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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 notesMHT-CET Chemistry strategy

Why this matters

46 PYQs, none HARD. Of the twenty-seven set from 2021 to 2025, 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

Every alpha-amino acid is H2N-CH(R)-COOH\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: H3N+-CH2-COO−\text{H}_3\text{N}^+\text{-CH}_2\text{-COO}^- — both groups charged, the molecule neutral overall.
Amino acid3-letter / 1-letterSide chain RClass
GlycineGly / G–HNeutral, achiral
AlanineAla / A–CH₃Neutral
SerineSer / S–CH₂OHNeutral
ThreonineThr / T–CH(OH)CH₃Neutral, essential
MethionineMet / M–CH₂CH₂SCH₃Neutral, essential, has S
Leucine / ValineLeu / L · Val / Visobutyl · isopropylNeutral, essential
TryptophanTrp / WindolylmethylNeutral, essential, heterocyclic
Aspartic acidAsp / D–CH₂COOHAcidic
D is aspartic acid; E is glutamic acid.
Glutamic acidGlu / E–CH₂CH₂COOHAcidic
LysineLys / K–(CH₂)₄NH₂Basic, essential
ArginineArg / RguanidinoBasic
HistidineHis / HimidazolylmethylBasic, 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.
Practise this conceptself-check · 4 quick reps

The same idea in a real exam question:

MHT-CET · 2025 · 22 April Shift I · Q53Moderate

Example 1 · Biomolecules · Amino Acids, Peptides and Proteins

Which from following amino acids contains heterocyclic ring at a side chain (R)(R) group?

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

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: -CO-NH-\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, CH3CH(NH2)CH2COOH\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 amino acids→(n−1) peptide bonds;α-helix: 3.6 residues per turnn\ \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?
Practise this conceptself-check · 4 quick reps

The same idea in a real exam question:

MHT-CET · 2023 · 15th May Shift 1 · Q51Easy

Example 2 · Biomolecules · Amino Acids, Peptides and Proteins

How many amino acids are linked together by (n−1)(n-1) amide bonds?

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 amino acids→(n−1) peptide bonds;α-helix: 3.6 residues per turnn\ \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 acid3-letter / 1-letterSide chain RClass
GlycineGly / G–HNeutral, achiral
AlanineAla / A–CH₃Neutral
SerineSer / S–CH₂OHNeutral
ThreonineThr / T–CH(OH)CH₃Neutral, essential
MethionineMet / M–CH₂CH₂SCH₃Neutral, essential, has S
Leucine / ValineLeu / L · Val / Visobutyl · isopropylNeutral, essential
TryptophanTrp / WindolylmethylNeutral, essential, heterocyclic
Aspartic acidAsp / D–CH₂COOHAcidic
D is aspartic acid; E is glutamic acid.
Glutamic acidGlu / E–CH₂CH₂COOHAcidic
LysineLys / K–(CH₂)₄NH₂Basic, essential
ArginineArg / RguanidinoBasic
HistidineHis / HimidazolylmethylBasic, 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)

Test yourself on Biomolecules

20 past MHT-CET questions from this chapter, timed at 18 minutes and marked the way the exam marks it. You see your score and every answer the moment you finish. Free to start.

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