Why an Enzyme Fits Its Substrate Like a Key in a Lock

Muscle, hair, antibodies, haemoglobin and the enzymes that digest food are all proteins — long chains of amino acids folded into precise shapes. The order of amino acids decides the shape, and the shape decides the job, which is why heat or acid can change how a protein behaves.

This lesson covers amino acids and the peptide bond, the four levels of protein structure, and enzymes as biological catalysts.

**Amino acids contain both an amino group and a carboxyl group, and a peptide bond, $-\mathrm{CO}-\mathrm{NH}-$, forms when the carboxyl group of one amino acid condenses with the amino group of another, releasing a water molecule.

Structure of alpha-amino acids:**

- General formula ${\mathrm{H}}_2\mathrm{N}-\mathrm{CH}(\mathrm{R})-\mathrm{COOH}$, with both groups on the same carbon
- About twenty amino acids make up proteins, differing only in their side chain R
- Glycine, with R = H, is the only one that is not optically active

Classification:

- Neutral, acidic or basic, depending on the numbers of amino and carboxyl groups: glycine is neutral, glutamic acid acidic and lysine basic
- Essential amino acids, such as lysine and valine, must come from food; non-essential ones, such as glycine and alanine, are made in the body

Zwitterions. In solution, an amino acid exists mainly as the dipolar ion ${\mathrm{H}}_3{\mathrm{N}}^{+}-\mathrm{CH}(\mathrm{R})-\mathrm{CO}{\mathrm{O}}^{-}$, acting as both acid and base, which explains its high melting point and water solubility.

Forming a peptide bond:

$${\mathrm{H}}_2\mathrm{NC}{\mathrm{H}}_2\mathrm{COOH}+{\mathrm{H}}_2\mathrm{NCH}(\mathrm{C}{\mathrm{H}}_3)\mathrm{COOH}\to {\mathrm{H}}_2\mathrm{NC}{\mathrm{H}}_2\mathrm{CONHCH}(\mathrm{C}{\mathrm{H}}_3)\mathrm{COOH}+{\mathrm{H}}_2\mathrm{O}$$

Glycine and alanine give the dipeptide glycylalanine; many amino acids give a polypeptide, and a polypeptide with a defined shape and function is a protein.

Worked example. Glycine (75 g mol${}^{-1}$) and alanine (89 g mol${}^{-1}$) give glycylalanine of molar mass $75+89-18=146$ g mol${}^{-1}$. A single chain of n amino acids has $n-1$ peptide bonds, so human insulin, with 51 amino acids in two chains, has $51-2=49$.

An everyday example. Dal and rice eaten together give a better balance of essential amino acids than either alone, because pulses are rich in lysine and cereals in methionine.

The substance. Glycylalanine and alanylglycine are different dipeptides — the order in which amino acids join matters, just as the order of letters matters in a word.

Protein structure has four levels: the primary structure is the amino acid sequence, the secondary structure is local folding into alpha-helices or beta-pleated sheets held by hydrogen bonds, the tertiary structure is the overall three-dimensional fold, and the quaternary structure is the arrangement of several chains.

Primary structure. The exact sequence of amino acids joined by peptide bonds; changing even one amino acid can change the protein's shape and function.

Secondary structure:

- Alpha-helix — the chain coils into a right-handed spiral, held by hydrogen bonds between the C=O of one residue and the N-H of a residue four places along
- Beta-pleated sheet — chains lie side by side in a zigzag, held by hydrogen bonds between neighbouring chains, as in silk

Tertiary structure:

- The overall folding of one chain, held by hydrogen bonds, disulphide bridges between cysteine residues, ionic attractions and hydrophobic interactions
- Produces long, insoluble fibrous proteins such as keratin, or compact, soluble globular proteins such as albumin and insulin

Quaternary structure. The arrangement of two or more polypeptide subunits, as in haemoglobin, with two alpha and two beta chains.

Denaturation. Heat, a change of pH or certain chemicals disrupt the forces holding the secondary and tertiary structure, so the protein loses its shape and function while its primary structure stays intact.

An everyday example. Paneer is made by adding lemon juice to hot milk, which denatures the milk proteins so that they clump and separate from the whey.

The substance. Denaturation destroys shape, not sequence — the proteins in paneer have lost their fold, but every peptide bond is still intact.

Enzymes are mostly globular proteins that speed up biochemical reactions by binding their substrate at an active site and lowering the activation energy; they are highly specific, work under mild conditions and can be inhibited.

How enzymes work:

$$\mathrm{E}+\mathrm{S}\rightleftharpoons \mathrm{ES}\to \mathrm{E}+\mathrm{P}$$

- The substrate binds to the active site, forming an enzyme-substrate complex
- The complex lowers the activation energy, the reaction occurs, and the products leave, freeing the enzyme
- In the lock-and-key model the active site fits the substrate exactly; in the induced-fit model it changes shape slightly as the substrate binds

Characteristics:

- Highly specific — maltase acts on maltose, sucrase on sucrose and urease on urea
- Optimum conditions — about 310 K for most human enzymes, pH about 2 for pepsin in the stomach and about 8 for trypsin in the small intestine
- Inhibition — competitive inhibitors block the active site, while non-competitive inhibitors bind elsewhere and change its shape

Worked example — rate enhancement. An enzyme that lowers the activation energy of a reaction from 86 to 50 kJ mol${}^{-1}$ at 310 K speeds it up by a factor of about

$$e^{(86000-50000)/(8.314\times 310)}=e^{13.97}\approx 1.2\times 10^6$$

An everyday example. Enzyme washing powders contain protease enzymes that break down protein stains such as blood and egg even in cool water.

The substance. Enzymes do not shift the position of equilibrium — like every catalyst, they only help a reaction reach equilibrium faster.