Proteins

An amino acid consists of a central carbon atom bonded to four groups: an amino group (—NH₂), a carboxyl group (—COOH), a hydrogen atom and a variable R group (side chain).

It is the R group that differs between the twenty amino acids and gives each its particular chemical properties.

(a) Every protein always contains the elements carbon (C), hydrogen (H), oxygen (O) and nitrogen (N). The nitrogen is the feature that distinguishes proteins from carbohydrates and lipids, which contain only C, H and O.

(b) Some R groups also contain sulfur (S) — for example in the amino acid cysteine. Two cysteine R groups can form a disulfide bridge (—S—S—), a strong covalent bond that helps to hold the tertiary structure of the protein in place.

A peptide bond forms by a condensation reaction between the carboxyl group (—COOH) of one amino acid and the amino group (—NH₂) of another. A water molecule is removed, and a peptide bond (—CO—NH—) is created between the two amino acids.

The peptide bond is broken by hydrolysis: a water molecule is added across the bond, splitting the —CO—NH— linkage and releasing the separate amino acids. In the gut this is catalysed by protease enzymes during protein digestion.

The tertiary structure is the overall three-dimensional shape of a single polypeptide chain. It develops as the secondary structures (α-helices and β-pleated sheets) fold and coil further, and it is stabilised by interactions between the R groups of the amino acids.

Four types of interaction hold the tertiary structure in place. Hydrogen bonds form between polar R groups; they are individually weak but very numerous. Ionic bonds form between R groups carrying opposite charges, such as a positively charged —NH₃⁺ group and a negatively charged —COO⁻ group. Disulfide bridges are strong covalent bonds (—S—S—) that form between the R groups of two cysteine amino acids. Hydrophobic interactions cause non-polar R groups to cluster together in the centre of the molecule, away from the surrounding water, while hydrophilic R groups face outward.

Because most of these bonds are weak and non-covalent, the tertiary structure can be disrupted by heat or changes in pH, which denatures the protein and changes its shape so that it can no longer carry out its function.

The primary structure is the specific sequence of amino acids in a polypeptide chain, joined by peptide bonds. The order of amino acids is determined by the gene that codes for the protein.

The secondary structure is the regular, local folding of the polypeptide backbone into an α-helix (a coil) or a β-pleated sheet. Both are held in place by hydrogen bonds between the —C=O group of one amino acid and the —N—H group of another along the backbone.

The quaternary structure exists only in proteins made of two or more polypeptide chains. It describes how those separate chains, together with any prosthetic groups (such as the haem groups in haemoglobin), are assembled into a single functional protein.

The secondary structure is the first level of folding of the polypeptide. It is the regular, repeating, local folding of the polypeptide backbone (not the R groups) into one of two patterns.

The first pattern is the α-helix, in which the chain coils into a right-handed spiral. The second is the β-pleated sheet, in which sections of the polypeptide lie alongside one another and the backbone zig-zags to give a pleated, sheet-like arrangement.

Both patterns are held together by hydrogen bonds. These form between the slightly negative oxygen of a —C=O group of one amino acid and the slightly positive hydrogen of an —N—H group of another amino acid further along the chain. Because these hydrogen bonds form at regular intervals along the backbone, they hold the helix or sheet in a stable, repeating shape.

Each individual hydrogen bond is weak, but there are very many of them, so collectively they make the secondary structure stable. However, because they are weak and non-covalent, they can be broken by heat or extremes of pH, which is one reason proteins denature.

(a) Trend. As temperature increases from 10 °C to 40 °C the rate increases to a peak (the optimum) of 48 arbitrary units at 40 °C. Above 40 °C the rate decreases sharply, falling to 6 units at 60 °C and reaching 0 units at 70 °C, where the reaction has stopped.

(b) Explanation. Up to the optimum, the rise in rate occurs because the higher temperature gives molecules more kinetic energy, so there are more frequent successful collisions between enzyme and substrate.

Above 40 °C, the extra kinetic energy makes the atoms in the enzyme vibrate more, which breaks the weak hydrogen bonds and ionic bonds holding the tertiary structure together. The enzyme's three-dimensional shape changes, so the shape of the active site is altered and is no longer complementary to the substrate. The substrate can no longer bind to form an enzyme–substrate complex, so fewer reactions are catalysed. By 70 °C the enzyme is fully denatured, the active site shape is permanently lost and the rate is zero.

