3.1.4 Proteins and Enzymes

Proteins do almost every active job in a cell. The shape they fold into is what decides what they do, and the shape comes from the amino acid sequence the gene specifies. Enzymes are folded proteins whose shape catches one specific molecule and changes it.

Proteins are built from twenty amino acids joined by peptide bonds.

Proteins are polymers built from amino acid monomers. Every amino acid shares the same backbone, but the side chain at one position varies. Twenty different side chains are in use in human proteins, and that small alphabet is what gives proteins their range of shape and function.

Two amino acids joined this way produce a dipeptide. Three or more in sequence produce a polypeptide, and most functional proteins are polypeptides hundreds of residues long. Hydrolysis is the reverse of condensation: a water molecule is added across the peptide bond, splitting it back into the two amino acids. Protein digestion in the gut and protein turnover inside cells both happen this way.

Protein structure is built in four hierarchical levels.

Protein structure exists at four hierarchical levels. Each level builds on the one beneath it, and the chemistry at one level dictates what is possible at the next. The bond types involved differ at every level, which matters when you need to predict what disrupts what.

The bond hierarchy at tertiary level decides what gives way first when conditions change. Disulfide bridges are covalent; they resist heat and pH change. Hydrogen bonds and ionic bonds are weaker, and they are the bonds disrupted first when temperature rises past the optimum or pH moves out of range. Hydrophobic interactions hold non-polar R groups in the interior of the fold.

Write tertiary structure. Don't write 3-D structure, 3-D shape, or 3°. AQA rejects all three substitutions.

In denaturation, hydrogen bonds and ionic bonds give way. Don't write peptide bonds broken or disulfide bonds broken. Peptide bonds hold the backbone; disulfide bridges are covalent and resist heat and pH change.

The one-mark definition AQA credits for quaternary structure is a protein made of more than one polypeptide chain. Haemoglobin has four subunits, each with a haem group. Insulin has two chains held together by disulfide bridges. The haem groups in haemoglobin are prosthetic groups: non-protein components permanently bound to the protein.

Proteins divide by overall shape into globular and fibrous.

Proteins split into two functional categories defined by their overall tertiary shape. Globular proteins fold into compact rounded structures and are the proteins that do dynamic work, like catalysis and transport. Fibrous proteins fold into elongated structures and provide mechanical support across tissues that need to hold weight or run between attachment points. Enzymes are always globular.

Write active site for enzymes only. Non-enzyme proteins have binding sites. AQA rejects active site applied to haemoglobin, antibodies, or any other non-enzyme protein.

The Biuret test detects peptide bonds.

The Biuret test detects peptide bonds, and by extension the presence of protein. The chemistry targets the peptide bond directly, so anything with two or more peptide bonds tests positive.

1. Add an equal volume of sodium hydroxide solution to the protein sample.
2. Add a few drops of dilute (around 0.05%) copper(II) sulfate solution to the mixture.
3. Shake the test tube gently to mix the reagents through the sample evenly.
4. Observe the colour: pale blue indicates no peptide bonds present; lilac or purple confirms a positive result.

The test cannot identify which protein is present or how much. A dipeptide tests positive; a fully folded enzyme tests positive; both give the same colour change. It is the only protein test on the A-level specification, and it requires no heating and no acid digestion; the colour change happens in seconds at room temperature.

Enzymes lower activation energy through a complementary active site.

Enzymes are biological catalysts. Almost all enzymes are globular proteins, and they accelerate metabolic reactions without being consumed by the process. One enzyme molecule cycles through many reactions in succession, processing one substrate after another.

Don't write provides energy for the enzyme mechanism. The enzyme lowers the activation energy threshold. It does not supply energy to the reaction.

1. The enzyme lowers the activation energy that the substrate's bonds need to overcome for the reaction to proceed.
2. It does this by bending or stressing the bonds in the bound substrate, so the bonds open more easily than they would on their own.

Two models describe substrate-active site interaction. The lock-and-key model treats the active site as a rigid cavity; the substrate fits the cavity exactly. The induced fit model adds that the active site flexes as the substrate approaches, and this flex strains the substrate's bonds. Induced fit is the credited mechanism.

Write induced fit. Lock and key is the older model and does not earn the active-site shape-change mark. AQA expects awareness of both models but credits induced fit.

Phosphorylation regulates enzyme activity through this same structural logic. A phosphate group added to a specific amino acid residue, typically a serine, threonine, or tyrosine, introduces a strong negative charge. The charge alters the local R-group interactions, changes the tertiary structure, and reshapes the active site. Phosphorylation is reversible; a separate enzyme removes the phosphate.

Five factors set the rate at which an enzyme works.

Five factors affect the rate of an enzyme-controlled reaction. Each one changes the rate through a specific mechanism, and each has a characteristic curve shape on graphs.

Write higher temperature or increase the temperature. Temperature alone is rejected. When two temperatures are compared, the higher one carries more kinetic energy and disrupts bonds faster. The kinetic-energy step is the most consistently dropped mark on temperature comparisons.

On rate-against-time graphs, falling substrate concentration means the enzyme is consuming substrate and therefore working. It does not mean the enzyme has denatured. The x-axis variable decides the interpretation.

Inhibitors block enzymes in two distinct ways.

Inhibitors reduce or block enzyme activity. AQA examines two categories of reversible inhibitor, distinguished by where on the enzyme they bind and by what happens when more substrate is added.

Write similar in shape for the competitive inhibitor. Don't write same shape. Same implies the inhibitor is chemically identical to the substrate.

For non-competitive binding, write at a site other than the active site or at an allosteric site. Don't write beside the active site or next to the active site. AQA does not credit the proximity phrasing.

1. The inhibitor binds at a site other than the active site, or at an allosteric site.
2. The tertiary structure changes, altering the shape of the active site.
3. The active site is no longer complementary to the substrate, so the enzyme-substrate complex no longer forms.

Read the direction of the rate change before committing to a mechanism. A novel molecule binding to an enzyme might increase the rate (an activator) or decrease it (an inhibitor). The graph direction settles which.

Key terms

• active site
• tertiary structure
• enzyme-substrate complex
• complementary
• induced fit
• activation energy
• hydrogen bonds
• ionic bonds
• competitive inhibitor
• non-competitive inhibitor