Protein Structure & Enzymes

Proteins are made up of long chains of amino acids. There are four levels of protein structure, each determined ultimately by the sequence of amino acids:

1. Primary structure - the sequence of amino acids, joined by peptide bonds.
2. Secondary structure - the coiling or folding of sections of the chain into an alpha helix or a beta-pleated sheet (plus loops, coils and turns), held by hydrogen bonds between amino acids; this gives the final protein its stability.
3. Tertiary structure - the three-dimensional shape of the entire polypeptide chain, driven by hydrophobic interactions between non-adjacent amino acids and stabilised by hydrogen, ionic and disulfide bonds between R-groups.
4. Quaternary structure - the three-dimensional shape of a whole protein made up of several polypeptide chains (for example haemoglobin, collagen and insulin).

The four levels of protein structure: amino-acid sequence, local coiling and folding, the 3-D shape of one chain, and the assembled multi-chain protein.

Quaternary proteins often require helper molecules to assemble. Haemoglobin's four chains need iron to assemble into a functional protein; collagen is three polypeptides supercoiled like a rope; insulin has two chains; and antibodies are glycoproteins made of two light and two heavy chains, produced by B-lymphocytes.

STRUCTURE DETERMINES FUNCTION

The three-dimensional structure of a protein is critical to its function. A protein's structure determines the way it recognises, binds to and responds to other molecules: a biological reaction will only take place between an enzyme and a substrate if their shapes are complementary. Equally, if the structure of a protein is changed - denatured, for example by excessive heat - it loses its function.

WHAT PROTEINS DO

Proteins carry out most of the work of the cell. The main functional classes, with examples:

Two points deserve emphasis. Not all hormones are proteins, but protein hormones fold into shapes recognised by only one specific receptor on their target cell. Receptors themselves may sit in the membrane (integral proteins) or in the cytoplasm; when their signal molecule binds, signalling cascades inside the cell end with new gene products being made.

ENZYMES

Enzymes are proteins that catalyse biological reactions: they speed up a reaction without changing the amount of product formed and without being changed themselves, so each enzyme molecule can be reused and the cell needs only small amounts of each. Reactions take place at a small region of the enzyme called the active site, and each enzyme is specific to its substrate.

For any reaction to begin, an initial input of energy is required - the activation energy. Enzymes increase reaction rates by lowering the activation energy: they place stress on bonds within the substrate, making them easier to break, and they align substrates so that collisions are more likely to result in reactions. Without enzymes, biological reactions would require extreme temperatures and pH levels that are incompatible with life.

LOCK-AND-KEY AND INDUCED FIT MODELS

According to the traditional lock-and-key model, an enzyme binds a substrate only if their shapes fit together exactly. This is now considered an oversimplification, and an alternative, the induced fit model, is widely used. In this model the fit does not have to be perfect: when the substrate comes into close contact, the enzyme changes shape slightly to mould around it, forming an enzyme-substrate complex and creating a better fit. This places extra stress on the substrate's bonds. As the reaction proceeds an enzyme-product complex forms; finally the enzyme releases the product and returns to its original shape, ready for the next substrate.

In summary: enzyme + substrate → enzyme-substrate complex → enzyme-product complex → enzyme + products.

ANABOLIC AND CATABOLIC REACTIONS

FACTORS AFFECTING ENZYME FUNCTION

Enzymes usually function within a narrow range of conditions. The main factors affect the rate by altering the active site:

1. Temperature - each enzyme has an optimum temperature at which it works best (about 37 °C for human enzymes). Warming increases the kinetic energy of molecules, so enzyme-substrate collisions become more frequent and the rate rises. Above the optimum, excessive heat destroys chemical bonds within the enzyme and it denatures - a permanent change of shape and loss of function. Cooling merely slows and eventually stops the reaction, with no permanent damage.
2. pH - each enzyme has an optimum pH. Changes in pH change the charges within the enzyme and alter hydrogen bonding between amino acids, distorting the active site and reducing the enzyme's affinity for its substrate; extreme pH denatures the enzyme permanently. For example, certain digestive enzymes work only in the acidic (low pH) stomach and lose function in the alkaline (high pH) intestine.
3. Substrate concentration - the rate rises with substrate concentration until every active site is continuously occupied (saturation); after that the rate plateaus.
4. Enzyme concentration - more enzyme provides more active sites and a faster rate, until substrate runs short and the rate plateaus again.

The effect of temperature on enzyme function: the rate rises to an optimum, then falls sharply as the enzyme denatures.

INHIBITORS

Inhibitors are molecules that slow or stop enzyme activity - the working principle behind many drugs and pesticides. There are two types, distinguished by where they bind:

• Competitive inhibitors - similar in structure to the substrate, so they bind to the active site in place of the normal substrate and physically block the reaction. Because inhibitor and substrate compete for the same site, the effect can be overcome by increasing the substrate concentration.
• Non-competitive inhibitors - bind to the enzyme at a separate site away from the active site, called the allosteric site. The binding causes changes in the structure of the enzyme, including the active site, so that it no longer fits the substrate. Adding extra substrate makes no difference.

The effect of inhibitors on enzyme function: a competitive inhibitor occupies the active site; a non-competitive inhibitor binds an allosteric site and distorts the active site's shape.