Enzymes

All enzymes are globular proteins (water soluble), act as catalysts, are specific, have an active site and their activity is affected by temperature and pH.

The active site of an enyme is where the catalytic activity of the enzyme occurs. It has a very specific, individual active site shape maintained by the tertiary structure. Often fewer than 10 amino acids form the actual active site, while the enyme consists of 100's.

They are often referred to as biological catalysts. A catalyst is defined as a molecule that speeds up a chemical reaction but doesn't get used up. Industries have started using enzymes. Metabolism can be described as enzyme-driven.

The substrate is turned into a product.

Extracellular enzymes catalyse reactions outside the cell. Intracellular enzymes catalyse reactions inside the cell.

Lactase - Catalyses the breakdown of lactose (milk sugar) into glucose and galactose

Catalase - Catalyses the breakdown of hydrogen peroxide to water and oxygen gas

Ribulose biphosphate carboxylase (Rubisco) - Catalyses the binding of carbon dioxide to ribulose biphosphate

ATP-ase - Catalyses the breakdown of ATP to produce ADP and a phosphate group

Glycogen synthase - Catalyses the joining together of glucose molecules to form glycogen

Covalently bonded molecules are very stable. The activation energy is the amount of energy that must be applied for the reaction to proceed.

Enzymes drive metabolic reactions by lowering the activation energy needed. They are essential as otherwise reactions would be far too slow. The lock and key hypothesis is that the substrate is the key and the enzyme is the lock. Once they are in place then the reaction will proceed.

A new hypothesis is the induced-fit hypothesis. This is that when a substrate molecule collides with an enyme then the active site shape changes slightly by fitting more closely around the substrate. Oppositely charged groups on the substrate and active site are close to each other to hold the substrate in place. This forms an enyme-substrate complex. This puts a strain on the substrate making it easier to destabilise it. The products formed are a different shape and so can move out of the enzyme, leaving it free to catalyse the same reaction with a new substrate.

Increasing temperature increases the kinetic energy the molecules have. There are more frequent collisions and this increases the rate of reaction. However, the vibrations in the enzyme can break the weaker bonds holding together the tertiary structure which can unravel and the active site can be lost, so the enzyme stops working. This is irreversible and is known as denaturation. 

The lower the pH, the more hydrogen ions there are. These can interfere with hydrogen bonds and ionic bonds in the tertiary structure. The hydrogen ions can replace the hydrogen bonds by being attracted to the negative charges in the enzyme. This could also alter the charges in the active site which hold the substrate in place. At the optimum pH, the protons would give the active site it's best overall shape.

Increasing the concentration of enzymes means that more enzyme-substrate complexes can form and so rate of reaction increases. However the substrate concentration become a limiting factor. Increasing the concentration of substrates also has the same effect until the number of enzmes become a limiting factor.

An inhibitor is any substance or molecule that slows down the rate of an enzyme-controlled reaction by affecting the enzyme molecule in some way.

Competitive inhibitors have a similar shape to that of the substrate. They compete with the substrate molecules for a place in the active site. This reduces the rate of reaction as less enzyme-substrate complexes are formed. Increasing the substrate concentration will dilute the effect of a competitive inhibitor and increase the rate of reaction. It is usually reversible.

Non-competitive inhibitors attach to part of the enzyme far away from the active site. They distort the tertiary structure and so the shape of the active site so the substrate no longer fits in. Increasing the substrate concentration will have no effect. This is usually irreversible but not always.

A cofactor is any substance that must be present in order for an enzyme-controlled reactions to take place at the appropriate rate.

A coenzyme is a small, organic, non-protein molecule that binds to the active site for a short period of time. It takes part in the reaction but is then recycled. Often it carries chemical groups between enzymes in enzyme-controlled reactions that are part of a sequence. An example is when nicotinamide makes a cofactor that is essential for pyruvate dehydrogenase to work.

A prosthetic group is a permanent coenzyme that contributes to the final 3D shape and the overall charge. An example is the zinc-based prosthetic group in carbonic anhydrase.

An inorganic ion cofactor is when the presence of a certain ion increases the rate of reaction. This can be by binding to either the enzyme or the substrate and making the enzyme-substrate complex easier to form. An example is chloride ions and amylase.

A poison can be because it inhibits or overactivates an enzyme. An example is potassium cyanide which is a non-competitive inhibitor for cytochrome oxidase which is used in respiration. 

Snake venom also contains an inhibitor of acetylcholinesterase which is involved in nerve transmission, causing paralyis.

Ethylene glycol (used in car antifreeze) when digested can be broken down by alcohol dehydrogenase into oxalic acid which is toxic. To treat this, fomepizole can be used which inhibits the action of the enzyme.

In cystic fibrosis, a symptom is that digestive enzyme passage is blocked. An enzyme covered in acid-resistant coat cant be prescribed,

Infections by viruses can be treated by inhibitors of the enzyme protease to stop viruses from replicating.

How and why different variables are kept constant:

• Temperature can be kept constant by using a water bath. This is because fluctuations in temperature can affect enzyme-controlled reactions.
• Enzyme concentration can be in an accurately measured solution. This is because reaction rate depends on concentration of enzyme molecules. In live tissues you must assume that all pieces of tissue contain the same amount of enzymes so you measure the mass.
• Substrate concentration can be in an accurately measure volume. This also affects the rate of the reaction.
• pH value can be maintained by using buffer solutions to keep H+ concentration constant.This is because the pH has an effect on the shape of the active site.

The turnover number of an enzyme molecule is how many reactions it can catalyse in one second.

Uncontrolled enzymes are dangerous. An example is in multiple sclerosis when there is uncontrolled synthesis of enzymes that are set against nerve cells.

In metabolic processes, the product of an enzyme-controlled reaction is usually the substrate for the next enyme-controlled reaction in the sequence. This is called a metabolic pathway. The end product is often a non-competitive inhibitor for an enzyme earlier on to prevent excess products.

A vital enzyme is ATP-synthase. It makes ATP from ADP and an inorganic phosphate group.

An inborn error of metabolism is when an enzyme is mutated due to incorrect instructions. An example is phenylketonuria. The enzyme phenylalanine hydroxylase doesn't function correctly to break down phenylalanine. This forms phenylpyruvic acid which can cause irreversible damage to developing brain tissue.