Haemoglobin is a globular protein with quaternary structure, consisting of four polypeptide chains (two α-globin and two β-globin). Each chain holds a haem prosthetic group containing an Fe²⁺ ion, giving four oxygen-binding sites per molecule. Its hydrophobic R groups point inward and hydrophilic R groups point outward, so the molecule is soluble and rounded in shape. These features suit its transport function: it dissolves in the cytoplasm of red blood cells and binds oxygen reversibly, loading oxygen where the concentration is high (the lungs) and releasing it in respiring tissues.

Collagen is a fibrous protein made of three polypeptide chains wound tightly around one another into a triple helix, stabilised by hydrogen bonds. Many collagen molecules then line up with staggered ends and form covalent cross-links, building long, rope-like fibres. Collagen is insoluble and has high tensile strength. These features suit its structural role: it can withstand large pulling forces without breaking, which is why it provides support and strength in tendons, ligaments, skin, bone and the walls of arteries.

The contrast is therefore one of soluble, compact, oxygen-carrying globular protein versus insoluble, elongated, load-bearing fibrous protein — a clear illustration of how molecular structure determines biological function.

The primary structure of a protein is the specific sequence of amino acids joined by peptide bonds. This sequence is determined by the sequence of bases in the gene that codes for the protein.

The primary structure determines the higher levels of structure. Each amino acid has a particular R group, and the chemical properties of these R groups (whether they are charged, polar or non-polar) decide where bonds can form as the chain folds. Hydrogen bonds between backbone groups create the secondary structure (α-helices and β-pleated sheets), and interactions between R groups — hydrogen bonds, ionic bonds, disulfide bridges and hydrophobic interactions — fold the chain into its tertiary structure, the precise three-dimensional shape.

If one amino acid in the sequence is changed, its R group is different. This can mean that a bond which previously formed can no longer form, or that a new bond forms in a different position. For example, a hydrophilic amino acid replaced by a hydrophobic one may now sit on the surface or in the core in the wrong place, or a cysteine needed for a disulfide bridge may be lost.

As a result, the chain folds differently and the tertiary structure changes, so the overall three-dimensional shape is altered. If the protein is an enzyme, the shape of the active site changes, so the substrate no longer fits, the enzyme–substrate complex cannot form and the reaction is not catalysed. In a transport protein such as haemoglobin, an altered shape can change how it binds oxygen. In each case the change in primary structure has, through the levels of structure, led to a loss of the protein's normal function.

Both haemoglobin and collagen are built from the same kind of monomers — amino acids joined by peptide bonds — but they differ in how the higher levels of structure are organised, and this is what suits each to its role.

Haemoglobin is a globular protein. Its polypeptides fold so that the tertiary structure is compact and roughly spherical, with hydrophilic R groups on the outside and hydrophobic R groups buried in the core. Its quaternary structure brings together four chains, and each holds a haem prosthetic group with an Fe²⁺ ion. Because the molecule is compact and its surface is hydrophilic it is soluble, so it can be transported dissolved in the cytoplasm of red blood cells. The four haem groups give four oxygen-binding sites, and the precise three-dimensional shape allows oxygen to bind reversibly — it is loaded in the lungs and released in respiring tissues. So a globular tertiary/quaternary shape is ideal for a transport role.

Collagen is a fibrous protein. Here the higher structure is dominated not by a compact fold but by a secondary/quaternary arrangement in which three polypeptide chains coil around one another into a triple helix, held by hydrogen bonds, and many such molecules line up with staggered ends and form covalent cross-links to build long fibres. This makes collagen insoluble and gives it high tensile strength, so it resists pulling forces and provides structural support in tendons, skin, bone and artery walls.

In conclusion, the contrast is structural: a compact, soluble globular molecule with a quaternary shape built for binding and transport, versus an elongated, insoluble fibrous molecule built from repeating cross-linked helices for mechanical strength. The same chemistry of amino acids and peptide bonds, organised differently at the higher levels of structure, therefore produces two proteins with opposite properties and roles.