Amino acids and peptides

Every protein in your body — the keratin in your hair, the haemoglobin carrying oxygen, the enzymes digesting your last meal — is built from the same small alphabet of about twenty amino acids, strung together one peptide bond at a time. An amino acid is a deceptively simple molecule: an amino group and a carboxyl group sitting on the same carbon, with a variable side chain that gives each amino acid its personality. But that simplicity hides a trick. In water, an amino acid does not sit as the neutral structure you draw on paper — it flips into a doubly-charged zwitterion, and that single fact explains why amino acids behave like ionic solids rather than ordinary organic molecules: high melting points, water solubility, and a net charge that swings from positive to negative as the pH changes. This article builds the general structure and classification of amino acids, the zwitterion and isoelectric point, and the condensation reaction that links amino acids into peptides and polypeptides — the last piece of groundwork before protein structure itself.

The core insight

An amino acid's amino and carboxyl groups undergo an internal proton transfer to form a charged zwitterion whose net charge — cationic below its isoelectric point, anionic above it — controls its physical behaviour, while successive condensation reactions between the –COOH of one amino acid and the –NH₂ of the next build peptide bonds into polypeptide chains.

The core idea

General structure. An α-amino acid carries an amino group (−NH2-\text{NH}_2) and a carboxyl group (−COOH-\text{COOH}) on the same carbon (the α-carbon), plus a hydrogen and a side chain R:

H2N–CH(R)–COOH\text{H}_2\text{N–CH(R)–COOH}

where: R is the side chain that distinguishes one amino acid from another (H for glycine, CH3\text{CH}_3 for alanine, and so on). Except for glycine, the α-carbon has four different groups attached, so it is chiral — amino acids are optically active, and the ones built into proteins are almost exclusively the L-configuration.

Two ways to classify. By the balance of acidic and basic groups: acidic amino acids have more −COOH-\text{COOH} than −NH2-\text{NH}_2 (aspartic acid, glutamic acid); basic have more −NH2-\text{NH}_2 than −COOH-\text{COOH} (lysine, arginine); neutral have equal numbers of each (glycine, alanine). By dietary origin: essential amino acids cannot be made by the body and must come from food (valine, leucine); non-essential ones the body synthesises itself (glycine, alanine).

The zwitterion. Because the same molecule carries an acidic and a basic group, an internal acid-base reaction transfers a proton from −COOH-\text{COOH} to −NH2-\text{NH}_2:

H2N–CH(R)–COOH  ⇌  +H3N–CH(R)–COO−\text{H}_2\text{N–CH(R)–COOH} \;\rightleftharpoons\; {}^{+}\text{H}_3\text{N–CH(R)–COO}^{-}

This dipolar form — the zwitterion — is the dominant species in the solid state and in neutral solution. It is why amino acids resemble ionic solids: strong electrostatic attractions between −NH3+-\text{NH}_3^+ and −COO−-\text{COO}^- of neighbouring molecules give unusually high melting points, good solubility in water, and poor solubility in non-polar solvents.

Isoelectric point. Because the zwitterion holds one positive and one negative charge, an amino acid's net charge depends on the pH of its surroundings. The isoelectric point (pIpI) is the pH at which the amino acid exists predominantly as the neutral zwitterion, with zero net charge, so it does not migrate toward either electrode in electrophoresis. Below pIpI, excess H+\text{H}^+ keeps the amino group protonated, giving a net positive (cationic) species; above pIpI, the carboxyl group is deprotonated and the molecule is net negative (anionic). Each amino acid has its own pIpI, fixed by how acidic or basic its side chain is — acidic amino acids sit at a low pIpI, basic ones at a high pIpI.

