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Most students can define a peptide bond. Fewer can draw glycylalanine without hesitating over which end is which, or explain why Gly-Ala and Ala-Gly are different compounds. Those are the questions that turn up as one-mark traps. This post gives a four-step method for drawing any small peptide, the naming rule, and the counting questions that go with them.
Where is this in the syllabus?
The JEE (Main) 2026 syllabus and the NEET (UG) 2026 syllabus both list the "peptide bond" and "polypeptides" in the Biomolecules unit, and the JEE (Advanced) 2026 brochure lists "Peptide linkage" and the "Structure of peptides". The chemistry is in the NCERT Class 12 chapter Biomolecules (2026-27 reprint), section 10.2.3. NEET students should also read the protein section of the NCERT Class 11 Biology chapter Biomolecules, which sets out the left-to-right convention used below. Check the current year's syllabus for your exam.
What exactly is a peptide bond?
NCERT defines it as an amide formed between a –COOH group and an –NH2 group. The amino group of one amino acid combines with the carboxyl group of the other, a molecule of water is eliminated, and the link –CO–NH– remains. Its example is the one in this post's title: when the carboxyl group of glycine combines with the amino group of alanine, the dipeptide is glycylalanine.
The key word is *which* carboxyl and *which* amino group. Glycine and alanine can join in two ways, and the two products are different molecules.
How do you draw a dipeptide in four steps?
Take glycylalanine, Gly-Ala.
Write the first amino acid with its amino group on the left. Glycine: H2N–CH2–COOH.
Write the second amino acid to its right, also amino group first. Alanine: H2N–CH(CH3)–COOH.
Remove OH from the left acid's COOH and H from the right acid's NH2. That is the water lost.
Join the C=O to the N. H2N–CH2–CO–NH–CH(CH3)–COOH.
Now reverse the order. Alanylglycine, Ala-Gly, is H2N–CH(CH3)–CO–NH–CH2–COOH. The methyl group now sits next to the free amino end rather than the free carboxyl end.
Both have the formula C5H10N2O3: add glycine (C2H5NO2) and alanine (C3H7NO2) and subtract H2O. Same formula, different connectivity, so they are structural isomers. Hydrolysis of either gives back glycine and alanine, which is why a hydrolysis result alone cannot tell you the sequence.
How are peptides named?
The IUPAC-IUB recommendations on amino acid and peptide nomenclature (rule 3AA-13.1, published in Pure and Applied Chemistry in 1984) give the rule. Every residue except the C-terminal one is named as an acyl group ending in -yl. Only the C-terminal residue keeps its full amino acid name. IUPAC uses the same example: if glycine acylates alanine, the product is glycylalanine; in the reverse order it is alanylglycine. It adds that formulas should normally be written with the N-terminal residue on the left.
So:
Gly-Ala: glycylalanine
Ala-Gly: alanylglycine
Ala-Gly-Val: alanylglycylvaline
Worked example: name and analyse a tripeptide
Name H2N–CH(CH3)–CO–NH–CH2–CO–NH–CH(CH(CH3)2)–COOH.
Find the free NH2 end. It carries a CH3 side chain, so the N-terminal residue is alanine.
Move right. The next α-carbon is CH2, so glycine.
The last α-carbon carries (CH3)2CH–, which NCERT's Table 10.2 gives as the side chain of valine. It has the free COOH, so it is C-terminal.
Sequence Ala-Gly-Val; name alanylglycylvaline.
Three residues, two peptide bonds, two waters lost. Formula: alanine C3H7NO2 + glycine C2H5NO2 + valine C5H11NO2 = C10H23N3O6, minus 2H2O, gives C10H19N3O4.
How many peptides can a set of amino acids make?
Because order matters, this is a counting question.
From glycine and alanine, with repeats allowed, there are 2² = 4 dipeptides: Gly-Gly, Gly-Ala, Ala-Gly and Ala-Ala.
From glycine, alanine and valine, each used once, there are 3! = 6 tripeptides.
With repeats allowed, the same three give 3³ = 27 tripeptides.
From 20 amino acids, 20² = 400 dipeptides are possible.
A question that says "containing one each of" means no repeats. One that just says "from" usually allows them, so read it twice. Our post on counting permutations and combinations covers the reasoning.
Which mistakes cost marks?
Writing the C-terminal residue on the left, or naming it with -yl.
Treating Gly-Ala and Ala-Gly as the same compound.
Drawing the bond between two side chains, or between the α-carbon and nitrogen of the same residue.
Forgetting to subtract one water per peptide bond in a formula.
Counting n peptide bonds for n residues. It is n − 1.
A practice routine
Draw Gly-Ala and Ala-Gly side by side from memory and circle the peptide bond in each.
Write the six tripeptides of Gly, Ala and Val, with full names.
Work out the formula of Val-Ala and check it is C8H16N2O3.
Then link this to charge: our post on amino acids and zwitterions explains what the free ends do in water, and levels of protein structure takes the chain further.
If a structure in your book will not make sense on paper, the Fermi Concept Library covers every concept in chemistry and biology with its own lesson, so you can work through the idea one step at a time.
Start now: draw Ala-Gly-Val, label both ends, and write its name.
