine has R = H, so its alpha-carbon has two hydrogens and is the one achiral amino acid. Ten cannot be made in the body and must be eaten — the essential ones. In water the acid exists as a zwitterion: the NH₂ takes the COOH's proton.

Definition

Acidic: aspartic acid (Asp, D, R = –CH₂COOH), glutamic acid (Glu, E). Their amides asparagine (Asn) and glutamine (Gln) are NEUTRAL.
Basic: lysine (Lys, K), arginine (Arg, R), histidine (His, H — imidazole ring, a heterocycle). Proline is NOT basic (its N is in a ring, an imino acid).
Neutral: glycine (Gly, R = H, achiral), alanine (Ala, R = –CH₃), valine (Val, isopropyl), leucine (Leu, isobutyl), serine (Ser, –CH₂OH), threonine (Thr, –CH(OH)CH₃), cysteine (Cys, –CH₂SH), methionine (Met, –CH₂CH₂SCH₃), phenylalanine, tyrosine, tryptophan (Trp, indole), proline.
Sulphur: methionine and cysteine. Heterocyclic ring in R: histidine (imidazole), tryptophan (indole); proline's ring includes the alpha-N.
Essential (not synthesised in the body): histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine (arginine is semi-essential). Tyrosine, serine, glycine, glutamine, proline, cysteine, glutamic acid are non-essential.
Zwitterion of glycine: $\text{H}_3\text{N}^+\text{-CH}_2\text{-COO}^-$ — both groups charged, the molecule neutral overall.

Amino acid	3-letter / 1-letter	Side chain R	Class
Glycine	Gly / G	–H	Neutral, achiral
Alanine	Ala / A	–CH₃	Neutral
Serine	Ser / S	–CH₂OH	Neutral
Threonine	Thr / T	–CH(OH)CH₃	Neutral, essential
Methionine	Met / M	–CH₂CH₂SCH₃	Neutral, essential, has S
Leucine / Valine	Leu / L · Val / V	isobutyl · isopropyl	Neutral, essential
Tryptophan	Trp / W	indolylmethyl	Neutral, essential, heterocyclic
Aspartic acid	Asp / D	–CH₂COOH	Acidic D is aspartic acid; E is glutamic acid.
Glutamic acid	Glu / E	–CH₂CH₂COOH	Acidic
Lysine	Lys / K	–(CH₂)₄NH₂	Basic, essential
Arginine	Arg / R	guanidino	Basic
Histidine	His / H	imidazolylmethyl	Basic, essential, heterocyclic The one that is basic, essential and heterocyclic at once — the favourite answer.

Class follows the side chain: a second COOH is acidic, a second basic N is basic, everything else neutral.

Practice this conceptself-check · 4 quick reps

From the bank · past-year question

Example 1BiomoleculesMODERATE

Which from following amino acids contains heterocyclic ring at a side chain

(R)

group?

[Q53 · 22 April Shift I · 2025]

Gln and Asn read as acidic

Glutamine and asparagine are the AMIDES of the acidic pair — neutral. Only Glu and Asp, the free side-chain acids, are acidic; the three-letter codes differ by one letter.

Drill 16 more on the amino acids by side chain: class, code and the essential ones

Concept 2 of 2

Peptide Bonds, Protein Shape and Structure Levels

Intuition

A peptide bond is the amide –CO–NH– between the COOH of one amino acid and the NH₂ of the next, with loss of water; a chain of n residues has n − 1 of them, and the residues are named from the N-terminal end (glycylalanine = Gly then Ala). Proteins are FIBROUS (long threads: keratin, myosin, collagen, fibroin) or GLOBULAR (folded balls, water-soluble: insulin, albumins, legumelin, haemoglobin, enzymes). Structure has four levels; the secondary alpha-helix turns every 3.6 residues, held by N–H···O=C hydrogen bonds.

Definition

Peptide bond: $\text{-CO-NH-}$ ; dipeptide = 2 residues, 1 bond (glycylalanine, Gly-Ala); n residues ⇒ n − 1 bonds, so (n − 1) bonds link n amino acids.
Fibrous: keratin (hair, nails), myosin (muscle), collagen, fibroin (silk). Globular: insulin, egg albumin, serum albumin, legumelin, haemoglobin, myoglobin, enzymes.
Structure levels: primary = sequence; secondary = alpha-helix (3.6 residues per turn) or beta-pleated sheet, by hydrogen bonds; tertiary = overall fold (disulphide, ionic, H-bonds, hydrophobic); quaternary = several chains (haemoglobin).
Denaturation: heat or pH unfolds secondary/tertiary structure (boiled egg, curdled milk); the primary structure survives.
Proteases: pepsin (stomach) and trypsin (intestine) hydrolyse proteins to alpha-amino acids. 3-Aminobutanoic acid, $\text{CH}_3\text{CH(NH}_2)\text{CH}_2\text{COOH}$ , is an amino acid too — a beta one; COOH stays the principal group in the name.

Peptide-bond count

n\ \text{amino acids} \to (n-1)\ \text{peptide bonds};\qquad \alpha\text{-helix: } 3.6\ \text{residues per turn}

Worked example

A polypeptide has 51 residues. How many peptide bonds does it contain, and how many complete alpha-helical turns could 18 of those residues make?

Practice this conceptself-check · 4 quick reps

From the bank · past-year question

Example 2BiomoleculesEASY

How many amino acids are linked together by

(n-1)

amide bonds?

[Q51 · 15th May Shift 1 · 2023]

Insulin as fibrous

Insulin, albumins and legumelin are globular. In every 'NOT globular' or 'identify fibrous' question the answer has been myosin.

Drill 9 more on peptide bonds, protein shape and structure levels

Summary — formulas & gotchas at a glance

A revision cheat-sheet for the formulas and gotchas above. Click any concept name to jump back to its full explanation.

Formulas (1)

Peptide Bonds, Protein Shape and Structure Levels
Peptide-bond count
$n\ \text{amino acids} \to (n-1)\ \text{peptide bonds};\qquad \alpha\text{-helix: } 3.6\ \text{residues per turn}$

Reference tables (1)

The Amino Acids by Side Chain: Class, Code and the Essential Ones12 rows

Amino acid	3-letter / 1-letter	Side chain R	Class
Glycine	Gly / G	–H	Neutral, achiral
Alanine	Ala / A	–CH₃	Neutral
Serine	Ser / S	–CH₂OH	Neutral
Threonine	Thr / T	–CH(OH)CH₃	Neutral, essential
Methionine	Met / M	–CH₂CH₂SCH₃	Neutral, essential, has S
Leucine / Valine	Leu / L · Val / V	isobutyl · isopropyl	Neutral, essential
Tryptophan	Trp / W	indolylmethyl	Neutral, essential, heterocyclic
Aspartic acid	Asp / D	–CH₂COOH	Acidic D is aspartic acid; E is glutamic acid.
Glutamic acid	Glu / E	–CH₂CH₂COOH	Acidic
Lysine	Lys / K	–(CH₂)₄NH₂	Basic, essential
Arginine	Arg / R	guanidino	Basic
Histidine	His / H	imidazolylmethyl	Basic, essential, heterocyclic The one that is basic, essential and heterocyclic at once — the favourite answer.

Class follows the side chain: a second COOH is acidic, a second basic N is basic, everything else neutral.

Watch out for (2)

Gln and Asn read as acidic
→ The Amino Acids by Side Chain: Class, Code and the Essential Ones
Insulin as fibrous
→ Peptide Bonds, Protein Shape and Structure Levels

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