Figure
A charge diagram showing an amino acid as cationic below its isoelectric point, neutral zwitterion at the isoelectric point, and anionic above it, with an arrow for increasing pH
Net charge of an amino acid as pH rises past its isoelectric point increasing pH +H3N–COOH cationic, pH less than pI +H3N–COO- zwitterion, net zero at pI H2N–COO- anionic, pH greater than pI migrates to cathode stays put at electrophoresis start line migrates to anode

The peptide bond. Two amino acids join by a condensation reaction: the −COOH-\text{COOH} of one attacks the −NH2-\text{NH}_2 of another, expelling a water molecule and leaving an amide linkage called the peptide bond (−CO–NH−-\text{CO–NH}-):

H2N–CH(R1)–COOH+H2N–CH(R2)–COOH⟶H2N–CH(R1)–CO–NH–CH(R2)–COOH+H2O\text{H}_2\text{N–CH(R}_1\text{)–COOH} + \text{H}_2\text{N–CH(R}_2\text{)–COOH} \longrightarrow \text{H}_2\text{N–CH(R}_1\text{)–CO–NH–CH(R}_2\text{)–COOH} + \text{H}_2\text{O}

Two amino acids give a dipeptide; more amino acids joined in sequence give a polypeptide, and proteins are large, biologically functional polypeptides (or assemblies of them).

Derivation APeptide bonds and water lost when n amino acids condense

The goal is a quantitative accounting rule for building any polypeptide chain: given n amino acid units joining end to end by the condensation reaction above, find how many peptide bonds form, how many water molecules are released, and how the polypeptide's molar mass relates to the sum of the free amino acids' masses — a relation used constantly to check peptide-synthesis and hydrolysis problems.

Step 1. Start with two amino acids. One condensation reaction consumes two free amino acid molecules and produces one dipeptide plus one water molecule. That is exactly one peptide bond formed for one water molecule lost — the bond count and the water count move together, one-for-one.

Step 2. Extend to three amino acids joined in sequence (a tripeptide). Joining amino acid 1 to amino acid 2 forms the first peptide bond and releases the first water. Joining that dipeptide to amino acid 3 forms a second peptide bond and releases a second water. Three amino acids therefore need two condensation steps, not three — every new unit added to an existing chain contributes exactly one new bond and one new water molecule, but the very first unit has nothing to bond to yet.

Step 3. Generalise to n amino acids joined into one polypeptide chain. Each amino acid after the first one added to the growing chain contributes exactly one peptide bond and releases exactly one water molecule, so a chain of n amino acids contains (n−1)(n-1) peptide bonds and releases (n−1)(n-1) water molecules overall:

number of peptide bonds=number of water molecules lost=n−1\text{number of peptide bonds} = \text{number of water molecules lost} = n - 1

Step 4. Turn this into a mass relation. If the n free amino acids have individual molar masses M1,M2,…,MnM_1, M_2, \ldots, M_n, condensation removes one water molecule (18 g mol−118\ \text{g mol}^{-1}) per bond formed, so the polypeptide's molar mass is

Mpolypeptide=(∑i=1nMi)−(n−1)(18)M_{\text{polypeptide}} = \left(\sum_{i=1}^{n} M_i\right) - (n-1)(18)

This is the same bookkeeping used later for full protein hydrolysis, run in reverse: hydrolysing a polypeptide back to n free amino acids adds back exactly (n−1)(n-1) water molecules.

Worked example

Question. Four amino acids — glycine (M=75 g mol−1M = 75\ \text{g mol}^{-1}), alanine (M=89 g mol−1M = 89\ \text{g mol}^{-1}), alanine again, and glycine again — condense in that order into a single tetrapeptide (Gly-Ala-Ala-Gly). Find the number of peptide bonds formed, the mass of water released, and the molar mass of the tetrapeptide.

Step 1. Count the amino acid units: n=4n = 4. By the derivation above, the number of peptide bonds is n−1=3n - 1 = 3, and the number of water molecules released is also 33.

Step 2. Sum the free amino acid masses: 75+89+89+75=328 g mol−175 + 89 + 89 + 75 = 328\ \text{g mol}^{-1}.

Step 3. Subtract the mass lost as water: 3×18=54 g mol−13 \times 18 = 54\ \text{g mol}^{-1} is released, so

Mtetrapeptide=328−54=274 g mol−1M_{\text{tetrapeptide}} = 328 - 54 = 274\ \text{g mol}^{-1}

Step 4. Sanity-check against the definition: a tetrapeptide has exactly one fewer peptide bond than it has amino acid residues, because the first residue in the chain has no bond behind it. Answer: 3 peptide bonds, 54 g of water released per mole of tetrapeptide formed, and the tetrapeptide's molar mass is 274 g mol⁻¹.

Competitive stretch

If instead you are told a polypeptide's molar mass is 274 g mol−1274\ \text{g mol}^{-1} and that it hydrolyses completely into four amino acids of total free mass 328 g mol−1328\ \text{g mol}^{-1}, you can work backwards: the mass gained on hydrolysis is 328−274=54 g mol−1328 - 274 = 54\ \text{g mol}^{-1}, which is 54/18=354/18 = 3 water molecules added — confirming n−1=3n - 1 = 3 bonds were broken, so n=4n = 4 amino acids were present, without ever being told the sequence.

Common traps

  • Drawing the neutral, non-ionised structure when asked to explain physical properties — high melting point and water solubility follow from the zwitterion, not the textbook neutral form.
  • Treating isoelectric point as a fixed universal value like pH 7 — pIpI is unique to each amino acid's side chain; acidic amino acids sit well below 7, basic ones well above.
  • Counting peptide bonds equal to the number of amino acids — a chain of nn amino acids has only (n−1)(n-1) peptide bonds and releases only (n−1)(n-1) water molecules, not nn.
  • Forgetting that the peptide bond forms by condensation (loss of water), not by simple mixing or addition of the two amino acids.

Ask the tutor: want to work through predicting an amino acid's net charge at several pH values around its pIpI, or extend the bond-counting relation to a full protein hydrolysis problem?

Why does the zwitterion form at all — why would an amino acid ionise itself internally with no external acid or base added

Because the molecule already contains both an acidic group (−COOH-\text{COOH}) and a basic group (−NH2-\text{NH}_2) on the same small structure, close enough together that the carboxyl proton simply hops onto the amino nitrogen — an intramolecular acid-base reaction needing no outside reagent. The equilibrium strongly favours the zwitterion in the solid state and near-neutral solution because the resulting dipolar ion is electrostatically stabilised, much like how a salt is more stable as separated ions than as a covalent pair. This is exactly why amino acids behave like ionic solids rather than ordinary small organic molecules.

If glycine's isoelectric point is around pH 6, does that mean it is basic at pH 6

No — at pH=pIpH = pI the amino acid is neutral overall, not basic or acidic; it exists predominantly as the zwitterion with equal positive and negative charge, so the net charge is zero. "Basic" and "acidic" as classification labels (by number of −NH2-\text{NH}_2 versus −COOH-\text{COOH} groups) describe the amino acid's side-chain chemistry and its typical pIpI range, not its charge state at any one specific pH. Below its own pIpI any amino acid picks up a net positive charge, and above it a net negative charge, regardless of whether it is classified as acidic, basic, or neutral.

Does a peptide bond ever break back apart into two amino acids on its own

Not spontaneously under normal conditions — the peptide bond is a stable amide linkage. It is broken deliberately by hydrolysis, the reverse of the condensation reaction: adding a water molecule back across the −CO–NH−-\text{CO–NH}- bond regenerates the free −COOH-\text{COOH} and −NH2-\text{NH}_2 groups, usually helped along by acid, base, or an enzyme (a protease) as a catalyst. This is exactly why the mass-balance relation in the derivation above works in both directions — build a chain and lose water, or break it apart and gain water back, one molecule per bond each time.

Before this

Where this leads